Entropy and information
Evgenii Rudnyi
http://blog.rudnyi.ru/2012/02/entropy-and-information.html
No doubt, this is my personal viewpoint. If you see that I have missed
something, please let me know.
Evgenii
Steve McGrew
I am neither a thermodynamicist nor an information theorist. However, I would like to offer the following points in response to your summary.
- Every system has structure that can in principle be described from the macroscopic level all the way down to sub-atomic.
- A complete* description of that structure could reasonably be
called "information", and its amount can be measured in suitable
units (e.g., "bits").
- Thus, every system contains a certain amount of information.
- The macroscopic behavior of a system can be described
accurately enough for almost all purposes, by using a much
smaller amount of information than is actually contained in the
system.
- In an entirely deterministic, closed system, the amount of information never changes, and the change in the information contents may change, but only with a single degree of freedom which corresponds to the passage of time.
- In a closed probabilistic system (e.g. closed quantum-mechanical system), again, the amount of information does not change but the information contents may change with a very large number of degrees of freedom corresponding to the "bits" in the description.
- Calculation of the evolution of a probabilistic system over
time, based on an initial incomplete description, becomes less
and less accurate as it is extrapolated further and further into
the future, because, in effect, the "known" fraction of the
complete description available for the calculation becomes
smaller, and the "unknown" fraction becomes larger,
In doing their calculations, thermodynamicists and chemists work
with an infinitesimally small fraction of the complete description
of a system. Physicists tend to do the same, of course.
By the way, a "chaotic" system would be one in which the behavior
cannot be accurately described (for practical purposes) without
taking a large fraction of the total amount of information into
account.
Steve McGrew
Evgenii Rudnyi
I would agree that we are free to give a meaning to a term (assuming
that we do have free will). Yet, in my view in the discussion about the
entropy and information, clear definitions are just missing.
Evgenii
On 26.02.2012 16:38 Steve McGrew said the following:
> Evgenii, I am neither a thermodynamicist nor an information theorist.
> However, I would like to offer the following points in response to
> your summary.
>
> * Every system has structure that can in principle be described from
> the macroscopic level all the way down to sub-atomic. * A complete*
> description of that structure could reasonably be called
> "information", and its amount can be measured in suitable units
> (e.g., "bits"). * Thus, every system contains a certain amount of
> information. * The macroscopic behavior of a system can be described
> accurately enough for almost all purposes, by using a much smaller
> amount of information than is actually contained in the system. * In
> an entirely deterministic, closed system, the /amount/ of
> information never changes, and the change in the /information
> contents/ may change, but only with a single degree of freedom which
> corresponds to the passage of time. * In a closed probabilistic
> system (e.g. closed quantum-mechanical system), again, the amount of
> information does not change but the information contents may change
> with a very large number of degrees of freedom corresponding to the
> "bits" in the description. * Calculation of the evolution of a
> probabilistic system over time, based on an initial incomplete
> description, becomes less and less accurate as it is extrapolated
> further and further into the future, because, in effect, the "known"
> fraction of the complete description available for the calculation
> becomes smaller, and the "unknown" fraction becomes larger,
>
> In doing their calculations, thermodynamicists and chemists work with
> an infinitesimally small fraction of the complete description of a
> system. Physicists tend to do the same, of course.
>
> By the way, a "chaotic" system would be one in which the behavior
> cannot be accurately described (for practical purposes) without
> taking a large fraction of the total amount of information into
> account.
>
> Steve McGrew
>
>
> On 2/26/2012 5:54 AM, Evgenii Rudnyi wrote:
>> I have written a summary for the discussion in the subject:
>>
>> http://blog.rudnyi.ru/2012/02/entropy-and-information.html
>>
>> No doubt, this is my personal viewpoint. If you see that I have
>> missed something, please let me know.
>>
>> Evgenii
>>
> -- You received this message because you are subscribed to the Google
> Groups "EmbryoPhysics" group. To post to this group, send email to
> embryo...@googlegroups.com. To unsubscribe from this group, send
> email to embryophysic...@googlegroups.com. For more
> options, visit this group at
> http://groups.google.com/group/embryophysics?hl=en.
Evgenii Rudnyi
I have thought more about your suggestion to define information in such
a way in order to completely describe a physical system. This could make
sense but then the thermodynamic entropy, in my view, is not related.
Some problem is to define what it means to describe a physical system.
Say, I could do it at the macroscopic level, at atomic level, at the
level of elementary particles, then now at the level of superstings.
Evgenii
On 26.02.2012 16:38 Steve McGrew said the following:
> Evgenii,
> I am neither a thermodynamicist nor an information theorist. However, I would
> like to offer the following points in response to your summary.
>
> * Every system has structure that can in principle be described from the
> macroscopic level all the way down to sub-atomic.
> * A complete* description of that structure could reasonably be called
> "information", and its amount can be measured in suitable units (e.g., "bits").
> * Thus, every system contains a certain amount of information.
> * The macroscopic behavior of a system can be described accurately enough for
> almost all purposes, by using a much smaller amount of information than is
> actually contained in the system.
> * In an entirely deterministic, closed system, the /amount/ of information
> never changes, and the change in the /information contents/ may change, but
> only with a single degree of freedom which corresponds to the passage of time.
> * In a closed probabilistic system (e.g. closed quantum-mechanical system),
> again, the amount of information does not change but the information
> contents may change with a very large number of degrees of freedom
> corresponding to the "bits" in the description.
> * Calculation of the evolution of a probabilistic system over time, based on
> an initial incomplete description, becomes less and less accurate as it is
> extrapolated further and further into the future, because, in effect, the
> "known" fraction of the complete description available for the calculation
> becomes smaller, and the "unknown" fraction becomes larger,
>
> In doing their calculations, thermodynamicists and chemists work with an
> infinitesimally small fraction of the complete description of a system.
> Physicists tend to do the same, of course.
>
> By the way, a "chaotic" system would be one in which the behavior cannot be
> accurately described (for practical purposes) without taking a large fraction of
> the total amount of information into account.
>
> Steve McGrew
>
>
> On 2/26/2012 5:54 AM, Evgenii Rudnyi wrote:
>> I have written a summary for the discussion in the subject:
>>
>> http://blog.rudnyi.ru/2012/02/entropy-and-information.html
>>
>> No doubt, this is my personal viewpoint. If you see that I have missed
>> something, please let me know.
>>
>> Evgenii
>>
Steve McGrew
A crystal in its lowest energy state) has low algorithmic complexity, and therefore low information content, because one sentence or a short formula can describe the arrangement of its atoms in complete detail. A bottle of CO2 has high algorithmic complexity, and therefore high information content, because the position and momentum, orientation, electronic state and spin vector of every molecule would need to be listed in order to describe it in complete detail.
However, we are usually satisfied to describe the bottle of CO2 with a few numbers: volume, pressure, and temperature, because that is enough for us to calculate its behavior in situations that usually matter to us. If the crystal, on the other hand, has an appropriately structured arrangement of electronic states, it might be able to perform complex calculations or even accurately model a bottle of CO2 down to the molecular level. The bottle of CO2 simply is itself; the crystal simulating the bottle of CO2 needs its electronic states highly structured.
According to the widely accepted notion, a system with the absolute maximum algorithmic complexity necessarily contains the maximum possible information. And, it must contain a minimum of internal correlations because every correlation reduces the algorithmic complexity. So, the arrangement of its parts need to be maximally random according to all possible measures of randomness. This equivalence of maximum randomness and maximum complexity suggests to me that neither randomness nor algorithmic complexity refer to things of importance to biology. Rather, we need a definition and measure of what I think of as "structure". Both a crystal (low algorithmic complexity for a complete description) and a gas (high algorithmic complexity for a complete description) would be low on the scale of "structure", while living organisms would rank high on the scale of "structure"
Steve
Newman, Stuart
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Steve McGrew [ste...@nli-ltd.com]
Sent: Monday, February 27, 2012 6:40 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics158:: Entropy and information
Evgenii,
Steve
Evgenii
Steve McGrew
http://blog.rudnyi.ru/2012/02/entropy-and-information.html
Evgenii
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to
embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>.
Newman, Stuart
William R. Buckley
Consider this model. Assume we have two adiabatic vessels. One has volume, the other does not.
Inside the volumetric adiabatic vessel we have an ideal gas at STP. Inside the non-volumetric adiabatic vessel, there is only
heat energy. Now, the STP gas has some entropy, and that entropy describes fully the state of the gas - it is *this much* disordered.
Now, we connect the two adiabatic vessels, and open the valve between them. Because there is no volumetric change, the V is
constant. Yet, the added energy to the gas increases the entropy state of the gas, and in order to properly describe this new
entropy state corresponds to an equal increase in the information needed to describe this changed state.
Is this argument based upon some fallacy?
wrb
Steve McGrew
Evgenii Rudnyi
Could please try your notation to the IT devices that surround us (a
hard disk, a flesh memory, a DVD, etc.)? Will it work to describe for
example their information capacity?
Evgenii
On 28.02.2012 00:40 Steve McGrew said the following:
> Evgenii,
>
> A crystal in its lowest energy state) has low algorithmic complexity, and
> therefore low information content, because one sentence or a short formula can
> describe the arrangement of its atoms in complete detail. A bottle of CO2 has
> high algorithmic complexity, and therefore high information content, because the
> position and momentum, orientation, electronic state and spin vector of every
> molecule would need to be listed in order to describe it in complete detail.
>
> However, we are usually satisfied to describe the bottle of CO2 with a few
> numbers: volume, pressure, and temperature, because that is enough for us to
> calculate its behavior in situations that usually matter to us. If the crystal,
> on the other hand, has an appropriately structured arrangement of electronic
> states, it might be able to perform complex calculations or even accurately
> model a bottle of CO2 down to the molecular level. The bottle of CO2 simply is
> itself; the crystal simulating the bottle of CO2 needs its electronic states
> highly structured.
>
> According to the widely accepted notion, a system with the absolute maximum
> algorithmic complexity necessarily contains the maximum possible information.
> And, it must contain a minimum of internal correlations because every
> correlation reduces the algorithmic complexity. So, the arrangement of its parts
> need to be maximally random according to all possible measures of randomness.
> This equivalence of maximum randomness and maximum complexity suggests to me
> that /neither/ randomness nor algorithmic complexity refer to things of
Evgenii Rudnyi
the state of the gas"?
The entropy is a function of a number of moles, temperature and pressure
S(n, T, p). If you take the same gas, I am pretty sure that you will
find many states
S(n1, T1, p1) = S(n2, T2, p2) = S(n3, T3, p3) = ...
So it is not clear what you mean. The situation is even more complex as
there are many different gases, say O2, N2, Ar, and so on. Again we can
find many states when the entropy has the same numerical values for
different gases.
Evgenii
On 28.02.2012 17:46 Steve McGrew said the following:
Steve McGrew
I think that it is reasonable to equate the information capacity of a system to the number of distinct accessible states, or perhaps to log(2) of that number if we want to talk about bits.
In a flash memory, there are specific locations with binary states. Each location, of course, is composed of a large number of atoms so the state of a location is a collective state of the atoms in that location. In a hard disk, the locations are not necessarily pre-defined, but again the states of the locations are collective states. The number of locations is the number of bits, and the number of accessible states is 2^(number of bits)
Evgenii Rudnyi
>>> A crystal in its lowest energy state) has low algorithmic
complexity, and
>>> therefore low information content, because one sentence or a short
formula can
>>> describe the arrangement of its atoms in complete detail. A bottle
of CO2 has
>>> high algorithmic complexity, and therefore high information
content, because the
You cannot use gas to store information for IT, you need a solid, and
higher temperatures are not good for IT either.
Evgenii
On 28.02.2012 20:46 Steve McGrew said the following:
Steve McGrew
I guess I didn't understand your question the first time.
Of course it is difficult to store information (for doing computations) in a gas specifically because the states are not easily accessible. Accessibility requires a sizable degree of "structure", but of course a gas has nearly negligible structure. To the extent that the relevant structural features are degraded by increased temperatures, heat can reduce the accessibility of states and thus reduce the effective information storage capacity. However, if there is no structure then the amount of information required to completely describe the state of the system is maximized even if the useful information storage capacity is consequently minimized.
So, the bottom line is that the term "information" has several meanings that are related but not equivalent. In any debate about such things, the participants need to make sure they are using the same meanings.
I guess "useful information storage capacity" is loosely comparable to what I've termed "structure".
Steve
William R. Buckley
Steve McGrew
It is important because electromagnetic radiation has entropy. Coherent laser light has extremely low entropy. Thermal radiation that is absorbed and re-emitted by the interior walls of a closed vessel has very high entropy.
Steve
Evgenii Rudnyi
Could you please say what is the relationship between information in IT
and in the CO2?
"A bottle of CO2 has high algorithmic complexity, and therefore high
information content"
I completely agree that information has several meaning and this is
probably the main problem when people discuss about the entropy and
information. But then it would be good to make definitions for different
meaning of information. It might help to understand the problem better.
Evgenii
On 28.02.2012 22:18 Steve McGrew said the following:
> Evgenii,
> I guess I didn't understand your question the first time.
> Of course it is difficult to store information (for doing computations) in
> a gas specifically because the states are not easily accessible.
> Accessibility requires a sizable degree of "structure", but of course a gas
> has nearly negligible structure. To the extent that the relevant
> structural features are degraded by increased temperatures, heat can reduce
> the accessibility of states and thus reduce the effective *information
> storage capacity*. However, if there is no structure then the amount of
William R. Buckley
While it is generally understood that such a case is nigh on impossible, it is also accepted to be a possibility, that a coffee cup
which is now at a temperature of 10 degrees C might suddenly obtain a large input of energy, and so be found at a temperature
of 20 degrees C. Highly unlikely but not impossible under the strictures of QM.
I don't care the form of the energy, so you pick one with no inherent entropy. Heck, idealised problems are the life-blood of physics.
This is how Einstein was able to understand the limit of travel, and the consequences to observation; such as by travel at the speed
of light.
So, the argument is that suddenly there is the appearance of a unit of energy that has no inherent entropy and which alters the
state of the adiabatically contained gas.
wrb
Steve McGrew
I'll try to answer your question.
In CO2, "high algorithmic complexity" and the corresponding high information content, equates to the number of bits needed to specify the position and momentum (within the uncertainties of QM) of each molecule. Of course, a complete description would also need to include the atomic-level details of the vessel containing the CO2. Because there are very few correlations in a gas, the number of bits is on the order of the number of molecules in the gas-- on the order of 10^24. The number of different states is horrendously large: on the order of 2^(10^24)
In, say, a flash memory, we do not care about the atomic-level details of the device. Rather, we care only about the accessible states of the device: those states we can control and detect via the input and output ports of the device. The biggest currently available flash memories have a number of accessible bits on the order of 10^12.
The number of accessible bits if we wanted to use a liter of gas at room temperature and normal atmospheric pressure as a computer data storage device is probably limited to about ten bits ((2^10) accessible states: whatever is necessary to specify the temperature to a practical degree of precision). This is because we cannot control the motions of individual molecules; all we can do is heat or cool the gas and measure its temperature.
The number of accessible bits in a terabyte flash drive is about 8 trillion bits ( 2^(8 trillion) states).
The algorithmic complexity of the contents of a flash drive depends on the contents. If the whole drive is filled with logical "0's", then the algorithmic complexity is very low because it would take only a very small number of bits to say, "filled completely with zeroes". This would be analogous to the algorithmic complexity of a CO2 crystal at absolute zero. If the whole drive is filled with a maximally compressed portion of the Library of Congress, it would contain a collection of 0's and 1's with no detectable internal correlations. That is, it would be random according to all statistical measures. In order to describe the contents of the drive in that case, the state of each bit would need to be specified individually. It would require at least 8 trillion bits to describe it.
In a living organism, the position and momentum of each molecule makes very little difference to the behavior and survival of the organism. In a cell membrane, there is some degree of organization that is important. The arrangement of the various organelles and cytoskeletal components is important but does not need to be controlled to the last detail. Similarly, the arrangement of the various types of cells and extracellular components of a multicellular creature does not need to be controlled to the last detail. If we fully understood a simple organism, we would be able to specify its state adequately in a relatively small number of bits, I'd guess something on the order of a thousand bits. (I could be off by a couple of orders of magnitude, but don't think so). "Adequately" here means well enough to predict its behavior accurately. On the other hand, it might take a substantially larger number of bits to specify the equations needed to *predict* the behavior, given the state. The accessible information capacity of a bacterium would correspond roughly to the amount of information we could write into it and get back out without killing it. Maybe that is on the order of ten thousand bits, maybe a couple of orders of magnitude higher. But to specify the bacterium's structure in full detail -- to transmit it in a Star Trek type transporter -- would take something on the order of 10^18 bits.
When we describe the information contained in a flash memory, we ignore the structure. But if we are comparing different kinds of data storage media, the atomic-level structure is very important. In the first case, "information" is what we store in the device. In the second case, "information" might be the full set of process steps and blueprints needed to make the device.
Regards,
Steve
Steve McGrew
If an unconstrained, collisionless blob of gas is illuminated by a fully coherent (zero entropy) laser beam, I think its entropy does not change. The distribution of states in the gas changes, but in a highly constrained way.
Lots of experiments have been done in which seemingly irreversible processes can be reversed. In those cases, it is clear that the *information* needed to specify the original state is transformed, but not lost. Reversing the transformation restores the original state. Although it *looks* like entropy has increased when the transformation is first done, it turns out that it really hasn't.
If I understand your thought experiment correctly, the second vessel has zero volume, so the fact that it's a vessel is irrelevant. You just want to abruptly introduce zero-entropy energy into the gas in the first vessel. This of course is very different from illuminating an unconstrained blob of gas with a pulse of laser light. In a very short time after the pulse, every molecule in the gas has hit other molecules or has hit the walls of the vessel, rebounding in unpredictable ways.
You're right, of course, that quantum mechanics complicates things. If molecules were billiard balls, then complete knowledge of the initial state of gas and vessel and the details of the laser pulse would be sufficient to predict any later state, and therefore sufficient to describe the later state after a given time. So, the entropy would not change.
Steve
Evgenii Rudnyi
I see a big difference between a flash memory and a gas. We write
information on a flesh memory in order to use it. The same concerns
books. A book is written to read it.
A gas, on the other hand, is just a gas. When I model it, I need to
define some variables, this is true. But this concern the gas model and
not the gas as such. When you speak about information to define a gas
model, I could understand. When you speak about information in the gas
as such, I cannot follow you.
Evgenii
P.S. By the way, I am not sure if I understand why you say that the
content of the Library of Congress is random. I would say not. Either
the content is compressed or not, in my view, this does not change the
fact that the information in the books is not random.
Even if the compressed form looks random, it is actually not, as one can
decompress the archive and restore normal books.
On 29.02.2012 22:34 Steve McGrew said the following:
> Evgenii,
>
> bits to specify the /equations/ needed to *predict* the behavior, given the
Evgenii Rudnyi
...
> Lots of experiments have been done in which seemingly irreversible processes can
> be reversed. In those cases, it is clear that the *information* needed to
> specify the original state is transformed, but not lost. Reversing the
> transformation restores the original state. Although it *looks* like entropy has
> increased when the transformation is first done, it turns out that it really hasn't.
Could you please give an example? But please not a thought experiment,
rather a real one.
Evgenii
Steve McGrew
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
Regards,
Steve
Newman, Stuart
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Steve McGrew [ste...@nli-ltd.com]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics176:: Entropy and information
Regards,
Steve
Evgenii
Regards,
Steve
Evgenii
Steve McGrew
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
Dr. Richard Gordon Ph.D.
Dear Stuart & Steve,
I tend to agree with Steve. What I call his LOGO program is “the genetic program”. But the physics is the component of the genetic program that is usually taken for granted. In the case of the LOGO program, this physics has to do with the operation of the compiler and the structure and operation of the computer. In the case of the embryo the physics is what the Embryo Physics Course is about: forces generated and responded to by cells, cytoskeletal physics, differentiation waves, etc. That there is a stochastic component is part of the physics, whether it be due to a random number generator or Brownian motion.
Yours, -Dick
On 2012-03-01, at 10:18 PM, Steve McGrew wrote:
> Stuart,
> Physical laws are the background principles that drive the processes.
> I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
>
> Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
>
> Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
>
> Steve
Dr. Richard (Dick) Gordon
Theoretical Biologist, Embryogenesis Center
Gulf Specimen Marine Laboratory (http://www.gulfspecimen.org)
Visiting Professor, Micro & Nanotechnology Institute, Old Dominion University
1-(850) 745-5011 or Skype: DickGordonCan
DickGo...@gmail.com
Newman, Stuart
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
William R. Buckley
I rather think the analogy is quite accurate. The key is abandoning the notion that all software is procedural. The genes of any organism, as a collective, act in the fashion of a highly
parallel program which is functional, not procedural.
wrb
William R. Buckley
Again, I strongly disagree with the notion that DNA does NOT constitute a program. Rather, the genes of DNA represent a set of independently operating components of a massively parallel processes, which are
effected by the transcription and translation of that information which is represented by the nucleic acid residue sequence of each gene.
Reliance upon the procedural view of computer programs in coming determine that DNA is not a program is a mistake, and a big one.
wrb
William R. Buckley
I hold the latter view, that physical laws are "just the constant background to everything, applying equally and everywhere to every parcel of" matter.
wrb
William R. Buckley
Is your point that you disagree with the position of physicists, that physics is constant throughout the universe?
wrb
Steve McGrew
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
Evgenii Rudnyi
I understand that one needs a decompression algorithm. Yet, when we
compress the Library of Congress, we know that such an algorithm exists.
If we take a really random string, then presumably such a decompression
algorithm just do not exist.
I personally do not think that a data compression is a good analogy with
DNA. I would say that here we have something different. Yet, I do not
know what happens there.
The video is nice, thanks a lot. Yet, at the end one sees that
dissipation does happen even in this case. If you have meant something
like this, then why not.
Evgenii
On 02.03.2012 00:36 Steve McGrew said the following:
> Evgenii,
> effectively /contains/ part of the information that's to be decompressed. A
> bigger compression/decompression algorithm can allow a higher degree of compression.
>
> Embryo development provides a very good analogy. DNA is a highly compressed
> description of an organism (/highly/ compressed, not /maximally/ compressed).
> The decompression algorithm resides in both the DNA and in the cellular
> machinery. The genetic code and all the cellular machinery are themselves
> encoded in the DNA, but cannot do their job unless there is already some tRNA
> along with other key machinery waiting in the fertilized ovum to "boot up" the
> system. And, it's worth noting that the principles of physics and chemistry are
> crucial parts of the decompression algorithm. If we sent all the DNA in an /e.
> Coli/ bacterium to alien scientists on Alpha Centauri, they would not be able to
> "decompress" it. If we included a set of tRNAs, they just might have a chance of
> success.
>
> We can assign a meaning to a randomly generated string of bits, and as long as
> we don't forget what meaning we assigned to the string, the string has that
> meaning and is thus no longer "random" in the sense that you're saying that the
> compressed archive is non-random.. If we forget, the string has not changed but
> it has lost its meaning. If we lose the decompression algorithm, the compressed
> string that "contains" the Library of Congress can lose its meaning.
>
> You asked for an example of a real experiment in which seemingly irreversible
> processes can be reversed. Spin echo and photon echo experiments are real
> examples. Here is a good one involving viscous liquid flow:
> http://www.youtube.com/watch?v=p08_KlTKP50. In the photon& spin echo
Evgenii Rudnyi
I have a question to your last sentence. I would say that physical laws
is a creation of mind. Then where physical laws existed when there was
no mind? How the next sentence could work in practice?
"physical laws just the constant background to everything, applying
equally and everywhere to every parcel of matter"
Does it imply that we have the matter and then additionally the physical
laws?
I am not kidding. This question troubles me indeed.
Evgenii
On 02.03.2012 03:58 Newman, Stuart said the following:
Evgenii Rudnyi
Let us a take a bacterium. How would you define a computation in order
to make sense for a sentence "A bacterium computes"?
Evgenii
On 02.03.2012 17:49 William R. Buckley said the following:
Steve Grand
Steve Grand
Steve Grand
laws?
> I am not kidding. This question troubles me indeed.
And so it should, Evgenii! But I'd say you attached the "additionally" to
the wrong part of the sentence. We have what can best be described as the
physical laws and it is matter that's the additional part. I think matter is
what you get when the laws that govern energy cause fields to wrap around on
themselves in certain ways. Ways that have the property of
self-reinforcement. Despite our intuition, I'd argue matter is not nearly as
"solid" and "primal" as it seems. It's no more primal than a wave on the
surface of the sea. It's no more solid than the force you experience as you
try to push one magnet closer to another. Imagine pushing two magnets
towards each other's identical pole and then imagine the same thing
happening without the actual magnets and that's what matter is like, imho.
-----Original Message-----
From: Evgenii Rudnyi
Sent: Friday, March 02, 2012 12:45 PM
To: embryo...@googlegroups.com
Stuart,
Evgenii
--
Dr. Richard Gordon Ph.D.
Dear Steve Grand,
I’m just going to disagree with one point, liking very much the rest:
“Embryology doesn’t just depend on simple physical factors such as diffusion and electrostatics, when it comes to the brain especially, development often depends heavily on the existence of quite complex environmental influences such as the presence of sound and the behavior of the mother.“
You’ve been coddled. In most of the real world, embryos are dispersed and lucky if their parents don’t eat them. The only environmental input before hatching may be temperature. Basically all the “information” is stored inside the embryo, and nothing of significance comes from the environment, in the vast majority of embryos. Sure, brains may be a different case, but early development is pretty brainless, and brains could be regarded as finishing touches. If you want to keep brains in the picture, then lets have separate tracks for early and later embryogenesis.
Yours, -Dick
On 2012-03-02, at 3:17 PM, Steve Grand wrote:
> I’ve been watching this with fascination but too busy to get involved. Nevertheless, I thought I’d just jump in about Steve’s comment:
>
> > We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
>
> Actually I think it’s fair to say that a computer’s hardware is ALSO software, so the distinction isn’t that much clearer in the computer world than it is in the biological one. When you think about it, the hardware of a computer exists in the ARRANGEMENT of its parts, and even the arrangement of “impurities” in the surface layers of its silicon. The hardware of a computer isn’t silicon and germanium and copper and metal oxides – a simple heap of these materials doesn’t compute. Come to that, even silicon and germanium are simply different arrangements of things – protons, neutrons and electrons (and protons and the like are themselves configurations of some sort...).
>
> So it’s not as if biology is really that much messier than computing. The arrangement of pools or cycles of electrons in memory cells that we call 1s and 0s, and therefore the “software” of the system, only do anything useful because of another layer of software – the arrangement of pools of contaminants in a slab of silicon. It’s software all the way down! The backbone of a DNA molecule is somewhat like a memory chip and the arrangement of its bases are somewhat like the memory contents. In computing we can differentiate between two kinds of content - program and data, but this is an extremely blurred distinction too (in fact the lack of a distinction is what makes a Universal Turing Machine so damned powerful). In DNA we get a similar blurring, in that the sequence of bases has a direct effect on protein synthesis but also affects the shape of the overall molecule and thus alters gene expression. The laws of physics are to biology like the “hardware” of a computer is to computing, but this too is really software. Philosophically speaking there’s barely any such thing as hardware in the so-called physical universe – even time and space are pretty “soft” concepts.
>
> It seems to me that making a distinction between the information content of the DNA and the information content of the physical world which that DNA acts on (and is acted upon by) can be misleading if you place too much trust on this distinction being true in other areas. A human being is constructed from the interaction between various sources of information, some of which lie in the DNA and the vast bulk of which lie in the outside world. Even the laws of physics are only a relatively small part of this information. Again it’s the CONFIGURATION of so-called physical objects that make up a lot of the relevant information. Embryology doesn’t just depend on simple physical factors such as diffusion and electrostatics, when it comes to the brain especially, development often depends heavily on the existence of quite complex environmental influences such as the presence of sound and the behavior of the mother.
>
> The only significant distinction that I can see between DNA and the rest-of-the-world, or a program and its computer, is that the rest-of-the-world is presumed to be sufficiently constant and robust for embryology to ASSUME its existence and reliability (as someone already said). DNA is the tiny part of the equation that COORDINATES the laws of physics and the usefulness of light and dark, sound and movement to creating a complete embryo. But information manipulation is happening all over the place.
>
> For a neat example of how informationally complex yet robust factors in the real world can influence very precise and complex structure formation in the developing brain with no explicit genetic control at all (just implicit control, since the external factors wouldn’t have this effect if neurons didn’t behave in the ways they do for other reasons), I recommend Stryker and Strickland’s work on the development of monocular stripes and binocular disparity cells in V1 of the visual cortex. The whole things is beautiful – it relies entirely on the facts that a) a baby in the womb gets no visual input, so the retinas start to strobe spontaneously, and b) a baby after being born receives correlated inputs to both eyes because the environment is heterogeneous. From these two facts and Hebb’s rule that “neurons which fire together wire together” a really striking pattern of nerve connections grows, very robustly.
>
> Just my two-pennyworth to add to a fascinating conversation!
>
> - Steve2 (Steve Grand)
Dr. Richard (Dick) Gordon
Newman, Stuart
It would be hard to disagree with the position stated that way, but not every physical law pertains equally to every scale and composition of matter. NASA doesn't do quantum mechanical calculations to send up satellites, though no one would argue with the fact that satellite trajectories do not violate quantum mechanics.
My point about biological development is that there are genes that are optional for life which, when they are present, capacitate cells and cell clusters to mobilize distinct physical effects. Cell-cell adhesion is not obligatory for survival, but if cells contain genes for cadherins, and enough calcium is present, they can form multicellular aggregates by mobilizing adhesive forces. Once such aggregates exist, there are many other such effects that come into play, which Ramray Bhat and I have encapusulated under the concept of "dynamical patterning modules."
Does this mean that there is a DNA program for cell aggregation (an important step in evolution, and an essential one for multicellular development)? Clearly not. Ancestral cells had many cadherin genes, but remained unicellular. Maybe all it took for Ediacaran organisms to take the first step toward metazoan evolution was a change in ambient calcium levels. Where is this reflected in the purported DNA program?
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 12:06 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics185:: Entropy and information
Stuart:
Is your point that you disagree with the position of physicists, that physics is constant throughout the universe?
wrb
On Fri, Mar 2, 2012 at 8:58 AM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
Relative William’s comment below, I have recently published the attached article.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley
Sent: Friday, March 02, 2012 11:51 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics183:: Entropy and information
Stuart:
I hold the latter view, that physical laws are "just the constant background to everything, applying equally and everywhere to every parcel of" matter.
wrb
On Thu, Mar 1, 2012 at 6:58 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Regards,
Steve
Evgenii
Regards,
Steve
Evgenii
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
Newman, Stuart
I think you are correct that physical laws are a construct of the human mind. I was using the term loosely to refer to objective physical reality, which I believe, probably like most member of this discussion group, to operate in a consistent way. Our imperfect laws capture and codify part of this consistency.
My main point here, which I made in an earlier response to William, is that we do not need to consider every scale of matter and the regularities of their behavior to understand the development of entities on a relatively narrow range of scales. And when cell aggregates are considered, not all of them are susceptible to exactly the same set of mesoscale effects.
Stuart
________________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Evgenii Rudnyi [use...@rudnyi.ru]
Sent: Friday, March 02, 2012 2:45 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics188:: Entropy and information
Stuart,
Evgenii
--
Steve Grand
> The only environmental input before hatching may be temperature. Basically
> all the �information� is stored inside the embryo, and nothing of
> significance comes from the environment, in the vast majority of embryos.
It's true, I have mammalian brains very definitely on my mind at the moment
and wasn't exactly thinking of C.elegans! I'll take your word for it that
neurogenesis is qualitatively separate from other aspects of morphogenesis
(although I'm pretty sure I remember you describing learning as an extension
of embryology, so maybe it depends on your perspective - from a
neuroscientific perspective I could say that embryology is merely an early
stage in the development of intelligence! :-)
> Basically all the �information� is stored inside the embryo
This was the core of the discussion, wasn't it? Whether this statement is
true or not? I came into this late.
-----Original Message-----
From: Dr. Richard Gordon Ph.D.
Sent: Friday, March 02, 2012 2:39 PM
To: embryo...@googlegroups.com
Cc: Steve Grand
Subject: Re: EmbryoPhysics193:: Entropy and information
Friday, March 2, 2012 4:32 PM, Panacea, FL, USA
Dear Steve Grand,
I�m just going to disagree with one point, liking very much the rest:
�Embryology doesn�t just depend on simple physical factors such as diffusion
and electrostatics, when it comes to the brain especially, development often
depends heavily on the existence of quite complex environmental influences
such as the presence of sound and the behavior of the mother.�
You�ve been coddled. In most of the real world, embryos are dispersed and
lucky if their parents don�t eat them. The only environmental input before
hatching may be temperature. Basically all the �information� is stored
inside the embryo, and nothing of significance comes from the environment,
in the vast majority of embryos. Sure, brains may be a different case, but
early development is pretty brainless, and brains could be regarded as
finishing touches. If you want to keep brains in the picture, then lets have
separate tracks for early and later embryogenesis.
Yours, -Dick
On 2012-03-02, at 3:17 PM, Steve Grand wrote:
> I�ve been watching this with fascination but too busy to get involved.
> Nevertheless, I thought I�d just jump in about Steve�s comment:
>
> > We go to great lengths in the design of digital computers to separate
> > software from hardware. Nature doesn't distinguish between the two, so
> > we're sure to get confused if we try to draw a line between the two in a
> > natural organism.
>
> Actually I think it�s fair to say that a computer�s hardware is ALSO
> software, so the distinction isn�t that much clearer in the computer world
> than it is in the biological one. When you think about it, the hardware of
> a computer exists in the ARRANGEMENT of its parts, and even the
> arrangement of �impurities� in the surface layers of its silicon. The
> hardware of a computer isn�t silicon and germanium and copper and metal
> oxides � a simple heap of these materials doesn�t compute. Come to that,
> even silicon and germanium are simply different arrangements of things �
> protons, neutrons and electrons (and protons and the like are themselves
> configurations of some sort...).
>
> So it�s not as if biology is really that much messier than computing. The
> arrangement of pools or cycles of electrons in memory cells that we call
> 1s and 0s, and therefore the �software� of the system, only do anything
> useful because of another layer of software � the arrangement of pools of
> contaminants in a slab of silicon. It�s software all the way down! The
> backbone of a DNA molecule is somewhat like a memory chip and the
> arrangement of its bases are somewhat like the memory contents. In
> computing we can differentiate between two kinds of content - program and
> data, but this is an extremely blurred distinction too (in fact the lack
> of a distinction is what makes a Universal Turing Machine so damned
> powerful). In DNA we get a similar blurring, in that the sequence of bases
> has a direct effect on protein synthesis but also affects the shape of the
> overall molecule and thus alters gene expression. The laws of physics are
> to biology like the �hardware� of a computer is to computing, but this too
> is really software. Philosophically speaking there�s barely any such thing
> as hardware in the so-called physical universe � even time and space are
> pretty �soft� concepts.
>
> It seems to me that making a distinction between the information content
> of the DNA and the information content of the physical world which that
> DNA acts on (and is acted upon by) can be misleading if you place too much
> trust on this distinction being true in other areas. A human being is
> constructed from the interaction between various sources of information,
> some of which lie in the DNA and the vast bulk of which lie in the outside
> world. Even the laws of physics are only a relatively small part of this
> information. Again it�s the CONFIGURATION of so-called physical objects
> that make up a lot of the relevant information. Embryology doesn�t just
> depend on simple physical factors such as diffusion and electrostatics,
> when it comes to the brain especially, development often depends heavily
> on the existence of quite complex environmental influences such as the
> presence of sound and the behavior of the mother.
>
> The only significant distinction that I can see between DNA and the
> rest-of-the-world, or a program and its computer, is that the
> rest-of-the-world is presumed to be sufficiently constant and robust for
> embryology to ASSUME its existence and reliability (as someone already
> said). DNA is the tiny part of the equation that COORDINATES the laws of
> physics and the usefulness of light and dark, sound and movement to
> creating a complete embryo. But information manipulation is happening all
> over the place.
>
> For a neat example of how informationally complex yet robust factors in
> the real world can influence very precise and complex structure formation
> in the developing brain with no explicit genetic control at all (just
> implicit control, since the external factors wouldn�t have this effect if
> neurons didn�t behave in the ways they do for other reasons), I recommend
> Stryker and Strickland�s work on the development of monocular stripes and
> binocular disparity cells in V1 of the visual cortex. The whole things is
> beautiful � it relies entirely on the facts that a) a baby in the womb
> gets no visual input, so the retinas start to strobe spontaneously, and b)
> a baby after being born receives correlated inputs to both eyes because
> the environment is heterogeneous. From these two facts and Hebb�s rule
> that �neurons which fire together wire together� a really striking pattern
> of nerve connections grows, very robustly.
>
> Just my two-pennyworth to add to a fascinating conversation!
>
> - Steve2 (Steve Grand)
Dr. Richard (Dick) Gordon
Theoretical Biologist, Embryogenesis Center
Gulf Specimen Marine Laboratory (http://www.gulfspecimen.org)
Visiting Professor, Micro & Nanotechnology Institute, Old Dominion
University
1-(850) 745-5011 or Skype: DickGordonCan
DickGo...@gmail.com
--
Newman, Stuart
________________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Dr. Richard Gordon Ph.D. [dickgo...@gmail.com]
Sent: Friday, March 02, 2012 4:39 PM
To: embryo...@googlegroups.com
Cc: Steve Grand
Subject: Re: EmbryoPhysics193:: Entropy and information
Friday, March 2, 2012 4:32 PM, Panacea, FL, USA
--
Newman, Stuart
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Steve McGrew [ste...@nli-ltd.com]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [mailto:embryo...@googlegroups.com] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Evgenii,
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>.
William R. Buckley
William R. Buckley
Newman, Stuart
This is not clear at all. If you take a present day amphibian or mammalian embryo and reduce the calcium ion concentration in its environment it will fall apart. Why could the reverse not have happened in pre-matazoan evolution, i.e., a cell surface cadherin having evolved in association with exclusively single-celled functions being recruited for a new function with absolutely no change in the organism's DNA?
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 9:17 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics199:: Entropy and information
Stuart:
Just because you haven't (or can't) find something does not mean it does not exist!
I would suggest that the mechanisms and processes of the cell (what happens in the cytoplasm, as opposed to what happens in the nucleus) are clearly directed by the information represented in the
base sequences of DNA. How this is accomplished is the $64,000.00US question and I suspect that further investigation will reveal the control mechanism and attendant information store; i.e. how the
genes control this process.
Your argument that NASA does not use quantum mechanics to develop flight plans for a missile is a Red Herring.
That genes for cadherin production were present long ago does not mean that in no way implies that they alone were sufficient to facilitate cell-cell adhesion; your suggestion otherwise is a non-sequitur.
Clearly, subsequent genetic change in the DNA of affected cell lineages yielded a new function for the cadherins; i.e. cell-cell adhesion.
wrb
On Fri, Mar 2, 2012 at 2:13 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
It would be hard to disagree with the position stated that way, but not every physical law pertains equally to every scale and composition of matter. NASA doesn't do quantum mechanical calculations to send up satellites, though no one would argue with the fact that satellite trajectories do not violate quantum mechanics.
My point about biological development is that there are genes that are optional for life which, when they are present, capacitate cells and cell clusters to mobilize distinct physical effects. Cell-cell adhesion is not obligatory for survival, but if cells contain genes for cadherins, and enough calcium is present, they can form multicellular aggregates by mobilizing adhesive forces. Once such aggregates exist, there are many other such effects that come into play, which Ramray Bhat and I have encapusulated under the concept of "dynamical patterning modules."
Does this mean that there is a DNA program for cell aggregation (an important step in evolution, and an essential one for multicellular development)? Clearly not. Ancestral cells had many cadherin genes, but remained unicellular. Maybe all it took for Ediacaran organisms to take the first step toward metazoan evolution was a change in ambient calcium levels. Where is this reflected in the purported DNA program?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 12:06 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics185:: Entropy and information
Stuart:
Is your point that you disagree with the position of physicists, that physics is constant throughout the universe?
wrb
On Fri, Mar 2, 2012 at 8:58 AM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
Relative William’s comment below, I have recently published the attached article.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of William R. Buckley
Sent: Friday, March 02, 2012 11:51 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics183:: Entropy and information
Stuart:
I hold the latter view, that physical laws are "just the constant background to everything, applying equally and everywhere to every parcel of" matter.
wrb
On Thu, Mar 1, 2012 at 6:58 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Regards,
Steve
Evgenii
Regards,
Steve
Evgenii
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
William R. Buckley
William R. Buckley
Newman, Stuart
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Evgenii,
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
Newman, Stuart
It's the case that you acknowledge the feasibilty of, but call an "exception," that I am focusing on. I believe it's what happened in fact, but even if it did not, it at least proves that my argument is not a non sequitur.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 9:51 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics203:: Entropy and information
Stuart:
In order for the cadherin to evolve, the corresponding DNA would have to change; mutation occurs! Recruitment implies some alteration to the system; and this will only occur by some alteration of the organismal
DNA. With perhaps one exception; the alteration of the niche in which the organism lives. If the cadherins were already extant, and the organism were to occupy a niche rich in calcium, then observation might have
included cell-cell adhesion without alteration to the organism DNA.
Clearly, your statement implies the necessity of calcium ions at some threshold, for you argue that reducing the available calcium ion concentration yields destruction of cell-cell adhesion.
Again, I claim you are involved in a non-sequitur.
wrb
On Fri, Mar 2, 2012 at 6:28 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
>Clearly, subsequent genetic change in the DNA of affected cell lineages yielded a new function for the cadherins; i.e. cell-cell adhesion.
This is not clear at all. If you take a present day amphibian or mammalian embryo and reduce the calcium ion concentration in its environment it will fall apart. Why could the reverse not have happened in pre-matazoan evolution, i.e., a cell surface cadherin having evolved in association with exclusively single-celled functions being recruited for a new function with absolutely no change in the organism's DNA?
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:17 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics199:: Entropy and information
Stuart:
Just because you haven't (or can't) find something does not mean it does not exist!
I would suggest that the mechanisms and processes of the cell (what happens in the cytoplasm, as opposed to what happens in the nucleus) are clearly directed by the information represented in the
base sequences of DNA. How this is accomplished is the $64,000.00US question and I suspect that further investigation will reveal the control mechanism and attendant information store; i.e. how the
genes control this process.
Your argument that NASA does not use quantum mechanics to develop flight plans for a missile is a Red Herring.
That genes for cadherin production were present long ago does not mean that in no way implies that they alone were sufficient to facilitate cell-cell adhesion; your suggestion otherwise is a non-sequitur.
Clearly, subsequent genetic change in the DNA of affected cell lineages yielded a new function for the cadherins; i.e. cell-cell adhesion.
wrb
On Fri, Mar 2, 2012 at 2:13 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
William,
It would be hard to disagree with the position stated that way, but not every physical law pertains equally to every scale and composition of matter. NASA doesn't do quantum mechanical calculations to send up satellites, though no one would argue with the fact that satellite trajectories do not violate quantum mechanics.
My point about biological development is that there are genes that are optional for life which, when they are present, capacitate cells and cell clusters to mobilize distinct physical effects. Cell-cell adhesion is not obligatory for survival, but if cells contain genes for cadherins, and enough calcium is present, they can form multicellular aggregates by mobilizing adhesive forces. Once such aggregates exist, there are many other such effects that come into play, which Ramray Bhat and I have encapusulated under the concept of "dynamical patterning modules."
Does this mean that there is a DNA program for cell aggregation (an important step in evolution, and an essential one for multicellular development)? Clearly not. Ancestral cells had many cadherin genes, but remained unicellular. Maybe all it took for Ediacaran organisms to take the first step toward metazoan evolution was a change in ambient calcium levels. Where is this reflected in the purported DNA program?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>>]
Sent: Friday, March 02, 2012 12:06 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics185:: Entropy and information
Stuart:
Is your point that you disagree with the position of physicists, that physics is constant throughout the universe?
wrb
On Fri, Mar 2, 2012 at 8:58 AM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>>> wrote:
Relative William’s comment below, I have recently published the attached article.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of William R. Buckley
Sent: Friday, March 02, 2012 11:51 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics183:: Entropy and information
Stuart:
I hold the latter view, that physical laws are "just the constant background to everything, applying equally and everywhere to every parcel of" matter.
wrb
On Thu, Mar 1, 2012 at 6:58 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>>> wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Regards,
Steve
Evgenii
Regards,
Steve
Evgenii
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
William R. Buckley
William R. Buckley
Newman, Stuart
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Evgenii,
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
Steve McGrew
The cloning of an extinct Pyrenean ibex ibex by inserting its DNA into the eggs of a domestic goat would seem to argue against the position you've taken: http://www.telegraph.co.uk/science/science-news/4409958/Extinct-ibex-is-resurrected-by-cloning.html.
Steve
>> wrote: Steve, My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA. Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology. What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development. Stuart ________________________________ From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com&g t;& gt;] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>] Sent: Friday, March 02, 2012 1:27 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> Subject: Re: EmbryoPhysics186:: Entropy and information Stuart, I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with. I think the issue boils down to the question of what distinguishes a program from the computer on which it runs. We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism. Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment. I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that. Steve On 3/2/2012 7:48 AM, Newman, Stuart wrote: Steve, I understand that you can write a program that generates tree morphologies. But you designed the program. An organism�s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism�s zygote, and only part of that is inscribed in DNA sequence. The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials. Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program. Stuart From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups .com> ;>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew Sent: Thursday, March 01, 2012 10:18 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c om>< /a>>> Subject: Re: EmbryoPhysics178:: Entropy and information Stuart, Physical laws are the background principles that drive the processes. I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics. Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program. Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe. Steve On 3/1/2012 6:58 PM, Newman, Stuart wrote: In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter? Stuart ________________________________ From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups .com> ;>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@goo glegroup s.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>] Sent: Thursday, March 01, 2012 6:36 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c om>< /a>>> Subject: Re: EmbryoPhysics176:: Entropy and information Evgenii, Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element! A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression. What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence. A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression. When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression. Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success. We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning. You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment. Regards, Steve On 3/1/2012 11:46 AM, Evgenii Rudnyi wrote: Steve, I see a big difference between a flash memory and a gas. We write information on a flesh memory in order to use it. The same concerns books. A book is written to read it. A gas, on the other hand, is just a gas. When I model it, I need to define some variables, this is true. But this concern the gas model and not the gas as such. When you speak about information to define a gas model, I could understand. When you speak about information in the gas as such, I cannot follow you. Evgenii P.S. By the way, I am not sure if I understand why you say that the content of the Library of Congress is random. I would say not. Either the content is compressed or not, in my view, this does not change the fact that the information in the books is not random. Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books. On 29.02.2012 22:34 Steve McGrew said the following: Evgenii, I'll try to answer your question. In CO2, "high algorithmic complexity" and the corresponding high information content, equates to the number of bits needed to specify the position and momentum (within the uncertainties of QM) of each molecule. Of course, a complete description would also need to include the atomic-level details of the vessel containing the CO2. Because there are very few correlations in a gas, the number of bits is on the order of the number of molecules in the gas-- on the order of 10^24. The number of different states is horrendously large: on the order of 2^(10^24) In, say, a flash memory, we do not care about the atomic-level details of the device. Rather, we care only about the accessible states of the device: those states we can control and detect via the input and output ports of the device. The biggest currently available flash memories have a number of accessible bits on the order of 10^12. The number of accessible bits if we wanted to use a liter of gas at room temperature and normal atmospheric pressure as a computer data storage device is probably limited to about ten bits ((2^10) accessible states: whatever is necessary to specify the temperature to a practical degree of precision). This is because we cannot control the motions of individual molecules; all we can do is heat or cool the gas and measure its temperature. The number of accessible bits in a terabyte flash drive is about 8 trillion bits ( 2^(8 trillion) states). The algorithmic complexity of the contents of a flash drive depends on the contents. If the whole drive is filled with logical "0's", then the algorithmic complexity is very low because it would take only a very small number of bits to say, "filled completely with zeroes". This would be analogous to the algorithmic complexity of a CO2 crystal at absolute zero. If the whole drive is filled with a maximally compressed portion of the Library of Congress, it would contain a collection of 0's and 1's with no detectable internal correlations. That is, it would be random according to all statistical measures. In order to describe the contents of the drive in that case, the state of each bit would need to be specified individually. It would require at least 8 trillion bits to describe it. In a living organism, the position and momentum of each molecule makes very little difference to the behavior and survival of the organism. In a cell membrane, there is some degree of organization that is important. The arrangement of the various organelles and cytoskeletal components is important but does not need to be controlled to the last detail. Similarly, the arrangement of the various types of cells and extracellular components of a multicellular creature does not need to be controlled to the last detail. If we fully understood a simple organism, we would be able to specify its state adequately in a relatively small number of bits, I'd guess something on the order of a thousand bits. (I could be off by a couple of orders of magnitude, but don't think so). "Adequately" here means well enough to predict its behavior accurately. On the other hand, it might take a substantially larger number of bits to specify the /equations/ needed to *predict* the behavior, given the state. The accessible information capacity of a bacterium would correspond roughly to the amount of information we could write into it and get back out without killing it. Maybe that is on the order of ten thousand bits, maybe a couple of orders of magnitude higher. But to specify the bacterium's structure in full detail -- to transmit it in a Star Trek type transporter -- would take something on the order of 10^18 bits. When we describe the information contained in a flash memory, we ignore the structure. But if we are comparing different kinds of data storage media, the atomic-level structure is very important. In the first case, "information" is what we store in the device. In the second case, "information" might be the full set of process steps and blueprints needed to make the device. Regards, Steve On 2/29/2012 12:14 PM, Evgenii Rudnyi wrote: Steve, Could you please say what is the relationship between information in IT and in the CO2? "A bottle of CO2 has high algorithmic complexity, and therefore high information content" I completely agree that information has several meaning and this is probably the main problem when people discuss about the entropy and information. But then it would be good to make definitions for different meaning of information. It might help to understand the problem better. Evgenii -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma ilto:em bryop...@googlegroups.com>>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma ilto:em bryop...@googlegroups.com>>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma ilto:em bryop...@googlegroups.com>>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com. To unsubscribe from this group, send email to embryophysic...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
Newman, Stuart
The story seems to imply that the ibex's DNA was used for the cloning experiment. I have never heard of such a procedure - cloning typically uses a cell nucleus from the donor, whuch contains hundreds of proteins in addition to the DNA (in a weight ratio of at least 2:1 protein to DNA) and an organizational state of the DNA in chromatin that makes certain genes accessible to transcription and others not. To call this highly organized, complex, multicomponent material "DNA" is an example of ideological thinking, such as i mentioned in an earlier message. And then there is the goat's egg, without whose ingredients (similar to those of the extinct ibex because of common evolutionary history) the "DNA" would be entirely inert.
Then the article goes on to say that the fact that the clone died right after its birth was probably due to a flaw in the DNA used to make the clone. For sure; what else could it have been?
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Steve McGrew [ste...@nli-ltd.com]
Sent: Saturday, March 03, 2012 12:11 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics209:: Entropy and information
Stuart,
The cloning of an extinct Pyrenean ibex ibex by inserting its DNA into the eggs of a domestic goat would seem to argue against the position you've taken: http://www.telegraph.co.uk/science/science-news/4409958/Extinct-ibex-is-resurrected-by-cloning.html.
Steve
On 3/2/2012 7:09 PM, Newman, Stuart wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com&g
t;<mailto:embryo...@googlegroups.com>&
gt;] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
.com>
;<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c
om><
/a>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: <mailto:embryo...@googlegroups.com> embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
.com>
;<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@goo
glegroup
s.com><mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c
om><
/a>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: <mailto:embryo...@googlegroups.com> http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>.
Steve McGrew
But evidently the animal that developed was an ibex, not a goat.� I must agree with you that the organization of the DNA is important-- and is part of the data that "describes" the ibex.
Steve
> wrote: William, It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA. Stuart ________________________________ From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups.c om>< /a>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com>] Sent: Friday, March 02, 2012 9:33 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information Stuart: Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction. DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide. Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you. It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps."). The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy. wrb On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>
>> wrote: Steve, My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA. Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology. What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development. Stuart ________________________________ From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>> [embryophysics@googlegrou ps.com< /a><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com&g
t;<mailto:embryo...@googlegroups.com>& gt;] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>] Sent: Friday, March 02, 2012 1:27 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
> Subject: Re: EmbryoPhysics186:: Entropy and information Stuart, I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with. I think the issue boils down to the question of what distinguishes a program from the computer on which it runs. We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism. Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment. I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that. Steve On 3/2/2012 7:48 AM, Newman, Stuart wrote: Steve, I understand that you can write a program that generates tree morphologies. But you designed the program. An organism�s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism�s zygote, and only part of that is inscribed in DNA sequence. The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials. Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program. Stuart From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@goog legroup s.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups .com>
;<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew Sent: Thursday, March 01, 2012 10:18 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@google groups. com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c om>
< /a>>> Subject: Re: EmbryoPhysics178:: Entropy and information Stuart, Physical laws are the background principles that drive the processes. I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics. Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program. Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe. Steve On 3/1/2012 6:58 PM, Newman, Stuart wrote: In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter? Stuart ________________________________ From: <mailto:embryo...@googlegroups.com> embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@googleg roups.c om>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups .com>
;<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@goo glegrou ps.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@goo glegroup s.com><mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>
>>] Sent: Thursday, March 01, 2012 6:36 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@google groups. com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c om>< /a>>> Subject: Re: EmbryoPhysics176:: Entropy and information Evgenii, Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element! A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression. What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence. A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression. When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression. Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success. We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning. You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: <mailto:embryo...@googlegroups.com> http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment. Regards, Steve On 3/1/2012 11:46 AM, Evgenii Rudnyi wrote: Steve, I see a big difference between a flash memory and a gas. We write information on a flesh memory in order to use it. The same concerns books. A book is written to read it. A gas, on the other hand, is just a gas. When I model it, I need to define some variables, this is true. But this concern the gas model and not the gas as such. When you speak about information to define a gas model, I could understand. When you speak about information in the gas as such, I cannot follow you. Evgenii P.S. By the way, I am not sure if I understand why you say that the content of the Library of Congress is random. I would say not. Either the content is compressed or not, in my view, this does not change the fact that the information in the books is not random. Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books. On 29.02.2012 22:34 Steve McGrew said the following: Evgenii, I'll try to answer your question. In CO2, "high algorithmic complexity" and the corresponding high information content, equates to the number of bits needed to specify the position and momentum (within the uncertainties of QM) of each molecule. Of course, a complete description would also need to include the atomic-level details of the vessel containing the CO2. Because there are very few correlations in a gas, the number of bits is on the order of the number of molecules in the gas-- on the order of 10^24. The number of different states is horrendously large: on the order of 2^(10^24) In, say, a flash memory, we do not care about the atomic-level details of the device. Rather, we care only about the accessible states of the device: those states we can control and detect via the input and output ports of the device. The biggest currently available flash memories have a number of accessible bits on the order of 10^12. The number of accessible bits if we wanted to use a liter of gas at room temperature and normal atmospheric pressure as a computer data storage device is probably limited to about ten bits ((2^10) accessible states: whatever is necessary to specify the temperature to a practical degree of precision). This is because we cannot control the motions of individual molecules; all we can do is heat or cool the gas and measure its temperature. The number of accessible bits in a terabyte flash drive is about 8 trillion bits ( 2^(8 trillion) states). The algorithmic complexity of the contents of a flash drive depends on the contents. If the whole drive is filled with logical "0's", then the algorithmic complexity is very low because it would take only a very small number of bits to say, "filled completely with zeroes". This would be analogous to the algorithmic complexity of a CO2 crystal at absolute zero. If the whole drive is filled with a maximally compressed portion of the Library of Congress, it would contain a collection of 0's and 1's with no detectable internal correlations. That is, it would be random according to all statistical measures. In order to describe the contents of the drive in that case, the state of each bit would need to be specified individually. It would require at least 8 trillion bits to describe it. In a living organism, the position and momentum of each molecule makes very little difference to the behavior and survival of the organism. In a cell membrane, there is some degree of organization that is important. The arrangement of the various organelles and cytoskeletal components is important but does not need to be controlled to the last detail. Similarly, the arrangement of the various types of cells and extracellular components of a multicellular creature does not need to be controlled to the last detail. If we fully understood a simple organism, we would be able to specify its state adequately in a relatively small number of bits, I'd guess something on the order of a thousand bits. (I could be off by a couple of orders of magnitude, but don't think so). "Adequately" here means well enough to predict its behavior accurately. On the other hand, it might take a substantially larger number of bits to specify the /equations/ needed to *predict* the behavior, given the state. The accessible information capacity of a bacterium would correspond roughly to the amount of information we could write into it and get back out without killing it. Maybe that is on the order of ten thousand bits, maybe a couple of orders of magnitude higher. But to specify the bacterium's structure in full detail -- to transmit it in a Star Trek type transporter -- would take something on the order of 10^18 bits. When we describe the information contained in a flash memory, we ignore the structure. But if we are comparing different kinds of data storage media, the atomic-level structure is very important. In the first case, "information" is what we store in the device. In the second case, "information" might be the full set of process steps and blueprints needed to make the device. Regards, Steve On 2/29/2012 12:14 PM, Evgenii Rudnyi wrote: Steve, Could you please say what is the relationship between information in IT and in the CO2? "A bottle of CO2 has high algorithmic complexity, and therefore high information content" I completely agree that information has several meaning and this is probably the main problem when people discuss about the entropy and information. But then it would be good to make definitions for different meaning of information. It might help to understand the problem better. Evgenii -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m ailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma ilto:em bryop...@googlegroups.com><mailto:embryo...@googlegroups.com>>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mai lto:embr yophysics%252Buns...@googlegroups.com>>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m ailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma ilto:em bryop...@googlegroups.com><mailto:embryo...@googlegroups.com>>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mai lto:embr yophysics%252Buns...@googlegroups.com>>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m ailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma ilto:em bryop...@googlegroups.com><mailto:embryo...@googlegroups.com>>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mai lto:embr yophysics%252Buns...@googlegroups.com>>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>. To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com>. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en. -- You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group. To post to this group, send email to embryo...@googlegroups.com. To unsubscribe from this group, send email to embryophysic...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
William R. Buckley
Your view of software is the source of limitation on your ability to see that the genes of DNA comprise a program.
Now, at no time have I claimed that the program effected by the transcription and translation of genes is procedural, nor have
I claimed that they provide a blueprint (as that term is understood by those who construct, for instance, high rise buildings) of
the organism which develops. Yet, I do claim that the totality of actions which derive from the production of polypeptides and
RNAs is never the less identical with the action of a program.
I know that many will want to argue with me on this point, and I claim that such argumentation against my position is totally
the consequence of myopic views of the nature of software.
wrb
Evgenii Rudnyi
possible by means of a simple example.
Evgenii
On 02.03.2012 21:17 Steve Grand said the following:
> I�ve been watching this with fascination but too busy to get
> involved. Nevertheless, I thought I�d just jump in about Steve�s
> comment:
>
>> We go to great lengths in the design of digital computers to
>> separate software from hardware. Nature doesn't distinguish between
>> the two, so we're sure to get confused if we try to draw a line
>> between the two in a natural organism.
>
> Actually I think it�s fair to say that a computer�s hardware is ALSO
> software, so the distinction isn�t that much clearer in the computer
> world than it is in the biological one. When you think about it, the
> hardware of a computer exists in the ARRANGEMENT of its parts, and
> even the arrangement of �impurities� in the surface layers of its
> silicon. The hardware of a computer isn�t silicon and germanium and
> copper and metal oxides � a simple heap of these materials doesn�t
> compute. Come to that, even silicon and germanium are simply
> different arrangements of things � protons, neutrons and electrons
> (and protons and the like are themselves configurations of some
> sort...).
>
> So it�s not as if biology is really that much messier than computing.
> The arrangement of pools or cycles of electrons in memory cells that
> we call 1s and 0s, and therefore the �software� of the system, only
> do anything useful because of another layer of software � the
> arrangement of pools of contaminants in a slab of silicon. It�s
> software all the way down! The backbone of a DNA molecule is somewhat
> like a memory chip and the arrangement of its bases are somewhat like
> the memory contents. In computing we can differentiate between two
> kinds of content - program and data, but this is an extremely blurred
> distinction too (in fact the lack of a distinction is what makes a
> Universal Turing Machine so damned powerful). In DNA we get a similar
> blurring, in that the sequence of bases has a direct effect on
> protein synthesis but also affects the shape of the overall molecule
> and thus alters gene expression. The laws of physics are to biology
> like the �hardware� of a computer is to computing, but this too is
> really software. Philosophically speaking there�s barely any such
> thing as hardware in the so-called physical universe � even time and
> space are pretty �soft� concepts.
>
> It seems to me that making a distinction between the information
> content of the DNA and the information content of the physical world
> which that DNA acts on (and is acted upon by) can be misleading if
> you place too much trust on this distinction being true in other
> areas. A human being is constructed from the interaction between
> various sources of information, some of which lie in the DNA and the
> vast bulk of which lie in the outside world. Even the laws of physics
> are only a relatively small part of this information. Again it�s the
> CONFIGURATION of so-called physical objects that make up a lot of the
> relevant information. Embryology doesn�t just depend on simple
> physical factors such as diffusion and electrostatics, when it comes
> to the brain especially, development often depends heavily on the
> existence of quite complex environmental influences such as the
> presence of sound and the behavior of the mother.
>
> The only significant distinction that I can see between DNA and the
> rest-of-the-world, or a program and its computer, is that the
> rest-of-the-world is presumed to be sufficiently constant and robust
> for embryology to ASSUME its existence and reliability (as someone
> already said). DNA is the tiny part of the equation that COORDINATES
> the laws of physics and the usefulness of light and dark, sound and
> movement to creating a complete embryo. But information manipulation
> is happening all over the place.
>
> For a neat example of how informationally complex yet robust factors
> in the real world can influence very precise and complex structure
> formation in the developing brain with no explicit genetic control at
> all (just implicit control, since the external factors wouldn�t have
> this effect if neurons didn�t behave in the ways they do for other
> reasons), I recommend Stryker and Strickland�s work on the
> development of monocular stripes and binocular disparity cells in V1
> of the visual cortex. The whole things is beautiful � it relies
> entirely on the facts that a) a baby in the womb gets no visual
> input, so the retinas start to strobe spontaneously, and b) a baby
> after being born receives correlated inputs to both eyes because the
> environment is heterogeneous. From these two facts and Hebb�s rule
> that �neurons which fire together wire together� a really striking
Evgenii Rudnyi
in the language of mathematics. Does mathematics has existed when there
was no mind?
Evgenii
On 02.03.2012 21:39 Steve Grand said the following:
Evgenii Rudnyi
have a question. In my view, to understand better what is exactly
information in this context, it could be useful to include into
consideration not living things as well.
I would suggest a following chain:
1) A rock;
2) A ballcock in the toilet;
3) An analog PID controller;
4) A self-driving car;
5) A living cell (a bacterium should suffer).
The question is at what level information comes into the play and how.
By the way, it is not that easy to exclude the information processing
even from the rock, see for example Jim Holt
�Take that rock over there. It doesn�t seem to be doing much of
anything, at least to our gross perception. But at the microlevel it
consists of an unimaginable number of atoms connected by springy
chemical bonds, all jiggling around at a rate that even our fastest
supercomputer might envy. And they are not jiggling at random. The
rock�s innards �see� the entire universe by means of the gravitational
and electromagnetic signals it is continuously receiving. Such a system
can be viewed as an all-purpose information processor, one whose inner
dynamics mirror any sequence of mental states that our brains might run
through.�
More to my question:
Information: a basic physical quantity or rather emergence/supervenience
phenomenon
http://blog.rudnyi.ru/2012/01/information.html
Evgenii
Steve McGrew
Seen in the close-up view, software *is* hardware.� The value of a bit is represented by the binary state of a somewhat isolated, small physical system whose state can be controlled and detected.� The state can be the location of a charge, the orientation of a cluster of spins, the temperature of a cluster of molecules, etc. �
The lac operon is a great example of hardware and software being inextricably mingled in DNA.� Something very akin to Boolean logic is performed by the control region of the operon, to determine whether or not a set of genes will be expressed.� Some of the products expressed by those genes in turn serve as inputs to the control region of the lac operon, and possibly to the control regions of other operons.� The enzymes that enable the function of the operon are the expressed products of genes in other operons.� These interactions can all be mapped out (in principle) and modeled as a Boolean network.� That network can be implemented as a computer program, or in an enormous FPGA, or in many other forms.�
To avoid confusion, we probably need new terminology.� Suppose we had a universal constructor that could extract minerals from rock and build anything we wanted it to make.� Then suppose we gave it blueprints of itself and instructed it to build what is described in the blueprints.� Usually we would have no problem calling the blueprints "software".� But the self-copy that results -- we would call "hardware".� On the other hand, suppose we had two "universal copiers", each with the ability to analyze any other system and construct a copy of it.� Set them to work on each other, and we would end up with copies of each.� In this case it is hard to point at a blueprint, but the end result is much the same as in the first case.� If we attempt to draw a clean line between hardware and software in the two cases, I think we will fail.
This may seem a bit academic, but really I think it might be important to try to come up with concepts a bit different from "hardware" and "software", and come up with names for those concepts, that work well in the context of cells and embryos.
Steve McGrew
On 3/3/2012 12:23 AM, William R. Buckley wrote:
Stuart:
Your view of software is the source of limitation on your ability to see that the genes of DNA comprise a program.
Now, at no time have I claimed that the program effected by the transcription and translation of genes is procedural, nor have
I claimed that they provide a blueprint (as that term is understood by those who construct, for instance, high rise buildings) of
the organism which develops.� Yet, I do claim that the totality of actions which derive from the production of polypeptides and
RNAs is never the less identical with the action of a program.
I know that many will want to argue with me on this point, and I claim that such argumentation against my position is totally
the consequence of myopic views of the nature of software.
wrb
On Fri, Mar 2, 2012 at 7:09 PM, Newman, Stuart <NEW...@nymc.edu> wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. �These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). �This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. �You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. �This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. �Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: �embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism�s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism�s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the �contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. �It could easily generate a forest containing vastly more pixels than the number of bits in the program. �Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. �They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. �What word would you use? �It wasn't a blueprint, because the trees and forest were different each time. �It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). �It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. �For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. �It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. �"Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. �The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. �Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. �In practice, no attempt is made to maximally compress data. �Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. �Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. �It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. �A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. �DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). �The decompression algorithm resides in both the DNA and in the cellular machinery. �The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. �And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. �If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. �If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. �If we forget, the string has not changed but it has lost its meaning. �If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. �Spin echo and photon echo experiments are real examples. �Here is a good one involving viscous liquid flow: http://www.youtube.com/watch?v=p08_KlTKP50. �In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
�Steve,
�Could you please say what is the relationship between information in IT and in
�the CO2?
�"A bottle of CO2 has high algorithmic complexity, and therefore high
�information content"
�I completely agree that information has several meaning and this is probably
�the main problem when people discuss about the entropy and information. But
�then it would be good to make definitions for different meaning of
�information. It might help to understand the problem better.
�Evgenii
William R. Buckley
If nothing else, information manipulation in biology is exemplified by gene therapy.
wrb
How would you define information manipulation in the biology? If possible by means of a simple example.
Evgenii
On 02.03.2012 21:17 Steve Grand said the following:
I’ve been watching this with fascination but too busy to get
involved. Nevertheless, I thought I’d just jump in about Steve’s
comment:
We go to great lengths in the design of digital computers to
separate software from hardware. Nature doesn't distinguish between
the two, so we're sure to get confused if we try to draw a line
between the two in a natural organism.
Actually I think it’s fair to say that a computer’s hardware is ALSO
software, so the distinction isn’t that much clearer in the computer
world than it is in the biological one. When you think about it, the
hardware of a computer exists in the ARRANGEMENT of its parts, and
even the arrangement of “impurities” in the surface layers of its
silicon. The hardware of a computer isn’t silicon and germanium and
copper and metal oxides – a simple heap of these materials doesn’t
compute. Come to that, even silicon and germanium are simply
different arrangements of things – protons, neutrons and electrons
(and protons and the like are themselves configurations of some
sort...).
So it’s not as if biology is really that much messier than computing.
The arrangement of pools or cycles of electrons in memory cells that
we call 1s and 0s, and therefore the “software” of the system, only
do anything useful because of another layer of software – the
arrangement of pools of contaminants in a slab of silicon. It’s
software all the way down! The backbone of a DNA molecule is somewhat
like a memory chip and the arrangement of its bases are somewhat like
the memory contents. In computing we can differentiate between two
kinds of content - program and data, but this is an extremely blurred
distinction too (in fact the lack of a distinction is what makes a
Universal Turing Machine so damned powerful). In DNA we get a similar
blurring, in that the sequence of bases has a direct effect on
protein synthesis but also affects the shape of the overall molecule
and thus alters gene expression. The laws of physics are to biology
like the “hardware” of a computer is to computing, but this too is
really software. Philosophically speaking there’s barely any such
thing as hardware in the so-called physical universe – even time and
space are pretty “soft” concepts.
It seems to me that making a distinction between the information
content of the DNA and the information content of the physical world
which that DNA acts on (and is acted upon by) can be misleading if
you place too much trust on this distinction being true in other
areas. A human being is constructed from the interaction between
various sources of information, some of which lie in the DNA and the
vast bulk of which lie in the outside world. Even the laws of physics
are only a relatively small part of this information. Again it’s the
CONFIGURATION of so-called physical objects that make up a lot of the
relevant information. Embryology doesn’t just depend on simple
physical factors such as diffusion and electrostatics, when it comes
to the brain especially, development often depends heavily on the
existence of quite complex environmental influences such as the
presence of sound and the behavior of the mother.
The only significant distinction that I can see between DNA and the
rest-of-the-world, or a program and its computer, is that the
rest-of-the-world is presumed to be sufficiently constant and robust
for embryology to ASSUME its existence and reliability (as someone
already said). DNA is the tiny part of the equation that COORDINATES
the laws of physics and the usefulness of light and dark, sound and
movement to creating a complete embryo. But information manipulation
is happening all over the place.
For a neat example of how informationally complex yet robust factors
in the real world can influence very precise and complex structure
formation in the developing brain with no explicit genetic control at
all (just implicit control, since the external factors wouldn’t have
this effect if neurons didn’t behave in the ways they do for other
reasons), I recommend Stryker and Strickland’s work on the
development of monocular stripes and binocular disparity cells in V1
of the visual cortex. The whole things is beautiful – it relies
entirely on the facts that a) a baby in the womb gets no visual
input, so the retinas start to strobe spontaneously, and b) a baby
after being born receives correlated inputs to both eyes because the
environment is heterogeneous. From these two facts and Hebb’s rule
that “neurons which fire together wire together” a really striking
pattern of nerve connections grows, very robustly.
Just my two-pennyworth to add to a fascinating conversation!
- Steve2 (Steve Grand)
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysics+unsubscribe@googlegroups.com.
William R. Buckley
I hold that things exist whether or not an intelligent mind is present to view such existence.
It is foolishness to hold otherwise.
wrb
William R. Buckley
You are preaching to the choir. I fully recognise the interconversion of hardware and software, and the interconversion of software and data. I am a very well experienced computer programmer who has at least one toe worth
of experience and expertise in electronic engineering.
I think you have not well described the details of the lac operon. It is a very well analysed system, which constitutes a negative feedback relationship.
On the notion of building a universal copier that can analyse any other system, I think you have run into the Halting Problem. To point, it is well known (owing to the work of Len Adelman and his student Fred B. Cohen,
following the work of Turing) that you cannot have one program (or machine) analyse another program (or machine) so as to determine the function of the analysed program (or machine), If this were not so, we would
have long ago written anti-virus software that was perfect at detecting and thwarting computer virus software.
wrb
William and Stuart,
Seen in the close-up view, software *is* hardware. The value of a bit is represented by the binary state of a somewhat isolated, small physical system whose state can be controlled and detected. The state can be the location of a charge, the orientation of a cluster of spins, the temperature of a cluster of molecules, etc.
The lac operon is a great example of hardware and software being inextricably mingled in DNA. Something very akin to Boolean logic is performed by the control region of the operon, to determine whether or not a set of genes will be expressed. Some of the products expressed by those genes in turn serve as inputs to the control region of the lac operon, and possibly to the control regions of other operons. The enzymes that enable the function of the operon are the expressed products of genes in other operons. These interactions can all be mapped out (in principle) and modeled as a Boolean network. That network can be implemented as a computer program, or in an enormous FPGA, or in many other forms.
To avoid confusion, we probably need new terminology. Suppose we had a universal constructor that could extract minerals from rock and build anything we wanted it to make. Then suppose we gave it blueprints of itself and instructed it to build what is described in the blueprints. Usually we would have no problem calling the blueprints "software". But the self-copy that results -- we would call "hardware". On the other hand, suppose we had two "universal copiers", each with the ability to analyze any other system and construct a copy of it. Set them to work on each other, and we would end up with copies of each. In this case it is hard to point at a blueprint, but the end result is much the same as in the first case. If we attempt to draw a clean line between hardware and software in the two cases, I think we will fail.
This may seem a bit academic, but really I think it might be important to try to come up with concepts a bit different from "hardware" and "software", and come up with names for those concepts, that work well in the context of cells and embryos.
Steve McGrew
On 3/3/2012 12:23 AM, William R. Buckley wrote:
Stuart:
Your view of software is the source of limitation on your ability to see that the genes of DNA comprise a program.
Now, at no time have I claimed that the program effected by the transcription and translation of genes is procedural, nor have
I claimed that they provide a blueprint (as that term is understood by those who construct, for instance, high rise buildings) of
the organism which develops. Yet, I do claim that the totality of actions which derive from the production of polypeptides and
RNAs is never the less identical with the action of a program.
I know that many will want to argue with me on this point, and I claim that such argumentation against my position is totally
the consequence of myopic views of the nature of software.
wrb
On Fri, Mar 2, 2012 at 7:09 PM, Newman, Stuart <NEW...@nymc.edu> wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
Steve,
Could you please say what is the relationship between information in IT and in
the CO2?
"A bottle of CO2 has high algorithmic complexity, and therefore high
information content"
I completely agree that information has several meaning and this is probably
the main problem when people discuss about the entropy and information. But
then it would be good to make definitions for different meaning of
information. It might help to understand the problem better.
Newman, Stuart
You seem to need the most sophisticated concept of software in order to designate DNA as the exclusive repository of the system's program, in what are actually multiscale dynamical/soft matter systems with distributed causality (Steve McGrew: "Hardware = software"). I prefer to think of present-day biological systems as having evolved from less precise chemical systems in which DNA could not have possibly begun with the role it has in modern forms (which I contend even now is not software).
Either you envision many steps along the way in which living systems were more what I (and I believe Steve McGrew) thinks they are, and therefore, in your definition, not true (i.e., DNA-programmed) life), or you must have recourse to some version of intelligent design, where things were always as you conceive them to be now.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Saturday, March 03, 2012 3:23 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics212:: Entropy and information
Stuart:
Your view of software is the source of limitation on your ability to see that the genes of DNA comprise a program.
Now, at no time have I claimed that the program effected by the transcription and translation of genes is procedural, nor have
I claimed that they provide a blueprint (as that term is understood by those who construct, for instance, high rise buildings) of
the organism which develops. Yet, I do claim that the totality of actions which derive from the production of polypeptides and
RNAs is never the less identical with the action of a program.
I know that many will want to argue with me on this point, and I claim that such argumentation against my position is totally
the consequence of myopic views of the nature of software.
wrb
On Fri, Mar 2, 2012 at 7:09 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>
Evgenii,
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>.
Newman, Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Saturday, March 03, 2012 10:17 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics218:: Entropy and information
Evgenii:
I hold that things exist whether or not an intelligent mind is present to view such existence.
It is foolishness to hold otherwise.
wrb
On Sat, Mar 3, 2012 at 3:15 AM, Evgenii Rudnyi <use...@rudnyi.ru<mailto:use...@rudnyi.ru>> wrote:
Let me put it then this way. The physical laws that we know are written in the language of mathematics. Does mathematics has existed when there was no mind?
Evgenii
On 02.03.2012 21:39 Steve Grand said the following:
Does it imply that we have the matter and then additionally the
physical
laws?
I am not kidding. This question troubles me indeed.
And so it should, Evgenii! But I'd say you attached the
"additionally" to the wrong part of the sentence. We have what can
best be described as the physical laws and it is matter that's the
additional part. I think matter is what you get when the laws that
govern energy cause fields to wrap around on themselves in certain
ways. Ways that have the property of self-reinforcement. Despite our
intuition, I'd argue matter is not nearly as "solid" and "primal" as
it seems. It's no more primal than a wave on the surface of the sea.
It's no more solid than the force you experience as you try to push
one magnet closer to another. Imagine pushing two magnets towards
each other's identical pole and then imagine the same thing happening
without the actual magnets and that's what matter is like, imho.
-----Original Message----- From: Evgenii Rudnyi Sent: Friday, March
02, 2012 12:45 PM To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> Subject: Re:
EmbryoPhysics188:: Entropy and information
Stuart,
I have a question to your last sentence. I would say that physical
laws is a creation of mind. Then where physical laws existed when
there was no mind? How the next sentence could work in practice?
"physical laws just the constant background to everything, applying
equally and everywhere to every parcel of matter"
Does it imply that we have the matter and then additionally the
physical laws?
I am not kidding. This question troubles me indeed.
Evgenii
On 02.03.2012 03:58 Newman, Stuart said the following:
In my opinion there is no sense at all in which DNA is a
"description of an organism," compressed or not. To believe it is
completely invalidates the notion of "embryo physics." Is DNA
supposed to encode the laws of physics? Or are physical laws just
the constant background to everything, applying equally and
everywhere to every parcel of matter?
Stuart
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com.
William R. Buckley
Your last sentence is non-sense.
I don't need a sophisticated concept of software. And, I never said that the cell had no other store of information than is represented by DNA; that is your supposition; cf. the work of Barbieri. Further, I hold that neither
has Steve McGrew made any such claim. What is program and what is data changes from moment to moment, and the functionality which one can obtain by the manipulation of matter (like electronic engineering) can
just as easily be obtained by the manipulation of software; simply modify the algorithm. Indeed, I hold that electronic engineering is not much different than is software engineering, and here I think Steve and I agree.
wrb
Newman, Stuart
Since the nucleus they used was from an ibex, the DNA (other than the mitochondrial genome) would have to have been ibex-specific, which is all the article claimed. Anatomically, ibexes and goats are fairly similar at embryonic, fetal and newborn stages. I think it would be difficult to ascertain that the animal that developed was an ibex, not a goat, from an animal that died at birth.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Steve McGrew [ste...@nli-ltd.com]
Sent: Saturday, March 03, 2012 12:40 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics211:: Entropy and information
Stuart,
But evidently the animal that developed was an ibex, not a goat. I must agree with you that the organization of the DNA is important-- and is part of the data that "describes" the ibex.
Steve
On 3/2/2012 9:34 PM, Newman, Stuart wrote:
Steve,
The story seems to imply that the ibex's DNA was used for the cloning experiment. I have never heard of such a procedure - cloning typically uses a cell nucleus from the donor, whuch contains hundreds of proteins in addition to the DNA (in a weight ratio of at least 2:1 protein to DNA) and an organizational state of the DNA in chromatin that makes certain genes accessible to transcription and others not. To call this highly organized, complex, multicomponent material "DNA" is an example of ideological thinking, such as i mentioned in an earlier message. And then there is the goat's egg, without whose ingredients (similar to those of the extinct ibex because of common evolutionary history) the "DNA" would be entirely inert.
Then the article goes on to say that the fact that the clone died right after its birth was probably due to a flaw in the DNA used to make the clone. For sure; what else could it have been?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>]
Sent: Saturday, March 03, 2012 12:11 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics209:: Entropy and information
Stuart,
The cloning of an extinct Pyrenean ibex ibex by inserting its DNA into the eggs of a domestic goat would seem to argue against the position you've taken: http://www.telegraph.co.uk/science/science-news/4409958/Extinct-ibex-is-resurrected-by-cloning.html.
Steve
On 3/2/2012 7:09 PM, Newman, Stuart wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups.c
om><
/a>] On Behalf Of William R. Buckley [<mailto:embryo...@googlegroups.com>bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>> [embryophysics@googlegrou
ps.com<
/a><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com&g
t;<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>&
gt;] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@goog
legroup
s.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
.com><mailto:embryo...@googlegroups.com>
;<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@google
groups.
com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c
om><mailto:embryo...@googlegroups.com><
/a>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: <mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@googleg
roups.c
om><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
.com><mailto:embryo...@googlegroups.com>
;<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@goo
glegrou
ps.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@goo
glegroup
s.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@google
groups.
com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c
om><mailto:embryo...@googlegroups.com><
/a>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: <mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m
ailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
%20.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mai
lto:embr
yophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m
ailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
%20.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mai
lto:embr
yophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m
ailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
%20.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mai
lto:embr
yophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com>.
Newman, Stuart
>Your last sentence is non-sense.
Then are you saying that DNA always had the privileged role of being the exclusive repository of the organism's program throughout evolution, or that its role was different at earlier stages?
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Saturday, March 03, 2012 10:47 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics222:: Entropy and information
Stuart:
Your last sentence is non-sense.
I don't need a sophisticated concept of software. And, I never said that the cell had no other store of information than is represented by DNA; that is your supposition; cf. the work of Barbieri. Further, I hold that neither
has Steve McGrew made any such claim. What is program and what is data changes from moment to moment, and the functionality which one can obtain by the manipulation of matter (like electronic engineering) can
just as easily be obtained by the manipulation of software; simply modify the algorithm. Indeed, I hold that electronic engineering is not much different than is software engineering, and here I think Steve and I agree.
wrb
On Sat, Mar 3, 2012 at 7:36 AM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
You seem to need the most sophisticated concept of software in order to designate DNA as the exclusive repository of the system's program, in what are actually multiscale dynamical/soft matter systems with distributed causality (Steve McGrew: "Hardware = software"). I prefer to think of present-day biological systems as having evolved from less precise chemical systems in which DNA could not have possibly begun with the role it has in modern forms (which I contend even now is not software).
Either you envision many steps along the way in which living systems were more what I (and I believe Steve McGrew) thinks they are, and therefore, in your definition, not true (i.e., DNA-programmed) life), or you must have recourse to some version of intelligent design, where things were always as you conceive them to be now.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Saturday, March 03, 2012 3:23 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics212:: Entropy and information
Stuart:
Your view of software is the source of limitation on your ability to see that the genes of DNA comprise a program.
Now, at no time have I claimed that the program effected by the transcription and translation of genes is procedural, nor have
I claimed that they provide a blueprint (as that term is understood by those who construct, for instance, high rise buildings) of
the organism which develops. Yet, I do claim that the totality of actions which derive from the production of polypeptides and
RNAs is never the less identical with the action of a program.
I know that many will want to argue with me on this point, and I claim that such argumentation against my position is totally
the consequence of myopic views of the nature of software.
wrb
On Fri, Mar 2, 2012 at 7:09 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>>]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>>>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>>
Evgenii,
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com><mailto:embryophysics%25252Bun...@googlegroups.com<mailto:embryophysics%2525252Bu...@googlegroups.com>>>>.
William R. Buckley
The modern means of identifying species is the use of a DNA sample from the individual. As the nuclear DNA was ibex, the birth was of an ibex.
What I could expect form a successful transnuclear experiment would be that the various molecules which constitute the host cell would with time be replaced by
molecules constructed according to the ibex genome; the cell would transmute from that of goat to that of ibex. I will accept that such transition takes time, so
that the transition period observes a chimera of goat and ibex characters.
wrb
William R. Buckley
What I said equates to "Your last sentence is unintelligible."
I did not say that DNA has always been the source of information store for biological organisms.
wrb
Newman, Stuart
Now I understand your position. If an organism is defined by its DNA sequence (rather than by any mrophological, physiological or behavioral traits), then certainly the organism's DNA sequence contains everything needed to characterize (i.e., represent or progam) it.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Saturday, March 03, 2012 10:57 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics225:: Entropy and information
Stuart:
The modern means of identifying species is the use of a DNA sample from the individual. As the nuclear DNA was ibex, the birth was of an ibex.
What I could expect form a successful transnuclear experiment would be that the various molecules which constitute the host cell would with time be replaced by
molecules constructed according to the ibex genome; the cell would transmute from that of goat to that of ibex. I will accept that such transition takes time, so
that the transition period observes a chimera of goat and ibex characters.
wrb
On Sat, Mar 3, 2012 at 7:48 AM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
Steve,
Since the nucleus they used was from an ibex, the DNA (other than the mitochondrial genome) would have to have been ibex-specific, which is all the article claimed. Anatomically, ibexes and goats are fairly similar at embryonic, fetal and newborn stages. I think it would be difficult to ascertain that the animal that developed was an ibex, not a goat, from an animal that died at birth.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>]
Sent: Saturday, March 03, 2012 12:40 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics211:: Entropy and information
Stuart,
But evidently the animal that developed was an ibex, not a goat. I must agree with you that the organization of the DNA is important-- and is part of the data that "describes" the ibex.
Steve
On 3/2/2012 9:34 PM, Newman, Stuart wrote:
Steve,
The story seems to imply that the ibex's DNA was used for the cloning experiment. I have never heard of such a procedure - cloning typically uses a cell nucleus from the donor, whuch contains hundreds of proteins in addition to the DNA (in a weight ratio of at least 2:1 protein to DNA) and an organizational state of the DNA in chromatin that makes certain genes accessible to transcription and others not. To call this highly organized, complex, multicomponent material "DNA" is an example of ideological thinking, such as i mentioned in an earlier message. And then there is the goat's egg, without whose ingredients (similar to those of the extinct ibex because of common evolutionary history) the "DNA" would be entirely inert.
Then the article goes on to say that the fact that the clone died right after its birth was probably due to a flaw in the DNA used to make the clone. For sure; what else could it have been?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Saturday, March 03, 2012 12:11 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics209:: Entropy and information
Stuart,
The cloning of an extinct Pyrenean ibex ibex by inserting its DNA into the eggs of a domestic goat would seem to argue against the position you've taken: http://www.telegraph.co.uk/science/science-news/4409958/Extinct-ibex-is-resurrected-by-cloning.html.
Steve
On 3/2/2012 7:09 PM, Newman, Stuart wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>>]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryophysics@googlegroups.c<mailto:embryophysics@googlegroups.c>
om><
/a>] On Behalf Of William R. Buckley [<mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>><mailto:bill.b...@gmail.com<mailto:bill.b...@gmail.com>>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryophysics@googlegrou
ps.com<http://ps.com><
/a><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>&g
t;<mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>&
gt;] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism’s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism’s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryophysics@goog<mailto:embryophysics@goog>
legroup
s.com<http://s.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups<mailto:embryophysics@googlegroups>
.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
;<mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryophysics@google<mailto:embryophysics@google>
groups.
com<mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups.c<mailto:embryophysics@googlegroups.c>
om><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><
/a>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. It could easily generate a forest containing vastly more pixels than the number of bits in the program. Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. What word would you use? It wasn't a blueprint, because the trees and forest were different each time. It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: <mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryophysics@googleg<mailto:embryophysics@googleg>
roups.c
om><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups<mailto:embryophysics@googlegroups>
.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
;<mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryophysics@goo<mailto:embryophysics@goo>
glegrou
ps.com<http://ps.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@goo<mailto:embryophysics@goo>
glegroup
s.com<http://s.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><mailto:embryophysics@google<mailto:embryophysics@google>
groups.
com<mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups.c<mailto:embryophysics@googlegroups.c>
om><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><
/a>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. "Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. In practice, no attempt is made to maximally compress data. Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). The decompression algorithm resides in both the DNA and in the cellular machinery. The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. If we forget, the string has not changed but it has lost its meaning. If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. Spin echo and photon echo experiments are real examples. Here is a good one involving viscous liquid flow: <mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> http://www.youtube.com/watch?v=p08_KlTKP50. In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
Regards,
Steve
Steve,
Evgenii
Evgenii,
order of 2^(10^24)
( 2^(8 trillion) states).
Regards,
Steve
Steve,
the CO2?
information content"
Evgenii
--
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><m
ailto:embryo...@googlegroups.com<mailto:ailto%3Aembry...@googlegroups.com><mailto:embryophysics@googlegroups<mailto:embryophysics@googlegroups>
%20.com<http://20.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><ma
ilto:em
bryop...@googlegroups.com<mailto:bryop...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mai
lto:embr
yophysics%252Buns...@googlegroups.com<mailto:yophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><m
ailto:embryo...@googlegroups.com<mailto:ailto%3Aembry...@googlegroups.com><mailto:embryophysics@googlegroups<mailto:embryophysics@googlegroups>
%20.com<http://20.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><ma
ilto:em
bryop...@googlegroups.com<mailto:bryop...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mai
lto:embr
yophysics%252Buns...@googlegroups.com<mailto:yophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>><m
ailto:embryo...@googlegroups.com<mailto:ailto%3Aembry...@googlegroups.com><mailto:embryophysics@googlegroups<mailto:embryophysics@googlegroups>
%20.com<http://20.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><ma
ilto:em
bryop...@googlegroups.com<mailto:bryop...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mai
lto:embr
yophysics%252Buns...@googlegroups.com<mailto:yophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><https://email.nymc.edu/owa/UrlBlockedError.aspx>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><mailto:embryophysics%252Buns...@googlegroups.com<mailto:embryophysics%25252Bun...@googlegroups.com>><https://email.nymc.edu/owa/UrlBlockedError.aspx>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
Evgenii Rudnyi
independent from an intelligent mind or not?
This first concern physical laws, because if mathematics is dependent on
a mind, it is unclear how physical laws has guided the matter when there
was no mind.
This also concerns the discussion about hardware and software. When we
speak about software, I guess, we mean an algorithm. The latter is a
pure mathematical construct and it is unwise to search for it in the
Nature. We may find some physical system that implements some algorithm,
but in my view this is not exactly what the term algorithm refers to.
Again, if mathematics is mind dependent then there were no algorithms
(software) in the Nature when there was no mind.
Evgenii
On 03.03.2012 16:37 Newman, Stuart said the following:
Evgenii Rudnyi
What is then information manipulation in the patient during this process?
Or do you mean the use of huge databases by scientists to find out what
sections of DNA to use?
Evgenii
On 03.03.2012 16:14 William R. Buckley said the following:
Steve Grand
Information is as relevant to the nature of life as cement is to the nature
of a house. You can't build a house unless you have enough cement, but the
amount of cement says nothing about the "houseness" of the system. A thing
can't be alive unless it has enough "information content" (in BIG
scare-quotes) but information is not the essence of life. Information
manipulation isn't really either, I don't think.
Two thought experiments to show the lack of a relationship between pure
Shannon-style information and lifeness or even "interestingness":
Take an old man on his deathbed and wait for him to die. One second he's
living; the next he's non-living. Where did all the supposed information go?
Virtually nothing changes as he crosses that threshold! It's not like
information has flowed out of him and gone up to heaven, leaving him a
simplified caricature of a living being. Some of the chemistry has altered
slightly, breaking some key feedback loops, but the information content of a
dead man is about the same as a live one. The information is necessary but
not sufficient.
Take two single-chip computers. Cut one chip into two pieces and rotate on
half before fusing them back together again. Hook them up to peripherals and
see which one computes. They have virtually identical information content to
many decimal places, but one's a computer and one is a lump of dirty
silicon.
Ideas like information, hardware, software, mathematics, complexity are all
human abstractions, and nature is under no obligation to adhere to them.
It's like asking whether light is a particle or a wave - of course it's
neither; it's light.
The essence of life is that it is a feedback system that preserves itself by
one or more of the following means: metabolism, reproduction, adaptive
reflex, and prediction. We give names to phenomena that are persistent and
recognizable (i.e. recur frequently). A rock is called a thing because there
are a lot of them and they hang around for a while. A ripple or a cloud are
called things because there are a lot of them and they hang around in a
rather more interesting way than a rock - they preserve their form
dynamically, through feedback. On the surface of a lake there are only two
possible things - two stable phenomena: ripples and vortices. There are an
infinite variety of other ways you can disturb the surface of a lake but
they all vanish quickly and these are the only two that have a means to
ensure their persistence.
An organism is a "disturbance in the fabric of the universe" much like a
ripple or a vortex, except very much more complex. This complexity isn't
what MAKES it alive, though; it's just what ENABLES it to be alive. It's an
arrangement of atoms that has some highly sophisticated feedback loops which
enable it to persist. At a minimum it is an autocatalytic set of enzyme
reactions, capable of making more copies of its own enzymes from raw
ingredients. One step up from that, metabolism becomes reproduction - the
splitting of the mass of reacting chemicals into two when it gets big.
Reproduction in which the structure of the network is preserved symbolically
between copies and is thus susceptible to natural selection in a more robust
and profound sense than mere accidents in the production of individual
molecules, has turned out to be highly successful, so all the autocatalytic
systems we know of have this property. These chemical feedback loops are
also nested and hence adaptive. Poke the thing with a stick and its internal
cycles of cause and effect will probably make it shrink from the stimulus.
Intelligent responses like this are also characteristic ways in which such
networks preserve themselves. Up nearer the top end of things, human beings
can even maintain their persistence by predicting the future and
pre-adapting to it, instead of waiting for something bad to happen and then
trying to respond to it. In all cases it's just chemistry and in all cases
it's a means by which the phenomenon persists over time for long enough to
deserve a name. You need a lot of chemistry to make such clever tricks
possible, but it's not the number of molecular species or the amount of
structural information PER SE that makes it into a living thing; it's the
QUALITATIVE way in which they are arranged. The bulk of all the possible
arrangements of a million proteins would fail miserably to maintain
themselves and would vanish quickly; it's only certain ones that survive but
they differ from the others qualitatively, not quantitatively.
I think information is an important concept; complexity an even more
important one (i.e. at least the ATTEMPT to differentiate between stupid
information and useful information, so that randomness is not the top of the
scale); but information is not life. Whether life is computation is another
question, but definitely an abstract one, since the definition of
computation is somewhat circular (a computer is that which computes;
computation is that which is performed by a computer) and so we can choose
to apply it as widely as we like (as we can the definition of life - it's
not an absolute category in nature but an artificial one). In Strong
Artificial Life it's a primary tenet that life can exist in a computer, but
I think it's a dangerous slip to conclude from this that life is
computation.
Anyway, I just wanted to suggest that life is a qualitative construct not a
quantitative one. Biology should beware of falling foul of physics envy,
even if that makes it an art as much as a science.
Steve2
-----Original Message-----
From: Evgenii Rudnyi
Sent: Saturday, March 03, 2012 4:12 AM
To: embryo...@googlegroups.com
William R. Buckley
> You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
> To post to this group, send email to embryo...@googlegroups.com.
Evgenii Rudnyi
also there). I do not see though information manipulation.
Evgenii
On 03.03.2012 19:14 William R. Buckley said the following:
Evgenii Rudnyi
that is an important concept but you do not say what it is.
I agree that information is an idea, human abstraction. On the other
hand, I do not understand how chemistry could develop such an idea. In
order to explain this better, I would suggest following. Let us consider
a situation where two mathematicians talks with each other about pi. I
would agree that after all this is just a bunch of molecules even with
very complicated autocatalitic reactions. What I do not understand how
the number pi appears from that chemistry.
Evgenii
On 03.03.2012 18:56 Steve Grand said the following:
Newman, Stuart
The field of biosemiotics deals with just such questions: http://en.wikipedia.org/wiki/Biosemiotics. The symbolic level, according to theortists in this area, does not apppear only with animal and human societies, but emerges along with the increasing autonomy of protobiological and biological systems from purely chemical ones during the evolution of life.
In this respect the triplet codons of DNA serve as symbols in the context of cellular systems, not solely as as molecules. Similarly with cyclic AMP and other intracellular messages, and hormones, neurotransmitters, and other extracellular ones.
Stuart
________________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Evgenii Rudnyi [use...@rudnyi.ru]
Sent: Saturday, March 03, 2012 4:42 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics233:: Entropy and information
Evgenii
--
William R. Buckley
Steve McGrew
You're right, of course, about the Halting Problem.� Note, however, that to copy something does not require analyzing it or determining its function.
Steve
On 3/3/2012 7:30 AM, William R. Buckley wrote:
Steve:
You are preaching to the choir.� I fully recognise the interconversion of hardware and software, and the interconversion of software and data.� I am a very well experienced computer programmer who has at least one toe worth
of experience and expertise in electronic engineering.
I think you have not well described the details of the lac operon.� It is a very well analysed system, which constitutes a negative feedback relationship.
On the notion of building a universal copier that can analyse any other system, I think you have run into the Halting Problem.� To point, it is well known (owing to the work of Len Adelman and his student Fred B. Cohen,
following the work of Turing) that you cannot have one program (or machine) analyse another program (or machine) so as to determine the function of the analysed program (or machine),� If this were not so, we would�
have long ago written anti-virus software that was perfect at detecting and thwarting computer virus software.
wrb
On Sat, Mar 3, 2012 at 6:25 AM, Steve McGrew <ste...@nli-ltd.com> wrote:
William and Stuart,
Seen in the close-up view, software *is* hardware.� The value of a bit is represented by the binary state of a somewhat isolated, small physical system whose state can be controlled and detected.� The state can be the location of a charge, the orientation of a cluster of spins, the temperature of a cluster of molecules, etc. �
The lac operon is a great example of hardware and software being inextricably mingled in DNA.� Something very akin to Boolean logic is performed by the control region of the operon, to determine whether or not a set of genes will be expressed.� Some of the products expressed by those genes in turn serve as inputs to the control region of the lac operon, and possibly to the control regions of other operons.� The enzymes that enable the function of the operon are the expressed products of genes in other operons.� These interactions can all be mapped out (in principle) and modeled as a Boolean network.� That network can be implemented as a computer program, or in an enormous FPGA, or in many other forms.�
To avoid confusion, we probably need new terminology.� Suppose we had a universal constructor that could extract minerals from rock and build anything we wanted it to make.� Then suppose we gave it blueprints of itself and instructed it to build what is described in the blueprints.� Usually we would have no problem calling the blueprints "software".� But the self-copy that results -- we would call "hardware".� On the other hand, suppose we had two "universal copiers", each with the ability to analyze any other system and construct a copy of it.� Set them to work on each other, and we would end up with copies of each.� In this case it is hard to point at a blueprint, but the end result is much the same as in the first case.� If we attempt to draw a clean line between hardware and software in the two cases, I think we will fail.
This may seem a bit academic, but really I think it might be important to try to come up with concepts a bit different from "hardware" and "software", and come up with names for those concepts, that work well in the context of cells and embryos.
Steve McGrew
On 3/3/2012 12:23 AM, William R. Buckley wrote:
Stuart:
Your view of software is the source of limitation on your ability to see that the genes of DNA comprise a program.
Now, at no time have I claimed that the program effected by the transcription and translation of genes is procedural, nor have
I claimed that they provide a blueprint (as that term is understood by those who construct, for instance, high rise buildings) of
the organism which develops.� Yet, I do claim that the totality of actions which derive from the production of polypeptides and
RNAs is never the less identical with the action of a program.
I know that many will want to argue with me on this point, and I claim that such argumentation against my position is totally
the consequence of myopic views of the nature of software.
wrb
On Fri, Mar 2, 2012 at 7:09 PM, Newman, Stuart <NEW...@nymc.edu> wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. �These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). �This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. �You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. �This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. �Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: �embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism�s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism�s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the �contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. �It could easily generate a forest containing vastly more pixels than the number of bits in the program. �Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. �They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. �What word would you use? �It wasn't a blueprint, because the trees and forest were different each time. �It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). �It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. �For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. �It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. �"Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. �The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. �Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. �In practice, no attempt is made to maximally compress data. �Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. �Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. �It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. �A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. �DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). �The decompression algorithm resides in both the DNA and in the cellular machinery. �The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. �And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. �If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. �If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. �If we forget, the string has not changed but it has lost its meaning. �If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. �Spin echo and photon echo experiments are real examples. �Here is a good one involving viscous liquid flow: http://www.youtube.com/watch?v=p08_KlTKP50. �In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
�Steve,
�Could you please say what is the relationship between information in IT and in
�the CO2?
�"A bottle of CO2 has high algorithmic complexity, and therefore high
�information content"
�I completely agree that information has several meaning and this is probably
�the main problem when people discuss about the entropy and information. But
�then it would be good to make definitions for different meaning of
�information. It might help to understand the problem better.
�Evgenii
Steve McGrew
The cellular components that are self-replicating (e.g., mitochondria) and are in the ovum into which the ibex DNA is inserted will be replicated into all of the cells in the developing embryo, and passed along to eventual offspring.� So, the final organism would, indeed, be a chimera. That leads to the question, "What is ibex DNA?" -- should we limit it to nuclear DNA?� And why limit it to DNA? Any self-replicating cellular components are certainly part of the heritable package that defines "ibex".� That of course, leads to the further question, "What is an ibex?".� I will happily assert that the concept of "ibex" has rather fuzzy boundaries.
Steve
On 3/3/2012 7:57 AM, William R. Buckley wrote:
Stuart:
The modern means of identifying species is the use of a DNA sample from the individual.� As the nuclear DNA was ibex, the birth was of an ibex.
What I could expect form a successful transnuclear experiment would be that the various molecules which constitute the host cell would with time be replaced by
molecules constructed according to the ibex genome; the cell would transmute from that of goat to that of ibex.� I will accept that such transition takes time, so
that the transition period observes a chimera of goat and ibex characters.
wrb
On Sat, Mar 3, 2012 at 7:48 AM, Newman, Stuart <NEW...@nymc.edu> wrote:
Steve,
Since the nucleus they used was from an ibex, the DNA (other than the mitochondrial genome) would have to have been ibex-specific, which is all the article claimed. Anatomically, ibexes and goats are fairly similar at embryonic, fetal and newborn stages. I think it would be difficult to ascertain that the animal that developed was an ibex, not a goat, from an animal that died at birth.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of Steve McGrew [ste...@nli-ltd.com]
Sent: Saturday, March 03, 2012 12:40 AM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics211:: Entropy and information
Stuart,
But evidently the animal that developed was an ibex, not a goat. �I must agree with you that the organization of the DNA is important-- and is part of the data that "describes" the ibex.
Steve
On 3/2/2012 9:34 PM, Newman, Stuart wrote:
Steve,
The story seems to imply that the ibex's DNA was used for the cloning experiment. I have never heard of such a procedure - cloning typically uses a cell nucleus from the donor, whuch contains hundreds of proteins in addition to the DNA (in a weight ratio of at least 2:1 protein to DNA) and an organizational state of the DNA in chromatin that makes certain genes accessible to transcription and others not. To call this highly organized, complex, multicomponent material "DNA" is an example of ideological thinking, such as i mentioned in an earlier message. And then there is the goat's egg, without whose ingredients (similar to those of the extinct ibex because of common evolutionary history) the "DNA" would be entirely inert.
Then the article goes on to say that the fact that the clone died right after its birth was probably due to a flaw in the DNA used to make the clone. For sure; what else could it have been?
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com>]
Sent: Saturday, March 03, 2012 12:11 AM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics209:: Entropy and information
Stuart,
The cloning of an extinct Pyrenean ibex ibex by inserting its DNA into the eggs of a domestic goat would seem to argue against the position you've taken: http://www.telegraph.co.uk/science/science-news/4409958/Extinct-ibex-is-resurrected-by-cloning.html.
Steve
On 3/2/2012 7:09 PM, Newman, Stuart wrote:
William,
All of this is true, but none of it supports the idea that the DNA contains any sort of program for, or representation of, the organism.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 10:01 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics206:: Entropy and information
Stuart:
The molecular components of the zygote came from the mother of the zygote; so called maternal effects; the presence of RNAs etc that originated with the mother. �These molecules which implement maternal effects
were derived from cells which are controlled by the same DNA as is present in the zygote (even if some alleles are different between mother and daughter). �This is the hand-off from one generation to another, and even
this kind of thing occurs within modern computers; its called a context switch.
wrb
On Fri, Mar 2, 2012 at 6:51 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>> wrote:
William,
It seems to me that DNA represents a long-lived storage medium for some of the (evolving) system's data, which is very different from being a program for the system's development, even though the data in question are used during development. There are numerous embryo types in which several dramatic morphogenetic and patterning changes occur based on stored molecular components of the zygote, with no involvement of the zygote's DNA. These steps are not programmed by any information in that DNA.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@googlegroups.c
�om><
/a>] On Behalf Of William R. Buckley [<mailto:embryo...@googlegroups.com>bill.b...@gmail.com<mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com><mailto:bill.b...@gmail.com>]
Sent: Friday, March 02, 2012 9:33 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics202:: Entropy and information
Stuart:
Programming involves a correspondence between a group of bits (often in the form of the octet that we call a BYTE) and a consequence, which is the processing of data yielded by execution of the instruction.
DNA has an identical correspondence, between triplet codons (effectively a group of bits; six bits, actually) and a cognate RNA molecule, which in the processing of the data yields the production of a polypeptide.
Just as with the presupposition of cell machinery to process DNA, etc., there is also the presuppostion of the existence of a computer to process programs. On this point, I agree with you.
It would be easy to implement computer programs which turn on and off certain sections of the component codes, just as occurs through the action of the cell on DNA (which you say "is itself a product of earlier steps.").
The fact that software does not traditionally work this way in no way means that software cannot work this way. �You are involved in a philosophical fallacy.
wrb
On Fri, Mar 2, 2012 at 3:22 PM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu<mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu><mailto:NEW...@nymc.edu>>> wrote:
Steve,
My understanding is that a program requires a programming language. As far as I know the only incontrovertible lingusitic aspects of DNA are the correpondences between its triplet codons and the sequences of cognate RNA molecules, and indirectly, the primary sequences of proteins. �This, and any other effects of the sequence of DNA molecules presuppose the machinery of the cell, which acts on the DNA and RNA but (unlike a computer program) not necessarily under instructions based on information in the DNA.
Since much of what the cell does to the the DNA (e.g., methylate it in certain places) or the RNA (choose which alternative splice forms to make) involves proteins, it is easy to assume that all information flows from some original zygotic DNA sequence. But that sequence, and the way it is packed into chromatin, is itself a product of earlier steps. So I have come to the opinion that considering the DNA to contain a description of, or a program for constructing, an organism, is a kind of ideology.
What this position seem to be saying is that "if the information is not in the DNA where else can it possibly reside?" But I suggest that the information resides in the system as a whole, and that DNA sequence changes over evolution constrained by the survival requirements of whole cellular and organismal systems. So while an organism's DNA sequence reflects the evolution of development, and participates in development, it doesn't "program" development.
Stuart
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>> [embryophysics@googlegrou
�ps.com<
/a><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com&g
�t;<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>&
gt;] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>]
Sent: Friday, March 02, 2012 1:27 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>
Subject: Re: EmbryoPhysics186:: Entropy and information
Stuart,
I enjoyed reading your article, "The Developmental Specificity of Physical Mechanisms", and found all points in it easy to agree with.
I think the issue boils down to the question of what distinguishes a program from the computer on which it runs.
We go to great lengths in the design of digital computers to separate software from hardware. �Nature doesn't distinguish between the two, so we're sure to get confused if we try to draw a line between the two in a natural organism.
Your position, and William Buckley's (and mine), I think, are all in agreement with this statement: �embryo development results from physical and chemical processes whose sequence, timing, physical location, duration, etc., are largely controlled by DNA sequences and their interactions with their environment.
I am inclined to call the contents of DNA a "program", and call the other cellular machinery "hardware", but this is just by analogy, and an imperfect analogy at that.
Steve
On 3/2/2012 7:48 AM, Newman, Stuart wrote:
Steve,
I understand that you can write a program that generates tree morphologies. But you designed the program. An organism�s DNA does not contain such a program. The program, if you want to call it that, resides in the entire material composition of the organism�s zygote, and only part of that is inscribed in DNA sequence.
The forms that we see unfolding in a present-day organism are not the execution of information in the DNA, but outcomes of a complex set of physical processes, only some of which are predictable based on the physics acting on the �contemporary materials (including the DNA). Some of the forms arose much earlier in evolutionary history based on the cellular materials present at that time and the physical effects relevant to those materials.
Those original forms (if they were consistent with survival) acted as structural templates for subsequent canalizing evolution, so that the present-day unfolding process can neither be attributed to present-day DNA, or present-day DNA plus present-day physics. The explanation of the forms and the means of their generation must also take the historical dimension into account. The DNA sequence reflect this history, but only partially, and not in the form of a program.
Stuart
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@goog
�legroup
s.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
�.com><mailto:embryo...@googlegroups.com>
;<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>> [mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>] On Behalf Of Steve McGrew
Sent: Thursday, March 01, 2012 10:18 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@google
�groups.
com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c
�om><mailto:embryo...@googlegroups.com><
/a>>>
Subject: Re: EmbryoPhysics178:: Entropy and information
Stuart,
Physical laws are the background principles that drive the processes.
I probably haven't communicated what I mean by "description of an organism", if you think that to believe DNA is a "description of an organism" invalidates the notion of embryo physics.
Once I wrote a simple LOGO program that generated a forest of trees on a computer screen.. �It could easily generate a forest containing vastly more pixels than the number of bits in the program. �Every time I ran the program, it generated a different forest with different trees, but the forest and trees had the same general character each time. �They always looked like spruce trees or oak trees, depending on the small handful of control parameters I gave to the program.
Maybe you wouldn't say that the LOGO program was a "description" of the trees or forest. �What word would you use? �It wasn't a blueprint, because the trees and forest were different each time. �It was a set of rules, and it made the forest grow but did not fully control the growth of the forest (because it included random functions). �It was a "prescription", maybe.
Steve
On 3/1/2012 6:58 PM, Newman, Stuart wrote:
In my opinion there is no sense at all in which DNA is a "description of an organism," compressed or not. To believe it is completely invalidates the notion of "embryo physics." Is DNA supposed to encode the laws of physics? Or are physical laws just the constant background to everything, applying equally and everywhere to every parcel of matter?
Stuart
________________________________
From: <mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@googleg
�roups.c
om><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
�.com><mailto:embryo...@googlegroups.com>
;<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryophysics@goo
�glegrou
ps.com><mailto:embryo...@googlegroups.com>><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@goo
�glegroup
s.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>] On Behalf Of Steve McGrew [ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com<mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com><mailto:ste...@nli-ltd.com>>>]
Sent: Thursday, March 01, 2012 6:36 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><mailto:embryophysics@google
�groups.
com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups.c
�om><mailto:embryo...@googlegroups.com><
/a>>>
Subject: Re: EmbryoPhysics176:: Entropy and information
Evgenii,
Of course there are enormous differences. I just wanted to note that a vessel filled with gas could, in fact, serve as a memory element if its temperature were controlled and detected by a computer. �For example, if the gas temperature is over 100 degrees C it might represent a "1", and if below 100 C it might represent a "0". Or, if the temperature could be controlled and detected to within one degree C in the range from 100 K to 400K, it could be in any of 300 states -- on the order of six or seven bits. �It certainly wouldn't be a very useful memory element!
A maximally compressed digital version of any information (i.e., the Library of Congress) is devoid of internal correlations -- because those internal correlations are what is reduced by data compression. �"Maximally compressed" would mean that there are no further internal correlations to exploit for compression.
What distinguishes a random sequence of bits from a nonrandom sequence is precisely the internal correlations. �The "degree of randomness" of a sequence corresponds to the length of the shortest possible algorithm that can generate the same sequence. �Any algorithm to generate the sequence efficiently will take advantage of internal correlations in the sequence. That is, it corresponds to the algorithmic complexity of the sequence.
A maximally compressed version of a sequence *IS* effectively the shortest algorithm that can generate the original sequence. �In practice, no attempt is made to maximally compress data. �Instead, a standard algorithm is used to detect and exploit a very limited subset of the possible correlations to produce a new sequence which, when run through an inverse of the algorithm, will regenerate the original sequence. �Consequently, some correlations always remain after ordinary data compression.
When you say, "Even if the compressed form looks random, it is actually not, as one can decompress the archive and restore normal books", I think you're stepping into a very messy topic. �It is not possible to decompress the archive without using the decompression algorithm, so the decompression algorithm effectively contains part of the information that's to be decompressed. �A bigger compression/decompression algorithm can allow a higher degree of compression.
Embryo development provides a very good analogy. �DNA is a highly compressed description of an organism (highly compressed, not maximally compressed). �The decompression algorithm resides in both the DNA and in the cellular machinery. �The genetic code and all the cellular machinery are themselves encoded in the DNA, but cannot do their job unless there is already some tRNA along with other key machinery waiting in the fertilized ovum to "boot up" the system. �And, it's worth noting that the principles of physics and chemistry are crucial parts of the decompression algorithm. �If we sent all the DNA in an e. Coli bacterium to alien scientists on Alpha Centauri, they would not be able to "decompress" it. �If we included a set of tRNAs, they just might have a chance of success.
We can assign a meaning to a randomly generated string of bits, and as long as we don't forget what meaning we assigned to the string, the string has that meaning and is thus no longer "random" in the sense that you're saying that the compressed archive is non-random.. �If we forget, the string has not changed but it has lost its meaning. �If we lose the decompression algorithm, the compressed string that "contains" the Library of Congress can lose its meaning.
You asked for an example of a real experiment in which seemingly irreversible processes can be reversed. �Spin echo and photon echo experiments are real examples. �Here is a good one involving viscous liquid flow: <mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com> http://www.youtube.com/watch?v=p08_KlTKP50. �In the photon & spin echo experiments, the 180 degree phase reversal pulse serves essentially the same purpose as reversing the direction of rotation in the viscous liquid experiment.
�Steve,
�Could you please say what is the relationship between information in IT and in
�the CO2?
�"A bottle of CO2 has high algorithmic complexity, and therefore high
�information content"
�I completely agree that information has several meaning and this is probably
�the main problem when people discuss about the entropy and information. But
�then it would be good to make definitions for different meaning of
�information. It might help to understand the problem better.
�Evgenii
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m
ailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
%20.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
�ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mai
�lto:embr
yophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m
ailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
%20.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
�ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mai
�lto:embr
yophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com>>>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>><m
ailto:embryo...@googlegroups.com<mailto:embryophysics@googlegroups
%20.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<ma
�ilto:em
bryop...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com>>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysic...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><https://email.nymc.edu/owa/UrlBlockedError.aspx>><mailto:embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com><mailto:embryophysics%252Buns...@googlegroups.com><mai
�lto:embr
Steve McGrew
I'm almost totally in agreement with you, and like very much what you had to say about names and persistent phenomena.
One point of disagreement: "One second he's living; the next he's non-living." I'm not convinced that there is a perfectly sharp boundary between "living" and "non-living", especially in the case of a human being on his deathbed. Perhaps there is a boundary that could be at the transition between "revivable" and "non-revivable", but that is obviously a very fuzzy boundary that moves as our medical technology improves.
Steve McGrew
On 3/3/2012 9:56 AM, Steve Grand wrote:
Do I detect a general lingering neo-vitalism in this conversation?
Information is as relevant to the nature of life as cement is to the nature of a house. You can't build a house unless you have enough cement, but the amount of cement says nothing about the "houseness" of the system. A thing can't be alive unless it has enough "information content" (in BIG scare-quotes) but information is not the essence of life. Information manipulation isn't really either, I don't think.
Two thought experiments to show the lack of a relationship between pure Shannon-style information and lifeness or even "interestingness":
Take an old man on his deathbed and wait for him to die. One second he's living; the next he's non-living. What does this mean? Where did all the supposed information go? Virtually nothing changes as he crosses that threshold! It's not like information has flowed out of him and gone up to heaven, leaving him a simplified caricature of a living being. Some of the chemistry has altered slightly, breaking some key feedback loops, but the information content of a dead man is about the same as a live one. The information is necessary but not sufficient.
Take two single-chip computers. Cut one chip into two pieces and rotate on half before fusing them back together again. Hook them up to peripherals and see which one computes. They have virtually identical information content to many decimal places, but one's a computer and one is a lump of dirty silicon. True: but the *structure* is altered.
Dr. Richard Gordon Ph.D.
Ah death and the soul next = information? However, in practical terms Steve McGrew is right: we use that fuzzy boundary to harvest transplantable organs and tissues from “dead” people. Which then takes us to Schroedinger’s cat, which while fuzzy in other ways, we now see as not dead/alive as a binary variable. If the cat is not just dead/alive, can it still be a quantum mixture of uncollapsed states? Has Schroedinger’s paradox itself collapsed?
Yours, -Dick Gordon
On 2012-03-03, at 9:52 PM, Steve McGrew wrote:
> Steve2,
> I'm almost totally in agreement with you, and like very much what you had to say about names and persistent phenomena.
>
> One point of disagreement: "One second he's living; the next he's non-living." I'm not convinced that there is a perfectly sharp boundary between "living" and "non-living", especially in the case of a human being on his deathbed. Perhaps there is a boundary that could be at the transition between "revivable" and "non-revivable", but that is obviously a very fuzzy boundary that moves as our medical technology improves.
>
> Steve McGrew
Dr. Richard (Dick) Gordon
Theoretical Biologist, Embryogenesis Center
Gulf Specimen Marine Laboratory (http://www.gulfspecimen.org)
Visiting Professor, Micro & Nanotechnology Institute, Old Dominion University
1-(850) 745-5011 or Skype: DickGordonCan
DickGo...@gmail.com
Steve Grand
Steve Grand
numbers in a computer. If <0.5V is zero and >4.5V is 1, it's entirely
possible for a bit in a computer's memory to represent a half and be at
2.5V. In fact it HAS to pass through that voltage on the way from one state
to the other. It just doesn't spend very long there! Phase transitions tend
to occur in systems with positive feedback - once they get started they get
harder and harder to stop. Quite possibly quantum ones, too. Schroedinger
was trying to make a point about the absurdity of superposition, as I
understand it, rather than defend it.
-----Original Message-----
From: Dr. Richard Gordon Ph.D.
Sent: Saturday, March 03, 2012 8:15 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics239:: Entropy and information
Saturday, March 3, 2012 10:09 PM, Panacea, FL, USA
Ah death and the soul next = information? However, in practical terms Steve
McGrew is right: we use that fuzzy boundary to harvest transplantable organs
and tissues from �dead� people. Which then takes us to Schroedinger�s cat,
which while fuzzy in other ways, we now see as not dead/alive as a binary
variable. If the cat is not just dead/alive, can it still be a quantum
mixture of uncollapsed states? Has Schroedinger�s paradox itself collapsed?
Yours, -Dick Gordon
On 2012-03-03, at 9:52 PM, Steve McGrew wrote:
> Steve2,
> I'm almost totally in agreement with you, and like very much what you had
> to say about names and persistent phenomena.
>
> One point of disagreement: "One second he's living; the next he's
> non-living." I'm not convinced that there is a perfectly sharp boundary
> between "living" and "non-living", especially in the case of a human being
> on his deathbed. Perhaps there is a boundary that could be at the
> transition between "revivable" and "non-revivable", but that is obviously
> a very fuzzy boundary that moves as our medical technology improves.
>
> Steve McGrew
Dr. Richard (Dick) Gordon
Theoretical Biologist, Embryogenesis Center
Gulf Specimen Marine Laboratory (http://www.gulfspecimen.org)
Visiting Professor, Micro & Nanotechnology Institute, Old Dominion
University
1-(850) 745-5011 or Skype: DickGordonCan
DickGo...@gmail.com
--
Steve McGrew
I wouldn't say there is no quantitative difference.� There is a real, physical difference: the electronic states of the memory and buffers-- and physics has everything to say about how the states subsequently evolve.� On the other hand, I'm not sure what would constitute a qualitative difference without in fact being a physical difference.
Steve McGrew
On 3/3/2012 7:23 PM, Steve Grand wrote:
...Or take two electronic circuits with absolutely identical constituents and complexity but slightly different configurations � one might be an oscillator and �live� while the other does nothing at all. There�s no quantitative difference, just a qualitative one. Physics doesn�t have much to say about qualities. Nor does information theory!�S2�
Steve Grand
Steve McGrew
On 3/3/2012 7:23 PM, Steve Grand wrote:
...Or take two electronic circuits with absolutely identical constituents and complexity but slightly different configurations – one might be an oscillator and “live” while the other does nothing at all. There’s no quantitative difference, just a qualitative one. Physics doesn’t have much to say about qualities. Nor does information theory!S2
Evgenii Rudnyi
means. You use this term and according to you it is very important in
biology. Yet, it is still unclear to me what do you mean by information.
I know that it is hard to make a definition. I guess that for life or
consciousness there is still no solid definition. Thereafter it is
possible to talk about something without a formal definition but still
it is good to explain what it is by means of examples.
The difference of information with life and consciousness is that the
last two are immediately observable. Even I cannot define exactly what
they are, I can at least show on them. Well, with consciousness it is
more complicated because each one has its own conscious experience but
it is there after all.
Information on the other hand is some abstract term. There is a formal
definition by Shannon but it is just a mathematical construct. If we
speak of a gene, then it is good to say what you mean. DNA is after all
is just a normal molecular and at the level of chemistry I do not see
information there. Do you mean molecular modeling fails to describe DNA
and we should add some new laws to this end?
In a loose sense, as a analogy, I see the point in saying that genes
transfer information. Yet, if we speak about science, then the goal
would be to convert this loose saying to some formal statements. Could
you please do it with an example of gene therapy?
Scientists always blame philosophers for being unclear. With information
in biology however, the situation, in my view, is even worse. Everybody
talks about information but it is very hard to follow. The word
information has many different meanings and it is unclear which meaning
has being employed when.
Evgenii
On 04.03.2012 00:35 William R. Buckley said the following:
Evgenii Rudnyi
Barbieri, M. (2007). Is the cell a semiotic system? In: Introduction to
Biosemiotics: The New Biological Synthesis. Eds.: M. Barbieri, Springer:
179-208.
http://www.springerlink.com/content/n0143kh20946g050/
Barbieri proves that the cell is also a semiotic system. He has found
the way on how to play with definitions in order to find meaning during
work of DNA/RNA/proteins. His paper is quite logical though, he gives
definitions and then applies them. It is more easier to follow his logic
in the paper as the logic of using the term information in the current
discussion. By the way his conclusion about information at the DNA level
is quite different.
See also
http://embryogenesisexplained.com/2012/02/is-the-cell-a-semiotic-system.html
I doubt however, that this will help us to understand how the number pi
appears when we consider two mathematicians at the chemistry level.
Evgenii
On 03.03.2012 23:11 Newman, Stuart said the following:
Steve McGrew
OK, you and I meant different things by "quantitative".� You're saying that typical measures of information content or complexity don't even come close to capturing the important differences between "living" and "dead", or between the computer that functions and the one that doesn't when the physical difference can be as small as the location of a single atom.� Of course you're right.
Steve McGrew
On 3/3/2012 9:50 PM, Steve Grand wrote:
Yeah, a physical difference, I agree, but not a quantitative one. And the electronic states arise solely from the qualitative difference. Until you apply power there is no quantifiable difference at all. Same masses, same number of protons, same Shannon entropy, same everything, except in one case you swap a couple of wires over. The two circuits are different but not in any way you can usefully put a number on.
�I think this is about abstraction. You or somebody else brought up gases as highly abstractable systems - 10^23 molecules, all with their own momentum vectors and high information content, and yet in practical terms you can squidge the whole thing down to just three numbers � P, T, V. Yet take a somewhat similar parallel system of identical interacting parts like Conway�s Life game. You can�t do much with numbers there at all. The behavior of the system AS a system - the difference between an �interesting� starting pattern and an uninteresting (static or short-lived) one, say - can�t be determined by any abstraction � you have to play the game and see what it does, because the system is its own best description. Just five dots can give you a pattern that lasts one timestep and then disappears, a pattern that explodes into amazing complexity and lasts hundreds of timesteps, never repeating itself, and the glider configuration, which lasts infinitely (on an infinite board) and even maintains its form. The first time I saw a glider I fell off my chair and it completely changed my life and the way I view the universe! Conway�s game is qualitative � numbers tell you nothing. Numbers are useful for describing the class of cellular automata in general � Chris Langton�s K constant, for instance, and the idea of rising complexity hitting a distinct phase transition into chaos. But in the game itself there is no way you can say what the thousandth timestep will look like without calculating the other 999, because it�s a chaotic system. Lots of stuff is like this, but I sometimes feel as if we�ve all become hypnotized by the huge success of Newton and Boyle with their linearly decomposable systems. Biology is incredibly nonlinear and in many aspects chaotic, so quantifying things doesn�t always work as well as expected. Information theory being a case in point, perhaps?�Steve2���
From: Steve McGrewSent: Saturday, March 03, 2012 9:36 PMSubject: Re: EmbryoPhysics242:: Entropy and information
�
Or take two identical plugged-in computers, the first of which is running a program and the second of which is not.
I wouldn't say there is no quantitative difference.� There is a real, physical difference: the electronic states of the memory and buffers-- and physics has everything to say about how the states subsequently evolve.� On the other hand, I'm not sure what would constitute a qualitative difference without in fact being a physical difference.
Steve McGrew
On 3/3/2012 7:23 PM, Steve Grand wrote:
...Or take two electronic circuits with absolutely identical constituents and complexity but slightly different configurations � one might be an oscillator and �live� while the other does nothing at all. There�s no quantitative difference, just a qualitative one. Physics doesn�t have much to say about qualities. Nor does information theory!�S2
�
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
Steve Grand
OK, you and I meant different things by "quantitative". You're saying that typical measures of information content or complexity don't even come close to capturing the important differences between "living" and "dead", or between the computer that functions and the one that doesn't when the physical difference can be as small as the location of a single atom. Of course you're right.
Steve McGrew
On 3/3/2012 9:50 PM, Steve Grand wrote:
Yeah, a physical difference, I agree, but not a quantitative one. And the electronic states arise solely from the qualitative difference. Until you apply power there is no quantifiable difference at all. Same masses, same number of protons, same Shannon entropy, same everything, except in one case you swap a couple of wires over. The two circuits are different but not in any way you can usefully put a number on.
I think this is about abstraction. You or somebody else brought up gases as highly abstractable systems - 10^23 molecules, all with their own momentum vectors and high information content, and yet in practical terms you can squidge the whole thing down to just three numbers – P, T, V. Yet take a somewhat similar parallel system of identical interacting parts like Conway’s Life game. You can’t do much with numbers there at all. The behavior of the system AS a system - the difference between an “interesting” starting pattern and an uninteresting (static or short-lived) one, say - can’t be determined by any abstraction – you have to play the game and see what it does, because the system is its own best description. Just five dots can give you a pattern that lasts one timestep and then disappears, a pattern that explodes into amazing complexity and lasts hundreds of timesteps, never repeating itself, and the glider configuration, which lasts infinitely (on an infinite board) and even maintains its form. The first time I saw a glider I fell off my chair and it completely changed my life and the way I view the universe! Conway’s game is qualitative – numbers tell you nothing. Numbers are useful for describing the class of cellular automata in general – Chris Langton’s K constant, for instance, and the idea of rising complexity hitting a distinct phase transition into chaos. But in the game itself there is no way you can say what the thousandth timestep will look like without calculating the other 999, because it’s a chaotic system. Lots of stuff is like this, but I sometimes feel as if we’ve all become hypnotized by the huge success of Newton and Boyle with their linearly decomposable systems. Biology is incredibly nonlinear and in many aspects chaotic, so quantifying things doesn’t always work as well as expected. Information theory being a case in point, perhaps?Steve2
From: Steve McGrewSent: Saturday, March 03, 2012 9:36 PMSubject: Re: EmbryoPhysics242:: Entropy and information
Or take two identical plugged-in computers, the first of which is running a program and the second of which is not.
I wouldn't say there is no quantitative difference. There is a real, physical difference: the electronic states of the memory and buffers-- and physics has everything to say about how the states subsequently evolve. On the other hand, I'm not sure what would constitute a qualitative difference without in fact being a physical difference.
Steve McGrew
On 3/3/2012 7:23 PM, Steve Grand wrote:
...Or take two electronic circuits with absolutely identical constituents and complexity but slightly different configurations – one might be an oscillator and “live” while the other does nothing at all. There’s no quantitative difference, just a qualitative one. Physics doesn’t have much to say about qualities. Nor does information theory!S2
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
William R. Buckley
I think my use of the term *information* is thoroughly consistent, and from that consistency you ought to be able to discern my meaning.
Still, let me be quite blunt regarding the DNA posited for gene therapy. Clearly, a well selected chunk of new DNA has a one-to-one
correspondence (by virtue of the transcription and translation process inherent in the host cell) to a particular polypeptide, which particular
polypeptide could not be constructed by the host cell prior to the act of gene therapy (introduction of the new DNA unit into the host
genome) but which particular polypeptide can be constructed by the host cell, post gene therapy.
I think that any rational observer would agree with me that such an act of gene therapy introduces a unit of information to the host genome.
And, all would agree even without understanding the nature of information; they would simply agree that such information exists.
wrb
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysics+unsubscribe@googlegroups.com.
Newman, Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Sunday, March 04, 2012 1:38 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics248:: Entropy and information
Evgenii:
I think my use of the term *information* is thoroughly consistent, and from that consistency you ought to be able to discern my meaning.
Still, let me be quite blunt regarding the DNA posited for gene therapy. Clearly, a well selected chunk of new DNA has a one-to-one
correspondence (by virtue of the transcription and translation process inherent in the host cell) to a particular polypeptide, which particular
polypeptide could not be constructed by the host cell prior to the act of gene therapy (introduction of the new DNA unit into the host
genome) but which particular polypeptide can be constructed by the host cell, post gene therapy.
I think that any rational observer would agree with me that such an act of gene therapy introduces a unit of information to the host genome.
And, all would agree even without understanding the nature of information; they would simply agree that such information exists.
wrb
On Sun, Mar 4, 2012 at 1:02 AM, Evgenii Rudnyi <use...@rudnyi.ru<mailto:use...@rudnyi.ru>> wrote:
What do I claim? Just that you have not explained what information means. You use this term and according to you it is very important in biology. Yet, it is still unclear to me what do you mean by information.
I know that it is hard to make a definition. I guess that for life or consciousness there is still no solid definition. Thereafter it is possible to talk about something without a formal definition but still it is good to explain what it is by means of examples.
The difference of information with life and consciousness is that the last two are immediately observable. Even I cannot define exactly what they are, I can at least show on them. Well, with consciousness it is more complicated because each one has its own conscious experience but it is there after all.
Information on the other hand is some abstract term. There is a formal definition by Shannon but it is just a mathematical construct. If we speak of a gene, then it is good to say what you mean. DNA is after all is just a normal molecular and at the level of chemistry I do not see information there. Do you mean molecular modeling fails to describe DNA and we should add some new laws to this end?
In a loose sense, as a analogy, I see the point in saying that genes transfer information. Yet, if we speak about science, then the goal would be to convert this loose saying to some formal statements. Could you please do it with an example of gene therapy?
Scientists always blame philosophers for being unclear. With information in biology however, the situation, in my view, is even worse. Everybody talks about information but it is very hard to follow. The word information has many different meanings and it is unclear which meaning has being employed when.
Evgenii
On 04.03.2012 00:35 William R. Buckley said the following:
So, you claim that genes represent nothing? I think you will regret
holding to such a position.
On Saturday, March 3, 2012, Evgenii Rudnyi<use...@rudnyi.ru<mailto:use...@rudnyi.ru>> wrote:
Some chemical reactions are taking place indeed (feedback is presumably
also there). I do not see though information manipulation.
Evgenii
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com>.
For more options, visit this group at http://groups.google.com/group/embryophysics?hl=en.
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com.
William R. Buckley
While what you say is important to DNA which occurs naturally, I was quite specific - please read again - that a "WELL SELECTED" chunk of DNA has such a one-to-one correspondence with a polypeptide,
and that is all that is important to my point - it matters not how that polypeptide later folds or doesn't fold.
The point is a thought experiment, and you missed the point.
wrb
Newman, Stuart
I understood the terms of your thought experiment. My reply, however, was informed by the fact that RNAs that are alternatively spliced in the natural state will typically not have a route into the cytoplasm without shuttle proteins that participate in the splicing process in the nucleus. Moreover, the cell that previously lacked the protein in question may have compensatory expression patterns of other proteins which coud indeed make the new protein take on the wrong conformation. If you want to stipulate in your thought experiment that none of this will happen, it's your privilege. My repsonse was intended to contribute to the ongoing discussion of whether DNA-based information can be defined unambigously and in a context-independent fashion.
Stuart
________________________________
From: embryo...@googlegroups.com [embryo...@googlegroups.com] On Behalf Of William R. Buckley [bill.b...@gmail.com]
Sent: Sunday, March 04, 2012 2:10 PM
To: embryo...@googlegroups.com
Subject: Re: EmbryoPhysics250:: Entropy and information
Stuart:
While what you say is important to DNA which occurs naturally, I was quite specific - please read again - that a "WELL SELECTED" chunk of DNA has such a one-to-one correspondence with a polypeptide,
and that is all that is important to my point - it matters not how that polypeptide later folds or doesn't fold.
The point is a thought experiment, and you missed the point.
wrb
On Sun, Mar 4, 2012 at 11:01 AM, Newman, Stuart <NEW...@nymc.edu<mailto:NEW...@nymc.edu>> wrote:
The DNA sequence does not have a one-to-one correpondence to a particular polypeptide if the RNA specified by the DNA sequence is alternatively spliced, as is the case with at least 70 percent of all human genes. And once a particlular polypeptide gets made, its structure and function are not uniquely determined by its primary structure. Many proteins are intrinsically unstructured, only achieving a specific role in the cell in the context of other optionally present proteins. And even proteins that are not intrinsically unstructured can take on can alternative tertiary structures by virtue of the effect of the rate of translation on on folding pathways.
________________________________
From: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com> [embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>] On Behalf Of William R. Buckley [bill.b...@gmail.com<mailto:bill.b...@gmail.com>]
Sent: Sunday, March 04, 2012 1:38 PM
To: embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>
Subject: Re: EmbryoPhysics248:: Entropy and information
Evgenii:
I think my use of the term *information* is thoroughly consistent, and from that consistency you ought to be able to discern my meaning.
Still, let me be quite blunt regarding the DNA posited for gene therapy. Clearly, a well selected chunk of new DNA has a one-to-one
correspondence (by virtue of the transcription and translation process inherent in the host cell) to a particular polypeptide, which particular
polypeptide could not be constructed by the host cell prior to the act of gene therapy (introduction of the new DNA unit into the host
genome) but which particular polypeptide can be constructed by the host cell, post gene therapy.
I think that any rational observer would agree with me that such an act of gene therapy introduces a unit of information to the host genome.
And, all would agree even without understanding the nature of information; they would simply agree that such information exists.
wrb
On Sun, Mar 4, 2012 at 1:02 AM, Evgenii Rudnyi <use...@rudnyi.ru<mailto:use...@rudnyi.ru><mailto:use...@rudnyi.ru<mailto:use...@rudnyi.ru>>> wrote:
What do I claim? Just that you have not explained what information means. You use this term and according to you it is very important in biology. Yet, it is still unclear to me what do you mean by information.
I know that it is hard to make a definition. I guess that for life or consciousness there is still no solid definition. Thereafter it is possible to talk about something without a formal definition but still it is good to explain what it is by means of examples.
The difference of information with life and consciousness is that the last two are immediately observable. Even I cannot define exactly what they are, I can at least show on them. Well, with consciousness it is more complicated because each one has its own conscious experience but it is there after all.
Information on the other hand is some abstract term. There is a formal definition by Shannon but it is just a mathematical construct. If we speak of a gene, then it is good to say what you mean. DNA is after all is just a normal molecular and at the level of chemistry I do not see information there. Do you mean molecular modeling fails to describe DNA and we should add some new laws to this end?
In a loose sense, as a analogy, I see the point in saying that genes transfer information. Yet, if we speak about science, then the goal would be to convert this loose saying to some formal statements. Could you please do it with an example of gene therapy?
Scientists always blame philosophers for being unclear. With information in biology however, the situation, in my view, is even worse. Everybody talks about information but it is very hard to follow. The word information has many different meanings and it is unclear which meaning has being employed when.
Evgenii
On 04.03.2012 00:35 William R. Buckley said the following:
So, you claim that genes represent nothing? I think you will regret
holding to such a position.
On Saturday, March 3, 2012, Evgenii Rudnyi<use...@rudnyi.ru<mailto:use...@rudnyi.ru><mailto:use...@rudnyi.ru<mailto:use...@rudnyi.ru>>> wrote:
Some chemical reactions are taking place indeed (feedback is presumably
also there). I do not see though information manipulation.
Evgenii
--
You received this message because you are subscribed to the Google Groups "EmbryoPhysics" group.
To post to this group, send email to embryo...@googlegroups.com<mailto:embryo...@googlegroups.com><mailto:embryo...@googlegroups.com<mailto:embryo...@googlegroups.com>>.
To unsubscribe from this group, send email to embryophysic...@googlegroups.com<mailto:embryophysics%2Bunsu...@googlegroups.com><mailto:embryophysics%2Bunsu...@googlegroups.com<mailto:embryophysics%252Buns...@googlegroups.com>>.
William R. Buckley
The mere fact that a previously unobserved polypeptide becomes a regular feature of some host organism is prima facie evidence of the presence of introduced information, and that is what Evgenii argues against.
Please, do not try frosting the cake before it is baked.
wrb
Dr. Richard Gordon
Friday, March 9
THE SECOND LAW OF EVERYTHING
A deck of cards being shuffled, a basement becoming ever more cluttered, a car relentlessly rusting - these are all cited as examples of entropy, the reason things fall apart. But as Ian Wilkinson discovers, entropy is really about the transference of energy, and it underlies absolutely everything.