Phillip E. Johnson now on the WWCW!
ma...@superb.com
I recently added a number of articles by Phillip Johnson to the WWCW
Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
answers to questions such as:
-- What is Darwinism?
--How can we tell science from religion?
--Can Darwinism really stand close scrutiny?
See you there,
Mark
WWCW.org
Mike
work. I had a quick read of one article (What is Darwinism?). It's
absolute crap but it's nice to know that the criticism aimed at the man is
warranted.
<ma...@superb.com> wrote in message
news:36e32e77...@news.extremezone.com...
ThomasPaine_II
>Hi all,
>
>I recently added a number of articles by Phillip Johnson to the WWCW
>Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
>answers to questions such as:
>
>-- What is Darwinism?
>
>--How can we tell science from religion?
>
>--Can Darwinism really stand close scrutiny?
>
>See you there,
>
>Mark
>WWCW.org
>
Great for a laugh; but mostly more creationist crap and lies.
Bonz
<36e32e77...@news.extremezone.com> :
>Hi all,
>
>I recently added a number of articles by Phillip Johnson to the WWCW
>Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
>answers to questions such as:
>
>-- What is Darwinism?
>
>--How can we tell science from religion?
>
>--Can Darwinism really stand close scrutiny?
>
>See you there,
>
>Mark
>WWCW.org
No thanks. Johnson knows less about evolution than I do about
collateral estoppel.
Why would you pay much attention to a man who 1) knows nothing
about the subject and 2) is in a profession devoted not to
finding the truth, but to winning by selectively citing the
evidence?
Law is an adversarial enterprise. Science is not.
Wesley R. Elsberry
Bonz <tea...@bbtel.HORMEL.com> wrote:
>On 7 Mar 1999 20:56:43 -0500, ma...@superb.com wrote in message
><36e32e77...@news.extremezone.com> :
[...]
B>No thanks. Johnson knows less about evolution than I do
B>about collateral estoppel.
B>Why would you pay much attention to a man who 1) knows
B>nothing about the subject and 2) is in a profession devoted
B>not to finding the truth, but to winning by selectively
B>citing the evidence?
I pay attention to Johnson because of his influence in the
anti-evolution movement.
B>Law is an adversarial enterprise. Science is not.
Law is adversarial by nature. Science is not *necessarily*
adversarial, but sometimes works out that way. There have
been some notable "feuds" conducted in the literature, of
which the not-so-friendly rivalry betwen Marsh and Cope last
century. I anticipate having various and sundry adversaries
crop up in my submissions of future publications due to my
participation in particular research projects. Incipient
paranoia? I don't think so.
--
Wesley R. Elsberry, Student in Wildlife & Fisheries Sciences, Tx A&M U.
Visit the Online Zoologists page (http://www.rtis.com/nat/user/elsberry)
Email to this account is dumped to /dev/null, whose Spam appetite is capacious.
"It's never said at all, on the map that Carrie reads" - BOC
maf...@my-dejanews.com
>Hi all,
>
>I recently added a number of articles by Phillip Johnson to the WWCW
>Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
>answers to questions such as:
>
>-- What is Darwinism?
>
>--How can we tell science from religion?
>
>--Can Darwinism really stand close scrutiny?
So when are going to establish your theocratic dictatorship?
<http://x12.dejanews.com/getdoc.xp?AN=426163336>
>
>Mark
>WWCW.org
-----------== Posted via Deja News, The Discussion Network ==----------
http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own
z@z
much better indeed than most neo-Darwinist high priests
(e.g. Richard Dawkins) and believers.
Here some excerpts from Philip E. Johnson's article
"How Can We Tell Science from Religion?":
http://www.wwcw.org/q-johnson1.html
" It is easy to see why ambitious scientists would be attracted to
a philosophy that maximizes the explanatory power of science,
but this very advantage creates a paradox. If science explains
literally everything in terms of physical causes, then it also explains
the scientific mind and its thoughts. If matter is ultimately all
there is, and if our brains are the product of mindless chemical
combinations, and if "the mind is merely what the brain does,"
then our thoughts and theories are products of mindless forces.
This disquieting point remains valid even if the relationship
between chemistry and thought is deemed to be complex, as
in the "computational theory of the mind. "
" Don't misunderstand me; I am no anti-rationalist. I am convinced
that we really do have the ability to reason from sound premises
to true conclusions, when our minds are operating as they should,
and that our best theories correspond at least approximately to
"the way things really are." The question is whether the ability to
theorize. which is different in kind from anything in the animal
world, can be explained from a materialist starting point. "
" Everybody with even a cursory knowledge of the literature knows
that the textbook examples (Kettlewell's peppered moths,
Grant's finch beaks) describe relatively trivial changes that involve
no innovation or increase in genetic information. Debate this
point (as I have) and you will find that most Darwinists quickly
retreat to the vague claim that "evolution has occurred." But when
materialism is assumed as the very basis of science, they can
re-emerge a few logical steps later in triumph. Something had
to guide evolution, to produce those wonders of apparent design,
and natural selection is just about the only materialist contender. "
" Putting these points together: we see that to account for life
(in this case, the cell), we have to explain not only the origin of the
chemicals but also the origin of the information. The neo-Darwinian
explanation is well-known. It assumes that a very simple replicating
organism started one way or another. Thereafter, the theory
ascribes the increases in information to random mutation, and
insists that the vast quantity of information can be provided by
mutation in very small doses, if each dose immediately adds to
the ability of the organism to survive and reproduce. "
" There are many excellent reasons for doubting the adequacy of
this kind of explanation. Random changes (such as copying errors
in the DNA) do not generate increases in information, whether
they are small or large. It is not necessarily easier to provide the
same amount of information in multitudinous small doses, rather
than a single large one. Each increment is less unlikely, but the
price one pays is that one has to have a great many increments,
each of which must supply the precise kind of new information
required. To illustrate the point with an analogy: It is hard enough
to earn one million dollars by winning the grand prize in a lottery,
but it is no easier to achieve that feat by winning a $100 prize
10,000 times. "
Wolfgang
http://members.lol.li/twostone/E/psychon.html
(presentation of a non-reductionist evolution theory)
z@z
> his work. I had a quick read of one article (What is Darwinism?).
> It's absolute crap but it's nice to know that the criticism aimed at
> the man is warranted.
A excerpt from "What is Darwinism?":
http://www.wwcw.org/q-johnson4.html
" Persons who advocate the compromise position called "theistic
evolution" are in my experience always vague about what they
mean by "evolution." They have good reason to be vague. As we
have seen, Darwinian evolution is by definition unguided and
purposeless, and such evolution cannot in any meaningful sense
be theistic. For evolution to be genuinely theistic it must be guided
by God, whether this means that God programmed the process
in advance or stepped in from time to time to give it a push in the
right direction. To Darwinists evolution guided by God is a soft
form of creationism, which is to say it is not evolution at all. To
repeat, this understanding goes to the very heart of Darwinist
thinking. Allow a preexisting supernatural intelligence to guide
evolution, and this omnipotent being can do a whole lot more
than that. "
Do you really think that this is absolute crap? On what is your
judgement based?
I suppose that it is based on orthodoxy, dogmatism, authority
and prejudices!
z@z
>> Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
>> answers to questions such as:
> No thanks. Johnson knows less about evolution than I do about
> collateral estoppel.
> Why would you pay much attention to a man who 1) knows nothing
> about the subject and 2) is in a profession devoted not to
> finding the truth, but to winning by selectively citing the
> evidence?
> Law is an adversarial enterprise. Science is not.
What gives you the right to criticize an author you have not read or you
don't understand?
Mike
>Philip E. Johnson seems to me a great logician and epistemologist,
>much better indeed than most neo-Darwinist high priests
>(e.g. Richard Dawkins) and believers.
>
>Here some excerpts from Philip E. Johnson's article
>"How Can We Tell Science from Religion?":
>
>http://www.wwcw.org/q-johnson1.html
>
<snip>
All the paragraphs were pretty lame. I'll concentrate on just one.
Although it doesn't need me to think long. You think Johnson is a great
logician...
>" There are many excellent reasons for doubting the adequacy of
> this kind of explanation. Random changes (such as copying errors
> in the DNA) do not generate increases in information, whether
> they are small or large. It is not necessarily easier to provide the
> same amount of information in multitudinous small doses, rather
> than a single large one. Each increment is less unlikely, but the
> price one pays is that one has to have a great many increments,
> each of which must supply the precise kind of new information
> required. To illustrate the point with an analogy: It is hard enough
> to earn one million dollars by winning the grand prize in a lottery,
> but it is no easier to achieve that feat by winning a $100 prize
> 10,000 times. "
When I walk to the shops at lunchtime (they are a kilometre away
approximately), I get there through 1,000 steps, not one huge leap. Also,
if instead of buying a lottery ticket each week I deposit that money in a
bank account I will definitely be a millionaire in the long run.
I suggest that Mr Johnson should walk to the shops and put some money in his
bank account. He may learn something.
Mike
>> Thanks for the link. I had heard about Phillip Johnson but not read
>> his work. I had a quick read of one article (What is Darwinism?).
>> It's absolute crap but it's nice to know that the criticism aimed at
>> the man is warranted.
>
>A excerpt from "What is Darwinism?":
>http://www.wwcw.org/q-johnson4.html
>
>" Persons who advocate the compromise position called "theistic
> evolution" are in my experience always vague about what they
> mean by "evolution." They have good reason to be vague. As we
> have seen, Darwinian evolution is by definition unguided and
> purposeless, and such evolution cannot in any meaningful sense
> be theistic. For evolution to be genuinely theistic it must be guided
> by God, whether this means that God programmed the process
> in advance or stepped in from time to time to give it a push in the
> right direction. To Darwinists evolution guided by God is a soft
> form of creationism, which is to say it is not evolution at all. To
> repeat, this understanding goes to the very heart of Darwinist
> thinking. Allow a preexisting supernatural intelligence to guide
> evolution, and this omnipotent being can do a whole lot more
> than that. "
>
>Do you really think that this is absolute crap? On what is your
>judgement based?
Yes. I think it is crap. "For evolution to be genuinely theistic it must
be guided by God"... Why? Those theistic evolutionists I know believe that
God created the universe with conditions such that life may evolve, not that
God has guided every step or preprogrammed life. They have not been "vague"
on this point at all. Perhaps some of the "theistic evolutionists" in this
group would like to elaborate.
For further information, see: Straw man, begging the question.
>
>I suppose that it is based on orthodoxy, dogmatism, authority
>and prejudices!
No, it is based on a much sounder knowledge of the debate than Johnson seems
, on the strength of your quote, to have.
R. Tang
>Philip E. Johnson seems to me a great logician and epistemologist,
>much better indeed than most neo-Darwinist high priests
>(e.g. Richard Dawkins) and believers.
Unforunately, this does not make one a good biologist or
biochemist, where Johnson fails miserably.
Logic and epistemology are limited without a command of the facts.
--
-Roger Tang, gwan...@u.washington.edu, Artistic Director PC Theatre
- Editor, Asian American Theatre Revue [NEW URL]
- http://www.abcflash.com/a&e/r_tang/AATR.html
-Declared 4-F in the War Between the Sexes
Evan W. Steeg
z@z wrote in message <7c1jof$fjb$3...@pollux.ip-plus.net>...
>A excerpt from "What is Darwinism?":
>http://www.wwcw.org/q-johnson4.html
>
>" Persons who advocate the compromise position called "theistic
> evolution" are in my experience always vague about what they
> mean by "evolution." They have good reason to be vague. As we
> have seen, Darwinian evolution is by definition unguided and
> purposeless, and such evolution cannot in any meaningful sense
> be theistic. For evolution to be genuinely theistic it must be guided
> by God, whether this means that God programmed the process
> in advance or stepped in from time to time to give it a push in the
> right direction. To Darwinists evolution guided by God is a soft
> form of creationism, which is to say it is not evolution at all. To
> repeat, this understanding goes to the very heart of Darwinist
> thinking. Allow a preexisting supernatural intelligence to guide
> evolution, and this omnipotent being can do a whole lot more
> than that. "
>
>Do you really think that this is absolute crap?
Pretty close. It seems to be the tired and simple-minded "God versus
Evolution" false dichotomy being served to us once again. Only this time
it's cooked with a little sophistry instead of appearing in its usual raw
form (e.g., "Any so-called Christian who accepts 'theistic' evilution is not
a REAL Christian!!").
So the professional liar Johnson asserts, more or less, that if God can be
involved in evolution, then that God could also do anything else (presumably
including instant creation of all "kinds" by fiat). Well, that's as true as
it is useless and stupid. One might as well say that "such a God could
also make apples fall up instead of down, allow us to build perpetual motion
machines, and produce dogs that bark the complete works of Goethe". Yes, it
is theoretically possible that God might have done things in a way that
contradicts the heaps of physical and observational evidence, but why are
Johnson and his scientificially ignorant ilk so wedded to this idea? And
why must sensible, open-minded people follow them in their idiocy?
There is no evidentiary or logical reason why the existence of a
supernatural being is incompatible with an observable gradual process which
explains the vast majority of geological, archaeological and molecular
biological and genetic data. I understand quite well why dogmatic atheists
and dogmatic adherents of particular ancient mideastern religions try to
pretend there is. Which are you?
Evan
Wesley R. Elsberry
[...]
B> No thanks. Johnson knows less about evolution than I do about
B> collateral estoppel.
B> Why would you pay much attention to a man who 1) knows nothing
B> about the subject and 2) is in a profession devoted not to
B> finding the truth, but to winning by selectively citing the
B> evidence?
B> Law is an adversarial enterprise. Science is not.
W>What gives you the right to criticize an author you have not
W>read or you don't understand?
Present evidence that Bonz has not read Johnson.
It is a good question, though, when applied correctly. For
example, go to p.30 in Johnson's "Darwin On Trial" and look at
the first complete paragraph. Johnson thoroughly
misunderstands Darwin there. What's his excuse?
--
Wesley R. Elsberry, Student in Wildlife & Fisheries Sciences, Tx A&M U.
Visit the Online Zoologists page (http://www.rtis.com/nat/user/elsberry)
Email to this account is dumped to /dev/null, whose Spam appetite is capacious.
"freddy is no more but he died game" - archy
Bonz
<7c1job$fjb$1...@pollux.ip-plus.net> :
>Philip E. Johnson seems to me a great logician and epistemologist,
>much better indeed than most neo-Darwinist high priests
>(e.g. Richard Dawkins) and believers.
Well, yeah, I guess, if you're brain dead.
<<snip more of the same Creationist double talk>>
Bonz
<7c1job$fjb$1...@pollux.ip-plus.net> :
>Philip E. Johnson seems to me a great logician and epistemologist,
>much better indeed than most neo-Darwinist high priests
>(e.g. Richard Dawkins) and believers.
>
>Here some excerpts from Philip E. Johnson's article
>"How Can We Tell Science from Religion?":
>
>http://www.wwcw.org/q-johnson1.html
>
>" It is easy to see why ambitious scientists would be attracted to
> a philosophy that maximizes the explanatory power of science,
> but this very advantage creates a paradox. If science explains
> literally everything in terms of physical causes, then it also explains
> the scientific mind and its thoughts. If matter is ultimately all
> there is, and if our brains are the product of mindless chemical
> combinations, and if "the mind is merely what the brain does,"
> then our thoughts and theories are products of mindless forces.
> This disquieting point remains valid even if the relationship
> between chemistry and thought is deemed to be complex, as
> in the "computational theory of the mind. "
Why is that even vaguely disquieting? That is pretty close to my
ordinary, day to day working assumption, and has been for
decades. I don't find it disquieting in the least.
>
>" Don't misunderstand me; I am no anti-rationalist. I am convinced
> that we really do have the ability to reason from sound premises
> to true conclusions, when our minds are operating as they should,
> and that our best theories correspond at least approximately to
> "the way things really are." The question is whether the ability to
> theorize. which is different in kind from anything in the animal
> world, can be explained from a materialist starting point. "
Why is he worrying about 'true conclusions', when he is talking
about science? That makes it seem as if science is some sort of
quest for the truth.
>" Everybody with even a cursory knowledge of the literature knows
> that the textbook examples (Kettlewell's peppered moths,
> Grant's finch beaks) describe relatively trivial changes that involve
> no innovation or increase in genetic information.
I have somewhat more than a cursory knowledge, and I think this
statement is pure bull shit.
> Debate this
> point (as I have) and you will find that most Darwinists quickly
> retreat to the vague claim that "evolution has occurred."
Why does he keep saying Darwinists? Does he mean as opposed to
neo-Darwinists? Or Kimura's neutralists? Or what?
> But when
> materialism is assumed as the very basis of science, they can
> re-emerge a few logical steps later in triumph. Something had
> to guide evolution, to produce those wonders of apparent design,
> and natural selection is just about the only materialist contender. "
This makes no sense at all.
>" Putting these points together: we see that to account for life
> (in this case, the cell), we have to explain not only the origin of the
> chemicals but also the origin of the information. The neo-Darwinian
> explanation is well-known. It assumes that a very simple replicating
> organism started one way or another. Thereafter, the theory
> ascribes the increases in information to random mutation, and
> insists that the vast quantity of information can be provided by
> mutation in very small doses, if each dose immediately adds to
> the ability of the organism to survive and reproduce. "
>
>" There are many excellent reasons for doubting the adequacy of
> this kind of explanation. Random changes (such as copying errors
> in the DNA) do not generate increases in information, whether
> they are small or large.
Then you are using a VERY strange definition if information. Why
is Johnson saying this in words, instead of in equations? Because
he knows it would make no sense that way?
> It is not necessarily easier to provide the
> same amount of information in multitudinous small doses, rather
> than a single large one. Each increment is less unlikely, but the
> price one pays is that one has to have a great many increments,
> each of which must supply the precise kind of new information
> required. To illustrate the point with an analogy: It is hard enough
> to earn one million dollars by winning the grand prize in a lottery,
> but it is no easier to achieve that feat by winning a $100 prize
> 10,000 times. "
And no one organism or line has to win any lottery. It does not
matter whether humans - or mammals for that matter -- go extinct
or not.
That's why all life is at the same 'level'.
Once again, Johnson is a transparent charlatan.
ThomasPaine_II
>much better indeed than most neo-Darwinist high priests
>(e.g. Richard Dawkins) and believers.
Do you believe in the tooth fairy too?
(snip)
ThomasPaine_II
>>> Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
>>> answers to questions such as:
>
>
>> Why would you pay much attention to a man who 1) knows nothing
>
>> Law is an adversarial enterprise. Science is not.
>
>don't understand?
A. Freedom of speech.
B. We understand him enough to recognize that he is a biased moron.
ThomasPaine_II
>> Thanks for the link. I had heard about Phillip Johnson but not read
>> his work. I had a quick read of one article (What is Darwinism?).
>> It's absolute crap but it's nice to know that the criticism aimed at
>> the man is warranted.
>
>http://www.wwcw.org/q-johnson4.html
>
>" Persons who advocate the compromise position called "theistic
> evolution" are in my experience always vague about what they
> mean by "evolution."
"In my experience", is, by no means, a meaningful (or scientific) statement.
In my experience, all lawyers are greedy assholes.
(BTW ... my experience is only with two - divorce attorneys; one on my side
and one on the ex's).
They have good reason to be vague. As we
> have seen,
Where have we seen? .... and what have we seen?
Not only are there no specifics listed here, it is asinine to assume that
anyone else has seen he same things Johnson has.
Darwinian evolution is by definition unguided and
> purposeless,
No. It is not. It is guided, and it's purposes, have nothing to do with some
supernatural invention. Chemistry, physics and survival are very good guiding
forces.
and such evolution cannot in any meaningful sense
> be theistic.
What?
A creationist that claims evolution (science) is not a religion?
That's a rare quirk of reality recognition.
For evolution to be genuinely theistic it must be guided
> by God, whether this means that God programmed the process
> in advance or stepped in from time to time to give it a push in the
> right direction.
Since there is no proof of god; then I guess that does mean evolution is
science, not religion.
To Darwinists evolution guided by God is a soft
> form of creationism, which is to say it is not evolution at all.
What?
First of all, he doesn't speak for "Darwinists"; to assume that takes a
totally arrogant asshole.
Secondly; whether he likes it or not, there are many christians who believe
evolution is guided by god.
To
> repeat, this understanding goes to the very heart of Darwinist
> thinking.
Which he, by examples above, does not represent; and has little, if any,
understanding of what "Darwinists" think.
Allow a preexisting supernatural intelligence to guide
> evolution, and this omnipotent being can do a whole lot more
> than that. "
What is this sentence supposed to be saying?
That if god did guide evolution - god can do more?
SWTF.
Totally meaningless
>
>Do you really think that this is absolute crap? On what is your
>judgement based?
>
>I suppose that it is based on orthodoxy, dogmatism, authority
>and prejudices!
No. It's based on the fact that this is absolute crap!
Jamie Schrumpf
>
>> Thanks for the link. I had heard about Phillip Johnson but not read
>> his work. I had a quick read of one article (What is Darwinism?).
>> It's absolute crap but it's nice to know that the criticism aimed at
>> the man is warranted.
>
>A excerpt from "What is Darwinism?":
>http://www.wwcw.org/q-johnson4.html
>
>" Persons who advocate the compromise position called "theistic
> evolution" are in my experience always vague about what they
> have seen, Darwinian evolution is by definition unguided and
> purposeless, and such evolution cannot in any meaningful sense
> be theistic. For evolution to be genuinely theistic it must be guided
> by God, whether this means that God programmed the process
> in advance or stepped in from time to time to give it a push in the
> form of creationism, which is to say it is not evolution at all. To
> repeat, this understanding goes to the very heart of Darwinist
> evolution, and this omnipotent being can do a whole lot more
> than that. "
>
>judgement based?
>
>I suppose that it is based on orthodoxy, dogmatism, authority
>and prejudices!
No, on the following. Pay close attention:
>" Persons who advocate the compromise position called "theistic
> evolution" are in my experience always vague about what they
> mean by "evolution."
This is vague in itself. What have his experiences been? Have they been with
scientists, or with other lawyers? Unless he tells us more detail about his
experiences, this statement is nearly meaningless.
"They have good reason to be vague. As we
> have seen, Darwinian evolution is by definition unguided and
> purposeless, and such evolution cannot in any meaningful sense
> be theistic."
It is neither totally unguided, as natural selection is indeed guided by the
environmental pressures with which an organism is faced, nor purposeless, as
its function is to make populations more fit within their environments. It
certainly is not designed to result in human beings, or to move toward "higher"
life forms. If he had said, "intelligently guided" and "apparently
purposeless," then he would have been more accurate.
His other fallacy here is that evolution is a process as much as a fact of
life, and a god could use the process of evolution to shape organisms into a
desired form much as a sculptor uses a chisel to form a piece of stone or wood.
This is why the qualifier "theistic" is placed before evolution, to
differentiate it from the purely naturalistic and non-intelligently-guided
version.
"For evolution to be genuinely theistic it must be guided
> by God, whether this means that God programmed the process
> in advance or stepped in from time to time to give it a push in the
> right direction. To Darwinists evolution guided by God is a soft
> form of creationism, which is to say it is not evolution at all."
This is Johnson's opinion only. Charles Darwin, at the end of "Origin," gives
credit to a Creator who started the process. Most scientists of the time
believed in a God who created various processes that continued on in a
naturalistic mode -- consider gravity and Newton's Laws. Deriving the orbits
of the planets did not automatically make God "go away," and neither does
deriving the evolution of life on earth.
"To repeat, this understanding goes to the very heart of Darwinist
> thinking. Allow a preexisting supernatural intelligence to guide
> evolution, and this omnipotent being can do a whole lot more
> than that. "
Sure, and He could personally be holding atoms together as well, but the strong
and weak nuclear forces are well-accepted in the world at large. Just because
God "could" do something doesn't mean that He "did" do it that way. One has to
follow the evidence in the earth itself, and the evidence indicates that the
biodiversity of life on earth didn't just "poof" appear, nor did it _require_
intelligence to design.
I'm not a biological scholar, but these are just the weakness I can see in
Johnson's argument after a basic reading of popular literature. I'm sure that
experienced biologists can do much better than I to expose Johnson's position.
--
-------------------------------------------------------------------------------
Jamie Schrumpf http://www.fred.net/hatteras
Gavin Tabor
>
> Philip E. Johnson seems to me a great logician and epistemologist,
> much better indeed than most neo-Darwinist high priests
> (e.g. Richard Dawkins) and believers.
Do you really think that he is so wonderful? On what is your
judgement based? I suppose that it is based on orthodoxy, dogmatism,
authority and prejudices!
Where have I heard that before? Whenever I read
stuff that Johnson writes I am strongly of the opinion that he is
attempting to communicate the least possible ammount in the maximum
number of words. I am reminded of Dawkin's comment about those who are
educated beyond their capacity for coherent thought. All of his
material is opinion : very rarely does he resort to a consideration
of facts.
>
> Here some excerpts from Philip E. Johnson's article
> "How Can We Tell Science from Religion?":
>
> http://www.wwcw.org/q-johnson1.html
>
> " It is easy to see why ambitious scientists would be attracted to
> a philosophy that maximizes the explanatory power of science,
> but this very advantage creates a paradox. If science explains
> literally everything in terms of physical causes, then it also explains
> the scientific mind and its thoughts. If matter is ultimately all
> there is, and if our brains are the product of mindless chemical
> combinations, and if "the mind is merely what the brain does,"
> then our thoughts and theories are products of mindless forces.
> This disquieting point remains valid even if the relationship
> between chemistry and thought is deemed to be complex, as
> in the "computational theory of the mind. "
Why is this a paradox? I don't find it at all disquieting that
we may eventually have a mechanistic model for the brain. If
Johnson does, then thats his problem.
>
> " Don't misunderstand me; I am no anti-rationalist. I am convinced
> that we really do have the ability to reason from sound premises
> to true conclusions, when our minds are operating as they should,
> and that our best theories correspond at least approximately to
> "the way things really are." The question is whether the ability to
> theorize. which is different in kind from anything in the animal
> world, can be explained from a materialist starting point. "
>
> " Everybody with even a cursory knowledge of the literature knows
> that the textbook examples (Kettlewell's peppered moths,
> Grant's finch beaks) describe relatively trivial changes that involve
> no innovation or increase in genetic information. Debate this
> point (as I have) and you will find that most Darwinists quickly
> retreat to the vague claim that "evolution has occurred." But when
> materialism is assumed as the very basis of science, they can
> re-emerge a few logical steps later in triumph. Something had
> to guide evolution, to produce those wonders of apparent design,
> and natural selection is just about the only materialist contender. "
This is just a recycling of the usual claim that NS selects pre-existing
genetic information, and evolution cannot generate new information. This
can be shown not to be the case. Consider the work presented at
http://www.newscientist.com/ns/971115/features.html
This describes the use of genetic algorithm techniques to evolve a
circuit that not only does a particular job, but does it in a way
not previously thought possible by humans.
>
> " Putting these points together: we see that to account for life
> (in this case, the cell), we have to explain not only the origin of the
> chemicals but also the origin of the information. The neo-Darwinian
> explanation is well-known. It assumes that a very simple replicating
> organism started one way or another. Thereafter, the theory
> ascribes the increases in information to random mutation, and
> insists that the vast quantity of information can be provided by
> mutation in very small doses, if each dose immediately adds to
> the ability of the organism to survive and reproduce. "
>
> " There are many excellent reasons for doubting the adequacy of
> this kind of explanation. Random changes (such as copying errors
> in the DNA) do not generate increases in information, whether
> they are small or large.
Yes they can.
> It is not necessarily easier to provide the
> same amount of information in multitudinous small doses, rather
> than a single large one. Each increment is less unlikely, but the
> price one pays is that one has to have a great many increments,
> each of which must supply the precise kind of new information
> required. To illustrate the point with an analogy: It is hard enough
> to earn one million dollars by winning the grand prize in a lottery,
> but it is no easier to achieve that feat by winning a $100 prize
> 10,000 times. "
This is only true if the events are random and uncorrelated. In
evolution
the events are not random and they are correlated : NS sees to that.
>
> Wolfgang
>
> http://members.lol.li/twostone/E/psychon.html
> (presentation of a non-reductionist evolution theory)
Gavin
--
Dr.Gavin Tabor
email : ga...@ic.ac.uk
home page : monet.me.ic.ac.uk/people/gavin/gavin.html
Department of Mechanical Engineering,
Imperial College,
London SW7 2BY
z@z
>> Philip E. Johnson seems to me a great logician and epistemologist,
>> much better indeed than most neo-Darwinist high priests
>> (e.g. Richard Dawkins) and believers.
> Do you really think that he is so wonderful? On what is your
> judgement based? I suppose that it is based on orthodoxy,
> dogmatism, authority and prejudices!
I'm not a theist (at the most a pantheist), but an evolutionist even
more consequent than Darwinists, because I do not accept such
a discontinuity in evolution as the magical appearence of
consciousness some billions years after 'big bang'.
So I do not think that all of Johnson's opinions are wonderful. My
judgement on Johnson is primarily based on his texts about AIDS,
which I really do appreciate. In my opinion the AIDS hysteria
(comparable with the medieval witch-hunting) shows better than
anything else that modern science is only quantitatively better than
medieval theology.
I proved my unprejudiced attitude by the fact that I have changed
my mind about evolution and many other things over the last
12 years. My own ideas cannot be based on orthodoxy, dogmatism
and authority, because they are too different from all prevailing ideas.
see: http://members.lol.li/twostone/E/psychon.html
> Where have I heard that before? Whenever I read
> stuff that Johnson writes I am strongly of the opinion that he is
> attempting to communicate the least possible ammount in the
> maximum number of words. I am reminded of Dawkin's comment
> about those who are educated beyond their capacity for coherent
> thought. All of his material is opinion : very rarely does he resort
> to a consideration of facts.
In my opinion Johnson (contrary to Dawkins) is able to recognize
the real (philosphical) problems and to discriminate between what
is important and what not.
It is quite normal that material in agreement with one's own
prejudices seems to be facts whereas the rest seems to be opinion!
It is my, Johnson's and many others' right to find it disquieting (or
even absurd) that "the mind is merely what the brain does" and
that "our thoughts and theories are products of mindless forces".
see for instance: http://members.lol.li/twostone/E/reductionism.html
> This is just a recycling of the usual claim that NS selects
> pre-existing genetic information, and evolution cannot generate
> new information. This can be shown not to be the case.
> Consider the work presented at
http://www.newscientist.com/ns/971115/features.html
> This describes the use of genetic algorithm techniques to evolve
> a circuit that not only does a particular job, but does it in a way
> not previously thought possible by humans.
It is not difficult to make computer games or AI programs where
also chance influences the result. It may even happen that the result
is one not expected by the programmers, but I do not believe in results
which are in principle different from what could have thought possible
by the programmers.
In any case, such algorithms are rather evidence for a guided (there
are engineers and programmers) evolution than for a purely random.
J>" There are many excellent reasons for doubting the adequacy of
J>" this kind of explanation. Random changes (such as copying errors
J>" in the DNA) do not generate increases in information, whether
J>" they are small or large.
> Yes they can.
They can in principle under special conditions, but it is much more
probable that random mutations have negative effects. At least
point mutations do not increase the information size (as measured
in bytes).
J>" To illustrate the point with an analogy: It is hard enough to
J>" earn one million dollars by winning the grand prize in a lottery,
J>" but it is no easier to achieve that feat by winning a $100 prize
J>" 10,000 times.
> This is only true if the events are random and uncorrelated. In
> evolution the events are not random and they are correlated :
> NS sees to that.
My opinion is quite similar to Johnson's:
"If it cannot be denied that the probability for random emergence
of a system (e.g. a living organism) is unrealistically low, the system
is taken apart to smaller and smaller sub-systems until random
emergence gets realistic. But it is ignored that the probability for
the whole system is calculated by multiplying the probabilities for
the emergence of all systems from their respective sub-systems.
Reductionist causal laws do not explain why sub-systems which are
useful for the whole reproduce themselves instead of disappearing
after having appeared by chance."
( http://members.lol.li/twostone/E/psychon.html#a03 )
Wolfgang
Clark Dorman
tea...@bbtel.HORMEL.com (Bonz) writes:
> On 8 Mar 1999 17:41:05 -0500, "z@z" <z...@z.lol.li> wrote in message
> <7c1job$fjb$1...@pollux.ip-plus.net> :
>
> >much better indeed than most neo-Darwinist high priests
> >(e.g. Richard Dawkins) and believers.
Johnson is a Christian evangelist. His goal is to get people to
believe in the Christian god. If you don't believe me, read
"Defeating Darwininism by Opening Minds", the last two chapters.
[snip]
> >" Don't misunderstand me; I am no anti-rationalist. I am convinced
> > that we really do have the ability to reason from sound premises
> > to true conclusions, when our minds are operating as they should,
> > and that our best theories correspond at least approximately to
> > "the way things really are." The question is whether the ability to
> > theorize. which is different in kind from anything in the animal
> > world, can be explained from a materialist starting point. "
>
> Why is he worrying about 'true conclusions', when he is talking
> about science? That makes it seem as if science is some sort of
> quest for the truth.
Because Johnson believes, and explicitly claims that the Truth is
the the Christian God is the the Creator. Anything that does not
support this is naturalistic and hence assumes and therefore
states that God does not exist.
--
Clark Dorman "Evolution is cleverer than you are."
http://cns-web.bu.edu/pub/dorman/D.html -Francis Crick
Loren King
> Philip E. Johnson seems to me a great logician and epistemologist,
How do you figure? I certainly see no evidence of this in the two books
of his that I've read. I expect he's a good professor of law, perhaps
very good; but the history, philosophy and methodology of the sciences
doesn't seem to be his strong suite.
Loren
--------------------------------------
Loren King lk...@mit.edu
http://web.mit.edu/lking/www/home.html
Ken Cox
> What gives you the right to criticize an author you have not read or you
> don't understand?
What makes you think either of the above are true?
If it helps any, I did read Johnson's book, and I did understand it,
and I also say that Johnson knows less about evolution than I do
about collateral estoppel. And I don't even know what collateral
estoppel *is*.
--
Ken Cox k...@research.bell-labs.com
Wesley R. Elsberry
W>Hello (Dr.) Gavin (Tabor)
[...]
GT> This is just a recycling of the usual claim that NS selects
GT> pre-existing genetic information, and evolution cannot generate
GT> new information. This can be shown not to be the case.
GT> Consider the work presented at
GT>http://www.newscientist.com/ns/971115/features.html
GT> This describes the use of genetic algorithm techniques to evolve
GT> a circuit that not only does a particular job, but does it in a way
GT> not previously thought possible by humans.
W>It is not difficult to make computer games or AI programs
W>where also chance influences the result. It may even happen
W>that the result is one not expected by the programmers, but
W>I do not believe in results which are in principle different
W>from what could have thought possible by the programmers.
W>In any case, such algorithms are rather evidence for a
W>guided (there are engineers and programmers) evolution than
W>for a purely random.
Nobody is claiming that the results are "purely random".
The claim at issue is whether the information provided by
the programmer is somehow infused into the information of
the solution state. An analysis of GA operation shows that
this is not a tenable argument. See
<http://inia.cls.org/~welsberr/zgists/wre/papers/antiec.html>
and look at Creationist Objection #5.
J>" There are many excellent reasons for doubting the adequacy of
J>" this kind of explanation. Random changes (such as copying errors
J>" in the DNA) do not generate increases in information, whether
J>" they are small or large.
GT> Yes they can.
W>They can in principle under special conditions, but it is
W>much more probable that random mutations have negative
W>effects. At least point mutations do not increase the
W>information size (as measured in bytes).
[...]
An increase in information is not necessarily dependent upon
an increase in message length. Going from a message of
AA
to
AB
is an increase in information. Information is also not about
meaning, so the claim about negative effects is irrelevant.
See <http://x6.dejanews.com/getdoc.xp?AN=424416762> for
discussion of observed increases in genetic information.
Johnson claims counter-factual things.
--
Wesley R. Elsberry, Student in Wildlife & Fisheries Sciences, Tx A&M U.
Visit the Online Zoologists page (http://www.rtis.com/nat/user/elsberry)
Email to this account is dumped to /dev/null, whose Spam appetite is capacious.
"And now the time has come at last to crush the motif of the rose" - BOC
Ken Cox
> z@z quoted Philip Johnson:
> > If matter is ultimately all
> > there is, and if our brains are the product of mindless chemical
> > combinations, and if "the mind is merely what the brain does,"
> > then our thoughts and theories are products of mindless forces.
> Why is this a paradox? I don't find it at all disquieting that
> we may eventually have a mechanistic model for the brain.
It's certainly nowhere near as disquieting as the thesis of Greg
Egan's science-fiction novel _Distress_. Talk about kicking the
supports out from under the table...
--
Ken Cox k...@research.bell-labs.com
ThomasPaine_II
>
>>> Philip E. Johnson seems to me a great logician and epistemologist,
>>> much better indeed than most neo-Darwinist high priests
>>> (e.g. Richard Dawkins) and believers.
>
>> Do you really think that he is so wonderful? On what is your
>> judgement based? I suppose that it is based on orthodoxy,
>> dogmatism, authority and prejudices!
>
>more consequent than Darwinists, because I do not accept such
>a discontinuity in evolution as the magical appearence of
>consciousness some billions years after 'big bang'.
>
>So I do not think that all of Johnson's opinions are wonderful. My
>judgement on Johnson is primarily based on his texts about AIDS,
>which I really do appreciate. In my opinion the AIDS hysteria
>(comparable with the medieval witch-hunting) shows better than
>anything else that modern science is only quantitatively better than
>medieval theology.
The only hysteria I saw about AIDS came from the conservative religious right.
Some even went so far as to call it a curse (on homosexuality) from god.
What this means is that some "modern" theologists are no better than their
medieval counterparts. Science had nothing to do with that.
>
>I proved my unprejudiced attitude by the fact that I have changed
>my mind about evolution and many other things over the last
>12 years.
Changing your mind does not prove non prejudices.
My own ideas cannot be based on orthodoxy, dogmatism
>and authority, because they are too different from all prevailing ideas.
>see: http://members.lol.li/twostone/E/psychon.html
>
>
>> Where have I heard that before? Whenever I read
>> stuff that Johnson writes I am strongly of the opinion that he is
>> attempting to communicate the least possible ammount in the
>> maximum number of words. I am reminded of Dawkin's comment
>> about those who are educated beyond their capacity for coherent
>> thought. All of his material is opinion : very rarely does he resort
>> to a consideration of facts.
>
>In my opinion Johnson (contrary to Dawkins) is able to recognize
>the real (philosphical) problems and to discriminate between what
>is important and what not.
So the fact that he lies, knows little about science and offers nothing but
his personal opinion without substantiation means nothing?
>
>It is quite normal that material in agreement with one's own
>prejudices seems to be facts whereas the rest seems to be opinion!
Since Johnson provides little or no meaningful facts; it all must be just his
personal opinion.
>
>
>It is my, Johnson's and many others' right to find it disquieting (or
>even absurd) that "the mind is merely what the brain does" and
>that "our thoughts and theories are products of mindless forces".
SO? It troubles you and Johnson.
Certainly not enough reason to assume it can't happen that way.
(snip "I don't believe it - so it's wrong")
Gavin Tabor
>
> Gavin Tabor wrote:
> > z@z quoted Philip Johnson:
> > > there is, and if our brains are the product of mindless chemical
> > > combinations, and if "the mind is merely what the brain does,"
> > > then our thoughts and theories are products of mindless forces.
>
> > we may eventually have a mechanistic model for the brain.
>
> Egan's science-fiction novel _Distress_. Talk about kicking the
> supports out from under the table...
>
> --
> Ken Cox k...@research.bell-labs.com
You know, that was a really sadistic reply. I positively demand
that you give me a synopsis of this novel - I've not heard of
it, and want to know more.
z@z
J>" As we have seen, Darwinian evolution is by definition unguided
J>" and purposeless, and such evolution cannot in any meaningful
J>" sense be theistic.
> It is neither totally unguided, as natural selection is indeed
> guided by the environmental pressures with which an organism
> is faced, nor purposeless, as its function is to make populations
> more fit within their environments. It certainly is not designed
> to result in human beings, or to move toward "higher" life forms.
> If he had said, "intelligently guided" and "apparently purposeless,"
> then he would have been more accurate.
Nothing is 'guided', 'unguided', 'random' or 'determined' in every
respect. One should always choose the most consistent
interpretation of a text. So the meanings of 'unguided' and
'purposeless' as used by Johnson are clear, at least for me.
You think Johnson would have been more accurate if he had said
"apparently purposeless". This shows that you do not understand
what Johnson wants to say: according to neo-Darwininism the
apparent purposefulness of nature (which cannot be denied) is
based on an (ontological) purposelessness.
> Sure, and He could personally be holding atoms together as well,
> but the strong and weak nuclear forces are well-accepted in the
> world at large.
That "the strong and weak nuclear forces" as conceived by modern
physics are holding atoms together, seems to me not much better
(maybe even worse in some respects) than an explanation by God.
-----------------------------------------
An excerpt from a correspondence with a physician:
>> Electrostatic attraction cannot even be explained qualitatively in this
>> way because under momentum conservation two bodies can only
>> drift apart by exchanging photons, and momentum conservation
>> of photons has been experimentally confirmed!
> It's not that simple. If it were, don't you think
> somebody would have noticed by now?
That's really an interesting answer!
-----------------------------------------
> One has to follow the evidence in the earth itself, and the evidence
> indicates that the biodiversity of life on earth didn't just "poof"
> appear, nor did it _require_ intelligence to design.
The evidence in the earth can inform us that there has been a
continuous evolution of live, but this evidence certainly can
not inform us whether reductionist causal laws are enough to
explain the actual biodiversity on earth! And the very basis of
at least neo-Darwinism is the rejection of any teleological
principle.
see: http://members.lol.li/twostone/E/psychon.html#a04
or: http://members.lol.li/twostone/E/reductionism.html
Wolfgang
Thomas Scharle
|> z@z <z...@z.lol.li> wrote:
|>
|> > Philip E. Johnson seems to me a great logician and epistemologist,
|>
|> of his that I've read. I expect he's a good professor of law, perhaps
|> very good; but the history, philosophy and methodology of the sciences
|> doesn't seem to be his strong suite.
There is the famous quotation from Oliver Wendell Holmes:
"The life of the law has not been logic" ("The Common Law",
as quoted in "The Essential Holmes", ed. R. A. Posner, p. 237).
--
Tom Scharle scha...@nd.edu "standard disclaimer"
Clark Dorman
Ken Cox <k...@lucent.com> writes:
> z@z wrote:
> > What gives you the right to criticize an author you have not read or you
> > don't understand?
>
> What makes you think either of the above are true?
>
> If it helps any, I did read Johnson's book, and I did understand it,
> and I also say that Johnson knows less about evolution than I do
> about collateral estoppel. And I don't even know what collateral
> estoppel *is*.
Not only did I not know what collateral estoppel was, I had never
heard of the term before. However, I note that a good dictionary
is an invaluable resource. Collateral estoppel is not in my
Merriam Webster, but estoppel is, and it refers to being legally
barred from denying an action or statement by previously doing or
saying something. The fact that it is a legal term allowed me to
go to the on line legal dictionary for the definition (see the
very end, definition (2)).
see <http://www.nolo.com/dictionary/wordindex.cfm> where
I obtained the following:
estoppel
(1) A legal principle that prevents a
person from asserting or denying
something in court that contradicts what
has already been established as the
truth.
equitable estoppel
A type of estoppel that bars a person
from adopting a position in court that
contradicts his or her past statements
or actions when that contradictory
stance would be unfair to another
person who relied on the original
position. For example, if a landlord
agrees to allow a tenant to pay the rent
ten days late for six months, it would be
unfair to allow the landlord to bring a
court action in the fourth month to evict
the tenant for being a week late with
the rent. The landlord would be
estopped from asserting his right to
evict the tenant for late payment of rent.
Also known as estoppel in pais.
estoppel by deed
A type of estoppel that prevents a
person from denying the truth of
anything that he or she stated in a
deed, especially regarding who has
valid ownership of the property. For
example, someone who grants a deed
to real estate before he actually owns
the property can't later go back and
undo the sale for that reason if, say, the
new owner strikes oil in the backyard.
estoppel by silence
A type of estoppel that prevents a
person from asserting something when
she had both the duty and the
opportunity to speak up earlier, and her
silence put another person at a
disadvantage. For example, Edwards'
Roofing Company has the wrong
address and begins ripping the roof
from Betty's house by mistake. If Betty
sees this but remains silent, she cannot
wait until the new roof is installed and
then refuse to pay, asserting that the
work was done without her agreement.
estoppel in pais
See equitable estoppel.
promissory estoppel
A type of estoppel that prevents a
person who made a promise from
reneging when someone else has
reasonably relied on the promise and
will suffer a loss if the promise is
broken. For example, Forrest tells
Antonio to go ahead and buy a boat
without a motor, because he will sell
Antonio an old boat motor at a very
reasonable price. If Antonio relies on
Forrest's promise and buys the
motorless boat, Forrest cannot then
deny his promise to sell John the motor
at the agreed-upon price.
(2) A legal doctrine that prevents the
relitigation of facts or issues that were
previously resolved in court. For
example, Alvin loses control of his car
and accidentally sideswipes several
parked cars. When the first car owner
sues Alvin for damages, the court
determines that Alvin was legally drunk
at the time of the accident. Alvin will not
be able to deny this fact in subsequent
lawsuits against him. This type of
estoppel is most commonly called
collateral estoppel.
--
Clark
z@z
J>" Everybody with even a cursory knowledge of the literature knows
J>" that the textbook examples (Kettlewell's peppered moths,
J>" Grant's finch beaks) describe relatively trivial changes that involve
J>" no innovation or increase in genetic information.
> I have somewhat more than a cursory knowledge, and I think this
> statement is pure bull shit.
It is a fact that all experimentally produced changes are relatively small.
Do you know an exception?
I know an 'exception', but this exception refutes reductionist
Darwinism: the instinctive behaviour of rats could be substantially
changed by breeding and training rats over a few generations.
See: http://members.lol.li/twostone/E/aa1.html
J>" But when materialism is assumed as the very basis of science,
J>" they can re-emerge a few logical steps later in triumph. Something
J>" had to guide evolution, to produce those wonders of apparent
J>" design, and natural selection is just about the only materialist
J>" contender.
> This makes no sense at all.
This makes no sense for you because you lack knowledge in
epistemology! This makes a lot of sense and your reasoning
even elegantly shows how much sense it makes.
Wolfgang
Thomas Scharle
[...snip...]
|> That "the strong and weak nuclear forces" as conceived by modern
|> physics are holding atoms together, seems to me not much better
|> (maybe even worse in some respects) than an explanation by God.
Could you tell us how God is an *explanation* of any fact about
the material world?
I am *not* denying that God is the Creator and Sustainer of
everything in the world.
What I am asking is what connection there is between any
attributes of God and some properties of (to take your example)
atomic nuclei. (Not every true statement is an *explanation*.)
As far as I can tell, when we give an explanation for something,
we make some attempt to say "why this and not that". But saying
that "God did it" doesn't tell us why the proton is made up of three
quarks rather than four. (For if God is powerful enough to determine
how many quarks make up a proton, He's surely powerful enough to make
intelligent life with four-quark protons. Or, if He's not, then I
think that *that* should be part of the explanation.)
z@z
J>" There are many excellent reasons for doubting the adequacy of
J>" this kind of explanation. Random changes (such as copying errors
J>" in the DNA) do not generate increases in information, whether
J>" they are small or large. It is not necessarily easier to provide the
J>" same amount of information in multitudinous small doses, rather
J>" than a single large one. Each increment is less unlikely, but the
J>" price one pays is that one has to have a great many increments,
J>" each of which must supply the precise kind of new information
J>" required. To illustrate the point with an analogy: It is hard enough
J>" to earn one million dollars by winning the grand prize in a lottery,
J>" but it is no easier to achieve that feat by winning a $100 prize
J>" 10,000 times.
> When I walk to the shops at lunchtime (they are a kilometre away
> approximately), I get there through 1,000 steps, not one huge leap.
> Also, if instead of buying a lottery ticket each week I deposit that
> money in a bank account I will definitely be a millionaire in the long
> run.
> I suggest that Mr Johnson should walk to the shops and put some
> money in his bank account. He may learn something.
If for a first organism with the power of reproduction to apppear
only twenty different conditions with a probability of each 0.001
were necessary, then the probability of such an organism to appear
would be only 10^60. Even if 19 of the 20 conditions were fulfilled,
the organism could not replicate and evolution of life could not
start. In realty certainly more conditions with lower probabilties
are necessary for such a self-replicating system with the additional
capacity to undergo further improvement by mutation and selection.
Probabilities must be multiplied!
See: http://members.lol.li/twostone/E/psychon.html#a03
Here a quotation from a genuine orthodox believer:
"But no one knows what that first organism was, for it naturally had
no bones and thus left no fossils, and it certainly would have been
vastly overpowered and driven to extinction by its more advanced
children who were born after successive mutation and selection."
( http://www.columbia.edu/~rcc20/foster9.html )
Within neo-Darwinian framework one must not take it for granted
that the "first organism" "certainly would have been vastly
overpowered and driven to extinction by its more advanced
children who were born after successive mutation and selection."
Wolfgang
Kalandros M
Only if the events are independent you nitwit. If not, then the
calculations get MUCH more complicated. Every prob. of life
calculation I have seen assumes this and ignores the effects
of chemistry. Thus all such calculations are useless.
Mike
Gavin Tabor
>
> Hello (Dr.) Gavin (Tabor)
>
> >> much better indeed than most neo-Darwinist high priests
> >> (e.g. Richard Dawkins) and believers.
>
> > Do you really think that he is so wonderful? On what is your
> > judgement based? I suppose that it is based on orthodoxy,
> > dogmatism, authority and prejudices!
>
> more consequent than Darwinists, because I do not accept such
> a discontinuity in evolution as the magical appearence of
> consciousness some billions years after 'big bang'.
>
> So I do not think that all of Johnson's opinions are wonderful. My
> judgement on Johnson is primarily based on his texts about AIDS,
> which I really do appreciate. In my opinion the AIDS hysteria
> (comparable with the medieval witch-hunting) shows better than
> anything else that modern science is only quantitatively better than
> medieval theology.
>
> my mind about evolution and many other things over the last
> and authority, because they are too different from all prevailing ideas.
> see: http://members.lol.li/twostone/E/psychon.html
>
> > stuff that Johnson writes I am strongly of the opinion that he is
> > attempting to communicate the least possible ammount in the
> > maximum number of words. I am reminded of Dawkin's comment
> > about those who are educated beyond their capacity for coherent
> > thought. All of his material is opinion : very rarely does he resort
> > to a consideration of facts.
>
> the real (philosphical) problems and to discriminate between what
> is important and what not.
>
> prejudices seems to be facts whereas the rest seems to be opinion!
This is indeed true.
>
> It is my, Johnson's and many others' right to find it disquieting (or
> even absurd) that "the mind is merely what the brain does" and
> that "our thoughts and theories are products of mindless forces".
However, please do not confuse your personal prejudices with
some global disquiet.
>
> see for instance: http://members.lol.li/twostone/E/reductionism.html
>
> > This is just a recycling of the usual claim that NS selects
> > pre-existing genetic information, and evolution cannot generate
> > new information. This can be shown not to be the case.
> > Consider the work presented at
> http://www.newscientist.com/ns/971115/features.html
> > This describes the use of genetic algorithm techniques to evolve
> > a circuit that not only does a particular job, but does it in a way
> > not previously thought possible by humans.
>
> It is not difficult to make computer games or AI programs where
> also chance influences the result. It may even happen that the result
> is one not expected by the programmers, but I do not believe in results
> which are in principle different from what could have thought possible
> by the programmers.
In that case I suggest you actually read the article whose link
I provided. I quote :
[the researcher]
set the system a task that appeared impossible for a human
designer. Using only 100 logic cells, evolution had to
come up
with a circuit that could discriminate between two tones,
one at
1 kilohertz and the other at 10 kilohertz.
By generation
2800, the fittest circuit was discriminating accurately
between
the two inputs, but there were still glitches in its
output. These
only disappeared completely at generation 4100. After
this,
there were no further changes.
>
> In any case, such algorithms are rather evidence for a guided (there
> are engineers and programmers) evolution than for a purely random.
a. Evolution is not purely random.
b. Johnson, in his article, doubts that the mechanism of evolution
can generate genuinely new properties in a system. This evolutionary
approach described in the NS article demonstrates that this is in
fact not true - the mutation and selection process used generates
a result which is not predicted by the scientist setting it up.
Yes, the scientist has played a role, in setting a goal for the
genetic algorithm to reach - but this is exactly equivalent to
the role of NS in evolution. It is not being guided. OK, the
experiment as a whole is more exactly equivalent to theistic
evolution (as properly understood, ie not by Johnson), but there
is no real distinction between that and atheistic evolution, in
practical terms.
>
> J>" There are many excellent reasons for doubting the adequacy of
> J>" this kind of explanation. Random changes (such as copying errors
> J>" in the DNA) do not generate increases in information, whether
> J>" they are small or large.
>
> > Yes they can.
>
> They can in principle under special conditions, but it is much more
> probable that random mutations have negative effects. At least
> point mutations do not increase the information size (as measured
> in bytes).
Other (more knowledgeable) people have discussed this. You are wrong
on all issues.
>
> J>" To illustrate the point with an analogy: It is hard enough to
> J>" earn one million dollars by winning the grand prize in a lottery,
> J>" but it is no easier to achieve that feat by winning a $100 prize
> J>" 10,000 times.
>
> > This is only true if the events are random and uncorrelated. In
> > evolution the events are not random and they are correlated :
> > NS sees to that.
>
> My opinion is quite similar to Johnson's:
>
> "If it cannot be denied that the probability for random emergence
> of a system (e.g. a living organism) is unrealistically low, the system
> is taken apart to smaller and smaller sub-systems until random
> emergence gets realistic. But it is ignored that the probability for
> the whole system is calculated by multiplying the probabilities for
> the emergence of all systems from their respective sub-systems.
> Reductionist causal laws do not explain why sub-systems which are
> useful for the whole reproduce themselves instead of disappearing
> after having appeared by chance."
> ( http://members.lol.li/twostone/E/psychon.html#a03 )
>
> Wolfgang
Again, the events are not uncorrelated : hence you cannot get an overall
probability just by multiplying the sub-probabilities. Selection
correlates
the events. In addition, the estimates that I have seen (not provided by
Johnson in his article) are usually much too small : they neglect the
effects of chemistry in a big way.
Rick Gillespie
[snip]
>You think Johnson would have been more accurate if he had said
>"apparently purposeless". This shows that you do not understand
>what Johnson wants to say: according to neo-Darwininism the
>apparent purposefulness of nature (which cannot be denied) is
>based on an (ontological) purposelessness.
Perhaps you can expand on this undeniable purposefulness of
nature for, somehow, I seem to have missed it.
[snip]
Rick Gillespie
Bruce Stephens
> Ken Cox wrote:
> > It's certainly nowhere near as disquieting as the thesis of Greg
> > Egan's science-fiction novel _Distress_. Talk about kicking the
> > supports out from under the table...
>
> You know, that was a really sadistic reply. I positively demand that
> you give me a synopsis of this novel - I've not heard of it, and
> want to know more.
Well buy it, then. You should find it in all good bookshops, in the
science fiction section. (It's my favourite of his, along with the
two excellent collections of short stories.)
Victor Eijkhout
> For evolution to be genuinely theistic it must be guided
> by God, whether this means that God programmed the process
> in advance or [...]
"For humans not to have free will they must be guided by God, whether
this means that God predetermined their every action in advance or [...]"
In other words, if you believe that random acts are compatible with
a God, then you should extend that courtesy to other situations as well.
--
Victor Eijkhout
`In Papua New Guinea, he said, he cancelled There's a Girl in My Soup,
"because I thought it might give them ideas".'
[traveling comedian Derek Nimmo, Times 1999/02/25]
Jamie Schrumpf
>
>Hello Jamie Schrumpf!
>
>J>" As we have seen, Darwinian evolution is by definition unguided
>J>" and purposeless, and such evolution cannot in any meaningful
>J>" sense be theistic.
>
>> It is neither totally unguided, as natural selection is indeed
>> guided by the environmental pressures with which an organism
>> is faced, nor purposeless, as its function is to make populations
>> more fit within their environments. It certainly is not designed
>> to result in human beings, or to move toward "higher" life forms.
>> If he had said, "intelligently guided" and "apparently purposeless,"
>> then he would have been more accurate.
>
>Nothing is 'guided', 'unguided', 'random' or 'determined' in every
>respect. One should always choose the most consistent
>interpretation of a text. So the meanings of 'unguided' and
>'purposeless' as used by Johnson are clear, at least for me.
>
>"apparently purposeless". This shows that you do not understand
>what Johnson wants to say: according to neo-Darwininism the
>apparent purposefulness of nature (which cannot be denied) is
>based on an (ontological) purposelessness.
"What Johnson wants to say" is more or less the problem here. He is not
reaching for truth, but -- in his lawyerly way -- is merely arguing the point
in which _he_ wants to believe. If he has, as most lawyers have, ever defended
someone whom he believes is guilty, then we can certainly imply that the truth
is incidental to any position he may take.
Not to put too fine a point on it, he doesn't _care_ what the truth may be. He
has an agenda to push and if he can twist words to advance it, that is what
he'll do.
>
>> Sure, and He could personally be holding atoms together as well,
>> but the strong and weak nuclear forces are well-accepted in the
>> world at large.
>
>That "the strong and weak nuclear forces" as conceived by modern
>physics are holding atoms together, seems to me not much better
>(maybe even worse in some respects) than an explanation by God.
Oh? Can you use the God Hypothesis to predict what particles will be given off
by certain interactions? You do know that these interactions are very well
explained by nuclear physics, don't you?
>
>-----------------------------------------
>An excerpt from a correspondence with a physician:
>
>>> Electrostatic attraction cannot even be explained qualitatively in this
>>> way because under momentum conservation two bodies can only
>>> drift apart by exchanging photons, and momentum conservation
>>> of photons has been experimentally confirmed!
>
>> It's not that simple. If it were, don't you think
>> somebody would have noticed by now?
>
>That's really an interesting answer!
Especially as I don't see the relevance. How do you think that "electrostatic
attraction" is related to the conservation of momentum?
>-----------------------------------------
>
>> One has to follow the evidence in the earth itself, and the evidence
>> indicates that the biodiversity of life on earth didn't just "poof"
>> appear, nor did it _require_ intelligence to design.
>
>The evidence in the earth can inform us that there has been a
>continuous evolution of live, but this evidence certainly can
>not inform us whether reductionist causal laws are enough to
>explain the actual biodiversity on earth! And the very basis of
>at least neo-Darwinism is the rejection of any teleological
>principle.
>
Well, thank you for admitting that the evidence indicates constant evolution of
life on earth. And you do understand that one of the basic principles of
science in general -- not just evolution -- is to "assume no unnecessary
entities"? You can't ignore the proven explanatory and predictive powers of
the theory of evolution just because it doesn't require a god to work.
Bonz
<7c3p0t$6cq$1...@pollux.ip-plus.net> :
>Hi Mike!
>
>J>" There are many excellent reasons for doubting the adequacy of
>J>" this kind of explanation. Random changes (such as copying errors
>J>" in the DNA) do not generate increases in information, whether
>J>" they are small or large. It is not necessarily easier to provide the
>J>" same amount of information in multitudinous small doses, rather
>J>" than a single large one. Each increment is less unlikely, but the
>J>" price one pays is that one has to have a great many increments,
>J>" each of which must supply the precise kind of new information
>J>" required. To illustrate the point with an analogy: It is hard enough
>J>" to earn one million dollars by winning the grand prize in a lottery,
>J>" but it is no easier to achieve that feat by winning a $100 prize
>J>" 10,000 times.
>
>> When I walk to the shops at lunchtime (they are a kilometre away
>> approximately), I get there through 1,000 steps, not one huge leap.
>> Also, if instead of buying a lottery ticket each week I deposit that
>> money in a bank account I will definitely be a millionaire in the long
>> run.
>> I suggest that Mr Johnson should walk to the shops and put some
>> money in his bank account. He may learn something.
>
>If for a first organism with the power of reproduction to apppear
>only twenty different conditions with a probability of each 0.001
>were necessary, then the probability of such an organism to appear
>would be only 10^60.
Not true. Show your math.
>Even if 19 of the 20 conditions were fulfilled,
>the organism could not replicate and evolution of life could not
>start.
Not true, Show your math.
> In realty certainly more conditions with lower probabilties
>are necessary for such a self-replicating system with the additional
>capacity to undergo further improvement by mutation and selection.
Probably not true. Show your math.
Suppose I fill a huge balloon with oxygen, hydrogen, and argon.
Then I stick a lit match to it. There are trillions of atoms
there. What happens, and how long does it take? Do you have to
pay attention to the argon, or not?
Bonz
<7c3p0t$6cq$1...@pollux.ip-plus.net> :
> In realty certainly more conditions with lower probabilties
>are necessary for such a self-replicating system with the additional
>capacity to undergo further improvement by mutation and selection.
There is no requirement for 'improvement' of any sort.
>
>Probabilities must be multiplied!
>See: http://members.lol.li/twostone/E/psychon.html#a03
>
>Here a quotation from a genuine orthodox believer:
>
>"But no one knows what that first organism was, for it naturally had
>no bones and thus left no fossils, and it certainly would have been
>vastly overpowered and driven to extinction by its more advanced
>children who were born after successive mutation and selection."
>( http://www.columbia.edu/~rcc20/foster9.html )
>
>Within neo-Darwinian framework one must not take it for granted
>that the "first organism" "certainly would have been vastly
>overpowered and driven to extinction by its more advanced
>children who were born after successive mutation and selection."
Why not? It took that first life millions and millions of years
before it became cellular life, and the simplest life we have
today is cellular as far as we know.
hrgr...@my-dejanews.com
hatt...@NOSPAM.fred.net (Jamie Schrumpf) wrote:
> In article <7c3jgv$2jd$1...@pollux.ip-plus.net>, z...@z.lol.li says...
> >
> >Hello Jamie Schrumpf!
> >-----------------------------------------
> >An excerpt from a correspondence with a physician:
I can only hope it *was* a physician and not a physicist! ;-)
> >>> Electrostatic attraction cannot even be explained qualitatively in this
> >>> way because under momentum conservation two bodies can only
> >>> drift apart by exchanging photons, and momentum conservation
> >>> of photons has been experimentally confirmed!
> >
> >> It's not that simple. If it were, don't you think
> >> somebody would have noticed by now?
> >
> >That's really an interesting answer!
>
> Especially as I don't see the relevance. How do you think that
"electrostatic
> attraction" is related to the conservation of momentum?
The explanation must have been that electrostatic attraction/repulsion, as a
specific case of electromagnetic interactions, is mediated by the exchange of
virtual photons.
While this may be an rough and intuitive way of describing the underlying
mathematics (Feynman diagrams etc.), for many questions it is "too rough". If
one has an over-realistic picture of virtual photons as ping-pong balls going
back and forth, I can imagine how one might think that only repulsion could be
achieved in that manner.
The question why opposite charges attract while similar charges repel is
actually quite subtle and has to do with the vector nature (i.e. photons are
particles of spin one) of electromagnetism.
Regards,
HRG.
<snip>
-----------== Posted via Deja News, The Discussion Network ==----------
http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own
z@z
>> If for a first organism with the power of reproduction to apppear
>> only twenty different conditions with a probability of each 0.001
>> were necessary, then the probability of such an organism to appear
>> would be only 10^60.
> Not true. Show your math.
You are right!
0.001^20 = (10^-3)^20 = 10^-60
>> Even if 19 of the 20 conditions were fulfilled, the organism
>> could not replicate and evolution of life could not start.
> Not true, Show your math.
No math is necessary, because my argument is based on the
premise that all 20 (independent from each other) conditions
must be fulfilled for replication to start.
>> In realty certainly more conditions with lower probabilties
>> are necessary for such a self-replicating system with the additional
>> capacity to undergo further improvement by mutation and selection.
> Probably not true. Show your math.
No math is necessary. A look at the complexity of living systems should
be enough.
Regards
Wolfgang
z@z
>> If for a first organism with the power of reproduction to apppear
>> only twenty different conditions with a probability of each 0.001
>> were necessary, then the probability of such an organism to appear
>> would be only 10^-60. Even if 19 of the 20 conditions were fulfilled,
>> the organism could not replicate and evolution of life could not
>> start. In realty certainly more conditions with lower probabilties
>> are necessary for such a self-replicating system with the additional
>> capacity to undergo further improvement by mutation and selection.
>>
>> Probabilities must be multiplied!
> Only if the events are independent you nitwit. If not, then the
> calculations get MUCH more complicated. Every prob. of life
> calculation I have seen assumes this and ignores the effects
> of chemistry. Thus all such calculations are useless.
Certainly at least 20 (independent) conditions with a probability
of at most 0.001 are necessary for a self-replicating system to
appear. If it were less, it should be possible to show how such a
system could appear and work or even to produce one in the
laboratory.
I agree with you that it useless to calculate exactly such probabilites!
However, it is possible to estimate upper limits. It is my opinion that
everybody who deals with this problem in a logically correct and
unprejudiced way must recognize that reductionist causal laws
cannot explain the appearence of such a self-replicating organism.
Regards
Wolfgang
Loren King
>>> ... In realty certainly more conditions with lower probabilties are
>>> necessary for such a self-replicating system with the additional
>>> capacity to undergo further improvement by mutation and selection.
>>> Probabilities must be multiplied!
>> Only if the events are independent you nitwit. If not, then the
>> calculations get MUCH more complicated. Every prob. of life
>> calculation I have seen assumes this and ignores the effects
>> of chemistry. Thus all such calculations are useless.
>
> Certainly at least 20 (independent) conditions with a probability
> of at most 0.001 are necessary for a self-replicating system to
> appear.
Why is this certain? If we don't understand the details of the process
(or even the generalities), then how could we estimate how many
conditions are involved, whether they are independent, and what their
respective probabilities are? It is not sufficient to argue that,
> if it were less, it should be possible to show how such a system could
> appear and work or even to produce one in the laboratory.
That doesn't follow. You are presenting present-day scientific
ignorance about a process as the basis of a claim to certain knowledge
about important features of that process.
> I agree with you that it useless to calculate exactly such probabilites!
> However, it is possible to estimate upper limits.
How, precisely? If you know little or nothing about the generating
mechanisms or the resultant distributions, how could you possibly infer
anything about the distributions?
> It is my opinion that everybody who deals with this problem in a
> logically correct and unprejudiced way must recognize that
> reductionist causal laws cannot explain the appearence of such a
> self-replicating organism.
What, precisely, is the basis of your opinion?
In my ivew, anyone who approaches this question in an unprejudiced and
scientific way should recognize that: (a) "reductionist causal laws" is
a vague statement, open to several plausible interpretations; and (b)
scientists have not yet explained the appearance of self-replicating
organisms.
It appears to me that you believe the following: some interpretation of
the phrase "reductionist causal laws" gives force to the claim that
existing scientific methods and theories are critically insufficient for
the task of explaining the appearance of self-replicating organisms.
But I'm not at all clear why you believe this; it certainly isn't an
obvious point.
z@z
>> You think Johnson would have been more accurate if he had said
>> "apparently purposeless". This shows that you do not understand
>> what Johnson wants to say: according to neo-Darwininism the
>> apparent purposefulness of nature (which cannot be denied) is
>> based on an (ontological) purposelessness.
> "What Johnson wants to say" is more or less the problem here.
> He is not reaching for truth, but -- in his lawyerly way -- is merely
> arguing the point in which _he_ wants to believe. If he has, as
> most lawyers have, ever defended someone whom he believes is
> guilty, then we can certainly imply that the truth is incidental to any
> position he may take.
Are you sure that what you are insinuating here, is not relevant for
you yourself? My personal impression is that Johnson is reaching
for truth, in the same way as you do. There are many things where I
do not agree with Johnson or with you, but I respect both your and
Johnson's opinions, even if I'm convinced that they are false.
I'm sure that Johnson is or was a much more unbiased lawyer than
the average.
> Not to put too fine a point on it, he doesn't _care_ what the truth
> may be. He has an agenda to push and if he can twist words to
> advance it, that is what he'll do.
Why do you know that? Are you sure that you are not pushing an
agenda which will seem absurd to future generations?
>> The evidence in the earth can inform us that there has been a
>> continuous evolution of live, but this evidence certainly can
>> not inform us whether reductionist causal laws are enough to
>> explain the actual biodiversity on earth! And the very basis of
>> at least neo-Darwinism is the rejection of any teleological
>> principle.
> Well, thank you for admitting that the evidence indicates constant
> evolution of life on earth. And you do understand that one of the
> basic principles of science in general -- not just evolution -- is to
> "assume no unnecessary entities"? You can't ignore the proven
> explanatory and predictive powers of the theory of evolution just
> because it doesn't require a god to work.
If reductionist causal laws cannot explain life, neo-Darwinism is
refuted and it is necessary to look for new entities or principles
which can explain life. I'm sure that neo-Darwinism will seem to
future generations a completely absurd theory, because it denies
the most obvious.
Whereas Johnson suggests God for what cannot be explained
by causal laws, I suggest final laws of nature and immaterial
unities undergoing evolution which I call psychons or souls.
Cheers
Wolfgang
z@z
!!
!! >>> Electrostatic attraction cannot even be explained qualitatively
!! >>> in this way because under momentum conservation two bodies
!! >>> can only drift apart by exchanging photons, and momentum
!! >>> conservation of photons has been experimentally confirmed!
!!
!! >> It's not that simple. If it were, don't you think
!! >> somebody would have noticed by now?
!!
!! >That's really an interesting answer!
> I can only hope it *was* a physician and not a physicist! ;-)
I'm sorry, it was a physicist (Sverker Johanson).
>> Especially as I don't see the relevance. How do you think that
>> "electrostatic attraction" is related to the conservation of
>> momentum?
> The explanation must have been that electrostatic attraction/repulsion,
> as a specific case of electromagnetic interactions, is mediated by the
> exchange of virtual photons.
> While this may be an rough and intuitive way of describing the
> underlying mathematics (Feynman diagrams etc.), for many
> questions it is "too rough". If one has an over-realistic picture of
> virtual photons as ping-pong balls going back and forth, I can
> imagine how one might think that only repulsion could be achieved
> in that manner.
One must never abstain from correct logical reasoning! This must
be valid also for theoretical physics, which in several respects plays
nowadays the same role theology played in the past.
The empirical evidence for most elementary particles is no better
than for angels and demons.
> The question why opposite charges attract while similar charges
> repel is actually quite subtle and has to do with the vector nature
> (i.e. photons are particles of spin one) of electromagnetism.
Here another quotation from my correspondence (Darwinism refuted
by adverse selection experiments) with Sverker Johansson:
"There are physical theories with no predictive value at all. The
explanation of the simple Coulomb law by obscure mathematical
formulas in QED is a good example. Photons as postulated by
Einstein are concrete, measurable things with frequency, energy
and momentum. Can you tell me how much photons of what kind
are active in a concrete situation of electrostatic attraction?"
There is an infinity of possible explanations of the fact that opposite
charges attract! However, only the simplest explanations should be
taken seriously according to sound epistemology.
Wolfgang
Kalandros M
> Hello Mike!
>
> >> If for a first organism with the power of reproduction to apppear
> >> only twenty different conditions with a probability of each 0.001
> >> were necessary, then the probability of such an organism to appear
> >> would be only 10^-60. Even if 19 of the 20 conditions were fulfilled,
> >> the organism could not replicate and evolution of life could not
> >> start. In realty certainly more conditions with lower probabilties
> >> are necessary for such a self-replicating system with the additional
> >> capacity to undergo further improvement by mutation and selection.
> >>
> >> Probabilities must be multiplied!
>
> > Only if the events are independent you nitwit. If not, then the
> > calculations get MUCH more complicated. Every prob. of life
> > calculation I have seen assumes this and ignores the effects
> > of chemistry. Thus all such calculations are useless.
>
> Certainly at least 20 (independent) conditions with a probability
> of at most 0.001 are necessary for a self-replicating system to
> appear. If it were less, it should be possible to show how such a
> system could appear and work or even to produce one in the
> laboratory.
You realize, of course that they have discovered replicating molecules
around 32 molecules long? And furthermore that molecules do not
form randomly? What independent events are you proposing need
to happen? Can you use the above ideas to predict the yield of
Miller's experiements?
>
>
> I agree with you that it useless to calculate exactly such probabilites!
> However, it is possible to estimate upper limits.
I think you mean lower limits. If the results are not independent the
probability of occurence could be MUCH higher.
> It is my opinion that
> everybody who deals with this problem in a logically correct and
> unprejudiced way must recognize that reductionist causal laws
> cannot explain the appearence of such a self-replicating organism.
Why not? because you can't?
Mike
Gavin Tabor
>
> Hi Bonz!
>
> >> If for a first organism with the power of reproduction to apppear
> >> only twenty different conditions with a probability of each 0.001
> >> were necessary, then the probability of such an organism to appear
>
> > Not true. Show your math.
>
> You are right!
>
> 0.001^20 = (10^-3)^20 = 10^-60
>
> >> could not replicate and evolution of life could not start.
>
>
> No math is necessary, because my argument is based on the
> premise that all 20 (independent from each other) conditions
> must be fulfilled for replication to start.
Where did you get the figure of 20 independent conditions, all
with such low probabilities from? I think that thats the real question.
My understanding is that the smallest self-replicating protein
has 32 base units in it. If there are say 10 different amino
acid choices for each block, that implies there are 10^32
such proteins which can form - ignoring any issues of
chemistry. In a liquid molecules interact at a rate of around
10^14 interactions/sec : lets say new arrangements are formed
at that rate. In 1 mole of amino acids that means there are
10^22 32-element proteins, and in 1 second, there are
thus 10^36 proteins being tried. Thus in 1 second, 10^4
of these self-replicating proteins will be formed.
Sounds like pretty good odds to me.
(Note to the biochemists : yes I know chemistry don't work
like this. Its just a back-of-envelope calculation).
Gavin
>
> >> In realty certainly more conditions with lower probabilties
> >> are necessary for such a self-replicating system with the additional
> >> capacity to undergo further improvement by mutation and selection.
>
> > Probably not true. Show your math.
>
> No math is necessary. A look at the complexity of living systems should
> be enough.
>
> Regards
> Wolfgang
--
z@z
I have seen that you have published some online texts on the
subject we are discussing. As far as I have read in them, they
give me a positive impression of you.
But I think that you overestimate science and scientists.
Representative of modern science is Galilei. At a time when
the Copernican theory was already spreading he usurped
this theory and fought the theories of Johannes Kepler.
Kepler had been the first to surpass substantially the
astronomy of Aristarchus by smashing the whole epicycle
theory and by introducing modern physical laws.
Also Kepler's explanation of life which was quite similar to
mine was ridiculed and fought.
>> Certainly at least 20 (independent) conditions with a probability
>> of at most 0.001 are necessary for a self-replicating system to
>> appear.
> Why is this certain? If we don't understand the details of the process
> (or even the generalities), then how could we estimate how many
> conditions are involved, whether they are independent, and what their
> respective probabilities are?
For a self-replicating system at least 20 molecules which are at least
as complex as nucleotids or amino acids are necessary. According
to neo-Darwinism the movements of molecules depend on random
thermal collisions (apart from chemical and physical laws).
Now I assume that 20 molecules are enough for a self-replicating
system to appear, if every molecule has the right position in space.
A further simplification is needed. I assume that all 20 molecules
are in a cube which is subdivided into 1000 mini-cubes, and for the
right position nothing more is required than the center of gravity of
the molecule being located within the right mini-cube.
In this simpified case the probability for the self-replicating system
to appear is 10^-60. Common sense is enough to show that for a
self-replicating system to appear in nature, the probability is even
much much lower.
Here a quotation of my text 'Arguments against Reductionism':
"How impossible it is that random thermal motions determine the
happenings in living cells would become obvious, if one created an
enlarged model of the DNA helix with a helix diameter of 50 cm,
and if persons had to take over the functions of the many enzymes
which are involved in the DNA replication. The whole human DNA
(of one single cell), which normally is tightly packed, would be at
such an enlargement about 500'000 km long. This model would
also show how improbable it is that transcription factors could find
a given DNA position, if there were only random motions and if
recognition of the position were possible only by direct contact.
Because of the enzyme size, this improbability cannot be hidden
behind the Heisenberg uncertainty relations."
( http://members.lol.li/twostone/E/psychon.html#a06 )
>> I agree with you that it useless to calculate exactly such probabilites!
>> However, it is possible to estimate upper limits.
> How, precisely? If you know little or nothing about the generating
> mechanisms or the resultant distributions, how could you possibly
> infer anything about the distributions?
It is possible to calculate upper limits of such probabilities, because
we can recognize conditions which must be fulfilled in any case.
>> It is my opinion that everybody who deals with this problem in a
>> logically correct and unprejudiced way must recognize that
>> reductionist causal laws cannot explain the appearence of such a
>> self-replicating organism.
> What, precisely, is the basis of your opinion?
The basis of my opinion you can find in 'The End of Reductionism':
http://members.lol.li/twostone/E/reductionism.html
> In my view, anyone who approaches this question in an unprejudiced
> and scientific way should recognize that: (a) "reductionist causal laws"
> is a vague statement, open to several plausible interpretations; and (b)
> scientists have not yet explained the appearance of self-replicating
> organisms.
(a) For me "reductionist causal laws" is not vague, see:
http://members.lol.li/twostone/E/psychon.html#a04
(b) I think I have explained at least in principle the appearance
of self-replicating systems.
> It appears to me that you believe the following: some interpretation
> of the phrase "reductionist causal laws" gives force to the claim that
> existing scientific methods and theories are critically insufficient for
> the task of explaining the appearance of self-replicating organisms.
> But I'm not at all clear why you believe this; it certainly isn't an
> obvious point.
If after having read 'the psychon theory' you are still unclear why I
believe this, I'll willingly explain you.
Cheers
Wolfgang
Bonz
message <7c61qa$mp3$1...@pollux.ip-plus.net> :
>Hi Bonz!
>
>>> If for a first organism with the power of reproduction to apppear
>>> only twenty different conditions with a probability of each 0.001
>>> were necessary, then the probability of such an organism to appear
>>> would be only 10^60.
>
>> Not true. Show your math.
>
>You are right!
>
>0.001^20 = (10^-3)^20 = 10^-60
No no no no no.
>
>
>>> Even if 19 of the 20 conditions were fulfilled, the organism
>>> could not replicate and evolution of life could not start.
>
>> Not true, Show your math.
>
>No math is necessary, because my argument is based on the
>premise that all 20 (independent from each other) conditions
>must be fulfilled for replication to start.
Yes. The question is, how do you know it is twenty, and not two?
That's sort of like saying that eating scrambled eggs is
impossible, because if egg shells are made of titanium steel
they'd be too hard to crack.
Try this one. Take a deck of cards. You cannot know how many
cards are in the deck. You get to deal them, one at a time, until
you get a 'woofie'. You do not know how many cards there are,
what is on their faces, not what cards comprise a "woofie'. What
are the odds of dealing a woofie?
So. What chemicals are you starting with? What is the range of
temperatures? What chemicals are you ending with?
>>> In realty certainly more conditions with lower probabilties
>>> are necessary for such a self-replicating system with the additional
>>> capacity to undergo further improvement by mutation and selection.
>
>> Probably not true. Show your math.
>
>No math is necessary. A look at the complexity of living systems should
>be enough.
I don't know of any living systems today that are not cellular.
What will they tell me?
Loren King
> "z@z" <z...@z.lol.li> wrote:
>> ... my argument is based on the premise that all 20 (independent from
>> each other) conditions must be fulfilled for replication to start.
> Yes. The question is, how do you know it is twenty, and not two?
> That's sort of like saying that eating scrambled eggs is impossible,
> because if egg shells are made of titanium steel they'd be too hard to
> crack.
And don't forget that it is exceedingly impossible that all of the tools
necessary to crack the titanium egg-shell would converge at the
requisite points in time and space for you to enjoy your breakfast. And
don't even get me started on the impossibility of the (at least 20)
independent components that need to come together all at once, fully
assembled, so that these tools can work as required to crack the
fiendishly robust egg.
Scrambled eggs are indeed impossible ... unless you set out to make an
omlette, which in my experience often degenerates into scrambled eggs
... but this of course doesn't solve the problem of impenetrable shells,
and the utter improbability of breaking them with improbable tools of
inordinate and irreducible complexity.
L.
z@z
>> Certainly at least 20 (independent) conditions with a probability
>> of at most 0.001 are necessary for a self-replicating system to
>> appear. If it were less, it should be possible to show how such a
>> system could appear and work or even to produce one in the
>> laboratory.
> You realize, of course that they have discovered replicating molecules
> around 32 molecules long? And furthermore that molecules do not
> form randomly? What independent events are you proposing need
> to happen? Can you use the above ideas to predict the yield of
> Miller's experiements?
That's actually new for me: the existence of "replicating molecules
around 32 molecules long". The only possibility I see is the following:
there are RNA enzymes 32 bases long which replicate by base
pairing. Are you sure that such molecules actually have been
discovered, molecules replicating independently? However, even if
they actually exist, they are not enough to start evolution.
Do you know the results of Miller's experiment? A mixture of simple
organic molecules. This result is almost irrelevant to the explanation
of life and evolution.
"It is revealing that the chemosynthesis of urea of the year 1828
symbolizes the victory of the reductionist view on life. Whereas
an urea molecule consists only of eight atoms, enzymes consist
of thousands of atoms and behave in an astonishingly versatile
and purposeful way. Enzymes construct and modify cells and
macroscopic organisms in a similar way termites construct
and modify their mounds. That enzymes also work in vitro (e.g.
polymerase chain reaction) does not prove the reductionist view.
For such a proof it would be necessary to explain roughly how
complex behaviour of enzymes (e.g. the ability of orientating
themselves in cells) could emerge from physical and chemical
laws, if probabilities are estimated in a reasonable way."
( http://members.lol.li/twostone/E/reductionism.html )
Further answers you can find in my last message to Loren King.
Wolfgang
z@z
>> >> If for a first organism with the power of reproduction to apppear
>> >> only twenty different conditions with a probability of each 0.001
>> >> were necessary, then the probability of such an organism to
>> >> appear would be only 10^-60.
. . .
>> >> Even if 19 of the 20 conditions were fulfilled, the organism
>> >> could not replicate and evolution of life could not start.
>>
>> > Not true, Show your math.
>>
>> No math is necessary, because my argument is based on the
>> premise that all 20 (independent from each other) conditions
>> must be fulfilled for replication to start.
> Where did you get the figure of 20 independent conditions, all
> with such low probabilities from? I think that thats the real question.
Look at the complexity of living cells!
I have answered this question in my last message to Loren King.
Here an excerpt:
"For a self-replicating system at least 20 molecules which are at least
as complex as nucleotids or amino acids are necessary. According
to neo-Darwinism the movements of molecules depend on random
thermal collisions (apart from chemical and physical laws).
Now I assume that 20 molecules are enough for a self-replicating
system to appear, if every molecule has the right position in space.
A further simplification is needed. I assume that all 20 molecules
are in a cube which is subdivided into 1000 mini-cubes, and for the
right position nothing more is required than the center of gravity of
the molecule being located within the right mini-cube.
In this simpified case the probability for the self-replicating system
to appear is 10^-60. Common sense is enough to show that for a
self-replicating system to appear in nature, the probability is even
much much lower."
> My understanding is that the smallest self-replicating protein
> has 32 base units in it. If there are say 10 different amino
> acid choices for each block, that implies there are 10^32
> such proteins which can form - ignoring any issues of
> chemistry. In a liquid molecules interact at a rate of around
> 10^14 interactions/sec : lets say new arrangements are formed
> at that rate. In 1 mole of amino acids that means there are
> 10^22 32-element proteins, and in 1 second, there are
> thus 10^36 proteins being tried. Thus in 1 second, 10^4
> of these self-replicating proteins will be formed.
> Sounds like pretty good odds to me.
Are you telling a joke?
What is a self-replicating protein? To assume that every collision
between molecules corresponds to a new arrangement of a
sequence of 32 amino acids seems absurd to me. Incorrect
chemical bonds between amino acids are possible. Bonds with
other molecules cannot be excluded. Where could a soup with
such a high proportion of amino acids have existed?
Regards
Wolfgang
Kalandros M
> Hello Mike!
>
> >> Certainly at least 20 (independent) conditions with a probability
> >> of at most 0.001 are necessary for a self-replicating system to
> >> appear. If it were less, it should be possible to show how such a
> >> system could appear and work or even to produce one in the
> >> laboratory.
>
> > You realize, of course that they have discovered replicating molecules
> > around 32 molecules long? And furthermore that molecules do not
> > form randomly? What independent events are you proposing need
> > to happen? Can you use the above ideas to predict the yield of
> > Miller's experiements?
>
> That's actually new for me: the existence of "replicating molecules
> around 32 molecules long". The only possibility I see is the following:
> there are RNA enzymes 32 bases long which replicate by base
> pairing. Are you sure that such molecules actually have been
> discovered, molecules replicating independently?
Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of
symbiosis in peptide self-replication through a hypercyclic network..
Nature , 390: 591-4, 1997 Dec 11
Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, A
self-replicating peptide.. Nature , 382: 525-8, 1996 Aug 8
> However, even if
> they actually exist, they are not enough to start evolution.
Why not? They posses the ability to reproduce. They probably will not
reproduce perfectly each time. So now we have variation. Thus
the effects of natural selection can take over. Boom! Evolution.
>
>
> Do you know the results of Miller's experiment? A mixture of simple
> organic molecules. This result is almost irrelevant to the explanation
> of life and evolution.
>
What holds together those "simple" organic molecules? Chemical bonds.
what holds together more complex molecules? Chemical bonds.
The point is that your probability calculations ignore chemistry. Some
combinations will encourage others. There are catalysts, there are
different reactions at different energy levels. You way oversimplify
by trying to boil this down to a nice uniform probability density.
Mike
Loren King
> I have seen that you have published some online texts on the subject
> we are discussing. As far as I have read in them, they give me a
> positive impression of you.
I've read Johnson's books, and have a short essay in defense of
naturalism on my website, that directly addresses his strategy of
critiqe. Is this what you're referring to?
> But I think that you overestimate science and scientists.
How so?
> Representative of modern science is Galilei. At a time when the
> Copernican theory was already spreading he usurped this theory and
> fought the theories of Johannes Kepler. Kepler had been the first to
> surpass substantially the astronomy of Aristarchus by smashing the
> whole epicycle theory and by introducing modern physical laws.
I'm not sure I understand your point: is the suggestion that Galileo was
somehow dishonest or petty? Or that his ideas and general methods were
flawed in some way relevant to present-day reseach?
> Also Kepler's explanation of life which was quite similar to mine was
> ridiculed and fought.
So what? Incidently, I'm not at all clear just what your explanation of
life is. I've read your posts here and most of your website, but it
still is unclear. You make reference to soul-like properties of living
things, and to processes of incarnation and soul-transfer. These souls
seem to be incorporeal and intangible, and yet they somehow they retain
certain experiences and information across their various material
manifestations. While these speculative conjectures might comport with
some outcomes of breeding experiments, I'm not at all clear on the
specific mechanisms involved, and how you would identify and study them.
>>> Certainly at least 20 (independent) conditions with a probability
>>> of at most 0.001 are necessary for a self-replicating system to
>>> appear.
>> Why is this certain? If we don't understand the details of the process
>> (or even the generalities), then how could we estimate how many
>> conditions are involved, whether they are independent, and what their
>> respective probabilities are?
> For a self-replicating system at least 20 molecules which are at least
> as complex as nucleotids or amino acids are necessary.
But you have no idea whether the processes by which these molecules come
together is sudden, or cumulative and incremental. If the latter, you
have no idea how probable or improbable each stage of the process is,
nor what conditions constrain these probabilities. So I ask again: how
can you be certain that "at least 20" independent and mutually
improbable conditions all have to be satisfied, in one particular
sequence? How could you possibly know this?
> According to neo-Darwinism the movements of molecules depend on random
> thermal collisions (apart from chemical and physical laws).
I don't see why this is a necessary part of neo-darwinian models and
theories. What do you mean by "random" here? What about
order-generating processes in complex dynamic systems? Are they
"random" or not? Are they incompatible with neo-darwinian approaches?
If so, why?
It sounds to me as though your real beef is with some version of
philosophical naturalism, materialism or emiricism; or with
anti-holistic epistemologies; but not with neo-darwinism per se.
Once again (and with reference to your quote on the impossibility of
emergent complexity in material systems), it seems to me that, unless
you know a fair bit about the generating mechanisms and the
distributions they create, claims about the possibility (or
impossibility) of particular distributions arising from particular
mechanisms lack persuasive force. As I said,
>> ... If you know little or nothing about the generating mechanisms or
>> the resultant distributions, how could you possibly infer anything
>> about the distributions?
> It is possible to calculate upper limits of such probabilities,
> because we can recognize conditions which must be fulfilled in any
> case.
How is this possible? Again, you've said nothing specific about how you
can make such estimates; instead you've appealed to incredulity and
present-day scientific ignorance. And that isn't convincing.
>>> It is my opinion that everybody who deals with this problem in a
>>> logically correct and unprejudiced way must recognize that
>>> reductionist causal laws cannot explain the appearence of such a
>>> self-replicating organism.
>
>> What, precisely, is the basis of your opinion?
> The basis of my opinion you can find in 'The End of Reductionism':
> http://members.lol.li/twostone/E/reductionism.html
Yes, and I'm afraid I didn't find that very persuasive. Again, your
claim seems to amount to little more than the following assertion: `life
(whatever it is) appears really, really complex; we don't yet understand
how it works or where it came from; therefore, life cannot be explained
by naturalistic science.' I'm not convinced, especially by the stuff on
holism and teleology; I could not grasp your point.
>> In my view, anyone who approaches this question in an unprejudiced
>> and scientific way should recognize that: (a) "reductionist causal
>> laws" is a vague statement, open to several plausible
>> interpretations; and (b) scientists have not yet explained the
>> appearance of self-replicating organisms.
> (a) For me "reductionist causal laws" is not vague, see:
> http://members.lol.li/twostone/E/psychon.html#a04
No, it's still vague. I cannot find any clear definition of
"reductionist causal laws" on this page you've cited. You talk about
reductionism, but really only define it as some sort of world-view
premised on humans being outside of nature, an ambiguous and contestable
claim. Then you go on to make a distinction between causal and final
laws in describing phenomena, and assert -- without sufficient
clarification and argument -- that when phenomena cannot be described by
stochastic and deterministic models, then they can only be described by
appeal to a "higher" final law. I have no idea why this follows; nor do
I understand how you could glean these "final" teleological facts about
the world without appeal to the observable "causal" stuff that you seem
to think is the domain of reductionism. But nowhere do you make clear
what the connection is between your initial (vague) claim about
reductionism and your claims about causal and final laws.
In short, I have no idea what you mean when you throw about terms like
"causal" and "final", "reductionist" and "law". Are you making
ontological claims here? or claims about how we know things about the
world? I really am confused as to what you are trying to say.
> (b) I think I have explained at least in principle the appearance
> of self-replicating systems.
No, you haven't.
>> It appears to me that you believe the following: some interpretation
>> of the phrase "reductionist causal laws" gives force to the claim that
>> existing scientific methods and theories are critically insufficient for
>> the task of explaining the appearance of self-replicating organisms.
>> But I'm not at all clear why you believe this; it certainly isn't an
>> obvious point.
>
> If after having read 'the psychon theory' you are still unclear why I
> believe this, I'll willingly explain you.
I have read your `psychon theory', and I am still utterly unclear on
what you believe, and why. As I said, your strong claims about the
failings of reductionist, naturalistic science in explaining the origins
of life seem to be based on nothing more than incredulity, an
unjustifiable application of probability, and a willingness to believe
in an intangible, inscrutible soul that somehow interacts with matter.
Loren
Evan W. Steeg
z@z wrote in message <7c6rn3$bvq$1...@pollux.ip-plus.net>...
>[...]
>> Where did you get the figure of 20 independent conditions, all
>> with such low probabilities from? I think that thats the real question.
>
>Look at the complexity of living cells!
>
>I have answered this question in my last message to Loren King.
>Here an excerpt:
>
>to neo-Darwinism the movements of molecules depend on random
>thermal collisions (apart from chemical and physical laws).
>
>system to appear, if every molecule has the right position in space.
>
>A further simplification is needed. I assume that all 20 molecules
>are in a cube which is subdivided into 1000 mini-cubes, and for the
>right position nothing more is required than the center of gravity of
>the molecule being located within the right mini-cube.
>
>In this simpified case the probability for the self-replicating system
>to appear is 10^-60. Common sense is enough to show that for a
>self-replicating system to appear in nature, the probability is even
>much much lower."
Why do you insist on ignoring chemistry and probability theory?
Chemistry: There is such a thing as cooperativity in protein (and RNA
and other polymers) formation and folding. Read a real scientific paper,
e.g. something by Chan and Dill, or Peter Wolynes or Joe Bryngelson on
cooperativity. The specifics of various kinds of interactions (covalent
bonds, hydrogen bonds, van der Waals forces and the "hydrophobic effect",
etc.) make it very clear that the substructural interactions that -- viewed
kinetically or structurally -- comprise the whole object/process are NOT
independent.
Statistics: When probabilities are not known to be independent, the
joint probabilities are not formed by multiplying the component marginals.
You must deal with conditional probabilities, and you've given no indication
whtsoever that you know how to even grossly estimate the conditional probs.
In general, Wolfgang, you seem very ignorant of any research into
self-organizing systems. Evolutionary theory (even "Darwinism", if we are
allowed to view the latter more broadly as the neo-Darwinian synthesis) does
NOT presuppose atheism, philosphical naturalism, or even "reductionism".
Indeed, researchers like Bryngelson, Kauffman, Peter Schuster and others are
actively looking into mathematical laws that are "wholistic" and "emergent"
in nature. (One can -- if one feels the emotional need -- even attach
"God" to the manifestation and actions of these newly-discovered rules of
self-organization in physical, chemical, biological and even economic and
social systems).
You seem to be stuck on this silly, discredited false dichotomy of
"random and reductionist" versus something you feel is better. (And you
smuggle in misleading and incorrect definitions of "random" while you're at
it). Well, this something "better" is in fact the subject of much real
scientific research, though if you're looking for the conclusions to support
your or my or anyone's particular favorite religious story you shouldn't
hold your breath.
What is this grudge you have against science that compels you to
represent it so falsely?
Cheers,
Evan
Mike
Kalandros M <kala...@hubble.colorado.edu> wrote in message
news:36E56990...@hubble.colorado.edu...
>"z@z" wrote:
>
>> Hi Mike!
>>
>> J>" There are many excellent reasons for doubting the adequacy of
>> J>" this kind of explanation. Random changes (such as copying errors
>> J>" in the DNA) do not generate increases in information, whether
>> J>" they are small or large. It is not necessarily easier to provide the
>> J>" same amount of information in multitudinous small doses, rather
>> J>" than a single large one. Each increment is less unlikely, but the
>> J>" price one pays is that one has to have a great many increments,
>> J>" each of which must supply the precise kind of new information
>> J>" required. To illustrate the point with an analogy: It is hard enough
>> J>" to earn one million dollars by winning the grand prize in a lottery,
>> J>" but it is no easier to achieve that feat by winning a $100 prize
>> J>" 10,000 times.
>>
>> > When I walk to the shops at lunchtime (they are a kilometre away
>> > approximately), I get there through 1,000 steps, not one huge leap.
>> > Also, if instead of buying a lottery ticket each week I deposit that
>> > money in a bank account I will definitely be a millionaire in the long
>> > run.
>> > I suggest that Mr Johnson should walk to the shops and put some
>> > money in his bank account. He may learn something.
>>
>> only twenty different conditions with a probability of each 0.001
>> were necessary, then the probability of such an organism to appear
>> the organism could not replicate and evolution of life could not
>> are necessary for such a self-replicating system with the additional
>> capacity to undergo further improvement by mutation and selection.
>>
>
>Only if the events are independent you nitwit. If not, then the
>calculations get MUCH more complicated. Every prob. of life
>calculation I have seen assumes this and ignores the effects
>of chemistry. Thus all such calculations are useless.
>
>
Perhaps he should have read the paragraph he quoted from in his post, where
one will find the words:
"To actually calculate the odds of 'life' developing from inanimate matter,
one must be acquainted not only with a vast arrangement of data and know how
to estimate all the statistical relationships involved, but one must even
know things that no one on Earth presently knows, or ever may know."
Mike (A different one to that immediately above, but the same Mike as the
one at top)
srgould
z@z <z...@z.lol.li> wrote in article <7c61qa$mp3$1...@pollux.ip-plus.net>...
> Hi Bonz!
>
> >> If for a first organism with the power of reproduction to apppear
> >> only twenty different conditions with a probability of each 0.001
> >> were necessary, then the probability of such an organism to appear
> >> would be only 10^60.
>
> > Not true. Show your math.
>
> You are right!
>
> 0.001^20 = (10^-3)^20 = 10^-60
>
>
> >> Even if 19 of the 20 conditions were fulfilled, the organism
> >> could not replicate and evolution of life could not start.
>
> > Not true, Show your math.
>
> No math is necessary, because my argument is based on the
> premise that all 20 (independent from each other) conditions
> must be fulfilled for replication to start.
>
>
> >> In realty certainly more conditions with lower probabilties
> >> are necessary for such a self-replicating system with the additional
> >> capacity to undergo further improvement by mutation and selection.
>
> > Probably not true. Show your math.
>
> No math is necessary. A look at the complexity of living systems should
> be enough.
Which is known as begging the question. You ask us to assume 20
independent conditions that need to be satisfied.
We know enough about chemical/biological interaction to know that often
enough conditions do not have to be independent. Further, implicitly you
exclude ANY other conditions bar those 20 - given how many times evolution
has independently evolved major structures, it tends to suggest, by an
argument you yourself should logically approve of, that there are somewhat
more than 20 conditions. You exclude the time interactions will take. You
exclude the number of independent objects (molecules, etc.) out there that
can interact - probabilities of random interaction are different when we're
dealing with 10^large than 10^small units. And all that is ASSUMING your
20 units of irreducible complexity, which assumption is also questionable.
Finally, you have no idea of how complexity may be generated. Your
perception is uninformed.
S.
Jamie Schrumpf
>
>Hello Jamie Schrumpf!
>
>>> You think Johnson would have been more accurate if he had said
>>> "apparently purposeless". This shows that you do not understand
>>> what Johnson wants to say: according to neo-Darwininism the
>>> apparent purposefulness of nature (which cannot be denied) is
>>> based on an (ontological) purposelessness.
>
>> "What Johnson wants to say" is more or less the problem here.
>> He is not reaching for truth, but -- in his lawyerly way -- is merely
>> arguing the point in which _he_ wants to believe. If he has, as
>> most lawyers have, ever defended someone whom he believes is
>> guilty, then we can certainly imply that the truth is incidental to any
>> position he may take.
>
>Are you sure that what you are insinuating here, is not relevant for
>you yourself? My personal impression is that Johnson is reaching
>for truth, in the same way as you do. There are many things where I
>do not agree with Johnson or with you, but I respect both your and
>Johnson's opinions, even if I'm convinced that they are false.
It may be relevant for myself. If so, then Johnson and I are both wrong. Of
course, I have never defended a position I _know_ to be wrong.
>
>I'm sure that Johnson is or was a much more unbiased lawyer than
>the average.
Why would you say that? What is your evidence?
>
>> Not to put too fine a point on it, he doesn't _care_ what the truth
>> may be. He has an agenda to push and if he can twist words to
>> advance it, that is what he'll do.
>
>Why do you know that? Are you sure that you are not pushing an
>agenda which will seem absurd to future generations?
Again, my point is that if he has ever knowingly defended a position that he
knew was wrong, i.e., a defendant he thought was guilty, then we can not be
sure that he is reaching for truth. That's not what lawyers do: their goal is
to win, at any cost.
I don't have an agenda, because I have nothing to gain or lose with
evolutionary theory. If scientists decide it's wrong, and have good evidence
for their decision, then that's the way the ball bounces.
Unlike most practitioners of religions, I have no personal stake in
evolutionary theory.
>
>>> The evidence in the earth can inform us that there has been a
>>> continuous evolution of live, but this evidence certainly can
>>> not inform us whether reductionist causal laws are enough to
>>> explain the actual biodiversity on earth! And the very basis of
>>> at least neo-Darwinism is the rejection of any teleological
>>> principle.
>
>> Well, thank you for admitting that the evidence indicates constant
>> evolution of life on earth. And you do understand that one of the
>> basic principles of science in general -- not just evolution -- is to
>> "assume no unnecessary entities"? You can't ignore the proven
>> explanatory and predictive powers of the theory of evolution just
>> because it doesn't require a god to work.
>
>If reductionist causal laws cannot explain life, neo-Darwinism is
>refuted and it is necessary to look for new entities or principles
>which can explain life. I'm sure that neo-Darwinism will seem to
>future generations a completely absurd theory, because it denies
>the most obvious.
>
>Whereas Johnson suggests God for what cannot be explained
>by causal laws, I suggest final laws of nature and immaterial
>unities undergoing evolution which I call psychons or souls.
>
"Reductionist causal laws" have yet to be written off, however. Science moves
slowly sometimes, in fits and starts. Folks like you seem to believe that "if
we don't know the answer now, we'll never know it." Science didn't know the
laws of nuclear physics that explain how the sun burns hydrogen to helium for
over 2000 years, but that doesn't mean that stars were actually God's holes in
the firmament though which the Light of Heaven showed up until that time.
You are also overly fond of your own hypotheses, a usually-fatal affliction in
science.
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
On 10 Mar 1999 16:48:54 -0500, "z@z" <z...@z.lol.li> wrote:
>Hello Mike!
>
>>> Certainly at least 20 (independent) conditions with a probability
>>> of at most 0.001 are necessary for a self-replicating system to
>>> appear. If it were less, it should be possible to show how such a
>>> system could appear and work or even to produce one in the
>>> laboratory.
What are these events? How do you know they are independent? How have
you estimated their probabilities? How do they relate to the chemistry
of peptides or nucleotides?
>> You realize, of course that they have discovered replicating molecules
>> around 32 molecules long? And furthermore that molecules do not
>> form randomly? What independent events are you proposing need
>> to happen? Can you use the above ideas to predict the yield of
>> Miller's experiements?
>
>That's actually new for me: the existence of "replicating molecules
>around 32 molecules long". The only possibility I see is the following:
>there are RNA enzymes 32 bases long which replicate by base
>pairing. Are you sure that such molecules actually have been
>discovered, molecules replicating independently?
Yep, see
Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of
symbiosis in peptide self-replication through a hypercyclic network.
Nature 390: 591-4, 1997 Dec 11
Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, A
self-replicating peptide. Nature 382: 525-8, 1996 Aug 8
There is also von Kreidowskis self replicating RNA's of various
lengths and the recent von K paper in Nature on tethered nucleotides.
>However, even if
>they actually exist, they are not enough to start evolution.
Why not, the Ghadiri groups peptide also mutates and forms
hypercycles!
>Do you know the results of Miller's experiment? A mixture of simple
>organic molecules. This result is almost irrelevant to the explanation
>of life and evolution.
However, the amino acids that turn up aremostly the modern ones. This
is not insignificant. In fact, most of the kinds of molecules that are
necessary for life turn up in Miller style experiments, even those
using more recent model atmospheres. However, what the original
questioner was trying to get accros is that chemistry is not random.
The biogenic chemicals in Millers experiments turn up in particular
ratios, due to the laws of chemistry. Does your approach yeild these
ratios?
>"It is revealing that the chemosynthesis of urea of the year 1828
>symbolizes the victory of the reductionist view on life. Whereas
>an urea molecule consists only of eight atoms, enzymes consist
>of thousands of atoms and behave in an astonishingly versatile
>and purposeful way. Enzymes construct and modify cells and
>macroscopic organisms in a similar way termites construct
>and modify their mounds. That enzymes also work in vitro (e.g.
>polymerase chain reaction) does not prove the reductionist view.
>For such a proof it would be necessary to explain roughly how
>complex behaviour of enzymes (e.g. the ability of orientating
>themselves in cells) could emerge from physical and chemical
>laws, if probabilities are estimated in a reasonable way."
>( http://members.lol.li/twostone/E/reductionism.html )
Stuart Kauffman has some ideas on this. He suggests it is an
inevitable consequence of sparsely connected chemical networks.
>Further answers you can find in my last message to Loren King.
>
>Wolfgang
>
=====================================================
Ian Musgrave Peta O'Donohue and Jack Francis Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
a collection of Dawkins inspired weasle programs http://www-personal.monash.edu.au/~ianm/whale.htm
Southern Sky Watch http://www.abc.net.au/science/space/default.htm
Gavin Tabor
>
> Hi Gavin!
Hi.
>
> >> >> If for a first organism with the power of reproduction to apppear
> >> >> only twenty different conditions with a probability of each 0.001
> >> >> were necessary, then the probability of such an organism to
> >> >> appear would be only 10^-60.
> . . .
> >> >> Even if 19 of the 20 conditions were fulfilled, the organism
> >> >> could not replicate and evolution of life could not start.
> >>
> >> > Not true, Show your math.
> >>
> >> No math is necessary, because my argument is based on the
> >> premise that all 20 (independent from each other) conditions
> >> must be fulfilled for replication to start.
>
> > Where did you get the figure of 20 independent conditions, all
> > with such low probabilities from? I think that thats the real question.
>
> Look at the complexity of living cells!
Noone (to my knowledge) thinks that currently-living cells were
the first reproducing entities. This is the area of abiogenesis
(not evolution) which is admittedly speculative : but it seems
likely that much simpler protein molecules which were able to
construct copies of themselves from simple amino acids were
first (see below).
>
> I have answered this question in my last message to Loren King.
> Here an excerpt:
>
> "For a self-replicating system at least 20 molecules which are at least
> as complex as nucleotids or amino acids are necessary. According
> to neo-Darwinism the movements of molecules depend on random
> thermal collisions (apart from chemical and physical laws).
Excuse me? Since when has neo-Darwinism had anything to do with
kinetic theory? (I really thought I'd seen it all by now).
The movement of molecules in a gas or liquid is the result of
collisions which are usually modelled using classical Newtonian
mechanics. In something like a cell they are likely to be attached
to each other electrostatically if in no other way, and will
vibrate. These _are_ chemical and physical laws :nothing to
do with biology.
>
> Now I assume that 20 molecules are enough for a self-replicating
> system to appear, if every molecule has the right position in space.
>
> A further simplification is needed. I assume that all 20 molecules
> are in a cube which is subdivided into 1000 mini-cubes, and for the
> right position nothing more is required than the center of gravity of
> the molecule being located within the right mini-cube.
Actually, all you want is the right topology for the interconnections.
Distances will be irrelevant : since these will be determined by the
physics of the situation, not by the probabilities. IE you are
estimating the wrong things here.
>
> In this simpified case the probability for the self-replicating system
> to appear is 10^-60. Common sense is enough to show that for a
> self-replicating system to appear in nature, the probability is even
> much much lower."
>
> > My understanding is that the smallest self-replicating protein
> > has 32 base units in it. If there are say 10 different amino
> > acid choices for each block, that implies there are 10^32
> > such proteins which can form - ignoring any issues of
> > chemistry. In a liquid molecules interact at a rate of around
> > 10^14 interactions/sec : lets say new arrangements are formed
> > at that rate. In 1 mole of amino acids that means there are
> > 10^22 32-element proteins, and in 1 second, there are
> > thus 10^36 proteins being tried. Thus in 1 second, 10^4
> > of these self-replicating proteins will be formed.
> > Sounds like pretty good odds to me.
>
> Are you telling a joke?
Do I look like I'm joking? I'm providing you with an example
of how to go about estimating the likelyhood of generating the
simplest self-replicating entity given a flask of amino acids.
This seems much more useful for the discussion than the probability
of 20 marbles forming a pretty pattern in space (which is what
you have worked out).
>
> What is a self-replicating protein?
One capable of reproducing itself from spare amino acids.
> To assume that every collision
> between molecules corresponds to a new arrangement of a
> sequence of 32 amino acids seems absurd to me.
What I am doing is assuming that every time two molecules
collide they are going to react to create a new molecule. This
is rather dubious : but even if only 1% of collisions result in
a reaction, I'm still ahead of the game.
> Incorrect
> chemical bonds between amino acids are possible. Bonds with
> other molecules cannot be excluded.
And I am taking account of these effects.
> Where could a soup with
> such a high proportion of amino acids have existed?
Didn't say it did in this concentration. The concentration
would be lower, and the rate of formation of new molecules
lower (if the biochemists in the audience would like to provide
some figures, we can factor these effects in). OTOH, there
would have been far more than 1 mole of amino acids around,
and its quite likely that the process of abiogenesis
took O(100myr) - thats 10^15 seconds.
I'd say this (which is definitely a back-of-envelope calculation)
still holds up pretty well.
Gavin
z@z
It actually were your texts concerning Naturalism and Creationism
which gave me a good impression of you. Your summaries of
my convictions show me that you also tried to understand at least
parts of my texts.
I think we have a problem of communication, and that's quite normal.
Therefore it will be necessary for mankind to create efficient artificial
languages with clear words and linguistic structures!
The problem of unclear words and expressions unfortunately cannot
be resolved by definitions, because they themselves depend on
other words. The best way is to give concrete examples.
However, to explain every word or expression is somewhat tiring.
The concepts 'causality' and 'finality' are very old philosophical
concepts. Maybe until the time of Descartes (1596-1650) they had
equal rights in philosophy and science. There is, however, no
apriori reason why 'causality' should be more scientific than 'finality'.
Johnson's concept 'naturalistic' is in some respect almost the same
as my concept 'reductionist', but there is also a (maybe only linguistic)
difference: according to my usage of 'natural' there is nothing
supernatural. Final laws or souls are totally natural entities.
In this context it may be interesting to look at the history of
'naturalism'. A certainly questionable and maybe subjective
simplification is the assumption that there was an evolution from
animism to polytheism, to monotheism with God outside the world,
to monotheism with God inside the world, to pantheism and finally
to atheism. The difference between atheism and pantheism is not
big, because in pantheism 'God' is only a synomym for 'world' and
'nature', or means a special aspect of the world.
The basis of modern science was build in the 17th century. One of
the first consequent naturalists was Baruch Spinoza (1632-1677),
who explained the world in a panpsychist and panmaterialist way:
space or matter is one aspect of the world (or of God or of nature),
and thinking or consciousness a second. Johannes Kepler (1571-
1630) had explained the world in a quite similar way, based on a
monotheism with God inside the world.
Both Kepler and Spinoza were fought and ridiculed especially by
theologians but also by scientists. The alternative was the philosophy
of Descartes: on the one hand was the material world and on the
other human souls and God. Animals were considered pure
machines without consciousness. The current scientific world view
is based on the philosophy of Descartes. The big inconsistency of
Cartesianism (animals as pure machines, humans having souls)
was removed by removing the concept 'soul' (and 'God').
So why do you consider panpsychism as something supernatural?
One main reason for its defeat was that it was a naturalistic
explanation of the world not in agreement with theology.
According to my usage of the word 'reductionist', Descartes'
philosophy is reductionist with the exception of the concepts
'human soul' (and 'God'), whereas all explanations involving final or
teleological principles, or based on vitalism or panpsychism are not.
I have put together some further extracts on this subject in:
http://members.lol.li/twostone/E/evidence.html#epistemology
Many enzymes work at defined places in a cell. If we create an
enlarged model, where enzymes are like little balls, then the volume
of the whole cell is about 1000 cubic metres. Imagine concretely
this situation: a little ball must come very near to a substrat and the
substrat recognition even depends on the correct alignment of the
little ball. In addition to that, enzymes often have to pass cell
membranes in order to reach their destination. What is the moving
force of enzymes? It cannot be electromagnetic attraction or
repulsion. So the moving force must primarily depend on random
thermal motions (as Brownian movements do).
You certainly will object that we do not know well enough the
chemistry of enzymes in order to conclude that: there may always
be the needed chemical forces responsible for the 'apparently'
very purposeful motions of enzymes. This implies that the information
for these motions to desired destinations is somehow stored in
the amino acid sequence of an enzyme, in addition to to the
information for folding, substrat specifity and so on, because even
similar enzymes can have very different destinations. A mutation
could change a description factor in such a way that the protein
would search its usual substrate in a wrong chromosome.
The voyage of transcription factors to their destiny can be compared
with the voyages of migratory birds and other migratory animals.
You ask me, how can I "be certain that 'at least 20' independent
and mutually improbable conditions all have to be satisfied, in one
particular sequence". I have the same right to ask you, how can you
be certain that not at least 20 different conditions with low probablilty
must be at the same time satisfied for a replicating system to appear.
Within the reductionist framework there is no sound reason to
assume that stages which could give rise to a self-replicating system
are rather conserved than other stages, or that steps in the right
direction have somehow a higher probability than steps in a wrong
direction.
The present-day scientific ignorance is no better evidence for
reductionism than for panpsychism! But is it really a necessary
ignorance? Ignorance is often the result of false premises.
I'm convinced that physical laws as described by classical physics
or by QM cannot be responsible for the fact that living organisms
evolved and survive. The often cited 'complex dynamic systems' as
e.g. the appearance of ordered vortices, waves or similar things
doesn't affect evolution much more than the appearance of solar
systems does. And the appearance of crystals (carefully studied
by Kepler) is rather evidence for panpsychism than for reductionism.
One must not confuse logical reasoning with empirical facts.
Calculations of probability must be based on clear and sound
assumptions, but the calculations themselves must not be
influenced by empirical facts. From the fact that evolution has
occured we cannot conclude that it can be explained on the basis
of the generally accepted metaphysical principles of current science.
Philip E. Johnson:
"But when materialism is assumed as the very basis of science, they
can re-emerge a few logical steps later in triumph. Something had
to guide evolution, to produce those wonders of apparent design,
and natural selection is just about the only materialist contender."
Cheers
Wolfgang
Loren King
> The concepts 'causality' and 'finality' are very old philosophical
> concepts. Maybe until the time of Descartes (1596-1650) they had equal
> rights in philosophy and science. There is, however, no apriori reason
> why 'causality' should be more scientific than 'finality'.
I'm familiar with the philosophical history of the concepts; I'm just
not sure why you think that some sufficiently complex phenomena can only
be explained in terms of final ends. Defining such ends has always been
a problem, since we generally have to infer such ends (consciously or
inadvertently) from the observation and interpretation of causes. But
if final ends in natural systems are inferred from causes, it isn't
clear why the concept of cause alone isn't sufficient to explain natural
phenomena. To my knowledge, no one has ever satisfactorily addressed
this objection to strong teleological claims about final ends in nature.
But let me just say at the outset what I think is a reasonable
definition `reductionism': it is the tendency of scientific explanations
of phenomena to go as far down as possible along the chains of cause and
effect. We try to figure out what causes what, by identifying and
understanding the characteristic features and consequences of each
causal relation involved in producing a phenomena.
> Johnson's concept 'naturalistic' is in some respect almost the same as
> my concept 'reductionist', but there is also a (maybe only linguistic)
> difference: according to my usage of 'natural' there is nothing
> supernatural. Final laws or souls are totally natural entities.
Johnson's big problem with naturalism is that it seems to remove the
supernatural from our explanations of various phenomena (natural and
social). But as I've said elsewhere, I don't think the methodological
naturalism characteristic of science is the same naturalism that Johnson
takes issue with. Johnson's naturalism is a blending of a bare
materialist ontology (i.e. everything is ultimately material) with a
rationalist epistemology (i.e. everything real is knowable through
experience and cognition) ... is this analogous to what you mean by
reductionism?
> [stuff on Spinoza and Kepler snipped] ... The current scientific world
> view is based on the philosophy of Descartes. The big inconsistency of
> Cartesianism (animals as pure machines, humans having souls) was
> removed by removing the concept 'soul' (and 'God').
I think it's a bit simplistic to say that "the current scientific
world-view" (whatever that is) is based on Cartesian ideas. A lot of
water has gone under the bridge since Descartes.
> So why do you consider panpsychism as something supernatural?
I don't. I'm just not at all clear about what "stuff" this term refers
to. Which is to say that I can't make sense of that view, given my
(provisional) commitment to methodological naturalism (namely that the
external world exists independent of our experiencing and thinking about
it, and our senses and reasonings are roughly accurate in conveying to
us basic facts about this world, and explaining causal relations). Nor
have I any reason to dispense with this provisional committment: there
are no glaring and persistent anomalies that lead me to radically revise
my assumptions about the basic reality and comprehensibility of the
world.
> According to my usage of the word 'reductionist', Descartes'
> philosophy is reductionist with the exception of the concepts 'human
> soul' (and 'God'), whereas all explanations involving final or
> teleological principles, or based on vitalism or panpsychism are not.
Why do you think that teleological reasoning cannot be reductionist?
You might find Ernst Mayr's views on this informative, particularly his
discussion of Aristotle, in his excellent GROWTH OF BIOLOGICAL THOUGHT:
DIVERSITY, EVOLUTION AND INHERITANCE (Harvard UP, 1982).
> You certainly will object that we do not know well enough the
> chemistry of enzymes in order to conclude that: there may always
> be the needed chemical forces responsible for the 'apparently'
> very purposeful motions of enzymes.
We don't, and what we do know doesn't suggest that our basic logic of
scientific inference is radically inadequate. There have been a lot of
advances in the study of abiogenesis and the origins of primitive
self-replicating systems; all of it is in accord with naturalistic
processes and reductionist explanatory principles (at least as I
understand that term).
> The voyage of transcription factors to their destiny can be compared
> with the voyages of migratory birds and other migratory animals.
It's a vague analogy, and I can't see how it could be rendered more
precise without quickly becoming incorrect as a causal explanation.
> You ask me, how can I "be certain that 'at least 20' independent
> and mutually improbable conditions all have to be satisfied, in one
> particular sequence". I have the same right to ask you, how can you
> be certain that not at least 20 different conditions with low probablilty
> must be at the same time satisfied for a replicating system to appear.
The burden of proof isn't on my shoulders: after all, you're the one
making claims about the certainty of your probability estimates. I'm
just asking you how you can meaningfully make such estimates, given that
you and no one else yet understands very much about the mechanisms and
processes involved.
> Within the reductionist framework there is no sound reason to
> assume that stages which could give rise to a self-replicating system
> are rather conserved than other stages, or that steps in the right
> direction have somehow a higher probability than steps in a wrong
> direction.
Why not? I see nothing preventing such incrementalist processes in
standard evolutionary theory.
> The present-day scientific ignorance is no better evidence for
> reductionism than for panpsychism! But is it really a necessary
> ignorance? Ignorance is often the result of false premises.
Huh? Reductionism seems to me to characterize a methodology, not a set
of hypotheses. The "evidence" in favour of reductionist methods is
their extraordinary success in leading us to knowledge about
cause-effect relations in the world around us. You've given us no
reason to think that reductionist research programmes will be any less
successful in eventually leading us to an understanding of the origins
of self-replicating systems in nature.
> I'm convinced that physical laws as described by classical physics
> or by QM cannot be responsible for the fact that living organisms
> evolved and survive.
What, specifically, convinces you of this?
> The often cited 'complex dynamic systems' as e.g. the appearance of
> ordered vortices, waves or similar things doesn't affect evolution
> much more than the appearance of solar systems does.
Do you have specific evidence to support this strong claim?
> And the appearance of crystals (carefully studied by Kepler) is rather
> evidence for panpsychism than for reductionism.
I don't see this at all.
Also, is panpsychism now a method, or a conjecture about certain natural
systems? I mean, you keep pairing reductionism against this psychic
position, but reductionism is a characteristic of scientific method, not
a sweeping claim about the subject matter of science (except in the
basic sense that reductionism supposes that we can in fact understand
wholes by studying their parts).
So, what gives? Do you have a non-reductionist method with which to
study panpsychic phenomena? Or is panpsychism itself a method? If the
latter, what is the "stuff" that this method studies, and how does it
approach this "stuff" in ways distinct and more fruitful than
reductionist approaches?
Mark Isaak
>"For a self-replicating system at least 20 molecules which are at least
>as complex as nucleotids or amino acids are necessary.
>In this simpified case the probability for the self-replicating system
>to appear is 10^-60.
You are assuming that there is only one self-replicating arrangement of
the 20 molecules. How do you know the number isn't closer to 10^59?
Your other assumptions are unreasonable, too. Molecules don't arrange
themselves randomly.
--
Mark Isaak atta @ best.com http://www.best.com/~atta
"My determination is not to remain stubbornly with my ideas but
I'll leave them and go over to others as soon as I am shown
plausible reason which I can grasp." - Antony Leeuwenhoek
George Acton
>
[snip]
>
> Many enzymes work at defined places in a cell. If we create an
> enlarged model, where enzymes are like little balls, then the volume
> of the whole cell is about 1000 cubic metres. Imagine concretely
> this situation: a little ball must come very near to a substrat and the
> substrat recognition even depends on the correct alignment of the
> little ball. In addition to that, enzymes often have to pass cell
> membranes in order to reach their destination. What is the moving
> force of enzymes? It cannot be electromagnetic attraction or
> repulsion. So the moving force must primarily depend on random
> thermal motions (as Brownian movements do).
>
> You certainly will object that we do not know well enough the
> chemistry of enzymes in order to conclude that: there may always
> be the needed chemical forces responsible for the 'apparently'
> very purposeful motions of enzymes. This implies that the information
> for these motions to desired destinations is somehow stored in
> the amino acid sequence of an enzyme, in addition to to the
> information for folding, substrat specifity and so on, because even
> similar enzymes can have very different destinations. A mutation
> could change a description factor in such a way that the protein
> would search its usual substrate in a wrong chromosome.
>
> The voyage of transcription factors to their destiny can be compared
> with the voyages of migratory birds and other migratory animals.
I'm sorry to contradict you, because I enjoyed your account of the
history of ideas in this area, and looking at some of these issues
from your perspective. But I'm afraid your description of the
cellular localization of enzymes misses the point. The cellular
"traffic control" that directs enzymes and other substances to
their destination is entirely mechanical. Not only does the enzyme
have the information to assume its shape and form the active site,
but it has portions that tag it as destined for different destinations.
The transport systems that move the enzymes recognize these "bar
codes" and move the enzyme to the appropriate site. The obvious
experiment is to alter that portion of the enzyme without changing
the active site. And the result is an active enzyme located in
the wrong place. And you are correct that a mutation could change
the protein so it would wind up in the wrong place, although
"Search" is more anthropomorphic than most people in science would
prefer.
More generally, all theories that impute knowledge or purpose
to subcellular or cellular structures have been discarded. One of
the classic instances was discovered by Monod. When the bacterium
E. coli is placed in an enviroment with a high concentration of
the sugar lactose, it makes more of the tramsporter protein in the
cell membrane, which imports more of the compound. The naive
explanation is that the transporter "knows" how much of itself is
needed by sensing how much sugar it contacts. It turns out that
the sensor is an entirely separate mechanism, with a different
protein, and that it doesn't sense exactly the same shape of
sugar at all. One can use chemically modified sugars recognized
by the sensor, which cannot be transported or provide nutrition.
And the systems can be mutated separately to have different
specificities for different sugars. So what appeared to be
an intelligent, purposive response by the cell turns out to be
totally mechanical. The story is told in The Eigth Day of
Creation, by Jodson.
(A small pedagogic point. Your model is correct in size, but
the thermal motion at the molecular level is much faster than
we would guess from everyday objects. Some enzymes can catalyze
thousands of reactions per second, and the calculations show that
random encounters will indeed expose them to that many substrate
molecules in a second.)
The general doctrine of purpose or intelligence at the
cellular level is known in the Twentieth Century as "vitalism".
This is confusing, since the term has had several contradictory
meanings in philosophy and biology. Some people consider that
the "death of vitalism" was in the explanation of antibody
diversity. Our blood contains perhaps a million different kinds
of antibody proteins, out of billions of possibilities. The
intuitively obvious explanation is that the immune system "sees"
a foreign antigen and somehow molds the shape of the appropriate
antibody. This is the "instructive theory". But the immune
system doesn't work that way. It assembles a random sample of
the billions of possibilities, each on a separage cell, then kills
or inacivates those that react to "self" and allows the cells that
encounter antigens to proliferate to make large quantities of
antibody. This is the "clonal selection" theory, and the Nobel
prizes for it were give out 40-50 years ago. Any immunology text
will give an account.
So in general, there are no subcellular or biochemical systems
that embody purpose in their present-day operation. Reductionism
has been triumphant for many years, and is embodied on the once-
controversial slogan "anything organisms can do, cells can do;
anything cells can do, molecules can do".
The history of ideas on this subject interests me, because I
have an ancestor who was a medium-wattage bulb of the Enlightenment,
and he left a large body of letters and notes, including some
related to his scientific interests. His life was shadowed by the
prematire deaths of his father and his wife, so he certainly had
some motivation to be interested in the biology of disease. But
he left no comments to the effect that anything non-material was
involved in biological processes. He and his contemporaries
seemed to have a aversion to any supernatural theories, although
by our standards they were totally ignorant of biology. Did they
believe mechanistic explanations would be forthcoming, after the
pattern of their favored scientific model of planetary motion?
Or were they stoic, after the Classical writers they had all
read. We don't know, since they were very reticent about their
psychology and the everyday theories by which they operated. It
is imposssible to recapture the mind-set of educated people even
200 years ago, and that would be far more interesting, if we could
have it, than the accounts of their travels and garden plantings.
--George Acton
John Wilkins
<gac...@softdisk.com> wrote:
[an excellent and literate article, of which I am going to excerpt a small
piece]
| The general doctrine of purpose or intelligence at the
|cellular level is known in the Twentieth Century as "vitalism".
|This is confusing, since the term has had several contradictory
|meanings in philosophy and biology. Some people consider that
|the "death of vitalism" was in the explanation of antibody
|diversity. Our blood contains perhaps a million different kinds
|of antibody proteins, out of billions of possibilities. The
|intuitively obvious explanation is that the immune system "sees"
|a foreign antigen and somehow molds the shape of the appropriate
|antibody. This is the "instructive theory". But the immune
|system doesn't work that way. It assembles a random sample of
|the billions of possibilities, each on a separage cell, then kills
|or inacivates those that react to "self" and allows the cells that
|encounter antigens to proliferate to make large quantities of
|antibody. This is the "clonal selection" theory, and the Nobel
|prizes for it were give out 40-50 years ago. Any immunology text
|will give an account.
The previous two directors of the Institute I work at were the researchers
who developed this theory. Macfarlane Burnet, whose centenary is this
year, won the Nobel Prize for his work on immunology, and the clonal
selection theory in particular, and Gustav Nossal, who retired a couple of
years ago, did the validation and confirmation of the theory. Mac got his
Nobel around 68, I think, and the theory was developed a decade earlier.
The Nobel site will have details.
--
John Wilkins
Head, Graphic Production
The Walter and Eliza Hall Institute of Medical Research
Melbourne, Australia
<mailto:wil...@WEHI.EDU.AU><http://www.wehi.edu.au/~wilkins>
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
On 11 Mar 1999 05:51:35 -0500, Gavin Tabor <g.t...@ic.ac.uk> wrote:
>z@z wrote:
[big snip]
>> > My understanding is that the smallest self-replicating protein
>> > has 32 base units in it. If there are say 10 different amino
>> > acid choices for each block, that implies there are 10^32
>> > such proteins which can form - ignoring any issues of
>> > chemistry. In a liquid molecules interact at a rate of around
>> > 10^14 interactions/sec : lets say new arrangements are formed
>> > at that rate. In 1 mole of amino acids that means there are
>> > 10^22 32-element proteins, and in 1 second, there are
>> > thus 10^36 proteins being tried. Thus in 1 second, 10^4
>> > of these self-replicating proteins will be formed.
>> > Sounds like pretty good odds to me.
I've done a very similar calculation but under more limiting
conditions, using all 20 amino acids, the synthesis rate in Ferris
"assembled on clay" chemistry (a week for an approx 40 aa long chain,
note that this is much slower than the Wacherhauser polymerisation),
an amino acid concentration of 10^-6 M, derived from Sagan and
Chybas's work. Under these conditions you get at least one self
replicating peptide a year.
see http://www-personal.monash.edu.au/~ianm/prob.htm for more details
and references.
>> Are you telling a joke?
No, he's not, his synthesis rate is a high, but otherwise it's okay.
>Do I look like I'm joking? I'm providing you with an example
>of how to go about estimating the likelyhood of generating the
>simplest self-replicating entity given a flask of amino acids.
>This seems much more useful for the discussion than the probability
>of 20 marbles forming a pretty pattern in space (which is what
>you have worked out).
and given that the Lee peptide is just one of a number of possible
self-relicating peptides, the probabilities are even better.
I personally like Kaufmanns catalytic closure ideas, whereby any
sufficently large population of enzymes becomes autocatalytic. This
remove the dependence on a particular peptide sequence. However,
Kaufmanns results have yet to be generalised to more realistic
chemistries.
>> What is a self-replicating protein?
>
>One capable of reproducing itself from spare amino acids.
>
>> To assume that every collision
>> between molecules corresponds to a new arrangement of a
>> sequence of 32 amino acids seems absurd to me.
>
>What I am doing is assuming that every time two molecules
>collide they are going to react to create a new molecule. This
>is rather dubious : but even if only 1% of collisions result in
>a reaction, I'm still ahead of the game.
The actual rate of formation of peptide bonds in free solution without
condensing agents is quite low. However, in the Wachterhauser
catalytic synthesis rates not too far from your 1% level occur. In the
drying and clay polymerisation scenarios, the reaction rates are
slower but still enough to make lots of sizable petides in a
reasonably short time.
>> Incorrect
>> chemical bonds between amino acids are possible. Bonds with
>> other molecules cannot be excluded.
>
>And I am taking account of these effects.
>
>> Where could a soup with
>> such a high proportion of amino acids have existed?
The oceans of early earth could have between 10^-4 and 10^-6 molar
amino acids, depending on the relative efficency of atmospheric
synthesis in various model atmospheres, and the rate of delivery of
organics via comets and dust grains. The contribution of Wachterhauser
type synthesis has been ignored.
Drying of beach lagoons could have easily boosted this concentration
to between 1mM and 1M.
>Didn't say it did in this concentration. The concentration
>would be lower, and the rate of formation of new molecules
>lower (if the biochemists in the audience would like to provide
>some figures, we can factor these effects in). OTOH, there
>would have been far more than 1 mole of amino acids around,
Something like 10^44 mole
>and its quite likely that the process of abiogenesis
>took O(100myr) - thats 10^15 seconds.
>
>I'd say this (which is definitely a back-of-envelope calculation)
>still holds up pretty well.
It's not bad at all.
Cheers! Ian
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
Following up on my own message, sorry.
On 11 Mar 1999 02:03:48 -0500,
reyn...@RemoveInsert.werple.mira.net.au (Ian Musgrave & Peta
O'Donohue) wrote:
>G'Day All
>Address altered to avoid spam, delete RemoveInsert
>
>On 10 Mar 1999 16:48:54 -0500, "z@z" <z...@z.lol.li> wrote:
[snip]
>>> You realize, of course that they have discovered replicating molecules
>>> around 32 molecules long? And furthermore that molecules do not
>>> form randomly? What independent events are you proposing need
>>> to happen? Can you use the above ideas to predict the yield of
>>> Miller's experiements?
>>
>>That's actually new for me: the existence of "replicating molecules
>>around 32 molecules long". The only possibility I see is the following:
>>there are RNA enzymes 32 bases long which replicate by base
>>pairing. Are you sure that such molecules actually have been
>>discovered, molecules replicating independently?
>
>Yep, see
>Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of
>symbiosis in peptide self-replication through a hypercyclic network.
>Nature 390: 591-4, 1997 Dec 11
>
>Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, A
>self-replicating peptide. Nature 382: 525-8, 1996 Aug 8
>
>There is also von Kreidowskis self replicating RNA's of various
>lengths and the recent von K paper in Nature on tethered nucleotides.
For those who want, here are even more references:
Self replicating peptides using a different structure to the Lee
peptide:
Yao S, Ghosh I, Zutshi R, Chmielewski J. Selective amplification by
auto and cross-catalysis in a replicating peptide system.
von Kiedrowski's latest:
Luther A. Brandsch R. von Kiedrowski G. Surface-promoted replication
and exponential amplification of DNA analogues. Nature.
396(6708):245-8, 1998 Nov 19
A review of self replication:
Bag. BG, von Kiedrowski G. Templates, autocatalysis and molecular
replication. Pure & Appl Chem 68, 2145-2152, 1996.
And here are some websites
The Ghadiri home page, go to publications and download the Current
Opinions PDF for a more detailed explanation
http://www.scripps.edu/pub/ghadiri/
A plain langauge description of the properties of the Lee peptide
http://www.newscientist.com/ns/970426/protein_nf.html
Another description, with comments by Stuart Kauffman
http://www.santafe.edu/sfi/publications/Bulletins/bulletin-summer97/turning.html
Yet another description by Kauffman
http://www.santafe.edu/sfi/People/kauffman/sak-peptides.html
Some other self-replicating molecules
http://w3.mit.edu/newsoffice/tt/1990/may09/23124.html
Von Kiedrowski's work:
http://p6-1.orch.ruhr-uni-bochum.de/kiedrowski/research.html
An overview of the RNA world, with comments on hypercycles, several of
the suggested experiments in the conclusion have been performed, with
results compatible with the RNA world.
http://biotech.chem.indiana.edu/pages/science/RNA.html
An American Scientist article on origin of life by C. de Duve:
http://www.sigmaxi.org/amsci/articles/95articles/cdeduve.html
This account was written before the ribozymal polymerases were
described, and a number of other issues resolved so is slightly more
pessimistic than needs be.
A discovery article on Deamers work on protocells
http://www.discover.com/
From the Discover site, go to the Archives, search on
November 1995 and click on the First Cell link.<p>
[snip]
>Stuart Kauffman has some ideas on this. He suggests it is an
>inevitable consequence of sparsely connected chemical networks.
Kauffmans web site
http://www.santafe.edu/sfi/People/kauffman/index.html
and an article about catalytic closure and his phase transition ideas
http://www.santafe.edu/sfi/People/kauffman/Investigations.html
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
On 11 Mar 1999 17:46:14 -0500, "z@z" <z...@z.lol.li> wrote:
>Hello Loren!
[snip intro to philosophy]
>Many enzymes work at defined places in a cell. If we create an
>enlarged model, where enzymes are like little balls, then the volume
>of the whole cell is about 1000 cubic metres. Imagine concretely
>this situation: a little ball must come very near to a substrat and the
>substrat recognition even depends on the correct alignment of the
>little ball.
Sometimes, but sometimes the enzymes are thethered to mebranes or
other structures (eg some of the respiritory enzymes, signal
transducing G-protiens etc). As Gavin tTabor pointed out, in aquoes
solution there are around 10^14 interactions/sec between molecules,
and the volume involved is nanoliters, which is miniscule compared to
the free diffusion paths of these molecules, so it is not particularly
difficult for a substrate to meet it's enzyme in the right orientation
just by randomly bouncing around in the cell.
>In addition to that, enzymes often have to pass cell
>membranes in order to reach their destination.
This happens very rarely, and then the enzymes are usually secreted
via a specific membrane targeting peptide. (Unless you are talking
about passage of transcription factors into the nucleus, where they
pass through the pores in the nuclear membrane)
>What is the moving
>force of enzymes? It cannot be electromagnetic attraction or
>repulsion.
Sometimes it is a contributor, many proteins have a small net charge,
but for untethered proteins, simple random motion works nicely.
>So the moving force must primarily depend on random
>thermal motions (as Brownian movements do).
Okay. Whats the mean free path of a small molecule such as say,
glycine in free solution. What is the mean free path of a haeomglobin
molecule
>You certainly will object that we do not know well enough the
>chemistry of enzymes in order to conclude that: there may always
>be the needed chemical forces responsible for the 'apparently'
>very purposeful motions of enzymes.
What apparent purposeful motion of proteins?
>This implies that the information
>for these motions to desired destinations is somehow stored in
>the amino acid sequence of an enzyme, in addition to to the
>information for folding, substrat specifity and so on, because even
>similar enzymes can have very different destinations.
For tethered proteins, certainly yes. As an example, signal
transducing GTPases (G-proteins) are targeted to the membrane by a
palmitoyl group attached to the enzyme, for protein kinase B, it the
plextrin homolgy domain that does the job of targeting. For things
like the monoamine oxidases, its a combination of structure and local
production that confines them to the mitochondrial wall.
>A mutation
>could change a description factor in such a way that the protein
>would search its usual substrate in a wrong chromosome.
Most certainly.
>The voyage of transcription factors to their destiny can be compared
>with the voyages of migratory birds and other migratory animals.
Not really, you're missing the scale of the cell and thermal motions.
A transcription factor can cross the cell in a nanosceond, the
observed rates of transcription factor initiation is entirely
compatible with the enzymes just randomly boncing around in the cell.
>You ask me, how can I "be certain that 'at least 20' independent
>and mutually improbable conditions all have to be satisfied, in one
>particular sequence". I have the same right to ask you, how can you
>be certain that not at least 20 different conditions with low probablilty
>must be at the same time satisfied for a replicating system to appear.
Well, that's a nice way to avoid the question. But from model self
replicators, and our current knowledge of chemistry, we can say that
the steps (however many they are) are not independent and at least
some are not particularly improbable.
Where do the "at least 20 steps" come from? is there a mathematical
analysis? what is the "granularity" of the steps? Are you refering to
the sequential formation of 20 discrete molecules? or are the steps
something else for example:
1) formation of building blocks
2) formation of a self-replicating molecule from bulding blocks
3) expansion of the replicator to a catalytic hypercycle
4) encapsulation of the hypecycle in a membrane
5) compartmentalization of the hypercycle into a genetic and a
metabolic compartment
6) formation of a genome from the genetic hypercycle
(this is the Eigen style model, a Kaufmann model would replace steps 2
and 3 with formation of catalysits and catalytic closure respectively)
>Within the reductionist framework there is no sound reason to
>assume that stages which could give rise to a self-replicating system
>are rather conserved than other stages, or that steps in the right
>direction have somehow a higher probability than steps in a wrong
>direction.
Depend on whether you are using a Eigen style "single replicator"
hypercycle model, an RNA/ribopeptide world co-operative hypercycle or
Kaufmanns catalytic closure. In the latter two self replicating
systems are significantly advantaged in their chemistry.
>The present-day scientific ignorance is no better evidence for
>reductionism than for panpsychism! But is it really a necessary
>ignorance? Ignorance is often the result of false premises.
How often, example please.
What is a prediction of panpsycism in chemistry that can be tested.
>I'm convinced that physical laws as described by classical physics
>or by QM cannot be responsible for the fact that living organisms
>evolved and survive.
Why, what is it about, say bacterial respiration that can't be
explained in modern physics and chemistry.
>The often cited 'complex dynamic systems' as
>e.g. the appearance of ordered vortices, waves or similar things
>doesn't affect evolution much more than the appearance of solar
>systems does. And the appearance of crystals (carefully studied
>by Kepler) is rather evidence for panpsychism than for reductionism.
Crystals from by well studied physical laws. Name an aspect of crystal
formation that is explained by panpsycism and not modern chemisrty and
physics. Can you predict from panpscism which molecules will
crystalise to form face centered cubic structures?
>One must not confuse logical reasoning with empirical facts.
>Calculations of probability must be based on clear and sound
>assumptions, but the calculations themselves must not be
>influenced by empirical facts.
Ahh, nice try, but in probability you must always check your empirical
facts (if you assume you have a normal distribution, when you in fact
don't have one, your calculations are meaningless).
>From the fact that evolution has
>occured we cannot conclude that it can be explained on the basis
>of the generally accepted metaphysical principles of current science.
z@z meet William of Occam, he has a razor he thinks you should use.
>Philip E. Johnson:
>
> "But when materialism is assumed as the very basis of science, they
> can re-emerge a few logical steps later in triumph. Something had
> to guide evolution, to produce those wonders of apparent design,
> and natural selection is just about the only materialist contender."
Of course, there is the little problem of all this _evidence_ for
selection (both natural and sexual) that people keep turning up.
maf...@my-dejanews.com
SIR FRANK MACFARLANE BURNET
1960 Nobel Laureate in Medicine
for discovery of acquired immunological tolerance.
Background
1899-1985
Residence: Australia
Affiliation: Walter and Eliza Hall Institute for Medical Research,
Melbourne
http://nobelprizes.com/nobel/nobel.html
-----------== Posted via Deja News, The Discussion Network ==----------
http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own
Gavin Tabor
>
> G'Day All
> Address altered to avoid spam, delete RemoveInsert
>
> >> > has 32 base units in it. If there are say 10 different amino
> >> > acid choices for each block, that implies there are 10^32
> >> > such proteins which can form - ignoring any issues of
> >> > chemistry. In a liquid molecules interact at a rate of around
> >> > 10^14 interactions/sec : lets say new arrangements are formed
> >> > at that rate. In 1 mole of amino acids that means there are
> >> > 10^22 32-element proteins, and in 1 second, there are
> >> > thus 10^36 proteins being tried. Thus in 1 second, 10^4
> >> > of these self-replicating proteins will be formed.
> >> > Sounds like pretty good odds to me.
>
> conditions, using all 20 amino acids, the synthesis rate in Ferris
> "assembled on clay" chemistry (a week for an approx 40 aa long chain,
> note that this is much slower than the Wacherhauser polymerisation),
> an amino acid concentration of 10^-6 M, derived from Sagan and
> Chybas's work. Under these conditions you get at least one self
> replicating peptide a year.
>
> see http://www-personal.monash.edu.au/~ianm/prob.htm for more details
> and references.
Yah know, I just knew there would be people listening to me
shout my mouth off who knew a lot more about this than me. Thanks for
the
link - I'm looking through it.
>
> >> Are you telling a joke?
>
> No, he's not, his synthesis rate is a high, but otherwise it's okay.
>
> >Do I look like I'm joking? I'm providing you with an example
> >of how to go about estimating the likelyhood of generating the
> >simplest self-replicating entity given a flask of amino acids.
> >This seems much more useful for the discussion than the probability
> >of 20 marbles forming a pretty pattern in space (which is what
> >you have worked out).
>
> and given that the Lee peptide is just one of a number of possible
> self-relicating peptides, the probabilities are even better.
How many are known? Is it 10s, 1000's 10^6's?
>
> I personally like Kaufmanns catalytic closure ideas, whereby any
> sufficently large population of enzymes becomes autocatalytic. This
> remove the dependence on a particular peptide sequence. However,
> Kaufmanns results have yet to be generalised to more realistic
> chemistries.
Presumably this would make construction of large peptide sequences
much easier than my simple random reactions would suggest - less
fragmentation.
>
> >> What is a self-replicating protein?
> >
> >One capable of reproducing itself from spare amino acids.
> >
> >> To assume that every collision
> >> between molecules corresponds to a new arrangement of a
> >> sequence of 32 amino acids seems absurd to me.
> >
> >What I am doing is assuming that every time two molecules
> >collide they are going to react to create a new molecule. This
> >is rather dubious : but even if only 1% of collisions result in
> >a reaction, I'm still ahead of the game.
>
> The actual rate of formation of peptide bonds in free solution without
> condensing agents is quite low. However, in the Wachterhauser
> catalytic synthesis rates not too far from your 1% level occur. In the
> drying and clay polymerisation scenarios, the reaction rates are
> slower but still enough to make lots of sizable petides in a
> reasonably short time.
>
> >> Incorrect
> >> chemical bonds between amino acids are possible. Bonds with
> >> other molecules cannot be excluded.
> >
> >And I am taking account of these effects.
> >
> >> Where could a soup with
> >> such a high proportion of amino acids have existed?
>
> The oceans of early earth could have between 10^-4 and 10^-6 molar
> amino acids, depending on the relative efficency of atmospheric
> synthesis in various model atmospheres, and the rate of delivery of
> organics via comets and dust grains. The contribution of Wachterhauser
> type synthesis has been ignored.
>
> Drying of beach lagoons could have easily boosted this concentration
> to between 1mM and 1M.
I thought that might be the case. Presumably if the surface of clays
has an afinity for amino acids, this would boost the concentration,
as well as making reaction easier.
>
> >Didn't say it did in this concentration. The concentration
> >would be lower, and the rate of formation of new molecules
> >lower (if the biochemists in the audience would like to provide
> >some figures, we can factor these effects in). OTOH, there
> >would have been far more than 1 mole of amino acids around,
>
> Something like 10^44 mole
>
> >and its quite likely that the process of abiogenesis
> >took O(100myr) - thats 10^15 seconds.
> >
> >I'd say this (which is definitely a back-of-envelope calculation)
> >still holds up pretty well.
>
> It's not bad at all.
Thank you!
>
> Cheers! Ian
> =====================================================
> Ian Musgrave Peta O'Donohue and Jack Francis Musgrave
> reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
> a collection of Dawkins inspired weasle programs http://www-personal.monash.edu.au/~ianm/whale.htm
> Southern Sky Watch http://www.abc.net.au/science/space/default.htm
Gavin
Kalandros M
> G'Day All
> Address altered to avoid spam, delete RemoveInsert
>
> Following up on my own message, sorry.
>
> On 11 Mar 1999 02:03:48 -0500,
> reyn...@RemoveInsert.werple.mira.net.au (Ian Musgrave & Peta
> O'Donohue) wrote:
>
> >G'Day All
> >Address altered to avoid spam, delete RemoveInsert
> >
Just out of curiosity, are these replicators considered likely to form in
the pre-biotic earth scenarios?
Mike
James G. Acker
In response to:
Hi all,
I recently added a number of articles by Phillip Johnson to the WWCW
Q&A page (http://www.wwcw.org/qa.html). Come on over and read his
answers to questions such as:
-- What is Darwinism?
--How can we tell science from religion?
--Can Darwinism really stand close scrutiny?
---> I did a quick evaluation of the last one.
My quick summary:
PJ is the most mealy-mouthed, two-faced propagandist I've
ever encountered.
Jim Acker
===============================================
| James G. Acker |
| REPLY TO: jga...@neptune.gsfc.nasa.gov |
===============================================
All comments are the personal opinion of the writer
and do not constitute policy and/or opinion of government
or corporate entities.
Ian Musgrave & Peta O'Donohue
Email modified to foil spammers, delete RemoveInsert to repy
On 12 Mar 1999 05:26:19 -0500 Gavin Tabor <g.t...@ic.ac.uk> wrote:
>Ian Musgrave & Peta O'Donohue wrote:
[snip]
>> >> Are you telling a joke?
>>
>> No, he's not, his synthesis rate is a high, but otherwise it's okay.
>>
>> >Do I look like I'm joking? I'm providing you with an example
>> >of how to go about estimating the likelyhood of generating the
>> >simplest self-replicating entity given a flask of amino acids.
>> >This seems much more useful for the discussion than the probability
>> >of 20 marbles forming a pretty pattern in space (which is what
>> >you have worked out).
>>
>> and given that the Lee peptide is just one of a number of possible
>> self-relicating peptides, the probabilities are even better.
>
>How many are known? Is it 10s, 1000's 10^6's?
Currently there are 8 self replicating peptides known, however Ghadiri
thinks that there are a lot more, and Yao's work suggests that his
idea is right. _Exactly_ how many is not certain, but I would bank on
thousands to millions, even just using the AB helical groove system
that Ghadiri uses.
>> I personally like Kaufmanns catalytic closure ideas, whereby any
>> sufficently large population of enzymes becomes autocatalytic. This
>> remove the dependence on a particular peptide sequence. However,
>> Kaufmanns results have yet to be generalised to more realistic
>> chemistries.
>
>Presumably this would make construction of large peptide sequences
>much easier than my simple random reactions would suggest - less
>fragmentation.
Yes, even catalysis on clay and mineral surfaces provides much less
fragmentation, when you get peptide catalysis, it's all down hill :-)
[snip]
>> Drying of beach lagoons could have easily boosted this concentration
>> to between 1mM and 1M.
>
>I thought that might be the case. Presumably if the surface of clays
>has an afinity for amino acids, this would boost the concentration,
>as well as making reaction easier.
Again, correct, sme recent work suggests that certain clays act as
"mini-reactors" with just this combination of concentration and
catalysis.
>> >Didn't say it did in this concentration. The concentration
>> >would be lower, and the rate of formation of new molecules
>> >lower (if the biochemists in the audience would like to provide
>> >some figures, we can factor these effects in). OTOH, there
>> >would have been far more than 1 mole of amino acids around,
>>
>> Something like 10^44 mole
>>
>> >and its quite likely that the process of abiogenesis
>> >took O(100myr) - thats 10^15 seconds.
>> >
>> >I'd say this (which is definitely a back-of-envelope calculation)
>> >still holds up pretty well.
>>
>> It's not bad at all.
>
>Thank you!
I had to sweat for two days with a calculator and a pile of references
to get a similar result to your back of the envelop stuff, so you did
a bloody good job.
Cheers! Ian
=========================================================
Ian, Peta and Jack Francis, reynella at werple dot mira dot net dot au
http://werple.mira.net.au/~reynella/ (no TO stuff)
http://www-personal.monash.edu.au/~ianm/whale.htm (weasle prgrams)
http://www-personal.monash.edu.au/~ianm/hols1.htm (ruminations on the Ark)
http://www-personal.monash.edu.au/~ianm/ssky.htm (southern sky watch)
Tree planters, Terry Pratchett fans and sometime scientists (De Chelonian Mobile)
Ian Musgrave & Peta O'Donohue
Email modified to foil spammers, delete RemoveInsert to repy
On 12 Mar 1999 11:16:56 -0500 Kalandros M
<kala...@hubble.colorado.edu> wrote:
>Ian Musgrave & Peta O'Donohue wrote:
[snip "are there_really_ peptide replicators" question]
>> >Yep, see
>> >Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of
>> >symbiosis in peptide self-replication through a hypercyclic network.
>> >Nature 390: 591-4, 1997 Dec 11
>> >
>> >Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, A
>> >self-replicating peptide. Nature 382: 525-8, 1996 Aug 8
>> >
>> >There is also von Kreidowskis self replicating RNA's of various
>> >lengths and the recent von K paper in Nature on tethered nucleotides.
>>
>> For those who want, here are even more references:
>>
>> Self replicating peptides using a different structure to the Lee
>> peptide:
>>
>> Yao S, Ghosh I, Zutshi R, Chmielewski J. Selective amplification by
>> auto and cross-catalysis in a replicating peptide system.
>>
>> von Kiedrowski's latest:
>> Luther A. Brandsch R. von Kiedrowski G. Surface-promoted replication
>> and exponential amplification of DNA analogues. Nature.
>> 396(6708):245-8, 1998 Nov 19
>>
>> A review of self replication:
>> Bag. BG, von Kiedrowski G. Templates, autocatalysis and molecular
>> replication. Pure & Appl Chem 68, 2145-2152, 1996.
>>
>
>Just out of curiosity, are these replicators considered likely to form in
>the pre-biotic earth scenarios?
In another part of this thread, Gavin Tabor and myself calculate that
one of these various peptide replicators could be produced in between
a minute to a year, depending on how rigorously you limit the
prebiotic environment. Whether they would contribute significantly to
the development of more complex self replicating sytems is another
story, and one I will elaborate on later.
The nucleotide self-replicators are another story, because of
questions over the ease of forming ribonucleotides.
The weird wonders that replicate in chloroform, sadly, are not for
this earth.
James J. Lippard
>Philip E. Johnson seems to me a great logician and epistemologist,
I don't see that he has any particular skills or qualifications in either
field. (Speaking as someone with an advanced degree in epistemology who
took and taught many logic courses.)
See my critique of some of Johnson's work at
http://www.talkorigins.org/faqs/johnson.html
and my review of _Man and Creation_ (which includes a chapter by Johnson)
at
ftp://ftp.primenet.com/pub/lippard/manreview.txt
ftp://ftp.primenet.com/pub/lippard/manreview2.txt
ftp://ftp.primenet.com/pub/lippard/manreview3.txt
ftp://ftp.primenet.com/pub/lippard/manreview4.txt
--
Jim Lippard lippard@(primenet.com discord.org ediacara.org)
Phoenix, Arizona http://www.primenet.com/~lippard/
PGP Fingerprint: B130 7BE1 18C1 AA4C 4D51 388F 6E6D 2C7A 36D3 CB4F
John Finkbiner
> G'Day All
> Email modified to foil spammers, delete RemoveInsert to repy
>
> On 12 Mar 1999 05:26:19 -0500 Gavin Tabor <g.t...@ic.ac.uk> wrote:
>
> >Ian Musgrave & Peta O'Donohue wrote:
> [snip]
> >> >> Are you telling a joke?
> >>
> >> No, he's not, his synthesis rate is a high, but otherwise it's okay.
> >>
> >> >Do I look like I'm joking? I'm providing you with an example
> >> >of how to go about estimating the likelyhood of generating the
> >> >simplest self-replicating entity given a flask of amino acids.
> >> >This seems much more useful for the discussion than the probability
> >> >of 20 marbles forming a pretty pattern in space (which is what
> >> >you have worked out).
> >>
> >> and given that the Lee peptide is just one of a number of possible
> >> self-relicating peptides, the probabilities are even better.
> >
> >How many are known? Is it 10s, 1000's 10^6's?
>
> Currently there are 8 self replicating peptides known, however Ghadiri
> thinks that there are a lot more, and Yao's work suggests that his
> idea is right. _Exactly_ how many is not certain, but I would bank on
> thousands to millions, even just using the AB helical groove system
> that Ghadiri uses.
>
I'm sure you've posted refrences to this work, but I can't always read as much
Usenet as I would like. If you (or somebody else) would suggest some papers,
a certain chemistry undergraduate would be very greatful.
John "I suppose biochem can be interesting occasionally" Finkbiner
z@z
>> I'm sure that Johnson is or was a much more unbiased lawyer
>> than the average.
> Why would you say that? What is your evidence?
If have read some texts of Johnson about AIDS which I really
do appreciate. These texts have shown me that Johnson
is very conscious of the problem of bias. All his texts I have
read are much sounder than his opponents try to give the
impression.
> You are also overly fond of your own hypotheses, a usually-fatal
> affliction in science.
I don't think that this is necessarily a usually-fatal affliction. Many
great scientific successes would have been impossible if not
at least the scientists themselves had been fond of their
own hypotheses.
Cheers
Wolfgang
z@z
Didn't you intentially try to twist what I have said in order to portray
my position absurd? I use the word 'reductionism' very frequently
and always in the same way (I'm very conscious with linguistic
problems). 'Methodological reductionism' is nothing more than the
only sound scientific method and in the main it is almost the same
as 'Occam's razor'.
My use of 'reductionism' is: to reduce all phenomena of nature to
a purely material basis.
> Defining such [final] ends has always been a problem, since we
> generally have to infer such ends (consciously or inadvertently)
> from the observation and interpretation of causes. But if final
> ends in natural systems are inferred from causes, it isn't clear
> why the concept of cause alone isn't sufficient to explain
> natural phenomena.
What you write here is a very elegant example of a well-known
philosophical fallacy: circular reasoning!
If you actually are "familiar with the philosophical history of the
concepts", then what I have written in 'Causal and Final Laws'
should be enough to understand my meanings of 'causality' and
'finality'. It is not enough to know something primarily from the
perspective of modern Darwinism.
> Johnson's naturalism is a blending of a bare materialist
> ontology (i.e. everything is ultimately material) with a
> rationalist epistemology (i.e. everything real is knowable
> through experience and cognition) ... is this analogous to
> what you mean by reductionism?
Yes.
I am a friend of a rationalist epistemology. But I am aware that
the theories by which we explain the world cannot be explained
themselves in the same way. The rationalist epistemology is
sometimes used to explain the simple (gravitation) by something
complicated (material gravitons).
> I think it's a bit simplistic to say that "the current scientific
> world-view" (whatever that is) is based on Cartesian ideas.
> A lot of water has gone under the bridge since Descartes.
But the way was pointed at that time for our current materialist
reductionism and against panpsychism. Leibniz was the last
well-known panpsychist, but the many inconsistencies of his
'monadology' (a compromise between panpsychism and christian
theology) were rather harmful.
> ... given my (provisional) commitment to methodological
> naturalism (namely that the external world exists independent
> of our experiencing and thinking about it, and our senses and
> reasonings are roughly accurate in conveying to us basic facts
> about this world, and explaining causal relations).
What you describe as methodological naturalism, I would rather
call 'naive realism'. Do you know the ideas of Immanual Kant?
> there are no glaring and persistent anomalies that lead me to
> radically revise my assumptions about the basic reality and
> comprehensibility of the world.
There are a lot of glaring and persistent anomalies, but in order
to recognize them, an unprejudiced attitude is a prerequisite.
>> You ask me, how can I "be certain that 'at least 20' independent
>> and mutually improbable conditions all have to be satisfied, in one
>> particular sequence". I have the same right to ask you, how can you
>> be certain that not at least 20 different conditions with low probablilty
>> must be at the same time satisfied for a replicating system to appear.
> The burden of proof isn't on my shoulders: after all, you're the one
> making claims about the certainty of your probability estimates.
> I'm just asking you how you can meaningfully make such estimates,
> given that you and no one else yet understands very much about
> the mechanisms and processes involved.
That's a reasoning based on authority and dogmatism. The fact
that we do not understand very much about the mechanisms and
processes involved, is unconsciously taken as evidence for God,
neo-Darwinism or any other world view we believe in.
When Pythagoras said, the earth is not flat, the burden of proof
seemed to be only on his shoulders. Despite a lot of evidence
most people continued to believe in a flat earth for many centuries.
Kepler has provided much empirical evidence for his three laws,
but not even Galilei did accept the evidence!
I repeat myself: "The present-day scientific ignorance is no better
evidence for reductionism than for panpsychism!"
>> Within the reductionist framework there is no sound reason to
>> assume that stages which could give rise to a self-replicating system
>> are rather conserved than other stages, or that steps in the right
>> direction have somehow a higher probability than steps in a wrong
>> direction.
> Why not? I see nothing preventing such incrementalist processes
> in standard evolutionary theory.
I agree that such incrementalist processes are necessary for
evolution to occur.
Let us assume that there are two stages of the same appearance
probability. One stage could be part of a self-replicating system,
whereas the other could not. Within the reductionist causal
framework there is really no reason at all to assume that the first
stage is rather conserved than the second, only because it could
be part of a self-replication system in future.
That's exactly one of the reasons why I have introduced final laws
of nature: steps in the right direction can have a higher probability
than steps in a wrong direction. There is some kind of 'causal
effect' from the future. You know, in relativity theory the present,
past and future are given in some respect 'at the same time'.
That events of different times are correlated in a non-causal way,
is in principle similar to actions at a distance, where events of
different places (e.g. motions of the earth and of the sun) are
correlated without mediating material causes such as gravitons.
>> I'm convinced that physical laws as described by classical physics
>> or by QM cannot be responsible for the fact that living organisms
>> evolved and survive.
> What, specifically, convinces you of this?
The fact that the behaviour of matter or particles is explained
only by relatively simple mathematical relations.
>> The often cited 'complex dynamic systems' as e.g. the appearance
>> of ordered vortices, waves or similar things doesn't affect evolution
>> much more than the appearance of solar systems does.
> Do you have specific evidence to support this strong claim?
Yes. Waves and vortices are incomparably less complex than
simple living cells. They really can be understood on the basis of
simple physical principles. They appear under certain conditions
and disappear with these conditions.
>> And the appearance of crystals (carefully studied by Kepler) is
>> rather evidence for panpsychism than for reductionism.
> I don't see this at all.
Do you understand at least in principle the appearance of very
elaborate snow crystals? I understand the emergence of the
highly ordered planetary movements (described by Kepler's laws)
from two simple hypothesis (law of inertia, reciprocal attraction),
but I do not understand the formation of crystals. If a sound
(and therefore simple and elegant) explanation existed, this
explanation should be more widespread.
For me it is not enough that a problem is declared to have
been resolved. The fact that computer simulations of crystal
formation are possible, explains not very much.
Cheers
Wolfgang
z@z
Ian, why do call persons with religious, philosophical or scientific
convictions you don't like, damned liars? I think this should
not be the attitude a of scientist, it's rather the attitude of a
fundamentalist.
I am convinced that the HIV AIDS thesis represents maybe
even the biggest medical error of all times. Nevertheless, I do
not call the persons believing in AIDS orthodoxy damned liars,
even if I cannot exclude that some members of the AIDS
establishment are consciously lying.
>> Many enzymes work at defined places in a cell. If we create an
>> enlarged model, where enzymes are like little balls, then the volume
>> of the whole cell is about 1000 cubic metres. Imagine concretely
>> this situation: a little ball must come very near to a substrat and the
>> substrat recognition even depends on the correct alignment of the
>> little ball.
It is necessary to have a concrete imagination of the proportions
between cells, enzymes, molecules and so on. Therefore I have
introduced the enlarged model where 1mm corresponds to 1nm.
The 'diameters' of enzymes are then in the order of a few millimetres
and the 'diameter' of a water molecule is about 0.3 mm (there is
room for 33.3 water molecules in 1 cubic millimetre).
> Sometimes, but sometimes the enzymes are thethered to mebranes
> or other structures (eg some of the respiritory enzymes, signal
> transducing G-protiens etc). As Gavin tTabor pointed out, in aquoes
> solution there are around 10^14 interactions/sec between molecules,
> and the volume involved is nanoliters, which is miniscule compared to
> the free diffusion paths of these molecules, so it is not particularly
> difficult for a substrate to meet it's enzyme in the right orientation
> just by randomly bouncing around in the cell.
One nanolitre gives a cube with a side length of 0.1mm, and in
our model this corresponds to 100 m !!! You even claim that such
lenghts are minuscule compared to the free diffusion paths of the
enzymes. Are you confusing kinetic theory of gases with diffusion
in aqueous solutions, are you telling us a joke, or are you even
telling us a ... ?
It seems that you do not know the theory of Brownian motion.
Einstein calculated in a 1905 paper that a particle with a
diameter of 0.001mm (the size of a bacterium) would result
in an average motion of 0.0008mm in a second and of 0.006mm
(less than the length of normal cell) in a minute (at a temperature
of 17°C). The average motions per time unit of enzymes are
certainly longer because they are much smaller. The bigger
the particles, the slower random thermal motions. The reason
is simple: random collisions with many surrounding molecules
can cancel each other out and the remaining change in
momentum does not increase proportionally to the mass
of the moving particle.
In our model, a normal living cell with a diameter of about
10m consists of 10^12 different cubes of 1mm length. So its
rather difficult for a substrate to meet it's enzyme in the right
orientation "just by randomly bouncing around in the cell".
Don't forget, most of the 10^14 random collisions primarily with
water molecules have no effect at all! Every square millimetre
of the enzyme surface corresponds to about 10 water
molecules.
>> In addition to that, enzymes often have to pass cell
>> membranes in order to reach their destination.
> This happens very rarely, and then the enzymes are usually secreted
> via a specific membrane targeting peptide. (Unless you are talking
> about passage of transcription factors into the nucleus, where they
> pass through the pores in the nuclear membrane)
Only at the most 5 percent of the hundreds of different
mitochondrial proteins are coded by mitochondrial DNA. The
proteins even have to pass a double membrane in order to
reach their destination. According to the very convincing
endosymbiont theory, at least most of these proteins (or their
ancestors) were coded once by the mitochondrial DNA itself.
How do you explain the fact that the proteins could find
even after the transfer of the genetic code to the nucleus
their destinations within the mitochondrion?
>>What is the moving force of enzymes? It cannot be
>> electromagnetic attraction or repulsion.
> Sometimes it is a contributor, many proteins have a small net charge,
> but for untethered proteins, simple random motion works nicely.
>> So the moving force must primarily depend on random
>> thermal motions (as Brownian movements do).
> Okay. Whats the mean free path of a small molecule such as say,
> glycine in free solution. What is the mean free path of a haeomglobin
> molecule
There is no free path at all!
>> You certainly will object that we do not know well enough the
>> chemistry of enzymes in order to conclude that: there may always
>> be the needed chemical forces responsible for the 'apparently'
>> very purposeful motions of enzymes.
> What apparent purposeful motion of proteins?
For instance motions of transcription factors or of ribosomal
proteins. There are many other examples: look for instance at
the many enzymes involved in DNA replication. If there were
only random thermal motions, only a very small percentage of
the enzymes would work (by chance).
>> This implies that the information
>> for these motions to desired destinations is somehow stored in
>> the amino acid sequence of an enzyme, in addition to to the
>> information for folding, substrat specifity and so on, because even
>> similar enzymes can have very different destinations.
> For tethered proteins, certainly yes. As an example, signal
> transducing GTPases (G-proteins) are targeted to the membrane by a
> palmitoyl group attached to the enzyme, for protein kinase B, it the
> plextrin homolgy domain that does the job of targeting. For things
> like the monoamine oxidases, its a combination of structure and local
> production that confines them to the mitochondrial wall.
>> A mutation
>> could change a description factor in such a way that the protein
>> would search its usual substrate in a wrong chromosome.
> Most certainly.
>> The voyage of transcription factors to their destiny can be compared
>> with the voyages of migratory birds and other migratory animals.
> Not really, you're missing the scale of the cell and thermal motions.
> A transcription factor can cross the cell in a nanosceond, the
> observed rates of transcription factor initiation is entirely
> compatible with the enzymes just randomly boncing around in the cell.
If this is true and transcription factors generally reach their
destinations some micrometres away in a nanosecond, than
(materialist) reductionism is dead !!!
>> You ask me, how can I "be certain that 'at least 20' independent
>> and mutually improbable conditions all have to be satisfied, in one
>> particular sequence". I have the same right to ask you, how can you
>> be certain that not at least 20 different conditions with low probablilty
>> must be at the same time satisfied for a replicating system to appear.
> Well, that's a nice way to avoid the question. But from model self
> replicators, and our current knowledge of chemistry, we can say that
> the steps (however many they are) are not independent and at least
> some are not particularly improbable.
I don't speak of steps but of conditions. If in an experiment
the necessary amino acids are are put together in an optimal
concentration, than we have a condition whose probability is
certainly less than 10^-100.
> Where do the "at least 20 steps" come from? is there a mathematical
> analysis? what is the "granularity" of the steps? Are you refering to
> the sequential formation of 20 discrete molecules? or are the steps
> something else for example:
> 1) formation of building blocks
> 2) formation of a self-replicating molecule from bulding blocks
> 3) expansion of the replicator to a catalytic hypercycle
> 4) encapsulation of the hypecycle in a membrane
> 5) compartmentalization of the hypercycle into a genetic and a
> metabolic compartment
> 6) formation of a genome from the genetic hypercycle
> (this is the Eigen style model, a Kaufmann model would replace steps 2
> and 3 with formation of catalysits and catalytic closure respectively)
These are also conditions which must have been satisfied for a
self-replicating cell to appear. And the probabilty for each
condition is very low or almost zero (within the reductionist
causal framework).
>> Within the reductionist framework there is no sound reason to
>> assume that stages which could give rise to a self-replicating system
>> are rather conserved than other stages, or that steps in the right
>> direction have somehow a higher probability than steps in a wrong
>> direction.
> Depend on whether you are using a Eigen style "single replicator"
> hypercycle model, an RNA/ribopeptide world co-operative hypercycle or
> Kaufmanns catalytic closure. In the latter two self replicating
> systems are significantly advantaged in their chemistry.
>> The present-day scientific ignorance is no better evidence for
>> reductionism than for panpsychism! But is it really a necessary
>> ignorance? Ignorance is often the result of false premises.
> How often, example please.
For instance ignorance about a cure for AIDS.
> What is a prediction of panpsycism in chemistry that can be tested.
Unfortunately panpsychism predicts what you think can be
explained by reductionist causal laws.
I ask you: can you imagine anything which would convince you
that neo-Darwinism is not generally correct?
If it would be possible to produce large amounts of rare proteins
such as luminous proteins by biotechnological means, this would
be strong evidence against the psychon theory.
>> I'm convinced that physical laws as described by classical physics
>> or by QM cannot be responsible for the fact that living organisms
>> evolved and survive.
> Why, what is it about, say bacterial respiration that can't be
> explained in modern physics and chemistry.
>> The often cited 'complex dynamic systems' as
>> e.g. the appearance of ordered vortices, waves or similar things
>> doesn't affect evolution much more than the appearance of solar
>> systems does. And the appearance of crystals (carefully studied
>> by Kepler) is rather evidence for panpsychism than for reductionism.
> Crystals from by well studied physical laws. Name an aspect of crystal
> formation that is explained by panpsycism and not modern chemisrty and
> physics. Can you predict from panpscism which molecules will
> crystalise to form face centered cubic structures?
In the same way you cannot predict from an evolution theory,
what kind of animals have appeared you cannot predict from
the psychon theory what kind of behaviour molecules have
developed during evolution.
>> One must not confuse logical reasoning with empirical facts.
>> Calculations of probability must be based on clear and sound
>> assumptions, but the calculations themselves must not be
>> influenced by empirical facts.
> Ahh, nice try, but in probability you must always check your empirical
> facts (if you assume you have a normal distribution, when you in fact
> don't have one, your calculations are meaningless).
I think your calculations are meaningless because they are
based on premises which represent themselves very improbable
conditions.
>> From the fact that evolution has
>> occured we cannot conclude that it can be explained on the basis
>> of the generally accepted metaphysical principles of current science.
> z@z meet William of Occam, he has a razor he thinks you should use.
My razor is certainly much better than yours. It has no sense
to cut off not only the hair but also the ears (Mike Tyson would
rather bite them off).
>> Philip E. Johnson:
>>
>> "But when materialism is assumed as the very basis of science, they
>> can re-emerge a few logical steps later in triumph. Something had
>> to guide evolution, to produce those wonders of apparent design,
>> and natural selection is just about the only materialist contender."
> Of course, there is the little problem of all this _evidence_ for
> selection (both natural and sexual) that people keep turning up.
I don't understand what you mean here and probably you don't
understand what Johnson means.
We all make errors, it's almost impossible to avoid them, but we
should try to correct them as soon as possible.
Cheers
Wolfgang
z@z
>> Many enzymes work at defined places in a cell. If we create an
>> enlarged model, where enzymes are like little balls, then the volume
>> of the whole cell is about 1000 cubic metres. Imagine concretely
>> this situation: a little ball must come very near to a substrat and the
>> substrat recognition even depends on the correct alignment of the
>> little ball. In addition to that, enzymes often have to pass cell
>> membranes in order to reach their destination. What is the moving
>> force of enzymes? It cannot be electromagnetic attraction or
>> repulsion. So the moving force must primarily depend on random
>> thermal motions (as Brownian movements do).
> I'm sorry to contradict you, because I enjoyed your account of the
> history of ideas in this area, and looking at some of these issues
> from your perspective. But I'm afraid your description of the
> cellular localization of enzymes misses the point. The cellular
> "traffic control" that directs enzymes and other substances to
> their destination is entirely mechanical. Not only does the enzyme
> have the information to assume its shape and form the active site,
> but it has portions that tag it as destined for different destinations.
> The transport systems that move the enzymes recognize these "bar
> codes" and move the enzyme to the appropriate site. The obvious
> experiment is to alter that portion of the enzyme without changing
> the active site. And the result is an active enzyme located in
> the wrong place. And you are correct that a mutation could change
> the protein so it would wind up in the wrong place, although
> "Search" is more anthropomorphic than most people in science
> would prefer.
Now it's me who is afraid that the explanation of the purposeful
movements of enzymes by an entirely mechanical "traffic control"
misses the point. How do you explain such a "transport system"?
Are there some kind of currents in the cell or even some kind of
taxis which transport the enzymes to their needed destinations?
When I wrote "the information for these motions to desired
destinations is somehow stored in the amino acid sequence
of an enzyme" I did not mean some kind of "bar code" on the
enzyme, which is interpreted by a cellular transport system being
responsible for the motions of the enzyme. It seems to me even
much more difficult to explain how such a "traffic control" could
transport all the enzymes to their very different destinations
depending on such a "bar code".
That enzymes may consist of several parts or domains and that
one such domain can be resonsible for the destination of the
whole enzyme is obvious. There is no clear transition line between
simple proteins and protein complexes. But my explanation goes
rather in a different direction:
"Also relations analogous to the one between horse and rider or between
shepherd, dog and herd are possible on different complexity levels. An RNA
nucleotide consists of three parts which are evolutionarily older than the
whole nucleotide: 1) RNA base, 2) ribose and 3) chain of phosphate groups."
( http://members.lol.li/twostone/E/psychon.html#a09 )
> More generally, all theories that impute knowledge or purpose
> to subcellular or cellular structures have been discarded. One of
> the classic instances was discovered by Monod. When the bacterium
> E. coli is placed in an enviroment with a high concentration of
> the sugar lactose, it makes more of the tramsporter protein in the
> cell membrane, which imports more of the compound. The naive
> explanation is that the transporter "knows" how much of itself is
> needed by sensing how much sugar it contacts. It turns out that
> the sensor is an entirely separate mechanism, with a different
> protein, and that it doesn't sense exactly the same shape of
> sugar at all. One can use chemically modified sugars recognized
> by the sensor, which cannot be transported or provide nutrition.
> And the systems can be mutated separately to have different
> specificities for different sugars. So what appeared to be
> an intelligent, purposive response by the cell turns out to be
> totally mechanical. The story is told in The Eigth Day of
> Creation, by Jodson.
It is actually a fact that "all theories that impute knowledge or
purpose to subcellular or cellular structures have been discarded"
by mainstream science. But my suspicion is that reductionist
(materialist) prejudices have been the main reason. In physics,
actions at a distance have been discarded despite the fact that
experiments (electrostatic attraction and repulsion) showed and
show their existence.
Normally the first who detects a new mechanism has the
possibility to provide a philosophical interpretation. I do not
agree with Monod's interpretation, because it is not based on
facts. The same facts can be interpreted in very different ways.
According to Monod's interpretation, every system we have
examined carefully enough can be called mechanical.
> (A small pedagogic point. Your model is correct in size, but
> the thermal motion at the molecular level is much faster than
> we would guess from everyday objects. Some enzymes can catalyze
> thousands of reactions per second, and the calculations show that
> random encounters will indeed expose them to that many substrate
> molecules in a second.)
In my model, little proteins have diameters of few millimetres, e.g.
myoglobin with 153 amino acids about 4.5mm x 3.5mm x 2.5mm.
The major groove of DNA is about 2mm large. The whole human
DNA (both chromosome sets) is about 2000 km long. The major
groove is even longer. If the recognition by transcription factors
depends on direct contact, then a transcription factor must
come very near (maybe 1mm or 2mm) to its destination and
should even have the correct alignment. A normal living cell
with a diameter of about 10m would consists of 10^12 different
cubes of 1mm length.
> The general doctrine of purpose or intelligence at the
> cellular level is known in the Twentieth Century as "vitalism".
> This is confusing, since the term has had several contradictory
> meanings in philosophy and biology. Some people consider that
> the "death of vitalism" was in the explanation of antibody
> diversity. Our blood contains perhaps a million different kinds
> of antibody proteins, out of billions of possibilities. The
> intuitively obvious explanation is that the immune system "sees"
> a foreign antigen and somehow molds the shape of the appropriate
> antibody. This is the "instructive theory". But the immune
> system doesn't work that way. It assembles a random sample of
> the billions of possibilities, each on a separage cell, then kills
> or inacivates those that react to "self" and allows the cells that
> encounter antigens to proliferate to make large quantities of
> antibody. This is the "clonal selection" theory, and the Nobel
> prizes for it were give out 40-50 years ago. Any immunology text
> will give an account.
There is an essential difference between panpsychism and vitalism.
Vitalism starts with dead matter and introduces some kind of 'vital
forces' or souls. In panpsychism, however, there is no dead matter,
because even elementary particles have two aspects, a 'materialist'
and a 'vitalist'.
In a similar way a human soul influences the behaviour of a
human body, some kind of primitive soul is responsible for the
astonishingly complex behaviour of photons.
The immun system has turned out to be more complex than
assumed by the "instructive theory". To kill or inactivate those
cells whose antibodies react to "self" is not so easy.
There was once the following problem:
How can the immune system distinguish between "self"
and "foreign"?
It was 'resolved' in this way:
Cells or antibodies reacting to "self" are inactivated or killed
by the immune system whereas those reacting to "foreign"
are not.
Once I read somewhere (or I dreamt to have read) that if we put
antigens to one of two glasses with the same fresh blood, also
in the glass without antigens corresponding antibodies appear.
If it is true, it would be very strong evidence for the psychon theory.
(It would be quite similar to the improvement of Agars control line
rats in learning: http://members.lol.li/twostone/E/aa1.html )
> So in general, there are no subcellular or biochemical systems
> that embody purpose in their present-day operation. Reductionism
> has been triumphant for many years, and is embodied on the once-
> controversial slogan "anything organisms can do, cells can do;
> anything cells can do, molecules can do".
I go even further. I assume a continuity from elementary particles
to human souls. The mind body problem, one of the oldest
philosophical problems, has never been resolved by materialist
reductionism, it only has been declared a pseudo problem.
Also the appearance of consciousness some billions years after
big bang is an open question. In addition to that, it is impossible
to localize the memories in the brain. Theories have seriously been
proposed where one memory is somehow stored in the whole
brain (in a holistic way). That seems to me rather evidence that
such memories are not stored in the brain.
Regards
Wolfgang
James J. Lippard
>I am convinced that the HIV AIDS thesis represents maybe
>even the biggest medical error of all times. Nevertheless, I do
>not call the persons believing in AIDS orthodoxy damned liars,
>even if I cannot exclude that some members of the AIDS
>establishment are consciously lying.
Check out Steven Harris's letter in response to Johnson's _Reason_
magazine article:
http://www.reason.com/9504/letterstext.apr.html
as well as Harris's _Skeptic_ magazine article on this subject:
http://www.skeptic.com/03.2.harris-aids.html
John Wilkins
|On 11 Mar 1999 23:56:33 -0500, wil...@wehi.edu.au (John Wilkins) wrote:
|
|>In article <36E88A...@softdisk.com>, George Acton
|><gac...@softdisk.com> wrote:
|>
|>[an excellent and literate article, of which I am going to excerpt a small
|>piece]
|>
|> | The general doctrine of purpose or intelligence at the
|> |cellular level is known in the Twentieth Century as "vitalism".
|> |This is confusing, since the term has had several contradictory
|> |meanings in philosophy and biology. Some people consider that
|> |the "death of vitalism" was in the explanation of antibody
|> |diversity. Our blood contains perhaps a million different kinds
|> |of antibody proteins, out of billions of possibilities. The
|> |intuitively obvious explanation is that the immune system "sees"
|> |a foreign antigen and somehow molds the shape of the appropriate
|> |antibody. This is the "instructive theory". But the immune
|> |system doesn't work that way. It assembles a random sample of
|> |the billions of possibilities, each on a separage cell, then kills
|> |or inacivates those that react to "self" and allows the cells that
|> |encounter antigens to proliferate to make large quantities of
|> |antibody. This is the "clonal selection" theory, and the Nobel
|> |prizes for it were give out 40-50 years ago. Any immunology text
|> |will give an account.
|>
|>The previous two directors of the Institute I work at were the researchers
|>who developed this theory. Macfarlane Burnet, whose centenary is this
|>year, won the Nobel Prize for his work on immunology, and the clonal
|>selection theory in particular, and Gustav Nossal, who retired a couple of
|>years ago, did the validation and confirmation of the theory. Mac got his
|>Nobel around 68, I think, and the theory was developed a decade earlier.
|>The Nobel site will have details.
|
|SIR FRANK MACFARLANE BURNET
|1960 Nobel Laureate in Medicine
| for discovery of acquired immunological tolerance.
|
|Background
|
| 1899-1985
| Residence: Australia
| Affiliation: Walter and Eliza Hall Institute for Medical Research,
| Melbourne
|http://nobelprizes.com/nobel/nobel.html
Well, I knew there was a "6" in the date :-) I was temporarily unwebbed,
or I'd have checked.
Ian Musgrave & Peta O'Donohue
In article <7chajo$b9l$4...@pollux.ip-plus.net>, "z@z" <z...@z.lol.li> wrote:
> Hello Ian Musgrave!
>
> Ian, why do call persons with religious, philosophical or scientific
> convictions you don't like, damned liars? I think this should
> not be the attitude a of scientist, it's rather the attitude of a
> fundamentalist.
Huh? what are you talking about? I haven't called anybody a liar, not even
Adamski, and that takes a LOT of self control.
> I am convinced that the HIV AIDS thesis represents maybe
> even the biggest medical error of all times. Nevertheless, I do
> not call the persons believing in AIDS orthodoxy damned liars,
> even if I cannot exclude that some members of the AIDS
> establishment are consciously lying.
> >> Many enzymes work at defined places in a cell. If we create an
> >> enlarged model, where enzymes are like little balls, then the volume
> >> of the whole cell is about 1000 cubic metres. Imagine concretely
> >> this situation: a little ball must come very near to a substrat and the
> >> substrat recognition even depends on the correct alignment of the
> >> little ball.
>
> It is necessary to have a concrete imagination of the proportions
> between cells, enzymes, molecules and so on. Therefore I have
> introduced the enlarged model where 1mm corresponds to 1nm.
> The 'diameters' of enzymes are then in the order of a few millimetres
> and the 'diameter' of a water molecule is about 0.3 mm (there is
> room for 33.3 water molecules in 1 cubic millimetre).
>
> > Sometimes, but sometimes the enzymes are thethered to mebranes
> > or other structures (eg some of the respiritory enzymes, signal
> > transducing G-protiens etc). As Gavin Tabor pointed out, in [aqueos]
> > solution there are around 10^14 interactions/sec between molecules,
> > and the volume involved is nanoliters, which is miniscule compared to
> > the free diffusion paths of these molecules, so it is not particularly
> > difficult for a substrate to meet it's enzyme in the right orientation
> > just by randomly bouncing around in the cell.
>
> One nanolitre gives a cube with a side length of 0.1mm, and in
> our model this corresponds to 100 m !!! You even claim that such
> lenghts are minuscule compared to the free diffusion paths of the
> enzymes. Are you confusing kinetic theory of gases with diffusion
> in aqueous solutions, are you telling us a joke, or are you even
> telling us a ... ?
No, free diffusion of molecules in solution is very rapid. Have you actually
had anything to do with diffusion in solutions. A fair bit of my work deals
with intracellular diffusion, and the molecules diffuse across the cells in
microseconds, which is not their actual rate of diffusion, as they first have
to saturate uptake sites in the cell. I haven't personally done flash
photolysis of caged compounds, but I used to work in a lab that did, and
photolysis diffusion is in the sub-microsecond range. I've also dialysed
cells with fairly hefty molecules, and one of my collegues has dialysed cells
with antibodies. Guess what, equilibrim dialysis of antibodies is quite
rapid. (Later this year I hope to be microinjecting cells with antisense
oligonucleotides and antibodies myself).
> It seems that you do not know the theory of Brownian motion.
> Einstein calculated in a 1905 paper that a particle with a
> diameter of 0.001mm (the size of a bacterium) would result
> in an average motion of 0.0008mm in a second and of 0.006mm
> (less than the length of normal cell) in a minute (at a temperature
> of 17°C). The average motions per time unit of enzymes are
> certainly longer because they are much smaller.
Good heavens, just look at your own calculations, a bacteria sized particle
travels 800 micrometers a second, thats roughly 8 times the diameter of an
average mamalian cell!!! And that's at 17 degrees, whereas mammalian cells
are at 37 deg C! Protein sized particles travel much faster as you say. Your
_own_ calculations show you are wrong. Now add in diffusion down a chemical
gradient, and you are way out of field.
[snip slower random motions bit]
> In our model, a normal living cell with a diameter of about
> 10m consists of 10^12 different cubes of 1mm length. So its
> rather difficult for a substrate to meet it's enzyme in the right
> orientation "just by randomly bouncing around in the cell".
On the contrary, it can visit all 10^12 cubes nearly 100 times via a random
walk.
> Don't forget, most of the 10^14 random collisions primarily with
> water molecules have no effect at all! Every square millimetre
> of the enzyme surface corresponds to about 10 water
> molecules.
But not all of that surface is water, there are also ions, substrate molecules
and other proteins.
Acording to you, enzyme reactions can't take place at all, even in a test
tube. However, they take place in test tubes at rates that are entirely
consistent with substrates and enzymes meeting randomly in a diffusion
limited way (with the exception of enzymes with lipid soluble substrates).
This is all elementary enzyme kinetics.
Heck, according to you most normal _chemistry_ can't take place, however, why
not read a college level text on physical chemistry (my own is rather old, so
I don't recomend it).
If your theroy was right, you might expect substantial differences between
hormone/receptor interactions in broken cell preparations, and in intact
cells. However, you don't.
> >> In addition to that, enzymes often have to pass cell
> >> membranes in order to reach their destination.
>
> > This happens very rarely, and then the enzymes are usually secreted
> > via a specific membrane targeting peptide. (Unless you are talking
> > about passage of transcription factors into the nucleus, where they
> > pass through the pores in the nuclear membrane)
>
> Only at the most 5 percent of the hundreds of different
> mitochondrial proteins are coded by mitochondrial DNA. The
> proteins even have to pass a double membrane in order to
> reach their destination.
And they do so via specific targeting peptide sequences. This is all
reasonably well known, a modern biochemistry text would explain this, or have
a look in the Annual Review of Biochemistry aand Trends in Biochemical
sciences.
> According to the very convincing
> endosymbiont theory, at least most of these proteins (or their
> ancestors) were coded once by the mitochondrial DNA itself.
> How do you explain the fact that the proteins could find
> even after the transfer of the genetic code to the nucleus
> their destinations within the mitochondrion?
Specific targeting peptide sequences. These can be tailored to particular
phospholipid ratio's in differnt membranes, or bind to a peptide receptor.
[snip for space]
> > Okay. Whats the mean free path of a small molecule such as say,
> > glycine in free solution. What is the mean free path of a haeomglobin
> > molecule
>
> There is no free path at all!
Good heavens, yes there is. It is small, but cells are small.
> >> You certainly will object that we do not know well enough the
> >> chemistry of enzymes in order to conclude that: there may always
> >> be the needed chemical forces responsible for the 'apparently'
> >> very purposeful motions of enzymes.
>
> > What apparent purposeful motion of proteins?
>
> For instance motions of transcription factors or of ribosomal
> proteins. There are many other examples: look for instance at
> the many enzymes involved in DNA replication. If there were
> only random thermal motions, only a very small percentage of
> the enzymes would work (by chance).
All examples of proteins with specific binding recognition sequences for
their targets. It doesn't help your argument that these complexes have been
formed "by chance" in test tubes, and work quite nicely thank you, and that
the cell traffic has been followed by labeled protiens.
[snip voyage of transcription factors]
> > Not really, you're missing the scale of the cell and thermal motions.
> > A transcription factor can cross the cell in a nanosceond, the
> > observed rates of transcription factor initiation is entirely
> > compatible with the enzymes just randomly boncing around in the cell.
>
> If this is true and transcription factors generally reach their
> destinations some micrometres away in a nanosecond, than
> (materialist) reductionism is dead !!!
That should be "in nanosecond_s_" [so much for proof reading]. Even by you own
calculations it would take nanoseconds to cross a cell, and remember, the
trancription factors don't have to cross the whole cell, but somewhere between
10-50 micrometers (depending on cell type).
> >> You ask me, how can I "be certain that 'at least 20' independent
> >> and mutually improbable conditions all have to be satisfied, in one
> >> particular sequence". I have the same right to ask you, how can you
> >> be certain that not at least 20 different conditions with low probablilty
> >> must be at the same time satisfied for a replicating system to appear.
>
> > Well, that's a nice way to avoid the question. But from model self
> > replicators, and our current knowledge of chemistry, we can say that
> > the steps (however many they are) are not independent and at least
> > some are not particularly improbable.
>
> I don't speak of steps but of conditions. If in an experiment
> the necessary amino acids are are put together in an optimal
> concentration, than we have a condition whose probability is
> certainly less than 10^-100.
You are still unclear as to what you mean here.
> > Where do the "at least 20 steps" come from? is there a mathematical
> > analysis? what is the "granularity" of the steps? Are you refering to
> > the sequential formation of 20 discrete molecules? or are the steps
> > something else for example:
>
> > 1) formation of building blocks
> > 2) formation of a self-replicating molecule from bulding blocks
> > 3) expansion of the replicator to a catalytic hypercycle
> > 4) encapsulation of the hypecycle in a membrane
> > 5) compartmentalization of the hypercycle into a genetic and a
> > metabolic compartment
> > 6) formation of a genome from the genetic hypercycle
> > (this is the Eigen style model, a Kaufmann model would replace steps 2
> > and 3 with formation of catalysits and catalytic closure respectively)
>
> These are also conditions which must have been satisfied for a
> self-replicating cell to appear.
But is this what you mean with your "20 steps"?
> And the probabilty for each
> condition is very low or almost zero (within the reductionist
> causal framework).
This is not true, for step 1, the probability is 1.0 for most building blocks,
step 2 is unknown at present, but may be quite low from contemporaneous
experiments, for step 3 p is around 1.0, depending on the system analysed
(Kaufmann would claim it is 1.0), step 4 is almost certainly around 1.0, and
the probability of step 5 is unknown.
[snip discussion of Kaufmann model robustness]
> >> The present-day scientific ignorance is no better evidence for
> >> reductionism than for panpsychism! But is it really a necessary
> >> ignorance? Ignorance is often the result of false premises.
>
> > How often, example please.
>
> For instance ignorance about a cure for AIDS.
Seeing as the public health strategies aimed at limiting aids based on the
viral model have been as successsful as funding and advertisment allows (in
AUutralia they have been spectacularly successful in abolishing AIDS from
blood transfusion patients, and greatly reducing the incidence in the the gay
community, less so in injecting drug users), and given that anti-virals have
significantly slowed the progression of AIDS, and our understanding of the
Tcell receptor mutants that confer resistance to AIDS, why do you think this
represents "false premises"?
> > What is a prediction of panpsycism in chemistry that can be tested.
>
> Unfortunately panpsychism predicts what you think can be
> explained by reductionist causal laws.
If there is no way to distinguish panpsycism from standard chemistry, it is a
useless hypothesis, there must be be _some_ prediction that it can make that
will alow one to dertemine the difference between panscyism and normal
chemistry.
> I ask you: can you imagine anything which would convince you
> that neo-Darwinism is not generally correct?
I can imagine several things, including showing that that DNA relationships
between organisms do not form patterns of descent (they do, but that is one
potential test). But what has this to do with your claims that the
biochemistry of the cell cannot be explained by "normal" chemistry?
> If it would be possible to produce large amounts of rare proteins
> such as luminous proteins by biotechnological means, this would
> be strong evidence against the psychon theory.
Bad news, the rare jelly fish fluorescent protein Aequorin can be made in
large quantitites by biotechnology see
http://www.probes.com/handbook/ch22-5.html#Recombinant as can things like
luciferase. There are receptors that occur in only one or two copies per cell
(like the Beta receptors) which can made in large copy number by
biotechnology, you can even artifically synthesise some (smallish) peptide
hormones that have the full biological activity of their natural
counterparts.
[snip]
> >> The often cited 'complex dynamic systems' as
> >> e.g. the appearance of ordered vortices, waves or similar things
> >> doesn't affect evolution much more than the appearance of solar
> >> systems does. And the appearance of crystals (carefully studied
> >> by Kepler) is rather evidence for panpsychism than for reductionism.
>
> > Crystals from by well studied physical laws. Name an aspect of crystal
> > formation that is explained by panpsycism and not modern chemisrty and
> > physics. Can you predict from panpscism which molecules will
> > crystalise to form face centered cubic structures?
>
> In the same way you cannot predict from an evolution theory,
> what kind of animals have appeared you cannot predict from
> the psychon theory what kind of behaviour molecules have
> developed during evolution.
But you are talking about _crystals_, how the appearance of crytals is
evidence for panpsycism, if panpsycism is to have any value, it must be able
to make _some_ kind of prediction at this simple level that will alow you to
distinguish it from standard chemistry. It is _your_ claim that crystal
apearance is evidence for panpsycism, _how_ is it evidence?
> >> One must not confuse logical reasoning with empirical facts.
> >> Calculations of probability must be based on clear and sound
> >> assumptions, but the calculations themselves must not be
> >> influenced by empirical facts.
>
> > Ahh, nice try, but in probability you must always check your empirical
> > facts (if you assume you have a normal distribution, when you in fact
> > don't have one, your calculations are meaningless).
>
> I think your calculations are meaningless because they are
> based on premises which represent themselves very improbable
> conditions.
I'm afraid this sentence makes no sense.
> >> From the fact that evolution has
> >> occured we cannot conclude that it can be explained on the basis
> >> of the generally accepted metaphysical principles of current science.
>
> > z@z meet William of Occam, he has a razor he thinks you should use.
>
> My razor is certainly much better than yours. It has no sense
> to cut off not only the hair but also the ears (Mike Tyson would
> rather bite them off).
Again this sentence makes no sense.
> >> Philip E. Johnson:
> >>
> >> "But when materialism is assumed as the very basis of science, they
> >> can re-emerge a few logical steps later in triumph. Something had
> >> to guide evolution, to produce those wonders of apparent design,
> >> and natural selection is just about the only materialist contender."
>
> > Of course, there is the little problem of all this _evidence_ for
> > selection (both natural and sexual) that people keep turning up.
>
> I don't understand what you mean here and probably you don't
> understand what Johnson means.
Selection (both natural and sexual) is cited as the reason for apparent design
because of _evidence_ that selection
> We all make errors, it's almost impossible to avoid them, but we
> should try to correct them as soon as possible.
Think about the aquorin example.
Cheers!
--------------------------------
#44 Most original poster on TO for November
Ian Musgrave Peta O'Donohue and Jack Francis Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
-----------== Posted via Deja News, The Discussion Network ==----------
Ken Cox
> Ken Cox wrote:
> > It's certainly nowhere near as disquieting as the thesis of Greg
> > Egan's science-fiction novel _Distress_. Talk about kicking the
> > supports out from under the table...
> You know, that was a really sadistic reply. I positively demand
> that you give me a synopsis of this novel - I've not heard of
> it, and want to know more.
I think you should read it. Any further description of the thesis
would be a huge spoiler for the novel.
However, since Greg Egan has been mentioned, may I (sadistically)
also recommend _Permutation City_. I found it just as disturbing
to my world-view, simply because I could find no logical way to
rebut its central thesis. (However, the thesis is based on the
premise that artificial intelligence is possible, so perhaps the
conclusion I should reach is that AI is not possible.)
--
Ken Cox k...@research.bell-labs.com
Ken Cox
> I am convinced that the HIV AIDS thesis represents maybe
> even the biggest medical error of all times. Nevertheless, I do
> not call the persons believing in AIDS orthodoxy damned liars,
> even if I cannot exclude that some members of the AIDS
> establishment are consciously lying.
When Edward Jenner invented vaccination, he exhibited the courage
of his convictions by first vaccinating himself and then deliberately
exposing himself to smallpox.
Curiously, none of the people who claim that HIV does not cause
AIDS have shown the same willingness to prove their thesis, by
participating in the obvious experiment.
--
Ken Cox k...@research.bell-labs.com
Gavin Tabor
I'll keep a look out for these novels (always interested to read
some new SF).
dstev...@my-dejanews.com
"z@z" <z...@z.lol.li> wrote:
> Hello Jamie Schrumpf!
>
> >> I'm sure that Johnson is or was a much more unbiased lawyer
> >> than the average.
>
> > Why would you say that? What is your evidence?
>
> If have read some texts of Johnson about AIDS which I really
> do appreciate. These texts have shown me that Johnson
> is very conscious of the problem of bias. All his texts I have
> read are much sounder than his opponents try to give the
> impression.
Ah. So you're saying that Johnson has no bias towards reality in preference to
fantasy.
I'm sure many people would agree with you there.
Ian Musgrave & Peta O'Donohue
Email modified to foil spammers, delete RemoveInsert to repy
Following up to myself to correct a few mistakes (slaps sloping
forehead)
On 15 Mar 1999 02:04:50 -0500 "Ian Musgrave & Peta O'Donohue"
<ian.mu...@med.monash.edu.au> wrote:
>G'Day All
>
>In article <7chajo$b9l$4...@pollux.ip-plus.net>, "z@z" <z...@z.lol.li> wrote:
>> Hello Ian Musgrave!
[snip visualisable models]
>> One nanolitre gives a cube with a side length of 0.1mm, and in
>> our model this corresponds to 100 m !!! You even claim that such
>> lenghts are minuscule compared to the free diffusion paths of the
>> enzymes. Are you confusing kinetic theory of gases with diffusion
>> in aqueous solutions, are you telling us a joke, or are you even
>> telling us a ... ?
Actually, on checking my physical chem books, and my old favorite,
Metzler, you _can_ use the gas diffusion laws as a first
approximation, you have to add in viscosity, and the fact that enzyme
substrate interactions are non-elastic, but it does suprisingly well.
(See Metzler, "Biochemistry", international edition, Chapter 6, pp
307-310)
[snip what I did on my holidays]
>> It seems that you do not know the theory of Brownian motion.
>> Einstein calculated in a 1905 paper that a particle with a
>> diameter of 0.001mm (the size of a bacterium) would result
>> in an average motion of 0.0008mm in a second and of 0.006mm
>> (less than the length of normal cell) in a minute (at a temperature
>> of 17°C). The average motions per time unit of enzymes are
>> certainly longer because they are much smaller.
>
>Good heavens, just look at your own calculations, a bacteria sized particle
>travels 800 micrometers a second, thats roughly 8 times the diameter of an
>average mamalian cell!!!
Bugger, that's wrong, 100 micrometers is about the size of the Ovum,
an average cell ranges more between 10-20 micrometers, sorry, so
that's 40 times the diameter of an average cell in one second. For an
enzyme like ribonuclease, it's more like a thousand times the
diameter of the average cell in a second.
But you should actually use the Stokes_Einstein equation, for more
accurate comparison.
>And that's at 17 degrees, whereas mammalian cells
>are at 37 deg C! Protein sized particles travel much faster as you say. Your
>_own_ calculations show you are wrong. Now add in diffusion down a chemical
>gradient, and you are way out of field.
>
>[snip slower random motions bit]
>
>> In our model, a normal living cell with a diameter of about
>> 10m consists of 10^12 different cubes of 1mm length. So its
>> rather difficult for a substrate to meet it's enzyme in the right
>> orientation "just by randomly bouncing around in the cell".
>
>On the contrary, it can visit all 10^12 cubes nearly 100 times via a random
>walk.
Actually, no. You have to consider viscosity, corrections for charge
and the fact that the molecule can wander in _any_ 3 dimensional
orientation, (doing the cubic latice thing actually hinders rather
than helps, how you think of this, I calculated for only 4 directions
of movement, bugger) and non-sphericity of some molecules. Also, the
collision radius is 4 times the particle radius.
The number of encounters between two particles a and b (say an enzyme
and its substrate, where the substrate is smaller than the enzyme) per
second per ml of solution is given by
4[pi](Da+Db)(ra +rb)na*nb
Where D is the diffusion constant, r is the radius and n the number of
molecules, given a realistic concentration of substrate (about 10^-6M)
and even just one enzyme (for a typical enzyme D is around 1x 10^-6),
this is roughly 10^9 collisions per ml per second between substrate
and enzyme (or around 10^3 collisions per cell per second)! This is
not correcting for charge, which ups the interaction rate. Now, as I
said before, the collisions are inelastic, because of water molecules
forming a "cage" around the enzyme and its substrate, so you can get
_100-200_ collisions per encounter!!!
So, far from enzymes not being able to meet a substrate in the correct
orientation, they can certainly meet them in the correct oreintation
quite rapidly.
From the French-Metzler formula a single enzyme can sweep through
roughly 20% of a standard cells _volume_ (or all of it's nucleus) in
one second.
The full derivation is in Metzler, and has too many greek letters and
subscripts to make it worthhile transcribing, but a quick trip to the
library will confirm the above work.
Of course, experimental work shows that reaction rates of enzymes are
consistant with being diffusion limited. Heck, my research revolves
around comparisons of drug actions on membranes vs whole cells, if
there was some discrepanct, I would have noticed by now.
Ian Musgrave & Peta O'Donohue
In article <7chajf$b9l$2...@pollux.ip-plus.net>, "z@z" <z...@z.lol.li> wrote:
> Hello George Acton!
>
> >> [snip] What is the moving
> >> force of enzymes? It cannot be electromagnetic attraction or
> >> repulsion. So the moving force must primarily depend on random
> >> thermal motions (as Brownian movements do).
>
> > I'm sorry to contradict you, because I enjoyed your account of the
> > history of ideas in this area, and looking at some of these issues
> > from your perspective. But I'm afraid your description of the
> > cellular localization of enzymes misses the point. The cellular
> > "traffic control" that directs enzymes and other substances to
> > their destination is entirely mechanical. Not only does the enzyme
> > have the information to assume its shape and form the active site,
> > but it has portions that tag it as destined for different destinations.
> > The transport systems that move the enzymes recognize these "bar
> > codes" and move the enzyme to the appropriate site. The obvious
> > experiment is to alter that portion of the enzyme without changing
> > the active site. And the result is an active enzyme located in
> > the wrong place. And you are correct that a mutation could change
> > the protein so it would wind up in the wrong place, although
> > "Search" is more anthropomorphic than most people in science
> > would prefer.
>
> Now it's me who is afraid that the explanation of the purposeful
> movements of enzymes by an entirely mechanical "traffic control"
> misses the point. How do you explain such a "transport system"?
> Are there some kind of currents in the cell or even some kind of
> taxis which transport the enzymes to their needed destinations?
Yes, there are, what ones depend on the kind of cell to a certain extent. In
the case of nerves there is ATP dependent _fast_ transport, where synaptic
vesicles bind to microtubules and are transported along these microtubules
like trams on a track at 400 mm/day. There is also _slow_ transport which is
mostly mediated by cytoplasmic flow down the axons at 6-10 mm/day.
Also there is the process in many cells whereby small patches of the
endoplasmic reticulum with their synthesized enzymes are pinched off and
transported to desired places by microtubbules or occasionally actin
filaments.
And as I've said before, some soluble proteins have peptide sequences that
will insert in specific lipid structures, or look for protein recpetors to
target them to the right places in the cell.
This is all fairly standard cellular biology, and is explained in any modern,
undergraduate level University text book.
> When I wrote "the information for these motions to desired
> destinations is somehow stored in the amino acid sequence
> of an enzyme" I did not mean some kind of "bar code" on the
> enzyme, which is interpreted by a cellular transport system being
> responsible for the motions of the enzyme. It seems to me even
> much more difficult to explain how such a "traffic control" could
> transport all the enzymes to their very different destinations
> depending on such a "bar code".
You have one part bind the microtubule, and when the other part reaches the
site with a specific receptor, allosteric changes results in the protein
unbinding from the microtubule. You can disrupt the traffic by removing ATP,
or unwinding the microtubules, heck, with appropriate antibdoy tags you can
even watch the transport of substances along the microtubuels under the
microscope!
> That enzymes may consist of several parts or domains and that
> one such domain can be resonsible for the destination of the
> whole enzyme is obvious. There is no clear transition line between
> simple proteins and protein complexes. But my explanation goes
> rather in a different direction:
>
> "Also relations analogous to the one between horse and rider or between
> shepherd, dog and herd are possible on different complexity levels. An RNA
> nucleotide consists of three parts which are evolutionarily older than the
> whole nucleotide: 1) RNA base, 2) ribose and 3) chain of phosphate groups."
> ( http://members.lol.li/twostone/E/psychon.html#a09 )
How is this an explanation of protein transport and targeting?
> > More generally, all theories that impute knowledge or purpose
> > to subcellular or cellular structures have been discarded.
[snip evidence and Jacob & Monods experiments]
>
> It is actually a fact that "all theories that impute knowledge or
> purpose to subcellular or cellular structures have been discarded"
> by mainstream science. But my suspicion is that reductionist
> (materialist) prejudices have been the main reason.
No, _experiments_, such as the ones described by Gavin Tabor, have been the
reason that these theories have been discared, they don't fit the evidence.
> In physics,
> actions at a distance have been discarded despite the fact that
> experiments (electrostatic attraction and repulsion) showed and
> show their existence.
Huh!
> Normally the first who detects a new mechanism has the
> possibility to provide a philosophical interpretation. I do not
> agree with Monod's interpretation, because it is not based on
> facts. The same facts can be interpreted in very different ways.
What is Monods data if not "facts"? How can you possibly interpret this data
in a "purposive" manner?
> According to Monod's interpretation, every system we have
> examined carefully enough can be called mechanical.
Where "mechanical" means an abscence of purposful intent, yes. Lots of
experiments show this. What is your point?
> > (A small pedagogic point. Your model is correct in size, but
> > the thermal motion at the molecular level is much faster than
> > we would guess from everyday objects. Some enzymes can catalyze
> > thousands of reactions per second, and the calculations show that
> > random encounters will indeed expose them to that many substrate
> > molecules in a second.)
Around 10^3 per second, depending on substrate concentration.
> In my model, little proteins have diameters of few millimetres, e.g.
> myoglobin with 153 amino acids about 4.5mm x 3.5mm x 2.5mm.
> The major groove of DNA is about 2mm large. The whole human
> DNA (both chromosome sets) is about 2000 km long. The major
> groove is even longer. If the recognition by transcription factors
> depends on direct contact, then a transcription factor must
> come very near (maybe 1mm or 2mm) to its destination and
> should even have the correct alignment.
More like 8 mm, allowing for charge effects and contact surfaces. And the
water "cage" effect will hold interacting molecules together so that about
100-200 collisions occur for every close enclounter, considering the rotation
rate spherical molecules, there is likely to be at _least_ one correctly
oriented collision per encounter.
But how does your model system relate to Gavins point that themal motion at
molecular scales is fast, as are reaction times?
> A normal living cell
> with a diameter of about 10m would consists of 10^12 different
> cubes of 1mm length.
An a single, averaged sized enzyme could visit 2 x 10^11 of them in one
second.
[snip vitalism and it's "death" from among other things, immunology]
> There is an essential difference between panpsychism and vitalism.
> Vitalism starts with dead matter and introduces some kind of 'vital
> forces' or souls. In panpsychism, however, there is no dead matter,
> because even elementary particles have two aspects, a 'materialist'
> and a 'vitalist'.
And how do you distinguish the two.
> In a similar way a human soul influences the behaviour of a
> human body, some kind of primitive soul is responsible for the
> astonishingly complex behaviour of photons.
Why do you need a primitive soul for photons, what aspect of the soul is
needed for reflection or refraction? How does a primitive soul contribute to
constructive interference? I'm not saying these things to be silly, but do
you have any form of quantitative theroy that will actually produce
predictions of photon behavior (or, as in another post, crystal appeareance)
and how will these predictions allow you to differentiate between the
materialist theory and your theory?
> The immun[e] system has turned out to be more complex than
> assumed by the "instructive theory".
In what way?
> To kill or inactivate those
> cells whose antibodies react to "self" is not so easy.
>
> There was once the following problem:
> How can the immune system distinguish between "self"
> and "foreign"?
>
> It was 'resolved' in this way:
> Cells or antibodies reacting to "self" are inactivated or killed
> by the immune system whereas those reacting to "foreign"
> are not.
Where did you read this? This is not correct.
> Once I read somewhere (or I dreamt to have read) that if we put
> antigens to one of two glasses with the same fresh blood, also
> in the glass without antigens corresponding antibodies appear.
You dreamt it, no such thing happens (actually, the experiment can't even
work in the way you describe it, antigens have to interact with B cells in
tissues such as liver and spleen to start generating clonal, antibody
generating cells). You _can_ present antigens to a culture dish of antigen
generating hybridoma cells, but hybridomas in an adjacent dish, not presented
with antigen don't produce antibody, people do this all the time.
> If it is true, it would be very strong evidence for the psychon theory.
> (It would be quite similar to the improvement of Agars control line
> rats in learning: http://members.lol.li/twostone/E/aa1.html )
Sorry, it doesn't happen.
[snip rest]
Cheers! Ian
--------------------------------
#44 Most original poster on TO for November
Ian Musgrave Peta O'Donohue and Jack Francis Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
-----------== Posted via Deja News, The Discussion Network ==----------
Ian Musgrave & Peta O'Donohue
with a cc to John as this turned up late on my server.
In article <john-14039...@m001.parrish-dorm01.swarthmore.edu>,
jo...@cs.swarthmore.edu (John Finkbiner) wrote:
> In article <36f96444...@news.mira.net.au>,
> reyn...@RemoveInsert.werple.mira.net.au (Ian Musgrave & Peta O'Donohue)
> wrote:
>
> > G'Day All
> > Email modified to foil spammers, delete RemoveInsert to repy
> >
> > On 12 Mar 1999 05:26:19 -0500 Gavin Tabor <g.t...@ic.ac.uk> wrote:
> >
> > >Ian Musgrave & Peta O'Donohue wrote:
> > [snip]
> > >> >> Are you telling a joke?
> > >>
> > >> No, he's not, his synthesis rate is a high, but otherwise it's okay.
> > >>
> > >> >Do I look like I'm joking? I'm providing you with an example
> > >> >of how to go about estimating the likelyhood of generating the
> > >> >simplest self-replicating entity given a flask of amino acids.
> > >> >This seems much more useful for the discussion than the probability
> > >> >of 20 marbles forming a pretty pattern in space (which is what
> > >> >you have worked out).
> > >>
> > >> and given that the Lee peptide is just one of a number of possible
> > >> self-relicating peptides, the probabilities are even better.
> > >
> > >How many are known? Is it 10s, 1000's 10^6's?
> >
> > Currently there are 8 self replicating peptides known, however Ghadiri
> > thinks that there are a lot more, and Yao's work suggests that his
> > idea is right. _Exactly_ how many is not certain, but I would bank on
> > thousands to millions, even just using the AB helical groove system
> > that Ghadiri uses.
> >
>
> I'm sure you've posted refrences to this work, but I can't always read as much
> Usenet as I would like. If you (or somebody else) would suggest some papers,
> a certain chemistry undergraduate would be very greatful.
>
> John "I suppose biochem can be interesting occasionally" Finkbiner
Try the Ghadiri home page, if you have access to the acrobat PDF reader go to
publications and download the Current Opinions PDF for a nice overview
http://www.scripps.edu/pub/ghadiri/
Otherwise the paper
Autocatalytic networks: the transition from molecular
self-replication to molecular ecosystems, David H Lee, Kay Severin and M Reza
Ghadiri, Current Opinion in Chemical Biology 1997, 1:491–496 is a good work.
Less accesible is
Bag. BG, von Kiedrowski G. Templates, autocatalysis and molecular
replication. Pure & Appl Chem 68, 2145-2152, 1996.
A bit older, but sure to be in the library is
Orgel LE, Molecular replication. Nature 358: 203-9, 1992 Jul 16
for the original papers in all their glory
Yao S, Ghosh I, Zutshi R, and Chmielewski J, Selective amplification by auto-
and cross-catalysis in a replicating peptide system. Nature 396: 447-50, 1998
Dec 3
Luther A. Brandsch R. von Kiedrowski G. Surface-promoted replication
and exponential amplification of DNA analogues. Nature.
396(6708):245-8, 1998 Nov 19
Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of
symbiosis in peptide self-replication through a hypercyclic network.
Nature 390: 591-4, 1997 Dec 11
Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, A
self-replicating peptide. Nature 382: 525-8, 1996 Aug 8
Cheers! Ian
--------------------------------
#44 Most original poster on TO for November
Ian Musgrave Peta O'Donohue and Jack Francis Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
-----------== Posted via Deja News, The Discussion Network ==----------
Bonz
message <7chajf$b9l$2...@pollux.ip-plus.net> :
>Hello George Acton!
>
<snip>
>> (A small pedagogic point. Your model is correct in size, but
>> the thermal motion at the molecular level is much faster than
>> we would guess from everyday objects. Some enzymes can catalyze
>> thousands of reactions per second, and the calculations show that
>> random encounters will indeed expose them to that many substrate
>> molecules in a second.)
>
>In my model, little proteins have diameters of few millimetres, e.g.
>myoglobin with 153 amino acids about 4.5mm x 3.5mm x 2.5mm.
Is this what you meant to say?
James J. Lippard
>Hello Jim Lippard!
>
>>> I am convinced that the HIV AIDS thesis represents maybe
>>> even the biggest medical error of all times. Nevertheless, I do
>>> not call the persons believing in AIDS orthodoxy damned liars,
>>> even if I cannot exclude that some members of the AIDS
>>> establishment are consciously lying.
>
>> _Reason_ magazine article:
>
>> http://www.reason.com/9504/letterstext.apr.html
>
>the few paragraphs of the reply of Charles Thomas, Kary Mullis,
>and Phillip Johnson at the end.
>
>The following quote is representative insofar is it shows
>better than anything else that the HIV AIDS thesis is
>primarily based on authority and dogmatism:
That's not much of a response to the wealth of data in Harris's letter,
most of which is ignored in the authors' response.
> "I thought the Thomas/Mullis/Johnson article an unusually
> bitter one for REASON to be running, since its authors
> suggest not only that the U.S. government has failed with
> AIDS but that just about everyone else has failed to think
> properly as well. The authors essentially suggest that the
> scientific method itself failed when it has come to this
> problem--that instead, hundreds of independent working
> groups in public and private labs in scores of countries are
> even now participating in the same shared conspiracy or
> mass delusion. Supposedly, every major HIV study lab has
> been afraid to acknowledge openly that the emperor has
> no clothes. Does this really seem likely to the reader? I am
> strongly reminded of the conspiracy theories of creationists
> and UFO-coverup enthusiasts when I read this kind of thing."
>
>Karry Mullis is nobel laureate in chemistry of 1993 for discovery
>of polymerase chain reaction, and because of the importance
>of his discovery he is certainly one of great nobel laureates!
>Without his method not even in all HIV antibody positive AIDS
>patients the virus could be detected.
So? He also believes in astrology and seems to be something of a kook--a
conclusion I draw from examining his own book about himself. Why are you
arguing from authority after you just told us that it's wrong to argue
from authority?
[rest deleted]
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
On 10 Mar 1999 15:33:38 -0500, "z@z" <z...@z.lol.li> wrote:
>Hello Loren!
[snip]
>Here a quotation of my text 'Arguments against Reductionism':
>
>"How impossible it is that random thermal motions determine the
>happenings in living cells would become obvious, if one created an
>enlarged model of the DNA helix with a helix diameter of 50 cm,
>and if persons had to take over the functions of the many enzymes
>which are involved in the DNA replication. The whole human DNA
>(of one single cell), which normally is tightly packed, would be at
>such an enlargement about 500'000 km long. This model would
>also show how improbable it is that transcription factors could find
>a given DNA position, if there were only random motions and if
>recognition of the position were possible only by direct contact.
>Because of the enzyme size, this improbability cannot be hidden
>behind the Heisenberg uncertainty relations."
>( http://members.lol.li/twostone/E/psychon.html#a06 )
Having read this, and your site, I think that you could do an easy
empirical test. If psycons are responsible for "targeting" enzymes to
their substrate in some way, then reaction rates should go faster than
a simple diffusion limited reaction. Take an enzyme (say trypsin), and
a simple substrate, and meaure the reaction rate at differing
substrate concentrtions, with fixed enzyme concemntration, then
measure the reaction rate with differing enzyme concentrations.
The diffusion theory gives rough predictions for the rate of the
reaction, and precise predictions for the change of rate with changing
substrate and enzyme concentrations. If psychon theory is correct, the
rates should be faster by an amount that depends on the mathematical
details of your theory.
Have you considered doing such a test?
Cheers! Ian
[snip]
=====================================================
Ian Musgrave Peta O'Donohue and Jack Francis Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
z@z
[several snips]
I'm sorry that I wrote in another post to you that you call other
persons 'damned liars'. You answered that you do not, so I
believe you. My claim was primarily based on your site "Lies,
Damned lies, Statistics and Probability Abiogenesis Calculations"
http://www-personal.monash.edu.au/~ianm/prob.htm .
I had found this site through a link of Richard C. Carrier and I
thought it was your main page. In the meanwhile I have seen
also your main page giving a much better impression of you.
Nevertheless, you call my convictions and claims "damned lies".
Even if such convictions are wrong, they are no lies! If you
don't want that people can get the impression that you call them
"damned liars", then you should change at least the name of
your site.
>>> ... As Gavin Tabor pointed out, in [aqueos]
>>> solution there are around 10^14 interactions/sec between molecules,
>>> and the volume involved is nanoliters, which is miniscule compared to
>>> the free diffusion paths of these molecules, so it is not particularly
>>> difficult for a substrate to meet it's enzyme in the right orientation
>>> just by randomly bouncing around in the cell.
>> One nanolitre gives a cube with a side length of 0.1mm, and in
>> our model this corresponds to 100 m !!! You even claim that such
>> lenghts are minuscule compared to the free diffusion paths of the
>> enzymes. Are you confusing kinetic theory of gases with diffusion
>> in aqueous solutions, are you telling us a joke, or are you even
>> telling us a ... ?
> No, free diffusion of molecules in solution is very rapid. Have you
> actually had anything to do with diffusion in solutions. ...
>> It seems that you do not know the theory of Brownian motion.
>> Einstein calculated in a 1905 paper that a particle with a
>> diameter of 0.001mm (the size of a bacterium) would result
>> in an average motion of 0.0008mm in a second and of 0.006mm
>> (less than the length of normal cell) in a minute (at a temperature
>> of 17°C). The average motions per time unit of enzymes are
>> certainly longer because they are much smaller.
> Good heavens, just look at your own calculations, a bacteria sized
> particle travels 800 micrometers a second, thats roughly 8 times
> the diameter of an average mamalian cell!!! And that's at 17 degrees,
> whereas mammalian cells are at 37 deg C! Protein sized particles
> travel much faster as you say. Your _own_ calculations show you
> are wrong. Now add in diffusion down a chemical gradient, and you
> are way out of field.
I don't understand: according to Einstein's calculation a bacteria
sized particle travels 0.8 and not 800 micrometers in a second. The
mean path is proportional to the square root of both the absolute
temperature and the time, and inversely proportional to the square
root of the diameter (of a spherical particle). The mean path of a
spherical enzyme with a diameter of 10 nanometers is roughly
10 micrometers in a second and roughly 10 nanometers in a
microsecond. For a mean path of 1 nanometer (about three times
the lenght of a water molecule) ten nanoseconds are needed!
The mean path of a little protein such a trypsin in 10 nanoseconds
is about 2 nanometers.
Why is a 100-fold increase in time needed for 10-fold increase in
the mean path? Because the movements are purely random and
the particle will come back to the starting point over and over
again (in infinite time).
>> In our model, a normal living cell with a diameter of about
>> 10m consists of 10^12 different cubes of 1mm length. So its
>> rather difficult for a substrate to meet it's enzyme in the right
>> orientation "just by randomly bouncing around in the cell".
> On the contrary, it can visit all 10^12 cubes nearly 100 times
> via a random walk.
(That this is impossible, you have recognized yourself.)
Here you assume that collisions of the enzyme result in
movements substantially longer than 1 millimeter and that
the enzymes are regularly reflected in the cell walls.
"The 'diameters' of enzymes are then in the order of a few
millimetres and the 'diameter' of a water molecule is about
0.3 mm (there is room for 33.3 water molecules in 1 cubic
millimetre)."
"The bigger the particles, the slower random thermal motions.
The reason is simple: random collisions with many surrounding
molecules can cancel each other out and the remaining
change in momentum does not increase proportionally to
the mass of the moving particle."
Please imagine very concretely the many water molecules
(0.3 millimeters) colliding with the enzyme (e.g. a diameter of
some millimeters). Think about the effect of such a collision on
a protein whose mass is thousands of times bigger than the
the mass of the water molecule.
>> Don't forget, most of the 10^14 random collisions primarily with
>> water molecules have no effect at all! Every square millimetre
>> of the enzyme surface corresponds to about 10 water
>> molecules.
> But not all of that surface is water, there are also ions, substrate
> molecules and other proteins.
The objection seems not relevant to me.
> Acording to you, enzyme reactions can't take place at all, even in a test
> tube. However, they take place in test tubes at rates that are entirely
> consistent with substrates and enzymes meeting randomly in a diffusion
> limited way (with the exception of enzymes with lipid soluble substrates).
> This is all elementary enzyme kinetics.
On the contrary, according to your reductionist Darwinism enzyme
reactions can't take place at all. The main principle of this modern
word view is the hypothesis that biology can be reduced to chemistry
and chemistry to physics. But if we explain chemistry by physics we
should do it in a careful and consistent way. It has no sense to put
forward some formulas which are in agreement with the experiments,
and to simply assume or claim that they are consistent with physics.
> If your theroy was right, you might expect substantial differences
> between hormone/receptor interactions in broken cell preparations,
> and in intact cells.
I suppose that in the meanwhile you know that this is not true.
It would be true for at least some forms of vitalism.
>> Only at the most 5 percent of the hundreds of different
>> mitochondrial proteins are coded by mitochondrial DNA. The
>> proteins even have to pass a double membrane in order to
>> reach their destination. According to the very convincing
>> endosymbiont theory, at least most of these proteins (or their
>> ancestors) were coded once by the mitochondrial DNA itself.
>> How do you explain the fact that the proteins could find
>> even after the transfer of the genetic code to the nucleus
>> their destinations within the mitochondrion?
> Specific targeting peptide sequences. These can be tailored to
> particular phospholipid ratio's in differnt membranes, or bind to
> a peptide receptor.
How probable is it that hundreds of mitochondrial genes received
during or after their transfer into the nucleus by random mutations
(blind chance) exactly such specific sequences which direct their
corresponding enzymes back to the mitochondria?
>> I ask you: can you imagine anything which would convince you
>> that neo-Darwinism is not generally correct?
> I can imagine several things, including showing that that DNA
> relationships between organisms do not form patterns of descent
> (they do, but that is one potential test).
The assumption that DNA relationships between organisms form
patterns of descent is valid for most sound evolution theories. It can
not even discriminate between Darwinism and the psychon theory.
>> If it would be possible to produce large amounts of rare proteins
>> such as luminous proteins by biotechnological means, this would
>> be strong evidence against the psychon theory.
> Bad news, the rare jelly fish fluorescent protein Aequorin can be
> made in large quantitites by biotechnology see
> http://www.probes.com/handbook/ch22-5.html#Recombinant
> as can things like luciferase. There are receptors that occur in
> only one or two copies per cell (like the Beta receptors) which
> can made in large copy number by biotechnology, you can even
> artifically synthesise some (smallish) peptide hormones that have
> the full biological activity of their natural counterparts.
Have you actually read the Aequorin site? How do you define
"large amounts"? I define it in the following way: at least bigger
amounts than there are in nature.
The biological activity of small peptide hormones depends rather
on the enzymes reacting to them than on them themselves.
Ian, it will be necessary to clarify why our figures are so different.
I hope that the error is on your side you probably hope that it is
on my side.
Cheers
Wolfgang
Kalandros M
If I'm reading this correctly your actually talking about the
net distance traveled, not the path length. If I walk one
mile going north and come back, I have a net distance traveled
of 0, but a path length of 2 miles. It is possible to have very
many interactions along that path, even if the net motion of
the particle is zero.
>
>
> >> In our model, a normal living cell with a diameter of about
> >> 10m consists of 10^12 different cubes of 1mm length. So its
> >> rather difficult for a substrate to meet it's enzyme in the right
> >> orientation "just by randomly bouncing around in the cell".
>
> > On the contrary, it can visit all 10^12 cubes nearly 100 times
> > via a random walk.
>
> (That this is impossible, you have recognized yourself.)
>
> Here you assume that collisions of the enzyme result in
> movements substantially longer than 1 millimeter and that
> the enzymes are regularly reflected in the cell walls.
>
> "The 'diameters' of enzymes are then in the order of a few
> millimetres and the 'diameter' of a water molecule is about
> 0.3 mm (there is room for 33.3 water molecules in 1 cubic
> millimetre)."
>
> "The bigger the particles, the slower random thermal motions.
> The reason is simple: random collisions with many surrounding
> molecules can cancel each other out and the remaining
> change in momentum does not increase proportionally to
> the mass of the moving particle."
This only hold for very still water. If I take that same water and
boil it, the particles will travel quite a distance, in a very short
period of time. There are theories about the formation of life
by underwater thermal plumes that would fit this scenario.
>
>
> Please imagine very concretely the many water molecules
> (0.3 millimeters) colliding with the enzyme (e.g. a diameter of
> some millimeters). Think about the effect of such a collision on
> a protein whose mass is thousands of times bigger than the
> the mass of the water molecule.
>
> >> Don't forget, most of the 10^14 random collisions primarily with
> >> water molecules have no effect at all! Every square millimetre
> >> of the enzyme surface corresponds to about 10 water
> >> molecules.
>
> > But not all of that surface is water, there are also ions, substrate
> > molecules and other proteins.
>
> The objection seems not relevant to me.
>
> > Acording to you, enzyme reactions can't take place at all, even in a test
> > tube. However, they take place in test tubes at rates that are entirely
> > consistent with substrates and enzymes meeting randomly in a diffusion
> > limited way (with the exception of enzymes with lipid soluble substrates).
> > This is all elementary enzyme kinetics.
>
> On the contrary, according to your reductionist Darwinism enzyme
> reactions can't take place at all. The main principle of this modern
> word view is the hypothesis that biology can be reduced to chemistry
> and chemistry to physics. But if we explain chemistry by physics we
> should do it in a careful and consistent way. It has no sense to put
> forward some formulas which are in agreement with the experiments,
> and to simply assume or claim that they are consistent with physics.
So the psychon theory supplants not just evolutionary biology but
chemistry as well?
Mike
James J. Lippard
expression in English. If you do a search on the phrase at
www.infoseek.com, you will find numerous examples of its use.
I forget who originally used it. Mark Twain?