This is a repaste of a reply to very similar sweetnes comments (linked
sweetnes_n_li...@yahoo.com wrote in message <news:firstname.lastname@example.org>...You have shown that short amino acid sequences can come together to
> I have presented you with proof (laboratory proof, in many instances)
> that your statements are incorrect.
form a new unified function that is indeed unique and of greater
complexity. The only problem you have here is that the minimum amino
acid number required for your most complex example is only 3 or 4
hundred amino acids. My argument is that evolution becomes more and
more difficult the greater the minimum amino acid requirement until it
becomes impossible this side of zillions of years when the minimum
requirement reaches a few thousand amino acids in fairly specified
order. Where are your examples of evolution requiring such a level of
minimum amino acid specificity? I see a lot of hot air coming from
you, but no such example. Where is the reference for such a
demonstration? And, by the way, your lame bacterial swarming example
doesn't even come close (see discussion below).
Recently I have been referred to the example of the bcr-abl chimeric
But, before you become excited about the bcr-abl function, there is a
> I have provided you with at least three examples of exactly thatActually it has everything to do with this. What you have shown are
> happening: simpler systems combining to produce a novel, complex
> system with a different, novel function. The fact that there are more
> ways to combine systems nonfunctionally does not have a bearing on
simpler systems combining to produce a novel function that requires,
at minimum, only 3 or 4 hundred amino acids. You have also provided
examples of a simple function requiring less than a few hundred amino
acids at minimum evolving a new type of function within the same level
of complexity, but not anything much greater. Please, I think you can
at least try and do better than this.
> The system does not work by searching randomly throughYou haven't explained how my ideas are wrong in this regard. All you
> thousands of different combinations of amino-acids, until it "hits"
> the right combination. This has been explained to you over and over
> again. It simply does not happen, and your refutation of this does not
> refute anything that is a part of evolutionary theory.
have shown is how the same type of function can be up-regulated and
down-regulated (See discussion below of Myxococcus xanthus swarming
evolution demonstrated by Gregory J. Velicer and Yuen-tsu N. Yu of the
Max Planck Institute for Developmental Biology) but not how new types
of function within higher levels of complexity can be evolved without
searching randomly through a very large non-beneficial sequence space.
Sequences with the same types of functions can be clustered around
each other like little islands of stepping stones - very much like a
sentence who's individual letters can be rearranged somewhat without a
complete loss of beneficial meaning, but who's type of meaning is
fairly isolated from other sentences with different types of meaning
or significantly different ways of achieving the same meaning. How to
cross the non-beneficial gap between these two different types of
meaning? That is the question? For shorter sequences, the random
walk required is easier to overcome. However, with each amino acid
increase in the minimum random walk required to achieve the success of
any new type of beneficial function within that level of functional
complexity, the time required grows exponentially.
> Please show me how would it be possible for a change in biologicalOk - take, for example, a particular function that requires, at
> systems, such as it happens NOW, at this moment, to go on for, say,
> ten thousand years, WITHOUT producing a novel, complex system?
minimum 5,000aa at minimum to be realized. Say this sequence happens
to get duplicated so that it can undergo various mutations without
risking significant loss to the original beneficial function (which
has been optimized for its host by now - as far as *level* of function
is concerned). The sequence space at this level of complexity is more
than 10e6500 sequences. The question is, out of all of these
universes of possibilities, how many are or would be beneficial to the
given organism in question? If the organism could use a million
different types of functions to some benefit at this level of
complexity and if each of these million different types of functions
had at least 10e1000 different sequences with at least some selectably
advantageous level of function, then there would be 10e1006 total
beneficial sequences in sequence space with a different type of
function. The question is, how long, on average, would it take to
find any one of these other beneficial sequence islands? Well, you
have to think of ratios at this point. What is the ratio of
beneficial vs. non-beneficial sequences in sequence space? Well,
10e1006 divided by 10e6500 equals 10e5494. That means that for every
one beneficial sequence there are literally universes of
non-beneficial sequences (i.e., there are only around 10e80 atoms in
the entire known universe). With a mutation rate of one mutation per
sequences of 5000aa per generation in a population the size of all the
bacteria on earth, it would literally take zillions of years on
average for even one member of the population to find even one
beneficial sequence with a new type of beneficial function at this
level of complexity.
Of course, you will say that evolution doesn't work like this.
You certainly haven't been able to provide me yet with any such real
> I am only now begining to understand the depthA bit of clarification: I am well aware that many multi-domain
> of what you are saying. The depth of ignorance in it, that is. I
> didn't understand before that you believe that multiudomain proteins
> are just "as complex as the most complex domain" *literally*. Gods.
> And, to top this, you don't belive in the (slightly more intelligent)
> idea that funcitonalities have to evolve suddenly, in a poof, from
> proteins searching through all possible random combinations; you
> actually believe that long proteins with functions can never arise?!?
proteins use all or many of their domains at the same time for a
collective function. However, when you are taking about a particular
function, multiple domains may not be required to achieve this type of
function. The question is, what is the minimum amino acid part
requirement to achieve a particular type of function to a level where
it becomes selectably advantageous? I'm not asking how one can make
the most complex Rube Goldberg-type mousetrap here. I'm asking how
one can make the most simple, bare bones, function of a particular
type that will work to at least some minimal degree of selectable
advantage. Once you have this function, refining it by increasing or
decreasing its level of function (i.e., more or less lactase ability)
is not a problem.
Now, if you can add to this minimum part requirement to achieve a new
> There are hundreds of observed instances. Hell, just last week we hadInteresting. Give me the details of this demonstration and/or the
> a seminar on two insect proteins that mutated (independently), and
> formed a complex with third one; the total complex is over five
> thousand residues long. It performs a function totally unrelated to
> any of its three constituents (two constituents are structural
> proteins, one is, of all things, a kinase; new function has to do with
> mitochondrial RNA repair).
reference for the publication of this demonstration. Does it involve
the deregulation of the kinase function, as is the case with the
chimeric bcr-able function mentioned above?
> >If such differences really do exist between suchAs I have said over and over again in this forum, I do not think we
> >otherwise similar creatures, then yes, such systems
> >could not evolve in trillions of years and so they
> >must have been designed. I cannot comment specifically
> >on the differences between chickens and turkeys, but I
> >can on the differences between several other life forms.
> Such as men and monkeys, eh? Of course.
know enough about the functional genetic differences between humans
and apes to rule out the possibility of common origin with the use of
> By your standards, practically every species on earth was designedThe definition of "species" is rather subjective. I do not believe
> separately and recently. This makes you a YEC. How do you explain away
> the fossil record, the geological data, the radiological evidence,
> cosmological/astronomical evidence, etc?
that all of what are now referred to as "separate species" where
designed separately - although I do believe that they were all here
relatively recently. The fossil record and geologic data, to include
the radiological evidence, is not nearly as solid in support of the
long ages of deposition that evolutionists claim it is. It shows very
clear evidence of rapid deposition over the course hundreds and
thousands of years, but certainly not anything even close to a
million, much less a billion years.
> >These sequences do not have beneficial functions withoutWhen such sequences are beneficial (which not all of the possibilities
> >the cell being what it is - in other words, it defines
> >such sequences as beneficial based on many other systems
> >of function that recognize and use such short beneficial
> >sequences in a beneficial way.
> Incorrect. Single amino acids and short polypeptides can (and do)
are), they are useful only because the system of the organism
"recognizes" them as useful in a particular environment. Not all such
sequences, even short sequences, are useful to all organisms. Just
because a particular sequence might be useful in one particular
organism does not mean that all organisms will also recognize it as
> >Try evolving this short word, one letter at a time, intoTry it. Give a demonstration here. Provide us with an environment or
> >a longer and longer word or phrase. See how far you can go.
> Quite long, actually. Since words get copied, not just single letters,
situation. Start with a short word that would be beneficial in such a
situation. Then, adding letters to that word, evolve it were each
addition makes beneficial sense in that situation. Spelling does not
have to be exactly correct, just understandable in a beneficial way.
See how far you can go. Try it here in this forum and include your
demonstration in your reply to this post.
Plus, proteins are not words.
No, they are not. They are even a lot more flexible in their
> >Again, a multi-domain protein is no more complex inYou will notice that I use the word, "necessarily". A many types of
> >functional ability than its most complex functional domain.
> >The functional domains work independently. It is like multiple
> >proteins stuck together. But, these domains do not necessarily
> >work at the same time to give a greater unified function.
> This is perhaps the best example of how poorly you understand
protein functions do not necessarily require multiple domains in order
to be realized. You yourself admitted as much in your first post when
you claimed that the lactase function is actually much simpler than
its usual 1000 acids would make it appear.
> Practically every large protein is formed of multiple domains, whichCertainly this is true. If you can present the evolution of such a
> ALL work TOGETHER to produce the function of the protein.
collective function that requires, at minimum, all of the various
amino acids in all of the various domains of a particular protein
working at the same time, then you will have something. You have
tried to do this, but your total number of specified amino acids falls
rather short - being less than 500aa so far. You claim to know of
functions that require much more than this, but you have yet to
provide me with the details of such observations and/or a reference to
support such claims.
> One domainYes - I agree and know full well about such collective functions. I
> recognizes the substrate, another may carry the active site of
> catalysis, the third may be involved in carrying the product (or
> recognizing and binding a coenzyme or second substrate...). If you
> don't have specifically defined domains, you have so-called motifs,
> which are smaller sub-domain like structures.
think you have misinterpreted what I was trying to say.
> Large proteins that do not work like this are *extremely* rare (whichCertainly . . .
> is to be expected).
> >Beyond a few hundred amino acids required at minimum, suchWhere? You made a blanket statement but you provided no details or
> >functions simply do not evolve.
> I gave you examples of them evolving.
references to support this statement.
> Sean. I am a biochemist. I work with this stuff every day. How stupidI don't think you are stupid and I do not assume to teach you how to
> do you think I am? You are trying to teach me how to do my job, and
> you are not very good at it.
do your job. However, I highly doubt that your job invokes the use of
evolution beyond the lowest levels of functional complexity. You
claim that it does or that you do in fact observe such levels of
evolution all the time, but you have yet to support such claims beyond
those that require more than a few hundred amino acids. What I am
talking about here are those types of beneficial functions that
require, at minimum, several thousand amino acids working together at
the same time in a rather specified order.
> Novel proteins of sizes measured in thousands of kD have arisenReferences?
> through evolution, in laboratory conditions.
> Well, since the examples I gave you so far simply don'tActually the M. xanthus bacteria did not develop their extracellular
> count for some reason (mostly that you refuse to accept that things
> happen if your theory says they cannot happen), let me give you a
> relatively recent one. Velicer and Yu, at Max Planck institute in
> Germany; the bacteria, under pressure, developed a complex
> etracellular fibril matrix, and adapted it to achieve a form of
> primitive cooperation.
matrix de novo. They were in fact already able to make this matrix
via the use of pre-existent genes. What happened is that when Velicer
and Yu deleated the genes that gave these bacteria that ability to
achieve S-type swarming, they increased their ability to make more
matrix necessary for A-type swarming. What they evolved was the
ability to make "enhanced quantities" of a matrix which they already
made. In fact, genetic mutants of the evolved strains were constructed
by Velicer and Yu that were unable to make this fibrilar matrix even a
little bit, and guess what, these bacteria never could evolve any type
of significant swarming ability, much less the A-type or S-types.
"Both the genetic and chemical inhibition of fibril-matrix
construction inhibited the evolved swarming phenotypes."
Basically, this is no different than the evolution of penicillin
Please! You really should try to do better than this! I really
In any case, this is all the nonsense I have time for today. Hope you
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