glenn
see http://www.glenn.morton.btinternet.co.uk/dmd.htm
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>
>> Pay attention to the issue at hand. I am saying that ignoring the data I
>> posted above is exactly LIKE, ANALOGOUS, SIMILAR to the way the YECs act.
>> And indeed, you skipped right by it without any comment.
>
>The issue at hand is random evolution of novel protein functionality,
>and, in particular, the first minimal functionality of a novel protein,
>before natural selection can set in. This has nothing to do with
>artificial selection of RNA in vitro, particularly if some of the
>functionality selected is already present. It's you who are evading the
>issue, not I.
This is a rigging of the roulette wheel. What you seem to be doing is ruling
out any experimental evidence which can be collected today. If it is in
vitro, you say it has nothing to do with the origin of life and the
emergence of useful proteins. If we put it in a metal dish and do the same,
or in a rock dish, does it suddenly become ok? I doubt you would accept any
experiments with zeolites which might show interesting effects merely
because they took place on a university campus. We have no time machine
with which to return to 3.8 Gyr and watch the process. So what you do by
ruling out the discussion of any experimental evidence is firmly plant your
head below the ground so that one can not see observational data.
>
>> >>So, given that I am mentioning this work for a second time,
>will you respond
>> >> to it's import now?
>> >
>> >You have not mentioned these papers (if I remember correctly), but
>> >similar ones, and I responded in detail. But I may do it again, giving
>> >you a new example if you insist. A. Lombardi, et al., "Miniaturized
>> >metalloproteins: Application to iron-sulfur proteins", PNAS 97 (2000),
>> >11922, attempted to design a minimal redox enzyme, but haven't achieved
>> >their goal as yet. Their dimeric undecapeptide can hold an iron atom,
>> >but is unstable, being too small to shield off the environmental water.
>> >The invariant of their (intelligently designed) construct amounts to at
>> >least 5 specific amino acid occupations, which is too much to be
>> >attainable by an evolutionary process without selection.
>>
>> What Lombardi is doing is not at all what Joyce, Szostak and
>Ellington are
>> doing. Lombardi is trying to shrink the proteins down to
>miniature versions,
>> of smaller length.
>
>This is exactly my point, see above. These miniature proteins are the
>ones which may give indications about the origin of semantic or
>functional biological information, about which I was talking (case a).
We weren't discussing the minimum length proteins can be. We were discussing
if other families of proteins could perform a given task than the one we
find doing it today. That was the issue. Not how short a protein can be.
Tell me how short the sequence for 'be' can be and still have you understand
what is meant? And to assume that the original proteins performed precisely
the same task as evolved proteins do today is quite a leap.
I
>did not want to deal with improvement of a preexisting functionality
>(case b), because there you may just be taking over some "information"
>from the environment by means of selection. And I did not doubt there
>are some RNA functions (case c) that are not very difficult to find (if
>you do have RNA!), just as Joyce, Szostak and others have found, even if
>you are looking for a function not yet present in the starting mix.
>Again, we have no means of telling whether any information has emerged
>de novo. With proteins, there is a way of dealing with semantic
>information (II), cf. Yockey's book.
All Yockey did was to substitute hydrophobic amino acids for hydrophobic,
hydrophilic for hydrophylic in cytochrome c and then count the
possibilities. That is not predicting the function. That is merely saying
that there are x number of sequences which appear to be able to perform the
same task. I think Yockey is correct, or close to it. But it isn't taking a
novel sequence and deciding what it does.
With RNA, I know of no similarly
>promising way of dealing with functional information, because residue
>conservation is much less clearly definable (you have only 4
>nucleotides, and there is the additional complication of base pairing).
>
>So, I am looking for examples of case a, but you keep pointing to
>examples of case b and/or case c.
I disagree here. Yockey is speaking of using pre-existing functionality to
predict similarity of function in similar molecules. The importance of what
he did was to show that the silly anti-evolutionary argument of past years
in which only one sequence is allowed to perform a given function is false.
Case c, the RNA shows probability is much much less. And with Case a, the
proteins, I posted references to multifunctionality yesterday. That is
evidence that proteins will be subject to the same thing.
And I have to ask a really dumb question here. NO ONE IN THE ORIGIN OF LIFE
ISSUE BELIEVES THAT LIFE AROSE FROM PROTEINS FIRST. THAT HASN'T BEEN
BELIEVED FOR A LONG TIME. SO WHY ON EARTH ARE YOU LOOKING FOR THE ORIGIN OF
INFORMATION AMONG THE PROTEINS? IS THIS ANOTHER CASE OF YOU BEING WAY BEHIND
THE TIMES ON THE TOPIC YOU WANT TO DISCUSS?
Consider this from 1991:
Sydney Fox's Experiment
"By repeatedly heating amino acids and dissolving them in water,
he induced them to coagulate into tiny spheres composed of short
protein strands.
"Fox argued then - and continues to do so - that these
'proteinoids' represent the first cells, but his work has fallen
out of favor among many scientists. Once proteinoids are formed,
'that's it,' says Gerald F. Joyce of the Research Institute of
Scripps Clinic. "They can't reproduce or evolve."~John Horgan,
"In the Beginning", Scientific American, February, 1991, p. 118-
119.
This from 1959:
"According to Dr. Pirie, the fact that all forms of life known
today do use protein 'will have no more relevance (to primitive
life being dependent on protein) for a discussion about the
origins of life than the now almost universal use of paper has
for the origin of writing or the use of matches for the original
making of fire."~N. W. Pirie, "Chemical Diversity and Origins of
Life,", The Origin of Life on Earth, (New York: MacMillan Co.,
1959), p. 78
And Fox's protenoid idea has been reduced to cartoon extents:
"Although Fox continued to champion his ideas through
numerous papers, popular articles, books, and talks until he died
in the summer of 1998, his work is now almost universally
dismissed. Over time, he became more and more a maverick in the
field. Sadly, at the Eleventh international Conference on the
Origin of Life, held in Orleans, France, in 1996, he was reduced
to having placards of proteinoid microspheres paraded around in
the manner of a cartoon sandwich man predicting the Second
Coming." Christopher Wills and Jeffrey Bada, The Spark of Life,
(Cambridge,MA: Perseus Publishing, 2001), p.55
>No, Glenn, they are not at all similar. There are fundamental
>differences between proteins and RNAs. Structure-function relationships
>are completely different; and with proteins, you need the
>genotype-phenotype code translation - to just mention two factors. You
>questioned my concept of semantic biological information, but you refuse
>to consider my definition of it. I don't see anything relevant to this
>type of information in the RNA artificial selection work - although it
>certainly is of interest in other respects. It's just not applicable to
>what I said and you questioned.
I agree that they are different and given that no one but you seems to think
that proteins were the first biopolymers to evolve means that this entire
discussion about proteins and the origin of information is nothing but a
discussion about that which no one believes. It is a strawman set up to
appear as if scientists actually believed that information first arose via
proteins. They don't any more. Most believe in the RNA world, which is why
I am discussing RNA rather than a 50-year out dated and rejected
proteinaceous concept.
>
>> >> >This only works because you first give me the book, which
>contains all
>> >> >the relevant semantic information. With the signal, you just send me
>> >> >ln(3) bits of information, not lots.
>> >>
>I don't dispute these calculations at all. But again and again, I have
>emphasized that we have to distinguish between
>(I) Maximum information carrying capacity;
>(II) Functional information relevant for biological systems.
>Shannon entropy is related to (I), not directly to (II). Meaning
>(biological or otherwise) is found in (II) and is a function of a
>functional system like a given language or biological system. (I), which
>is a function of sequence length and alphabet size, specifies nothing
>but a maximum amount of functional information (II) which can be stored
>in a given sequence having a maximal capacity (I). Never have I claimed
>a 1-to-1 correspondence between a "value" of (I) and a "value" of (II).
ANd over and over, I keep asking you to recognize this II. Even if you can't
quantify it, you seem to be unable to recognize it when offered a chance to
tell me if a sequence has this II functional information. You never ever
try to tell me which sequence has it. If you can't even recognize it, can't
quantify it, do you really expect us to believe it is real?
Lets give you another chance.
ken quine monie hiv a wyme
wyme a monie quine hiv ken
ken wyme a monie quine hiv
a ken monie quine hiv wyme
ken quine a hiv wyme monie
hiv a quine wyme ken monie
quine monie a ken wyme hiv
Which sequence in Doric has functional information. Can you recognize it
when you see it. We can't quantify modern art, but we can at least
recognize it. So, if you want me to believe that functional information is
a real concept then pass 5 tests like tis with only 1 failure. Which
sequence has meaning?
>
>You may compute the Shannon entropy of a given DNA sequence (4-letter
>alphabet) or a given protein (20-letter alphabet). You'll get different
>values, even for a length ratio of 3:1.
So what? Ratio has no place in the definition of shannon's entropy. What
you say shows you don't know much about Shannon entropy.
>Yockey also shows the connection to meaningful biological information:
>"Let us consider evolution as a communication system from past to
>present. At some time in the history of life the first cytochrome c
>appeared. As a result of drift, random walk and natural selection, this
>ancestor genetic message was communicated along the dendrites of a
>fractal ... representing a phylogenetic tree ... Some dendrites lead to
>modern organisms, the sequence having changed with time. Thus the
>original genetic message of the common ancestor specifying cytochrome c,
>regarded as an input, has many outcomes that nevertheless carry the same
>specificity. The evolutionary processes can be considered as random
>events along an ergodic Markov chain ... that have introduced
>uncertainty in the original genetic message. This uncertainty is
>measured by the conditional entropy in the same manner as the
>uncertainty of random genetic noise is measured ... Since the
>specificity of the modern cytochrome c is preserved, although many
>substitutions have been accepted, this conditional entropy may be
>subtracted from the source entropy ..., to obtain the mutual entropy or
>information content needed to specify at least one cytochrome c sequence
>... The information content of the sequence that determines at least one
>cytochrome c molecule is the sum of the information content of each
>site. The total information content is a measure of the complexity of
>cytochrome c" (p.132). For the mathematical formulation, please refer to
>Yockey's book.
I don't have a problem with Yockey's point. All he is pointing out is that
one must account for degeneracy in functionality, i.e. that many sequences
will perform the same function, which is what I keep telling you.
>
>> >Homonyms may be difficult to find in biology! They occasionally occur in
>> >our languages, even within the same language.
>>
>> See Szostak and Ellington above and Joyce. They are finding homonyms in
>> biology but you don't seem to want to discuss them.
>
>This is in vitro RNA chemistry using some biochemical molecules. It may
>not have much to do with biology. The RNA world is completely
>hypothetical, and we have no idea how it might have emerged. Presumed
>natural evolutionary processes in it are completely different from known
>evolutionary processes in living organisms.
And no one believes, like you seem to, that proteins were the first
biopolymers. They weren't, and you are arguing for a 50-year-old rejected
idea. At least stay with the program and the current thinking on the topic.
Most researchers beleive that life evolved through the RNA.
>
>Of course, today one cannot predict biological function (if any) from a
>sequence alone. I never claimed this.
You said Yockey did it above.
However, as researchers are
>getting better at understanding the biological systems which can "read"
>and express such sequences in the appropriate functional environment, a
>measure of meaningful prediction will emerge. This is what the new field
>of proteomics is all about. This confirms the relationship between
>information (I) and information (II).
As Shannon pointed out, and I have repeated many times in this exchange,
there is NO relationship between Shannon entropy and your information II.
For some reason you don't seem to be able to understand what SHannon
actually wrote. I repeat it again.
"The fundamental problem of communication is that of reproducing
at one point either exactly or approximately a message selected
at another point. Frequently the messages have _meaning-, that
is they refer to or are correlated according to some system with
certain physical or conceptual entities. These semantic aspects
of communication are irrelevant to the engineering problem." C.
E. Shannon, " A Mathematical theory of Communication" The Bell
System Technical Journal, 27(1948):3:379-423, p. 379
What part of the term 'irrelevant' do you not understand?
glenn
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