Information and Genetics

This seems to be a major topic, so I thought I'd
pop a thread up on it.If there already is one, apologies and point me to it I've seen a lot of claims that information theory can be used to refute ToE, and would like to know why.I'm not going to belabour the issue of defining information ...
well not to start with ... but want to question the principle
of applying information theory to genetics.Is there any information content in an organism's genetics ?We use the analogy of a genetic code, but is it actually
a code ?

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Originally posted by Fred Williams:
If you insist that a computer is not an intelligent device, or represents intelligence, then what is the point in debating further? Like Mark, you have concocted a version of information that is not falsifiable.

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Pedantic bit:: A computer is not an intelligent device, it is a
deterministic, electronic 'machine'. Check the definition of
intelligence that you provide if you don't believe me.You assert that a change to an existing 'algorithm' isn't
new information (in the sense that you define info.).What if successive small changes to an algorithm ultimately
produce an algorithm that's function is radically
different from the start-point ? Is that still not new information ?To attempt an analogy using words::If we start with 'cat' and modify one letter to make 'bat'
is the information conveyed by the second word (to an english
speaking individual) new or not ?It's just a modification, but once 'interpreted' to provide
information within the recipient isn't it new information ?

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Originally posted by Fred Williams:
It depends. Was it the intent of the sender? If not, the receiver lost information even in the Shannon sense because of loss of certainty. Is it a typo in a dictionary? Again, a clear loss of information. Is it an intentional addition of a new word to the language by the sender? This would be new information.

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The point I was trying to make is also relate to ::

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By your logic a single bug in a subroutine should deem that subroutine as something new. No, it’s BROKEN. You are trying to call it new because you want new information. You are grasping at straws.

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Which is at the hub of the whole question of 'information' let alone
information in a bilogical context.The sub-routine with a bug has a functionally different output
to that intended (otherwise there wouldn't be a bug) so it contains
a 'new' algorithm compared to that originally envisaged.'Information' cannot be transmitted at all, only data can.And there IS a difference between data and information (which
distinction, incidentally, Shannon (nor any other communications
experts of the past) ever explicitly make).In my word analogy it doesn't actually matter what I intended to
convey by putting 'bat' on the page ... the fact is that any
english speaking individual on reading that word will flash mental
images through their mind of baseball bats, cricket bats,
fruit bats, vampire bats, or what-have-you. Information is
ONLY formed in the conscious mind of the individual observing
the data, and is highly context and historically sensitive.So now we have the problem that I see with applying the term
'information' to biology.Information is something that a 'viewer' obtains from data, whether
or not that data was intended to hold that 'information'.Saying that the change from 'cat' to 'bat' is a loss of information
pre-supposes that I originally intended to convey 'cat'. In
the biological/genetic sense this is to start with the assumption
that there IS a creator of genetic code, and that that data was
intended to contain/convey some kind of 'information'.This is why a large part of my question here is 'Does the genetic
content of a cell convey information ?'If so, what form does that information take ?Since information can only be derived from a subjective
viewing of data, is it even relevent to biological
systems in the context of evolution/creation hypotheses ?

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Proteins, DNA, irreducibly complex systems, etc., all contain detectable design.

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How do you detect design ? I thought IC was put forward as an
evidence of design, but I don't find it compelling.Effectively the argument of IC is one of incredulity. That is
since we cannot imagine a way that such a thing could have evolved
then it can't have.

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It's not that they aren't explained naturalistically at the time being, it is that they almost can't be--unless a natural process can be shown that can assemble such a system or meet requirements such as left-handedness, which bring us back to my question, and of which neither of us know the answer.

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Two things about the above ... the unless part defines the
not explained now part so I don't see what you are driving at.As far as left-handedness is concerned check out
the 2001 Nobel prize for chemistry:: http://www.nobel.se/chemistry/laureates/2001/public.htmlThe background to which points out that ::"In the early sixties it was not known whether catalytic asymmetric hydrogenation was feasible, i.e. would it be possible to catalyse an asymmetric reaction to produce an excess of one of the enantiomers? The breakthrough came in 1968 when William S. Knowles was working at the Monsanto Company, St Louis, USA. He discovered that it was possible to use a transition metal to produce a chiral catalyst that could transfer chirality to a non-chiral substrate and get a chiral
product. The reaction was a hydrogenation in which the hydrogen atoms in H2 are added to the carbons in a double bond. A single catalyst molecule can produce millions of molecules of the desired enantiomer. "So the potential existence of catalysts that will produce this
effect has been known for over thirty years ... if they can
exist in a lab isn't it at least possible that they could
have existed on earth billions of years ago ... after all none
of us know exactly what the conditions were when life began to
emerge. The possibility of a catalyst being responsible is
quite telling I feel.We don't even have to mention that cosmic radiation can promote
one handedness to dominate ... oh I just did

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It sounds to me as if they're
(a) setting conditions just right,
(b) half of the time making the catalysts themselves, and
(c) isn't menthol from peppermint oil?

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(a):: Well, yes, but for life to form spontaneously the conditions
would have had to be 'just right' ... the possibility of a chemical
precedent for the dominance of one-handedness is a first step in
placing reasonable doubt on chirality as a bar to the naturalistic
emergence of life.(b):: But the catalysts are much more simple than amino-acids,
and could perhaps emerge naturally.(c):: I think they use this process to make menthol.

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It depends. Of course they could be present (at least that's what I'm thinking logically--I know nothing about this), but the transition elements they mention seem all to be very rare--and it seems to hint that researchers actually made them--they are synthetic.

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My understanding of 'Transition Metal' is the bunch of chemical
elements in the middle of the periodic table ... in which case
they can occur naturally. Even if they are rare now, that doesn't
mean they have always been rare ... it's unknowable, but adds to the
reasonable doubt (over this one issue).

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The fact is that L- and D-forms occur at roughly equal frequency in nature, and bind with amino acids of the opposite handedness quite readily. There cannot be one, single R-form in a protein. Sure, perhaps there is an excessive amount of L-forms in the part of the ocean where the certain catalyst metal is--R-forms are going to form everywhere else, and move in.

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I thought there were some Right handed proteins in some
bacterial cells ... might be wrong about that as I'm dredging up
memories from a debate on this issue I had about two years ago ...
I've got some e-mails stored somewhere Anyhow ... that is a problem, but then a part of the anti-abiogenesis
argument is that amino-acids wouldn't even survive that long.So perhaps we have localised conditions were we generate amd
maintain a left-handed dominance. The catalysts I pointed out would
allow this if we can find another set of conditions that allows
amino-acid survival and combination into peptides. [b] [QUOTE] Secondly, the amino acids that they manage to get to be L-forms don't just 'get together'. All of these products have a specific amino acid sequences. The scientists have to acquire L-forms by using synthetic catalysts, and then put the amino acids in the right order to form the right substance. About half of the amino acid sites are called active sites, at which a wrong amino acid could be fatal (take sickle-cell anemia for an example). Did I mention that peptide and non-peptide bonds occur at roughly equal frequency in nautre, as well? You also have to get all of the amino acids to form peptide bonds with each other.
[/b][/QUOTE]I think that's jumping ahead (unless I mis-understand) to DNA
isn't it ?Your talking about 'fatality' while I'm just discussing prdocution
of proteins structurally similar to those required for life
as we know it.

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By the way, being in the oceans (you know, the 'soup') would have but the kabosh (sp?) on protein synthesis. Behe says on pp. 169-170 of his book:

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What year was Behe's book ?I read about some Japanese research in a news article two years
ago that said that they had found poly-peptides forming around
deep sea thermal vents. The vents act as a kind of poly-peptide
factory where some amino-acids join in the vent, come out on currents,
and are fed back into the system.I'll try to dig out anything on that too.

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By the way, we don't even have to mention that ultraviolet radiation destroys ammonia and many organic compounds that would have been present in the ocean... oh I just did

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How deep into water can UV penetrate ? I seem to remember that
it's not far, but I could be wrong.[Hope you have/had a nice trip ]

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[This message has been edited by Peter, 07-23-2002]

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Originally posted by ChaseNelson:

That is not jumping ahead to DNA. A wrong amino acid site in the hemoglobin molecule will cause sickle cell anemia.

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I think I must have mis-understood the context in which you
raised the issue.

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Originally posted by ChaseNelson:

Behe’s book is 1996. About the hydrothermal vents, Sarfati has written an article on that (which is very short) in CEN Technical Journal, which is available online at http://www.trueorigin.org/hydrothermal.asp . I encourage you to read that--it should be no trouble, because it's very short.

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The article makes four points::1) It questions the starting/environmental assumptions made.
This seems to be pot calling kettle black to me.
What were the exact conditions on Earth at the time of the
emergence of the first amino-acids. Niether of us know so this
objection seems contrived.2) Raises temperature objection ... when the research itself suggests
a 'quenching' effect to combat this. And then mentions chirality.
... which is kinda what we were talking about anyhow so I'll come
back to that.3) Seems a little odd. In a limited experiment don't you expect
limited, but indicative results ?
Perhaps the claims that this IS how it all started are overstated
but to say that it is categorically not the way it happened
based upon one small-scale experiment is equally dogmatic.My feeling is that it lends credibility to the potential for
naturalistic formation of the first amino-acids, and possibly
proteins.4) Pretty much as above.I don't claim to have the answer (I'd certainly be up for
a Nobel prize if I did ) but the refutation article appears to me
(as a trained researcher) to be a knee-jerk, assuming invalidity
style of article. It has not critiqued the methods and conclusions
from an impartial stand-point, but sought problems because the
position is contrary to those held by the author. Inevitably some
of the raised objections are not really relevant.

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Originally posted by ChaseNelson:

About the handedness evidence you raise, Tim Wallace states that the required catalyst only adds complexity to the scenario, further decreasing the chances of achieving the final product. Likewise, Dr. Jonathan Sarfati states that As always, no chiral imbalance can be produced in the products that's not in the reactants. It's crystal clear from the article that the catalyst ITSELF was chiral, and transferred its ALREADY-EXISTING chirality to the amino acids it helped generate. As a chemist, I would [have] automatically assumed that there had to be chirality to start with, and this is indeed the case. In the primordial soup, there were no organometallic chemists to synthesise homochiral catalysts! (Both quotes from personal communication.) So it turns out that the metals were synthetic (I'm not really into geology much, so I couldn't quite tell when I read the article).

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Transition metals are just elements, and they occur in nature
(otherwise we wouldn't know about them ... i.e. they are not
transuranic elements manufactured via 'atomic' processing).The catalysts are relatively simple ... and perhaps are not
the oly chiral catalysts possible. One molecule of catalysts
can produce millions of molecules with a chiral imbalance.How does that complicated matters. If producing a simple
molecule can increase the yield of the right kind of
more complex molecules doesn't that help ?Always wondered about this chirality issue in any case ...
R- and S-Limonene are lemon and orange smells ... doesn't that
mean that either the orange or the lemon has a left-handed
protein that works fine ? And don't some bacteria have
left-handers in their cell membranes ?We don't appear to need ALL r-handed, only a tendancy for R-handed.The possibility of catalysing such a dominance surely has a little
bearing.

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Originally posted by ChaseNelson:

I will inquire about how deep in water UV rays can penetrate.

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EO - 404 ErrorI found the above, which, even discounting the organic carbon
impurities, suggests that UV-B (at least) is rapidly
disapated in water.So if the amino-acids were at deep-sea location, that would
not be such a bar to production I guess.

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Originally posted by ChaseNelson:

I’m sorry that this post is so very short, but I’m extremely busy. I look forward to your reply.

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BTW, thanks for wishing me a good time. It had its ups and downs, .

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No problem, I've been a bit busy myself.

[QUOTE]Originally posted by John:
[B][QUOTE]Originally posted by Peter:
[B][QUOTE]I found the above, which, even discounting the organic carbon
impurities, suggests that UV-B (at least) is rapidly
disapated in water.So if the amino-acids were at deep-sea location, that would
not be such a bar to production I guess.
[/b][/quote]Lipid molecules, major players in the abiogenesis debate, would float on the surface.
[/B][/QUOTE]Oh.What if it was all sparked off by an asteroid impact ?Sudden random thought I know, but the collection of thoughts leading
up to the wondering is::Some scientists postulate that organic compounds could survive
on asteroids enetering earth atmosphere.Cosmic radiation can affect the distributions of enatiomersA dust cloud resulting from a large enough asteroid collision could
produce particles in the atmosphere which would dissipate UV radiationIt is considered that in the early life of the solar system such impacts were not that rare.Could provoke siesmic activity resulting in heat release from
mantle (energy source).---------> Just a thought ....

...but could the high presence of incoming rocks
have promoted an atmosphere much different to today
which would block UV for extended periods.As I understand current thinking it is considered that
many (varying sized) asteroid impacts happened in the
early life of the earth.

... but is there actually any information content
of DNA, or is it just the way we view it?

But with a hard-disk we start with the assumption that
the data on it was put there by someone ... and the binary
digits stored are data not information.The main reason that I started this thread was to discuss the line of reasoning put forward by some YEC's that the information
content of DNA is an indication of design.DNA contains sequences that are used in the cell to create
proteins etc. and that process in itself is pretty complex,
but does DNA actually, objectively contain information (can you
even have objective information?) ?The issue of information and genetics is important in the
consideration of design ... but is extremely complex, compounded
by the abstract nature of information.Another contention, within the context of the information = design
line of reasoning, is that information has to come from an
intelligent source.Is this true?If I write a computer program to randomly generate a three letter
sequence, and eventually that comes up with 'cat', and english
reading individual will read that sequence and glean information
from it ... it is related to all things feline in the
consciousness of the observer.There is no intelligence behind the emergence of the sequence
above, the intelligence is in the observer, who assigns meaning
to it, and thus forms information.

If I have a group of chemicals and I put them together
in a flask, give 'em a whisk, add some heat energy maybe,
and they react to form something else ... does that mean
that the starting molecules contained the information
required to perform the reaction?

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If this GA truly emulates evolution as you have clearly implied, then why do GAs only permit uphill movement on the fitness terrain?

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Evolution DOES move uphill on the fitness terrain -- that
doesn't mean that things have to go from simple to complex.It means they have to tend toward the more suitable wrt the
selection criteria.If there was any merit to the line of reasoning you seem to be
implying (that evo. requires movement toward the complex)
then surely there would be no single-celled critters on earth.Haven't amoeba been evolving for billions of years too? (within
the evolutionary framework that is ... not in your opinion)[This message has been edited by Peter, 09-16-2003]

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* I claimed GAs are rarely used in engineering. Rei objected and provided a few examples (fallacy of exception supporting the rule).

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In what way is the frequency of use of such techniques relevant to
the discussion of whether or not they can illuminate the issue
of natural processes being capable of design?

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1) unrealistic truncation selection,
2) unrealistic assumption of positive mutations, both in quantity and frequency,
3) extinction is ignored or not permitted,
4) an information source is always required to prune any useful information created by a GA.

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In no particular order:Re (2): Mutations are allowed, they are random ... that some help
to progress toward an acceptable solution suggests that mutation
can lead to design-like qualities (when coupled with selection).In EA's the mutations are not directed, they are simply governed
by 'natural' laws and minimal components.Re (3): How do you develop a solution with a EA without rejecting
some 'results' completely? That is extinction.Re (4): Depending on your definition. The selection criteria are
just that something to compare outputs to ... that's what natural
selection is saying -- the outputs tend toward a fit with the
environmental conditions.Re (1): Eh? EA's use the supposed mechanism of evolution, but act
upon different components. The results are designs which were
not generated by an 'intelligence' but by a mechanistic process