An Interesting Pattern

I've finally posted my 50th entry in the Biotic Reality section of my web page. Enjoy.

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This entry was posted on Wednesday, January 9th, 2008 at 11:51 pm and is filed under Origin of Life. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/an-interesting-pattern/trackback/

51 Responses to “An Interesting Pattern”

The Pixie Says:
January 10th, 2008 at 5:39 am
Hi Mike

The pattern is that the authors only descuss big amino acids, while the Miler-Urey experiment produced mostly small amino acids. The latter is to be expected. Is any reason given in the paper for why the authors chose those 8 amino acids (like, had they already tried the smaller ones and found no effect). I would guess you would see a more significant stereochemical effect is larger amino acids, so that may be why the authors chose those eight (but maybe they only saw the effect in those eight).

One thing that seemed rather obvious to me was that this list of eight amino acids could have been more varied.

Besides avoiding the small amino acids, from your Venn diagram, they look to cover most options to me (the only obvious ommision would be glutamate, E, for an example of a anionic (negative) amino acid).

Like I said, could the Duck being causing us to see more ducks?

You mean, they assume abiogenesis+evolution, and so are rationalising the data to support that? I could believe that. At the end of the day, they have a statistic sample of 8, which is not much to hang a hypothesis on.

Comment by The Pixie — January 10, 2008 @ 5:39 am

Doug Says:
January 10th, 2008 at 9:37 am
Heading over there right now to read it. I've been excited for the new entry for awhile. I had just been re-reading over the tubulin/ftsZ paper…
Thanks for updating.

Comment by Doug — January 10, 2008 @ 9:37 am

Zachriel Says:
January 10th, 2008 at 10:46 am
MikeGene: I have often been told that this review outlines very powerful evidence that shows the genetic code gradually evolved over time and sometimes been challenged to respond.

The authors only claim evidence which "suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid"“binding sites to become modern codons and anticodons".

The Pixie: had they already tried the smaller ones and found no effect

They write "for seven of eight biological amino acids that have been tested", indicating that those were the ones tested.

ORIGINS OF THE GENETIC CODE: The Escaped Triplet Theory: There is very significant evidence that cognate codons and/or anticodons are unexpectedly frequent in RNA-binding sites for seven of eight biological amino acids that have been tested. This suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid"“binding sites to become modern codons and anticodons. We explicitly show that this stereochemical basis is consistent with subsequent optimization of the code to minimize the effect of coding mistakes on protein structure. These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself.

Any reasonable discussion of abiogenesis has to start with an acknowledgment of what we know with some certainty, including the primary claims of the Theory of Evolution, as well as dispensing with fallacious claims that there is some inherent reason why the genetic code could not *conceivably* evolve.

Comment by Zachriel — January 10, 2008 @ 10:46 am

Bradford Says:
January 10th, 2008 at 11:50 am
There is very significant evidence that cognate codons and/or anticodons are unexpectedly frequent in RNA-binding sites for seven of eight biological amino acids that have been tested. This suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid"“binding sites to become modern codons and anticodons.

What "function" would a codon enable in a binding site prior to the existence of a code that allows for information storage and translation? How would the binding site and the larger protein containing it be synthasized? Where do these amino acids and codons come from and what mechanisms ensure their availability and specificity for imagined functions?

Comment by Bradford — January 10, 2008 @ 11:50 am

Doug Says:
January 10th, 2008 at 1:33 pm
Even if, what is the mechanism that maintains the integrity of the information in the RNA molecule? Allowing it to duplicate its information and pass it onward into future generations?
Even with all of the mechanisms an advanced genome (such as ours) has to prevent a mutational crash…. even we are trending towards genetic entropy - a net accumulation of deleterious mutations.
Even with the machinery to correct errors; compounded with a secure enviroment (housed in the relatively safe confines of a cellular surrounding - or again in our case - cell membrane and nuclear membrane) deleterious mutations are accumulating.

Comment by Doug — January 10, 2008 @ 1:33 pm

Raevmo Says:
January 10th, 2008 at 1:52 pm
Bradford:

What "function" would a codon enable in a binding site prior to the existence of a code that allows for information storage and translation?

Good question. Maybe it would help catalyze the replication of an RNA molecule. That function in itself could be regarded as a "code" and as such represent "information". Of course you prefer the answer "we don't know, therefore goddidit".

Comment by Raevmo — January 10, 2008 @ 1:52 pm

Doug Says:
January 10th, 2008 at 2:04 pm
Of course you prefer the answer "we don't know, therefore goddidit".

Is this sarcasm? If not, I've never seen such a lame response on here from you before.

Comment by Doug — January 10, 2008 @ 2:04 pm

Rob R. Says:
January 10th, 2008 at 2:08 pm
course you prefer the answer "we don't know, therefore goddidit".

Not nearly as intellectually satisfying, I'm sure, as "we don't know, but however it may have happened, goddidn'tdoit." "Most probably, anyway."

But, we all need our hobbies.

Comment by Rob R. — January 10, 2008 @ 2:08 pm

Bradford Says:
January 10th, 2008 at 2:31 pm
What "function" would a codon enable in a binding site prior to the existence of a code that allows for information storage and translation?

Raevmo: Good question. Maybe it would help catalyze the replication of an RNA molecule.

Why is that a likely chemical scenario and why refer to it as a function?

That function in itself could be regarded as a "code" and as such represent "information".

Codes are not catalytic reactions. Biomolecules are represented by other biomolecules in coded systems. The reason you have to use quotes is your lack of comfort with the implications of those words.

Of course you prefer the answer "we don't know, therefore goddidit".

What I prefer is a realistic depiction of what is going on. A self-catalytic reaction is not analogous to the transcription- translation- synthesis mechanisms we observe in real cells. The Escaped Triplet Theory is a nice story. A molecular Houdini but not to be mistaken for sound theory.

Comment by Bradford — January 10, 2008 @ 2:31 pm

MikeGene Says:
January 10th, 2008 at 5:16 pm
Hi Pixie,

The pattern is that the authors only descuss big amino acids, while the Miler-Urey experiment produced mostly small amino acids.

That's clear now that I have illustrated this. Do you know if anyone else noticed this before me?

Is any reason given in the paper for why the authors chose those 8 amino acids (like, had they already tried the smaller ones and found no effect).

Nope. If they tested and found no effect, we'd see more blue dots. The only blue dot is up there among the non-tested. And this reminds me of something. Remember your discussion of predictions in science? One thing you said was, "In real science, a failed prediction should falsify the hypothesis (all else being equal). And the predictions should be bold, that is, they should predict a different outcome to the competing hypotheses."

Why not use your knowledge of abiogenesis to make a bold, differentiating prediction about the remaining unscored 12 amino acids? What color should they be?

I would guess you would see a more significant stereochemical effect is larger amino acids, so that may be why the authors chose those eight (but maybe they only saw the effect in those eight).

So perhaps, just perhaps, this has nothing to do with a non-teleological origin of the Code.

Comment by MikeGene — January 10, 2008 @ 5:16 pm

MikeGene Says:
January 10th, 2008 at 5:25 pm
Hi Zachriel,

The authors only claim evidence which "suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid"“binding sites to become modern codons and anticodons".

Indeed. So it's more like a supported suspicion than powerful evidence.

They write "for seven of eight biological amino acids that have been tested", indicating that those were the ones tested.

So why didn't they test a random sampling?

Any reasonable discussion of abiogenesis has to start with an acknowledgment of what we know with some certainty, including the primary claims of the Theory of Evolution,

Yes, but the evidence for evolution is not evidence for abiogenesis. These are distinct subjects.

as well as dispensing with fallacious claims that there is some inherent reason why the genetic code could not *conceivably* evolve.

Agreed. I do not, and would never argue that the genetic code could not conceivably evolve. This is explained, in depth, in my book.

Comment by MikeGene — January 10, 2008 @ 5:25 pm

0112358 Says:
January 10th, 2008 at 7:10 pm
Mike,

I have a love/hate relationship with science. I hate it because it attempts to provide an explanation of everything, robbing me of a sense of wonder. A butterfly becomes a machine and something to be explained away. . . . I love it because the more it uncovers the more we realize we don't know.

Thanks for the great post.

Comment by 0112358 — January 10, 2008 @ 7:10 pm

Raevmo Says:
January 10th, 2008 at 7:10 pm
Bradford:

What "function" would a codon enable in a binding site prior to the existence of a code that allows for information storage and translation?

Raevmo: Good question. Maybe it would help catalyze the replication of an RNA molecule.

Bradford: Why is that a likely chemical scenario and why refer to it as a function?

Here's what the paper says:

What was the function of these amino acid"“binding structures? One possibility is that they were templates on which activated amino acids were directly ordered for polymerization.
The possibility that the primordial template for coded peptide assembly was an RNA-like oligomer of ordered amino acid"“binding sites is called the DRT (Direct RNA Template) hypothesis (35). DRT is compared with three alternative roles for primordial amino acid"“binding sites in Knight & Landweber (36). Conversely, some coding assignments may have been made by other processes,
although this notion depends on a negative result (cf. Table 1). In particular, the adaptive hypothesis, which suggests that optimization has improved the code's error-minimizing properties, is still plausible given a broad range of amino acids whose coding was predetermined by stereochemistry (Figure 2). In addition, coevolution may have played a role. However, once it is accepted that the code's history records more than one effect (for example, it is stereochemical but evolved along pathways also), uncertainty about the specific pathways to be chosen for partial coevolution makes it difficult to estimate a fraction of the
code potentially attributable to coevolutionary codon assignment (see Coevolution above). Because associations between coding triplets and RNA-binding sites have no meaning until the appearance of an RNA-like molecule, the fact that binding sites
selected from random RNA sequences recapitulate features of the genetic code suggests that these primordial assignments occurred in an RNA world, rather than at a hypothetical earlier stage of evolution. This idea does not rule out the possibility
that short peptides were important in metabolism before the origin of RNA but suggests that such peptides were not encoded by a mechanism resembling the present translation system. Because an RNA world itself implies a fairly complex metabolic repertoire (37), the initial genetic code would not necessarily have been limited to amino acids produced by prebiotic mechanisms. To put this another way, the properties of RNA in the translation system make clear that genetic coding was introduced by our immediate biological progenitors (23, 24), not by ancient ancestors near the origin of life. This idea is reemphasized here in the finding that amino acids with complex
biosyntheses, like tryptophan, histidine, and arginine, were included in the presumably primordial stereochemical core of the genetic code. Amino acids, such as histidine, produced by pathways related to nucleotide metabolism, but not found
in spark-tube experiments, are in fact excellent candidates for inclusion because they interact well with the RNA that must be present. This underscores the notion that the origin of the genetic code is a different and later event than the origin of
life; it employed amino acids that lie at the end of what must have been highly evolved anabolic pathways. These pathways must have evolved before the code, and ribozymes are obvious candidates for their catalysis.

Bradford:

Codes are not catalytic reactions. Biomolecules are represented by other biomolecules in coded systems. The reason you have to use quotes is your lack of comfort with the implications of those words.

Oh, you can read my mind. How impressive. In fact, chemistry as a whole can be regarded as a code that specifies the likelihood of reactions A+B (backandforth) C+D. Same for codon (backandforth) ac, as this paper shows.

[note: I use (backandforth) because I can't use "arrows"]

Bradford:

What I prefer is a realistic depiction of what is going on. A self-catalytic reaction is not analogous to the transcription- translation- synthesis mechanisms we observe in real cells. The Escaped Triplet Theory is a nice story. A molecular Houdini but not to be mistaken for sound theory.

A nice mechanistic story indeed, with testable predictions. What's your mechanistic theory?

Comment by Raevmo — January 10, 2008 @ 7:10 pm

Bradford Says:
January 10th, 2008 at 7:59 pm
Raevmo: In fact, chemistry as a whole can be regarded as a code that specifies the likelihood of reactions A+B (backandforth) C+D. Same for codon (backandforth) ac, as this paper shows.

Chemistry is a code?! Talk about impressive. This does not answer the question I posed. What do you know about nucleotides and ribose that suggests the likelihood of a genetic code arising from their chemical properties. Chemists are precise. Could we have some precision in an answer?

The paper deals in generalities like this:

What was the function of these amino acid"“binding structures? One possibility is that they were templates on which activated amino acids were directly ordered for polymerization.

The term function is used with reference to organizational structures- cells because biological function is understood within the context of survival and replication of cells. What organizational structure would contain amino acid polymers prior to the existence of a code which would make possible orderly synthesis and inheritance?

Then there is this:

In addition, coevolution may have played a role. However, once it is accepted that the code's history records more than one effect (for example, it is stereochemical but evolved along pathways also), uncertainty about the specific pathways to be chosen for partial coevolution makes it difficult to estimate a fraction of the code potentially attributable to coevolutionary codon assignment (see Coevolution above). Because associations between coding triplets and RNA-binding sites have no meaning until the appearance of an RNA-like molecule, the fact that binding sites selected from random RNA sequences recapitulate features of the genetic code suggests that these primordial assignments occurred in an RNA world, rather than at a hypothetical earlier stage of evolution.

Associations between coding triplets and RNA-binding sites have no meaning until the appearance of an RNA-like molecule? They have no meaning unless an encoding convention exists. This is a materialist dog chasing his own tail in a desperate attempt to avoid the teleology inherent in a genetic code. What is the selection criteria that assures us that chemical reactions proceeed to create a genetic code? Why would RNA itself be selected in a sea of molecules indifferent to a cellular outcome? RNA is far from being known for its stability. Why would we presume an RNA soup apart from an attempt to insert chemical causality without the supporting data for it?

A nice mechanistic story indeed, with testable predictions.

This study has been around for awhile. Make my day. Throw some testable predictions out there and specify how they would be tested.

Comment by Bradford — January 10, 2008 @ 7:59 pm

Rock Says:
January 10th, 2008 at 8:20 pm
The very idea of an "error-correcting" code runs deep.

To correct code requires feedback.

I don't think we will ever decode the genetic code until we appreciate the fact that DNA performs operations upon itself (via the products of translation). Feedback. That's the "DNA-code."

DNA X DNA.

Comment by Rock — January 10, 2008 @ 8:20 pm

Raevmo Says:
January 10th, 2008 at 8:24 pm
Bradford:

Chemistry is a code?! Talk about impressive. This does not answer the question I posed. What do you know about nucleotides and ribose that suggests the likelihood of a genetic code arising from their chemical properties. Chemists are precise. Could we have some precision in an answer?

Hahaha. Very rich seeing you complaining about a lack of precision. As if you have ever made a precise (or indeed any) prediction based on ID "theory". But please correct me if I'm wrong. Make your precise prediction right here to prove me wrong.

A prediction from the paper:

This requires storage and duplication of biological information, for which there is no empirical example outside of nucleic acids [although other possibilities are sometimes asserted (51)]. In fact, this prediction can be confirmed by the isolation of a rudimentary RNA replicase ribozyme (52, 53). To progress to nucleoprotein cells from the ribocyte era, the RNA cell must devise translation. Therefore, the four essential reactions of translation must be part of the RNA repertoire. This prediction has been confirmed by the discovery of amino acid"“activating (54), "“aminoacylating (55, 56), peptidyl-transfer RNAs (57), as well as RNAs that retain a residue of the genetic code (23) (see above).

Can you improve on this prediction based on ID "theory"

Comment by Raevmo — January 10, 2008 @ 8:24 pm

Bradford Says:
January 10th, 2008 at 9:08 pm
This requires storage and duplication of biological information, for which there is no empirical example outside of nucleic acids [although other possibilities are sometimes asserted (51)]. In fact, this prediction can be confirmed by the isolation of a rudimentary RNA replicase ribozyme (52, 53). To progress to nucleoprotein cells from the ribocyte era, the RNA cell must devise translation. Therefore, the four essential reactions of translation must be part of the RNA repertoire. This prediction has been confirmed by the discovery of amino acid"“activating (54), "“aminoacylating (55, 56), peptidyl-transfer RNAs (57), as well as RNAs that retain a residue of the genetic code (23) (see above).

You're kidding. Cite RNAs, which owe their existence to intelligent design, and then claim these are evidence of a rudderless process.:lol:

Comment by Bradford — January 10, 2008 @ 9:08 pm

Bradford Says:
January 10th, 2008 at 10:06 pm
Rock:

The very idea of an "error-correcting" code runs deep.

To correct code requires feedback.

I don't think we will ever decode the genetic code until we appreciate the fact that DNA performs operations upon itself (via the products of translation). Feedback. That's the "DNA-code."

DNA X DNA.

My favorite topic Rock. Built in error correction allowing for genomic integrity. Those errors are built into the very nature of nucleic acids IOW, they are inevitable. So how did the road to genomic complexity proceed at the outset when the multiple components needed for feedback and correction could not have been in place? A naturalistic miracle?:shock:

Comment by Bradford — January 10, 2008 @ 10:06 pm

The Pixie Says:
January 11th, 2008 at 5:14 am
Hi Mike

That's clear now that I have illustrated this. Do you know if anyone else noticed this before me?

So when you said "One thing that seemed rather obvious to me was that this list of eight amino acids could have been more varied." you were thinking they could have looked at a small amino acid too? Why not just say that outright? You make it sound as if there are huge gaps that need to be filled in, when this is not actually case.

Why not use your knowledge of abiogenesis to make a bold, differentiating prediction about the remaining unscored 12 amino acids?

Because my knowledge of abiogenesis is pretty minimal. Why no e-mail the authors, and see if they are williing to?

Pix: I would guess you would see a more significant stereochemical effect is larger amino acids, so that may be why the authors chose those eight (but maybe they only saw the effect in those eight).

Mike: So perhaps, just perhaps, this has nothing to do with a non-teleological origin of the Code.

Ceratainly "perhaps". If the pattern was random, they would have a 1 in 32 chance of scoring 7 out of 8, so these results are not exactly emarkable. They do explain the failed point, but that sounds like an after the event rationalisation that modifies the hypothesis, rather than a before the event prediction.

Do you (or anyone) have an electronic copy of the paper? If you do, could you e-mail it to the underscore pix at hotmail dot com?

Comment by The Pixie — January 11, 2008 @ 5:14 am

chunkdz Says:
January 11th, 2008 at 12:09 pm
Doug (to Raevmo)

"I've never seen such a lame response on here from you before."

You must have missed this gem .:smile:

Comment by chunkdz — January 11, 2008 @ 12:09 pm

Doug Says:
January 11th, 2008 at 12:41 pm
Wow. I usually considered Raevmo one of the more level-headed critics. I mean that too. The posts I read from him usually seemed calm and considerate.
When I 1st read his 'goddidit' comment I thought it was sarcasm. Not because the context of the comment hinted at sarcasm, I just never read him reply in such a….. childish manner.
But reading that link you posted is starting to paint a new picture of him.
He can't keep his own emotions in check enough to avoid such pathetic taunts, I would have to doubt his ability to even consider the validity of something that ran contrary to a position that he held prior entering into a discussion.

Comment by Doug — January 11, 2008 @ 12:41 pm

Doug Says:
January 11th, 2008 at 12:44 pm
Bradford, do you still have my email? If so, send me an email please. I keep on losing yours (more accurately, Chase's lotus notes is terrible and information is constantly being lost).
Also, please delete this post after reading.. if you wish.

Comment by Doug — January 11, 2008 @ 12:44 pm

Zachriel Says:
January 11th, 2008 at 1:06 pm
Zachriel: The authors only claim evidence which "suggests …"

MikeGene: Indeed. So it's more like a supported suspicion than powerful evidence.

It's evidence which, in conjunction with other lines of evidence, lends support to the general hypothesis of a spontaneous origin.

Zachriel: Any reasonable discussion of abiogenesis has to start with an acknowledgment of what we know with some certainty, including the primary claims of the Theory of Evolution,

MikeGene: Yes, but …

You may want to discuss that with Kornbelt888.

MikeGene: Yes, but the evidence for evolution is not evidence for abiogenesis. These are distinct subjects.

The Theory of Evolution is distinct from theories of abiogenesis, but the evidence supporting the theory of evolution overlaps that for abiogenesis. Much of the relevant evidence is found in highly derived extant organisms, so we need to have a thorough understanding of evolutionary processes in order to decipher this evidence. Furthermore, evolutionary processes are evident even in the earliest ephochs of life's known history, and there is evidence that these processes are important in even the dimmest periods.

These are some of the primary areas of evidence:

HISTORICAL
* Life did not always exist on Earth, but originated soon after liquid water formed.
* Once life originated, it evolved through a process of evolution and divergence.
* Lines of descent point to a primitive ancestral population.

CHEMICAL
* All life processes have a chemical foundation.
* Macromolecules spontaneously assemble under a variety of conditions.
* Autocatalytic molecules exist in nature and can form from random assemblages of nucleotides.

ABIOGENETIC
* The genetic code is highly resistant to errors relative to random codes consistent with evolutionary selection.
* There is a statistical association between at least some codons and the RNA binding sites for their cognate amino acid.
* Multiple mechanisms for chemical segregation, including spontaneous formation of lipid membranes.

The evolution of the genetic code is still obscure, but there have been significant strides in understanding the relative roles of selection, chemistry and historical processes. Yarus, the author of the abovementioned study, has done some other important work in this area.

Comment by Zachriel — January 11, 2008 @ 1:06 pm

chunkdz Says:
January 11th, 2008 at 1:39 pm
Doug,

"Wow. I usually considered Raevmo one of the more level-headed critics."

To be fair, he did later apologize. Sort of.:grin:

Although I'm not sure if he was apologizing for the Baby Jesus comment or for calling Bradford a "plague on our society."

Comment by chunkdz — January 11, 2008 @ 1:39 pm

Raevmo Says:
January 11th, 2008 at 2:18 pm
Hey, it's not my fault, my monkey genes made me do it!

Comment by Raevmo — January 11, 2008 @ 2:18 pm

Bradford Says:
January 11th, 2008 at 3:29 pm
Raevmo: Hey, it's not my fault, my monkey genes made me do it!

Don't denigrate monkeys with your comparison.:wink:

Comment by Bradford — January 11, 2008 @ 3:29 pm

Bradford Says:
January 11th, 2008 at 3:33 pm
Zachriel: It's evidence which, in conjunction with other lines of evidence, lends support to the general hypothesis of a spontaneous origin.

Sounds like supporting evidence for an ET scenario or for creation. A chemical trail does not convey spontaneity; at least not the complex, multi-stage type that one would expect to see leading to a cell.

Comment by Bradford — January 11, 2008 @ 3:33 pm

Doug Says:
January 11th, 2008 at 5:26 pm
Hey, it's not my fault, my monkey genes made me do it!

Typical, stupid creationist. It's apes!!!! Not monkeys.

Comment by Doug — January 11, 2008 @ 5:26 pm

Bradford Says:
January 11th, 2008 at 6:27 pm
Raevmo: Hey, it's not my fault, my monkey genes made me do it!

Doug: Typical, stupid creationist. It's apes!!!! Not monkeys.

Comment by Bradford — January 11, 2008 @ 6:27 pm

Raevmo Says:
January 11th, 2008 at 6:31 pm
Doug:

Doug: Typical, stupid creationist. It's apes!!!! Not monkeys.

Speak for yourself! I have monkey genes. The ways of the Designer are mysterious.

Comment by Raevmo — January 11, 2008 @ 6:31 pm

MikeGene Says:
January 11th, 2008 at 10:37 pm
Hi Zachriel,

You write:

It's evidence which, in conjunction with other lines of evidence, lends support to the general hypothesis of a spontaneous origin.

Like I said, it's more like supporting a suspicion (your presentation makes it sound more sciencey). Either that, or an elaborate case of confirmation bias.

I would like to thank you for laying out the "primary areas of evidence." Unfortunately, I won't have much time for TT these days, but they should come in handy. I would just point out that the strength of this circumstantial case is probably a function of one's predisposition to embrace spontaneous generation (what you call "strides" look more like epicycles to me). I'd score the strongest piece of evidence as follows:

There is a statistical association between at least some codons and the RNA binding sites for their cognate amino acid.

Yet they didn't test a random sample.

There is no compelling reason to think this is relevant to abiogenesis. But what makes this one stand out is that it poses a problem for the design inference "“ why would a designer have codons and anticodons bind their cognate amino acid?

Answer that question and its all just ducks and rabbits.

Comment by MikeGene — January 11, 2008 @ 10:37 pm

Zachriel Says:
January 11th, 2008 at 11:39 pm
MikeGene: Like I said, it's more like supporting a suspicion (your presentation makes it sound more sciencey).

Well, that's a problem with hypothesis-testing. It's sorta sciencey.

Comment by Zachriel — January 11, 2008 @ 11:39 pm

MikeGene Says:
January 12th, 2008 at 10:27 am
Well, that's a problem with hypothesis-testing. It's sorta sciencey.

Sure, like the hypothesis testing of the wife who suspects cheating. It's hypothesis-testing, but not really science.

But we're supposed to be talking Science here. So why didn't the hypothesis-testing begin with a randomly chosen sample of amino acids?

Furthermore, since you have spent so much time preaching about science, predictions, hypotheses, and testing, why don't you actually do it?

There are 12 amino acids that have not been scored. Why not use the important work of Yarus and your evidence of abiogenesis and propose a hypothesis that predicts how these 12 will score? Remember, a scientific hypothesis should also predict a different outcome to the competing hypotheses, so failed predictions should have meaning, right?

Of course, if you are just trying to sound all sciencey and that, I can understand why you don't want to answer my question or put up a testable hypothesis. But it would seem that those who claim their views are Science and who preach endlessly about the scientific method would be happy to show the way.

Comment by MikeGene — January 12, 2008 @ 10:27 am

Rock Says:
January 12th, 2008 at 1:28 pm
A naturalistic miracle?"”Bradford

LOL Bradford, scoffing at miracles! To me, life is a miracle, Bradford, regardless of the whole "evolutionist/cretinist" thing. I won't be so easily dissuaded from my belief in miracles. These discussions are not going to shake my faith. LOL

As an aside, Bradford (I know its not really topical), but when I wrote that ("DNA X DNA") I reminded myself of Yockey's argument for Crick's "Dogma": Because the forward map is not "one-to-one" and because of irreversible logical operations (deriving one "alphabet" from the other; translation), the Central Dogma is mathematically proved (or supported by communications theory).

http://laplace.compbio.ucsf.ed...

Except that the "Central Dogma" is materially false (LOL It was falsified by Temin and Baltimore in the edition of Nature previous to the one in which it appeared!) and no mathematical argument can save it.

I re-read Yockey's paper and noticed immediately the communications-theoretic equivalent of Haeckel's embryos. Figures 1 & 2 are truncated. The do not accurately depict real world communications systems, which are not linear and unidirectional, but contain feedback.

Yockey finds it a "curious phenomenon" that the introduction of a feedback loop (kinetic proofreading) improves error-correction (in translation) by four orders of magnitude!

Given that result, Dr. Yockey, should you reconsider the previous "Dogma" argument?

Here is the corrected (or extended) theory:

http://citeseer.ist.psu.edu/ma...

(And is prediction a function of data or theory?)

Comment by Rock — January 12, 2008 @ 1:28 pm

Bradford Says:
January 12th, 2008 at 2:13 pm
Rock:

Yockey finds it a "curious phenomenon" that the introduction of a feedback loop (kinetic proofreading) improves error-correction (in translation) by four orders of magnitude!

Given that result, Dr. Yockey, should you reconsider the previous "Dogma" argument?

Yes or risk the suspicion he is ideologically motivated.

Here is the corrected (or extended) theory:

http://citeseer.ist.psu.edu/ma...

(And is prediction a function of data or theory?)

I have to read and reread what you referenced before I feel comfortable framing my thoughts around them. Rock, I've noticed some people claim they have trouble understanding you and some of that may result from your writing style but for what it is worth I think some of your comments reveal a deeply analytical mindset that contrasts sharply with the shallowness of so many others.

Comment by Bradford — January 12, 2008 @ 2:13 pm

Zachriel Says:
January 12th, 2008 at 5:49 pm
The Pixie: Certainly "perhaps". If the pattern was random, they would have a 1 in 32 chance of scoring 7 out of 8, so these results are not exactly remarkable.

Close. They calculated 5.4 x 10^-11 "on the assumption that there was *no* connection between coding triplets and aminoacid binding RNA sequences."

MikeGene: So why didn't the hypothesis-testing begin with a randomly chosen sample of amino acids?

Primarily historical reasons. Because of the strong correlation, it was important to publish with the available data. They plan on testing all twenty. They're currently working on methionine and threonine.

MikeGene: Why not use the important work of Yarus and your evidence of abiogenesis and propose a hypothesis that predicts how these 12 will score?

Stereochemical associations seem the rule rather than the exception. The correlation is very significant, hence we would expect the pattern to continue.

Comment by Zachriel — January 12, 2008 @ 5:49 pm

Bradford Says:
January 12th, 2008 at 6:30 pm
Zachriel: Stereochemical associations seem the rule rather than the exception. The correlation is very significant, hence we would expect the pattern to continue.

How would a correlation lead to an assignment of causality?

Comment by Bradford — January 12, 2008 @ 6:30 pm

Raevmo Says:
January 12th, 2008 at 6:56 pm
Bradford:

How would a correlation lead to an assignment of causality?

Correlation is not causation, but highly correlated with it.

Comment by Raevmo — January 12, 2008 @ 6:56 pm

Bradford Says:
January 12th, 2008 at 7:05 pm
How would a correlation lead to an assignment of causality?

Raevmo: Correlation is not causation, but highly correlated with it.

Thanks for that bit of circumlocution but let me try again. What specifically (if anything) would correlation indicate? Don't know is an acceptable answer.

Comment by Bradford — January 12, 2008 @ 7:05 pm

Raevmo Says:
January 12th, 2008 at 7:26 pm
Bradford:

Thanks for that bit of circumlocution but let me try again. What specifically (if anything) would correlation indicate? Don't know is an acceptable answer.

Well, what do you think? You are the OOL expert around here. You tell us. And you might want to throw in a few testable predictions. I swear I won't publish your hypotheses without proper acknowledgments.

Comment by Raevmo — January 12, 2008 @ 7:26 pm

Bradford Says:
January 12th, 2008 at 7:31 pm
Thanks for that bit of circumlocution but let me try again. What specifically (if anything) would correlation indicate? Don't know is an acceptable answer.

Raevmo: Well, what do you think? You are the OOL expert around here. You tell us. And you might want to throw in a few testable predictions. I swear I won't publish your hypotheses without proper acknowledgments.

Since you're the chemistry expert why don't you at least give us a clue as to a chemical pathway suggested by a codon bias.

Comment by Bradford — January 12, 2008 @ 7:31 pm

Zachriel Says:
January 12th, 2008 at 7:41 pm
Bradford: How would a correlation lead to an assignment of causality?

Untangling causation can often be difficult. That's why, absent a complete understanding, scientists often couch their words with "suggests" or "consistent with" or "strengthens the argument". Generally, the stronger the correlation, the stronger the evidence of some causal link. Continued testing of various aspects of the hypothesis, using different methodologies, can help provide that confidence as well as a greater understanding of the phenomena in question. For example, support for the Theory of Evolution includes evidence from such diverse areas as geology and genetics.

Comment by Zachriel — January 12, 2008 @ 7:41 pm

Raevmo Says:
January 12th, 2008 at 7:41 pm
Bradford:

Since you're the chemistry expert why don't you at least give us a clue as to a chemical pathway suggested by a codon bias.

Why so evasive? This is your chance to be the creative genius behind some novel OOL hypotheses.

BTW, I'm no chemistry expert at all. I took some obligatory biochemistry, organic chemistry and physical chemistry courses that all biology students take. Unfortunately, most of it I've forgotten already.

Comment by Raevmo — January 12, 2008 @ 7:41 pm

hrun Says:
January 13th, 2008 at 11:26 am
I scanned through this thread but could not find an answer to this question: What would possibly be the 'teleological' reason for amino acids having any kind of affinity for their codons or anti-codons. Irrespective of the number of amino-acids tested or number of positives found, why would ANY of the amino-acids show such an affinity?

Comment by hrun — January 13, 2008 @ 11:26 am

MikeGene Says:
January 13th, 2008 at 7:32 pm
Now yer thinkin' like a design theorist! The clues are right in front of our eyes. I'm going to be very, very busy for the time being, so I will have to cut back significantly on this blog. But I'll devote the 51st installment of my web page to following up those clues and try to get it up by the end of the month.

Comment by MikeGene — January 13, 2008 @ 7:32 pm

hrun Says:
January 13th, 2008 at 9:09 pm
Now yer thinkin' like a design theorist!

I hope this was not in response to me. Because if that is the case, then 'design theorists' are in bigger trouble than I thought.

The clues are right in front of our eyes. I'm going to be very, very busy for the time being, so I will have to cut back significantly on this blog. But I'll devote the 51st installment of my web page to following up those clues and try to get it up by the end of the month.

Darn. Patience is required?

Comment by hrun — January 13, 2008 @ 9:09 pm

Rock Says:
January 14th, 2008 at 12:16 pm
Rock, I've noticed some people claim they have trouble understanding you"¦–Bradford

The feeling's mutual, I assure you. Don't let it bother ya. I don't. LOL

I think some of your comments reveal a deeply analytical mindset"¦.

Nah. I'm just BSing, Bradford. Brainstorming. Entertaining my idle mind with interesting puzzles.

You're wrong about me. But you are a creationist and therefore wrong about everything. LOL

Anyway, Bradford, you've got to "Delinearize your Thimking!" You have that part where DNA is "decoded" (transcription-translation) into RNA and protein, but you missed that part where RNA and protein "encode" DNA (reverse transcription-translation). That's a critical part of the error-correcting repertoire, Bradford. You have the basic concept of feedback control, error-correction, and all that fantastic error-correcting machinery of the cell, but you haven't fit it into a system. A system the evident object of which is to generate adaptive variation. (In part by "DNA self-catalysis.")

The widely discussed alternative, Bradford, is that information is encoded into DNA by a "scientific miracle"! By a highly improbable confluence of unintended events. Or what most of us call an "Accident." LOL

I don't see the produstion of RNA and protein from DNA as anything other than an intermediary step in the process.

(And I incorrectly attributed the misleading diagrams to communications theorists, when it is obviously the "systems-thing-to-do." But the mathematicians taught us how to do it, so I blame them. Better yet, I blame the critics! LOL)

Comment by Rock — January 14, 2008 @ 12:16 pm

Bradford Says:
January 14th, 2008 at 3:47 pm
Anyway, Bradford, you've got to "Delinearize your Thimking!" You have that part where DNA is "decoded" (transcription-translation) into RNA and protein, but you missed that part where RNA and protein "encode" DNA (reverse transcription-translation). That's a critical part of the error-correcting repertoire, Bradford.

I'm aware of this Rock. My emphasis is on causes rather than mechanisms because I'm aware that once some find a possible mechanism they can assume causality. Reverse transcription does not solve any of the mysteries inherent in an extra-cellular (or intracellular) chemical trail to error correction.

Comment by Bradford — January 14, 2008 @ 3:47 pm

Rock Says:
January 17th, 2008 at 9:59 pm
Bradford, life forms are not composed of self-replicating molecules. A life form is composition (system) of non-self-replicating molecules. A life form is a reproducible system of irreproducible parts. Fact.

Hypothesis: A "code," "plan," "program," a "design" is required to construct such a system; transforming a collection of irreproducible parts into a reproducible system.

Every one of your critics, Bradford, recognizes the fact. They assume it.

Carefully observe what your critics have to say.

Comment by Rock — January 17, 2008 @ 9:59 pm

Bradford Says:
January 17th, 2008 at 10:56 pm
Rock:

Bradford, life forms are not composed of self-replicating molecules. A life form is composition (system) of non-self-replicating molecules. A life form is a reproducible system of irreproducible parts. Fact.

You're right Rock. You're one of the more knowledgeable commenters at TT and I value your input. You also have a subtle sense of humor which I did not initially recognize.

Comment by Bradford — January 17, 2008 @ 10:56 pm

valerie Says:
January 17th, 2008 at 11:00 pm
A life form is a reproducible system of irreproducible parts. Fact.

Rock,

I don't think that's what you meant to say. In any case, it's not true.

Comment by valerie — January 17, 2008 @ 11:00 pm

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An Interesting Pattern

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