Bradfords Hammer

Posted: December 30, 2007 in Intelligent Design

elephant.jpg

Bradford over at Telic thoughts wields the hammer and hits the nails squarely on the head:

He says :

‘He mentioned how struck he was by the reaction of biologists to the genetic code. They (and others) act as if this were an ordinary biological feature. It is far from it. The Big Bang and quantum physics get the attention of philosophers while the genetic code flies under philosophical radar. A symbolic molecular coding system is presumed to be a consequence of unobserved chemical reactions. But why? Because we find parallel results in chemistry? No, that’s not it. There are vague references to complexity arising. But the type of complexity cited (crystals for example) is of a different nature. All of this leads me to believe a philosophical predilection underlies which lens we choose to view data through. If the lens orients one to a telic perspective it is not likely to see the light of day.

When Darwinians challenge IDers to come up with some empirical results that strikes me as a strange demand. The empirical data is being churned out every day in labs all across the world.

Excellent point. Data is neutral with respect to where it comes from. Whether researchers believe in ID or oppose it the data remains the same.’

I am in complete agreement with the above statement,the data is there -there are no exclusively naturalistic empirical driven scenarios for how we got to the complexity of structure and function including the systems we see in place for maintaining fidelity of the message; that we find in the genome. Just as there are no exclusively naturalistic empirically driven scenarios for the cause of Hoyle’s distasteful ‘Big bang’ , that is why the field is wide open for interpretation.

History teaches that a consensus is not to be trusted, another bus will be along shortly. I read again and again that Intelligent design is dead ,yet not one piece of evidence is brought to the table to demonstrate its demise,while the big elephant in the room everyone is ignoring remains to be explained,where did this complexity and diversity we have recently and unexpectedly uncovered originate ?

Is it naive to expect the data to always lead and our ideas to meekly follow ?Are we unsullied by metaphysics and so free to see the data as it is ? The big invisible elephant suggests otherwise.

 

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Comments
  1. Alden says:

    I agree. There is, I believe, no known case where information did not arise from an existing intelligence. You may be able to argue that some limited order or complexity can arise out of chaos (although I would argue that this, too, points to design), but not information (or intelligence, for that matter). Therefore, a conclusion that the information in DNA arose apart from intelligence is not based on any known scientific theory but seems to fall into the category of faith. In other words, a “science of the gaps” approach. A consistent approach to genetic information would seem to point to a preexisting intelligence of some sort.

  2. Art says:

    What Bradford isn’t telling you is that there is interesting (even compelling) positive experimental evidence indicating that the genetic code has a definite chemical underpinning. This sort of dashes the assertion that

    “A symbolic molecular coding system is presumed to be a consequence of unobserved chemical reactions. But why? Because we find parallel results in chemistry? No, that’s not it.”

    Fact is, the “chemical reactions” that are the basis of the genetic code are observed and observable.

    A good place to start for more on this subject:

    http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.74.082803.133119

  3. Mike Godfrey says:

    Hi Alden and Art,
    thanks for visiting the site and commenting.
    Im in the middle of a week long internet downtime-troubles at the ISP -Im at an internet cafe -so limited comments for now.
    Alden Im with you regarding the origin of information-as the resolution of what is involved in transcription/translation is increased and we find more and more complexity in the system -insistance on chance or necessity as a cause for the complexity we see, seems a faith position, forced on the believer by the fact that design is unthinkable for no other reason than metaphysics-how scientific is that ?
    Art there’s a very interesting chapter regarding the chemical basis of DNA and redundancy in Simon Conways Morris’s book ‘Life’s Solution: Inevitable Humans in a Lonely Universe’
    so that transcription mistakes mistakes are most likely to lead to amino acids that code for similar ie hydrophilic or hydrophobic amino acids to those originally intended by the DNA code causing the least damage to the protein the amino acids are part of.
    This redundancy and safeguard indicates to me design rather than chance, as the possibilities of getting the optimal DNA -Amino acid coding by another means than design are extremly rare.
    check out this post:https://fluorescentflicker.wordpress.com/2006/05/16/one-in-a-million/

  4. Mike Godfrey says:

    Art,
    I’ve seen this article by Mike Gene regarding the paper you cited :Yarus M, Caporaso JG, Knight R. Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem. 2005;74:179-98.

    Check out this paper in response :
    http://www.idthink.net/biot/aminocode/index.html

  5. Art says:

    Hi Mike,

    Sorry about being slow in responding.

    Mike Gene’s discussion of Yarus et al. is strained and confusing. It’s obvious that he will not accept that the positive evidence for an underlying stereochemical basis for the genetic code is strong. I don’t understand why he would point to experiments not done as a way to argue against this. But that is what he is doing. Makes no sense to me.

    One other thing I noticed about Mike Gene’s essay – he totally misses the reason why those amino acids mentioned by Yarus et al. were the ones that were tested for affinities with codons and anticodons. I’ll be coy for now and point you to Fig. 1 in Majerfeld and Yarus (Nat. Struct Biol. 1, 287-292, 1994). Think about it a bit and you’ll see that Mike Gene has pretty much missed the boat in his remarks.

    I’ll try to be more prompt in keeping up my end of the discussion.

  6. Art, let’s assume for the sake of argument that there is a correlation between codons and amino acids evidenced in tRNAs for the twenty conventional amino acids discussed. Let’s further grant the presumption that there are chemical properties of tRNA (and all other elements of the biological processes enabling protein synthesis) which make the translation function possible. How does this indicate that the specific causal process, leading to the generation of the translation cellular function (or cells for that matter) was devoid of intelligent input?

  7. Art says:

    Bradford, Yarus’ work refutes a common, oft-repeated, and WRONG claim – that the genetic code is arbitrary and has no chemical basis. The ID vanguard makes this claim, you make it. And it’s wrong.

    As for the proposition that the establishment of the genetic code via chemical means is “devoid of intelligent input”, I find your question to be meaningless. That the genetic code has an underlying stereochemical basis does not speak to “underlying intelligent input”, any more than it speaks to the possibility that we’re all living in some orbital of a giant plutonium atom, or that all of existence is just a fleeting and fanciful figment of my imagination. It tells us how the genetic code came about, and establishes some conditions that the future development of life are constrained by.

    People like you see design anywhere and everywhere. There’s not much that can be said or done about this, except to point out that your musings are entirely without scientific support (scientific meaning supported by controlled and repeatable experiments). There’s no reason for anyone to pay attention, let alone try and refute, any and all of the unsupported assertions that you make. When “intelligent input” gets to the point where it’s a (even wildly unlikely) scientific hypothesis, then we can visit the matter. As it stands now, it’s just another way for you to avoid the science.

    Sorry for being blunt. But that’s how things are.

  8. Art: Bradford, Yarus’ work refutes a common, oft-repeated, and WRONG claim – that the genetic code is arbitrary and has no chemical basis.

    Of course there is a chemical interaction of biochemical components that can be explained by referencing common well known concepts of basic chemistry. That is not to be confused with a chemical explanation outlining a causal trail accounting for the biological function of translation. You are confusing a predominance of a biochemical component with refutation of arbitriness which holds that the relations currently existing between tRNAs and amino acids are chemically determinsitic from a causal perspective. Are they the only relations that are chemically plausible? No.

    As for the proposition that the establishment of the genetic code via chemical means is “devoid of intelligent input”, I find your question to be meaningless.

    Of course you do. You are determined to eliminate the possibility in the absence of conclusive evidence supporting your belief.

    That the genetic code has an underlying stereochemical basis does not speak to “underlying intelligent input”, any more than it speaks to the possibility that we’re all living in some orbital of a giant plutonium atom, or that all of existence is just a fleeting and fanciful figment of my imagination. It tells us how the genetic code came about, and establishes some conditions that the future development of life are constrained by.

    It does not tell us how the genetic code came about. Showing the chemical properties of components does nothing to illustrate the process. If this were not so you would point to a study that has an initial starting point of no code and ends with a demonstration of one coming about through a series of precisely delineated reactions.

    People like you see design anywhere and everywhere.

    If I did I might be right and unless you are in a position to show me empirical evidence ruling out design at a pre-Big Bang point in the causal chain. But why should you or anyone else even want to go there since these issues are ultimately reducible to philosophical assumptions. Darwin did not rule out teleology when he proposed a natural selection concept. He merely proposed an explanation that did not require an intelligent agency at the point wherein a biologically self-sustaining self-replicator already existed. He did not explore or even attempt to explore the origin of underlying reductionist forces we refer to by laws of physics. Why would you think design was obviated by Darwin? The Paley refutation is itself a myth.

  9. Art says:

    Bradford, I find your latest attempt to dismiss the significance of Yarus et al. to be especially feeble. Of course, much of what you say is pretty confusing, so it may be the way you are presenting things.

    You said: “Of course there is a chemical interaction of biochemical components that can be explained by referencing common well known concepts of basic chemistry.”

    LOL. What “common well-known concepts of basic chemistry”, presumably taught in Chem101 in community colleges throughout the land, teach the concept that “UUY = phe” is a commonly-held notion? IMO, you’re just pulling arguments out of thin air to try and refute the basic refutation of your position (remember, “A symbolic molecular coding system is presumed to be a consequence of unobserved chemical reactions. But why? Because we find parallel results in chemistry? No, that’s not it. “) Fact is, we do have an interesting underlying stereochemical basis for the genetic code, and your attempts to confuse the issue with obtuse reference to “common knowledge” that is not at all common fall far short of rescuing your mistake.

    You also said: “That is not to be confused with a chemical explanation outlining a causal trail accounting for the biological function of translation.”

    But the results we are talking do begin to define a “causal trail”. That’s anathema to you and your ilk, I know. This is, I suspect, why you try to confuse matters in debate (with endless reference to experiments not done), rather than explore the ramifications of these positive experimental results. And why MikeGene also hides behind the experiment not done, rather than pause and look into the matter more thoroughly and critically.

    You also said: “You are confusing a predominance of a biochemical component with refutation of arbitriness which holds that the relations currently existing between tRNAs and amino acids are chemically determinsitic from a causal perspective. Are they the only relations that are chemically plausible? No.”

    Pardon the frankness, but this is gobbledygook. The fact is, the genetic code is not an arbitrary construct of some unknowable intelligence. It is a manifestation of the interactions between amino acid and RNA. It has an underlying chemical basis. Get over it.

    You later say: “It does not tell us how the genetic code came about. “

    Absolutely wrong.

    To be sure, Yarus et al. have not incubated a primordial singularity in a test tube and obtained the universe (this is the only “evidence’ I know you will accept, and even then you will resort to the “Creationist Uncertainty Principle”). But their results are a positive answer to one piece of the puzzle. Any scenario for the origins of the genetic code must account for these results.

    (I realize that it really, really bothers the telic thinkers that the RNA World is so spectacularly supported by these results. It’s revealing that this crew cannot get past this.)

    “Showing the chemical properties of components does nothing to illustrate the process.”

    Again, completely false.

    “If this were not so you would point to a study that has an initial starting point of no code and ends with a demonstration of one coming about through a series of precisely delineated reactions.”

    Ah yes, the experiment not done refutes positive experimental data. I’ll admit that this reasoning is foreign to me.

    Why should I be able to point to such a study? How many people work on OOL questions in the lab? How many experiments have been done? What would be the scope or scale of a study such as you imagine has been done?

    Science is about hypothesize, test using controlled and repeatable experiment, revise. Part of the process is to devise a hypothesis that is amenable to testing. It usually brings us to a better understanding of “big picture” things, not by reproducing each and every detail of a long and drawn out process in one fell swoop, but by breaking down things into manageable and focused questions. Yarus et al. does this. End of story.

    Bradford, I’ll note that you are unable to call upon any positive experimental results that contradict the conclusions of Yarus et al. I’ll also note that, when it comes to the OOL, the positive case has a litany of positive (if limited and focused) positive results that support their position and guides ongoing research. The deniers have zero positive support. (Another foreign concept to me – deniers keep insisting that zero, the quantity of supporting data for their position – is greater than the hundreds (or more) of positive experimental results that contradict their claims. I missed that lecture in math class.)

    A suggestion – when you get over your reflexive reaction to the RNA World, then you will really begin to make progress in understanding the OOL. Even from a design perspective. Until then, you’ll continue to make claims like “0 is greater than 1000”. That ain’t gonna take you anywhere.

  10. Mike Godfrey says:

    Hi Art,
    Thanks for your references and replies; it’s been a while since I did any Biochemistry so I’ve had to revisit the concepts behind these ideas.
    One thing I miss is the luxury of being able to download an article from the academic journals; as it stands I can only view the abstract, I can view the diagram you mentioned from Yarus-roll on open source!
    Regarding the short article by Mike Gene, I think he is trying to suggest that, yes there is binding between some codons or anticodons and amino acids, but that the basis for that binding is not as simple as stereochemistry alone, other factor(s) are involved, one that explains the patterns he outlines.
    He says:
    ‘It is not clear that we should conclude “stereochemical associations seem the rule.” From these data alone, we might alternatively conclude that stereochemical associations occur among a distinct and clustered subset of amino acids.’

    He also points to other problems with the OOL scenario that of production of amino acids within the supposed scenario of a prebiotic environment via the miller Urey experiment; this produced only two of the binding amino acids, according to Gene.
    Of course this could be a limitation with Urey’s experiment-but I don’t know what that limitation could be. Apart from the assumptions of the experiment for a reducing prebiotic atmosphere, which have been criticised by geochemists –Miller has stated:

    ‘“Either you have a reducing atmosphere, or you’re not going to have the organic compounds required for life.”

    Art you said in reply to Bradford:

    ‘People like you see design anywhere and everywhere. There’s not much that can be said or done about this, except to point out that your musings are entirely without scientific support (scientific meaning supported by controlled and repeatable experiments).’

    I think the folks at Telic thoughts-of which Bradford is a part and Mike Gene is prominent, are not apt to find design in every case –they allow for natural causes but view the sum of these causes as unable to explain the complexity and breadth of responses organism demonstrate.
    We all come to science with a prior metaphysical assumptions, and I have mine, you have yours; with my assumptions I find it not unreasonable to state that the control of one molecule by another such that a meaningful code would emerge seems a bridge too far. –stereochemistry alone does not produce a code with administrative read write access
    ID maverick David Berlinski writes regarding OOL:

    ‘The question, of course, is which of the two steps came first. Without life acquiring some degree of foresight, neither step can be plausibly fixed in place by means of any schedule of selective advantages. How could an ancestral form of RNA have acquired the ability to code for various amino acids before coding was useful? But then again, why should “ribozymes in an RNA world,” as the molecular biologists Paul Schimmel and Shana O.Kelley ask, “have expedited their own obsolescence?”

  11. Art says:

    Hi Mike,
    I realize that it may be hard to get ahold of the figure I pointed to above, so I thought I would summarize the figure and what it means vis-a-vis our discussion here.
    Briefly, the figure was an illustration of the method used to isolate amino acid-binding RNAs. What is relevant here is that the amino acid in question is linked, via a somewhat lengthy linker, to a solid matrix. Moreover, for most amino acids, the pools of RNAs are “scrubbed” with just immobilized linker and with immobilized glycine (which explains why glycine does not appear in the collection of amino acids that have been studied). This is done to remove RNAs that bind the linker, or the peptide bond.
    A consequence of this approach is that there is a possibility that small amino acids will not present enough novel chemical signature to allow the method to work. Naively, if the amino acid is considerably smaller than the linker, it may be hard or impossible to use this approach to find RNAs that bind the small amino acid.
    So what does this mean as far as Mike Gene’s attempt to dismiss these studies? Mike Gene imagines a “pattern”, and concocts reasons why the pattern argues against the obvious conclusion. But the pattern has nothing to do with some biases on the parts of OOL researchers, an inability of Urey-Miller amino acids to bind RNAs, or anything else. It is just a reflection of the technical limitations of the experiment. Nothing more.
    So, it turns out that Mike Gene has no basis for saying “It is not clear that we should conclude “stereochemical associations seem the rule.”” He has jumped on the experiment not done and leapt to a very wrong conclusion.
    The facts are these – 11/12 amino acids tested preferentially bind RNAs that have cognate codons or anticodons. This includes 100% of tested Urey-Miller amino acids. Clearly, stereochemical associations that link amino acid with either codon or anticodon are the rule. The overwhelming rule. (The fact that at least one amino acid does not seem to be governed by this rule is also interesting, but it doesn’t dispel the other positive results. Indeed, it speaks to an evolution of an incipient genetic code in the RNA World. Which is why telic thinkers are so adamantly opposed to this sort of research.)
    Of course, these considerations also lay to rest Berlinski’s objections. (At least, once one brings into the discussion the effects that co-factors have on chemically-active RNA species.)

  12. Art: “You also said: “That is not to be confused with a chemical explanation outlining a causal trail accounting for the biological function of translation.”

    But the results we are talking do begin to define a “causal trail”. That’s anathema to you and your ilk, I know. This is, I suspect, why you try to confuse matters in debate (with endless reference to experiments not done), rather than explore the ramifications of these positive experimental results. And why MikeGene also hides behind the experiment not done, rather than pause and look into the matter more thoroughly and critically.”

    Art, claiming that a causal trail is anethema to me is indicative of the emotion that clouds your judgement. If this is the begining of the trail then the entire trail needs mapping out and the end of it should back up what you believe to be true. The fact is such a trail does not exist. We do not see a set of conditions in which tRNAs and other elements of tranlation arise in extra-cellular envirnments. The study you cite is claimed as the begining of a tral leading to that outcome but until the trail actually does lead to the outcome you are left with your personal beliefs and your faith in an undemonstrable outcome.

  13. Art, have you read the ‘Design Matrix’? Mike mentioned your name et. al. along with his appreciation of “stimulating questions, commentary, and/or kind words.”

  14. Guts says:

    Art wrote:

    “The facts are these – 11/12 amino acids tested preferentially bind RNAs that have cognate codons or anticodons. ”

    Over at Art’s blog, he is now saying it’s 6/8

    “This includes 100% of tested Urey-Miller amino acids.”

    1/2 , Ile but not Leu

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