Saturday, November 19, 2016

The DNA Code and Evolution

My Dear Watson

The DNA code is used in cells to translate a sequence of nucleotides into a sequence of amino acids, which then make up a protein. In the past fifty years we have learned four important things about the code:

1. The DNA code is universal. There are minor variations scattered about, but the same canonical code is found across the species.

2. The DNA code is special. The DNA is not just some random, off the shelf, code. It has unique properties, for example that make the translation process more robust to mutations. The code has been called “one in a million,” but it probably is even more special than that. For instance, one study found that the code optimizes “a combination of several different functions simultaneously.”

3. Some of the special properties of the DNA code only rarely confer benefit. Many of the code’s special properties deal with rare mutation events. If such properties could arise via random mutation in an individual organism, their benefit would not be common.

4. The DNA code’s fitness landscape has dependencies on the DNA coding sequences and so favors stasis. Changes in the DNA code may well wreak havoc as the DNA coding sequences are suddenly not interpreted correctly. So the fitness landscape, at any given location in the code design space, is not only rugged but often is a local minimum, thus freezing evolution at that code.

Observation #1 above, according to evolutionary theory, means that the code is the ultimate homology and must have been present in the last universal common ancestor (LUCA). There was essentially zero evolution of the code allowed over the course of billions of years.

This code stasis can be understood, from an evolutionary perspective, using Observation #4. Given the many dependencies on the DNA coding sequences, the code can be understood to be at a local minimum and so impossible to evolve.

Hence Francis Crick’s characterization, and subsequent promotion by later evolutionists, of the code as a “frozen accident.” Somehow the code arose, but was then strongly maintained and unevolvable.

But then there is Observation #2.

The code has been found not to be mundane, but special. This falsified the “frozen accident” characterization, as the code is clearly not an accident. It also caused a monumental problem. While evolutionists could understand Observation #1, the universality of the code, as a consequence of the code being at a fitness local minimum, Observation #2 tells us that the code would not have just luckily been constructed at its present design.

If evolution somehow created a code to begin with, it would be at some random starting point. Evolution would have no a priori knowledge of the fitness landscape. There is a large number of possible codes, so it would be incredibly lucky for evolution’s starting point to be anywhere near the special, canonical code we observe today. There would be an enormous evolutionary distance to travel between an initial random starting point, and the code we observe.

And yet there is not even so much as a trace of such a monumental evolutionary process. This would be an incredible convergence. In biology, when we see convergence, we usually also see variety. The mammalian and cephalopod eyes are considered to be convergent, but they also have fundamental differences. And in other species, there are all kinds of different vision systems. The idea that the universal DNA code is the result of convergence would be very suspect. Why are there no other canonical codes found? Why are there not more variants of the code? To have that much evolutionary distance covered, and converge with that level of precision would very strange.

And of course, in addition to this strange absence of any evidence of such a monumental evolutionary process, there is the problem described above with evolving the code to begin with. The code’s fitness landscape is rugged and loaded with many local minima. Making much progress at all in evolving the code would be difficult.

But then there is Observation #3.

Not only do we not see traces of the required monumental process of evolving the code across a great distance, and not only would this process be almost immediately halted by the many local minima in the fitness landscape, but what fitness improvements could actually be realized would not likely be selected for because said improvements rarely actually confer there benefit.

While these problems obviously are daunting, we have so far taken yet another tremendous problem for granted: the creation of the initial code, as a starting point.

We have discussed above the many problems with evolving today’s canonical code from some starting point, all the while allowing for such a starting point simply to magically appear. But that, alone, is a big problem for evolution. The evolution of any code, even a simple code, from no code, is a tremendous problem.

Finally, a possible explanation for these several and significant problems to the evolution of the DNA code is the hypothesis that the code did not actually evolve so much as construct. Just as the right sequence of amino acids will inevitably fold into a functional protein, so too perhaps the DNA code simply is the consequence of biochemical interactions and reactions. In this sense the code would not evolve from random mutations, but rather would be inevitable. In that case, there would be no lengthy evolutionary pathway to traverse.

Now I don’t want to give the impression that this hypothesis is mature or fleshed out. It is extremely speculative.

But there is another, more significant, problem with this hypothesis: It is not evolution.

If true this hypothesis would confirm design. In other words, a chemically determined pathway, which as such is written into the very fabric of matter and nature’s laws, would not only be profound but teleological. The DNA code would be built into biochemistry.

And given Observation #2, it is a very special, unique, detailed, code that would be built into biochemistry. It would not merely be a mundane code that happened to be enabled or determined by biochemistry, but essentially an optimized code.

Long live Aristotle.

The problem is there simply is no free lunch. Evolutionists can try to avoid the science, but there it is.

32 comments:

  1. There is up to a 10 million dollar offer to anyone that can demonstrate that a code can arise via stochastic processes. And it is very telling that no one has collected it.

    Technology Prize for Origin of Information


    Only intelligent agencies are capable of producing codes...

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  2. As Bill Gates has noted, "DNA is like a computer program, but far, far more advanced than any software we've ever created."

    ReplyDelete
    Replies
    1. Complexity does not require intelligence to form. Some day creationists will realize that simple fact.

      Delete
    2. No one said that mere complexity requires intelligence. Dembski and others have said the opposite. Someday you will stop attacking your cartoon version of ID.

      Delete
  3. It's encouraging to see CH offer a hypothesis.

    What about the next step - constructing tests to support the hypothesis (or not?). What would such tests look like CH?

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    Replies
    1. Yes, we try to find some way that physics and chemistry can account for a code and all the physical means to carry it out. I don't know if anyone is working on it though. No one seems interested in testing the claims of evolutionism.

      We already know that intelligent agencies can produce codes. To our knowledge the only way that codes arise is via intelligent agency intervention.

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    2. Joe G

      To our knowledge the only way that codes arise is via intelligent agency intervention.


      That is demonstrably false. Codes that use arbitrary symbols as abstractions to map inputs to outputs require an intelligence but the genetic code doesn't use arbitrary symbols as abstractions in its mapping. There are plenty of well known natural non-intelligent processes that follow physical laws to map inputs to outputs. Things like the climate information encoded in tree rings, the spectral data encoded in starlight, and the morphological information encoded in DNA.

      Hopefully this post won't vanish too.

      Delete
    3. Ghostrider:
      That is demonstrably false.

      If that were true then you could win 10 million dollars.

      Codes that use arbitrary symbols as abstractions to map inputs to outputs require an intelligence but the genetic code doesn't use arbitrary symbols as abstractions in its mapping.

      Of course it does. RNA codons represent amino acids they do not become them. It is as arbitrary as Morse Code. Even biochemist Larry Moran admits to that. He thinks nature can do it but he hasn't a clue how. http://sandwalk.blogspot.com/2007/02/real-genetic-code.html

      The genetic code, as with ALL codes, is arbitrary with RNA codons representing amino acids. Biology 101.

      Thank you for proving your ignorance on the matter.

      Things like the climate information encoded in tree rings,

      LoL! Tree rings are not a code.

      Buy a vowel...

      Delete
    4. Joke G

      If that were true then you could win 10 million dollars.


      LOL! Creationists sure love their phony "challenges", don't they? I bet you fell for Kent Hovind's phony $250K "prove evolution" challenge too.

      Of course it does. RNA codons represent amino acids they do not become them. It is as arbitrary as Morse Code.

      If the mapping is arbitrary then show how any codon can produce any arbitrary amino acid. Or better yet, make a codon sequence out of TinkerToys and see if it produces a TinkerToy protein.

      Joke fails Science 101 yet again. :)

      Delete
    5. It isn't a phony challenge and only a coward would say that it was.

      If the mapping is arbitrary then show how any codon can produce any arbitrary amino acid.

      That isn't what arbitrary means in this case. It is arbitrary in that it isn't determined by any laws nor is it necessary to be the way it is.

      The arbitrariness of the genetic code

      Delete
    6. Joke G

      It isn't a phony challenge


      Only a moron Creationist would think that phony "challenge" was above board.

      "If the mapping is arbitrary then show how any codon can produce any arbitrary amino acid."

      That isn't what arbitrary means in this case


      It's exactly what "arbitrary" means when talking about using arbitrary symbols as abstractions in a designed code Joke. As always your attempts to pull your foot out of your mouth by digging up an unrelated paper fail miserably.

      Delete
    7. The onus is on the coward claiming the challenge to be phony. I cannot prove a negative

      If the mapping is arbitrary then show how any codon can produce any arbitrary amino acid.

      It isn't mine to change, duh. However it is arbitrary in that it is not determined by any law. There isn't any physio-chemical reason the code has to be the way it is.

      Read a biology book on the subject- google is also your friend.

      AGAIN: The arbitrariness of the genetic code:

      Abstract

      The genetic code has been regarded as arbitrary in the sense that the codon-amino acid assignments could be different than they actually are. This general idea has been spelled out differently by previous, often rather implicit accounts of arbitrariness. They have drawn on the frozen accident theory, on evolutionary contingency, on alternative causal pathways, and on the absence of direct stereochemical interactions between codons and amino acids. It has also been suggested that the arbitrariness of the genetic code justifies attributing semantic information to macromolecules, notably to DNA. I argue that these accounts of arbitrariness are unsatisfactory. I propose that the code is arbitrary in the sense of Jacques Monod's concept of chemical arbitrariness: the genetic code is arbitrary in that any codon requires certain chemical and structural properties to specify a particular amino acid, but these properties are not required in virtue of a principle of chemistry. This notion of arbitrariness is compatible with several recent hypotheses about code evolution. I maintain that the code's chemical arbitrariness is neither sufficient nor necessary for attributing semantic information to nucleic acids.

      And yes the mRNA codon is a symbol representing the amino acid output.

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    8. Here is another article that supports my claim: Code Biology:

      The genetic code

      In protein synthesis, a sequence of nucleotides is translated into a sequence of amino acids, and the bridge between them is realized by a third type of molecules, called transfer-RNAs, that act as adaptors and perform two distinct operations: at one site they recognize groups of three nucleotides, called codons, and at another site they receive amino acids from enzymes called aminoacyl-tRNA-synthetases. The key point is that there is no deterministic link between codons and amino acids since it has been shown that any codon can be associated with any amino acid (Schimmel 1987; Schimmel et al. 1993). Hou and Schimmel (1988), for example, introduced two extra nucleotides in a tRNA and found that that the resulting tRNA was carrying a different amino acid. This proved that the number of possible connections between codons and amino acids is potentially unlimited, and only the selection of a small set of adaptors can ensure a specific mapping. This is the genetic code: a fixed set of rules between nucleic acids and amino acids that are implemented by adaptors. In protein synthesis, in conclusion, we find all the three essential components of a code: (1) two independents worlds of molecules (nucleotides and amino acids), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed.


      Two for me and still zero for you

      Delete
    9. I missed this piece of unsupported whining:

      As always your attempts to pull your foot out of your mouth by digging up an unrelated paper fail miserably.

      The paper refutes you. Is that why you claim it is unrelated? Or are you too stupid to understand what it says?

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    10. LOL! Joke the moron still doesn't get that if you can't make any existing mRNA map through any known tRNA to create any known amino acid with the existing rules of chemistry and physics then the mapping isn't arbitrary. Certain combinations work Joke, most other combinations don't. Linking to IDiot websites with their unsupported claims doesn't help you Joke, any more than citing Behe, Axe, or Meyer helps your ID-Creationist claims.

      How are you coming with that codon to protein using TinkerToys? If it's all arbitrary then why can't you demonstrate it? Joke fails again.

      Delete
    11. that if you can't make any existing mRNA map through any known tRNA to create any known amino acid with the existing rules of chemistry and physics then the mapping isn't arbitrary.

      Please support your claim with some academic reference. I have supported my claim with two.

      How are you coming with that codon to protein using TinkerToys?

      Strawman at best and most likely a red herring.

      Why do you think that you can just pull something from your arse and it means something?

      If it's all arbitrary then why can't you demonstrate it?

      I told you why it is arbitrary and provided two references to support my claim.

      Just because "certain combinations work" doesn't make it any less arbitrary than Morse code.

      The whole reason for Crick's "frozen accident" as an explanation for the genetic code is due to its arbitrary nature. There isn't any known law nor any force that determines what codon represents which amino acid.

      That is the definition of arbitrary with respect to the genetic code.

      So please either support your claims with something other than your own spewage or admit that you are ignorant of the subject.

      Delete
    12. BTW, arbitrary means that the existing rules of chemistry and physics don't apply- just as they don't apply to Morse code.

      mRNA map through any known tRNA to create any known amino acid

      So in your world the tRNA creates the amino acid? Really?

      with the existing rules of chemistry and physics

      They don't apply in an arbitrary situation.

      What definition of "arbitrary" are you using and why?

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    13. Joke G

      Please support your claim with some academic reference. I have supported my claim with two.


      LOL! Sorry Joke but an ID-Creationist website making unsupported claims isn't an academic reference.

      Where's that TinkerToy protein you formed from some TinkerToy DNA? Looks like Mr. "it's all arbitrary!!" fell on his face again. :D

      Delete
    14. Joke G

      BTW, arbitrary means that the existing rules of chemistry and physics don't apply-


      LOL! Go ahead Joke. Tell us how you'd go about changing the existing laws of chemistry and physics. In the world of non-IDiots all reactions obey those physical laws.

      Delete
    15. OK, seeing that you won't support your claims as I have- then please tell us what determined the pairings- what determined which mRNA codon corresponds to its amino acid? If you can't say then it is clear the pairings are arbitrary.

      BTW there is no need to change any existing laws because they have nothing to do with the genetic code. It's as if you are proud of your ignorance

      Delete
    16. So ghostrider thinks tat tRNAs create amino acids-> they don't.

      It also thinks that the genetic code is governed by the laws of physics and chemistry-> It isn't and that is what makes it arbitrary. And that proves GR doesn't understand the meaning of the word "arbitrary".

      And finally this - The arbitrariness of the genetic code- is a peer-reviewed article and no amount of cowardly whining will ever change that.

      And to top it off the moron thinks its strawman/ red herring is an actual argument!

      Where's that TinkerToy protein you formed from some TinkerToy DNA?

      Please make your case as to why you think that is relevant. I dare you to try. If you can't then just admit that you are an ignorant troll.

      Delete
    17. Ghostrider: If the mapping is arbitrary then show how any codon can produce any arbitrary amino acid. Or better yet, make a codon sequence out of TinkerToys and see if it produces a TinkerToy protein.

      Wikipwdia:
      Expanded genetic codes (synthetic biology)[edit]
      Main article: Expanded genetic code
      See also: Nucleic acid analogues
      Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins.[71] [72]

      H. Murakami and M. Sisido have extended some codons to have four and five bases. Steven A. Benner constructed a functional 65th (in vivo) codon

      Xie J, Schultz PG (Dec 2005). "Adding amino acids to the genetic repertoire". Current Opinion in Chemical Biology. 9 (6): 548–54. doi:10.1016/j.cbpa.2005.10.011. PMID 16260173.
      Jump up ^ Wang Q, Parrish AR, Wang L (Mar 2009). "Expanding the genetic code for biological studies". Chemistry & Biology. 16 (3): 323–36. doi:10.1016/j.chembiol.2009.03.001. PMC 2696486Freely accessible. PMID 19318213.


      Fullfil this data your requirements?

      Delete
  4. 4. The DNA code’s fitness landscape has dependencies on the DNA coding sequences and so favors stasis. "Changes in the DNA code may well wreak havoc as the DNA coding sequences are suddenly not interpreted correctly. So the fitness landscape, at any given location in the code design space, is not only rugged but often is a local minimum, thus freezing evolution at that code."

    Population genetics dealt with this issue decades ago. Your point may be true if there wasn't genetic variation within a population.

    Yes, the nature of DNA has likely not changed in billions of years. But there has certainly been extensive change in the order of base pairs and genes along the DNA strands.

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  5. WS
    "Population genetics dealt with this issue decades ago. Your point may be true if there wasn't genetic variation within a population. "

    I think CH is talking about the constraint on the variation due to population genetics. Variation is there it is just minimized due to the fitness landscape.

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  6. Why did I have three posts vanish?

    ReplyDelete
    Replies
    1. Google figured out you were fake news...

      Delete
    2. Everything apparently runs in threes. I had three disappear as well. That seems to be a common behaviour of moderators at ID sites.

      Delete
  7. "More fake news."

    What part was fake? The part where I pointed out that DNA is not universal, just global? Or the part where I pointed out that if DNA is the only game in town that it must have unique properties? Or the part where I pointed out that most mutations are detrimental? Although, in re-reading your OP, I admit that my latter point did not really address your OP.

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    1. Your response to #4 is fake news. While evolutionists now attempt to contrive these sorts of explanations, years agoe before the code's special properties were fully appreciated, evolutionists understood and agreed that evolving the code was problematic.

      Oh how incredible it would be if the normal levels of genetic variation somehow aligned with the code's evolutionary changes.

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    2. "Your response to #4 is fake news."

      Nice assertion. Yet, you allowed that one to be posted and not the other three.

      But let's examine your false assertion. Yes, before knowledge of mutations, and other sources of available variation, were understood, the evolutionists were stumped. But guess what? The scientists kept working on it and found these sources. Maybe IDists should try the same approach. Actually do some research.

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    3. Nice assertion. Yet, you allowed that one to be posted and not the other three.

      Sorry, Darwin's God had nothing to do with whatever happened to your comments.

      Delete