Tuesday, May 19, 2015

Amino Acid Frequency Correlates With the Number of Codons

An Optimal Code

One of the powerful evidences for evolution is the DNA code, at least according to evolutionists. The DNA code is essentially the same across all of life and, evolutionists explain, there is no reason for such universality. The code is ubiquitous across all life, but it is not special or unique. It is a mundane code, like any other, which just happened to evolve early in evolutionary history. But once in place it could not evolve, so it has been preserved ever since. In other words, the DNA code is the result of contingency, not law. As usual the evolutionary reasoning makes no sense. There is no credible, scientific, explanation for how a code could arise spontaneously in some primitive cell. And if it could not evolve once it was in place, then how could it evolve in the first place? Beyond all this, it certainly is not just another code. For instance, consider Morse code shown below:



The Morse code encodes letters and numbers using short and long signals called “dots” and “dashes.” It was used with telegraph systems in the nineteenth century. The letter codes are shorter for those letters that are used more frequently, such as A, E, I, N and T. This serves to minimize the length of the transmitted message and maximize the information conveyed by the telegraph.

Similarly the DNA code is an optimized code. Unlike the Morse code which is a variable word length code, the DNA code uses a constant word length. Each word consists of three chemical “letters” and the code has four different letters in all. This means there are 4^3 or 64 different words that are possible in this code. Each word codes for an amino acid, but only 20 different amino acids are coded for.

So an amino acid can have more than one code word assigned to it. One way that the DNA code is optimized is by assigning more code words to those amino acids that appear more frequently. This serves to maximize the additional information that can be overlaid on the genetic message.

For instance, if you need to code for an alanine amino acid, then you have four different code words available to you. This choice might encode for some other type of information, such as an overlapping gene. Many DNA segments code for more than one gene, for instance, by reading backwards. Not very mundane. Below is a chart of the DNA code (Lewin, Genes VII). On the right is a graph showing the number of code words for each amino acid plotted against the typical amino acid frequency. You can see that the higher frequency amino acids have more code words assigned to them.



Like the Morse code, the DNA code is optimized to maximize the information conveyed. When evolutionists say the DNA code is powerful evidence for evolution they are manipulating science to support their preconceived truth.

29 comments:

  1. Dr. Hunter,

    Your site very often makes compelling cases for ID. Unfortunately, I think you need to reexamine your facts on this one. The title of your second graph says:


    Figure 7.2
    The number of codons for each amino acid does not correlate closely with its frequency of use in proteins.

    If DNA were just the throw of a dice, those that code 6 different ways should be 6 times as common as those that code only 1 way.

    The most active of the 1s shows as about 2.2 on your chart. The least active of the 6s shows as about 5.5. Your theory should suggest that the highest of the 1s should be less than six times the lowest of the 6s. Instead it is a ration of 2.5 to 1.

    This pattern continues between the 2s and the 6s. The most frequent of the 2s is actually significantly more frequent than the least frequent of the 6s, where it should be less than 1/3 the frequency if the DNA code were to show evidence of intelligence.

    ReplyDelete
    Replies
    1. bFast:

      Let me try explaining it a different way. First, the point of the OP is that the claim that the DNA code is strong evidence for evolution is not backed up by the science (it is a metaphysical claim), and in fact the science shows that the DNA code is evidence against evolution.

      Lewin’s header on that figure states that these two quantities do not “correlate closely”. Similarly, in the text he states “There is only a slight tendency for amino acids that are more common to be represented by more codons, and therefore it does not seem that the genetic code has been optimized with regard to the utilization of amino acids.”

      Both of these are subjective statements. Just as an example, the correlation coefficient for the amino acid frequencies plotted versus the respective number of codons is about 0.7. That is statistically significant (especially in biology!). Evolutionists routinely appeal to such relationships to argue that a pattern is not random, and therefore confirms common descent. There are problems with that argument, but my point merely is that what qualifies as significant for evolutionists seems to depend on how it bears on their theory.

      To downplay the significant of this correlation is misleading. Evolution has no explanation for how it could have arisen (let along a code of any kind). Lewin’s point that “it does not seem that the genetic code has been optimized with regard to the utilization of amino acids” is not very informative. Was he expecting a correlation coefficient of 1? Is that what it takes for evolutionists to admit to a correlation?

      These two quantities (amino acid frequencies and the number of codons assigned to each amino acid) are merely two factors in an enormously complex system. There are all kinds of other influences and constraints at play, that would bear on these factors. For instance, the code has several other functions in addition to transmitting information. One of them is minimizing the effect of transcription and translation errors. This is a completely different problem, that would bring different constraints on the amino acid frequencies versus #codons relationship. Or again, to support the encoding of overlapping genes, it might be necessary for certain amino acids to have more, or less, codons, compared to other amino acids. The same could be said of any of several other functions, such as the tuning of the mRNA transcript stability. Furthermore, the DNA code needs to be implemented by the aminoacyl-tRNA synthetase proteins which bring their own constraints.

      Obviously I’m not making any claims of exactly what these constraints are. I’m merely pointing out that, as usual in biology, structures and processes exist in the context of a complex environment with many mitigating factors. You don’t often get a relationship as obvious as this one, and to downplay it as not significant is just not good science. Of course it is significant.

      If DNA were just the throw of a dice, those that code 6 different ways should be 6 times as common as those that code only 1 way.

      No, if DNA were just the throw of a dice then there would be no genes, no proteins, no DNA code, etc.


      Your theory should suggest that the highest of the 1s should be less than six times the lowest of the 6s. Instead it is a ratio of 2.5 to 1.

      I’m afraid this is the usual evolutionary reasoning of erecting some scientifically unrealistic criterion that must be met for evolution to be in question.

      Delete
    2. I've been able to get a hold of a later version of the textbook - "Genes X".

      In "Genes VII" it says, and I'm quoting your comment above, that:

      "There is only a slight tendency for amino acids that are more common to be represented by more codons, and therefore it does not seem that the genetic code has been optimized with regard to the utilization of amino acids."

      In the later version, "Genes X", it says:

      "In general, amino acids that are more common are represented by more codons. This suggests that there has been some optimization of the genetic code with regards to the utilization of amino acids."

      Thoughts?

      Delete
    3. Interesting, thanks Glenn. I think what you are seeing there is the evolving sentiment from the earlier "proteins are slightly edited random sequences and the genetic code is a frozen accident" to the realization that the code is unique and performs a set of specialized functions simultaneously.

      Delete
  2. If there is one concept in the study of the history of life that points decisively to the conclusion that life was intelligently designed, it is the genetic code.

    A code is an intellectual concept the creation of which requires foresight and planning. It must be able to code for all the various body plans that have ever come into existence. I would say the code would be irreducibly complex.

    Add to that the fact that the code has error correction and is also able to code for two different languages in a given segment of DNA (i.e., proteins and gene control), it becomes almost impossible to claim that the code originated by molecules bumping together.

    Until how the genetic code originated is elucidated, the theory of evolution rests on very shaky ground.

    ReplyDelete
  3. *"You can see that the higher frequency amino acids have more code words assigned to them."*

    Can't tell if my brain just isn't working or whether this is exactly what I would expect if it were random. The more code words assigned to an amino acid would naturally result in that amino acid appearing more frequently would it not?

    ReplyDelete
    Replies
    1. Yes, true, but if the DNA gene sequences were random, then you wouldn't have folding, functional proteins to begin with. Protein sequences are not just some random sequence. For instance, if you randomly substitute in different amino acids, at random locations in a protein, one at a time, the protein function degrades pretty rapidly. It only takes a few percentage substitutions to lose meaningful function. So the assumption is that protein sequences are mostly the way they are for functional reasons, not because of the DNA code.

      On the other hand, if protein sequences were to have a lot of flexibility in their amino acid composition, then yes, the relationship could be explained as the structure of the code driving the protein sequences.

      Delete
    2. So you just agreed that the main point of the OP is incorrect???

      And no, there is quite a lot of redundancy in protein sequences - my "go-to" cytochrome C substitution study demonstrates this quite clearly. No reason to think that other proteins are less redundant.

      Delete
    3. http://www.ncbi.nlm.nih.gov/pubmed/3005287

      Delete
    4. So you just agreed that the main point of the OP is incorrect???

      Yes, I do if, for example, we have good reason to think protein sequences are essentially random. They have been described this way in the past, but the evidence does not support that very well.

      there is quite a lot of redundancy in protein sequences

      I'm not sure what exactly you mean by redundancy, but proteins do not hold up very well under random substitutions, as I mentioned above. I would not characterize that as "a lot of redundancy."

      my "go-to" cytochrome C substitution study demonstrates this quite clearly

      which one was that?

      Delete
    5. So I don't see how the Sherman paper suggests that protein sequences are essentially random. Yes proteins can often sustain a single substitution. They can usually sustain a few substitutions. But function degrades pretty rapidly as you do that.

      Delete
    6. What the paper shows is that there is an incredibly strong correlation between the variation in wild type sequences and the variation allowed in empirical testing. It also shows that much of the protein sequence is redundant.

      As for proteins being random strings of amino acids, that's not what I'm saying; clearly some parts of the sequence are highly conserved and that's not random at all. What I _AM_ saying is that the more codons that code for an amino acid, the more likely that amino acid is likely to occur if the DNA is random. There is no analogy to Morse Code whatsoever.

      Delete
    7. And incidentally, as I've argued before, it is this redundancy that infers common descent and contradicts common design.

      Delete
    8. As for proteins being random strings of amino acids, that's not what I'm saying

      OK, good.


      What I _AM_ saying is that the more codons that code for an amino acid, the more likely that amino acid is likely to occur if the DNA is random.

      OK, but then, according to your own logic, you don’t have a protein.

      Delete
    9. Wow. I do recall that you tried to pull me up once on formal logic, so your response surprises me.

      You are the one claiming an optimisation analogy exists between Morse Code and the codon table. I am saying that no such optimisation exists - that's quite clear in the graph. You need something that's NOT that graph, because the graph roughly reflects the codon frequency *IF* the underlying DNA is random. That's why I was questioning whether my brain was working properly earlier because the entire post seems to be completely upside down.

      This is NOT the same as me saying that proteins are just strings of random DNA - clearly they have a specific function which degrades as you change the sequence, and most random strings of amino acids wouldn't fold into anything. This is not necessarily a function of the relative frequencies of amino acids - that's the point of difference.

      Delete
    10. no such optimisation exists - that's quite clear in the graph.

      http://www.ncbi.nlm.nih.gov/pubmed/3933772
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC60310/


      You need something that's NOT that graph

      The similarity is that both are codes and both reflect the letter frequencies of the messages they encode.

      Delete
    11. Okay, that first citation is one you've used before - it's in French, and it's a one line abstract. Please stop using it if you can't provide a translation and/or an explanation.

      The second one is quite interesting - and I've read it twice this afternoon, and still don't have a good grasp on it. One thing I *CAN* say about the study is that it actually takes into account the DEVIATIONS from the expected frequency. So for example, there are 61 out of 64 codons that can be used, and if a particular amino acid has 6 codons, then you would expect it to make up roughly 9.8% of the sequence. If in practice, it makes up 8.5% of the sequence, then it is that 1.3% difference that is measured in the paper.

      I'm a bit concerned that taking into account the amino acid frequencies is a little bit circular, but I'll need to sleep on it ...

      Delete
    12. I should point out that his first article is from 1985

      Delete
  4. Codon to amino acid map is a formal coded system just like a Morse code is (in a different domain of course).

    I sometimes use Morse during my ham radio contacts. In case of Morse code forward error coding is processed in our minds. For example when receiving English text there is no problem when noise obliterates one or two characters in a word. There is enough information left for mind to fill in missing info.

    There is certainly level of redundancy in codon to AA map. Usually in fixed mapped coded systems redundancy is sign of forward error coding scheme. It's has been couple of years since I read about this so I'll have to refresh the knowledge. Biology prefers to evaporate from my mind.

    ReplyDelete
  5. I learned that over the years there were attmpets to make a universal computer programming language. There was PL/1, ADA, ect. It seems that there are advantages to having a universal code. So maybe there are good design reasons for having a universal genetic code as well. For example if horizontal gene transfer is an important phenomenon then a universal code is required. There needs to be portability across platforms, just like with computer programs.

    ReplyDelete
  6. You need to take account of potential confounding factors that bias distributions away from 'random' expectations. There's no evidence that transition/transversion bias has been taken into account, for example. Fourfold degenerate sites are less susceptible to this than twofold or singlet sites. Over time, this would lead to under-representation of the latter, since these substitutions are not silent. And certain amino acids are just less generally substitutable than others.

    This seems a classic case of a conclusion in search of some supporting data.

    ReplyDelete
    Replies
    1. Good luck getting him to admit this.

      Delete
    2. Allan:

      There's no evidence that transition/transversion bias has been taken into account

      Evolutionists commonly make these sorts of "there's no evidence ..." statement as though they mean something. There's no evidence he has stopped drinking. Ah, haa, very interesting.

      If you are looking for something that has "no evidence," it would be that transitions and transversions created the DNA code. The shell game is to get you to swallow the camel, and pretend that transition/transversion bias is a confounding factor that can explain the code's optimality.

      Delete
  7. Great Post! anybody ever try this amino acid? I would love opinions http://www.amazon.com/Cellucor-Alpha-Amino-Supplement-Count/dp/B00HM9OJFY

    ReplyDelete
  8. Great Post! anybody ever try this amino acid? I would love opinions http://www.amazon.com/Cellucor-Alpha-Amino-Supplement-Count/dp/B00HM9OJFY

    ReplyDelete
  9. very nice article. this blog surely enhance my knowledge. Thank you for sharing. I enjoyed reading.
    Digestive enzymes Canada

    ReplyDelete
  10. Tindakan menggugurkan kandungan adalah keputusan yang sangat sulit , jika anda tidak ada pilihan untuk berdiskusi dengan pelayanan kesehatan atau dokter , Kami menasehatkan untuk membicarakannya dengan teman baik atau anggota keluarga . Apabila anda perempuan yang masih muda , bicarakanlah tentang situs obat aborsi dengan orang tua atau orang dewasa lain yang anda percayai , karena pembicaraan ini lebih penting . Dan bila anda sudah merasa mantap yakin akan menggugurkan dan tidak mempunyai pilihan lain , pelajarlah intruksi-intruksi yang ada di situs ini dulu atau diskusikan dengan teman atau seseorang yang anda percaya . Semoga artikel cara menggugurkan kandungan dengan cepat dan selamat ini dapat membantu mengatasi masalah anda .

    ReplyDelete
  11. This article gives the light in which we can observe the reality. This is very nice one and gives indepth information. Thanks for this nice article.
    jual obat aborsi

    ReplyDelete