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The Sound of the Genetic Code Exploding

Scientists Discover Parallel Codes In Genes

Explosion
“These parallel codes were probably exploited during evolution to allow genes to support a wide range of signals to regulate and modify biological processes in cells.” says Shalev Itzkovitz at The Weizmann Institute of Science.

Not exploding as in destroyed but exploding as in discovery that it’s far from a complete description of how heritable information is encoded in living things. Probably exploited during evolution? How about purposely exploited by an intelligent designer, Shalev. This finding comes as no surprise from a design theoretic point of view. We expected it and much more like it. Several times in the past year (here and here) I wrote about how the genome resembles an NTSC broadcast television signal where multiple independent information channels ride on the same underlying carrier. It’s nice to be right. This is yet another example of the value of presuming life to be the product of intelligent design and thinking like an intelligent design engineer instead of an accidental design biologist.

Scientists Discover Parallel Codes In Genes
Science Daily — Researchers from The Weizmann Institute of Science report the discovery of two new properties of the genetic code. Their work, which appears online in Genome Research, shows that the genetic code — used by organisms as diverse as reef coral, termites, and humans — is nearly optimal for encoding signals of any length in parallel to sequences that code for proteins. In addition, they report that the genetic code is organized so efficiently that when the cellular machinery misses a beat during protein synthesis, the process is promptly halted before energy and resources are wasted.

“Our findings open the possibility that genes can carry additional, currently unknown codes,” explains Dr. Uri Alon, principal investigator on the project. “These findings point at possible selection forces that may have shaped the universal genetic code.”

The genetic code consists of 61 codons–tri-nucleotide sequences of DNA–that encode 20 amino acids, the building blocks of proteins. In addition, three codons signal the cellular machinery to stop protein synthesis after a full-length protein is built.

While the best-known function of genes is to code for proteins, the DNA sequences of genes also harbor signals for folding, organization, regulation, and splicing. These DNA sequences are typically a bit longer: from four to 150 or more nucleotides in length.

Alon and his doctoral student Shalev Itzkovitz compared the real genetic code to alternative, hypothetical genetic codes with equivalent codon-amino acid assignment characteristics. Remarkably, Itzkovitz and Alon showed that the real genetic code was superior to the vast majority of alternative genetic codes in terms of its ability to encode other information in protein-coding genes–such as splice sites, mRNA secondary structure, or regulatory signals.

Itzkovitz and Alon also demonstrated that the real genetic code provides for the quickest incorporation of a stop signal–compared to most of the alternative genetic codes–in cases where protein synthesis has gone amiss (situations that scientists call “frameshift errors”). This helps the cell to conserve its energy and resources.

“We think that the ability to carry parallel codes–or information beyond the amino acid code–may be a side effect of selection for avoiding aberrant protein synthesis,” says Itzkovitz. “These parallel codes were probably exploited during evolution to allow genes to support a wide range of signals to regulate and modify biological processes in cells.”

The results of this study will be useful for researchers seeking to identify DNA sequences that regulate the expression and function of the genome. Many currently known regulatory sequences reside in non-protein-coding regions, but this may give scientists incentive to delve deeper into the protein-coding genes in order to solve life’s mysteries.

Note: This story has been adapted from a news release issued by Cold Spring Harbor Laboratory.

Use the link at the top for the full article.

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21 Responses to The Sound of the Genetic Code Exploding

  1. The finding that this property exists in “reef coral, termites, and humans” which are in different phyla means that the process must have developed before the Cambrian Explosion or else this remarkable feature “evolved” independently several times.

    What are the odds of multiple evolutions? We are talking about some really small numbers approaching the epsilon used in calculus.

    Of course if life is designed, then the probability is close to one that multiple phyla would have it.

    If it is pre Cambrian then it should be in all the members of the phyla in which these organisms belong. What are the odds that such a sophisticated mechanism evolved in the short time before the Cambrian.

  2. jerry,

    “We are talking about some really small numbers approaching the epsilon used in calculus.”

    As someone with an undergradute degree in Mathematics, I have to confess that I found it very helpful to use really big epsilons.

  3. Douglas,

    I was in a Ph.D program in mathematics at one time and we used really small epsilons there.

    I used this expression in a similar way before and want to revise it to how I previously used it. “We are talking about some really small numbers here that make the epsilon used in calculus look huge.”

    But these numbers are probably not small enough for Darwinists or experts like religious professor, Scott Paeth.

  4. As jerry points out above, NDE is put in the position once again of having to explain the “evolution” of more and more complex things, with less and less time available.

    Of course, they could give up, and then start talking about “panspermia”.

  5. PaV,

    We should try to develop a list of all the sophisticated mechanisms that had to be in a pre Cambrian organism. The Hox genes, the eye, this mechanism for parallel coding etc.

    There must be hundreds of complicated systems/genes across phyla that can only be explained by the naturalisitc paradigm if they existed pre-Cambrian in a common organism. And this extremely complicated monster(s) never survived nor left any traces in the fossil record.

    How can they look at each other with a straight face when they discuss things like this? They will probably make up some mechanism such as cross phyla gene transfer as the basis for this appearance of the same systems in different phyla. They are good at making up things. You have to give them credit there.

  6. It sounds to me like this “code” is the same as the neutral substitution issue we discussed. That is, that neutral substitutions are generally not actually neutral because they change protein folds.

    Does anybody recall that discussion? What am I missing?

  7. Nice article DS. We are seeing the tip of the iceberg when it comes to biotic information encoding.

    My additional prediction: when we discover ALL of the different layers of signal, the code won’t be “near” optimal for what it does, it will be optimal. Furthermore, since this optimality will only be operative relative to the ENTIRE set of signals, it will show forethought and foreward selection, further providing confirming evidence for the Design hypothesis.

  8. Jerry:
    What are the odds of multiple evolutions?

    Canned evo response:
    “It happemed so the odds are 1:1.”

    If eyes can “evolve” 20-40 times…

  9. DaveScot:
    Several times in the past year (here and here) I wrote about how the genome resembles an NTSC broadcast television signal where multiple independent information channels ride on the same underlying carrier.

    Contact had the famous “signal within a signal” also.

    Some computer codes also layer information- eg programs running in the background, statements etc.

  10. “As jerry points out above, NDE is put in the position once again of having to explain the “evolution” of more and more complex things, with less and less time available.”- PaV

    Yes, but according to Dawkins, the more complexity in nature, the more complex, and therefore more improbable, the designer!

  11. “…the more complexity in nature, the more complex, and therefore more improbable, the designer!”

    In fact the “designer” is indeed infinitely complex and has no limits. But it isn’t improbable because instead is absolutely certain. Nature itself is the proof that the infinite designer is. Moreover its “infiniteness” and “unlimitedness” grants that it has no “parent” upon it, because there cannot be two infinities (they would limit each other and outside infinity there is nothing).

  12. jerry,

    “I was in a Ph.D program in mathematics at one time and we used really small epsilons there.”

    Well, people who study mathematics are weird.

  13. Well, people who study mathematics are weird.

    No doubt about that!

  14. So sweet.

    Have you heard the joke where there is a man drowning and 2 boats come by to help him, but he refuses their help b/c God will save him. He drowns and goes to heaven and asks God why he didn’t save him and God replies, “I sent you 2 boats!”

    God is sending these people way more than 2 boats, but I guess they’re still missing it.

    I hope I’m alive when we scientists unravel the parallel codes.

    Let’s just add another point to the prb of abiogenesis.

  15. [SLIGHTLY OFF-TOPIC]

    Audi has just released a new TV advert (seen in South African) showing the human body as a series of intricate machines (heart, eyes, DNA etc)and the words ‘Intelligently Designed’ on it followed by the ‘design’ aspect of their cars. I nearly fell off my chair when I saw it! I guess Ad companies are not restricted to the Darwin dogma!!!

    Has anyone else seen it?? I can’t seen to find it posted on the net yet. DaveScot if you’re reading this please mail me (you should be able to get my address off my profile as an Administrator). I think it would make a great new topic.

  16. lucID,

    Obviously, you must be hallucinating, as per your name. ;)

  17. Have you heard the joke where there is a man drowning and 2 boats come by to help him, but he refuses their help b/c God will save him. He drowns and goes to heaven and asks God why he didn’t save him and God replies, “I sent you 2 boats!”

    God is sending these people way more than 2 boats, but I guess they’re still missing it.

    Wasn’t that used in an episode of The West Wing?

    But, if you think about it, isn’t the moral of that little parable that the victim was foolish to turn down the naturalistic offers of help – the boats – that were available and wait for some sort of supernatural aid that wasn’t?

    So, in terms of biology, wouldn’t that mean that we would be foolish to reject the best available naturalistic explanation for the diversity of life – the theory of evolution – even though it’s not perfect, just because some people think it doesn’t allow for God?

  18. “If the mutations prove harmful, some plants in the next generation revert to their grandparents’ DNA sequence with the help of the RNA. “It does make sense,” Pruitt says.

    Such a mechanism would be especially useful to plants that self-pollinate and so are not as genetically variable as other plants. But it might happen in all plants and even animals.”

    This is a big problem, in my thinking, for Darwinism. The overall Darwinian process creates advantages through mutational errors. That system, hypothetically, creates an error-control mechanism which runs counter to the overall mechanism.

  19. Whoops. Wrong thread.

  20. Douglas

    Are you not confusing LSD with Lucid (which had almost a diametrically opposed meaning)????

  21. Hi DaveScot,

    you might be interested in this link (or probably already aware):

    http://www.evolutionnews.org/2......html#more

    it talks about how a different message can be found encoded in DNA when you shift the reading-frame.

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