'Junk DNA' Cornell Conference

Open Mike: Cornell OBI Conference Chapter 11—Not Junk After All—Conclusion

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Biological Information

To facilitate discussion, we are publishing the abstracts and conclusions/summaries/Introduction excerpts of the 24 papers from the Cornell Conference on the Origin of Biological Information here at Uncommon Descent, with cumulative links to previous papers at the bottom of each page. You can get from anywhere to anywhere in the system.

Note: A blow-by-blow account of the difficulties that the authors experienced from Darwin lobby attempts to censor the book by denying it publication with Springer are detailed here. Fortunately, the uproar resulted in an opportunity for readers like yourself to read the book online. That said, the hard cover version is now shipping.

The Conclusion for “Not Junk After All” by Jonathan Wells:

The concept of information as applied to a linear sequence — such as letters in an English sentence or nucleotides in a DNA molecule — has been extensively analyzed [133-143]. Although protein-coding DNA constitutes less than 2% of the human genome, the amount of such information in such DNA is enormous. Recent discoveries of multiple overlapping functions in non-protein-coding DNA show that the biological information in the genome far exceeds that in the protein coding regions alone.

Yet biological information is not limited to the genome. Even at the level of gene expression — transcription and translation — the cell must access information that is not encoded in DNA. Many different RNAs can be generated from a single piece of DNA by alternative splicing, and although some splicing codes occur in intronic DNA there is no empirical justification for assuming that all of the information for tissue- and developmental-stage-specific alternative splicing resides in DNA. Furthermore, even after RNA has specified the amino acid sequence of a protein, additional information is needed: Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149].

Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152].

So non-protein-coding regions of DNA that some previously regarded as “junk”turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life. More.

See also: Origin of Biological Information conference: Its goals

Open Mike: Origin of Biological Information conference: Origin of life studies flatlined

Open Mike: Cornell OBI Conference— Can you answer these conundrums about information?

Open Mike: Cornell OBI Conference—Is a new definition of information needed for biology? (Chapter 2)

Open Mike: Cornell OBI Conference—New definition of information proposed: Universal Information (Chapter 2)

Open Mike: Cornell OBI Conference—Chapter Three, Dembski, Ewert, and Marks on the true cost of a successful search

Open Mike: Cornell OBI Conference—Chapter Three on the true cost of a successful search—Conservation of information

Open Mike: Cornell OBI Conference—Chapter Four: Pragmatic Information

Open Mike: Cornell OBI Conference—Chapter Four, Pragmatic information: Conclusion

Open Mike: Cornell OBI Conference Chapter Five Abstract

Open Mike: Cornell OBI Conference Chapter Five – Basener on limits of chaos – Conclusion

Open Mike: Cornell OBI Conference Chapter Six – Ewert et all on the Tierra evolution program – Abstract

Open Mike: Cornell OBI Conference Chapter Six – Ewert et all on the Tierra evolution program – Conclusion

Open Mike: Cornell OBI Conference Chapter 7—Probability of Beneficial Mutation— Abstract

Open Mike: Cornell OBI Conference Chapter 7—Probability of Beneficial Mutation— Conclusion

Open Mike: Cornell OBI Conference Chapter 8—Entropy, Evolution and Open Systems—Abstract

Open Mike: Cornell OBI Conference Chapter 8—Entropy, Evolution and Open Systems—Conclusion

Open Mike: Cornell OBI Conference Chapter 9—Information and Thermodynamics in Living Systems—Abstract

Open Mike: Cornell OBI Conference Chapter 9—Information and Thermodynamics in Living Systems—Conclusion

Open Mike: Cornell OBI Conference Chapter 10—Biological Information and Genetic Theory: Introductory Comments—Abstract

Open Mike: Cornell OBI Conference Chapter 10—Biological Information and Genetic Theory: Introductory Comments— Excerpt

Open Mike: Cornell OBI Conference Chapter 11—Not Junk After All—Abstract

13 Replies to “Open Mike: Cornell OBI Conference Chapter 11—Not Junk After All—Conclusion

  1. 1
    Mung says:

    One genome’s junk is another genome’s evolutionary treasure.

  2. 2
    drc466 says:

    Wait til somebody figures out to examine DNA for compression, encryption, and RAID-type redundancy…

  3. 3
    Mung says:

    My copy has shipped!

  4. 4
    AVS says:

    “the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]”

    Can someone with the full text please point me to whatever “144-147” is please.

  5. 5
    AVS says:

    Yeah, I’m pretty sure that statement is completely wrong. Which leads me to believe this just another bogus-science, fact-twisting load of crap.Why am I not surprised?
    They can’t even get the basic stuff right, and I thought you guys might have been on to something. Ha, yeah right.

  6. 6
    wd400 says:

    AVS,

    The same amino acid sequence can fold differently – that’s what a prion is, after all. That’s not to say it’s a widespread phenomenon, or really relevant to the discussion in that passage.

  7. 7
    AVS says:

    Ha, no don’t try and bail him out. That’s such bullshit. Protein folding is dependent on amino acid sequence. One sequence forms one protein. Prion proteins force correctly folded proteins into a different conformation.

  8. 8
    wd400 says:

    I have no desire bail someone as hopelessly wrong as Wells out. But it’s just true that proteins can switch fold, and that’s been known for some time.

    Influenza Haemagglutinin is one such protein – physiological changes caused by infection make it partially unfold, revealing a functional domain that is usually in the core of the protein.

    Wells is wrong about the big picture, but he’s not wrong to say some protein can switch folds.

  9. 9
    AVS says:

    No. That is not an example of a different fold. That is an example of a conformational change in the protein. That is what proteins do, they change shape while retaining the same overall fold. You do not know what you are talking about. What he said is that a single amino acid sequence can form various proteins and he is wrong. This alone gets your whole book thrown in the trash.

  10. 10
    wd400 says:

    Check out the structures, and note that the protein actually partly unfolds before snapping into the new stable form:

    http://www.rcsb.org/pdb/101/motm.do?momID=76

  11. 11
    AVS says:

    I think youre confused about protein folding terminology. It is a change in conformation that activates the protein and results in virus infection. This is what every paper says on it, heres the first one:
    “The hemagglutinin of influenza virus undergoes a conformational change at low pH, which results in exposure of a hydrophobic segment of the molecule, crucial to expression of viral fusion activity.”

    Conformation changes keep 99% of the protein fold intact while specific domains are swung into new positions by loop regions.

  12. 12
    wd400 says:

    I’m fairly confident I know which of us is confused here. why don’t you download the paper, which is open access, and read the cited sources. Or indeed, some that aren’t.

  13. 13
    Joe says:

    wd400:

    The same amino acid sequence can fold differently …

    Or not fold at all, that is why genetic engineering has been a failure outside of the little advantages such as insulin production.

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