Home » Intelligent Design » Tuning Knobs and Other Features of the Genome

Tuning Knobs and Other Features of the Genome

There is a growing body of experimental knowledge about the evolution of genomes, which shows that decidedly directed forces at work. The genome is best viewed, not as a happenstance gathering of parts, but as a holistic mechanism which functions as a whole. A good summary paper of these sorts of ideas is Mutation is modulated: implications for evolution. While the author does attempt to reconcile this directed view of evolution with Darwinism, ultimately it is the directed mutation, not the reconciliation with Darwinism, which is supported experimentally.

Some interesting points about the genome:

  • Tandem repeats can be used as tuning knobs to quickly and reversibly adjust biological function of genes
  • The vertebrate immune system has “an integrated set of mechanisms that focus mutation at the binding sites of potential antibodies and T-cell receptors” (emphasis mine)
  • Mutation tends to occur at binding sites rather than structural sites, allowing a protein to diversify in a useful way (note to readers — this means the cell must contain intelligence of some sort about which sites are binding sites and which sites are structural sites)
  • A global method of gene regulation exists in methylation. Methylation can be used to tag certain sequences for conservation, variation, and repair, and can also tag transposons to be mobile or non-mobile
  • Bacteria can sample foreign DNA and incorporate it into its genome for adaptation, which process is regulated by stress

This is an area which is just beginning to be explored, and certainly in the coming years we will learn more and more about the way that mutation is modulated.

Where the author goes wrong is in assuming that Darwinistic evolution can account for such evolutionary strategies. The general argument is that the author confuses the difference between whether or not something is “favored by selection”, and whether or not it could be produced without following a higher-order pattern. The assumption present throughout the paper was that anything which would be favored by selection would necessary come into being. The contention of ID is that the search constraints require that a higher-order pattern exist, and cannot be derived in and of itself from a lower-order pattern (for justification, see here and here).

Anyway, it was a fascinating paper (one of several excellent papers by the author). This field is just beginning to see the fruits of the search for directed forms of mutation, and I think in the long run we will get a much, much different view of the genome than what is currently seen and taught.

Caporale, L.H. “Mutation is modulated: implications for evolution”. Bioessays 22(4):388-395.
Kashi, Y. and D.G. King. “Simple sequence repeats as advantageous mutators in evolution”. Trends in Genetics 22(5):253-259.

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22 Responses to Tuning Knobs and Other Features of the Genome

  1. Very interesting article. I have a feeling that johnnyb is going to be a great addition to UD.

  2. I notice that progress like this is impossible without admitting an influence that is in opposition to the forces of entropy and therefore, outside the laws of thermodynamics and hence, pre Big-Bang.

    The origin of the universe and the origin of life would then seem to share the same first cause. I think I shall consider this first cause to be “The Management” or even “The Owner”.

    Now WHO is a science stopper?

    ID is starting to bear fruit. Mmmm. Now that’s good doctrine!

  3. bFast really woke up to some weaknesses in my argument for the relevance of intron behaviour to ID.

    I will certainly recant any suggestions I might have made that introns don’t mutate. Of course they do. But, according to the following paper, they are ‘under less selection pressure’.

    http://genomebiology.com/2006/7/5/R41

    To me, that is the same as saying that they somehow are more resistant to entropy than exons. That is like discovering anti-gravity!

    They are just amino acids, but they are also information. Does information itself inherently posses an enduring quality?

  4. Collin, I think your comment belongs in the “Berlinski on Chomsky…” thread.

  5. Welcome as a contributor johnnyb!

    Directed mutations are in evidence at the organismal level (single organism) in the immune system. Here is a paper by my friend Royal Truman on the topic The Unsuitability of B-Cell Maturation as an Analogy for Neo-Darwinian Theory.

    It’s very reasonble to think that if directed mutations happen at the organismal level that they surely can happen at the population level (directed evolution).

    Caporale (the author of the paper) works in the pharmaceutical industry. Apparently because of the life critical role of her research, her work on the whole seems light years better than what comes out of most evolutionary biologists.

    Salvador

  6. Sal –

    Very interesting! My talk at the BSG conference this week is on V(D)J recombination, and some design-based predictions of function in that system. If you happen to be in Cedarville, Ohio on Friday you could come and listen :)

  7. My point is simply that evolution is bunk. Genomes don’t evolve – they adapt. The complexity of the adaptation mechanisms are sufficient and reasonable proof of design.

    When we include evidence that adaptation is managed in a way that defies the laws of thermodynamics, overcoming entropy istelf, we are getting at evidence of a designer exists simultaneuosly inside and outside of this universe. The topic of this thread even suggests ressurective abilities.

    Acts 17:23-33 to me gives stunning insight to this debate, and the nature of ID. God is not unknown. He is the owner and manager (Lord) of all. We are his offspring. Physical death is reversible, but spiritual death (unbelief) is not.

    My time on Mars’ Hill (place of struggle) coming to some sort of closure. I have learned I can uphold my faith, but also learned that this should not have to be a struggle.

    I also have learned that there is only one place where faith is upheld without struggle. It is in the private place of the mind: the hill (colline) of the skull (du crâne).

    I leave in love, and ask that you reflect on Philippians, chapter 2 verse 1. Thanks very much for your time.

  8. Darn deletion mutations – Philippians – Chapter 2 verse 11.

    Jesus is Lord.

  9. johnnyb,

    Is there a way I can contact you outside of this weblog? I’m trying to figure a way to join in on the fun in Cederville, but if I can’t make it around this time, I’d still be glad to be in touch through other means. I’m hoping 3 of the GMU PhD biology alums will be at the BSG: Gordon Wilson, Tim Brophy, and Timothy Standish. Please give Gordon Wilson my greetings!

    Salvador

  10. Any chance of you giving the citations to the papers, not just the links? I’m getting an error trying to look at the first paper you link to, and because you don’t give the citation, I have no alternative way of finding the paper.

    Thanks!

    Bob

  11. Simple sequence repeats as advantageous mutators in evolution
    Yechezkel Kashi1 and David G. King

    “Concluding remarks
    In a changeable world, long-term stability of fitness is
    found in the adaptive variation that mutability provides.

    Implicit in the genome are many ‘ingenious and unexpected mechanisms’ or ‘protocols’ [53,54], for regulating, modifying and restructuring genetic information with minimal risk to ongoing adaptation.

    The quantitative adjustment and on–off switching provided by site specific mutation of SSRs might be one of the simplest of these protocols, but it might also be one of the most widespread and powerful means of providing genetic variation for evolution.

    This hypothesis raises several questions (Box 4) that should be addressed by direct experiment and comparative analysis of genome sequence data.”

    Ingenious; Having or arising from an inventive or cunning mind; clever.

    Please note. This work in no way supports Intelligent Design.

  12. Ditto that, Bob OH!

    Johnny, could you PLEASE provide a citation for said paper, because I encountered an error as well, and searching on Wiley’s website for keywords “mutation is modulated” produced no matches.

    Many thanks!!

  13. Johnny, regarding post #10, you may want to re-instate your e-mail as “[email protected] (replace “nospam” with “johnnyb”)”.

    This way, spammers who troll the internet for e-mails will not be able to log your e-mail and bombard your butt with their crap.

    See the top page fineprint of Dr. Dembski’s website http://www.designinference.com that deals with permissions-he uses this trick!

    Best regards,

    apollo230

  14. Physical death is reversible, but spiritual death (unbelief) is not.

    And here I thought the good news is that spiritual death (unbelief) is reversible. Perhaps you have it backwards. :)

  15. Thanks for the tip, but I’m very sure my name is already in every spam engine known to man. I’d rather just make it easy for everyone else.

    Anyway, the article should be updated, with an updated link and references at the bottom. Why science paper sites can’t simply put you on a linkable URL is beyond me. Pubmed seems to do it just fine.

  16. Mung,

    “And here I thought the good news is that spiritual death (unbelief) is reversible. Perhaps you have it backwards”

    The only backwards thing around here is a doctrine that encourages belief in Creation, but at the same time steps back from knowledge the Creator. That is simply an altar to an unknown god.

    The spiritual danger here is that ID could easily become the religion of genetic designers who worship themselves and their creations, discouraging belief in the true Creator.

    Scriptures are replete with warnings about this, but I am not here to do anybody’s extremely late homework.

    Doesn’t scripture inform genetic engineers that they were created in God’s likeness? -ds

  17. First of all…
    “Mutation tends to occur at binding sites rather than structural sites, allowing a protein to diversify in a useful way (note to readers — this means the cell must contain intelligence of some sort about which sites are binding sites and which sites are structural sites)”
    –No it doesn’t. The processes are random. That which works persists. That which doesn’t is eliminated. Binding sites are TA rich, meaning they are held together electrochemically less strongly than other regions. That grants them a number of interesting properties, one of which is that they mutate more readily.

    Secondly…
    That Introns mutate at a faster rate is true. that they are under less selection pressure is also true. That has nothing whatsoever to do with Entropy. Geeze. Those regions don’t code for specific amino acids, so the order of nucleotides in them is less significant. If they change it matters less. So, they change more. And, it’s important to note that it is not the case that mutations occur more frequently in those areas. Mutations occur at steady rates. The mutation rate, in this case, applies to the rate of survivial in the species of those mutations. When a mutation causes a deleterious effect, it is rarely around long enough for anyone to know about it or count it up.

  18. ds,

    The notion of ministering to genetic engineers is an excellent idea.

    Thanks

  19. Mung,
    “And here I thought the good news is that spiritual death (unbelief) is reversible. Perhaps you have it backwards”

    Meant to respond earlier… agreed, spiritual “unbelief” is reversible and so to belief. If it were not so, then the seeds would all fall on good ground or pavement. Judgement of Spiritual Death however is final – referred to as the “2nd death” of which those who did not believe are blotted out from the Book of Life.

    Physical death as recorded is reversible. But, once past, it is the passing of an old vessel where a seed was deposited and thru ultimate grace born anew in spiritual form(a higher form) even by those who believe without seeing.

    Collin, evolution worships the creature. True, ID does not state who the designer is, but that is a secular scientific principle that must be met for scholarship in this world. But if I were to make a tent and sell it like Paul and refuse to sell it to those who do not believe, of what profit is it to the House of the Lord? The message is not in ID itself and never was, but in individual testimony and always has been. The casting of the net was a mere realization of trust once the fish were caught. ID cast a large net, a 153 fish does not include all possible fish. Many creationist detest this part of ID. However the body of Christ is made of many parts. Should we do away with one to please the other? Who is to say how the Lord will call his sheep and thru whom will they be called? Each have gifts and are called by the will of the Father even at his timing and his ways, not ours. Is heroin a call? Not by us, but thru Him, all things are possible. Maybe I misunderstood your post, but ID was never my reason to believe. If anyone places their faith on such thin ice(creature design no matter how wonderfully created), they’ll fall thru.

    Dave, I even heard some bulldogs were made in his likeness ;-)

  20. “No it doesn’t. The processes are random. That which works persists. That which doesn’t is eliminated. Binding sites are TA rich, meaning they are held together electrochemically less strongly than other regions. That grants them a number of interesting properties, one of which is that they mutate more readily.”

    Perhaps you should read the paper. Did you also miss the tuning knobs? Other examples of directed mutation:

    http://jb.asm.org/cgi/content/full/182/11/2993
    http://baraminology.blogspot.c.....istic.html
    http://baraminology.blogspot.c.....nesis.html

    Also, there is an element to “randomness” which both isn’t random and is directed. See my comments here:

    http://baraminology.blogspot.c.....rling.html

    Basically, if a mutation is partially specified, then a random search can be a fast way to it.

  21. Michaels7

    “agreed, spiritual “unbelief” is reversible and so to belief. If it were not so, then the seeds would all fall on good ground or pavement”

    Belief is not an intellectual excerise, requiring a constant effort of will. To know your saviour is to accept your salvation. This is a permanent condition, requiring zero effort to maintain.

    Evolution rejects salvation, making it impossible to know your saviour. You cannot have it both ways. Let me draw you a picture:

    Creator Creation
    IE NO NO
    ID NO YES
    Salvation YES YES

    Any questions?

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