Home » Darwinism, Genomics, Intelligent Design » Interactome? Well, remember genome, proteome, old folks home …

Interactome? Well, remember genome, proteome, old folks home …

File:Arabidopsis thaliana.jpg

leafy green lab rat

Old folks home? (For not-quite-dead-enough yet ideas like Darwinism)

From “Clue or Clueless on Plant Evolution” (Creation-Evolution Headlines, August 01, 2011), we learn that, from studies of arabidopsis, the leafy green lab rat,  the interactome is bad news for Darwinism – not that the story in The Scientist quite spells it out:

The protein products of duplicated genes, for example, might be expected to take on different functions, as one can maintain the original task while the other is free to accumulate mutations. But the researchers found that most gene duplicates in Arabidopsis tended to interact with many of the same proteins, even though those duplicates had originated more than 700 million years ago, suggesting that the interactome somehow reduces the freedom of duplicated proteins to diverge

To which Creation-Evolution Headlines replies,

This seems a serious blow to a common notion among evolutionists that duplicated genes comprise raw material for evolutionary innovation. The authors of the paper confirmed the problem: “Whether or not natural selection shapes the evolution of interactome networks remains unclear,” they said, even though gene duplication is considered “a major driving force of evolutionary novelty” among evolutionists, and has been studied in yeast. “However, the difficulty in dating ancient gene duplication events and the low coverage of available protein-protein interaction data sets limit the interpretation of these studies.”

Rest.

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16 Responses to Interactome? Well, remember genome, proteome, old folks home …

  1. For those who are reading Evolution, a View from the 21st Century, by Shapiro, page 30 Genome Formatting for Proper Access to Information would seem to be relevant. Especially
    “The use of repetitive elements to construct transcriptional regulatory circuits reflects two basic functional aspects of biochemical control: etc.

  2. But the researchers found that most gene duplicates in Arabidopsis tended to interact with many of the same proteins, even though those duplicates had originated more than 700 million years ago, suggesting that the interactome somehow reduces the freedom of duplicated proteins to diverge

    Silly creationists. It’s the other duplicated genes that evolve, you know, the ones that take on different functions so the original one can maintain the original task while the other is free to accumulate mutations.

    duh

  3. 3

    Mung,

    Silly creationists.

    Yes indeed.

    How old is the Earth Mung?

  4. You’re a funny sort. You accuse me of not bothering to read what has been written on a topic when you obviously haven’t bothered yourself to read what I’ve written.

    I think the earth is created anew ever planck time.

    So the earth never gets old enough for the question “how old is the Earth Mung” to even be meaningful.

  5. I’m surprised and impressed to see UD mention research that contradicts Behe’s Edge of Evolution stuff. (Of course, I am referring to the results with plant defense proteins, that plainly show how easily new “CCC’s” evolve, and how these newly-evolved “CCC’s” affect the interplay with the biosphere. Very nifty stuff.)

  6. One more pleasant surprise – that UD would mention a study that draws on my own research. (The trail is a bit hard to follow, but it is there, and ends in the Supplemental Materials.)

  7. So Art, are you saying in that we can expect a cure to malaria after only 700 million more years?

  8. Arthur Hunt:

    I’m surprised and impressed to see UD mention research that contradicts Behe’s Edge of Evolution stuff.

    In what way does it do that Arthur?

    Do you have any evidence that duplicated genes are a Darwinian process? Do you have any evidence that dupicated genes followed by protein changing mutations and integration into the existing system is a darwinian process?

  9. Do you have any evidence that duplicated genes are a Darwinian process?

    Yes.

    Do you have any evidence that dupicated genes followed by protein changing mutations and integration into the existing system is a darwinian process?

    ??

    Why would one suspect that the protein product of a newly-duplicated gene would not retain its original “place” in an interaction network?

    The question should be – can the products of duplicated genes bring new functionalities to existing networks? The answer, as I am alluding to, is clearly yes.


  10. Do you have any evidence that duplicated genes are a Darwinian process?

    Arthur Hunt:

    Yes.

    What is that evidence and is it in peer-review?


    Do you have any evidence that dupicated genes followed by protein changing mutations and integration into the existing system is a darwinian process?

    Arthur Hunt:

    ??

    Why would one suspect that the protein product of a newly-duplicated gene would not retain its original “place” in an interaction network?

    Many problems there- First you are assuming that the gene and all the proper binding sites were duplicated. And then that the existing TFs would then get to work to produce that protein at the right time. Also the “place” would be taken by the original, meaning the new protein would be left to diffuse about the cell, ready to attach to some other unsuspecting protein or system.

    Arthur Hunt:

    The question should be – can the products of duplicated genes bring new functionalities to existing networks? The answer, as I am alluding to, is clearly yes.

    Yes, in a designed world. Definitely not in a blind watchmaker world.

    And the question you missed:

    In what way does this contradict Behe’s edge of evolution?

  11. Joseph:

    Many problems there- First you are assuming that the gene and all the proper binding sites were duplicated.,

    I’m not sure that’s correct. If a gene that causes a protein to be created is duplicated then the binding sites are already present. They don’t need to be duplicated themselves for the proteins created by the duplicated gene to bind as the binding sites from the “original” gene continue to exist.

    Or have I misunderstood your point?

  12. Hi Elsie,

    I am talking about the DNA binding sites for the gene- the DNA sequence that transcription factors bind to in order to promote or repress experession.

    It isn’t part of the gene. And without regulation what have you?

    Also the duplicated gene has to wind up in a part of the strand that is accessible- not part of the inside of histone spool.

  13. I am talking about the DNA binding sites for the gene- the DNA sequence that transcription factors bind to in order to promote or repress experession.

    It isn’t part of the gene.

    That’s just plain silly.

    Next, people will be claiming that UTRs aren’t parts of genes. Or introns. Or, well, gee, what have we got left?

    The fact is, gene duplication necessarily and inevitably will involve duplication of the whole kit and kaboodle, promoter, untranslated parts of the primary transcript, all of the regulatory sites in the promoters and RNA (including all of the miRNA target sites), all of the original protein sequence (including all of the protein interaction domains, catalytic residues, etc.), everything.

    If we don’t understand this, them I’m afraid an intelligent discussion of gene duplication, networks, etc. is going to be pretty difficult.

  14. Introns are not part of genes :)

    By the way, James Shapiro says of genes:

    Why and How to Avoid Using the Term Gene

    Throughout the book, the term “gene” appears in quotation marks to indicate its hypothetical nature. The term has no rigorous and consistent definition. It has been used to designate countless different features of genome organization. In other words, the use of “gene” gives the false impression of specifying a definite entity when, in fact, it can mean any number of different genomic components.

    In some cases, such as when “gene” is used to indicate a continuous human DNA sequence encoding a specific protein, it actually means something that has no real existence in nature. This is because the genomic DNA coding regions usually comprise several separated exons and are only joined at the level of the RNA transcript. In place of “gene,” therefore, the term coding sequence indicates DNA regions that determine protein primary structure, in keeping with the contemporary use of CDS to indicate protein-encoding regions in genome sequence annotations. Moreover, the term genetic locus is preferable, because it indicates a discrete identifiable region of the genome, including signals formatting transcription and post-transcriptional processing, that encodes one or more messenger RNA molecules, which in turn encode one or more specific protein products. The reason for this preference is that a genetic locus can be defined operationally by either genetic or molecular analysis, and the two-word phrase does not carry the same theoretical and confusing implications s the multifarious term “gene.”

    See also:

    Scientists and Philosophers Find That ‘Gene’ Has a Multitude of Meanings


  15. I am talking about the DNA binding sites for the gene- the DNA sequence that transcription factors bind to in order to promote or repress experession.

    It isn’t part of the gene.

    Arthur Hunt:

    That’s just plain silly.

    Next, people will be claiming that UTRs aren’t parts of genes. Or introns. Or, well, gee, what have we got left?

    That’s just plain dumb.

    Promoters are located near the genes but are not part of the gene (typically upstream->5′)

    Silencers and enhancers can be thousands of base-pairs away from the gene they control

    Gene- starts with the START codon and ends with the STOP codon. The binding sites are not between the start and stop, hence they are not part of the gene.

    If you don’t understand that, then I’m afraid an intelligent discussion of gene duplication, networks, etc. is going to be pretty difficult. :razz:

    Arthur Hunt:

    The fact is, gene duplication necessarily and inevitably will involve duplication of the whole kit and kaboodle, promoter, untranslated parts of the primary transcript, all of the regulatory sites in the promoters and RNA (including all of the miRNA target sites), all of the original protein sequence (including all of the protein interaction domains, catalytic residues, etc.), everything.

    And there is evidence for this- that it happens like that 100% of the time?

    And the fact is even if you are right (doubtful) all you are getting is more of a protein you already have.

    And you still don’t have any evidence it was via darwinian processes.

  16. BTW I say introns are part of a gene- a very important part and also very good evidence for Intelligent Design-> alternative gene splicing requires knowledge, knowledge of what to splice, how to splice, when to splice, how to edit, what to edit-> what exons get spliced together and how, with all the proof-reading and error-correction, geez it’s a wonder that any biologist can still hold a darwinian or neo-darwinian PoV.

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