Tuesday, September 16, 2014

Making New Genes Just Got More Exotic—Yes They Evolve, But How?

Gene Duplication Meets Epigenetics

Making new genes is not easy. For several decades now it has been thought that the only process for gene construction is to start by duplicating an existing gene and then making adjustments to it (it is not the only process, but that is another story). Naturally evolutionists interpreted this duplication process as another example of an evolutionary mechanism. What they don’t consider, however, is how subtle this process is.

Too often the origins debate focuses on the simplistic opposites of stasis and change. Evolutionists would have it that creationism and Intelligent Design require complete stasis in the biological world—no changing of the species. Any change that is discovered, such as the construction of new genes, is interpreted as yet another proof text of evolution.

But why? Why should we think that adaptation to the environment immediately implies random mutations, natural selection, common descent, a strictly blind naturalistic origin of the world via chance, and so forth?

It simply doesn’t follow. In fact, research has consistently shown that the species have a fantastically complicated built-in adaptation capability. Organisms respond rapidly to environmental challenges with directed changes, not slowly with blind, random changes.

As research continues, this story just continues to grow. For instance, regarding the construction of new genes via duplication of an existing gene, a recent study added yet another layer of incredible subtlety and nuance. It turns out that after a duplication event, the organism often labels one of the genes, as though marking it for change. The technical term for this is “epigenetics,” and it amounts to small chemicals being attached to either the gene or to the proteins about which the gene is wrapped. This chemical “barcode” technology is fantastic, as it involves several different chemicals, each conveying a different message, and the message varies depending on just where the chemical is attached. The chemicals can even be attached to other small chemicals that were previously attached.

So the question is not, “Do organisms change and adapt?” It would be silly to make that the test for the truth of blind, random evolution.

There is no question that organisms adapt. And so there is no question that species undergo evolution in the sense that they respond and change. But evolution can be a loaded term. For most of us, evolutionists included, “evolution” automatically means the undirected origins of, well, pretty much everything.

That simply is not what the science shows. The science shows that the species adapt via fantastically exotic, creative and nuanced processes. Perhaps all of this arose from an undirected origins, but that would call for an enormous serendipity. In other words, it would mean that the incredible processes by which evolution occurs were, themselves, created by evolution. That would be highly serendipitous.

We need to stick to what the evidence tells us, and be careful not to make unwarranted claims beyond the evidence.


  1. Shorter version: Cornelius Hunter actually does accept that it is reasonable to think that natural evolutionary processes can and do produce at least some new genes. Too bad for Stephen Meyer's no-new-information-ever-except-from-intelligence argument!

    1. NickM, that knife cuts both ways.
      In a recent post, "When I Pointed Out the De Novo Gene Evidence an Evolutionist Came Unglued" I challenged you as follows:

      NickM, " So I guess you are agreeing that most genes could evolve naturally. Therefore I was right to say the origin of new genes is a solved problem."

      Huh? Most genes ..., therefore those genes that are not "most" are a solved problem. How logical is that?!

      You didn't respond.

      You say "... can and do produce at least some..." But CH continues to challenge with examples that appear to be beyond the reach of natural processes.

      Whose theory is the most vulnerable here. If a gene is found to be the product of natural processes does it blow ID out of the water, or if a gene is found which could not with any conceivable probability have been produced by natural processes, which the naturalistic hypothesis be blown out of the water?

    2. NickM:

      From the paper:

      Remarkably, for a majority of duplicate gene pairs, a specific duplicate partner is consistently hypo- or hypermethylated across highly divergent tissues. Our results indicate that epigenetic modifications are intimately involved in the regulation and maintenance of duplicate genes.

    3. Dr. Hunter, I fail to see how this can be classified as a genuinely 'new' gene in that it is merely the duplication, and subsequent stability, (with perhaps modest modification) of a pre-existing sequence. ,,, I'm sure you are well aware of the search space problem for finding functional sequences.

      Stephen Meyer (and Doug Axe) Critique Richard Dawkins's "Mount Improbable" Illustration - video

      Thus why did you say a 'new' gene evolved? For ID proponents, a genuinely new gene, from an existing gene, would entail traversing that vast sequence space to a brand new sequence (which even immunity responses can't do). ,,, The example you cite fits much more easily into Dr. Shapiro's falsification of the modern synthesis of neo-Darwinism than it does to the claim that a 'new' gene evolved.

      Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009
      Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).

      Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigenetic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.

      Revisiting Evolution in the 21st Century - James A. Shapiro, PhD - video

      How life changes itself: the Read-Write (RW) genome. - 2013
      Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

    4. ba77:

      Thank you for your posts and great citations.

      Thus why did you say a 'new' gene evolved? For ID proponents, a genuinely new gene, from an existing gene, would entail traversing that vast sequence space to a brand new sequence

      Good question. I think that "new" is a tricky concept. What if you created a computer program that processed and analyzed a large amount of data, and discovered some very simple trends in the data that otherwise were not visible or apparent? Is the program's output "new"? It was not in the program, and not explicitly in the raw data. You could argue that the output is "new," even though the obviously it derives from the data and the software algorithm.

      Likewise information is a tricky concept. Shannon gave us a pretty simple definition (and probably the most useful). But using letter frequencies, or letter pair frequencies, it says next to nothing about the actual information in a sentence, as we normally understand the word.

      I'm simply saying there are subtleties here, and these are not clear cut, simple concepts.

      So consider a physiological response of an organism, or an epigenetic response of a population. We understand the mechanisms somewhat. They, in combination with the environment, create something "new" in the organism. I can understand the concern that using the word "evolution" for this is too confusing, because it suggests RM+NS creating the world. But I think, properly understood, "evolution" may be the best term for these examples, and likewise, for the "new" gene that arises.

      Evolutionists can continue to extrapolate on all of this, and think that evolution does create everything. But that is not a fact. It is not even supported by the evidence.

      I think evolutionists really need to reckon with this, and avoid the over reach they have repeatedly done. But OTH, I think we need to avoid putting unnecessary stakes in the ground, like fixity of species (I know we're not doing that these days, but it is a good historical example), or that structures that are "new" in some sense cannot arise. Why can't something new arise? Given all the data that are pouring in from the environment, and the incredible built-in processing power, one would expect something "new," in most senses of the word.

      I think the subtlety of the problem here is in this built-in processing power. Newton figured out a way to explain how the solar system worked. It was brilliant, but he realized his explanation did not account for how the solar system *arose*. Operation is different than origin. In biology, operation includes adaptation. But adaptation does not account for how the thing arose.

      Make sense?

    5. Dr. Hunter, as far as molecular biology is concerned, I disagree that Shannon gave us 'the most useful' definition of information.

      The Evolution-Lobby’s Useless Definition of Biological Information - Feb. 2010
      Excerpt: By wrongly implying that Shannon information is the only “sense used by information theorists,” the NCSE avoids answering more difficult questions like how the information in biological systems becomes functional, or in its own words, “useful.”,,,Since biology is based upon functional information, Darwin-skeptics are interested in the far more important question of, Does neo-Darwinism explain how new functional biological information arises?

      Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors
      Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

      Mathematically Defining Functional Information In Molecular Biology - Kirk Durston - video

      Measuring the functional sequence complexity of proteins - Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors - 2007
      Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,,
      Programming of Life - Information - Shannon, Functional & Prescriptive – video

      Dr. Don Johnson explains the difference between Shannon Information and Prescriptive Information, as well as explaining 'the cybernetic cut', in this following Podcast:

      Programming of Life - Dr. Donald Johnson interviewed by Casey Luskin - audio podcast
      The GS (genetic selection) Principle – David L. Abel – 2009
      Excerpt: The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.”

  2. Evolution by Gene Duplication Falsified - December 2010
    Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.


    Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution - 21 February 2013
    We suggest that the overall trends of gene emergence are more compatible with a de novo evolution model for orphan genes than a general duplication-divergence model. Hence de novo evolution of genes appears to have occurred continuously throughout evolutionary time and should therefore be considered as a general mechanism for the emergence of new gene functions.

    Yup, Orphan genes (comprising 10 to 30% of every new genome sequenced, including humans) can now just ‘poof’ into existence. That whole evolutionary model of functional sequences being selected for in small increments is no good anymore. Need a new gene? Just call on ‘de novo evolution’ to do your dirty work.

    Orphan Genes (And the peer reviewed 'non-answer' from Darwinists) - video

  3. Heh, strife amongst the creationists? Say it ain't so!

    1. Nick:

      Serious question for you. Feel free to defer if this is too personal, but my question is: Are you a Christian? I'm not looking for an argument or anything like that, I'm just trying to understand all the different categories in the origins debate. Again, I understand if you'd prefer not to answer.

    2. Nick, I just want to say I really appreciate your participation on this forum. Your contributions carry weight. You seem to bring out the best in Dr. Hunter and perhaps he brings out the best in you. The best posts of all time on this forum in my opinion were recorded during those times that the back and forth between the two of you was heaviest.

      PS. I am a creationist and an "IDist" if that is a word. The distinctions between the two are very clear to me. I do not see ID as a faith-based view in any manner whatsoever. ID, the theory, appears to be founded upon what is known about intelligence and what is known about things known to be designed. Designed things conspicuously serve complex purposes separate from their design. To me, the theory is a fact based, present tense view of the physical, mechanical and biological world.

    3. C`mon Nick. Twice I have challenged you, above and in a recent post mentioned above. Give an answer -- how do you explain de novo genes? You seem pretty sure that some genes may be explainable by natural means. What about the hard cases? Aren`t there any? Have they all been solved?

      Or are you happy to interpret dialog by a community that is not of one great lock-step mind, but is a mind of independent thinkers as `strife`?

  4. NickM is such a cowardly equivocator- Earth to NickM-> not all evolution is blind watchmaker evolution. Grow up.

    1. Joe G, NickM would conclude that if there is a tidbit of truth in the blind watchmaker hypothesis, then the whole thing must be true. Evidence to the contrary is to be ignored.