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Surprise: 10-20% of each organism’s genome protein coding sequence is actually new. Not inherited.

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In “Orphan genes: A Guide to the Perplexed,” Ann Gauger of the Biologic Institute explains why there is a continuing debate about protein evolution:

As scientists sequence more genomes from different organisms, they are discovering roughly 10-20% of each genome’s protein-coding sequence is new, that is, unlike any other known protein-coding sequence. This was one of the biggest surprises to come out of the whole genome-sequencing project, though by no means the biggest.

Why? The working assumption had been that, given common descent and the fact that most house-keeping genes are shared among living things, and the hither-to assumption that evolution occurs by incremental small changes, orphan genes (protein-coding sequences without known protein-coding antecedents) were assumed to be rare if not non-existent.

At this point it is necessary to explain a little about how such orphan sequences come to be identified. More.

4. Given the fact that such surprising species- or clade-specific proteins exist, it raises interesting questions about where orphans come from. Some might have come from gene duplication followed by rapid adaptive evolution (see #3 above). If that is the case we should see traces left behind in the orphan protein’s three-dimensional structure. Some propose recruitment from non-coding DNA by a combination of mechanisms, including insertion of transposable elements. This is possible, but it would require that the insertion or other mechanism(s) be lucky events in order to produce a stable, functional protein, that is, one that is of use to the organism. Exactly how lucky is one of the issues we are debating.

5. Then there is the elephant in the room that evolutionary biologists don’t want to acknowledge. Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Certainly, this runs contrary to the expectation of common descent.

It’s convenient that discussing these problems is “religion”—unless researchers suggest that space aliens dunit. Maybe they’ll have to do that in order to enable a discussion.

7 Replies to “Surprise: 10-20% of each organism’s genome protein coding sequence is actually new. Not inherited.

  1. 1
    Mung says:

    This is exactly what one would expect if Darwinism were true.

  2. 2
    ericB says:

    Mung, Darwinism would lead to the expectation of change over time, but not to this much change in this short of a time.

    Because Darwinism operates by blind watchmaker accidental (i.e. unintended, unplanned) variation, there is no capacity for tossing in so many new genes with no ancestral connections or commonalities even with supposedly recently separated cousin species.

    Too much novelty separating chimps and humans, for example, is a deal breaker for a Darwinian account of a recent common ancestor for both species.

    Or to put it another way, if you really want to say that there could never be “too much” novelty separating species such as chimps and humans, such that it would never be a deal breaker for Darwinism, then you have just conceded that the Darwinian claim is unfalsifiable in that regard. If we are to accept that any amount of difference is expected by Darwinism, then that becomes a faith proposition, not a scientific proposition the evidence could defeat.

  3. 3

    So what would the ID take on this be – that these genes are miraculously inserted, or rearranged from existing sequences, from time to time as and when organisms need them?

    I don’t use the word “miraculously” sarcastically, here, I’m genuinely interested in how, and how often, people think this might happen.

    It seems like rather a large molecular event to be smuggled in under the cloak of quantum chaos.

  4. 4
    Joe says:

    So what would the ID take on this be

    That they were designed- either directly or via the organisms’ internal programming.

  5. 5
    lifepsy says:

    Apparent genetic sequence homology was used as evidence for Evolution, and now of course, discovering the exact opposite as a rule of biology just sheds more light on how evolution works. What a great theory.

    Interesting how blind and unguided mutation and selection processes on most of the Earth’s biodiversity coincidentally hit around the 20% mark for orphan sequences.

    An evolutionist is honest and admits how troubling orphan genes are for evolution.

    How Can There Be Orphan Genes?
    by Ken Weiss (Professor of Biological Anthropology and Genetics PSU)

  6. 6
    bornagain77 says:

    lifepsy himself (who is much too bashful) has done an excellent video on this topic;

    Orphan Genes (And the peer reviewed ‘non-answer’ from Darwinists) – video

  7. 7
    johnnyb says:

    Elizabeth –

    There are several possibilities:

    (1) As you mention, supernatural intervention
    (2) Teleological organisms – that is, organisms themselves have a minimalistic agency that allows them to operate as micro-designers
    (3) Maximal Front-loading – the genes could have been all present in a common ancestor, and then the ones not needed for the organism were tossed out
    (4) Minimal Front-loading – the parts for the genes and the feedback systems necessary to detect when new genes are needed and the ability to put them together in likely-working ways was pre-existing in the organism. This is the quintessential non-Darwinian evolution.
    (5) Symbiosis – the genes may originate as a response to new symbiotic relationships, either as borrows or integrations from the host
    (6) Semi-Symbiosis – the genes could be carried and inserted by foreign organisms such as viruses and bacteria

    #1 and #2 are hard to determine evidentially, but #2-#6 have all been shown to be present in nature, and they point to either #1 or #2 in a larger sense (i.e. in #6, if there are beneficial genes floating around, why are they floating around, except as part of a design or teleological relationship?) #4 is highly active in the immune system, both through V(D)J recombination and somatic hypermutation.

    If the ways in which genes are made are highly teleological, and all presuppose information present at the beginning, then it is reasonable to presume #1 or #2 as the ultimate origin for that information. If #1 or #2 can create the information at the beginning, there is no a priori reason to presume that they can’t create information going forward.

    Just for completeness, I should also add a #7, which I think is Behe’s view:

    (7) The universe itself has “accidents” setup so that mutational events will just happen to lead to the right information. In other words, there may be a cosmic ray that hits DNA at just the right spot to make just the right mutation, because God ordered the cosmos from the beginning so that this apparently “lucky” coincidence would be sure to happen.

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