Orphan genes as Fatherly providence

The questioning of natural selection in my last two posts should be seen as a simple lack of conviction that classical Neodarwinianism is robust enough to account for, in a well-worn phrase, the origin of the species. I should emphasise again that theologically, an adequate scientific theory of evolution is perfectly compatible with the providence (ie supervision and direction) of a wise God: the denial of teleology is categorically an unscientific and metaphysical claim.

At the same time, the astonishing complexity of life, as its wonders are exponentially proving, makes some kind of teleological mechanism within biology ever more likely, if we are to avoid a high contingency theory that is unsatisfactory both scientifically and theologically. I am happy with the God of miracles, but given the mechanisms already seen at all scales of the science of life, the use of secondary causes by the Son for the unfolding purposes of the Father seems, to me, to be more plausible than a chain of pure miracles. Providence would still rule those mechanisms.

And so neutral theory, as I understand it, is anything but an advance on the “Modern Synthesis,” at least without some less random, more physiological view of mutation as postulated by Denis Noble, Jim Shapiro or, recently J Scott Turner.

One aspect that seems to move things forward, or at least increase possibilities, is the developing understanding of “orphan genes”, which are protein-coding genes unique to species, or other taxa, and which appear to have no evolutionary relationship whatsoever to their ancestors. Given the emphasis on homology as evidence for evolution, it is something of a surprise that every new genome sequenced so far expands the number of “orphans” considerably, the average of new genes in each now being estimated at between 10 and 30%. That is quite a lot of new genetic information, especially as many such genes actually code for unique protein folds not related to the common “families” of proteins. It rather pushes the envelope for “gradual development” as the defining feature of evolution if each species is 20% brand new. That’s getting close to saltation.

There is also a growing consensus that orphans may be responsible for, or at least associated with, many of the specific features of taxa. For example, new genes have been suggested as handling key features of the human brain.

There is a good, recent, overview of the state of play in the orphanage in the New Scientist, by Helen Pilcher, who is a journalist but with a PhD in stem cell biology. You’ll see there that the original thought was that orphans derive from gene duplication events, but evolved so rapidly that all resemblance to the parent gene was quickly lost – very much a Just-So story: only a Darwinian would establish a relationship from total dissimilarity! One of the early researchers in the filed, Tautz, recorded why this was:

Susumu Ohno’s passionate support for gene (and genome) duplication as the major mechanism for creating evolutionary novelty has, for a long time, set the stage for thinking about gene emergence.

It’s passion and fashion that sometimes dictates the science. But the trend has been, as Pilcher’s article shows, towards seeing orphans as de novo genes arising from non-coding areas of the genome (see, for example, Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes).

The idea is that sequences of “Junk DNA” of various kinds pick up initiators, promoters and so on fortuitously and so become genes. As Pilcher points out, this may well be happening with some frequency, the majority of such attempts being nonsensical or deleterious, but the occasional one being selected, and therefore being refined by mutation.

On her own blog, Pilcher says this:

Creationists have cited the apparent incompatibility between orphan genes and evolutionary theory as evidence of intelligent design. It’s not. They’re actually an example of natural selection at its finest.

The majority of orphan genes, it now seems, lack obvious parents because they’ve sprung up from junk DNA. The idea, once considered totally implausible, is gathering credence as scientific papers pinpoint the non-coding sequences and processes that have forged these foundlings.

Our cells may be constantly experimenting with new genes all the time – ‘testing’ random stretches of non-coding DNA to see if they can produce anything useful. The cell’s cytoplasm is bustling with well-coordinated activity, so most of the proteins manufactured from these sequences won’t fit in. The wannabe gene won’t be selected for, and reverts to plain old, non-coding DNA. But once in a while, junk DNA throws up something useful. The sequence may then start to pick up useful mutations, and over millions of years of natural selection it becomes shaped it into a fully functional gene.

Now, there’s a question here about the pervasiveness of natural selection – once non-coding DNA is brought into the equation, the genome is pushing the theoretical limit of c.30K genes that Ohno proposed as the upper boundary to natural selection. The constraints I mentioned in my last two posts apply even more to any new, barely beneficial, genes newly formed as to mutations of old genes.

That aside, note the teleological language employed by Pilcher in her very dismissal of creationism: “experimenting”, “testing”, “wannabe”. One has become used to the employment of “purpose” language in a context supposedly denying purpose, but her use of typical functional terminology says one thing clearly: evolution here is viewed as a physiological mechanism, and the non-coding DNA as the raw material on which it works.

Junk DNA may, then, may be as validly seen as “functional” for cells to use for evolution as genes are for coding the functional genes by which they routinely operate. Whether cells are simply co-opting parasitic DNA is irrelevant if macroevolution would not happen without it, as is becoming apparent. Evolution is a physiological function, and non-coding DNA the database it employs.

There is still a probability question, mind you. The non-coding genome is big, but not infinite. Just what likelihood is there that any randomly selected sequence of nonsense code will form anything functional on which natural selection might operate? Let alone novel protein folds in a context of control functions appropriate to a new species or order? I have no way of knowing, but my hunch is that it’s not going to make the tree of life a done job. One way or another, providence still seems to be the master-planner.

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About Jon Garvey

Training in medicine (which was my career), social psychology and theology. Interests in most things, but especially the science-faith interface. The rest of my time, though, is spent writing, playing and recording music.
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