There are some interesting conclusions to be drawn from Jeffrey Tomkins article for today – called Newly Discovered ‘Orphan Genes’ Defy Evolution. This may seem odd, not least because a) all three of those pairs of words are common and uninteresting Tomkins-isms and b) the “recent review paper” he begins by talking about was actually published in 2009, but bear with me here.
What’s an orphan gene? The basic idea is that you have many cases of genes common to say, rats, but which can be found in no other organism. While for most genes you can see that there is a very similar version in mice, or the platypus, or some other visible interspecies relationship, these “orphaned” genes look very much like they appeared out of nowhere without any visible family – prime targets for creationists, then.
There are two main mechanisms that have been proposed to create these genes (excluding, of course, the obvious “goddidit”). One is the idea that they were originally created by the duplication of other existing genes, but evolved away too fast for the connection to be still visible – evidence for this includes the observation that many of these genes still are evolving quickly. The other option is that they come from sections of non-coding DNA – which can be, but don’t have to be, Junk DNA – that become able to produce proteins by inheriting the required promotor sequences etc. The second option sounds quite far-fetched (what are the odds?) but it turns out that we know that it can happen – what’s under dispute is exactly how common it is. For more information I recommend this New Scientist article – you’ll certainly not find any of that in Tomkins’ posting.
Also debatable is exactly how common orphaned genes really are. Tomkins quotes the aforementioned 2009 review article like so:
The authors of a recent review paper, published in Trends in Genetics, on the subject of orphan genes stated, “Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species.”
It turns out that he could have quoted a 2013 paper for a figure of 10-30% if he so desired, but the actual number is not hugely significant. Less than half of a given species’ genes are orphaned, but it is still a significant chunk.
Complicating matters somewhat is the definition of orphaned gene used: does it still count if the gene is present in two very closely related species (like the two species of chimpanzee), or must it be found only in bonobos and absolutely nothing else? Changing that criterion could be partially responsible for the differing figures and wide range given.
The other explanation for the range, however, is that some species just have more orphan genes than others. Tomkins’ second reference is to a paper talking about how many orphan genes have functions related to the specific adaptations of that organism (his thesis is that God gave each baraminological “kind” of organism special genes, but lets not get ahead of ourselves). That paper mentions the water flea Daphnia pulex “harbours a large number of orphan genes and orphan gene families, some of which become specifically activated in response to environmental changes.” While the figure is not given directly there, the paper cited for that information claims that “more than a third” of Daphnia‘s 30,907 genes (humans have around 20,000, to give that number some context) are orphans, at least so far as we can tell with the number of related animals sequenced.
Returning to Tomkins, he ignores completely the potential mechanisms that could have produced these genes without divine intervention and says:
The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms). And several new studies in both fish and insect genomes are now highlighting this important fact.
What’s he got?
In the recent fish study [link], researchers sequenced the protein-coding genes in zebrafish and then compared the DNA sequences to other animal’s gene sequences. The researchers classified the zebrafish genes into three different groups: 1) Genes commonly found in many types of animals, 2) genes that are only found in ray-finned fishes (the broad group of Teleost fishes), and 3) genes that are species-specific to only zebrafish. This third category refers to orphan genes. Thus there was a distinct group of genes found only associated with zebrafish and no other animal or type of fish.
That’s unsurprising, in light of what we’ve already seen. What is interesting here is that we have confirmation of a pattern that we would expect to see if evolution were producing these genes. Suppose we have one type of organism, which has a certain set of genes. This organism type has multiple descendant varieties, each of which have produced their own set of orphaned genes by whatever mechanism produces them. Each of those varieties have more descendants, which carry on their ancestors’ orphans along with new ones of their own. This cycle repeats until we get to modern animals, such as the zebrafish.
In that case we would see, as we do, zebrafish having some orphaned genes of their own, but also sharing some semi-orphaned genes with wider and wider groupings of fish and animals. In contrast, a divine creator could just as easily have given all animals a common set of genes, and then each animal variety its own set, in which case we would see no such hierarchy.
It is the second paper that is more important, though it may look like just more of the same:
In another study, researchers compared the genomes of seven different types of ants with other known insect genomes. When comparing the ant genes to other insects, researchers discovered 28,581 genes that were unique only to ants and not found in other insects. While the various ant species shared many groups of genes, only 64 genes were common to all seven ant species.
The researchers concluded that on average, each ant species contained 1,715 unique genes—orphan genes. Researchers not only found dramatic differences for protein-coding genes, but also for other types of regulatory DNA sequences that control how and when genes are turned off and on.
The genomes of seven species of ant, along with the honey bee, have so far been sequenced. Each of these seven, according to this study, have many genes that no other ant shares – although as more genomes are sequenced some of these will no doubt be found in closely related groups. As I hope I’ve already made clear, the mere existence of orphaned genes can not be called a problem for evolution without at least discussing possible mechanisms of how they may have come to be. But I think Tomkins’ may be a victim of his own success here, for while so many orphaned genes needn’t be a problem for evolution they are for the creationist pseudoscience of baraminology.
You have, I’m sure, heard of the sentiment that God must be “inordinately fond of beetles” – there are, after all, an awful lot of them. But if you talk to a modern young-Earth creationist they will say that God need not have created each individual beetle species (there are hundreds of thousands of the things, which would have thrown out His back), but just one or several beetle “kinds” which radiated out into what we see today. This kind of attitude allows them to avoid crowding the Ark with every single species that ever existed, though in the case of insects such as beetles and ants they don’t actually include them on the boat: as everyone knows, “every creeping thing of the earth” does not mean every creeping thing of the earth – that would be absurd.
Now, Tomkins is saying that if a species has orphan genes when compared to another, then they must be in different “kinds.” With the limited number of genomes available for comparison this may not yet seem all that difficult – seven kinds of ant isn’t too large. But it doesn’t look like stopping there.
You see, two of those seven species of ants that have already been sequenced and compared are closely related species of leaf-cutter ant: Acromyrmex echinatior, and the more famous Atta cephalotes. This suggests that kinds would have to be very small indeed, if two species of ant that, to the layman, do exactly the same thing nevertheless merit independent special creation with their own set of unique genes. It does not seem far fetched to predict, in fact, that once we have sequenced every genome available almost every species of animal will be shown to have at least some orphaned genes. If so then every species is must be, according to Tomkins, its own “kind.” And in that case, baraminology is dead and the Ark is sunk to boot.
What Tomkins should be trying to show is not that orphaned genes exist, but that they don’t. What he needs to be true is that every species of animal shares all of its genes will a small, sharply defined group of relatives – its “kind.” If not then every species is its own kind and YECs will no-longer be able to whittle down 10s of thousands of vertebrate species down to something manageable.
I believe the phrase is “hoisted by own petard.”
It is the ability to only see what they want to see, and the tendency to be oblivious to facts, as well as completely lacking a logical thought process that is capable of connecting the dots, that makes me fond of saying “There ain’t nuthin scares me more than a bunch of good (insert religion here)”
The bits about many ant “kinds” and ants not being on the ark are what struck me the most. With how much ground Tomkins is giving up, while not making too much of a case against Evolutionary theory, I think ICR would have been better off to skip this one.
Tomkins recognizes that the 64 common genes among the seven ant species is too much diversity for a bottleneck caused by the flood 4,000 years ago. So he actually speculates that ants weren’t on the ark, going against the bible that says God set out to destroy all flesh with breath, unless insects are all excluded from the flesh/breath requirement. So with ICR’s magical flood, that created all tall mountains, broke up Pangaea, included meteors and tsunamis, and led to a single Ice Age, it was still not enough to kill the humble ant. Apparently, ants floated for the entire duration of the flood (over a year) on flotsam. QED.
And when BT was discrediting the Eunotosaurus in June, he insisted that it was just a turtle kind. But with ants, now there are multiple kinds.
Ok I’m not a science geek just a fan but i’m trying to understand you argument. you say
“each of which have produced their own set of orphaned genes by whatever mechanism produces them.”
you mention 2 or 3 “mechanisms” but i read your links and i didn’t see, “mechanisms”. I saw for lack of a better word assertions.
and cobbled together speculations. the Harvard article mentions possible options for strings them together and at the end assert they ARE probably what did it. but there’s no solid evidence. “de Novo” still means out of no where. and it’d seem the time line for the development for the fully functioning parts would be FAR to short. seems there are lot of intermediate hurdles before the speculative gene could shoe horn in a functioning new gene, A function fit for the organism (will housing poisonous venom help a org live without self protection, heck and extra tooth? or muscles), new function x integrated seamlessly into it nervous system, circulatory system, growth pattern, and survive the wild with the new unique feature and finally find a mate that would carry the new gene as dominant. to mention a few broad strokes.
the pre-human ancestor to man timeline is to short. for any De novo process described to develop it seems.
Saying that “well it happened” is no more scientific than ICR.
But again the de Novo processes described are admittedly, “unlikely”.
Yet the empirical finding is de novo gene that appear to have no links. Saying that “De novo evolution is clearly a strong force– constantly generating new genes over time,” does not explain it . it just shows that gene’s do seem to pop up out of nowhere A LOT. saying evolution did it is no better than saying God did it.
add to that that the idea of Junk areas of DNA are fading away in the light of recent research. it seem to me that’d leave far less wiggle room for NEW gene to POP UP out of parts that are already functional.
I just don’t get the tone of your rebuttal. The science points ICR made seem to have some merit, even if you don’t like the conclusions drawn from them.
De novo genes ARE a problem for evolution. As evidenced by the new research and speculation to give an evolutionary solution for it’s unexpected prevalence.
am i way of base here.
I’m not here be snarky or anything just looking at the facts i hope. please don’t hit me insults, i’m sincerely curious about the data.