Trading Genes

A Bdelloid rotiferBdelloid rotifers are amazing animals. They are capable of withstanding harsh conditions – including radiation exposure – and they also reproduce asexually, having apparently lost their ability to use sexual reproduction millions of years ago. This is, in fact, a bit of a contradiction. Sexually reproducing animals appear to have and edge over those that do not, being at least theoretically better able to adapt and withstand environmental pressures. A recent paper in PLoS Genetics looked at horizontal gene transfer (HGT) – the same mechanism used by bacteria and archea to transfer genetic material with a similar effect to sexual reproduction – in the Bdelloid species Adineta ricciae. They discovered that an abnormally large percentage of A ricciae sequences seemed to have been acquired from non metazoan (that is, non animalian) organisms, even when compared to HGT levels in other, non Bdelloid rotifers. They hypothesise that this may be the cause of the Bdelloid’s resilience in the face of their disability. Jeffrey Tomkins writes, in the first DpSU of the month, Are Rotifers Gene Stealers or Uniquely Engineered?

The tools of DNA sequencing are becoming cheaper to use and more productive than ever, and the deluge of DNA comparison results between organisms coming forth are becoming a quagmire for the evolutionary paradigm. To prop it up, biologists resort to ever more absurd explanations for discrepancies. A prime example of this trickery is in a recent DNA sequencing project performed in a microscopic aquatic multi-cellular animal called a rotifer.

Given that the ICR has in the past tried to explain away viruses as originally being a mechanism to transfer genetic material between organisms I don’t know where Tomkins got the idea that he could cast the first stone here – HGT is a perfectly reasonable concept to invoke given the evidence, the viruses less so.

Before he can go on to the actual results of the research, however, Tomkins cannot resist taking a dig at what he perceives as discarded evidence:

In this effort, the researchers targeted those gene sequences that are expressed as proteins for DNA sequencing because the genome was too large and complex to sequence and assemble all of its DNA. They recorded over 61,000 gene sequences that were expressed from rotifers grown in stressed and non-stressed conditions. Of these, they could only find sequence similarities between rotifers and other creatures for 28,922 sequences (less than half). The researchers tossed the unknown DNA sequences out of their analysis since the non-similar genes were novel, apparently specific to rotifer, and essentially difficult for evolution to explain.

The reason, of course, why they ignored sequences that did not match with anything known from other organisms because you have no way of determining that a sequence is the result of horizontal gene transfer if you have no other organism that it could have originated from that has stuff that matches with it. It would be entirely useless to use these other sequences in further comparison. Tomkins has a belief that novel genes cannot be explained by evolution, something that will have to wait for another day, which explains why he seems to think they were “tossed out” here.

Now, the angle that Tomkins is going for is that because you have all these sequences (about 10% of the 29,000) that, to him, don’t fit “evolutionary expectations of common descent,” common descent must be bunk, right? To do so, of course, he needs to dismiss the horizontal gene transfer option. It’s worth pointing out that the methods used by the researchers exclude any HGT between the rotifers and other animals, so when he talks about how the organisms with matching sequences include algae and bacteria and the like he is only stating the obvious. Continuing:

In the present report, the rotifer under study was asexual, limiting heredity as an option for aiding in gene transfer. So the researchers concluded that it stole hundreds of genes via HGT from a plethora of other creatures.

Tomkins has no objection to the concept of HGT itself, noting that he had himself contributed to a paper in Science on the subject of gene transfer from bacteria to eukaryotes. But he is apparently unable to accept the volume of elements transferred in these rotifers:

How will rotifer researchers account for the massive transfer of hundreds of genes from a broad range of hosts that they believe includes 533 supposed source genomes for which no biological host-based relationships exists? Some sort of causal host relationship must occur for the transfer of one gene, let alone hundreds of genes from hundreds of sources.

While a host relationship no doubt helps, I think “must” is too extreme here – Tomkins cites the PLoS paper in support, but I can’t find where they say it. It’s a fairly weak objection in any case, as if nothing else there have been millions of years for the Bdelloids to associate with the relevant organisms.

Another problem is that the researchers showed that the so-called “stolen genes” were well-integrated into the rotifer cell biochemistry and its environmental adaptation mechanisms. A separate 2012 study showed that highly expressed native genes could not be shared via HGT, even among bacteria, because they would severely disrupt essential cell biochemistry. And these are exactly the types of genes that were surveyed in the rotifer.

The paper has a different take:

HGT in the bdelloid has the potential to radically extend and complement metazoan biochemistry, since approximately 80% of foreign sequences are concerned with enzyme activity, much of which is novel in animals. This supports the complexity hypothesis, which states that genes whose products are involved in relatively few protein-protein interactions, such as those specifying enzymes, are more likely to be horizontally transferred than those with a higher degree of connectivity, like transcription factor genes [17][39][40]. Thus, although the complexity hypothesis was developed to explain observations in prokaryotes, it also seems to apply to the large scale HGT observed in the bdelloid. It would be interesting to investigate in the bdelloid a more recent suggestion from a study in prokaryotes that highly expressed genes are less likely to be horizontally transferred between organisms [41]. Technically, this might be difficult to achieve, as we estimate there are at least 533 source organisms that have contributed to the bdelloid genome by HGT, but we will explore this in future work.

Citation #41 is the one given by Tomkins above also. We don’t actually know if this contradicts the high expression study, contrary to what Tomkins says. Meanwhile, many of the new enzymes add things that weren’t already present, rather than disrupting what is already there. In other cases non-metazoan genes were found to have replaced the original genes that had the same function, but this too wouldn’t require major disruption, just that the original gene got damaged some time after the new gene was added.

Tomkins concludes:

The unique mix of rotifer genes along with their flawless biochemical integration into the rotifer’s cell system, clearly and abundantly supports the special creation described in the Bible.

A Bible that never mentions rotifers, I will note. Instead, Tomkins is both bending the science and scripture to support his views – the Bible makes no claims about the underlying genetics of the animals it describes.

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