Why Science Works - Doing It Like Adults

The basic difference between science and religion is that science is grown up while religion is essentially childish. This is illustrated by a controversy which has suddenly blown up in a fairly obscure but nonetheless interesting aspect of evolutionary biology in the last week.

An interesting paper was published a few days ago which seemed to show that horizontal gene transfer (HGT) may account for up to 18% of the tardigrade ('water bear') genome, suggesting that HGT could have played a bigger role in the evolution of multicellular organisms than is generally recognised.

HGT is widely suspected to have played a part in the evolution of prokaryote cells so that acquiring genes evolved in another species could have been a short-cut to evolution or a way for new combinations of genes to come together, analogous to sexual reproduction. In eukaryote cells, the incorporation of prokaryotes was a form of HGT after all, but for HGT to have played a wider role in the evolution of multicellular species would be surprising - hence the interest in this paper and why I wrote about it.

Now, however, another group has published a paper which suggests that the result of the genome analysis may have been an artifact produced by contamination:

Abstract
Tardigrades are meiofaunal ecdysozoans and are key to understanding the origins of Arthropoda. We present the genome of the tardigrade Hypsibius dujardini, assembled from Illumina paired and mate-pair data. While the raw data indicated extensive contamination with bacteria, presumably from the gut or surface of the animals, careful cleaning generated a clean tardigrade dataset for assembly. We also generated an expressed sequence tag dataset, a Sanger genome survey dataset and used these and Illumina RNA-Seq data for assembly validation and gene prediction. The genome assembly is ~130 Mb in span, has an N50 length of over 50 kb, and an N90 length of 6 kb. We predict 23,031 protein-coding genes in the genome, which is available in a dedicated genome browser at http://www.tardigrades.org. We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.*

Georgios Koutsovoulos, Sujai Kumar, Dominik R Laetsch, Lewis Stevens, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Aziz Aboobaker, Mark Blaxter
The genome of the tardigrade Hypsibius dujardini
bioRxiv doi: http://dx.doi.org/10.1101/033464

*Copyright © the author/funder.
Reprinted under terms of Creative Commons International Licence (CC-BY 4.0)

So what is the response to this paper which, not to put too fine a point on it, tells the publishers of the original paper that they may have been less than thorough and so got it wrong. Imagine for a moment trying to suggest something like that to, say, a theologian, fundamentalist apologist or a creationist.

To find out how grown up scientists react to news that they may have been wrong, go to the paper and scroll down through the comments where you will find:

This paper reports an independent genome for the tardigrade Hypsibius dujardini and raises some reasonable concerns about contamination in our recent paper (1). We thought seriously about the possibility of contamination—it was of course the most likely initial explanation for the large amount of foreign DNA found in our assembly—and much of the analysis in our paper was designed specifically to address this issue. We view the independent data and analysis of Koutsovoulos and coauthors, including their analysis of our data, as valuable toward resolving questions of broad interest. We will work now to try to further resolve the issues that were raised. We plan to refrain from commenting more until we've done additional analyses that can shed more light on this issue, and we'll be happy to share what we learn between groups.

We appreciate that the bioRxiv preprint server is a valuable way to move science like this forward without delay, and we're grateful to Koutsovoulos and coauthors for making use of it.

-Thomas Boothby and Bob Goldstein

(1) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Osborne Nishimura E, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B. Proc Natl Acad Sci USA. 2015 Nov 23. [Epub ahead of print]

This as good as anything illustrates why science and the scientific method eventually get things right. It is always willing to admit mistakes and accept corrections. It does this because the single most important idea in science is that truth matters; that truth is the ultimate and only aim of science, far more important than precious egos, and far more important than trying to persuade people to believe something regardless of whether it's actually right or wrong because your power, privileges and livelihood depends on them believing it.

This is why science and technology, and societies founded on them, continue to advance whilst religion struggles to keep up and continually tries to drag society back to the Dark Ages when it reigned supreme. It is the reason all the major churches of whatever religion are now losing members through disgust at their backward teaching and repugnant 'morality' which has never progressed much beyond the Bronze Age because religion, unlike science, is incapable of admitting it is wrong. The entire edifice depends on selling the idea that it can't be.

And as though to illustrate this contrast for me, The Discovery Institute - the organization that tries to mislead people about science and to present biblical literalism as an alternative - is sending out begging letters with the following motivational argument for intelligent design:

Intelligent design is a common sense idea. Research has shown that children intuitively recognize design in the world around them. You and I make design inferences every day. It has taken a long time for the scientific community to catch up with the kids. But that day is coming.

That's right! Uneducated children believe it so it must be true. Ignorance and immaturity are better measures of reality than science!

So, when you're next sick, just ask an uneducated child what to do. No need to bother with doctors and all that science-based stuff. What do they know? They haven't caught up with the children yet!

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