Common ancestry: Bioinformaticist Julian Gough on the SUPERFAMILY database on proteins in genomes

_{Denyse O'Leary

March 18, 2017

Informatics}

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Julian Gough In an interview with Suzan Mazur at Huffington Post. Mazur explains,

Plug certain information into SUPERFAMILY and it can analyze a vast assortment of genomes and assist you in building a Tree of Life using superfamilies — i.e., domains with an evolutionary relationship — and the conserved part of thousands and thousands of protein structures called protein domains.

…

Suzan Mazur: Do protein Superfamilies represent the current limits of our ability to identify common ancestry?

Julian Gough: Yes. That is exactly what their definition is. So if you want to group two protein structural domains into the same Superfamily, the question that you ask is whether there is structural sequence and functional evidence for common evolutionary ancestry. So they’re classified based on that.

The most powerful part of that classification comes from the structure. Structure is far more conserved than sequence and so the knowledge of the structure allows you to classify very distantly related things that have no apparent or detectable similarity in sequence.More.

Suzan Mazur is the author of Public Evolution Summit.

See also: Axe on specific barriers to macro-level Darwinian Evolution due to protein formation (and linked islands of specific function)

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Comments

PaV: Do you think that feathers and helium balloons are a problem for the theory of gravity? According to gravitational theory (both Newton's and Einstein's), everything should fall at the same rate, but feathers fall slower than they should and helium balloons "fall" up. Don't see the relevance of that question? Here's the point: gravitation theory predicts that everything will fall at the same rate if gravity is the only force acting. If there are other forces acting (as there are in those cases), they need to be taken into account; and with those forces taken into account, there's no conflict. The same thing holds with most of the "problems" I've seen for common ancestry: they're conflicts with what we should see if common ancestry were the only relevant factor. But there are other factors at work, like horizontal transfer, selection-driven convergence, coalescence effects, statistical noise, etc. As with the gravity example, if you take all of those into account the conflicts pretty much vanish. This sort of thing is entirely normal in science. In a controlled experiment, you can try to design it to isolate out just the one thing you're trying to test. But if you're studying real phenomena, you have to take them as they are: usually results of a messy combination of interacting processes and causes. If you want to understand what's going on, you have to tease out what all the relevant causes and processes are, and how they all come together to give the phenomenon you're studying. Furthermore, if you really want to refute common ancestry, you have to come up with a better explanation for the pattern of similarities we see among organisms. In science, a theory that often makes correct predictions but sometimes makes wrong predictions is better than one that makes no predictions at all; it's clearly not right as is, but it may just be incomplete or only partly right, and thus is a useful step toward a better theory. Branching common ancestry -- even without taking other factors into account -- does a very good job of predicting the pattern of similarities and differences between organisms. Taking those other factors into account, it's even better. Evolutionary theory and intelligent design with common ancestry thus have a good explanation for these patterns. Intelligent design without common ancestry doesn't have any explanation at all, unless you add something else to explain the pattern. And I haven't seen any proposed replacements that explain the pattern anywhere close to as well as common ancestry does. Unless you can come up with a decent replacement, intelligent design needs common ancestry.Gordon Davisson_{March 20, 2017
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Gordon Davisson: The problem is the same problem of phylogenetic trees, and the molecular clock hypothesis: it works over here, but not over there; which means that it is of little utility, contrary to Darwinian (random is always random, and common descent is a given) thinking. We will find, in the end, that these protein superfamilies will cause all kinds of problems for Darwinism. It always does.PaV_{March 19, 2017
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PaV @ 1: I don't see any problem for evolution here. Note that he's talking about superfamilies of proteins (and protein domains), not superfamilies of organisms -- they're completely different. Here's an extension of the excerpt Denyse gave (with my emphasis):
Suzan Mazur: Do protein Superfamilies represent the current limits of our ability to identify common ancestry? Julian Gough: Yes. That is exactly what their definition is. So if you want to group two protein structural domains into the same Superfamily, the question that you ask is whether there is structural sequence and functional evidence for common evolutionary ancestry. So they’re classified based on that.
Our ability to identify common ancestry of organisms goes way beyond the Linnaean superfamily level. If you read the article, he talks (a little bit) about the limits of our ability to identify common ancestry among organisms... well, if you consider viruses organisms:
Julian Gough: I’m not aware of many people who have attempted to reconstruct an evolutionary tree of viruses. To put the evolution of viruses in context, you have different categories of viruses. You have double-stranded DNA, single-stranded DNA, double-stranded RNA, single-stranded RNA. They’re not even using the same way of storing genetic code. So to try to make an evolutionary tree of viruses, bringing these together, I think it goes too far back.
He does talk a bit about using his database to reconstruct the tree of life (i.e. common ancestry of organisms):
Suzan Mazur: Who else is building a ToL using SUPERFAMILY besides Kurland and Harish? Julian Gough: We have a paper on doing exactly that, although maybe not in the same way. But I think the first person to publish using the SUPERFAMILY database to attempt to build a tree was a student with Phil Bourne. That was more than 10 years ago.
The tree-of-life tool is at http://supfam.org/SUPERFAMILY/sTOL. Just select some species you'd like to include, click Submit, then Plot Tree, and it'll infer a tree from the protein superfamily data, and draw you a picture. Note that it has no trouble relating any of the organisms in the database, even across different superkingdoms. Here is one I did, just by selecting some interesting-looking names from the list. The group at the top is archaea, the group at the bottom is bacteria, and the ones in between are eukaryotes. Humans are near the middle. Note that I'm far more familiar with animals (and mammals in particular) than anything else, so those are overrepresented in the list I chose.Gordon Davisson_{March 18, 2017
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Congratulations to Mazur on capturing this particular exchange. Nicely done -- and very interesting.Upright BiPed_{March 18, 2017
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Pav@1 please expand on your commentes58_{March 18, 2017
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Another day; another bad day for Darwinism.PaV_{March 18, 2017
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