Criticizing from a foundation of skimming

Last week, PZ Myers briefly commented on my earlier posting about the Archaean expansion.  So I edited the original posting to point out that all of his criticisms failed largely because he was lashing out against a straw man.  In fact, the criticisms were so far off base that one can conclude Myers hasn’t even read anything about the hypothesis of front-loading.  This should not be surprising, as there is a very funny twist to his whole post that clearly stems from someone who roots their criticism in superficial skimming.

Beta catenin-like protein in Volvox?

Earlier, I presented some evidence that the green algae, Volvox, appears to possess a homlog of beta-catenin. We saw that when this hypothetical protein was aligned with human beta catenin, there was a 27% sequence identity over the entire 525 amino acids of the Volvox protein with an E value of 1e-25. Also, the Conserved Domain Database representation predicts an almost identical domain arrangement of the two proteins (although beta catenin has an extra 100 amino acids on both ends).

Yet it is quite possible that the homology between this Volvox protein and beta catenins is merely a reflection of the fact that they share Armadillo (ARM) repeats. The ARM domain is about 40 amino acids in length and functions in many different proteins simply to mediate protein-protein interactions. Thus, the hypothetical Volvox protein could simply be a protein with multiple ARM repeats yet possess no beta catenin-like function.  It would simply stick to some other proteins using a homologous domain.

Unfortunately, we won’t be able to resolve this issue until biochemical evidence is provided that a) establishes the hypothetical protein is truly expressed and b) shows some level of beta-catenin like function. However, we can use a phylogenetic approach to compare the Volvox sequence with both beta catenins (and alpha importins) and a random selection of ARM repeat proteins. If the Volvox protein has a beta catenin-like function, we would expect it to nest with the known beta catenins. If it is just an ARM repeat protein, we would not expect it to nest with beta catenins and instead find itself situated among the randomly selected ARM repeat proteins. So let’s give it a try.

Easter Bunny

An article from The Scientist

Here’s some excerpts from an article you might enjoy reading:

Conventional thought on evolutionary change has led researchers to believe that genetic innovations underlie the transition. Advances in genomics research, however, are revealing that more and more of the genes associated with complex processes also exist in simpler animals and even in their unicellular cousins.

[…]

Choanoflagellates, unicellular organisms that look remarkably similar to the feeding structures of sponges, are the closest living relatives of metazoans. It turns out that they also share a number of genes once thought to be unique to multicellular animals. Tyrosine kinases (TK), for example, enzymes that function in cell-cell interactions and regulation of development in animals, were identified in the choanoflagellates in the early part of this decade, and the first sequenced choanoflagellate genome, published in 2008, revealed that they have more TK genes than any animal—and many other components of the TK signaling pathway as well.

“So this gene family that was thought to be essentially a trigger that unleashed animal origins, we can now say with great confidence evolved long before the origin of animals,” says evolutionary biologist Nicole King of the University of California, Berkeley, who has been studying choanoflagellate biology for over 10 years.

Scientists have also identified choanoflagellate homologs of cadherins, known to be involved in cell-cell adhesion and signaling in animals. And more recently, a widespread search for genes associated with integrin-mediated adhesion and signaling pathways revealed that the integrin adhesion complex originated much earlier than even the choanoflagellates, dating back to the common ancestor of animals and fungi.

“It’s pretty surprising to find these adhesion genes in far-flung species,” says Srivastava. “We would have thought that integrin signaling has to do with cells sticking together, but it goes much further back in time than our most recent unicellular cousins.”

The genomic exploration of the evolution of multicellularity is really just beginning, but already, a trend is emerging. “Almost every month now we are seeing genes that were supposed to be exclusive to metazoans that are already present in their single-cell relatives,” says evolutionary biologist Iñaki Ruiz-Trillo of the University of Barcelona. “I think that means co-option of ancestral genes into new functions is important for evolutionary innovations like the origin of multicellularity.”

“Probably the more data we collect, the fewer and fewer animal-specific genes there are going to be,” agrees Dunn. “And we’re going to have to explain the origins of multicellularity in terms of changes in the way these gene products interact with each other.”
Read more: From Simple To Complex – The Scientist – Magazine of the Life Sciences http://www.the-scientist.com/article/display/57883/#ixzz1JuiPZdUx

Familiarity

Here is the conclusion from the recent Science paper I mentioned:

In either case, our results identify unexpected similarities in tissue organization between two groups of distantly related organisms that were thought to have independently evolved multicellularity, and thus reveal molecular factors and organizational principles that may have contributed to the early evolution and diversification of animals.

“Molecular factors” and “organizational principles” that “contributed” the emergence of animals.  This description nicely maps to the way in which I described front-loading in the context of social engineering about a year ago.

Lesson from a Receptor

Over at BioLogos, Dennis Venema writes a very nice summary of recent research that resurrected a likely ancestral protein state.  Here is the meaty portion:

In vertebrates, two hormone – receptor pairs were of interest to the Thornton group: the mineralocorticoid receptor (MR), which binds a steroid hormone called aldosterone, and the glucocorticoid receptor (GR), which binds a second steroid hormone called cortisol (see diagram above). Cortisol can also activate MRs, but an enzyme that breaks down cortisol is present in tissues where MR is used so cortisol cannot accumulate. Aldosterone, on the other hand, cannot activate GR – it is specific to its binding partner MR. Even though these two hormone / receptor pairs regulate different processes in modern organisms, the two receptors are the result of an ancient gene duplication that occurred early in vertebrate evolution, around 450 MYA (million years ago). As time has gone by, the derivatives of the original gene have picked up distinct binding partners and physiological roles. Thornton and colleagues wanted to tease out the details of these important changes.

They started out by determining the ancestral sequence of the original receptor gene, prior to the duplication, and recreating it in the lab. When they tested this lab-designed protein, they found that it, like modern MRs, (but not GR’s)could bind either cortisol or aldosterone indicating that the ancestral protein must have been able to bind both. This result suggested that somewhere along the line the GR lost its ability to bind aldosterone and became specific to cortisol. This is interesting, because at the time the ancestral receptor was present, aldosterone didn’t exist. Aldosterone is a relative newcomer on the scene: it is present only in four-limbed vertebrates (tetrapods), which arose around 390 MYA. So, the ancestral receptor present prior to 450 MYA already had the ability to bind a hormone that wouldn’t evolve for tens of millions of years. Of course, the ancestral receptor “didn’t mind” – it had its own binding partner – a steroid hormone closely related to cortisol and aldosterone. It wasn’t sitting around doing nothing in the meantime.

More Epithelial Nudging

If you’ll recall, back in December, I provided evidence that unicellular organisms were endowed with components (beta catenins) that served as preadaptations to nudge epithelial tissue into existence when needed.

Well, feast your eyes on a paper that was published in Science just a couple of weeks ago.