Posts Tagged Protein evolution

Epistasis in living colour—mapping an evolutionary trajectory

ResearchBlogging.orgReconstruction of evolutionary trajectories will be a favourite topic on this blog, since it’s a very interesting area that is currently growing rapidly. I already wrote about nice new work showing how heat stability can evolve in thermophiles (heat-loving organisms). Now there’s a new paper looking at how blue color vision arose in the lineage leading to human beings. Both studies asked the same basic and important question: how did evolution get from A to B, given that most of the paths leading from A to B are dead ends? Read the rest of this entry »

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In which I propose that creationist rubbish can be turned to gold (and discuss latest creationist “publication”)

Most creationist publishing is rubbish, taking the form of religious argumentation and shamelessly inaccurate propaganda. Creationist writers on both sides of the Atlantic are almost uniformly unworthy of any scientific or scholarly attention, and the only serious question among scientists is whether and how to engage creationist tactics to limit their damaging influence on science education and literacy.

It is quite unusual, then, to see a creationist group publish a scientific paper—containing experimental data—in a peer-reviewed journal. When this happens (about once every two years), it seems worthwhile to read the paper and see whether the creationists are at least doing valid experiments. Read the rest of this entry »

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Reuse, recycle, repurpose …. how evolution makes do

ResearchBlogging.orgOne well-known metaphor for the process of biological evolution is ‘tinkering.’ First proposed by François Jacob in 1977 in a now-famous paper in the journal Science, the idea captures two facets of evolution: the fact that new things must be developed from pre-existing things, and the apparent fact that evolution does not proceed with guidance. The picture is one of an actor mindlessly fiddling with implements, tossing them into the mix to see what happens. A believer might prefer the actor to be mindful, perhaps even goal-driven, but the process shows no evidence of this—Hume’s “stupid mechanic” seems a more apt metaphor to me. But mystical preferences aside, a view of evolution as tinkering brings a set of expectations or predictions to evolutionary thought.

One of those predictions is that innovations in evolution should be rare. More precisely, whenever something “new” appears, we expect it to be built from old stuff, from the components already there. No matter how innovative the new thing looks, we expect it to be a subtle reworking of whatever came before. Read the rest of this entry »

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Proteins in a boiling kettle? No worries.

One challenge in writing about basic evolutionary concepts is finding the balance between the creation of jargon-filled geek indulgences and the tedious rehashing of well-known facts and principles. Proteins are a case in point. Many readers will already know that proteins are the workhorses of life, nanomachines with finely-tuned functions and exquisite 3D structures to match. Many, I hope, already know that proteins are manufactured by reference to the famous genetic code, a universal DNA- and RNA-based system. Some perhaps know that proteins must be folded into those exquisite 3D structures, often with help from other proteins, in order to function. And one way to destroy a protein functionally, to cause it to unfold and perhaps even turn inside-out, is to heat it. We’re not talking about extreme heat (say, 500 degrees C as in a self-cleaning oven) that cooks everything down to carbon. We’re talking the kind of heat one finds in the kettle, or in bubbling hot springs in places like Yellowstone National Park in the US. Say, 95 degrees C.

Amazingly, there are life forms (aptly named ‘thermophiles’) that thrive in serious heat. The bacterium Thermus aquaticus is one of the best known—originally discovered in those Yellowstone hot springs, its DNA-copying protein made feasible decades of DNA copying in labs the world over, through a process called the polymerase chain reaction.

This is amazing because proteins in, well, normal organisms like us cannot tolerate 95 C. They unfold, and usually this is permanent. They don’t re-fold when the temperature goes back down. The process is called ‘denaturation.’ Cooking meat is a basic example of this. The heat denatures proteins, and essentially all of the denaturation is irreversible. The meat stays cooked. (Thank heaven. No one wants the haggis coming back to life.)

Somehow, then, the proteins in thermophiles like Thermus aquaticus have become super-stable. They refuse to unfold even when heated to near boiling. We should expect that natural selection, acting on the basic protein structure (the sequence of building blocks, which are amino acids), can hone the nanomachine into a heat-tolerating nanomachine. Read the rest of this entry »

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