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Evolutionary biologist Joe Thornton came up with an excellent idea: to "resurrect" or rather recreate in the lab proteins from animals that have been extinct for many millions of years. His findings refute creationists' claims of "irreducible complexity" and show how different protein families evolved and gained new functions. Before becoming an evolutionary biologist, he was an environmental scientist working for Greenpeace. Because of the effect of pollutants on steroid hormone receptors, he started to study this receptor family. in vertebrates, there are 6 steroid hormone receptors; however, none had been found in arthropods or other invertebrates. Creationist claim these genes appeared from nowhere, hence, a creator. But in 2003, Thornton discovered an estrogen receptor-like gene from the mollusk Aplysia californica. What he did next was genius: starting with the genes for steroid hormone receptors from a bunch of vertebrates, and the Newly discovered mollusk gene, he "walked backwards", down the evolutionary tree, and using computational biology, deduced the most likely sequence of the common ancestor of all these receptors. Such protein existed 600-800 million years ago, in the last common ancestor that mollusks and vertebrates shared. This ancestral gene was lost in the lineage leading to arthropods and nematodes.  Thornton did not stop there: he built the gene in the lab, inserted it in cells, and studied its function. He showed that the ancient receptor responded to estrogen only, but not to other steroids, and that its function was lost somewhere along the Aplysia lineage. He also studied the mineralocorticoid receptor (MR; this receptor binds the hormone aldosterone and regulates salt and water balance), and the closely related glucocorticoid receptor (GR), which binds cortisol and controls stress response. The two related proteins arose from gene duplication > 450 million years ago. Strangely, aldosterone did not evolve until millions of years later! God! yelled the creationists, asking "where was the drive to evolve the two separate receptors if the hormone did not exist back then?  By resurrecting the ancestor of both receptors, Thornton solved the puzzle. To his surprise, the ancestral protein was sensitive to aldosterone, suggesting that it had been activated by an ancient ligand with a similar structure. Once aldosterone evolved, evolution, as usual, works with what's already there, and co-opted the receptor to control a new biological function. The phenomenon is called "molecular exploitation". The crystal structure of the common ancestor of the GR and MR was determined, showing that 2 crucial mutations altered the binding pocket of the ancestral receptor so that it favored cortisol, and identified another five mutations that were crucial for cortisol binding, but prevented the binding of other ligands. Evolution opens some doors, but closes others. This year, Thornton and his collaborators dissected the evolution of V-ATPase, a proton pump that regulates acidity within the cell. He showed that random mutations that actually corrupted proteins had led to "irreducible complexity." I highly recommend bookmarking and reading the entire article.

Prehistoric proteins: Raising the dead


To dissect evolution, Joe Thornton resurrects proteins that have been extinct for many millions of years. His findings rebut creationists and challenge polluters.

21 March 2012

SHAWN RECORDS

Halfway through breakfast, Joe Thornton gets a call from his freezer. A local power cut has triggered an alarm on the −80 °C appliance in his lab at the University of Oregon in Eugene, and it has sent out an automatic call. Thornton breaks off our conversation and calls his senior research scientist, Jamie Bridgham, to make sure that the back-up generator has kicked in. If the freezer starts warming up, a lot could be lost — not least a valuable collection of proteins that had been extinct for hundreds of millions of years until Thornton and his team brought them back from the dead.

One deep-frozen vial holds the more-than-600-million-year-old ancestor of the receptors for oestrogen, cortisol and other hormones, which Thornton brought to life1 nine years ago. Other tubes house proteins more than 400 million years old, which Thornton resurrected a few years later to show how an ancient receptor had changed its preferences — and how the march of evolution cannot be reversed234. In another corner of the freezer rest the ancient protein components of a sophisticated cellular machine that acquired a more complex form through random mutations rather than selection for superior function, as the group showed in Nature this January5. The sheer awe of working with long-dead proteins doesn't fade, says Thornton. “It's amazing. The ability to do this type of time travel is fantastic.”

Thornton is a leader in a movement to do for proteins what the scientists in Jurassic Park did for dinosaurs: bring ancient forms back to life, so that they can be studied in the flesh. “Instead of passively observing things as most evolutionary biologists do, you actively go in and test the hypotheses experimentally,” says Antony Dean, a molecular biologist at the University of Minnesota in St Paul who heads another major group in the field. “His is one of the leading labs, no doubt.” And Thornton is tackling some important questions, says Kenneth Miller, a molecular biologist at Brown University in Providence, Rhode Island. “He's helping to put some flesh on the bones of speculation about how complexity arises.”

What isn't so widely known is that evolutionary biology is Thornton's second career: in his first, he was an activist for Greenpeace, campaigning vigorously against the release of toxic chemicals. He wrote a controversial book on organochlorines: industrial chemicals that include dioxins, polychlorinated biphenyls (PCBs) and pesticides such as DDT. That activist legacy bleeds into his work today, for example in his focus on the oestrogen receptor, which is corrupted by many pollutants. The grubby, sea-green tiles under Thornton's lab benches were carefully sourced to be free of polyvinyl chloride (PVC), one of the organochlorines that worries him most. His activist past also helps to explain why he has been fearless — almost enthusiastic — about highlighting the challenge that his work presents to a creationist argument called intelligent design: the claim that complex molecular systems can only have been created by a divine force. Thornton shows how evolution did the job, leaving no need for a designer.


Read the rest here

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His original article:

Science. 2003 Sep 19;301(5640):1714-7.

Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling.

Source

Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA. joet@uoregon.edu

Abstract

Receptors for sex and adrenal steroid hormones are absent from fully sequenced invertebrate genomes and have not been recovered from other invertebrates. Here we report the isolation of an estrogen receptor ortholog from the mollusk Aplysia californica and the reconstruction, synthesis, and experimental characterization of functional domains of the ancestral protein from which all extant steroid receptors (SRs) evolved. Our findings indicate that SRs are extremely ancient and widespread, having diversified from a primordial gene before the origin of bilaterally symmetric animals, and that this ancient receptor had estrogen receptor-like functionality. This gene was lost in the lineage leading to arthropods and nematodes and became independent of hormone regulation in the Aplysia lineage.

His latest article on vATPases:

Nature. 2012 Jan 9;481(7381):360-4. doi: 10.1038/nature10724.

Evolution of increased complexity in a molecular machine.

Source

Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.

Abstract

Many cellular processes are carried out by molecular 'machines'-assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine--the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump--increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

Just the same way they build research satellites these days --off the shelf components where possible, off the shelf components but modified to suit the research mission and completely new components when the other to ways fails to give what is required to fulfil the mission.

Good analogy, Davy.

LOL! This is a bit beyond me.

But I'm always amazed at the lengths creationists will go - up to studying genetics - to look for "holes." They are like the stupid worm burrowing a hole in the tree; when he gets to the other side of the trunk, he expects the tree to fall.

Awww...I guess I did not explain it very well; I tried to explain the work without being too technical, because what this guy did is brilliant. But it is very hard to put in non-technical terms, at least for me, because it's my field. Sorry...

No worry =)
I'm missing too many bricks to appreciate the technical prowess. I barely get the drift, but I get it. 

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