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Resurrecting extinct proteins shows how a machine evolves

By bringing long-dead proteins back to life, researchers have worked out the process by which evolution added a component to a cellular machine. The result, they say, is a challenge to proponents of intelligent design who maintain that complex biological systems can only have been created by a divine force.

Cells rely on ‘machines’ made of multiple different protein components to carry out many vital functions in the cell, and molecular and evolutionary biologists have puzzled about how they evolved. In an effort to find out, Joe Thornton at the University of Oregon in Eugene chose to study a particular machine called the V-ATPase proton pump, which channels protons across membranes and is vital for keeping cell compartments at the right acidity. Part of this machine is a ring of six proteins that threads through the membrane.

In animals and most other eukaryotes, this ring is composed of two types of protein; fungi are alone in having a ring with three. Thornton wanted to know how the machine evolved from the simple to the more complex form. And, because he has built a lab that specializes in resurrecting ancient proteins, he had just the tools to find out at hand.

The team first scoured databases and pulled out 139 genetic sequences that encode the ring’s component proteins in a range of eukaryotic organisms. They then used computational methods to work backwards and find the most likely sequences of these proteins hundreds of millions of years ago, at key branching points on the evolutionary tree: just before and just after the ring increased in complexity. The team synthesized DNA that encoded these ‘ancestral’ proteins and put it into yeast, which had had parts of its own proton pump deleted. The technique allowed Thornton’s team to test in yeast whether various combinations of ancestral proteins produced a working, proton-pumping, machine.

The work, published online in Nature, reveals the pathway by which the two-component ancestral protein (let’s call the components A and B) became a three-component one (A, B and C). The gene encoding protein A duplicated, and two identical copies of the gene started making proteins A1 and A2. Then, A1 and A2 started to accumulate mutations so that they could no longer substitute for each other in the ring. To work out the exact sequence of events, the team identified the likely historical mutations and engineered them, one by one, into their version of ancestral A.

They found that just one key mutation in each of A1 and A2 created proteins that could no longer bind promiscuously with neighbouring proteins in the ring, and instead had to occupy specific spots. The proteins “went from being a generalist to a specialist,” Thornton says. And A2 eventually became C, the third part of the three-component ring now made up of A1, B and C.

The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage. In this case, the more complex version doesn’t seem to work better or have any other obvious advantage compared with the simpler one; it is more likely that A1 and A2 proteins were just corrupted by random mutation. (The yeast didn’t seem worse off when they were stripped of their own three-protein ring and instead used one built of two ancestral proteins.) “What’s surprising to me is the idea that greater complexity doesn’t require acquisition of new functions. It can come from partial degeneration of the ancestor,” Thornton says.

To those studying evolutionary theory, the result “is an expectation rather than a surprise”, says Michael Lynch, who carries out such studies at Indiana University in Bloomington. “But science does not advance with theoretical work alone,” he says. The new results “bring the theory to life”.

And to intelligent-design proponents, Thornton adds, the results say that “complexity can appear through a very simple stepwise process — there is no supernatural process required to create them.” Still, evolution of a three-protein machine is unlikely to silence those proponents — there are many far more complicated biological machines with far more protein parts and intricate internal mechanisms. Thornton says that his and other groups will now probably use the same tools to dissect the evolution of more complex molecular machines.


  1. Report this comment

    Abd Al said:

    the “evolution” is not an act of “creation” it is rather an act of “transformation”. That is, the change of the state of an element from state A into a state B. The creation on the other hand, is the act of causing the existence of something that did not exist before (like some say out of thin air).

    According to these universal definitions, evolution is just a process of transformation, not a process of creation.
    The properties of a created element (such as protein) provide that element with the ability to evolve from one state to the other. therefore the act of creation causes the act of evolution to happen, not the other way around.

    Evolving from one state to the other needs an act of decision to take place, this decision is based on a complex and huge number of factors surrounding the phenomena. Taking a decision means deciding for a choice, and as we can see the choice made causes life to happen.
    That choice keeps happening every fraction of second in the life of every living. That systematic choice needs knowledge and intelligence and can not result based on a random process. As systematic actions need a process definition and action plan.

    Therefore, taking decision, defining goals, planing and executing can not be done through evolution but through creation first. and for each physical action that happens in this world is causes by an actor (elementary knowledge in physics that behind every action there is a force F to trigger it) we can conclude that actor who decides, defines, and sets a plan for the evolution is simply your creator.

    People can deny these facts based on “Science” but they forgot that science is only human-made activity to try to explain phenomena, but if humans live in a box and use science which was defined in that box, how can human be able to judge what’s beyond that box? simply they cannot, the human brain is so limited that it’s not able to create a fly!

    if one day somebody can create a fly, i’ll stop thinking there is a creator! but till then you people denying the creator have to try harder …
    take care

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