Enzyme Evolution

[foursixand2]

I am familiar with the fallacy, i may be mistaken is called irreducible complexity? Its the idea that certain things could not have evolved because their intermediates would be useless, thus requiring a god or supernatural force to have come into existence at all. Examples would be eyes, wings, and disguises. I know explanations to disprove the fallacy at least for those examples. The simplest one: any type of eye is better than none, from being able to simply tell light from dark, to constructing crude shapes and shades, to more accurate visual equipment. Precursors to a wing may be a flap of skin that produces some amount of air resistance. An individual with this precursor to a wing would be able to survive a fall from a certain height, while its contemporaries would not. Its descendants would be driven by the benefit of any improvement of this flap that would make, being able to fall from higher heights, eventually being able to glide, eventually having a sophisticated flying mechanism. A chicken might not be able to really fly, but it can escape the ground for a few moments, thus potentially escaping certain predators. Though if i remember right a chicken is technically not the proper example since its ancestors technically were capable of true flight? Finally a disguise, no matter how crude is better than none. An insect that resembles a leaf from a certain distance, could fool a predator at this distance, surviving undetected, while its brother or sister, not quite as much resembling a leaf from the same distance, would be more likely to be eaten. This individuals genes are passed on, and some descendants will resemble a leaf at an even closer distance, driving the gradient toward eventual perfection of the disguise.

 

Sorry to bore anyone with a principle you may already understand, i was just illustrating that i understand it also. I am no silly creationist. So finally to my question. Enzymes are complex protein constructs capable of metabolizing various specific compounds. At first glance it may seem these interactions are too complex to have arisen from simpler forms.

 

So please demonstrate otherwise!! As another note i am an avid Dawkins reader, i would not be surprised if he covers this dilemma somewhere in his works, nor would i be surprised if ive even read it and do not recall at this moment. If you know of where he might cover the issue, please direct me there, i probably own whichever book it might be. and if i dont, i should, and will. Thanks for the help science forumers

[foodchain]

There is "field" of study in this that uses physics and chemistry for such questions really. IN fact the question you raise was specifically defeated by a group at a university. Not only did they discover a chemical evolution to speak of molecules they actually recreated such molecules. So if say a key and lock type of molecular pair existed, and one mutated, you would have evolution going on that level then. This is a problem I believe even Darwin recognized that could defeat evolution.

 

Evolution though is not by just classical Darwinism anymore though. For instance using molecular techniques the variation in aids and is passes around through people can be specifically tracked to individuals. The basic methodology behind this is a common tool applied at larger levels such as with species, this is done all from a molecular/cellular viewpoint.

 

Lastly a good deal of evolution is not simply more genetic code. It can just be rearrangement of existing code. A rat for instance as such a level in what might be coined epigenetic effects that can effectively remodel at a genetic level such as with histones, and that is but one example of many. Stephan J Gould also noted this in that pure genetic variation as you might find centered in a genecentric view could not explain diversity well enough, and that the epigenetic level also played a huge role.

[foursixand2]

do you have more details about that study at that university that i could read up on?

[iNow]

I guess what I'm missing in your question is this. If evolution is valid, and you agree with that point, why would the enzyme NOT have evolved as a feature which slowly and progressively became more useful just like everything else?

[foodchain]

http://www.nytimes.com/2007/08/21/science/21prot.html?_r=1&oref=slogin

 

"Offering insight into how evolution progresses inside a gene, scientists have pinpointed mutations in an ancient protein that transformed its shape and function more than 400 million years ago."

[iNow]

http://www.nytimes.com/2007/08/21/science/21prot.html?_r=1&oref=slogin

 

"Offering insight into how evolution progresses inside a gene, scientists have pinpointed mutations in an ancient protein that transformed its shape and function more than 400 million years ago."

 

Here's the actual article that the newspaper is referencing:

 

 

 

 

http://www.sciencemag.org/cgi/content/abstract/1142819

 

The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein—the 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations—substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes—played a major role in determining GR's evolutionary trajectory.

 

 

You can see supplementary work by the same author at Professor Joseph Thorton's site.

 

 

 

To be frank, I don't know if it's really relevant to the thread topic, but it's always best to cite the actual study, not the news report discussing it.

[foursixand2]

I guess what I'm missing in your question is this. If evolution is valid, and you agree with that point, why would the enzyme NOT have evolved as a feature which slowly and progressively became more useful just like everything else?

 

I do assume it would i just dont know anything about the process, i'd like to know more about how it does, which hopefully ill learn from reading that article

[lucaspa]

I do assume it would i just dont know anything about the process, i'd like to know more about how it does, which hopefully ill learn from reading that article

 

The article is in Science, which will be in your local library.

8. http://www.sciencemag.org/cgi/content/full/312/5770/97 JT. Bridgham, SM Carroll, J W Thornton Evolution of Hormone-Receptor Complexity by Molecular Exploitation Science 7 April 2006: Vol. 312. no. 5770, pp. 97 - 101

 

There are some other papers that trace the molecular evolution of enzyme systems. For instance, evolution of the blood clotting system (one of Behe's original IC structures) is summarized here:

Thromb Haemost 1993 Jul 1;70(1):24-28

The evolution of vertebrate blood coagulation: a case of Yin and Yang.

Doolittle RF

 

That one might be tough for you to find. PM me with your e-mail address and I can send you the PDF file.

 

A paper summarizing the different routes of Darwinian evolution (with lots of references) is here:

http://www.cbs.dtu.dk/dave/JTB.html

 

 

Other papers looking at the evolution of protein shapes are:

1. E Wilson-Miles and DR Davies, On the ancestry of barrels. Science 289: 1490. Sept. 1, 2000. "the structure arose from the duplication and fusion of the gene of acommon half-barrel ancestor"

3. http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030139 Formation of gene families and protein folding