Posted: Jul 02, 2010 10:22 am
by Calilasseia
Oh dear. I see someone's erecting the "beneficial mutations don't exist" canard. Yawn. Time for this:

Protein engineering of hydrogenase 3 to enhance hydrogen production by T. Maeda, V. Sanchez-Torres and T. K. Wood, Applied Microbiology and Biotechnology, 79(1): 77-86 (May 2008)

Here's the abstract:

Maeda, Sanchez-Torres & Wood, 2008 wrote:The large subunit (HycE, 569 amino acids) of Escherichia coli hydrogenase 3 produces hydrogen from formate via its Ni-Fe-binding site. In this paper, we engineered HycE for enhanced hydrogen production by an error-prone polymerase chain reaction (epPCR) using a host that lacked hydrogenase activity via the hyaB hybC hycE mutations. ... The best epPCR variant contained eight mutations (S2T, Y50F, I171T, A291V, T366S, V433L, M444I, and L523Q) and had 17-fold higher hydrogen-producing activity than wild-type HycE. In addition, this variant had eightfold higher hydrogen yield from formate compared to wild-type HycE. Deoxyribonucleic acid shuffling using the three most-active HycE variants created a variant that has 23-fold higher hydrogen production and ninefold higher yield on formate due to a 74-amino acid carboxy-terminal truncation. Saturation mutagenesis at T366 of HycE also led to increased hydrogen production via a truncation at this position; hence, 204 amino acids at the carboxy terminus may be deleted to increase hydrogen production by 30-fold. This is the first random protein engineering of a hydrogenase.


So, what did the authors of this paper do?

Basically, they wanted to improve the performance of the hydrogenase-3 enzyme that is used by Escherichia coli, with a view to using it as a commercial producer of hydrogen gas. Now, there were two possible approaches to solving this problem. The first approach would have been to dissect the enzyme, amino acid by amino acid, determine how that enzyme worked based upon its structure, then try and design a better one with a more economical structure with improved performance. However, the authors realised that this process would keep them up to their necks in supercomputer analyses of the molecules for the next 50 years. Needless to say, they wanted a quicker route. So what they did was this. They decided to let evolution do the hard work for them.

Now, in order to understand the neat trick employed here, bear in mind that in order to copy DNA molecules, scientists use what is known as a polymerase enzyme, which is an enzyme that is present (in various forms) in all living organisms. Everything from bacteria to humans possesses a polymerase enzyme of some sort. Indeed, these enzymes were first pressed into service on a large scale in forensic science, where they are used to amplify the contents of a DNA sample, so that there is sufficient material available for gel electrophoresis (the so-called "DNA fingerprinting" technique). However, forensic scientists are interested in eliminating copying errors, so that the amplified DNA fragments are all faithful copies of the original. So, forensic scientists have been looking for high-fidelity polymerase enzymes (and have found them) to perform this task. What the authors of the above paper were interested in was not the production of high-fidelity copies of their hydrogenase gene, but accelerated generation of mutant versions of that gene. So, they deliberately looked for a polymerase enzyme with low copying fidelity in order that mutations would be introduced into the gene population at an accelerated rate.

Once they had their population of mutants, they then tested each of the mutants for efficiency in producing hydrogen. The abject failures were discarded, whilst those that produced hydrogen more efficiently than the original were used as seed material for a second round of the same process - accelerated mutation, followed by selection of the successful mutants. In other words, the classic Darwinian process, just speeded up a little. And, when they did this experimentally in the laboratory, it worked. Not only did their accelerated evolution process produce lots of nice mutants to select from, but it eventually produced a mutant that was thirty times better than the original wild type enzyme at producing hydrogen.

In other words, evolution has been demonstrated experimentally to work in the laboratory and to be capable of producing improvements in a function coded for by a given gene.

And before anyone tries to erect apologetic bullshit to the effect that the above paper somehow supports "design" (despite the fact that, with typical lack of rigour, creationists use the word "design" for two entirely different processes, and perform a duplicitous bait and switch based on this), what happened in the above experiment was this:

[1] Generate lots of mutants;

[2] Test the mutants for competence with respect to the desired function;

[3] Discard the failures;

[4] Use the successful ones as seed material for a repeat round of mutation and selection.

The idea that this supports creationist assertions about "design" is ludicrous. Plus, it nails the lie that beneficial mutations don't exist. Indeed, in vitro evolution, with the fitness function being determined by increased success at production of a given end product, is being harnessed in research laboratories for such tasks as the production of new pharmaceuticals, and large R&D budgets are being expended upon this.

Indeed, that's how nature works - if a gene producing a given product gives an organism a competitive advantage, it is selected for, and if better versions of that gene arise, they are in turn selected for. No magic needed, and certainly no magic man.

Next?