One Of These Again

And finally, Today’s DpSU was New Study Shows Enzymes Couldn’t Evolve.

CS2 hydrolase enzyme - click through for more pictures

Yes, this is one of those DpSUs when a study works out a way for x to evolve, and the Mr Thomas tries to reinterpret their results to show otherwise.

What the study has done is found, analysed, compared and finally mutate an apparently previously unknown enzyme, which is apparently what you have to do to get published in Nature. In the mutation phase they tinkered with the tunnels leading to the active site of the enzyme. They found that they could both decrease and increase the reactivity of the enzyme with these mutations, depending on what they did to the enzyme. Knowing this, why does Mr Thomas say this?

On one hand, evolution’s story requires that, at some point in time, something altered what would become the enzyme core again and again, as each structural piece evolved into place over eons. On the other hand, science shows that altering the enzyme core in the slightest is impossible without making the whole structure useless.

Am I to take it that I’ve read more of the paper than he has? I have recently acquired a Nature subscription, which is why I can read that far – is it now he that is only reading the abstract? I need more data…

The researchers found a clue in the DNA that suggested to them an idea of how the enzyme could have evolved. The DNA that codes for the tunnel portion of the CS2 hydrolase gene is surrounded by unique sequences, indicating that this DNA portion may have been added to the main enzyme’s DNA. Perhaps some unknown cellular mechanism “stitched in” this extra bit at just the right place among the bacteria’s 1.8 million DNA bases, adding the tunnel portion to a CO2-converting enzyme through “lateral gene transfer” and thereby forming CS2 hydrolase. If so, could this process properly be called “evolution”?

I don’t know where he’s going with this “unknown cellular mechanism” thing – DNA gets moved around all the time. Evolution is change, so this is evolution.

Actually, I do know where he’s going – he’s back on his Lamarckian adaptation mechanisms thing again.

No—if the gene jumped from another bacterium to this one, it did not evolve because it already existed elsewhere. But in order for a lateral gene transfer to even work, in addition to the enzymes themselves, another mechanism had to already exist that could recognize, accept, and insert the foreign DNA in just the right place. Only then could it retrofit an enzyme in just the right way to enable the bacterium to live on sulfur.

that doesn’t mean it’s not evolution, and he has no evidence to suggest that any mechanism was needed to “recognize, accept, and insert the foreign DNA in just the right place” nor that any process like that had to happen. This brings me back up to the second paragraph, for another example of Mr Thomas’ logic:

[E]nzymes are highly engineered miniaturized machines. Even intelligent human scientists armed with the most sophisticated technology cannot reproduce their design and manufacture—so, logically, neither can unintelligent chemicals or the laws that govern them.

That doesn’t follow. Now, back to where we were.

Where’s the evidence here for evolutionary innovation? Pre-existing DNA and pre-existing DNA transfer and splicing programs appear to have existed from the beginning.

Read the paper. (I am ranting a lot tonight, aren’t I – that’s what English exams do to you, along with stupidity on this scale.)

The authors asserted that CS2 hydrolase “emerged owing to the evolution of a new quaternary [final protein] structure.” But this ignores the facts that no new DNA actually “emerged,” and the proper placement of transferred DNA required just the opposite of evolution—purposeful design.

They’re not even saying that “new DNA” emerged – that’s not necessary for evolution to take place. And he has no evidence that “purposeful design” was required.

CS2 hydrolase did not evolve. In fact, experimental science shows that this enzyme functions today only because of its precise and specific arrangement of parts. And like any machine with multiple, inter-connected parts, whether biological or man-made, all the correct parts assembled in the correct configuration were needed from the very beginning.

I’ll quote from the paper this time:

To test whether active site accessibility determines the reaction specificity, we designed seven CS2hydrolase mutants, with the amino acid residues that form the tunnel wall being replaced by smaller or larger residues. Furthermore, the C terminus was truncated (mutant Gly199Stop) (Fig. 4a). The activities of the mutant CS2 hydrolases were quantified (Fig. 4b) and were visualized on native PAGE activity gels (Supplementary Fig. 5). The mutants with a change in Phe 78 lost most or all of their activity (Fig. 4b). Phe 78 is close to the active site (Fig. 4a), and any change in this region of the protein adversely affected enzyme activity. By contrast, widening the entrance of the tunnel by shortening the C terminus or by replacing large hydrophobic residues with smaller ones (for example, Phe77Ala or Phe96Ser) (Fig. 4a) reproducibly increased the catalytic efficiency of the mutants by up to twofold (Fig. 4b).

I don’t think he read it. (For one thing, he would be misguidedly harping on the “designed” aspect of the mutants – the fact that he isn’t is pretty damning evidence in my opinion.)

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2 thoughts on “One Of These Again

  1. Pingback: Anammox « Eye on the ICR

  2. Pingback: Mistakes Were Made – But Not By Us « Eye on the ICR

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