I need help with language to use in regard to evolution

[T_aquaticus]

In a previous post I mentioned that part of the function of polymerases is to create mutations. Here is an interesting paper that led me to that conclusion:

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15803-8. Epub 2005 Oct 25.
Probing the active site tightness of DNA polymerase in subangstrom increments.
Kim TW, Delaney JC, Essigmann JM, Kool ET.

We describe the use of a series of gradually expanded thymine nucleobase analogs in probing steric effects in DNA polymerase efficiency and fidelity. In these nonpolar compounds, the base size was increased incrementally over a 1.0-A range by use of variably sized atoms (H, F, Cl, Br, and I) to replace the oxygen molecules of thymine. Kinetics studies with DNA Pol I (Klenow fragment, exonuclease-deficient) in vitro showed that replication efficiency opposite adenine increased through the series, reaching a peak at the chlorinated compound. Efficiency then dropped markedly as a steric tightness limit was apparently reached. Importantly, fidelity also followed this trend, with the fidelity maximum at dichlorotoluene, the largest compound that fits without apparent repulsion. The fidelity at this point approached that of wild-type thymine. Surprisingly, the maximum fidelity and efficiency was found at a base pair size significantly larger than the natural size. Parallel bypass and mutagenesis experiments were then carried out in vivo with a bacterial assay for replication. The cellular results were virtually the same as those seen in solution. The results provide direct evidence for the importance of a tight steric fit on DNA replication fidelity. In addition, the results suggest that even high-fidelity replicative enzymes have more steric room than necessary, possibly to allow for an evolutionarily advantageous mutation rate.

A quick summary for those who don’t know sciencese. They allowed a polymerase to copy DNA using larger and larger bases. As the size of the bases increased there was a reduction in the number of mutations and an increase in enzyme effeciency which indicates that mutations are due to a loose fit between the polymerase and the incoming

If perfect fidelity is advantageous it would seem to me that polymerases would evolve that feature, but they haven’t. Instead, the active site is just loose enough to allow for mutations. Of course, this is in E. coli so it may not apply to all other species, but it is an interesting finding.

[Rumraket (Mikkel R.)]

@T_aquaticus

A quick summary for those who don’t know sciencese. They allowed a polymerase to copy DNA using larger and larger bases. As the size of the bases increased there was a reduction in the number of mutations and an increase in enzyme effeciency which indicates that mutations are due to a loose fit between the polymerase and the incoming

If perfect fidelity is advantageous it would seem to me that polymerases would evolve that feature, but they haven’t. Instead, the active site is just loose enough to allow for mutations. Of course, this is in E. coli so it may not apply to all other species, but it is an interesting finding.

I think the drift-barrier hypothesis accounts for this. It is not that polymerases are actually somehow selected to cause mutations, but rather improving their replication fidelity beyond a certain point would require unrealistically enormous population sizes because the fitness gains from reducing the mutational load when the mutation rates are already so low would be effectively invisible to selection.

[Mercer (John Mercer)]

@AJRoberts

Yep, but way off topic if we start sharing everything we know about somatic hypermutations.

I’m not “sharing everything I know.”

I’m just heading off attempts to insert teleology where there’s no evidence to support doing so.

[gbrooks9 (GeorgeB)]

@Mercer

I’m just heading off attempts to insert teleology where there’s no evidence to support doing so.

@Mercer

@AJRoberts, and all of us here, are allowed to insert teleology everywhere … “design by God” is one of the foundation stones of this site.

This is not the same thing as saying Science can see this teleology. In fact, I’m convinced that only the human heart sees this teleology. Which means, by definition, there will never be “scientific evidence” supporting teleology.

It is not the belief in teleology that is a problem to me and @swamidass.

It is the belief that teleology can be proven that is the problem belief here.

[Mercer (John Mercer)]

@gbrooks9

This is not the same thing as saying Science can see this teleology. In fact, I’m convinced that only the human heart sees this teleology. Which means, by definition, there will never be “scientific evidence” supporting teleology.

So you’re agreeing with my pointing out that

@Mercer

there’s no evidence to support doing so.

[gbrooks9 (GeorgeB)]

@Mercer

So you’re agreeing with my pointing out that

Mercer:

@Mercer,

Yes, technically I agree there is no scientific evidence… but that’s not to say there is no evidence. Nor does it mean @AJRoberts can’t legitimately assert that God guides evolution with a heft slice of teleology. This is one of the places on the internet where she is allowed and encouraged to make observations like that!