Correcting a Quote Mine on Deleterious Mutations

[thoughtful (Valerie (non-scientist))]

@ProfBravus

Do they?

Yes.

@CrisprCAS9

You can just read what they actually say… Reduced selection, to the extent they say it at all. Implying of course that a) normal levels of selection would not result in fitness reductions and b) none of it applies to any other species necessarily, and c) the reductions will reach a new equilibrium and then stop.

It’s not in his book, but this paper is referenced on Sanford’s website as a new development. It doesn’t come to that conclusion - it’s sort of opposite of everyone else and what you were saying - granted they say selection will increase. But all of this seems to be begging the question.

Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes

We estimate that humans and chimpanzees have accumulated approximately 140,000 slightly deleterious mutations each, mutations that would have been eliminated by selection in murids. These mutations have small effects, since it can be inferred that they have selection coefficients less than 1/ Ne for hominids, i.e., less than 10−4. It should be noted that it is unlikely that the mutation accumulation is due to a recent relaxation of natural selection in humans due to an improvement in our living conditions [32], since the time of this improvement is short relative the overall length of human evolution. We would not expect the decline in fitness to continue indefinitely, since the absolute strength of selection on new mutations, both advantageous and deleterious, may increase as fitness declines [33]. Furthermore, this accumulation of deleterious mutations may have been compensated in part by adaptive substitutions in gene expression control regions and elsewhere in the genome.

@CrisprCAS9

And yet it does apply to viruses, in spite of even higher population sizes… Odd, that. All most like they’re just making stuff up to fit whatever they need as they say it.

It seems like this is a silly argument when I can look up basic biology info about replication and find that selection obviously plays a role as they explain below.

@Rumraket

*Edit: Forgot to mention, bacteria generally have huge population sizes, which would imply that mutations of smaller effect are visible to selection.

Yes, but also this:

Bacteria have an amazing growth rate. The entire world population of a species like E. coli turns over very fast (perhaps once per hour). Trillions upon trillions of these cells die for many different reasons each and every hour. Thus, this may be a system where natural selection can actually halt the inevitable decay. Why? Because any mutation that confers even a small disadvantage (and most do) can be removed through differential reproduction, given enough time. (Time in this case is measured in generations.)

@Rumraket thanks for sharing this paper with me. The irony is that it has some of the same authors as the paper above, even though they seemed to refute some of their same research. But all the fitness distributions in the graphs were uneven.

http://www.lifesci.susx.ac.uk/home/Adam_Eyre-Walker/Website/Publications_files/EWNRG07.pdf

What I thought was key:

This raises a crucial question: can we ever really know what the DFE is? For a simple organism like a virus, this does seem to be possible, because most mutations have large effects that can be assayed in the laboratory. For most other organisms, and particularly
for multicellular organisms, quite the opposite is the case; most mutations, even if they are deleterious, have such small effects that one cannot measure their fitness consequences. Furthermore, the environment in which most organisms live is probably sufficiently complex that laboratory assays give only the crudest measure of fitness. However, comparative methods using DNA sequence data potentially allow us to circumvent both of these problems. By examining the pattern of polymorphism in a species, we can estimate the effects of mutations with very small effects and we can infer the overall fitness consequences of mutations in the environment in which the species evolved. Furthermore, if we are prepared to sequence hundreds, if not thousands, of alleles then we can, in principle, measure the DFE for both strongly and weakly selected mutations. So, the DFE is knowable, but uncovering it might require a large amount of sequencing and effort.

Isn’t this what Sanford and Carter did?

Isn’t this what they’re doing with SARS-CoV-2? No undisputed increase in fitness in any mutant so far?

So…this is the reason why I think GE has merit based on what I’ve seen in the forum so far:

• When human degeneration is pointed out as evidence of GE, then scientists say natural selection must have acted (this is begging the question based on your/their view of evolutionary theory)

• I haven’t seen proof of how scientists think natural selection acts or how scientists have researched/posited it, other than how Sanford says they do.

• Sanford convincingly (IMO) refutes how scientists think or have posited how natural selection acts.

• I have seen no one try to state or prove he’s wrong on natural selection.

• Others bring up beneficials and their distribution, and we go back to Bullet #1

For those that haven’t read the book, this is the point I’m up to and Sanford goes beyond the Kimura’s no selection zone.

As always, let me know what I’m getting wrong or missing. This is my non-scientist brain, trying to understand a science world. It’s interesting