Wednesday, October 18, 2006

Update of Haldane's Dilemma on ARN?

On the ARN bulletin board, there is discussion about this paper, "Estimate of the Mutation Rate per Nucleotide in Humans".

The first reply, by somebody with the handle "Life Engineer", says:
This has been discussed many times. The harmful and even neutral mutations predicted by Neo-Darwinian dogma don't actually occur. They are selectively eliminated by intelligent error correction mechanisms. As has been often discussed, the almost non-existent harmful mutations is an example of the evidence clearly contradicting the theory, but the soft science procedures intentionally ignoring the evidence in claiming the theory is still valid.
The argument then moves in a different direction, but I wanted to react specifically to this, without the 100 or so further responses that follow.

The assertion is that the harmful/neutral mutations are selectively eliminated. This sounds great, but I was left thinking - "at what stage?" My understanding was that gametes are formed by meiotic division, rather than mitotic - but in their nature, much of their functionality remains unexpressed whilst still in their haploid form. So, from the point of view of the parent, or for that matter the process of cell reproduction, there is no way to differentiate between harmful and beneficial mutations, let alone apply "intelligent error correction mechanisms" to get rid of harmful mutations. There is little evidence to show that the vast majority of human eggs contain harmful mutations - yes, up to 50% of fertilization events may not result in a live birth, but this doesn't approach the "female 40 offspring for 2 to survive" that the authors of the paper put forward. I also don't know whether there is evidence that this intelligent error correction occurs before the egg cells are included in the ovary - in other words, that the error correction takes place at an even earlier stage. And how would this relate to the production of male gametes?

On the other hand, it is interesting that this (5%) survival rate is consistent with what David Stove says Darwin's theory as he set it out implies.

More generally, as the original poster (Salvador, IDEA GMU) suggests, there does seem to be something circular happening in the argument here. Something along the lines of:

- We know that beneficial mutations (sorry - that implies teleology - what I mean by "beneficial" there is simply steps towards the new species that we see today) must be occuring at a specified rate, to allow for the evolution from (say) proto-hominid to homo sapiens.

- But this would entail a significant number of "harmful" mutations - that is, mutations that reduce the organism's fitness.

- Therefore, since evolution is true, either harmful mutations must be selectively eliminated (harmful mutations are "non-existent", according to Life Engineer - and the evidence in support of this is apparently the lack of harmful mutations, not a mechanism to eliminate them), or there must be another mechanism at work (the authors of the paper propose something called "synergistic epistasis").

Now this is a reasonable scientific approach. Here is a scientific "world-view" (macro-evolution). Here is an implication of it (required mutation rate). Here is an implication of that (the impact of harmful mutations). And here is a suggestion as to how this can be resolved (synergistic epistasis, or some mechanism for intelligent elimination of harmful mutations). However, it is important to think through the scientific implications. Macro-evolution was presented to start with as an assumption. You can't use an assertion of the truth of macro-evolution to support an argument when it is the truth of macro-evolution that you are seeking to demonstrate. Ultimately, if evidence doesn't support that assumption, then you have to throw away the assumption, and at least say: "We don't know".

In my job, we are warned about the danger of "confirmation bias". An event happens, which we have indications to interpret, and we come to some conclusion about what that event is. We then fit all subsequent evidence into that interpretive framework. We are told that, having dealt with what we perceive to be the problem, we need to be prepared to "review" evidence as carefully as time allows, in the hope that stepping back and looking again at everything might allow us to pick up something that will break the risk of confirmation bias.

My perception is that, in the case of evolution, confirmation bias has set in in a big way - exacerbated by what I would consider to be the erroneous assumption that good science requires philosophical naturalism. All evidence is fitted into the evolutionary paradigm, no matter how stretched it ends up, no matter how many contradictions it contains.

There are a limited number of ways in which this specific conundrum (the impact of harmful mutations) can be solved. I suspect that Life Engineer's solution is already moving too far in the direction of teleology for some people (he distinguishes himself from the "neo-darwinian dogma") in talking about "intelligent error correction mechanisms" - what does he mean by "intelligent"? can he reword this using concepts that don't imply purpose? What happens if and when these solutions are shown not to work, I wonder?

One more thought, relating to the bias against Intelligent Design as a worldview. Suppose this research had been done and written up by somebody from the Discovery Institute, and rather than proposing synergistic epistasis, they had simply highlighted this as a problem for macro-evolution. Would such a paper have been published in a mainstream journal? I would suggest not, despite the fact that synergistic epistasis currently has no more scientific basis than intelligent design - EXCEPT that it apparently avoids the risk of external agency, and so allows people to hold on to darwinian macro-evolution for a bit longer.