The Electric Eel - more evidence against evolution

Yes. We have enough factors to make equations to estimate, e.g., the amount of time it will take for a particular complex adaptation to arise. Yes, it could be.

So the great deal of sequence similarity between human and chimp genomes could be due to convergence, rather than common ancestry? Because, ya know, we don't know all the details, so we can't rule out convergence? Yes, that's generally how science works. Even if a hypothesis doesn't fit very well, it usually remains until replaced by a more robust hypothesis. When was the last time I said that? I concur.

I don't think convergent evolution is a better explanation for the genomic sequence similarity than common ancestry. The reason I don't think so has precisely to do with probability -- despite the fact that we don't know all about genome evolution. Improbability or implausibility of a hypothesis is not enough to support an alternative model; it is simply enough to cast the hypothesis into doubt and intensify efforts to look for other explanations. It's perfectly relevant to gauge the robustness of a particular hypothesis for the origin of a given system.

Nothing else, unless you have some other idea that wouldn't boil down to probability. The reason we can say with confidence that certain human and chimp proteins are homologous is precisely because of statistical significance of the match. Of course just saying "it's improbable" doesn't suffice; one must detail reasons to support that thesis. So when choosing one phylogenetic hypothesis over another, why does one choose the one with the greatest probability? Because, ya know, improbability isn't relevant.

Then what is your view on all those disciplines of science that base conclusions on the basis of improbability, when obviously we still don't have all the possible information? How do you determine when (a) we lack all information, and (b) we don't? I'm just a bit confused on this, since you immediately follow up with: Those "certain aspects of science" use speak of include population genetics and evolutionary biology.

Surely. For starters (references not in journal format since it's easy enough just to google the titles):Lynch, M., Abegg, A."The Rate of Establishment of Complex Adaptations," 2010.This is just from the abstract -- I encourage you to read the whole paper to get an idea of what's going on:
"A central problem in evolutionary theory concerns the mechanisms by which adaptations requiring multiple mutations emerge in natural populations. We develop a series of expressions that clarify the scaling of the time to establishment of complex adaptations with population size, mutation rate, magnitude of the selective disadvantage of intermediate-state alleles, and the complexity of the adaptation. In general, even in the face of deleterious intermediate steps, the time to establishment is minimized in populations with very large size."Also from Michael Lynch:
"Scaling expectations for the time to establishment of complex adaptations," 2010.The abstract:
"Although the vast majority of research in evolutionary biology is focused on adaption, a general theory for the population-genetic mechanisms by which complex adaptations are acquired remains to be developed. The issue explored here is the procurement of novel traits that specifically require multiple mutations to achieve a fitness advantage. By highlighting the roles played by the forces of mutation, recombination, and random genetic drift, and drawing from observations on the joint constraints on these factors, the ways in which rates of acquisition of specific types of adaptations scale with population size are explored. These general results provide insight into a number of ongoing controversies regarding the molecular basis of adaptation, including the adaptive utility of recombination and the role of drift in the passage through adaptive valleys."See also:Durrett, R., Schmidt, D. "Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution," 2008."...we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second of which creates a new one. Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take >100 million years."So as not to be accused of quote-mining:
"In addition, we use these results to expose flaws in some of Michael Behe's arguments concerning mathematical limits to Darwinian evolution."There are other papers on the subject, as well. The point is this: we do indeed have tools to make estimates of the amount of time it would take for a particular complex adaptation to evolve. The next challenge, then, would be to find ways to determine the categories of complex adaptations current molecular systems fall into. It does not matter who is making the claim so long as the claim is supported by evidence. When did qualifications become a part of this? As long as the claim is supported by evidence, qualifications do not matter. It's easier to back up claims when one is familiar with the pertinent literature and does not make a claim unless it can be supported. Edited by Genomicus, : No reason given.

That doesn't work because theories aren't complete explanations. Even theories lack all information. Sure. But we now have a workable theory of molecular evolution, population genetics, and related disciplines. We have tools and techniques in population genetics and evolutionary biology to allow us to make rough estimates of the plausibility of evolutionary pathways. To be sure, such techniques cannot be applied to all systems. However, the point stands: we're not in a phase where we're "in the dark." Evolutionary biology and related disciplines have developed past that point. Edited by Genomicus, : No reason given.