This is most probably wrong. For example, nearly unique among vertebrates, bats constitutively express
IFN alpha genes, likely resulting in less viral replication, hence less GE.
In summary, we present an evolutionarily unique bat type I IFN locus with the discovery of only three functional bat IFN-α genes. Although bats have fewer IFN-α family members, the constitutive and ubiquitous expression pattern of IFN-α in bats may provide bats with a highly effective system for controlling viral replication.
Sure but without those particular values, all you have is handwaving. GE isn’t testable because you have no way to predict a magnitude of effect.
The point is that the whole idea with natural reservoirs is just his vague idea you point to when we point out life is really really old. But your vague idea doesn’t save GE because it has no content. There is no actual testing of the GE idea going on because you have no values to plug into any formula that shows deep time is consistent with GE given the natural reservoir. This meets the criterion for pseudo-science.
I think I’m a billionaire. Since I am, I must have billions in the bank. How did I get it? Where is it? I don’t know, but that I don’t know doesn’t mean it doesn’t exist, right?
This would seem to conflict with observations of viruses in known contexts. And what do you mean by “natural reservoirs”? I don’t think you have any idea. The default hypothesis should be that there is no such thing.
Not only don’t you know, it’s difficult to imagine how higher fidelity replication would be accomplished. The default hypothesis should be that there is no such thing.
Obviously. But I would suggest that the credible range of particular values doesn’t include the magic “reservoirs” you need. Sanford attempts to get out of this problem by postulating an extremely young biota. But how can you? Forget viruses. Shouldn’t all life be extinct by this point?
…and then you go on not to respond at all to that claim.
Significantly less? Do bat viruses evolve unusually slowly? That would be a test of your hypothesis. Of course when we say “bats” here, we’re referring to exactly one species, as the paper mentions nothing about any other bat species.
Bats are a concern because they are a reservoir with spillover potential. Given that bats are often found in vast packed together colonies, it is not surprising that they exhibit defensive antiviral adaptations. That this might result in preservation from GE, however, is nonsense.
If such preservation were the case, we would expect that viral surveys would review a preserved strain. As has been stated above, and any search of the literature would confirm, is that natural reservoirs, bats included, manifest variation. For just one of several studies…
Through detailed research on 13,064 bat samples from 14 provinces of China, 1141 CoV strains are found across 10 subgenera and one unclassified Alpha-CoV, generating 399 complete genome sequences. Within bat CoVs, 11 new CoV species are identified and 425 recombination events are detected. Bats in southern China, particularly in Yunnan province, exhibit a pronounced diversity of CoVs.
Whenever bat hosted viruses are inventoried, it is the same story. There will be a spectrum of variation, often leading to constructions of deep phylogenic trees. Undoubtedly, the cataloged strains are but a narrow portion of those actually existing in the here and now, and the strains existing in the here and now but a portion of strains which have come and gone. There is no single dominant or static wild strain. There are thousands of mutations represented. Any evaluation of the host-viral interaction and variation must be consistent with the observation that there is nothing close to genetic preservation in bat reservoirs, even over relatively brief intervals. The self inconsistency of GE remains.
Given neodarwinism only, yes, I believe that all life should be extinct by this point. So something else is at play. I proposed an hypothesis at 88. Let me quote myself: For example, one can hypothesized that stem organisms played similar role in phylogeny than stem cells in ontogeny. We know that the mutation rate is lower in stem cells than in somatic cells. Similarly, the mutation rates of these putative stem organisms could also be much lower than the ones observed in non stem organisms, making them much less prone to GE
No, given the hypothesis of GE. Not “neodarwinism”(whatever that is even supposed to be).
There isn’t anything in contemporary evolutionary theory that entails life can’t be billions of years old. You have to assert some premise that just isn’t part of standard evolutionary theory. You have to make assumptions that have no empirical support.
So you are hypothesising a completely unobserved (and likely unobservable) lower “mutation rates of these putative stem organisms” (which are likely all extinct) as an explanation for the fact that we fail to observe GE? Wouldn’t a simpler explanation be simply that Sanford hallucinated GE?
Likewise, the only basis for your hypothesis seems to be the fact that Stem Cells and ‘Stem Organisms’ share a similarity in labels – hardly the basis for a strong analogy, let alone a strong argument that they should share this particular similarity.
You are ignoring that bat virus populations are permeated with mutation. The reality does not conform to the rhetoric of GE.
The proof is in the pudding, is it not? We have long known that tolerance in bats does not preserve viral purity, as variation is the observed state. Tolerance in bats does not offer any sort of mutation free zone. Sanford does not get to have it both ways.
But do the evolutionary rates of bat viruses drastically slow down relative to the rates of virus evolution in other hosts? You have nothing so far that says this, so your references are not relevant to the main issue.
But those animal reservoirs, as far as we can tell, do not have the characteristics you demand in order to save viruses from GE.
I mean it’s difficult to imagine a credible mechanism. And you have no data to indicate such a mechanism, or a lower mutation rate for any reason.
Great. But what organisms are stem organisms? Shouldn’t we be able to identify them easily? On phylogenetic trees, they should show unusually short terminal branch lengths. And by “unusually”, I mean many orders of magnitude. Where are these stem organisms? And what would their biology look like, for that matter? You’re just postulating a form of magic here.
These stem organisms existed at widely varying times scattered across evolutionary history. Your hypothesis suggests that we should be able to look at extant species, see which ones (if any) have much lower mutation rates than their relatives, and determine that these species are the stem organisms for future clades. Since humans don’t have a lower mutation rate than other mammals, or even other primates, your hypothesis suggests our lineage won’t thrive and diversify.
Your hypothesis also suggests that the stem organisms, with their lower mutation rates, would not have been able to evolve as fast as their competitors in response to changing environmental or ecological conditions, and so would have gone extinct - which would have course prevented them from becoming stem organisms at all.
You didn’t consider the possible consequences of your hypothesis at all, did you?
Not only the rate of evolution of RNA viruses can be order of magnitude less in some ecological distinct host species (see my answer to @John_Harshman ) but there is also the possibility of abiotic preservation of viruses (see below). So no, as far as RNA viruses are concerned, GE is not necessarily inconsistent. To argue that it is, one has to assume that we have a comprehensive understanding of the world of viruses, which is far, far from being the case.
Two problems: 1) the rate of evolution isn’t the same thing as the mutation rate unless all mutations are neutral; 2) even the slowest observed rate of evolution is very fast, enough that if GE were true the virus would have gone extinct long ago. So where’s your magic reservoir? Are you now going to claim that it’s glaciers? But how old, even if we believe this bizarre hypothesis, are the oldest glaciers? Hold old do you think the oldest virus lineages are?
The evidence is direct. We observe diversity, not fidelity. What is the point in postulating mechanisms for an end state that doesn’t exist? If there is some high fidelity strain, please provide an example.