Without a consistent molecular clock how does the theory make predictions?
You cite a paper that contradicts you outright, in the abstract?
It was emphasized that departures from exact clockwise progression of molecular evolution by no means invalidates the neutral theory.
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… and a partridge in a pear tree.
Okay. So what are you saying? Are these numbers implausible in your opinion? If so, why? What, in your estimation, would be more plausible ones? Please, provide some, if crude, calculation, that illustrates why exactly your estimates are more plausible than what the consensus says the data shows.
In my opinion any chromosome change based on reproductive errors becoming fixed in large population is difficult to justify because the mutations eventually impede reproduction in that population. The most likely event is the variants get removed from the population.
This is a tentative opinion based on the papers previously cited here.
The word exact and consistent are different. Models require consistent mechanisms. This is what the paper you cited shows you are missing to support your model.
Fair enough. So in lieu of genetics - since we are, it would seem, tentatively opining that none of it is a thing at all - how would you propose to account for the effects of selective breeding, or generally any observed systematic change in any population of any organism?
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We can observe a lot of changes that are not dependent on the general gene arrangements and chromosome counts.
There is natural variation combining two different dogs with different features through the combination of the genetic differences between the mother and the father along with genetic recombination. There can also be epigenetic differences that can be independent of gene arrangements and chromosome
counts.
No. Neutral theory does not require a “consistent” molecular clock. It doesn’t have to be consistent, constant, exact, or anything of the sort. Bill you’re just making shit up again.
No, models require mechanisms that can be modeled. They can change over time, a lot. As long as that can be represented mathematically, the output of a model can be compared do data and tested in that way.
You also don’t understand what models are in the slightest. Is there no end to things you will opine on with no comprehension?
No paper I have cited has shown anything of the sort. None of your papers have supported any statement you’ve made. You’re just blathering on a topic where you understand nothing yet you’ve just memorized a couple of vacuous catchphrases.
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How would you propose making a predictive model of a mechanism whose output varied unpredictably?
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Then how do you predict the amount of time for a process (chromosome change) to be completed?
You could make a lot of model runs with parameters set to different values (within some range deemed to be realistic) and you get some range of outputs and within this range, some outcomes are more likely than others. That would then tell you how often you’d expect a lineage with a higher(or lower)-than-average rate. That’d be one way to do it.
So maybe instead of using the word consistent the chromosome mutation rate driving the molecular clock has to operate in a “realistic range”.
I’m not sure what you meant to say, but if you meant to say the allowed range for the mutation rate has to be within a certain range, it could be. It could also be defined by some probability distribution where the rate is more likely to be within a certain range, and it becomes increasingly unlikely the more it deviates from the mean(like in a gaussian distribution for example). Obviously if the range is allowed to be completely unconstrained with equal probability for any imaginable value the model is meaningless as you could get anything from none to an infinite rate of change and all outputs being equally likely. Then yes, you couldn’t predict anything other than “anything goes.”
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But even this would not violate Neutral Theory, it would just mean that, in that specific (and unlikely) instance, the outcome of Neutral Theory would be inscrutable.
Neutral Theory =/= always yields a predictable model.
Right, but to be clear that just isn’t neutral theory. It isn’t a theory where the mutation rate can take any value with equal probability from an infinite range. That would be silly and nobody posits such a thing.
But it is a model that makes predictions, it just has to be understood statistically.
It’s no different than modeling dice, or coinflips, or whatever. There’s going to be variation in the outcomes and you can evaluate that statistically when you do lots of runs. Model throwing 50 dice, record the results. Do it again. Do it a million times. There’s going to be a range of outcomes with some being more likely than others. You can then compare it to actually physically throwing the dice.
That’s why you do many model runs exactly because the values can fluctuate. That way you get an expected range of outcomes with a sufficiently large number of runs.
When modeling evolution, you can compare the range of values and distribution of outcomes you get, to a phylogeny (where you infer the rate of molecular evolution in different lineages from branch lengths).
If your model is good it will produce outcomes that look like the phylogeny in the sense that you get approximately the same range of values for rates of evolution in your model runs, as the different branches in the tree imply. And you can compare those to more directly observed rates of molecular evolution in pedigree mutation rate studies, to see if the different types of data agree. And you can do statistics on how well they agree. And if they show significant agreement you have reason to think your model is capturing something about reality.
This idea that a higher than average rate of mutation in some lineage of deer somewhere is somehow an issue for the idea of common descent is ridiculous. It just doesn’t work like that.
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Right… So you accept that genes can not only be fetched in sexually reproducing species from either parent, but can also be inherited in parts from both. “Along with” that there is recombination, just to drop the technical term for it. I mean, fair enough. We are denying still the existence of any and all mutations - since if “gene arrangements” is to mean anything at all, then it must be something that some accumulation of point mutations, insertion mutations, deletion mutations, and duplication mutations would at one point or another alter, and when I asked how many such alterations are realistic in your opinion you said the equivalent of “zero” - but at least, and I stand corrected, we are not denying quite all of genetics…
So, since recombination of parent genes requires two or more parents to partake in the reproductive process, how do you propose to account for the effects of selective breeding, or generally any observed systematic change in any population of non-sexually reproducing organisms, seeing as recombination in that classical sense is not available to them?
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I think you are conflating gene arrangements with chromosome counts.
I think you would agree it depends on how much higher.
As the paper acknowledges the mechanism driving the hypothesized chromosome change is not known.
Although the molecular mechanism driving these karyotype changes is unknown, we found that one fusion event in the M. muntjak lineage reversed a chromosome fission that occurred earlier in the cervid lineage; in another case, we found that a pair of ancestral cervid chromosomes likely fused independently in the M. muntjac and M. reevesi lineages. These findings suggest that some chromosomes may be more prone to karyotype changes than others and that care should be taken in applying the parsimony principle due to the possibility of convergent change
That’s okay. I said what I meant. I know what chromosome counts are. I don’t know what gene arrangements are. But, if they are anything at all, then changing DNA sequences is bound to alter them at some point also. The only way for gene arrangements to be fixed, as you tentatively opine they must be, is for genes to never mutate. Since if there is any chance for them to mutate within any lineage, and the mechanism by which genes mutate is Markovian, then there is a chance for them to mutate any number of times, including how ever much it takes to alter the “gene arrangement”, what ever that is. If “gene arrangements” mean something that cannot be altered by any amount of mutation, then “gene arrangement” has nothing at all to do with actual genes, and is naught more than a buzzword we do not mean anything concrete by.
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