Do all deer share a common ancestor?

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They is no objective way to define reasonable. It’s generally consent and agreement along those actually familiar and knowledgeable about the topic.

Take for example this quote about Peter Duesberg from his Wikipedia article.

Blockquote
…although the Berkeley virologist raises provocative questions, few researchers find his basic contention that HIV is not the cause of AIDS persuasive. Mainstream AIDS researchers argue that Duesberg’s arguments are constructed by a selective reading of the scientific literature, dismissing evidence that contradicts his theses, requiring impossibly definitive proof, and dismissing outright studies marked by inconsequential weaknesses. – Jon Cohen.[11]

This sums up why Duesberg’s opinions about HIV and AIDS are not considered reasonable. Of course Duesberg absolutely believes his ideas aren’t just ‘reasonable’ but also correct. I don’t expect you, colewed, to believe you are being ‘unreasonable’. I don’t believe it is even possible to convince people that they are being unreasonable. Like anti-vaxxers, AIDS skeptics, anti-evolutionists and flat earthers, and any other host of similar ‘skeptics’ this is just what happens in human brains.

Given that people who may appear perfectly normal in some areas can nonetheless have crazy-shit bonkers ‘reasonable’ ideas that nobody can dissuade them from, I have to assume that I likely have blind spots as well. Everyone probably does. However, the best self-evaluation for that is to bounce the ideas off others. In scientific matters I consult other scientists in the fields for their opinions. And I can only report that from the feedback received, I don’t seem to carry any ideas where I strongly believed I was right and the experts are wrong. So if I’m infected with a meme that’s overriding my rationality like some imp of the perverse, it’s probably in a different area, like music appreciation or engaging people in debates about evolution long after the ‘reasonable doubt’ train left the station.

So in summary and in conclusion: Colewed, you may never believe that your deductions in this area are unreasonable. But I see that it is, as do so many others that have bothered to engage you in this area. Most full-time scientists with deep knowledge won’t even bother engaging – it’s not worth their time. None of that matters. None of that will ever penetrate the perception of certainly in one’s belief in their own rationality. What Jon Cohen described is something very few people would admit of themselves even after a lifetime of reflection. It’s just an odd kink of being human. Sometimes that is tragic, such as how Duesberg’s irrational confidence contributed to the premature death of perhaps 300,000 Africans, but often it’s benign.

Not that change isn’t possible. It took an embarrassingly long time to grok that debating creationism on Internet forums is about as productive and satisfying as pissing into a strong headwind and so I had to work on why that felt compelling. Turned out it was about figuring out why people think the crazy things they do.

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Hi Argon
Thanks for the thoughtful response. I agree it is very awkward to take a contrarian position to a theory which is as well established as evolutionary theory or Universal common descent.

The issue I have with it is the data we are getting with high frequency sequencing does not appear to support the UCD hypothesis yet this hypothesis is used as an axiom for most evolutionary papers.

In all these Venn diagrams, the first (Howe Venn) posted by @stcordova at TSZ several years ago the gene arrangements are very different between species. If you use common descent as an axiom this is explained by gene gain and gene loss.

If you do not infer common descent then you need to explain how reproduction generated these changes. No one has come close to explaining this for a group of species we all assumed share a common ancestor. What do you think scientists should do with this? Simply stay with the status quo model and ignore the challenge.

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And yet, somehow, you struggle to articulate exactly what the conflict between the data and the hypothesis is supposed to be. Are you sure your objection is actually rooted in the data? That does not seem to be the general impression others are getting.

Is it? Can you cite two papers that (a) use universal common descent as an axiom and (b) go on to construct one or more arguments that would actually fall apart, were it not for that premise?

Assuming that there is an actual problem to solve there, I should think relying on mechanisms the workings of which can be experimentally confirmed is the reasonable way to approach them. What alternative do you propose?

Wait, so which is it? Is there a functional explanation of the data by gene gain and loss at the ready under common descent assumptions, or did nobody come close to explaining the data under common descent assumptions? Please, pick one to stick with, at least for the duration of any one given post…

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Where has some one offered a solution to reproduction generating different gene arrangements?

I agree.

John Harshman explained the pattern under common descent assumptions. The explanation is gene gain and gene loss.

If you do not assume common descent then you need to explain how the different gene patterns originated. This is the unsolved problem as we have little to no evidence that reproduction and associated variation is a gene producing mechanism.

648

Do we in fact know that the genes are “very different”?

Do we know whether the ‘different’ genes in the Venn diagrams are 95% (99%?) the same, 50% the same, as genes of other species in the Venn diagrams, or that they are entirely different?

It would seem to me that we need the answers to these sorts of questions, that the Venn diagrams cannot answer, before we can say that the genes are “very different”.

It is entirely possible, and in fact likely, that these Venn diagrams exaggerate the gene differences.

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The issue I have is that you don’t look at the data.

1000x no. The data from sequencing support common descent. At best you can quibble about the “U” part, but the data completely support common descent of apes, mammals, vertebrates, and even deuterostomes.

Your Humpty Dumpty words (gene arrangement, etc.) appear to be chosen only as a way to mask your refusal to deal with the actual data–and the math required to understand them.

The problem is that the Venn diagrams aren’t the data you should be analyzing for yourself. Why are you afraid to do so?

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False. There were no assumptions. Please quit projecting.

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Not exactly. The pattern is explained by gene gain and loss on a phylogenetic tree. That’s evidence for the hypothesis of phylogeny. It’s unexplained under the hypothesis of independent creation. And that hypothesis gets worse as you add species. Remember: you have no explanation for the pattern. Why?

Bill confuses assumptions with models. And models do incorporate assumptions. But the purpose is to test the model, not just assume that it’s true.

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I have made a claim how design explains the various Venn diagrams. Do you remember the claim?

I don’t see how this is evidence for the hypothesis unless gene gain shown to be feasible. Separate origins eliminates the need for gene gain/loss claim.

We know some that are claimed to be the result of gene duplication are from a sequence divergence standpoint. Your point is a good one however and needs to be explored for closer related species like deer.

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Perhaps you can refresh my memory. Try to be a clear as you can.

Yes, you don’t see a lot of things. Not my problem, though. Once again you confuse the pattern with the causes of mutation. And of course separate origins explains nothing, since any pattern or no pattern is equally unpredicted.

Whatever does that mean?

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  1. Which specific genes are “claimed to be the result of gene duplication”?

  2. Who made that claim?

  3. On what basis are you claiming that duplicated-and-diverged genes must be “very different”?

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Right. So if we assume common descent, then mechanisms we can observe and study experimentally appear to be an adequate account of the data.

Right. So either different gene patterns occur by loss and gain irrespective of common descent, or they occur by some other mechanism. If they occur by gain and loss even without assuming common descent, then common descent becomes rather an inference than a premise. If they occur by some other mechanism, then common descent is not indicated. So, what do the experiments show? Do variations in gene patterns occur by gene gain and gene loss? If yes, why is this not consistent with common descent? If no, what other mechanisms do they occur by, and how do those conflict with common descent? If they occur both by gene gain and loss and other mechanisms, how is this combined picture in conflict with common descent? I feel like this is a problrem for those among us trying to deny common descent moreso than for those asserting it. Perhaps you can point out the flaw in my logic here. I’d appreciate it.

Is that so? Does germ cell mutation not count as reproduction-associated variation and a gene producing mechanism? Does recombination not count as reproduction-associated variation and a gene producing mechanism? In your opinion, what might evidence that reproduction and associated variation is a gene producing mechanism look like? What experimental data we have to date not gathered is it biologically plausible that we might gather one day, that may satisfy this standard of yours?

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Recent (within the last 7-8 years) research auggests that the Eukaryotes root in the Archaea among the Asgard superphylum and particularly with the recently discovered Lokiarchaeota. Laura Eme’s work is a good place to start.

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The alternative to common descent is separate origin of some or all of the species. In the case of separate origin we do not have to invoke gene/gain or loss to explain the different gene patterns in the Venn diagram’s.

An experiment like the Lenski experiment where he looks at the genetic data would work if that experiment ws able to produce a unique functioning enzyme sequence. be used.

If it happens I believe it will not be from the mechanisms that are currently being proposed. I think random processes with some selective filter will simply move complex sequences away from function.

The WNT and Frizzled are ligand and receptor gene families that are believed to have diverged from gene duplication in the past. The different versions have around 200 different amino acid positions or similar positions on only about 40-50% of the proteins.

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Then again, one could say that for separate origin we would have to explain gain of all genes, many times independently. And you in fact have no such explanation. Hey, if all species were independently created, shouldn’t we expect to see that happening occasionally? Shouldn’t new species just poof into existence before our eyes every so often? Where’s the evidence of that?

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I’m not sure how this relates to the portion of my message you quoted. Is there some particular advantage in avoiding to invoke gene gain or loss? If yes, what is it? If no, why try? By which specific predictions are models that do not require them superior to ones that do?

Why? Does selection favour non-functional genes in your opinion, such that it puts organisms that inherit less functional genes at an advantage? If yes, please explain how this could be the case generally, rather than in a specific circumstance. If no, please explain how your impression that random processes with selective filtering would simply move complex sequences away from function is consistent with your picture of how either random processes or selection, or a conjunction of the two work.

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If animals are specially created (the multiple origin theory) then different gene patterns is how they were created based on what we are observing. Gene gain/loss is a claim based on the single origin hypothesis.

This may take a few back and forth to get mutual understanding. My claim has to do with the size of the sequence space and the number of mutations required to find a functional advantage.

Gene/protein sequences are very large combinatorial spaces. For many proteins the amount of functional space is orders of magnitude larger than the amount total sequence space.

This is a hard concept because these spaces (possible arrangements of nucleotides/amino acids) can be orders of magnitude larger than the known sub atomic particles in the universe. Even if the solutions are this large the non functional space is so large the number of solutions does not matter.

The bottom line is the odds of a sequence moving away from function is much higher than moving toward it so the long term trend is toward non function.

Separate origin according to Behe’s model is a fully delivered gene arrangement at the origin of the species.

You mean like UFO’s.

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Amusing typo. Of course that situation is physically impossible.

This reveals a fundamental misunderstanding of how natural selection works.

That’s not actually true. That’s your model, not Behe’s. But my point is that it falls upon you to explain the origin of that fully delivered gene arrangement, including why some genes are similar and others are different between these separately created species. Of course it’s not just genes. You have to explain the similarities and differences across the genome as well as the packaging of the various sequences into chromosomes. You have nothing.

No idea what you mean, but you certainly managed not to answer any of my questions, almost as if you’re avoiding them. Perhaps you want to avoid even having to think about them. If so, you should know that your avoidance is transparent to anyone reading this thread.

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  1. So only one out of the tens of thousands of deer genes. This is NOT “very different”.

  2. I would note that WNT is shared across a very wide range of remotely-related species, including Drosophila. This would account for the low similarity you assert (I would note however that this claim does not appear to be contained in the cited paper). I would expect to see a far higher similarity for more closely related species, such as deer. Do you have, with citation, WNT & Frizzled similarity figures for Deer Bill? If not, you have no evidence that even this gene is in any way dissimilar.

Summarising:

  1. We have no evidence that deer genetics are “very different” from each other.

  2. We have no evidence that, for deer, “the different chromosome counts and the different gene patterns are an indication they do not all share a common ancestor.”

  3. We have no evidence that we cannot “reconcile the common ancestry of deer based on population genetics for chromosome variation and gene family variation”.

In other words we appear to remain at the status quo ante that was in place before this thread was started, approximately three months ago.

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So you mean to say that gene gain and loss is not something one can experimentally observe, irrespective of what origin hypothesis one first presumes? Very well…

Alright. I’m looking forward to seeing the numbers you’ll surely present.

In order of the emphases:

  • How large?
  • How many?
  • How large, each?

(please, also provide either your sources for or a way to verify your numbers)

That’s unsurprising, actually. Sub-atomic particles tend to be smaller than an atom. Pretty much everything is orders of magnitude larger than them. Atoms themselves are some five orders of magnitude larger already when we are talking of hadrons. And that’s not even considering that to the best of our knowledge elementary particles might well be point-like, rendering them literally infinitely smaller than anything else. What makes any of it a hard concept, though, escapes me. Most everyone I know was taught this before their mid-teens.

Not sure how solution size (what ever that is) matters. Regardless, how large are we talking here, respectively?

That would be an interesting bottom line indeed. Now all we have to do is show that this is actually the case. I was not even aware we were talking about odds here. Maybe it’s on me, but I did not notice you mention any odds until this very bottom line. Same for the long-term trend, which is yet a different, separate claim. Please, continue. Whence do you draw any part of this bottom line?