Re: What goes around comes around

Cornelius and all,

I have cut out some stuff that I'm not responding to.

P.

>
>>>>Let me ask you about about related evidence. Are you not at all
>>>>struck by the obvious assembly of human chr 2 (if I remember right)
>>>>from 2 ape chromosomes?
>>>>Why are there 2 sets of telomere repeats
>>>>fused head to head internally at the expected position?
>>>
>>>Probably because there was a fusion event in the human lineage.
>>
>>If so, then the human lineage started out looking very much like the
>>ape lineage. Why would that be so on your alternate hypothesis,
>>whatever its is?
>
>Folks this is a great example. We have evidence that the human
>lineage underwent a chromosomal fusion. OK, fine. But this,
>therefore, is compelling evidence for evolution? How can this be?
>This has nothing to do with common descent or evolution.

When you say it is only evidence for a fusion in the human line, you
ignore the fact that the 2 partners for the fusion look extremely
like 2 chromosomes in the closest related species. You simply discard
that part of the evidence. Another way to frame this is as a
violation of parsimony. You multiply entities, in this case
chromosomes, unnecessarily, positing 2 primordial human chromosomes
when the extremely similar ape chromosomes are there before you.
Logically, those 2 human-like chromosomes could have been present in
any one of a zillion distant species or present nowhere. But there
they are in the one species where they would be predicted to be by
common descent, and you say this has no significance as evidence. I'm
sorry, but this just seems tendentious to me. I'm trying to
understand your refusal to connect the two parts of the evidence, but
I can't.

I'm curious about what others in the group think about this
particular piece of evidence. I've been wanting to try it on some
non-molecular biologists and see if they think it has any weight in
favor of common descent of human and ape. Any comments?

>And when this is pointed out, the claim is defended by asking for a
>better explanation. If you can't supply the rationalist with an
>explanation, then his is right.

I didn't say that. I just asked if you had another hypothesis.
Cornelius, surely it is the common practice in science to try to
provide a better hypothesis. I wouldn't ask for one if you were a
layman, but since you are a scientist it seems like a reasonable
request. Since you reject a bit of evidence that looks obviously
relevant to me and I would guess others, I wondered if you are making
the judgement in comparison to another hypothesis which you think is
much better. If you have one, I'd like to know what is it and why is
it better? If you don't have one, why shouldn't I stick with one that
looks pretty good? I haven't asserted certainty at any point.

>>For the record, for a long time I was rather
>>non-committal on the issue despite being raised in a fundamentalist
>>background, but the genomic evidence seems pretty convincing to me in
>>that common descent seems to account for a lot of things very nicely.
>
>Fair enough, but so does geocentrism. The problem lies in the
>details. I can't respond to statements like "seems convincing." The
>key question is: why do you think this? You seem to be unfamiliar
>with details such as HERVs and mutational hotspots.

I'm familiar enough with both concepts. I haven't covered the whole
literature. This is not the main thing I do. I've looked at a number
of papers where large groups of insertions were examined across
multiple species. In every case the proportion of insertions with an
anomalous phylogenetic pattern was very small. Most of them are
accountable as lineage sorting of an element that is not fully fixed.
Since their fixation is slow and uncertain due to their neutrality,
this seems like a quite reasonable account when the speciation times
are close. A few were found to be likely homoplasies (independent
insertions), but not the large proportion you insist on. As to
hotspots, if you are talking about hotspots for point mutations, they
are irrelevant to transposable elements. I've seen reference to a
couple of insertion hotspots for TEs, not thousands. If there are
HERVs that are grossly anomalous in their pattern, I've never seen
them referred to. There's no way I can evaluate it if you won't
provide references. I don't have time to search a large literature on
a concept that isn't easily defined for a search. When you make these
kind of assertions, it really is customary to provide references. If
you want the ones I refer to, I have them. If this is from your own
research, why don't you publish a paper?

>
>>>Actually, that burden is on you, not me. You are the one who is
>>>making the claim that a duplicated mutation is conspicuous, and of
>>>low probability in a vast pool of repeated mutations that cannot be
>>>due to common descent (that is a non intuitive claim). I believe you
>>>will fail to make the point because there literally are many more of
>>>these mutations that cannot be due to common descent. Have you
>>>looked at them?
>>
>>I'm not aware of any that can't be explained. Examples please.
>
>independent mutations are common across the board--viruses,
>bacteria, higher organisms. Within the field this is not
>controversial (it is a biological fact).
>

It is not my impression that this is true for transposable elements.
Every discussion I have seen in the literature has concluded that
independent insertions of the same element at the same position are
rare.

>
>>>Everything that is known about LINE elements, endogenous
>>>>retroviruses, Alu elements indicates that they only have mild
>>>>biases about target locations. To suggest that this is analogous to
>>>>mutational hotspots is ludicrous. There is one example of an HERV
>>>>which is present in only one copy in human and several ape genomes.
>>>>In all it is at the same position.
>>>
>>>Yes, and there are also HERVs at the same positions that do not
>>>follow the common descent pattern. Again, this is special pleading.
>>
>>Again, examples, please.
>
>Same answer as above. There are HERVs found in the human and distant
>species like old world monkeys, yet not in chimps or gorillas. Then
>there are HERVs found in widespread species but not humans. Both
>falsify the prediction of common descent.

I thought you liked tentative probabilistic conclusions. That sounds
like an assertion of absolute certainty. Deletions do happen.
Genetics throws up all kind of complexities. Like you said, it's all
in the details, and I can't look at the details if you won't supply
the references.

>
>>Do you have any alternative hypothesis for these things that doesn't
>>reduce to "God just did it that way?" I don't mean to be offensive,
>>but if special creation of every species is your hypothesis, I don't
>>see how you avoid that, and as Ted pointed out, that is the most
>>unfalsifiable hypothesis of all.
>
>No offense taken. However, I do disagree with the unfalsifiable
>part. All that is needed is compelling evidence for evolution.

I don't see why. No matter how good the evidence for evolution might
be, one could always still say "God just did it that way." You might
change your mind, but it wouldn't be because special creation had
been falsified.

What would you regard as compelling evidence for evolution? You've
rejected lots of things that the people who are most familiar with
the evidence regard as compelling. I'd sure like to know what you
would accept.

Finally, do you see theological problems with common descent per se?
Omit the Darwinian mechanism and the bugaboo of randomness, bring in
ID type insertions of new sequences. You still have to have animal
death before the Fall. Do you see theological problems with that?

If you've had enough for now, ignore the last question. Just curious.

Shalom,

Preston
Received on Thu Oct 6 23:04:51 2005