Re: What goes around comes around

Preston:

I thought it was obvious that we were discussing truth claims of evolution,
not operational science. Of course a prediction that fails, now and then, is
nonetheless operatinally useful. But it is entirely another matter to use
such predictions as confirmations. One need look no further then geocentrism
to see the danger of making truth claims about a theory and downplaying a
few failed predictions because they can be explained by this or that
epicycle.

You cannot add epicycles to your theory, as a result of a failed
prediction, and still maintain the confirmation status of the prediction. If
your epicycle is not limited in application (as appears to be the case with
the HERV epicycles), then there is no end to their explanatory power.

In other words, let's say tomorrow we discover 10 more such anomalous HERVs.
The next day 100 more. Evolution would have no problem, because the epicycle
could be applied. If 50% of the HERVs were anomalous in the ways we have
observed, evolution would have no problem. The epicycles are ready and
waiting to be applied. It would be a different matter if you could say that
we have reason to believe that this epicycle can work only on a few limited
cases.

By the way, I'm not denying that there are evidences for evolution. And who
knows, perhaps HERVs are yet another such evidence. Perhaps the epicycles
are reasonable ones. These are non trivial questions in my view. However,
what is quite obvious is there are significant problems with evolution.
Instead of ignoring these, TEs ought to be saying "Well it is quite obvious
that evolution, alone, is not doing the job. Oh, by the way, there is some
interesting evidence for limited application of evolutionary processes. Stay
tuned to this channel ..."

> Cornelius,
>
> A few comments.
>
> It seems that for you a class of evidence must be absolutely flawless to
> count at all. There must be no anomalies, even if anomalies are reasonably
> expected. You say, "It can't be a prediction if it is explained away when
> it fails." Nonsense. A prediction that is born out in 95% of cases is a
> pretty good prediction. The fact is that any competent population
> geneticist could predict that things like lineage sorting will happen if
> you look at enough cases. This is not a "wild speculation." It's a
> reasonable prediction. In some cases you can find out what happened by
> looking at the details, as someone mentioned for a TE that was largely
> deleted. In some cases you can't. That's genetics.
>
> You dogmatically assert that no HERV can ever delete cleanly.

Actually that assertion comes from evolutionists claiming that HERVs provide
a particularly powerful evidence.

> First, there's just no basis for such an absolute assertion in genetics.

And therefore, there is no basis for the evidential claim that HERVs are
special because they cannot delete cleanly.

> My whole career in science could be marked off by the things that "can
> never ever happen" that then happened. When I was in grad school it was
> gospel, believe it or not, that antibodies do not bind to denatured
> proteins. Surprise. They can! But all that aside, consider this. Here's a
> sequence. It forms a tandem duplication, as often happens. A HERV inserts
> in one copy. Later, homologous recombination removes one copy of the
> duplication, with the HERV. Also a common event. Appears to be a clean
> deletion. It's predictable that such things will happen. These kind of
> events are not wild speculations. Genomes are full of evidence for them,
> and watching cells in culture will give you a lot more. It didn't even
> take a geneticist, only a lowly biochemist to think of this one. So, part
> of what is sensibly predicted is that there will be anomalies.

Agreed, this is not wild speculation. I was thinking of another HERV that
fails to show up in the chimp and gorilla, so *two* independent yet
identical, clean deletes are required in those two different lineages.

In any case, I think you missed my point. I'm not saying these anomalies
cannot be explained. They can be. In fact, you are arguing such explanations
are readily available. My point is simply that this leaves the evidence much
more ambiguous. Exactly what was predicted, vis-a-vis HERVs? And why? And
what bounds are there on these predictions? And just what would falsify the
predictions?

> You say that you didn't mean to imply a high rate of homoplasies. You said
> "...literally are many more of these mutations that cannot be due to
> common descent" and "vast pool of repeated mutations." Sounds like a high
> rate to me.

Yes, for point mutations there are many such examples.

> But anyway. If you don't really have a high rate of homoplasy, we're back
> to go. How do you account for the original simple observation of thousands
> of TE insertions in the same place in different species, quite apart from
> any phylogenetic patterns. And remember, you don't just have to get an L1
> or an Alu in the position, it has to be the same subsubtype. It seems to
> me you are brushing this off too easily, but I've given up on
> comprehending your reasoning. If you have any other refs than the one from
> Pim, I would appreciate them.

Here is anohter HERV reference, for the one I mentioned above:

Johnson, W.E. & Coffin, J.M. 1999. Constructing primate phylogenies from
ancient retrovirus sequences. Proceedings of the National Academy of
Sciences, 96: 10254-10260

Transposable Elements (TEs; not Theistic Evolutionists) often do not align
phylogenetically very well, so in that regard do not serve as very good
evidence for evolution. And some are known to be site specific. And there
are TEs at similar, but not the exact same insertion location. So I've never
thought of them as very good evidences. But I'm not saying there is no
evidence for evolution here. I'd like to see the "thousands of TE
insertions" to which you are referring.

> Your list of things that would convince you on evolution seem to focus
> almost entirely on matters of mechanism. If matters of mechanism are
> you're overriding concern, why not think about CD + ID as a solution?

Sure, I'm not the one rejecting such a solution.

> One more thing. Why would making a cell in vitro affect your judgement of
> evolution?

Even the most basic cell that can be conceived is phenomenally complex. This
is why the OOL problem is difficult, and why Crick said it is tantamount to
a miracle.

--C

>
> Cheers,
>
> Preston
Received on Fri Oct 7 19:52:12 2005