Re: Stereotypes and reputations

Cornelius Hunter wrote:

> Pim:
>
> The problems with common descent are not minor issues that can be
> glossed over. I recall speaking with an evolutioniist about abruptness
> in the fossil record (Cambrian explosion, etc.). She said she did not
> think that constituted evidence against the theory. So there was no
> evidence against evolution. Do you see the problem here?
>
The Cambrian explosion, while to some, may have appeared problematic to
Darwinian theory (Darwin himself acknowledged it), more and more
evidence shows that what appears to be a morphological explosion may
fall well within the paradigm of Darwinian/evolutionary theory. In fact,
the evidence of common descent extends through the Cambrian.

> If one cannot admit to what are clear counter indications, then there
> is a problem. Woese is not saying that HGT explains early life. He is
> appealing to a far more aggressive explanation -- HGT on a massive
> scale -- nothing like it has ever been observed. You also have
> understated Doolittle, who is one of the early evolutionists to admit
> to what the data say: the tree model doesn't work very well. You wrote:
>
Again this is misleading. There are indications of a problem namely our
ignorance of the exact circumstances surrounding the Cambrian explosion.
I am not sure why such ignorance should pose a problem to Darwinian
theory. Would it not pose a problem to any theory? Woese argues for
massive HGT followed by clearly identifiable common descent. Woese's
claims hardly seem to be problematic for common descent, although it
does pose a problem to extract horizontal versus vertical gene transfer.
And yet recent studies have quantified this and found for a set of
bacteria that horizontal gene transfer accounts for a relatively small
amount of the variation compared to the vertical transfer. The reason
why Doolittle states that tree model does not work very well is because
of the horizontal transfer, a tree needs to have additional links.
Once more research becomes available science resolves many of these
'problems' quite easily.

See
http://www.pandasthumb.org/archives/2005/07/carl_zimmer_tan.html
The net of life: Reconstructing the microbial phylogenetic
network Victor Kunin1, Leon Goldovsky, Nikos Darzentas and Christos A.
Ouzounis

[quote]
Abstract:It has previously been suggested that the phylogeny of
microbial species might be better described as a network containing
vertical and horizontal gene transfer (HGT) events. Yet, all
phylogenetic reconstructions so far have presented microbial trees
rather than networks. Here, we present a first attempt to reconstruct
such an evolutionary network, which we term the "net of life." We use
available tree reconstruction methods to infer vertical inheritance, and
use an ancestral state inference algorithm to map HGT events on the
tree. We also describe a weighting scheme used to estimate the number of
genes exchanged between pairs of organisms. *We demonstrate that
vertical inheritance constitutes the bulk of gene transfer on the tree
of life.* We term the bulk of horizontal gene flow between tree nodes as
"vines," and demonstrate that multiple but mostly tiny vines
interconnect the tree. Our results strongly suggest that the HGT network
is a scale-free graph, a finding with important implications for genome
evolution. We propose that genes might propagate extremely rapidly
across microbial species through the HGT network, using
certain organisms as hubs.
[/quote]

>> That there are problems with morphological and molecular data does
>> not mean that there is no common ancestry. It merely shows that
>> resolving difficulties may be hard. Again, the argument common
>> ancestry is wrong because two methods disagree, is hardly sufficient.
>
>
> Unfortunately this is always the explanation, and it makes common
> descent unfalsifiable.

Not at all. Common descent would be easily falsifiable. THe problem is
that some look at minor/major disagreements about mechanisms and their
relative importance as evidence of a larger problem namely that of
common descent being wrong

> With every problem, one hears, "well, that doesn't mean the theory is
> wrong." So here we have all kinds of incongruities -- phylogenetic
> mismatches abounding.

Compared to the matching data, the mismatches are in most cases quite
minor and often resolve themselves when more accurate data becomes
available.

> Non homologous development patterns that make utterly no sense on
> common descent.

Why not?

> Detailed designs evolving independently over and over.

Again no problem for evolutionary theory, once you realize that it is
not surprising for similar solutions to be found by natural selection.

> Did I mention fundamental differences at the DNA level where common
> descent predicts there should be none (proteins involved in DNA
> replication)?

Again, you need to be more specific. Where was this prediction made and
what evidence was found?

> And of course that little problem that we have no idea how these
> designs could are arisen. Sure, one can always contrive just-so
> stories. How many different evidential problems, from how many
> different angles, do we need before we acknowledge problems? You
> mentioned, Douglas Theobald's site -- this is yet another problem with
> talkorigins. That page is problematic. You wrote:
>
I agree that the page IS problematic for those arguing against common
descent as Douglas has described a wealth of data establishing common
descent beyond much reasonable doubt.

>> Convergence is also not necessarily a problem for common descent. Nor
>> are ORFans for instance. We should not let our ignorance lead us
>> astray from the solid evidence in favor of common descent.
>
>
> I'm sorry but this is not tenable. ORFans and massive convergence not
> problems? This is a joke right?

Not at all. Please explain why you believe that these are problems to
Darwinian theory or common descent? It may be tempting to reject the
vaste amounts of data supporting common descent because of some minor
issues, most of them due to our ignorance. Once you realize that
evolution is 'constrained' by environment, laws of nature. mechanical
constraints etc, finding convergence becomes far less an issue.

Although convergence may make recovering accurate trees more difficult,
it should not be considered a major problem for common descent/.
Received on Sun Jul 31 00:00:41 2005