Re: Stereotypes and reputations

Pim van Meurs wrote:

>
>>> 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/.
>
The mystery of ORFans is slowly being resolved. Until we understand
ORFans, the conclusion that they disprove Common Descent seems a bit
premature.

Could bioinformatics tools have predicted the approximate structures of
those ORFans having previously observed folds? Fold-recognition (FR)
methods,30,31 applied without using the information from the recently
released structures,27 but using as templates previously determined
structures, correctly predicted the structures of six of the
19 ORFans. Figure 1 shows the highly confident FR prediction of a
Mycoplasma-specific hypothetical protein (1q8cA).

See also an early paper
http://bioinformatics.oxfordjournals.org/cgi/reprint/15/9/759

That ORFans are still poorly understood should not be confused with it
being a problem for common descent. It's merely an interesting
evolutionary puzzle

[quote]
Abstract
ORFans are open reading frames (ORFs) with no detectable sequence
similarity to any other sequence in the databases. Each newly sequenced
genome contains a significant number of ORFans. Therefore, ORFans entail
interesting evolutionary puzzles. However, little can be learned about
them using bioinformatics tools, and
their study seems to have been underemphasized. Here we present some of
the questions that the existence of so many ORFans have raised and
review some of the studies aimed at understanding ORFans, their
functions and their origins. These works have demonstrated that ORFans
are an untapped source of research, requiring
further computational and experimental studies. [/quote]
Received on Sun Jul 31 00:18:57 2005