Gene Trees and Species Trees

How ironic that this topic follows one about AIG.

Think about it: AIG and the DI base nearly all of their arguments on their perceived weaknesses of "Darwinism," but rarely address their own radical differences, let alone provide independent evidence for their particular "theory."

At the DI, the only one to offer some detail on his "theory" is Michael Behe. While he rejects "evolution" as a cause, he agrees that the "trees" - and the "biological continuum" that they imply - are real, as are their ~4 billion year chronology. Behe also stated that the Bible should not be used as a source of evidence, and indeed his conclusions from the evidence look nothing like AIG's interpretation of Genesis or any of the common OEC interpretations.

Meanwhile AIG starts with the Bible and admits to picking and choosing only that "evidence" that fits.

Thus there are two "kinds" of debate that AIG and the DI (with Behe or other old-earther as a representative) can, and must, conduct if either is ever to have any hope that their ideas will be taken seriously by the scientific community. One concerns "what happened when," and the other concerns whether evidence that doesn't fit the Bible (Genesis) should be included or excluded. Both debates should be far easier that any "creation/evolution" debate, because neither party has a prior commitment to "naturalism," which invariably makes all debates between creationism/ID and evolution degrade into a no-win debate about "naturalism."

Yesterday I started a thread on Talk.Origins specifically for anti-evolutionists to debate their differences. So far no takers (not that I expected any). And 2 years ago I posted a "call for proposals" for any alternate explanations regarding human origins. The stipulation was that they stick to the whats, whens and hows, and test their ideas independent of any problems they may have with "Darwinism" or "naturalism." As you might expect, no takers there too.

In case anyone wonders why I bother, I don't expect any changes in anti-evolution activists' behavior, but I also think that most people are sill unaware of the extent of their antics.

Have you completely lost your minds?

Another Sandefur "article" consisting of a comments-barred, adulatory link to the hyper-controversial, widely-believed-to-be-racist, and climate-change-denying site "Little Green Footballs"?

To clarify, the problems, again, are -

1) Lack of comments section, blocking any expression from those who disagree. This is particularly outrageous because LGF is also a comments-blocked site.

2) Representation of a political site as "scientifically accurate" when it's far more likely that the site in general is scientifically uninformed and inaccurate on most issues, and when, frankly, "support for evolution" is probably nothing more than an epiphenomenon of "support for social Darwinism".

This isn't funny; it's direct fuel for any creationist who seeks to muddy the waters and an absolute violation of any hypocritical claims that this isn't a political site.

Why on earth you allow a political extremist who advocates ending all federal funding for research to use your site as a billboard for his extremist political views is beyond me.

I don't have a lot of power here. I'm not a PT volunteer, I don't maintain a blog that links to PT, and I also am not even a very prolific commenter.

So all I can do is express my disgust at the hypocrisy and favoritism, as well as the cowardice of those who cannot handle even collegial critique of their views.

I urge you to remove the Sandefur post, and frankly, to consider whether or not Timothy Sandefur is adding anything of value whatsoever.

Alright, deep breath, and a final conciliatory comment -

Of course it's true that many people who hold "conservative" political views are not evolution deniers.

In short, although there is an intensely strong association between evolution denying and the American (and UK and Canadian and Australian) political right, there are some people on the right who do not deny evolution. And there are plenty of self-identified liberals or leftists who are scientifically ignorant or superstitious.

The strong association between evolution denial and the political right wing is not a one-to-one matching function.

But -

1) Timothy Sandefur is using THE WRONG METHOD to make this point. A comments-allowed, original content post would be the way to go, not a blind link to a far right web site.

2) The point is so obvious that it barely needs to be addressed.

3) More importantly, the American political right is currently associated with a plethora of science-denying positions - evolution denial, HIV denial, contraception evidence denial (and related denial of studies of the effect of abstinence-only education), climate change denial (and science denial on other environmental issues), and even some old hold-outs on things like denial of the relationship between smoking and disease (a staple of the American right for many years).

There must be one or two serious political conservatives who accept scientific consensus on all of these major issues (accept as current scientific consensus, that is). John Kwok? Maybe?

But they're hard to find, and Sandefur undermines his own point by cherry picking sites that don't deny evolution, while glossing over the fact that such sites are a far cry from scientifically enlightened.

Meanwhile, the article that this thread is actually about is excellent. I've said enough.

There must be one or two serious political conservatives who accept scientific consensus on all of these major issues (accept as current scientific consensus, that is). John Kwok? Maybe?

RBH,

The party left you too, huh?

Frank J said: RBH, The party left you too, huh?

Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two environmental-temperature-related phases during the evolutionary history of the tree of life. In the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea–Eukaryota; in the second period, it decreased.

Oops! Browser trouble made me drop a note: I believe high Archaean sea water temperatures, if real, can be explained by an, IIRC, putative early dense CO2 atmosphere trapping the initially relatively weak solar radiation.

Torbjörn Larsson, OM said: Thanks, it was informative (especially for me personally, as it taught me some more complications of phylogenies) and a good read, as well as other posts on that site.

RBH said:

Torbjörn Larsson, OM said: Thanks, it was informative (especially for me personally, as it taught me some more complications of phylogenies) and a good read, as well as other posts on that site.

Don't be afraid to let Mailund know that on his site. :)

I also agree that the article was excellent; in fact I bookmarked it for future reference.

Torbjorn -

Despite your kind words to the author, I can't resist commenting that you also changed the subject slightly, as prokaryotes and LGT are only mildly related to great ape/hominid relationships :).

harold said: I also agree that the article was excellent; in fact I bookmarked it for future reference.

Thomas Mailund said: I've just posted the first of two posts on the coalescence process and its consequences when we compare two genomes. It is a bit more technical than the species trees vs gene trees post, but I hope you will enjoy it anyway.

Thomas,

Excellent articles, though I need to review a lot of math to truly appreciate them, especially the second article. But the graphics are excellent. A simplified version for high school biology might be ideal for a critical analysis (e.g. "what data would be required to support a different conclusion?"). It would also show that anti-evolution activists do not advocate a real critical analysis, only a phony one, specifically "designed" to promote unreasonable doubt.

Thomas Mailund -

Thanks very much for your contributions and for drawing my attention to all of this.

By a funny coincidence, for completely different reasons, I've been reviewing my old Probability book.

Although I was mainly a neuroscience type as an undergraduate, population genetics (which this reminds me of, except following alleles instead of sequences of individual nucleotides, of course) was one of my favorite courses. I believe I took it because it filled a requirement and was scheduled at a convenient time, but it ended up being a great choice.

It's my impression that when evolution is looked at in a quantitative way, it does a great deal to eliminate the emotional biases that result from anthropomorphising it.

Frank J said: Thomas, Excellent articles, though I need to review a lot of math to truly appreciate them, especially the second article. But the graphics are excellent. A simplified version for high school biology might be ideal for a critical analysis (e.g. "what data would be required to support a different conclusion?").

Frank J said: But the graphics are excellent. A simplified version for high school biology might be ideal for a critical analysis

harold said: Thomas Mailund - Thanks very much for your contributions and for drawing my attention to all of this. By a funny coincidence, for completely different reasons, I've been reviewing my old Probability book. Although I was mainly a neuroscience type as an undergraduate, population genetics (which this reminds me of, except following alleles instead of sequences of individual nucleotides, of course) was one of my favorite courses. I believe I took it because it filled a requirement and was scheduled at a convenient time, but it ended up being a great choice. It's my impression that when evolution is looked at in a quantitative way, it does a great deal to eliminate the emotional biases that result from anthropomorphising it.