A Thor point

Rooting the tree - and finding the cenancestor?

A study done by the EMBL in Heidelberg, Germany, has reconstructed the universal tree of life shown here by eliminating lateral transfer (genes crossing taxonomic lineages, increasingly shown to be rampant in bacteria). Using a number of genes rather than the single gene trees previously done (16sRNA, a mitochondrial gene), helps present a more accurate tree.

The tree strongly supports the hypothesis that the last common ancestor of all life (the cenancestor) was a gram-positive thermophile, which means that the cenancestor evolved in high temperature environments like volcanic pools or black smoker thermal vents on the sea floor. "Gram positive" means that the cell walls are composed of a particular protein, peptidoglycan, which makes the cell walls thick and strong.

One interesting aspect of this reconstruction is that it notes how the phyla of the Eukaryotes (organisms whose cells have a nuclear membrane surrounding the DNA) are much "smaller" than the phyla of the rest of the tree, emphasising that this is an artificial taxonomic level, and is relative to the group one thinks are significantly different or not. They note:

As expected, the hierarchy of taxonomic groups correlates with phylogenetic diversity measured between and within them (e.g., species belonging to the same family have a shorter branch length distance than species belonging only to the same phylum). Within each taxonomic level, branch lengths distances vary considerably ..., apparently owing to factors that influence substitution rates, such as differences in life-style or population size. However, even when taking this effect into account, we observe a strong discrepancy between taxonomic divisions within Eukaryota and Prokaryota ... . Organisms that have been assigned to separate phyla in Eukaryota would clearly belong to the same phylum in the prokaryotic classification. Historically, eukaryotes have obviously been given more taxonomic resolution than prokaryotes, a testament to their greater morphological diversity.

Here I disagree - the morphological diversity of eukaryotes rests largely on the fact that some of them are multicellular, and thus exhibit differences we find striking, nothing more.

Trouble brewing in science?

Applied mathematical theology

Gregory Benford, one of my favourite science fiction writers (because, I suspect, he's also a scientist) has a cute piece in Nature on what would happen if there was a clearly nonrandom pattern to the cosmic background radiation that could "only be" a message. He mentions "applied mathematical theology" as a discipline that tries to decode it. At the end of the piece, it remains untranslated, with plenty of wiggle room for religion and science. But do you think it would bother any of these applied mathematical theologians if the did decode it, and it said:

Best before 15 billion years A. C.

Testing the Designer

Thought Pimp says:

Let's bring intelligent design into biology, and take the vague theory and refine it into mutually exclusive families of clearer hypotheses. Each of which we analyze for explanatory power, corroborating and disconfirming evidence, and so on.

And in the process, we will show that the Christian concept of God is scientifically false---we can say with a fair degree of scientific confidence that there is no god much like the God they want.

But of course, that will never happen. They'd accuse us of violating their boundary between 'science' and 'religion,' and taking a 'religious' stance. (Well, anti-religious, and in a sense they'd be right on that.) If we said the truth, which is that scientists know orthodox Christianity to be scientifically false, we'd be lynched.

Well, I don't know about the extent of this claim. But it does suggest a slightly different angle - if ID is taken to mean a substantive claim, that is if they managed to actually assert something about the Designer rather than rely on vague generalities and attacks of (straw) evolution, then the knife cuts both ways. If we have an actual hypothesis about design, we can test it, and hence it is vulnerable to disproof. So in that sense, bring it on.

Note, though, that this is not the same thing as putting the Christian God under scrutiny. Thought Pimp seems to have bought into the idea that ID represents the Christian, or even just a general theistic, God. From what I know of theology that is a very bad assumption. For example, Tillich's, Bultmann's and Barth's differing accounts of God are neither scientifically impossible nor vulnerable to disproof. I don't even think Aquinas' God is, despite his rather dated metaphysics (which nevertheless still interests philosophers). Moreover, most theists treat God's actions as being what underlies the continuous existence of the physical world. So it follows that for those theists, whatever science uncovers must be not only consonant with the God's creativity, but identical to it.

But the Designer now, he's vulnerable to confirmation and disconfirmation. Which is why the ID folk say absolutely nothing about him.

[Late note: I changed the title - I forgot to edit it when using BlogThis]

Chocolate - not ... quite... a panacaea?

It's been a while since I blogged on chocolate, which as some of you may know I consider to be the quintessence, and the highest state of matter. This is in part because I haven't been eating very much of it, due to, well, health. (I know, there's a higher state of consciousness that takes priority over mere health, but then there are those who force me to go to the gym, the mongrels.) So here is a piece on chocolate at FrinkTank that gives me hope. It seems (or perhaps only seems) that chocolate is good for the chronologically advanced. Not me, of course. But when I get there, it's good to know I can rationalise it because Science Says So.

I might just go test this incrementally now...

A new association in biogeography

SEBA - Systematic and Evolutionary Biogeographical Association has just been announced. It will be the home of the forthcoming International Code of Area Nomenclature, which my wicked fingers already think of as the International Area Code...

The aim of this association is to standardise, so that research can be directly cross-compared, the terminology of biogeographic areas, areas of endemism, biotas, and the like, and to relate systematics and evolution with biogeography, which has suffered a decline in funding and interest over the years.

Recently it has become important in the arena of conservation biology, due to an increasing interest in "ecological hotspots", areas of high biodiversity and potential vulnerability. Part of the difficulty lies in being able to identify the natural boundaries for areas, and as biodiversity relies heavily on the evolutionary history of the species in a region, knowing what is endemic and what is not is essential. Being able to be sure that when one study identifies an area, it is the same area as another study, is vital.

Blonds going extinct!

In the "humans are still evolving, folks" category comes this:

Cavegirls were first blondes to have fun - Sunday Times - Times Online: "A study by the World Health Organisation found that natural blonds are likely to be extinct within 200 years because there are too few people carrying the blond gene. According to the WHO study, the last natural blond is likely to be born in Finland during 2202."

This has two obvious implications:

1. Gene frequencies (in this case the alleles of the hair colour gene MC1R) are still changing in modern society, and

2. There is shortly going to be a global hydrogen peroxide shortage, so put your money in hydrogen peroxide mines immediately!

Oh, and book tickets to Finland.

[Late note: it's apparently a hoax, as Ian notes in the responses. I can't tell because the journal is offline right now. But the exactness of the date of extinction should have been a giveaway.]

[Much later note: It's not a hoax, except for the WHO bit. There are indeed changes in the gene frequency.]

Judge Jones speaks

'The opinion speaks for itself.' Well, yes, yes it does. As any good judgement should, and in this case it certainly does. Jones has naturally enough been demonised for his judgement in the Kitzmiller v. Dover case against ID by the conservative spinmeisters, but if you read it, you'll find that as Jones says, it is indeed a primer on the topic, and yes, Phyllis, he really is the best placed judge in the US to rule on the matter. He heard the evidence, remember?

We can only hope

I can do math, me

at least, to Year 8 level...

You Passed 8th Grade Math

Congratulations, you got 10/10 correct!

Could You Pass 8th Grade Math?

Via Grrlscientist