Methylomes

DNA methylation is the term for a modification to certain DNA bases that involves the addition of a methyl group. This slows down gene expression, which may or may not be advantageous in context – though if you remove it entirely in mice you kill them outright. To cut to the chase, in late August a paper – Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution (pdf, supplemental data) – came out comparing levels of methylation, concentrating on the brain, between humans and chimpanzees. They found differences, particularly in regions apparently associated with diseases that we suffer from more than chimps do. Here’s a figure stolen from their supplemental information:

"The mean fractional methylation levels (± S.E.) of different genomic regions." (From page two)

“NS” stands for “not significant,” but the ones with stars are. Something to note with that graph is that there is a hidden 20% below the axis, so the differences are not quite as large as they would appear. Continue reading

The Denisova …Human?

Mouth of the Densova caveThe Denisova hominins were a group of humans that, similar to the more famous Neanderthals, survived until just a few tens of thousands of years ago. Their discovery was announced only in 2010, in the form of a portion of a child’s little finger extracted from the Denisova cave in Siberia. Since then it has been determined that a tooth found in 2000 was from the same group. Curiously, given the finds location in Russia, the Denisovans are believed to have interbred with the ancestors of people that now live in the vicinity of Melanesia.

We can tell all this from such scant evidence because conditions in the cave allowed the aforementioned finger bone to preserve the complete genome of its owner. Most recently this has been sequenced with as much fidelity as you would get from an analysis of a living person. Brian Thomas writes: Is Fossil Finger Genome Human?

The Denisovans are similar enough to modern humans that creationists must include them on our side of their rather arbitrary human-ape division. They have inherited the “fully human” epithet of the Neanderthals. For example: Continue reading

Humans Were Made for Walking – Quick DpSU June 3

Brian Thomas – in an ungodly blend of Fine Tuning and Irreducible Complexity – claims that Humans are so good at walking that they must have been designed. New study that doesn’t really deal with the subject at hand: Check. Ten year old studies on the evolutionary side of things that could easily be obsolete by now in such a dynamic field: Check. Ending paragraph containing statements that could really do with a nice, juicy citation: Check. In short, a classic type Io DpSU (in contrast with type Amber/Embryo) from Mr Thomas.

As in added bonus, here’s the last paragraph:

Without all of the bones, ligaments, tendons, and muscles properly integrated with one another all at the same time, it would be impossible to walk like a man—let alone to switch to a whole separate running gear. Evolutionists must put their faith in imaginary physical “transitions” that could not work because they would require long time spans of creatures with not-yet-formed leg structures that would render any such animal immobile. Those who “walk humbly with [their] God,” however, can rely on the data showing that the mechanics of walking were well-created.6

The citation at the end implies that Mr Thomas has “data showing that the mechanics of walking were well-created”. Instead, the link at the bottom is to “Micah 6:8” in the version of the bible that the ICR prefers: The New Defenders Study Bible. The NDSB remands me somewhat of the Conservapedia Bible Project (but not nearly as audacious) – they seem to be adding annotations that retrofit the whole thing so as to “resolve its alleged contradictions, point out the evidences of its divine origin, confirm its historical accuracy, note its remarkable anticipations of modern science, demonstrate its fulfilled prophecies and in general remove any doubts about its inerrancy, its authority and its ability to meet every human need”. They didn’t go so far as to actually change the text, however – it’s seems to be copied wholesale from the KJV (compare this and this). As an example of an annotation, take the annotation to the passage Thomas links to (“He hath showed thee, O man, what is good; and what doth the LORD require of thee, but to do justly, and to love mercy, and to walk humbly with thy God?” in both the KJV and NDSB).

6:8 walk humbly with thy God. These characteristics are not enough to earn salvation (actually no one could achieve them perfectly anyway), but they should characterize all who have been saved through faith in Christ, whose perfect sacrifice for sin was anticipated in type by all the previous animal sacrifices.

This is the Old Testament, you know… Basically, they interpret the whole O.T. as a giant case of foreshadowing for the New.

As for the actual argument in the article, Thomas thinks that we could only have been created because we are so efficient at walking. To stopper the holes caused by applying fine tuning to biology (it’s usually used to explain why the universe is so “perfect for life” from a religious perspective), he invokes Irreducible Complexity as well. Look, IC is for Bacteria. This is too big. As mentioned above, Thomas fails to provide any reference for the claim that intermediary forms “could not work because they would require long time spans of creatures with not-yet-formed leg structures that would render any such animal immobile”. Is he really saying that all other similar ways that you could have a human leg and foot could not work? My feet naturally fall at ninety degrees to each other, but I can walk perfectly well…

If you then disregard the alleged IC through lack of evidence, you find no problem at all. Adaptation and efficiency is what evolution does best.