Open Access Journals and the Evil Darwinian Orthodoxy

Geotimes has an interesting discussion of open access journals:

Open-access publishing has been heralded both as the savior of scientific literature and the death of publishing, but after less than a decade of the practice, its impact remains uncertain. A new review indicates that the success of these free and open journals also remains to be seen.
The movement to make scientific journals freely available has been growing worldwide in recent years.

About 1,600 journals have followed the open-access model, whereas more than 20,000 non-open-access journals are regularly published around the world. The movement to make scientific journals freely available has been growing worldwide in recent years, with added attention in the United States due partly to a policy introduced last year by the National Institutes of Health. The federal agency encourages its researchers to enter their papers in an online database open to the public, within six months of publication.

Does anybody know the URL of this Online Database?

The entire article is worth reading in it’s own right, but I have different motives for mentioning it. You may notice a section on my sidebar, named “The Evil Darwinian Orthodoxy”. It contain’s link to a number of scientific journals dealing with evolution. I am alway’s on the lookout for more and since the above quote mentions 1,600 open access journals and 20,000 non-open access journals I figure I’ve barely scratched the surface here. In a word, even though I beg and plead some of my readers are holding out on me! So I’m going to beg and plead some more! Please, pretty please with sugar on top, leave some journal titles in the comments (links would be nice but are not required). Don’t make me show up at your site and whine pathetically! You won’t (to paraphrase Bruce Banner) like me when I get whiney!

I was inspired to create the list based on an idea of Josh Rosenau at Thoughts From Kansas. You see Josh created The Evolution Prject and the Non-Evolution Project wherein he documents the relative contibutions of evolutionists and Intelligent Design proponents to the advancement of science (we are still waiting for a contribution from ID …). So I thought wouldn’t it be a grand idea if we had a list of all the science journals dealing with evolution. So that we could refer people to them. Refering people to say, Talk Origins or the NCSE, is great but I think it would be helpful if we could also send to to some journals where they could see how science actually works. Doesn’t that sound worthwhile? How can you still hold out? You will be amply rewarded with the warm fuzzies that come from knowing you helped halt the spread of stupidity in America, so come on pony up with the Journals!

Transitions News

The next post in Evolgen’s series on Detecting Natural Selection has been crossposted on Transitions: The Genetics Page. The series gets more fascinating with each post, and would dare I say, make a great book (just a hint)! Check it out!

In the meantime, I am in the process of selecting a new site of the week but the competition is tough!

Tangled Bank Reminder

Just a reminder, I’ll be hosting Tangled Bank 44 on January 4th. You all know what to do…

The Tangled Bank

Footprints are Springing Up All Over the Place

From Yahoo News:

Hundreds of human footprints dating back to the last Ice Age have been found in the remote Australian Outback, an official and media reported Thursday.
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The 457 footprints found in Mungo National Park in western New South Wales state is the largest collection of its kind in the world and the oldest in Australia, The Sydney Morning Herald newspaper reported.

The prints were made in moist clay near the Willandra Lakes 19,000 to 23,000 years ago, the newspaper reported ahead of archeologists’ report on the find to be published in the Journal of Human Evolution.

*snip*

“We see children running between the tracks of their parents; the children running in meandering circles as their parents travel in direct lines,” Debus told Australian Broadcasting Corp. radio.

“It’s a most extraordinary snapshot of a moment or several moments in the life of Aboriginal people living on the edge of the lake in western New South Wales 20,000 years ago,” he added.

Interesting Website

I’ll probably do a post later, but in the meantime I thought I would bring this website to your attention Paleobiology Website.

It’s pretty cool to play around with.

Fish with Two Mouths

Here

Two Mouths

“It’s probably a genetic deformity,” he said. “I don’t think there’s anything wrong with it.”

Ummm, I don’t really have anything to add (other than to recommend that somebody should check pollution levels in the lake it came from – Montgomery Burns would be so proud).

Mammoth Nuclear DNA says African Elephant, Mitochondrial DNA Says Asian

Okay, now I’m confused! I have posted on the Mammoth DNA study several times. One The articles I read stated that one of the conclusions was that Mammoths are more closely related to Asian elephants than African. Yet the story linked to above claims the exact opposite:

A mammoth was chosen for the study, in part, because of its close evolutionary relationship to the African elephant, whose nuclear DNA sequence has been made publicly available by the Broad Institute in Cambridge, Massachusetts (USA). Using comparisons with elephant DNA, the researchers identified 13-million base pairs as being nuclear DNA from the mammoth, which they showed to be 98.5 percent identical to nuclear DNA from an African elephant.

This, I hasten to point out, is a completely different study than the one I posted about previously. One obvious difference is that the first article used mitochondrial DNA while this one used nuclear DNA. I don’t see how this would make a difference in basic results though. One of these studies has to be flawed…

At any rate here is what the Penn State (the mitochondrial DNA study was done by the Max Planck Institute)team did:

The project became possible through the discovery of exceptionally well preserved remains of a mammoth skeleton in the permafrost soil of northern Siberia, in combination with a novel high-throughput sequencing technique that could cope with the heavily fragmented DNA retrieved from the organism’s mandible, its jaw bone. “The bone material used in this study is approximately 28,000 years old, as was shown by beta carbon dating analysis,” said Hendrik N. Poinar, associate professor of anthropology at McMaster University. “This was a surprising finding, as it demonstrated that the analyzed material was frozen for more than 10,000 years before the maximum of the last ice age.” The research team used a comparative computational approach to demonstrate that an unprecedented large percentage of the bone DNA was indeed mammoth DNA, while the remaining genetic material was shown to belong to microorganisms and plants living the tundra soil.
“Analyzing DNA from the organelles of mitochondria has been the only method of studying ancient DNA in the past, as it is more tractable due to its 1000-fold higher copy number per cell,” Schuster explains. However, the mitochondrial genome codes for only a tiny fraction of an organism’s genetic information — 0.0006 percent in the case of a mammal. “We focused on sequencing nuclear DNA in this study because most hereditary information is organized on chromosomes located in the cell’s nucleus,” Schuster says.

The mitochondrial research appears in Nature and the Penn State research will appear in Science…

Added Later: Ahh, here is the explanation:

Poinar sent the DNA-rich sample to genomicist Stephan C. Schuster at Pennsylvania State University, University Park, who is working with a new genome sequencer developed by a team at Stanford University and 454 Life Sciences Corp. of Branford, Connecticut (Nature, 15 September, p. 376). This rapid, large-scale sequencing technology sidesteps the need to insert DNA into bacteria before amplifying and sequencing it. Instead, scientists break DNA into small fragments, each attached to a tiny bead and encapsulated by a lipid bubble where the DNA is multiplied into many copies for sequencing. Because each fragment is isolated before copying, the method avoids bias from copying large amounts of contaminant DNA from bacteria or humans.

The researchers were stunned by how well the method worked on ancient DNA, which is notoriously difficult to extract and sequence: “I would have been happy if we got 10,000 bases of mammoth DNA,” said Poinar. Instead, they got 28 million basepairs, 13 million from the mammoth itself. Their preliminary analysis shows that the mammoth was a female who shared 98.55% of her DNA with modern African elephants. But mammoths were apparently closest kin to Asian elephants, as shown by Pääbo’s mitochondrial study, which retrieved about 17,000 basepairs.

Apparently, both groups helped each other…