Is “X-woman” really a new species?

The discovery of the creature nicknamed “X-woman” has to rank as one of the most exciting science stories of the year so far. She — if X-woman is indeed a “she” — is known only from a little finger bone, found in a Siberian cave and dated to between 48,000 and 30,000 years ago. But according to a research team led by Johannes Krause and Svante Pääbo, of the Max Planck Institute in Leipzig, she may represent an entirely new human species.

At the time X-woman lived, the only hominins known in Eurasia were modern humans and Neanderthals (Homo floresiensis, the “Hobbits”, were also around in Indonesia). Yet analysis of mitochondrial DNA from the bone has suggested that X-woman belongs to neither species (the nickname, incidentally, was chosen because mitochondrial DNA is passed down the female line — there is no indication of sex just yet).

Krause and Pääbo believe that this suggests the creature belongs to a new lineage of humans, and perhaps to a new species. As Pääbo put it:

“Whatever carried this DNA out of Africa is some new creature that has not been on our radar screens. It suggests there were perhaps three different families of humans in this area about 40,000 years ago, and also the hobbits in Indonesia.”

Read the rest of this interesting article from TimesOnline here.

Why do herbicides become ineffective in just a few generations? And what does that have to do with people?

“While the long term effects of genome mutations are quite well understood, we did not know how often new mutations arise in the first place,” said Detlef Weigel, director at the Max Planck Institute in Germany. It is routine today to compare the genomes of related animal or plant species. Such comparisons, however, ignore mutations that have been lost in the millions of years since two species separated. The teams of Weigel and his colleague Michael Lynch at Indiana University therefore wanted to scrutinize the signature of evolution before selection occurs. To this end, they followed all genetic changes in five lines of the mustard relative Arabidopsis thaliana that occurred during 30 generations. In the genome of the final generation they then searched for differences to the genome of the original ancestor.

The painstakingly detailed comparison of the entire genome revealed that in over the course of only a few years some 20 DNA building blocks, so called base pairs, had been mutated in each of the five lines. “The probability that any letter of the genome changes in a single generation is thus about one in 140 million,” explains Michael Lynch.

To put it differently, each seedling has on average one new mutation in each of the two copies of its genome that it inherits from mum and dad. To find these tiny alterations in the 120 million base pair genome of Arabidopsis was akin to finding the proverbial needle in a haystack, says Weigel: “To ferret out where the genome had changed was only possibly because of new methods that allowed us to screen the entire genome with high precision and in very short time.” Still, the effort was daunting: To distinguish true new mutations from detection errors, each letter in each genome had to be checked 30 times.

The number of new mutations in each individual plant might appear very small. But if one starts to consider that they occur in the genomes of every member of a species, it becomes clear how fluid the genome is: In a collection of only 60 million Arabidopsis plants, each letter in the genome is changed, on average, once. For an organism that produces thousands of seeds in each generation, 60 million is not such a big number at all.

Turning to the larger picture, Weigel suggests that changes in the human genome are at least as rapid as in Arabidopsis: “If you apply our findings to humans, then each of us will have on the order of 60 new mutations that were not present in our parents.” With more than six billion people on our planet, this implies that on average each letter of the human genome is altered in dozens of fellow citizens.

Read the full article here.

Why continue to post about unjustified beliefs and criticize them?

I have often been asked why I bother to post every day, why I take the time and effort to expose unjustified beliefs as stories and articles about them hit the media. Why cannot I leave them and their unjustified beliefs well enough alone?

The short answer is that I can’t because it is wrong to do nothing. Because I can do something, I feel that I must do my small part at the very least… hence my posting. Ignorance must be challenged and brought into the light of critical thinking to expose it for what is usually is: an expression of cancerous fear that is not worthy to be held respectable but owed our justified and published contempt.

The longer version of the answer I will borrow from a poster with whom I have the greatest respect: Calilasseia, who writes here…

To those like myself who have followed a scientific academic career, such are the things of beauty that fill our intellectual realms; such are the fragrant blossoms of our requisite enchanted gardens. They speak of the way the world works, they allow us not only to marvel at that world, but to work within it and build upon it. From the world of biology, the butterfly that forms my avatar, Morpho rhetenor from Peru, is another scintillating marvel about which I can wax lyrical – did you know that its wing scales, when viewed under the electron microscope, possess structural features allowing them to act as light amplifiers for specific regions of the visible spectrum via constructive interference? Breathtaking as the butterfly is in life, and one day I hope to see it for myself in its natural habitat and experience the wonder of its flashes of blue iridescence as it flies upon those jewelled wings, the thought that its scintillating beauty has an explanation that can be deduced by the mind of Man should also be something we pause for a moment to gasp at.

But there are those whose eyes and whose minds are closed to such things. Not for them the joys of inquiry, of discovery, of learning: rather, they seek their sustenance not in the bright sunshine of free thought, but in the perennial darkness of doctrine. Worse still, these persons are not content with inhabiting those catacombs themselves – they seek to cage others within the darkness, shut them out from the light, deny them forever the fragrant blossoms of the enchanted gardens I have just described. To do so, they will resort to subterfuge and intrigue, eating away at the wonderful edifice of learning that, if they paused for a moment to consider, gives them too gifts in their lives for which they appear to show not one atom of gratitude.

They must be stopped.

It is indeed an imperative that they are, for if that magnificent, hard-won product of the Enlightenment is lost to us, the consequences will be disastrous. From an era in which we can sit at home, and at the touch of a button be connected with manned spaceflight in real time, or with thousands upon thousands of other people on different continents in media such as this forum, living lives free from the perils of famine and pestilence, we shall descend into a new Dark Age, in which those vanquished spectres will emerge wraith-like to claim more, and those who are left will be subject to arbitrary, Inquisitional terror.

If some, like myself, are inclined to be polemical about this, it because we know precisely what is at stake if the purveyors of ignorance and bigotry win – we know how much of a calamity it will be for our very species. We know intimately how precious those gifts of the Enlightenment are, and what will befall us if they are wrested from our hands. We know also that to perpetuate those gifts is something we cannot leave to chance, it must be worked for, the price that the rational man must pay for the wonders of free thought is eternal vigilance in the face of those forces that would destroy it. That is why I, for one, am not only prepared to launch polemically into the fray, but consider it my moral duty so to do, because the consequences of indolence, were they to result in the victory of the forces of ignorance and bigotry, would be worse than calamitous, they would be truly apocalyptic. And make no mistake, those who would replace the glories of free thought with the concentration camp of mysticism seek not only to destroy those glories, but from their own words have given a chilling insight into the pleasure they would derive from that destruction, and the pleasure they would derive from having people like us at their mercy.

What we have is far more beautiful, inspiring, and worthy of defending than any doctrine. Let the hordes come – my sword is at the ready.

Evidence for dark matter… in Minnesota?

Laurence Krauss is one of my favourite science writers because his writings are accurate, fascinating, and accessible. Read his entire article here.

In early December, the Cold Dark Matter Search (CDMS) experiment located in the deep Soudan Mine in northern Minnesota leaked a tantalizing hint that they may have discovered something remarkable. The experiment is designed to directly detect new elementary particles that might make up the dark matter known to dominate our own Milky Way galaxy, all galaxies, and indeed all mass in the universe—so news of a possible breakthrough was thrilling.

The actual result? Two pulses were detected over the course of almost a year that might have been due to dark matter, CDMS announced on Dec. 17. However, there is a 25% chance that the pulses were actually caused by background radioactivity in and around the detector.

So when the physics community heard rumors that one of these experiments had detected something, we all waited with eager anticipation. A convincing observation would vindicate almost half a century of carefully developed, if fragile, arguments suggesting a whole new invisible world waiting to be discovered.

For the theorist working at his desk alone at night, it seems almost unfathomable that nature might actually obey the delicate theories you develop on pieces of paper. This is especially true when the theories involve ideas from so many different areas of science and require leaps of imagination.

The reported results are intriguing, but less than convincing. Yet if the two pulses observed last week in Minnesota are followed by more signals as bigger detectors turn on in the coming year or two, it will provide serious vindication of the power of human imagination. Combined with rigorous logical inference and technological wizardry—all the things that make science worth celebrating—scientists’ creativity will have uncovered hidden worlds that a century ago could not have been conceived.