Jablonski taking a sledgehammer to race - MUCH more impressed with this woman than I am with myself...,

Edge | Race has always been a vague and slippery concept. In the mid-eighteenth century, European naturalists such as Linnaeus, Comte de Buffon, and Johannes Blumenbach described geographic groupings of humans who differed in appearance. The philosophers David Hume and Immanuel Kant both were fascinated by human physical diversity. In their opinions, extremes of heat, cold, or sunlight extinguished human potential. Writing in 1748, Hume contended that, "there was never a civilized nation of any complexion other than white."

Kant felt similarly. He was preoccupied with questions of human diversity throughout his career, and wrote at length on the subject in a series of essays beginning in 1775. Kant was the first to name and define the geographic groupings of humans as races (in German, Rassen). Kant's races were characterized by physical distinctions of skin color, hair form, cranial shape, and other anatomical features and by their capacity for morality, self-improvement, and civilization. Kant's four races were arranged hierarchically, with only the European race, in his estimation, being capable of self-improvement.

Why did the scientific racism of Hume and Kant prevail in the face of the logical and thoughtful opposition of von Herder and others? During his lifetime, Kant was recognized as a great philosopher, and his status rose as copies of his major philosophical works were distributed and read widely in the nineteenth century. Some of Kant's supporters agreed with his racist views, some apologized for them, or—most commonly—many just ignored them. The other reason that racist views triumphed over anti-racism in the late eighteenth and nineteenth centuries was that racism was, economically speaking, good for the transatlantic slave trade, which had become the overriding engine of European economic growth. The slave trade was bolstered by ideologies that diminished or denied the humanity of non-Europeans, especially Africans. Such views were augmented by newer biblical interpretations popular at the time that depicted Africans as destined for servitude. Skin color, as the most noticeable racial characteristic, became associated with a nebulous assemblage of opinions and hearsay about the inherent natures of the different races. Skin color stood for morality, character, and the capacity for civilization; it had become a meme. The nineteenth and early twentieth centuries saw the rise of "race science." The biological reality of races was confirmed by new types of scientific evidence amassed by new types of scientists, notably anthropologists and geneticists. This era witnessed the birth of eugenics and its offspring, the concept of racial purity. The rise of Social Darwinism further reinforced the notion that the superiority of the white race was part of the natural order. The fact that all people are products of complex genetic mixtures resulting from migration and intermingling over thousands of years was not admitted by the racial scientists, nor by the scores of eugenicists who campaigned on both sides of the Atlantic for the improvement of racial quality.

The mid-twentieth century witnessed the continued proliferation of scientific treatises on race. By the 1960s, however, two factors contributed to the demise of the concept of biological races. One of these was the increased rate of study of the physical and genetic diversity human groups all over the world by large numbers of scientists. The second factor was the increasing influence of the civil rights movement in the United States and elsewhere. Before long, influential scientists denounced studies of race and races because races themselves could not be scientifically defined. Where scientists looked for sharp boundaries between groups, none could be found.

Despite major shifts in scientific thinking, the sibling concepts of human races and a color-based hierarchy of races remained firmly established in mainstream culture through the mid-twentieth century. The resulting racial stereotypes were potent and persistent, especially in the United States and South Africa, where subjugation and exploitation of dark-skinned labor had been the cornerstone of economic growth.

After its "scientific" demise, race remained as a name and concept, but gradually came to stand for something quite different. Today many people identify with the concept of being a member of one or another racial group, regardless of what science may say about the nature of race. The shared experiences of race create powerful social bonds. For many people, including many scholars, races cease to be biological categories and have become social groupings. The concept of race became a more confusing mélange as social categories of class and ethnicity. So race isn't "just" a social construction, it is the real product of shared experience, and people choose to identify themselves by race.

Clinicians continue to map observed patterns of health and disease onto old racial concepts such as "White", "Black" or "African American", "Asian," etc. Even after it has been shown that many diseases (adult-onset diabetes, alcoholism, high blood pressure, to name a few) show apparent racial patterns because people share similar environmental conditions, grouping by race are maintained. The use of racial self-categorization in epidemiological studies is defended and even encouraged. In most cases, race in medical studies is confounded with health disparities due to class, ethnic differences in social practices, and attitudes, all of which become meaningless when sufficient variables are taken into account.

Race's latest makeover arises from genomics and mostly within biomedical contexts. The sanctified position of medical science in the popular consciousness gives the race concept renewed esteem. Racial realists marshal genomic evidence to support the hard biological reality of racial difference, while racial skeptics see no racial patterns. What is clear is that people are seeing what they want to see. They are constructing studies to provide the outcomes they expect. In 2012, Catherine Bliss argued cogently that race today is best considered a belief system that "produces consistencies in perception and practice at a particular social and historical moment".

Race has a hold on history, but it no longer has a place in science. The sheer instability and potential for misinterpretation render race useless as a scientific concept. Inventing new vocabularies of human diversity and inequity won't be easy, but is necessary.

first computational genomics, now computational ethology...,

academia |  Abstract: For the past two decades, it has widely been assumed by linguists that there is a single computational operation, Merge, which is unique to language, distinguishing it from other cognitive domains. The intention of this paper is to progress the discussion of language evolution in two ways: (i) survey what the ethological record reveals about the uniqueness of the human computational system, and (ii) explore how syntactic theories account for what ethology may determine to be human-specific. It is shown that the operation Label, not Merge, constitutes the evolutionary novelty which distinguishes human language from non-human computational systems; a proposal lending weight to a Weak Continuity Hypothesis and leading to the formation of what is termed Computational Ethology. Some directions for future ethological research are suggested.

 Keywords: Minimalism; Labeling effects; cognome; animal cognition; formal language theory; language evolution

Individual Genetic Variation 5X Greater Than Thought

The First Diploid Sequence of an Individual Human: The highly accurate sequence suggests that our genetic code is five times as variable as we thought

SOURCE: "The Diploid Genome Sequence of an Individual Human" Samuel Levy et al.
PLoS Biology 5: e254

RESULTS: Genomics pioneer Craig Venter and his colleagues have generated a highly accurate sequence of Venter's genome, one that includes the DNA sequences inherited from both his mother and his father.

WHY IT MATTERS: The genome sequence generated by the Human Genome Project, the massive, distributed effort to sequence human DNA that was completed in 2003, was a milestone in the history of biology. But the DNA sequence produced by the project represented just one set of chromosomes (every human has two sets, one inherited from each parent), and it drew on DNA samples from many individuals. As a result, it didn't reflect some of the variability between individuals. ­Venter's diploid genome suggests that genetic variation between individuals is approximately 0.5 percent, not the 0.1 percent that earlier sequencing projects suggested.

METHODS: In the new study, researchers used a method of gene sequencing called Sanger sequencing. The method is more expensive than newer approaches, but it generates longer strings of DNA that are easier to assemble into a complete genome.

NEXT STEPS: Venter and his colleagues plan to add phenotypic information, such as medical records and physical characteristics, to the database housing his genome. This will allow scientists to begin analyzing an individual's genomic information in the context of his or her actual traits.

biologists finally catching on?

Video - Craig Venter on Genomics from Human to the Environment.

Bytesize Biology | An article published today in Science shows the first case of animals synthesizing carotenoids. Nancy Moran and Tyler Jarvik form the University of Arizona looked at the recently sequenced genome of the pea aphid. The pea aphid is known for having two different colors: green and red. It was not very clear though how the aphids got their color. Aphids feed on sap, and sap does not contain carotenoids. When looking at the genomes of the aphids, Moran and Jarvik found that they contained genes for synthesizing carotenoids: this is the first time carotenoid synthesizing genes are found in animals. The question they naturally asked is “where did those genes come from”? The animal kingdom does not contain genes for making carotenoids, so how come aphids have them? Indeed, when they looked for the most similar genes to the aphid carotenoid synthesizing genes they found that they came from fungi, which means they somehow jumped between fungi and aphids, in a process known as horizontal gene transfer. Horizontal gene transfer is not unheard-of in animals, and is actually quite common in plants (yeah, fungi are not plants, I know that), but this is the first time someone has shown a jump from fungi to animals, and that the trait that this gene conveys — color — became embedded and functional in the genome.

Aphid color is important: red aphids get picked easily by predators off green plants, and vice-versa. So there is an evolutionary aspect here: the carotenoid genes play a role in the predator-driven selection of aphids. So in the case of aphids, as opposed to puffins and flamingo, the selective pressure is that of predation, not of mating. (I’ll refrain from comments about Auntie Mae.)

"Long ago, an ancestor to today's pea aphid somehow internalized a large important chunk of DNA from a fungus. This DNA now allows the aphid to generate its own carotenoid molecules. All animals need carotenoids for body functions as important as eyesight. However this aphid is the only organism in the Animal Kingdom so far to have been reported capable of producing it internally. The rest of us must forage for foods such as carrots, containing carotenoids. The precise way the DNA transfer occurred is not yet understood; however patterns within the DNA conclusively show a link to a fungus. DNA transfer from fungus to animal is unprecedented." (text taken from the NSF announcement). Credit: Zina Deretsky, National Science Foundation

As an aside, many of our pseudogenes and other contents of “junk DNA” are thought to have been acquired by horizontal gene transfer. Still, this is the first time a case of gene transfer that is so clear between two different kingdoms. However, I have the sneaking suspicion that as we sequence more animal, plant, fungal and other genomes of multicellular organism, we would find more cases of “large-leap” HGT of functional genes happening: we just don’t have enough genomes yet to appreciate the frequency of these occurrences! Fist tap Dale.

genomic science: keeping it 100%

The Scientist | Meet the species whose DNA has recently been sequenced:

Species: The marijuana plants Cannabis sativa and Cannabis indica
Genome size: Around 400 million base pairs
Interesting fact: The marijuana plant is most well known for the high produced by THC, its active ingredient, which binds to cannabinoid receptors in the body. But Cannabis contains dozens of other active compounds, some of which are being studied as potential treatments for cancer and inflammation. Researchers at Medicinal Genomics hope that sequencing the entire genome will allow them to pinpoint therapeutic compounds while removing the psychoactive effects of THC.

The science dudes did some fungus and other stuff too....whatever.

science: the breakthroughs of 2010 and insights of the decade

AAAS | Until this year, all human-made objects have moved according to the laws of classical mechanics. Back in March, however, a group of researchers designed a gadget that moves in ways that can only be described by quantum mechanics—the set of rules that governs the behavior of tiny things like molecules, atoms, and subatomic particles. In recognition of the conceptual ground this experiment breaks, the ingenuity behind it, and its many potential applications, Science has called this discovery the most significant scientific advance of 2010.

Physicists Andrew Cleland and John Martinis from the University of California at Santa Barbara and their colleagues designed the machine—a tiny metal paddle of semiconductor, visible to the naked eye—and coaxed it into dancing with a quantum groove. First, they cooled the paddle until it reached its “ground state,” or the lowest energy state permitted by the laws of quantum mechanics (a goal long-sought by physicists). They then raised the widget’s energy by a single quantum to produce a purely quantum-mechanical state of motion. They even managed to put the gadget in both states at once, so that it literally vibrated a little and a lot at the same time—a bizarre phenomenon allowed by the weird rules of quantum mechanics.

Science and its publisher, AAAS, have recognized this first quantum machine as the 2010 Breakthrough of the Year. They have also compiled nine other important scientific accomplishments from this past year into a top 10 list, appearing in a special news feature in the journal’s 17 December 2010 issue. Additionally, Science news writers and editors have chosen to spotlight 10 “Insights of the Decade” that have transformed the landscape of science in the 21st century.

Science’s list of the nine other groundbreaking achievements from 2010 includes:

Synthetic Biology. In a defining moment for biology and biotechnology, researchers built a synthetic genome and used it to transform the identity of a bacterium. The genome replaced the bacterium’s DNA so that it produced a new set of proteins—an achievement that prompted a Congressional hearing on synthetic biology. In the future, researchers envision synthetic genomes that are custom-built to generate biofuels, pharmaceuticals, or other useful chemicals.

Neandertal Genome. Researchers sequenced the Neandertal genome from the bones of three female Neandertals who lived in Croatia sometime between 38,000 and 44,000 years ago. New methods of sequencing degraded fragments of DNA allowed scientists to make the first direct comparisons between the modern human genome and that of our Neandertal ancestors.

HIV Prophylaxis. Two HIV prevention trials of different, novel strategies reported unequivocal success: A vaginal gel that contains the anti-HIV drug tenofovir reduced HIV infections in women by 39% and an oral pre-exposure prophylaxis led to 43.8% fewer HIV infections in a group of men and transgender women who have sex with men.

Exome Sequencing/Rare Disease Genes. By sequencing just the exons of a genome, or the tiny portion that actually codes for proteins, researchers who study rare inherited diseases caused by a single, flawed gene were able to identify specific mutations underlying at least a dozen diseases.

Molecular Dynamics Simulations. Simulating the gyrations that proteins make as they fold has been a combinatorial nightmare. Now, researchers have harnessed the power of one of the world’s most powerful computers to track the motions of atoms in a small, folding protein for a length of time 100 times longer than any previous efforts.

Quantum Simulator. To describe what they see in the lab, physicists cook up theories based on equations. Those equations can be fiendishly hard to solve. This year, though, researchers found a short-cut by making quantum simulators—artificial crystals in which spots of laser light play the role of ions, and atoms trapped in the light stand in for electrons. The devices provide quick answers to theoretical problems in condensed matter physics and they might eventually help solve mysteries such as superconductivity.

Next-Generation Genomics. Faster and cheaper sequencing technologies are enabling very large-scale studies of both ancient and modern DNA. The 1000 Genomes Project, for example, has already identified much of the genome variation that makes us uniquely human—and other projects in the works are set to reveal much more of the genome’s function.

RNA Reprogramming. Reprogramming cells—turning back their developmental clocks to make them behave like unspecialized “stem cells” in an embryo—has become a standard lab technique for studying diseases and development. This year, researchers found a way to do it using synthetic RNA. Compared with previous methods, the new technique is twice as fast, 100 times as efficient, and potentially safer for therapeutic use.

The Return of the Rat. Mice rule the world of laboratory animals, but for many purposes researchers would rather use rats. Rats are easier to work with and anatomically more similar to human beings; their big drawback is that methods used to make “knockout mice”—animals tailored for research by having specific genes precisely disabled—don’t work for rats. A flurry of research this year, however, promises to bring “knockout rats” to labs in a big way.

Finally, to celebrate the end of the current decade, Science news reporters and editors have taken a step back from their weekly reporting to take a broader look at 10 of the scientific insights that have changed the face of science since the dawn of the new millennium. Here are their 10 “Insights of the Decade”:

the minimal cell

theatlantic |  In 2010, a team of scientists announced that they had created a synthetic living cell. The team, led by Nobel laureate Ham Smith, microbiologist Clyde Hutchison III, and genomics pioneer Craig Venter, fashioned the full genome of a tiny bacterium called Mycoplasma mycoides in their lab, and implanted the DNA into the empty cell of another related microbe. They nicknamed it Synthia. Some news sources claimed that the team had, for the first time, created artificial life.Others noted that they had merely photocopied life, putting an existing genome into a new chassis, like a “hermit crab taking up residence in an abandoned shell.”

But amid the hyperbole and skepticism, the team continued working. “The 2010 paper was basically the control experiment,” says Venter. Their true mission was to create a cell with a minimal genome.

All living things evolved from a common ancestor, so despite our grand variety, we all share genes that are essential for our survival. They’re at the core of our operating systems: the fundamental software without which we would die. Smith, Hutchinson, Venter, and their colleagues wanted to create an organism with just these essential genes—only those it needed to survive, and nothing more. A minimalist microbe. Kondococcus, perhaps.

Why bother? Because they ultimately want to intelligently design new life-forms from scratch—say, bacteria that can manufacture medical drugs, or algae that churn out biofuels. And creation requires understanding. “We had to start with a system where we knew and understood all the components, so that when we added specific ones to it, we could do so in a logical design way,” Venter says. They needed a minimal genome—a vanilla model that they could later kit out with deluxe accessories.

And they’ve done it. Six years after Synthia, they’ve finally unveiled their bare-bones bacterium. And in piecing together its components, they realized that they’re nowhere close to understanding them all. Of the 473 genes in their pared-down cell, 149 are completely unknown. They seem to be essential (and more on what that means later). Many of them have counterparts that are at work in your body right now, probably keeping you alive.

And they’re a total mystery.

“We’ve discovered that we don’t know a third of the basic knowledge of life,” says Venter. “We expected that maybe 5 percent of the genes would be of unknown function. We weren’t ready for 30 percent. I would have lost a very big bet.”