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For the last time, redheads are not going extinct

Pictured: Your great-grandchildren?

As a redheaded science journalist, I hear this "fact" a lot. Reality is, though, we aren't going anywhere. Yes, as Cara Santa Maria points out at Huffington Post, redheads represent only about 1% of the world's population. And this hair color is related to a recessive gene. Both your parents have to have a copy in order for you to be a redhead, so a redheaded person can have non-redheaded babies. But that's not the same thing as going extinct. Because here's our little secret: We redheads are stealthily infiltrating the rest of humanity. Only 1% of humans are redheads, but 4% of humans carry a copy of the gene that makes redheads. You could be a carrier and not even know it. So could your spouse. Two redheads are unlikely to make a brunette, but two brunettes can make a redhead. Good luck wiping us out. *Insert evil laughter here*

You can learn more about this at Cara Santa Maria's Talk Nerdy To Me vidcast, but I'll add a little piece of anecdata, too. My parents are both brunettes. So were their parents. I am largely an anomaly on both sides of my family. In fact, besides my brother and I, the only other redhead in my Mom's entire family (that anyone remembers) was her grandfather. And yet still, we rise.

How Stuff Works also has a great debunking of the redhead extinction myth

Some more info on how redheads are in yer genome, gingerin' yer descendants from the Stanford University Tech Museum

Image: Four shades of Red, part II, a Creative Commons Attribution Share-Alike (2.0) image from e3000's photostream

Why cilantro-haters hate cilantro

I have loved cilantro (also known as coriander) passionately since first eating it in a Vietnamese restaurant in a former gas station in downtown Chicago when I was 10. And most people seemed to agree with me that it is the best herb ever. Only in recent years did I stumble upon the vocal minority of cilantro-haters—the people who think my beloved cilantro tastes like soap. I do not understand them. But Nature News offers some insight. Turns out, dislike of cilantro is linked to a variation in a gene associated with our sense of smell. Bonus: If you hate cilantro whole, there's some evidence to suggest you might like it pulverized in a pesto.

ENCODE, the media, and what we really know about the human genome

If you've read anything in the past week about ENCODE—a group of laboratories that recently published their latest work on the human genome—then you need to read John Timmer's excellent piece over at Ars Technica.

What ENCODE has actually done, and why it matters, has been widely misrepresented in the mainstream press—largely because of misleading press releases put out by ENCODE, itself. Timmer sets the record straight. It's a long read, but a fascinating one. Highly recommended.

This week, the ENCODE project released the results of its latest attempt to catalog all the activities associated with the human genome. Although we've had the sequence of bases that comprise the genome for over a decade, there were still many questions about what a lot of those bases do when inside a cell. ENCODE is a large consortium of labs dedicated to helping sort that out by identifying everything they can about the genome: what proteins stick to it and where, which pieces interact, what bases pick up chemical modifications, and so on. What the studies can't generally do, however, is figure out the biological consequences of these activities, which will require additional work.

Yet the third sentence of the lead ENCODE paper contains an eye-catching figure that ended up being reported widely: "These data enabled us to assign biochemical functions for 80 percent of the genome." Unfortunately, the significance of that statement hinged on a much less widely reported item: the definition of "biochemical function" used by the authors.

This was more than a matter of semantics. Many press reports that resulted painted an entirely fictitious history of biology's past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge (this happens to be the exact opposite of what journalism is intended to accomplish). But you can't entirely blame the press in this case. They were egged on by the journals and university press offices that promoted the work—and, in some cases, the scientists themselves.

Read the rest of John Timmer's story at Ars Technica

Image: Micah's DNA, a Creative Commons Attribution Share-Alike (2.0) image from micahb37's photostream

Rare is relative

Rare genetic mutations turn out to not be quite as rare as we previously thought.

NYT series on genetically-targeted cancer treatments

When you have been diagnosed with cancer, as I have, you quickly grow accustomed to "friendly cancer spam." Friends, relatives, and well-meaning acquaintances routinely forward you a gazillion identical links to whatever this week's hot cancer news headline may be.

So it was for me with this New York Times story on Lukas Wartman, a leukemia doctor and researcher at Washington University who developed leukemia. As he faced death last Fall, his cancer genome was sequenced by his colleagues.

What was revealed then led to a treatment plan that targeted the specifics of his genetic makeup. And so far, according to Gina Kolata's report, that experimental treatment plan has been an amazing success. Snip:

Dr. Ley’s team tried a type of analysis that they had never done before. They fully sequenced the genes of both his cancer cells and healthy cells for comparison, and at the same time analyzed his RNA, a close chemical cousin to DNA, for clues to what his genes were doing.

The researchers on the project put other work aside for weeks, running one of the university’s 26 sequencing machines and supercomputer around the clock. And they found a culprit — a normal gene that was in overdrive, churning out huge amounts of a protein that appeared to be spurring the cancer’s growth.

Even better, there was a promising new drug that might shut down the malfunctioning gene — a drug that had been tested and approved only for advanced kidney cancer. Dr. Wartman became the first person ever to take it for leukemia.

And now, against all odds, his cancer is in remission and has been since last fall. While no one can say that Dr. Wartman is cured, after facing certain death last fall, he is alive and doing well.

Suffice it to say that this stuff is relevant to my interests. It is routine for breast cancer patients like me to receive genetic screening for the BRCA mutation, and sometimes a few additional known genetic factors. But there is so much that we do not know, and a growing sense that this infinite array of genetic unknowns could lead to more saved lives, and better quality of life for those of us who have been diagnosed with the disease.

Read the rest

Probably false article claims Madonna worries that her fans want her DNA

An report in the Melbourne Herald-Sun, quoting an unlinked article in the UK Mirror (a truly awful tabloid) claims that Madonna has a DNA cleanup crew who sterilize all the surfaces and vacuum all skin cells and hair follicles after Madonna uses a dressing room, to prevent fans from getting hold of her genetic material. Given the stupid provenance, it's almost certainly not true, but it's a great plot-point for some future science fiction story.

Madonna thinks fans want her DNA | Herald Sun (via Kottke)

Open-source human genomes

Yesterday, during a World Science Festival panel on human origins and why our species outlasted other species of Homo, geneticist Ed Green mentioned that there were thousands of sequenced human genomes, from all over the world, that had been made publicly available. Our code is open source.

But where do you go to find it? Several folks on Twitter had great suggestions and I wanted to share them here.

The 1000 Genomes Project—organized by researchers at the Wellcome Trust, the National Institutes of Health, and Harvard—is working on sequencing the genomes of 2500 individuals. The data they've already collected is available online. Read a Nature article about The 1000 Genomes Project: Data management and community access.

The Personal Genome Project is interactive. Created by a researcher at Harvard Medical School, the program is aimed at enrolling 100,000 well-informed volunteers who will have their genomes sequenced and linked to anonymized medical data. Everything that's collected will be Creative Commons licensed for public use.

The University of California Santa Cruz Genome Browser is a great place to find publicly available genomes and sequences.

Thanks to Eva Rose, Aatish Bhatia, and Edward Banatt.

The discovery of DNA

Fifty-nine years ago this week, James Watson and Frances Crick published their first description of the structure of DNA. You can read the full, historic paper online. Note that the "unpublished experimental results and ideas" of Dr. R. E. Franklin get a shout-out at the end. (Via Pourmecoffee)

"My Favorite Museum Exhibit": The cyclops

"My Favorite Museum Exhibit" is a series of posts aimed at giving BoingBoing readers a chance to show off their favorite exhibits and specimens, preferably from museums that might go overlooked in the tourism pantheon. I'll be featuring posts in this series all week. Want to see them all? Check out the archive post. I'll update the full list there every morning.

From Australia's McLeay Natural History Museum at Sydney University comes ... dun dun dun ... the Cyclops!

Sorry. I've got a bit of THE TRIUMPH OF MAN stuck in my head. Actually, this skull belonged to a foal, says Justin Cahill, who sent in the photos. It's part of a long, natural history museum tradition of exhibiting the weird and often grotesque, preserving them as examples of how the natural way isn't always ideal. The same forces that shape evolution can also seriously screw you up. So much of what we call "normal" is based on chance.

Nobody ever actually saw this foal alive, by the way. The skull was found in the Hawkesbury River in 1841. But there have been attempts to reconstruct what the horse might have looked like during it's brief time alive. You can see that photo after the cut:

Read the rest

Twins: Nature, nurture, and epigenetics

National Geographic has a really interesting story on what we can learn about human biology and human culture from studying the lives of twins. (Last week, Mark blogged about some of the photos in the story.) The story explains the chance beginnings of the now-massive Minnesota Study of Twins Reared Apart; introduces you to twin girls from China who were adopted by two different Canadian families that now work to keep the girls in each other's lives; and delves into what we know and don't know about why some identical twins are different from each other in very conspicuous ways.

One example of this last bit is the story of Sam and John, identical twin brothers. Both are on the autism spectrum, but they appear to be on entirely different parts of that spectrum, with John experiencing much more severe symptoms that led the boy's parents to enroll him in a special school. Why would identical twins, raised in the same family, have such an obvious difference in the expression of characteristics that are probably mostly inherited? That's where epigenetics comes in.

A study of twins in California last year suggested that experiences in the womb and first year of life can have a major impact. John's parents wonder if that was the case with him. Born with a congenital heart defect, he underwent surgery at three and a half months, then was given powerful drugs to battle an infection. "For the first six months, John's environment was radically different than Sam's," his father says.

Shortly after Sam and John were diagnosed, their parents enrolled them in a study at the Kennedy Krieger Institute in Baltimore. Blood samples from the boys were shared with a team at nearby Johns Hopkins University looking into the connection between autism and epigenetic processes—chemical reactions tied to neither nature nor nurture but representing what researchers have called a "third component." These reactions influence how our genetic code is expressed: how each gene is strengthened or weakened, even turned on or off, to build our bones, brains, and all the other parts of our bodies.

If you think of our DNA as an immense piano keyboard and our genes as keys—each key symbolizing a segment of DNA responsible for a particular note, or trait, and all the keys combining to make us who we are—then epigenetic processes determine when and how each key can be struck, changing the tune being played.

Image: Twins, a Creative Commons Attribution (2.0) image from missbossy's photostream

Study raises new concerns about safety of genetically modified food

A study at Nanjing University in China found that ingested "microRNA" (very small pieces of ribonucleic acid, or RNA) from plants were able to survive digestion and influence the function of human cells.

Food columnist Ari Levaux has a piece digging into the implications, in The Atlantic. The basic idea: if this research stands up to the rigors of scientific scrutiny, it could prove that when we eat food, we consume not just fuel and nutrients, but information that changes us on a cellular level, and influences health.

Snip:

Monsanto's website states, "There is no need for, or value in testing the safety of GM foods in humans." This viewpoint, while good for business, is built on an understanding of genetics circa 1950. It follows what's called the "Central Dogma" (PDF) of genetics, which postulates a one-way chain of command between DNA and the cells DNA governs.

The Central Dogma resembles the process of ordering a pizza. The DNA knows what kind of pizza it wants, and orders it. The RNA is the order slip, which communicates the specifics of the pizza to the cook. The finished and delivered pizza is analogous to the protein that DNA codes for.

We've known for years that the Central Dogma, though basically correct, is overly simplistic. For example: Pieces of microRNA that don't code for anything, pizza or otherwise, can travel among cells and influence their activities in many other ways. So while the DNA is ordering pizza, it's also bombarding the pizzeria with unrelated RNA messages that can cancel a cheese delivery, pay the dishwasher nine million dollars, or email the secret sauce recipe to WikiLeaks.

Monsanto's claim that human toxicology tests are unwarranted is based on the doctrine of "substantial equivalence." This term is used around the world as the basis of regulations designed to facilitate the rapid commercialization of genetically engineered foods, by sparing them from extensive safety testing.

via The Very Real Danger of Genetically Modified Foods - The Atlantic. You'll also want to read the actual study, and make up your own mind.

Update: Here's a critical take on the linked-to Atlantic piece. Ari responds here.

(via @coopportunity)

Did genetic adaptation help early African-Americans survive harsh conditions of slavery?

Did natural selection help African-Americans adapt to the harsh conditions of their new lives as slaves in the Americas? A team of researchers at the Chinese Academy of Sciences in Shanghai report in the journal Genome Research that "certain disease-causing variant genes became more common in African-Americans after their ancestors reached American shores — perhaps because they conferred greater, offsetting benefits." Read more at the New York Times.

Image: The Africans of the slave bark "Wildfire"--The slave deck of the bark "Wildfire," brought into Key West on April 30, 1860. Library of Congress.

Forget love, biological sex is a battlefield

Gender isn’t a simple thing. A person can be male, female, both, neither, and more—and that identity doesn’t have to have anything to do with the particular genital plumbing they were born with.

Read the rest

Genomics X-Prize looking for centenarians


[Video Link]

The Archon Genomics X-Prize is offering $10 million to the first research team to sequence the genomes of 100 people who are age 100 or older. The goal: Get a clear view, for the first time, of what makes centenarians different on a genetic level.

That's pretty cool. And will probably be a lost more useful than the usual answer to, "How did you live so long?," which seems to usually involve something about piss, vinegar, and ironically unhealthy lifestyle choices.

But, before the fun can start, the Prize needs to find 100 centenarians willing to donate samples of their DNA to science. That's where you come in. Do you have a friend, grandparent, or great-grandparent who'd be interested in participating in the project? If so, you should nominate them to be one of the "100 Over 100."

This team of genomic pioneers will also have opportunities to document their lives and experiences for the benefit of future generations, through the Life@100 online community. (It's pretty awesome to see a sign-up page with a disclaimer that says you must have been born before January 3, 1913 to join.) The video above comes from the profile 105-year-old investment broker Irving Kahn.

(Thanks, Miles O'Brien!)

Science Saturday: Allergies, symbiotic bacteria, and scientific literacy

I had a great conversation with Christina Agapakis, a science blogger at Scientific American and a scientist studying synthetic biology. In this episode of Bloggingheads.tv's Science Saturday, you'll find out what Christina learned when she traced her allergies on a phylogenetic tree, why she's currently obsessed with symbiotic bacteria, why I think adults need more opportunities for informal science education after they've left school, and how scientists and educators are trying to address clashes between science and culture.

In the video, I talked about my experience at the 6th Science Center World Congress. For a little more on that, check out the story I wrote about why adults need science museums to pay more attention to them.

Encoding text with GM bacteria


Science Now reports on a project from David Walt (Tufts) and George Whitesides (Harvard) to come up with a steganographic text-encoding scheme that uses bacteria to encode messages and selective antibiotics to reveal them. It was conceived of in response to a DARPA challenge to devise non-electrical text-encoding, but its applications include adding text-based information to GM crops that can be read in the field (or in the market) to determine what's being grown.

The new scheme replaces the fuse with seven colonies of Escherichia coli bacteria, each given a gene for a different fluorescent protein. When, and only when, these genes are turned on do the bacteria make these proteins and light up. The colors, including yellow, green, and red, vary based on which gene is expressed. All are clearly visibly different to the naked eye. With their colorful bacterial colonies in hand, the researchers then created a code using pairs of different colored bacteria. Having seven colors gave them 49 combinations, which they used to encode the 26 different letters and 23 alphanumeric symbols such as "@" and "$." They wrote a message by simply blotting pairs of colored bacteria in rows. To "print" the message, the researchers transferred the bacteria onto a plate containing agar, a bacterial growth medium, into which they pressed a sheet of nitrocellulose "paper" that immobilizes the bacteria.

At this point, the bacteria on the nitrocellulose paper remain invisible. But the message receiver can turn on the key genes and make the colors light up by pressing the nitrocellulose paper into an agar plate containing a chemical trigger that activates expression of the fluorescent proteins. (The proteins chosen to light up are ones the bacteria don't normally use, so unless the researchers activate them, they stay quiescent.) As long as the receiver knows which colors correspond to which characters, the message is revealed. But Walt and his colleagues added one more safeguard as well. Into some bacteria they inserted genes for resistance to particular antibiotics; the idea is that only the antibiotic-resistant bacteria are carrying the real message. If the message fell into the wrong hands, the receiver would see a mix of colors once the genes were activated and be unable to read it. But if the decoder added the right antibiotic, nonresistant bacteria and their colors die away, and the message becomes clear. The first example, reported in today's issue of the Proceedings of the National Academy of Sciences reads "this is a bioencoded message from the walt lab @ tufts university 2010."

(via /.)

(Image: Manuel A. Palacios/Tufts University)

The psychopathic neurobiologist

James Fallon studies the brain. Then he studied his own, and found out that he has the same brain malfunctions as psychopathic serial killers. What happened next is a fascinating story about the brain, the mind, and the dueling influences of nature and nurture.

Primer on GM crops

Check out this great primer on the science behind the safety of genetically engineered food crops.(Via Kate Clancy)