Scientists sequence the coelacanth genome

The coelacanth is one of a small handful of living fishes that are probably closely related much more ancient, extinct creatures — including, the first fish to haul itself up onto land. Now scientists have sequenced its genes and are digging through the data in search of genetic clues to how fish and land-dwelling animals are connected to one another. Among the finds so far, a gene that seems to be connected to how animals grow placentas. Coelacanths don't have placentas, but they do have eggs that hatch inside their own bodies.

Some kinds of DNA ancestry tests are basically astrology

If you want to learn about your family tree, you're probably better off doing the work of compiling history than getting a $500 DNA test.

Resurrecting the dead — one piece at a time

Thanks to Jurassic Park, we tend to focus on one use for the DNA of extinct creatures — resurrecting them, in full, to live here in the modern age. But it's not necessary to go that far to learn a lot about those animals, and the evolution of life, in general. At the Experimental Podcast, Stephanie Vogt talks about the paleophysiologists who are reconstructing the proteins of extinct animals using fragments of DNA found in long-dead remains. Those proteins, simple as they may seem, hold some amazing stories. For instance, reconstructed haemoglobin from wooly mammoths could someday help doctors get oxygen to the brains of high-risk human surgery patients.

Coming in late summer — human baby season

There is definitely a seasonality to human births, writes Beth Skwarecki at Double X Science. The complicated bit is that human baby season isn't necessarily the same (or as strongly expressed) from place to place and culture to culture. In the United States, significantly more babies are born in July, August, and September. Meanwhile, in Europe, babies seem to make their way into the world in spring. So there's clearly a cultural component to this — but culture doesn't explain it, entirely. Skwarecki's piece explores a messy place where culture, genetics, and circadian rhythms intersect.

Getting to know "Mitochondrial Eve"

By studying the way it has mutated and changed over time, scientists can trace human mitochondrial DNA — the DNA that is passed from mother to daughter — back to a single woman. Basically, everybody alive is descended from her. But that's not the same thing as saying that Mitochondrial Eve was once the only woman alive. In a very nice piece — with helpful illustrations — the Christian (but evolution-accepting) scientists at BioLogos explain what Mitochondrial Eve really means and why she can't be used as an argument for creationism. Whether or not you've ever found yourself arguing this point with a family member or friend, the piece is really useful for deepening your understanding of a pop-science concept that's often thrown around without a clear explanation behind it.

How bad research gets published (and promoted)

In 2010, a group of scientists claimed to have found bacteria that could build its DNA using arsenic, instead of the phosphorous used by the rest of Earth's life forms. Within days, the research behind "arsenic life" was under serious scrutiny and we now know that it was totally wrong. But the work was peer-reviewed. It was sponsored by NASA. How do so many experts make such a big mistake? Dan Vergano at USA Today has an excellent article looking at just that — and it includes the peer review comments that helped the arsenic life paper get published. Though normally secret, Vergano got a hold of them through a Freedom of Information Act request.

The super history of supertasters

Last week, I posted a link to a story on the Atlantic, all about the history of research into supertasters — humans with the ability to taste a bitter compound called phenylthiocarbamide. It's a big part of why some people can't stand the taste of broccoli, and others love it. But that one piece isn't the full story. According to taste geneticist Stephen Wooding, it wasn't even totally accurate. Instead, he suggested three articles that anybody curious about supertasting should read. First, a history of the science that he wrote for the journal Genetics. Second, a long read by Cathryn Delude about research that might, someday, make broccoli delicious for everybody. And a University of Utah site that explains the genetics of taste.

The bones of Richard III (or, possibly, someone else entirely)

Before you get excited about the bones of Richard III being found under a parking lot, consider this — the announcement included no mention of how common the DNA sequences that ostensibly identified the body as Richard really are. Those sequences might match Richard's descendants, but if the sequences are also really common, well, that's not saying much.

No cloned Neanderthal baby for Harvard (at least not yet)

For the record, a Harvard scientist is NOT looking for an "adventurous woman" to give birth to a cloned Neanderthal. Ladies, you can stop filling out those application forms. Apparently, geneticist George Church and the German magazine Der Spiegel had a bit of a translation problem.

The evolution of white fur and an animal sex scandal

Up north — in Canada and other places where snowy winters are reliable (and reliably heavy) — you find more animals whose fur comes in various shades of white. This is true even for species that are brown or black further south. The difference is obvious. But how does it happen? Carl Zimmer presents two possible paths to paleness — random mutation, and fortuitous cross-species mating. In related news: Golden retrievers are probably getting it on with Canadian coyotes.

How humans evolved to explore

Boldly going where nobody's gone before. In a lot of ways, that idea kind of defines our whole species. We travel. We're curious. We poke our noses around the planet to find new places to live. We're compelled to explore places few people would ever actually want to live. We push ourselves into space.

This behavior isn't totally unique. But it is remarkable. So we have to ask, is there a genetic, evolution-driven, cause behind the restlessness of humanity?

At National Geographic, David Dobbs has an amazing long read digging into that idea. The story is fascinating, stretching from Polynesian sailors to Quebecois settlers. And it's very, very good science writing. Dobbs resists the urge to go for easy "here is the gene that does this" answers. Instead, he helps us see the complex web of genetics and culture that influences and encourages certain behaviors at certain times. It's a great read.

Not all of us ache to ride a rocket or sail the infinite sea. Yet as a species we’re curious enough, and intrigued enough by the prospect, to help pay for the trip and cheer at the voyagers’ return. Yes, we explore to find a better place to live or acquire a larger territory or make a fortune. But we also explore simply to discover what’s there.

“No other mammal moves around like we do,” says Svante Pääbo, a director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where he uses genetics to study human origins. “We jump borders. We push into new territory even when we have resources where we are. Other animals don’t do this. Other humans either. Neanderthals were around hundreds of thousands of years, but they never spread around the world. In just 50,000 years we covered everything. There’s a kind of madness to it. Sailing out into the ocean, you have no idea what’s on the other side. And now we go to Mars. We never stop. Why?”

Why indeed? Pääbo and other scientists pondering this question are themselves explorers, walking new ground. They know that they might have to backtrack and regroup at any time. They know that any notion about why we explore might soon face revision as their young disciplines—anthropology, genetics, developmental neuropsychology—turn up new fundamentals. Yet for those trying to figure out what makes humans tick, our urge to explore is irresistible terrain. What gives rise to this “madness” to explore? What drove us out from Africa and on to the moon and beyond?

Read the full story

Sequencing of barley genome could have implications for home brewers

When scientists from the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany sequenced the genome of barley, they were thinking primarily about the impact on food. Understanding the genetics behind certain traits could help us breed barley varieties that have built-in resistance against disease, or that contain more fiber. (Contrary to popular understanding, there's actually a lot of overlap between what we might think of as genetic engineering and what we might think of as breeding. Crop researchers can use genome maps to select specific plants to cross pollinate, enabling them to reliably breed a trait into a new variety much faster than was previously possible.)

But, this is barley. And we don't just eat barley. With this plant, sequencing the genome also has implications for the way we brew beer. At Popular Science, Martha Harbison explains what we're learning about barley's genetic code and why it matters in beer making. In particular, she says it's significant that the researchers sequenced the genomes of more than one variety of barley.

Why should aspiring homebrewers care? Because two-row and six-row barley behave slightly differently in the mash, which can have profound effects on brewing efficiency and characteristics of the finished beer (a complex phenomenon I'll get into in a future column). I figured anyone nerdulent enough to want to know about genetic differences of cultivars would be curious as to which kind of barley was used in the single-nucleotide-variation study.

Read the rest of the story at Popular Science

You can read more about the surprisingly complex world of plant breeding in two articles I wrote — one for Popular Science, and one for Discover.

Image: Beers and Glassware, a Creative Commons Attribution No-Derivative-Works (2.0) image from cambridgebrewingcompany's photostream

What does the $1000 genome really mean for you?

The cost of genome sequencing is starting to sink into the affordable range. (In comparison to its previous cost. We're talking "within reach" the same way Design Within Reach uses the phrase.)

Companies are starting to claim that a $1000 personal genome sequence is on the horizon. But what does that mean for you? Should you save up and get one? Can it really tell you anything meaningful at all? Who is going to sift through all the information your genome represents — and how will they do it?

Tonight, starting at 7:00 Eastern, Science Online New York City is hosting a round-table to discuss these issues, especially the problems associated with collecting, making sense of, and protecting a massive new stream of personal data. The live event is sold out, but you can watch whole thing streaming online.

Panelists: Ronald Crystal, the Chairman of the Department of Genetic Medicine at Weill-Cornell Medical College, who has had his genome sequenced and analyzed it himself. Virginia Hughes, a freelance author who has written about her experience with the 23andMe genotyping service. Manish Ponda of Rockefeller University, who has experimented with other -omic type analyses.

SoNYC's livestream feed

Via Lou Woodley

Court to hear argument on the privacy implications of "junk" DNA databases

The Ninth Circuit is hearing arguments today about the privacy implications of gathering and retaining "junk" DNA, which has been treated as merely identifying, like a fingerprint, and not unduly invasive. Modern genetics shows that it's possible to extract information about health, ancestry, and other potentially compromising traits. From the Electronic Frontier Foundation's blog:

In this case, Haskell v. Harris, the ACLU of Northern California is challenging the California law, arguing that it violates constitutional guarantees of privacy and freedom from unreasonable search and seizure.  This is the first court hearing to address DNA privacy since the research on “junk” DNA has become widely known, and in its role as amicus, EFF asked the court to consider the ground-breaking new research.  The oral argument is open to the public at the federal courthouse at 95 7th Street in San Francisco.  The hearing starts at 10am, in courtroom 1 on the third floor.

Wednesday Hearing in 9th Circuit Tackles DNA Privacy

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