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Genomic sequencing finds no single gene basis for extreme longevity

Misao-OkawaWhole genome sequencing has not found any single gene variation responsible for extreme longevity, according to a paper published in PLOS ONE:

We have sequenced the genomes of 17 supercentenarians (over 110 years of age) to see if we could uncover the genetic basis for their extreme longevity. We analyzed rare protein-altering variants, but found no strong evidence for enrichment of either a single variant or a single gene harboring different variants in female Caucasian supercentenarians compared to controls.

The full genomic sequences have been published, allowing other researchers to build on the data set.

 

Video: Bringing back extinct species

In recent years, the possibility of reviving extinct species by recreating their genomes has become a reality. First on deck for "de-extinction" are the woolly mammoth and passenger pigeon. But is this a good idea? KQED's QUEST takes a look: "Reawakening Extinct Species"

"Duon" is just a new name for something we already knew about

Over the last couple of days, you might have heard about the "duon" — a "second" genetic code that's being hyped as a radical new "breakthrough" in science.

Based solely on the number of words I've put in quotations here, you can probably guess that the actual news doesn't really match the hype.

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Why 23andMe can't tell you everything about yourself (yet)

How can a mild-mannered grasshopper turn into a ferocious locust? Why are humans humans when we have share 80 percent of the same genetic material with a cow? In a fascinating long read at Aeon, David Dobbs delves into the differences between genetic change (evolution as you probably learned it in school) and genetic expression (the amazing powers of natural selection that scientists are only now starting to really understand).

23AndMe issues statement on FDA smackdown

Distributed today to all users of the 23andMe home genetic testing service, after the FDA ordered the firm to halt sales of new kits:

Dear 23andMe Customers,

I wanted to reach out to you about the FDA letter that was sent to 23andMe last Friday.

It is absolutely critical that our consumers get high quality genetic data that they can trust. We have worked extensively with our lab partner to make sure that the results we return are accurate. We stand behind the data that we return to customers - but we recognize that the FDA needs to be convinced of the quality of our data as well.

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23andMe vs. the FDA in less than 4 minutes

At what point does interesting-but-potentially-incorrect-or-misleading information become a potential threat to health? How do you regulate a product that current regulations were never set up to handle? The University of Michigan's Risk Science Center put together this quick cartoon that neatly summarizes the problems and questions at the heart of the FDA's crackdown on 23andMe, which Xeni wrote about on Monday.

A couple of other smart takes on this that have come out in the past couple of days:
• Genomics expert Michael Eisen delves deeper into the question of how we should regulate personal genetic testing.
Journalist David Dobbs rounded up some diverse opinions. You should pay attention to his blog. He's been doing a lot of great reporting on genetics and culture and is planning on publishing a longer piece on the 23andMe stuff later this week.

Is the yeti related to an ancient polar bear?

Abominable snowman 520169

Is the yeti actually some hybrid of ancient polar bear and brown bear? University of Oxford geneticist Bryan Sykes has analyzed DNA from what's purported to be yeti hair samples.

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Do IQ test results mean anything at all?

The answer is yes — but only in certain circumstances and that "yes" comes with a whole bunch of caveats. At Discover, Emily Sohn has a nice basic primer on what we know now about intelligence testing and what your score on an IQ test does and doesn't mean.

Two redheads can have a brunette child

Turns out, whether or not you are a ginger is not determined by the simple genetics of a single gene. In fact, the pigment that causes red hair is likely present in many brunettes. What matters more seems to be how much of the ginger-hiding brunette pigment you have — and the genetics that determine that are a lot more complicated. Which, frankly, makes the brunette-guy-with-red-beard phenomenon make a whole lot more sense.

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Genetics: Not a "miracle", but still pretty damn strange

Besides magnetism, there's another thing that the Insane Clown Posse was on-track in categorizing as a mind-blowing mystery — Why do Shaggy 2 Dope's kids look just like him? As with the magnets, this is another situation where the obvious answer (it's genetics!) masks a much more complicated issue that science hasn't totally figured out yet. At Pacific Standard, Michael White explains why genetics is still messing with our heads, almost 150 years after Mendel:

The problem: most of the genetic differences discovered have only a very small effect. And when you add up all those effects, the result can’t possibly explain the full influence of our genes on those traits. For example, researchers have identified hundreds of DNA differences between people that influence the very strongly heritable trait of human height, but the total effect of those differences added together explains only about 10 percent of the genetic influence on height. In other words, we still can’t explain why tall parents have tall children.

Scientists have named this discrepancy the “missing heritability,” and they’ve spent the last half-decade trying to find it.

Scientists experiment with "turning off" excess chromosome that causes Down's

Down's syndrome happens when a human being ends up with an extra copy of chromosome 21 — three copies, instead of the normal two. But scientists say they might have found a way to make that extra chromosome functionally irrelevant. If they're right, it could lead to treatments that could someday reduce the symptoms of Down's. The trick is connected to another extra chromosome that the human body "turns off" all the time — the X. Women have two X chromosomes, of course, but only one ever gets to express itself. Scientists put the same mechanism to use on chromosome 21 in petri dish experiments.

Making sense of the confusing Supreme Court DNA patent ruling


Nine people who have not recently made any sweeping judgements about biotechnology.

Last week, I told you about the US Supreme Court ruling that made it illegal to patent naturally occurring DNA. In that article, I talked briefly about the fact that the new ruling doesn't cover all DNA. It's still perfectly legal to patent synthetic DNA, and the court documents referred specifically to complementary DNA (aka cDNA).

This is where things get murky. Complementary DNA is a thing that can be both natural and synthetic. And, as a laboratory creation, it's an important step in a common method of replicating naturally occurring DNA. All of which leaves some holes in the idea that the Supreme Court ruling is a simple "win" for open-access science, patent activists, and patients. After all, if you can't patent a gene, but you can patent the laboratory copy of the gene, what's that mean? It's sort of like not being able to patent a novel, but being able to patent a copy of its contents that's had all the white space removed. It seems like everybody is a bit confused by this. So I wanted to take a moment to at least clarify what cDNA is and what some people, on different sides of the science/law/biotech divides, are thinking about it.

It starts with some stuff you learned back in junior high — how information from your DNA gets turned into actual working proteins.

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Blunders of Genius: interesting errors by Darwin, Pauling, and Einstein

History has shown us that even some of the greatest scientific luminaries, towering figures such as the naturalist Charles Darwin, the twice-Nobel-Laureate chemist Linus Pauling, and the embodiment of genius — Albert Einstein — have made some serious blunders.

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Supreme Court: You can't patent (naturally occurring) genes

In an unanimous decision, the United States Supreme Court ruled today that companies can't patent genes, or parts of genes — at least, so long as that genetic material is identical to what occurs in nature. The lawsuit dealt specifically with Myriad Genetics, the company that isolated and has claimed a patent on BRCA 1 and BRCA 2 — genes associated with an increased risk of breast and ovarian cancers. From a practical perspective, Myriad's hold on the genes has meant that tests for genetic cancer risk are strikingly expensive — Xeni paid more than $3000 for hers. It's also meant that, if you get a positive result, there's been nowhere you could go for a second opinion.

That's a big deal. Mutations in the BRCA 1 and 2 genes mean an increased risk of cancer, but there's more than one kind of mutation that can happen. In fact, BRCA 1, alone, has hundreds of known mutations. Some increase your risk of cancer. But, even if you narrow it down to just those, they don't all increase the risk by the same amount. The health choices you make could be very different depending on whether you have an 80% risk of developing breast cancer by age 90 (the worst-case scenario for BRCA 1 mutations), or something much lower. That's the kind of situation where you might really like to have more than one lab run more than one kind of test.

This ruling opens the door for that, and the competition should (theoretically) also lower the cost.

Read the rest

What we can learn from the clones that walk among us

Genetically speaking, identical twins ought to be two copies of the same person. Environmentally speaking, if the twins grow up together, they ought to even be influenced by the same things. But if you actually pay attention to identical twins, they aren't identical in personality or interests. How do naturally occurring clones become individual people? That's the subject of a mouse study that Scicurious writes about on her blog. Fascinating stuff.

Did a volcanic eruption nearly kill off ancient humans?

Short answer: We don't know. What makes this story by Erin Wayman interesting is the way it carefully breaks down an almost Hollywood-ready narrative and finds the fascinating uncertainty lurking underneath. The truth is, uncertainty is cool. Because it means there's more stuff left to discover.

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