Why did humans lose our tails? Blame a "jumping gene"

 

Most animals have tails, including almost all mammals. For some reason, we humans don’t. This difference has been the source of much speculation among scientists over the years, and many arguments have been made about why we don’t tails.

One line of reasoning goes like this: tails are very useful for animals that live in trees, but once our ancestors came down from the trees and started living on the open plain, they didn’t need those tails any more. But why lose them? Lots of animals don’t live in trees, and they still have tails.

Even among the primates, most species have tails, but chimpanzees, gorillas, orangutans, and bonobos–the great apes–don’t. In fact, one way to tell great apes apart from other apes is by the presence of a tail. We humans are simply great apes without so much hair. Or, as the English scientist Desmond Morris called us in his famous book, humans are “The Naked Ape.”

So why am I writing about this now? Well, in a newly published article in Nature, a group of scientists from NYU, led by Itai Yanai and Jef Boeke, seem to have figured out what made us lose our tails. It’s all due to a piece of DNA that copies itself and jumps around our genome.

It’s a bit geeky, but stay with me and I’ll try to explain.

It seems that sometime around the divergence of the great apes from other primates, about 15-20 million years ago, a “jumping gene” popped into a gene called TBXT in our ancestor. (The B in TBXT stands for brachyury, which means “short tail.”)

The jumping gene here is just a piece of DNA a few hundred letters long*, not really a gene all by itself. But once that jumping gene got into TBXT, it was in just the right position to make the cells in our ancestor produce a shorter version of TBXT. The shortened gene was missing one of its pieces, but it still worked – well, sort of. Our ancestors managed just fine, but they lost their tails.

(Aside: the piece that’s chopped out is called exon 6, for those who really want to know.)

Given that this happened over 15 million years ago, how did the scientists prove their hypothesis? Well, other mammals have the same gene, but they make a longer version. So the authors of the new paper created a version of the TBXT gene in mice that included the jumping gene–and, as predicted, some of the mice lost their tails entirely.

Admittedly, this doesn’t exactly prove that one jumping gene caused us to lose our tails. Without a time machine to take us back 15 million years (with a DNA sequencing machine in tow), we can’t truly prove what happened eons ago. But it’s a compelling story, because we know that our genomes, and those of other great apes, have this unique jumping gene that other mammals lack.

So now we know how we lost our tails. We still don’t know exactly why, though. Some scientists speculate that being tail-less might have helped us to walk upright, or that it might have been better to lose the tails once our ancestors stopped living in trees.

On the other hand, guinea pigs don’t have tails either, and they don’t walk on two legs. And koalas don’t have tails, even though they live in trees. Some of these questions may just have to remain a mystery.

*Technically, the jumping genes in this story are called Alu elements, and they occur all over our genome. Famed geneticist Haig Kazazian, a former Hopkins colleague who passed away just two years ago, explained in a 2004 paper that Alus are a form of “nonautonomous retrotransposon.”

Jurassic World fact check: can we clone dinosaurs?

One of this summer’s biggest hits was the movie Jurassic World, which earned a record $209 million on its opening weekend back in June. It's so popular that it’s still showing in theaters now, more than two months later.

Like its predecessors, the fourth movie in the Jurassic Park series features a theme park filled with dinosaurs that were created by cloning dinosaur DNA. In the movie, the dino DNA was collected from mosquitos preserved in amber, which (in the fictional movie world) had sucked the blood of dinosaurs 65 million years ago.

The success of the movie spurred YouGov.com to conduct a poll, asking Americans if they believed it was currently possible to create dinosaurs from DNA found in fossils. 28% said yes.

It makes for a fun story, but is there any science behind it? Well, yes and no.

Can we clone a living organism entirely from scratch, just from its DNA sequence alone? Yes! Not only can we do it, but it has already been done. Genome scientists Craig Venter and Hamilton Smith, both former colleagues of mine, achieved this at least twice, creating bacteria by synthesizing the necessary DNA and then “booting up” a new bacterial cell, which went on to replicate itself and grow into colonies of brand-new bacteria. Very impressive work, although bacterial genomes are quite small, only a few million nucleotides long.

Moving up a step, just last year, Hopkins scientist Jef Boeke (who is now at NYU) and his team synthesized an entire yeast chromosome. Yeast are single-celled like bacteria, but they're eukaryotes, evolutionarily closer to humans and dinosaurs than bacteria. Eukaryotes keep their DNA sequestered inside a nucleus, which in turn makes them way harder to clone from scratch. Synthesis of the remaining yeast chromosomes is under way, and it’s entirely feasible that we’ll have artificial yeast in just a year or two.

As of today, though, no one has even come close to synthesizing a multi-cellular creature like a dinosaur–or a chicken, or a frog, or a human. But in principal, it is possible to create a living animal just from its DNA, though it might take a few more decades to do it.

So yes, we might someday create animals from DNA. But dinosaurs? Alas, this half of the Jurassic World question gets a big “no.”

The problem is, despite the compelling story in the movie, there is no dinosaur DNA left on the planet. None at all, despite what you might have read. Dinosaurs went extinct about 65 million years ago, mostly likely because of a massive asteroid impact in the Yucatan peninsula, and DNA simply doesn’t last that long.

But wait, you might ask: what about all these stories about Neandertal DNA, or woolly mammoth DNA, or other ancient species? These studies are true and are very exciting. Scientists have reconstructed the genome of our Neanderal relatives from very old bones, around 30,000-40,000 years old. We can extract DNA from bones that old, although the DNA is badly degraded. I worked on an ancient DNA project myself, using an 11,000 year old mammoth thigh bone to reconstruct part of its genome. We were able to recover quite a lot of mammoth DNA from that bone.

Other work on ancient samples has demonstrated that in the most extreme conditions, where the bones have been continuously frozen in the Greenland ice sheet, DNA may survive as long as 1 million years. However, dinosaurs lived in temperate climates where DNA degrades far more quickly, and virtually all dinosaur DNA was probably gone within a few thousand years after the dinosaurs became extinct.

(By the way, that same YouGov poll that asked about cloning dinosaurs also asked "Do you believe that dinosaurs and humans once lived on the planet at the same time?" 40% of Americans said yes, demonstrating once again that Americans are woefully misinformed about evolution and the history of the planet.)

So alas, a mosquito that sucked the blood of a Tyrannosaurus rex, and then got swallowed and preserved in tree sap, would not yield any T. rex DNA for present-day cloning experiments.

This doesn’t mean we’ll never have a Jurassic Park, but if we do, we’ll have to guess at what that dino DNA looked like, perhaps using the DNA of birds. Perhaps, though, we should focus on saving the species we have left, which we are rapidly wiping out, before worrying about reviving long-lost dinosaurs.

Ted Cruz is not as smart as Galileo, whatever he claims

Global temperatures for the past 125 years. It's getting hot!

The word in Washington lately is that Senator Ted Cruz–who just announced that he’s running for President–is supposed to be a very smart guy. Some of this comes from Harvard Law professor Alan Dershowitz, who said last year that Cruz was “clearly among the top students” at the prestigious Harvard Law School. Dershowitz is very liberal, while Cruz is very conservative, so one assumes that Dershowitz wouldn't say this if it weren't true.

Perhaps Cruz was an excellent law student. But when it comes to science, Cruz is no whiz kid. On the contrary, he seems to be woefully ignorant. We know this because despite his lack of expertise, he doesn’t hesitate to make sweeping pronouncements about scientific matters.

In just the past week, Cruz has weighed in on two major science issues, and he's been wrong on both. First, in an interview a few days ago with the Texas Tribune, Cruz stated that global warming isn’t happening. This wasn’t the first time he’s made that claim, but this time he threw in what’s known in skeptical circles as the "Galileo gambit," a well-known ploy of conspiracy theorists. He compared his global warming denialism to Galileo thusly:

“Today, the global warming alarmists are the equivalent of the flat-Earthers. It used to be [that] it is accepted scientific wisdom the Earth is flat, and this heretic named Galileo was branded a denier.”

Cruz managed to get at least two things wrong in a single sentence here. 

First, Galileo did not become famous for arguing against flat-Earthers: he argued that the Earth revolved around the sun (the heliocentric model of the solar system) rather than the sun revolving around the earth (the geocentric or Ptolemaic model, after the Greek philosopher Ptolemy).

Second, Galileo was not a denialist, nor was he called one. He was not denying a vast array of scientific data to make his point–just the opposite, in fact. The data showed that the Earth and other planets revolved around the sun, and the Catholic church (among other institutions) didn’t want to believe it, and therefore they forced him to recant. The Church didn't call Galileo a "denier."

Cruz's statement is not just wrong: it's also arrogant. Cruz is comparing himself to Galileo, one of the greatest scientists in history, as if he (Cruz) were making a brave scientific stand against a dogmatic opponent. This is the crux of the Galileo gambit: the speaker claims to take a heroic stand against a powerful foe while defending the truth. Sorry, Senator Cruz: you’re no Galileo. Not even a little bit.

And let's not ignore Cruz’s scientific claim: that the Earth isn't getting warmer. Here's one of his quotes:

"And many of the alarmists on global warming, they’ve got a problem cause the science doesn’t back them up. And in particular, satellite data demonstrate for the last 17 years, there’s been zero warming. None whatsoever."

Oh good. Ted Cruz has evaluated the satellite data and figured this out. Who knew that he was not only a lawyer but also a scientist? Real climate scientists–who understand this issue far, far better than Cruz–disagree. For example, NASA and NOAA recently announced that 2014 was the warmest year on record. They also explained that 

“The 10 warmest years in the instrumental record, with the exception of 1998, have now occurred since 2000. This trend continues a long-term warming of the planet, according to an analysis of surface temperature measurements by scientists at NASA’s Goddard Institute of Space Studies.” (See the Figure.)

There’s no mystery about why Cruz and others deny global warming: the oil and coal industries have conducted a vigorous campaign for years now, primarily targeting Republicans, to cast doubt on the science. The reason is simple: fossil-fuel companies are worried that if we take global warming seriously, we might burn less fossil fuel. Their lobbying campaign is working: Cruz has certainly fallen into line.

Meanwhile, coastal areas are fighting rising sea levels, and the Arctic and Antarctic are melting. Lobbying might change the minds of politicians, but the planet doesn't care.

Now let’s look at the second bit of dodgy science that Senator Cruz endorsed this week. He announced his candidacy at Liberty University, a Christian fundamentalist college in Virginia that was founded by Jerry Falwell, an evangelical Southern Baptist minister. Liberty University’s Center for Creation Studies teaches students that the the Earth is only a few thousand years old and that all species were placed here by an all-powerful god, exactly as described in the Bible. Not surprisingly, students and faculty at Liberty University deny the facts of evolution. To a scientist, Cruz's appearance at Liberty University is an in-your-face endorsement of creationism.

I should be clear that Ted Cruz didn’t explicitly embrace creationism and deny evolution when he announced his candidacy, but he did choose Liberty University, and he must know its views about evolution. I wrote to Senator Cruz to see if he believed in young-Earth creationism, or if he believed that species evolved over millions of years, as science has demonstrated. He didn’t reply.

Virtually all of modern biology and medicine has its basis in evolution. No serious scientist disputes that evolution is by far the best explanation for the species around us, and for a thousand other phenomena that scientists study every day. The debate about the fact of evolution is long over. As a scientist, I find it just embarrassing to have prominent U.S. politicians publicly deny evolution.

Actually, I suspect that Ted Cruz isn’t really a creationist. I find it hard to believe that a guy who went to Princeton and Harvard, and apparently did quite well at both schools, can really believe the Earth was created 4,000 years ago. I also wonder if he truly believes that the world's leading climate scientists are just making stuff up about the Earth warming. Maybe he’s just pandering to his right-wing audience and his campaign donors.

Do politicians need to make decisions about science? Of course they do. But science can be incredibly complex and specialized. A good president (or prime minister, or governor) will identify experts–independent ones, without conflicts of interest–and seek their advice. Ted Cruz is no scientist, as his recent comments demonstrate, but I predict he won't be the only U.S. presidential candidate to make misguided remarks about science.

South Carolina lawmaker wants to force Creationism down students' throats

Well, it’s happened again. The great state of South Carolina has demonstrated that when it comes to ignorance of science, its legislators take a back seat to no one. They must have been jealous of Kansas, Louisiana, and Texas.

Last week, SC legislator Mike Fair, a Republican, proposed a new standard for teaching high school biology that encourages teachers to teach alternatives to evolution, by which he means creationism. He's been working on this for months; last spring he tried to pass a law that would have required students and teachers to construct arguments against evolution. After failing to get that through his committee, he has proposed a new law that says: 

“evolution is continually open to and subject to experimental and observational testing.”

Except of course that's not what he really means.

Let’s be clear: Mike Fair doesn’t want evolution to be taught in public schools. Instead, he wants to force students, using the power of government, to adopt his conservative Christian views, which teaches that God created all living things just as they are today, about 6000 years ago (or 4000 years, depending on who you ask). 

Fair has a history of trying to dumb down the teaching of science.  Back in February, he blocked the state education oversight committee from using the phrase “natural selection” in the state science standards. Speaking to the (SC) Post and Courier, Fair said 

“To teach that natural selection is the answer to origins is wrong. I don't think it should be taught as fact.” [Mike Fair, S.C. legislator]

Ignorant barely begins to describe this statement. Mike Fair clearly doesn’t have the faintest grasp of biology or genetics. He’s the last person that anyone should want to weigh in on science standards. His behavior goes far beyond mere ignorance, though: not only is he wrong, but he wants to use the power of the state to impose his religious views, under the guise of science, on every student in South Carolina’s schools. No wonder South Carolina is perennially ranked near the bottom of the country in public education. 

I have a confession to make. I grew up in South Carolina and went through the public schools there, from kindergarten right through high school. I met lots of guys like Mike Fair: popular, plays on the football team, student body president. These guys are usually bullies (we've all seen the movie), and that’s just what Fair is demonstrating now: he wants to bully every teacher, and every child, into listening to his ignorant views of science. I’ve no doubt that if Fair could require prayer in every school — Christian prayer, that is — he’d do that too. I grew up surrounded by this kind of nonsense, but I didn't speak up then because I would have been ostracized. Well, I'm speaking up now. 

Fair and his colleagues in the Republican-dominated S.C. House of Representatives argue that no, they aren’t forcing teachers to teach creationism — they just want to teach the controversy. Equally appalling is the position of the S.C. Superintendent of Education, Mick Zais, who agreed with this sentiment, saying: 

"We ought to teach both sides and let students draw their own conclusions."

No, you shouldn't. There is no scientific controversy about evolution. Evolutionary theory is based on an enormous edifice of facts, with literally tens of thousands of scientific papers providing evidence to support it. There is no competing theory out there.

Ironically, three years ago Fair introduced a bill to prevent the imposition of Islamic-based Sharia law in South Carolina. He justified this by saying 

“A growing concern is the immigration of people who are accustomed to their religion and their civil laws being inextricably connected. For those newcomers to our state, this bill will be helpful to them as they are assimilated into our culture maintaining complete freedom to worship as they please."

Reading this sent my irony meter way into the red zone. Let me see if I understand: Mike Fair doesn’t want religion and civil laws to be “inextricably connected” — but he does want to require that public, state-funded schools teach his religious view of the creation myth. I guess what he meant to say is that it’s okay to mix religious fundamentalism and civil law, as long as it’s Mike Fair's brand of Christian fundamentalism.

South Carolina doesn't need its own set of science standards, nor does Texas, Louisiana, or Kansas. The laws of science don't change when you cross state lines or national borders. Allowing politicians to set science standards is a recipe for disaster, and is one reason why the U.S. continues to lag the rest of the world in science education—as South Carolina has once again demonstrated.

Another humanoid species walked the earth

[I'm on vacation, and this short post will appear while I'm away.]

One of the coolest scientific discoveries of the past few years was a small bone found in a remote region of Siberia.  The scientists who found it initially thought it was just an early human fossil, or else a Neanderthal fossil, but something about it looked a bit off.  It was just one small finger bone, not much to go on.

But DNA sequencing told a different tale.  The bone belonged to a female who was neither human nor Neanderthal, but something in between.  She and her kind appear to be closer to Neanderthals than to modern humans, but there is no doubt that she represents a new hominid species, one that died out only recently in evolutionary terms.  The evidence indicates that this previously unknown group, called the Denisovans after the cave in which the bone was found, actually interbred with humans.

The latest findings were published last fall in the journal Science, by a team led by Matthias Meyer and Svante Paabo.  With just one small, 75,000-year-old finger bone, they knew that extracting DNA would be a challenge.  Most of the DNA from ancient samples comes from bacteria and other creatures that have infiltrated the bone over the millenia.  But they were lucky in one respect: Siberia is cold, and has been for a very long time, which helps to preserve DNA.  Still they had to develop an entirely new method of extracting ancient DNA for this bone.

Meyer and colleagues extracted enough DNA to cover the entire genome of this ancient female.  They estimated that Denisovans and human diverged over 175,000 years ago.  They also discovered that modern Papuans contain vestiges of Denisovan DNA in their genomes, about 6%, suggesting that interbreeding occurred when humans were spreading across Asia.

Just this month, National Geographic's Jamie Shreeve published a feature article on the discovery, providing a fascinating look at how a single finger bone revealed a previously lost sister species.  (I highly recommend it, even for those who read the original Science article.) Now that we know what to look for, we might find more, and learn more, about these almost-humans from ancient Siberia.  And maybe we'll eventually figure out why they disappeared.

A final note: this discovery is yet another example of how evolution has shaped the history of life on this planet, but somehow I suspect the anti-evolution forces in the U.S. will find a way to deny it.

What do the Presidential candidates think about science?

ScienceDebate.org recently posed 14 questions to President Obama and Republican presidential nominee Mitt Romney, and just a few days ago, the candidates answered all 14.  Can we learn what they actually think about science from these answers?  Well, maybe just a little bit.  

My first inclination, on going to the ScienceDebate2012 website, was to look for the candidates' positions on the two biggest scientific topics in the political arena today: evolution and global warming.  Somehow, ScienceDebate2012 only asked about one of these, which I'll get to in a minute.

The ScienceDebate2012 organization calls its list "the top American science questions: 2012", but the questions themselves are a disappointment.  They're what you'd expect from a committee: lots of nice-sounding, polite questions, but nothing that really challenges the candidates.  I guess SD2012 was afraid that the candidates might get all offended, or maybe that fewer scientists would sign their petition.  But if you read the answers, you'll see that the candidates just answered the question they wanted to hear, as politicians love to do.  Most of the answers describe policies we already know (for those who are paying attention to the campaigns), but an interesting surprise popped up: Mitt Romney has no fondness for NASA.  Jump to the bottom to learn more.

Most of the questions are big fat softballs, starting with the first one: "What policies will best ensure that America remains a world leader in innovation?" http://www.sciencedebate.org/debate12/   Good tough question, guys!  We only have 14 questions, and you waste one on this?  Unsurprisingly, the answers to this one just repeated campaign talking points.

Before looking at some real answers, let's start with the howlingly obvious question that ScienceDebate2012 failed to ask.  

The Un-asked Question: do you believe that evolution should be taught in public schools, and that it should be presented as the only explanation for how species arose?  

This question has only one right answer, as any biologist worthy of the name knows.  Evolution is the foundation of all of modern biology, genetics, infectious disease research, you name it.  And the U.S. is one of the few advanced countries where a significant number of its citizens don't accept evolution, opting instead for an archaic religious position that claims Earth is only a few thousand years old.  

We should know the candidates' answers.  In 2008, ten Republican presidential candidates were asked if they believe in the theory of evolution.  Only 7 said yes--but one was Governor Romney.  Back in 2007, he told the New York Times that "the science class is where to teach evolution," and that intelligent design was "for the religion class or philosophy class."  President Obama also supports evolution, and opposes teaching creationism in the science classroom. 

So the candidates agree on this one - at least they did in the past.  But Romney's fellow Republicans don't all agree. In particular, we need to ask Governor Romney: do you support the crazy religious extremism of your fellow Republican, Congressman Paul Broun from Georgia, who just announced that evolution, embryology, and the Big Bang theory are

 "lies straight from the pit of hell"?  

And Broun also stated that the Bible - and his wacko interpretation of it - should be used to run our government.  Any candidate for president should denounce this call for theocratic rule.

And by the way, if a Democratic Congressman said anything like this, I'd throw the same question at President Obama.

Now on to one of the real questions, on global warming. ScienceDebate2012 posed the question this way:

"The Earth’s climate is changing and there is concern about the potentially adverse effects of these changes on life on the planet. What is your position on cap-and-trade, carbon taxes, and other policies proposed to address global climate change—and what steps can we take to improve our ability to tackle challenges like climate change that cross national boundaries?"  

Obama's short answer acknowledges that "climate change is one of the biggest issues of this generation," and goes on to say he will "continue efforts to reduce our dependence on oil and lower our greenhouse gas emissions."  Vague generalities, and nothing he hasn't said before, but consistent at least.

Romney's answer, though, tries to have it both ways.  He first says that global warming is indeed happening and then says, basically, we need more research because it's controversial.  Here's how his lengthy answer begins: 

"My best assessment of the data is that the world is getting warmer, that human activity contributes to that warming, and that policymakers should therefore consider the risk of negative consequences."  

But then he pivots in the very next sentence and claims 

"there remains a lack of scientific consensus on the issue ... and I believe we must supported continued debate and investigation within the scientific community."  

So there you go: yes, global warming is a problem, but let's study it rather than do something.  At the end of his answer, Romney recovers a bit by saying he supports "robust government funding for research on efficient, low-emissions technologies."  So it appears he would support some action on global warming.  But his answer offers a troubling false claim about a lack of scientific consensus: the consensus is rock solid.

Now, I promised one surprise: a bit of new information.  Question 12 covers space exploration and is another softball: 

"What should America's space exploration and utilization goals be in the 21st century and what steps should the government take to help achieve them?" 

I expected some vague answers about how great America is (and both candidates did indeed deliver on that), but Romney surprised me with his answer.

Here's the surprise: Romney comes right out and says he will probably cut the NASA budget.  What he actually said in his answer was: 

"A strong and successful NASA does not require more funding, it needs clearer priorities."

In Washington-speak, this means "NASA has too much money and I will probably cut it."

So at least we know where Romney stands on space exploration.  He wants to downsize it and, apparently, outsource it to other countries.  Here's how he puts it later in his answer: 

"Part of leadership is also engaging and working with our allies and the international community. I will be clear about the nation’s space objectives and will invite friends and allies to cooperate with America in achieving mutually beneficial goals."  

If I worked for NASA, I'd be worried.  

Evolution bugs me

Cover illustration for the forthcoming textbook
by Carl Zimmer and Douglas Emlen

This is a real photo.  It's the cover for a new biology textbook by Carl Zimmer and Douglas Emlen.  The photo shows three "walking leaves," or leaf insects, which have evolved to look just like the leaves around them.

These little bugs must be one of the best examples of natural selection ever.  The more closely they resemble a leaf, the more difficult it is for predators to find them.  Over the millenia, the bugs who evaded predators survived better, and eventually walking leaves looked like they do today.

In fact, these guys have been around for a long time, at least 47 million years, according to a fossil discovery published in 2006.  That paper described a fossilized leaf insect found in an ancient lake bed in Germany, which looks remarkably similar to its modern descendants.

Yes despite this amazing evidence, only 40% of Americans believe in evolution. State legislatures continue to pass bills attempting to teach children the creation myth that the world was created less than 10,000 years ago.  Just last week, a committee in Alabama's legislature proposed a new law that would give students credit for courses on creationism.  The bill's sponsor, local legislator Blaine Galliher, was very clear about his motivation:

"They teach evolution in the textbooks, but they don't teach a creation theory…. Creation has just as much right to be taught in the school system as evolution does." 

I feel sorry for the students in Alabama whose education might suffer thanks to the ignorance of their lawmakers.  But there is some hope: in the national poll showing that 40% of Americans overall accept evolution, among young adults that percentage was 49%, while among over-55 set it was just 31%, as shown in this graph:

So perhaps in another hundred years or so, Americans will start to "get" evolution.  But it might take longer: apparently 18% of Americans still believe that the sun revolves around the earth.  So it's taken us 500 years to get to 80% for that one.

Indiana's clumsy attempt at theocracy

An edible FSM

Those state legislators are meddling with science again.  This time it's Indiana, trying to promote their religious views in public schools by dictating what science teachers will teach.  As usual when legislators try to do science, they messed up badly.

What happened?  Just a few days ago, the Indiana state Senate passed a bill, sponsored by Republican Dennis Kruse, that required the teaching of creationism.  Actually, the original bill called for schools to teach "creation science," but then the Senate amended it to make it much funnier.  Thanks Indiana!

The amended bill, which was approved 28-22, says:

"The governing body of a school corporation may offer instruction on various theories of the origin of life. The curriculum for the course must include theories from multiple religions, which may include, but is not limited to, Christianity, Judaism, Islam, Hinduism, Buddhism, and Scientology."

Holy cow!  I can't wait to see what Indiana students will be spouting when they go on to college.  Maybe they'll learn Scientology, which is one of the religions listed in the new law.  Scientologists believe that life on Earth started 75 million years ago, when an evil galactic warlord named Xenu brought 13.5 trillion of his people to Earth in a spaceship, stacked them around volcanoes, and vaporized most of them with hydrogen bombs.  (No, I'm not making this up.)

If I were teaching in Indiana schools, I'd be sure to cover the Church of the Flying Spaghetti Monster, which has a wonderful theory about the origin of life:

"We believe the Flying Spaghetti Monster created the world much as it exists today, but for reasons unknown made it appear that the universe is billions of years old (instead of thousands) and that life evolved into its current state (rather than created in its current form). Every time a researcher carries out an experiment that appears to confirm one of these “scientific theories” supporting an old earth and evolution we can be sure that the FSM is there, modifying the data with his Noodly Appendage. We don’t know why He does this but we believe He does, that is our Faith."

Now that's a theory you can sink your teeth into.

Finally, a little bit of science education for Indiana's legislators.  The next time you write a law trying to force the teaching of creationism instead of evolution, get the wording right.  You see, you wrote the bill incorrectly, because evolution is not a theory of the origin of life, as any good high school science teacher could have told you.  (Note to Indiana teachers: I've no doubt that you tried to teach these legislators back when they were in school. Apparently they're still not listening.)  Instead, evolution is a theory that explains how species arise: how a single species can evolve into many, through the process of natural selection.  You might have guessed this from the title of Darwin's book: The Origin of Species.  Scientists do have theories about the origin of life, but evolution isn't one of them.

Two years ago, South Dakota's legislature declared that astrology can explain global warming, which gave the rest of the country a bit of entertainment. Last week, it was Indiana's turn to look foolish.  After a huge flurry of embarrassing publicity, it appears that Indiana's legislature has changed its mind, and the bill will not become law.  But if they try again, I'd be happy to send them some materials on the Flying Spaghetti Monster.

[Note: I also recommend the blog posts by PZ Myers at Pharyngula and Jen McCreight at BlagHag.]

The black death is dead

Evolution tells us a lot about death. Of course it's about life too, but it's really about survival, which involves both life and death.

As most people know, the Black Death was a horrible plague that swept through Europe, Asia, and Africa in the 1300's, killing tens of millions of people at a time when there weren't so many people to begin with. The world's population prior to the plague, about 450 million, dropped to 350 million. About one-third of the entire population of Europe, and half the population of China, may have died. Centuries earlier, the Plague of Justinian in 541-542 C.E. may have killed even more, up to half of Europe and untold millions elsewhere around the world. In ancient and medieval times, people thought the plague was caused by rats, but the true cause wasn't discovered until 1894, when Alexandre Yersin of France and Kitasato Shibasaburo of Japan finally traced it to a bacterium now called Yersinia pestis, which is transmitted by fleas, which in turn are carried around by rats.

The plague kills all of its hosts, even the fleas:

"The bacteria multiply inside the flea, sticking together to form a plug that blocks its stomach and causes it to starve. The flea then bites a host and continues to feed, even though it cannot quell its hunger, and consequently the flea vomits blood tainted with the bacteria back into the bite wound. The bubonic plague bacterium then infects a new victim, and the flea eventually dies from starvation. " Source: Wikipedia

Gross, I know. But the original plague, the Black Death, has never returned. Why not? A study last year and another one published just this week provide the answer.

Last year, Barbara Bramanti and colleagues collected DNA from mass graves dating to the Black Death, and showed conclusively that the victims were infected with Yersinia pestis. Until this study, some scientists were uncertain about whether Yersinia pestis was the true cause, but Bramanti's research should settle that question once and for all. They also showed that at least two distinct strains of plague bacteria infected Europe, each arriving via a different route.

Further evidence appears in a remarkable new study published this week by Hendrik Poinar and colleagues. They exhumed over 100 skeletal remains from victims of the Black Death, collected from a ancient London cemetery, East Smithfield, which has been conclusively dated to the plague years, 1348-1350. Using the latest DNA sequencing methods, they identified Yersinia pestis DNA in 20 of the 109 victims.

Both studies collected enough DNA to show that the strain of Yersinia pestis from 1350 C.E. is unlike any modern strain. In other words, the original plague died out, probably long ago. The likely explanation is just this: the Black Death was simply too deadly to persist. Evolutionary theory tells us that a pathogen that kills all its victims will eventually run out of victims, leading to its own extinction. The plague bacteria needed to evolve into something less virulent, and that seems to be what happened. A bug that doesn't kill its host is far more successful evolutionarily. (Just look at the common cold, which we can't seem to get rid of.)

The same thing happened to the "Spanish" flu virus, the one that cause the terrible 1918 flu pandemic. It too evolved into a milder pathogen, and it is still with us today - the 2009 influenza pandemic was caused by a direct descendant of the 1918 virus.

The Black Death was so widespread that it even affected human evolution. In 1998, Stephen O'Brien and colleagues showed that a mutation that confers resistance to HIV first appeared in the human population in the 1300's. They concluded that this mutation can best be explained by "a widespread fatal epidemic"; in other words, the Black Death. I should be careful to explain that the plague didn't actually cause the mutation: the mutation occurred naturally. The Black Death selectively killed more people without the mutation, leaving us with a population of humans that tended to have the mutation.

In light of these new results about evolution, I can't help pointing out that, finally, that evolution has been in the news recently for another reason. Several U.S. politicians, some campaigning for President, have been attacking evolution, saying that it has "got some gaps in it" and even supporting the teaching of creationism. Scientific facts aren't affected by political statements, of course, but the future of the U.S. is. Politicians who attack evolution, whether from ignorance or from some political or religious agenda, only hurt our future potential as a technology leader. I can only hope that the public won't support these anti-science positions.

Meet the new flu, same as the old flu*

Next year we’ll be back to one flu vaccine, thank goodness. The flu vaccine protects you against three different strains of the influenza virus, but for the past year, we had a separate vaccine for the new pandemic (“swine”) flu. It’s always hard to get people to take their shots (or “jabs,” as they say in England – why can’t we come up with a less painful-sounding word?), and asking everyone to go out and get two shots was never ideal.

For the next flu season, the vaccine will include these 3 strains:

1. The 2009 “swine flu” strain, H1N1
2. The previous seasonal flu, H3N2
3. Influenza B, a milder flu that has been around for decades.

What happened? Well, the WHO, the CDC, and the FDA have decided to replace one of the three strains in the flu vaccine with the new H1N1. The strain they replaced was also called H1N1, which is rather confusing. Let’s look at the history of these strains, which is an interesting picture of virus evolution.

In 1918, the Spanish flu (which originated in the U.S., despite its name) spread throughout the world and killed an estimated 30-40 million people, in the worst flu epidemic in recorded history. This was the original H1N1 flu. It soon evolved into a milder flu, which was around until...

In 1957, a new pandemic strain appeared, H2N2 or "Asian flu." This completely replaced H1N1 in the human population, although H1N1 continued to fluorish in pigs (more on that below). H2N2 dominated until...

In 1968, the Hong Kong flu pandemic, H3N2, swept the world and replaced H2N2.

Then, very suspicously, in 1977 the H1N1 strain reappeared in Russia. It is widely believed that this was an accidental escape from the Soviet Union’s biowarfare program. This H1N1 strain didn’t replace H3N2, but both strains have co-circulated ever since, with H3N2 generally causing more serious illness.

All along, the milder influenza B strain has been around as well. That’s why the vaccine contains 3 strains: H3N2 (from 1968), H1N1 (from 1918 via Russia in 1977), and flu B.

That brings us to late 2008. Several strains of Spanish flu (H1N1) had been circulating in pigs for decades. Two of those strains combined to create the new pandemic flu, which jumped from pigs to humans. Oddly enough, we don’t have any reports of a pandemic among pigs, which is why “swine flu” is a misnomer. Here are the latest statistics for human infections in the U.S., for the last week of March 2010:

• 3.7% of people tested turned out to have influenza. (In other words, the season is over, as I predicted in mid-January.)
• 98% of positive influenza specimens were pandemic H1N1.
• 2% of positive specimens were influenza B.

So it seems that the swine flu has replaced the Russian flu. At least it has in the vaccine. It might even be safe to get rid of H3N2 in the vaccine, but there’s little harm in keeping it in the vaccine for one more season, just in case H3N2 stays with us a bit longer. So next fall we’ll be back to one shot, and “pandemic flu” will be just plain old “seasonal flu” once again.

The CDC's advisory panel also (rather quietly) expanded their recommendation on who should get vaccinated “to include all people aged 6 months and older.” That’s right, everyone, even the elderly. Wait until the anti-vaccination movement gets hold of this – they’ll have a field day. Actually I’m surprised they haven’t already. Maybe they don’t know about the nanobots we’ll be putting in vaccines in the very near future.

*with apologies to The Who.

10,000 genomes – why?

In the genomics world that I inhabit, a consortium has just published an intriguing proposal to sequence the genomes of 10,000 vertebrate species. It’s described an article in the current Journal of Heredity – unusual in that this is not a research article, but a proposal. Nonetheless, the article is full of interesting facts about what we know (and don’t know) about vertebrate species and how they’re all related. It makes a good read for anyone interested in evolution; for example, how many people know that all vertebrates have a common ancestor who lived about 500-600 million years ago? Perhaps more interesting, evidence is emerging that we all share about 10,000 genes – which means that these 10,000 genes are so useful that their functions have been preserved for 500 million years.

The consortium is led by a number of outstanding scientists, including UCSC’s David Haussler and NIH’s Stephen O’Brien, both of whose work I like and have followed for years. And some aspects of this proposal are terrific: for example, they want to start collecting DNA now from 16,203 vertebrate species. This will make a great specimen collection for future work. (Heck, maybe I’ll even sign on to the project myself.)

But this proposal is more than that: it is also the opening salvo in an effort to raise $50-100 million for the sequencing of these species. The paper was announced with press releases and news articles in both Science and Nature, demonstrating that it is clearly a lobbying effort for new funding. Fair enough – science takes funding, and sometimes you have to build support for new ideas. However, given that two of the three leaders of the consortium are primarily funded by NIH, I can only guess at who they’re expecting to cough up the money. The NIH's human genome funding has been led by NHGRI, which continues to look for new ways to justify maintaining the size of its three enormous sequencing centers (the Broad Institute, Washington University in St. Louis, and Baylor College of Medicine). Now, let me say here that genomes are the bread and butter of my own work, and these centers have done terrific work for the past 10-15 years - and I've often collaborated with them. And I hope they will continue. But it hasn’t escaped my attention that the new NIH Director, Francis Collins, was a key force in building up those centers while he was Director of NHGRI, and we all know that the centers are near and dear to him.

But wait a minute: 10,000 genomes, none of which are human? Exciting idea, sure, but not for NIH. The NIH-led centers are already participating in the 1000 Genomes project, which is attempting to sequence 1000 individuals (at a low-level “draft” quality). If NIH wants to scale up, there are 6 billion more of us available. Admittedly, not everyone wants to have his/her genome sequenced, but plenty of us would be happy to volunteer. Take a look at the Personal Genome Project, which was started by George Church at Harvard, and is trying to sign up 100,000 humans to have their genomes sequenced.

So I’m going to be the skeptic here: if NIH is thinking of throwing its sequencing dollars at 10,000 more genomes, I suggest that it focus on humans rather than a broad collection of other vertebrates. (I know, this should be obvious, right? But sometimes NIH gets distracted.) We still have only scratched the surface of what there is to know about the human genome, and there’s plenty of DNA sequencing to do in the human population. The 10,000 genomes project sounds like a great mission for the National Science Foundation, which has ceded much of large-scale sequencing work to the NIH in the past 10 years, except for plant genomes and some bacteria. In fact, maybe this is a chance for NSF to have its own large-scale sequencing center – I’d be all for that. But I’m not at all convinced that NIH should spend its biomedical research dollars on 10,000 vertebrates. Let’s see how this plays out.

Dinosaur proteins from T. rex and hadrosaurs

The controversy over the finding of Tyrannosaurus rex proteins in a fossilized bone
continues, with a long article in Wired magazine this week exploring the issue. The Wired reporter, Evan Ratliff, takes a refreshingly skeptical view through much of the article. It's a good read, and I recommend it.

But first, an update on the science: Mary Schweitzer, John Asara and colleagues published a new report in Science on May 1 describing their analysis of an 80-million-year-old fossil from the dinosaur Brachylophosaurus canadensis, a hadrosaur that is 12 million years older than T. rex. Once again, they found fragments from collagen, the protein that is a major component of bone, and as with their original T. rex study, they claim that these represent original dinosaur proteins. And as before, they found that the dinosaur proteins most closely resemble modern birds – in particular, ostrich.

The new study spends a significant amount of effort addressing the question of contamination. This question has been raised in at least two ways. Tom Kaye and colleagues reported in PLoS ONE that the soft tissue found by Schweitzer could be explained as a bacterial biofilm, rather than as preserved dinosaur tissue. I still like the biofilm explanation, and I don’t see how the new study refutes it. The study contains many microscope photos showing how the fine structure of the fossilized bone resembles modern ostrich bone, but preserved physical structure is not in question. The real question is, did dinosaur proteins survive for 80 million years in these bones?

The second contamination question emerges from this: Marty McIntosh discovered – after Asara released his mass spec data to the public – that the original T. rex sample contained hemoglobin. This finding has been discussed in the mass spec community, and privately among a group of scientists (including me) following this story, but it has not been published (as far as I know) until the Wired article.

Hemoglobin! Now, from what I know, we don’t expect to find much hemoglobin in bone tissue, and we sure don’t expect to find it in 68-million-year-old fossils. Could this be another big discovery? Or could it, perhaps, be that the sample is contaminated with modern proteins, perhaps from ostrich?

Upon further inquiry, a number of scientists learned that John Asara’s lab had indeed used its mass spec equipment to analyze samples of ostrich bone. Asara reports (in the Wired article) that the ostrich sample had been analyzed long before either of the dinosaurs:

“Asara conducted his ostrich and T. rex experiments a year and a half apart, separated by roughly 1,500 mass spectrometry runs. According to Asara, none of those spectra, nor samples of the soil surrounding the fossils, nor his daily control runs—in which he sequences known solutions to check for contaminants—turned up any ostrich hemoglobin.”

The new Science paper on the hadrosaur proteins doesn’t mention the (unpublished) hemoglobin fragments in the T. rex data, so this important question was not addressed. Well, if Asara’s lab handled ostrich material, then I remain skeptical of their assurances that ostrich couldn’t have possibly contaminated the original T. rex samples. And Marty McIntosh explained to the Wired reporter that “a chemical modification on the hemoglobin makes it more likely to be contamination.” McIntosh submitted a paper on his results to Science, but they rejected it – perhaps because it called into a question a finding that Science’s editors have obviously endorsed. That’s too bad.

If the T. rex sample was contaminated, that throws all the results into question. It also throws into question the new hadrosaur results – if contamination was a problem before, it might be still. The best way to resolve this is for an independent group to take the original fossils and repeat the study. I know that there are groups trying to do exactly this, but the fossils are controlled by paleontologist Jack Horner, who thus far has refused to share them with anyone but Schweitzer.

Extraordinary claims require extraordinary evidence, as any good skeptic knows. The finding of intact collagen protein in dinosaur fossils is certainly an extraordinary claim, and the finding of hemoglobin is even more stunning. Alas, the alternative explanations (statistical artifacts - see my earlier blogs and Pavel Pevzner's article in Science - and contamination by bacteria and/or ostrich tissue) are much more likely. I'd love for these results to be true - intact dinosaur proteins! Think of all the evolutionary comparisons we could do if we can reconstruct the past 80 million years directly from the molecular record! But I'm afraid I remain skeptical.

A tale of two pigs

I don't usually mix my own research into this blog, but I make exceptions for influenza. As everyone knows (if you're awake and sentient), there's been a huge outbreak of swine flu recently, starting a few weeks ago in Mexico, which has now spread all over the U.S., Europe, New Zealand, and elsewhere. You can read all about it in the major news media, so I'll just focus on a couple of things you might not find elsewhere.

First, the swine flu has been reported to be a mixture of human, avian, and swine influenza viruses. Although the source of these reports is the CDC, that's not an accurate picture. I read today in The Washington Post that this epidemic started when a single pig was infected simultaneously by bird, pig, and human viruses. That's a reasonable inference from the reports in the media, but it's not true.

In fact, as a number of researchers have now discovered, the new swine flu is a mixture of two different swine flu viruses. It's definitely a novel strain, but it's pretty clearly a mixture of two already-circulating pig strains. That sounds less exotic than the "human-bird-pig" theory, and it is. The reason for the "triple reassortant" story is a bit complex, but (to simplify a bit): the history of one of the two parental swine flu strains indicates that part of that strain originated in birds - well over a decade ago. That strain is sometimes called "avian-like" as a result, but it's not an avian flu strain now. Second, the history of the other strain includes a small piece (one gene) that appears to have originated in humans - over 15 years ago. Again, it's a swine flu virus now, but there's a piece of it that might have come from humans. The event that created today's swine flu - the one we're worried about - is a combination (called a reassortment) between two pig strains, pure and simple.

The other point I wanted to make is about data sharing. The sequences from the U.S. isolates have been deposited in GenBank - the public DNA database - immediately, and this allows people like me to start our analysis without delay. Many of us have been arguing for years how important it is to get the data out to the community fast, in order to accelerate the pace of scientific discovery. However, the isolates from Mexico have NOT been put into GenBank, even though these sequences first went through the CDC. Instead, they went into a database called GISAID, which was originally set up to facilitate sharing of avian influenza. Unfortunately, GISAID changed their data release policy about six months ago, and there's no guarantee that sequences deposited there will ever become public.

The CDC has been depositing influenza sequences in GISAID as if this were equivalent to making them public. It's not, and they shouldn't pretend otherwise. The CDC has not always been supportive of publicly releasing flu data - in fact, for years they deposited some of their sequences in a private database. They've recently made public statements about their commitment to public data release of influenza sequences, but it doesn't seem that they are following through with this commitment for all of the sequences from the swine flu outbreak. (Don't get me wrong: the CDC is doing a fantastic job in trying to track and understand this outbreak, and their work is incredibly important to public health, especial concerning the flu. I'd just like them to be a big more open with their data.)

One last note, a technical one. I've looked at the Mexican sequences (I have a GISAID account) and the California sequences, and they are virtually identical. So it would appear that any differences in virulence are due to differences in the people being infected, not to the virus itself. At least that's what it looks like so far - the situation is changing rapidly.

Creationism in the journal Proteomics

Last year, a controversial paper on the mitochondrion, including a claim that amounted to "God did it" (created life), almost slipped into the journal Proteomics. I say "almost" because the article appeared online before print, and then caused such a furor that the journal withdrew it from their website and the print version never appeared.

I wrote a brief account of the whole episode, including the journal editor's attempts to justify their sloppy reviewing, which just appeared online in the National Center for Science Education's magazine, NCSE Reports. I also blogged about this when it happened, one year ago, as did PZ Myers (Pharyngula), Attila Csordas, and Lars Juhl Jensen. The article appears as "retracted" on the journal website, with the explanation that the retraction was due to plagiarism (most of the article was blatantly plagiarized), but no comment at all about the Creationism claims.

Ironically, this article - although retracted! - was the #2 most-accessed article for the journal for the entire year of 2008, according to the journal's website. I guess people were interested in seeing what all the fuss was about.

The Creationist claim and the plagiarism were discovered by bloggers and blog readers, and sent to the journal. The journal's chief editor was initially very concerned, but he quickly became defensive, and never made a public statement on the Creationist claims, instead defending the review process and the anonymous reviewers.

Luckily we stopped them this time. But it's a cautionary tale for those of us who regularly review papers in the scientific literature.