Blogs / The Loom

Over at the Origins blog on Science’s web site, I take a look at what means to have sex–especially if you happen to be bacteria. Check it out.

Last month, I asked you how to handle the ever-growing pile of science books I receive (before I donate most of them to the library, of course). A plurality of you voted in favor of frequent thumbnail descriptions, rather than alternatives like the less frequent all-out review. That’s a relief, because that was my own preference. So let me pull off the top book from the pile,  Life Ascending: The Ten Great Inventions of Evolution by Nick Lane.

The reason it’s on the top is that it happened to be very useful to me right now with an article I’m working on (more on that next month). Lane has selected a handful of key features of the natural world, from DNA to sex to warm-bloodedness to consciousness, and has written a chapter about each, explaining what we understand about it and how it evolved. The list is, as Lane himself admits, a bit arbitrary, and on first inspection it may give off a whiff of Scala Naturae, arranging life on a ladder from lower to higher. But once you delve into Lane’s writing, those minor qualms will evaporate. Lane, the author of two previous books about biology, writes about tricky topics like the chemistry of photosynthesis with grace and ease. On the topics I’m familiar with, I can vouch that he has picked good studies to showcase. Lane is also a scientist himself, and he not only reports on the latest research on each topic but also sometimes steps in with intriguing ideas of his own.

As with future posts of this ilk, this is not a full-blown book review. Call it a book (p)review: a heads-up about a book that has grabbed my attention. While I started reading Life Ascending for work, I look forward to finishing it for my own enjoyment.

I just loved this speech John Hodgman made at the Radio and TV Correspondents’ Dinner yesterday. Hodgman spoke for all us nerds, perhaps even including the president himself. And best of all, while talking about that fine nerd novel Dune, he showed the president a painting of a giant sand worm from Dune by John Schoenherr. (It shows up at 11:20.)

I grew up a couple miles from Schoenherr and spent much of my nerdy youth with his son Ian, hanging out in his fabulous old barn-slash-studio, filled with his classic science fiction art, new paintings of bears and geese, assorted Japanese swords, many cameras, a complete collection of National Geographic, and lots of bones and stuffed animal heads. I’m grateful to Hodgman for bringing back  those times, and for showing off the work of a wonderful artist. I return Hodgman the final words of his speech: I extend that most American of greetings–I have been and always shall be your friend. Live long and prosper.

The Kyoto Prize has gone to Peter and Rosemary Grant, I see from 80 Beats. Congratulations to them both for this Nobel-esque honor. If you don’t immediately recognize their names, you can start with this post I wrote last fall about the Grants’ research on the evolution of Darwin’s Finches, and then finish up with a couple books: their own How and Why Species Multiply: The Radiation of Darwin’s Finches and the Pulitzer-Prize winning The Beak of the Finch: A Story of Evolution in Our Time by Jonathan Weiner.

I wrote about the two sides of our brains in April for Discover. Now some of the scientists whose research I highlighted have an article of their own in Scientific American, focusing on the ancient evolutionary origins of specializations in each hemisphere. So if you still have interhemispheric cravings, check it out!

Meet Limusaurus. It is not–I repeat NOT–the missing link between anything. And yet it is still an important fossil that may help us understand how birds evolved from dinosaurs.

The recent splash about a certain fossil primate has revealed yet again just how much a lot of people (sadly, including a lot of journalists) want to cling to the notion that paleontologists are only interested in missing links–which, I guess, are supposed to be the direct ancestors of some living group of organisms that are precisely halfway between primitive forerunners and the advanced living creatures.

This notion is wrong in many ways. First of all, the entire body plan shared by, say, living birds did not leap into existence in a single ancestor. In fact, what we today consider the bird body plan actually evolved through a long series of steps. Different parts of bird anatomy evolved at different times. It’s now generally agreed that birds descend from a group of dinosaurs called theropods that includes lots of famous two-legged species like T. rex and Velociraptor. Many studies show that feathers had already evolved in forms seen on birds today on dinosaurs long before they had wings, beaks, or lots of other adaptations that all birds today have. So looking for “the” missing link for birds is ridiculous from the get-go.

The obsession about missing links is wrong-headed for another reason. Paleontologists can learn a lot about the history of a living group of organisms without unbroken chain of direct ancestors (which is fortunate, because the fossil record is far too scrappy to ever uncover such a series). That’s because the evolution of animals is, in many ways, like branches growing from a tree. So paleontologists can look at the branches of a related group of species and note which species have which traits. There are some traits that all the species share, which were already in place in their common ancestor. And there are some traits that are only found among a smaller group of related species within the tree. Those are new traits that evolved later than the earlier traits. Scientists can then mark nodes along the tree to show how new traits evolved, and how old ones got modified into new ones. And as scientists discover new fossils, they can come up with more detailed hypotheses for the pattern of this change.

Limusaurus, which makes its debut in tomorrow’s issue of Nature, sheds light on one particularly contentious matter about the origin of birds: how the fingers in a dinosaur hand got transformed into the end of a wing. A bird wing starts out as a limb bud, inside of which tiny clusters of cartilage cells start to form. Eventually, these clusters stretch out into wrist and finger bones, which later fuse together to provide a bendable spar that can support flight feathers. (To the left here is a simple diagram of the bones in a chicken’s hand.)

Only three digits form in a bird limb bud. Many lineages of land vertebrates have lost one or more digits over the course of their evolution. But which digits did the birds lose?

Scientists have generally argued for one of two possibilities. One possibility is that the thumb and pinky were lost, as I’m illustrating with my own hand here. That’s the pattern that has evolved in other land vertebrates, such as in horses. And when developmental biologists look at the clusters of cells that first develop in bird limb buds, they appear where the middle three digits appear in other land vertebrates. This alternative goes by the name 2-3-4. (Scientists name the five digits of the hand or foot starting from the thumb [1] and going out to the pinky [5].)

Yet a number of paleontologists have argued that the fingers in a bird’s wing are actually 1-2-3, as I’m showing in my second self-portrait. In early birds, such as Archaeopteryx, the fingers were not yet fused. As a result, they can give a clearer look at the anatomical connections between the bones and how they compare to other land vertebrates. I’ve lined up Archeopteryx’s three-fingered hand with the five-fingered hand of an alligator, the closest living relative of birds. That top white digit looks a lot more like a stout thumb than a slender index finger. More evidence offered in favor for the 1-2-3 hypothesis comes from how the digits of early birds and related dinosaurs make contact with wrist bones as digits 1, 2, and 3 do in other land vertebrates.

Last year scientists at Yale decided to investigate this intriguing paradox by investigating the genes that build bird wings. In all land vertebrates, the same set of genes help set the identities of the digits. They found that in both mammals and alligators, there’s a key difference in the genes that are active in the thumb and in the four other digits. In the four other digits, a gene called HoxD-11 is active late in development. In the thumb, it’s silent. That difference may be a crucial reason why thumbs are so different from other fingers.

But in birds, the scientists found, something odd happens. In digit 2 (corresponding to our index finger), HoxD-11 is silent. One way to interpret this result is as follows: birds really do have 2-3-4 hands. Their dinosaur ancestors lost their thumb and pinky. And they also evolved a shift in the pattern of gene activity in their hands, so that HoxD-11 stopped switching on in the index finger. As a result, it became thumbish.

Enter Limusaurus. This 1.7-meter-long dinosaur was recently discovered in China. It’s interesting for a lot of reasons, such as the fact that it appears to be one of several examples of a carnivorous theropods giving up meat and becoming a plant-eater. (The simple feathery covering is inferred from discovery of feathers on other dinosaurs.) Limusaurus is also interesting for its hands, shown here. After carefully analyzing the different bones that make it up, Limusaurus’s discoverers have concluded that it has digits 2,3, and 4–plus a tiny digit 1.

This vestigial thumb has only a single bone left, the metacarpal at its base. The scientists conclude that by the time Limusaurus evolved, some features of the bird hand had already evolved–namely, a lost pinky and a vestigial thumb. But the remaining fingers had not yet undergone further changes seen today in birds, such as the thumbiness of the index finger.

To see how the Limusaurus  hand fits into the overall hypothesis about bird evolution, you can take a look at the tree the authors publish in their paper, reproduced below. Limusaurus belongs to the branch marked Ceratosauria. All living birds belong to Neornithes at the top. It will take future fossil discoveries to put this hypothesis to the test. But it’s already a fascinating synthesis, showing how an ordinary five-fingered hand evolved over millions of years into many new forms, including one three-fingered arrangement that you can see soaring overhead today.

Update: Co-author Jim Clark gets into some of the details of the research in his comment on my post. Thanks, Jim.

Reference: Xing Xu et al, “A Jurassic ceratosaur from China helps clarify avian digital homologies,” Nature 459:940 doi:10.1038/nature08124

Images: Limusaurus hand and tree from Nature paper. Hand diagrams from Vargas et al, PLOS One 2008. Limusaurus reconstruction by Portia Clark Sloan.

Here’s a vision of how science may work in the future.

Last month I scrambled to write a story about the evolution of swine flu for the New York Times. I talked to some of the top experts on the evolution of viruses who were, at that very moment, analyzing the genetic material in samples of the virus isolated around the world. One scientist, whom I reached at home, said, “Sure, I’ve got a little time. I’m just making some coffee while my computer crunches some swine flu. What’s up?”

All of the scientists were completely open with me. They didn’t wave me off because they had to wait until their results were published in a big journal. In fact, they were open with the whole world, posting all their results in real-time on a wiki. So everyone who wanted to peruse their analysis could see how it developed as more data emerged and as they used different methods to analyze it.

Now, a little over a month later, they’re publishing their results in the journal Nature. Normally we press folks would get a press release about the paper a week before publication, and it would be under strict embargo till it appeared in the journal. This morning, however, I got a press release pointing me to the published paper. And while Nature normally requires you to subscribe to read a paper, the flu paper is published under a Creative Commons license, which means anyone can get it and use it under the license’s terms.

While that’s all very exciting, the paper itself is an anxiety-triggering read. The new swine flu (which the authors now call S-IOV S-OIV) is only distantly related to other known swine flus, which means that there are a lot of flu viruses circulating around about which we know very little. And, as I mentioned in my article, it had already entered the human population several months before it came to light earlier this spring. Be sure to check out figure 1 (I’m inserting it below from the wiki–thanks, Creative Commons!), which shows how lots of bird, swine, and human season flu viruses mixed together to produce the new beast. The authors warn that the pattern of evolution they see is the sort of pattern the big flu pandemics followed when they emerged in the past.

With this sort of urgent situation at hand, the patient process of old-fashioned science publishing may have to be upgraded.

[Image: CDC]

“We do not even in the least know the final cause of sexuality; why new beings should be produced by the union of the two sexual elements…The whole subject is as yet hidden in darkness.”

So wrote Charles Darwin in 1862. In this week’s issue of Science, I write an essay on what we know now about this mystery. The essay is here (subscription required), and you can listen to me talking about why sex is weirder than you know on this week’s Science Podcast.

To continue this celebration of sex in all its evolutionary glory, I’ll be guest-blogging a few times this month over at Science’s Origins blog. I’ll let you know here when each post goes up.

Image: From Robert F. on Flickr/Creative Commons Licence

More and more, scientists are figuring out the molecular changes that have taken place over the course of our evolution. It’s one thing, however, to have a good idea of the ways in which our DNA was altered, but it’s quite another to figure out how those changes affected our ancestors, and how those changes may have spread from an individual to the entire species through a process such as natural selection.

Knowing how genes work makes it possible to come up with hypotheses about how changes to those genes evolved. And today scientists can engineer animals to see if those hypotheses hold up. A couple years ago I blogged about a study on the evolution of our color vision, in which scientists gave mice the power to see the colors that we (and other primates) can see. Now comes a similar study on the evolution of language. The mice involved may not be able to talk, but their brains have changed in some very interesting ways.

This story begins with a family in London who had trouble with language. Some members of the family had trouble speaking and understanding grammar. They turned out to have an inherited language disorder, and scientists were able to use the family’s genealogy to pinpoint the gene involved, which they dubbed Foxp2. Foxp2 encodes a transcription factor, a protein that switches other genes on or off. That can make a gene very powerful, but it can also make it hard for scientists to figure out what it does, since its ultimate effects on a person’s body must first be carried down through a cascade of other genes. But it’s pretty clear at this point that Foxp2 influences the development of the brain.

Foxp2 exists in other animals, and in many cases it appears to have an influence on communication. When scientists have knocked out the gene in mouse embryos, for example, the mice are born having trouble producing the ultrasonic squeaks they need to make in order to get help from their mother. In 2002, Wolfgang Enard of the Max-Planck Institute for Evolutionary Anthropology and his colleagues compared the version of Foxp2 in humans to other animals and found that it had undergone a dramatic evolution in our own ancestry after our ancestors branched off from those of chimpanzees and bonobos. Our hominid ancestors aquired two mutations to the gene that each changed an amino acid in the Foxp2 protein. In 2007, Max Planck researchers announced that they had found the Foxp2 gene in the DNA of Neanderthals, our closest hominid relatives. It turned out they shared that same altered sequence. If Neanderthals share our version of Foxp2 thanks to common descent, that means that the two amino acids changed before our common ancestors split off, some 800,000 years ago. It presumably was one of many changes that took place to many genes in our hominid ancestors on the road to full-blown language.

To get a sense of how this new version of Foxp2 might have changed the brains of our ancestors, Enard and his colleagues have now tweaked Foxp2 in mice into a human form. Because Foxp2 has changed very little in mammal evolution (except in humans), a mouse version of Foxp2 is a fairly good model for what the gene looked like in our own ancestors. And so this experiment can, in very rough form, replay the transition from the old Foxp2 to the new.

As the scientists report in Cell tomorrow, the mice are generally healthy, but their behavior has changed. Their squeaks are lower in frequency. They explore less. They have less dopamine in the brain, a neurotransmitter that we need to control our bodies and to pursue rewarding things like food. Dopamine is produced in the base of the brain by a clump of neurons called the basal ganglia.

Scientists who have studied people with Foxp2 defects have noticed that part of the basal ganglia, called the striatum, is altered. So the researchers looked closely at the striatum of the humanized mice. They discoverd that certain kinds of neurons had longer branches and could sprout new connections with other neurons than in regular mice.

None of these changes should be accepted blindly as having happened in our own ancestors. The effect of a mutation to a gene depends a lot on the other genes it interacts with. When Foxp2 changed in our ancestors, it was interacting with many other hominid genes, not with genes in mice.

Nevertheless, there are many intriguing clues from this study that hint that perhaps these mice are pointing to at least a few changes that gave rise to language. It turns out, for example, that people who produce less dopamine in the basal ganglia do a better job of breaking down the sounds of speech into smaller chunks in the brain in order to undertand the words someone is saying. It’s also intriguing that songbirds have independently evolved Foxp2 as they’ve become excellent singers, and when scientists block Foxp2 expression in the basal ganglia of birds, they do a worse job of singing.

Obviously, mice are no better at singing like birds than they are at talking like us. But it’s possible that their brains have been tweaked in a crucial way, much as happened independently in the ancestors of both birds and people.

Source: Enard et al.: “A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice.” Cell 137, 961–971, May 29, 2009. DOI 10.1016/j.cell.2009.03.041 www.cell.com. Publishing in

A friend passed on this ad that aired for “The Link,” the show about Darwinius on May 25. Take a look.

Yep. That’s right. May 25 will be more important than 9/11. Than Pearl Harbor. Than every date in human history. Pre-human, too.

Let this be the starting point from now on for all discussions of science hype.

Update: A commenter asked if this was a spoof. It’s not. This is a real ad for the show.

Update #2: The TV producers who passed on this video to me are now wondering if this particular piece is actually some kind of mash-up, using an original teaser ad and encrusting it with even more over-the-top-itude. Are there any YouTube-ologists who can parse such things? Take a look at this and this and this and, in particular, this, which was posted by someone who suspected it was a semi-hoax.

If I had to guess, the original ad, which aired on or around May 14, was a series of historic dates (including 9/11–classy!) with voiceovers, ending with Darwinius Day (which from now on will be the day I celebrate beautiful fossils by hyperventilating into a paper bag).

Then somebody decided the ad was so ridiculous that he or she had to take it up an extra crazy notch–grafting some of the original design from the History Channel web site. If my hypothesis is correct, there is one seriously funny amateur video editor out there.

Question: did anyone see the original on TV?

Just a quick note–I’ve updated my post on the Darwinius affair. The journal where the paper was published has responded to my enquiries. They say the authors of the paper were responsible for the secrecy over the paper.

In a remarkable feat of commenter-blogger synergy, the Loom has helped give Darwinius its name back.

As I posted yesterday, some commenters on the Loom pointed out that, amidst all the hullaballoo over the unveiling of this primate fossil (oh, don’t get me started), it looked as if the scientists who wrote the paper failed to follow the rules for naming a new species. The people who make the rules (the International Commission on Zoological Nomenclature) require paper copies of a scientific paper, not just a digital one, as was the case of Darwinius.

Today, the executive secretary of the ICZN used the Loom to confirm that, yes, Darwinius was not yet Darwinius.

But at last, it is. Here’s an update from Peter Binfield, the managing editor of Plos ONE, the journal that published the paper.

Regarding the requirements for making the name Darwinius masillae nomenclaturally available in the eyes of the ICZN, we have been in discussion with Ellinor Michel (the ICZN Executive Secretary) and have additionally consultated with Richard L. Pyle (an ICZN Commissioner). They have advised us that by doing the following, we have met the ICZN code and therefore the name should be considered nomenclaturally available.

A print-run of fifty copies of the paper has been created on May 21st. The top sheet of each copy has the following text appended to the footer: “This document was produced by a method that assures numerous identical & durable copies, and those copies were simultaneously obtainable for the purpose of providing a public and permanent scientific record, in accordance with Article 8.1 of the International Code of Zoological Nomenclature. Date of publication: 21st May 2009”

Apart from this wording, these copies are identical to the electronic version that is freely available from our web site at: http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0005723&representation=PDF

These copies are now obtainable from our offices at 185 Berry Street, Suite 3100, San Francisco, CA 94107, USA. Anyone who requests a copy, and tenders a fee of $10 (towards the cost of postage and printing) will receive a copy.

Having made the printed copies available, we have been told by the individuals named above that we have conformed with the relevant ICZN codes. They have also indicated that the proposed resolution is an interim step, which should meet the requirements of the Code until a formal amendment is published within the next few years.

We are very grateful to the ICZN for their actions to resolve this matter.

Richard Pyle of the ICZN thought that Peter’s update required a small clarification, which he just sent in:

The pending proposed Amendment to the ICZN Code for allowing electronic forms of publication (see: http://www.iczn.org/electronic_publication.html) is currently in review, as is required for all such major amendments to the Code.  This process will likely be completed within the next year, and if adopted, the amendment should go into effect at that time.

What will require “a few years” to be published is the next (Fifth) Edition of the ICZN Code (see: http://iczn.ansp.org ). Presumably, this Edition of the Code will also support the electronic publication of nomenclatural acts (especially if the proposed amendment to the existing 4th Edition of the Code is approved).

To those not steeped in species, genera, suborders and suprafamilies, all of these bylaws and codes may trigger vertigo. But keeping the world’s biodiversity in order is not for the faint of heart. With 1.8 million species on the books, and tens of thousands of new ones being added every year, taxonomists need an intricate set of rules to keep it all straight. The fact that taxonomists share a set of rules, no matter how intricate, was one of the great advances in the history of biology. (See my lecture [audio] for a sense of the chaos that came before.)

But who knows how Linneaus would have dealt with the Internet….