I guess it’s only appropriate that the week of Darwin’s birthday is seeing a bunch of new reports about evolutionary transitions. On Monday there was news about how ancient whales with teeth turned into whales with baleen–thanks to the discovery of a fossil of an ancient whale that appears to have had both teeth and baleen. Today’s news takes us from the sea to the trees–the fossil of a primitive bat. The transition that the ancestors of bats made from scampering shrew-like mammals to masterful flyers has remained particularly mysterious. Today’s new fossil lets us look back further than ever into this transition.

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It’s time to add a new chapter to the Whale Chronicles….

…more below the fold…

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I’m always learning something from the readers of the Loom. Yesterday, I wrote about how scientists had inserted their names into a synthetic genome, and how such signatures would erode away like graffiti inside real organisms. But how about the opposite case–what if evolution has produced sequences of DNA that happen to form words?

In the comment thread, Peter Ellis asked,

What actually is the longest word (in any language) encoded by the reference human genome? If I had the time and computer power I’d have a look…

Guesstimate – it’ll be somewhere in the 4-5 letter range, depending on letter frequency in the target language.

Bear in mind the rules of this game…the letters are the amino acids specified by codons (three bases of DNA). There are 20 amino acids in most living things, so you can’t spell every word–or you can use alternatives, like using V for U. (Here’s a table.)

Ron then replied:

Just wander over to NCBI and blast to your hearts content. Taking “gvesstimate” (note the classical spelling) and checking against the protein refseq database finds:

>ref|NP_939322.1| Putative peptide ABC transport system ATP-binding protein [Corynebacterium
diphtheriae NCTC 13129]
Length=560

GENE ID: 2649530 DIP0959 | protein coding
[Corynebacterium diphtheriae NCTC 13129] (10 or fewer PubMed links)

Score = 26.1 bits (54), Expect = 215, Method: Composition-based stats.
Identities = 9/11 (81%), Positives = 10/11 (90%), Gaps = 0/11 (0%)

Query 1 GVESSTIMATE 11
GVESS I+ATE
Sbjct 278 GVESSEILATE 288
(sorry about the lack of proper formating)

Knock yourself out. I do have vague recollections of someone doing something similar a long time ago, when the database was much, much smaller.

I had not heard about anyone trying this before, but it sounds like a lot of fun. I’m a complete novice when it comes to reading genomes with BLAST, so I won’t try. But if anyone wants to post the longest word they can find, let’s see what you get. (Maybe I’ll get my word-guru brother to team up with a geneticist…that would be interesting.)

If you think about it, life on Earth is probably coming up with stray words in its many genomes, which then turn to gibberish (to our eyes), only to produce new words for us to find. The four-billion-year world search, as it were.

Update: Stephen Matheson offers easy step-by-step instructions. Thanks! Without a Z in the genetic code, I can’t make an egotistic search for Zimmer. But here’s Darwin lurking in bacteria.

How do new kinds of bodies evolve? It’s a question that obsesses many scientists today, as it has for decades. Yesterday, Olivia Judson, an evolutionary biologist and book author, published a blog post entitled “The Monster is Back, and It’s Hopeful,” in which she declared that these transitions can happen in sudden steps.

(I’m posting this at about 11 am EST without links. This afternoon I should have enough free time to add links in. So if you want to follow up on this essay, come back.) Update: Links are in.

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Sorry to start the New Year on a down note, but the January 1, 2008 issue of the New York Times has a review I wrote about a book called No Way Home. It’s a sobering look at the decline of the world’s great migrations. I’ve written a fair amount about the marvels of migration in recent months (here, here, and here), so it’s sad to see that there might not be much to write about in years to come unless the world gets its act together.

Last week I wrote about a new study that identified a fossil mammal as the closest relative to whales, helping to shed light on how whales moved from land to sea. The mammal, Indohyus, was a small four-legged creature that probably spent a fair amount of time in water and ate vegetation. The authors of the new study proposed that the ancestors of whales originally lived this way. Gradually, the whale lineage became more adapted to life in water and shifted to eating meat, as exemplified by early whales like Ambulocetus, which was something like a furry alligator.

In the comment thread, Noumenon asked this question:

I don’t understand how Indohyus and Ambulocetus, both dated to around 47 mya, can both be the ancestors of today’s whales. You say carnivory was an important transition for whales. Then Indohyus would have had to split off before Pakicetus, before whales became carnivorous.

Via email, I got a similar question from a biologist I know who is working on a book about evolution. He had read about the discovery in this article by Ian Sample in the Guardian, who declared:

Fossil hunters have discovered the remains of the earliest ancestor of the modern whale: a small deer-like animal that waded in lagoons and munched on vegetation.

So how can an ancestor be younger than its descendants?

Simple answer: It can’t.

If you head back to the original paper, you’ll see that the scientists compared the skeletons of a lot of living and dead mammals in order to draw a tree. Each species they studied is a twig on that tree. Each twig is linked to other twigs through a shared ancestry. But the scientists did not line up species in a chain of ancestors and descendants.

It is sometimes possible to find the fossil of one extinct species that evolved into another extinct species. But if scientists only studied evolution that way, they’d be ignoring a wealth of other clues to how evolution unfolded. As a lineage of mammals evolves, it acquires traits that will set all its subsequent members apart from other mammals. Roughly 150 million years ago our ancestors evolved a placenta. Placentas are found in humans, bats, elephants, whales, and thousands of other species. They are not found in platypus or echidnas. Platypus and echnidnas, thanks to their position on neighboring branches in the tree of life, tell us something about our ancestry. Like them, our own ancestors once lacked a placenta. That does not mean, however, that echidnas or platypuses are our ancestors.

By using these methods, scientists can look to Indohyus and get some ideas about what the ancestors of whales were like, even if Indohyus lived after the oldest known whales. Indohyus is the closest relative to the group of mammals called cetaceans. Only after it branched off did cetaceans gradually become more like the whales around us today. I’ve put together a simple tree showing how those traits appear to have evolved in early whales, based on what scientists know about fossil whales and how they’re related. You can find it at the end of the post.

Of course, this is a scientific hypothesis that needs to be tested. And the way to test it is to find more species like Indohyus. If paleontologists are lucky, they’ll be able to draw more branches at the base of the whale tree. And if the current hypothesis is right, a lot of the species belonging to those deep lineages will be a lot like Indohyus. They may turn out to have lived before the oldest whales, or they may have lived millions of years later. But that’s not the heart of the matter. What matters is kinship.

In the annals of misleading science reporting, this may be pretty small potatoes. But mistaking relatives for ancestors does lead to confusion, and it gets in the way of appreciating some very elegant research. And, of course, some people pretend that the fact that relatives are not direct ancestors means that evolution is false. So it’s worth getting right–not just for whales, but for humans, flowers, or any other organism.

[Update Thursday--8:30 am: changed "kangaroos" to "echidnas." Thanks to Alan for pointing out that kangaroos have (primitive) placentas.]

When I first met Hans Thewissen, he spending an afternoon standing on a table, pointing a camera at a fossil between his feet. He asked me to hold a clip light to get rid of some shadows. I felt like I was at a paleontological fashion shoot.

Thewissen was taking pictures of bones from a whale that walked. As I later wrote in my book At the Water’s Edge, Thewissen has discovered some crucial clues to the transitions that the ancestors of whales made from land to sea. In Pakistan, he discovered a 47-million-year-old fossil called Ambulocetus natans, that had an otter-like body. It was the first whale fossil ever found with functional legs. New fossils of other ancient whales have since surfaced. The bones Thewissen was photographing, for example, belonged to an even older, even more terrestrial relative of today’s whales, called Pakicetus.

When Thewissen and other have compared these fossils to those of other mammals, they’ve found that whales either evolved from even-toed ungulates (known as artiodactyls) or a close relative of artiodactyls. Meanwhile, other scientists have been comparing the genes of whales to other mammals, and they’ve found that one kind of artiodactyl–hippos–is the closest living relative to whales. But the fossil record of hippos is pretty sketchy. The oldest member of the family is only 15 million years old.

So I was pretty excited to read the newest paper from Thewissen and his colleagues, published in tomorrow’s issue of Nature. They’ve identified what they believe is the closest fossil relative of whales. It’s a raccoon-sized beast named Indohyus that lived 48 million years ago in Kashmir. Analyzing the bones of Indohyus, the scientists discovered that it shares some–but not all–of the traits previously considered unique to cetaceans from Pakicetus to today’s whales and dolphins.

Even more intriguing is the evidence suggesting that Indohyus was fairly aquatic. The evidence comes from isotopes in the fossils, as well as from the structure of the bones. Living mammals that spend a lot of time underwater tend to have heavy bones that they use to keep them from floating up to the surface of the water. So does Indohyus. Its teeth appear adapted for eating vegetation. It might have eaten underwater, like muskrats do today, or on land, as hippos do. Its adaptations to water may have helped it find refuge from predators on land. (The inimitable Carl Buell, who illustrated walking whales for me in At the Water’s Edge, has painted this portrait of Indohyus.)

If Thewissen’s right, then a key step in the origin of whales was the transition from eating plants to eating meat. (Pakicetus and other early whales show signs of having been meat-eaters.) But that transition came after the ancestors of whales had already started to take the plunge.

For more, watch Thewissen talks about Indohyus and whales on this video

Source: Thewissen et al, “Whales originated from aquatic artiodactyls in the Eocene epoch of India,” Nature, http://www.nature.com/doifinder/10.1038/nature06343

In tomorrow’s New York Times, I have a story about some very fun research–the study of the world’s biggest gulp. Some new research indicates that the biggest species of whales eat by gulping their own weight in water every thirty seconds. They do so in much the same way a parachute stops a race car.

Here’s the article.

Here’s the podcast (I come on at about 8:30)

Here’s the original paper.

And here are the web sites of two of the authors, Nick Pyenson and Jeremy Goldbogen.

My bad–for some reason I thought my piece on NPR would air this morning. It was on the news tonight. And you can listen to it here.

A quick heads-up: I’ll be talking about the tree of life tomorrow morning on NPR’s Saturday Weekend Edition. The segment will be archived on their “Science Out of the Box” web page. We’ll be talking about everything from animals to mushrooms to the unclassifiable viruses that graft the tree of life into a web.

Update: 12/1 10 am: …or maybe not. As far as I could tell over the breakfast din, the piece didn’t run this morning. I’ll let you know when and if it does.

Update: 12/1 5:30 pm: The piece just ran. I don’t think I made any major gaffes, but fact-check away. Here’s where you can listen online.

I just noticed that in the new issue of the New Yorker Michael Specter has written an article on the viruses in our genome. I wrote about this research in the New York Times a year ago. I haven’t had a chance to read the article through yet, but I was mortified to come across this line…

Until recently, the earliest available information about the history and the course of human diseases, like smallpox and typhus, came from mummies no more than four thousand years old. Evolution cannot be measured in a time span that short.

What happened to the New Yorker’s legendary fact-checking staff? Scientists can make important observations of virus evolution in their labs in a matter of weeks. HIV evolved from a chimpanzee disease to a human one over the past few decades. Perhaps Specter meant something more specific than “evolution,” like the evolution of human beings and their viruses over the past few million years. But that’s a charitable interpretation.

Anyway–let me know what you think of the piece.

Update: Wed. 11/28 4:20–Having read the piece, I must say it’s very good. It gets into a lot of cool experiments and the even cooler implications about how viruses may have shaped us. Some of the wording could have been made more precise, like the sentence I cited above, but having struggled to convey this sort of material myself, I shouldn’t be casting too many stones. I am also a bit confused by the ending, in which a scientists claim that HIV is driving the evolution of resistance mutations in humans and that resistant humans will acquire viruses in their genomes that will mark the creation of an entirely new species. I can’t tell if he’s saying that a reproductive barrier will emerge between the resistant humans and other humans, or if the resistance genes are supposed to simply take over the world population through selection. No matter which he means, speciation doesn’t work that way.

For my latest “Dissection” column in Wired, I take a look at the tree of life, and the way it changed dramatically thirty years ago this month. To get a sense of what the tree looks like today, I pointed readers to the wonderful interactive tree of life at the European Molecular Biology Lab. But I didn’t realize until after I finished the column that when you scroll over the branches of the tree, pictures pop up of species at their tips. Most of the pictures are of assorted chains, blobs, and other microbial portraits. But things get more interesting in the animal kingdom. Iz very nice!

Hat tip: Delightfully So