Category: Evolution

Why Whales Are Weird: Joy Reidenberg Explains

By Carl Zimmer | July 20, 2012 10:14 am

Here’s a video of a great talk about the evolution of whales that anatomist Joy Reidenberg gave at the recent PopTech conference. You may have seen her on the show Inside Nature’s Giants. Here’s my profile of Reidenberg this spring in the New York Times, in which I focused on what it’s like to take apart whales for a living.

Joy Reidenberg: Weird whales from PopTech on Vimeo.

The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger

By Carl Zimmer | July 19, 2012 5:21 pm

[Note: This is the second of a four-part series:

Part One: The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)

Part Three: Four Days of Fusion Chromosome Freak-Out

Part Four: And Finally the Hounding Duck Can Rest]

Wow, what people will do to avoid answering your question.

Last night I started asking the people who run a creationist Facebook page for the evidence to back up a claim of theirs about evolution. I was told to buy their book. When I was asked again, I was told nothing.

I ended up researching the latest on this particular aspect of human evolution–the fusion of two of our chromosomes millions of years ago–and wrote a blog post today.

This afternoon I got an email from the creationists.

Dear Carl,

I edit Discovery Institute’s Evolution News & Views website. We’d be interesting [sic] in hosting an online debate between you and a contributor to Science and Human Origins. There are interesting issues to address and this is, I think, a much better format for that than Facebook. Please let me know if you’re agreeable in principle. If so, we can nail down a specific topic to debate and go over any further parameters. The format would be a simple point-counterpoint-point-counterpoint, with each post limited to 1000 words and focusing strictly on the ideas, not on personalities.

Best wishes,
David

I’m fairly sure that this is legitimate, because it comes from a discovery.org address, and because another Discovery Institute employee hinted at the same idea on the Facebook page.

I thought the question I asked was pretty simple. I wasn’t asking to hold a Lincoln-Douglas debate. I just asked what the evidence was for one of the claims made by the creationists.

Now it seems that in order to get that answer, I can either buy a book–which apparently is based on no peer-reviewed research of the authors, but just cherry-picked quotes from a ten-year old paper–or I can donate my time to write several thousands words for free for a creationist web site.

Making this offer even richer is Klinghoffer’s ground rules about focusing “strictly on the ideas, not on the personalities.” Klinghoffer himself has used Evolution News & Views to call people pathetic, a worthless bully, cowards, illiterate, and “a tyranny of the unemployed” (referring to Wikipedia editors). In one piece he wrote for Evolution New and Views, Klinhoffer mocked a post by a science blogger as “preening and self-congratulatory.”

That blogger happened to be me.

I will answer Mr. Klinghoffer publicly: no thanks. I never asked for a debate, and your arbitrary decrees, such as a mysterious thousand-word cutoff (my blog post on the chromosomes alone clocked in at over 2,000 words) make it even less appealing. I am particularly opposed to web sites that do not allow readers to comment. That’s how I ended up on Facebook in the first place–because the Discovery Institute’s web sites do not permit commenting. You, on the other hand, are more than welcome to leave a comment on my blog. My comment policy is very lax: I only throw out commenters who curse uncontrollably, hawk their own wares, or can’t stay on topic after repeated warnings. We have a thriving, fascinating discussion here, one from which I regularly learn new things from my readers. You might too.

Update: Klinghoffer confirms it was indeed he who emailed. He is also very tired of my asking the same question again and again, likening me to a duck. A preening duck, no doubt.

CATEGORIZED UNDER: Evolution

The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)

By Carl Zimmer | July 19, 2012 12:13 pm

[Note: This post ended being the first of a series of four.

Part Two: The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger

Part Three: Four Days of Fusion Chromosome Freak-Out

Part Four: And Finally the Hounding Duck Can Rest]

There’s something fascinating about our chromosomes. We have 23 pairs. Chimpanzees and gorillas, our closest living relatives, have 24. If you come to these facts cold, you might think this represented an existential crisis for evolutionary biologists. If we do indeed descend from a common ancestor with great apes, then our ancestors must have lost a pair after our lineage branched off, some six million years ago. How on Earth could we just give up an entire chromosome.

A close look at our genome and the genome of our close relatives reveals that we didn’t. We just combined a couple of them. Every now and then, chromosomes fuse. This fusion occurs as sperm and eggs develop, as pairs of chromosomes fold over each other and swap chunks of DNA. Sometimes two different chromosomes grab onto each other and then fail to separate.

Scientists have observed both humans and mammals with fused chromosomes. Chromosomes typically have distinctive stretches of DNA in their center and at their ends. From time to time, scientists will find an individual that’s short a chromosome, but one of the chromosomes it retains now has an odd structure, with chromosome endings near the middle and other peculiar features.

This might seem like a fantastic mutation–something like a human and a horse being joined into a centaur. Remarkably, however, fused chromosomes are real, and there are surprising number of normal, healthy people carrying them.

If humans and apes did indeed share a common ancestor, then it would make sense that two chromosomes fused in our ancestors. The rise of genome sequencing allowed them to test that hypothesis. They found that human chromosome two bears the hallmarks of an ancient chromosome fusion, with remnants of chromosome ends nestled at its core. In 2005, it became possible to test the hypothesis again, when a team of scientists sequenced the chimpanzee genome and could compare it to the human genome. The chimp genome team were able to match human chromosome two to two unfused chromosomes in the chimpanzee genome.

Ken Miller, a biologist at Brown who was an expert witness in the 2005 Dover creationism trial, includes this research in his lectures on evolution. Here’s a video of one of those lectures, where he lays out some of the evidence with impressive clarity.

What makes evolutionary biology such a fun subject to write about is that it does not stay still. While Miller’s description is entirely accurate, the past five years have rendered it obsolete. Last month, Evan Eichler at the University of Washington and his colleagues published a study in the journal Genome Research in which they deeper into the history of our missing chromosome.

They were able to do so thanks to the publication earlier this year of the gorilla genome. A comparison of the human, chimpanzee, and gorilla genomes confirms that the ancestors of gorillas branched off from the ancestors of chimpanzees and humans about ten million years ago. Humans and chimpanzees then branched apart later. A comparison between all three species provides a clearer picture of what our chromosomes looked like before they fused, and how they’ve changed since.

Eichler and his colleagues put together a diagram to illustrate this ten-million-year saga, which I’ve adapted here.

By comparing human chromosome two to the unfused versions in the chimpanzees and gorillas, Eichler and his colleagues reconstructed the chromosomes in the common ancestor of all three species:

The bands correspond to segments of each chromosome. The colors represent the two ancestral chromosomes (I’ll just call them green and red to keep from getting bogged down in confusing numbers). The hash marks represent regions of very unstable DNA. These areas, which are full of repeating sequences, are prone to accidentally getting duplicated, expanding the chromosome. They’re also where chromosomes are likely to trade chunks with other chromosomes. That’s why the red chromosome has a little green at the end. It had picked up part of the green chromosome earlier than the common ancestor of us, chimpanzees, and gorillas.

The green chromosome then changed:

Three key events are illustrated here. First, the top of the green chromosome flipped (another common type of mutation, called an inversion). Then a chunk of yet another chromosome got stuck to the end of the green chromosome, marked here in pink. And then a new piece of DNA got stuck at the end of the green chromosome, known as StSat, and marked here as a yellow dot.

The ancestors of gorillas then diverged from the ancestors of chimpanzees and humans. They underwent some ten million years of independent evolution, during which time a lot happened. For one thing, the cap on the green chromosome got duplicated and pasted onto other chromosomes, including the red one, and even on the other end of the green one itself. In the illustration below, the yellow and pink segments, along with the adjoining green segment, are represented by a brown oval:

Meanwhile, the ancestors of chimpanzees and humans were evolving. The two chromosomes continued to change, as shown here.

A copy of StSat got glued to the end of the red chromosome, and then the pink and green segments at the top of the green chromosome got flipped.

The chromosomes at the right of the figure show you what our two chromosomes looked like before they got fused. When the human and chimpanzee lineages split, each lineage inherited them. And in each lineage, they evolved in a different way.

In the chimpanzee lineage, the chromosomes didn’t fuse. Instead, this happened:

The caps on both the green and red chromosomes were duplicated massively and ended up on lots of other chromosomes.

And finally, here’s what happened to humans after our ancestors split from chimpanzees:

The two chromosomes fused, and the cap was deleted, inclusing StSat. It could no longer spread around our genome, the way it did in chimpanzees and gorillas.

This study is an important advance in our understanding of how human chromosomes evolved–a subject of medical significance, too, since the duplication of the DNA at the end of chromosomes can cause dangerous mutations that can cause genetic disorders. Plus, it is very cool to see how our chromosomes are, in fact, an ancient patchwork.

It just so happens that I came across this paper by a very roundabout way–but an instructive one. Over at the Panda’s Thumb, I learned yesterday that biologist Nick Matzke was trying to set things straight on a creationist Facebook page. The page is set up by an outfit called The Biologic Institute, which is promoting a new book by two of its employees that purports to reveal all the flaws in the evolutionary account of human beings. They linked to a post on a site run by the intelligent design clearinghouse, the Discovery Institute, which provided some details from the book. It’s called, “A Veil Is Drawn Over Our Origin as Human Beings,” and it’s written by David Klinghoffer.

Matzke left several comments explaining why they were wrong, and what some of the evidence for human evolution actually is. The Biologic Institute didn’t take this well: they suddenly announced that Facebook was not the appropriate venue for debate, and would limit comments to 100 words, or maybe shut the whole thing down.

I found this deliciously ironic and had to jump in too. I pointed out that the site they linked to does not allow comments (which is fairly typical of creationist web sites). So there was no other way to ask questions than to post them to Facebook. And my question concerned fused chromosomes.

Klinghoffer declares:

The evidence from chromosomal fusion, for one, is strikingly ambiguous. In the Darwinian presentation, the fact that humans possess 23 chromosome pairs and great apes 24 clearly points to an event in which human chromosome 2 formed from a fusion, leaving in its wake the telltale sign of telomeric DNA — normally appearing as a protective cap at the end of the chromosome — in the middle where it doesn’t belong. Ergo, common descent.

But Casey [Luskin, of the Discovery Institute and co-author of the book] explains, there’s a lot wrong with this inference. Even if there was such an event and humans once had 24 chromosome pairs, it doesn’t at all follow that this happened in some prehuman past. Nothing stands in the way of picturing a human population bottleneck accomplishing the spread of a fused chromosome 2 from part of an early human community to all of it.

But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.

I was baffled, so I asked on Facebook for the evidence that the form of the chromosome wasn’t what you’d expect if it fused six million years ago.

What followed was a ridiculous runaround, some of which I’ll reproduce here:

Biologic Institute: Sorry, Carl, what link contains that particular quote?

Me: I am quoting from the page that YOU linked to.

Biologic Institute: Ah! That evidence is in the book that the post describes.

Carl Zimmer: In other words, the only way we can check these claims is to purchase the book? There’s no evidence published in peer-reviewed journals?

[No response]

Carl Zimmer: The book you are pointing us to is written by two Biologic Institute employees–the same Institute that puts out this Facebook page. Why can’t you describe your evidence about the chromosome fusion here?

[An hour passes. No response.]

Carl Zimmer: Hello? Is anyone there? Are you choosing not to respond to my request for evidence from your own book? How do you calculate what the chromosome fusion DNA should look like if it fused six million years ago?

Biologic Institute: Carl, you write books for a living. Do you rehearse their content on your blog for anyone who asks?

Carl Zimmer: Hello, Biologic Institute. If I make a strong claim about science in an online forum, and someone asks me for evidence for that claim, I do not say, “Well, you’ll just have to read my book.” I provide the evidence–I point to the peer-reviewed research on which I based my statement. But, hey, I’d be perfectly satisfied if you pointed me to a scientific paper that presents calculations showing that the chromosome fusion could not have happened six million years ago. I can go find it for myself–if such a paper actually exists.

Well, that was the last I heard from the Biologic Institute. They still haven’t piped back up on their own thread. However, I did hear from someone who had read the book, Paul MacBride. (He even reviewed it here.) Here’s the comment he left on Facebook:

Carl, I can tell you the answer to your question, as I have read the book. Luskin provides no evidence for this. Well, more correctly, he quotes a question from this paper http://www.ncbi.nlm.nih.gov/pubmed/12421751 “If the fusion occurred within the telomeric repeat arrays less than ∼6 Mya, why are the arrays at the fusion site so degenerate?” but not their three suggested answers. Luskin asserts that if a chromosomal fusion occurred it should have been a neat and tidy joining of the two chromosomes in question, anything else is a Problem For Evolution. Dave Wisker addressed this succintly in a comment at Panda’s Thumb http://pandasthumb.org/archives/2012/07/paul-mcbrides-r.html#comment-288503

That paper MacBride mentions? It’s the 2002 paper I mentioned at the start, the one that presented evidence for fusion based on a study of the human genome. In other words, the authors of this new intelligent design book cherry-pick a quote out of a paper that’s ten years old (you can check for yourself, the paper’s free). That, it seems, is all the evidence they have. If anyone tells you how impressive the science is behind intelligent design, how superior it is to evolutionary biology, may I suggest you use this example to show them how wrong they are.

I read the 2002 paper long ago, but MacBride’s link led me to reread it. I also noticed that it was cited by a number of more recent papers, including Eichler’s new one. It just goes to show how you can end up learning something new in the most unexpected places.

Update: Man, these folks will do anything to avoid just pointing me to some evidence.

Update #2: Actually, they’ll do a lot more–here’s my round up of the four days since I posted this.

Update #3: After five days, I finally got my answer. And it shows why the creationists are wrong. And thus ends this strange story.

[Image of centaur: Wikipedia]

CATEGORIZED UNDER: Evolution, The Tangled Bank, Top posts

Presenting "Evolution: Making Sense of Life" (and a free app!)

By Carl Zimmer | July 8, 2012 7:54 am

As I’ve mentioned a couple times, I’ve been working for a couple years with biologist Douglas Emlen on a new textbook about evolution, intended for biology majors. It’s scheduled to be published next month, and we’ve gathered some gratifying endorsements. Here are a selection:

Exciting is a word not often used to describe a new textbook. But, by using powerful examples, beautiful images, and finely wrought prose Zimmer and Emlen have produced a text that not only conveys the explanatory power of evolution, but one permeated with the joy of doing science. Their text can only be described as an exciting moment for our field: it is an important accomplishment for our students and for evolutionary biology at large.” –Neil Shubin, University of Chicago, author of Your Inner Fish.

“A richly illustrated and very clearly written text, Evolution: Making Sense of Life brings forth the excitement, power, and importance of modern evolutionary biology in an accessible, yet sophisticated overview of the field.” –Sean B. Carroll, University of Wisconsin, Madison, author of Endless Forms Most Beautiful.

“If there was ever a book that makes it obvious why evolution is a fascinating topic—and a topic that goes to the core of understanding what biology is about—this is it. It truly makes you better understand and appreciate the biological world around us.” –Svante Paabo, Director, Max Planck Institute for Evolutionary Anthropology

“Two master craftsmen in the art of scientific communication have combined to produce an excellent basic text on evolution: it informs, explains, teaches and inspires. The illustrations are outstanding.” –Peter R. Grant, Princeton University

“Carl Zimmer and Douglas Emlen have captured in this stunning new book the excitement and richness of twenty-first century evolutionary biology. They describe clearly and elegantly not only what, but also how, we are learning about evolutionary processes and the patterns they produce. The writing is compelling, the illustrations beautiful and truly informative, and the balance between breadth and depth of discussion on each topic just right. This is a book that would make anyone think about becoming an evolutionary biologist today.” –John N. Thompson, University of California, Santa Cruz

“Beautifully written and lavishly illustrated, here’s a superb textbook that can do double duty gracing the coffee table. This book is bound to attract many more students into the field of evolutionary biology.” –Richard Lenski, Michigan State University

“This is not your grandmother’s evolution text. Breathtakingly illustrated, this book covers not only the usual topics in evolution – adaptation, drift, phylogenetic analysis – but also a host of new and exciting areas where groundbreaking research is occurring.” –Marlene Zuk, University of Minnesota

You can pre-order the book on Amazon here. And here is information at the web site at our publisher, Roberts & Company. Excitingly, they are also creating an iPad version of the book, with many interactive features. The app itself is free, and you can use it to download the first chapter (also free). The remaining chapters will be rolling out soon, with the price to be determined later. (No Android version, I’m afraid!)

Turning doctors into wildlife managers: my story in tomorrow's New York Times

By Carl Zimmer | June 18, 2012 5:27 pm

This month has seen a flood of new studies and reviews on the microbiome, the collection of creatures that call our bodies home. In tomorrow’s New York Times, I look at why scientists are going to so much effort to map out these 100 trillion microbes.

The microbiome is not just an opportunistic film of bugs: it’s an organ that play an important part in our well-being. It starts to form as we’re born, develops as we nurse, and comes to maturity like other parts of the body. It stabilizes our immune system, keeps our skin intact, synthesizes vitamins, and serves many other functions. Yet the microbiome is an organ made up of thousands of species–an ecosystem, really. And so a number of scientists are calling for a more ecological view of our health, rather than simply trying to wage warfare against infections.

Check it out.

Monkey Heart Attacks and Barnacle Penises: My take on the new book "Zoobiquity"

By Carl Zimmer | June 17, 2012 3:39 pm

A new book is out, called Zoobiquity: What Animals Can Teach Us About Health and the Science of Healing, coauthored by cardiologist Barbara Natterson-Horowitz and science writer Kathryn Bowers. They take a look at the surprising parallels between animal and human health. The Daily Beast asked me to review it, and you can read my piece here.

The facts that animals and humans share an evolutionary heritage, and that we can gain medical insights through a comparison between species, are not new. And Zoobiquity contains some misconceptions about how evolution works and how to analyze it. Nevertheless, I think the book well-worth reading. I learned a lot from it about things ranging from cancerous rhino horns to anorexic pigs.

Check out my review here. (You can also read a fairly long excerpt from the book in the New York Times here.)

We Are Viral From the Beginning

By Carl Zimmer | June 14, 2012 1:42 pm

We all started out as a fertilized egg: a solitary cell about as wide as a shaft of hair. That primordial sphere produced the ten trillion cells that make up each of our bodies. We are not merely sacs of identical cells, of course. A couple hundred types of cells arise as we develop. We’re encased in skin, inside of which bone cells form a skeleton; inside the skull are neurons woven into a brain.

What made this alchemy possible? The answer, in part, is viruses.

Viruses are constantly swarming into our bodies. Sometimes they make us sick; sometimes our immune systems vanquish them; and sometimes they become a part of ourselves. A type of virus called a retrovirus makes copies of itself by inserting its genes into the DNA of a cell. The cell then uses those instructions to make the parts for new viruses. HIV makes a living this way, as do a number of viruses that can trigger cancer.

On rare occasion, a retrovirus may infect an egg. Now something odd may happen. If the egg becomes fertilized and gives rise to a whole adult individual, all the cells in its body will carry that virus. And if that individual has offspring, the virus gets carried down to the next generation.

At first, these so-called endogenous retroviruses lead a double life. They can still break free of their host and infect new ones. Koalas are suffering from one such epidemic. But over thousands of years, the viruses become imprisoned. Their DNA mutates, robbing them of the ability to infect new hosts. Instead, they can only make copies of their genes that are then inserted back into their host cell. Copy after copy build up the genome. To limit the disruption these viruses can cause, mammals produce proteins that can keep most of them locked down. Eventually, most endogenous retroviruses mutate so much they are reduced to genetic baggage, unable to do anything at all. Yet they still bear all the hallmarks of viruses, and are thus recognizable to scientists who sequence genomes. It turns out that the human genome contains about 100,000 fragments of endogenous retroviruses, making up about eight percent of all our DNA.

Evolution is an endlessly creative process, and it can turn what seems utterly useless into something valuable. All the viral debris scattered in our genomes turns out to be just so much raw material for new adaptations. From time to time, our ancestors harnessed virus DNA and used it for our own purposes. In a new paper in the journal Nature, a scientist named Samuel Pfaff and a group of fellow scientists report that one of those purposes to help transform eggs into adults.

In their study, Pfaff and his colleagues at the Salk Institute for Biological Sciences examined fertilized mouse eggs. As an egg starts to divide, it produces new cells that are capable of becoming any part of the embryo–or even the membrane that surrounds the embryo or the placenta that pipes in nutrients from the animal’s mother. In fact, at this early stage, you can pluck a single cell from the clump and use it to grow an entire organism. These earliest cells are called totipoent.

After a few days, the clump becomes a hollowed out ball. The cells that make the ball up are still quite versatile. Depending on the signals a cell gets at this point, it can become any cell type in the body. But once the embryo reaches this stage, its cells have lost the ability to give rise to an entirely new organism on their own, because they can’t produce all the extra tissue required to keep an embryo alive. Now the cells are called pluripotent. The descendants of pluripotent cells gradually lose their versatility and get locked into being certain types of cells. Some become hematopoetic cells, which can turn into lots of different kinds of blood cells but can no longer become, say, skin cells.

Pfaff and his colleagues examined mouse embryos just after they had divided into two cells, in the prime of their totipotency. They catalogued the genes that were active at that time–genes which give the cells their vastly plastic potential. They found over 100 genes that were active at the two-cell stage, and which then shut down later on, by the time the embryo had become a hollow ball.

One way cells can switch genes on and off is producing proteins that latch onto nearby stretches of DNA called promoters. The match between the protein and the promoter has to be precise; otherwise, genes will be flipping on at all the wrong times, and failing to make proteins when they’re needed. Pfaff and his colleagues found that all the two-cell genes had identical promoters–which would explain how they all managed so become active at the same time.

What was really remarkable about their discover was the origin of those promoters. They came from viruses.

During the earliest stage of the embryo’s development, these virus-controlled genes are active. Then the cells clamp down on them, just as they would clamp down on viruses. Once those genes are silenced, the totipotent cells become pluripotent.

Pfaff and his colleagues also discovered something suprising when they looked at the pluripotent ball of cells. From time to time, the pluripotent cells let the virus-controlled genes switch on again, and then shut them back down. All of the cells, it turns out, cycle in and out of what the scientists call a “magic state,” in which they become temporarily totipotent again. (The pink cells in this photo are temporarily in that magic state.)

Cells in the magic state can give rise to any part of the embryo, as well as the placenta and other tissue outside the embryo. Once the virus-controlled genes get shut down again, they lose that power. This discovery demonstrated that these virus-controlled genes really are crucial for making cells totipotent.

Pfaff and his colleagues propose that the domestication of these virus promoters was a key step in the evolution of mammals with placentas. The idea that viruses made us who were are today may sound bizarre, except that Pfaff is hardly the first person to find evidence for it. Last year, for example, I wrote about how placental mammals stole a virus protein to build the placenta.

A discovery this strange inevitably raises questions that its discoverers cannot answer. What are the virus-controlled genes doing in those first two cells? Nobody knows. How did the domestication of this viral DNA help give rise to placental mammals 100 million years ago? Who knows? Why are viruses so intimately involved in so many parts of pregnancy? Awesome question. A very, very good question. Um, do we have any other questions?

We don’t have to wait to get all the answers to those questions before scientists can start to investigate one very practical application of these viruses. In recent years, scientists have been reprogramming cells taken either from adults or embryos, trying to goose them back into an early state. By inducing cells to become stem cells, the researchers hope to develop new treatments for Parkinson’s disease and other disorders where defective cells need to be replaced. Pfaff suggests that we should switch on these virus-controlled genes to help push cells back to a magic state.

If Pfaff’s hunch turns out to be right, it would be a delicious triumph for us over viruses. What started out as an epidemic 100 million years ago could become our newest tool in regenerative medicine.

(For more on these inner passengers, see my book A Planet of Viruses.)

[Image: Courtesy Salk Institute.]

This morning's interview subject

By Carl Zimmer | June 12, 2012 12:46 pm

Connecticut isn’t exactly the Amazon. But our spotted salamanders are pretty handsome. And, as an added bonus, they’re evolving in some interesting ways. Full details to come!

CATEGORIZED UNDER: Evolution, The Tangled Bank

Drawing two million branches: My story in tomorrow's NYTimes on building the full tree of life

By Carl Zimmer | June 4, 2012 6:40 pm

Even the most elaborate pictures of the tree of life you can find online are gaunt shadows of life’s full diversity. In tomorrow’s New York Times, I write about a team of scientists who are setting out to build a tree with every described species on Earth–and program it so that the entire scientific community can help tease out its branches and add more branches as they discover the six, sixty, or six hundred million more unnamed species on Earth. Check it out.

In The Beginning Was the Mudskipper?

By Carl Zimmer | May 23, 2012 1:00 pm

In 1893, the Norwegian zoologist Fridtjof Nansen set off to find the North Pole. He would not use pack dogs to cross the Arctic Ice. Instead, he locked his fate into the ice itself. He sailed his ship The Fram directly into the congealing autumn Arctic, until it became locked in the frozen sea. Nansen was convinced that the ice itself would drift up to the pole, taking him and his crew along for the ride.

For two and a half years they drifted with the pack. It gradually became clear to Nansen that The Fram had stopped moving north and was now traveling east instead, back towards Europe. He leaped out of the ship and tried to sled up to the pole, only to discover that the ice he was now traveling on was moving south. Only four degrees away from true north, he decided to retreat. He bolted back for Franz Josef Land.

The Fram meanwhile continued to drift east. After several months, it broke free of the ice, and the crew sailed the ship south to the island of Spitzbergen. There on the bare flats they saw a giant balloon.

Its pilot was a young Swedish engineer named Salamon Andrée. Andrée had decided that ships like the Fram could never reach the Pole, and that flight offered the only hope. He had convinced the king of Sweden and Alfred Nobel to pay for a balloon which he had brought by ship to Spitzbergen. And there he mixed tons of sulfuric acid and zinc to create hydrogen gas, which filled his silk canopy for four days. But gales hit the island before he was ready to launch the balloon, and then the Fram arrived with stories of how Nansen was racing on sleds towards the pole. Andrée let the canopy fall back to the ground.

When he got back to Sweden, Andrée discovered that Nansen had actually failed and had returned to Norway. He began to plot a second attempt. He returned to Spitzbergen in 1897 and this time he succeeded in launching his balloon. For a few days Andrée floated north with his crew of two, bobbing up and down with the sudden changes in temperature and moisture of the Arctic atmosphere. But as he crossed over the edge of the polar ice, the voyage took a turn for the worse. The balloon became burdened with rain and snow, until the guidelines dragged across the ice, until the gondola bounced like a ball on the ground, until the balloon came to a rest.

For a week the crew huddled in cramped fog. Andrée decided to pack sledges with food and a collapsible boat, which they dragged over the drifting ice. Hauling them across sloshing leads, they hoped, like Nansen, that they could find refuge in Franz Josef Land. But the ice wandered in the wrong direction under their feet, and after two months of this polar treadmill they reached a little hump of Arctic rock called White Island. In 1930 whalers came to the island and discovered their decrepit boat, their journals, and Andrée’s corpse still sitting in the snow.

But in 1897, no one knew where Andrée had gone. His fellow Swedish scientists searched for him by ship in the following summers, first travelling around Spitzbergen, and then heading to Greenland. As the pack ice opened, they traveled for eight weeks along its eastern edge in their sail- and steam-powered ship. They mapped the tentacled coast, and in one fjord along an elephant-backed mountain they named Celsius Berg, the explorers found bones.

They weren’t the bones of Andrée and his crew. They were the bones of fish that had been resting in the Greenland rocks for over 350 millions years.

Other fossils of these fish had been found elsewhere in late Devonian rocks, but to those who studied that era, Greenland was a revelation. It was as if a new continent suddenly appeared on the map: other Devonian rocks were hid for the most part under a woody, bushy carpet in places like England and Pennsylvania, while the mountains of Greenland were mercilessly bare. Unfortunately the new fossils were also so remote that only some greater pretext–like the search for a famous explorer–could get the paleontologists to this far corner of the Arctic.

Another rationale came about thirty years later, when Denmark and Norway began competing in the late 1920s for control of Eastern Greenland, and the oil and minerals that it might hold. The Danes brought Swedish scientists with them, and they found bones of more fish, including lobe-fins, as well as a few things they didn’t know what to make of, simply marking them as “scales of a fish-like vertebrate of uncertain affinities.”

These expeditions were a bit less brutal than Andrée’s and Nansen’s trips. The scientists still traveled in wooden steamers with three square-rigged masts, and while they could now bring a hydroplane for their surveys they still wore polar bear suits when they flew. In 1931 an energetic 22-year old geologist named Gunnar Säve-Söderbergh was put in charge of the expeditions. For sixteen hours a day he could climb mountains, throwing rocks into his rucksack and sketching out stratigraphy along the way.

He had a book of numbered tags made for the expeditions, P. for fishes, and A. for amphibians–a supremely confident system, considering that no one had ever found a Devonian amphibian. The fossil record of land vertebrates with legs–known as tetrapods–only went back about 300 million years and stopped cold.

That first summer, Säve-Söderbergh made his way around the northern slope of Celsius Berg and found more fish. In the cones of fallen rocks below the mountain’s eastern plateau, he also found more than a dozen scraps of a flat skull that didn’t look like any species of fish he had seen before. Optimistically, he marked them with A. tags.

Back in Stockholm that fall, Säve-Söderbergh slowly worked the bones free of the hard sandstone, painting them with alchohol and balsam to reveal the sutures between the bones. Looking down on the flat roof of the skull, he could see that some of the bones were patterned like the skulls of a group of fish known as lobe-fins–represented today only by lungfishes and coelacanths. Many naturalists argued that tetrapods had evolved from an lobe-fin ancestor. But Säve-Söderbergh could also see that it had some traits–like a long snout–that had only been found in early tetrapod fossils.

Looking at that skull, Säve-Söderbergh realized that he had found the earliest tetrapod. He named it Ichthyostega–”fish plate”–after the top of the animal’s skull.

The discovery was a great hit in Denmark, not only with the politicians who wanted to tighten their grip on Greenland, but with the public as well. In celebration one newspaper cartoonist drew a trout with dog legs carrying a pipe-smoking caveman, as snakes encircled moutain peaks and elephants flapped their wings overhead.

Säve-Söderbergh spent the following few summers mapping more of the region by foot, boat, and Icelandic horse. Fossils practically fell out of the rocks for him–mostly fish but on rare occasion another piece of Ichthyostega. The strange scales that had been found in 1929 turned out to be Ichthyostega’s ribs, massive and overlapping like Venetian blinds of bone. His assistants, particularly a student from the University of Upssala named Erik Jarvik, found more Ichthyostega skulls. One skull, unearthed in 1934, was so handsome the paleontologists brought it back across the Atlantic resting on a blue velvet pillow.

After five years Säve-Söderbergh was appointed a professor at the University of Uppsala, but in that year he was diagnosed with tuberculosis. He lingered in bed, managing to write a few papers about some of the fish he had collected, and died in June 1948 at only 40. The summer of Säve-Söderbergh’s death, the expedition to Greenland finally found the legs and shoulders and tail of Ichthyostega. At last it had most of a body.

In the 64 years since Säve-Söderbergh’s death, scientists have discovered many more early tetrapods and their extinct lobe-fin relatives. They’ve found some of these beasts on return trips to Greenland. But they’ve also found other species in places like Pennsylvania, northern Canada, Latvia, and, most recently, Nevada. Together, these fossils now offer an illuminating look at one of the most crucial transitions in the history of life. Without it, we’d still be fish in the sea.

Despite all the new company Ichthyostega has enjoyed lavish attention ever since its discovery, thanks to the quality and quantity of the fossils it left behind. For decades, Erik Jarvik pored over the fossils, and then, after his death, Jennifer Clack of the University of Cambridge and other paleontologists took a look for themselves.

Ichthyostega’s legs, while short and squat, had the elbows, knees, ankles, wrists, and toes that qualified it as a tetrapod. (Strangely, it had seven digits on its feet.) Its spine was sturdy, its hips and shoulders massive, its skull rigid. Yet Ichthyostega’s rigid skull still shared some traits with the flexible skull of lobe fins. It had a distinctive suture in the skull at the same place where a lobe-fin skull has a hinge. Under the tetrapod palimpsest its ancestry could be seen.

Ichthyostega’s tail was a similar mix of tetrapod and fish. Tetrapods have simple tails consisting of a long series of tapering vertebrae encased in flesh (ours has dwindled to a mere sprout, the coccyx). A lobe-fin’s tail, the motor that the animal uses to move through water, is a much more elaborate affair. Each vertebra has two long rods, one on top and one below. Attaching to each of these rods are more slender bones, called radials, and attaching to the radials is a wide fan of fin rays: a completely differerent kind of bone called dermal bone that also makes up scales. This complex anatomy allows a fish to set up waves in its tail either forward or backwards, to let it dart through the water or suddenly brake.

The bottom of Ichthyostega’s tail had a simplified tetrapod form, but the top still retained all the geegaws of a fish. It was, in a sense, still half in the water.

Clack and her colleagues have used the anatomy of Ichthyostega to figure out what it did in life–and, by extension, to get some clues to how the tetrapod body plan evolved. Long before Ichthyostega came on the scene, lobe-fins were already evolving some of the crucial pieces of that body plan–legs and wrists, for example. These ancient relatives lived unquestionably like fish, using gills to breath and depending on water to support much of their weight. It’s clear, in other words, that even though the tetrapod body is very good for getting around on land, it didn’t start evolving on land.

How far had things gotten by the time Ichthyostega showed up 360 million years ago? Clack has found that Ichthyostega’s ear was tuned for hearing underwater. But when she and her colleagues looked at a series of Ichthyostega skeletons, going from young to old, they found a different story. As the animals matured, their shoulders changed shape, providing more space for anchoring arm muscles. It’s possible that they spent a lot of time in the water when they were young and then spent more time on land when they became adults.

In 2005 Clack and her colleagues did a thorough study of Ichthyostega’s trunk–its spine and rib cage. They concluded that the tetrapod was weirdly stiff, unable to bend from side to side. They suggested two possible ways for Ichthyostega to get around on land. It might walk, but without bending its body the way, for examplpe, a salamander does. Or it might mimic an inchworm. It would bend its spine upwards, reach forward with its front legs, and then straighten out, pushing forward with its hind legs.

Today in Nature, Clack offers more clues to this puzzling creature. She collaborated with John Hutchinson of the Royal Veterinary College, an expert on biomechanics, and his postdoctoral researcher Stephanie Pierce. They have brought Ichthyostega back to life through a detailed computer reconstruction.

They started by making high-resolution scans of its fossils, which they then assembled into a virtual skeleton. Hutchinson has, over the past decade, figured out a way to estimate how animals moved based on this kind of reconstruction. By placing virtual muscles on the virtual bones, he can estimate their range of motion. Hutchinson knows his models are reliable, because he can test them on living animals. His estimates for the movements of animals such as otters and alligators are close to how they really move.

Here are a couple videos showing their results. I’ll explain them below.

The whole body:

The hind leg in action:

Simply put, Ichthyostega could not have been very impressive on land. No matter how hard it tried, it could not walk with its back legs. The limbs could move forward and back, but they could not swivel into a position that would allow Ichthyostega to plant its feet on the ground. Its forelimbs were a little more useful. It could bend its elbows. But its shoulders had little range of motion.

Combined with their rigid trunk, these new findings lead Clack and her colleagues to conclude that the best living analogy for Ichthyostega is a mudskipper. Mudskippers are not lobe-fins. Instead, they are ray-finnsed fish, more closely related to goldfish or trout. In an independent transition from the ocean, they evolved the ability to move around on land by crutching along on their front pair of fins. As the delightful video below from David Attenborough shows, mudskippers are quite successful in their peculiar ecological niche, crawling on muddy beaches, sucking up food from the muck, and then swimming through their underwater burrows to care for their young. But they are hardly an inspiring vision of tetrapods emerging on land.

Clack’s new study stands in intriguing contrast to one that I blogged about in December. University of Chicago scientists reported then that lungfish–our closest living aquatic relatives–can walk underwater with their pelvic fins–which correspond to the hind legs of tetrapods. The Chicago team argued that hind-leg-driven walking could have started out long before the tetrapod body evolved. Clack and her colleagues, on the other hand, propose that hind legs came late to the terrestrial party.

But if there’s one thing that the past couple decades of fossil-hunting has made clear is that the origin of tetrapods was not some linear march of progress. Starting about 380 million years ago, some lobe fins independently evolved tetrapod-like traits in a grand, unplanned experiment. Different species ended up with different combinations of those traits, perhaps adapting them to different ways of getting around underwater or on land. Ichthyostega might be a good model for the ancestor of all living tetrapods. Or it may have been a very weird beachcomber with hind legs that were only good as underwater paddles. To find out, scientists need to build more virtual skeletons of early tetrapods. And they need to head out to find more fossils.

Let’s just hope that they don’t have to follow doomed explorers to find them.

For more information about the discovery of tetrapod evolution, see my book At the Water’s Edge, from which parts of this post were adapted.

[Images: skeleton from Clack's site. Skull from Tree of Life. Images of the Fram and the failed balloon from Wikipedia.]

NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
ADVERTISEMENT

See More

ADVERTISEMENT
Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »