Blogs / The Loom

The warming climate may earn carbon dioxide all the headlines (including ones about senators who can’t tell the difference between a couple blizzards and a 130-year climate record), but the gas is having another effect that’s less familiar but no less devastating. Some of the carbon dioxide we pump into the air gets sucked into the ocean, where it lowers the pH of seawater. We’ve already dropped the pH of the ocean measurably, and as we burn more fossil fuels we will drop it more. Ocean acidification has the potential to wreak world-wide havoc on marine life.

Today in Yale Environment 360, I write about scientists comparing today’s ocean acidification to the last time something comparable happened–55 million years ago. Short answer: today’s is big. Really, really big. Check it out.

Suddenly this obscure, blind cave dweller has become extremely interesting. It turns out to be a close cousin of the most diverse group of animals on Earth, the insects.

Insects–all one-million-plus-species of them–belong to a lineage of animals called arthropods. The arthropods emerged early in the history of animals, and while many of the early arthropods such as trilobites disappeared long ago, a vast diversity thrive on Earth today. Living arthropods share a number of traits in common, such as a hardened, segmented exoskeleton and compound eyes. But they’ve evolved into lots of different forms, ranging from scorpions to horseshoe crabs to centipedes to daddy longlegs to butterflies. They fly through the sky, plunge to the bottom of the sea, thrive in scorching deserts, and hang out in your kitchen.

In order to understand how the arthropods evolved into all this diversity, scientists have labored for many decades to figure out how they are related to one another. It has been a tricky undertaking for many reasons. For one thing, different lineages of arthropods have frequently evolved the same traits independently. So just because two species have long stalk-shaped eyes doesn’t mean that they share a close stalk-shaped ancestor. It’s possible they might have each evolved from two separate ancestors with ordinary eyes.

When scientists started to sequence DNA from arthropods, they hoped that they would be able to get a sharper picture of arthropod evolution. It has helped clear up some things. For example, for a long time scientists believed that insects were closely related to centipedes and millipedes. Along with their anatomical similarities, these two groups are also both mainly land-dwellers. But studies on DNA have pretty clearly demonstrated that, in fact, insects are closer to crustaceans like lobsters and shrimp than they are to centipedes and millipedes. So the two groups descend from two separate invasions of land.

However, studies on DNA did not immediately make all the uncertainties about arthropods disappear. And there’s no reason to have expected it would. DNA is not magic. It’s a great repository of information about the history of life, but it’s not perfect. For example, just as two insects may independently evolve stalk eyes, two lineages may evolve a similar sequence in a particular stretch of DNA. Another problem arises with groups like arthropods that blossomed very quickly into many lineages a long time ago. It’s hard to tease apart the ordering of the branches, just as it’s hard to tease apart distant galaxies in a telescope.

So scientists have been gathering more arthropod DNA and analyzing it in new ways, in order to find strong evidence for kinships. In Nature today, a team of scientists at the University of Maryland, Duke University, and the Natural History of Museum in LA have presented a particularly massive analysis. They lined up 41,000 bases of DNA from 62 genes in 75 species spanning the diversity of arthropods. They found that a number of the branches of the tree held up under a number of different statistical tests. The tree, in all its full glory, is reproduced at the bottom of this post.

In some respects, it supports a lot of traditional taxonomy. For example, everything we call an insect are closer to each other than to any arthropod not considered an insect. But there are also some intriguing surprises.

The one I’ll mention here is the cave-dwelling critter I mentioned at the top of the post. It’s called Speleonectes tulumensis. It lives only in the pitch-black, oxygen-free waters at the bottom of deep caves in the Bahamas. It belongs to a group of arthropods, which the authors of the new study dub Xenocarida, that have mystified scientists ever since they were discovered in the 1980s. Some researchers argued that they were the most primitive of all crustaceans. Yet some xenocarids have remarkably elaborate brains. Thanks to the fact that they live at the bottom of deep caves, scientists haven’t given them quite the attention they’ve lavished on fruit flies and honeybees and other arthropods in easier reach.

According to the new study, however, they deserve the attention of anyone interested in where insects came from. That’s because they are the closest living relative to the insects (along with springtails and other six-legged arthropods, the hexapods).  They can therefore offer clues to what the forerunners of insects were like. Insects may not have evolved out of deep caves–it’s possible that xenocarids lived in other parts of the ocean in the past but have only survived in one extreme habitat. But before there were insects, this new study suggests, the proto-insects may have looked like this. It’s yet another demonstration of the knowledge that we can get even from rare, obscure species. If we had accidentally wiped out the xenocarids, no one would have ever known the important place they have in the history of this arthropod-dominated world.

Here’s the course of Charles Darwin’s ancestors out of Africa over the past 50,000 years or so. It’s based on an analysis of the Y chromosome belonging to his great-great grandson. Details here.

I seem to have ended up as the Dinosaur Feather Color Bureau Chief at the New York Times. After discovering colors in fossil bird feathers, scientists found colors in dinosaurs last week. But this week another group of scientists has got the color pattern across a dinosaur’s entire body.

Imagine: Silver Spangled Hamburgs of the Jurassic!

Image courtesy of National Geographic. Check out their 3-D version.

Dinosaurs in color! I’ve got a story tomorrow in The New York Times on scientists who are using the microscopic structure of dinosaur feathers to figure out their colors.

My new article is just one chapter in a multi-part story. Back in September, I wrote in the Times about how paleontologists developed this method and used it to determine the color of a 47-million-year-old bird feather. On the blog, I promised you here to stay tuned, and now here we are.

The new paper is important, but, as I note in the article, the scientists analyzed a single sample from each fossil. They didn’t look at a large number of samples from a single specimen. Such an analysis could give a broader picture of the color pattern of a dinosaur.

Again, you may guess where this is going. And so, again, stay tuned…

[Update: Times link fixed]

I’ve been following the research of primatologist Frans de Waal on peacemaking among primates for a long time. Earlier this month I finally got to meet him in New York, where we had a conversation about his new book, The Age of Empathy: Nature’s Lessons for a Kinder Society.

I’ve embedded the first of a series of excerpts you can watch on YouTube. You can find all the excerpts here.

Here’s a talk I just gave on Big Think–about viruses, synthetic biology, and tapeworms that carry my name. The sound quality isn’t as good as I’d like, but I hope the words make up for it.

Anthony Lane reviews the new Darwin biopic Creation in the New Yorker. As is his habit, Lane manages to write some lovely stuff about a movie he doesn’t care much for (”at once slow and overwrought”). I have to agree with him on this, for example:

[Actor Paul] Bettany, with his jungly sideburns and smooth pate, offers a reasonable likeness of the great man, although he lacks the shaggy overhang of brow, extending far beyond the sunken eye sockets, which lent Darwin not only his solemn frown but, it must be said, his semi-simian air. I sometimes wonder if his tracing of our ancestry began not on his travels, or at his desk, but one morning when he glanced into his shaving mirror.

[Image: Wikipedia]

I’m just back from ScienceOnline 2010, a conference unlike anything I’ve been to before. I usually go to conferences where my role is the journalistic fly on the wall, gathering story leads from presentations and hallway chats. Sometimes I go to meetings of fellow science writers, where it’s mostly hard-core job talk (with sporadic wailing and gnashing of teeth). ScienceOnline was a strange merging, where scientists talk about how to blog from a research vessel in the middle of the Pacific and journalists talked about how to teach Hollywood producers about quantum physics.

It is futile for me to distill all the stuff I learned into a blog post. There’s just too much, from the inspiring to the mundane. For example, for good podcasting sound quality, why not sit in a closet with a towel draped over your head? I’m also spending much of today surfing around to new web sites I heard about. Allow me to give a shout-out to fellow Discover-ite Darlene Cavalier’s newly launched Science For Citizens. It’s like Amazon.com for all sorts of possibilities for doing cool citizen science (such as studying fireflies).

Fortunately, later this week you can watch just about all the sessions on this YouTube channel. In the meantime, some audience members have already started uploading their own recordings. Embedded below is my seven-minute spiel. I was part of a panel on “rebooting science journalism.” Moments before I stood up to dispense my wisdom, I decided that nothing summed up the situation today with science journalism better than duck sex. And, as I discovered, ScienceOnline is just the sort of place where the audience gets it.

[More on Uff da here]

Here’s a talk by Ian Couzin, a scientist who does fascinating studies on crowds and their wisdom. I wrote about Ian a couple years in the New York Times. It’s funny now to actually see him in the virtual flesh. And to hear him talk about how much he loves the Pixies.

Last month I wrote an essay about the future of evolution for Science. I paid particularly close attention to what will happen to our own species, describing some recent research and ideas from scientists. Natural selection will not stop, nor will the emergence of new, neutral mutations.

But this week, the evolutionary biologist Michael Lynch has published a provocative paper (to mark his inauguration into the National Academy of Sciences) in which he makes another kind of forecast. Our future evolution, he warns, is going to lead to a devastating decline in our health.

The idea is not new. Hermann Muller, who won the Nobel Prize for his work on mutations, first raised the specter of evolutionary decline in 1950. He pointed out that many mutations that arise in a population are harmful. They can cause various diseases, cutting lives short or making it harder for organisms to reproduce. Left to themselves, these mutations can drive down the reproductive rate of a population. But their harmful effects can be balanced by natural selection. If individuals with harmful mutations have fewer offspring than other individuals, the mutations become less common. Overall, the population can continue to reproduce at a healthy rate.

As Lynch points out, Muller’s argument depended on the actual rate of mutations and other vital statistics that no one in the 1950s could know with much precision. But in his new paper, Lynch surveys recent studies that make it possible to know the mutation rate quite well. Lynch concludes that every gamete (a sperm or egg) acquires the following:

–38 base-substitution mutations (a single “letter” of DNA changes to another one).

–3 small insertions or deletions of a stretch of DNA

–1 splicing mutation (which changes the combination of segments of a gene that cells use to build proteins)

–Plus some assorted other mutations (gene duplications, insertions of DNA copied by transposable elements, and so on).

All told, Lynch estimates a total of 50 to 100 mutations.

Compared to other species, Lynch points out, we mutate a lot. Any base in our DNA is twice as likely to mutate as a base in a fruit fly’s DNA, for example. Part of our special burden is our long life. As sperm divide rapidly during a man’s life, they pick up lots of new mutations. We are also left prone to cancer, as our skin, intestines, and other tissues continue to divide and sometimes pick up new mutations.

A lot of the new mutations in every new baby are harmless. But each baby may acquire a few harmful ones. These mutations rarely cause a swift death. Instead, in their totality, they slice off a tiny fraction of the total offspring an entire population can produce. Lynch estimates that mutations to protein-coding DNA cause the fitness of a population to decline by 1%. That’s assuming natural selection does not favor other mutations over these harmful ones.

Lynch acknowledges that natural selection is still in effect in humans, particularly in places where people never see doctors, let alone get clean drinking water. But as the world’s standard of living goes up, he argues, more and more people are being shielded from natural selection’s most intense effects–and harmful mutations are piling up.

In a matter of a few centuries, Lynch predicts, industrialized societies may experience a huge increase in harmful genes–”with significant incapacitation at the morphological, physiological, and neurobiological levels,” he writes.

Battling this decline won’t be easy, says Lynch. Rather than a few big mutations causing the trouble, the decline will be brought about by a vast number of mutations, each with a very small effect. The fantasies of selective breeding dreamed of by eugenicists aren’t just loathesome–they’re also useless. Instead, Lynch argues for something that would make the eugenicists crazy. “Ironically, the genetic future of mankind may reside predominantly in the gene pools of the least industrialized segments of society,” he writes.

Image: IU

This fall, I gave a number of lectures about the evolution of swine flu. By the time I got to the end of the talk, I could tell that a lot of people in the audience were feeling a bit resigned, given the way evolution allows viruses like the flu to evade our best attacks. (Here’s the full video of my lecture at the University of British Columbia.)

To try to cheer up the crowd, I’d offer a note of hope–the notion that we could turn the evolution of viruses against them, by pushing them into mutation overdrive. (This slide gets across the basic idea–the flu virus is like a sports car. Going fast is cool. Going too fast–not so cool.)

In tomorrow’s New York Times, I lay out this intriguing idea, that goes by the profoundly cool name of lethal mutagenesis. Check it out.