Ever upwards

Of course it would be Phil who would remind me: today is the 38th anniversary of the first manned landing on the moon. I remember lying on my stomach on the floor with my chin in my hands, watching TV in the way only 12 year olds can and which would nowadays leave me wondering if I’ll be able to get up again, the front door open, a summer breeze blowing through the screen, the sound of someone down the street mowing their lawns, and right there in front of me, in this ordinary day in a boring little small town, I saw these grainy echos of a human being stepping onto the moon. We can do that. It was hard, and only a tiny few of us have ever accomplished it, but here in our hands and in our minds we have this amazing power to accomplish astonishing things.

How are we going to accomplish our next miracle, do you think?

Middle World

One of the traditional ways to explain a scientific subject is the historical approach: start at the beginning of the endeavor and explain why people asked the questions they did, how they answered them, and how each answer blossomed into new potential. It’s a popular way of teaching science, too, because it emphasizes the process that leads to new discovery. Middle World: The Restless Heart of Matter and Life(amzn/b&n/abe/pwll), by Mark Haw, exemplifies the technique. Not only is it effective, but this one slim book manages to begin with a simple, curious observation in 1827 and ends up synthesizing many of the major ideas of modern physics, chemistry, and biology!

[Read more…]

Evolution of a sex ratio observed

i-38dd94616ec7d013e7ee71a091e77669-y_the_last_man.jpg

If you’ve been reading that fascinating graphic novel, Y: The Last Man(amzn/b&n/abe/pwll), you know the premise: a mysterious disease has swept over the planet and bloodily killed every male mammal except two, a human named Yorick and a monkey named Ampersand. Substantial parts of it are biologically nearly impossible: the wide cross-species susceptibility, the near instantaneous lethality, and the simultaneity of its effect everywhere (there are also all kinds of weird correlations with other sort of magical putative causes, which may be red herrings). On the other hand, the sociological part of the story seems very plausible. There is no feminist utopia, the world goes on in a traumatized and rather complicated way, and the reactions everywhere vary from crazed euphoria to a more common despair. One thing that isn’t at all implausible, and actually has been observed, is a plague that selectively exterminates males.

[Read more…]

Reinventing the worm

i-1bc8375bf73650319bed813cbac1e39a-buddenbrockia_sm.jpg

Sometimes, I confess, this whole common descent thing gets in the way and is really annoying. What we’ve learned over the years is that the evolution of life on earth is constrained by historical factors at every turn; every animal bears this wonderfully powerful toolbox of common developmental genes, inherited from pre-Cambrian ancestors, and it’s getting rather predictable that every time you open up some fundamental aspect of developmental pattern formation in a zebrafish, for instance, it is a modified echo of something we also see in a fruit fly. Sometimes you just want to see what evolution would do with a completely different starting point — if you could, as SJ Gould suggested, rewind the tape of life and let it play forward again, and see what novelties arose.

Take the worm. We take the generic worm for granted in biology: it’s a bilaterally symmetric muscular tube with a hydrostatic skeleton which propels itself through a medium with sinuous undulations, and with most of its sense organs concentrated in the forward end. The last common ancestor of all bilaterian animals was a worm, and we can see that ancestry in the organization of most animals today, even when it is obscured by odd little geegaws, like limbs and armor and regional specializations and various dangly spiky jointed bits. You’ll even see the argument made that that worm is the best of all possible simple forms, so it isn’t just an accident of history, it’s a morphological optimum.

But what if we could rewind the tape of life a little bit, to the first worms? Is it possible there are other ways such an animal could have been built? It seems nature may have carried out this little experiment for us, and we have an example of a reinvented worm, one not constructed by common descent from that initial triumphal exemplar in the pre-Cambrian — an alternative worm.

[Read more…]

Common elements of eumetazoan gene organization in an anemone

We now have a draft of the sea anemone genome, and it is revealing tantalizing details of metazoan evolution. The subject is the starlet anemone, Nematostella vectensis, a beautiful little animal that is also an up-and-coming star of developmental biology research.

i-da53b70f97ff878afc87b689369ca148-nematostella.jpg
(click for larger image)
Nematostella development. a. unfertilized egg (~200 micron diameter) with sperm head; b. early cleavage stage; c. blastula; d. gastrula; e. planula; f. juvenile polyp; g. adult stained with DAPI to show nematocysts with a zoom in on the tentacle in the inset; h, i. confocal images of a tentacle bud stage and a gastrula respectively showing nuclei (red) and actin (green); j. a gastrula showing snail mRNA(purple) in the endoderm and forkhead mRNA (red) in the pharynx and endoderm; k. a gastrula showing Anthox8 mRNA expression; l. an adult Nematostella.

A most important reason for this work is that the anemone Nematostella is a distant relative of many of the animals that have already been sequenced, and so provides an essential perspective on the evolutionary changes that we observe in those other organisms. Comparison of its genome with that of other metazoans is helping us decipher the likely genetic organization of the last common ancestor of all animals.

[Read more…]

What do you want to be when you grow up?

David Ng is asking if biologists have physics envy, which is both a common and a peculiar question (short answer: no, physicists should have biology envy). Then he follows up with a few brief questions to determine if scientists are actually pining away, wishing they’d gone into some different field … and here are my answers.

1. What’s your current scientific specialty?

Developmental biology.

2. Were you originally pursuing a different academic course? If so, what was it?

I started my undergraduate career with a general interest in marine biology, but quickly focused on neurobiology and development as more interesting problems (but not more interesting environments or organisms!) I went into graduate school thinking neuroscience was the bee’s knees, but again shifted focus to more development — starting from a developmental perspective was the practical way to approach the complexity of the nervous system. Now I also think it is the practical way to approach the complexity of metazoan evolution. Actually, I’m with D’Arcy Thompson that “everything is the way it is because it got that way” and that development is the lens we should use to examine everything. The process is all.

3. Do you happen to wish you were involved in another scientific field? If so, what one?

Yes, all of them.

Well, all of the biological disciplines, anyway. The problem is that I tend to think of mathematics, physics, and chemistry as subsets of biology, so they all tend to get sucked into my domain of desired knowledge.

On the other hand, maybe my answer should be “no.” My interests are my interests, and I’m currently free to pursue them exactly as I will, so I can’t quite imagine changing who I am. If I were to switch to another scientific field it would only be because I saw it as a useful tool to better understand the process of development.

Go ahead, everyone, answer the questions yourselves. If you aren’t a scientist, you can still always answer questions 2 and 3 (hint: the correct answer to #3 will always be some variant of evo-devo. Different answers will be marked down accordingly.)

You are a mutant, and your genome is full of junk. What’s the problem?

These kinds of calculations are always handy. Larry Moran estimates the number of novel mutations you carry: the textbooks say about 300, he calculates something over 120. So next time a creationist tells you all mutations are deleterious, just tell him he’s a mutant himself with somewhere around a few hundred random nucleotide changes from either of his parents. What Larry doesn’t mention in this estimate, but I know he’s familiar with the idea, is that most of those mutations will be neutral: about 95% will fall into junk DNA, many won’t affect the amino acid sequence of any proteins, others may cause slight changes in the protein sequence that don’t detectably affect the phenotype.

In the category of utterly baffling pronouncements from scientists, Larry also chastises John Greally for misrepresenting junk DNA in an interview with Ira Flatow. I could scarcely believe it myself, but I listened to the interview, and Greally actually seems to be conflating regulatory sequences with junk, and Flatow introduces the story as suggesting that junk DNA may all have a function. He also claims that if you have a mutation in a gene, the “gene is dead” and will have no function. None of this is correct. It’s bizarre—I think Larry and I are fairly familiar with the genetics literature, and there’s nothing to support these contentions and quite a bit to contradict them.

It’s good to be home, especially when welcomed by Natalie Angier

I’m home from our vacation, and our painfully tiring redeye flight from Seattle, and I get a treat right as I step through the door: a copy of Natalie Angier’s The Canon(amzn/b&n/abe/pwll) arrived in the mail while I was away. What did I do? Right after we got all the luggage into the house, I flopped down on the bed with it and read it until the lack of sleep caught up with me — and it’s good enough that I actually made it through the first two chapters before passing out. It’s a passionate and enthusiastic survey of basic principles in science, and it’s fun to read.

Then I discovered that onegoodmove had a video interview of Angier talking about her book. She’s very good; check it out. She’s the kind of science journalist I want to see more of, and everyone should go out and buy her book to encourage her to do more.

One annoyance: several of the commenters at onegoodmove seem to be of the concern troll variety. Here’s this smart, fluent, talented writer who is also a world-class science geek and atheist, and they start picking over her appearance and body language — it’s rather dismaying, in particular since her gestures are no more flamboyant than those of her (male) interviewer. I’ve long thought that Natalie Angier would make an excellent spokesperson for godless science, and wondered why we don’t see more of her … and I wonder if part of the reason is that the same troglodytes who grunt in disgust at the sight of someone who doesn’t respect their sky-god are also appalled at the sight of a woman speaking confidently about high geek factor subjects and also dismissing their primitive superstitions.