Eppur si muove!

Blogging on Peer-Reviewed Research

The Harvard multimedia team that put together that pretty video of the Inner Life of the Cell has a whole collection of videos online (including Inner Life with a good narration.) Go watch the one titled F1-F0 ATPase; it’s a beautiful example of a highly efficient molecular motor, and it’s the kind of thing the creationists go ga-ga over. It’s complex, and it does the same rotary motion that the bacterial flagellum does; it has a little turbine in the membrane, a stream of protons drives rotation of an axle, and the movement of that axle drives conformation changes in the surrounding protein that promote the synthesis of ATP. It’s a molecular machine all right. Makes a fellow wonder if possibly it’s “irreducible”, doesn’t it?

Well, it’s not. It can be broken down further and it still retain that rotary motion.

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Reproductive history writ in the genome

Blogging on Peer-Reviewed Research

Fossils are cool, but some of us are interested in processes and structures that don’t fossilize well. For instance, if you want to know more about the evolution of mammalian reproduction, you’d best not pin your hopes on the discovery of a series of fossilized placentas, or fossilized mammary glands … and although a few fossilized invertebrate embryos have been discovered, their preservation relied on conditions not found inside the rotting gut cavity of dead pregnant mammals.

You’d think this would mean we’re right out of luck, but as it turns out, we have a place to turn to, a different kind of fossil. These are fossil genes, relics of our ancient past, and they are found by digging in the debris of our genomes. By comparing the sequences of genes of known function in different lineages, we can get a measure of divergence times … and in the case of some genes which have discrete functions, we can even plot the times of origin or loss of those particular functions in the organism’s history.

Here’s one example. We don’t have any fossilized placentas, but we know that there was an important transition in the mammalian lineage: we had to have shifted from producing eggs in which yolk was the primary source of embryonic nutrition to a state where the embryo acquired its nutrition from a direct interface with maternal circulation, the placenta. We modern mammals don’t need yolk at all … but could there be vestiges of yolk proteins still left buried in our genome? The answer, which you already know since I’m writing this, is yes.

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Dicyemid mesozoa

Blogging on Peer-Reviewed Research

You know how people can be going along, minding their own business, and then they see some cute big-eyed puppy and they go “Awwwww,” and their hearts melt, and then it’s all a big sloppy mushfest? I felt that way the other day, as I was meandering down some obscure byways of the developmental biology literature, and discovered the dicyemid mesozoa … an obscure phylum which I vaguely recall hearing about before, but had never seriously examined. After reading a few papers, I have to say that these creatures are much more lovable then mere puppy dogs. Look at this and say “Awwwww!”

i-67abe67694eea42539187c64ab322994-dicyemid.jpg
Light micrograph of Dicyemid japonicaum rhombogen. AX, axial cell; C, calotte; IN, infusorigen; P, peripheral cell.

O dicyemid mesozoan, how do I love thee? Let me count the ways.

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The choanoflagellate genome and metazoan evolution

Blogging on Peer-Reviewed Research

What are the key innovations that led to the evolution of multicellularity, and what were their precursors in the single-celled microbial life that existed before the metazoa? We can hypothesize at least two distinct kinds of features that had to have preceded true multicellularity.

  • The obvious feature is that cells must stick together; specific adhesion molecules must be present that link cells together, that aren’t generically sticky and bind the organism to everything. So we need molecules that link cell to cell. Another feature of multicellular animals is that they secrete extracellular matrix, a feltwork of molecules outside the cells to which they can also adhere.

  • A feature that distinguishes true multicellular animals from colonial organisms is division of labor — cells within the organism specialize and follow different functional roles. This requires cell signaling, in which information beyond simple stickiness is communicated to cells, and signal transduction mechanisms which translate the signals into different patterns of gene activity.

These are features that evolved over 600 million years ago, and we need to use a comparative approach to figure out how they arose. One strategy is to pursue breadth, cast the net wide, and examine divergent forms, for instance by
comparing multicellular plants and animals. This approach leads to an understanding of universal properties, of how general programs of multicellular development work. Another is to go deep and examine closer relatives to find the step by step details of our specific lineage, and that’s exactly what is being done in a new analysis of the choanoflagellate genome.

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The genome is not a computer program

The author of All-Too-Common Dissent has found a bizarre creationist on the web; this fellow, Randy Stimpson, isn’t at all unusual, but he does represent well some common characteristics of creationists in general: arrogance, ignorance, and projection. He writes software, so he thinks we have to interpret the genome as a big program; he knows nothing about biology; and he thinks his expertise in an unrelated field means he knows better than biologists. And he freely admits it!

I am not a geneticist or a molecular biologist. In fact, I only know slightly more about DNA than the average college educated person. However, as a software developer I have a vague idea of how many bytes of code is needed to make complex software programs. And to think that something as complicated as a human being is encoded in only 3 billion base pairs of DNA is astounding.

Wow. I know nothing about engine repair, but if I strolled down to the local garage and tried to tell the mechanics that a car was just like a zebrafish, and you need to throw a few brine shrimp in the gas tank now and then, I don’t think I would be well-received. Creationists, however, feel no compunction about expressing comparable inanities.

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We’re having a lunar eclipse tonight!

Check out Phil for the details. For us Minnesotans, the events start around 8pm, should reach totality around 9, and should be over around 11.

Here’s the good news: we’re supposed to have clear skies!

And now the bad news: it’s about -27°F outside right now, and while we’re supposed to warm up a little today, it’s still going to be about -15°F tonight. Don’t let your eyeballs freeze while you’re doing your moongazing.

Beelzebufo: best frog name ever

Blogging on Peer-Reviewed Research

It means “devil toad,” and it was a 10 pound monster that lived 70 million years ago, in what is now Madagascar. It’s huge, and judging by its living cousins, was a voracious predator. If it were alive today, it would probably be eating your cats and puppies.

In other words, this was an awesome toad, and I wish I had one for a pet.

Here’s what it looks like, with some very large extant toads for comparison.

i-e5b6bbd646907dd5b6e43f29f30c0653-beelzebufo.jpg
Beelzebufo ampinga, Late Cretaceous of Madagascar. (A) Skull
reconstruction showing parts preserved (white areas, Left) and distribution of
pit-and-ridge ornament (stippling, Right). (B) Skeletal reconstruction and
inferred body outline of average-sized (skull width, 200 mm; SVL, 425 mm)
adult female B. ampinga based mainly on Lepidobatrachus asper. White
areas indicate parts represented by fossil specimens. For size comparison,
dorsal view silhouettes of Ceratophrys aurita (the largest extant ceratophryine) (C), and Mantidactylus guttulatus (the largest extant Malagasy frog) (D),
are shown. cp, crista parotica; fm, foramen magnum; frp, frontoparietal; mx,
maxilla; n, nasal; pmx, premaxilla; qj, quadratojugal; qu, quadrate; sq, squamosal. (Scale bars: 50 mm.)
i-4ad5439499d731bfc005d4c6572bade4-deviltoad.jpg

There are some biogeographical puzzles associated with this beast. It’s found in Madagascar, but it’s closest extant relatives are South American…and since frogs and toads do a poor job of crossing salt water, that implies the existence of land bridges between those continents around the Cretaceous. It’s not a major puzzle, though, although some of the news reports I’ve seen play up the concern, as if it were a significant controversy. As the authors explain,

We suggest that extant ceratophryines are remnants
of a Gondwanan hyloid clade that once ranged from at least
South America to Indo-Madagascar. Whether this clade was
more broadly distributed and on which Gondwanan landmass it
originated cannot be determined on current evidence. However,
as the Late Cretaceous fauna of the Maevarano Fm,
including its ceratophryine anuran, bears little resemblance to
that of modern Madagascar, major biotic changes clearly occurred on the island in the intervening period. When and how the ancestors of the endemic mantellid and microhylid anurans arrived on Madagascar remains controversial,
but there is general agreement that these frogs did not diversify
significantly until the Paleogene. Their radiation
has been linked, at least in part, to the expansion of rainforests,
but may also have been facilitated by the extinction of archaic
faunal elements, including ceratophryines.

It was a diverse, widespread group once upon a time, and it’s not at all challenging to report that the continents have shifted in 70 million years. It’s just very cool that anurans achieved the status of charismatic megafauna*, once upon a time.

*For a generous definition of “mega”.

Evans SE, Jones MEH, Krause DW (2008) A giant frog with South American affinities from the Late Cretaceous of Madagascar. Proc Nat Acad Sci USA 105(8):2951-2956.