A major change in stem cell policy

Today, President Obama signed a bill lifting the Bush restrictions on stem cell research. You really must go listen to his speech on the occasion — he seems to get what scientific research is all about. Man, it’s been a long eight years, and oh is it wonderfully good to hear an eloquent defense of scientific research from our president, for a change.

The ugly little goblins of the Bush years still plague us, though; compare the uplifting message of knowledge from Obama with this fundamentally fallacious opinion piece from the carnie barker of junk science, Steven Milloy. And by “fundamentally fallacious”, I mean that it’s problems are far deeper than his usual slithery tweaking of the facts to misrepresent the evidence and the science — I mean that right at the core of Milloy is an absolute lack of comprehension of the very nature of science, and it’s right there, exposed and naked and hideous.

His problem? He thinks his ignorance of the field is an accurate picture, and he thinks science ought to be more like a vending machine: put in your nickel, and the bubble gum you wanted pops out.

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Elephantine errors from Ray Comfort

So Ray Comfort is now complaining on the revered pages of the respected publication, World Net Daily about me. The article is full of dishonest misquotes, but let’s zip right to Ray’s scientific misunderstandings. They are deep and painful. He has this bizarre idée fixe that the necessity of every species having males and females somehow greatly reduces the probability that new species could arise. It’s total nonsense, and I dismissed it briefly when I commented on it before.

“I know Ray is rather stupid, but who knew he could be that stupid. This has been explained to him multiple times: evolution does explain this stuff trivially. Populations evolve, not individuals, and male and female elephants evolved from populations of pre-elephants that contained males and females. Species do not arise from single new mutant males that then have to find a corresponding mutant female – they arise by the diffusion of variation through a whole population, male and female.”

Ray has read that, and failed to grasp the central concept. Take a look at the workings of Ray Comfort’s mind as he attempts to wrestle with a simple idea: the hamster wheel is wobbling, but the poor beast lies dead with legs up in its cage, and nothing is turning over.

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The best article title this week goes to…

I had to read it just for the title alone: “Harmonic Convergence in the Love Songs of the Dengue Vector Mosquito”. It’s got romance, it’s got harmony, it’s got singing, and best of all, it has that delicious dramatic tension of being all about biting insects known to carry a nasty disease. Even in the lowliest, most obnoxious creatures, biologists find beauty.

I’d tell you all about it — in short, courting mosquitos synchronize their wingbeats to sing in harmony — but Neurotopia beat me to it. When summer comes to Minnesota, I’ll have to remember that the incessant whines are actually tiny little liebeslieder.

A brief moment in the magnificent history of mankind

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Isn’t that beautiful? It’s an ancient footprint in some lumpy rocks in Kenya…but it is 1½ million years old. It comes from the Koobi Fora formation, familiar to anyone who follows human evolution, and is probably from Homo ergaster. There aren’t a lot of them; one series of three hominin trails containing 2-7 prints, and a stratigraphically separate section with one trail of 2 prints and an isolated single print. But there they are, a preserved record of a trivial event — a few of our remote relatives taking a walk across a mudflat by a river — rendered awesome by their rarity and the magnitude of the time separating us.

Here’s one of the trails:

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Tessellated swath of optical laser scans of the main footprint trail on the upper footprint surface at FwJj14E. Color is rendered with 5-mm isopleths.

It’s an interesting bridge across time. There they were, a couple of pre-humans out for a stroll, perhaps on their way to find something for lunch, or strolling off to urinate, probably nothing dramatic, and these few footprints were left in drying mud to be found over a million years later, when they would be scanned with a laser, digitized, and analyzed with sophisticated software, and then uploaded to a digital network where everyone in the world can take a look at them. Something so ephemeral can be translated across incomprehensible ages…I don’t know about you, but I’m wondering about the possible future fate of the debris of my life that has ended up in landfills, or the other small smudges across the landscape that I’ve left behind me.

And what have we learned? The analysis has looked at the shape of the foot, the angle of the big toe, the distribution of weight as the hominins walked across the substrate, all the anatomical and physiological details that can be possibly extracted from a few footprints.

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Optical laser scan images color-rendered with 5-mm isopleths for footprints at both FwJj14E and GaJi10. (A) Isolated left foot (FUI1) on the upper footprint surface at FwJj14E. (B) Photograph of FUI8 on the upper footprint surface at FwJj14E, showing good definition of the toe pads; the second toe is partially obscured by the third toe. (C) Second trail on the upper footprint surface at FwJj14E, showing two left feet. (D) Third trail on the upper footprint surface at FwJj14E, showing a right and a left foot. (E) Print R3 from GaJi10 (22), re-excavated and scanned as part of this investigation. (F) Partial print (FUT1-2) on the upper footprint surface at FwJj14E; the heel area has been removed by a later bovid print. (G) Print FLI1 on the lower footprint surface at FwJj14E, rendered with 5-mm alternating black and white isopleths. (H) Inverted image of the toe area of print FUT1-1 with alternating 5-mm black and white isopleths. Note the locations of the pads of the small toes and the presence of a well-defined ball beneath the hallucial metatarsophalangeal joint. The first, third, and fifth toes are marked D1, D3, and D5, respectively.

The answer is that these beings walked just like us. The tracks are noticeably different from the even older footprints of australopithecines found at Laetoli, from 3.5 million years ago. The foot shape and the stride of Homo ergaster was statistically indistinguishable from those of modern humans, even though we know from the bones associated with these species that they were cranially distinct from us. This is not a surprise; it’s been known for a long time that we evolved these bipedal forms long ago, and that the cerebral innovations we regard as so characteristic of humanity are a relative late-comer in our history.

Remember, though, these are 1½ million years old, 250 times older than the age of the earth, according to creationists. That’s a lot of wonder and history and evidence to throw away, but they do it anyway.

Bennet MR, Harris JWK, Richmond BG, Braun DR, Mbua E, Kiura P, Olago D, Kibunjia M, Omuombo C, Behrensmeyer AK, Huddart D, Gonzalez S (2009) Early Hominin Foot Morphology Based on 1.5-Million-Year-Old Footprints from Ileret, Kenya. Science 323(5918):1197-1201.

Exposing the intimate details of the sex lives of placoderms

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The media is getting another science story wrong. I keep seeing this discovery of an array of fossil placoderms as revealing the origins of sex, and that’s not right. Sex is much, much older, and arose in single-celled organisms. Come on, plants reproduce sexually. A fish is so far removed from the time of origin of sexual reproduction that it can’t tell us much about its origins.

Let’s get it right. These fossils tells us about the origin of fu…uh, errm, mating in vertebrates.

What we have are a set of placoderm fossils from the Devonian (380 million years ago) of Western Australia (The Aussies are going to be insufferable, now that they can claim to be living in the birthplace of shagging) that show two interesting features: some contain small bits of placoderm armor that show no signs of digestion, and so are not likely to be relics of ancient cannibal feasts, but are the remains of viviparous broods — they were preggers. The other suggestive observation is that the pelvic girdle has structures resembling the claspers of modern sharks, an intromittent organ or penis used for internal fertilization.

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Weird-eyed fish

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This is a photograph of Macropinna microstoma, also called barreleyes. It has a very peculiar optical arrangement. When you first look at this photo, you may think the two small ovals above and behind its mouth are the eyes, and that it looks rather sad…wrong. Those are its nostrils. The eyes are actually the two strange fluorescent green objects that look like they are imbedded in its transparent, dome-like head.

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Video frame-grab of Macropinna microstoma at a depth of 744 m, showing the intact, transparent shield that covers the top of the head. The green spheres are the eye lenses, each sitting atop a silvery tube. Visible on the right eye, just below the lens on the forward part of the tube, is the external expression of a retinal diverticulum. The pigmented patches above and behind the mouth are olfactory capsules. High-definition video frame grabs of Macropinna microstoma in situ are posted on the web at: http://www.mbari.org/midwater/macropinna.

It gets the name “barreleyes” because it’s are cylindrical, rather than spherical; this is an adaptation for better light collection in the dim depths where it lives, using very large lenses but not building a giant spherical eye to compensate. It’s ore like a telescope than a wide-angle camera. Here’s what a single eye in a side view looks like — the lens (L) is what is glowing so greenly in the photos.

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Chapman’s (1942) mesial view of the left eye of Macropinna microstoma. Abbreviations: RS = rectus superior, L =lens, OS = obliquus superior, OI = obliquus inferior, RIN = rectus internus, RI = rectus inferior, RE = rectus externus, OP = optic nerve.

As if that weren’t weird enough, the animal has a completely transparent skull cap, and the eyes swivel about within the skull to look out through that translucent cranium. In the two pictures below, the animal is first looking straight up through its head (the eyes are in the same orientation as in the diagram above), and in the right frame it has rotated the binocular-shaped eyes forward to look ahead.

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Lateral views of the head of a living specimen of Macropinna microstoma, in a shipboard laboratory aquarium: (A) with the tubular eyes directed dorsally; (B) with the eyes directed rostrally. The apparent differences in lip pigmentation between (A) and (B) are because they were photographed at slightly different angles. (A) was shot from a more dorsal perspective and it shows the lenses of both eyes; the mouth is not sharply in focus. (B) shows only the right eye, with the lips in sharper focus.

Nature is always coming up with something stranger than we would imagine, and Macropinna is a perfect example. Apparently, the function of this arrangement is to give the animal a sensitive light detector for tracking its prey, bioluminescent jellyfish, and at the same time to shield the eyes from the stinging tentacles of the jelly while it’s eating it.

Robison BH, Reisenbichler KR (2008) Macropinna microstoma and the Paradox of Its Tubular Eyes. Copeia 2008(4):780-784.

Neandertal genome? Or a premature announcement?

In a potentially exciting development, researchers have announced the completion of a rough draft of the Neandertal genome in a talk at the AAAS, and in a press conference, and the latest issue of Science has a number of news articles on the subject. And that is a reason for having some reservations. There is no paper yet, and science by press release raises my hackles, and has done so ever since the cold fusion debacle. Not that I think this is a hoax or error by any means, but it’s not a good way to present a scientific observation.

Also, the work has some major limitations right now. They’ve got about 60% of the genome so far, and it’s all entirely from one specimen. From the age of these bones, degradation is inevitable, so there are almost certainly corrupted sequences in there — more coverage would give me much more confidence.

With those caveats, though, there are some tantalizing hints, and the subject is so exciting that it’s understandable why there’d be rush to announce. So far, they’ve identified approximately 1000-2000 amino acid differences in the coding part of the genome (human-chimp differences are about 50,000 amino acids), but there’s no report of any detectable regulatory differences.

I’m withholding judgement until I see a real paper; for now, you have to settle for a podcast with a science journalist, which just isn’t meaty enough yet.

Schinderhannes bartelsi

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Fans of the great Cambrian predator, Anomalocaris, will be pleased to hear that a cousin lived at least until the Devonian, over 100 million years later. That makes this a fairly successful clade of great-appendage arthropods — a group characterized by a pair of very large and often spiky manipulatory/feeding arms located in front of the mouth. Here’s the new fellow, Schinderhannes bartelsi:

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Holotype of Schinderhannes bartelsi. (A) Ventral. (B) Interpretative drawing of ventral side. l, left; r, right; A1, great appendage; A2, flaplike appendage; sp, spine; fm, flap margin; te, tergite; ta, trunk appendage. (C) Partly exposed dorsal side, horizontally mirrored. (D) Interpretative drawing of dorsal side. (E) Interpretative drawing of great appendages, combining information from the dorsal and ventral sides. (F) Radiograph. (G) Reconstruction. Scale bar, 10 mm [for (A) to (G)]. (H) Mouth-part. Scale bar, 5 mm.

There are some significant differences between familiar old Anomalocaris and Schinderhannes. Anomalocaris was a monster that grew to about a meter long; this little guy is about a tenth of that, around 4 inches. He also has those interesting “wings” behind his head, which presumably aided in swimming.

Another significant feature of this animal is that it has characters that place it in the Euarthropoda, which makes great appendages paraphyletic and primitively present in euarthropods. Those great appendages have long been a curiousity, and we’ve wondered whether they are a unique innovation that was completely lost in modern arthropods, or whether they evolved into one of the other more familiar cephalic appendages; the authors suggest that this linkage with the euarthropod family tree implies that chelicera (what you may recognize as the big paired ‘fangs’ of spiders) are modified great appendages.

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Cladogram; tree length, 87. Consistency index, 0.5402; retention index, 0.6552. (1) Peytoia-like mouth sclerites, terminal mouth position, lateral lobes, loss of lobopod limbs, and stalked eyes. (2) Great appendages. (3) Sclerotized tergites, head shield, loss of lateral lobes, and biramous trunk appendages. (4) Stalked eyes in front and loss of radial mouth. (5) Post-antennal head appendages biramous and antenna in first head position. (6) Free cephalic carapace, carapace bivalved, and two pairs of antennae. (7) Maxilla I and II. (8) Exopods simple oval flap. (9) Two pre-oral appendages and a multisegmented trunk endopod. (10) Post-antennal head appendages biramous and tail appendages fringed with setae. (11) Long flagellae on great appendage and exopods fringed with filaments. (12) Trunk appendages uniramous and eyes not stalked. (13) No posterior tergites. (14) Tail spines and chelicere/chelifore on first head position. (15) Proboscis. (16) Six post-antennal head appendages.

Kühl G, Briggs DEG, Rust J (2009) A Great-Appendage Arthropod with a Radial Mouth from the Lower Devonian Hunsrück Slate, Germany. Science 323(5915):771-773.

Jerry Coyne has a blog

I know! It’s hard to believe! Why, any of the riff-raff can just charge in and start a blog anymore. You write a book or a few, do some internationally recognized research in evolution, and suddenly you get cocky and think you have the talent to write a blog. Back in the day when I started in this, I had to struggle with none of that. And I liked it!

Despite his awesome handicaps, it is a pretty good blog.

I especially like this image from his book, Why Evolution is True(amzn/b&n/abe/pwll):

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©Kalliopi Monoyios

So…no transitional forms, huh? Look at that australopithecine between modern Homo and Pan. It’s definitely not a chimp — the pelvis alone would tell you that — yet it’s also definitely far from fully human. Very cool.