Physics is important to us biologists, too

The Canadian Undergraduate Physics Conference is in trouble — government support has been flat, and corporate support has been declining. They are really in trouble: here’s what I got from one of the people working on it:

The CUPC is the largest conference in North America organized entirely by undergraduate students. It brings together students from across Canada and the world studying a vast array of subject areas from mathematical and theoretical physics to medical biophysics to engineering and applied physics. This important event gives many students their first experience with academics outside of the classroom, and helps to cultivate an interest in research and higher study. I, and every one else working on the organization of this event, would therefore be extremely grateful if you would be willing to post a link to your blog for the conference (http://cupc.ca/) and ask for donations (which are accepted on the site). The conference is in only a few short days and we are desperate for funds. If the we cannot find adequate support, this will be the 44th and final CUPC, which will be a tremendous shame for science education.

If you can, donate. If you know any potential sponsors who care about undergraduate physics research, pass the word on.

Fossil daisy-chain

Blogging on Peer-Reviewed Research

Here’s a very strange fossil from the Chengjiang Lagerstätte, an early Cambrian fossil bed from 525 million years ago. It’s a collection of Waptia-like arthropods, nothing unusual there; these are ancient creatures that look rather like headless shrimp. What’s weird about it is the way the individuals are locked together in a daisy chain, with the telson (tail piece) of each individual stuck into the carapace of the animal behind. It’s not just a fluke, either — they have 22 fossil chains, and just one animal all by its lonesome.

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(Click for larger image)
Waptia-like arthropod, Lower Cambrian, Haikou, Yunnan. (A) Individual with twisted abdomen, part of chain, Yunnan Key Laboratory for Palaeontology, YKLP 11020a. (B) Chain, about 20 individuals, various dorsoventral-lateral orientations, composite image (joined at cpt/p arrow), YKLP 11020a and YKLP 11020b. (C) Individual linked to carapace behind, lateral view, part of chain of nine individuals, YKLP 11021. (D) Isolated individual, subventral view, YKLP 11019. (E to G) Reconstruction shown in dorsal, ventral, and right lateral views, respectively. Scale bars in (A), (C), and (D) indicate 1 mm; in (B) and (E) to (G), 5 mm. b, s, and t indicate bent, stretched, and telescoped individuals, respectively; cpt, counterpart; f, facing direction; p, part; and tw, twisted.

They do not look like animals that were constrained in a burrow, or that were crawling over the surface. Rather, they had been swimming together in a chain at death, and the whole chain fell to the sea bed, bending and kinking but still remaining firmly locked together.

Why were they doing this? My first thought was of sex; everyone knows how dragonflies and damselflies lock together for mating, but of course that would predict pairs of individuals, not 20 at a time. It also reminded me of the Drosophila mutant fruitless, in which male flies court other male flies, and they spontaneously form conga lines in the culture bottles. That’s also unlikely, since that kind of behavior doesn’t lead to a consistent pattern of successful reproduction, but maybe if these animals were hermaphroditic, it might work. It’s not a behavior that any modern arthropods show, however.

The authors consider the possibility it is a feeding strategy, but that’s even worse: they’re locked basically mouth to anus, which would mean the fellow at the end of the line gets a very unpleasant diet. They conclude that the most likely explanation is that this represents a migratory behavior, perhaps involved in daily vertical migration. It may have been that strings of these animals would link up and paddle together to move to new feeding sites, where they separated and dispersed until the time came to move elsewhere.

Hou X-G, Siveter DJ, Aldridge RJ, Siveter DJ (2008) Collective Behavior in an Early Cambrian Arthropod. Science 322(5899):224.

Jellyfish gettin’ it on, baby

This is too much verisimilitude. The movie below is of the mating behavior of the jellyfish Carybdea sivickisi, and the first thing you’ll notice is that the scientists have set it to good old classic porn music.

The second thing you’ll notice, that I found annoying, is that they used too high a power objective to film it, so everything is jerking everywhere and none of the participants stay in the field of view for any length of time. Why is it that porn is afflicted with so many gynecological close-ups? Come on, set the mood, show us whole individuals instead of fragmented zooms of body parts.

Hawaii’s shame

This is shocking news, but not too surprising: I know a few of the people in this facility, and when I talked to them last they were deeply concerned about this possibility. The University of Hawaii is planning to shut down the Kewalo Marine Laboratory. They’re doing it so they can funnel more money into the expansion of a cancer research center, which is certainly valuable, but not at the expense of closing half of their marine facilities. This is especially shocking because heck, when students here in the cold and land-locked midwest talk to me about going into marine biology, many of them ask about Hawaii — it’s only natural that they’d imagine a tropical island would be a haven for that kind of research, and it is. It’s just that the state doesn’t support it. This is an ironic fact:

The Kewalo scientists said that Florida, also an ocean state, has 22 marine labs. “Even Georgia would have more marine labs (four) than Hawaii” if the Kewalo facility goes, said Michael Hadfield, biosciences research center faculty member and former director.

So I should tell my students that Georgia would be a better place to study marine biology? That’s nice for the South, not so nice for Hawaii.

And it’s not as if Kewalo has been unproductive — they’ve turned out some amazing work. Mark Martindale is there, as the director. The man is a Very Big Name in the field of evo-devo — go back through my evo-devo posts, and he keeps popping up everywhere. He’s working on early pattern formation in the metazoans, and his papers are indispensable in understanding early evolutionary events.

An old friend of mine, Elaine Seaver, is also there and doing fabulous work on a promising new system, the polychaete worm Capitella. If you want to know about body plan evolution, we need the kind of comparative approach she’s taking.

Write. Contact:

Gary Ostrander

Vice Chancellor for Research & Graduate Education
Hawaiʻi Hall 211
2500 Campus Road
Honolulu, HI 96822
808-956-7837

Let them know what an incredibly short-sighted decision this is, and what a failure of vision in the making. Not only does it harm the university immediately, damaging their reputation and costing them a useful facility, but think of the message it’s sending, that productive and esteemed faculty at the University of Hawaii can have their work so cavalierly dismissed and their laboratories demolished.

GFP wins Nobel Prize!

The Nobel in Chemistry this year goes to Osamu Shimomura, Martin Chalfie, and Roger Tsien for the discovery of Green Fluorescent Protein, GFP. That’s well deserved — GFP is a wonderful tool, a simple protein that fluoresces. There are lots of fluorescent compounds out there, and most of them require some kind of artificial injection or application to get them into cells — they basically allow you to determine that “a needle was stuck in here“, and also to allow us to visualize the morphology of individual cells, which is all very useful, and there’s quite an industry built around making new probes of this sort. GFP is different. It allows one to use the molecular biology of the cell to generate your green glowing compound. If you want to know when and where a particular gene of interest is expressed, for instance, you just make a construct that couples the regulatory elements of that gene to a GFP gene, and presto, where ever the gene you’re following is turned on, so is GFP, and the cell lights up like a little Christmas tree decoration. That’s powerful stuff: it gives us a tool to follow patterns of gene expression visually, in real time, in living cells.

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Wave those arms in praise of MSKGEELFTG VVPVLVELDG DVNGQKFSVS GEGEGDATYG KLTLNFICTT GKLPVPWPTL VTTFSYGVQC FSRYPDHMKQ HDFFKSAMPE GYVQERTIFY KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK MEYNYNSHNV YIMGDKPKNG IKVNFKIRHN IKDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSALSKD PNEKRDHMIL LEFVTAARIT HGMDELYK!

    1 atgagtaaag gagaagaact tttcactgga gtggtcccag ttcttgttga attagatggc 
   61 gatgttaatg ggcaaaaatt ctctgtcagt ggagagggtg aaggtgatgc aacatacgga 
  121 aaacttaccc ttaattttat ttgcactact gggaagctac ctgttccatg gccaacactt 
  181 gtcactactt tctcttatgg tgttcaatgc ttctcaagat acccagatca tatgaaacag 
  241 catgactttt tcaagagtgc catgcccgaa ggttatgtac aggaaagaac tatattttac 
  301 aaagatgacg ggaactacaa gacacgtgct gaagtcaagt ttgaaggtga tacccttgtt 
  361 aatagaatcg agttaaaagg tattgatttt aaagaagatg gaaacattct tggacacaaa 
  421 atggaataca actataactc acataatgta tacatcatgg gagacaaacc aaagaatggc 
  481 atcaaagtta acttcaaaat tagacacaac attaaagatg gaagcgttca attagcagac 
  541 cattatcaac aaaatactcc aattggcgat ggccctgtcc ttttaccaga caaccattac 
  601 ctgtccacac aatctgccct ttccaaagat cccaacgaaa agagagatca catgatcctt 
  661 cttgagtttg taacagctgc taggattaca catggcatgg atgaactata caaa

And the Nobel Prize goes to…

It looks like Alex’s predictions for the Nobel Prise this year did not come to pass — although I was thinking McCulloch and Till were likely, so I was wrong, too. The Nobel for Physiology or Medicine has just been announced, and the winners are Harald zur Hausen, for discovering that HPV causes cervical cancer, and Françoise Barré-Sinoussi and Luc Montagnier for the discovery of HIV. It’s a viral year this time around.

My human lineage

This is a very simple, lucid video of Spencer Wells talking about his work on the Genographic Project, the effort to accumulate lots of individual genetic data to map out where we all came from.

I’ve also submitted a test tube full of cheek epithelial cells to this project, and Lynn Fellman is going to be doing a DNA portrait of me. I had my Y chromosome analyzed just because my paternal ancestry was a bit murky and messy and potentially more surprising, and my mother’s family was many generations of stay-at-home Scandinavian peasantry, so I knew what to expect there. Dad turned out to be not such a great surprise, either. I have the single nucleotide polymorphism M343, which puts me in the R1b haplogroup, which is just the most common Y haplogroup in western Europe. I share a Y chromosome with a great many other fellows from England, France, the Netherlands, etc., which is where the anecdotal family history suggested we were from (family legend has it that the first American Myers in my line was a 17th or 18th century immigrant from the Netherlands). Here’s a map of where the older members of my lineage have been from: Africa (of course!) by way of a long detour through central Asia.

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Hello, many-times-great-grandpa! That’s quite the long walk your family has taken. Howdy, great big extended family! We’ll have to get together sometime and keep in touch.

If you’re interested in finding out what clump of humanity you belong to, it’s easy: you can order a $100 kit, swab out a few cheek cells (just like they do on CSI or Law & Order!), mail it back, and a few weeks later, they send you your results. It’s not very detailed — they only analyze a small number of markers — but it’s enough to get a rough picture of where your branch of the family tree lies. And for a bit more, Lynn can turn it into something lovely for your wall.

By the way, Lynn and I will be talking about the science and art of human genetics in a Cafe Scientifique session in Minneapolis in February.

That’s an old rock

Geologists have just discovered the oldest terrestrial rock yet: some badly battered bit of something called a faux-amphibolite from Northern Quebec, Canada that has been dated to 4.28 billion years ago. I’m afraid most of the paper is way above my head — lots of radioisotope measurements, discussions of the details of the local geology, etc. — but I can at least note that this means Ken Ham is wrong by a factor of over 713,000. I am impressed by both the age of the rocks and the magnitude of the error a creationist can sustain without exploding into a cloud of pink pixie dust that fades to the sound of waning calliope music.

O’Neil J, Carlson RW, Francis D, Stevenson RK (2008) Neodymium-142 Evidence for Hadean Mafic Crust. Science 321(5897):1828-1831.