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.

i-3e2d5a2a71247b754798265bf82dda3e-squid.gif

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

I need to take a shower after reading that

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Occasionally, John Derbyshire gets kudos from the pro-science side of the national snarl because he at least manages to recognize that Intelligent Design creationism is a load of lies and pseudoscience. I’ve been less than thrilled with the guy; he’s generally a creepy fellow who only advocates science as a prop to his bizarre ideological fantasies. The latest example: he opposes Obama because he will destroy the biological sciences. Why, you might ask? It’s a peculiar assertion, since virtually every biologist I know considers the Republican party to have been a disaster for American science, and like Obama’s positions on science policy. Just the fact that he’s willing to encourage stem cell research is a major step forward.

The reason Derbyshire predicts Obama will stop science cold is that the presidential candidate is a black man who dislikes the idea that modern genetics will demonstrate the inferiority of certain races.

To support his claim, he babbles approvingly about Herrnstein and Murray’s awful book, The Bell Curve, and cites a “genomics researcher” who must remain anonymous because the cultural Marxists who dominate the research industry will destroy him…unfortunately, he uses a pseudonym familiar to me — “Godless Capitalist” — and I know his internet ravings well. He’s a garden-variety racist who misuses genetics as window-dressing for his delusions. Just to give you an idea of how repugnant and stupid this guy is, here’s a little anecdote told by Derbyshire that tells you how clueless Derbyshire is, and how vilely misogynist and bigoted “Godless Capitalist” is:

When “Godless” was helping me get up to speed on this stuff, I asked him at one point: “What’s the difference between a geneticist and a genomicist?” He gave a very cute answer: “Geneticists are female, genomicists are male.” Asked to elaborate, he offered this: “Imagine you are walking down a corridor in a research institute, looking in through the glass panels in doors. In one lab you see a young woman of nontrivial attractiveness carefully adding drops to a Petri dish from a pipette. That’s a geneticist. A couple of doors along you look into another lab and there are two young guys arguing about some long string of numbers displayed on a computer screen. Those are genomicists …”

I guess this guy never heard of Pardis Sabeti or Anne Carpenter or Dannie Durand or any of a bunch of other female genomics researchers I can think of. Or the even larger number of male geneticists out there. And why does attractiveness even come into this?

That’s a rhetorical question. It’s because these happy chatting bigots are always judging ideas by superficial appearances, by sex or skin color or racial and sexual stereotypes.

Obama vs. Cranky Grampa

We have another debate coming up shortly, so here’s an open thread for you all to chatter on…if the software lets you.

There will be no drinking games allowed that encourage alcohol consumption every time POW is mentioned.

<sigh> If ever I hear the words “my friends” again, I shall gag.

Defining moment for me was when McCain insisted that Obama was dangerous because he would speak too loudly (while later castigating him for advocating diplomacy), and Obama came back to point out that McCain was the one singing “bomb bomb bomb, bomb Iran”. In other words, McCain was a desperate fraud while Obama was calm and well-spoken.

Although I also felt Obama was thin on specifics and rich in politician-speak. He didn’t thrill me, but he was solidly better than his opponent.

Oh, yeah…and when McCain called Obama “that one”. That was condescending and creepy.

Site problems

Scienceblogs is experiencing some technical difficulties right now: the guts of the machine are being very recalcitrant and generating time-out errors all over the place. Please be patient and heed the message when making comments: getting an error when posting does not necessarily mean the comment did not get posted. Most often, it just means that the MovableType software has gotten very, very stupid.

And if you think you’re having problems with comments, you can’t imagine how bad it is for us trying to post articles. I just tried to create a new entry, and went off to a doctor’s appointment while waiting for the window to open.

Very peculiar

I’ve read Steve Jones’ books and enjoyed them — so I’m really baffled by this bizarre report of a talk he gave. It’s either a massive example of misreporting, or Jones has a solid grip on everyone’s ankles and he’s straining to pull our legs right off.

He claims human evolution is over. The reason? Because not enough fathers over 35 are having children. That’s bad because mutations are the source of evolutionary novelty, and older fathers are more likely to have accumulated errors in the replication of sperm, and therefore pass on more mutations.

This is because cell divisions in males increase with age. “Every time there is a cell division, there is a chance of a mistake, a mutation, an error,” he said. “For a 29-year old father [the mean age of reproduction in the West] there are around 300 divisions between the sperm that made him and the one he passes on – each one with an opportunity to make mistakes.

“For a 50-year-old father, the figure is well over a thousand. A drop in the number of older fathers will thus have a major effect on the rate of mutation.”

This is true, but it makes no sense. It’s not as if younger fathers produce no mutations — they generate plenty. It’s a difference in degree, nothing more, so we still have plenty of new mutations percolating into the population. And of course, over most of human history parents have been relatively young, since you couldn’t count on living to the age of 35.

And then there’s this odd argument.

Another factor is the weakening of natural selection. “In ancient times half our children would have died by the age of 20. Now, in the Western world, 98 per cent of them are surviving to 21.”

That makes even less sense. Natural selection is going to eliminate variants; by reducing its effects, we permit more mutations to persist in the population. One moment he’s complaining that fewer mutations are being produced, the next he’s complaining that the mutants are thriving. Which is it?

I’m thinking Jones must be making some colossal joke here, or maybe he’s testing his audience to see how much illogic and absurdity they will accept. That’s the only way I can explain these strange claims.

I see that Larry Moran has just thrown up his hands in exasperation at all the errors.

Grrrr

My email was just beginning to calm down, and now Bill Donohue rants again. He names me and fsmdude, and since people can’t find a mailing address for a guy named “fsmdude”, all these cranky little old Catholic ladies are sending me their shrill denunciations of youtube videos, instead.

Oh, and Bully Billy has conveniently forgotten the history already: “It was a professor from the University of Minnesota, Morris campus, Paul Z. Myers, who started the war on the Eucharist this past summer by intentionally desecrating a consecrated Host.” I guess he never ever called for the expulsion and arrest of a student for violating a Catholic sacrament now.

Here comes the bride

Remember Rachel Bird and Gideon Codding, the spoiled, petulant little whiners who wanted their state issued marriage license to call them “bride and groom”? The ones who were being used as a wingnut cause celebre to argue that gender neutrality really does hurt heterosexual marriages?

Bad news. They won. California caved and changed the wording on the licenses.

Now gay couples getting married in California will have to get their revenge: they should cheerfully appropriate the terms bride and groom, too. Rachel Bird can call herself a bride (she could all along, of course), but so can the biggest, butchest, bristly-bearded gay leatherman with a biker mustache…and he should be able to get state recognition of his status as a bride.

It’s only fair, after all.