Martin Chalfie: GFP and After

Chalfie is interested in sensory mechanotransduction—how are mechanical deformations of cells converted into chemical and electrical signals. Examples are touch, hearing, balance, and proprioception, and (hooray!) he references development: sidedness in mammals is defined by mechanical forces in early development. He studies this problem in C. elegans, in which 6 of 302 nerve cells detect touch. It’s easy to screen for mutants in touch pathways just by tickling animals and seeing if they move away. They’ve identified various genes, in particular a protein that’s involved in transducing touch into a cellular signal.

They’ve localized where this gene is expressed. Most of these techniques involved killing, fixing, and staining the animals. He was inspired by work of Shimomura, as described by Paul Brehm that showed that Aequorin + Ca++ + GFP produces light, and got in touch with Douglas Prasher, who was cloning GFP, and got to work making a probe that would allow him to visualize the expression of interesting genes. It was a gamble — no one knew if there were additional proteins required to turn the sequence into a glowing final product…but they discovered that they could get functional product in bacteria within a month.

They published a paper describing GFP as a new marker for gene expression, which Science disliked because of the simple title, and so they had to give it a cumbersome title for the reviewers, which got changed back for publication. They had a beautiful cover photo of a glowing neuron in the living animal.

Advantages of GFP: heritable, relatively non-invasive, small and monomeric, and visible in living tissues. Roger Tsien worked to improve the protein and produce variants that fluroesced at different wavelengths. There are currently at least 30,000 papers published that use fluroescent proteins, in all kinds of organisms, from bunnies to tobacco plants.

He showed some spectacular movies from Silverman-Gavrila of dividing cells with tubulin/GFP, and another of GFP/nuclear localization signal in which nuclei glowed as they condensed after division, and then disappeared during mitosis. Sanes and Lichtman’s brainbow work was shown. Also cute: he showed the opening sequence of the Hulk movie, which is illustrated with jellyfish fluorescence (he does not think the Hulk is a legitimate example of a human transgenic.)

Finally, he returned to his mechanoreceptor work and showed the transducing cells in the worm. One of the possibilities this opened up was visual screening for new mutants: either looking for missing or morphologically aberrant cells, or even more subtle things, like tagging expression of synaptic proteins so you can visually scan for changes in synaptic function or organization.

He had a number of questions he could address: how are mechanotransducers generated, how is touch transduced, what is the role of membrane lipids, can they identify other genes important in touch, and what turns off these genes?

They traced the genes involved in turning on the mec-3 gene; the pathway, it turned out, was also expressed in other cells, but they thought they identified other genes involved in selectively regulating touch sensitivity. One curious thing: the mec genes are transcribed in other cells that aren’t sensitive, but somehow are not translated.

They are searching for other touch genes. The touch screen misses some relevant genes because they have redundant alternatives, or are pleiotropic so other phenotypes (like lethality) obscure the effect. One technique is RNAi, and they made an interesting observation. Trying about 17000 RNAis, they discovered that 600 had interesting and specific effects, 1100 were lethal, and about 15,000 had no effect at all. The majority of genes are complete mysteries to us. They’ve developed some techniques to get selective incorporation of RNAis into just neurons of C. elegans, so they’re hoping to uncover more specific neural effects. One focus is on the integrin signaling pathway in the nervous system, which they’ve knocked out and found that it demolishes touch sensitivity — a new target!

They are now using a short-lived form of GFP that shuts down quickly, so they’ve got a sharper picture of temporal patterns of gene activity.

Chalfie’s summary:

  • Scientific progress is cumulative.

  • Students and post-docs are the lab innovators.

  • Basic research is essential. Who would have thought working on jellyfish would lead to such powerful tools?

  • All life should be studied; not just model organisms.

Chalfie is an excellent speaker and combined a lot of data with an engaging presentation.

Privileging belief

A horrible little cult in Baltimore committed an ugly crime.

…they denied a 16-month-old boy food and water because he did not say “Amen” at mealtimes. After he died, they prayed over his body for days, expecting a resurrection, then packed it into a suitcase with mothballs. They left it in a shed in Philadelphia, where it remained for a year before detectives found it last spring.

The child’s mother, Ria Ramkissoon, and others are on trial for murder, reasonably enough. Here’s the kicker, though:

Psychiatrists who evaluated Ramkissoon at the request of a judge concluded that she was not criminally insane. Her attorney, Steven Silverman, said the doctors found that her beliefs were indistinguishable from religious beliefs, in part because they were shared by those around her.

“She wasn’t delusional, because she was following a religion,” Silverman said, describing the findings of the doctors’ psychiatric evaluation.

Well. Why should the religion label excuse delusional beliefs?

Promoting a few links up top

The open thread produced a couple of interesting articles I thought worthy of highlighting.

The first is a story from Canada about the growing godless movement. It’s very positive and avoids the cheap tactic of presenting this as a scary or worrisome prospect.

Ms. Gaylor [of the Freedom From Religion Foundation], who said her group has grown from 7,000 to more than 10,000 since the fall, is not sure that the recent rash of books is winning converts to atheism, but she is certain it is emboldening those in the closet.

When Herb Silverman became a professor of mathematics at the College of Charleston in South Carolina in 1976, people would say to him: “You’re the only atheist I know,” and he would respond: ” No I’m not. You know hundreds of atheists, I’m just the only one who acknowledges they’re an atheist.”

I predict a slow, steady growth of atheism in the coming years — not because all these vocal atheists have been converting people, but because they are removing the stigma from atheism and getting people to take some pride in their freedom from faith. And what are all these atheists going to do? One of the annoying, baffling habits some people have is to dismiss the idea, because all atheists could possibly do is sit around and talk about nothing. Not true!

“Big questions have been monopolized by religious institutions,” says Justin Trottier, 24, who has a degree in engineering, comes from a secular Jewish background and is the centre’s executive director. “Atheists are just as interested in questions of meaning, purpose and beginning. Why shouldn’t we have a place where we can chat?”

See, we can talk about and do important stuff, the same as goes on in religious institutions … we just do it without larding it full of supernatural monkeypoop, or worse, elevating the monkeypoop to the status of the Most Important Issue. A secular institution should be more effective than a religious one in any significant endeavor, since it doesn’t bear the burden of commitment to dogmatic malarkey.

This other story from the LA Times is more depressing. It’s about a reporter, a fervent Christian, who joyously leapt into the religion beat, and steadily lost his faith to the incessant corruption of pedophilic priests, greedy Prosperity Christians, and faith-healing frauds. I see another goal for the godless here:

My soul, for lack of a better term, had lost faith long ago — probably around the time I stopped going to church. My brain, which had been in denial, had finally caught up.

Clearly, I saw now that belief in God, no matter how grounded, requires at some point a leap of faith. Either you have the gift of faith or you don’t. It’s not a choice. It can’t be willed into existence. And there’s no faking it if you’re honest about the state of your soul.

It’s a painful piece, and you can tell the writer is grieving for the loss of his faith — but faith is not a gift. Faith is a delusion. This is a man who should be grateful that he has opened his eyes. He’s opened them to an ugly, disillusioning world, true enough, but now he is better able to do something about it. Something far better than praying for an intervention that will never come from an entity that doesn’t exist. There should be no sorrow in casting the scales from your eyes.

Should we be happy about this?

So today we learn that Rep. Pete Stark admits to being godless.

There is only one member of Congress who is on record as not holding a god-belief.

Rep. Pete Stark (D-Calif.), a senior member of the powerful House Ways and Means Committee, Chair of the Health Subcommittee, and member of Congress since 1973, acknowledged his nontheism in response to an inquiry by the Secular Coalition for America.

Although the Constitution prohibits religious tests for public office, the Coalition’s research reveals that Rep. Stark is the first open nontheist in the history of the Congress. Recent polls show that Americans without a god-belief are, as a group, more distrusted than any other minority in America. Surveys show that the majority of Americans would not vote for an atheist for president even if he or she were the most qualified for the office.

Herb Silverman, president of the Secular Coalition for America, attributes these attitudes to the demonization of people who don’t believe in God. “The truth is,” says Silverman, “the vast majority of us follow the Golden Rule and are as likely to be good citizens, just like Rep. Stark with over 30 years of exemplary public service. The only way to counter the prejudice against nontheists is for more people to publicly identify as nontheists. Rep. Stark shows remarkable courage in being the first member of Congress to do so.”

In November, 2006 the Secular Coalition for America, a national lobby representing the interests of atheists, humanists, freethinkers, and other nontheists, announced a contest. At the time, few if any elected officials, even at the lowest level, would self-identify as a nontheist. So the Coalition offered $1,000 to the person who could identify the highest level atheist, humanist, freethinker or any other kind of nontheist currently holding elected public office in the United States.

In addition to Rep. Stark only three other elected officials agreed to do so: Terry S. Doran, president of the School Board in Berkeley, Calif.; Nancy Glista on the School Committee in Franklin, Maine; and Michael Cerone, a Town Meeting Member from Arlington, Mass.

Surveys vary in the percentage of atheists, humanists, freethinkers and other nontheists in the U.S, with about 10% (30 million people) a fair middle point. “If the number of nontheists in Congress reflected the percentage of nontheists in the population,” Lori Lipman Brown, director of the Secular Coalition, observes, “there would be 53-54 nontheistic Congress members instead of one.”

I’m a bit amused that after Stark, the next highest elected officials who aren’t afraid to admit their unbelief are three (count ’em, three) school board members scattered across the country. Is there active discrimination to exclude non-believers from the democratic process? You know there is.

Oh, and I don’t know a thing about Stark’s politics, other than that he’s a Democrat. Any of his constituents out there who want to let us know if he’s a representative we should be proud of?