A creationist at the Chicago meeting

Last week, I described the lectures I attended at the Chicago 2009 Darwin meetings (Science Life also blogged the event). Two of the talks that were highlights of the meeting for me were the discussions of stickleback evolution by David Kingsley and oldfield mouse evolution by Hopi Hoekstra — seriously, if I were half my age right now, I’d be knocking on their doors, asking if they had room for a grad student or post-doc or bottle-washer. They are using modern techniques in genetics and molecular biology to look at variation in natural populations in the wild, and working out the precise genetic changes that led to the evolution of differences in development and morphology. They are doing stuff that, back when I actually was a graduate student, would have been regarded as technically impossible; you needed model systems in the laboratory to have the depth of molecular information required to track down the molecular basis of novel morphs, and you couldn’t possibly just grab some interesting but otherwise unknown species out on a beach or a pond and work out a map and localize genetic differences between individuals. They’re doing it now, though, and making it look easy.

Then there were all the other talks in population genetics and paleontology (and the talks on history and philosophy, which I almost entirely neglected)…this was a meeting that everywhere demonstrated major advances in our understanding of evolution. Every talk was about the successes of evolutionary theory and directions to take to overcome incomplete areas of understanding; this was a wonderfully positive and promising event that should have impressed all the attendees with the quality of the work that has been done and the excitement of the potential for future research. Like I said, there were a whole bunch of people here that I want to be when I grow up.

Well, normal people would feel that way. Paul Nelson, that creationist, was also there. Nelson is a weird guy; he’s always hanging around the edges of these scientific meetings, and you’d think that after all these years of lurking, he’d actually learn something, but no…the only skill he has mastered is the art of ignoring what he doesn’t like and incorporating fragments of sentences into his armor of ignorance. It’s very sad.

I talked with Nelson briefly at a reception at the meetings, and we both agreed on the quality of Kingsley’s work — but that’s about all. Nelson thought it supported ID better than neo-Darwinian evolutionary theory. His argument was that a) all anybody ever described was loss of features, and b) a large parent population was the source of all the allelic variation in the sub-populations studied, which is what ID predicts. He didn’t mention their favorite magic word of “front-loading”, but I could see what he was thinking.

How Nelson can hang about on the fringes of the evo-devo world and not notice that what was described by modern empirical research is exactly what the evo-devo theoreticians expected is a mystery — these were results that fit beautifully what science, not the wishful voodoo of intelligent design creationism, predicts.

Both Kingsley and Hoekstra are looking at recent species, subpopulations that separated from parent populations within the last ten thousand years, and have adapted relatively rapidly to new environmental conditions. The sticklebacks are fragments of marine species that were isolated in freshwater streams and lakes, while the beach mice are parts of a widespread population of oldfield mice that are adapting to gulf coast islands. They are also working with populations that can be bred back to the root stock, that retain the ability to do genetic crosses, so of course the variation is not on the magnitude of turning fins into limbs (we need large amounts of geological time to do that; it’s the kind of work Neil Shubin would do, and unfortunately, he can’t cross Tiktaalik with Acanthostega). Complaining that the variants the real scientists are looking at aren’t the kind that the creationists want is a particularly clueless kind of whine, since the scientists are intentionally focusing on the variants that are amenable to dissection by their techniques.

The other aspect of their work that confirms evo-devo expectations is that what they’re discovering is that the genetic mechanisms behind morphological variants are changes in regulatory DNA — that what’s happening is that regulatory genes like Pitx1 or Mc1r are being switched off or on. We anticipate that a lot of morphological novelty is going to be generated by switching genes off and on, and by recombination of patterns of gene expression. Nelson and Behe are reduced to carping on the sidelines that observed variants are just the product of getting large effects by trivially flipping switches, while all the real biologists are out there in the middle of the work happily announcing that we can get large-scale morphological effects by simply flipping switches, and hey, isn’t that cool, and doesn’t that tell us a lot about the origins of evolutionary novelties? It’s not just a to-may-to/to-mah-to difference in interpretation, this is a case of the creationists wilfully and ignorantly missing the whole point of an exciting line of research.

There’s also a fundamental failure of comprehension. Creationists see loss of a feature like pelvic spines, or a reduction in pigmentation, and declare that the evolutionary evidence is “all breaking things and losing things”. Wrong. What we have here is a complete lack of understanding of developmental genetics. What we typically find are changes in the pattern of expression of developmental genes, not wholesale losses. In the stickleback, Pitx1 is still there; what’s different is that the places in the embryo where it is turned on have changed, the map of the pattern of gene expression has shifted. You cannot describe that as simply a broken gene. Similarly, in the mouse, Hoekstra showed that the expression of genes that reduce pigmentation has expanded. We’ve seen the same thing in the blind cavefish; a creationist looks at it and says it’s just broken and has lost its eyes, but the scientists look closer and see that no, the fish have actually increased gene expression and expanded the domain of a midline gene.

Just wait for the detailed analysis of jaw morphology in cichlid fishes. These animals have radically different variants in feeding structures, which is thought to be the root of their adaptability and the radiation of different forms, and I guarantee you that the creationists will ignore the morphological novelties and focus on the fact that to achieve that, some genes will be downregulated (I also guarantee you that there will be such shifts in expression). It’s “all breaking things and losing things”, after all; just like baking a cake involves breaking eggs.

I don’t know how the creationists fit known variations in the coding sequences of genes (how do you translate a single-nucleotide polymorphism into their vision of all change being a matter of losses?) into their idea that all evolution is a matter of breaking DNA, or how they can claim all novelty requires a designer when people can track the progression of morphological shifts in the tetrapod transition, for instance, across tens of millions of years. It seems to be their desperate 21st century excuse in the face of the overwhelming progression of information from 21st century biological science.

Nelson ends his skewed summary of the meeting with the comment that “It’s a heck of a lot of fun to attend a conference like this, if you don’t mind being the butt of jokes.” I’m sure. I suppose Nelson could have even more fun if he put on a dunce cap and drooled a lot, because that’s basically his role at these meetings anyway — he’s the butt of jokes because he shows up and then happily demonstrates his ignorance about what’s going on. It’s not a role I’d enjoy, but the gang at the clown college called the Discovery Institute have a slightly different perspective, I suppose.

Eric Lander—Genomics and Darwin in the 21st Century

Lander began by saying he wasn’t an evolutionist — an interestingly narrow definition of the term. He’s a fan of the research, but considers himself a biomedical geneticist, as if that was something different.

Having entire genomes of many species available for quantitative analysis is going to lead to a qualitative change in the science we can do.

He gave a pocket summary of the human genome project. Mouse genome followed, then rat and dog, and now have sequence (to varying degrees of completeness) of 44 species, out of 4600 mammals. Within Homo, there’s the hapmap project and the 1000 genomes project, so at least in us we’re going for depth and breadth of coverage.

Sequencing technology is rapidly accelerating. Exponential growth in the number of nucleotides sequenced per year. Exponentially on a log scale! We’re developing a tremendous amount of data acquisition capability. We’ll be able to address mechanisms of physiology and evolution, and learning about the particulars of history.

Lander focuses on genome-wide studies. Evolutionary conservation is a guide to extracting information from the genome. Showed synteny diagrams of mouse and human, and discussed analyses that allow you to identify highly conserved pieces, bits that might have significant function.

Number of genes is low, 20,500. Early higher numbers he admitted were inflated a bit by prior expectations; when they had a good estimate of 30,000, they decided to waffle and call it 30-40,000.

If genes are counted by homology, how do we know there aren’t many more genes that don’t have homology. If that were case, the number of genes in humans would still be close to the estimated numbers in chimp and macacque.

There are also well-conserved non-coding regions in DNA. 5% of the genome is under selection: coding 1.2%, non-coding 3.8%. Found 200 gene poor regions that contain key developmental genes, and many of the conserved non-coding regions are associated with them.

Long intergenic non-coding DNA: pretty much all of the genome is transcribed, but the vast majority of this is simply noise. There about a dozen regions known where transcription of non-coding DNA seem to be conserved evolutionarily, and have some function: they be transcriptional repressors.

Mechanism of evolutionary innovation in coding genes: examples of whole genome duplication, divergence and loss, all of which can be demonstrated by comparison with an outgroup. Outgroup comparisons can demonstrate whole genome duplications.

Mechanisms of innovation in non-coding regions: about 84% of conserved DNA is shared between marsupials and placentals, suggesting that about 16% of changes are novel. About 15% of placental specific CNEs are derived from transposons.

With 29 mammalian genomes compared, they have 4 substitutions per site, a detection limit of about 10 bp, and 2.8 million features detected. We have a lot of detail that can be extracted from the data sets.

We can find evidence of positive selection. Using chicken as an outgroup, we can identify genes that have undergone major changes in humans but not chimps. Comparision across 29 mammals shows even more. What we’re finding is that these evolutionarily significant genes are enriched for developmental genes.

Analysis within the human species shows that we are a young population that expanded rapidly from a small initial population of 10,000 individuals. Can now screen for associations between single-nucleotide polymorphisms and disease. We can now screen for 2 million polymorphisms in a single pass on a chip. Have now identified 500 loci associated with common traits. Most have very modest effects and only contribute to a small part of the heritability of the trait. Where is all the missing heritability? Missing loci, missing alleles, and non-additive effects of loci.

Positive selection in human history: can use hapmap data to find 300 regions with outlier distributions that suggest they have been the target of selection. Combining statistical tests narrows the specificity of identification to a size roughly equal to a single gene making it possible to identify specific genes with an interesting selective history (work in press by Pardis Sabeti). There are themes: many of these genes are involved in resisting infectious disease.

Genomics is experiencing an explosion of data that represents a huge opportunity for future discovery.

How badly can a paper summary be botched?

Perhaps you are a scientist. And perhaps you have wondered how badly the popular press could possibly mangle your research. Wonder no more: we have discovered a new maximum.

Behold this research summary in The Daily Galaxy, and be amazed!

It’s about a paper in the ACS Journal of Physical Chemistry B. It’s straightforward physical chemistry using some cool tools to image the formation of double helices of DNA: it’s simply addressing the question of how complementary strands align themselves in solution. It’s physical chemistry, OK? It’s about tiny molecular interactions…until the Daily Galaxy gets ahold of it. Now it’s about how DNA uses telepathy.

DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.

Scientists are reporting evidence that contrary to our current beliefs about what is possible, intact double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. Somehow they are able to identify one another, and the tiny bits of genetic material tend to congregate with similar DNA. The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.

In the study, scientists observed the behavior of fluorescently tagged DNA strands placed in water that contained no proteins or other material that could interfere with the experiment. Strands with identical nucleotide sequences were about twice as likely to gather together as DNA strands with different sequences. No one knows how individual DNA strands could possibly be communicating in this way, yet somehow they do. The “telepathic” effect is a source of wonder and amazement for scientists.

Cue the theremins, everyone, and bring on the reanimated corpse of Rod Serling to narrate this sucker. Audience, say “OOOOOoooooOOOOOOOOooOOH!”

Oh, wait. Read the actual paper, first. It turns out that not only are the scientists not mystified, but they provide a reasonable explanation for the phenomenon, and go on to give some alternatives, even. None of them involve molecular telepathy. They actually are amazed at the ability of these molecules to align…at distances of one whole nanometer!

Pay especially careful to the first sentence of the following paragraph. If you are a journalist writing a summary of a paper, claiming that it says no one knows how the two molecules recognize each other, you should probably read more closely a paragraph that begins, “We hypothesize that the origin of this recognition may be as follows.” It’s a clue that an explanation will follow.

We hypothesize that the origin of this recognition may be as follows. In-register alignment of phosphate strands with grooves on opposing DNA minimizes unfavorable electrostatic interactions between the negatively charged phosphates and maximizes favorable interactions of phosphates with bound counterions. DNAs with identical sequences will have the same structure and will stay in register over any juxtaposition length. Nonhomologous DNAs will have uncorrelated sequence-dependent variations in the local pitch that will disrupt the register over large juxtaposition length. The register may be restored at the expense of torsional deformation, but the deformation cost will still make juxtaposition of nonhomologous DNAs unfavorable. The sequence recognition energy, calculated from the corresponding theory is consistent with the observed segregation within the existing uncertainties in the theoretical and experimental parameters. This energy is ˜1 kT under the conditions utilized for the present study, but it is predicted to be significantly amplified, for example, at closer separations, at lower ionic strength, and in the presence of DNA condensing counterions.

So, their preferred explanation is that there are electrostatic interactions between the molecules that favor pairs that fit together well. Not telepathy. As cautious investigators, they also suggest some alternative explanations; perhaps telepathy will appear here? Or maybe elves?

Presently, we cannot exclude other mechanisms for the observed segregation. For instance, sequence-dependent bending of double helices may also lead to homology recognition by affecting the strand-groove register of two DNA molecules in juxtaposition. The juxtaposition of bent, nonhomologous DNAs may also be less energetically favorable under osmotic stress, since it may reduce the packing density of spherulites. In addition, formation of local single-stranded bubbles and base flipping may cause transient cross-hybridization between the molecules, as proposed to explain Mg2+ induced self-assembly of DNA fragments with the same sequence and length. We consider it to be rather unlikely in this instance, since the probability of bubble formation in unstressed linear DNA of the studied length is very small in contrast to the case where topological strain is relieved by bubble formation in small circular DNA molecules. Furthermore, bubble formation would distort the cholesteric order of spherulites and we see no evidence of this in spherulites composed of a single type of DNA molecule.

I’m so disappointed. Telepathy isn’t mentioned once in the whole danged paper, and there aren’t even tiny diaphanous fairies tugging at the molecules. And no, the Intelligent Designer doesn’t appear, either.

Baldwin GS, Brooks NJ, Robson RE, Wynveen A, Goldar A, Leikin S, Seddon JM, Kornyshev AA (2008) DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment. J. Phys. Chem. B 112(4):1060-1064.

Gene regulatory networks and conserved noncoding elements


We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can’t see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.

[Read more…]

The future is roaring your way…

Edge hosted an amazing session that described the looming future of biology — this is for the real futurists. It featured George Church and Craig Venter talking about synthetic genomics — how we’re building new organisms right now and with presentiments for radical prospects in the future.

Brace yourself. There are six hours of video there; I’ve only started wading into it, but what I’ve seen so far also looks like a lot of material that will be very useful for inspiring students about the future of their field. There is also a downloadable book (which is a dead link right now, but I’m sure will be fixed soon) if you don’t want to watch the talks…but the talks are pretty darned good. Somehow, I’m going to have to make time to soak these up. Here’s the overview of the six sessions:

  • Dreams & Nightmares
    Overview, safety/security/policy, nanotechnology, molecular manufacturing

  • Smaller than life
    What is life, origins, in vitro synthetic life, mirror life, computing and DNA, computing with DNA

  • Engineering microbes
    Bio-petrochemicals & pharmaceuticals, accelerated lab evolution

  • Engineering humans
    Electronic-biological interfaces, bioengineered personal stem cells, humanized mice, bringing back extinct species

  • The sorceror
    The diversity of life, constructing life, from Darwin to new fuels

  • The near future, big questions
    Terraforming earth, creating extraterrestrials, the singularity, human nature

There goes your weekend.

The evolution of Hedgehog


PLoS has recently published a highly speculative but very interesting paper on how a particular signaling pathway, the Hedgehog pathway, might have evolved. It’s at a fairly early stage in hypothesis testing, which is one of the things that makes it interesting — usually all you see published is the product of a great deal of data collection and experiment and testing, which means the scientific literature gives a somewhat skewed view of the process of science, letting the outsider mainly see work that has been hammered and polished, while hiding the rougher drafts that would better allow us to see how the story started and was built. It’s informative in particular for those who follow the creationist “literature”, which often crudely apes the products of actual working science, but lacks the sound methodological underpinnings. In particular, creationism completely misses the process of poking at the real world to develop ideas, since they begin with their conclusion.

So take this description as a work in progress — we’re seeing the dynamic of building up a good working model. As usual, it starts on a sound foundation of confirmed, known evidence, makes a reasonably hypothesis on the basis of the facts, and then proposes a series of research avenues with predicted results that would confirm the idea.

[Read more…]

What caused the Cambrian explosion? MicroRNA!


No, not really — my title is a bit of a sensationalistic exploitation of the thesis of a paper by Peterson, Dietrich, and McPeek, but I can buy into their idea that microRNAs (miRNAs) may have contributed to the pattern of metazoan phylogenies we see now. It’s actually a thought-provoking concept, especially to someone who favors the evo-devo view of animal evolution. And actually, the question it answers is why we haven’t had thousands of Cambrian explosions.

In case you haven’t been keeping up, miRNAs are a hot topic in molecular genetics: they are short (21-23 nucleotides) pieces of single stranded RNA that are not translated into protein, but have their effect by binding to other strands of messenger RNA (mRNA) to which they complement, effectively down-regulating expression of that messenger. They play an important role in regulating the levels of expression of other genes.

One role for miRNAs seems to be to act as a kind of biological buffer, working to limit the range of effective message that can be operating in the cell at any one time. Some experiments that have knocked out specific miRNAs have had a very interesting effect: the range of expressed phenotypes for the targeted message gene increases. The presence or absence of miRNA doesn’t actually generate a novel phenotype, it simply fine-tunes what other genes do — and without miRNA, some genes become sloppy in their expression.

This talk of buffering expression immediately swivels a developmental biologist’s mind to another term: canalization. Canalization is a process that leads organisms to produce similar phenotypes despite variations in genotype or the environment (within limits, of course). Development is a fairly robust process that overcomes genetic variations and external events to yield a moderately consistent outcome — I can raise fish embryos at 20°C or at 30°C, and despite differences in the overall rate of growth, the resultant adult fish are indistinguishable. This is also true of populations in evolution: stasis is the norm, morphologies don’t swing too widely generation after generation, but still, we can get some rapid (geologically speaking) shifts, as if forms are switching between a couple of stable nodes of attraction.

Where the Cambrian comes into this is that it is the greatest example of a flowering of new forms, which then all began diverging down different evolutionary tracks. The curious thing isn’t their appearance — there is evidence of a diversity of forms before the Cambrian, bacteria had been flourishing for a few billion years, etc., and what happened 500 million years ago is that the forms became visible in the fossil record with the evolution of hard body parts — but that these phyla established body plans that they were then locked into, to varying degrees, right up to the modern day. What the authors are proposing is that miRNAs might be part of the explanation for why these lineages were subsequently channeled into discrete morphological pathways, each distinct from the other as chordates and arthropods and echinoderms and molluscs.

[Read more…]

Roger Y. Tsien: Building and Breeding Molecules to Spy on Cells, Tumors, and Organisms

The difference between biology and chemistry: biologists ask how natural systems and molecules work, while chemistry wants to know how to artificially re-synthesize natural biomolecules. Tsien favors a synthetic approach, asking hwo to build new molecules that will perform amusing and useful functions in biology. He compares it to architecture on a molecular scale that is also a rigorous test of one’s understanding of molecular function.

He thinks biology has the most interesting grand questions in all of science (hooray!). He also likes pretty colors. However, he thinks that interdisciplinary barriers prevent most biologists from knowing how to manipulate molecules other than nucleotides and proteins. Anyone who knows how to make non-linear molecules has an advantage.

His first target was intracellular Ca++, which we all know is central to cellular signaling. He gave a quick overview of Ca++ properties and functions, as a rationale for why he began looking at Ca++ indicators like aequorin. He started looking for something new, started with something selective for calcium, the calcium chelator EGTA, which lacks any chromophore. One way would be to add benzene rings (chromophores) to EGTA, which led to BAPTA, basically EGTA with two benzene rings. It has high calcium sensitivity and did exhibit a color shift, but a poor one. This work led to Fura-2 synthesis, in which you can still see the EGTA ancestor, but has a much more complex set of rings attached to it. Fura-2 requires microinjection, which Tsien wasn’t good at, so he synthesized a protected form of the molecule with a methyl ester protecting group that would be stripped by enzymes in the cell.

He showed a gorgeous image of the Ca++ wave in sea urchin fertilization, visualized with pseudo-colored images of calcium concentration visualized with Fura-2.

Next step: Tsien wanted to visualize cAMP, an important second messenger in cell processes. They needed a non-destructive way to assay the dynamics of cAMP, which is present at very low concentration in the presence of many other nucleotides. The idea again was to find a specific binding agent and coupling it to a chromophore. He chose to use a specific PKA subunit that binds to cAMP, and use fluorescence resonance with a pair of adjacent chromophores. It worked, and they built proteins with rhodamine and fluorescein that did the job.

They wanted a general means to fluorescently label designated proteins. This led to the discovery of Douglas Prasher’s work on cloning GFP.

What was wrong with wild-type GFP? It’s main excitation was at 395nm (UV), and only minor excitation peak at 475 (blue). We don’t like to zap cells with UV. He puzzled out which components of the molecule were responsible for particular peaks in the spectrum (which he got wrong), but by empirically juggling in different amino acids, he came up with a variant that emphasized suitable peaks in the spectrum. This work was done without the aid of knowing the 3D structure.

They worked out the crystal structure, and then with rational design, made more variants with different colors. The work was rejected by Science for amusing reasons: reviewers didn’t understand the significance. They got it published by sending a brief note to Science that announced the imminent publication of the crystal structure of wild-type GFP in Nature.

Tsien wanted to make a red version. A Russion group found a red GFP variant in a coral, which they then analyzed and found the structure. This work has led to lots of fluroescent proteins with colors from blue to red.

Problems: Sometimes FPs are too big, the excitation wavelengths are hard to get through mammalian tissues, and a few others I was too slow to get down. Darn.

They are now developing an infrared fluorescent protein based on biliverdin, and are also studying the role of proteases in cancer. They are using polycationic proteins sequences as tools to transport payload proteins into cells, with some clever tricks to regulate accessibility and make it chemically triggerable by enzymes present in tumors. They have a probe that selectively labels tumor cells, which can be a very useful guide for surgical removal of tumors. He also combines it with in vivo labeling of nerves, which surgeons don’t want to cut, making it a way to color-code living tissue for tumor resection, a technique called molecular fluorescence imaging guidance, MFIG.

This was another excellent talk — Tsien has an entertaining sense of humor.

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.