Osamu Shimomura: Chemistry of Bioluminescence

Bioluminescence is common, especially in marine organisms. Shimomura classified thes into a couple of types: luciferain, photoprotein, and an undefined “other”. Luciferin requires an enzymatic (luciferase) reaction, and luminescence is proportional to the concentration of the substrate. The photoprotein type requires a single molecule — aequorin, symplectin, pholasin, etc.

He summarized how D-Luciferin is converted to Oxyluciferin in the presence of O2 and ATP, catalyzed by luciferase, to produce light, either red light in acidic media or yellow green in alkaline media. There is also a variant of this reaction called coelenterazine-luciferase luminaescence, found in many marine organisms, like Periphylla, a ellyfish, and Chiroteuthis, a squid. Coelenterazine is converted to coelenteramide in the presence of O2 to produce light and CO2.

Another organism is Cyprodana, a crustacean that uses a luciferin variant — produces a very pretty blue glow.

Luminiscent bacteria convert luciferin into a fattye acid, FMN, to produce light, which is also luciferase-catalyzed. Luciferase seems to be popping up all over the place — unfortunately, Shimomura doesn’t talk much at all about variations in the enzyme, but is more focused on giving us the chemical intermediates produced in the reaction. Typical chemist!

This is especially unfortunate since the luciferase reaction in different organisms seems to produce very different reaction products…it’s getting me very curious about how these different forms of the protein must differ to be yielding such different outcomes, all only similar in that they also produce light as a byproduct. And then we see that some very different phyla, such as krill and dinoflagellates, use nearly identical reactions.

Photoproteins: he talks about Aequorea aequorea, which produces green light with a protein called aequorin that binds a complex molecule that resembles coelenterazine, that undergoes a conformational change in the presence of calcium ions to produce green light. If GFP is used, it produces green light.

A squid, Symplectoteuthis, converts dehydrocoelenterazine to symplectin which then produces light.

Then he switches to talking about fungal biolominescence in Mycena and Panellus, mushrooms that glow green. The precursor is decanoylpanal is conferted to luciferin, which produces light in the presence of superoxides, O2, and tetradecanoylcholine. The reaction can take place in the absence of any enzyme.

Shimomura is not exactly a dynamic speaker — he basically just read off his list of reactions — but at least he had lots of pretty pictures of glowing organisms. If only he’d said something about the relationships and evolutionary differences between them all!

Warming up for the big meeting

It’s another exciting day of exciting lectures, I hope. I know that this morning was the most anticipated one on my dance card; here’s what we’re looking forward to.

Osamu Shimomura: Chemistry of Bioluminescence

Martin Chalfie: GFP and After

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

Richard Royce Schrock: Recent Advances in Olefin Metathesis Catalyzed by Molybdenum and Tungsten Alkylidene Complexes

Werner Arber: Molecular Darwinism

OK, I confess, Schrock’s lecture won’t be my cup of tea, and I have no idea what his title says, but the rest sound fun, and the last one sounds controversial. I’ll be back in a few hours with some short summaries.

I was wondering about that

I received Chris Mooney’s last two books as review copies, before the simple folk could get theirs, and I also gave them positive (and sincere!) reviews. I’d noticed that he’s got a new book out, but strangely, I hadn’t been sent a copy this time. I was wondering what was up with that, but now Ophelia Benson has read part of the book, and all is explained. He spends part of one chapter singling me out for criticism! Gosh, I guess he felt he wouldn’t get a friendly review this time.

The focus of his ire? Crackergate. He regards destroying a sacred symbol to be inflammatory and obnoxious, completely ignoring the insanity it exposed. That insanity — and I am not using that word casually — is what Mooney thinks the spokespeople for science in our country ought to treat deferentially. Here’s why he thinks we need to do that:

America is a very religious nation, and if forced to choose between faith and science, vast numbers of Americans will select the former. The New Atheists err in insisting that such a choice needs to be made. Atheism is not the logically inevitable outcome of scientific reasoning…A great many scientists believe in God with no sense of internal contradiction…[pp 97-98]

Ah, yes, the policy of cowardice. We are weak, and the loons are numerous and strong, and therefore we must avoid telling them the truth. If the masses prefer their silly religion to science, well then, we shall give them a neutered science, a weak science, an inoffensive science that does not challenge anyone’s beliefs.

If atheism is not the logical outcome of scientific reasoning, then let us pretend that gods that turn into a cracker that cures you of sin is logical and unquestionable and harmless…oh, wait, let’s pretend that belief doesn’t exist, and doesn’t poison minds. We’ll blame the American problem of unreason on the atheists, instead.

Sheril Kirshenbaum assures me that I will be receiving a review copy of their book; I’m not being intentionally snubbed, it is merely a matter of timing, and the review copies are only now being sent out. I look forward to it with grim anticipation. I am hoping that the rest of the book isn’t as awful as chapter 8, or I’ll have to be brutal.

Argentina takes over the world!

I am in awe — they did it without anyone noticing. They just infiltrated nations all around the planet, smuggling in individuals to form vast new colonies of billions, all loyal to the overlords back home. Of course, these are very, very short Argentinians, which made them harder to notice: they’re all ants.

In Europe, one vast colony of Argentine ants is thought to stretch for 6,000km (3,700 miles) along the Mediterranean coast, while another in the US, known as the ‘Californian large’, extends over 900km (560 miles) along the coast of California. A third huge colony exists on the west coast of Japan.

While ants are usually highly territorial, those living within each super-colony are tolerant of one another, even if they live tens or hundreds of kilometres apart. Each super-colony, however, was thought to be quite distinct.

But it now appears that billions of Argentine ants around the world all actually belong to one single global mega-colony.

You better start practicing your tango is you hope to get along with our new arthropod overlords.

wednesday morning at Lindau, part 2

This morning was a long session broken into two big chunks, and I’m afraid it was too much for me — my recent weird sleep patterns are catching up with me, which didn’t help at all in staying alert.

Robert Huber: Intracellular protein degradation and its control

This talk was a disaster. Not because it wasn’t good, because it was; lots of fine, detailed science on the regulation of proteases by various mechanisms, with a discussion of the structure and function of proteasomes, accompanied by beautiful mandalas of protein structure. No, the problem was that this listener’s jet lag has been causing some wild precession of my internal clocks, and a quarter of the way through this talk all systems were shutting down while announcing that it was the middle of the night, and I really couldn’t cope. I’m going to have to look up some of his papers when I get home, though.

Walter Kohn: An Earth Powered Predominantly by Solar and Wind Energy

Kohn has made a documentary to illustrate the power of solar energy. It was very basic, a bit silly — John Cleese narrates it — but might be useful in educating the pubic. He showed excerpts from it, and while it was nice, it didn’t fire me up.

Peter Agre: Canoeing in the Arctic, a Scientist´s Perspective

This was a bit strange. We’ve had all these science talks on global warming, so Agre decided to just show us what we stand to lose, and showed us photos of his vacations on canoeing trips in Canada and Alaska. They were gorgeous photos, but please don’t show me your photo album when I’m crashing hard.

I think my new and revised plan is to take a nap this afternoon and try to recharge a bit. I really must be alert for tomorrow’s session with Shimomura, Chalfie, and Tsien, which are the talks I was most anticipating. There’s also a curious talk by Werner Arber on something called Molecular Darwinism which has my skeptical genes tingling; I’ve got to see what kinds of evidence he provides for that. So brain must not melt down now.

Wednesday morning at Lindau

I’m here for another long session of talks. Unfortunately, this is Big Chemistry day, and I’m struggling to keep up with the unfamiliar. I need more biology for it all to make sense!

Rudolph Marcus: From ‘On Water’ and enzyme caalysis to single molecules and quantum dots. Theory and experiment.

I was afraid of this. This Lindau conference has a primary focus on chemistry, and I am not a chemist…and I just knew there would be a talk or two at which I would be all at sea, and that was the case in Marcus’s talk, which was all hardcore chemistry. I got the general gist — he’s making an argument that you need both a solid grounding in theory in order to carry out computational chemistry, which seemed fairly obvious to me — but I confess that his discussion of the details of on-water catalysis, single molecule enzyme catalysis, and quantum dots lost me, through no fault of his. I don’t have the background to follow the context of the discussion.

Kurt Wüthrich: Structural genomics — exploring the protein universe

This was more of that tricky chemistry stuff, but at least it was related to biology. Wüthrich studies 3D protein structures, specializing in using NMR of proteins in solution. He fave a little background, and talked especially about his particular interest in hemoglobin, an interest that continues — he currently works at catching EPO doping in athletes. The more interesting part of the work is his current contributions to analyzing the structure of proteins in the genome. He made the point that there are currently over 6 million gene sequences tucked away in databases, but we know the the 3D structure of only about 50,000 of them. He’s part of a very large research consortium that is trying to fill in the gaps with high throughput, automated techniques.

Harold Kroto: Science, society and sustainability

If you’ve ever heard a Kroto talk, you know it is pretty much indescribable.

He did present all of chemistry in 30 seconds, but much of it was about about science education, science’s role in society, and how science is going to be necessary to save the world. There was a good strong bit of promotion of atheism (he’s one of us!), and an amusing tour of the Creation “Museum”, which he visited recently. All I can recommend is that you keep an eye on the Lindau site — they will make the lectures available online at some time.

Old fossil “disproves” Darwin!

The old fossil is Pat Buchanan, who has published a freakishly antiquated diatribe against Darwin. It’s extremely old school — he uses arguments straight out of 1960s era “scientific creationism”, trying to tar Darwin with guilt by association with Karl Marx and Adolf Hitler. He is apparently inspired by a “splendid little book,” The End of Darwinism: And How a Flawed and Disastrous Theory Was Stolen and Sold, by a creationist crank named Eugene G. Windchy. You can get an idea of Windchy’s level of scholarship by this quote:

That Darwinism has proven “disastrous theory” is indisputable.

“Karl Marx loved Darwinism,” writes Windchy. “To him, survival of the fittest as the source of progress justified violence in bringing about social and political change, in other words, the revolution.”

“Darwin suits my purpose,” Marx wrote.

John Lynch has rebutted this claim; I rather doubt that Marx could love someone as bourgeois as Darwin, a prosperous landowner and investor, a fellow who thought his greatest success in life was his talent as a businessman, and I can be fairly confident that any affection would not have been returned. And please, don’t even mention the false claim that Marx wanted to dedicate Das Kapital to Darwin.

It’s not enough to link Darwin to Marx; Windchy also has to turn Hitler into a committed Darwinist. You’d think he’d stop to marvel at the idea that Darwin could have inspired two such antagonistic philosophies, but Windchy and Buchanan aren’t quite that thoughtful.

Darwin suited Adolf Hitler’s purposes, too.

“Although born to a Catholic family Hitler become a hard-eyed Darwinist who saw life as a constant struggle between the strong and the weak. His Darwinism was so extreme that he thought it would have been better for the world if the Muslims had won the eighth century battle of Tours, which stopped the Arabs’ advance into France. Had the Christians lost, (Hitler) reasoned, Germanic people would have acquired a more warlike creed and, because of their natural superiority, would have become the leaders of an Islamic empire.”

Charles Darwin also suited the purpose of the eugenicists and Herbert Spencer, who preached a survival-of-the-fittest social Darwinism to robber baron industrialists exploiting 19th-century immigrants.

For being a “hard-eyed Darwinist”, Hitler certainly seems to have failed to make much use of the theory. Read Mein Kampf and you will find nothing about Darwin or evolution, but you will find much about God. And don’t his strange notions about an Aryan Islamic empire simply mark Hitler as a crazy crackpot, and say nothing at all about Darwin?

They do make some outrageous accusations against Darwin: he was a thief and a liar who stole his whole theory from Wallace.

Darwin, he demonstrates, stole his theory from Alfred Wallace, who had sent him a “completed formal paper on evolution by natural selection.”

“All my originality … will be smashed,” wailed Darwin when he got Wallace’s manuscript.

Unfortunately for their thesis, Darwin’s writings are preserved to an amazing degree — the history of his idea can be traced almost to the day. We know that he was putting together an outline of his theory within a few years of returning from the voyage of the Beagle; we have an early draft of his thesis written in 1842, well before the contact with Wallace; we have his correspondence where he bounced these ideas off his colleagues. He didn’t steal his theory at all, but had it well formulated before Wallace wrote his fateful letter, triggering him to finally publish.

You only have to read Wallace’s own gracious account of his interactions with Darwin to see how false Windchy’s claims are.

In conclusion I would Only wish to add, that my connection with Darwin and his great work has helped to secure for my own writings on the same questions a full recognition by the press and the public; while my share in the origination and establishment of the theory of Natural Selection has usually been exaggerated. The one great result which I claim for my paper of 1858 is that it compelled Darwin to write and publish his Origin of Species without further delay. The reception of that work, and its effect upon the whole scientific world, prove that it appeared at the right moment; and it is probable that its influence would have been less widespread had it been delayed several years, and had then appeared, as he intended, in several bulky volumes embodying the whole mass of facts he had collected in its support. Such a work would have appealed to the initiated few only, whereas the smaller volume actually written was read and understood by the educated classes throughout the civilised world.

There’s another case where Windchy/Buchanan accuse Darwin of lying.

Darwin also lied in “The Origin of Species” about believing in a Creator. By 1859, he was a confirmed agnostic and so admitted in his posthumous autobiography, which was censored by his family.

He doesn’t claim to believe in a Creator in the Origin. There is a brief mention of the possibility of a Creator initiating the universe in later editions of the book, but it’s more compatible with a deistic view than anything. He was an unbeliever in any specific religious doctrine, but that does not make him at all hypocritical to have considered the possibility of a creator beginning the whole process.

How much more can Buchanan get wrong? How about everything.

Darwin’s examples of natural selection — such as the giraffe acquiring its long neck to reach ever higher into the trees for the leaves upon which it fed to survive — have been debunked. Giraffes eat grass and bushes. And if, as Darwin claimed, inches meant life or death, how did female giraffes, two or three feet shorter, survive?

Like most animals, they’ll eat whatever is physiologically advantageous…but they prefer the leaves and shoots of acacia trees, where a long neck to reach the branches is advantageous. If you actually read the Origin, Darwin proposes several advantages of the long neck: for feeding, but also for observing predators, for combat, and as part of the defensive strategy of growing to large body size, and he uses the giraffe as an example of a general principle: “The preservation of each species can rarely be determined by any one advantage, but by the union of all, great and small.”

None of this has been debunked.

All Buchanan can do is a standard Gish Gallop, next bringing up canards like Piltdown Man, Nebraska Man, and a typically distorted version of punctuated equilibrium. It’s quite a performance, and it really takes a lot of work to distill stupid down to something quite as concentrated as what Buchanan presents.

This man actually ran for president? There are times I have to stand appalled at the lack of discrimination in our political process.

Irwin Neher: Chemistry helps neuroscience: the use of caged compounds and indicator dyes for the study of neurotransmitter release

Ah, a solid science talk. It wasn’t bad, except that it was very basic—maybe if I were a real journalist instead of a fake journalist I would have appreciated it more, but as it was, it was a nice overview of some common ideas in neuroscience, with some discussion of pretty new tools on top.

He started with a little history to outline what we know, with Ramon Y Cajal showing that the brain is made up of network of neurons (which we now know to be approxiamately 1012 neurons large). He also predicted the direction of signal propagation, and was mostly right. Each neuron sends signals outwards through an axon, and receives input from thousands of other cells on its cell body and dendrites.

Signals move between neurons mostly by synaptic transmission, or the exocytosis of transmitter-loaded vesicles induced by changes in calcium concentration. That makes calcium a very interesting ion, and makes calcium concentration an extremely important parameter affecting physiological function, so we want to know more about it. Furthermore, it’s a parameter that is in constant flux, changing second by second in the cell. So how do we see an ion in real time or near real time?

The answer is to use fluorescent indicator dyes which are sensitive to changes in calcium concentration — these molecules fluoresce at different wavelenths or absorb light at different wavelengths depending on whether they are bound or not bound to calcium, making the concentration visible as changes in either the absorbed or emitted wavelength of light. There is a small battery of fluorescent compounds — Fura-2, fluo 3, indo-1 — that allow imaging of localized increases in calcium.

There’s another problem: resolution. Where the concentration of calcium matters most is in a tiny microdomain, a thin rind of the cytoplasm near the cell membrane called the cortex, which is where vesicles are lined up, ready to be triggered to fuse with the cell membrane by calcium, leading to the expulsion of their contents to the exterior. This microdomain is tiny, only 10-50nm thick, and is below the limit of resolution of your typical light microscope. If you’re interested in the calcium concentration at one thin, tiny spot, you’ve got a problem.

Most presynaptic terminals are very small and difficult to study; they can be visualized optically, but it’s hard to do simultaneous electrophysiology. One way Neher gets around this problem is to use unusually large synapses, the calyx of Held synapse, which is part of an auditory brainstem pathway. It’s an important pathway in sound localization, and the signals must be very precise. They have a pecial structure, a cup-like synapse that envelops the post-synaptic cell body — they’re spectacularly large, so large that one can insert recording electrodes both pre- and post-synaptically, and both compartments can be loaded with indicator dyes and caged compounds.

The question being addressed is the concentration of Ca2 at the microdomain of the cytoplasmic cortex, where vesicle fusion occurs. This is below the level of resolution of the light microscope, so just imaging a calcium indicator dye won’t work — they need an alternative solution. The one they came up with was to use caged molecules, in particular a reagent call Ca-DMN.

Caged molecules are cool, with one special property: when you flash UV light of just the right wavelength at them, they fall apart into a collection of inert (you hope) photoproducts, releasing the caged molecule, which is calcium in this case. So you can load up a cell with Ca-DMN, and then with one simple signal, you can trigger it to release all of its calcium, generating a uniform concentration at whatever level you desire across the entire cell. So instead of triggering an electrical potential in the synaptic terminal and asking what concentration of calcium appears at the vesicle fusion zone, they reversed the approach, generating a uniform calcium level and then asking how much transmitter was released, measured electrophysiologically at the post-synaptic cell. When they got a calcium level that produced an electrical signal mimicking the natural degree of transmitter release, they knew they’d found the right concentration.

Caged compounds don’t have to be just calcium ions: other useful probes are caged ATP, caged glutamate (a neurotransmitter), and even caged RNA. The power of the technique is that you can use light to manipulate the chemical composition of the cell at will, and observe how it responds. These are tools that can be used to modify cell states, to characterize excretory properties, or to generate extracellular signals, all with the relatively noninvasive probe of a brief focused light flash.