Lagniappe (science, business, and culture)

Thursday, January 30, 2003
Size Matters
I've been working with some biomolecules that are just large enough to stop being recognizable as friends. I obviously can't tell you what they are, or why I'm working with them, but I hope I can get across what makes them odd.

A "normal" molecule, by synthetic organic standards, is one that we can get our hand around. Molecular weight of up to 500 or 600, say. The largest thing I've ever made (ever made deliberately, that is) is about 800, and even while I was making it I was pretty sure it was too large to be a drug. (I was right.) Molecules in that range - there are untold zillions of them - can do all sorts of things, but they generally have shapes that we can roughly picture in our heads. They're pretty lumpy, and they can flex around in different ways, but if you make a model of them (by hand or on the computer screen) you can get a feel for what they're like.

A real biomolecule isn't like that. Large proteins, for example, have shapes that are too complicated. Folds, convolutions, twists upon twists - you can't hold the shape in your mind. Unless it's a very unusual one, you'd never recognize it again if you saw it on a screen after a month, or if you see it from another angle. It's like trying to compare the shapes of cumulus clouds.

It's hard to say when a molecule crosses over and becomes one of those, rather than one of ours. I'd say when it starts to have structure on top of structure. That is, when it's able to fold around on itself and start to pile up; that's when the real complications start. Most organic size molecules can't really touch their toes, so to speak - they can bend and twist, but you can't usually get one end of the molecule to touch the other end. A large polysaccharide or RNA, though, has no problem doing that, or in folding into who-knows-how-many other possible forms.

I'm working in that border country right now. What's odd is that the biologists regard these things as pretty tiny, and they're suspicious of them from the other direction. Those suspicions aren't relieved when they see an organic chemist working with the stuff - "We knew it all along," I can see them thinking. "Not a real one at all, just another molecule that a chemist can mess around with."

Wednesday, January 29, 2003
Optimism, And What It's For
I know that Lagniappe isn't a politics and current events site. Anyone coming here the morning after the State of the Union found, uniquely in the world of punditry, an essay on genetically engineered rodents. I assume that no one was surprised, and that people don't stop by here for political commentary. But there are parts of the speech that I find touch on some of the points that I make here.

I think the phrase I'm looking for is technological optimism. My recent posts about Norman Borlaug are what I have in mind. In that case, it's the idea that through better agricultural productivity we can grow enough food for everyone without turning the entire Earth into farmland. And the mention I made of the trends in population growth bear on this, too: as countries become more affluent and knowledge-centered, their birth rate drops. You don't have to have kids to breed the free labor, and people realize that they have to provide larger amounts of education to the ones they have. A strong back isn't enough to make your way in such a world; a strong mind is needed.

That's why I'm such a supporter of global free trade: I honestly feel that the solution is to get as many countries as possible pulled up into the knowledge economy, the world where fewer people have to do manual labor and science and art can become priorities. And I think that free trade is the best way to do it. This means jump-starting countries past some stages that the Western world spent a long time in, but I think it's possible. For a small-scale example, look at how many countries are skipping over the land-line phone stage, and going straight to wireless. It's cheaper to do it that way, it works better, and it consumes less land and resource.

One thing in Bush's speech that made me think of all this was his proposal on HIV in Africa. Well, no matter how bad you think that situation is, it's probably worse in reality. Incomprehensibly worse. The only way that anti-retroviral drugs are going to have a chance is if they come attached to a lot of medical infrastructure. By that I mean clinics with reliable electric power and clean water, for starters. The sort of work that's going to be needed to get these drugs administered to people will benefit the entire population, not just the fraction with HIV (a terrifyingly large fraction, though, in some places.)

It takes an optimistic person to propose something like this. Africa has caused many well-intentioned development schemes to vanish with no sign they ever existed. But if Norman Borlaug can come out of retirement to try to feed the continent, then we can go and try to heal their sick. In the same spirit, I applaud the initiatives going on now to fund work into pharmaceutical cures for tropical diseases. I can think up reasons all day for why all these things might not work out, but the hell with it. Let's try. If we don't, they're certain not to work, aren't they?

The other thing last night that started me thinking on these lines was Bush's proposal on fuel cells. There's already been a huge amount of effort in this area, of course. But it was inspiring to hear someone point out that we could really get there, could really end up on a hydrogen economy in the foreseeable future. That's the techo-optimist fix for things, and I'm glad to see it.

Oil giving you trouble? Invent your way out of using it. Not enough food? Figure out how to grow more. Terrible diseases stalking the earth? Get in the lab and get cracking. This taps into a longstanding part of our national character: from backyard tinkerers, through the likes of Edison, and on to today's American prowess in so many scientific fields. Instead of looking at situations and giving a fatalistic shrug - eh, what can you do? - we've charged in, more often than not, and tried to do something.

I've written before about the spring of 1989, when the abortive cold fusion story broke. I was living in Germany, on a post-doctoral fellowship. I was deeply overjoyed at the news - and just as disappointed when it didn't pan out. But one incident in particular stands out. I went with my labmate to have dinner at his family's house that day, Easter Sunday. And his father asked him "Hast du schoen gehoert? Die Amis hat die kern-fusion gemacht." ("Have you heard? The Yanks have done nuclear fusion.") He was grinning, and his expression said "Those Americans. . ."

You see, he and his family didn't seem to doubt that such a thing might be possible. And if such a breakthrough were to happen, the US was where they expected to see it coming from. Let's prove them right.

Tuesday, January 28, 2003
More on Knockouts, For Those Who Care
So, is anyone wondering how you get a gene knocked out in just one specific tissue? Sure you are! (I'll look the other way while anyone who wants to can discreetly make for the exits.)

Tissue-specific knockouts are harder to do than whole-animal ones (and even those aren't really routine, although they're getting closer.) I mentioned the "Cre/lox" system for making those the other day. Cre is a recombinase enzyme, capable of cutting and splicing whole regions of DNA. It's guided by specific DNA sequences on either side of the region it's supposed to work on - these are the "lox" regions.

The entire system was borrowed from prokaryotic cells, and it actually works in mice, to everyone's surprise. What you do is generate one line of mice with the lox sequences inserted in front of and behind the gene you want deleted. Then you generate another strain that expresses the Cre enzyme. These two strains are virtually normal - but when you breed them, some of the progeny will have both modifications. And that means that the Cre enzyme goes to work immediately, slicing out the gene that you marked - and the mice are left to develop without it.

So much for the whole animal. It's more complicated than it sounds, because (as it turns out) different strains of mice can react differently to having a particular gene knocked out. It's not something that we like to think about a lot, but it's true. (Of course, when that happens, you have the chance to learn some other unusual things - just not the ones you set out to learn.)

For tissue-specific knockouts, you take advantage of the way that different tissues control their gene expression. For example, a DNA sequence called aP2 gets used as a marker, upstream of some key genes that are only expressed in fat cells. The fat-specific insulin receptor knockout was done, then, by taking the same lox-modified mice (those in the field say that the gene has been "floxed") that you'd use for a whole-body knockout. On the other side, you generate a line of mice that have the Cre enzyme's gene downstream of an aP2 promoter. That should mean that it'll only get expressed in fat cells. Cross them, and the ones that have both modifications will have Cre doing its job only in the fat.

You'd better have a specific promoter if you want to get this to work. Some tissues have them, and some don't, at least not that we know about yet. The insulin receptor has been knocked out specifically in pancreatic tissue, muscle, neurons, brown fat, and skin (that I'm aware of.) No doubt there are other tissues that await a more detailed knowledge of their expression systems.

For diagrams, and a more detailed explanation of the whole thing from some people who actually do it, try this NIH site.

Live Long and Prosper
I spoke just the other day about the role of IGF-1 in life span - well, this is a lively area, and now there's another publication that bears on this issue. In the latest issue of Science (299, 572) researchers at Harvard describe another knockout mouse model. In this one, the insulin receptor itself has been taken out, but very selectively: it's only missing in the fat tissue.

These animals were first reported last year (Dev. Cell 3, 25), and have a number of interesting qualities. For one thing, they have a low amount of body fat, and they seem to be almost incapable of getting obese. They didn't get fatter as they got older, which is the norm in mice. The researchers went to the extreme of using a technique that damages an area of the hypothalamus, which sets the appetite-control system completely off. After that, animals eat three times as much as normal. These did, too, but their weight didn't change.

And since they don't get fatter as they get older, they don't show up with the equivalent of type II diabetes, either. In fact, their glucose handling seems normal, which is something you always worry about when you start disrupting insulin receptors. (In contrast, knocking out the IR in muscle tissue leads to a very sick animal indeed, with galloping high blood sugar. Muscle tissue is where most glucose gets taken up, and insulin signaling there is essential.)

You'd think that inability to get fat would be enough of a dramatic result. But the latest paper reports that these animals also have mean increase in life span of 18%. It seems that this increase comes in two ways - they're older before they start showing appreciable death rates, and the death rate is slower once it starts becoming significant. For example, after 3 years all the control mice were dead, but a quarter of the knockouts were still hanging in there. The oldest made it another five months after that, a very advanced age indeed for a mouse.

They showed no ill effects for all this. Their fat cells were distributed into different sizes than the norm, but otherwise, no abnormalities showed up. As the authors point out, this result leads to an interesting possibility regarding the known life-extending effects of caloric restriction. CR seems to decrease metabolic rate, although there's a lot of disagreement about how to measure that, and how it varies among different animals (and people.) This, says one camp, leads to less oxidative damage by free radicals.

But these latest mice don't have a decreased metabolic rate. Perhaps the effects of caloric restriction work through lowering the amount of body fat, and these knockout animals get to the same state by a different route. (One way to investigate that would be to restrict the diet of the knockout animals - would you get an even longer lifespan, or would their low-body-fat state react poorly?)

The insulin (and IGF) pathways have always been interesting, and they're looking more so all the time. What's intruiging isn't just the possibility of longer life, although I'm sure that would do well in a marketing survey. But longer, healthier lives? Effects that could potentially break the cycle of larger and larger health expenditures on ever-more-graying populations? It's going to be a slowly developing story - I think - but it could be the one with some of the largest consequences.

Monday, January 27, 2003
Making Big Ones Into Even Bigger Ones
News reports the last few days have it that Novartis has upped its stake in Roche to 32.7%. This odd figure is no accident: Swiss securities law (one of those things that I only wish I was in a position to know better) seems to require an effort to buy the company once you cross 33.3%

Novartis has been accumulating shares for some time; it's no secret. But no one can figure out what they're up to. Their chairman says he isn't interested in a hostile takeover of Roche, which is a good thing, since that would probably be impossible. Two families control just over 50% of Roche's voting shares (we're talking serious piles of Swiss francs here,) and they've shown no interest in selling out to anyone. Besides, hostile takeovers aren't exactly a feature of the Swiss business landscape.

"Long-term investment" is the official explanation from Novartis, but that doesn't make any sense at all. Think of all the money they've spent buying those shares. What they're saying is that it was better spent buying into a competitor than it was plowed back into their own research efforts. Were that reason the real one, I'd be flattered if I worked for Roche, and vaguely disturbed if I worked for Novartis.

Roche, though, is disturbed, and there's nothing vague about it. Their chairman stated "I am absolutely convinced that a large merger would destroy the inherent value of Roche." And as the Wall Street Journal was good enough to note, "he may have a point." I've made my disdain for big pharma mergers clear; it's nice to see some other people coming around to that view.

Sunday, January 26, 2003
How Not to Do It - Part of a Continuing Series
Once in a while I take a break from pronouncing on the Big Issues That Affect Our Very Beings and tell a lab story or two. Previous installments can be found on August 29 and May 15. (That last page also has the infamous patent illustration, which is worth a look if you haven't seen it.)

Every organic chemist has a supply of these stories; when a new chemist joins a company or university, one of the things they add is some new lab disaster tales. Some of them have happened in similar fashion many times in many chemistry departments - the old one about scratching the bottom of the flask to induce crystallization is a good example. As Melville put it, "Genius all over the world stands hand in hand, and one shock of recognition runs the whole circle round."

But there are some errors that are unlikely to have been replicated. One that comes to mind happened in my graduate school group, just before I joined it. The witnesses were still very forthcoming, since they were still in awe of the achievement of a certain postdoc who'd joined the group at the time. He was from a European country which I won't name, a kindly one in which a PhD can seemingly be attained without too much actual laboratory work.

This fellow was going to set up a reaction with LAH, lithium aluminum hydride. This will be an old friend to my fellow chemists, but for those outside the field, it's a powerful reagent to reduce all sorts of functional groups on organic molecules. It doesn't go after unsaturated carbon-carbon bonds very quickly, but otherwise it reduces and spares not, especially if you heat it up. That's something you should think about before you do, by the way, since the reaction is often accompanied by excess heat of its own. If you're already supplying external heat, things can get a bit out of control - as I found out one day when I walked into my lab to see how my LAH reaction was going, and wondered, as I turned the corner, what all that glassware was doing on the floor.

But I digress. Our postdoctoral fellow had managed a PhD in organic chemistry without ever having used LAH, which is possible, though unlikely. He was about to run a large reduction, and was taking all the necessary precautions along with one flagrantly unnecessary one. LAH reacts vigorously with water, as you'd figure. ("Reacts vigorously" is a polite phrase of the art, which translates in a range from "Heads up!" to "Flee for your life!") So he had dried the flask, a large one (let's-get-this-reaction-over-with,) and made sure to use dry solvent from the still. His starting material was on the vacuum pump, also a good idea, since things can sometimes hold a dismaying amount of moisture.

So far, so good. But he also decided that he needed to dry his LAH. This shows a special, highly corrosive form of incompetence: LAH is, perforce, as dry as anything can get. Because of its reactivity, it's actually a good reagent to dry other things (as long as they have only traces of water, that is.) But he dished out a good amount of the stuff into a big crystallizing dish. It's a grey powder, very sneeze-inducing if you breath it in; it's doing its best to reduce your nose. And he shoved this into the drying oven.

That oven wasn't the best choice to dry any reagent (and no oven is the best one to store an open dish of lithium aluminum hydride.) It was where people took their wet glassware to dry it off before storing it at their benches. After a bucket of that stuff went in, the inside was like a rain forest. As fate would have it, a bucket had gone in about five minutes before the LAH made its appearance.

It didn't stay long. Estimates varied, but everyone agreed that it didn't take more than a minute or two. WHA-DOOM! The door of the oven blew open, spewing a festive grey cloud of aluminum oxides and a shower of Pyrex shrapnel. Fortunately, no one was standing in the path of all this. Everyone dropped what they were doing and ran to the scene - including the group's research director, who came out of his office like he'd been launched from a slingshot.

"What on earth?!"
"I don't know, boss, I just don't - everything was fine, I had just put the LAH in the drying oven, and -"
"You put the what in the WHAT?"

And I'll pull a curtain over the rest of the scene, which probably has too much foul language anyway. A clearer example of Schiller's quote I've never encountered. "Gegen den Dummheit kaempfen Goetter selbst vergebens," or "Against stupidity, the Gods themselves struggle in vain."

New Links
I've added a few new links to the blogroll at left. I can recommend the frozen-North opinions of Colby Cosh, the medical insights of Docnotes, and the techno-futurism of the Z+Blog. (That last one is courtesy of Virginia Postrel.)

Friday, January 24, 2003
Food and Population, Revisited
Norman Borlaug, mentioned two days ago, isn't a household name, but he should be. One of my far-flung correspondents sent along a link to a 1997 profile, by Gregg Easterbrook in the Atlantic. It's an excellent summary of his work, and the recent obstacles that have come up to continuing it.

On exactly the same subject, there's an interesting article in today's Wall Street Journal on world population trends. They're being revised downward even more than previously, as countries like India, Iran, Brazil, and Mexico bring their birthrates down. This is very good news, although it's interesting to hear people's reaction to it. When I've mentioned these figures, I've heard things like "Those poor people," because some assume that the birth rate must be dropping due to even more abject poverty.

On the contrary: it's a virtuous cycle in many countries. Rising standards of living (and less dependence on an agricultural economy) lead to lower birth rates, which in turn helps raise the standard of living for the less-rapidly-growing population. You can get into trouble in a situation like Japan's, though, whose demographic pyramid is trying to turn upside down. A nation of retirees will be a problem, all right, until that generation clears out and the demographic bulge disappears.

My background in this is an upbringing in rural northeast Arkansas, on the Mississippi Delta. That's hardly the Sudan, but it's pretty off the beaten track as far as the US goes. It was generally the poorer farming families that had the most children, and as I got older I realized that it was the same around the world. Needless to say, the "disappearing family farm crisis" doesn't resonate with me very much. Like most jobs, the more it can be mechanized, the better off we are as a species. End of editorial. . .for now.

Thursday, January 23, 2003
Making Little Ones Out of Big Ones
The latest issue of Science has an article (299, 350) by researchers at Harvard and NIH titled "What Are the Right Targets for Psychopharmacology?" Longtime readers of this blog (a hardy breed) may recall my cri du couer last February 14th on this subject. These authors lay it all out, and a discouraging picture it is:

It is well known that there is a severe drought affecting drug targets in psychopharmacology. Put simply, the major targets of currently available medications. . .were discovered by investigating the mechanisms of action of existing drugs. . .As in many other medical illnesses, the molecular targets currently used for drug development in psychopharmacology have not been convincingly shown to play a role in pathophysiology.

In other words, we're like the drunk looking for his keys under the streetlight, because it's too dark over there where he lost them. And, you know what? I think they're right. I spent eight years working on targets against Alzheimer's and schizophrenia, and the mechanistic rationales we had were the best that the field could offer, and as thin as gold leaf. Simultaneously.

At least with Alzheimer's, progress hasn't come by figuring out how the existing drugs actually work, because (to a good approximation) there aren't any existing drugs that work. But the point is well taken for schizophrenia, bipolar disorder, depression, and so on: these fields are littered with the wreckage of discarded theories and failed drug development projects.

The authors go on to point out that there's almost certainly no single disease called schizophrenia (to pick one example.) Developing a monotherapy for what's likely to be a subtly related constellation of defects and symptoms is probably impossible. They call for dissecting these disorders past what the diagnostic and clinical manuals say, and for drug development to focus on their smaller components.

My hypothetical long-time readers may recall another post from last February 24th, in which I talked about the limited varieties of mental illness. People seem to go insane, for the most part, in certain ways: paranoia is common, but when did you ever hear of someone with the delusion that people are sneaking around behind his back helping him out? I don't think these two points of view contradict each other, actually. It's those very patterns that have led us to classify mental illness into well-defined categories in the first place. But the molecular and cellular mechanisms that get you into these alternate low-energy states are no doubt just as various and complicated as the current article suggests.

It's going to be tough to change, though. Drug companies like to be able to point at the disease that they're treating. Getting a program launched to treat only, say, the lack of motivation seen in schizophrenia is going to take some work - not least on the part of the marketing folks, who won't know how to deal with this at all. The National Institute of Mental Health has started a program to break the larger diagnostic categories down, and to identify individual clinical markers that could serve as surrogates for drug development. That's exactly what the field needs; without that, we'll have no way to know if we're on the right track with anything.

Not that this is enough to make me want to do CNS drug discovery again any time soon. A guy has his limits. As Voltaire put it, in quite another context, "Once, a philosopher. Twice. . ."

Wednesday, January 22, 2003
He Should Know
Today's Wall Street Journal has a fine article from Norman Borlaug, Nobel Prize winner for his "Green Revolution" work, and a good candidate for the person now alive who has done more to alleviate human suffering than any other. It's called "Science Vs. Hysteria," and it takes the European Union (and anti-biotech groups) out in the back yard and beats the dust out of them with a stick. Says Borlaug:

Genetic engineering of crops - plant breeding at the molecular level - is not some kind of witchcraft, but rather the progressive harnessing of the forces of nature to the benefit of feeding the human race. The idea that a new technology should be barred until proven conclusively that it can do no harm is unrealistic and unwise. . .If low-income food-defecit nations - which desperately need access to the benefits of science and technology - are being advised by governments and pressure groups in privileged nations to reject biotechnology, based on ideologically inspired pseudo-science, there is reason for serious concern.

There's more in that vein, and it's all excellent. I wrote on Nov. 26th about the improved rice (drought, cold- and salt-tolerant) that's been realized by addition of trehalose, and that's just the beginning of what's being accomplished. Malnutrition, hunger: these things could vanish from the earth. For the first time in human history, we're getting the power to do such a thing.

Should anyone of the anti-biotech persuasion read this site, greetings. Get your teeth into this: I really think that the solution to world hunger - and plenty of other problems besides - is to get all the regions of the earth up to speed economically and technologically. Birth rates actually drop in industrialized societies; that's been clear for years. If you want overpopulation, though, just keep people poor and backwards. The periodic starvation that results doesn't quite make up for it, you know. And if you want to save natural habitats, then help us grow more food on less land.

The waste of human capital, human potential in poor countries is completely appalling, as is the sheer amount of needless misery. Who knows what problems we could solve if these billions of people were well-off enough to help us think about them? Things don't have to be the way they are: the neo-Luddites and I can probably agree on that much. But if they've got plans with as good a chance of helping people as technology offers, I've yet to hear them.

More on IGF
I've had quite a bit of mail on this subject - I guess the idea of an anti-aging therapy hits a nerve with a lot of people. No venture capitalists have contacted me yet, though. One reader pointed out something I should have thought of: if a company does develop something like this - or any anti-aging therapy - the clinical trials required to show efficacy are going to be a real battle.

It's hard enough dealing with slow-progression diseases like Alzheimer's or osteoporosis (there are companies that have gotten out of those areas partly because of the clinical difficulties.) But aging. . .probably the way to do it is to agree on some sort of surrogate marker. Perhaps if everyone could agree on enhanced tolerance to oxidation as a worthwhile clinical endpoint you could get somewhere. But I don't think anyone's given it serious thought, because until recent years, it hasn't been a serious possibility.

As for why human growth hormone deficiency doesn't affect lifespan, a colleague of mine suggested that the reason could be IGF-II. In adult humans, that's a major form of circulating IGF, and it's not regulated through growth hormone. In adult rodents, it's not very important at all, though. So humans with GH deficiency don't necessarily have lowered IGF tone (there, that's how to sound like an endocrinologist at parties, not that that's always a desirable endpoint itself.)

Tuesday, January 21, 2003
Though Some Have Called Thee So
The January 9 issue of Nature has a very interesting article (p. 182) on a subject I've written about before: longevity. (See the August 1, June 3, and May 14 posts.) In 1997, it was shown that (partially) disabling a particular gene in everyone's favorite roundworm, Caenorhabditis elegans ("See-elegans" to its friends) makes them live twice as long. That attracted some interest, understandably, and in 2001 the same experiment was shown to work on fruit flies.

The leap to mammals has now been made by a team of French researchers. Mice are perfectly suited for this sort of experiment, because, uniquely among higher organisms, we have a system for completely knocking out their gene expression. (It's via a system called Cre-lox recombination, which I realize sounds like something you do after you drop a bagel on the floor.)

The equivalent roundworm/fly gene in mice is an insulin-growth-factor (IGF) receptor; that general pathway is what goes on in the other animals as well. Our signaling (I'm using the "mammalian we" here) is quite a bit more complex (for one thing, we have separate receptors and pathways for insulin and IGF.) If you knock it out completely (from both sides of the animal's inheritance,) you get very bad effects: stillbirth, with plenty of developmental abnormalities. But the heterozygous animals ("half knockouts" to chemists like me) show increased lifespan, with seemingly no ill effects at all. Metabolic rate, physical activity, fertility, body temperature, blood chemistry: all seemed to be unaffected.

This is news. Many doubted that the effects would translate this well across such a broad phylogenetic range. But a mouse is very much within shouting distance of a human, in general - and it would be hard to imagine something that can work on roundworms, flies, and mice and not be valid all the way to people as well. This is clearly a deep and conserved pathway, real metabolic source code.

Interestingly, the females showed a much more robust effect (33% increased lifespan) than the males (who showed a trend that didn't reach statistical significance.) A similar effect was seen in the fruit flies; as far as I know, no one has explained this. So how does it work? One clue is that the cells from these animals seem to be more resistant to oxidative stress (in line with the other species.) It's unclear how much of the extra lifespan is due to this, and how much to other pathways yet to be worked out.

As I mentioned in the earlier posts, this work ties in neatly with some other observations about aging. Caloric restriction, which also works across phyla (probably including humans; we'll know in another thirty years or so) decreases signaling through IGF-1. Mice with dwarfism, due to low amounts of growth hormone, also have longer life spans, and have lower IGF-1 levels as well. (Here's a question, though: why doesn't that translate to humans? Growth hormone deficiency - dwarfism - is associated with normal life expectancy. Excess growth hormone (acromegaly) seems to be a negative factor, though, but that seems to be through physical factors like heart trouble.)

There are a number of life-extending mutations that have been found in C. elegans and other simpler species by now, and you can bet that the race is on to try them out in mice. Do all these fit together, or are there numerous life-extension mechanisms? What will happen when they're combined? How will all this relate to the generally-perceived tradeoff between growth and lifespan?

As if this weren't turning into a hot enough field, there's a way to combine this with another huge area of research. As Charles Murtaugh rightly observes, RNA interference (and other odd RNA behavior) is going to be the subject of a Nobel (or two or three) very soon. It's that big. (The New York Times has a good overview today.) You can now use RNA techniques to do the rough equivalent of a knockout in an adult animal, and you're not limited to mice. Who's going to be the first to try it on the IGF-1 receptor gene?

And for my fellow medicinal chemists, who's going to be the first to make a small-molecule antagonist to the receptor? (Someone may already be at work on that, although it won't be an easy target. It's already an anticancer target due to its effects on cell proliferation. Anyone see a market for a drug that makes you live longer? No matter what you think of your sales force, they should be able to go out and detail that one. . .

A Word From Our Sponsor
Well, that'd be me. I just wanted to mention that I have a column today on TechCentral Station, summarizing the autism/thimerosal controversy.

(I'm at home this morning, thus the rare mid-morning update. This afternoon I'll be back at the Wonder Drug Factory, though.)

Monday, January 20, 2003
Dueling Enzymes
There was a good example last week of the importance of running your clinical trials the right way. (I last spent some time talking about this issue back when Imclone's drug was shot down.) This latest case is even more clear, because it involves virtually the same drug, but from two different companies.

Genzyme and Transkaryotic Therapies had been racing through the approval process for a treatment for Fabry's disease. The two filed with the FDA within a week of each other back in 2000, and they both came up for review last week. Genzyme got the go-ahead on Monday from the FDA advisory panel for their Fabrazyme. On Tuesday, Transkaryotic came up for review with their version of the same enzyme, Replagal - and it was turned down. Why? Their clinical trial data wasn't good enough to show whether the stuff worked. This must have been particularly galling, since Genzyme had been able to show efficacy, but it came down to how the trials were run.

Fabry's disease is a pretty rare disorder, fortunately. There are only a few thousand people in the whole country who have it (whichever company got approval first was planning to invoke the "Orphan Drug" exclusivity rights.) Patients have a defective form of the enzyme alpha-galactosidase, which is involved in lipid handling. Without the enzyme, abnormal amounts of trihexosylceramide, a lipid which would ordinarily be cleared out, start to accumulate in the lysosome organelles within various cells. A number of bad effects ensue. Its deposition inside neurons leads to attacks of severe pain and tingling, and other problems are caused by buildup in muscle and arterial tissue. Eventually the kidneys get damaged downstream of all this - most Fabry's patients need dialysis, and many eventually need kidney transplants.

Lipid handling is a real mess, technically speaking, and involves more enzymes than you could ever imagine were necessary. That leaves the door open for a lot of genetic breakdowns, when one or another of them get mutated. With so many pathways, losing one isn't always fatal during development (in contrast to what happens with many mutations.) The consequences are unpleasant, though, to say the least. There's a whole list of genetic lysosomal storage diseases, for example, and you don't want any of them.

If gene therapy ever gets off the ground, these disorders are candidates for treatment - just correct that mutation early enough, and you'll make the missing enzyme on your own. It's harder to work on this angle, though, than it is for SCID (the subject of the Murtaugh post I mentioned the other day.) That defect is more localized. Take Fabry's: since alpha-galactosidase is distributed throughout the body in a wide variety of cell types, you'd really have to do the switch as early in embryonic development as possible. In contrast, at a later age you can selectively kill off the cells that carry SCID mutations and replace them with fresh ones.

Transkaryotics seems to have set their sights too high: they tried to prove several things at once in their trial (improvement of pain, cardiac function, kidney function, etc.) That's a lot to ask from a small study. They had only 26 patients - finding patients to enroll in orphan disease trials is a major undertaking. In the end, they couldn't do it. Several of their clinical endpoints were just plain missed, others might have been there, but weren't statistically very convincing.

Genzyme, on the other hand, said that they might need hundreds of patients to have enough statistical power to prove a benefit in pain during a clinical trial. The disease, they pointed out, lasts for many years and progresses slowly. They picked a biochemical marker, clearance of lipid from kidney cells, and demonstrated it beyond any doubt. And that was all they needed. As the trade newsletter Biocentury pointed out today, if TKTX had tried to demonstrate just one important benefit (instead of all of them) they might have made it, too.

Well, both versions are approved in Europe, but Transkaryotics has to find a fallback strategy here. They'll probably be digging through all their clinical data to see if they can find a marker that showed a clear effect (but if they had one, last Tuesday would have been the time to unveil it. . .)

I've mentioned Transkaryotic Therapies before; they've been in protracted legal battles with Amgen and others over their business strategy. In that case, they're going after Amgen's erythropoetin by making in a different way, one that isn't protected by Amgen's patents (well, so says TKTX, anyway.) Amgen has rights to recombinant EPO, but Transkaryotics is trying to get around that by using a technique to make human cells produce the protein in useful quantities. That way, they claim, this isn't a recombinant protein at all, is it? It's just a matter of persuading the human cells to use their latent capabilities and produce the stuff on their own. . .

That rationalization ended up in court very quickly, as you'd imagine. There was another ruling in the case from the Court of Appeal for the Federal Circuit about a week ago, but I'm still trying to find the time to wrap my brain around it. There are numerous issues involved - some reasonably clear, some a complete bucket of ink - and there have been so many claims, counter-claims, partial victories and reversed rulings that I can hardly keep it all straight. I'll take another crack at it and try to report back.

Sunday, January 19, 2003
Per Bacteria Ad Astra
There's a bacterium called Deinococcus radiodurans that has been puzzling people for a long time now. It's not the cause of any disease (that I'm aware of!) and it doesn't clean up PCBs or extract gold out of seawater. What it can do is survive higher doses of radiation than any other organism. Much higher doses. One thousand times the dose that kills everything else known to man, and this critter crawls out of the wreckage and gets on with its life.

It's bizarre, and the reasons why this should be so aren't very clear. It's DNA damage that finishes off a cell exposed to radiation, usually. The other constituents are either a little harder to tear up, or are being broken up and remade often enough anyway. But you can't lose your primary data and still survive. So the first guess, a logical one, was that the bacteria must have extraordinarily efficient DNA repair enzymes.

A few years ago, though, sequencing showed that D. radiodurans has a plain-vanilla complement of repair enzymes - no super-efficient DNA error-checkers. It has a reasonable complement of free-radical-soaking substances, but those didn't seem to be enough to keep its DNA from suffering cartoonish levels of damage. The mystery deepened.

In the latest issue of Science (299, p 254), we may have the answer, or a large piece of it. It turns out that the bacterium has an unusual arrangement of its DNA, which is clear even on microscopic examination. It carries four copies of its genome, which was already known, and it stores them in separate compartments: a normal D. radiodurans cell looks like four smaller cells stuck together.

And the way it has each copy of the DNA packaged is unusual, too. Instead of the usual ball of yarn or twisted phone line of prokaryotic DNA, D. radiodurans has a tight, orderly doughnut. This kind of arrangement is also known, but it's usually found in dormant systems like spores. At any given time, only one or two of the compartments have their DNA "unwound" so it can be used for transcription. The toroidal DNA is quite constrained: the authors hypothesize that broken strands still end up sitting right next to each other, instead of flopping around. When the bacteria are exposed to their usual hideous doses of radiation, they first let their shattered chromosomes recombine in each compartment, then they mix compartments for a standard repair enzyme called RecA to reconcile any differences and errors.

Just how and why the bactierum ended up with this arrangement is a mystery. Presumably the organism evolved under stressful conditions, and its ancestor that hit on this stabilizing arrangement ended up owning whatever foul microenvironment it lived in. For the more fanciful readers out there, no, it won't be easy to appropriate this technique for our own use. Eukaryotes (wombats, crabgrass, Japanese beetles, you and I) handle DNA quite differently than prokaryotes do. For one thing, we don't keep spare copies of our DNA around. I can just barely imagine keeping a nuclear membrane and having it exist in a toroidal shape, but our transcriptional machinery makes things complicated enough to wipe out whatever advantages might accrue.

But what about keeping spares around in a spare nucleus - a sort of "break glass in case of emergency" DNA vault? That would require biological engineering beyond our current capabilities, but if and when we get there, I can think of a good use for such an organism. For some years now, Freeman Dyson (yep, him again) has been advocating what he's called an "astrochicken" space probe. That's a part-living device that is hardened to survive in vacuum, use solar power, furnish its own propulsion, obtain its fuel from local sources, and so on. A satellite that needs to eat, in other words. (You can find one description of such a device in his book Infinite in All Directions) I think he's got a very good point, and that biotechnology might well turn out to be a key for space exploration. What better way to package such an organism's DNA than to follow the durable example of Deinococcus radiodurans?

Friday, January 17, 2003
As Close to Instapundit as It's Going to Get Around Here
Two updates in one day! Hold on to your hats.

I mentioned the Medpundit discussion on gene therapy below; now Charles Murtaugh has expanded it on his site. Highly recommended. He's right that (so far) it just looks like extraordinarily bad luck that both of these events happened, hitting the same gene. No doubt the retrovirus inserted itself into all sorts of other genes, but silently. There may be something unusual about the LMO-2 gene, or some other factor that interacts with it to cause cancer; it's just too early to say. Gene therapy is going to be a long, hard path. But worth it.

Blame Canada?
Over at Asymmetrical Information, Jane Galt has a post inspired by my recent Canadian-reimportation rant below. Her answer to why pharmaceutical companies don't make the economic argument is that they'd almost certainly lose, which could well be right, unfortunately. She followed that up with a vigorous defense of pharma marketing, and a good look at how some of the numbers that are tossed around get used.

So far, none of my mail has defended the "can't guarantee the safety" argument against Canadian reimportation, and I've heard from people in the industry who are just as embarrassed as I am. (Glad it's not just me.) If it's true that this is the only argument the industry can make, then we're in a bad way. Perhaps we are. . .

Thursday, January 16, 2003
If You Want Something Done Right. . .
. . .do it yourself, especially if you're waiting for Blogger to fix it. I've manually put in links for my missing archives over to the left, because I can't get the site to do it automatically. It gave up listing them back in October, and no workaround has restored them (even though they still live on the server, fortunately.)

I've also added to and reworked the Lagniappe Bookshelf over there - the occasional non-science book will make an appearance there, starting this month with an unlikely collection of obituaries.

Lipitor, And How It Got That Way
While I'm linking, I should mention this article at Fortune about Lipitor. That drug is the single reason that Pfizer went after Warner-Lambert a couple of years ago. The article is a good pocket history of the entire class of statins, and a not-atypical look at how blockbuster drugs get discovered and marketed. There's hardly a major drug in the world that hasn't been almost killed off several times in development; Lipitor's no exception. Who would have thought there was room for another statin?

Gene Therapy Revisited
I was going to write about the latest troubles with gene therapy (I last wrote on this subject on October 14.) But the discussion between "Dr. Smith" and Charles Murtaugh over at Medpundit is a better place to read up on the topic. Let's hope that this retrovirus vector issue gets straightened out, because it's going to be hard method to replace.

Wednesday, January 15, 2003
Inhale, By Any Other Name
The former Inhale Therapeutics has officially changed names to Nektar. I can understand the reason for wanting a new name, since the company does more than work on inhaled forms of drugs - but changing from something that means the wrong thing to something that sounds like a destructive alien robot from a 1950s film isn't that big a step up.

Inhale, er, Nektar is more well-known for their work (with Pfizer) on an inhaled form of insulin. That may sound somewhat weird, but it makes a lot of sense. Large proteins like that are notorious for their lack of drug-like properties. They're digested in the gut, and anything that makes it past that is very poorly absorbed into the blood. So much for oral dosing. Even injected into the blood, they tend to have fairly short half-lives - thus all the tricks developed over the years to stabilize them.

Substituting amino acids near known cleavage sites can do the trick (if you don't lose efficacy or cause an allergic reaction in the process.) A popular method is "pegylation," attaching a big waxy ball of polyethylene glycol ("PEG" to its friends) to one end of the protein. All sorts of odd ways of delivering unmodified proteins have been tried, but they tend to have downsides. It's hard to get a patch to work - those have a better chance with smaller molecules, and you start to get close to skin damage when you try to drive really large peptides across.

It's been known for some time that the capillaries in the respiratory tract are rather permeable, although this route has been largely used for drugs of abuse. It turns out that even insulin, which is pretty large, gets across reasonably well - but the problem is getting it deep enough into the lungs to where it can hit the large capillary surface area it needs. That means very careful control of particle size, static and wetting properties and so on. Frankly, it's exactly the kind of thing you wouldn't want anyone working on biowarfare to learn about, a thought that just occurred to me as I was writing this.

Pfizer and Inhale knew that this was going to be hard, but it's turned out to be even harder than they thought. The other big problem with insulin is that there isn't much of a safety margin. If you take twice as much aspirin as you should, it'll be rough on your stomach - but if you take twice as much insulin, you're probably going to end up on the floor. The insulin response is rather "brittle," as the clinicians say. So getting a reproducible dose is critical. All those physical properties I just mentioned are the key to doing it, paired with a special inhaler device.

But there are some variables that are tough to control for: what if the patient has a cold? That's a nontrivial problem. And it turns out that some of the patients who've been trying the formulation have shown decreased pulmonary function over time. How bad that is, how bad it potentially gets, and how that affects the insulin delivery have all been objects of a lot of time, effort, and money. The quest to throw away the syringes goes on. . .

Tuesday, January 14, 2003
Idle Hands
Light blogging schedule tonight - taking care of our two children cuts into time for vital stuff like this. My boy is 4-and-a-few-months and asking questions nonstop; a good 40% of his sentences start out "What if. . ." I try to give reasonable answers (although it's not easy when the question is something like "What if a rocket ship fought a velociraptor?" I did mention that he was a little boy, didn't I?)

And work is keeping me busy, as it should. I have more than one project occupying space in my head these days, so each day one or another of them gets shortchanged. They're a mixed bag: one has an interesting situation in rodents that require a lot of literature-reading and staring out the window; one is a late-stage drug discovery project in let's-get-this-thing-finished mode, one is more a problem in analytical chemistry than anything else - how do we pick needle X out of haystack Y? - and another is straight organic synthesis.

Simultaneously one of the best things and one of the worst things about science is how the problems just never stop coming. Depending on your personality, it's either a guaranteed source of interest and entertainment, or a Sisyphusean slog. If I weren't so busy, I think I'd be pretty entertained.

Get Real
So Glaxo SmithKline has become the first major drug company to officially throw down the gauntlet to their Canadian buyers. No doubt most readers are familiar with the whole drug-reimportation issue: many prescription drugs are much cheaper in Canada, by government decree. So, as the slightest knowledge of economics (and human nature) would predict, there's a thriving business in bringing pharmaceuticals back across the border into the US. (Actually, it's impossible to really understand economics without understanding quite a bit about human nature. More than one social thinker has hit the rocks by not paying attention to that relationship. . .)

A bill was passed earlier this year officially ratifying this practice, but the language in it has kept it from ever being enforced. The Secretary of HHS is supposed to certify that the pharmaceuticals so imported are up to US standards, and Tommy Thompson hasn't shown any urgency to do that. But no one's cracked down on the current trade, either, leaving everything exactly as it was.

GSK has told its Canadian distributors that they'll consider cutting off business ties if they continue to abet the process. That's a nervy maneuver, but I can see their point: if no one says anything, this is just going to keep getting bigger. And while that might "heighten the contradictions" of the current system, as the Marxists used to say, heightening those has never seemed to do much good.

What's happening is simple, and seemingly unspeakable: American customers are subsidizing the low prices in Canada. The prices are higher here so they can be cheaper there. That Reuters article linked above, though, phrases it like this:

The United States is one of the few countries in the world without price controls on medicine, allowing drugmakers to charge higher prices in the United States than anywhere else in the world.

That would be more accurate if the word "allowing" were replaced by "causing." I know that the politically popular position is to say "See! Those big drug companies can sell their drugs for 40% less in Canada! That proves that they're gouging the little guys here at home." It proves no such thing. While I can't say that there are no little guys being gouged anywhere - no one in any free market can guarantee that, by the way - I can say that there's a good way to prove that the drug companies aren't doing that systematically.

How? Go back to another favorite charge against the industry: that it produces too many "me-too" drugs that just echo what's already out there. (I'll leave my oft-made point for now that these days plenty of companies would love to have even a couple of me-toos coming on the market.) Well, if that's true, how come more of them aren't competing on price? Wouldn't that be a good strategy in this cost-cutting environment?

There are examples of this, but mighty few. (And even those are usually supported by higher-margin products somewhere else in a company's portfolio.) The problem seems to be that no company thinks it can make a go of it with lower profit margins across the board. Too risky. Doesn't leave enough of a cushion for the inevitable down periods, when your patents are expiring and your sales aren't growing (like now.)

No, what happens more often is that a new drug in a category comes in firing all bow tubes, trumpeting its advantages over the older competition and trying to scoop up the whole category for itself. There's a fine example of this in the story of Lipitor - many people thought that there was no room for another statin, but look at the stuff fly off the shelves.

If you truly have an also-ran compound that can't at least look like an improvement, you're running the risk of not recouping your investment if you take it to market. That's the situation with my favorite whipping boys, Nexium and Clarinex, and it leads to some of the worst marketing excesses in an attempt to make up for the shortcomings. Note that neither drug is notable for its low price. And while Nexium is certainly paying the bills over at AstraZeneca, I'm not sure how much money Clarinex is ever going to make for Schering-Plough.

And while I'm in the mood to not let my own industry off the hook, let me get back to the Canadian reimportation issue. The whole HHS "certification" process is based on a red herring, as far as I'm concerned. You'd never know it from listening to the industry, though. A spokesman for the trade association, PhRMA, was in the papers today going on about how these Canadian drugs might be unsafe, don't know what those folks have been doing with them, got to protect consumers, and so on. Here's the boilerplate.

This argument is a disgrace. I can't imagine that these pharmaceuticals are in any worse shape than what's on the shelves here. No, the real problem is that PhRMA doesn't want to make the economic argument above - the real one - because they're afraid they might lose the battle. (So they've such lame positions that losing the battle is even more likely.) I really don't think that my industry's leaders understand how idiotic the "unsafe Canadian drugs" line sounds. It makes me grit my teeth, and I'm about as sympathetic a listener as you can find. We're in danger of sounding as out-of-it as the recording industry: like a joke, in other words. The last thing we need.

Sunday, January 12, 2003
Easy Parts and Hard Parts
I've been reading George Dyson's interesting history of Project Orion, the late-1950s attempt to design a spacecraft powered by sequential nuclear explosions. (A borderline crazy idea, it very likely would have worked. The big question became whether it should be allowed to work at all.)

He quotes his father, Freeman Dyson, about the early days of the project:

"Everybody did a little of everything. There was no division of the staff into phgysicists and engineers. The ethos of engineering is very different from that of physics. A good physicist is a man with original ideas. A good engineer is a man who makes a design that works with as few original ideas as possible."

There's a lot of truth to that. So in which category is work in medicinal chemistry? The answer isn't immediately obvious, especially for people just starting out in the business. In graduate school, the emphasis is (rightly) on the pure science: as many original ideas as possible (as long as you can get them to work, one way or another.) So when freshly coined PhDs or post-docs join a drug company, they're sometimes under the illusion that unusual new chemistry is what's called for at every opportunity.

And nothing could be further from the truth. From an organic chemistry standpoint, medicinal chemistry can be downright boring. The sooner that new researchers figure that out, the better off they are. You can do perfectly respectable medicinal chemistry using nothing but reactions and ideas from an undergraduate textbook. (As I've pointed out, those reactions got to be classics because they tend to work, which is just what you need.)

The point of medicinal chemistry isn't chemistry; that's just the means to the end. We do just as much cutting-edge chemistry as we have to, and no more. That stuff takes a lot of time to figure out - and we have plenty of other problems that are waiting to take plenty of our time. The chemistry had better just quietly work for the most part, if you're going to have a chance.

The original ideas come when it's time to decide what molecules to make, and when it's time to figure out why you're getting the biological effects from them that you are. In those areas, we'll take all the original thinking that anyone can provide. Any weird brainstorms about how to make a compound more potent or more selective are welcome. And if making those new molecules calls for nothing more than ancient reactions, yawners that bore the pants off everyone who does them, then so much the better: that means that the molecules will be made quickly and in a good quantity. (One of the worst binds you can be caught in is to have a wonderful lead structure that you can't find a way to make enough of.)

So, when it comes to chemistry, we're engineers. When it comes to medicines, though, we'd better be the next best thing to poets.

Saturday, January 11, 2003
I don't usually post on the weekends, but I noticed last night that today (January 11) is the one-year anniversary of Lagniappe. It's been one of those (increasingly frequent!) quick years. I'm glad, but a bit surprised, that I'm still finding enough material to write about. Actually, the supply still looks pretty good. I made a list early on of things that I should get around to covering, and there are still several things on it that I haven't done.

What surprises me is that it looks like Charles Murtaugh and I are still the only pharma/medical research bloggers around. I thought for sure that there would be more company, but I'll just have to continue to exploit my ecological niche in the Blogosphere alone for now.

Readership has grown from the inital "hit from someone I didn't know" about three days into things. That was a random hit off Blogger's "recently updated" list from some ISP in New Mexico. I was amazed. My first link from another blog came soon after that, from the Insolvent Republic of Blogistan. (Which, with the others mentioned, is on the blogroll at the left.) Getting Instapundited the first time was quite an experience, and a month or two into things I was linked to by Andrew Sullivan - setting a single-day hit record that was only equalled last week.

I'd like to thank Glenn Reynolds for helping to bring plenty of readers here over the last year, as well as Mickey Kaus, Virginia Postrel, the Arts and Letters Daily staff and many others. It's been fun, and I see no reason not to continue in the same fashion. And thanks to everyone who's visited, and everyone who continues to stop by.

Thursday, January 09, 2003
Back in the Stacks
I don't want to give the impression that there are hundreds of gems buried among the papers that no one references. Sometimes no one references them because they're not worth very much, or because no one can get ahold of the actual article. I had a old reference turn up the other day from the local "Proceedings" journal of an obscure Egyptian university - I should have threatened our library staff with a photocopy request. You probably couldn't find it short of London; I seriously doubt that any reference library on this continent has a copy. Heck, you'd probably have trouble tracking it down in Egypt. No one will ever know if it's any good.

But most journal articles in chemistry just disappear from view, because they say what they have to say and get off the stage: "We made compound Z for the first time," or "This palladium catalyst is great when you have exactly the sort of starting material that we have," or "Sometimes this reaction works well, and sometimes, darn it all, it doesn't."

These aren't groundbreaking classics, but they're still valid work. And thanks to modern literature-searching tools, they'll be found whenever someone might really need them (if ever.) Some paper that sits composting quietly for years can suddenly turn out to be vital for another researcher who wasn't even born when it first appeared (I've been that researcher a couple of times myself.) At least twice in my career I've gone to copy a paper out of a bound volume of an old journal and realized that a few years before I'd copied the paper right next to it, for a completely different research project. Last time that happened, I looked at the next paper after that one, wondering if I'd need to come copy it a few years from now. (On closer inspection, I hoped not.)

I've always enjoyed being back in the wilderness of the bound journals in a large library. Of course, as time goes on, I can't help but notice that some of these journals that I can remember seeing seeing as new issues are now in the back storage room. Hmmm. You mean to say they've filled out this entire shelving unit with Journal of Organic Chemistry since I was reading it my senior year of college? Let's see, at this rate, it'll be out to. . .here by the time I retire. Hey, J. Alfred Prufrock measured out his life with coffee spoons; things could be worse.

Wednesday, January 08, 2003
More Ricin
I've had some interesting e-mail on the subject, which I thought I'd address here for the curious. One person mentioned the possibility of ricin dissolved in DMSO. I have to say that that's a nasty thought, because DMSO certainly does increase skin permeability. But I don't know how soluble a large peptide like this would be - even in DMSO, which is generally a solvent of last resort in chemistry. And even if you could get some of the protein in there, odds are excellent that it would denature, change its conformation as it went into solution. Most enzymes shift around so much going into solvents like DMSO that they lose their activity completely. Not all of them, though - but I would put ricin in the category of unlikely to survive the transition. It has an important disulfide bond that would probably be labile to oxidation on storage in DMSO as well.

Others have mentioned food adulteration. If my guesstimate of a gram or two for lethality is right, a big problem would be that the stuff would probably alter the taste of whatever you added it to. I certainly have no idea of what ricin tastes like - and I'm not about to find out, because sublethal doses are still pretty unpleasant. But it's unlikely to be unnoticable. The heat of cooking is an even better denaturant than any organic solvent, usually, but ricin is said to be unusually heat-stable. That's not saying much in protein chemistry, though - boiling water is considered insane heat in the protein world. It's not likely to be a useful agent in someone's french fries; you'll just have to count on the acrylamide.

The Library of Babel
Spent some quality time in the library at work today, digging into another aspect of a project that I'm working on. As you get deeper into the literature on a given scientific subject, some things happen over and over. There will be articles that everyone refers to, the standards that are like showing a form of ID: "Yes, you can take me seriously, because I'm referring to the big papers that everyone in this field should know about."

And there will be papers that somehow got lost in the shuffle, things that are a lot more important than they look, that no one paid enough attention to. You really have to know the field well to recognize these when you see them. And there's always a nagging doubt: "Why doesn't anyone talk about this? What's wrong with it, anyway? If it were good, people would have referenced it. . .right?" The literature-searching tools we have now are gradually giving these papers a better chance to be noticed, but if they're published in an out-of-the-way journal, they still won't get read the way they should be.

Sometimes these papers are lost more in time than in space. More than once I've found that a topic I thought was the latest rage had been anticipated years before. Sometimes the nomenclature has changed enough so that people don't realize that the earlier work is relevant, and sometimes people just don't bother looking at the old literature. A recent project of mine turns out to have relevant papers from thirty years ago, which is remarkable since the same underlying idea is still of interest. Very few modern papers reference these at all; you have to look closely.

What strikes me every time I learn more about a field, though, is how the details start resolving as I get closer. From a distance, when you don't know much about an area, the main points of it look large and chunky: Enzyme X is involved in doing Reaction Y, and it's found in tissue Z. Then as you start to get into the primary literature, all these start breaking into pieces. . .turns out there are several subtypes of Enzyme X - at least, some people say there are, but this other group says that they can't verify that. . .and it does Reaction Y, all right, but it can also do three others, one of them both in forward and reverse - seems to vary depending on the species you look at. . .and here's a paper saying that it's in tissue Z, sure, but it's a lot more important in this other organ where you can barely find it. . .and so on. All these solid rocks of knowledge start turning into mica, exfoliating into piles of complicated details.

The same thing happens when science as a whole approaches a new area. Broad ideas are all we can see at first, but further inspection is rewarded by puzzling anomalies. We may come to a point where we understand things, but the complexity just keeps on increasing the closer we look. It's like a fractal image - just when you think you can see the outline of the whole thing, you realize that those curves have tiny curves on them, which really look as if they themselves have. . .and so it goes. It's just how the world is put together. And I have to say, it would be a lot less interesting if it were easier to understand.

Tuesday, January 07, 2003
There's a report today that British authorities have rounded up several terrorist suspects in London - and that they had small quantities of ricin. So, what is the stuff, how bad is it, where did they get it, and what did they plan to do with it?

Ricin's a protein from castor beans - yep, the same ones used to prepare castor oil. The parent plant is sometimes used as a warm-weather ornamental, and used to be an industrial crop. The leaves aren't a problem, but the beans contain up to 5% ricin, which is a rather high yield for a natural product. It's quite toxic, although there are certainly worse things out there. Botulinum toxin, for example, is a thousand times more potent, but you can't grow anerobic bacteria very well in your back yard.

The purification methods for ricin are in the open literature, and aren't particularly challenging. It's probably one of the easiest toxins to isolate. For that matter, you can order various forms of it from biochemical supply houses. I looked at a few catalogs today, and it's quite cheap, by the standards of peptidic natural products (which are usually priced rather steeply.)

And what does the stuff do? Briefly, it's a very potent inhibitor of protein synthesis, which it accomplishes by attacking one subunit of the ribosome (the central RNA-to-protein machinery of the cell.) Rather than just binding to ribosomes and gumming them up, ricin is actually an enzyme all by itself. It tears up a specific adenine base in the ribosomal RNA, which disables the whole thing, and then it moves on to the next ribosome. One ricin molecule can turn over thousands of times, and needless to say, a cell can't lose thousands of ribosomes and expect to survive.

Ricin's a reasonably large protein, and it suffers from the defects of large proteins. The least dangerous way to be exposed to it is by eating it, since most of it gets digested, and much of the rest has trouble crossing from the gut into the bloodstream. In rodents, oral dosing is about 4000 times less potent than inhalation, which is the worst way to be exposed. The assumption is that if ricin were weaponized, it would be treated like anthrax spores and dispersed for maximum effect. The US and Britain carried out research that led to a prototype of a ricin bomb during World War II, just another one of many nasty weapons that actually didn't get used in that conflict.

Needless to say, there's not a whole lot of public data on just how toxic ricin might be in that form, and it would certainly depend on particle size, static charge, and all the other variables we learned about during the anthrax scare. We have a single public data point about injected ricin, though: Georgi Markov, a Bulgarian exile who worked for Radio Free Europe. One day in 1978, he felt a sharp pain as a stranger poked him with the tip of an umbrella. He began to feel ill within a few hours, and three days later, he was dead. A small pellet containing ricin had been injected into the muscle of his leg, as it turns out, in one of the more exotic assassinations known to have been carried out by the KGB. The best guess is that at most half a milligram proved lethal.

Which sounds pretty bad - but consider that terrorists are unlikely to be able to give masses of people intramuscular injections. And if they want to use inhalation, which is certainly the way to cause real damage with the stuff, they're faced with manufacturing problems similar to the use of anthrax spores.

It's not particularly water-soluble, so dumping it into a reservoir would be a waste of time. And adulterating food would be almost useless, although I've seen mentions of this possibility since the news story broke today. It takes a good handful of the beans themselves to kill an adult (and they have to be crunched up, too, because whole beans tend to pass unchanged through the digestive tract.) A back-of-the-envelope calculation for the pure toxin suggests that it would take a gram or two to reliably kill someone by ingestion. That adds up to a few hundred casualties per pound of ricin, but only if you can get all your victims to eat enough of it.

How worrisome is the news from London? It depends on how much ricin these people had, and what form it was in. I'm betting that it was straight precipitate from the beans, and not something ready to disperse for inhalation. In which case, the suspects were set up to commit retail murder. And not wholesale, fortunately.

(For as much detail as anyone could want, see this PDF, a book chapter written by two colonels from the Army's Medical Research Institute at Fort Detrick.)

Monday, January 06, 2003
And Another Thing. . .
I've been staying away from all the Clonaid / Raelian hoo-hah. As soon as I realized who was behind this, I rolled my eyes and braced for the worst. I first read about the Raelians in Donna Kossy's extraordinary book Kooks (which I see is now in a second edition, which I must purchase very soon indeed.) With that as background, it's hard to take anything these people say seriously.

My opinion of the human clone claims can be easily expressed: bullshit. Look, you fools: extraordinary claims require extraordinary evidence. Come up with multiple blood samples now for DNA microsatellite analysis, in full view of multiple witnesses, or shut up. This is an important issue, and watching all of you hit each other with pies and try to cram yourselves back into the midget car isn't very instructive.

There. I feel better now.

Compare and Contrast
Dwight Meredith over at PLA pointed out to me that the UC-Davis study on the prevalence of autism in California is online. It hasn't been published in a journal yet, and the JAMA paper I mentioned last week doesn't reference it. But the editorial comment in the same issue does.

As it should, since there's certainly an issue to be resolved. The Davis authors feel that their evidence makes it more likely that autism is actually increasing, even after correcting for wider diagnostic criteria, and so on. They still couldn't correct for all the potential differences in case finding, though, and it's unknown how much this has affected the final numbers. The JAMA editorial points out a recent paper analyzing the same California data which concluded that "diagnostic substitution" had occurred - a decrease in the "mental retardation" category had been taken up by an increase in the autism category.

Dwight's view, I believe, is that there has indeed been a real increase in autism - although short of the epidemic that some in the press have spoken of. I look forward to seeing how more data prove or disprove this - if there really is an increase, it's a tragedy, of course, but it could also provide a rare chance to uncover some important facts about the etiology of the condition. You don't get many good shots at the causes of a complex syndrome like this.

I think that's one reason the thimerosal provision that worked its way into the Homeland Security bill upsets me. Unlike many, I don't see it as evidence of a conspiracy to cover up wrongdoing (although one of the worst parts is that it provides spectacular ammunition to those who do.) I think that the less political maneuvering and grandstanding there is on this topic, the better. Most things would be improved that way, come to think of it. I did a quick Google search while writing this post, and since it had "autism" as a search term, up popped a sponsored link on the right-hand side of the page: "Child vaccines are linked to autism. Free case review by our lawyers." I'm glad these guys are so certain.

It's going to be hard enough to figure all this out without all the bricks flying through the air. As I've said, I think that thimerosal is a red herring. But if autism really is on the increase - and I'm still on the fence about that - then finding the real cause would be the most important research priority in the whole field.

Sunday, January 05, 2003
Ratio Rationalizations
We spend a lot of time in drug discovery thinking about ratios. As we accumulate data about our compounds, we start ranking them by how selective they are - "This one's 10x versus the other receptor subtype and that one's 50x," you'll hear someone say, or "We've got to get compounds at least 100-fold over that other enzyme or side effects are going to kill us." Generally you have several secondary assays that the compounds have to jump through along the way, and the ratios are what everyone looks at.

And when compounds start to get dosed in animals, you try to look for cutoffs that can tell you which compounds are worth trying in longer assays. Maybe they only work, for example, when the ratio of peak blood concentration, Cmax (or time-averaged total exposure, AUC) to the binding potency is 100x or more. (Other things being equal, that means you could get the desired effect with a really potent compound that doesn't get into the system all that well, or a weaker compound that hangs around a long time.)

So, how good are these numbers? There's the problem - not as good as we tend to think. Even experienced medicinal chemists can get caught over-interpreting data when it's expressed in ratio form. The problem is, on a graph we all expect to see error bars (and we get pretty antsy if they aren't there - it means someone didn't run the experiment enough times, or they're sloppy about making their graphs, or they're trying to pull a fast one.) And for single data points from an assay, we try to remember the variability - looking at the various runs that went into the number you see is always recommended.

But when things get expressed as ratios, all that disappears. We throw around "40-fold" as if it's different from "20-fold," and it takes a conscious effort to remember that it almost certainly isn't. The variability of biological assays would completely curl the hair of a physicist or physical chemist - at times it curls ours in med-chem, and we're supposed to be used to it. Plus or minus 100% is considered a nice, tight assay for many systems - really, it is. They get worse as the system gets more realistic, too - cloned proteins are usually tighter than isolated ones, which are invariably tighter than cell assays, which are certainly tighter than tissue preps, and anything's less variable than some of the animal assays. If you have one of the jumpier ones in the denominator of your ratio, well, prepare to get all sorts of crazy results.

This is why no one, and I mean no one of any competence at all, really trusts "N of 1" data, especially if it's saying something interesting or unusual. If you haven't run the assay again, you're often better off not telling anyone about your numbers until you have. I have seen many people fall flat on their faces because they couldn't resist trumpeting some startling result that later turned out to be junk. It's tough, because we live for startling results. But we die by error bars, and they rule the drug discovery world in the end.

Friday, January 03, 2003
. . .to those of you visiting via the Washington Post web site. As you may have gathered from a look around, I'm a medicinal chemist in the pharmaceutical industry, and I spend my time going on about that line of work and science in general. As far as I know, I'm the only person in this position who's blogging - and there aren't too many other scientists in general, actually. You'll find a selection of them over on the blogroll to the left.

Hope you find it interesting enough to visit again occasionally. I try to update the site for every weekday, but events (large and small!) sometimes intervene.

Thursday, January 02, 2003
A Prophetic Vision
I seem to be recovering from my virus - of course, saying that so publicly almost ensures that I'll be on my flat on my back in the morning, wheezing at the ceiling and wondering if this is how Gregor Samsa felt.

But at least I have some idea where to get good medicines (although it's going to be a bit of a wait.) Take a look at what Jay Manifold over at A Voyage to Arcturus predicts. I figure that Charles Murtaugh will be the one raising the money for this venture, what with all those valuable contacts he's no doubt making at Harvard and all. Me, I have contacts in places like the Mississippi Delta.

Which reminds me - Jay may be right on target when it comes to my future, but he's laboring under some sort of delusion when he ranks Kansas City barbecue above even Memphis. Perhaps we two can divide the barbecue world between us, and consign beef-cooking Texans and vinegar-squirting Carolinians to the outer darkness together. . .

The Rate of Autism
There's a new study out in JAMA (free full text here) on the incidence of autism in the US population. Before getting to what the article actually says, it's worth seeing what the media are saying it says. The New York Times headlines it "Study Shows Increase in Autism", and Yahoo runs it as "Study Confirms Marked Rise in Autism."

The AP ("CDC Study Finds Autism To Be Less Rare") and Reuters ("Atlanta Study Finds Rise in Autism Diagnoses" do better. That's because it's very hard to tell if there's a real rise taking place or not. The numbers are going up, but the interpretation isn't as easy as it sounds. To quote the authors:

Debate continues about whether the overall prevalence of autism has increased or whether past rates underestimated true prevalence. This debate is difficult to resolve retrospectively.

It's difficult for these reasons:

In the United States, the increase in the number of individuals receiving services for autism may be attributed to several factors. Changes in diagnostic criteria have expanded the concept of autism to a spectrum of disorders. Heightened public awareness of autism also has had an effect, due in large part to efforts of parent and advocacy groups, availability of more medical and educational resources, increased media coverage of affected children and families, and more training and information for physicians, psychologists, and other service providers. Also, in 1991, the US Department of Education added autism as a category for special education services, possibly leading to increases in the number of children classified with autism because of the availability of these services. The mandate for early intervention services for children with DDs, including autism, also has contributed to greater attention being placed on autism. At the same time, studies are suggesting that some children with autism respond well to early, intense educational intervention. The combined influence of these factors has probably contributed to the identification of more individuals with autism. However, it remains unclear whether specific environmental, immunologic, genetic, or unidentified factors also have contributed to these higher reported prevalence rates.

I think that's a very fair statement. Some environmental factor might be at work, if the increase is a real one. If so, tracking it down is going to be a major undertaking, because instead of one smoking gun, there might be several - insufficient by themselves, but adding up to something. These things are very hard to unravel, because it's almost impossible to get statistically meaningful samples that represent the range of variables that you're trying to check.

As for clues to any environmental causes, one footnote from the article that I have access to is from 2000, in Environmental Health Perspectives (Medline abstract here.)

Epidemiologic studies indicate that the number of cases of autism is increasing dramatically each year. It is not clear whether this is due to a real increase in the disease or whether this is an artifact of ascertainment. A new theory regarding the etiology of autism suggests that it may be a disease of very early fetal development (approximately day 20-24 of gestation). This theory has initiated new lines of investigation into developmental genes. Environmental exposures during pregnancy could cause or contribute to autism based on the neurobiology of these genes.

I find this idea somewhat more plausible than the thimerosal hypothesis, or any other environmental factor acting in the first years after birth. For what it's worth, it makes more sense to me that any causative agent would be something that's present in very small amounts, which would overall have greater leverage to cause broad-based harm earlier in brain development. That's an Occam's razor approach, which doesn't always cut the right way, but that's how I'd call it now - if there's an environmental cause at all, and if there is indeed a rise in autism. And we're still not sure about either one.

Wednesday, January 01, 2003
Light blogging tonight - light everything tonight, because I'm in the grip of some sort of respiratory virus. And there's not much you can do with those except ride them out, unfortunately. (I caught a tremendous one two years ago, just in time to be thoroughly sick for a trip to a Keystone research conference in Colorado. Do not, in case you're thinking about it, fly to a week-long meeting at a ski resort in January when you have a galloping sinus infection.)

Antiviral therapies are mighty hard work, as I've pointed out many times over the last few months. Many viruses are simple enough to have only a few processes that you can even hope to interrupt - and if you strike out on those, you have nowhere left to go in drug discovery. Short of vaccines, the viral disease far and away the largest number of therapeutic options is AIDS - and given what's needed there, that tells you what the other diseases are like. Second is perhaps herpes, and past that you rapidly end up in "drink lots of fluids and get some rest" category. (And don't fly to Colorado, while you're at it.)