Traffic?
I notice that traffic continues at this site while I get everyone changed over to the new one. If you're reading this, you're not getting the latest, not for weeks now. I've moved the site, and this one won't be updated. For more Lagniappe, go here. Same blog, with a new site and a new name!
posted by Derek at 10:40 PM

 
Lagniappe has moved! Here's the new site.
posted by Derek at 5:57 PM

 
Ready To Move
Well, things are just about ready for the changeover. The next couple of days will be devoted to getting some new posts up at the new site, and making sure that everything's working the way it should. Drop by on Sunday night (EST) and I'll have the new URL up and more information. Leaving Blogspot will feel a bit strange, but I'm looking forward to a wider readership (and archives that work.) For a free service, though, I really can't complain. Blogger has been a great place to get all this going.

So, I'll see everyone next week over at the new place. It really feels like I should be ordering some cheese trays and vegetable platters or something. . .
posted by Derek at 9:44 AM

 
Beginning of the End?
If reports tonight are to be believed - always a good question - then the final assault on Baghdad may well have started. Who knows how long it will take, but here's hoping that it's short. As Phil Carter's excellent site points out, the whole thing is to make the other army fight on the coalition's terms. A "fair fight" is the absolute last thing you want, since the object is to win, not to have an exciting contest. So however long it takes to set up such conditions is how long things will take - if the key is a rapid advance that disorganizes the opposition, so much the better.

I find myself even with enough mental overage to start working on material for the site again. Article are in the works on a potential new method to use liver cells, the costly failure of an attempted new obesity therapy, some new insights into Alzheimer's, and more. The advent of renewed blogging will coincide with the change I spoke of the other day.

But much larger, more important changes are at work in the world this evening. I'm off to read some more news about them. See you all soon. . .
posted by Derek at 10:35 PM

 
Atmosphere
So far, there hasn't been much in the Iraq conflict that overlaps with what I have made the themes of this site. And that's a good thing (no, I mean a good thing for everyone, not just for those of you who'd have to read it!) No chemical weapons (yet,) no biological ones either (yet.) I'm still half-expecting to see some of this brought out when things get more desperate for the Iraqi military, but every day that goes by without these is a day that could have been much, much worse.

It's surprised me, the extent to which the war takes up mental space. It really makes a person think about what it must have been like during the immensely worse conflicts of the last 100 years (Paul Fussell's Wartime is one such look at what things were like in the Second World War. The way people are on edge now makes it hard to imagine what a year like 1942 must have been like.)

I notice some other blogs going on hiatus for the war, and I understand how they feel. As I've said, I'm going to stay only semi-active myself; it's still more than I'm good for to do my regular sorts of items in this environment.

posted by Derek at 9:56 PM

 
News of the Blog
I'd like to express my appreciation to everyone who keeps dropping by the site. I know that I haven't provided much for your trouble this week, but it's been hard to write about things with the world in the state it's in. I can tell that other blogs are feeling the same internal pressures - it's a strange time. This period is going to have a definite feel to it when we all remember it years from now, that's for sure. (I spent some time just recently looking into possible vacation ideas for the family this summer - when I finished, I realized that that was probably the longest I'd gone without thinking about the war situation since it started. . .no wonder I felt refreshed. . .)

I'm continuing to come across lots of good material, though, and I'm starting to work on some pieces for when regular science-and-pharma posting starts up again. When that will be is a good question, though. I think that the Iraq war will either come to some sort of eventful conclusion fairly soon, or settle into a less fraught situation for a matter of many weeks. Either way, I'll be back on my regular beat. But I'm waiting a bit longer to see if the first possibility happens - that's obviously the one I prefer, because I think that conclusion can only be the downfall of an indefensible regime. But there will be some nail-biting before we get to that point.

On the local blog news level, I wanted to also mention that there are some changes in the works. A move to a new URL is in the offing (no more Blogspot, ah well,) and that's the least of it. More details as we get closer to resumption of regular service here.
posted by Derek at 9:36 PM

 
Biology, Put to Bad Uses
I mentioned the other day that I haven't covered biological warfare agents in any great detail. For those interested, a good source of what has gone on in this area is the book
Biohazard. It's a truly alarming account of the Soviet biological weapons program written by a Kazakh scientist who held a high position in it.

A good deal of the stuff he recounts in this book is probably still out there, in one form or another. Some of the people who did it have dispersed to other countries willing to pay them for their expertise. Is it necessary to point out that all of it was done by a country that signed all the relevant international treaties outlawing such research?
posted by Derek at 9:34 PM

 
Signal to Noise
Posting will continue to be light here as the war goes on. Here's hoping for a victory as quickly as possible (and, personally, I'm encouraged by how things have gone so far.) Two sources I'm using for breaking news are the blog collective The Command Post and the one-man show The Agonist. These folks are combing pretty much all available sources.

But that brings up a key point: no one (outside of Central Command and anyone above them) has any idea of what's going on. Even that level of knowledge is only a recent development in warfare; plenty of battles have been fought under such confusing conditions that no one had a clear idea of what really happened to produce their outcome. The news reports that we've been getting are often extraordinary, and dispatches straight from the front make compelling reading. But keep in mind that reporters are assigned to whatever units the military wants them assigned to (nobody's with any Special Forces, to pick an obvious example.) And they can be blacked out from reporting, and quite properly.

What we get has a very low S/N. It's a patchy selection of a selection of what's going on, and I'm surprised that it even makes as much sense as it does (which isn't much, some days.) Just go back to all the reports about how the attack was going to proceed, and compare them to what took place (as far as we can tell.) And apply the same discount to the reports about what's coming next. The Vietnam-era suspicion is that because we're not getting the full picture, that things must be worse than they seem. I'm thinking that they may well be better. No matter what, it's for sure that they're different.

The "fog of war" is still there. It's less of a factor for our troops, because of advances in communication, but that just makes it a useful weapon all its own. The Iraqi leadership can watch everything on the satellite just like we can; it would be a sign of terrible incompetence were a useful picture of the fighting available that way. And as for the embedded reports - well, quick glances of fog under a magnifying glass don't resolve it into anything but more fog.

Not that I can keep myself from checking the news all day. . .!
posted by Derek at 7:10 AM

 
Cipro in Iraq?
News reports have surfaced that some Iraqi soldiers have been found to be carrying the antibiotic Cipro as part of their kit. This has immediately led to speculation that there is some connection with the possible use of anthrax.

Unfortunately, that can't be ruled out. Iraq most certainly seems to have produced a nightmarish amount of anthrax during its biological weapons program, and that's just the stuff we know about. Anthrax can take a few days to come on, and thus isn't as useful in a fast-evolving battlefield situation (which this one sure is.) But you can't really be sure that it wouldn't be used if it were around.

However, the presence of Cipro isn't a direct link to anthrax. It's true that the drug got a lot of publicity in the fall and winter of 2001-02 as an anthrax therapy, but it's not the only effective antibiotic against the bacterium. Just about everything in the fluoroquinolone class of drugs should be effective, and plenty of others as well. If it was found with other supplies, it's possible that this was just part of someone's idea of a good medical kit to have (to guard against gangrene, etc.) But if the antibiotic was there all by itself, then one does have to wonder. . .worth watching.
posted by Derek at 10:19 PM

 
How Do You ID a Chemical Weapons Plant?
As I write, there are reports all over the news wires that a suspected chemical weapons facility has been found in Iraq. If this holds up - and there's no certainly that it will, just as there's no certainly about any early reports in any war - how can the presence of these weapons be confirmed?

Well, if there's still some in the pipeline, that's the obvious shortcut. It's not a trivial matter to just open the stopcock and see what comes out, but you've if you've got the material there, it's impossible to mistake it once you've analyzed it. Chemical weapons are small molecules, which are easily identified - an undergraduate could tell some of them from their spectral data.

Residues inside the equipment are also pretty diagnostic. It's impossible to get all the stuff out of any chemical production facility without a thorough and meticulous cleaning. Unless great care has been taken, you're always going to have traces of what was being produced. (And even if such cleaning has taken place, there could well be washes and waste piled up - it has to go somewhere unless there's a very good incineration facility on site.)

And, finally, there's feedstock. No chemical plant operates without supplies of its raw starting materials around. If you find tanks of thiodiglycol, for example, their owners are going to have some explaining to do. That gets used in ballpoint pen ink, sure, but if it's in a well-hidden site, you're looking at mustard gas precursor. Meanwhile, the nerve agents all involve phosphorus compounds which can only be plausibly confused with insecticide starting materials. And the further down the synthesis they are, the further the structures diverge from something that only kills flies.

No, establishing that a given facility is involved in making chemical weapons isn't going to be hard at all. The tough part is finding them, and taking them.
posted by Derek at 10:30 PM

 
Still in War Mode
Like everyone else, I'm spending my time trying to keep up with what's happening. So far, no sign of any chemical or biological components, which is very good news.

I haven't spent much time talking about the latter weapons, except for a post on ricin and its mechanism of action back in the first week of January. It's an even scarier topic than chemical warfare, but (fortunately) the entry barrier is higher if you want to do bad things. I think, though, that biological terrorism is a major worry for the coming years, though. All the more reason, in my opinion, to take measures to keep it from happening.
posted by Derek at 9:58 AM

 
War Footing
I have several items to write about, but I'm holding off as the Iraq campaign gets under way. That's partly because I assume that everyone is going to be somewhere else keeping up with the news, and partly because I'm going to be occupied keeping up with it myself. To give a local example here at Lagniappe Central, my wife's mother landed in Tehran yesterday afternoon on a long-planned visit to her relatives for the Iranian New Year (Noh Ruz,) which begins tonight.

As for war-related blogging, a run through the links at left will point you to plenty. I desperately wish to have no opportunity for any follow-up postings about chemical weapons. But if the damned things do get used, check back here and I'll have comments.

Otherwise, posting will be light here while we all watch to see what comes next. I can only wish good fortune to everyone affected - with the large and total exception of anyone who sincerely supports the current government of Iraq on its merits.
posted by Derek at 6:07 AM

 
Antisense Ungood
Antisense company Isis Pharmaceuticals had a bad day yesterday. Well, actually, they've probably had several bad days recently, it's just that yesterday the rest of us got to hear about it. The stock had the bad day today. They've been plugging away for years at antisense technology, where a complementary "backwards" strand of nucleic acid is intoduced to gum up the expression of a specific gene. The idea is a slick one, and has been a slick one for a long time now. It's just that the execution is such a bear.

DNA and RNA molecules themselves have a pretty short half-life out in the body. They're not the most stable things in the world, not when they're ripped away from all the proteins that help them out in the cell nucleus, and the body probably isn't real keen on having naked nucleic acids wandering around all over the place, either. A major challenge in antisense has been getting reasonably long-lasting analogs that can still penetrate the cell membrane from outside (and get through the nuclear membrane after that.)

This latest compound was a joint venture with Eli Lilly on an antisense to protein kinase C-alpha, PKC-alpha to the trade. This is a reasonable cancer target, and it's one that small molecule therapies have had very little luck attacking. (PKC subtypes, which are legion, have been a real tar pit for drug development in several disease areas.) They made it all the way to Phase III, definitely the most advance thing that Isis has.

And then the wheels fell off. Phase III trials are larger than Phase IIs, and tend to be done under more real-world conditions. This studied non-small-cell lung cancer patients, half of whom got standard chemotherapy and half of whom got that plus the Isis drug, Affinitak. And there was no benefit whatsover. Of course, there have been some half-hearted attempts at putting a good face on the data, but from what I've seen, Affinitak is a goner - at least against NSCLC.

Truth to tell, this wasn't unexpected. Isis and Lilly were using a pretty strict standard (patient survival, not some secondary marker) against a very difficult cancer type. And word was getting out back in December that the trial might not look good.

All this is still a disappointment, but don't count Isis out yet. Affinitak was from an earlier generation of antisense, and they now have better structural classes that seem to have better activity. These are in earlier trials, so their main challenge is to hold on until those come in. But it's been tough: Isis had a good-sized deal with Merck for a diabetes therapy (another enzyme that no one has a good small molecule against.) Many people thought that one could pay off, but Merck dropped it back in December (which must have been a bad month for these guys.) They're still in there pitching, though, with deals with Amgen and Pfizer.

Someday antisense will pay off. . .maybe. The big question is whether RNA interference will come from behind to take over the same therapeutic space. Is that one going to be easier, or is its fate to be just as tough as this stuff is?
posted by Derek at 9:57 PM

 
France and the European Court
No, despite what the last couple of days have been like around here, this isn't going to be about Iraq (at least, not directly.) A co-worker pointed me to this article at Genomeweb. It's about the EU's Biotech Directive, which is an attempt to get the various member countries in line on matters of biotech policy and intellectual property law.

That's no small order, because many EU member countries still have their own patent offices. There's a central European Patent Office, but applications still issue as separate patents in Germany, England, and so on. There's usually not much difference between them, since they generally come from an EPO application, but there are areas of disagreement - especially on patenability. ANd when a patent gets challenged, it can get fought out country by country. Sometimes the EPO steps in and clears things up eventually, but sometimes not.

Among other things, the Biotech Directive says that gene sequences are patentable, as long as a clear utility is demonstrated for them. That's essentially the position of the US PTO, at least after they clarified things a couple of years back. The UK and others have implemented this, and it's now part of patent law in those countries. But several EU countries haven't gotten around to it yet. Including France. . .and they've just passed their own biotech law, which blatantly contradicts the EU directive at several key points. For example, gene sequences are specifically declared non-patentable.

According to the article, the French aren't even keeping up a pretense:

But the French government has made no attempt to suggest that the two pieces of legislation are compatible.  In fact, French Health Minister Professor Matthei, a sponsor of the bill, suggests that the best way forward would be for the Biotech Directive to be interpreted in accordance with the (French) Bioethics Bill.

That's a good one. Wouldn't you really rather do it the French way, now that you've thought about it? All you other countries, who negotiated and implemented the binding EU-wide policy - didn't you really mean to do it the way France thought it should be done?

There's room for disagreement on gene sequence patentability, and plenty of subtle points to keep everyone occupied. But this isn't subtle at all. It's, well, it's. . .unilateral. That's the word I was looking for. In theory, France should now be dragged before the European Court. Won't that be a spectacle. . .
posted by Derek at 9:55 PM

 
Chemical Attack
As we draw closer to the resolution of the Iraq situation, it's time for me to make good on my promise to update the chemical warfare posts that I did last fall (which are here, starting on the post dated Wednesday, Sept. 11. The date was not completely a coincidence.)

I think it quite possible that a military campaign in Iraq would cause Saddam Hussein's forces to use unconventional weapons. It's not a good decision, objectively, but the Iraqi government has made similarly poor decisions in the past. If things come to that, here are the possible chemical agents:

1. Hydrogen cyanide: industrial chemical, although not produced and stored in large quantities as such. Can be defended against by standard protective equipment.
Effectiveness: minimal against reasonable protection. Wasn't even useful in World War I.
Likelihood of use: If Iraq has weaponized HCN, they're more stupid or desperate than anyone's realized. Despite its reputation, HCN is a very poor choice for a war gas. Delivering enough of it rapidly enough to be effective is a problem not worth solving.

2. Chlorine: industrial gas, available in huge quantities. Made by the ton by anyone with a chlor-alkali chemical capacity, which can be quite low-tech. Powerful smell, not something that sneaks up on anyone. Can be defended against by standard protective equipment.
Effectiveness: minimal against reasonable protection. Considered obsolete as a weapon.
Likelihood of use: Iraq has plenty of chlorine. But I strongly doubt that it would be used in battle. If they're going to go chemical against a force like the one arrayed against them now, they're going to go all the way.

3. Phosgene: industrial gas, available in large quantities. Can be made by the ton by anyone with a supply of chlorine. Odd smell, though not as immediately detectable as chlorine. Can be defended against by standard protective equipment.
Effectiveness: minimal against reasonable protection. Considered obsolete as a weapon.
Likelihood of use: Iraq may have phosgene. But I also doubt that it would be used, for the same reason as given for chlorine above.

4. Mustard Gas: not really a gas, but an oily persistant liquid. It stays around long enough to be a problem for everyone involved, including the side that initially uses it. It's cheap to make, and requires only what a standard chemical industry would have already. It keeps indefinitely if reasonably clean. But it can be defended against by standard protective equipment.
Effectiveness: minimal, despite its reputation, at least against well-equipped soldiers. It can take a long time to incapacitate or kill, making it more of a terror weapon. As such, it's potentially horrific if used on civilians.
Likelihood of use: Iraq most certainly has produced this, and it was used against Iran. Its use now would be an extremely poor decision, because it would accomplish nothing except an even more overwhelming response. But it can't be ruled out.

5. Tabun (GA): one of the more volatile nerve gases, and the first one to be produced on a large scale (by a hideous process; see my September discussion for more.)
Effectiveness: well, all the nerve agents are pretty damned effective. That's the problem. But good protective gear will negate them, as long as it's coupled with discipline and good training.
Likelihood of use: Tabun is the "training wheel" nerve gas, and is considered to be essentially obsolete. Even if a country or group has never produced a nerve agent before, they'd be more likely to come up with Sarin. Saddam Hussein has worse.

5. Sarin (GB): still used as a nerve agent. Like the others, it's very stable on storage if it's clean to start with. This was what Aum released into the Tokyo subway, although their material wasn't as clean as it could have been, fortunately.
Effectiveness: worse than Tabun. Good protective gear will negate it.
Likelihood of use: Sarin has certainly been produced in Iraq, and could see use if it's still around. I'd say that VX is the most likely thing in this department.

5. Soman (GD): a little-used nerve agent, although it was produced on large scale and stockpiled during the Cold War.
Effectiveness: worse than Tabun and Sarin, overall. Good protective gear will negate it.
Likelihood of use: Unsure if this has ever been made in Iraq. Worse has, though.

5. VX: the bottom of the barrel, or the top, depending on the state of your soul. This was the state of the art before the 1971 agreement, and there's been no confirmed public report of anything past it.
Effectiveness: less volatile than the other nerve agents above, and more of a problem by skin contact than by inhalation. Skin contact is more than enough.
Likelihood of use: Appears to have been used in the infamous attack on the Kurds. If Iraq is going to deploy a nerve agent, which I fervantly hope they are not, then this is the one they're going to use.

So, how would they use any of these? The standard method has been by artillery, but there's a limited amount of agent that can be delivered that way. They can be dropped by aircraft, as Iraq has horribly shown by its own experience. The drone that's caused all the weapons-inspection furor would be one method, but it would have to be low- (and slow-)flying to disperse a chemical agent. (Biologicals could be a different story.) But there aren't going to be any Iraqi aircraft getting off the ground, or not for very damned long. (That's not bragging, nor is it wishful thinking, just a statement of fact.)

Chemical attack would be an act of revenge or desperation on the part of Iraq, and (after the first shock and suprise) would have no effect on the outcome of the conflict. The problem is, we can't rule revenge or desperation out. The effects would be worst on any civilian population in the area, of course, which is yet another reason to hope that we don't seem these weapons used.

For more on these, if you can deal with more, see this large PDF. An excellent one-stop reference.
posted by Derek at 10:54 PM

 
It's Here, Too
I've noticed that my traffic is down the last week or two, off a good 20%. And although this hasn't been the most content-heavy week in Lagniappe history, I'm assuming that the reason for the decline is the impending war, for which this blog isn't really a source of information.

It's hard not to write about it. I didn't have this site going before September 11, but it's easy to see how that changed what many people thought they'd spend their time talking about. It's hard not to write about politics and world events in general. After all, most people that set up shop as founts of opinion and information talk about those things. (The rest talk about the financial markets or sports, two other areas where arguments are, conveniently enough, almost never settled.)

I started out thinking that I would get right into the same area. I certainly have plenty of opinions on political issues (I've always been gently amazed at the many people who don't.) Charles Murtaugh wrote recently that, unlike him, I'd had the sense to keep out of political discussions on my site. But it didn't take long for me to feel that current-event opinions were well- (if not over-) represented in the blog world. Keep in mind that this was over a year ago; it hasn't gotten any less crowded since then. So, sensibly or not, I decided to carve out a different ecological niche, since I'd always enjoyed talking about what I do for a living.

So, compared to many others, this isn't as much of an opinion site. I try to keep the subject matter here in a certain zone - I don't cover the political ends of health-care issues that much, because I see that as more politics than science. But I also try not to make the scientific content so recondite that my readership disappears. When I can tie my site's areas of interest to broader events, I do - that seems like a legitimate pursuit, and a legitimate pursuit of a larger audience. Every time I get linked from one of the high-traffic opinion sites, a few more readers stay around. I like this stuff; my site's predicated on the idea that enough others like it to make writing it enjoyable. (Writing it for no one to see it wouldn't be too much fun at all, of course.)

And I really have little to complain about. Traffic has increased over the months, more or less steadily, and I've had feedback from a lot of places that I never could have expected. I'm writing a monthly column for a trade magazine (Contract Pharma) and that's something I never expected to be doing, either. Selling other occasional pieces of journalism has been fun, too, although I'm glad that I'm not trying to make a living at it.

But allow me to unburden myself, because it does seem a bit surreal to not mention the most massive subject on everyone's mind. (I note that fellow science-blogger Murtaugh is feeling the strain, too.) It shouldn't be a surprise to any regular readers that I favor the current Iraq campaign. And although I think it's going to be quick, I'm still nervous about it. Anyone who isn't, hasn't thought things through very much. This is a very large throw of the dice. Although I believe the odds are on our side - both in the short term and the long - even surer things have come to grief before.

(This isn't a view that's more widely held among scientists than the rest of the population, I have to say. We're as divided as any other group. For example, if Chad Orzel and I meet in person at some point, we'll have a much better time if we stick to science and shy away from the politics, I think.)

But the same optimism that people have noted in my writing informs my views of this coming conflict. I know many people from Europe and from the Middle East: I work with them, I'm married to one. And many of them tell me that they can't believe that America thinks that it can improve such a place. Don't we realize that it's been this way for hundreds, thousands of years? Can't we leave well enough alone?

No, for a variety of reasons that we've had terrible familiarity with these last months, I believe that we can't. And this may be naive of me, but deep down, I really refuse to admit to totally intractable problems. That's odd, considering that I do scientific research for a living, because most of the things that I try to accomplish fail regularly. All research does; it falls flat on its face day after day. But eventually some of it gets to where it's going, and some of it finds wonderful things that no one ever dreamed were there. Unlikely things happen; they're out there. And if I can't solve a particular problem, then someone else who comes after me will have a crack at it, and someone after that. We get somewhere.

Inoculating that region of the world with the values of the West may be a long shot. (I'm not so sure that it is. . .) But even if so, well, I see longer shots work all the time. Leaving well enough alone doesn't really seem to be in my nature. Leaving bad enough alone certainly isn't. As Jane Galt pointed out recently, many disagreements between liberals and conservatives aren't about problems, they're about what the best solution might be. Honorable and reasonable people can disagree about whether this war - which is certainly going to happen - is a good solution or not, and even its proponents argue about its chances of working.

But that's all going to be wasted breath in a few days, a very few now. Our questions are about to be answered - some slowly, some very quickly indeed.

Alea iacta est.
posted by Derek at 10:04 PM

 
Vaxgen and Its Numbers
The March 7 issue of Science has a summary of Vaxgen's presentation of their HIV vaccine results, under the discouraging headline of "Vaccine Results Lose Significance Under Scrutiny." The contents of the article will hold few surprises for readers of the posts here from the last week of February. The pitfalls of subgroup analysis are discussed, sometimes in exactly the same terms as my contributors and I used:

Cornell University's John Moor, a longtime critic of the vaccine and an expert on HIV antibodies, finds this reasoning absurd. "Lumping Blacks and Asians together is biological rubbish," says Moore. "They might as well do a subgroup analysis based on signs of the zodiac."

An interesting wrinkle occurred during that week after the criticism started. Many pointed out that the P values (used as a measure of statistical significance) really should have been corrected for how many subgroups were split out. A conservative way to do this, the Bonferroni correction, is to just multiply the P values by the number of subgroups. That way you have to have much more significance in the underlying data before you decide that you're seeing something real.

Did Vaxgen do this? Their initial press release sure didn't make it clear, but it didn't look as if they had. Then on February 27, their CEO told an investor conference that sure, you bet, they'd done that. In fact, he said, "a conservative version was applied, and it had no impact on statistical significance." This is the sound of someone who doesn't appear to understand what he's talking about. Of course doing the correction had an impact - if you're lucky, it doesn't push your results into nonsignificance, but there has to be an impact.

Later that day, Vaxgen issued a a press release "in response to media inquiries." As they said, seemingly through gritted teeth:

"The number of required adjustments for VaxGen's subgroup analyses is subject to interpretation and there are a variety of methods to calculate those adjustments. The company cannot predict the impact these adjustments may have on the findings since that determination will ultimately rest with regulatory authorities."

They're presenting at a Keystone meeting in Banff in about two weeks. Should be a mighty interesting session. . .
posted by Derek at 10:24 PM

 
Welcome Back
Paul Orwin, on the blogroll at left, has landed a faculty position and is back to blogging after a hiatus of several months. I'm always glad to see a dormant site return to life.
posted by Derek at 8:39 AM

 
A Quick One
Blogging time is in short supply tonight. Work and home are keeping me busy, and my blog items are part of the slack that disappears under those conditions.

I continue to get regular hits on this site from Baghdad, at least according to Geobytes. I'm now wondering if this is some Western journalist posted there. I wouldn't mind an e-mail from whomever it might be, since I'm quite curious.

And since I mentioned Iraq, I realize that I owe everyone that second look at chemical warfare that I promised. It's in the works. World events are giving me more time to get around to writing it than I thought I would have. . .

One thing that's unexpectedly taken up time is my book chapter I've mentioned once or twice, on oxazole chemistry. Turns out the index for it needs some reworking, and the long-suffering editor of the volumes has had to toss that one back to the individual authors. It's time well spent, because a decent index can really make the difference in whether a scientific book is used or not. I know from personal experience that a bad one can make a book go right back on the shelf.
posted by Derek at 9:27 PM

 
I Claim Stuff That's Good For What Ails You
The U. of Rochester patent defeat that I wrote about on Friday has some pretty interesting implications for Ariad's attempt to sew up the NF-kB transcriptional pathway. Much as I'd like for Rochester to have lost on general principles, the general principle that you can patent medical methods of treatment (and entire biological pathways) remains intact. It'll probably take statute law to change that. The reason Rochester lost was, basically, "lack of enablement."

That, translated from patent-speak, means that they didn't show how to do what they were claiming, and showed no evidence that they'd done it (or even knew how to.) It's one thing to claim the COX-2 enzyme; it's quite another to claim any compound that works by inhibiting it. Rochester had the enzyme in hand, and they'd done the background work to show what it could be used for. But they didn't have anything to accomplish those uses. As the judge's opinion said, they basically were expressing a wish, or outlining a plan - not carrying it out.

And you have to do that, or at least show enough work that you can claim that you know how to. Just saying that you think it would be a good idea isn't enough. Of course, the Rochester patent had already been issued in this form, which just goes to show you what the patent office is like these days. Now, if they'd shown some examples of compounds that inhibited COX-2, they'd have had a much stronger case - and the more compounds, and the more data they had on their effects, the better.

The people most likely to have plenty of data like that are, well, drug companies. It's much harder to invalidate big pharma patents, because they're generally backed up with more enablement. Not impossible, not at all - just harder. So will Ariad's hold up? Based on this decision, I'd be worried if I were them. They have no compounds in their patent at all, at least none that I recall seeing. So how can they say that all their claims of medical treatment are enabled? The whole patent looked to me like a gigantic shopping list.

And this brings up another point. Back in December, there was an article in The New Republic from two former editors of the New England Journal of Medicine. And it just raked the drug industry over the cheese grater, back and forth for pages on end. I kept meaning to take this article apart, but never got around to it (for one thing, it goes on at a beastly, New Yorker-ish length.) But there's one point that the authors harped on which always gets my blood up - the accusation that drug companies steal all their research from publicly funded discoveries.

I'd be the last to deny that we get a lot of useful stuff from NIH-funded research projects (and many others.) If someone working off an NIH grant discoverers that knocking out the XYZase gene leads to doubled lifespan with minty fresh breath, you can bet that we'll all try to make an inhibitor of its protein product (and try to make a fortune off it.) But that's not piracy - that's science. We build off each other's discoveries.

The attitude seems to be that it's only the people who find the pathway that have discovered anything. Someone who comes up with a drug that uses said pathway is just freeloading. On the contrary: it ain't that easy. If it were, I can assure you that we'd have a lot more useful drugs out there (and we'd all be making a lot more money.) Going from a biological target to a drug is about as hard a job as you could ask for. As I've mentioned before, I've been doing this since 1989, and I've never worked on anything that's come close to ever hitting the market. That's very typical. Years go by between working on something that even gets into a clinical trial, much less one that makes it all the way.

My message to anything who thinks differently is: come on down and try it. Get yourself some venture capital and grab some of that easy money. We're not scooping much of it up right now, for some reason - it's all here waiting for you.
posted by Derek at 10:06 PM

 
Couldn't Resist
My post on Scifinder and modern literature searching the other day reminds me of a story. Back in about 1985 or so, I became the grad student in my group who searched CAS (Chemical Abstracts Service) Online. We got a 90% discount, but it was still considered something that the boss wasn't going to let everyone go wild with.

As I mentioned, trying this out for the first time, I felt like I'd suddenly been given voodoo powers. Searching through bound volumes was slower, of course, and less thorough - but I quickly became aware that there were online searches that weren't just slower than the corresponding offline ones, they were downright impossible that way. (Multiple variable atoms and chain lengths, for example, would have been just nightmarish with the hard copies.)

Well, one day I was doing a search for one of the new grad students in the group. I ran the query and got a reasonable list of hits. As I scrolled down the screen, she suddenly pointed at the title of one of them: "That's it! That's exactly what I need!" I thought quickly - pointing at some of the arcane codes that littered each citation, I said "But that's going to be a hard one to get. . ."

"What! How? Why? I've got to have that one!"
"Well, do you see that part where it says "JPC"? That means that it's from the Journal of Pakistani Chemistry." (Sheer bull, of course, but I thought it rather inspired.)
"Journal of. . .what?"
"And that part that says "UR?" That means that the paper is written in Urdu."

Well, I let her rant for a bit, then broke the welcome news that the paper was actually from something like the Journal of Physical Chemistry - actually, I think I'd rather read that non-existent Pakistani journal instead, but at least we had J-Fizz-Chem right over on the shelf. And they don't publish in Urdu, although most folks would need about three issues to notice the switch even if they made it mandatory. So she calmed right down, after switching from berating Chemical Abstracts to berating me.

And a side effect of that one was that she wouldn't trust a word out of my mouth for about four months. "What time is it? " "Noon." "Yeah, sure, you expect me to believe that?"
posted by Derek at 9:15 PM

 
Holy Mackerel
Well, according to my Geobytes data, I had a hit on this site Tuesday from. . .Baghdad. I only wish I could have seen it in my referral log to see what led them here. . .I'm picturing the Google strings now. . .
posted by Derek at 9:46 PM

 
What's A Patent Buy You?
There have been some very large sums transferred over the answer to that question. Yesterday's decision in the long-running dispute over the University of Rochester's COX-2 patent may be ready to join the list. That's the enzyme behind money-spinners like Vioxx (from Merck) and Celebrex (now Pfizer's.)

It's beyond doubt that the university team discovered the enzyme, and realized its possible use in anti-inflammatory treatment. (Anyone who didn't catch on to that part wouldn't have been competent enough to have found the enzyme in the first place, but that's neither here nor there.) They filed a broad patent, and broad claims issued - including language that would seem to have claimed treatment of COX-2 mediated diseases with whatever inhibitor anyone might discover.

Long-time readers will recall that these patent claims really drive me insane. (See my articles on June 26 and July 2nd about Ariad's patent abuses, eventually to be followed up on.) Until a few years ago, no one tried to claim this sort of thing, but now that the USPTO has let these things issue, everyone's in on the act. Universities, companies, random strangers: they're all patenting their enzymes, the sequence that codes for them, cells that express them and vectors to make 'em do so, every assay that might use any of the above, the use of any of those assays to discover any drug, and the treatment of any disease with any of said drugs. That's only slightly exaggerated. Very, very slightly.

The Rochester group didn't have any chemical matter that might have been a COX-2 inhibitor, and they had no idea of what one might look like or how to make it. But they went after the companies that did the work of finding and developing them, wanting a generous piece of the pie. A summary judgement has tossed that on the trash heap - well, for another few days or weeks, until they appeal. Who knows when this will eventually get resolved?

Matthew Herper at Forbes does a fine job, by the way, of pointing out that Pfizer has been doing something very similar to its competitors who are working on drugs that go through the same pathway as Viagra. He hits it on the head:

Essentially, Pfizer draws the line of "invention" at the moment when researchers actually figure out how to make a drug. The University of Rochester picked a different "eureka" moment, when scientists figured out exactly what the drug should do. The question is whether the law should allow either of these discoveries to be protected as inventions.

Both of these patents are weird, or at least counterintuitive. It would be easy to make a host of philosophical or legalistic arguments for either patent. But the purpose of patents is not really all that complicated. They are supposed to encourage invention by giving companies a degree of monopoly over their products, but not squash it by preventing anyone from doing anything similar ever.

For this reason, Pfizer's PDE-5 patent is a bad idea. Having a whole host of medicines to treat a disorder is a good idea, even if they are similar. . .

Preach it! I couldn't agree more. We're going to ruin our industry with this nonsense if we don't watch out.
posted by Derek at 9:24 PM

 
Ker-thunk. Ker-thunk. Ker-thunk.
Schering-Plough was out with yet another revised earnings forecast. I've lost count of how many times they've done this in the last few months, but it's easy to remember what direction they've all been. (I have some SGP stock; believe me, it's easy to remember. It's a rule, by the way, that every time at least one financial news source has to run the news under the head "Schering Gets Ploughed.")

The problem has been that sales of Claritin haven't been what the company had expected. That's just weirdly incompetent (the Wall St. Journal called their situation "a textbook case of bad transition planning.") I think that they should have made provisions for Claritin revenue to drop off, say, 80% in the first three months after it went off patent. That would have been a blow to the stock at the time, but a preferable one to rolling down the entire flight of stairs one by one, which is what's been happening.

After all, look at what's happened that last few years with big patent expirations. Sales just vanish; managed care sees to that, and quite rightly. That's what an efficient market does. It responds quickly to price signals, turning quite literally on a dime. How could Schering-Plough think that things would be any different in their case?

(Well, OK, I know how: the usual way. A bunch of people got together and repeated the sales forecasts to each other until everyone believed it. Companies do all kinds of crazy stuff that way. But wasn't there anyone around who could burst the bubble?)
posted by Derek at 9:06 PM