I know, for example, that hardly anyone takes IR spectra any more. I've taken maybe one or two in the last ten years, and that was to confirm the presence of things like alkynes or azides, which show up immediately and oddly in the infrared. Otherwise, IR has just been overtaken by other methods for many of its application in organic chemistry, and it's no surprise that it's fallen off so much since its glory days. But I think that carbon-13 NMR is probably underused, as are a lot of 2D NMR techniques. Any other nominations?

This question has a lot of bearing on questions of protein evolution. The paper's intro brings up two competing hypotheses of how protein function evolved. One, the "inherent functionality model", assumes that primitive binding pockets are a necessary consequence of protein folding, and that the effects of small molecules on these (probably quite nonspecific) motifs has been honed by evolutionary pressures since then. (The wellspring of this idea is this paper from 1976, by Jensen, and this paper will give you an overview of the field). The other way it might have worked, the "acquired functionality model", would be the case if proteins tend, in their "unevolved" states, to be more spherical, in which case binding events must have been much more rare, but also much more significant. In that system, the very existence of binding pockets themselves is what's under the most evolutionary pressure.

The Skolnick paper references this work from the Hecht group at Princeton, which already provides evidence for the first model. In that paper, a set of near-random 4-helical-bundle proteins was produced in E. coli - the only patterning was a rough polar/nonpolar alternation in amino acid residues. Nonetheless, many members of this unplanned family showed real levels of binding to things like heme, and many even showed above-background levels of several types of enzymatic activity.

In this new work, Skolnick and Gao produce a computational set of artificial proteins (called the ART library in the text), made up of nothing but poly-leucine. These were modeled to the secondary structure of known proteins in the PDB, to produce natural-ish proteins (from a broad structural point of view) that have no functional side chain residues themselves. Nonetheless, they found that the small-molecule-sized pockets of the ART set actually match up quite well with those found in real proteins. But here's where my technical competence begins to run out, because I'm not sure that I understand what "match up quite well" really means here. (If you can read through this earlier paper of theirs at speed, you're doing better than I can). The current work says that "Given two input pockets, a template and a target, (our algorithm) evaluates their PS-score, which measures the similarity in their backbone geometries, side-chain orientations, and the chemical similarities between the aligned pocket-lining residues." And that's fine, but what I don't know is how well it does that. I can see poly-Leu giving you pretty standard backbone geometries and side-chain orientations (although isn't leucine a little more likely than average to form alpha-helices?), but when we start talking chemical similarities between the pocket-lining residues, well, how can that be?

But I'm even willing to go along with the main point of the paper, which is that there are not-so-many types of small-molecule binding pockets, even if I'm not so sure about their estimate of how many there are. For the record, they're guessing not many more than about 500. And while that seems low to me, it all depends on what we mean by "similar". I'm a medicinal chemist, someone who's used to seeing "magic methyl effects" where very small changes in ligand structure can make big differences in binding to a protein. And that makes me think that I could probably take a set of binding pockets that Skolnick's people would call so similar as to be basically identical, and still find small molecules that would differentiate them. In fact, that's a big part of my job.

But in general, I see the point they're making, but it's one that I've already internalized. There are a finite number of proteins in the human body. Fifty thousand? A couple of hundred thousand? Probably not a million. Not all of these have small-molecule binding sites, for sure, so there's a smaller set to deal with right there. Even if those binding sites were completely different from one another, we'd be looking at a set of binding pockets in the thousands/tens of thousands range, most likely. But they're not completely different, as any medicinal chemist knows: try to make a selective muscarinic agonist, or a really targeted serine hydrolase inhibitor, and you'll learn that lesson quickly. And anyone who's run their drug lead through a big selectivity panel has seen the sorts of off-target activities that come up: you hit someof the other members of your target's family to greater or lesser degree. You hit the flippin' sigma receptor, not that anyone knows what that means. You hit the hERG channel, and good luck to you then. Your compound is a substrate for one of the CYP enzymes, or it binds tightly to serum albumin. Who has even seen a compound that binds only to its putative target? And this is only with the counterscreens we have, which is a small subset of the things that are really out there in cells.

And that takes me to my main objection to this paper. As I say, I'm willing to stipulate, gladly, that there are only so many types of binding pockets in this world (although I think that it's more than 500). But this sort of thing is what I have a problem with:

". . .we conclude that ligand-binding promiscuity is likely an inherent feature resulting from the geometric and physical–chemical properties of proteins. This promiscuity implies that the notion of one molecule–one protein target that underlies many aspects of drug discovery is likely incorrect, a conclusion consistent with recent studies. Moreover, within a cell, a given endogenous ligand likely interacts at low levels with multiple proteins that may have different global structures.

"Many aspects of drug discovery" assume that we're only hitting one target? Come on down and try that line out in a drug company, and be prepared for rude comments. Believe me, we all know that our compounds hit other things, and we all know that we don't even know the tenth of it. This is a straw man; I don't know of anyone doing drug discovery that has ever believed anything else. Besides, there are whole fields (CNS) where polypharmacy is assumed, and even encouraged. But even when we're targeting single proteins, believe me, no one is naive enough to think that we're hitting those alone.

Other aspects of this paper, though, are fine by me. As the authors point out, this sort of thing has implications for drawing evolutionary family trees of proteins - we should not assume too much when we see similar binding pockets, since these may well have a better chance of being coincidence than we think. And there are also implications for origin-of-life studies: this work (and the other work in the field, cited above) imply that a random collection of proteins could still display a variety of functions. Whether these are good enough to start assembling a primitive living system is another question, but it may be that proteinaceous life has an easier time bootstrapping itself than we might imagine.

The United States spent more than US$3 billion last year across 209 federal programmes intended to lure young people into careers in science, technology, engineering and mathematics (STEM). The money goes on a plethora of schemes at school, undergraduate and postgraduate levels, all aimed at promoting science and technology, and raising standards of science education.

In a report published on 10 April, Congress’s Government Accountability Office (GAO) asked a few pointed questions about why so many potentially overlapping programmes coexist. The same day, the 2014 budget proposal of President Barack Obama’s administration suggested consolidating the programmes, but increasing funding.

What no one asked was whether these many activities actually benefit science and engineering, or society as a whole. My answer to both questions is an emphatic ‘no’.

And I think he's right about that. Whipping and driving people into science careers doesn't seem like a very good way to produce good scientists. In fact, it seems like an excellent way to produce a larger cohort of indifferent ones, which is exactly what we don't need. Or does that depend on the definition of "we"?

The dynamic at work here isn’t complicated. By cajoling more children to enter science and engineering — as the United Kingdom also does by rigging university-funding rules to provide more support for STEM than other subjects — the state increases STEM student numbers, floods the market with STEM graduates, reduces competition for their services and cuts their wages. And that suits the keenest proponents of STEM education programmes — industrial employers and their legion of lobbyists — absolutely fine.

And that takes us back to the subject of these two posts, on the oft-heard complaints of employers that they just can't seem to find qualified people any more. To which add, all too often, ". . .not at the salaries we'd prefer to pay them, anyway". Colin Macilwain, the author of this Nature piece I'm quoting from, seems to agree:

But the main backing for government intervention in STEM education has come from the business lobby. If I had a dollar for every time I’ve heard a businessman stand up and bemoan the alleged failure of the education system to produce the science and technology ‘skills’ that his company requires, I’d be a very rich man.

I have always struggled to recognize the picture these detractors paint. I find most recent science graduates to be positively bursting with both technical knowledge and enthusiasm.

If business people want to harness that enthusiasm, all they have to do is put their hands in their pockets and pay and train newly graduated scientists and engineers properly. It is much easier, of course, for the US National Association of Manufacturers and the British Confederation of British Industry to keep bleating that the state-run school- and university-education systems are ‘failing’.

This position, which was not my original one on this issue, is not universally loved. (The standard take on this issue, by contrast, has the advantage of both flattering and advancing the interests of employers and educators alike, and it's thus very politically attractive). I don't even have much affection for my own position on this, even though I've come to think it's accurate. As I've said before, it does feel odd for me, as a scientist, as someone who values education greatly, and as someone who's broadly pro-immigration, to be making these points. But there they are.

Update: be sure to check the comments section if this topic interests you - there are a number of good ones coming in, from several sides of this issue.

We're talking SG&A, "sales, general, and administrative". That's the accounting category where all advertising, promotion and marketing ends up. Executive salaries go there, too, in case you're wondering. Interestingly, R&D expenses technically go there as well, but companies almost always break that out as a separate subcategory, with the rest as "Other SG&A". What most companies don't do is break out the S part separately: just how much they spend on marketing (and how, and where) is considering more information than they're willing to share with the world, and with their competition.

That means that when you see people talking about how Big Pharma spends X zillion dollars on marketing, you're almost certainly seeing an argument based on the whole SG&A number. Anything past that is a guess - and would turn out to be a lower number than the SG&A, anyway, which has some other stuff rolled into it. Most of the people who talk about Pharma's marketing expenditures are not interested in lower numbers, anyway, from what I can see.

So we'll use SG&A, because that's what we've got. Now, one of the things you find out quickly when you look at such figures is that they vary a lot, from industry to industry, and from company to company inside any given group. This is fertile ground for consultants, who go around telling companies that if they'll just hire them, they can tell them how to get their expenses down to what some of their competition can, which is an appealing prospect.

Here you see an illustration of that, taken from the web site of this consulting firm. Unfortunately, this sample doesn't include the "Pharmaceuticals" category, but "Biotechnology" is there, and you can see that SG&A as a percent of revenues run from about 20% to about 35%. That's definitely not one of the low SG&A industries (look at the airlines, for example), but there are a lot of other companies, in a lot of other industries, in that same range.

So, what do the SG&A expenditures look like for some big drug companies? By looking at 2012 financials, we find that Merck's are at 27% of revenues, Pfizer is at 33%, AstraZeneca is just over 31%, Bristol-Myers Squibb is at 28%, and Novartis is at 34% high enough that they're making special efforts to talk about bringing it down. Biogen's SG&A expenditures are 23% of revenues, Vertex's are 29%, Celgene's are 27%, and so on. I think that's a reasonable sample, and it's right in line with that chart's depiction of biotech.

What about other high-tech companies? I spent some time in the earlier post talking about their R&D spending, so here are some SG&A figures. Microsoft spends 25%, Google just under 20%, and IBM spends 21.5%. Amazon's expenditures are about 23%, and have been climbing. But many other tech companies come in lower: Hewlett-Packard's SG&A layouts are 11% of revenues, Intel's are 15%, Broadcom's are 9%, and Apple's are only 6.5%.

Now that's more like it, I can hear some people saying. "Why can't the drug companies get their marketing and administrative costs down? And besides, they spend more on that than they do on research!" If I had a dollar for every time that last phrase pops up, I could take the rest of the year off. So let's get down to what people are really interested in: sales/administrative costs versus R&D. Here comes a list (and note that some of the figures may be slightly off this morning's post - different financial sites break things down slightly differently):

Merck: SG&A 27%, R&D 17.3%
Pfizer: SG&A 33%, R&D 14.2%
AstraZeneca: SG&A 31.4%, R&D 15.1%
BMS: SG&A 28%, R$D 22%
Biogen: SG&A 23%, R&D 24%
Johnson & Johnson: SG&A 31%, R&D 12.5%

Well, now, isn't that enough? As you go to smaller companies, it looks better (and in fact, the categories flip around) but when you get too small, there aren't any revenues to measure against. But jut look at these people - almost all of them are spending more on sales and administration than they are on research, sometimes even a bit more than twice as much! Could any research-based company hold its head up with such figures to show?

Sure they could. Sit back and enjoy these numbers, by comparison:

Hewlett-Packard: SG&A 11%, R&D 2.6%.
IBM: SG&A 21.5%, R&D 5.7%.
Microsoft: SG&A 25%, R&D 13.3%.
3M: SG&A 20.4%, R&D 5.5%
Apple: SG&A 6.5%, R&D 2.2%.
GE: SG&A 25%, R&D 3.2%

Note that these companies, all of whom appear regularly on "Most Innovative" lists, spend anywhere from two to eight times their R&D budgets on sales and administration. I have yet to hear complaints about how this makes all their research into some sort of lie, or about how much more they could be doing if they weren't spending all that money on those non-reseach activities. You cannot find a drug company with a split between SG&A and research spending like there is for IBM, or GE, or 3M. I've tried. No research-driven drug company could survive if it tried to spend five or six times its R&D on things like sales and administration. It can't be done. So enough, already.

Note: the semiconductor companies, which were the only ones I could find with comparable R&D spending percentages to the drug industry, are also outliers in SG&A spending. Even Intel, the big dog of the sector, manages to spend slightly less on that category than it does on R&D, which is quite an accomplishment. The chipmakers really are off on their own planet, financially. But the closest things to them are the biopharma companies, in both departments.

One good source for such numbers is Booz, the huge consulting outfit, and their annual "Global Innovation 1000" survey. This is meant to be a comparison of companies that are actually trying to discover new products and bring them to market (as opposed to department stores, manufacturers of house-brand cat food, and other businesses whose operations consist of doing pretty much the same thing without much of an R&D budget). Even among these 1000 companies, the average R&D budget, as a per cent of sales, is between 1 and 1.5%, and has stayed in that range for years.

Different industries naturally have different averages. The "chemicals and energy" category in the Booz survey spends between 1 and 3% of its sales on R&D. Aerospace and defense companies tend to spend between 3 and 6 per cent. The big auto makers tend to spend between 3 and 7% of their sales on research, but those sales figures are so large that they still account for a reasonable hunk (16%) of all R&D expenditures. That pie, though, has two very large slices representing electronics/computers/semiconductors and biopharma/medical devices/diagnostics. Those two groups account for half of all the industrial R&D spending in the world.

And there are a lot of variations inside those industries as well. Apple, for example, spends only 2.2% of its sales on R&D, while Samsung and IBM come in around 6%. By comparison with another flagship high-tech sector, the internet-based companies, Amazon spends just over 6% itself, and Google is at a robust 13.6% of its sales. Microsoft is at 13% itself.

The semiconductor companies are where the money really gets plowed back into the labs, though. Here's a roundup of 2011 spending, where you can see a company like Intel, with forty billion dollars of sales, still putting 17% of that back into R&D. And the smaller firms are (as you might expect) doing even more. AMD spends 22% of its sales on R&D, and Broadcom spends 28%. These are people who, like Alice's Red Queen, have to run as fast as they can if they even want to stay in the same place.

Now we come to the drug industry. The first thing to note is that some of its biggest companies already have their spending set at Intel levels or above: Roche is over 19%, Merck is over 17%, and AstraZeneca is over 16%. The others are no slouches, either: Sanofi and GSK are above 14%, and Pfizer (with the biggest R&D spending drop of all the big pharma outfits, I should add) is at 13.5%. They, J&J, and Abbott drag the average down by only spending in the 11-to-14% range - I don't think that there's such a thing as a drug discovery company that spends in the single digits compared to revenue. If any of us tried to get away with Apple's R&D spending levels, we'd be eaten alive.

All this adds up to a lot: if you take the top 20 biggest industrial R&D spenders in the world, eight of them are drug companies. No other industrial sector has that many on the list, and a number of companies just missed making it. Lilly, for one, spent 23% of revenues on R&D, and BMS spend 22%, as did Biogen.

And those are the big companies. As with the chip makers, the smaller outfits have to push harder. Where I work, we spent about 50% of our revenues on R&D last year, and that's projected to go up. I think you'll find similar figures throughout biopharma. So you can see why I find it sort of puzzling that someone can complain about the drug industry as a whole "only" spending 16% of its revenues. Outside of semiconductors, nobody spends more

Being a global pharmaceutical major, Ranbaxy took a deliberate decision to pool its resources to fight neglected disease segments. . .Ranbaxy strongly felt that generic antiretrovirals are essential in fighting the world-wide struggle against HIV/AIDS, and therefore took a conscious decision to embark upon providing high quality affordable generics for patients around the world, specifically for the benefit of Least Developed Countries. . .Since 2001, Ranbaxy has been providing antiretroviral medicines of high quality at affordable prices for HIV/AIDS affected countries for patients who might not otherwise be able to gain access to this therapy.

And here we have them in an advertorial section of the South African Mail and Guardian newspaper, earlier this year:

Ranbaxy has a long standing relationship with Africa. It was the first Indian pharmaceutical company to set up a manufacturing facility in Nigeria, in the late 1970s. Since then, the company has established a strong presence in 44 of the 54 African countries with the aim of providing quality medicines and improving access. . .Ranbaxy is a prominent supplier of Antiretroviral (ARV) products in South Africa through its subsidiary Sonke Pharmaceuticals. It is the second largest supplier of high quality affordable ARV products in South Africa which are also extensively used in government programs providing access to ARV medicine to millions.

Yes, as Ranbaxy says on its own web site: "At Ranbaxy, we believe that Anti-retroviral (ARV) therapy is an essential tool in waging the war against HIV/AIDS. . .We estimate currently close to a million patients worldwide use our ARV products for their daily treatment needs. We have been associated with this cause since 2001 and were among the first generic companies to offer ARVs to various National AIDS treatment programmes in Africa. We were also responsible for making these drugs affordable in order to improve access. . ."

And now we descend from the heights. Here, in a vivid example of revealed preference versus stated preference, is what was really going on, from that Fortune article I linked to yesterday:

. . .as the company prepared to resubmit its ARV data to WHO, the company's HIV project manager reiterated the point of the company's new strategy in an e-mail, cc'ed to CEO Tempest. "We have been reasonably successful in keeping WHO from looking closely at the stability data in the past," the manager wrote, adding, "The last thing we want is to have another inspection at Dewas until we fix all the process and validation issues once and for all."

. . .(Dinesh) Thakur knew the drugs weren't good. They had high impurities, degraded easily, and would be useless at best in hot, humid conditions. They would be taken by the world's poorest patients in sub-Saharan Africa, who had almost no medical infrastructure and no recourse for complaints. The injustice made him livid.

Ranbaxy executives didn't care, says Kathy Spreen, and made little effort to conceal it. In a conference call with a dozen company executives, one brushed aside her fears about the quality of the AIDS medicine Ranbaxy was supplying for Africa. "Who cares?" he said, according to Spreen. "It's just blacks dying."

I have said many vituperative things about HIV hucksters like Matthias Rath, who have told patient in South Africa to throw away their antiviral medications and take his vitamin supplements instead. What, then, can I say about people like this, who callously and intentionally provided junk, labeled as what were supposed to be effective drugs, to people with no other choice and no recourse? If this is not criminal conduct, I'd very much like to know what is.

And why is no one going to jail? I'm suggesting jail as a civilized alternative to a barbaric, but more appealingly direct form of justice: shipping the people who did this off to live in a shack somewhere in southern Africa, infected with HIV, and having them subsist as best they can on the drugs that Ranbaxy found fit for their sort.

On May 13, Ranbaxy pleaded guilty to seven federal criminal counts of selling adulterated drugs with intent to defraud, failing to report that its drugs didn't meet specifications, and making intentionally false statements to the government. Ranbaxy agreed to pay $500 million in fines, forfeitures, and penalties -- the most ever levied against a generic-drug company. (No current or former Ranbaxy executives were charged with crimes.) Thakur's confidential whistleblower complaint, which he filed in 2007 and which describes how the company fabricated and falsified data to win FDA approvals, was also unsealed. Under federal whistleblower law, Thakur will receive more than $48 million as part of the resolution of the case. . .

. . .(he says that) they stumbled onto Ranbaxy's open secret: The company manipulated almost every aspect of its manufacturing process to quickly produce impressive-looking data that would bolster its bottom line. "This was not something that was concealed," Thakur says. It was "common knowledge among senior managers of the company, heads of research and development, people responsible for formulation to the clinical people.

Lying to regulators and backdating and forgery were commonplace, he says. The company even forged its own standard operating procedures, which FDA inspectors rely on to assess whether a company is following its own policies. Thakur's team was told of one instance in which company officials forged and backdated a standard operating procedure related to how patient data are stored, then aged the document in a "steam room" overnight to fool regulators.

Company scientists told Thakur's staff that they were directed to substitute cheaper, lower-quality ingredients in place of better ingredients, to manipulate test parameters to accommodate higher impurities, and even to substitute brand-name drugs in lieu of their own generics in bioequivalence tests to produce better results."

You name it, it's probably there. Good thing the resulting generic drugs were cheap, eh? And I suppose these details render inoperative, as the Nixon staff used to say, the explanations that the company used to have about talk of such problems, that it was all the efforts of their big pharma competitors and some unscrupulous stock market types. (Whenever you see a company's CEO going on about a conspiracy to depress his company's share price, you should worry).

The whole article is well worth reading - your eyebrows are guaranteed to go up a few times. This whole affair has been a damaging blow to the whole offshore generics business, India's in particular, and does not help them wear their "Low cost drugs for the poor" halo any better. Not when your pills have glass particles in them along with (or instead of) the active ingredient. . .

The article, by Brian Till of the New America Foundation, seems somewhat confused, and is written in a confusing manner. The title is "How Drug Companies Keep Medicine Out of Reach", but the focus is on neglected tropical diseases, not all medicine. Well, the focus is actually on a contested WHO treaty. But the focus is also on the idea of using prizes to fund research, and on the patent system. And the focus is on the general idea of "delinking" R&D from sales in the drug business. Confocal prose not having been perfected yet, this makes the whole piece a difficult read, because no matter which of these ideas you're waiting to hear about, you end up having a long wait while you work your way through the other stuff. There are any number of sentences in this piece that reference "the idea" and its effects, but there is no sentence that begins with "Here's the idea"

I'll summarize: the WHO treaty in question is as yet formless. There is no defined treaty to be debated; one of the article's contentions is that the US has blocked things from even getting that far. But the general idea is that signatory states would commit to spending 0.01% of GDP on neglected diseases each year. Where this money goes is not clear. Grants to academia? Setting up new institutes? Incentives to commercial companies? And how the contributions from various countries are to be managed is not clear, either: should Angola (for example) pool its contributions with other countries (or send them somewhere else outright), or are they interested in setting up their own Angolan Institute of Tropical Disease Research?

The fuzziness continues. You will read and read through the article trying to figure out what happens next. The "delinking" idea comes in as a key part of the proposed treaty negotiations, with the reward for discovery of a tropical disease treatment coming from a prize for its development, rather than patent exclusivity. But where that money comes from (the GDP-linked contributions?) is unclear. Who sets the prize levels, at what point the money is awarded, who it goes to: hard to say.

And the "Who it goes to" question is a real one, because the article says that another part of the treaty would be a push for open-source discovery on these diseases (Matt Todd's malaria efforts at Sydney are cited). This, though, is to a great extent a whole different question than the source-of-funds one, or the how-the-prizes-work one. Collaboration on this scale is not easy to manage (although it might well be desirable) and it can end up replacing the inefficiencies of the marketplace with entirely new inefficiencies all its own. The research-prize idea seems to me to be a poor fit for the open-collaboration model, too: if you're putting up a prize, you're saying that competition between different groups will spur them on, which is why you're offering something of real value to whoever finishes first and/or best. But if it's a huge open-access collaboration, how do you split up the prize, exactly?

At some point, the article's discussion of delinking R&D and the problems with the current patent model spread fuzzily outside the bounds of tropical diseases (where there really is a market failure, I'd say) and start heading off into drug discovery in general. And that's where my quotes start showing up. The author did interview me by phone, and we had a good discussion. I'd like to think that I helped emphasize that when we in the drug business say that drug discovery is hard, that we're not just putting on a show for the crowd.

But there's an awful lot of "Gosh, it's so cheap to make these drugs, why are they so expensive?" in this piece. To be fair, Till does mention that drug discovery is an expensive and risky undertaking, but I'm not sure that someone reading the article will quite take on board how expensive and how risky it is, and what the implications are. There's also a lot of criticism of drug companies for pricing their products at "what the market will bear", rather than as some percentage of what it cost to discover or make them. This is a form of economics I've criticized many times here, and I won't go into all the arguments again - but I will ask:what other products are priced in such a manner? Other than what customers will pay for them? Implicit in these arguments is the idea that there's some sort of reasonable, gentlemanly profit that won't offend anyone's sensibilities, while grasping for more than that is just something that shouldn't be allowed. But just try to run an R&D-driven business on that concept. I mean, the article itself details the trouble that Eli Lilly, AstraZeneca, and others are facing with their patent expirations. What sort of trouble would they be in if they'd said "No, no, we shouldn't make such profits off our patented drugs. That would be indecent." Even with those massive profits, they're in trouble.

And that brings up another point: we also get the "Drug companies only spend X pennies per dollar on R&D". That's the usual response to pointing out situations like Lilly's; that they took the money and spent it on fleets of yachts or something. The figure given in the article is 16 cents per dollar of revenue, and it's prefaced by an "only". Only? Here, go look at different industries, around the world, and find one that spends more. By any industrial standard, we are plowing massive amounts back into the labs. I know that I complain about companies doing things like stock buybacks, but that's a complaint at the margin of what is already pretty impressive spending.

To finish up, here's one of the places I'm quoted in the article:

I asked Derek Lowe, the chemist and blogger, for his thoughts on the principle of delinking R&D from the actual manufacture of drugs, and why he thought the industry, facing such a daunting outlook, would reject an idea that could turn fallow fields of research on neglected diseases into profitable ones. "I really think it could be viable," he said. "I would like to see it given a real trial, and neglected diseases might be the place to do it. As it is, we really already kind of have a prize model in the developed countries, market exclusivity. But, at the same time, you could look at it and it will say, 'You will only make this amount of money and not one penny more by curing this tropical disease.' Their fear probably is that if that model works great, then we'll move on to all the other diseases."

What you're hearing is my attempt to bring in the real world. I think that prizes are, in fact, a very worthwhile thing to look into for market failures like tropical diseases. There are problems with the idea - for one thing, the prize payoff itself, compared with the time and opportunity cost, is hard to get right - but it's still definitely worth thinking about. But what I was trying to tell Brian Till was that drug companies would be worried (and rightly) about the extension of this model to all other disease areas. Wrapped up in the idea of a research-prize model is the assumption that someone (a wise committee somewhere) knows just what a particular research result is worth, and can set the payout (and afterwards, the price) accordingly. This is not true.

There's a follow-on effect. Such a wise committees might possibly feel a bit of political pressure to set those prices down to a level of nice and cheap, the better to make everyone happy. Drug discovery being what it is, it would take some years before all the gears ground to a halt, but I worry that something like this might be the real result. I find my libertarian impulses coming to the fore whenever I think about this situation, and that prompts me to break out an often-used quote from Robert Heinlein:

Throughout history, poverty is the normal condition of man. Advances which permit this norm to be exceeded — here and there, now and then — are the work of an extremely small minority, frequently despised, often condemned, and almost always opposed by all right-thinking people. Whenever this tiny minority is kept from creating, or (as sometimes happens) is driven out of a society, the people then slip back into abject poverty.

This is known as "bad luck."]]> http://pipeline.corante.com/archives/2013/05/16/the_atlantic_on_drug_rd.php http://pipeline.corante.com/archives/2013/05/16/the_atlantic_on_drug_rd.php Drug Development Thu, 16 May 2013 06:55:00 -0500 I was talking with someone the other day about the most difficult targets and therapeutic areas we knew, and that brought up the question: which of these has had the greatest number of clinical failures? Sepsis was my nomination: I know that there have been several attempts, all of which have been complete washouts. And for mechanisms, defined broadly, I nominate PPAR ligands. The only ones to make it through were the earliest compounds, discovered even before their target had been identified. What other nominations do you have?

]]> http://pipeline.corante.com/archives/2013/05/15/and_the_award_for_clinical_futility_goes_to_.php http://pipeline.corante.com/archives/2013/05/15/and_the_award_for_clinical_futility_goes_to_.php Clinical Trials Wed, 15 May 2013 13:51:40 -0500 Speaking about open-source drug discovery (such as it is) and sharing of data sets (such as they are), I really should mention a significant example in this area: the GSK Published Kinase Inhibitor Set. (It was mentioned in the comments to this post). The company has made 367 compounds available to any academic investigator working in the kinase field, as long as they make their results publicly available (at ChEMBL, for example). The people at GSK doing this are David Drewry and William Zuercher, for the record - here's a recent paper from them and their co-workers on the compound set and its behavior in reporter-gene assays.

Why are they doing this? To seed discovery in the field. There's an awful lot of chemical biology to be done in the kinase field, far more than any one organization could take on, and the more sets of eyes (and cerebral cortices) that are on these problems, the better. So far, there have been about 80 collaborations, mostly in Europe and North America, all the way from broad high-content phenotypic screening to targeted efforts against rare tumor types.

The plan is to continue to firm up the collection, making more data available for each compound as work is done on them, and to add more compounds with different selectivity profiles and chemotypes. Now, the compounds so far are all things that have been published on by GSK in the past, obviating concerns about IP. There are, though, a multitude of other compounds in the literature from other companies, and you have to think that some of these would be useful additions to the set. How, though, does one get this to happen? That's the stage that things are in now. Beyond that, there's the possibility of some sort of open network to optimize entirely new probes and tools, but there's plenty that could be done even before getting to that stage.

So if you're in academia, and interested in kinase pathways, you absolutely need to take a look at this compound set. And for those of us in industry, we need to think about the benefits that we could get by helping to expand it, or by starting similar efforts of our own in other fields. The science is big enough for it. Any takers?

]]> http://pipeline.corante.com/archives/2013/05/15/gsks_published_kinase_inhibitor_set.php http://pipeline.corante.com/archives/2013/05/15/gsks_published_kinase_inhibitor_set.php Academia (vs. Industry) Wed, 15 May 2013 06:28:27 -0500 I mentioned Microryza in that last post. Here's Prof. Michael Pirrung, at UC Riverside, with an appeal there to fund the resynthesis of a compound for NCI testing against renal cell carcinoma. It will provide an experienced post-doc's labor for a month to prepare an interesting natural-product-derived proteasome inhibitor that the NCI would like to take to their next stage of evaluation. Have a look - you might be looking at the future of academic research funding, or at least a real part of it.

]]> http://pipeline.corante.com/archives/2013/05/14/a_specific_crowdfunding_example.php http://pipeline.corante.com/archives/2013/05/14/a_specific_crowdfunding_example.php Cancer Tue, 14 May 2013 07:47:06 -0500 Crowdfunding academic research might be changing, from a near-stunt to an widely used method of filling gaps in a research group's money supply. At least, that's the impression this article at Nature Jobs gives:

The practice has exploded in recent years, especially as success rates for research-grant applications have fallen in many places. Although crowd-funding campaigns are no replacement for grants — they usually provide much smaller amounts of money, and basic research tends to be less popular with public donors than applied sciences or arts projects — they can be effective, especially if the appeals are poignant or personal, involving research into subjects such as disease treatments.

The article details several venues that have been used for this sort of fund-raising, including Indiegogo, Kickstarter, RocketHub, FundaGeek, and SciFund Challenge. I'd add Microryza to that list. And there's a lot of good advice for people thinking about trying it themselves, including how much money to try for (at least at first), the timelines one can expect, and how to get your message out to potential donors.

Overall, I'm in favor of this sort of thing, but there are some potential problems. This gives the general pubic a way to feel more connected to scientific research, and to understand more about what it's actually like, both of which are goals I feel a close connection to. But (as that quote above demonstrates), some kinds of research are going to be an easier sell than others. I worry about a slow (or maybe not so slow) race to the bottom, with lab heads overpromising what their research can deliver, exaggerating its importance to immediate human concerns, and overselling whatever results come out.

These problems have, of course, been noted. Ethan Perlstein, formerly of Princeton, used RocketHub for his crowdfunding experiment that I wrote about here. And he's written at Microryza with advice about how to get the word out to potential donors, but that very advice has prompted a worried response over at SciFund Challenge, where Jai Ranganathan had this to say:

His bottom line? The secret is to hustle, hustle, hustle during a crowdfunding campaign to get the word out and to get media attention. With all respect to Ethan, if all researchers running campaigns follow his advice, then that’s the end for science crowdfunding. And that would be a tragedy because science crowdfunding has the potential to solve one of the key problems of our time: the giant gap between science and society.

Up to a point, these two are talking about different things. Perlstein's advice is focused on how to run a successful crowdsourcing campaign (based on his own experience, which is one of the better guides we have so far), while Ranganathan is looking at crowdsourcing as part of something larger. Where they intersect, as he says, is that it's possible that we'll end up with a tragedy of the commons, where the strategy that's optimal for each individual's case turns out to be (very) suboptimal for everyone taken together. He's at pains to mention that Ethan Perlstein has himself done a great job with outreach to the public, but worries about those to follow:

Because, by only focusing on the mechanics of the campaign itself (and not talking about all of the necessary outreach), there lurks a danger that could sink science crowdfunding. Positive connections to an audience are important for crowdfunding success in any field, but they are especially important for scientists, since all we have to offer (basically) is a personal connection to the science. If scientists omit the outreach and just contact audiences when they want money, that will go a long way to poisoning the connections between science and the public. Science crowdfunding has barely gotten started and already I hear continuous complaints about audience exasperation with the nonstop fundraising appeals. The reason for this audience fatigue is that few scientists have done the necessary building of connections with an audience before they started banging the drum for cash. Imagine how poisonous the atmosphere will become if many more outreach-free scientists aggressively cold call (or cold e-mail or cold tweet) the universe about their fundraising pleas.

Now, when it comes to overpromising and overselling, a cynical observer might say that I've just described the current granting system. (And if we want even more of that sort of thing, all we have to do is pass a scheme like this one). But the general public will probably be a bit easier to fool than a review committee, at least, if you can find the right segment of the general public. Someone will probably buy your pitch, eventually, if you can throw away your pride long enough to keep on digging for them.

That same cynical observer might say that I've just described the way that we set up donations to charities, and indeed Ranganathan makes an analogy to NPR's fundraising appeals. That's the high end. The low end of the charitable-donation game is about as low as you can go - just run a search for the words "fake" and "charity" through Google News any day, any time, and you can find examples that will make you ashamed that you have the same number of chromosomes as the people you're reading about. (You probably do). Avoiding this state really is important, and I'm glad that people are raising the issue already.

What if, though, someone were to set up a science crowdfunding appeal, with hopes of generating something that could actually turn a profit, and portions of that to be turned over to the people who put up the original money? We have now arrived at the biopharma startup business, via a different road than usual. Angel investors, venture capital groups, shareholders in an IPO - all of these people are doing exactly that, at various levels of knowledge and participation. The pitch is not so much "Give us money for the good of science", but "Give us money, because here's our plan to make you even more". You will note that the scale of funds raised by the latter technique make those raised by the former look like a roundoff error, which fits in pretty well with what I take as normal human motivations.

But academic science projects have no such pitch to make. They'll have to appeal to altruism, to curiosity, to mood affiliation, and other nonpecuniary motivations. Done well, that can be a very good thing, and done poorly, it could be a disaster.

There was a paper last year from the Groves group at Princeton on fluorination of aliphatic CH bonds using a manganese porphyrin complex. These two papers are similar in my mind - they're modeling themselves on the CYP enzymes, using high-valent metals to accomplish things that normally we wouldn't think of being able to do easily. The more of this sort of thing, the better, as far as I'm concerned: new reactions will make us think of entirely new things

Both types of headlines are overblown, but I think that one set is more overblown than the other. The minimalist bladderwort genome (8.2 x 10⁷ base pairs) is only about half the size of Arabidopsis thaliana, which rose to fame as a model organism in plant molecular biology partly because of its tiny genome. By contrast, humans (who make up so much of my readership), have about 3 x 10⁹ base pairs, almost 40 times as many as the bladderwort. (I stole that line from G. K. Chesterton, by the way; it's from the introduction to The Napoleon of Notting Hill)

But pine trees have eight times as many base pairs as we do, so it's not a plant-versus-animal thing. And as Ed Yong points out in this excellent post on the new work, the Japanese canopy plant comes in at 1.5 x 10¹¹ base pairs, fifty times the size of the human genome and two thousand times the size of the bladderwort. This is the same problem as the marbled lungfish versus pufferfish one that I wrote about here, and it's not a new problem at all. People have been wondering about genome sizes ever since they were able to estimate the size of genomes, because it became clear very quickly that they varied hugely and according to patterns that often make little sense to us.

That's why the ENCODE hype met (and continues to meet) with such a savage reception. It did nothing to address this issue, and seemed, in fact, to pretend that it wasn't an issue at all. Function, function, everywhere you look, and if that means that you just have to accept that the Japanese canopy plant needs the most wildly complex functional DNA architecture in the living world, well, isn't Nature just weird that way?