The coltan controversy

The gaming internets were buzzing the last few days about a widely-publicized report from Toward Freedom that civil war and ongoing militia activity in the Democratic Republic of the Congo (DRC) have in part been fueled by the demand for coltan, a source of the tantalum powder that is necessary for capacitors in consumer electronics. Of course, this isn't a new issue, just a new press release, in which the Playstation 2 in particular is singled out as a cause of conflict. This would be an excellent reason to dislike gaming consoles were it not inflammatory nonsense.

It would be foolish to deny the destructive effects of coltan demand, of course. Although the civil wars in the DRC had political origins, the conflict was sustained in part by demand for this mineral resource. Neighboring countries used militias in the DRC as proxies to ensure access to coltan, which they then sold to a number of foreign companies, which then resold it to various manufacturers, including many American makers of capacitors. Prices for tantalum spiked significantly in the years 1999-2000, providing an even stronger incentive for the DRC's neighbors to seize its rich reserves of coltan. Conflict and deficiencies in infrastructure have at times limited industrial mining of coltan, meaning that it is often mined using less safe artisanal techniques, and often by children. While many responsible companies have taken steps to ensure that they do not use any coltan illegally seized from the DRC, monitoring any supply chain of this kind is very difficult and there are strong incentives for bad actors to lie. Moreover, the greatest damage was done by the '99-'00 price spike; adopting supply controls now can't undo what happened. The Toward Freedom article attributes the spike (and ongoing demand) to the Playstation 2. This is at best a highly selective interpretation of history.

Consider that as of 2007, the total number of cellular phone subscriptions worldwide was estimated at 3.3 billion, while the total number of PS2s sold to date is something like 150 million. According to statistics found at the Cellular Telecommunications and Internet Association website, the number of cellular phone subscriptions in the United States in 2000 was more than 100 million. By 2003 the number of cell phone subscriptions in the United States alone exceeded the number of Playstation 2 units sold worldwide in the entire production run to date. Keep in mind that those cell phone users are changing their phones regularly: the number of used and discarded phones in the United States (which has a low cellular penetration rate) substantially exceeds its human population. As such, we should expect that the actual number of cellular phones used by human beings since their introduction is significantly higher than the number of subscriptions, perhaps by a factor of two or more. Why blame game consoles for the coltan demand, then, rather than the far more prevalent cellular technology?

Of course, the demand for coltan doesn't end with game consoles or cellular phones. Tantalum is used in virtually every modern piece of electronics equipment, including pagers, laptop computers, digital cameras, and inkjet printers, as well as artificial joints, film, and various tools. Why blame game consoles for the ongoing conflict when their sales and usage are completely dwarfed by these other applications? The turn of the century saw a massive expansion in the use of all manner of electronics, all over the world. All of these factors contributed to the tantalum price spike. Yes, the 2000 shortfall of PS2s played a role, but the 6-fold change in price that year could not have happened without an existing huge demand for phones and laptops, and serious structural problems in the tantalum market.

How, then, did this conflict come to be known as the "Playstation War"? Reporter John Lasker doesn't provide any answers. He certainly doesn't quote anyone on the subject and it's not clear to me that the words "Playstation War" were used in reference to this conflict at any point before he did so in this article. In a fit of fairness late in the piece, Lasker acknowledges that the spike in tantalum prices that provided incentive for neighboring countries to interfere in DRC affairs was the result of multiple concurrent technology booms, but any good journalist knows that readers remember the lede. I don't know why Lasker made the choice to put the console reference so high up in the story, but doing so was inflammatory, irresponsible, and counterproductive.

The world does not have vast and plentiful reserves of tantalum, and existing electronics that contain tantalum are, in general, not properly recycled. Continued strong demand for consumer electronics and the still-increasing penetration of cellular phones in the global market are combining to bring the price of tantalum back up. Thus, a rejuvenation of resource warfare in central Africa is becoming increasingly likely. The best defense against this scenario is for consumers to keep strong pressure on manufacturers and regulators to prevent "blood coltan" from making its way into consumer goods. The typical purchaser of a cell phone doesn't know anything about tantalum or its uses, and in fact the typical American probably couldn't tell you what continent the DRC is on. Awareness, then, is a precious commodity, especially for an advocate-journalist. However, awareness is diminished when you make game consoles into a scapegoat.

Even if you manage to heighten awareness of mineral wars in Africa with a piece like this, no good is done if the reader doesn't make the proper connection with his own life. Can you imagine a person reading the lede paragraph on his laptop or cell phone and cursing those darn gamers for carelessly supporting resource wars? I can imagine nothing else. Calling the conflict a "Playstation War" allows the non-gaming reader to shift the blame onto those darn gamers and ignore his own contributions to resource scarcity and conflict.

Are gamers to blame for the sustained conflict in the DRC? Sure they are — to precisely the same degree as anyone who owns a cell phone, laptop, digital camera, artificial joint, anti-lock braking system, etc. All of us should try to be conscious of the origins (and destinations, you non-cell-phone-recycling jerks) of the materials in our electronics, and pressing the companies that make them to ensure that our sale price doesn't subsidize war in Africa. Inordinately emphasizing the importance of game consoles in the financial origins of war in the DRC, however, lets non-gamers think they are off the hook, and amounts to little more than blaming the "other" for the sins of all. A putatively progressive organization like Toward Freedom should be capable of recognizing that, and ought to feel ashamed at having done so.

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Great Game Music

For those of you who have missed it, Greg Tannahill has a fun series of posts about great gaming music up at his blog, The Dust Forms Words. While I don't agree with all his selections (I prefer "Hikari" to "Sanctuary", for instance), and I think he ommitted some really good ones (more on that below), it's a great series of posts. Greg, who will soon be standing for election in Canberra, brings back happy memories of some really good games with great music, but he also dug up some very interesting renditions, such as the one below the fold.

Yes, those are musical tesla coils, and yes, that is the Mario Level 1-1 theme.

One of my favorites among the games he's mentioned is the opening theme to Katamari Damacy. You should follow that link and watch the clip, but be forewarned that hearing this music even one time will burn it permanently into that part of your brain that keeps songs in your head all day. I also think this is one of the best introductory sequences to a video game. Watching the intro doesn't prepare you in any way for the gameplay or the story, but the wacky visuals and catchy music put you in the right mood.

As I said, Greg missed a couple of great soundtracks. Rather than leave a snarky comment on his blog, I thought I'd include put some of the omissions in my own post.

The most obvious of these is Kō Ōtani's soundtrack to Shadow of the Colossus. You can find the whole soundtrack about eight times over on YouTube, but the following video will give you a good start.

One of the best parts about the sound design in Shadow of the Colossus is that it doesn't make every battle an exercise in overwhelming horns and heavy, pounding rhythms. Several combat sequences feature calmer music that builds tension with sinister or mournful undertones. Shadow of the Colossus would probably make the shortlist for best game of all time even if the soundtrack consisted entirely of kids beating sticks together, but featuring some of the best music in the history of gaming certainly doesn't hurt. "Revived Power" is one of my favorite heroic themes ever.

Second on my list of omissions is Christophe Heral's soundtrack for Beyond Good and Evil, which is simply amazing. One of the recognized high points is "Home Sweet Home", which plays over the credits and out on the water before you complete the Black Isle Mission. And my god, this piano arrangement of the main theme by Mythili Mahendran is fantastic:

The game that really cemented my love affair with computer RPGs was Betrayal at Krondor, and this was certainly helped by Jan Paul Moorhead's excellent midi soundtrack. This is harder to get these days, but I remember coming across some .ogg files from it not too long ago. Amazingly, YouTube actually had a clip of the credits (German version) to this great game, with the main theme playing over them. I actually prefer the funkier "Jimmy the Hand", which plays during this walkthrough, starting at about 0:18.

The PS2 had an amazingly vast library of RPGs to choose from, but perhaps the best, and certainly the most unique, was Shadow Hearts: Covenant. Playing fast and loose with history, it featured cameos from Roger Bacon, Anastasia, and Rasputin, blending its bizarre humor in with three convoluted and emotional love stories. And then there was the character who fights with a doll that can only gain new attacks if you give a particular tailor gay porn. The soundtrack was fairly diverse, ranging from creepy electronic themes like this one from the battle with Astaroth, to very placid piano and string pieces. Almost all of it was excellent, but I am inordinately fond of "Getsurenka", which played over the closing credits. Yes, it's almost hilariously overwrought, but after the "good" ending of Covenant a cathartic love song is precisely what you need:

There are certainly more that could go in here, but that's enough embedding for one post. If you're interested in more technical discussions of video game music, you should check out Cruise Elroy. Click his category link on the side to find the music posts.

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Microwave Pfu CelB 5 minutes for highest activity

Like many bachelors, I regularly eat meals heated up in a microwave oven. I'd like to think I eat a somewhat lower percentage of frozen dinners than others in my situation, but even when it comes to food I cooked myself I usually don't have the time or patience to cook a recipe for one every night. That means I'm often eating reheated leftovers from the trusty Radar Range. The microwave oven works using dielectric heating, a process in which the movements of dipolar bonds are coupled to an oscillating external field. Water, for instance, is a molecule with a large dipole moment, and when you cook something in a microwave a lot of the heating occurs by the accelerated movements of water molecules. In principle this kind of excitation should also occur for other kinds of polar molecules, and thus we come to an interesting study from the lab of Alex Dieters, in which microwave radiation was used to activate a cellulase from a hyperthermophile.

Protein backbones consist of series of peptide bonds which include a carbonyl group, a classic example of a polar bond. Naturally, one might expect that the motion of these groups would be excited by microwave radiation. However, it does not directly follow that additional motion of the peptide backbone will actually accelerate chemical reactions, because this motion may be chaotic or unproductive. Moreover, from the fact that microwaves cook things (like eggs), we know that microwave radiation does a good job of denaturing proteins, sometimes at lower temperatures than we expect. Both of these problems can conceivably be avoided by studying a hyperthermophilic protein.

Proteins from hyperthermophiles such as Pyrococcus furiosus tend to be stable and optimally active at very high temperatures, at or even exceeding the boiling point of water. At lower temperatures, they retain their stability, but tend to become inactive. In many cases this reduction in activity appears to result from squelching internal motions that may be necessary to bind or properly orient substrates. Young et al. decided to study the β-glucosidase CelB from P. furiosus as a way of understanding whether microwaves might enhance enzymatic catalysis. Because CelB has optimal activity at 110° C it should be possible to see a significant difference in activity if microwave activation works. The stability of this protein at high temperatures also suggests that you will not accidentally cook it.

Sharp readers will have noticed an obvious problem with this idea—because heat activates this protein, and microwaves heat aqueous solutions, we must incorporate some kind of control in order to determine the pure effect of the radiation as opposed to the temperature. Young et al. resolve this problem by monitoring the heating of the sample during microwave irradiation, and then using a normal thermal apparatus to match this temperature profile (Figure 2). When a reaction reached 40° C using either heating method, it was quenched by the addition of a basic solution and the concentration of products was measured. Simply heating the Pfu CelB reaction to 40° C produced negligible activity, but microwaving it increased the activity by 4 orders of magnitude (i.e. a factor of 10,000). Less dramatic, but still significant, effects were observed for two other hyperthermophilic enzymes, but an enzyme from a mesophilic organism (the almond) was not activated by microwave irradiation.

That the microwaves caused increased backbone motion was supported by the finding that irradiating Pfu CelB at 75° C caused it to denature; this temperature is well below the normal melting temperature of this enzyme (115° C). The authors attribute the differences in activation between CelB and the other hyperthermophiles to their lower optimal activity temperatures, but it is also possible that the particular motions enhanced by microwaves are simply not as productive in those molecules. Although all the dipoles should be affected in similar ways by microwaves, they are all oriented differently with respect to each other in the protein molecule. As a result, the induced motion may be chaotic, perhaps specifically so, and therefore the activation of a particular thermophile may depend on the nature of the motions needed for its catalytic cycle. Enzymes that require large ensemble motions of subdomains, such as adenylate kinase, might not be activated as much as a protein that simply needs to be melted a little. Examining the differences in structural dynamics of enzymes differentially activated by microwaves may be an interesting area of future study.

While microwave activation is unlikely to revolutionize some of the more common uses of hyperthermophilic proteins (i.e. PCR), it does have promise. In ligations, for instance, hyperthermophilic enzymes can not be used at present because many DNA inserts denature at the optimal active temperature. With microwave activation, it may be possible to employ extremophilic ligases in these reactions, gaining the benefits of their speed and durability without having to worry about accidentally melting your DNA. Depending on the enzymes available, this technique may also prove valuable in improving mobile medical laboratories and developing novel diagnostic tools for field work.

1. Young, D.D., Nichols, J., Kelly, R.M., Deiters, A. (2008). Microwave Activation of Enzymatic Catalysis. Journal of the American Chemical Society DOI: 10.1021/ja802404g

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It really isn't

"I don’t think riding in a fighter plane and getting shot down is a qualification to become president."—Gen. Wesley Clark (ret.)

I'm finding it difficult to see why this statement is considered to be at all controversial, despite the firestorm it has ignited in the conservative set. It is not an attack on John McCain's service nor is it a smear against him. I could almost find the outraged Republican blowback on this quote to be funny, if I didn't have a memory. Instead, I find it positively revolting.

It amazes me that anyone has to defend this quote at all, as our history has amply demonstrated that military service has no bearing on Presidential quality. Yes, the Army gave us Washington and Eisenhower. It also gave us such perennial entries on the shortlist for worst President in U.S. history as Franklin Pierce and Ulysses S. Grant. Even successful leadership at the rank of General does not indicate that one will perform admirably as a President. For Clark, a military man (and former Presidential candidate) himself, to point this out hardly qualifies as a smear. It's fair to say this comment is unnecessary, but absent any additional context, the histrionics of the McCain campaign are just unwarranted foolishness.

However, we are not without additional context, because in an amazing coincidence, one of the men delivering those histrionics was Bud Day. Yes, the very same Bud Day who was a member of the Swift Boat Veterans for Truth and appeared in one of their commercials. This man, who through ignorance or foolishness attacked Clark's perfectly sensible statement, had the gall to follow it up with a defense of the Swift Boat smears as "the truth".

That's why I can't just dismiss the McCain response as a good laugh. The outrage, feigned or not, of conservatives is positively revolting in light of the Swift Boat campaign. To see those who winked at the SBVT's outright slander of an American serviceman treat Clark's statement as some kind of blood libel is a repellent display of hypocrisy. For McCain, who claimed to repudiate the SBVT tactics, to employ SBVT members and take their money in this campaign only heightens my disgust. The maverick, the straight-talker, the man for whom I felt a good deal of respect all seem to have perished in the pursuit of the Presidency.

McCain's experiences in the Vietnam War, heroic as they were, have no bearing on his qualifications for the Presidency. His reaction to Clark's statement of this obvious fact, however, has me more firmly convinced than ever that he lacks the judgment, the restraint, and the integrity to lead this nation.

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It's just a _____!

I didn't intend to write a separate post on this topic. I'm no authority on philosophy and can't claim that I adhere to some superior standard of rationality in daily life. I wanted to leave the "just a game" thing alone, and let my comments on the relevant post at Dan Bruno's site be my final word. But then someone left a comment at my Tin Man post, attempting to blunt the criticism with the idea that it was just entertainment. Now, despite the fact that I happen to think that some things really do fit into this category, the use of this phrase as an argument annoys me, because it is no argument at all. So here's my position. It's probably not art, but you might be entertained.

"It's just a game," or "It's just an action flick," and other statements of their ilk almost always betray a mental sloth, an unwillingness to actually engage the arguments presented. When someone responds to an argument in this way he displays a fundamental disinterest in the discussion, but also a foolish pride in that disinterest. Because he does not view the subject as worthy of discussion, he concludes that this viewpoint must be valid for everyone else, and proclaims it as a fact. However, even if it is true that some games are "just games", then that must be proven, not simply asserted. The statement incurs a burden of proof, and anyone unwilling to try meeting that burden probably shouldn't be saying anything at all.

Leaving aside for the moment the question of just how that statement can be proven, everyone ought to know that proving it doesn't put a close to the discussion. That a particular game is "just a game" doesn't preclude meaningful and interesting discussion about the way the game is made or the values that went into it. An example of this came up in the comments to Dan's article. Few people would dispute that a golf simulator is "just a game", and I am not one of them. Nonetheless, Michael Abbott says some very interesting things in comparing the presentation of the Tiger Woods games to Hot Shots Golf, and about simulations generally. Of course, we can also address the quality of the entertainment experience, i.e. its artisanship, which I tried to do in the Tin Man piece: I thought it didn't actually do a very good job of entertaining me because of its inconsistency. Even if everyone in the universe agrees that Ballistic: Ecks vs. Sever is so far from being art that it might not even deserve italics, we can still discuss whether the boom mike drops into the scene and what that does to the entertainment value of the film.

This brings me to another point: the failure of a piece of media to achieve anything artistically is a valid criticism of its entertainment value. We all accept that different people are entertained by different things. Gamers, whose tastes are often fragmented along genre (or even subgenre) lines should be especially aware of this. The other night I came across this fundamentally fair review of Baroque, which sent commenter Gen Eric Gui over the edge. His problem was that the author did not judge it strictly on its merits as a Roguelike, and he really likes Roguelikes, and thus loved Baroque. Everyone who has ever discussed games with any regularity has had a conversation just like that. Well, here's what I really, really like: games that do something interesting artistically. That plays a significant role in deciding whether a game (or book or movie, for that matter) entertains me. There's not some mystical wall dividing art on one side from entertainment on the other. Art does entertain, or at least it can; otherwise we probably wouldn't have it. So when considering whether a piece of media succeeds as entertainment, it's reasonable to ask whether it has some artistic merit that can help entertain people who get turned on by that sort of thing. Tin Man didn't have it, or at least not enough. Neither, in my opinion, did Baroque.

So does it matter that something is "just a game"? I think it does; achieving some kind of consensus on that point gives us a good idea of where to direct our mental energies. If it is true that a particular game (movie, etc.) is entirely without artistic merit then we ought to focus our discussions of it on the artisanal aspects of its construction. Halo probably isn't art, but it contains art, as well as artful design, from which much can be learned. Shadow of the Colossus is art, and we could do worse than discussing its artistic qualities, in addition to or instead of studying its artisanship. Directing the discussion into a particular area, however, shouldn't exclude efforts to see whether there is some merit.

Here we get to the question of how we can prove, or at least support, the statement that something is "just a game". I have to admit, I use a pragmatic rather than an analytical standard here. My experience is that it's virtually impossible to prove that a particular piece of media (let alone an entire medium) is art. My standard therefore is not analytical proof, but simply whether the premise "X is a work of art" leads us anywhere interesting. In plenty of cases, including Halo (Roger Travis' view notwithstanding) and sports simulations, I think it doesn't. We can say very interesting things about these games, but those things don't need the premise that the game is a work of art. In contrast, I think you would need to accept that No More Heroes or The Two Thrones are art in order to fully appreciate them. That doesn't mean that we have to uncritically accept every attempt at artistic discussion, but we are obligated to reply, with more than just "nuh-uh, it's just a game".

Sometimes a game is just a game, and I honestly don't have any problem with that. Plenty of games (and other media) are very entertaining without having much artistic merit at all. But the statement that a work is just entertainment is not a rebuttal of reasoned argument to the contrary, nor is it a valid way to deflect criticism. And really, because artistic content is (or at least can be) part of the entertainment value, it's not any kind of response at all. "It's just a game" isn't a response that's automatically invalid, but saying those words doesn't make them true. It's a statement that must be substantiated and shown to be relevant, just like any other argument. If you're not willing to go through with that, then perhaps you don't really have anything to say at all.

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Toccata and fugue in the postapocalyptic wasteland

Baroque is a Playstation 2 / Wii remake of a Playstation remake of a game originally made for the Sega Saturn, and although I am happy, in a way, that it traversed this long chain of production I cannot quite figure out why it did so. Even loose Roguelikes are not usually a winning commercial proposition, the popularity of Persona 3 notwithstanding, and Baroque lacks the concessions that would allow it succeed more broadly. For all its faults, though, there are some interesting ideas in Baroque that deserve some thought.

Spoilers, as usual, after this line of text right here, goddammit.

Baroque takes place in a post-apocalyptic wasteland, and while the fact that it is a wasteland is apparent immediately, that it is post-apocalyptic is something that you must learn, because the main character begins without any memory. Now, Wlad and Michael Abbott and maybe a few others of you know that I usually loathe amnesia as a narrative mechanic, but I did not mind it here. Mostly this is because the majority of games use amnesia as an excuse for long explanatory monologues, while Baroque just tosses you into the story without explaining much of anything. As you stumble forward in the world you encounter an Archangel who gives you a special gun and urges you to make your way to the bottom of a place called the Neuro Tower and use the gun there. "Use it," he urges, "There is meaning in you using it."

The Tower is a dungeon filled with creatures that were once human, but who became twisted into something else by "baroques", twisted ideas that come to dominate their minds. In the world that exists after the apocalypse, ideas that distort the mind can warp the body, and sometimes they remain in the form of a crystal after the body's destruction. By gathering these crystals, and exploring the tower, the nameless main character learns more about the world and its past. The catch, however, is that the Neuro Tower allows travel only in one direction (downwards). To depart the tower and learn from the people in the outer world, the hero must die. He then reappears in the world, having lost all his items (though some can be transferred from the dungeon and found outside) and progress (he is reverted to level 1). To proceed in the story, he usually must enter the dungeon and make his way to the bottom once more.

The hero learns that he, the surviving one of conjoined twins, was fused with God, whom the Archangel had driven mad in part by removing her pain. The Archangel separated the hero from God, causing the apocalypse. The hero must return certain ideas and pain to the multiple personalities that split off from God, and then fuse with her to adapt some kind of livable world from the current existence.

This whole scheme, in my opinion, is practically bursting with potential. One ideal route would be to highlight that the repetitive mechanics make the traversal of the tower a baroque for the main character (or the player). The idea of pain as necessary for sanity, and the parallels between the hero's and God's feelings of incompleteness make for interesting thematic territory. If you wanted to turn the game into a commentary on games and gaming (despite my love of No More Heroes this is not something I generally advise), the subversion of traditional RPG goals would give you a lot to work with. Yet Baroque never really does any of these things; it is simply satisfied to present its minimal story and its Roguelike dungeon and to let you imagine the wonderful things that could have been done with this premise.

Part of the problem here is the repetition; putting repetitive tasks in a game always involves walking a fine line between holding the player's interest and annoying him, and Baroque definitely teeters over into the latter. The real-time combat is dull, and the hero doesn't really become any stronger by leveling up. Instead, the character's strength is almost completely dependent on the items he finds in the tower. Because so many of the items he can find are harmful to him (a common element of Roguelikes), the hero's ability to fight and survive is almost totally random. Because of this, actually fighting through the levels is, after a certain point, a total waste of time. It's better just to run whenever you can. I am still on board for this, but if fighting through the levels is not a worthy end in itself then a game needs to have something else to draw the player along. Baroque doesn't.

Baroque just has too little content to support even the minimal amount of play necessary to finish the game (judging from some FAQs, the game can be completed only entering the Tower 3 times, though it took me 10 attempts to fumble through). Part of the problem here is that the most interesting parts of this tale happened in the past. The backstory of the game is very tense, very emotional, and involves some interesting ideas, but the reality is that you are just playing the epilogue of that epic. Although the pace at which the past is revealed is good, the story doesn't really have an arc, or develop any tension beyond the player's increasing annoyance at going through the Neuro Tower again again. Moreover, the Christian and Kabbalistic imagery is pretty worn at this point, though perhaps it was fresher when the game was first made.

I won't fault Baroque just for being a Roguelike. However, it is fair to complain that the dungeon crawl just isn't entertaining enough to sustain a game on its own, the story isn't strong enough to compensate, and the thematic possibilities never become realities. From its confusing beginning to its end, Baroque repeatedly flashes signs of brilliance, but it never really delivers on the promise. Somebody could make a great game out this.

Sadly, nobody did.

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EGCG disrupts amyloid oligomers

As I mentioned in my post on the recent paper by Kukar et al., the disruption of amyloid plaques has been an ongoing focus in Alzheimer's disease research. However, plaques and inclusions are of concern in many diseases, and as a result there is a great deal of interest in finding molecules that can either dissociate, or prevent the formation of, amyloids of many different kinds of proteins. In the most recent issue of Nature Structural and Molecular Biology there is a paper suggesting that (-)-epigallocatechin gallate (EGCG) may be able to interfere with multiple proteins that form β-rich aggregates.

EGCG is a chemical found in green tea (although it is doubtful you could realistically drink enough green tea to absorb the concentrations used in this study). Previous studies had suggested that it altered the aggregation behavior of α-synuclein (αS) and huntingtin. So, Ehrnhoefer et al. use highly purified EGCG in a number of experiments to determine what effect it had on αS and the amyloid-β peptide (Aβ) (1). What these proteins have in common, besides the fact that their aggregation is associated with disease, is that the single proteins take on a β-strand structure that assembles into fibrils.

Ehrnhoefer et al. find that EGCG interferes with some aspect of this process, reducing the formation of the fibrils while inducing the formation of some alternate oligomeric structure. In the case of αS, the result is a spherical oligomer (Figure 1), although the gel filtration results indicate that a large spectrum of oligomeric states is formed at lower concentrations (the trace suggests that these oligomeric forms are interconverting during elution). NMR and other data show that EGCG associates directly, but non-specifically, with the protein backbone, and that the compound has strongest affinity for the C-terminus of αS, which may play a role in preventing aggregation. The EGCG-treated oligomers had reduced β-strand content (as assayed by CD). Treatment with EGCG appeared to reduce αS toxicity in cultured cells, although this was measured strictly in terms of cell death.

Similar results were seen with Aβ—addition of EGCG reduced the formation of fibrils and the toxicity of amyloids towards cultured cells. Again, the oligomers formed in the presence of EGCG could be quite large, and took a spherical shape.

Based on these data, the authors propose that EGCG binds preferentially to unfolded proteins and interferes with the formation of regular β-strand structure. The EGCG-bound proteins are unable to form fibrils, and therefore EGCG oligomers compete with fibrils for monomers, slowing the formation of the latter. The net effect is to divert these unfolded proteins out of amyloidogenic pathways and into alternate oligomeric structures, which appear to be nontoxic, or at least less toxic.

Can EGCG or a derivative be turned into a drug to treat Alzheimer's disease, or a general treatment for amyloidoses? This is an uncertain proposition. As the authors of a commentary (2) in the same issue of NSMB note, EGCG's nonspecific assault on amyloids may damage some normal structures built on this architecture. Moreover, because EGCG seems to bind unfolded regions nonspecifically, it has the potential to interfere with any of the numerous signaling proteins that possess such regions. The potential for side effects is very high, and the continued viability of cultured cells in the presence of EGCG, while reassuring, is not a particular reason to believe the compound is safe at high concentrations in the human nervous system.

The promiscuity of EGCG's interactions with unfolded regions poses another problem, in that all these proteins will act to interfere with EGCG's action on its intended target. Fairly high ratios of EGCG were necessary in these assays, and they mostly involved purified proteins. In vivo, all unfolded proteins will act to titrate EGCG out of plasma, meaning that significant quantities of this (or any other non-specific molecule like it) would need to be used in order to achieve the desired effect. This again raises the likelihood of side effects.

Of course, the most severe complication arises from the nature of amyloidoses themselves. Although the obvious presence of plaques and inclusions naturally leads us to suspect that these aggregates are the agents causing the disease, increasing evidence suggests that amyloids are merely the endpoints of some other process that is the actual culprit. In the case of Alzheimer's disease, for instance, a recent article in Nature Medicine has provided very strong evidence that soluble Aβ dimers are the dominant contributors to Alzheimer's pathophysiology (go check out Ashutosh's excellent discussion of this article over at The Curious Wavefunction for more information). Now, given that these dimers do eventually form amyloid, it seems likely that they have β structure in their pathogenic form, which EGCG will probably disrupt, but this is not guaranteed. Small molecules like EGCG that prevent deposition into amyloid may actually exacerbate the problems they are meant to solve. Further research is needed to establish that the EGCG oligomers of αS and Aβ are not toxic in vivo.

Diseases associated with protein aggregation continue to pose a challenge precisely because we have such a poor handle on their pathogenesis. Ehrnhoefer et al. clearly demonstrate that EGCG possesses the ability to alter the behavior of amyloidogenic unfolded proteins. While that may imply that it has promise as a broad-spectrum drug to attack these diseases, the promiscuity of its action is a cause for concern from the perspective of dosage and side effects. And, because soluble oligomers may well be the pathogenic species in many (if not all) of these diseases, our optimism about this approach must be tempered with an awareness that the actual effect of EGCG may be to enhance, rather than diminish, the toxicity of the relevant protein targets.

1. Ehrnhoefer, D.E., Bieschke, J., Boeddrich, A., Herbst, M., Masino, L., Lurz, R., Engemann, S., Pastore, A., Wanker, E.E. (2008). EGCG redirects amyloidogenic polypeptides into unstructured, off-pathway oligomers. Nature structural & molecular biology, 15(6), 558-566. DOI: 10.1038/nsmb.1437

2. Roberts, B.E., Shorter, J. (2008). Escaping amyloid fate. Nature Structural & Molecular Biology, 15(6), 544-546. DOI: 10.1038/nsmb0608-544

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Recent play rundown

Most of the games I've played since finishing The World Ends With You simply haven't done much for me, regrettably. One or two were inspiring, and I'll talk about them at some point when I've had more of an opportunity to digest them, but the majority either disappointed me, or just didn't leave me with much to say about themes or characters. Still, I had some thoughts about these games I wanted to put down. So if you're interested in my opinion of Insecticide, Penny Arcade Adventures Part One, Fire Emblem: Radiant Dawn, or Final Fantasy Crystal Chronicles: Ring of Fates, read on. If you're not, well, screw you; it's my blog.

I didn't finish Insecticide; I may have only barely started it. This was a game I wanted desperately to like, and in fact, except for one incident of what Yahtzee might call "moon logic", I loved the hell out of the adventure portions of it. The ones I worked through weren't anything special in terms of the gameplay, but they were cleverly written and funny, and they successfully evoked happy memories of point-and-click adventure games. However, I loathed the combat portions, to the degree that I ultimately tossed the game aside in frustration. I'm not sure whether the combat segments seemed like a good idea earlier on or what, but at some point someone should have realized that movement was awkward, the controls were sluggish, and they would have a much better game if they skipped all this crap and just put more detective work in. Were the developers really convinced the shooter segments were good? Did they start down a road they couldn't back out of? I can't say. I just wish it had turned out differently.

Continuing with the DS, I followed Insecticide by trying out Final Fantasy Crystal Chronicles: Ring of Fates, a game I finished, but one I also felt fell short of the mark, at least as a single-player experience. The controls weren't so bad, but there were two significant problems. The first was that casting spells was just slow and clumsy. The second was that the only way to get maximum use from the game would be to use your hands for both sets of buttons and the stylus simultaneously, which was awkward and uncomfortable. The AI governing your allies was awful; about all they were good for was wasting your magicite. The platforming was needlessly complicated by your inability to look around the rooms you were passing through. And then there was the story, which worked in a perfunctory way, but strained credulity to the breaking point and ended in an incoherent, unsatisfying mess. If Chelinka really had sacrificed herself, if it had been a bittersweet ending instead of a saccharine one, I would have thought better of it.

Moving from the DS to the Wii, I finally finished Fire Emblem: Radiant Dawn. I loved the previous entry in this series, the Gamecube's Path of Radiance, but I felt let down by the sequel. Part of this was due to the fragmented nature of the narrative. What I liked most about Path of Radiance was taking the Greil Mercenaries from marginal competence to mastery; here there's no continuous arc. Rather, you get thrown back and forth between sides of a very large conflict, leaving some characters behind for several chapters. When you see them again, you've practically forgotten who they are, or why you care if they get killed. This will happen, because when you see them again they are often absurdly under-leveled. Perhaps to compensate for this, you are frequently given a vast army of high-level warriors, most of whom seem to have been lobotomized with a trebuchet. Due to their large numbers the ally turns take quite a while; their extraordinary stupidity makes these phases seem even longer.

A side effect of the construction is that the cast feels far too large, an impression only exacerbated by the replacement of the charming support conversations that took place in camp in Path of Radiance with boring, generic support conversations that take place in the field. This gives you much less of a handle on the characters' personalities, and excises the side plots of the first game. The story of Soren's lineage in that game was one of my favorite discoveries; there's nothing quite like that here. That's a pity, because the main plot of Radiant Dawn is an insipid mess. In Path of Radiance, Ashnard was crazy, but at least he had a goal and took concrete, sensible steps towards it. The villains of Radiant Dawn are apparently evil just to be evil, without any apparent aim or coherent strategy. This is a narrative sin in any game, but it's especially absurd when the gameplay is built around strategic and tactical thinking. The battles where you don't have too many allies are entertaining, but there's no basis for an emotional connection to the characters or the story. You're better off playing chess.

Well, enough being mean. Let's talk about something I really enjoyed: Penny Arcade's On the Rain Slick Precipice of Darkness. As writers of some of the excellent blogs in my sidebar and Blägroll have noted, OtRSPoD doesn't really do anything vastly original in terms of story or gameplay. It's a decent fusion of fairly standard RPG mechanics and point-and-click adventure that has two significant virtues. The first is that it does almost everything right, and the second is that it is great fun to play. The game world is populated by hilarious characters and enemies, and unlike many entries in the genre, OtRSPoD doesn't punish you for trying to see all of it. The concepts are funny, the dialogue is entertaining, and the combat is fun, although I found using items to occasionally be something of a drag. The humor probably isn't for everyone (does a creepy, libidinous juicer sound funny to you?), but if you can see the appeal in fighting a dread mime deity from beyond the edge of reality with a magic rake, it's worth giving Episode One a whirl. I'm pretty sure I'll be grabbing Episode Two.

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A conformational equilibrium controls the Vav DH domain

One emerging view of allostery, and protein behavior generally, describes function in terms of pre-existing equilibria. In this view, proteins are not like switches that get turned on and off, but rather are like dials that are turned "more on" or "more off" depending on the conditions. In this view, regulatory modifications such as phosphorylation do not enforce an active conformation so much as promote it. Because some relaxation measurements are sensitive to conformational exchange, NMR is well-suited to examine systems with this behavior. In the most recent edition of Nature Structural and Molecular Biology, a group from Michael Rosen's lab discover that this kind of equilibrium is governing the behavior of the DH domain from the Vav protein.

Vav activates Rho GTPases by inducing the exchange of GDP for GTP, making it a Guanine nucleotide Exchange Factor (GEF). This activity is performed by the DH domain, and is inhibited by a small neighboring element called the acidic region (Ac). As you can see from the figure of the combined Ac and DH domains (AD) at right, Ac (red) inhibits the DH domain (blue) by forming a helix that binds to the active site (explore this structure at the PDB, noting that the numbering is off by 167). Phosphorylation of Y174 (red side chain) unfolds the helix and exposes the active site, which would be a nice model except for two things. First, as you can see, Y174 is pretty well buried in this structure, which would make it difficult to phosphorylate. Second, mutation of Y174 to phenylalanine, a residue that cannot be phosphorylated, activates DH domain activity. How can Y174 get phosphorylated? What is phosphorylation actually doing?

One possible answer is that the existing structure doesn't tell the whole story. A protein, after all, doesn't have just a single structure, but rather an ensemble of structures across a population or time. While AD may spend most most of its time in this inhibited state, it's possible that sometimes it adopts an alternate conformation that allows Y174 phosphorylation. Li et al. set out to assess this possibility using measurements of R₂ relaxation dispersion. Residues that have a large field-dependence of transverse relaxation (ΔR₂) are undergoing some sort of conformational exchange process that changes their chemical shift between two or more states.

Using CPMG experiments on methyl-bearing side chains, Li et al. identified two groups of residues engaged in conformational exchange processes, shown at left. The first group (orange side chains) have a large ΔR₂ that vanishes once Y174 is phosphorylated. The second group (green side chains) have high ΔR₂ in both the phosphorylated and unphosphorylated states, but the rates are slightly higher in the former. Residues that were observed to have low ΔR₂ are shown with gray side chains. All of this indicates that there are two dynamic processes occuring on the microsecond-millisecond timescale. The first encompasses some change in the chemical shift of the acidic helix, while the second involves some unknown process. However, because the Group 2 residues react to the phosphorylation state, these processes are likely linked in some way. I notice that the Group 2 residues are clustered around loops and joints in the upper half of the domain (in this view), while residues not adjacent to loops or joints do not appear to have significant ΔR₂. It is possible that the observed dispersion represents some flexing of the domain around these loops, and that the rate of this motion increases slightly when the binding site is unoccupied.

That's all very interesting, but it's also bad news for the analysis, because it means the observed relaxation dispersion would have to be fit to a four-state model in order to obtain populations and kinetic parameters. Previous analysis by several groups has shown this to be a dubious proposition, so Li et al. take an alternative approach. Rather than try to fit out populations from the dispersion data, they make a series of mutations to AD to push the populations of the two states in one direction or the other. They find a number of states where the methyl peaks lie on a line between the open (phosphorylated) and bound (unmodified) states. The Y174F mutation lies very close to the phosphorylated state, interestingly enough, implying that the phosphate group itself is not a significant determinant of chemical shifts in the open state. Using a combination of HSQC peak positions and ΔR₂ measurements, Li et al. determine for each mutant or modification what population of the ensemble is in the open state. They find that this NMR-assigned population correlates with the rate constant (k_cat/K_M) for phosphorylation.

This implies a model in which regulation of DH by Ac involves an equilibrium between the bound and open states. In the bound state, Ac forms a helix in the binding site, an effect strongly dependent on a hydrogen bond to the OH of the Y174 (R332 may be the partner here). However, in this state Ac samples the open state about 10% of the time. While in the unbound state, Ac can be phosphorylated, a modification that prevents helix formation or binding; probably by steric interference in the binding site. This stabilization of the open state dramatically increases the chances that the Vav DH domain will be in an active state when it encounters a target. Thus, DH regulation depends on a population shift of an underlying equilibrium, not a singular on/off switch. This model has the advantage of accounting for how Y174 gets phosphorylated and why a mutation that prevents phosphorylation nonetheless leads to a constitutively activated state.

In vivo, Vav consists of many other domains in addition to the AD construct used here. These domains are known to contribute to the inhibition of DH; given these results it is probable that they do so by stabilizing the bound state. Because Ac binding causes the formation of a negatively-charged surface on one side of the helix, charge stabilization is a likely mechanism. Further research will hopefully identify these mechanisms, as well as the origin of the second conformational exchange process revealed by the experiments in this paper. This study is a good example of scientists making the best use of limited data to describe an instance of this important, but difficult to characterize, regulatory mechanism.

1. Li, P., Martins, I.R., Amarasinghe, G.K., Rosen, M.K. (2008). Internal dynamics control activation and activity of the autoinhibited Vav DH domain. Nature Structural & Molecular Biology, 15(6), 613-618. DOI: 10.1038/nsmb.1428

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Structural dynamics of PDZ allostery

If Michele Vendruscolo were trying to get me to blog about one of his papers, he could hardly have assembled a more perfect lure than his upcoming paper in JACS. It brings together all sorts of things I've been talking about on this webpage: NMR dynamics, MD simulations, and dynamics-driven allostery (in the PDZ domain, no less). Previous investigations of this PDZ domain indicated the existence of a network of residues that had a dynamic response to ligand binding. Dhuselia et al. extend this work using molecular dynamics simulations constrained by the existing dynamics results. This leads them to discover not one, but two networks in the PDZ domain, with different properties.

NMR experiments have enormous power to sensitively detect changes in dynamics resulting from a perturbation, but they are also quite limited. Because of the models we use, the parameters we can fit out of relaxation data only give us information about the magnitude and timescale of fluctuations. Chemical shift overlap and interference caused by nearby dipoles limit the number of probes. Moreover, because NMR can only measure an ensemble, it is practically impossible to extract anything other than the most general information about correlated motions. MD has answers to all of these problems, but as a general rule has done poorly at reproducing NMR data about side-chain motions, calling the validity of the conclusions into question. Vendruscolo has taken some interesting strides in this regard by employing the limited experimental dynamics data as a component of the energy function. By constraining the simulation to mimic the known dynamics, we can hopefully learn more about the sites to which we are blind, as well as what kinds of motions the experiment is sensing and how they are linked.

In this instance, the authors make use of the PDZ domain previously studied by Ernesto Fuentes in Drew Lee's lab (there was also some hack working there at the time). Ernie's research followed on previous evolutionary studies indicating a network of communication in PDZ domains (local summary here), and Ernie found, by comparing the dynamics of the free and ligand-bound states, that changes in motions propagated away from the binding site to two distal surfaces. The pathways of communication compared pretty well with the evolutionary results. Dhulesia et al. aim to extend these results by determining which motions are correlated and identifying the mechanisms by which energy is transmitted. They accomplished this by running multiple parallel simulations of the free and ligand-bound states of the PDZ domain constrained by Ernie's dynamics results, as well as NOE and ³J data.

They find that two regions of the protein have correlated motions internally and move in an anticorrelated fashion relative to each other (Figure 3A). One of these regions consists of part of the binding site and all of distal surface 2 (DS2), while the other includes the other half of the binding site and all of distal surface 1 (DS1). When the ligand binds, something interesting happens. The motions of DS2 become more tightly correlated to the motion of an area around V30. The tight correlation between the motions of DS1 and α2 (an element of the binding cleft) switch to a slight anticorrelation.

When a ligand binds to a protein we expect a broad increase in rigidity of the complex so that the proper orientations of bonding pairs are maintained. For the most part, the simulations affirm this expectation, but not for all regions. For the binding site and DS2, the backbone mobility decreases, as expected, but the backbone mobility of DS1 increases (I am going off the text and Table 3 here, rather than Figure 3). The side chains have a similar response. This agrees with other studies indicating that the change in conformational entropy upon binding a ligand need not be homogeneous. What is more interesting is that these results imply that opposite coherent responses can be induced in a small domain by a single stimulus.

Although (as far as I know) this PDZ domain has no allosteric behavior in vivo, one can imagine that the binding of a ligand at the cleft could alter the binding of other modules to this domain. The entropic penalty for binding to DS2 would be lower in this case, while the penalty for binding to DS1 would be higher. The opposed nature of the dynamic responses may be related to the broad regional anticorrelation of free-state motions; disruption of this mode (by linking the motion of β2 and α2) may shunt that energy into DS1.

The authors also find, using a series of structural parameters, that a set of residues have clear structural changes. Some of them appear to be associated with coupled changes in rotameric states; the authors map out one pathway in Figure 5. Because it is a rotameric pathway, it should be possible to test whether it is essential to communication experimentally—mutation of the intermediary residues should abolish the linkage. The authors also carry out a network analysis to identify the most connected residues, a prediction that may also be testable by mutagenesis. These "structural network" residues overlap only slightly with the dynamic network, and indeed do not generally intersect with the evolutionary network either. In the absence of identified allosteric behaviors or clear energetic connectivities it's difficult to say what this disjunction means. However, the residues undergoing structural changes surround most of the residues undergoing dynamic changes. It is possible that these changes in structure provide the context that allows the changes in dynamics (or vice-versa); the two properties are inextricably linked.

Although communication between the binding site and distal surfaces is proven in this PDZ domain, and appears to be a general feature of the fold, the absence of a known function for the propagation in this instance makes it tough to assess the quality of these results. However, the findings of Dhulesia et al. make it clear that this approach can produce testable predictions and explanations. Hopefully this approach will be employed in the near future to study PDZ domains known to possess allosteric properties.

1. Dhulesia, A., Gsponer, J., Vendruscolo, M. (2008). Mapping of Two Networks of Residues That Exhibit Structural and Dynamical Changes upon Binding in a PDZ Domain Protein. Journal of the American Chemical Society DOI: 10.1021/ja0752080

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Determinants and evolutionary mechanisms of homosexuality

Debates over the rights of homosexuals in the United States, particularly the right to marry, often get hung up on a thoroughly inane point: whether homosexuality is "chosen" or "innate". While this may seem to be a question of moral import, it is not, and moreover it presents a false dichotomy. Like nearly all human behaviors, sexuality is too complex to be reduced to a choice or a destiny; it is neither, or both, depending on your view. However, the degree to which different factors contribute to sexuality, and the mechanisms by which they do this, are fit subjects for scientific inquiry. Two articles this week present interesting findings, sure to be distorted by all sides of the argument, that may prove enlightening in this regard. I will endeavor, along with others, to be a resource providing an unbiased view.

First, however, a plea for sanity. If science finds, by some transcension of nature, that sexual orientation is entirely chosen, or entirely innate, it does not matter to any debate over the rights of homosexuals. Men may have an innate tendency to try to spread their genes as widely as possible, but we would not forgive adultery on this basis. Toddlers have an innate tendency to become frustrated and throw tantrums, but we still make them sit in the corner. That a behavior is innate is not a basis for withholding moral judgment. And if sexual orientation is a choice? Well, we frequently forbid discrimination on the basis of chosen behaviors—religion, for instance, or political affiliation. What is truly at issue is not choice, but whether it is just to deny rights and protections to one group of citizens for no reason beyond the moral opprobrium of another group.

Thus, the question of rights for homosexuals does not depend, one way or the other, on whether people choose to be gay. I firmly believe one side of this question to be in the right, but this opinion is not informed by my scientific knowledge, because it cannot be. I would urge my readers (all three of you) to view these results strictly as what they are: interesting scientific findings related to a political question that do not support one side of the argument or the other. I would ask advocates for both sides to refrain (for once) from distorting the conclusions of these reports, not only because of the raw immorality of lying, but because by misrepresenting these findings they will have sacrificed their integrity for no gain in the debate.

There, I feel better now. On to the science!

In the first study, a team analyzed the results of a survey of Swedish twins in hopes of parsing out the relative contributions of heredity, shared environment, and unshared environment in shaping sexuality (1). Although the survey was answered by a fairly large number of twins, the authors draw their conclusions using two questions that do not directly ask for sexual orientation. The survey only requested information about actual sexual partners, and did not address homosexual feelings that might not have been acted upon. After excluding twin pairs that were opposite-sex or unclear with respect to zygosity, they had 3826 pairs to work with, of which 5% of men and 8% of women reported at least one same-sex sexual encounter. Because it is suspected that the factors influencing homosexuality may differ between the sexes, males and females were treated separately. By comparing the concordance and discordance of sexual behaviors between monozygotic and dizygotic twins it should be possible to parse out the degree to which genetics and the environment contribute to sexuality.

Despite the limited materials, the authors were able to reach some conclusions, with the caveat that the 95% confidence intervals were quite wide. For instance, for males they found that genetic factors explained 39% of the observations with respect to whether a twin had any same-sex partner in his life. However, the 95% CI on this prediction was 0% to 59%. For men, shared environmental factors appeared to contribute nothing, while unique environmental factors explained 61%. For women, it was determined that genetic factors contributed 19%, shared environment 17%, and unique environment 64%. Similar distributions were seen for comparisons of total numbers of same-sex partners. While the confidence intervals for all factors are quite large, the numbers largely agree with a previous study on Australian twins (less so with a study on American twins).

Obviously, the small sample size and broad confidence intervals on these results suggest that they should be interpreted cautiously. It should also be noted that "unique environmental factors" may run the gamut from hormone exposure in utero to childhood illness to personal experiences. Many unique environmental factors, even for twins, are just as involuntary as genetics, but some result from conscious choices of the individual (which is different from choosing to be gay). Despite their limitations, these results generally support the idea that sexual orientation results from a confluence of genetic and environmental factors.

That genetics play a role in homosexuality may seem curious, because in terms of the classic expression, "survival of the fittest", homosexuality would appear to be a non-starter. After all, a reluctance or outright inability to mate with the opposite sex would seem to result in a substantial reduction in reproductive fitness. However, contrary to what a certain ignoramus would have you believe, the Theory of Evolution has advanced substantially since the days of Darwin, and we are aware of numerous additional evolutionary mechanisms that operate alongside the law of natural selection. In the case of male homosexuality, a new paper by Camperio Ciani et al. argues that sexually antagonistic selection may be at work (2). PLoS ONE is open access, so feel free to open up the article in another window and skim it yourself.

Camperio Ciani et al. begin with the observations that male homosexuality has a matrilineal association, and that the mothers (and maternal aunts) of homosexuals are somewhat more fecund than the population at large. From these pieces of data, and from the fact that homosexuality appears to have been present at low levels in every society that has left written records, the researchers created a set of requirements for some evolutionary simulations, based on different supposed properties of the genetic factors influencing male homosexuality (GFMH). Most of the simulations failed to satisfy the parameters. In many cases (especially with single-locus traits) the GFMH either became extinct or gained too high of a frequency; in others the matrilineal association was not preserved.

Ultimately, the researchers found that the model that best fit the parameters featured two alleles (one of them X-linked), and was sexually antagonistic. What this means is that the trait increases the reproductive fitness of one sex while decreasing that of the other. For instance, a heightened sexual response to men could make women more likely to pass on their genes, while making men possessing the trait less likely to do so. Provided that the effects of this trait are balanced with respect to the population proportion of each gender, it should be possible for it to survive in a population at a relatively constant level.

This result is interesting, and provides some hypotheses that can be tested with genetics. However, it does not prove that homosexuality is genetic, or even that it has a genetic component. Like all simulations, these results merely inform us that a particular possibility is consistent with what we already know. In this case, we now know that the observed aspects of homosexuality are consistent with a 2-locus trait that is sexually antagonistic. However, this model was arrived at simply through process of elimination, and there may be some superior model or more-accurate mechanism that simply hasn't yet been tested. There is always a model we haven't thought of; sometimes that model is the right one. Moreover, as Långström et al. note, some of the data used to determine criteria for successful simulations remain controversial. Camperio Ciani et al. convincingly show how the preservation of homosexuality through evolution could happen, but that is not the same as demonstrating how it did happen. That will require a positive identification of the actual GFMH.

The results of Långström et al. indicate that any GFMH eventually identified, whether or not they materially resemble the predictions of Camperio Ciani et al., will only give rise to a heightened propensity for homosexuality. Environmental factors play a significant, perhaps even dominant, role in determining sexual orientation. Whether genetic or environmental, most factors contributing to homosexuality are involuntary, but some are chosen. If that answer doesn't satisfy you, perhaps you were asking the wrong question.

1. Långström, N., Rahman, Q., Carlström, E., Lichtenstein, P. (2008). Genetic and Environmental Effects on Same-sex Sexual Behavior: A Population Study of Twins in Sweden. Archives of Sexual Behavior DOI: 10.1007/s10508-008-9386-1

2. Camperio Ciani, A., Cermelli, P., Zanzotto, G., Brooks, R. (2008). Sexually Antagonistic Selection in Human Male Homosexuality. PLoS ONE, 3(6), e2282. DOI: 10.1371/journal.pone.0002282 OPEN ACCESS

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NSAIDs bind to amyloid-β

One of the best-known features of Alzheimer's disease pathology is the formation of proteinaceous amyloid plaques in the brain. In Alzheimer's disease these plaques are primarily formed by the amyloid-β peptide (Aβ) derived from the amyloid precursor protein (APP) by the action of β- and γ-secretase. The length of the Aβ peptide varies, but the 42-residue form (Aβ42) is more likely to form plaques and fibrils. Although it remains uncertain whether plaques are a cause of Alzheimer's disease symptoms, or merely an effect of some underlying derangement, finding some way to prevent or reduce plaque formation is a major goal in the field. This week in Nature, a team of researchers from institutions all over the US and Europe show that non-steroidal anti-inflammatory drugs (NSAIDs) may be able to accomplish these goals by binding to APP and Aβ directly.

Previous research from the Koo lab indicated that some NSAIDs specifically reduced the production of the amyloidogenic Aβ42 fragment (1) both in cultured cells and in a mouse model of the disease. APP was still processed into peptides, but these were shorter and less likely to form amyloid plaques than Aβ42. Significantly, the cleavage of other γ-secretase targets was not affected, meaning that side-effects of NSAID treatment might be minimal. Although NSAIDs were expected to ameliorate Alzheimer's symptoms by reducing inflammation, Weggen et al. found that the beneficial effects were not the result of cyclooxygenase inhibition. In a follow-up paper (2), Weggen et al. used experiments on cultured cells to show that the drugs were directly modulating γ-secretase activity. These experiments also showed that mutations to presenilin-1, a core component of the γ-secretase complex, could either increase or decrease the effect of NSAIDs, suggesting that it was the protein directly affected by these drugs.

Kukar et al. set out to test this hypothesis using photaffinity labeling. They took a few compounds known to alter Aβ42 levels and added a functional group that would react with a protein in the presence of UV light. These covalently-labeled proteins could then be detected, and this would serve as a relatively easy way to determine which component of the γ-secretase complex was actually binding NSAIDs. Like many cleverly-designed experiments, this failed in an interesting way: no known components of the γ-secretase complex were labeled. Fortunately, the researchers realized that there was another component to the complex they hadn't tested yet: the substrate.

It turned out that the NSAIDs could label a 99-residue fragment of APP. Moreover, this labeling was reduced by other γ-secretase modulators (GSMs) and unaffected by non-GSM NSAIDs. Using a series of progressively shorter constructs, Kukar et al. localized the binding activity of GSMs to residues 28-36 of amyloid-β.

This on its own is a very useful finding because it provides a target for refinement of these compounds. Knowing where and to what protein a possible drug binds makes it easier to develop assays to test new potential drugs, as well as enabling structure-based design. However, the authors took the next step and asked whether these drugs, because they bind to a region of APP known to be involved in the formation of amyloid plaques, might inhibit plaque formation directly. In cultured cells, they found that treatment with certain substrate-targeting GSMs decreased the formation of Aβ dimers and trimers even under conditions where the overall concentration of Aβ42 was not altered.

This suggests that these GSMs may be able to fight the buildup of amyloid plaques in two ways. By altering where γ-secretase cleaves APP, they reduce the concentration of Aβ42. Moreover, by interfering with Aβ oligomerization they fight the formation of plaques directly. With luck, further work in medicinal chemistry will arrive at compounds that enhance both these activities. The development of compounds that significantly reduce or prevent the formation of amyloid plaques will be a great step forward for Alzheimer's research. Even if such drugs do not prove to be a cure, a clear indication that plaques don't cause Alzheimer's would be a critical insight.

I want to emphasize that although these results are quite promising, they do not prove the efficacy of NSAIDs in ameliorating actual Alzheimer's symptoms. Transforming these findings into a cure or even an effective treatment will require a great deal of additional research, if it is even possible. You should not attempt to treat Alzheimer's with NSAIDs, or begin a regimen of NSAIDs or any other kind of drug or supplement, unless you have first discussed the possible risks and benefits with your doctor. And no, Minnesota, I do not mean a naturopath.

1. Weggen, S., Eriksen, J.L., Das, P., Sagi, S.A., Wang, R., Pietrzik, C.U., Findlay, K.A., Smith, T.E., Murphy, M.P., Bulter, T., Kang, D.E., Marquez-Sterling, N., Golde, T.E., Koo, E.H. (2001). A subset of NSAIDs lower amyloidogenic Aβ42 independently of cyclooxygenase activity. Nature, 414(6860), 212-216. DOI: 10.1038/35102591

2. Weggen, S. (2003). Evidence That Nonsteroidal Anti-inflammatory Drugs Decrease Amyloid β42 Production by Direct Modulation of γ-Secretase Activity. Journal of Biological Chemistry, 278(34), 31831-31837. DOI: 10.1074/jbc.M303592200 OPEN ACCESS

3. Kukar, T.L., Ladd, T.B., Bann, M.A., Fraering, P.C., Narlawar, R., Maharvi, G.M., Healy, B., Chapman, R., Welzel, A.T., Price, R.W., Moore, B., Rangachari, V., Cusack, B., Eriksen, J., Jansen-West, K., Verbeeck, C., Yager, D., Eckman, C., Ye, W., Sagi, S., Cottrell, B.A., Torpey, J., Rosenberry, T.L., Fauq, A., Wolfe, M.S., Schmidt, B., Walsh, D.M., Koo, E.H., Golde, T.E. (2008). Substrate-targeting γ-secretase modulators. Nature, 453(7197), 925-929. DOI: 10.1038/nature07055

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