Wednesday, August 31, 2005

Good ways to handle scientific disagreements.

One of the things I think scientists like about doing science (besides the cool lab coats and safety glasses, of course) is that, in cases of disagreement, there's good reason to think you'll be able to work it out in the end. The reason this is so is that scientists share a commitment to testing their hypotheses and theories, whether by comparing them to the available empirical evidence, or by assessing its logical consistency, or evaluating it based on other agreed-upon standards of goodness.

Even when the going gets tough -- when the standards of theoretical goodness are not so agreed upon, or when one laboratory is having a hard time reproducing another laboratories experimental results -- scientists are looking to data that ought to be obtainable by anyone (once the equipment is working and the scientist has mastered the technique), trying to make their cases with reasons that are laid out for public scrutiny. Winning the argument only matters if you win because your reasoning and/or your experimental result is better. Better to lose the argument if it helps the community as a whole get closer to the truth.

In other words, scientists try hard to avoid disagreements that degenerate to the "Jane, you ignorant slut" level of discourse.

A nice example of a scientific disagreement in the literature is discussed by Ricardo Azevedo. The scientific dispute centers on whether evolutionary mechanisms like mutation are sufficient to explain the complex adaptive features of proteins. One set of authors presented a model to demonstrate that they were not. Another set of authors offered a detailed critique of the biological assumptions, modeling techniques, and logic upon which this model was based. Indeed, they looked to empirical evidence (about the frequencies of neutral versus deleterious mutations, in a number of experimental systems, in studies conducted by several different research groups) to undermine certain of the crucial assumptions in the earlier article.

Sadly, the response to this response seems not to really engage. Rather than taking seriously the empirical grounds for worrying about the central assumptions of the model, the advocates of that model seem to say the critics have misinterpreted what the experiments are really saying. There's no satisfying, side-by-side duel of competing models given a set of empirical results both sides can agree on. In the end, the attempt at engagement is followed by an attempt at disengagement. So dissatisfying.

Does it matter that one of the authors of the original article is a staunch advocate of ID, and that this model was supposed to demonstrate that ID is all that makes sense once evolutionary mechanism prove inadequate to the explanatory task?

I don't think it would matter so much, at least from the point of view of how dissatisfying it feels to not get the real scientist-on-scientist engagement one hopes to encounter in the literature. It might, however, give us clues to why that kind of serious scientific dialogue didn't end up happening here.

At least in the romantic ideal, the scientist cares only for the truth. Serious engagement with others is how to get there. You don't want to run from such engagement: you want to seek it out, to see if your theory is really as good as you think it is.

If the goodness of your theory can't be demonstrated with public reasons and public data, you're supposed to suck it up and be ready to cut that theory loose. You may get to keep tinkering with it to rehabilitate it, but you will at least understand why other scientists are skeptical. If you go for the underdog theory, you live for the day you can convince the doubters in a fair fight. And, you accept the possibility that it is you who will be convinced to change your point of view.

Good, clean scientific engagement yields a scientific community where everyone comes out smarter. Purposely dodging such engagement, on the other hand, leaves one feeling dirty.

Tuesday, August 30, 2005

Apparently the re-runs aren't just on TV...

Because Charles "co-authoring The Bell Curve didn't kill me" Murray is back with a piece in Commentary. You'll be pleased to know that in it, he defends not only the claims of that well-known book, but also the esteemed Lawrence Summers.

Where to start?

First, anyone who hasn't read Ned Block's paper, "How Heritability Misleads about Race", really should.

(Go on. I'm not going to read it for you.)

All I want to say about the scientific credibility (or ... not) of the arguments in The Bell Curve and their re-occurrence is that "heritability" is a concept scientists spend a good bit of effort trying to make precise, to the extent that they find it a helpful concept. Measuring the heritability of a trait (like intelligence, or IQ, which is supposed to be a reasonable proxy for intelligence), or even getting a sensible estimate, is wicked-hard most of the time. And, it's fair to say, heritability is not a straightforward concept that a lay person will be clear on.

Not, of course, that the policy wonks who opted out of serious science courses in college won't feel themselves entitled to take some scientist's word for it, even if other scientists are offering pretty serious reasons to question the work.

Murray says pretty much what you'd expect about what history tells us about the achievements of men and women, about women wanting babies, etc. I'm not in the mood to dissect it (as I have grading to do tonight, and I have to ration my bile accordingly). But, there are a couple claims I just can't leave alone:

"Among women who have become mothers, the possibilities for high-level accomplishment in the arts and sciences shrink because, for innate reasons, the distractions of parenthood are greater. To put it in a way that most readers with children will recognize, a father can go to work and forget about his children for the whole day. Hardly any mother can do this, no matter how good her day-care arrangement or full-time nanny may be."

OK, how many fathers are going to work and forgetting the kids for the whole day? Get those dads listed first on the Emergency Cards at school! On the other hand, how many women (given the societal realities) would admit after an engrossing day in the lab, "Gee, I was in the zone and forgot I even had offspring!" Do you want to be spending time on the phone with Child Protective Services?

"I have omitted perhaps the most obvious reason why men and women differ at the highest levels of accomplishment: men take more risks, are more competitive, and are more aggressive than women."

It all depends on how you define "risks", doesn't it? While I know studies have indicated that having kids during one's probationary period lessens the chances of getting tenure even for men, it has a profound effect on the tenuring rate for women. Yet there are serious scientists and scholars (chicks, no less) taking that risk. (Often, it seems the men on the promotions committees are the ones who are risk averse ...)

After commenting that tests show that on average males do better than females with abstract cognitive tasks:

"In the humanities, the most abstract field is philosophy—and no woman has been a significant original thinker in any of the world’s great philosophical traditions."

Dr. Murray, please pull over and give us a look at your license to practice philosophy.

I am optimistic that someone else will have the time, patience, and stomach to give Murray the point-by-point critique and analysis he deserves.

Monday, August 29, 2005

Try paying attention to that man behind the curtain.

In another round of maybe-the-blogosphere-can-save-us-from-the-mess-we've-made, there's a post at Weblogs in Higher Education that opines that "the blogging attitude" can help the public gain a better understanding of what real science looks like and shift science towards being more democratic and less authoritarian. From the post:

If science were more widely collaborative -- maybe not string theory physics, but certainly health and ecology and other more social and environmental sciences -- then more people would know theory from religion because they were involved in making science. For example, hundreds of people could participate in a survey of the species in a community and follow the studies that those surveys made possible. They, with the scientists down at the college, could create knowledge as scientists do.

Does it always come down to blogs? Of course not, but it does come down to the blogging attitude -- the collaboration, the shared work of making meaning, the authority won by work rather than by title, and so forth. If the scientific work of our society was more widely shared, then fewer people would be persuaded by non-science dressed up as science. This would be good for religion, too -- clarifying its real place in our lives.

I feel the appeal of this ... For sure, more people ought to understand what science is about and what strategies it uses to get the job done (and, what that job is and what that job is not). For sure, dialogue between scientists and lay people would be more satisfying (and would feel more like a bona fide dialogue) if it were based on a demonstration of reasons (and acknowledgment of uncertainties) rather than a "don't worry your pretty little head" appeal to authority. While most people don't become scientists to do PR, scientists should want people outside the community of science to have some inkling of why the things scientists study matter. (This may involve helping the public to understand how the object of scientific study is cool, quite apart from any actual or foreseeable practical applications of the knowledge.)

Of course, this would require some sweeping changes to business as usual.

Besides dope-slapping and purging the inept science teachers who drive all but the super-geniuses away from science, and beefing up educational requirements to expose every student to more science, scientists need to call bullsh*t on colleagues who give impenetrable talks. Doctor Theoretical Physicist talks for 45 minutes and loses most of the audience by minute 5. Why, oh why, do people walk out of the talk saying, "Wow, Doctor Theoretical Physicist is really smart!"? Why not, "Who the heck can tell if what he's saying has merit, since he sure as hell hasn't figured out how to communicate it coherently!"?

When scientists can't actually communicate with each other, they're already getting by on an appeal to authority.

The driving hope of empirical sciences is that there is a truth that we can get to by applying our sense organs and our powers of reason. The truth that scientists are after is one that, presumably, is there for any human to find -- given the same sense organs and cognitive machinery, any of us could get it. This is just the opposite of an appeal to authority ("Don't worry that you can't see it; take my word for it.").

So, a good scientific attitude, it seems to me, must include not only serious engagement with other scientists studying the same phenomena, but also an acknowledgment that lay people are not lesser beings than scientists -- given the proper training and, perhaps, different interests, they could have been doing science with you.

This doesn't mean one is obligated to administer a crash program in science to the lay person every time one tries to explain a cool new finding (or comes to ask for more public funding of science). But it does call for something a bit deeper than "Just trust me." The public often thinks of science as a product. Being more transparent about the process of science might be a step in the right direction.

Sunday, August 28, 2005

A little knowledge is a dangerous thing.

By which, of course, I mean too little knowledge is what gets you into trouble.

As has been wisely noted, there has been a fairly surprising reaction to Lisa Lloyd's book on attempts at evolutionary explanations of the female orgasm. Lloyd makes the case that the female organism was less likely selected for than a developmental byproduct of the selection for male orgasm. The surprising reaction, to which Lloyd herself responds at Philosophy of Biology, is from certain feminists claiming that somehow this argument means Lloyd thinks female orgasm is utterly valueless. Which, or course, means she's all for the subjugation of women.

Dude, there is no possible world in which Lisa Lloyd would make either of these claims. Trust me.

Since Lloyd does a fine job responding to these ill-founded concerns (and Pharyngula does, too), it's worth exploring just how the baseless accusations of anti-feminism get going. For which exploration, turn to the analysis at Big Monkey, Helpy Chalk:

The core problem is that most college educated feminists get little or no scientific training. They are not trained in scientific reasoning, or the basics of the dominant scientific theories. They can even become dismissive of science, abetted by a superficial reading of the great feminist philosophers of science...

The lack of science training is compounded by the fact that, by necessity, much of feminist scholarship is conducted in an unmasking mode. The first step in fighting the patriarchy is to recognize it, and this requires showing the true face of a lot of things that are taken for granted.

I would venture to add that it's not just feminists who are graduating colleges and universities innocent of scientific training. I suspect it's most graduates who haven't majored or minored in a science that fall into this category. (Except, of course, the nerds. I loves me some nerds!)

What do students know about science? Well, there are theories and such. And maybe somehow theories are different from facts, so if something is a theory, you can say it's just a theory. And, even though science also has a strong association with facts in people's minds, scientists get into these arguments. How can they be arguing? You have the facts or you don't.

So, the scientifically deficient student seems to bounce between thinking science is offering a perfectly established, complete picture of just how things are, and thinking scientists don't know a damn thing. What such a student is completely lacking is any understanding of how scientific knowledge is produced. Once you have a better understanding of that piece of science, you have a much better idea how wicked-hard getting absolute truth can be, but how committed scientists can do really well with what they've got.

Clearly, every college graduate would be better off graduating with at least the equivalent of a minor in a particular science. And just as clearly, I have no idea how to convince the folks with the power (most of whom seem to be in the B-School) to make the necessary changes. But, I think there's another reasonable place to lay blame and push for changes:

Every science teacher (especially in middle school and high school) who tries to convince his/her students that only really smart students could possibly understand anything scientific needs to be rounded up and administered a resounding dope-slap. Is it any wonder that people dodge science classes in college with this kind of early encouragement? Given our societal dumbening about matters scientific, we've got no room for science teachers who can't teach science to their students (which, really, is what's going on when a teacher says, "If you're not smart enough to understand this on your own, i can't help you.").

There are, of course, plenty of college-educated feminists who not only understand science, but are busy doing it. Somehow, they're not the ones approached to write book reviews for the Guardian or the San Francisco Chronicle. Probably something should be done about that, too.

Good science, bad science, or no science?

Once again, PZ Myers is showing justified dismay at the politically and religiously driven attempts to undermine science, this time as defined (for the purposes of transfer credits) by the University of California. Long story short: science departments in the UC system kinda feel like science credits leading toward a UC degree should reflect evidence of scientific knowledge. Whereas, there are folks suing the UC to accept as science credits credits earned from classes taught with textbooks that say "the Word of God" trumps science.

You can see the potential conflict here.

But here's the element that really jumped out at me from this particular rant (Pharyngula is perhaps my favorite online source of rants):

The press covering this battle, and the creationism vs. evolutionary theory war over all, have been portraying this as a battle between competing scientific theories. The struggle has been treated as one where the entrenched scientific view is refusing to deal with criticism, or where religious folks are striving to find a way to do science that's consistent with their beliefs. It's been treated as a question of "Which of these theories is good science?"

But, strategically, that doesn't seem to be what the proponents of creationism/ID are really after.

It's not that there are loads of scientists doing field or laboratory research guided by the theory of intelligent design whose requests for funding are being denied, whose research reports are being rejected, or whatever. ID-driven biology is not being offered as an alternative scientific research program.

Rather, the goal seems to be to undercut science altogether. You have the scriptures; why do you need science to answer questions that have already been answered?

Given how freaked out the average consumer of news is by science, the "theory vs. theory" storyline is pretty easy to sell. I wonder how the public would respond, however, if the press managed to illuminate the "science vs. no science" nature of the battle.

Saturday, August 27, 2005

Crackpottery, etiquette, and ethical duties.

There's scientific knowledge. There are the dedicated scientists who make it, whether slaving in laboratories or in the fields, fretting over data analysis, refereeing each other's manuscripts or second guessing themselves.

And, well, there are some crackpots.

I'm not talking dancing-on-the-edge-of-the-paradigm folks, nor cheaters. I mean the guy who has the crazy idea for revolutionizing field X that actually is crazy.

Generally, you don't find too much crackpottery in the scientific literature, at least not when peer review is working as it's meant to. The referees tend to weed it out. Perhaps, as has been suggested, referees also weed out cutting edge stuff because it's just so new and hard to fit into one's stodgy old referee's picture of what's field. That may just be the price of doing business. One hopes that, eventually, the truth will out.

But where you do see a higher proportion of crackpottery, aside from certain preprint repositories, is at meetings. And there, face to face with the crackpot, the gate-keepers may behave quite differently than they would in an anonymous referee's report.

Doctor Crackpot gives a talk intended to show his brilliant new solution to a nagging problem with an otherwise pretty well established theoretical approach. Jaws drop as the presentation proceeds. Then, finally, as Doctor Crackpot is aglow with the excitement of having broken the wonderful news to his people, he entertains questions.

Crickets chirp.

Doctor Hardass, who has been asking tough questions of presenters all day, tentatively asks a question about the mathematics of this crackpot "solution". The other scholars in attendance inwardly cheer, thinking, "In about 10 seconds Doctor Hardass will have demonstrated to Doctor Crackpot that this could never work!"

Ten minutes later, Doctor Crackpot is still writing equations on the board, and Doctor Hardass has been reduced to saying, "Uh huh …" Scholars start sneaking out as the chirping of the crickets competes with the squeaking of the chalk.

Granted, no one wants to hurt Doctor Crackpot's feelings. If it's a small enough meeting, you all probably had lunch with him, maybe even drinks the night before. He seems like a nice guy. He doesn't seem dangerous-crazy, just scientifically crazy. And, as he's been toiling in obscurity at a little backwater institution, he's obviously lonely for scientific company and conversation. So, calling him out as a crackpot seems kind of mean.

But ... it's also a little mean not to call him out. You're letting him wander through the scientific community with spinach in his teeth while trailing toilet paper from his shoe if you leave him with the impression that his revolutionary idea has any merit. Someone has to set this guy straight ... right? If you don't, won't he keep trying to sell this crackpot idea at future meetings?

So, in the continuum of "scientific knowledge", on whose behalf scientists are sworn to uphold standards and keep out the riff-raff, where do meetings fall? Do the scientists in attendance have any ethical duty to give their candid assessments of crackpottery to the crackpots? Or is it OK to just snicker about it at the bar? If there's no obligation to call the crackpot out, does that undermine the value of meetings as sources of scientific knowledge, or of the scientific communications needed to build scientific knowledge?

Who'd have thought problems might arise from scientists being too nice?

Friday, August 26, 2005

Science blogs for intra-scientific community communication.

There's been some interesting chatter in the blogosphere about science blogging, or the addition of blog-like features to electronic scientific archives. We're not talking about scientists blogging to educate their students and/or the public (a topic ably discussed by Geeky Mom). Instead, the focus is on the potential of blogging (and allied communication tools) as a way for scientists to communicate with other scientists.

Last month, Clifford Johnson at Cosmic Variance considered the use of group blogs as a research tool. He pointed out some potentially valuable outcomes - a flow of information between scientists that has less to do with the professional status of the person writing and more to do with the content of the contribution, a setting where it is possible to bounce ideas off each other even if they are not fully baked, communications that are not bound by geography, speed (of course), and searchability. This last element is especially attractive for those of us who value the exchange of ideas at the water cooler (or at the hotel bar at the professional meeting) but have less-than-perfect recall. (I am usually the only one at the bar scribbling in my notebook.) The searchability of science blogs not only means that the great ideas can be recovered, but you can even figure out who came up with them (or contributed to them).

More recently, Sean Carroll, also blogging at Cosmic Variance, noted that arxiv, the electronic preprint repository for physicists, has joined the blogosphere by introducing trackbacks on abstracts in the arxiv. Quoth Carroll,

As blog readers know, an individual blog post can inform other blog posts that it is talking about them by leaving a “trackback” or “pingback” — basically, a way of saying “Hey, I’m talking about that stuff you said.” This helps people negotiate their way through the tangles of the blogosphere along threads of common interest. Now your blog post can send trackbacks to the abstracts of papers at the arxiv!

In other words, not only is the electronic preprint depository allowing lightning-quick sharing of information between scientists, but with trackbacks it is now letting scientists see who is reacting to these findings out there in the ether.

I'm a big fan of scientific communication. But there are some interesting dimensions of these developments in scientist-to-scientist communication. For instance, here's what Carroll says about versus the "traditional" scientific literature in physics:

Any time you write a paper, you send it to the arxiv, where its existence is beamed to the world the next day, and it is stored there in perpetuity. Along with the SPIRES service at SLAC, which keeps track of which papers have cited which other papers, physicists have a free, flexible, and easy-to-use web of literature that is instantly accessible to anyone. Most people these days post to the arxiv before they even send their paper to a journal, and some have stopped submitting to journals altogether. (I wish they all would, it would cut down on that annoying refereeing we all have to do.) And nobody actually reads the journals — they serve exclusively as ways to verify that your work has passed peer review.

So, it's not like you have to worry that keeping up with the blogs and electronic preprints is going to be a huge addition to your keeping-up-with-the-literature time, because scientists have pretty much given up on keeping up with the journals anyway. (I can't really criticize that. When I was in grad school, there was just one Journal of Physical Chemistry; now there are two and they come out weekly. Even if no one is reading the journals, it seems like the number of journals there are not to read keeps growing!)

But if the journals now function almost entirely as certifications of quality control (which, we all know, is connected to important real-life issues for the scientist like tenure, promotion, and funding), this points to a potential downside to the rapid communication blogospherical mode of scientific discourse: there may not be a great signal to noise ratio. Seriously, I've seen some preprints that are pretty crackpot. Mostly, they never make it past pre- to plain old print. But, if the idea is that electronic archives plus trackbacks plus blogs will make for scientific discourse where everyone gets a fair shake, we may end up with a whole lot of crap to wade through.

On the other hand, people in the blogosphere (especially scientists) don't seem to be shy about calling out crap when they see it. Indeed, if you're evaluating someone's crackpottery online, it seems, you're more likely to give a reasoned argument indicating wherein the crappiness lies than you might be, say, as an anonymous referee. After all, if someone thinks your diagnosis is crappy, they'll call you out for it. So, possibly the relative transparency of communication via the blogosphere will cure some of the problems of anonymous refereeing.

It's hard to know whether the pseudonymous (or semi-pseudonymous) blogging would serve to democratize scientific exchanges (since you don't always know who's senior and who's junior, who's at a prestigious institution and who's laboring in obscurity), or whether this would mostly enable people to give props to their own work (or to shiv their enemies without being called to account). I suppose, if this all catches on, that it's an empirical question ...

Trying to put my finger on the relevant difference.

Trying to come back from my blogging hiatus (during which I wrote a couple things that my institution is more inclined to count as scholarship than they are a blog -- Luddites!). There are a couple big issues I've got in the hopper, but on at least one of them, I can't hold forth until my brother has sent me an article I asked him to send me.

So instead, I'm going to take up an issue where I haven't been able to work out an answer that satisfies me.

Months ago, PZ Myers discussed a biology teacher who dissected a dog for his class. A live dog. PZ Myers noted that, to the scientist trying to understand the phenomenon that is a mammal, dissection of dead tissue just doesn't give you the same sense of what an organism is. If the point of dissection is to teach you something about the organism, then arguably, live dissection is better.

Also important to note: The dog that was dissected was scheduled to be euthanized, as are many dogs in this country given our propensity to make more dogs and cats than we can take care of. And, the dog was anesthetized during the dissections (although some of the commenters at Pharygula wondered whether veterinarians really know all they should about adequate anesthesia for animals, let alone in situations like this.

I see the argument here. The dog is going to die no matter what. Isn't it less wasteful to get some useful educational experience out of this dog -- one that won't cause it any pain -- than to just put it down?

But ... there's a part of me that's uneasy about this. Not just because I'm a dog person (which I admit I am). There's an aspect of this transaction that feels ethically ... dangerous. It seems to feed into the conviction some folks have that animals are ours to do with as we please, or that the quest for scientific knowledge (even for secondary students in a biology class) is more important than the life of a dog. To get through a live-dog dissection, I suspect one might need to make oneself at least a little callous to the welfare of the dog, to shut off that flicker of empathy for the other creature. There are times that may be necessary, but I have a hunch that we're better off cultivating empathy than quashing it. (The lack of empathy for fellow scientists one sees in the halls of science can be striking...)

Here's the thing, though: I don't have any similar worries about what might be a parallel case, the use of "extra" embryos or aborted fetuses for stem cell research. Those extra embryos aren't going anywhere; they're just getting freezer burn. Why not learn something from them? People aren't (to my knowledge) getting pregnant and then terminating those pregnancies in order to support stem cell research. So this could be viewed as equivalent to getting some use out of the dog that's going to be put down.

Of course, we're talking human stem cells here. I'm not a card-carrying speciest (ran out of slots in the wallet, yo), but I'll confess that I probably favor human welfare over dog welfare more often than not. But I still don't get the ethical willies out of stem cell research that I do from live-dog dissection. Whether it's justified or not, I suspect the researchers working with the embryos and fetuses aren't risking the same sort of empathy callouses that someone doing live dissections needs to develop.

Am I wrong not to see a stronger equivalence here? Should I worry more about the stem cell research? Less about the dog?