This is the biggest problem with commercial scientific publishing, they have no incentive to publish correct science, only incentives to publish science that get them in the newpapers.
Science is not a commercial publication; it is produced by the American Association for the Advancement of Science, a non-profit organization. Many people have made the argument that the problem is with high-profile, "prestige" journals, who do frequently seem to favor publicity and high citation counts over sound science. However, the problem has absolutely nothing to do with commercial versus non-profit or open-access. Academics are just as hungry for publicity and trendiness as anyone else; we're certainly not in it for the money.
As I understand it, the controversy really heated up when this researcher started shouting 'SEXISM!' at the first sign of peer criticism.
I am not a fan of this research, but I do not recall ever seeing a claim of sexism being made, at least not by Wolfe-Simon or any of the people involved in the original work. What I do remember is them stating that they wouldn't respond to criticisms until they had been formally peer-reviewed, which most people thought was a bullshit response. Peer review doesn't just mean haggling with the editors at Science for several months and tailoring your manuscript to satisfy some anonymous curmudgeon.
If anything, I would not be surprised if some potential critics of the work were more muted, for fear of being accused of trying to tear down an ambitious female scientist. It's not like this never happens, either - I live in a very liberal area, and yet I've heard stories about some academic science departments at local universities that sound like something out of "Mad Men". In this case, however, the vast majority of the criticism I saw was based on sound scientific arguments and a general distaste for hand-waving. If Wolfe-Simon had been male, I imagine the response would have been somewhat more venomous - which, frankly, wouldn't have been any better for small-s science.
Hopefully some sort of selective breeding experiment can succeed where nature has failed, and give us an organism that substitutes some or all of its phosphorus for arsenic...
You're not going to be able to do any better than millions of years of evolution by random mutation and natural selection. The selective breeding we've done so far is penny-ante stuff compared to the amount of molecular changes needed to support an arsenate-dependent biochemistry. It's not just the DNA and RNA; the underlying components (nucleotide triphosphates) are the basic energy currency of the cell. Thousands of proteins would need to be adapted all at once to use the arsenate forms rather than phosphate. Adaptations that allow organisms to utilize what might otherwise be toxic molecules are not uncommon; a few years ago someone found a cadmium-dependent protein in a marine microorganism, and it wouldn't shock me if someone was able to find a protein that was able to use arsenate productively. But these are single proteins or pathways, not the entire metabolism and genetic infrastructure.
Moving beyond the molecular biology, there were sound chemical reasons why this type of adaptation was unlikely in a lifeform that lives in water, aside from the experimental issues with the original research. I heard somewhere (it may have been a biochemist friend of mine who said this) that the arsenate DNA backbone could be stable in a different solvent (e.g. ammonia), but I don't know enough to tell whether this is in fact true. It is unlikely to be viable for any terrestrial organism, however.
The only thing that would be newsworthy is if you managed to do something highly technical without having Linux play a vital role.
Agreed - I can't think of any large scientific facility that isn't bristling with Linux machines. Visit any particle accelerator and most of the workstations will be running Linux, not Windows. And nearly all of the backend servers will be running Linux as well. The Windows machines will mostly just be individual scientists' laptops (mixed in with a lot of Macs, at least in the US), and controllers for proprietary hardware that can't be run from Linux.
I think this is mostly historical legacy, as others have noted; 15 years ago these would have been entirely proprietary Unix systems, where typical prices were $50,000 for the workstation and $3000 just for the compilers. Switching to Linux was the obvious thing to do.
Lots of physicists talk like that, it's not a religious statement it's a common was to express ideas.
Biologists can be even worse sometimes - they'll make casual reference to evolution "designing" a particular adaptation. The urge to anthropomorphize natural processes is apparently very strong, even among people who are trained to look for rational and non-supernatural explanations. But I have to admit I wince every time I read something like that.
Oh HELL yes. My mom (!) introduced me to these as a child and I though they were terrific - definitely not "hard" science fiction but an excellent gateway to the genre. Perfect level for an 8-year-old (I doubt he'd have a problem reading it himself).
Some of the other books I've seen mentioned on this thread are probably going to go over the head of an 8-year-old; Ender's Game in particular is pretty dark. The Heinlein juveniles are great but I'd probably wait a couple more years unless you have an exceptionally precocious child. The Norby and Lucky Starr series are both excellent, however. I'd probably give "A Wrinkle In Time" a try too.
There is another kind of useless science that pervades academia: competing against other labs to finish a project! The project is going to get finished no matter what, so why spend your time working on it? This does not advance scientific knowledge, but is more of an ego trip for people who lack perspective...
I think you're fundamentally misunderstanding human nature, and how the academic scientific enterprise functions. We're not just in it for the knowledge; there have to be other incentives too, and while we're used to the relatively low pay, ego still plays a big part. People compete against other labs to finish a project because whoever finishes successfully, and first, will accrue most of the credit and prestige. The professor whose lab wins gets a cover article in a prestigious journal, gets invited to be keynote speaker at meetings, gets cited more, gets his/her postdocs into good faculty jobs, and maybe - many years down the line - ends up in the running for a Nobel prize. Oh, and the NIH will undoubtedly look favorably on future grant proposals.
It's easy to get on a high horse and say, "well, they should just be in it for the knowledge and good of humanity." Bullshit. Human beings (most of us, anyway) simply don't function that way; we're willing to make some sacrifices if we think it's in a good cause, but personal satisfaction and advancement is paramount. On the other hand, if you can harness all of that self-interest and ego in the interests of advancing human knowledge, you'll get far more accomplished than would otherwise be possible. If you want to motivate an exceptionally bright postdoc - someone capable of making tens of thousands more in a real job - to work 80 hours a week for $50,000 a year, which of these two arguments do you think will be more convincing?
1. "Just think of how enriched the field will be by this research! Someone might use it to cure cancer in twenty years! And everyone in the lab will know that you did the work!" 2. "We need to finish this experiment because my evil counterpart at Bastard U. is trying to scoop us, and if that happens, you'll never get that faculty job."
Now, it can be argued (quite fairly) that (2) has a tendency to lead to sloppy science and hand-waving, but there are trade-offs in any situation, and the solution isn't to rely more on the selfless motives of the scientists involved, but other institutional reforms to make this more difficult.
I must admit that you sound, on the whole, rather disillusioned with research in general.
Yes, although this goes well beyond institutional flaws. Part of my frustration is that it's very difficult to do anything truly revolutionary - not because of supposed scientific conservatism/closed-mindedness, but because everyone is so specialized and the low-hanging fruit is already picked. There are many "grand challenges" that will probably be addressed in the next few decades, but they're going to involve painstaking gruntwork by legions of people like me, most of whom will go unrecognized. Of course the same is true of most human endeavors, but when you're deliberately sacrificing youth and fortune in pursuit of knowledge, it's depressing to realize the inherent limitations of your work. I'm just barely starting to establish a reputation for myself in my chosen field, and while I'm thrilled that this is even possible, it's maybe a few tens of thousands of specialists at most who will ever be affected by my work.
If your work is just about competing with other groups tackling the same problem, it seems like whatever you're doing just isn't giving you the satisfaction that academia is supposed to.
It's not just about competing with other groups, but the competition in the biomedical sciences is ferocious. This is partly by design: the NIH funds competing proposals all the time (there will be differences in details, of course, but the broader scope and impact is often duplicated). Postdocs may be willing to work 60 hours a week if they think there's a faculty job and the end of the rainbow, but they'll work 80 hours if they think someone else might get there first, and their P.I. is cracking the whip to get a paper out ASAP so they can publish in Nature instead of Biochemistry. Since I'm a methods developer my goals are somewhat different, but it comes down to the same problem. The competition forces us all to work harder, but sometimes I have to wonder what the point is.
If you could invent a structural or institutional change to try and prevent people from ending up where you are, what would you do?
Admit fewer grad students. Honestly, I have no bright ideas, but I feel nauseous every time I come across some idiot suggesting that we need to increase enrollment in the basic sciences.
My advice is that you may actually want to consider computing more seriously.
Way ahead of you; I am effectively a full-time software engineer at this point, writing production code used by other researchers. (For reasons mostly unrelated to my rant above, I also turned out to be temperamentally unsuited for bench work.) The problem is that this is still pretty much a dead end, career-wise. My options are either to stay in academia making pretty much the same salary forever and groveling to the NIH for funding every few years, try to land one of the very few industry positions suitable for someone with my background, or leave science altogether and apply my technical skills elsewhere. The latter is starting to look increasingly appealing - much as I'd hate to give up on science, I'm starting to feel stupid working unpaid overtime to keep up with our competitors when the only reward is continued employment at a considerably lower salary than everyone I know in the private sector.
Wow, sounds like your "prestigious" grad program sucked. Mine was awesome. I really felt the faculty in my program wanted to make me into the best scientist I could possibly be.
And I am certain that there were a few people in my program who felt the same way. In fact, a few really did thrive, partly because the stars were in perfect alignment whenever they had to deal with faculty, and partly because they were simply better suited, temperamentally speaking, for the organized chaos of grad school.
There are probably a handful of students in every program who are so awesome that no amount of mismanagement can keep them down; all they need from senior scientists is a lab bench, adequate funding, and someone to bounce ideas off of. We should of course be encouraging these people to pursue scientific careers. But the average science grad student is not quite this awesome. Most of us are more than capable of understanding the material and performing the experiments, and even having good ideas on our own, but our success (and intellectual growth) really does depend on proper management, and genuinely poor management leaves us really helpless.
Any training-grant-funded program that produces a lot of unemployable graduates is in big trouble.
It depends how far down the road you're looking. Any idiot can find a postdoc position; look at science job sites (like Nature Jobs) and you'll see no shortage of openings in most fields. A very large fraction of biomedical grad students - the few who are ambitious and capable enough to succeed in an academic career path, and the majority who are too clueless to cut their losses while they can still salvage their dignity - will end up postdoc job shortly after graduation. I really doubt that the granting agencies track them beyond this point. Whether any of these poor souls are "employable" after spending several years as postdocs is debatable - and to whatever extent this is the case, it's largely because the more senior researchers expect that everyone else endure the same bullshit they had to put up with.
Some of the graduates may not have the greatest critical reasoning skills, but surviving in such a program most definitely requires significant determination and dedication.
Equally advantageous: extreme mismanagement at all levels.
I spent five years in one of the most prestigious biomedical science graduate programs and somehow managed to get a PhD (I say this not to brag, but to make the point that they'll give just about any asshole a degree). I have seen countless graduate students and postdocs coast along for years with no results to show for it, without any action from the supervisors. Sometimes bad luck is a factor - even the most talented scientist can be helpless when faced with an intractable experiment - but a good manager knows when to cut his/her losses. A good manager also knows when to say, "perhaps grad school isn't a good environment for you. Maybe you should quit now with an MS and go do something more useful with your life." A good manager realizes that when someone stops showing up for months on end, it's time to fire his sorry ass and hire someone useful, or buy more equipment. An HPLC never shows up at 3pm because it overslept after eating too many pot brownies. (True story!)
What makes this really depressing: most of the people I went to school with were far above average intelligence and capable of doing excellent work with the proper motivation and management. There are lots of exceptionally bright men and women in their 20s slaving away in laboratories on soul-crushing projects, supervised by an odd mix of micromanagers, passive-aggressives, and absentee landlords (for lack of a better term). Most of us are utterly unsuited for graduate school, either in theory or in practice. Only a fraction are cut out to be full research faculty, and even some of these I wonder if they'd be happier doing something different. (The remainder, I seriously wonder whether they'll be fucking up their grad students' lives in 20 years.) Most of us go to grad school because that seemed like the logical route at the time, and we enjoyed learning and experimenting. After 5-6 years of largely wasted effort, almost none of us would still recommend grad school to our younger selves. I still feel bad about a few of the younger students who didn't get the brutally honest advice they deserved, because we didn't want to hurt their feelings.
There are probably a few sub-fields where it is possible to stay on the cutting edge and be employable for years after graduation - next-gen sequencing, perhaps. But I get depressed every time I go to meetings and meet students and postdocs with IQs well above 120 slaving away on projects that are probably useful but certainly not world-changing, and who will probably end up with one or two papers in Journal of Molecular Biology, and eventually need to find jobs in their chosen fields. What jobs? Even if you're the most badass electron microscopist in all of New England, what does that prepare you to do other than perpetuate the cycle of mismanagement at another research institution? Assuming you can even get the job, of course; even a top-tier journal publication doesn't automatically get you anything when you're competing with several hundred other postdocs.
Sadly, I still haven't figured out what to do with the degree that took most of my youth and nearly all of my sanity. I never had any ambitions towards faculty posts, fortunately, but there aren't a ton of jobs in industry in my field either. I still work in the same field in academia in a full-time researcher position, which is relatively stable if you ignore the fact that my employer is $14 trillion in the red and counting. I'm probably marginally more employable because I managed to pick up very good programming skills along the way, but still, if I want to move into software engineering I'm either going to be competing with CS PhDs, or settling for bachelors-level jobs. Every time I read my alumni newsletter from college I cringe, and think "Jesus Christ, why didn't I just sell out like everyone with a brain?"
The "arsenic based bacteria" which were supposed to revolutionize the way we viewed biology didn't even turn out to be a hoax, but bad science. Although, after RTFA, it looks as if these scientists are being a bit more cautious before making outrageous declarations.
Biologists are finding fascinating new microorganisms in harsh environments all the time - this is mostly very good science, but nothing revolutionary or remotely controversial. The microbes in TFA are interesting because there isn't an obvious energy source available (since they're non-photosynthetic). This means that they may have evolved some unique metabolic strategy. But there is no inherent reason why these microbes can't or shouldn't exist; they're just something we haven't seen before.
The arsenic bacteria article was immediately controversial because for the claims of the authors were true, it would directly conflict with some very basic chemical phenomena, and didn't make sense in light of everything else we know about cellular biochemistry. (The mere existence of microbes in such high levels of arsenic is intrinsically interesting, since they would have had to evolve tolerance for what is effectively a poison, but again hardly revolutionary.) It was doubly controversial because it didn't do a very good job experimentally supporting the primary claim, that the bacteria preferred arsenate to phosphate in nucleic acid backbones. If you're going to put forward such an extreme hypothesis, you need to really nail the evidence 100%. The hand-waving science-by-press-release was an added slap in the face. Every scientist (especially the great ones) loves a bit of PR now and again - that's why universities issue press releases like TFA - but you have to know your limits.
With instruments like this, it will make the task of X-ray crystallography determination of protein structures much easier.
No, it won't. Two reasons:
1) You need "hard" X-rays for crystallography - with a wavelength similar to the chemical bond length. The maximum resolution you can achieve is equivalent to half the wavelength, and even that requires a complicated detector setup, so in practice you want a wavelength around 1 Å for crystallography. The wavelength of this device is 8Å, which is fine for spectroscopy and small-angle scattering studies, but useless for crystallography. While I suspect the technology could be made to work at shorter wavelengths, this usually involves tradeoffs such as higher cost, higher energy consumption, etc.
2) The intensity of the source is far less than a synchrotron (let alone a free-electron laser). This means that data collection times will take far longer. At a synchrotron beamline, in favorable conditions, you can collect an entire data set in seconds (of course, the detector alone costs more than $1 million). Usually it's not quite that fast, but you don't need to wait days for your data - and you can hedge your bets by collecting data on as many crystals as possible.
A secondary reason is that the improvement in synchrotron beamline technology has also made them more accessible - much of the work is now done remotely using robotic sample changers. Being able to grow decent crystals in the first place is a far more limiting factor. And my impression is that beamtime isn't terribly difficult to get; people do still use home X-ray sources while they're waiting for beamtime, but most people are content to wait for the synchrotron to get the truly publishable data.
A private company can re-incorporate elsewhere to save on taxes or avoid regulations in a heartbeat.
Wrong. Quoting a representative posting on the SpaceX careers page:
"To conform to U.S. Government space technology export regulations, applicant must be a U.S. citizen, lawful permanent resident of the U.S., protected individual as defined by 8 U.S.C. 1324b(a)(3), or eligible to obtain the required authorizations from the U.S. Department of State."
I guess this is one of those regulations they could theoretically avoid, but where exactly do you think would be a better place to do business, given that a large fraction of the potential customers will be in the US (either the government or companies)? And where else do you think has a sufficient labor pool? Right now the choices are the USA, Russia, or the EU. India might get there eventually. You'd have to be insane to relocate a commercial space flight company to China.
It was an exceptional school in many respects. But it was also typical of American public schools in many others: massive classes (30 was very typical, often more even though that was supposed to be the limit), chronically underfunded (my senior year the science classes started requesting a voluntary lab fee so they could afford basic supplies, like graph paper), and often incompetently managed (see my remarks about education bureaucrats above). A few years after I left, the school district "misplaced" $25 million - they simply couldn't account for it. A principal was fired for having sex with a student. My freshman year, a student emptied a 9mm in the cafeteria and hallways (fortunately, he was a poor shot). So it wasn't one of those ridiculously nice suburban schools like Scarsdale that feeds off high property tax income.
What made it exceptional was a critical mass of competent-to-excellent teachers, relatively bright (or at least hardworking) students, and very involved parents. No amount of standardized testing, union-busting, innovative techniques, or increased funding will substitute for these.
For the majority who need to go to public schools, our education system is terrible. The article points to the successes of those whose parents could afford to give them the best education money can buy.
This is not universally true. I have a PhD in biochemistry, and until college I had always attended American public schools. So did many of my close friends, who now have PhDs as well. The (large, urban) high school I attended had some massive systemic problems that are probably unfixable, but at least 60% of our graduating class went to four-year colleges, including about ten or so students who attended Ivy League schools. I have very little good to say about those four years of my life, but I honestly think most of the teachers did the best they could with what they had. The quality of the science education was very mixed, but we had some terrific innovative programs (especially marine science and tech ed) that were as good as anything the private schools could offer. I know I'm not the only student who was inspired to pursue a scientific career as a result of this.
The biggest problem I faced was that a faction of the education bureaucracy was fiercely opposed to college prep courses (because they were elitist) and wanted to homogenize the curriculum. This was not the fault of the teacher's union or the politicians; I still haven't figured out where these people get their ideas. (Just to clarify, "these people" were very racially diverse - a handful of white teachers were some of the loudest advocates at my school.) However, it was every bit as anti-intellectual a movement as the right-wingers trying to force pseudoscience into the classroom. By the time I was partway through high school, my parents decided they didn't like where things were headed, and sent my siblings to a private high school (where they appear to have received the same quality education, albeit with less senseless brutality).
The more general problem is that funding is indeed limited - the difference between a high-quality private school and a large public school is that the classes in the latter will be twice as large, so teachers can't give individual students they attention they require (or that their parents feel they deserve). The really smart students will always be screwed unless there are enough of them to fill a classroom - otherwise you have to explain to the PTA why five students get their own teacher for AP American History while the rest of the students get class sizes of 30.
My German friends were expected to be able to solve calculus problems in order to graduate high school. Calculus was considered college level when I went to high school, and still is.
The high school I attended had not one but two levels of calculus - I took AP Calculus I my senior year. All you need is enough students at that level to fill a classroom, and we had enough for two periods. That was actually one of my favorite courses in all of high school - it was the first time math seemed truly intuitive to me.
Steal from California? That state is flushing money down the sewer.
California's public debt is currently around $16 billion, almost three orders of magnitude less than the federal government's. California's contribution to federal revenues in 2007 was more than $300 billion, although I suspect this will have declined slightly since 2008.
You're probably right that losing CA and NY would force the rest of country to live within its means. However, it would be an even better deal for Californians, because some of the money wasted subsidizing red states could instead be spent fixing our own fiscal mess, and we'd still have plenty left over that could be refunded to taxpayers. Sadly, CA would also be crippled without federal intervention to ensure that the state gets an adequate water supply - I haven't figured out a solution to that yet.
The people who are most adamant that creationism is the right way are those who take what is written in the Bible word-for-word.
Actually, that's giving them too much credit. They actually take what is written in the English translations of the Bible word-for-word.
Of course, I'd argue that apart from issues of translating from ancient Hebrew (etc.), the convoluted authorship of the Bible - and the lack of a clear documentary record for much of the text itself - should be enough to deter any reasonable individual from interpreting it literally. This doesn't mean that the Bible is all nonsense (although I have my own opinions on that), but to take the Bible as absolute truth, you have to assume that the people who recorded it were infallible and uncorrupted by baser motives.
That has huge implications for taxonomy and phylogenetics
One of the most exciting potential projects I've seen recently is a proposal to sequence 10,000 vertebrate genomes, which would sample nearly every genus. One of the project leaders, David Haussler, has previously worked on extrapolating backward from known mammalian genomes to guess at the genome of the common ancestor (100-plus million years ago). That was with several orders of magnitude less data - if they actually pull this project off, we'll be able to understand vertebrate evolution at a level of detail unimaginable today. As usual with these kind of projects, of course, the data analysis is going to be far more difficult than the actual sequencing.
I was under the impression that you paid PNAS to publish your work because it was shit that you couldn't get published in a real journal.
This was very frequently true until the last decade or so. In fact, there were always some very good papers in PNAS, but there was also a lot more junk. Peter Duesberg, probably the most famous (and most reputable, until he went crazy) scientist to argue that HIV does not cause AIDS, is (or was) notorious for contributing an article to PNAS every year - since he was already an NAS member since the 1980s, they had to let him publish there. Since the editor who made the switch to direct submission, Nick Cozarelli, was a colleague of Duesberg's at Berkeley, I wouldn't be surprised if there's a direct link here.
Anyway, if the article says "communicated by" or "contributed by", that means it got in through the back door. Not all of these articles are crap, but many don't deserve to be there. According to the PNAS web site, 90% of articles submitted, and 79% of those published, are direct submission. I believe the "communication" route is now closed, but it is still possible to contact an NAS member directly and ask if he/she is willing to be an editor, in which case the footnotes will mention that the editor was "pre-arranged". The difference from before is that the peer review is more rigorous and the editorial board has veto power. I've done it both ways (as a minor co-author), and while I'd obviously feel better about getting in the front door, I can understand why we went directly to an NAS member in one case. Academic politics is a bitch.
Why is that 'politically correct' BS always is imposed over strict rationality?
I dunno, some of us have an instinctual aversion to totalitarian social engineering imposed in the name of "strict rationality"... might have something to do with the 20th century.
...it does publish great papers, but does require something of a personal connection to get into... Same for The Proceedings of the National Academy of Sciences
Actually, this isn't so true of PNAS any more. One of the previous editors decided in the late 1990s to raise the quality prestige of the journal by accepting more papers through a traditional peer-review route, as opposed to NAS members "communicating" or "contributing" articles (which would often have minimal peer review). This was very successful, and now most articles in PNAS get in through the front door, and they're slowly eliminating the back doors. The overall quality is pretty good - not as high-impact as Science or Nature or some of the top specialty journals, but it's definitely a journal that researchers are excited about publishing in if they can't get into the top tier. The fact that they're not part of Elsevier or one of the other big commercial publishers, and their open-access fee is very reasonable, is an added bonus. (Disclaimer: I've published there, so I'm not entirely unbiased.)
Now, as with any journal, knowing the right people always helps - sadly, this is true at any level.
If "private industry" did the same, they would face manslaughter charges. Only government can get away with that level of incompetence and disregard for human life, and survive.
Private industry did in fact do the same, and no, they did not face manslaughter charges. Contrary to common assumption, much of the launch infrastructure was already privatized, under "cost-plus" contracts which guaranteed a profit to the contractor no matter how expensive the final product was. In the case of Challenger, the contractor (Morton Thiokol) responsible for the SRBs ignored the warnings of its own engineers and told NASA to go ahead with the launch. (Doubtless NASA fucked up too, but it wasn't NASA's product that exploded.) They were ultimately fined for the disaster, but never had to admit legal liability.
The end result? The same company (after some corporate restructuring and a later merger - it's currently called ATK) continued manufacturing SRBs, and Congress recently tried to force NASA to continue using the same SRBs. So, the moral is that when your biggest customer by far is the US government, incompetence and failure is no barrier to success in the private sector.
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This is the biggest problem with commercial scientific publishing, they have no incentive to publish correct science, only incentives to publish science that get them in the newpapers.
Science is not a commercial publication; it is produced by the American Association for the Advancement of Science, a non-profit organization. Many people have made the argument that the problem is with high-profile, "prestige" journals, who do frequently seem to favor publicity and high citation counts over sound science. However, the problem has absolutely nothing to do with commercial versus non-profit or open-access. Academics are just as hungry for publicity and trendiness as anyone else; we're certainly not in it for the money.
As I understand it, the controversy really heated up when this researcher started shouting 'SEXISM!' at the first sign of peer criticism.
I am not a fan of this research, but I do not recall ever seeing a claim of sexism being made, at least not by Wolfe-Simon or any of the people involved in the original work. What I do remember is them stating that they wouldn't respond to criticisms until they had been formally peer-reviewed, which most people thought was a bullshit response. Peer review doesn't just mean haggling with the editors at Science for several months and tailoring your manuscript to satisfy some anonymous curmudgeon.
If anything, I would not be surprised if some potential critics of the work were more muted, for fear of being accused of trying to tear down an ambitious female scientist. It's not like this never happens, either - I live in a very liberal area, and yet I've heard stories about some academic science departments at local universities that sound like something out of "Mad Men". In this case, however, the vast majority of the criticism I saw was based on sound scientific arguments and a general distaste for hand-waving. If Wolfe-Simon had been male, I imagine the response would have been somewhat more venomous - which, frankly, wouldn't have been any better for small-s science.
Hopefully some sort of selective breeding experiment can succeed where nature has failed, and give us an organism that substitutes some or all of its phosphorus for arsenic...
You're not going to be able to do any better than millions of years of evolution by random mutation and natural selection. The selective breeding we've done so far is penny-ante stuff compared to the amount of molecular changes needed to support an arsenate-dependent biochemistry. It's not just the DNA and RNA; the underlying components (nucleotide triphosphates) are the basic energy currency of the cell. Thousands of proteins would need to be adapted all at once to use the arsenate forms rather than phosphate. Adaptations that allow organisms to utilize what might otherwise be toxic molecules are not uncommon; a few years ago someone found a cadmium-dependent protein in a marine microorganism, and it wouldn't shock me if someone was able to find a protein that was able to use arsenate productively. But these are single proteins or pathways, not the entire metabolism and genetic infrastructure.
Moving beyond the molecular biology, there were sound chemical reasons why this type of adaptation was unlikely in a lifeform that lives in water, aside from the experimental issues with the original research. I heard somewhere (it may have been a biochemist friend of mine who said this) that the arsenate DNA backbone could be stable in a different solvent (e.g. ammonia), but I don't know enough to tell whether this is in fact true. It is unlikely to be viable for any terrestrial organism, however.
The only thing that would be newsworthy is if you managed to do something highly technical without having Linux play a vital role.
Agreed - I can't think of any large scientific facility that isn't bristling with Linux machines. Visit any particle accelerator and most of the workstations will be running Linux, not Windows. And nearly all of the backend servers will be running Linux as well. The Windows machines will mostly just be individual scientists' laptops (mixed in with a lot of Macs, at least in the US), and controllers for proprietary hardware that can't be run from Linux.
I think this is mostly historical legacy, as others have noted; 15 years ago these would have been entirely proprietary Unix systems, where typical prices were $50,000 for the workstation and $3000 just for the compilers. Switching to Linux was the obvious thing to do.
Lots of physicists talk like that, it's not a religious statement it's a common was to express ideas.
Biologists can be even worse sometimes - they'll make casual reference to evolution "designing" a particular adaptation. The urge to anthropomorphize natural processes is apparently very strong, even among people who are trained to look for rational and non-supernatural explanations. But I have to admit I wince every time I read something like that.
Oh HELL yes. My mom (!) introduced me to these as a child and I though they were terrific - definitely not "hard" science fiction but an excellent gateway to the genre. Perfect level for an 8-year-old (I doubt he'd have a problem reading it himself).
Some of the other books I've seen mentioned on this thread are probably going to go over the head of an 8-year-old; Ender's Game in particular is pretty dark. The Heinlein juveniles are great but I'd probably wait a couple more years unless you have an exceptionally precocious child. The Norby and Lucky Starr series are both excellent, however. I'd probably give "A Wrinkle In Time" a try too.
There is another kind of useless science that pervades academia: competing against other labs to finish a project! The project is going to get finished no matter what, so why spend your time working on it? This does not advance scientific knowledge, but is more of an ego trip for people who lack perspective...
I think you're fundamentally misunderstanding human nature, and how the academic scientific enterprise functions. We're not just in it for the knowledge; there have to be other incentives too, and while we're used to the relatively low pay, ego still plays a big part. People compete against other labs to finish a project because whoever finishes successfully, and first, will accrue most of the credit and prestige. The professor whose lab wins gets a cover article in a prestigious journal, gets invited to be keynote speaker at meetings, gets cited more, gets his/her postdocs into good faculty jobs, and maybe - many years down the line - ends up in the running for a Nobel prize. Oh, and the NIH will undoubtedly look favorably on future grant proposals.
It's easy to get on a high horse and say, "well, they should just be in it for the knowledge and good of humanity." Bullshit. Human beings (most of us, anyway) simply don't function that way; we're willing to make some sacrifices if we think it's in a good cause, but personal satisfaction and advancement is paramount. On the other hand, if you can harness all of that self-interest and ego in the interests of advancing human knowledge, you'll get far more accomplished than would otherwise be possible. If you want to motivate an exceptionally bright postdoc - someone capable of making tens of thousands more in a real job - to work 80 hours a week for $50,000 a year, which of these two arguments do you think will be more convincing?
1. "Just think of how enriched the field will be by this research! Someone might use it to cure cancer in twenty years! And everyone in the lab will know that you did the work!"
2. "We need to finish this experiment because my evil counterpart at Bastard U. is trying to scoop us, and if that happens, you'll never get that faculty job."
Now, it can be argued (quite fairly) that (2) has a tendency to lead to sloppy science and hand-waving, but there are trade-offs in any situation, and the solution isn't to rely more on the selfless motives of the scientists involved, but other institutional reforms to make this more difficult.
I must admit that you sound, on the whole, rather disillusioned with research in general.
Yes, although this goes well beyond institutional flaws. Part of my frustration is that it's very difficult to do anything truly revolutionary - not because of supposed scientific conservatism/closed-mindedness, but because everyone is so specialized and the low-hanging fruit is already picked. There are many "grand challenges" that will probably be addressed in the next few decades, but they're going to involve painstaking gruntwork by legions of people like me, most of whom will go unrecognized. Of course the same is true of most human endeavors, but when you're deliberately sacrificing youth and fortune in pursuit of knowledge, it's depressing to realize the inherent limitations of your work. I'm just barely starting to establish a reputation for myself in my chosen field, and while I'm thrilled that this is even possible, it's maybe a few tens of thousands of specialists at most who will ever be affected by my work.
If your work is just about competing with other groups tackling the same problem, it seems like whatever you're doing just isn't giving you the satisfaction that academia is supposed to.
It's not just about competing with other groups, but the competition in the biomedical sciences is ferocious. This is partly by design: the NIH funds competing proposals all the time (there will be differences in details, of course, but the broader scope and impact is often duplicated). Postdocs may be willing to work 60 hours a week if they think there's a faculty job and the end of the rainbow, but they'll work 80 hours if they think someone else might get there first, and their P.I. is cracking the whip to get a paper out ASAP so they can publish in Nature instead of Biochemistry. Since I'm a methods developer my goals are somewhat different, but it comes down to the same problem. The competition forces us all to work harder, but sometimes I have to wonder what the point is.
If you could invent a structural or institutional change to try and prevent people from ending up where you are, what would you do?
Admit fewer grad students. Honestly, I have no bright ideas, but I feel nauseous every time I come across some idiot suggesting that we need to increase enrollment in the basic sciences.
My advice is that you may actually want to consider computing more seriously.
Way ahead of you; I am effectively a full-time software engineer at this point, writing production code used by other researchers. (For reasons mostly unrelated to my rant above, I also turned out to be temperamentally unsuited for bench work.) The problem is that this is still pretty much a dead end, career-wise. My options are either to stay in academia making pretty much the same salary forever and groveling to the NIH for funding every few years, try to land one of the very few industry positions suitable for someone with my background, or leave science altogether and apply my technical skills elsewhere. The latter is starting to look increasingly appealing - much as I'd hate to give up on science, I'm starting to feel stupid working unpaid overtime to keep up with our competitors when the only reward is continued employment at a considerably lower salary than everyone I know in the private sector.
And one other that is not there: http://philip.greenspun.com/careers/women-in-science [greenspun.com]
I had not seen this before, but thank you for pointing it out - his observations are dead-on.
Wow, sounds like your "prestigious" grad program sucked. Mine was awesome. I really felt the faculty in my program wanted to make me into the best scientist I could possibly be.
And I am certain that there were a few people in my program who felt the same way. In fact, a few really did thrive, partly because the stars were in perfect alignment whenever they had to deal with faculty, and partly because they were simply better suited, temperamentally speaking, for the organized chaos of grad school.
There are probably a handful of students in every program who are so awesome that no amount of mismanagement can keep them down; all they need from senior scientists is a lab bench, adequate funding, and someone to bounce ideas off of. We should of course be encouraging these people to pursue scientific careers. But the average science grad student is not quite this awesome. Most of us are more than capable of understanding the material and performing the experiments, and even having good ideas on our own, but our success (and intellectual growth) really does depend on proper management, and genuinely poor management leaves us really helpless.
Any training-grant-funded program that produces a lot of unemployable graduates is in big trouble.
It depends how far down the road you're looking. Any idiot can find a postdoc position; look at science job sites (like Nature Jobs) and you'll see no shortage of openings in most fields. A very large fraction of biomedical grad students - the few who are ambitious and capable enough to succeed in an academic career path, and the majority who are too clueless to cut their losses while they can still salvage their dignity - will end up postdoc job shortly after graduation. I really doubt that the granting agencies track them beyond this point. Whether any of these poor souls are "employable" after spending several years as postdocs is debatable - and to whatever extent this is the case, it's largely because the more senior researchers expect that everyone else endure the same bullshit they had to put up with.
Some of the graduates may not have the greatest critical reasoning skills, but surviving in such a program most definitely requires significant determination and dedication.
Equally advantageous: extreme mismanagement at all levels.
I spent five years in one of the most prestigious biomedical science graduate programs and somehow managed to get a PhD (I say this not to brag, but to make the point that they'll give just about any asshole a degree). I have seen countless graduate students and postdocs coast along for years with no results to show for it, without any action from the supervisors. Sometimes bad luck is a factor - even the most talented scientist can be helpless when faced with an intractable experiment - but a good manager knows when to cut his/her losses. A good manager also knows when to say, "perhaps grad school isn't a good environment for you. Maybe you should quit now with an MS and go do something more useful with your life." A good manager realizes that when someone stops showing up for months on end, it's time to fire his sorry ass and hire someone useful, or buy more equipment. An HPLC never shows up at 3pm because it overslept after eating too many pot brownies. (True story!)
What makes this really depressing: most of the people I went to school with were far above average intelligence and capable of doing excellent work with the proper motivation and management. There are lots of exceptionally bright men and women in their 20s slaving away in laboratories on soul-crushing projects, supervised by an odd mix of micromanagers, passive-aggressives, and absentee landlords (for lack of a better term). Most of us are utterly unsuited for graduate school, either in theory or in practice. Only a fraction are cut out to be full research faculty, and even some of these I wonder if they'd be happier doing something different. (The remainder, I seriously wonder whether they'll be fucking up their grad students' lives in 20 years.) Most of us go to grad school because that seemed like the logical route at the time, and we enjoyed learning and experimenting. After 5-6 years of largely wasted effort, almost none of us would still recommend grad school to our younger selves. I still feel bad about a few of the younger students who didn't get the brutally honest advice they deserved, because we didn't want to hurt their feelings.
There are probably a few sub-fields where it is possible to stay on the cutting edge and be employable for years after graduation - next-gen sequencing, perhaps. But I get depressed every time I go to meetings and meet students and postdocs with IQs well above 120 slaving away on projects that are probably useful but certainly not world-changing, and who will probably end up with one or two papers in Journal of Molecular Biology, and eventually need to find jobs in their chosen fields. What jobs? Even if you're the most badass electron microscopist in all of New England, what does that prepare you to do other than perpetuate the cycle of mismanagement at another research institution? Assuming you can even get the job, of course; even a top-tier journal publication doesn't automatically get you anything when you're competing with several hundred other postdocs.
Sadly, I still haven't figured out what to do with the degree that took most of my youth and nearly all of my sanity. I never had any ambitions towards faculty posts, fortunately, but there aren't a ton of jobs in industry in my field either. I still work in the same field in academia in a full-time researcher position, which is relatively stable if you ignore the fact that my employer is $14 trillion in the red and counting. I'm probably marginally more employable because I managed to pick up very good programming skills along the way, but still, if I want to move into software engineering I'm either going to be competing with CS PhDs, or settling for bachelors-level jobs. Every time I read my alumni newsletter from college I cringe, and think "Jesus Christ, why didn't I just sell out like everyone with a brain?"
The "arsenic based bacteria" which were supposed to revolutionize the way we viewed biology didn't even turn out to be a hoax, but bad science. Although, after RTFA, it looks as if these scientists are being a bit more cautious before making outrageous declarations.
Biologists are finding fascinating new microorganisms in harsh environments all the time - this is mostly very good science, but nothing revolutionary or remotely controversial. The microbes in TFA are interesting because there isn't an obvious energy source available (since they're non-photosynthetic). This means that they may have evolved some unique metabolic strategy. But there is no inherent reason why these microbes can't or shouldn't exist; they're just something we haven't seen before.
The arsenic bacteria article was immediately controversial because for the claims of the authors were true, it would directly conflict with some very basic chemical phenomena, and didn't make sense in light of everything else we know about cellular biochemistry. (The mere existence of microbes in such high levels of arsenic is intrinsically interesting, since they would have had to evolve tolerance for what is effectively a poison, but again hardly revolutionary.) It was doubly controversial because it didn't do a very good job experimentally supporting the primary claim, that the bacteria preferred arsenate to phosphate in nucleic acid backbones. If you're going to put forward such an extreme hypothesis, you need to really nail the evidence 100%. The hand-waving science-by-press-release was an added slap in the face. Every scientist (especially the great ones) loves a bit of PR now and again - that's why universities issue press releases like TFA - but you have to know your limits.
With instruments like this, it will make the task of X-ray crystallography determination of protein structures much easier.
No, it won't. Two reasons:
1) You need "hard" X-rays for crystallography - with a wavelength similar to the chemical bond length. The maximum resolution you can achieve is equivalent to half the wavelength, and even that requires a complicated detector setup, so in practice you want a wavelength around 1 Å for crystallography. The wavelength of this device is 8Å, which is fine for spectroscopy and small-angle scattering studies, but useless for crystallography. While I suspect the technology could be made to work at shorter wavelengths, this usually involves tradeoffs such as higher cost, higher energy consumption, etc.
2) The intensity of the source is far less than a synchrotron (let alone a free-electron laser). This means that data collection times will take far longer. At a synchrotron beamline, in favorable conditions, you can collect an entire data set in seconds (of course, the detector alone costs more than $1 million). Usually it's not quite that fast, but you don't need to wait days for your data - and you can hedge your bets by collecting data on as many crystals as possible.
A secondary reason is that the improvement in synchrotron beamline technology has also made them more accessible - much of the work is now done remotely using robotic sample changers. Being able to grow decent crystals in the first place is a far more limiting factor. And my impression is that beamtime isn't terribly difficult to get; people do still use home X-ray sources while they're waiting for beamtime, but most people are content to wait for the synchrotron to get the truly publishable data.
A private company can re-incorporate elsewhere to save on taxes or avoid regulations in a heartbeat.
Wrong. Quoting a representative posting on the SpaceX careers page:
"To conform to U.S. Government space technology export regulations, applicant must be a U.S. citizen, lawful permanent resident of the U.S., protected individual as defined by 8 U.S.C. 1324b(a)(3), or eligible to obtain the required authorizations from the U.S. Department of State."
I guess this is one of those regulations they could theoretically avoid, but where exactly do you think would be a better place to do business, given that a large fraction of the potential customers will be in the US (either the government or companies)? And where else do you think has a sufficient labor pool? Right now the choices are the USA, Russia, or the EU. India might get there eventually. You'd have to be insane to relocate a commercial space flight company to China.
Then you went to an exceptional school.
It was an exceptional school in many respects. But it was also typical of American public schools in many others: massive classes (30 was very typical, often more even though that was supposed to be the limit), chronically underfunded (my senior year the science classes started requesting a voluntary lab fee so they could afford basic supplies, like graph paper), and often incompetently managed (see my remarks about education bureaucrats above). A few years after I left, the school district "misplaced" $25 million - they simply couldn't account for it. A principal was fired for having sex with a student. My freshman year, a student emptied a 9mm in the cafeteria and hallways (fortunately, he was a poor shot). So it wasn't one of those ridiculously nice suburban schools like Scarsdale that feeds off high property tax income.
What made it exceptional was a critical mass of competent-to-excellent teachers, relatively bright (or at least hardworking) students, and very involved parents. No amount of standardized testing, union-busting, innovative techniques, or increased funding will substitute for these.
For the majority who need to go to public schools, our education system is terrible. The article points to the successes of those whose parents could afford to give them the best education money can buy.
This is not universally true. I have a PhD in biochemistry, and until college I had always attended American public schools. So did many of my close friends, who now have PhDs as well. The (large, urban) high school I attended had some massive systemic problems that are probably unfixable, but at least 60% of our graduating class went to four-year colleges, including about ten or so students who attended Ivy League schools. I have very little good to say about those four years of my life, but I honestly think most of the teachers did the best they could with what they had. The quality of the science education was very mixed, but we had some terrific innovative programs (especially marine science and tech ed) that were as good as anything the private schools could offer. I know I'm not the only student who was inspired to pursue a scientific career as a result of this.
The biggest problem I faced was that a faction of the education bureaucracy was fiercely opposed to college prep courses (because they were elitist) and wanted to homogenize the curriculum. This was not the fault of the teacher's union or the politicians; I still haven't figured out where these people get their ideas. (Just to clarify, "these people" were very racially diverse - a handful of white teachers were some of the loudest advocates at my school.) However, it was every bit as anti-intellectual a movement as the right-wingers trying to force pseudoscience into the classroom. By the time I was partway through high school, my parents decided they didn't like where things were headed, and sent my siblings to a private high school (where they appear to have received the same quality education, albeit with less senseless brutality).
The more general problem is that funding is indeed limited - the difference between a high-quality private school and a large public school is that the classes in the latter will be twice as large, so teachers can't give individual students they attention they require (or that their parents feel they deserve). The really smart students will always be screwed unless there are enough of them to fill a classroom - otherwise you have to explain to the PTA why five students get their own teacher for AP American History while the rest of the students get class sizes of 30.
My German friends were expected to be able to solve calculus problems in order to graduate high school. Calculus was considered college level when I went to high school, and still is.
The high school I attended had not one but two levels of calculus - I took AP Calculus I my senior year. All you need is enough students at that level to fill a classroom, and we had enough for two periods. That was actually one of my favorite courses in all of high school - it was the first time math seemed truly intuitive to me.
Steal from California? That state is flushing money down the sewer.
California's public debt is currently around $16 billion, almost three orders of magnitude less than the federal government's. California's contribution to federal revenues in 2007 was more than $300 billion, although I suspect this will have declined slightly since 2008.
You're probably right that losing CA and NY would force the rest of country to live within its means. However, it would be an even better deal for Californians, because some of the money wasted subsidizing red states could instead be spent fixing our own fiscal mess, and we'd still have plenty left over that could be refunded to taxpayers. Sadly, CA would also be crippled without federal intervention to ensure that the state gets an adequate water supply - I haven't figured out a solution to that yet.
The people who are most adamant that creationism is the right way are those who take what is written in the Bible word-for-word.
Actually, that's giving them too much credit. They actually take what is written in the English translations of the Bible word-for-word.
Of course, I'd argue that apart from issues of translating from ancient Hebrew (etc.), the convoluted authorship of the Bible - and the lack of a clear documentary record for much of the text itself - should be enough to deter any reasonable individual from interpreting it literally. This doesn't mean that the Bible is all nonsense (although I have my own opinions on that), but to take the Bible as absolute truth, you have to assume that the people who recorded it were infallible and uncorrupted by baser motives.
That has huge implications for taxonomy and phylogenetics
One of the most exciting potential projects I've seen recently is a proposal to sequence 10,000 vertebrate genomes, which would sample nearly every genus. One of the project leaders, David Haussler, has previously worked on extrapolating backward from known mammalian genomes to guess at the genome of the common ancestor (100-plus million years ago). That was with several orders of magnitude less data - if they actually pull this project off, we'll be able to understand vertebrate evolution at a level of detail unimaginable today. As usual with these kind of projects, of course, the data analysis is going to be far more difficult than the actual sequencing.
I was under the impression that you paid PNAS to publish your work because it was shit that you couldn't get published in a real journal.
This was very frequently true until the last decade or so. In fact, there were always some very good papers in PNAS, but there was also a lot more junk. Peter Duesberg, probably the most famous (and most reputable, until he went crazy) scientist to argue that HIV does not cause AIDS, is (or was) notorious for contributing an article to PNAS every year - since he was already an NAS member since the 1980s, they had to let him publish there. Since the editor who made the switch to direct submission, Nick Cozarelli, was a colleague of Duesberg's at Berkeley, I wouldn't be surprised if there's a direct link here.
Anyway, if the article says "communicated by" or "contributed by", that means it got in through the back door. Not all of these articles are crap, but many don't deserve to be there. According to the PNAS web site, 90% of articles submitted, and 79% of those published, are direct submission. I believe the "communication" route is now closed, but it is still possible to contact an NAS member directly and ask if he/she is willing to be an editor, in which case the footnotes will mention that the editor was "pre-arranged". The difference from before is that the peer review is more rigorous and the editorial board has veto power. I've done it both ways (as a minor co-author), and while I'd obviously feel better about getting in the front door, I can understand why we went directly to an NAS member in one case. Academic politics is a bitch.
Why is that 'politically correct' BS always is imposed over strict rationality?
I dunno, some of us have an instinctual aversion to totalitarian social engineering imposed in the name of "strict rationality"... might have something to do with the 20th century.
...it does publish great papers, but does require something of a personal connection to get into... Same for The Proceedings of the National Academy of Sciences
Actually, this isn't so true of PNAS any more. One of the previous editors decided in the late 1990s to raise the quality prestige of the journal by accepting more papers through a traditional peer-review route, as opposed to NAS members "communicating" or "contributing" articles (which would often have minimal peer review). This was very successful, and now most articles in PNAS get in through the front door, and they're slowly eliminating the back doors. The overall quality is pretty good - not as high-impact as Science or Nature or some of the top specialty journals, but it's definitely a journal that researchers are excited about publishing in if they can't get into the top tier. The fact that they're not part of Elsevier or one of the other big commercial publishers, and their open-access fee is very reasonable, is an added bonus. (Disclaimer: I've published there, so I'm not entirely unbiased.)
Now, as with any journal, knowing the right people always helps - sadly, this is true at any level.
If "private industry" did the same, they would face manslaughter charges. Only government can get away with that level of incompetence and disregard for human life, and survive.
Private industry did in fact do the same, and no, they did not face manslaughter charges. Contrary to common assumption, much of the launch infrastructure was already privatized, under "cost-plus" contracts which guaranteed a profit to the contractor no matter how expensive the final product was. In the case of Challenger, the contractor (Morton Thiokol) responsible for the SRBs ignored the warnings of its own engineers and told NASA to go ahead with the launch. (Doubtless NASA fucked up too, but it wasn't NASA's product that exploded.) They were ultimately fined for the disaster, but never had to admit legal liability.
The end result? The same company (after some corporate restructuring and a later merger - it's currently called ATK) continued manufacturing SRBs, and Congress recently tried to force NASA to continue using the same SRBs. So, the moral is that when your biggest customer by far is the US government, incompetence and failure is no barrier to success in the private sector.