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a debacle’s a-brewing on copied work in research publications. last year, some software was unveiled that checked papers on the physics archive (www.arXiv.org). the researchers showed just 0.2% cases of plagiarism (assuming their results scaled for the small sample size they analyzed). here’s the review.

last month, a similar analysis on arXiv turned up some 70 offending papers, mostly from turkish theoretical physicists (original story). forty alone were “coauthored” by one graduate student, who apparently was first flagged because he wasn’t able to answer simple mechanics questions at his oral exam, despite his publication record.

online this week, nature posted to more bits to the story. first, an angry turkish physicist weighs in on the accusations: “Plagiarism? No, we’re just borrowing better English.” second, another physicist suggests implementing a different submission method, in which all new papers would be plagiarism-checked and flagged before being accepted.

it sounds like there are two separate issues here. first, there’s the dire case of students who publish (or even pass) without knowing anything. there shouldn’t be much tolerance for this; it makes all of academia look bad. but second, there’s the slightly more innocuous case of poor english speakers. as the correspondence submitter, a turkish physicist, points out, “Even if our introductions are not entirely original, our results are — and these are the most important part of any scientific paper.” additionally, there are very different views of plagiarism (including none at all) in different cultures. for example, the student who was flagged for his poor oral exam couldn’t be expelled because, apparently, his university had no ethics policy regarding plagiarism!

it strikes me as bad practice to write up results while stealing introductions and backgrounds. but it does point out two different styles of science. some very original work synthesizes different sets of experiments in new ways, leading to new directions of research. these obviously require original background material, because they draw from different literatures. meanwhile, there are experiments in single fields that just beg to be done. usually, people in the field know that the question was there and why it was there. all they need is the answer. one can imagine a forum in which original experiments are inserted into a larger published work as the experiments are performed. At its root, scholarpediahas a form of this that might work on the long term. researchers just insert their contribution or experiment into the larger review article, and the knowledge is thus collected (introduced, contextualized, and reviewed) without extra work for the experimental scientist.

scientists often aren’t good writers. to what standard should scientists hold scientists?

as you probably know, this is the week of the 2007 nobel prize announcements. one field’s winners are announced each night; see here for the results so far. the major players in paving the way for gene knockouts, a staple of molecular biology research, were awarded the prize for physiology or medicine.

interestingly, the creators of a major citation index have been trying to predict the winners for several years now. they’re zero for two this time around, and i have a feeling the winner for chemistry, announced in 6 hours, also isn’t on their list. it’s bad karma to suggest his name, so just trust me when i say “i told you so” tomorrow.

UPDATE: here’s a nice post about the chemistry prize (tip to ah): “Very early tomorrow morning, some lucky biologist will receive a call that he’s won the Nobel Prize in chemistry. Just kidding—it will probably be a medical doctor or a physicist.”

for those in the area, james watson, of double helix fame, just finished a “public conversation” at the salk, and will be speaking at d.g. wills books in la jolla tonight at 7. according to the link, he may discuss his plans of “making all girls pretty.”

watson recently published Avoid Boring People: Lessons from a Life in Science (available for pre-order on amazon). if you think of attending tonight, remember the title’s deliciously double entendre! (photo credit: max gerber, la jolla village news)

first, rather than explain yet another virtual absence, i’ll point you to some things that have unapologetically stolen my time. with any luck, you’ll get lost in at least one of them, and forget that you haven’t read anything here for a while.
{google reader; tiddlywiki; enc of philosophy, eg the problem of induction; the ugly insides of data acquisition; etc}

ny times, glynis sweeny

at any rate, nytimes had a much-needed op-ed by mike males, a guy who helped to start youthfacts.org. the article and the site try dispelling myths about youths. males makes several interesting points as he demonstrates a “ballooning crisis” among americans aged 35-54 in traditionally adolescent issues like drug and alcohol abuse. beware of his numbers comparisons, though, such as this one: of all 35-54 years old americans, “21 million [are] binge drinkers (those downing five or more drinks on one occasion in the previous month), double the number among teenagers and college students combined…” here, the adult group range is twenty years, whereas “teenagers and college students” are an age-group spanning only ten years. that is, the population size is probably about double, making roughly the same percentage of binge drinkers in the two age groups.

what i especially appreciated about males’ piece, though, was his willingness to challenge claims about youths that are traditionally made on the basis of irrelevant or misrepresented research studies. i’m not the first to complain about this: the media’s science fetishism, mixed with its sound-byte sensationalism, render impossible any attempt to fully gather data and make fair interpretations. of course, the answer isn’t to downplay the significance or applicability of research… perhaps just to rein in the lay coverage of its conclusion.

for comparison, see also this interesting scientific american human behavioral and fMRI result regarding political disposition and internal conflict. here’s a quotation from the article, which was a review of a recent nature neuroscience paper: ” ‘They are more sensitive to the need for change and more sensitive to the need to change their behavior,’ Amodio says about the politically left-leaning subjects.”

if coding to europe seems too far-fetched, matlab today released their twice annual competition. you have a week to optimally solve the peg-jumping problem with the leanest code. the winners get bragging rights, and maybe a coffee mug. (thx to bc for the tip)

the flapperome

it’s not news that scientists aren’t all linguists. but that ain’t no excuse for the nominal slop that pervades biological appelation. perhaps the most notorious of cases, and the subject of today’s exposé, begins in the 1920s: flappers were a dime a dozen, histologists were still arguing over the neuron doctrine, and a forty-something german botanist was coining the term genome. with it, he unwittingly hacked open a pandora’s box of lingual lament, unleashing the phoneme-turned-meme -ome to a world poised to beat it to death. the inevitable ome-philia is now as annoyingly crazy as its shakespearean counterpart; one can only wish it were as self-destructive.

an ome-ome

these days, new *-omes appear daily. perhaps, as colleague dh pointed out in conversation, it’s due to the success of the human genome project, especially as compared to its drunk-in-a-gutter step-brother, the human brain project. here are a few of its more colorful manifestations: the human cytome project, the human epigenome project, the human GNU-ome project, the human Jen-ome project, the american meme-ome project.

the range of possibilities is much greater when it’s not a “human project”: the proteome (coined by mark wilkins, 1995), the metabolome (coined by oliver et al, 1998), the interactome, the transcriptome, the davematthewsome… the list goes on. what spawned my own expl-ome-ation was the new fix that the neuroscience community has with omomics… presenting [drum roll please]… the connectome (PLOS biology article and the obligatory dotcom attempt). it begs the question: what’s in an -ome? surely, people recognize how passé (and strange) it is to affix their favorite subject’s moniker to the -ome suffix: most of these things have nothing to do with chromosomes. but maybe that’s not the real origin of -ome…

et-ome-ology

in the 2 april 2001 edition of the scientist, lederberg and mccray offered a brief but entertaining account of the etymology: ‘ome sweet ‘ome-ics. the authors are iconoclastic enough to suggest that OED gets it wrong. OED suggests that botanist hans winkler, who was the first to use the term in 1920, coupled “gen” from gene and “ome” from chromosome. meanwhile, lederberg and mccray point out three other intriguing, if not all etymologically plausible, facts. 1) there are a number of botanical terms that predated winkler and his cronies in the 20’s, and may have provided more proximate motivation than the term “chromosome”; 2) in Greek, the suffix denotes “having the nature of” ([2], by way of [1]); 3) in Sanskrit, it means “fullness [and] completeness” [1]. beautiful, but winkler was a german at a time when indians were brits… and nobody likes brits.

in the end, skill and passion go hand in hand with the best of science, no matter how it’s dubbed. in that vein, perhaps the old aphorism says it best: ‘ome is where the ‘art is.

UPDATE: see notes from a recent seminar on connectomics (in case you’re still interested).

also see:
[1] Lederberg and McCray. ‘Ome Sweet ‘Omics–A Genealogical Treasury of Words.
[2] Roland Brown. Composition of Scientific Words.
[3] Walter Flood. Scientific Words.
[4] Sporns et al. The Human Connectome: A Structural Description of the Human Brain.

gateway electronics is closing its san diego doors after many years of faithful, if disorganized, service to the techies of SoCal.

our lab scavenged the place a few days back, mostly for personal projects, and walked out with easily more than $1000-worth of stuff, all for around fifty bucks. some of the more exciting purchases were multiple lasers, including this helium-neon one, which had a used pricetag of $100. i got it for one dollar.

i also bought near 100 7- and 11-segment LEDs, you know, just in case… you ever need to build an alarm clock from a couple of watch batteries, a paperclip, a rubber band, and a few LEDs.

the closing marks a well-recognized, but nevertheless sad, shift in our culture: people are increasingly using sophisticated equipment while avoiding the knowledge of how the heck any of it works. as a famous neuroanatomist, personal hero, and close lab friend emailed me regarding the event:

I guess I am of a different generation. No, I KNOW I am of a different generation. When I was a kid in NYC, the area around Hudson Street had dozens of stores that sold electronic components, army surplus transmitters and receivers, 807 vacuum tubes, 6au6 pentodes (?), and transistors hadn’t yet been invented. (Shit! Am I really that old?! Had they yet invented resistors?).

Sad day, and the end of electronics hobbying in San Diego. Hmm!! Maybe that explains why most of today’s kids don’t have the slightest idea how their various electronics toys work.

fortunately for tinkerers everywhere, the head salesman is planning to reopen the store under new guise nearby. plus, their website will still ship out of st. louis. phew!

sad but true.

just came across this guy’s comics and had to link.

the center for ethics in science and technology (CEST), based in san diego, is hosting a free public conference on stem cell ethics this friday at salk. it has some of the heavy hitters in the field (check the brochure). one has to wonder, though, why the organizers scheduled the event from 1-6pm on the most solemn and holy of days in the christian year… to wit, the very hours jesus hanged on the cross. they’ve insured that no practicing christian will attend the event; perhaps a more apt name for the organization would include the prefix “the in-group” (and thus, IN-CEST).

from the advertisement:

A free, public program for the San Diego Community in collaboration with the San Diego Research Ethics Consortium which includes the Burnham Institute for Medical Research, the Salk Institute for Biological Studies, The Scripps Research Institute, and UCSD.

the title says it all. visit here to celebrate, or here to appreciate the beauty that is pi. (gif credit: john reid and the wikipedia commons)

i generally stay away from the evolution-creation debate on this blog, but this story has more issues at stake than usual.

ny times offers up a strange dose of science-religion interaction today in its article Believing Scripture but Playing by Science’s Rules. it’s a discussion of a young-earth creationist who just received his phd from the university of rhode island in geology and now works at jerry falwell’s “liberty” university. while he apparently does first-rate science from an evolution/old-earth perspective, he holds a religious conviction that it’s false. the most interesting question to ask him, then, is how his position is intellectually honest… when asked, he replied, “‘I was working within a particular paradigm of earth history. I accepted that philosophy of science for the purpose of working with the people’ at Rhode Island,” according to nytimes.

the nytimes asks for readers’ comments on the question “Can a scientist produce intellectually honest work that contradicts deeply held religious beliefs?” there are really two questions here, and it looks from the over 200 comments that people are trying to answer both. first, can the science produced be sound? second, is the intellectual position of the scientist defensible?

the answer to the first question is a resounding yes. science is never done by omniscient people. instead, it’s usually done by people wanting to know how the natural world works, or more accurately, how far we can extend a physical explanation of the world based on certain logical assumptions, like measure theory, and a conviction that the scientific method actually works. successful science doesn’t require a belief in the underlying absolute truth of conclusions based on evidence. in fact, i imagine (and hope) that most scientists acknowledge that they have no reasoned account for demonstrating the absolute truth of even the most fundamental and general scientific results. with a nod to postmodernists, i’d submit that there are a set of assumptions required to do scientific work and that in principle such work can be done by anyone willing to use those assumptions when making measurements and synthesizing data into a coherent framework. this can include people with extremely bizarre convictions.

as for the second question, there are two answers. first, his position doesn’t seem to be intellectually honest. to the extent that the phd student, marcus ross, believes the inherently contradictory accounts of a young-earth creationism and an old-earth evolution/geology, his framework is fragmented. of course, he probably doesn’t believe both simultaneously. in order to be intellectually honest, though, it seems that his understanding of creation must satisfactorily account for the findings that he himself has made in geology. he probably has an account for this, but i don’t know it. but second, i’d argue that most scientists’ positions are intellectually dishonest! i disagree with michael dini, a texas tech prof cited in the article for refusing to give letters of recommendation to “anyone who would not offer ‘a scientific answer’ to questions about how the human species originated”:

Scientists “ought to make certain the people they are conferring advanced degrees on understand the philosophy of science and are indeed philosophers of science,” he said. “That’s what Ph.D. stands for.”

if that’s the case, virtually every science phd program fails. philosophy of science is a subtle business: most scientists i know hold convictions they deem scientific that are simply false. i agree with dini that, pedagogically, science phds should understand the major issues in philosophy of science. however, few do, and there’s no means of weeding them out. in the end, it would be unjust to deny a science phd to a student on a particular point in philosophy of science when his peers are guilty of other misunderstandings.

thanks to SL for pointing out the article.

see here (UPDATE: this is a better gallery of all publicly available hubble pics). “The Perfect Storm, a small region in the Swan Nebula, 5,500 light years away, described as ‘a bubbly ocean of hydrogen and small amounts of oxygen, sulphur and other elements’ .”

nature neuroscience ran an editorial this week arguing that scientists should counsel policy-makers. because science is becoming increasingly specialized, politicians will necessarily have more trouble interpreting results relevant to science-related law (as for medicine, space, geoscience, etc). the article describes the uk’s office of science and innovation, an examplar for dealing with scientific policy-advising. for a recent example, a ‘Foresight project’ committee recently studied the implications of neuroscience on society and identified several issues that the government should be considering now, especially regarding intelligence enhancement, addiction, and recreational drug use. by comparison, surprise surprise, the u.s. bureaucracy isn’t great:

The situation in the United States is more complicated. US science policy is largely managed by the Office of Science and Technology Policy (OSTP), which coordinates with the President’s Council of Advisors on Science and Technology (PCAST) and the National Science and Technology Council (NSTC). In theory, these organizations should have direct access to the White House; the NSTC is a cabinet-level council, and, as implied by its name, PCAST is expected to advise the president. In practice, however, the roles and access of these organizations depend on the preferences of the incumbent. For example, unlike in previous administrations, the PCAST now reports to the OSTP director, not to the president. Compared to other advisory institutions (such as the National Security Council), there is little continuity in science advice between administrations, making the sort of long-term policy making exemplified by the Foresight projects very difficult—a problem compounded by the scarcity of direct interaction between scientists and politicians.

the article goes on to mention another disappointing fact: “[…]the OSTP is significantly weaker under the present administration. Only two of four associate director positions are currently filled, and the offices have been relocated away from key White House staff.” man, even their website is clunky.

should we expect anything less of this president? alright, to be fair, we’d do well to remember, among all these “facts”, the wisdom from the great colbert: “reality has a well-known liberal bias.”

the onion reports that kansas has outlawed evolution. from the article:

From now on, the streets, forests, plains, and rivers of Kansas will be safe from the godless practice of evolution, and species will be able to procreate without deviating from God’s intended design…This is about protecting the integrity of all creation.

and again

“Barn swallows that develop lighter, more streamlined builds to enable faster migration, for example, could live out the rest of their brief lives in prison,” said Indiana University chemist and pro-intelligent-design author Robert Hellenbaum, who helped compose the language of the law. “And butterflies who mimic the wing patterns and colors of other butterflies for an adaptive advantage, well, their days of flouting God’s will are over.”

(tip to jd for the link)

an awesome reader (hat tip, kw) found the clip alluded to in an earlier post. skip to about 3:30 for the good stuff.

note that it’s actually on protein synthesis (not dna replication), and comes complete with an obligatory, if quizzical, reading of the jabberwocky along with smoke for gtp hydrolysis (and illicit inspiration, i’m sure).

mathematicians have just solved the age-old problem of how to cut birthday cake to keep everyone happy. they call it the surplus or equitability procedure, and it involves ‘weighting’ which parts of the cake you like best (icing, chocolate, etc). you get a piece that has the most of what you like, and distribute what’s left over of that piece to everyone else, each of whom does the same thing. this solution is relevant for more than just cakes… it works for pies, quiches, even casseroles. and anything else that requires optimizing the total value of weights for more than one decisionmaker.

i didn’t check the math, but i’m still a fan of my tried and true method: “half the cake and eat it too.” it’ll be interesting for some decision-making psychologists to test how this solution pans out for human subjects. also, i bet the folks at freakonomics will have something to say.
“gimme gimme gimme gimme gimme gimme gimme gimme gimme that cake!“

a friend just showed me this new animation exploring the vibrant biological milieu. it’s kind of gratuitous, and the music is wretched, but it does a nice job with DNA transcription, cytoskeletal reorganization, and stylized myosin trafficking (here’s one that takes fewer liberties). unfortunately, the animation doesn’t really capture the feverish pace or elegant complexity of these biochemical interactions…to get an intution for that, it’s better to watch a philip glass serial film. still, it’s a fun cartoon.

for my money, i’d stick with that hilarious 1970’s version of DNA transcription filmed by a bunch of bored, artistically-stifled grad students given afternoon access to a football field. if anybody can find a clip of that, pass it along.

(picture courtesy cgl.ucsf.edu)

for fear that i’ve been focusing too much on politics (it’s hard to avoid), i’m starting a new science series on fridays called science fridays, appropriately enough. first up, a scanning electron micrograph from thomas eisner, known for his love of biology and for his delicious pictures…in this case, a carpenter ant caught (literally) in the act of attacking a beatle.

but the real story for this week is the special oct 6 issue of the journal science. it focuses on computational neuroscience, which the introduction heralds as having now arrived as “a mature field of research”. it’s about time! to be fair, the field really started around 60 years ago when hodgkin and huxley modeled the action potential (the electrical event we think is most responsible for communication among cells in the nervous system) and lorente de no looked at the properties of signal propagation in and around these cells. these early works make for great reading (even for those solely interested in the sociology of ideas: historians of science are beginning to appreciate the circus of research and controversies still swirling as neuroscience continues in its heyday of naivety (see u washington’s timeline or check out the resources at the society for neuroscience site.

back to the issue, there are several nice articles:

• it’s nice to see simoncelli get some air time, even if it is slightly idolatrous.
• i’m so tired of hearing about jeff hawkins and neuroscience. i read some of his book, but didn’t find an original idea in it. it was a typical techy-turned-neuroscientist foray into the neuroscience a lot of us already know (i’m serious, it was a regurgitation of vernon mountcastle… 30 years late). in fairness, he’s contributed a lot of resources and enthusiasm. but his intellectual ‘contributions’ don’t warrant a page in science… there, i said it.
• i enjoyed floyd bloom’s assessment of the computational neuroscience terrain as he addresses pitfalls for collaboration in the past, and looks forward to emerging subfields like neuroinformatics.
• last, the journal had four reviews of recent neuroscience books, which i’ll list in toto, in case you’re stuck on finding a holiday gift for me…

1. moral minds: how nature designed our universal sense of right and wrong, by marc hauser. didn’t hear about this one till now… anxious to read it.

2. rhythms of the brain by gyorgy buzsaki (i really like this guy’s research… a fellow new joyseyite)

3. neurobiology of addiction by george koob (of ucsd fame… great speaker) and michel le moal.

4. social neuroscience: people thinking about thinking people, by cacioppo…snore…et al.

last, as a treat for making it this far along in the first installment of scifri, take a look at some pretty pictures from the winners of nikon’s recent science images competition. one of my favorites is of rat retinal astrocytes from a researcher here at ucsd.

ucsd’s guardian just ran an article on religion profs who strive and struggle to maintain objectivity in teaching. in response i wrote the following letter to the editor (link added when published, Oct 12).

**********

Dear Editor,

I enjoyed Ms. Buchanan’s carefully written Teacher Don’t Preach in Monday’s Guardian; I’d like to encourage more articles on the topic by pointing out two areas to explore. First, the author assumed that objectivity is possible in academics. In reality, this proposition has been actively debated among philosophers for a while. Rutgers philosopher Roy Clouser, in his lively book The Myth of Religious Neutrality (U Notre Dame Press, 2001), finds ‘religious beliefs’ in mathematics and the natural sciences after rigorously defining that phrase. UCSD Prof. Rahimi’s comment on the diversity of his religious beliefs affirms Clouser’s definition: “my religious beliefs range from a humanistic conception of moral conduct to ritually watching ‘Real Time’[…] I never separate my beliefs from my lectures.” Second, and in keeping with this broad understanding of religious conviction, Ms. Buchanan did not explore the extent to which religious beliefs permeate the science and philosophy lecture halls. To put it bluntly, if Daniel Dennett and UCSD Prof. Patricia Churchland don’t have strong religious convictions that influence their lectures and their work, no one does.

**********
hopefully, churchland won’t blacklist me. (picture credit, kedar reddy/guardian)

just found out about the very small release of mike judge’s new film idiocracy and read a nice review at slate. apparently, it’s everything you’d expect from the creator of beavis and butthead in the time of george w bush: a humor that laments incompetence and laziness. i’m in no rush to see it, thanks to a few other reviews, one of which sums it up best: the movie is “so puerile and gross that[,] though the movie wants to say something about the dumbing down of America, it winds up not so much commentary as part of the problem.” there’s also a conspiracy theory saying that the distributor (FOX) intentionally squelched the film…