Beta

Slashdot: News for Nerds

×

Welcome to the Slashdot Beta site -- learn more here. Use the link in the footer or click here to return to the Classic version of Slashdot.

Thank you!

Before you choose to head back to the Classic look of the site, we'd appreciate it if you share your thoughts on the Beta; your feedback is what drives our ongoing development.

Beta is different and we value you taking the time to try it out. Please take a look at the changes we've made in Beta and  learn more about it. Thanks for reading, and for making the site better!

Comments

top

Biology Help Desk: Volume 2^3

robotkid Re:"waiting list"? Actually, no. (19 comments)

There was a study in PNAS within the last year that was eye-opening, especially in that female faculty were just as biased against a fictional resume for a lab manager (read gap year student technician) if the name was feminine rather than masculine.

http://www.pnas.org/content/109/41/16474.full

Of all the numerous commentaries on why this might be so, I think the above-average but not stellar academic credentials (B+ student) is what did it. For a normal
(read male) evaluation, the narrative might be "this guy just needs some good mentoring while he figures out what to do next", whereas for a female name, it might be "she's OK but she's not stellar, and she needs to be stellar to succeed in this male dominated field, so let's not mislead her".

about 9 months ago
top

Biology Help Desk: Volume 2^3

robotkid Re:"waiting list"? Actually, no. (19 comments)

Oh, of course! I really enjoyed going to a school that had a much more balanced range of academic programs, and I guarantee all my engineering friends very much appreciated that environment as well, especially being able to meet motivated and smart people with very different and varied interests.

But even then, the number of female Ph.Ds or faculty members in, say, math, physics, or computer science is a tremendous problem, and noone believes for an instant it has anything to do with innate ability, it's clearly external.

In contrast, the local school's startcraft team is top seeded, and there are so few women in this department that I find myself constantly reprimanding grad students who think injecting innuendo into lab presentations is harmless and acceptable academic behavior.

Quick anecdote. My postdoc advisor was trying to decide between two foreign applicants for the Physics Ph.D program here, both top students from their respective schools, and not knowing the overseas academic institutions very well, he asked one of the scientists in our group from the same country to rank the two applicants. He took all of 30 seconds and said "admit the woman". My advisor was shocked it took so little time, he asked why, the credentials seemed equivalent. The scientist replied "she's the only woman in her graduating physics class from a top university, so she had to prove herself ten times harder than any man to end up with the same grades, she's clearly the better scientist though it doesn't show on paper".

It's hard to know if that'll be entirely necessary. I understand as a father you feel a profound need to protect, but it actually is getting better. You might want to consider sending her to another university, however; schools with an overall more balanced program tend to have an easier time drawing women to more polarized fields.

about 9 months ago
top

Biology Help Desk: Volume 2^3

robotkid Re:"waiting list"? Actually, no. (19 comments)

I'm reading this thread and I'm wondering: is this *really* happening? I'm glad, in a way, for not being a geek female. I'm worried for my daughter, just a bit.

Agreed and seconded.

I currently work at a university well known for it's engineering programs and I would be *very* scared to send my daughter here. The ~ 15% female population is alternatively fetishized and objectified, but also not expected to succeed in any highly technical endeavors. My daughter is 3 years old, I'm hoping to teach her to code when she's a little older (project Alice or something similar), but only if she also learns some sort of asymmetric self-defense such as Aikido first. . .

about 9 months ago
top

Anti-GMO Activist Recants

robotkid Re:GMO's aren't the problem, GMO patents are (758 comments)

I have nothing against GMOs. What I do have a problem with is patents on genetics.

I think that's what a lot of the more educated anti-GMO activists have a problem with as well. Nobody should be able to patent a life form or a DNA sequence.

The crazy thing is, unlike the DNA patent for testing for breast cancer which has finally gotten SCOTUS' attention, there is no indication that a GMO will ever not meet the bar of a utility patent given the amount of purposeful engineering involved. The issue is more about whether the government should allow the entire world's food chain to be completely at the whims of a single, monopolistic patent holder.

There are a variety of plant-variety-protection acts that were originally penned to protect fruit tree breeders from having their competitors just grow seedlings from their painstakingly cultivated strains that often took decades of greenhouse breeding. Such protections have exemptions built in allowing farmers to re-plant seeds, as well as research exceptions and other public-safety provisions (i.e. if the government can step in if licensing terms would cause a famine, for example). The fine line that Monsanto treads is that, to anti GMO activists, they claim that a GMO is really just a souped-up type of selective plant breeding that we have been doing for centuries, so it shouldn't require any special environmental or public health regulations. But when it comes to licensing disputes, they insist that GMOs are so sophisticated and totally unlike a traditional "plant variety" that they deserve a utility patent and not ordinary plant variety protection. They can't have their cake and eat it too. Someone needs to found the AMD of GMOs and take away their cake. And then maybe they'll stop using lawyers to force 20-year-old genetic technology down farmer's throats and actually innovate for a change.

about a year and a half ago
top

Anti-GMO Activist Recants

robotkid Re:Is he OK w/ Monsanto's lawsuits? (758 comments)

Most likely not. Saying that GMO is not evil is not the same as condoning Monsanto's actions in court. Strawman much?

Agreed the two should not be conflated, although it's hard not to since Monsanto has 90%+ of the market share, so it's their way of the highway. If there were an AMD-like underdog, the first thing they would compete on would be reasonable licensing terms. But instead, we have a company that is acting like MicroSquash in the '90s, and just as with MS they prefer their critics to promote Luddite-ism rather than focusing in on the antitrust aspects of this.

I do disagree with TFA, however. It's not anti-GMO activism that kills small GMO startups, Monsanto does that very well on their own. If they don't buy out a promising startup outright they just deny it access to the market and it dies a slow death. For all the waving and shouting, anti-GMO activists can't even get labelling laws passed.

about a year and a half ago
top

Einstein@Home Set To Break Petaflops Barrier

robotkid Re:folding@home (96 comments)

I believe Folding@Home is a seperate standalone project, so it's all or nothing. In addition, there are a LOT of protein folding projects. I'd really like to see them work together - or explain why they are different.

Not only are there a lot of projects like this, most of them - whatever their intrinsic scientific merit - have very little direct application to fighting disease. Sure, the people directing the projects like to claim that they're medically relevant, but this is largely because the NIH is the major source of funding. It's also really difficult to explain the motivations for such projects to a general audience without resorting to gross oversimplifications. (This isn't a criticism of protein folding specifically, it's all biomedical basic research that has these problems.) My guess is that it will take decades for most of the insights gleaned from these studies to filter down to a clinical setting.

The project that is arguably more relevant to disease is Rosetta@Home, but that's because of the protein design aspect, not the structure prediction. (In fact, Rosetta doesn't even do "protein folding" in the sense that Folding@Home does - it is a predictive tool, not a simulation engine like Folding@Home.)

Someone please mod this up, as a researcher in the same field as F@H I can attest this is all quite correct.

First, I should preface this by saying I've interacted with several of the F@H folks professionally and they do excellent work. And that the NIH is under no pretenses when it funds this work that cures will magically pop out tomorrow - they think of it as a seed investment for a decade or two in the future. In terms of tax dollars spent, it's a good investment considering many biomedical labs spend more just keeping their mice alive every year than all the F@H lab's salaries combined (especially since the computing time is donated by volunteers).

That said, I've always been disappointed that they do not use their unique standing with the public enthusiast computing community to educate and provide the context of what is it they are actually doing and how it is unique among the literally hundreds of other similar protein folding research groups out there. I don't think it's hypocritical to claim basic research can have real world impact on real-world problems, but providing the proper context for an individual researcher's findings is sadly often at odds with their PR goals (in this case, convincing people to donate cycles to F@H and not to other similar projects). But so goes all of biomedical research, as the poster shrewdly notes, despite this being taxpayer funded research performed largely at non-profit, educational institutions.

FYI, federal grants are public record and you can search them to see brief descriptions of current funded research to get at least an idea of how much larger the field is than any one research group. Try one of the links below with the search term "protein folding" if you want a sense of how big this field truly is (and note that it does actually include projects run by actual doctors seeing actual patients). Considering the overall research budget is comprised of less than 2 cents from every tax dollar collected, it's not a bad ROI (obviously I'm biased as a federally funded researcher myself).

http://projectreporter.nih.gov/reporter.cfm
http://www.nsf.gov/funding/

about a year and a half ago
top

Biology Help Desk: Volume Seven

robotkid Re:Home PCR/EP, etc. (19 comments)

Related to biobricks, there are some good tutorials and short videos for basic lab techniques at the bottom of this page:
http://qb3.berkeley.edu/synberc/courses-college.html

Also that page has some links to slides and notes from intro courses in biological engineering and synthetic biology which would be appropriate as well.

about 2 years ago
top

Biology Help Desk: Volume Seven

robotkid Re:Home PCR/EP, etc. (19 comments)

I almost forgot. If by some chance your local CC does not offer a molecular biology course for lab techs, they certainly will offer a general microbiology course as that is required for oral hygienists, med techs, and nurses. It is traditionally taught as 50% lecture and 50% lab course with no prerequisites, so while you would not learn as many techniques as the pure lab course, you will learn more of the underlying biology involved and they will at least teach you how to do basic bacteria growth, plating, simple genetic manipulation and probably some microscope skills too.

I always found that course to be loads more fun than intro bio. Maybe because it's meant to be stand-alone and practical, as opposed to a mile-wide inch-deep preparation for future coursework, plus it's not required for medical school so all the hyper-competitive pre-med types aren't enrolled :-)

Cheers,
Alan

about 2 years ago
top

Biology Help Desk: Volume Seven

robotkid Re:Home PCR/EP, etc. (19 comments)

Community colleges aren't really the place to find biology, though. There are few (if any) disciplines where laboratory-grade biology knowledge can be applied without the kind of background a bachelor's degree would confer. You're more likely to find people who are both useful and open-minded around full-fledged universities.

I agree a community college is an unlikely environment to find someone who will understand your desire to tinker nor will you be exposed to cutting-edge science or be trained as a scientist would.

BUT...

Community colleges DO teach decent lab courses in molecular biology (i.e. e.coli manipulation) which would give you most of the skills you are looking for. Pretty much every community college offers such a course as there is a high demand for qualified lab technicians. It would be a stand-alone, hands-on course with few (if any) prerequisites, which your 10-year old bachelors degree probably satisfies. At my local CC, for example, they teach this course:

BIOL 285 - Molecular Laboratory Tech
This course is an introduction to the principles, concepts, and analytical methods of molecular laboratory techniques. Laboratory studies are conducted on the molecular level, and genetic engineering (recombinant DNA) is utilized in several laboratories. This course is recommended for students planning careers in biology, biotechnology, or advanced professional health. Offered Spring. A lab fee will be required.
3.000 Credit hours 1.000 Lecture hours 4.000 Lab hours

Additional points to consider:
1) At a 4-year college, the official answer is usually "no" to any request from a non-student, because they selfishly want you to pay $$$ for their continuing education or adult night school. If you ask a professor personally, however, they might be cool with you sitting in on a large lecture course, but not a lab course since those resources are strictly for degree seeking students. But never ask through official channels, the official answer will always say "no".

2) Departmental seminars, however, are usually open to the public, you can safely attend those without asking for permission. Universities often have special seminars by notable scientists aimed at the general public which are much more accessible, check the event calendars.

3) At a CC, you don't need to enroll in a degree program just to take one random course for your own self interest, nor will anyone care/notice that you aren't 18. Enrolling in a course is the best, most efficient way to get hands on training, perhaps after some self study with a good primer on molecular biology.

4) You can likely afford the cost of a CC course, which will be ~100-150$ per credit hour for residents , whereas at my university part-time enrollment costs 1,200$ a credit hour!!!

5) Home brew workarounds will make much more sense once you see how things are "normally" done with proper equipment. Actually, a poorer school will likely have the same old, beat-up equipment that homebrew folks pick up on ebay, so you might actually learn more applicable skills than if you trained with a cutting-edge setup.

I second the biobricks recommendation. When I become a prof I will definitely start an iGEM team and contribute some biobricks.

Cheers,
Alan

about 2 years ago
top

Function of 80% of the Human Genome Charted

robotkid Re:Junk DNA? (112 comments)

Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functionality.

There was a few surprising discoveries, sure. RNA enzymes were a real shock, for example. All in all, about just about 15-20% of human DNA now has 'putative junk' status that might be changed later with new discoveries.

You've listed the things we know are useless and pointed out that it adds up to >66%. No argument there. You also hypothesize that there's room for an order-of-magnitude increase in the things that *might* be useful from future, surprising discoveries. That's entirely my point!!

Exactly why are we arguing again?

I can't help but point out, though, that the RNA world folks were all saying "I told you so" when the RNA bits were discovered . . .

about 2 years ago
top

Function of 80% of the Human Genome Charted

robotkid Re:Junk DNA? (112 comments)

That 10% of the brain thing was the usual pop culture nonsense, but I've heard a lot of reputable scientists talk about junk DNA.

Yeah the analogy is imperfect but they are both rooted in the common assumption that if we can't assign a function to something then it doesn't do anything at all - which is troubling to me because we don't even know what alot of the "real" genes do yet to do an accurately accounting how much is NOT useful.

So while it'll probably remain true that "junk DNA" will outnumber "useful" DNA in the final accounting (80% is surely a headline-grabbing overreach), there will also continue to be a steady progression of sequences initially tagged as "junk" that turn out to have function. And my initial point was that THAT fact should not come as a surprise to molecular biologists, I can't remember a single year in recent history when there wasn't a discovery of a whole new class of noncoding RNAs, for example.

about 2 years ago
top

Function of 80% of the Human Genome Charted

robotkid Re:Junk DNA? (112 comments)

Actually, most molecular biologists KNOW that the majority of _eukaryotic_ DNA has no function. It's junk, deal with it. Fairly small parts of non-coding DNA perform useful functions: gene expression regulation (less than 0.1% of total DNA), mechanic 'handles' for cell replication machinery (about 5% of DNA), various RNA enzymes (less than 1%), etc. But most of it is still junk.

Sure, it'll never add up to an actual majority of the genome, but do you seriously believe the proportions you quote will still be valid in say, 5, 10 years? Just because something doesn't light up on your nifty hidden markov models doesn't mean there aren't any more epigenetic or non-coding regulatory bits hidden between those mountains of retrotransposon corpses just waiting to be discovered.

Show me a viable cell line with a 90% of the genome removed and then I'll believe you. Until then. . .

about 2 years ago
top

Function of 80% of the Human Genome Charted

robotkid Re:Junk DNA? (112 comments)

Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?

I don't think any serious molecular biologist ever thought the majority of DNA had no function, just as no neuroscientist ever believed that we only use 10% of our brain, but that's precisely the sort of sound bite that, when uttered in a press release somewhere, echos around the public consciousness forever and never dies because it provides a conveniently sciency premise for the next batch of rebooted superhero origin stories. The distinction is that before this study, we knew non-coding DNA was involved in regulation but not to what extent; i.e. there were plenty of specific anecdotal findings but nothing this systematic and large scale.

As for the significance of this sort of work, yes, it exactly like release day for a major software package, it's an anticipatory excitement and not a "we finally found the Higgs Boson after decades of searching" type of achievement. Molecular biologists and geneticists everywhere can now do a simple web search see how this affects the system they are working on without needing to perpetually beg the labs that possess the specialized high-throughput instrumentation to do a one-off experiment just for their favorite gene. . .

about 2 years ago
top

Dozens of Reported Plagiarism Incidents On Coursera's Free Online Courses

robotkid An obvious solution . . . (210 comments)

The largest enrolled courses on Coursera are on AI and machine learning.

Seems like it would be a good class exercise to make a plagiarism detector. I know such things exist commercially using proprietary algorithms and privately curated databases but doing a shoot-out using real world examples from the other courses on coursera could be a cool idea, not to mention a big dissuader for future plagarizers to know their essays are being vetted by ever-changing algorithms. And then you'd have to run them on each other to make sure people didn't copy each other's code :-)

Yes, of course, since coursera is free and not-for-credit right now plagarism "only" hurts the students. But the whole point of coursera is that all the big names in academia don't want to be left behind when whatever happens to higher education finally happens - and a large part of that is figuring out how online courses will be able to handle plagarism and even mundane things like exams and homework. Giving real credit and providing for a true alternative to a traditional brick and mortar education can not happen without addressing those first.

about 2 years ago
top

Researchers Seek Help Cracking Gauss Mystery Payload

robotkid It's a zombie virus! (229 comments)

Obviously it's looking for the DAYZmod files. Because, as I learned from watching Johnny Mnemonic, defeating military grade encryption is very much like winning a death match in a third-person shooter.

The insanely slow login times? That's your connection being tunneled through a secret proxy server in Qatar.

Every time you kill a bandit, somewhere in Iran a centrifuge explodes.

Zombie AI amazingly stupid? Turns out the Iranian Revolutionary Guards suck at video games, but you have to admire their persistence. . .

about 2 years ago
top

Antivirus Pioneer John McAfee Arrested In Belize

robotkid Re:Foreign Corrupt Practices Act (367 comments)

Bribing foreign officials is a violation of the US law Foreign Corrupt Practices Act. So it's surprising that he would admit this to a journalist.

Right, but according to the fastcompany article he's revoked his US citizenship to be a Belize permanent resident and seems to have gone to great pains to make his assets completely untouchable to the US what with the 5 civil suits pending against him.

more than 2 years ago
top

Antivirus Pioneer John McAfee Arrested In Belize

robotkid Re:Question: Why does this guy live in Belize? (367 comments)

There's quite alot of foreshadowing in the fastcompany article:

Then there is the $1 million patrol boat he donated to the Belizean coast guard. (In a letter to The New York Times, he described it as an act of philanthropy; later, he tells me he had to bribe members of the coast guard to prevent them from hassling his ferry business: "This is a third-world country. I had to bribe a whole bunch of folks.

indicating that he routinely gives large, overt, public bribes to get whatever he wants in Belize

Then there's this:

"And so a pair of police officers came to visit him. "We are sorry that we have to tell you to stop building that wall," they said. "I am sorry that I have to tell you that I am going to build it anyway," he told them, and they left. To McAfee, this exchange was proof of the evolved level of discourse in Belize, where a person is largely left to do as he pleases. . . At the time, I thought that he was simply being argumentative. But McAfee seems to want freedom without limitation. Needless to say, few of us exercise this sort of freedom. It tends to be very expensive."

Either he is willfully ignoring the fact that this seems to have been a small-time shakedown attempt or he is completely oblivious to it. Did he really think Belize patrolmen (note, not the environmental cops) are so genuinely concerned about shoreline regulations?? He doesn't seem to realize by being so brazen about describing large bribes to the press he's just inviting even bigger, less polite shake-downs in the future, which sounds exactly like what (unfortunately) just went down. Did he really think that request for a campaign contribution for the guy employing police hitsquads was purely optional when bribes for building permits, import permits, business titles, etc. for his dozens of shell companies were not?

Sure, it still sucks, and I feel sorry for him, but it really does sound like he specifically chose Belize because he liked how pliable the laws were if you had money and it never occurred to him that cuts both ways...

more than 2 years ago
top

Biology Help Desk: Volume 6

robotkid Re:Zombies (36 comments)

Dead tissue is useless tissue. Nothing in nature moves when it's dead unless it's being pushed. The moment metabolic activity has stopped (in humans, about three minutes after the heart stops) bacteria and other recyclers begin to do their jobs, destroying the ability of critical cells to function. Once rigor mortis sets in, three to four hours later, the body is completely incapable of being moved through electrical (or nervous) stimulation, as the muscles (which operate on a principle similar to a forklift) become fused due to the absence of ATP. When rigor mortis fades, 2-3 days after death, these frozen parts are destroyed, and the muscle cells are just useless bags of mush. In short, reanimating dead tissue is completely out of the question for anything short of a bad deus ex machina in a Hollywood film.

If you want a zombie, think less dead, more infected. There are lots of parasites that screw with behaviour in a dramatic way, and guarantee the animal will die in the near future. Worry about those. (And never travel to Africa.)

Great examples, I'd like to add the most zombie-relevant one, though, the wasp parasite that mind-controls a "zombie" spider into making a specially designed nest for the larva with its silk spinner, and then it parks itself in the center to be a snack larva when they hatch (it is still alive as Samantha points out, just somehow mind controlled via some injected toxin).

http://www.damninteresting.com/mind-controlling-wasps-and-zombie-spiders/

here's a whole gallery of zombie-insect examples:
http://discovermagazine.com/photos/04-zombie-animals-and-the-parasites-that-control-them

more than 2 years ago
top

Biology Help Desk: Volume 6

robotkid Re:does it matter if the govt bans flu research? (36 comments)

I assume you mean specifically a strain of bird flu which would be more harmful to humans, for use as a weapon. The answer in this case is that it isn't very prohibitive in terms of equipment; a well-stocked lab, general-purpose biology lab could probably be put together for under half a million dollars: thermal cyclers are cheap, reagents are cheap, incubators are cheap, pipettes are cheap. The most expensive piece would be the hardware to do DNA sequencing to confirm what changes have occurred; technically you could just leave this out. This would not be a particularly safe working environment, however; a BSL 3 lab (the kind appropriate to studying contagious human diseases) would be much more expensive to put together and easily cost a couple of million dollars. For test subjects, as morbid as this is, I'd probably recommend pigs or stray cats, both of which are known to be susceptible.

Much more challenging would be the task of getting well-trained researchers who are willing to engineer such a weapon. The people with substantial knowledge of influenza are either doctors (under the Hippocratic Oath) or PhDs in the life sciences (who got their knowledge because they were expressly interested in helping people.) You might also have a lot of trouble getting the equipment in the first place, since some more expensive pieces require licenses to operate.

A simpler route for the aspiring supervillian would be naturally supporting evolution through eugenics: infect a population of pigs with the disease, and then place the corpses of the pigs who die first into the next population, ad infinitum. This sort of process has been used commercially to make genetically-modified crops more resistant to disease and herbicides. For this, all you'd need is a big enough warehouse, a lot of pigs, and the various facilities to maintain them all. Perhaps also a clipboard or two.

The second route may appear to be slower, but I'm not sure if we know enough about the flu genome that directly modifying it would really make us any more efficient at getting it to do something specifically bad.

I would add a couple of zeroes to the estimate. You need an animal facility for studying emerging infectious diseases, as only the diseases that are so well understood that we can already treat them typically have established cell-culture models (and even them my pathogen colleagues don't trust them much). Sure, maybe you are in a 3rd world country where there is no PETA/OSHA/CDC etc and you are working for a despot. You still need containment to keep infected animals separate from healthy ones or you can't experiment. You still need to keep your PhD-equivalent researchers from constantly getting sick and dying (not because you care about them but because they are hard to replace). And anyone well educated enough to be useful will be acutely aware of how dangerous it is to work closely with sick animals without containment facilities. So you need a biocontainment lab along the lines of the beginnings of the movie "outbreak". Of which there are a few thousand in the world, so it's well within the means of a rogue nation-state or well connected corporation, but unlikely for garage terrorists because they will probably get really sick before they could make any progress on something weaponizable. Even the well-regulated containment labs in the states have tons of near-misses all the time, you can only imagine how hazardous to your health it would be to work without protections. I think at this point terrorists with a death wish are still probably better off trying to stuff IEDs in their underpants than playing with infectious agents without proper facilities.

Lastly, I'll point that although it only takes a PCR machine and some off-the-shelf chemicals to make recombinant E. coli, the procedures for making specific changes to virus genomes are a heck of a lot more complicated. So although you could theoretically cultivate and mutate a viruses you found in the wild using non-highly trained technicians, if you wanted to make the specific changes in the redacted papers you'd need PhD. level virologists to do it for you. To boot, it probably would fizzle because the authors have since clarified the mutations they identified only increase airborne transmission, they weren't actually that lethal to the ferrets. So people are much more worried about the precendent they are setting for how future findings are disseminated or classified rather than the exact findings in this set of papers (specifically, that we had no procedure or guidelines at all). The authors speculate that any similarly equipped facility (on the order of dozens worldwide that specialize in flu/ferret work) could replicate their work in six months or so given all the details, but they were much more worried about these mutations occurring naturally by chance in the future than a garage-terrorist group doing it first.

So what we have here is that public health experts say it's more important we address the inevitable natural evolution of the bug into something more dangerous by telling third world hospitals exactly what mutations to look for so we can have an early warning system, whereas security experts say any risk, however small, of terrorists using this data should be avoided at all costs. We'll see which side wins. .

more than 2 years ago
top

Biology Help Desk: Volume 2n+1, n=2

robotkid Re:Some questions about gene expression (34 comments)

I find it slightly ominous that you call data-driven research a thing of the past; I just got through a course that hailed it as a Big Deal—though the class's attitude was that it was a process for finding a hypothesis, not really testing one. Given that a full human gene expression microarray really is quite excessive for pointing fingers at only a handful of genes (those could be done through much cheaper RT-PCR, after all) my instinct is still to suspect that they're not as organized as you or I might like them to be—or, at least, they're prepared to fall back, and since they're grinding up such a valuable resource already, decided to go for broke with the gene chips, to make sure any negative confirmations they generate are as useful as possible.

Don't get me wrong, I think genechips are awesome tools. I've seen some really nice work on elucidating what changes at different points in the cell cycle, for example, that really couldn't have been done with anything else. But just because it's a high-throughput tool that could be used to brute force things doesn't mean we don't have to pay scientists to think anymore. I think genomics really planted the idea in people's heads that if you collected the data first, other people would be able to make it useful later, but then you have the luxury of there being a definite consensus sequence of an organism. With genechips, the results you get can depend alot on where you decide to focus your attention, I would argue if you don't know what to look for you just won't find it.

If these big, multi-center consortium projects had some sort of arrangement where after they identify "interesting" things they could then go in a more detailed study and pick the interesting things apart, that would be something. But they don't, because the people who are good at pushing the technological hi-throughput capabilities are usually not the people who know what a biologically interesting results might look like or where to look for them and that could be fatal if the community these projects are supposed to be serving have no ability to tell the ship it's headed in the wrong direction.

There's a great editorial from a personal hero of mine Sean Eddy (of pFam fame, we overlapped a bit when he was in St. Louis). He has a great point about how science is evolving to where ee completely divorce the people who have the technical knowledge of how to do an experiment with the people who care about the end results and why this might not be such a good idea.

http://selab.janelia.org/publications/Eddy05b/Eddy05b-reprint.pdf

I was at a conference lately where basically all the bigwigs were predicting the death of data-driven research simply due to a lack of bang for the buck an age of very tight pursestrings and technology that outdates itself in a matter of months. And there was a consortium guy there, whose passionate defense of it was "well, it kept the lights on in my lab so I could do the other cool stuff I wanted to do. Oh, and we standardized on data formats and have a central repository, that's good, right?"

more than 2 years ago

Submissions

top

fixing the "free rider" problem in politics

robotkid robotkid writes  |  more than 2 years ago

robotkid writes "The modern political process is universally acknowledged to be less responsive to the concerns of ordinary individuals compared to the influence of well-funded lobbying groups ranging from the AARP to unions and corporate trade groups. To ordinary individuals, donating money or time to a political cause comes at a high personal cost compared to the perceived impact on the ultimate outcome; therefore, they tend to donate less or nothing even for causes that are important to them while relying on the hope that many others share their concerns and will act differently. This is known as the "free rider" problem, which diminishes the the ability of a democracy to accurate represent the interests of its constituents. Law professor Jordan Barry from University of San Diego has recently proposed a clever solution to this dilemma through a program of "political dollars" that each voting citizen would have available to them solely for contributing to political causes. As this would enhance the aggregate political leverage of individuals without directly curtailing the "speech" of corporations and lobbying groups, this is a solution that would level the playing field without requiring the overturning of the Supreme Courts' "Citizens United" ruling."
Link to Original Source

Journals

robotkid has no journal entries.

Slashdot Account

Need an Account?

Forgot your password?

Don't worry, we never post anything without your permission.

Submission Text Formatting Tips

We support a small subset of HTML, namely these tags:

  • b
  • i
  • p
  • br
  • a
  • ol
  • ul
  • li
  • dl
  • dt
  • dd
  • em
  • strong
  • tt
  • blockquote
  • div
  • quote
  • ecode

"ecode" can be used for code snippets, for example:

<ecode>    while(1) { do_something(); } </ecode>
Create a Slashdot Account

Loading...