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Comment: Re:"waiting list"? Actually, no. (Score 1) 19

by robotkid (#45288355) Attached to: Biology Help Desk: Volume 2^3

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".

Comment: Re:"waiting list"? Actually, no. (Score 1) 19

by robotkid (#45285561) Attached to: Biology Help Desk: Volume 2^3

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.

Comment: Re:"waiting list"? Actually, no. (Score 1) 19

by robotkid (#45281867) Attached to: Biology Help Desk: Volume 2^3

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. . .

Comment: Re:GMO's aren't the problem, GMO patents are (Score 1) 758

by robotkid (#42481379) Attached to: Anti-GMO Activist Recants

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.

Comment: Re:Is he OK w/ Monsanto's lawsuits? (Score 4, Insightful) 758

by robotkid (#42481007) Attached to: Anti-GMO Activist Recants

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.

Comment: Re:folding@home (Score 1) 96

by robotkid (#42468231) Attached to: Einstein@Home Set To Break Petaflops Barrier

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/

Comment: Re:Home PCR/EP, etc. (Score 1) 19

by robotkid (#41757209) Attached to: Biology Help Desk: Volume Seven

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.

Comment: Re:Home PCR/EP, etc. (Score 1) 19

by robotkid (#41748887) Attached to: Biology Help Desk: Volume Seven

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

Comment: Re:Home PCR/EP, etc. (Score 1) 19

by robotkid (#41748769) Attached to: Biology Help Desk: Volume Seven

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

Comment: Re:Junk DNA? (Score 1) 112

by robotkid (#41243465) Attached to: Function of 80% of the Human Genome Charted

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 . . .

Comment: Re:Junk DNA? (Score 1) 112

by robotkid (#41243359) Attached to: Function of 80% of the Human Genome Charted

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.

Comment: Re:Junk DNA? (Score 1) 112

by robotkid (#41243017) Attached to: Function of 80% of the Human Genome Charted

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. . .

Comment: Re:Junk DNA? (Score 4, Insightful) 112

by robotkid (#41239693) Attached to: Function of 80% of the Human Genome Charted

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. . .

Comment: An obvious solution . . . (Score 1) 210

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.

Comment: It's a zombie virus! (Score 1) 229

by robotkid (#40987913) Attached to: Researchers Seek Help Cracking Gauss Mystery Payload

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. . .

An optimist believes we live in the best world possible; a pessimist fears this is true.

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