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.
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.
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).
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 . . .
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.
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. . .
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. . .
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.
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. . .
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.
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...
His definitions require replication with variations. So if someone found a way to suppress genetic mutation in humans, we would not be alive right? An artificial creation can also not be alive unless it can reproduce? Does factory production count? It seems we can shorten his definition even more if we embrace his bias:
Life is: from evolution.
I don't object to evolution, but I don't think it's correct to define life by this existing process. Or am I missing something?
There IS a blatant agenda here, and it has nothing to do with defining life.
This type of paper is what I would call "borderline scholarship". It was done by a real scientist, passed "real" peer review, and even ended up in a "real" journal (more on that in a bit). But I would estimate this sort of work took maybe one weekend in a library and 20 minutes in excel. "Top science" this is not. It was picked up by JBSD, a washed-up journal that used to publish edgy stuff a few decades ago, and has lately decided that the way to regain relevance in age of science-by-press-release is to publish edgy sounding papers (no matter the quality of their content), invite two dozen "expert commentaries" from actual experts in the field, make a press release, hope it gets picked up by popular media (such as slashdot) and then watch their citation index go up the wazoo.
It doesn't matter that most of the two-dozen expert comments are basically rehashes of "why is this being published, again, and why was I asked to comment on it?". Hey, it's such an edgy paper, 20 experts "couldn't wait" to submit their comments, and if they are not familiar with the publication they don't realize their commentary just got counted as an actual citation for the original paper and upped the citation index for the journal itself.
Oh, and make it "open access" to sound like they are so generous as to let the public in on this amazing breakthrough (actually, this is a journal that long ago stopped being able to charge anyone to subscribe to them).
As is typical from such self-serving PR exercises, I actually learned more from the criticisms than from the actual paper.
Here's what Eugene Koonin says, and he's the one that proved life exists in three separate branches (prokaryotes, eukaryotes, and archaea). So he's thought about this alot more deeply than TFA.
Yet, all its simplicity and appeal notwithstanding, the minimalist definition appears to be neither necessary nor sufficient, not even internally consistent. A simple implication of information theory (and more fundamentally, thermodynamics) is that error-free replication (more precisely, any information transmission process) is impossible (5). Hence the phrase self-reproduction with variation is actually redundant because any replication process will be characterized by some intrinsic error rate. The problem is exactly the opposite: it has been shown by Eigen and others that for stable information transfer (inheritance) down the chain of generations to be sustained, the error rate must not exceed a certain critical value known as error catastrophe or mutational meltdown threshold (6, 7). Thus, a necessary condition for life to evolve is not simply replication and not ‘replication with variation’ (a tautology) but replication with an error rate below the sustainability threshold..
How is it, then, that, say, in Poland you can do medical school as a 6 year integrated program, starting straight out of high school, while in the U.S. you need an undergrad degree followed by what, 5 more years? I don't think that the polish model produces any worse doctors...
I agree completely it could be done in 6 years in terms of the curriculum itself and once you've isolated the right student pool (med school here is 4 years, BTW, not 5, and there is not much to do your 4th year except applying and interviewing for residencies). But for a variety of competing interests in the US it is much harder to image a universal shift to 6-year integrated programs succeeding. Given that even the doctors that graduate last in their class here still have an automatic ticket to earning potentials in the top 1% of society, pre-med students will continue to bend to whatever admissions criteria are thrown their way.
I think the real question that differentiates the two models is if it's easier to judge on paper whether an 18 year old high school graduate vs a 22 year old who has attended college is going to make the final cut to be a successful doctor.
Consider that in the US, less than 50% of medical school applicants (i.e. premeds) are accepted to any medical school at all. Combined with the fact that somewhere between 60 and 80% of college freshman declaring pre-med intentions change their mind before even getting to the point of applying to medical school (either due to a change of heart or being "weeded out" by the pre-med curriculum). Medical schools have little incentive to increase their student capacity (due to vested interests such as maintaining their "elite" rankings and limiting the overall number of licensed physicians competing for jobs) so a universal shift to a 6-year integrated programs would also mean having to sift through an order of magnitude more applicants with much less data to compare them by (high schools in the US being notoriously uneven in quality and, on average, well below European standards in terms of college preparedness).
In the US, dropping out of med-school is NOT an option due to the obscene amount of loans one needs. Conversely, medical schools here covet high graduation rates to improve their standings, so try to do all their weed-out in the application process and then try their hardest to make sure everyone who is accepted makes it through. So within that framework, I think it's easier to judge candidates who proven university academic track record rather than just a high school diploma.
Maybe it works in poland because the secondary education system is more uniform? I would still expect a model like the Polish one would have to compensate for students who just don't prove to be up to the task by failing a substantial portion of them out over that 6-year period. I don't think that's necessarily better or worse than the US system, but given how the system is set up here (where rankings mean everything and students often have to go a quarter million dollars in debt to finance their M.D.) there's little incentive for medical schools here to change their requirement until society collectively decides that we need more doctors who are paid less rather than a restricted number of super-specialists who earn stratospheric sums.
MD degree is to long and the school mindset may be to much drilled in to people. Going to med school do they really need a full 4 year BA with all the filler classes before med school? Why not 2-3 years and then Med school? Now I can see what that setting in a class room for years with lot's of tests and some stuff that you will never use can do to your mindsets. Testes become more about craning for the test then studying the full topics. Now some of this comes from poor tests and the other part comes from the tech the test idea.
Well, it wasn't always this way. Used to be, you didn't need a B.A. to enter medical school. Heck, you didn't even need to have any contact with real patients before you set up your own practice (i.e. no residency or clerkships). Medical schools used to be giant diploma mills that would take any paying student. Accreditation and board certification were a complete joke.
Then the civil war came along, many of those doctors were drafted to help the army, and to the horror of wounded soldiers everywhere, it soon became clear that your chances of survival were often *better* if you were not treated at all than if you were allowed to be operated on by one of these diploma mill graduates with no real qualifications.
Since then, all medical schools have required a bachelor's degree.
I entirely agree one could theoretically teach all the relevant pre-med material in 2-3 years, nothing is stopping anyone from simply finishing a B.A. a year early if they want. Most pre-meds I knew could have too, they just chose not to because they wanted to live a little before going to med school, or buff their resume and get into a really good one.
And sure, you can always argue pre-meds are being weeded out with only slightly relevant material (yes, orgo II, I'm looking at you). But, you know what? I aced that class without really understanding it and all it took was applying a few key chemical concepts and a fair bit of rote memorization. If you can't hack that, I don't want you interpreting my MRI scan or prescribing me an immunomodulator that might or might not interact with my heart medication.
As a molecular biologist I have to ask: how would that matter? The MDs that have patients don't really need to be thinking about ATPases or the Michaelis–Menten equation. The MDs that are taking basic research and putting it into the field seem to be getting their PhDs which can't be easily faked. And the just regular PhDs are in theory doing the really basic research that involves knowledge of mobio, we don't go to med school or see patients.
Having gotten my Ph.D in the basic research wing of a major medical school, I can concur that MD's typically have only a vague understanding of mechanistic biochemistry, and that the Ph.D's designing future treatments have only a vague understanding of human physiology. Exactly how is this a satisfactory state of affairs?
If you were ill with some condition that presented in an unusual way, (say, a borderline metabolic deficiency), would you prefer your M.D. to actually be able to figure out on their own what's wrong with you, or just blindly follow diagnostic recipes they memorized from the New England Journal of Medicine?
The only reason I can see for wanting a premed student to take molecular biology is to add another level of selection to deter the weakest students from becoming doctors.
You are aware that intro molecular biology is now taught in the second year of any standard biology major, or sometimes combined with biochemistry in your third year? My wife is an ecologist and she took it. Pre-vets take it. Nurses take it in nursing school. Heck, my dentist took advanced biochemistry as well. So why are you against pre-meds taking it? You think a doctor doesn't need to be as capable as a nurse, vet, or dentist? It's not exactly quantum physics, and it's extremely useful since you may only get the abbreviated "molecular medicine" type of crash course in med school since they assume you already took it as a premed.
Interestingly, I've heard that the major that scores the highest on average on the MCAT is actually not premed, biology, or chemistry. Philosophy majors do the best on the MCAT. Granted, there's a lot of self-selection going on there, they probably make up at most 1% of the MCAT takers, and the MCAT is not necessarily an indicator of who will be a good doctor.
You can see a list of the topics covered on the MCAT below which covers (surprise!) molecular/cell biology and biochemistry. Unless the philosophy majors are cheating, they must have at least self-studied the material to score so highly, but more likely than not they took a course or two. I'm really puzzled what you are trying to prove here.
You know what's hilarious? We spend $700 billion/year on the "defense" budget vs. $30 billion/year on the NIH. I find that hilarious. All these stupid diseases could be cured in 15 years if we reversed those numbers.
Agreed. If it's any consolation, the NIH itself is the only government agency I can think of that is uniformly filled with the most frikkin brilliant researchers in the entire field and then some, better than you'll find in even the most highly-compensated strata of the private sector. NASA is just a shell of it's former self, the DOE is a cold-war dinosaur, the great industrial blue-sky labs are all gone or completely unrecognizable (Bell Labs, Kodak, GE, etc). Meanwhile, public universities are cutting "frills" like entire humanities departments due to budget cuts, while private universities are slowly morphing into elite boarding schools catering exclusively to the ultra-wealthy. Sure, they do alot of good research too, but only if someone else pays the bills for it like the NIH or NSF or a frikkin charity, but they still want YOU to donate to them because they argue they are almost like a charity. I mean, how are the 1%'s progeny supposed to *study* if they don't have 24 hour gourmet cooking and multimillion dollar fitness centers like they did in the upper east side?
The pharma industry has all but admitted that their entire economic model is broken, there will be no more blockbusters to make up for their research misses and they aren't agile enough to do the risky legwork to find the new drug candidates that require yet-undeveloped technology to even identify. Meanwhile, small startups basically stand no chance against the big guys unless they plan on being acquired first, at which point whatever risk-taking culture they had cultivated becomes superfluous. So if you hear oneday in the future that the NIH has become a dismal, depressing place to work full of do-nothings waiting to collect their federal pension, then we're all pretty screwed, it's the only part of the biomedical R&D ecosystem that is working the way it should.
We spend ~$30billion a year on research in the U.S. on the NIH, so a partial solution is already in place.
The other thing to keep in mind is this drug is only highly priced for the next 20 years. After that the generic versions will be cheap, so future patients will benefit hugely. That's the beauty of the patent system. It hasn't been outrageously extended to hell like the copyright system has.
It's worth pointing out that part of the calculus that goes into pricing a drug has to do with the fact that drugs rarely enjoy all 20 years of patent protection, due to the fact that the invention of the drug usually occurs in the R&D phase which predates the clinical trials, approvals, and manufacturing scale-up. The average effective patent life (i.e. the period during which a drug is actually for sale) is 7 to 12 years, so prices tweaked to compensate. The flip side is that it really discourages treatments for diseases that affect very small portions of the population,since you cannot count on recouping costs over long periods of time to compensate for the small patient pool. This is partially addressed by the Orphan Drug Act, but more often than not this is where charities funding disease-specific research really play a crucial role.
Good lord, we are animals not plants. There is no such thing as a "cell wall" in our cells! Call it what it is: the cell membrane.
Pedantic? Yes, but the definitions are precise and are intended to be used precisely. Journalism like this makes me want to gouge my eyes out; a single high-school biology class teaches cell wall vs. cell membrane!
I'm a scientist., I'll handle this!
By the power vested in me by science, I hereby retroactively flunk the original submitter's high school biology grades, and also raise the grade of the bookish, socially awkward lab partner you conned into doing all your work. The sentence is to correct 10 obnoxiously factually incorrect slashdot comments without invoking any of the following: Godwin's Law, correlation vs. causation, Ron Paul, or conspiracy theories of any kind. Oh, and just for good measure, rule 34.
Until then your slashdot submitting privileges are subject to double-secret probation.
Well, I have an issue with this. From the article:
While that will give an immediate boost, more is needed from governments, which have provided the bulk of the $22.6 billion that has been raised by the Geneva-based organization to date for its work in 150 countries.
The commitment of governments was shaken last year when the fund reported "grave misuse of funds" in four recipient nations, prompting some donors such as Germany and Sweden to freeze their donations.
Why do coutnries pay into this foundation that invests primarily in American funds and stocks? Why do they not setup their own charities that invest in their own stocks or -- better yet -- give it directly to the institutions of medical research?
This perplexes me to no end. This foundation is at the mercy of the stock market and rely on money managers to post returns every year so that it can give those returns to the targeted countries and research -- right up until a crisis causes those funds to greatly shrink.
I have complained about this before and been called "full of bullshit" and I guess this is just one thing that my opinion and concern diverges on from the rest of the readers here. This is charity in the form of keeping the capital inside America's border and shaving off returns. The money stays at work in America and no such stock or company or infrastructure is built up in the countries that could truly use it and truly need it.
When you're talking billions of dollars, you're talking enough money to start internal institutions and programs that could create jobs or better education as well as do medical research. Instead this money stays in the coffers of rich Western companies and even after the returns are "given" to the countries, it is given in the form of purchased medicines often made by American companies. And that strategy of deciding where your donations gets spent doesn't always work out like you would expect.
It's great he donates all that money but that method is never going to change anything. The real winners here are the companies that get huge cash infusions from the foundation in the form of investment (like Monsanto) and Big Pharma who gets the revenue from all the AIDS medicine that is bought and shipped. Exactly why are foreign governments investing in the Bill and Melinda Gates Foundation instead of finding a better solution?
Bring on the "look a gift horse in the mouth" posts. They may be right but there has to be a better way to use this money to accomplish these goals. It's almost designed to be a perpetual medicine exporting machine.
You are mixing up two things here. There's the Bill and Melinda Gates foundation, and there's the Global Aids Fund.
Bill Gates just donated money to the latter, which depends on donations from individual countries, is run out of Geneva (not by the Gates foundation) and has criticized for being poorly managed.
The Gate Foundation invested in Monsanto, which is the link you provided, not the Global Aids fund. I'm not aware of foreign countries investing in the Gates Foundation.
As unsavory as it might be for charities to be using donated money to invest, the purpose here is long-term viability. The purpose of the Gates Foundation is to fund things that might not show tangible results for decades that traditional, government-directed research and public health funds cannot address. This type of planning is pointless if you can't guarantee the Gates fund will be able to sustain funding for such projects on a decade timescale, which is simply not possible without some sort of long term financial investing. It would be nice if the inves
Is there some environment where sinkers get more nutrients and floaters get eaten or killed?
This is saccharomyces cerevisiae, the yeast used to make beer. Brewers have been selecting for floculent yeast since long before scientists started playing with them. The fact that this isn't mentioned once in the article invalidates the entire thing for me. This is not wild yeast learning a new trait. It's a well known trait being selected for. When I was brewing, I spent many hours watching yeast colonies, which vary wildly from strain to strain. Personally, I prefer the clearer taste that come from floculent yeast.
You, sir, are hereby promoted to "King of the Lab". I had this nagging feeling it would be something like this, but I missed the connection completely!
Also, the flamebait you so maticulously tried to avoid you yourself introduced when you dismissed the taxpayers rights with the word "COMMIE".
Since I helped pay for that research I do not feel it right that I have to pay AGAIN, this time to a middle man, for the previledge of reading about the research. And, if you knew as much about OpenSource as you apparently do about biology, you'd know that OpenSource isn't a Marxist philosophy, contrary to the assertions of the Ballmer, who heads the world's biggest monopoly and is in the process of extending that monopoly on PCs with the introduction of the EUFI HD bootlock. Since Windows is as susceptible as ever to malware the only reason for UEFI is to prevent users of Linux from being able to replace Windows with Linux or to dual boot with it. If Microsoft wants to lock up hardware they should take Apple's route and manufacture their own, and not force independent PC OEMs to act as wholly owned subsidiaries of Microsoft. But, if your flamebait meant anything it probably means that you use a Mac or Win7 and could care less if others wanted the freedom to choose another OS. As long as your ox is not getting gored...
You do understand that was sarcasm, right? Now I can't tell if you are being sarcastic too.
As scientists, we have to pay 3-5K$ of grant money to get something published in a journal in "page fees", after it passes peer review from experts volunteering their time. That's before any "open access" fee. Then, our parent institution has to pay exorbitant subscription fees so that the guy down the hall has the legal right to read the work I did, all using taxpayer money. And if I happened to work in cancer research (I don't), some taxpaying sick schmuck at a hospital somewhere might want to read my paper and they'd still have to pay like 30$ to read it. I think I can safely say >95% of scientists would prefer an overhaul of the cost structure so that anyone who wants to read an article can do so for free
I tried to print 50 copies of MY OWN paper once at Kinkos to hand out at a conference. Kinko's would not do it without a waiver from the copyright holder. I very self righteously (and erroneously) complained that as the author, I was a copyright holder, and as a taxpayer, everyone should have a right to see it. Kinkos pointed out that neither is true, the journal holds the copyright and technically I have to get written permission to reprint my own work.
So I went and bought my own color printer. Problem solved.
This has indeed been pondered! We're pretty sure that all life that presently exists all comes from one root, however. If there ever were alternative life-starting events, they didn't survive. The reason for this is that all extant organisms share a number of completely arbitrary decisions called chirality (if you know any physics, that's left-handed vs. right-handed molecular symmetry.) Chirality is completely random in the chemical reactions that produce amino acids and nucleotides, but absolutely fixed, in the same way, in every living organism we've studied. A number of environmental tests have been conducted specifically to look for organisms of contrary chirality, but we haven't found anything yet.
There are two points here. As for the single root of life, I saw Carl Woese give a talk on this - see timely PNAS perspective here if you have institutional access: http://www.pnas.org/content/early/2012/01/13/1120749109.short?rss=1
(he's a giant in evolutionary biology and the one who proved archaea were a separate lineage using ribosomal RNA sequences, thus redefining our understanding of microbiology, so I'm inclined to give large weight to his views)
His view was that some events almost certainly happened to one unique organism, you can do the backwards projection on the endosymbiosis of mitochondria and a very distinct genetic profile emerges from multiple, independent lines of evidence. But when you try and project all the way back to the LUCA (last universal common ancestor of all three kingdoms) the uncertainty becomes so large and some of the contradictions so severe that it is in fact best explained by groups of highly similar (but not identical) universal ancestors over a window of time, not just literally one unique genome at a specific point in time. So he thinks that the "base" of the tree of life ends up being more like a collection of small shrubbery or bushes instead of a singular point of origin. Carrying that thought a bit further, if there were indeed multiple bushes of life at the start it seems probable there were also other bushes that completely vanished without a trace (no fossil record possible).
As for the universal chirality, that speaks to the origin of self-replicating macromolecules that would have preceeded the last universal common ancestor by quite a spell, so we can only speculate what happened based on our knowledge of organic chemistry. NASA funds some rather creative chemists to think about this question to help define what life might be like elsewhere, and last time I saw one of them speak they seemed to be of the opinion that it was probably just a random chance that gave us one hand and not the other and that there were pools of similar chemical species being selectively concentrated by some sort of clay catalyst. But that means it could have occurred multiple times and only one pool resulted in a proto-cell, or multiple proto-cells arose and the rest died off, or maybe all steps really did only happen once, there's absolutely no projection or record to build upon except geological models of what the earth might have been like then.
I suspect it's not "evolution" at all, but subtly bad science (i.e. a scientist gunning for more grant money). DNA can express in many ways given varying environmental conditions, without the mutations that characterize true evolution -- and artificially forcing genetic drift by selecting for the bottom-clumpers is certainly VERY DIFFERENT from having gravity serve as the "selection pressure."
It's well known DNA can express in many different ways without true evolution. We've come a long way from the theory of Lamarckian evolutionary theory (evolution of acquired characteristics). One is example: exons, which can express differently across generations based on environmental conditions-- without actual change to the DNA.
I'm thinking this great discovery will get pounded upon by other biologists pretty quickly -- and put in its proper place as an interesting science experiment that really does not advance the field much if at all. INTERESTING evolution would be a group of mutations that lead to a multicellular outcome. That's NOT what these guys 1) demonstrated happened (multicellular DNA base-pair-causing mutations) or 2) proved was the actual genetic cause at the molecular-biology level.
IAAMBP (I am a molecular biophysicist) and I actually just finished discussing this article at work before seeing it on/. The parent post is an odd mix of insightful comments and flamebait so I'll respond to the former. BTW the actual research article itself is free for everyone to read, thanks to the authors shelling out an extra 1K$ to allow public access. I'll link it below:
If you would prefer having to pay 10-30$ for the privilege of reading what your tax dollars already paid for instead of this commie "open access" stuff, please call your congressman and tell him/her to support HR bill 3699.
To contextualize this work: the path that led from single-celled eukaryotes to multicellular organisms is one of those $64,000 questions in evolutionary biology, that weird crossover from outright competition to coordinated teamwork. The advantages of being multicellular really pay off for big, complex organisms, but why on earth would it have been advantageous for a small group of a few dozen cells? This paper does not answer the question by any stretch, but it does provide a few interesting, unexpected clues. Most groups asking this question focus on Volvocine algae, which evolved multicellularity so recently such that you can compare them side by side with their nearly identical single-celled cousins in the very same pond. But these are not the most convenient organisms to work with; they have a very complicated life cycle, and have a monster-sized genome for their diminutive size (~140 million bases) and doing genetics on such beasties is still quite difficult and tedious.
Yeast, on the other hand, are really easy to work with and are actually pretty boring in most respects; ~12 million base pairs which have all been sequenced many times over. You can actually custom order them with any gene you want deleted just to see what happens, it's that well characterized. So the observation that artificially selecting for clusters in boring yeast leads to weird snowflake-shape colonies with something that resembles "programmed cell death" in higher organisms is completely unexpected an novel. "Programmed cell death" literally means that the colony has found a way to promote what's good for the colony over what's good for the individual, even though these are only 60 days removed from being a pretty ordinary yeast.
Is this how it happened billions of years ago? Probably not, this is just boring yeast after all, and I can't think of a scenario where sinking to the bottom is a life-or-death advantage. In the case of the algae, it would in fact be suicidal to sink beyond where the
What I don't understand is why antibiotics can't be rotated in and out of use. If these bugs adapt in so few generations and have generations so quickly I'd think they'd lose adaptations for immunities that haven't been needed as quickly as they develop new ones.
So why can't we just put penicillin on the shelf for 20 years, use amoxicillian, and then some others and by the time we go through the list penicillin would be highly effective again?
This is a great question, actually. It would totally work if acquiring resistance relied on a really rare event and had a large cost (decreased growth rate or reproduction rate, etc) associated with maintaining it when it is not needed, which is very much the case with herbicides and pesticides. DDT, for example, works really, really well against mosquitoes now that we've stopped using it out of environmental concerns for decades. The issue here is that most bacteria have what's known as horizontal gene transfer, that is they can spontaneously acquire new genes on plasmids (think of them as firmware updates) from their brethren on a pretty much continual basis. So even if you wait a long time so that resistance has become very rare in the population, it'll never be completely gone, and the moment you reintroduce it the bacteria will start re-sharing it faster than you can torrent Crysis 5 (or whatever version they are up to now) from the Pirate Bay.
Horizontal gene transfer is why there's no way we can ever come up with new antibiotics faster than the bacteria can become resistant. The only hope I see on the horizon is to use viruses that specialize in targeting bacteria so that the cure can counter-evolve it's own adaptations. Yes, I do realize this sounds like a setup to a new Resident Evil movie. But it's been used extensively in former Soviet republics where they couldn't afford antibiotics. http://en.wikipedia.org/wiki/Phage_therapy
Maybe true, but the thought of three or more companies like Monsanto hiding the truth in secretly patented processes, the genetic mutations cross pollinating randomly reproducing in nature across borders of fields and its a complete mess, nature ceasing to accomodate support of life's natural processes. Who could even estimate what would happen? Evolution ceases? Life ceases? Win Win for everyone except for those of us who actually love life.. fundamentally speaking, no more corn in my mash potatoes. That would really suck.
I think it's like oil companies - everyone loves to hate them but fundamentally our society can't exist without them without making wholesale changes to our lifestyle we are unwilling to stomach. At least we can play oil companies off each other by boycotting whichever one is the naughtiest - imagine how much worse it would be if there were only *one* global oil company. But they are not going anywhere anytime soon no matter how much we dislike them.
It's not that farmers are so enamored with doing business with Monsanto - it's that they find they have no choice in an age where pesticides and herbicides are progressively more expensive and less effective (and I should add more environmentally damaging than roundup even with it's multiple bugaboos). Currently only 1% of the US works on a farm, a figure that dwindles every year, and unless we can convince 20% of our population to become organic farmers like in Cuba we cannot be self sufficient without GMOs.
So I think the conversation that is going on about yes/no to GMO's is misplaced, and that's severely to Monsanto's advantage because the need for their product will only increase with time. The conversation we SHOULD be having is about whether foodstuff GMOs should enjoy patent protection at all (for all the claims that this is just like selective breeding on steroids, those aren't patentable and somehow GMOs are), what type of environmental oversight should be required (did you know that only the USDA has authority to regulate GMO crops, not the EPA?) and whether Monsanto should be broken up Baby Bell style for anti-trust issues. The longer we fret about frankenfoods and avoid talking about the issues at hand, the stronger Monsanto's hand gets and the closer that market share gets to 100%. At which point history of monopolies tells us we are really in for a *** storm, and that's not something that has anything to do with the morality of your average Monsanto employee, it's just inevitable in our free market system.
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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.
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.
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/
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 . . .
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.
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. . .
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. . .
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.
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. . .
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.
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...
His definitions require replication with variations. So if someone found a way to suppress genetic mutation in humans, we would not be alive right? An artificial creation can also not be alive unless it can reproduce? Does factory production count? It seems we can shorten his definition even more if we embrace his bias:
Life is: from evolution.
I don't object to evolution, but I don't think it's correct to define life by this existing process. Or am I missing something?
There IS a blatant agenda here, and it has nothing to do with defining life.
This type of paper is what I would call "borderline scholarship". It was done by a real scientist, passed "real" peer review, and even ended up in a "real" journal (more on that in a bit). But I would estimate this sort of work took maybe one weekend in a library and 20 minutes in excel. "Top science" this is not. It was picked up by JBSD, a washed-up journal that used to publish edgy stuff a few decades ago, and has lately decided that the way to regain relevance in age of science-by-press-release is to publish edgy sounding papers (no matter the quality of their content), invite two dozen "expert commentaries" from actual experts in the field, make a press release, hope it gets picked up by popular media (such as slashdot) and then watch their citation index go up the wazoo.
It doesn't matter that most of the two-dozen expert comments are basically rehashes of "why is this being published, again, and why was I asked to comment on it?". Hey, it's such an edgy paper, 20 experts "couldn't wait" to submit their comments, and if they are not familiar with the publication they don't realize their commentary just got counted as an actual citation for the original paper and upped the citation index for the journal itself.
Oh, and make it "open access" to sound like they are so generous as to let the public in on this amazing breakthrough (actually, this is a journal that long ago stopped being able to charge anyone to subscribe to them).
As is typical from such self-serving PR exercises, I actually learned more from the criticisms than from the actual paper.
Here's what Eugene Koonin says, and he's the one that proved life exists in three separate branches (prokaryotes, eukaryotes, and archaea). So he's thought about this alot more deeply than TFA.
http://www.jbsdonline.com/mc_images/category/4317/4-koonin-jbsd_29_4_2012.pdf
Yet, all its simplicity and appeal notwithstanding, the minimalist definition appears to be neither necessary nor sufficient, not even internally consistent. A simple implication of information theory (and more fundamentally, thermodynamics) is that error-free replication (more precisely, any information transmission process) is impossible (5). Hence the phrase self-reproduction with variation is actually redundant because any replication process will be characterized by some intrinsic error rate. The problem is exactly the opposite: it has been shown by Eigen and others that for stable information transfer (inheritance) down the chain of generations to be sustained, the error rate must not exceed a certain critical value known as error catastrophe or mutational meltdown threshold (6, 7). Thus, a necessary condition for life to evolve is not simply replication and not ‘replication with variation’ (a tautology) but replication with an error rate below the sustainability threshold. .
And here's a snippet from the response from evolutionary biologist Richard Egel, author of "Origins of Life: The Primal Self-Organization", so yeah, he's thought alot about this question too:
http://www.jbsdonline.com/mc_images/category/4317/8-egel-jbsd_29_4_2012.pdf
In summary, the statistical voca
How is it, then, that, say, in Poland you can do medical school as a 6 year integrated program, starting straight out of high school, while in the U.S. you need an undergrad degree followed by what, 5 more years? I don't think that the polish model produces any worse doctors...
I agree completely it could be done in 6 years in terms of the curriculum itself and once you've isolated the right student pool (med school here is 4 years, BTW, not 5, and there is not much to do your 4th year except applying and interviewing for residencies). But for a variety of competing interests in the US it is much harder to image a universal shift to 6-year integrated programs succeeding. Given that even the doctors that graduate last in their class here still have an automatic ticket to earning potentials in the top 1% of society, pre-med students will continue to bend to whatever admissions criteria are thrown their way.
I think the real question that differentiates the two models is if it's easier to judge on paper whether an 18 year old high school graduate vs a 22 year old who has attended college is going to make the final cut to be a successful doctor.
Consider that in the US, less than 50% of medical school applicants (i.e. premeds) are accepted to any medical school at all. Combined with the fact that somewhere between 60 and 80% of college freshman declaring pre-med intentions change their mind before even getting to the point of applying to medical school (either due to a change of heart or being "weeded out" by the pre-med curriculum). Medical schools have little incentive to increase their student capacity (due to vested interests such as maintaining their "elite" rankings and limiting the overall number of licensed physicians competing for jobs) so a universal shift to a 6-year integrated programs would also mean having to sift through an order of magnitude more applicants with much less data to compare them by (high schools in the US being notoriously uneven in quality and, on average, well below European standards in terms of college preparedness).
In the US, dropping out of med-school is NOT an option due to the obscene amount of loans one needs. Conversely, medical schools here covet high graduation rates to improve their standings, so try to do all their weed-out in the application process and then try their hardest to make sure everyone who is accepted makes it through. So within that framework, I think it's easier to judge candidates who proven university academic track record rather than just a high school diploma.
Maybe it works in poland because the secondary education system is more uniform? I would still expect a model like the Polish one would have to compensate for students who just don't prove to be up to the task by failing a substantial portion of them out over that 6-year period. I don't think that's necessarily better or worse than the US system, but given how the system is set up here (where rankings mean everything and students often have to go a quarter million dollars in debt to finance their M.D.) there's little incentive for medical schools here to change their requirement until society collectively decides that we need more doctors who are paid less rather than a restricted number of super-specialists who earn stratospheric sums.
MD degree is to long and the school mindset may be to much drilled in to people. Going to med school do they really need a full 4 year BA with all the filler classes before med school? Why not 2-3 years and then Med school? Now I can see what that setting in a class room for years with lot's of tests and some stuff that you will never use can do to your mindsets. Testes become more about craning for the test then studying the full topics. Now some of this comes from poor tests and the other part comes from the tech the test idea.
Well, it wasn't always this way. Used to be, you didn't need a B.A. to enter medical school. Heck, you didn't even need to have any contact with real patients before you set up your own practice (i.e. no residency or clerkships). Medical schools used to be giant diploma mills that would take any paying student. Accreditation and board certification were a complete joke.
Then the civil war came along, many of those doctors were drafted to help the army, and to the horror of wounded soldiers everywhere, it soon became clear that your chances of survival were often *better* if you were not treated at all than if you were allowed to be operated on by one of these diploma mill graduates with no real qualifications.
Since then, all medical schools have required a bachelor's degree.
I entirely agree one could theoretically teach all the relevant pre-med material in 2-3 years, nothing is stopping anyone from simply finishing a B.A. a year early if they want. Most pre-meds I knew could have too, they just chose not to because they wanted to live a little before going to med school, or buff their resume and get into a really good one.
And sure, you can always argue pre-meds are being weeded out with only slightly relevant material (yes, orgo II, I'm looking at you). But, you know what? I aced that class without really understanding it and all it took was applying a few key chemical concepts and a fair bit of rote memorization. If you can't hack that, I don't want you interpreting my MRI scan or prescribing me an immunomodulator that might or might not interact with my heart medication.
As a molecular biologist I have to ask: how would that matter? The MDs that have patients don't really need to be thinking about ATPases or the Michaelis–Menten equation. The MDs that are taking basic research and putting it into the field seem to be getting their PhDs which can't be easily faked. And the just regular PhDs are in theory doing the really basic research that involves knowledge of mobio, we don't go to med school or see patients.
Having gotten my Ph.D in the basic research wing of a major medical school, I can concur that MD's typically have only a vague understanding of mechanistic biochemistry, and that the Ph.D's designing future treatments have only a vague understanding of human physiology. Exactly how is this a satisfactory state of affairs?
If you were ill with some condition that presented in an unusual way, (say, a borderline metabolic deficiency), would you prefer your M.D. to actually be able to figure out on their own what's wrong with you, or just blindly follow diagnostic recipes they memorized from the New England Journal of Medicine?
The only reason I can see for wanting a premed student to take molecular biology is to add another level of selection to deter the weakest students from becoming doctors.
You are aware that intro molecular biology is now taught in the second year of any standard biology major, or sometimes combined with biochemistry in your third year? My wife is an ecologist and she took it. Pre-vets take it. Nurses take it in nursing school. Heck, my dentist took advanced biochemistry as well. So why are you against pre-meds taking it? You think a doctor doesn't need to be as capable as a nurse, vet, or dentist? It's not exactly quantum physics, and it's extremely useful since you may only get the abbreviated "molecular medicine" type of crash course in med school since they assume you already took it as a premed.
Interestingly, I've heard that the major that scores the highest on average on the MCAT is actually not premed, biology, or chemistry. Philosophy majors do the best on the MCAT. Granted, there's a lot of self-selection going on there, they probably make up at most 1% of the MCAT takers, and the MCAT is not necessarily an indicator of who will be a good doctor.
You can see a list of the topics covered on the MCAT below which covers (surprise!) molecular/cell biology and biochemistry. Unless the philosophy majors are cheating, they must have at least self-studied the material to score so highly, but more likely than not they took a course or two. I'm really puzzled what you are trying to prove here.
https://www.aamc.org/students/download/85566/data/bstopics.pdf
You know what's hilarious? We spend $700 billion/year on the "defense" budget vs. $30 billion/year on the NIH. I find that hilarious. All these stupid diseases could be cured in 15 years if we reversed those numbers.
Agreed. If it's any consolation, the NIH itself is the only government agency I can think of that is uniformly filled with the most frikkin brilliant researchers in the entire field and then some, better than you'll find in even the most highly-compensated strata of the private sector. NASA is just a shell of it's former self, the DOE is a cold-war dinosaur, the great industrial blue-sky labs are all gone or completely unrecognizable (Bell Labs, Kodak, GE, etc). Meanwhile, public universities are cutting "frills" like entire humanities departments due to budget cuts, while private universities are slowly morphing into elite boarding schools catering exclusively to the ultra-wealthy. Sure, they do alot of good research too, but only if someone else pays the bills for it like the NIH or NSF or a frikkin charity, but they still want YOU to donate to them because they argue they are almost like a charity. I mean, how are the 1%'s progeny supposed to *study* if they don't have 24 hour gourmet cooking and multimillion dollar fitness centers like they did in the upper east side?
The pharma industry has all but admitted that their entire economic model is broken, there will be no more blockbusters to make up for their research misses and they aren't agile enough to do the risky legwork to find the new drug candidates that require yet-undeveloped technology to even identify. Meanwhile, small startups basically stand no chance against the big guys unless they plan on being acquired first, at which point whatever risk-taking culture they had cultivated becomes superfluous. So if you hear oneday in the future that the NIH has become a dismal, depressing place to work full of do-nothings waiting to collect their federal pension, then we're all pretty screwed, it's the only part of the biomedical R&D ecosystem that is working the way it should.
We spend ~$30billion a year on research in the U.S. on the NIH, so a partial solution is already in place.
The other thing to keep in mind is this drug is only highly priced for the next 20 years. After that the generic versions will be cheap, so future patients will benefit hugely. That's the beauty of the patent system. It hasn't been outrageously extended to hell like the copyright system has.
It's worth pointing out that part of the calculus that goes into pricing a drug has to do with the fact that drugs rarely enjoy all 20 years of patent protection, due to the fact that the invention of the drug usually occurs in the R&D phase which predates the clinical trials, approvals, and manufacturing scale-up. The average effective patent life (i.e. the period during which a drug is actually for sale) is 7 to 12 years, so prices tweaked to compensate. The flip side is that it really discourages treatments for diseases that affect very small portions of the population,since you cannot count on recouping costs over long periods of time to compensate for the small patient pool. This is partially addressed by the Orphan Drug Act, but more often than not this is where charities funding disease-specific research really play a crucial role.
Good lord, we are animals not plants. There is no such thing as a "cell wall" in our cells! Call it what it is: the cell membrane.
Pedantic? Yes, but the definitions are precise and are intended to be used precisely. Journalism like this makes me want to gouge my eyes out; a single high-school biology class teaches cell wall vs. cell membrane!
I'm a scientist., I'll handle this!
By the power vested in me by science, I hereby retroactively flunk the original submitter's high school biology grades, and also raise the grade of the bookish, socially awkward lab partner you conned into doing all your work. The sentence is to correct 10 obnoxiously factually incorrect slashdot comments without invoking any of the following: Godwin's Law, correlation vs. causation, Ron Paul, or conspiracy theories of any kind. Oh, and just for good measure, rule 34.
Until then your slashdot submitting privileges are subject to double-secret probation.
Well, I have an issue with this. From the article:
While that will give an immediate boost, more is needed from governments, which have provided the bulk of the $22.6 billion that has been raised by the Geneva-based organization to date for its work in 150 countries.
The commitment of governments was shaken last year when the fund reported "grave misuse of funds" in four recipient nations, prompting some donors such as Germany and Sweden to freeze their donations.
Why do coutnries pay into this foundation that invests primarily in American funds and stocks? Why do they not setup their own charities that invest in their own stocks or -- better yet -- give it directly to the institutions of medical research?
This perplexes me to no end. This foundation is at the mercy of the stock market and rely on money managers to post returns every year so that it can give those returns to the targeted countries and research -- right up until a crisis causes those funds to greatly shrink.
I have complained about this before and been called "full of bullshit" and I guess this is just one thing that my opinion and concern diverges on from the rest of the readers here. This is charity in the form of keeping the capital inside America's border and shaving off returns. The money stays at work in America and no such stock or company or infrastructure is built up in the countries that could truly use it and truly need it.
When you're talking billions of dollars, you're talking enough money to start internal institutions and programs that could create jobs or better education as well as do medical research. Instead this money stays in the coffers of rich Western companies and even after the returns are "given" to the countries, it is given in the form of purchased medicines often made by American companies. And that strategy of deciding where your donations gets spent doesn't always work out like you would expect.
It's great he donates all that money but that method is never going to change anything. The real winners here are the companies that get huge cash infusions from the foundation in the form of investment (like Monsanto) and Big Pharma who gets the revenue from all the AIDS medicine that is bought and shipped. Exactly why are foreign governments investing in the Bill and Melinda Gates Foundation instead of finding a better solution?
Bring on the "look a gift horse in the mouth" posts. They may be right but there has to be a better way to use this money to accomplish these goals. It's almost designed to be a perpetual medicine exporting machine.
You are mixing up two things here. There's the Bill and Melinda Gates foundation, and there's the Global Aids Fund.
Bill Gates just donated money to the latter, which depends on donations from individual countries, is run out of Geneva (not by the Gates foundation) and has criticized for being poorly managed.
The Gate Foundation invested in Monsanto, which is the link you provided, not the Global Aids fund. I'm not aware of foreign countries investing in the Gates Foundation.
As unsavory as it might be for charities to be using donated money to invest, the purpose here is long-term viability. The purpose of the Gates Foundation is to fund things that might not show tangible results for decades that traditional, government-directed research and public health funds cannot address. This type of planning is pointless if you can't guarantee the Gates fund will be able to sustain funding for such projects on a decade timescale, which is simply not possible without some sort of long term financial investing. It would be nice if the inves
Is there some environment where sinkers get more nutrients and floaters get eaten or killed?
This is saccharomyces cerevisiae, the yeast used to make beer. Brewers have been selecting for floculent yeast since long before scientists started playing with them. The fact that this isn't mentioned once in the article invalidates the entire thing for me. This is not wild yeast learning a new trait. It's a well known trait being selected for. When I was brewing, I spent many hours watching yeast colonies, which vary wildly from strain to strain. Personally, I prefer the clearer taste that come from floculent yeast.
You, sir, are hereby promoted to "King of the Lab". I had this nagging feeling it would be something like this, but I missed the connection completely!
>
Also, the flamebait you so maticulously tried to avoid you yourself introduced when you dismissed the taxpayers rights with the word "COMMIE".
Since I helped pay for that research I do not feel it right that I have to pay AGAIN, this time to a middle man, for the previledge of reading about the research. And, if you knew as much about OpenSource as you apparently do about biology, you'd know that OpenSource isn't a Marxist philosophy, contrary to the assertions of the Ballmer, who heads the world's biggest monopoly and is in the process of extending that monopoly on PCs with the introduction of the EUFI HD bootlock. Since Windows is as susceptible as ever to malware the only reason for UEFI is to prevent users of Linux from being able to replace Windows with Linux or to dual boot with it. If Microsoft wants to lock up hardware they should take Apple's route and manufacture their own, and not force independent PC OEMs to act as wholly owned subsidiaries of Microsoft. But, if your flamebait meant anything it probably means that you use a Mac or Win7 and could care less if others wanted the freedom to choose another OS. As long as your ox is not getting gored...
You do understand that was sarcasm, right? Now I can't tell if you are being sarcastic too.
As scientists, we have to pay 3-5K$ of grant money to get something published in a journal in "page fees", after it passes peer review from experts volunteering their time. That's before any "open access" fee. Then, our parent institution has to pay exorbitant subscription fees so that the guy down the hall has the legal right to read the work I did, all using taxpayer money. And if I happened to work in cancer research (I don't), some taxpaying sick schmuck at a hospital somewhere might want to read my paper and they'd still have to pay like 30$ to read it. I think I can safely say >95% of scientists would prefer an overhaul of the cost structure so that anyone who wants to read an article can do so for free
I tried to print 50 copies of MY OWN paper once at Kinkos to hand out at a conference. Kinko's would not do it without a waiver from the copyright holder. I very self righteously (and erroneously) complained that as the author, I was a copyright holder, and as a taxpayer, everyone should have a right to see it. Kinkos pointed out that neither is true, the journal holds the copyright and technically I have to get written permission to reprint my own work.
So I went and bought my own color printer. Problem solved.
This has indeed been pondered! We're pretty sure that all life that presently exists all comes from one root, however. If there ever were alternative life-starting events, they didn't survive. The reason for this is that all extant organisms share a number of completely arbitrary decisions called chirality (if you know any physics, that's left-handed vs. right-handed molecular symmetry.) Chirality is completely random in the chemical reactions that produce amino acids and nucleotides, but absolutely fixed, in the same way, in every living organism we've studied. A number of environmental tests have been conducted specifically to look for organisms of contrary chirality, but we haven't found anything yet.
There are two points here. As for the single root of life, I saw Carl Woese give a talk on this - see timely PNAS perspective here if you have institutional access: http://www.pnas.org/content/early/2012/01/13/1120749109.short?rss=1
(he's a giant in evolutionary biology and the one who proved archaea were a separate lineage using ribosomal RNA sequences, thus redefining our understanding of microbiology, so I'm inclined to give large weight to his views)
His view was that some events almost certainly happened to one unique organism, you can do the backwards projection on the endosymbiosis of mitochondria and a very distinct genetic profile emerges from multiple, independent lines of evidence. But when you try and project all the way back to the LUCA (last universal common ancestor of all three kingdoms) the uncertainty becomes so large and some of the contradictions so severe that it is in fact best explained by groups of highly similar (but not identical) universal ancestors over a window of time, not just literally one unique genome at a specific point in time. So he thinks that the "base" of the tree of life ends up being more like a collection of small shrubbery or bushes instead of a singular point of origin. Carrying that thought a bit further, if there were indeed multiple bushes of life at the start it seems probable there were also other bushes that completely vanished without a trace (no fossil record possible).
As for the universal chirality, that speaks to the origin of self-replicating macromolecules that would have preceeded the last universal common ancestor by quite a spell, so we can only speculate what happened based on our knowledge of organic chemistry. NASA funds some rather creative chemists to think about this question to help define what life might be like elsewhere, and last time I saw one of them speak they seemed to be of the opinion that it was probably just a random chance that gave us one hand and not the other and that there were pools of similar chemical species being selectively concentrated by some sort of clay catalyst. But that means it could have occurred multiple times and only one pool resulted in a proto-cell, or multiple proto-cells arose and the rest died off, or maybe all steps really did only happen once, there's absolutely no projection or record to build upon except geological models of what the earth might have been like then.
I suspect it's not "evolution" at all, but subtly bad science (i.e. a scientist gunning for more grant money). DNA can express in many ways given varying environmental conditions, without the mutations that characterize true evolution -- and artificially forcing genetic drift by selecting for the bottom-clumpers is certainly VERY DIFFERENT from having gravity serve as the "selection pressure."
It's well known DNA can express in many different ways without true evolution. We've come a long way from the theory of Lamarckian evolutionary theory (evolution of acquired characteristics). One is example: exons, which can express differently across generations based on environmental conditions-- without actual change to the DNA.
I'm thinking this great discovery will get pounded upon by other biologists pretty quickly -- and put in its proper place as an interesting science experiment that really does not advance the field much if at all. INTERESTING evolution would be a group of mutations that lead to a multicellular outcome. That's NOT what these guys 1) demonstrated happened (multicellular DNA base-pair-causing mutations) or 2) proved was the actual genetic cause at the molecular-biology level.
IAAMBP (I am a molecular biophysicist) and I actually just finished discussing this article at work before seeing it on /. The parent post is an odd mix of insightful comments and flamebait so I'll respond to the former. BTW the actual research article itself is free for everyone to read, thanks to the authors shelling out an extra 1K$ to allow public access. I'll link it below:
http://www.pnas.org/content/early/2012/01/10/1115323109.full.pdf+html
If you would prefer having to pay 10-30$ for the privilege of reading what your tax dollars already paid for instead of this commie "open access" stuff, please call your congressman and tell him/her to support HR bill 3699.
To contextualize this work: the path that led from single-celled eukaryotes to multicellular organisms is one of those $64,000 questions in evolutionary biology, that weird crossover from outright competition to coordinated teamwork. The advantages of being multicellular really pay off for big, complex organisms, but why on earth would it have been advantageous for a small group of a few dozen cells? This paper does not answer the question by any stretch, but it does provide a few interesting, unexpected clues. Most groups asking this question focus on Volvocine algae, which evolved multicellularity so recently such that you can compare them side by side with their nearly identical single-celled cousins in the very same pond. But these are not the most convenient organisms to work with; they have a very complicated life cycle, and have a monster-sized genome for their diminutive size (~140 million bases) and doing genetics on such beasties is still quite difficult and tedious.
Yeast, on the other hand, are really easy to work with and are actually pretty boring in most respects; ~12 million base pairs which have all been sequenced many times over. You can actually custom order them with any gene you want deleted just to see what happens, it's that well characterized. So the observation that artificially selecting for clusters in boring yeast leads to weird snowflake-shape colonies with something that resembles "programmed cell death" in higher organisms is completely unexpected an novel. "Programmed cell death" literally means that the colony has found a way to promote what's good for the colony over what's good for the individual, even though these are only 60 days removed from being a pretty ordinary yeast.
Is this how it happened billions of years ago? Probably not, this is just boring yeast after all, and I can't think of a scenario where sinking to the bottom is a life-or-death advantage. In the case of the algae, it would in fact be suicidal to sink beyond where the
What I don't understand is why antibiotics can't be rotated in and out of use. If these bugs adapt in so few generations and have generations so quickly I'd think they'd lose adaptations for immunities that haven't been needed as quickly as they develop new ones.
So why can't we just put penicillin on the shelf for 20 years, use amoxicillian, and then some others and by the time we go through the list penicillin would be highly effective again?
This is a great question, actually. It would totally work if acquiring resistance relied on a really rare event and had a large cost (decreased growth rate or reproduction rate, etc) associated with maintaining it when it is not needed, which is very much the case with herbicides and pesticides. DDT, for example, works really, really well against mosquitoes now that we've stopped using it out of environmental concerns for decades. The issue here is that most bacteria have what's known as horizontal gene transfer, that is they can spontaneously acquire new genes on plasmids (think of them as firmware updates) from their brethren on a pretty much continual basis. So even if you wait a long time so that resistance has become very rare in the population, it'll never be completely gone, and the moment you reintroduce it the bacteria will start re-sharing it faster than you can torrent Crysis 5 (or whatever version they are up to now) from the Pirate Bay.
Horizontal gene transfer is why there's no way we can ever come up with new antibiotics faster than the bacteria can become resistant. The only hope I see on the horizon is to use viruses that specialize in targeting bacteria so that the cure can counter-evolve it's own adaptations. Yes, I do realize this sounds like a setup to a new Resident Evil movie. But it's been used extensively in former Soviet republics where they couldn't afford antibiotics. http://en.wikipedia.org/wiki/Phage_therapy
Maybe true, but the thought of three or more companies like Monsanto hiding the truth in secretly patented processes, the genetic mutations cross pollinating randomly reproducing in nature across borders of fields and its a complete mess, nature ceasing to accomodate support of life's natural processes. Who could even estimate what would happen? Evolution ceases? Life ceases? Win Win for everyone except for those of us who actually love life.. fundamentally speaking, no more corn in my mash potatoes. That would really suck.
I think it's like oil companies - everyone loves to hate them but fundamentally our society can't exist without them without making wholesale changes to our lifestyle we are unwilling to stomach. At least we can play oil companies off each other by boycotting whichever one is the naughtiest - imagine how much worse it would be if there were only *one* global oil company. But they are not going anywhere anytime soon no matter how much we dislike them.
It's not that farmers are so enamored with doing business with Monsanto - it's that they find they have no choice in an age where pesticides and herbicides are progressively more expensive and less effective (and I should add more environmentally damaging than roundup even with it's multiple bugaboos). Currently only 1% of the US works on a farm, a figure that dwindles every year, and unless we can convince 20% of our population to become organic farmers like in Cuba we cannot be self sufficient without GMOs.
So I think the conversation that is going on about yes/no to GMO's is misplaced, and that's severely to Monsanto's advantage because the need for their product will only increase with time. The conversation we SHOULD be having is about whether foodstuff GMOs should enjoy patent protection at all (for all the claims that this is just like selective breeding on steroids, those aren't patentable and somehow GMOs are), what type of environmental oversight should be required (did you know that only the USDA has authority to regulate GMO crops, not the EPA?) and whether Monsanto should be broken up Baby Bell style for anti-trust issues. The longer we fret about frankenfoods and avoid talking about the issues at hand, the stronger Monsanto's hand gets and the closer that market share gets to 100%. At which point history of monopolies tells us we are really in for a *** storm, and that's not something that has anything to do with the morality of your average Monsanto employee, it's just inevitable in our free market system.