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Researchers Study Mystery of the Toddler Who Won't Grow

Iron (III) Chloride Re:Epigenetics (252 comments)

This keeps on getting repeated so as a biology grad student I feel the obligation to inform everyone: yes, epigenetics is very important and makes up much of the story, but while a lot about it is still unknown, we have just as many tools to tackle it as we do with genomic DNA. We can sequence the epigenome (both histone marks and DNA CpG methylation), the transcriptome, the translatome, and the proteome (by mass spec, though not de novo) - almost any "ome" that involves any combination of nucleic acids and proteins can be probably sequenced and profiled by technology that we have today. The only thing that we probably can't easily do yet is metabolomics, because small molecules are not built out of well-understood monomeric units, but I bet there are tens if not hundreds of labs around the world working on this kind of technology as we speak.

My point is, the explosion in sequencing technology that have occurred in the 10 years since the completion of the human genome have put us solidly in the "post-genomics" era. The technologies to find the needle in the haystack exist in the here and now - the only real constraints are time, manpower (brainpower?), sample availability, and (to some extent) cost, in the sense that you need to not be in the bottom 30% of labs in terms of your funding situation in order to have enough money to be able to use these technologies. Brooke is human so there will be limitations in terms of what kinds of samples we can take without harming her health, but the people working on this will be able learn a lot from her genome (and her epigenome, transcriptome, and so on and so forth) and then they will be able to find those mutant candidate genes and make mouse or Drosophila models so that we can get a really detailed understanding of what is going on at the mechanistic level, and in those model organisms we can then whatever we want in order to get whatever types of data we need.

A reference for those who haven't seen it yet: http://www.genome.gov/sequencingcosts/

about a year and a half ago
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Flexible Phones 'Out By 2013'

Iron (III) Chloride Feature Set (152 comments)

One question to ask would be the types of features that one would expect in these flexible phones in the near-term. Would they start out as having similar capabilities as current smartphones in the market, or would they be more "bread-and-butter" phones that will only see incorporation of additional capabilities in the long term?

Of greater interest to me is the possibility of flexible laptops and tablets. The reason why we have things like smartphones is because we can easily carry them around (e.g. in our pocket) and still have sufficient computational for day-to-day use. But if we can get flexible tablets/laptops to work, I think that'd be very useful in terms of packing greater amounts of computational power per (folded) surface area.

about a year and a half ago
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Genspace: New York City's Community Biolab (Video)

Iron (III) Chloride Re:science is for everyone, not just a chosen few (29 comments)

I find that to be a bit of an unfair characterization.

Sure, there are definite socioeconomic barriers - it favors someone who was exposed to science at a young age, or could afford to get a decent education (or be so good that he could get into a school where he didn't have to pay tuition), or did not have family obligations that would distract from a career - these things all unfairly inhibit participation in science. But I don't think that things like patience and dedication can be characterized as "hand-picking," certainly not in any sense of it being "unfair."

The truth of the matter is, science is hard, and requires intelligence, diligence, and patience. No institution or society or culture has artificially increased its difficulty - its very nature means that in order to be able to understand what you're doing, you're going to have to put a lot of effort into it. If it's not within your personality to be able to put up with the work involved (though personality to some degree can probably be taught, so there's probably some socioeconomic dependence there), then it's unlikely that you're going to be able to make substantial contributions to your field.

That said, I am quite supportive of the Genspace project, for the simple reason that it is a great endeavor from an educational point of view. But that also means that the science done there is probably not going to be of the same caliber as the research that you see done at top academic labs around the world.

about a year and a half ago
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Contest To Sequence Centenarians Kicks Off

Iron (III) Chloride Re:Judging accuracy (74 comments)

I'm actually having some trouble finding anything along the lines of "two genomes will be publicized, 110 will not" in the rules and guidelines (obtained from http://genomics.xprize.org/sites/genomics.xprize.org/files/docs/AGXP_Competition_Guidelines.pdf). In addition, I don't see why there would be any restriction on publication once the genomes have been de-anonymized, regardless of whether a competition was organized. While the technology behind the instrumentation may be proprietary, the resulting sequences most certainly will not be, given that they were not previously invented.

about 2 years ago
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Contest To Sequence Centenarians Kicks Off

Iron (III) Chloride Re:Judging accuracy (74 comments)

We already would've gotten the research (and possibly the algorithms, the assemblers for some of the commercial instruments are open-source, if I recall correctly) for free since the companies would've been published their results either way (or for whatever the cost is for you to access the publications), so I don't think that was the motivation for having the competition.

about 2 years ago
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Contest To Sequence Centenarians Kicks Off

Iron (III) Chloride Re:epigenetic data may be more important (74 comments)

ChIP-seq and bisulfite sequencing are used to capture histone modifications and 5-methylcytosines, two of the most heavily-studied epigenetic marks. Being that they're variations of "vanilla" sequencing (even though raising good antibodies can be moderately expensive), I'd say they're fairly low-cost.

about 2 years ago
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China Unblocks Sensitive Keywords

Iron (III) Chloride Re:Relation to possible revolution? (101 comments)

Just fyi since I'm not sure this was clear to you, but Wen Jiabao is part of the current leadership that will retire next year, so he's not going to make too much of a difference other than in any influence that he might have over the leadership transition in promoting those with similar agendas as his - at least in terms of the agenda that he has publicly expressed, in any case.

(Some critics believe that Wen Jiabao's pro-reformist rhetoric is just a smoke screen by the Party to placate the masses while stalling and not actually doing anything - sort of analogous to the concept "empty campaign promises" here in the US. I don't know whether those criticisms are warranted given my lack of knowledge about the situation, just putting the possibility out there.)

more than 2 years ago
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The Stroke of Genius Strikes Later In Life Than It Used To

Iron (III) Chloride Re:Longer life span (162 comments)

Erm, I'm not sure about your explanation for why Einstein never got a Nobel prize for relativity. His theory of GR was published in 1915, he won the Nobel in 1921, but the famous eclipse experiment (which was the first novel experimental validation of GR) was in 1919. He got the prize for the photoelectric effect (which, along with Brownian motion and SR, was published in 1905), and he died in 1955. That's a 32-year gap, and Einstein got quite famous for relativity well before his death. I'm quite sure the Nobel committee could've easily awarded Einstein the prize had they wanted to do so.

Also, it appears based on the MSNBC article (I generally don't trust the media for accurate reports about studies, so this is just for what it's worth), that the analysis appears to have done its calculation based on the age of the scientist at the time of discovery, not at the time of recognition. You might argue for some sort of selective bias in the sense that only longer-living scientists tended to get recognized in the early 20th century, but then you would still have to show a negative correlation between a propensity for longer lifespan living under early-20th-century medicine and the age at which one's best work was done. In other words, if, according to your explanation, only the "healthier" scientists got recognized in the early 20th-century led to a bias in the data, that would have to mean that their health somehow enabled them to do their best work at a younger age compared to their "less healthy" peers. That doesn't seem to be a likely possibility for me, so I'm not sure your explanation makes that much sense.

more than 2 years ago
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Mitsubishi Hack Stole Nuclear, Defense Data

Iron (III) Chloride Re:I Just Can't Understand It (78 comments)

The difference is that Western corporations do it out of self-interest (as in protecting the individual), whereas corporations in east Asia do it to protect the individual _and_ to "protect the group." That's two hurdles to transparency and accountability as opposed to one. I am not qualified to comment on the normalized (say, by economic influence) magnitudes of transparency and accountability violations in different countries (an empirical question), but at least in terms of underlying psychological motivation, that's one more mental barrier that needs to be overcome.

So no need to get all riled up about the follies of Western corporations because I am well aware of those - I am simply stating that from the perspective of culturally ingrained notions, east Asians tend to have even more misplaced loyalty than Westerners (who are already bad enough).

more than 2 years ago
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Mitsubishi Hack Stole Nuclear, Defense Data

Iron (III) Chloride Re:I Just Can't Understand It (78 comments)

I grew up in the States but am east Asian by ethnicity/heritage and have some knowledge of east Asian culture (though obviously my parents didn't think too highly of it, otherwise they probably would've made a more concerted effort to educate/indoctrinate me about it).

The concept is quite simple, it's primarily about bolstering external perception in order to promote the reputation of a group that one self-identities with - be that the family, the company, or the country. You define an in-group and an out-group, and within the in-group honesty and transparency is permitted (at least with respect to the domain of the in-group, you're not going to be sharing family secrets with your co-workers, for example). However, when it comes to the out-group, every effort is made to give the appearance that activities within the in-group are efficient, successful, "harmonious" (i.e. lack of conflict between members of the in-group) - in other words, bury all dirty secrets and make everything look utopian, even if it isn't. Transparency is discouraged because it is bad PR, and members of the out-group (i.e. the rest of society) are expected to have lower expectations as to the amount of information that is provided through "official" channels. So in order to obtain such information, members of the out-group turn to gossip, espionage, etc.

I wouldn't say that "Western" culture (I hate that term because I reject the existence of that distinction as philosophically valid) doesn't practice "face-saving" to some degree, it just isn't taken to the extremes that it is in east Asia because of societal expectations regarding transparency and accountability. I for one think that this is one area where people in China, Korea, and Japan can learn a lot from "Western" countries. After all, face-saving is simply an aspect of tribalism, institutionalized.

more than 2 years ago
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NASA Game Lets You Build Complex Space Networks

Iron (III) Chloride Re:Not for Mac OS either (47 comments)

An interesting proposal. I was not aware that the technology required to build and operate moonbases was within our reach. The ability to do large-scale construction in space is most definitely a very important goal.

However, a couple of questions:
1) What advantages (and disadvantages) would using the proposed moonbase to build large projects (mainly for deep-space exploration at this project) offer compared to building these projects on Earth?
2) You propose that this moonbase be industrially-oriented. By the time we finish building your putative moonbase, will we have the technology (and the market, for that matter) for companies to begin taking advantage of it such that activities on the moonbase become commercially viable?

It has always intuitively seemed to me that a mission to an asteroid, and then to Mars would be a more readily achievable goal at this point in time. Maybe a moonbase would have come next after that. But it would be interesting if you could show me otherwise.

more than 2 years ago
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NASA Game Lets You Build Complex Space Networks

Iron (III) Chloride Re:Not for Mac OS either (47 comments)

Look ... I'm not terribly enthusiastic about the way the US is spending its efforts either. And I think part of the reason so much is wrong with our culture (I say "our" because I'm an American) is the complacency that almost naturally follows from perceived superiority of self, in the economic and political domains. My bet is that if Europe was in a similar position, it wouldn't be in too different a situation compared to the US - I really think it's part of human nature. So, while your point is legitimate, I don't think it's endemic to the US, but rather a property of the nation's current and historical societal position.

That said, I really don't think your criticisms of NASA are fair. Sure, we're not doing manned spaceflight at the moment. But that overlooks two points: first, that manned spaceflight is more romantic than scientific (granted, the romantic aspect is not a bad thing by any means, but in terms of knowledge it doesn't exactly give us the most "bang for the buck") and second, that we are temporarily sacrificing ability to orbit around the Earth (interesting, but not exactly visionary) so that we can develop the ability to do deep-space missions. That's a perfectly long-term, visionary goal. And by relegating LEO manned spaceflight to companies, we're making exactly the right long-term decision - space must be commercialized if we are to eventually make it a very familiar part of our lives the way the computer and the automobile have been.

Complain about the details of the implementation - the politics that corrupts and entangles everything - all you want. But I don't think anyone can legitimately argue that the US's current space vision is the wrong thing to do in the long term. In my view, it is important that we continue to work within this framework to further promote space exploration in all of its aspects and to lead the way into the future.

more than 2 years ago
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NASA Tries To Save Hubble's Successor

Iron (III) Chloride Re:I'm sure the deficit hawks will be right on thi (134 comments)

Because the JWST yields scientific knowledge that does not have immediate forseeable potential for profit, companies aren't going to be paying for it (other than possibly for PR purposes). As to private charities, it appears to me that most of philanthropies sponsoring science research are aimed towards promotion of causes like human health, renewable energy, etc. - daily, practical concerns. Nothing lofty like the JWST which will help us view the cosmos. Even basic biology research that might have a medical impact 50 years down the road won't get sponsored by charities, because there is way too much uncertainty involved.

That's why government funding is necessary to sponsor basic science research - for those areas of science which are so far down the road in terms of turning a direct potential benefit to humanity, that can either radically change our view of the world and our way of living or simply be an interesting piece of trivia. Most of the time it's somewhere in between, in which even the interesting factoids will provide bits and pieces of the puzzle on our way to the Next Great Invention or Theory (TM).

more than 2 years ago
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Scientists Modify Organism With Artificial Amino Acid

Iron (III) Chloride Re:What's with the glowing? (149 comments)

Basically this. Glowing is one of the most easily measurable markers, without the need for any fancy tools or followup experimental procedures other than perhaps your fluorescent microscope (the other would probably be viability, but that kills the organism which you may not actually want). There's a reason green fluorescent protein won the chem Nobel prize a few years back.

more than 2 years ago
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Scientists Modify Organism With Artificial Amino Acid

Iron (III) Chloride Re:I'm a little uneasy about this (149 comments)

I don't mean like haha, "I, for one, welcome our new C. elegans overlords" or tagging the story with whatcouldpossiblygowrong. I mean The Stand. Could somebody with a reasonable knowledge of GM organisms please offer some reassurance that this technique couldn't backfire in some disastrous way?

IAABIT (I am a biologist in training) and based on my knowledge, there's honestly nothing to worry about for this, because it is fundamentally a chemical change. You're gaining the ability to use amino acids other than the 20 that naturally exist, but at that low of a level all that you're gaining is more biochemical versatility. You're going to have to go much higher in terms of complexity and organization before you get something that could potentially pose a danger or what not.

It's sort of like changing one of the instructions in the instruction set of your CPU - would you be worried about malware at that point? I wouldn't say so. It's at the much higher levels that you would start to become worried when these fundamental chemical units (or instructions) start getting combined in novel ways that are potentially dangerous that you would really begin to worry about things. A simple categorical change in amino acid may or may not alter the large-scale properties of macromolecules which are responsible for the majority of biological function. This advance will simply give us the ability to have a greater range of freedom on which to conduct genetic engineering by opening up the possibility of using non-natural amino acids (and "natural" just means one of the 20 amino acids who happen to have been adopted for use by the first biological life forms) - it doesn't really say what the end phenotype will be because that depends on the way the amino acid is used.

Hope that made sense.

more than 2 years ago
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Can the US Still Lead In Space Despite Shuttle's End?

Iron (III) Chloride Naive opinion (365 comments)

This is just my naive opinion as a biologist rather than say, an aeronautical engineer, but it would seem to me that the role of government is to sponsor and conduct high-risk, high-reward research that has little or no probability of foreseeable commercial payoff while the role of corporations is to sponsor and conduct research that has been sufficient well-established in such a way so as to commercialize it for the general public and to reduce its cost to a minimum? (And yes, I consider space exploration to be a form of research.) We've been doing loops around the Earth for about five decades now, so don't you think that low Earth orbit is sufficiently well understood for it to be outsourced to the private sector, while NASA focuses on loftier goals?

I realize I may be drastically oversimplifying the issue, but it seems to me that NASA is on the right track. Wouldn't American space exploration stagnate if we continue to fixate on the space shuttle (whose success has not been entirely unequivocal, imho)? Just my two cents.

about 3 years ago
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Human Genome Contaminated With Mycoplasma DNA

Iron (III) Chloride Re:Mindless drivel (123 comments)

First off, the fact that we are continuing to resequence individual human genomes through projects like the 1000 Genomes Project (and attempting to do de novo assemblies, so we're not just relying on the HGP reference genome) as well as articles telling out about such incidences makes it in my view unlikely that significant contamination will continue as research continues.

Putting that aside, I fail to see how how the usage of invalid DNA sequences in biomedical research, leading to problems with disease treatment as you've mentioned, will lead to selection of those genes in vivo in Mycoplasma. Sure, those efforts to research those diseases will be set back, but how will that confer selective advantage to Mycoplasma carrying genes containing those sequences unless Mycoplasma is directly involved (or affected) by treating the disease in humans (which will definitely not be true in general)? That's the missing biological link. There has to be a mechanism by which direct benefit is conferred onto Mycoplasma as a downstream consequence of those contaminants being in our databases, but unless the invalid sequences are in genes that are involved in some Mycoplasma infection, Mycoplasma doesn't stand to gain anything at all.

IAABIT [I am a biologist in training] and I personally work in genomics, so from my experience my guess of what likely got these sequences into the databases in the first place is a combination of their similarity to actual human sequence (despite the absence of homology), favorable sequence bias during the library generating process (the effects will be determined by what protocols you use), and possibly prevalence in the standard lab environment. None of these features are likely to confer evolutionary benefit to Mycoplasma "in the wild" under normal circumstances (i.e. the invalid sequences don't belong to genes involved in Mycoplasma infection), so I honestly don't see where this notion of the "arms race" is coming from.

more than 3 years ago
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Human Genome Contaminated With Mycoplasma DNA

Iron (III) Chloride Mindless drivel (123 comments)

I don't want to be excessively harsh but the summary was seriously a bunch of drivel. In silico either means it's data on the computer, or that you are simulating a biological process computationally. But as other posters have mentioned, unless you are purposely simulating evolution, mycoplasma sequences in your human databases isn't going to cause any "arms race." Yes, it seriously screws with validity, but that's a completely different issue.

This is a generalization, and no offense to fellow Slashdotters, but in my experience most of the computer scientists that I've met have a really crappy understanding of even basic biology. CS concepts don't directly translate to biology ones.

more than 3 years ago
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Secret Gov't Documents Will be Declassified 12/31

Iron (III) Chloride Re:Can't wait... (301 comments)

I agree that we should have a perspective of erudition as opposed to apathy. However, I think your reduction of causes might have been too general here. Those three causes, as you said, are the cause of any error. However, when we deal with car accidents we are dealing with human nature (most humans are quite ... lazy ... and will not take the time to clearly apply information towards future "goals" of driving safely) as well as a few millennia of culture. You have a significantly more complex issue at hand when dealing with mistakes such as these and to rectify them would take significantly less effort than to persuade people on a single issue of Iraqi War (or, if you have sufficiently political influence, directly influence the Bush administration). That is not to say we should attempt to rectify both problems; some problems take longer than others and perhaps it is a good idea to go "one step at a time." What do you think?

more than 7 years ago

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