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How to Maintain Lab Safety While Making Viruses Deadlier

MmmmAqua Re: So ... (213 comments)

Okay, I hope I've misunderstood you. I work in genomics research, and your post seems, on its face, misinformed at best. Are you seriously suggesting that the computer modeling common to physics and chemistry can be applied to biological systems? Even in the case of something as "simple" as a virus (which may consist of tens to hundreds of thousands of kb pairs, specifying dozens or hundreds of RNA transcripts), simply modeling the virus is meaningless. You would also have to completely model host organisms and their immediate environments. Not even the NSA has that kind of compute power. You're dealing with emergent behaviors in interdependent systems far beyond the scope of what computer modeling can handle. There is no "model it as a simple sphere" approach in biology that can yield meaningful results at this level. Until we can phone up whatever god you happen to believe in (if any), the only way to find out what changing a virus will do to the virus, is to change the virus. The information gained is valuable enough that it is worth the minor risk involved in gaining it.

about a week ago
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Neuroscientist: First-Ever Human Head Transplant Is Now Possible

MmmmAqua Re:head transplant, or body transplant? (522 comments)

Whoever modded this insightful has a pretty poor understanding of human physiology. The heart gets external maintenance constantly, in the form of oxygen supplied by the lungs, nutrients from the digestive system, waste export from the excretory system, and so on. The heart's surroundings are the human body, and while I see that the parent comment could be read in that context, it doesn't make sense in that context. The heart is necessary for the proper function of all systems in the body, but it is energetically expensive to operate; it does harm to its surroundings by consuming energy and resources.

While I will agree that, as a whole, the heart doesn't shut down for maintenance, individual cells within the heart certainly do as they die and are replaced, or as they commit more metabolic activity to repair than to other activities. The heart, or any other organ, is simply a collection of specialized tissues acting in concert. It's a large machine made up of millions of smaller machines. At any given moment, hundreds or thousands of those smaller machines can be out of service without affecting the overall function of the organ.

Sorry, but biology is fundamentally different from technology and you can't make car analogies here. Biology is a consequence of emergent behavior from chemical systems orders of magnitude more complex than anything we've come up with pushing electrons around or using controlled explosions to make wheels turn.

about a year ago
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Europe Needs Genetically Engineered Crops, Scientists Say

MmmmAqua Re:But, but - CLIMATE CHANGE will kill us ALL (586 comments)

Hi, I'm a former computer nerd, now a biologist.

Don't overestimate the role of mutation in short-term evolution. The rate of mutation per site per generation in almost all extant species is very low, and almost all mutations are deleterious. For any de novo allele to persist in a population, it must confer a significant benefit to survival or reproduction. If its selective benefit is only slight, its chance of persistence or fixation in a population is equal to its initial frequency, which is extremely low (except in very small populations, but then you have other problems). Mutation is certainly necessary for evolution, but it works on extremely long time scales.

From a biological standpoint, what Monsanto does is pretty irrelevant. They create populations that, barring mutation, don't reproduce. What they do does not affect the genetic variation of natural populations, except insofar as it restricts the total acreage occupied by non-GMO crops. But it's important to realize that those non-GMO crops are _not_ natural populations, nor are they "natural" plants. Such crops have been as thoroughly modified by man as has any Roundup-Ready plant. That's exactly what selective breeding for greater yield, better taste, etc. are - genetically modifying organisms. Corn, wheat, cabbage, mustard, and a whole host of other plants that are grown "organically" and eaten every day do not occur in nature in the forms we consume. The only difference is that companies like Monsanto target single genes, because they can. There is an argument to be made that, by selectively adding or modifying only beneficial alleles, biochemical engineering is a safer way to shape crop plants to our needs; selective breeding is sloppy, messy, and can't eliminate negative genes that, for example, are in linkage disequilibrium with selectively positive genes. And, if you don't want to grow GM seeds... don't. Agribusiness isn't preventing anyone from growing old crops the old way.

From what I have observed, most people's objections to Monsanto boil down to what one of my non-major humanities professors said: "It just doesn't seem natural." People don't seem to realize that when engineering these plants, what is happening is simply a refinement of a process that's been going on in agriculture since we first figured out planting seeds makes plants grow. It's just a more precise version, and able to avoid a whole host of problems presented by the old way of doing things. But it's happening in a lab, so it's automatically unnatural, and interfering with either God's plan or evolution. Evolution is a tricky subject, and far more complicated than most people realize.

I guess what I'm saying is, don't get a gut feeling about something and just call it good. There is a huge amount of propaganda on both sides of this issue, and the reality of the situation is more nuanced than 99% of people realize. I'm probably going to get attacked for this as a Monsanto shill, but please note that I didn't take a firm position either way. There's a reason for that: despite all the screaming from both sides, there is not enough reliable data available to do real, objective science on the broader effects of widespread GMO agriculture. Unfortunately, this dearth of data just feeds the gut feelings on both sides.

Lecture over. Feel free to flame.

about a year ago
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Researchers Study Mystery of the Toddler Who Won't Grow

MmmmAqua Re:Wouldn't They See That in the Endocrine System? (252 comments)

Just curious, is someone restricting you to only looking at her transcriptome or has her whole genome just not been sequenced yet? Given the differential development rates at play, my first inclination would be to look for SNPs or variation in STRs around common non-transcribed regulatory elements. That would of course be only a contributing factor to a condition this complex, but it would be a fascinating one.

about a year and a half ago
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Designers Criticize Apple's User Interface For OS X and iOS

MmmmAqua Mountain Lion shrunk widgets (484 comments)

I believe the reason Apple has moved to things like the disappearing scroll bars, etc. has less to do with eye candy tricks than it does with an attempt to push users to a different form of interaction. iOS demonstrated that touch UIs with physical-like behaviors (bounce back, inertial scrolling, and so on) are effective and easy to learn. As an anecdotal example, since my 93-year old grandmother began using an iPad as her primary computer, my phone support burden has decreased to zero.

Apple seems to be trying to extend this to OS X by pushing touch pads as primary interface devices. Apple sell more laptops and iOS devices by far than they do keyboard/mouse desktops, so they can assume the majority of their user base will be using touch devices. Hence the disappearing scroll bars - if you're two-finger inertial scrolling with a touch pad you don't really need scroll bars. They push desktop users to this interface by including a touch-based mouse with iMacs and Mac Pros and pushing the Magic Trackpad whenever you put an iMac or Mac Mini or Mac Pro in your cart at the online store.

Basically, they've figured out how to make touch an effective interface across all their devices. On the computers, they can assume that your hands will be close to the keyboard and touch pad at all times, so they are tailoring the OS to those devices. Because you rarely need to click buttons anymore, anyway, Fitts' law can go hang as far as they are concerned. Keyboard shortcuts and gestures for all!

Note that I am *not* commenting on the suitability or wisdom of this approach. I am simply proposing a motivation for it.

about 2 years ago
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Right-Wing German Extremists Tricked By Trojan Shirts

MmmmAqua Re:Parent summary is biased (457 comments)

*snip* because if it were cheaper, then you wouldn't *need* regulations.

That makes no sense whatsoever. The need for regulation is not predicated on the price of a service, but on the potential for damage, to the consumer and the economy as a whole, from incompetent practitioners.

Again, all of that is made up. It also assumes that the alternatives available are "fully licensed" and "totally unregulated with horrible quality." What about stuff like Underwriters Labratories, an "Independent, not-for-profit product safety testing and certification organization." In a dark and scary world where light bulbs were not tightly regulated by the government, couldn't you vote with your wallet and be like "Well I'm not buying light bulbs unless they're tested by this third party that has a good reputation."

The "vote with your wallet" argument is, in this context, disingenuous at best. Sure, the cost of waiting for the market to weed out shitty lightbulb manufacturers is relatively small, and the market will eventually produce a generally decent grade of lightbulb-makers. But we are not talking about lightbulbs. We are talking about professional services, many of which involve direct risk to human and economic health. It may cost the economy a few million dollars to weed out Shitty Lights, Inc., but the cost of weeding out shitty or marginally-competent doctors, engineers, and lawyers is astronomically higher. None of those people are going to be drummed out of business by one dissatisfied (or dead) client, or even a hundred, in a deregulated market.Consumers are generally poorly informed and unwilling to do much research when seeking professional services, and that is simply not going to change.

I would imagine for something important like surgery it would happen almost immediately. Now I have a choice. If I need a heart transplant, I'll go to an expensive doctor just like now. If I have a broken finger and I need some pain medication and a splint, well guess what it's not going to cost $1800 for a trip to the ER. I'll go to the hedge witch down the street for $50, no insurance required.

Yes, in that hypothetical. But you're pulling that out of thin air. You can't use it as an argument.

Unregulated services are not going to be uniformly horrible, but without a guarantee of minimum competence the services you get below a certain price point are going to tend to suck. Even if your $50 hedge witch gets things right 70% of the time, she is still screwing up 30% of peoples' broken fingers. Those mistakes have a much higher overall cost to the individual and the economy than the price difference between a licensed doctor and an unlicensed quack.

You are also ignoring the fact that you have a choice, now, too. The $1800 ER trip could just as easily be a $400 urgent care clinic trip, no insurance required. $400 is more than $50, but it's also much more reasonable to most people than $1800, and you also get the guarantee that the MD or RNFP seeing you knows what they're doing.

about 3 years ago
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Bing Is Cheating, Copying Google Search Results

MmmmAqua Re:Mountweazels (693 comments)

So every Tom Clancy novel from Rainbow Six on can't be copyrighted?

more than 3 years ago
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US Army Unveils 'Revolutionary' $35,000 Rifle

MmmmAqua Re:Hope It Helps End the Fighting (782 comments)

Someone's been watching too many movies.

I was in Iraq way back when it was still a war. I was an infantryman, and got to do all the fun infantry stuff you do in a shooting war (sarcasm intended). My personal weapon was an M249, but I trained and shot with M-16 variants my whole career. In an 18-month combat tour I only ever saw one M-4 jam. That was due to a double-feed because the FNG private liked to practically bathe his magazines in CLP. It's been a long time since the M-16 was introduced, and for some time the weak link in proper weapon operation has been the individual soldiers own PMCS. If you don't take care of your weapon, no shit, it's going to jam.

Except for calves and forearms, I also never saw anyone shot with a 5.56 round just ignore it and keep fighting. Hit someone anywhere near center mass and they all go down. They also tend not to die right away, and the screaming and gurgling definitely has a negative impact on their buddies' fighting effectiveness.

And the Army does still use M-14s for designated marksmen. They're great weapons in that role, and the round does have more energy at range than the 5.56, but they're heavy, unwieldy, and useless in close combat. Which you can't avoid in Iraq. Still, some did prefer it; to each his own, I suppose. Just don't believe the 'M-16s are plastic toys' myth.

[semantic mode]BTW, the 5.56 is a NATO standard rifle round.[/semantic mode]

more than 3 years ago
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Which Language To Learn?

MmmmAqua Re:Really? (897 comments)

I know people keep bringing up Mono, but mod_mono and FastCGI are available for hosting ASP applications outside of Microsoft operating systems.

more than 3 years ago
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Casio Unveils New Color Screen Graphing Calculator

MmmmAqua Re:Why? (313 comments)

Just try to talk a test proctor into letting you use your netbook instead of an approved graphing calculator.

more than 3 years ago
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Casio Unveils New Color Screen Graphing Calculator

MmmmAqua This won't end TIs dominance (313 comments)

But it will probably result in a color-screen nSpire sooner than we might otherwise have seen one. Which is A Good Thing (tm) - some of the graphing uses of my nSpire would be much nicer with color to distinguish the plots.

more than 3 years ago
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Disposable Toilet To Change the World

MmmmAqua Re:Perhaps a buy one donate several model? (413 comments)

Read the post again. I never said I can smell it.

...this is Slashdot, so I guess it's ridiculous of me to expect people to read my post before flexing their e-nuts.

more than 4 years ago
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Disposable Toilet To Change the World

MmmmAqua Re:Perhaps a buy one donate several model? (413 comments)

Cute. But, I never said I can smell buried crap; I can't.

Some animals can. Which is where reading the part where I said, "to most wildlife" might have helped - of course, then you wouldn't have any material to fire off half-assed attempts at wit.

I have had a couple of camping trips unpleasantly interrupted at night by bears because someone didn't properly bury their shit. And no, neither time had anything to do with food scent; after both ordeals we tracked the bears paths back to someone's badly covered shit the bears had dug up.

Also, how is stopping at the store to pick up some of these bags "great pains in their outdoor activity's preparation and costs"? You're going to have to go to the store for normal supplies, anyway, and the bags are only supposed to cost a few cents, each.

more than 4 years ago
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Disposable Toilet To Change the World

MmmmAqua Re:Perhaps a buy one donate several model? (413 comments)

I really don't have a problem with animal crap. It rarely causes problems when camping or hiking. My problem with human crap is that people rarely cover it well enough.

Poorly covered human crap has some annoying side effects not seen with everyday animal poop. First, the slippery splat factor which, while pretty rare even in heavily trafficked areas, is just disgusting; not usually a problem with animal dung unless you really aren't paying attention to where you're going. Second, to most wildlife human crap doesn't smell like it belongs, which can bring some really unwanted visitors.

6-8" isn't a deep enough hole to completely eliminate the smell of human poo, and I'm not advocating for people to crap in biodegradable bags and leave them around. I am advocating for people to crap in biodegradable bags and then bury them 6-8". Sanitary disposal which better masks the scent of human spoor and leaves the ground more fertile - where is the downside?

more than 4 years ago
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Disposable Toilet To Change the World

MmmmAqua Re:Perhaps a buy one donate several model? (413 comments)

Speaking as another hiker/camper/climber/yuppie, the idea that you are going to leave poorly covered piles of unsanitized excrement in the same areas others choose to hike/camp/climb, just because you either don't want to spend a few bucks on an environmentally sound product or feel you are above crapping in a bag, is ri-goddamn-diculous.

Someone comes up with a cheap way to make your shit literally not stink (figuratively, anyway), and you aren't going to buy it? Turn in your yuppie ID card. And don't take yourself so seriously - you'll never get out of this alive, anyway.

more than 4 years ago
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Throttle Shared Users With OS X — Is It Possible?

MmmmAqua Re:Mac Mini Server (403 comments)

Most (if not all) SAS controllers also support SATA disks. Dell, HP, and Sun/Oracle all sell 1U/2U x64 servers with 2.5" SATA disks - plain laptop hard drives. Dell and Sun/Oracle in particular are real dicks about bending you over for the upgrade to SAS.

more than 4 years ago

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