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Comment: Re:Basement Are Better for Isolation (Score 2) 88

by MaXintosh (#41859161) Attached to: Thousands of Lab Mice Lost In Sandy Flooding
This. And and unfortunately, the otherside is that administrations want to keep the 'dirty' bits of science away from where students study or alumni pay over-priced sums of money for sporting tickets. Point in case is when some animal facilities were told they had to move in Salt Lake City because they were going to be too close to the Olympic venues. They, too, got shoved in various basements.

Comment: Re:What drugs and what protections from failure? (Score 1) 439

by MaXintosh (#41858947) Attached to: Massachusetts May Soon Change How the Nation Dies
There's quite a few drugs that have very low lethal doses with multiple delivery routes. Fentnyl or carfentnyl can easily be delivered in a lethal dose in the microgram quantity. And there are more derivatives that we haven't explored much because they're too active that likely would suffice..

Comment: Re:Question... (Score 2) 315

We can, and do, try this. It's called 'ancestral state reconstruction' and its what I make my students do each year. There's a ton of assumptions that go into it, though, and few few are likely to be correct over long timescales. We can do that with closely related taxa (I can make some educated statements about the last common ancestor of, say, black-tailed and white-tailed deer DNA-wise), but the further back in time you go, the more homoplasy (convergent/parallel evolution), atavism, and just plain weird crap (macro-mutations) happens. Heck, for some species, we have two+ chromosome counts running around at the same time. Dinosaurs are probably beyond our reconstructive ken.

OTOH, people are clever. I'm open to someone coming up with an interesting statistical approach that proves me wrong for these deep coalescenceses.

Comment: Re:Question... (Score 5, Informative) 315

Scientist here (you can tell by my hat, and the fact that something like 90% of my comments on /. start with "I'm a biologist"). First, the DNA we get is from better preserved remains, which kicks the half life back further (It's in TFA, but not mentioned in the summary). There's still a 'deadline' around 7 MYA, where (allegedly) all the bonds would have pretty much been broken at that point - Frozen remains supposedly have a halflife around 158 kya. It's that dang phosphate backbone that's too willing to run off and go have reactions with any trallop of a molecule that wanders on by.

This means even in the relatively recent past, the amount of DNA we're looking at is pretty dang tiny. Part of the reason ancient DNA is so dang tricky is because the much of what you sequence is not actually what you're interested in - doubly so when you're sequencing something closely related to humans. For example, did some spot sequencing of ancient/historic polar bear remains, and had to toss out a chunk of the data we got back, as it was soil bacteria(/fungi/pollen) contamination. How do we know which is which? We had good scaffolds to align our bear sequences back up again, though not everyone is as fortunate as us.

In addition to being rare, what is left is fairly short. You can imagine if you start putting breaks in at random, your average length is going to start declining rapidly, and then level out at some small value that takes quite a while to get smaller. It'll get there, and given geologic time scales, a lot of what we want is that far back, but it'll take a while.

Finally, what isn't mentioned in this summary is that there was massive variance in the estimates of half-life. Supposedly only 40% of the variance in halflife was explained by age. Preservation, inter-lab differences, and good old fashioned luck probably contribute considerably to variance in half-life.

There are other factors too, but they're boring, and I should probably get work done instead of dragging out this reply.

(And to answer your latter question, Neanderthals have been sequenced whole genome, not just mtDNA).

Comment: Re:Rat murderer (Score 1) 356

by MaXintosh (#41388845) Attached to: Roundup Tolerant GM Maize Linked To Tumor Development
Here's the link for the article. http://www.sciencedirect.com/science/article/pii/S0278691512005637

I'm fairly underwhelmed with it. First is the issue you mention of "how many negative results did he not publish?" that is rather insidious. Then there's all the issues that come from his small data set size, and the fact that he did not use large portions of his actual data. And can't be bothered to report it. Or provide it. But it just wasn't useful data, for reasons not explained. I wouldn't accuse the authors of misconduct (no doubt the authors believe their ms is true), but the practices described is definitely a great way to get a false positive. Briefly skimming the interwebs show other people have some statistical issues with this too. http://www.science20.com/science_20/blog/gm_maize_causes_tumors_rats_here_how_experts_responded-94259

Sadly, only "GM crops evil!" will get reported, because it plays into a social narrative. Not "shitty stats continues to be shitty!"

Comment: Re:I'm really lucky ... (Score 2) 356

by MaXintosh (#41388523) Attached to: Roundup Tolerant GM Maize Linked To Tumor Development
Dose makes the poison. Any chemist or biochemist would tell you that. Selenium is either a mineral requirement or a toxic substance, depending purely on the dose. As is the case for sodium, potassium, and good old fashioned water. On the other hand, there's likely some amount of elemental mercury in your drinking water right this instant. But it's so trace that it's hard to detect without clever setups, and it undoubtedly has no health effects because it's so rare.

If you asked a homeopath, though, the ultra-rare nature of the pollutant is what makes it especially deadly. Heaven help us if the mercury in the water become any more dilute, we'll all die from its toxicity.

And in any event, any analytically chemist would tell you that in many regulations out there, we set unrealistically low requirements for some contaminants. Sometimes its because water naturally has a lot of junk in it, and getting it out on a utility scale is tricky, but more often than not, the 'safe levels' are picked as arbitrarily low numbers by middle manager types without any understanding that the analytical methods for detecting the analyte of interest at that low of a level aren't feasible.

Comment: Re:It's good to see... (Score 5, Insightful) 345

by MaXintosh (#41375709) Attached to: Judge Preserves Privacy of Climate Scientist's Emails
Your comment smacks heavily of "If he has nothing to hide, why is he fighting to hide things?" Here's an alternate explanation for why he's fighting too hard: The professor was personally offended by what he probably saw as a mob of science-denying jackals that were to sure to pick at his emails, find some quote, take it horribly out of context and trumpet it in the news as loudly as could be, front page headlines blaring. And then when a correction is published showing he did no wrong, that correction will be published on the 5th page of the middle section of the newspaper where none will ever see it.

It's hard not to be personally insulted in such a case. Hell. I'm starting to feel more than a touch offended on his behalf. I know in such a case, even if there was nothing I had ever written that could be misconstrued, I would fight bitterly and with all my reserves to thwart such an attack on purely personal grounds. As someone on slashdot, I'm surprised you don't realize that sometimes people fight even losing battles purely on principle.

Comment: Re:I never understood the traditional species conc (Score 2) 169

by MaXintosh (#41369455) Attached to: "Out of Africa" Theory Called Into Question By Originator
As a biologist, I'd say you've hit the nail on the head. There's probably no such thing as a species as a discrete entity, and the reason we have about 57 different species concepts is that they're all differing models for categorically explaining a continuous phenomenon that otherwise defies enumeration. But like other models, they're fantastically useful in some respects, and we keep them around for those purposes. When species concepts start to break down, we start talking about things like gene trees, or population dynamics, depending on the level of precision required. Even those things are models, but models that are useful for the level of question we're asking.

At its root, the only things that really 'exist' are probably genes, which struggle for existence in communities of other genes, trying to replicate themselves as much as possible because the ones who don't aren't around anymore. But working purely with genes, and nothing else, needlessly complicates a great many things.

Comment: Re:Educate? (Score 5, Interesting) 587

by MaXintosh (#39962795) Attached to: DVDs, Blu-Rays To Show 20-Second Unskippable Govt. Warnings
It'll probably get lost in the junk down here, but I was curious just how many human life equivellents was being sapped by these inane ads. If you look up the 2011 sales figures, the top 100 DVDs sold 147 million copies. Assuming each was watched only once, and by one person, the anti-piracy warnings waste a total of 93.27 years of human life per release-year (6.33775293*10^-7 Year Waste/DVD * ~147 million DVD/Release Year).

I'm comfortable with that dimensional analysis. Easy peezy. I'm less sure about the power consumption of warning: 20 seconds at 35 watts (A typical DVD player) would be 700 watt seconds. That times 147 million would come out to around 28.58 Megawatt Hours a year. That seems a bit much, though, so I may have made a mistake there. The average home supposedly uses around 11 megawatt hours a year. At 11 cents a kw/hr, that's 3,144.16666 dollars.
Now I'm not sure how to price leisure time, but I think the right economic thing to do would be to assume it's worth greater than or equal to the alternative activity (earning whatever per hour). I don't know what that number is, so I'm just going to assume it's a buck fifty arbitrarily. I don't think I could find many people to sit willing to sit being bored for 1.50 an hour, but I don't have time to dig through the lit to find a better one. At 1.50 an hour, the 20 seconds waste around 1.22 Million Dollars a year. which is a fair bit than the 3.1 Thousand dollars wasted electricity.

For those who must know, 93.27 years is 0.000213 Library of Congress equivalents, assuming you can read one book a week.

Comment: Re:Very brief summary (Score 2) 244

by MaXintosh (#39644577) Attached to: MIT Fusion Researchers Answer Your Questions
If you'd read, you'd see the number is 40 years off. That's 10 less than 50!

I think you're being unfair with the money begging. Basically, here's what they'd said (by my reading): Fusion power is going to happen. It's a matter of when, not if. But if we want it in a timeframe that most humans are used to working (before most of us are dead and buried) we need to start taking it seriously. Insert allusions to the Manhattan Project and the Apollo Missions, both of which involved pouring a ton of money into a specific scientific problem.

I'm pretty disappointed they didn't talk more about the NIF. Pretty much every article I read about "Yet another fusion problem solved; thinks rosier than we thought!" has been work coming out of the NIF.

Comment: Again, lacking the option... (Score 3, Interesting) 267

by MaXintosh (#39614973) Attached to: My gut feeling about fracking:
To quote the great, late Carl Sagan,
I try not to think with my gut. If I'm serious about understanding the world, thinking with anything besides my brain, as tempting as that might be, is likely to get me into trouble. Really, it's okay to reserve judgment until the evidence is in.

I don't know enough, for and against, to make a reasonable decision. And I'm not in a position to effect change, even if I had an opinion. I think it's better for me to leave the debate to the real experts, instead of trying to prognosticate from my armchair. It's a crazy idea. It just might work.

Comment: Re:Man is an intriguing being... (Score 1) 140

by MaXintosh (#38721794) Attached to: Drone Guides Fuel Shipment to Alaskan Town

That'd be nice. I wouldn't have to work. I could just play video games and play with robots forever.

That would be nice. Except it's entirely untrue. And there is money, it's not 3k, and it's not for `simply living there.` It's royalties on oil money and rent, which instead of directly being plugged back into education, or whatever, the state decided to let people spend as they see fit. The amount doesn't even cover cost of living, which is incredibly high due to logistics.

Comment: Re:Stop and think (Score 1) 145

by MaXintosh (#38441012) Attached to: India To Cut Out Animal Dissection
Are you kidding me? Lab quality animals are cheap compared to the site licenses for good software to do the same. Never mind you lose a crapton of the detail. Site licenses can run into the five plus digits, easily, depending on enrolment. Plus you need computers to run them all on, and people to support those computers (granted, that's usually dumped onto IT's workload without ever giving them more pay or new workers). And if enrollment is high enough, as it is in many A&P courses (since pre-med, pre-vet, nursing, EMT, and general biology students all get fed through there), you might need a dedicated room to house all that. It adds up incredibly quickly. And that's ignoring that simulations are currently vastly inferior.

Real Programmers don't write in PL/I. PL/I is for programmers who can't decide whether to write in COBOL or FORTRAN.

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