407 karma · joined August 20, 2016
...until there is a newline inside a field.
The moronic quoting mechanism of CSV is one half of the problem; people like you, who try to parse it by "just splitting strings" is the other half. The third half is that it's locale dependent and after 30+ years, people still don't use Unicode.
> Are you saying the Denisovan genome doesn't have unique mutations?
It sure does, but we don't know them. Anything unique to a single archaic individual can always be a sequencing error. (But it's high coverage! Right, but they couldn't compute proper genotype likelihoods for ancient DNA, so systematic errors end up in the final sequence.) And anything found only in Denisovans, however you define them, may or may not be fixed in them, and may or may not exist in other hominins. With so few archaic genomes, it's impossible to tell.
The actual analysis is done on variants that exist in extant humans. Which is why you never read sentence about the number of mutations unique to whoever, you always get something like "is more similar to X than to Y".
> So if Denisovans are more different from Neanderthals than that, why do you think the Denisovan bone was from a Modern x Neanderthal instead?
Distance is calculated by walking along the genome, calling a genotype for every base, and counting difference. This works well for modern humans, but for Neanderthals, a good chunk of the called genotypes are erroneous. This increases their apparent distance from humans, but it increases their apparent distance from each other even more. I'm saying, the Denisovan and Neanderthals may not really be more different from each other than French and San.
I'm not saying anything about the Denisovan in particular. I'm saying the gene flow was probably into Neanderthals, and we stumbled upon one affected individual. Interbreeding is a local event. It is easy to believe that we stumbled upon an individual that had some human ancestry. It is much harder to believe that such an individual ended up in a human population and ended up affecting the whole population uniformly.
The "hybrid" is just more confused terminology. If we simply acknowledged, that Neanderthals had higher genetic diversity than previously thought, the Denisovan and the so-called hybrid would just be a Neanderthal. We don't talk about hybrids of Europeans and Africans either, do we? If I remember correctly, the admixture wasn't confirmed in the hybrid, either. I think, nobody looked.
The root of this nonsense is that Neanderthals were thought to be genetically very similar, especially their mitochondria. The reason is that prior to 2009, it wasn't possible to routine sequence the mitochondrion, let alone the nuclear genome, of some random fossil. Therefore, all fossils were pre-screened using a PCR test for a mitochondrial mutation specific to Neanderthals. But not all Neanderthals have that mutation, so those that were sequenced were very similar due to a technical limitation.
Considering the topic at hand, you should know who David Reich is. He (co-) wrote every single paper on Neanderthal and Denisovan genetics.
It's a fantastic demonstration of modern science at work.
The dendrogram is right here: https://www.eva.mpg.de/genetics/genome-projects/neandertal/
The difference between the Denisovan and the Neanderthals is bigger than between San and French, but not by much. Keep in mind that the archaic genomes are noisy, and noise adds to their distance.
At the time, the debate was whether Neanderthals and the Denisovan constitute different species or just different subspecies. (Taxonomy is fun. You get to name species you discover after yourselves. I'd love to discover a new species, but in a pinch, a subspecies will do.)
You use the meaningless term "population". Whatever, let them be different populations. Now we have two populations, namely the "Denisovan" and the "Altai Neanderthal" living in the same cave, at roughly the same time.
Regarding the admixture, the analysis doesn't indicate the direction. If a Denisovan had offspring with an ancestor of present day Philippinos and the offspring stayed with the humans, that would create exactly the same D-statistics as if the child stayed with the Denisovans.
I think the most believable scenario is that humans migrated through an area that was already inhabited by Neanderthals, some of them had fun with the locals, and the Denisovan is an offspring of such a family. That's much easier to believe than Denisovans, who somehow never left traces in the fossil record, living all over Asia and contributing genes to all present day Melanesians.
[Reich2010] has a single sentence to rule out this scenario: the fossil is a tiny bit too old to be affected by the migrating modern humans. That relies on stratigraphic dating (C14 fails at around 50ka), and that relies on the assurance of the archaeologists that "most of the site was disturbed, but this fossil is from the undisturbed part!" Yeah, right.
As you said, Denisovans, assuming there was ever more than one, and assuming they weren't just Neanderthals, probably swam to the Philippines. Isn't it amazing how much we can learn from a single pinky bone?
My favorite counter example is "A Draft Sequence Of A Neandertal Genome". The article was accepted by both Nature and Science before it was written. The authors chose to publish in Science, because Science offered more on the side: the title page and an unlimited(!) number of "contributed" (this means unreviewed) companion papers. The article itself was about 20 pages of drivel; all the substantial content was relegated to the 200(!) pages of "Online Supplemental Material". Nobody ever read, let alone reviewed, all of that.
After that, I can't trust either Science or Nature, which offered pretty much the same crooked deal. If those two aren't "highest profile", who is?
> Glenfiddich has sold off spent grains left over from the malting process to be used for a high-protein cattle feed.
This sounds as if the leftovers used to be sold as cattle feed, but now they are turned into fuel. If correct, that's horrible! Valuable protein is destroyed in the process. That protein will now have to come from somewhere else, and that's plants fertilized with ammonia, which is in turn made from natural gas.
Destroying protein is not green! Never! Fueling the very same trucks with natural gas is as easy and more efficient, because it skips the intermediate steps.
> The Scottish whisky industry hopes to hit carbon net-zero targets by 2040.
I'm curious how they plan to do this while burning peat in the production process. My guess is by creative accounting.
That's almost completely false.
It obviously depends on the kind of plastic. PE and PP are made from ethene and propene, which are indeed byproducts of fuel refining. But demand far outstrips supply now, so these are now made on purpose. PS is made from styrene, which is not a byproduct. It is made from low-value chemicals, so it's upgraded waste. PET is made from terepthalic acid, which is very much not a waste product of any process.
Even if there were any waste products from fuel refining, they would certainly not be vented. They'd be burned as fuel. Which is also a sensible thing to do with waste plastics. (Someone is going to object that this releases CO2. It does. Burning fuel releases CO2. We can come back to this point once we longer burn coal or methane for energy.)
I'd have clicked it.
So what is the value of a paper journal over a website? That the pictures look better?
I love how you compare a scientific journal to a cinema. It really brings your point home. But you're wrong: Science isn't entertainment. (I have experienced both NPG and AAAS treat it as if it was, though.)
Not really. The publishers provide hardly any value, definitely not commensurate with their prices. So why don't the scientists simply walk away? Why not publish on the internet, why not simply upload to arxiv.org?
It's because funding through quasi government agencies (NSF, NIH, etc.) is tied to your publication record, which is evaluated in "impact points", and those are actually tied not to your own publications, but to the journals they appear in. So your funding as a scientist depends on you publishing in these expensive journals.
It's actually the politicians and bureaucrats stealing from the tax payers, funneling the money to the publishers, all the while claiming they are funding science.
As a scientist, you have little leverage in this fouled up system, but it is your civic duty to use it: Please refuse to review papers for commercial journals without appropriate payment. You owe it to your fellow scientists to not subsidize predatory business models.
Yes, that's the first thing a terrorist would think of.
Seriously, dirty bombs are a red herring. It's the "bomb" part you should be worried about, not the "dirty" part.
[Edit: And, as usual, downvotes rolling in for pointing out a verifiable fact. HN being HN, I guess.]
A 1GW nuclear power station consumes about 1t of U per year and produces about 8000GWh of electricity in that time. So we need about 1mg/8kWh. We got 12 times that much.
So, it sort of works out. Of course, this assumes a breeder reactor and I pretended that brine is purified uranium. If breeders are commercialized, it might be worth looking into this. Right now, it isn't.
Of course. But not on anything related to nuclear waste. In plain language, it has been stolen by the government.
If you don't like the taxpayer having to pick up the tab left by incompetent politicians, you should have voted differently.
> her grad school tuition that I had been saving to pay for her
> she has not worked for >90% of our ~10 year marriage
My friend, you are not abusing your wife. She is abusing you. She is also gaslighting you into thinking you are the problem. You're not. And she is using your child to blackmail you emotionally.
> things she has anxiety about doing -- driving the car to new places, walking the dog when it is dark outside
This isn't anxiety, it's laziness. But if you're merely reluctant about the exact same things, she calls it "a form of emotional abuse." Brilliant.
Unfortunately, the way the law is currently applied, there is nothing you can do without violating it.
Actually, it is, because there is so little of it.
However, in the Nuclear Waste Policy Act of 1982, the US government declared that only the US government can handle nuclear waster, and nuclear power plant operators have to pay into a fund so that the waste handling will be funded. It then spent the following 38 years doing a grand total of exactly nothing, forcing the power plant operators to store the waste. And not for lack of funds, because the Nuclear Waste Fund sits an an unspent $45 billion.
Please stop pretending nuclear waste was either a financial or a technical problem. It's purely a political problem.
> a law that puts upper cap to damages
Which US law places a cap on damages caused by nuclear power plants?
As long as electricity generation, transportation, and space heating are carbon intensive, there is just no point in worrying about steel and cement.
It's repeated a few times, that girls attend college more often than boys, and achieve higher grades. But college is a broad term; you can study electrical engineering or gender studies and get a master's degree either way, yet these are very different fields and require very different skills. Relatively more girls pick gender studies over electrical engineering.
It's possible that boys outperform girls in every single field, but averaged over all fields, it appears the other way around (Simpson's Paradox). I wonder if there is any data that shows girls' superior performance broken down by field.