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Comment Re:I miss Firefox in this regard (Score 1) 102

I like firefox though. They tell you you are SOL without the passkey. I have no idea how Chrome encrypts. It looks like it is linked to your google account. Google could easily be holding all the keys.

Chrome uses a passphrase to encrypt sync data. By default it will use your Google account password, but you can change it to use any passphrase. If the Chrome devs are doing it right, they should be running the passphrase through PBKDF2 to derive an AES symmetric key. It's worth noting, though, that the Dashboard for "Chrome sync" shows counts for the number of synced items of each type. Assuming they're doing the crypto correctly, I see only two ways the Dashboard could know those numbers: (a) if Chome sends the counts in plaintext as part of the sync, or (b) if the items are individually encrypted (which is generally a bad idea due to known plaintext).

I do know from personal experience that you're SOL if you lose the Chrome sync passphrase (or if you simply want to change it). You have to click the "Stop sync and delete data from Google" link in the Dashboard, wait 5 or 10 minutes for the delete to finish, then set up sync again for all your Chrome instances. Oh, and Chrome sync still doesn't support OAuth login, so setting up sync is a pain if you have 2-factor auth set up on your account (as you should).

Disclaimer: I happen to work at Google, but I don't interact with Chrome except as a user. I'm using knowledge gleaned only from using Chrome sync with my personal account.

Comment Re:tech is a fairly broad category (Score 1) 660

BTW 80k to start in SF seems pretty horrible considering the cost of living there [...]

No, that's actually not bad. Online cost of living calculators don't grok SF. When I moved to SF 5 years ago for a tech job I started out on $75k/year, and I did fine for myself living solo. Sure, you're probably going to drop an extra $15k-$20k/year on rent -- I moved into a ~650ft 1BR apartment for $2100/month, a bit of a premium for a good neighborhood -- but Craigslist is booming with roommate offers, and most other living expenses are about the same as other cities. Utilities are less (milder weather), eating out is more (higher wages, trendier places), groceries are the same. Entertainment is less (lots of free/cheap shows) but there's more of it, so you may wind up spending more.

Beyond rent, the only other thing that's noticeably more expensive than elsewhere is car ownership; parking garage fees of $300/month aren't uncommon if you work downtown and expect to park there every day, and there's the perennial delight of California gas prices if you're moving from out of state. But even before costing out the parking surprise, a $65/month Muni "M" pass is hella cheaper than gas + insurance + maintenance for owning your own car anyway. Throw in a ~$4/month ZipCar annual membership (partially or fully subsidized by some employers) and you can still have access to a car when transit won't cut it; the rental itself runs about $12/hour, which includes the cost of gas, insurance, and all the maintenance headaches. Even without an employer subsidy, that annual ZipCar fee is 1/3 the price of a WoW subscription, i.e. totally worth it at $75k/year.

Comment Re:Just more of the same (Score 1) 162

[...] If you read the word Bayesian in this sentence, you know for certain that you did. There is nothing probabilistic about it. [...]

Not quite. You've never had the experience of remembering having done something, then having someone contradict you, then asking around and finding out that your memory is faulty? If you were certain of your memory, no finite amount of evidence would ever convince you that you were mistaken. Your example instead demonstrates that we pick the most probable (most "familiar") explanation without conscious consideration of alternatives, and we only backtrack to alternatives when the first explanation is sufficiently falsified to demote it from the best explanation.

That's not to say that this has any bearing on Judea Pearl's research into causal networks. Causal networks complement a probabilistic approach, as each causal node operates on purely Bayesian principles; the only difference is the added operation of graph surgery to represent counterfactuals. It's certainly true that the naïve extension of Bayesian probability to a decision theory (Evidential Decision Theory) is silly -- it results in "Speeding on the way to work is correlated with being late to work, therefore if I don't speed I can't be late!", and it's also true that causal graphs naïvely extend to a decision theory (Causal Decision Theory) that fixes the most egregious silliness. But Bayesian probability is still a key piece of CDT, and even CDT doesn't fix everything (look up Newcomb's paradox).

Comment Re:Not that odd... (Score 2) 65

This is just an example of a MaCHO. We've theorized about them for a while. They are a strong candidate for a bulk of the dark matter we've detected. The other candidates are WIMPs.

Uh, no. MaCHOs were supposed to be Jupiter-size to brown dwarf-size lumps of mass, careening through galaxies without being associated with stars or other luminous matter. A black hole *can* count as a MaCHO *if* it has no accretion disk, but we think most black holes have accretion disks and therefore emit X-rays (and thus don't count as dark matter). This black hole is firmly in the not-a-MaCHO category; for that matter, what we today know about Big Bang baryogenesis pretty strongly rules out MaCHOs being the dominant type of dark matter, so they've mostly fallen by the wayside in modern cosmological thinking.

Comment Re:1st (Score 1) 96

If the microwave radiation is strong enough, it definitely is going to cause skin damage (and also a bit below the skin), by simply boiling the tissue.

Believe me, that's a risk I worry about every day. But I recently discovered that there are other frequencies that can cause such damage! I now refuse to allow my family within a mile of any restaurant with so-called "heat lamps" (or as I prefer, "death lamps"), and I'm seriously considering banning from my household anything that emits between 400 and 790 THz. I heard one of my neighbors actually bought an Easy-Bake Oven for their kids. An Easy-Bake Oven! Won't somebody please think of the children?

(Seriously, though, if you pour significantly more than a kilowatt per meter square of EM into living tissue, you're gonna have a bad time. There are a handful of cases, e.g. VHF, where you might be able to bump that figure by an order of magnitude (maaaybe two) because humans are reasonably transparent at those frequencies. But as a rule of thumb, all non-ionizing EM from visible light down cooks you the same way.)

Comment Re:This is cool. But... (Score 1) 357

If the 5th packet was lost, in standard TCP you'd need to retransmit packets 5-10. With this encoding, you could in theory transmit only 1 packet to complete the set, regardless of which was lost, based on how the new ACKs describe the algebraic degrees of freedom remaining in solving for the original packet bytes. That means that you put out 11 packets instead of 15 packets into the same noisy environment, and the existing TCP window controls perceive less losses.

Uhh, that sounds like an extremely convoluted reinvention of TCP SACK (RFC 2018) using some knockoff of Reed-Solomon instead of, y'know, "I got packets 1-4 and 6-10, please retransmit #5".

Comment Re:Favorite quote from the article (Score 1) 34

Not that I'm a pro or anything, but junk DNA was anything that didn't encode proteins, right?

No, that's "non-coding DNA". The Ars Technica article has a very nice Venn diagram. In short, we infer that most non-coding DNA is junk DNA because it shows signs of neutral drift (i.e. it doesn't matter to reproductive fitness), but non-coding DNA is different from junk DNA, and regulatory DNA is always non-coding but can be either junk or non-junk.

Some concrete examples (with Venn diagram colors in parens):

  • Coding DNA that isn't junk (white): a gene.
  • Coding DNA that is junk (blue): an endogenous retrovirus.
  • Regulatory non-coding DNA that isn't junk (orange/yellow): a promoter for a gene.
  • Regulatory non-coding DNA that is junk (orange/yellow/blue): a promoter for a pseudogene.
  • Non-regulatory non-coding DNA that isn't junk (yellow): hmm... an intron, I guess.
  • Non-regulatory non-coding DNA that is junk (yellow/blue): the letters "CGG" 30 times in a row on the X chromosome. (See aside below for more info.)

(Terminology: a "pseudogene" is a gene damaged so badly by frame shifts or early stop codons that it can't code for protein anymore. Before they break and become pseudogenes, they're often duplicates of some existing gene, which is why breaking them can be fitness-neutral. DNA transposons and sloppy cross-overs in meiosis make gene duplication reasonably common. Gene duplication is important for evolution as well: duplicated genes are free to mutate in random directions until they stumble on a new useful function, with the original free to keep the old one. For instance, the vertebrate blood clotting cascade was clearly formed from several rounds of dupe-then-mutate, and similarly with the huge family of myosin muscle proteins.)

(Terminology: an "intron" is a stretch of DNA that gets snipped out of the resulting RNA before the RNA can code for protein. It's not quite junk: an intron has recognition signals that say "please cut RNA here", and IIRC the intron needs to have roughly the correct length, but most of the intron is arbitrary nonsense. Some genes have alternative splices, where the same gene can code for different proteins by swapping in different coding regions -- "exons" -- like lego bricks. Alternative splices are important in the immune system, for instance: they're how antibodies work. And the alternative splicing stuff wouldn't be possible without introns, including the nonsense filler that helpfully spaces out the exons so the splice enzymes can operate correctly.)

(Aside: long sequences of repetitive DNA can trip up the DNA polymerase enzyme that copies DNA, causing the stretch of DNA to lengthen itself in the next generation... and the longer it gets, the better the chance is that DNA polymerase will screw up and make it longer still. The ...CGG-CGG-CGG... sequence I mentioned has about 30 repeats in healthy individuals; but if the number of repeats climbs high enough, it causes Fragile X syndrome. Apparently the nucleus tries to silence the repeat by attaching methyl groups (CH3), which is standard procedure in the nucleus for turning off misbehaving DNA, but methylation isn't terribly precise and a nearby promoter happens to live nearby. This promoter is responsible for a nearby gene that's important in brain development; if the promoter is silenced by methylation, the reduced gene expression causes a form of severe autism.)


Submission + - "80% Functional" Includes Junk DNA After All

CTachyon writes: "Last week the ENCODE project published a suite of papers, which were announced to the press with a claim that 80% of the human genome is "functional". But according to Ars Technica's science editor John Timmer, himself a Ph.D. in Molecular and Cell Biology, most of what you read was wrong: in their papers, the ENCODE team redefined the word "functional" so that known junk DNA (such as dormant viruses and broken pseudogenes) would meet the definition; and what's more, Timmer accuses individual ENCODE scientists of fostering confusion, rather than clearly explaining the semantic bait-and-switch."

Comment Re:What about the 'junk' DNA? (Score 1) 112

As PZ Myers asks, if the remaining 40% is all functional... why do onions need ten times as much as humans need,

When you question them, this is all the "Junk DNA" proponents' arguments ever boil down to: "I don't understand it, therefore it's junk."

We DO understand what 60% of the genome is doing. 45% of it is parasitic. Do you really think that LINEs, parasitic DNA strands that make copies of themselves over and over again, are NOT junk?

and why can the fugu pufferfish thrive without any of it?

Thrive....under what conditions? And what is your definition of "thrive"? Have you subjected the animal to every possible condition it could ever experience in life, to completely ensure that the DNA in question can never be triggered under any circumstances?

Of course you haven't--because you haven't the foggiest clue how it all even works. "Junk DNA", like many other idiocies in the long history of science, is the legacy of morons.

Fugu "thrive" in the sense that they're alive and reproducing. Fugu are not dying off. Fugu are not endangered. Fugu are not at an evolutionary dead end suffering under a genetic legacy that's handicapping them, like pandas or the various all-female species of parthenogenic whiptail lizard are. Like I said, thriving. The only thing that threatens them at all: their tasty lip-numbing tetrodotoxin convinces humans to turn them into sushi.

Why do fugu (390 megabases) get by with 3.5 times less DNA than zebrafish (1.4 gigabases)? Why do fruit flies eliminate non-coding "junk" DNA from their genome 40 times faster than crickets do? (And, for that matter, why do both fruit flies AND crickets AND most eukaryotes excise DNA from their genome at all?) Why does the common onion, Allium cepa (15876 megabases), need 2.3 times more DNA than its close relative the Blue Spear chive, Allium altyncolicum (6860 megabases)? Does bear's garlic, Allium ursinum (30870 megabases), have extra DNA stashed away in preparation for a future alien invasion that will sap the precious bodily fluids from lesser garlics? No. If two closely related Allium species both live in the same area, and look similar, and taste similar, and their cells have a similar appearance under a microscope, and they are equally prolific in their environment... but one has twice as much DNA as the other... then by definition at least half of the larger wad of DNA must be redundant. Maybe not inert, but "junk" in the sense of duplicate or obsolete functionality that doesn't need to be there to grow a successful, sexually mature plant that can compete in the real world.

In short, "junk DNA" is basically a shorthand for "DNA that could be deleted from all individuals in a species without harming the reproductive fitness of those individuals". By this standard, LOTS of DNA is junk -- at least the part that's known to be parasitic (45% of the human genome), and probably a lot more.

Are there regions of non-coding DNA, in the 40% of the human genome as yet not understood by humanity, that confer a benefit to their hosts? Almost certainly. But as a percentage of the genome, the 80% claim in the ENCODE press release is f***ing ridiculous. As best as I can tell, the ENCODE papers are using a shotgun approach that would categorize known parasites like LINEs, ERVs, and transposons as "functional". In one sense, such DNA is not passively sitting there, so it's not "junk" in the sense of being "inert". But for all the spinning of its little wheels, it's doing nothing to help you survive. Sure sounds like junk to me.

Beyond that... fine, call me a moron if you like, but PZ Myers is a Ph.D. professor of biology who studies genetics. This is his area of expertise, and his day job is to teach this stuff to people. If you don't have a Ph.D. in biology, maybe you shouldn't dismiss him as a moron; instead, shut up and watch his video. You might learn something, instead of emotionally flipping out and calling people names, as if "nuh uh, you're a poopy-head" were a valid form of argument. (Hmm... are you sure you're not a Creationist? Flipping out and calling people names is a rather Creationist style of "debate". Although there's such a high background level of it on Slashdot I'm not sure my priors are sound on the matter...)

Comment Re:What about the 'junk' DNA? (Score 1) 112

You haven't confirmed shit, other than you're a moron. Looking back in 20 years you'll feel stupid when it turns out that DNA actually does have a use after all.

Humanity and its arrogance. Jesus Fucking Christ.

Yes, we HAVE confirmed that most DNA is junk. See this talk by biologist PZ Myers. (Money quote starts at 35:20.) Cyberax's figures are an exaggeration, but... roughly 5% is functional (protein-coding, rRNA, tRNA, microRNA), 10% is structural (centromeres and telomeres), 45% of the human genome is known parasitic DNA (LINEs, SINEs, endogenous retroviruses, transposons), and only 40% is unexplained. As PZ Myers asks, if the remaining 40% is all functional... why do onions need ten times as much as humans need, and why can the fugu pufferfish thrive without any of it?

Comment Re:Superficially Bizarre (Score 1) 195

Bizarre, because the now dominiant language of Turkey, Turkish, isn't Indo-European. So it spread everywhere, but was pushed out of it's own back yard.

If I recall correctly from Jared Diamond's Collapse, the non-tonal Polynesian languages originated in South Asia but were pushed out by tonal ones, e.g. Vietnamese, who were themselves pushed out by Han expansion from China.

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