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dinosaur facts

I'm currently reading The Rise and Fall of the Dinosaurs by Steve Brusatte, a 2018 book on dinosaur history by a professional paleontologist, obviously way more up to date than my childhood reading. I've learned a lot, not all about dinosaurs. Supplemented by some Wiki reading about periods:

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sexless surprise

When you look at the multicellular part of the tree of life, almost everything reproduces sexually. Not all the time -- some plants can self-fertilize, many plants can spread vegetatively, some animals are optionally parthenogenetic. But almost everything has sex as an option. Not all: there are some animal species that only reproduce by parthenogenesis. But they're all twigs on the tree of life, not lush branches, suggesting that this approach to reproduction doesn't last long. Why not? That touches on the question of why sex evolved in the first place, but a rather plausible answer is that it helps protect against parasites and germs, by mixing things up. Asexual reproduction looks like a good short-term genetic bet for the parent -- 100% of genes pass on! -- but yields a population of clones that can be scythed through by the parasite that figures out the key.

Bacteria and archaea evolve fast enough to keep up with each other and with viruses, perhaps... and, also, they have their own forms of gene transfer: conjugation (like sex), or transformation (uptake of plasmids, say.) (A side note: modern GMOs are thus less unnatural than you might think; genes jump around, even between multicellular animals, and GMOs are made via 'natural' techniques.)

There is one big exception to the "all twigs" statement: the bdelloid rotifers, a clade of 450+ species that have apparently been asexual for 25 million years. How do they pull it off? I'd thought maybe their cuticles were tough enough that they thoroughly kept out viruses and such, unlike anything else. But The Tangled Tree by David Quammen gave a better explanation. As freshwater plankton, they've evolved to survive drying out and being rehydrated. And it's not that they're really good at preserving their DNA through such stages; rather, they're decent at repairing the damage after rehydration. 'Decent' meaning that in the process they may incorporate foreign bits of DNA.

...they found at least twenty-two genes from non-bdelloid creatures, genes that must have arrived by horizontal transfer. Some of those were bacterial genes, some were fungal. One gene had come from a plant. At least a few of those genes were still functional, producing enzymes or other products useful to the animal. Later work on the same rotifer suggested that 8 percent of its genes had been acquired by horizontal transfer from bacteria or other dissimilar creatures. A team of researchers based mostly in England looked at four other species of bdelloids and also found “many hundreds” of foreign genes. Some of the imports had been ensconced in bdelloid genomes for a long time, since before the group diversified, while some were unique to each individual species, and therefore more recently acquired. This implied that horizontal gene transfer is an ancient phenomenon among bdelloid rotifers, and that it’s still occurring.

...biologists suspect that such drying-and-rehydrating stresses cause bdelloid DNA to fracture and leave cell membranes leaky. Given that they’re surrounded in their environments by living bacteria and fungi, plus naked DNA remnants from dead microbes, the porous membranes and fracturing could make it easy for alien DNA to enter even the nuclei of bdelloid cells and to get incorporated into bdelloid genomes as they repair themselves. Let me say that again: broken DNA, as a cell fixes it, using ambient materials, may include bits that weren’t part of the original. If that mended DNA happens to be in cells of the germ line, the changes will be heritable. Baby rotifers will get them and, when the babies mature, pass the changes along to their own daughters. Thus a bacterial or fungal gene can become part of the genome of a lineage of animals.

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ridehail math

Ridehail being a more accurate name for Lyft and Uber than 'rideshare'.

Some people talk as if ridehail is the wave of the future, to become a dominant transit mode, despite neither company reporting profits yet. Let's see what that would be like.

The average American driver drives 15,000 miles a year. Ridehail cost per mile component is around $1. Total cost of urban trips (based on a sampling of the apps in Boston and LA) is $2-4/mile, going down the longer the drive is, maybe around $2/mile for 10 mile trips. If you replaced your car with ridehail, you'd be paying $30,000/year. Trés affordable! /s Now, maybe a lot of those miles are longer road trips you wouldn't use ridehail for, so your local driving might be 10,000 miles; that's only $20,000.

Different approach: the app prices are more constant in time units, about $1/minute. The average commute to work is 30 minutes; if you ridehailed to work, you'd be paying $60/workday, or $15,000 over 250 workdays (a year). That's just for your commute, never mind groceries, taking kids to school or things, going out...

That's all for the original product, single person on demand. If you do the Lyft Line/Uber Pool approach, that can halve costs. A mere $7,500 for your work commute! ...assuming no rush hour surge pricing. And car pooling has more time variability, of course. For the 10,000 miles of local driving, $10,000/year. Not that far from estimates of total cost of car ownership for 15,000 miles/year.

Urban car trips tend to be 15-30 MPH, I figure; 10,000 miles is 20,000 to 40,000 minutes, so $20-40K/yeared, or $10-20K pooled.

Competition is fierce, neither company is profitable, and there's doubt as to whether it's really profitable for drivers if they accounted for all costs, so prices are more likely to go up than down.

My T pass is $1014/year. Granted it's often slower (not at rush hour!) It's also 90-99% less likely to mangle or kill me, but most people don't worry about that.

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Aleppo Palace

There's a new restaurant in Central Square, at 25 Central Square Cambridge. It replaced a previous Mideast restaurant the name of which Google has forgotten. It's very new: opened in the past three days (I didn't go out Wed or Thurs.) Pure takeout -- no seating, though there's a ledge if you really wanted to wolf your food there. Prices in the $9 range.

I was given two small falafel for free; I thought they weren't as good as Falafel King's, but decent. I ordered a lamb kafta pita with hummus and fava beans. The guy kept asking if I wanted the ground lamb and not the beef shawarma, which seemed odd; maybe he has no faith in Americans knowing what they want. It rang up oddly: $8.99 turn into $10-something with tax, then back down to $9.60 with cash discount. I thought total sales tax was 7% here, meaning $9.62.

The actual food? Pretty tasty. It was a stuffed pita, not a wrap; the pita looked small, but came out to a decent amount of food; I could probably have made 2 small meals out of it. Tasty and juicy: I was foresighted enough to eat over a plate, the tinfoil covering would not have saved my clothes if eating over my lap.

There are breakfast specials at $6.49, though all vegetarian.

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Python is annoying

Our code works with binary data (hashes/digest) and hexstring representations of such data, a lot. It was written in Python 2, when everything was a string, but some strings were "beef" and some were "'\xbe\xef'"

Then we converted to Python 3, which introduced the 'bytes' type for binary data, and Unicode strings everywhere, which led to some type problems I had figured out, but a recent debugging session revealed I had to think about it some more. Basically we can now have a hexstring "beef", the bytes object b'\xbe\xef' described by that hexstring... and the bytes b"beef" which is the UTF-8 encoding of the string.

In particular, the function binascii.hexlify (aka binascii.b2a_hex) which we used a lot, changed what it returned.

Python 2:
>>> binascii.a2b_hex("beef")
>>> binascii.hexlify(_)

Python 3:
>>> binascii.a2b_hex("beef")
>>> binascii.hexlify(_)

>>> binascii.a2b_hex("beef")
>>> _.hex()

I found it easy to assume that if one of our functions was returning b"beef" and the other "beef" that they were on the same page, when really, not.

Bunch of examples in the cut.

Grah PythonCollapse )

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Factfulness 1

I'm reading Factfulness: Ten Reasons We're Wrong About the World – and Why Things Are Better Than You Think by Hans Rosling, on the state of the world and people's misconceptions of it. It's kind of like Pinker's Enlightenment Now except with less Enlightenment crowing and I think fewer people distrust Rosling, and more about "so, why are people so wrong?" Because that's his first point: people are very wrong about how things are going in income distribution, life expectancy, child mortality, etc. Worse-than-random-chimps wrong. I can confirm in a small way: a Facebook poll of my friends regarding global life expectancy was mostly wrong.

Gapminder link

Wall o' textCollapse )

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an Endless question

There are only six shrouds in the chamber beneath Litharge. Why?

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bitcoin ETF

A well-written 13 page PDF submitted to the SEC, arguing against the approval of a Bitcoin ETF. https://www.sec.gov/comments/sr-cboebzx-2018-040/srcboebzx2018040-4064523-169183.pdf

Highly manipulated penny stock equivalent, with no revenue and negative sum trading, used largely for illegal money transfer, plus unbacked claims of insurance by the ETF proposers, who would be in a position to manipulate the alleged value.

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I've been sort of into meditation for a while. I'm not going to push it as changing your life; I don't know that it's changed my life, or had any effect other than giving me a way to break negative thoughts in the moment. Not that I've done it very regularly; OTOH, studies claim to find medium-term benefits from even short practice. And having a way to break negative thoughts is actually pretty useful by itself. That said, Western studies do claim decent evidence for meditation helping treat anxiety and depression (or at least reducing depressive relapses.) They also claim many other things, but small sample size and file drawer effect justify skepticism.

I don't see a need for 'woo', even as metaphors. It makes sense to me that if you practice focusing your attention and discarding unwanted thoughts, which seem common to nearly all the multitudinous kinds of meditation, then you'll get better at focusing your attention and discarding unwanted thoughts. Also we know the body can influence mood: you smile when you're happy, but become a bit happier when you smile; you breathe slowly when calm, but calm down when your force yourself to breathe slowly. And a lot of meditations are about attending to if not controlling breath, too.

I did find, today, that very brief meditations -- 5 breaths or 'Oms' -- helped me refocus on reading some documentation I'm entirely unthrilled about reading.

In skimming through various articles, a few kinds jumped out at me.

* Breath-attention, supposedly distinct from 'mindfulness meditation' but I couldn't tell a difference. You focus on your breathing. Maybe you count durations, or try to control how you breathe, or maybe you just pay attention to how it feels. You'll have other thoughts, you note that you're having other thoughts, and go back to attending to your breathing without feeling guilty about having other thoughts.

* Mantra: you focus on reciting a mantra. I like 'Om'. Without needing any mysticism, it's a nice resonant sound, especially if you try to say it from deep in your chest, that can easily drive out other thoughts like a ringing gong or bell. Repeat the stuff above about labeling extraneous thoughts and going back to your mantra.

* Loving-kindness. I haven't tried this much. You dwell on wishing the best, or something, for yourself, your friends, acquaintances, people you hate... It sounds foofy at odds with my personality, but I can imagine how practicing feeling positive might get you better at feeling positive. Alternately, it at least gives you a period in which you're *not* dwelling on negative emotions that stress and anger you. There's also the gratitude variant, where you focus on things to feel grateful for.

* This thing I may have invented since I've found nothing like it. I could call it external mindfulness, maybe. (Edit: or mindful seeing.) The idea is to try to be attentive to everything around you. You'll fail, at least if you do it walking as I usually do, but the point is to saturate your attention with the current moment. I get started by trying to label everything I see, in detail, or else to imagine drawing it, particularly imagining tracing edges with my hand, which really means tracing them with my eyes. If you're *not* moving, then you can spend longer focusing on individual objects, staring at them until you've run out of detail. As an example, I was making dinner earlier, and there's a row of cups in my kitchen, but I went beyond "row of cups" to looking at each cup in turn, noting the color, reading any text, noticing anything else odd about them.

It disrupts your other thoughts since it demands so much attention. As a bonus, you're more likely to notice odd things about your environment, since you're actually paying attention to things rather than letting them blur by.

If you search "walking meditation" you find descriptions that are almost completely opposite: focusing on the movement of your body, the soles of your feet, the motion of your pelvis, and such, preferable in a small safe area so you won't hurt yourself when you stumble from paying so much attention to how you walk. I haven't really tried it and think I'd prefer my "focus on everything" method.

You'll note I don't say anything about posture or position. I suspect those aren't important, unless you *want* to be focusing on maintaining a particular position; some people tell you about precise postures and breathing regimens, other say sitting or lying down is fine. I rather think that focusing on *something* is the only key element.

Disclaimer: non-spiritual atheist Westerner dabbling in readings and occasional practice.

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2018 books

2018 book count: 109 fiction, 26 non-fiction. I'd meant to read more non.

32 fiction with female main characters, 36 male, 25 other (both?), 16 unlabeled (most of those are Spice and Wolf, which I guess should be mostly 'male' in terms of 3rd person POV but Horo is so important I was reluctant to go that way. That or I was lazy with cut and paste.)

47 by female authors, 55 male, 20 other, 13 unlabeled. other definitely means male/female author pairs, like the Liaden series, while unlabeled tends to mean "I don't know", like for fanfics by authors with opaque names.

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GMO safety and ignorance

GMO opposition study.
"about 75 percent of the population chose health and safety concerns" though this summary doesn't spell out "GMO being safe to eat" vs. "concerns about more pesticide use".
Opposition anti-correlates with knowledge of genetics: the more you know, the less concerned about GMO safety you are. And in the US (but not Europe), the ignorant considered themselves knowledgeable.
Opposition isn't a left-right thing.


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air dryer power

At the place I'm staying now, there's a hair dryer prominently labeled as 1875 Watts. That's... a lot. A 5000 BTU/hour window air conditioner is 1465 Watts. Small and effective [1] space heaters are often 1000 or 1500 Watts. No wonder hair dryers can trip breakers.

[1] Unless trying to heat a cavernous and leaky basement on low power.

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Study resolutions

As mentioned in my poll, I usually don't make New Year's resolutions. But I recently did make resolutions, and it's near New Year's, so hey. Anyway, there are various subjects I've wanted to become better at: Spanish, Japanese, physics (Feynman lectures), machine learning (Ng course), drawing. Many of which I started an embarrassingly long time ago, with limited progress or even effort. So my new goal is to spend at least 10 minutes a day on each. Or if that somehow feels too much, 1 minute. Something. Also, at least one new word a day of Spanish and Japanese.  Emphasis on "at least"; going longer is fine, but aim to do at least that much a day, every day.

This doesn't sound like much, and it's not, but it's something. The key idea is that I feel it's easier to keep doing something than to start doing something, so lower the mental barrier to starting as much as possible. Arguably a more efficient plan would be to budget 40 minute 'class periods' to each subject, maybe 2x a week. But beyond the fact that I'm not used to keeping such a regular schedule without outside structure, there's also that it's a lot easier to go "ugh, I don't have the time or energy for 40 minutes, I'll make it up later", with that later becoming never. And I'm speaking from experience. Whereas 10 minutes is like an extended potty break. 1 minute should be doable for anyone not feverish or critically depressed.

10 minutes a day is 60 hours a year, which still isn't a lot: a class at Caltech was budgeted for 90 hours (3 class, 6 homework a week, for 10 weeks.) But again, more than I've managed apart from Spanish. 1 minute a day is 6 hours, which is more than I've drawn most years.

Nice ideas; do I have any evidence? Yes: I've had the 40 minute class periods idea before, and not gotten far. Conversely, my daily Duolingo budget is a measly 10 points, on a scale of 10 to 50, and I have a streak longer than a year. I also use Anki flashcards for Spanish vocabulary, and going through them takes about 10 minutes a day, and I've been pretty regular with that. So: aim low but regular and hope for spillover, rather than aim high and miss and get discouraged and stop aiming at all.  And while my Spanish progress has been slow, there has been some detectable progress.
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fundamental blockchain problems

I haven't tried reading the proof yet, but there's an alleged trilemma: correctness, cost-effective, decentralized, pick two. It's plausible, sound very similar to the CAP theorem in distributed computing and databases. (Correctness, Availability, Partition-free -- basically if your nodes are partitioned, you can either shut down and stay correct, or be available and risk conflict when the nodes are re-connected.)

There's a list of various paradoxes about cryptocurrency: more users make it worse (more congested), quadratic total storage costs, conflict between users and miners... https://bankunderground.co.uk/2018/11/13/the-seven-deadly-paradoxes-of-cryptocurrency/

I can suggest some math. Say a blockchain is reasonably successful and has 100 million users (Bitcoin aims at competing with the global financial system!) doing an average of one transaction a day[1]. That's 1e8 transactions in under 1e5 seconds, so over 1000 transactions a second. The top blockchains, bitcoin and Ethereum, can handle around 5 transactions a second. See a problem? And a really global system could plausibly need 100,000 transaction a second.

There are some blockchains -- bitshares, EOS -- that claim such capacity, though I've also seen people say that they're not really decentralized, and one study claimed they didn't even measure up to their claims. https://www.prnewswire.com/news-releases/whiteblock-completes-industrys-first-eos-benchmark-testing-and-blockchain-investigation-300742130.html

But let's say some system can handle that many transactions. What's the storage? 20 bytes each for the From and To addresses, say 10 bytes for the amount, 50 bytes per transaction. At the small scale, each node needs to add 50 kB a second to the distributed ledger (which is what a blockchain at heart is.) No big deal. 5 MB at the big scale... still doable.

But imagine bringing up a new node after three years of such activity. 1e8 seconds in three years, so 5e12 or 5e14 bytes -- 5 or 500 Terabytes to download so that you can be a miner too. Eep!

I can imagine a way around that: a blockchain that every N blocks produces an explicit balance sheet, so that you don't have to go through the entire blockchain history to figure out how much someone has. I don't know if that's viable, such balance sheet blocks would be extra-attractive to attack, but I can't say it's unviable either. OTOH, how big is such a sheet? 100 million users, 20 bytes address per user, 10 bytes balance per user, 3 GB. If 3 billion users, 90 GB. Which has to be shipped around and validated by the mining nodes in the time it takes to make a block -- 10 minutes for Bitcoin, 10 seconds for Ethereum, IIRC. So we cut down on the total storage cost but need some really fat bandwidth.

[1] 30 per month. My own records show an average of 2 expenditures a day, or 60 a month. An average worker's month might see 2 paychecks, 1 rent or mortgage payment, 2-3 phone + utility bills, 4 grocery payments, 1 gas or transit pass payment... we're up to 10 a month right there.

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why key stretching re-salts

Good practice for a serving storing passwords is to not do so. Rather it hashes your password and stores that: when you log in, your password is hashed and compared to the stored value. This way someone who steals the password file doesn't get anything immediately useful. (Hashing is a one way function.) To prevent dictionary and other attacks, the password is combined with a non-secret 'salt' value, then hashed. (The password file contains the salt and the hash(password+salt) value.)

More recently, good practice has become to repeatedly hash the password like 1000 times. If a computer can do a billion hashes in a second then you won't notice a slower login, but it makes a brute force attack (of a stolen password file) 1000x harder. This is called "key stretching" or "key strengthening". The description on Wikipedia says to repeatedly hash the hash value with the salt, and I wondered why that was necessary. I think I figured it out.

Say the salt is applied just once, followed by 1000 consecutive hashings. It's possible that two passwords and their salts would collide, give the same value, samevalue, say on the 3rd iteration. Since they have the same value then, they'll have the same value on every subsequent hashing, and the same stored value in the file; they're basically locked in synchrony An attacker could see that they would get two accounts for the work of one.

But by repeatedly using the salt, that's foiled. In this case, the 4th iteration would see hash(samevalue, salt1) and hash(samevalue, salt2), and diverge again due to the different salts. You can still get collisions in the password file, but it has to actually be after 1000 iterations, not at any point in between.

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(Forward links: street land use and Google Street View browsing).

Back in college, I found a newspaper article talking about the decline of US cities (or not, of a few) and it gave population densities. Having read Jane Jacobs and turned into a wee amateur urbanist, I memorized the numbers. I still know them. But of course they were all in people/sq. mile. Since I'm on a one person campaign to get more comfortable with the units used by 96% of the human race, I thought I'd type up the numbers in /km2, for my better retention, with a lot more places, significant to me or friends, added. And then I'll do various botec/Fermi modeling, to try to show what's going on on the ground.

Density dataCollapse )

ModelsCollapse )

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qotd: holiday/birthday

[community profile] questionoftheday asks: Does your family have any unique holiday traditions? What's the story behind them?

My answer:

The properly non-standard one was my birthdays when I was a small kid. My parents had created our own maypole, painted and with tassels, and I and other kids would run around under it in a circle. Or something like that; I haven't thought about that in years.

A stronger memory is the food. Instead of cake and ice cream, we would make wontons -- bought the wrappers, but made the stuffing and stuffed and fried them -- and chocolate mousse (two flavors, rum and orange). Compared to most birthday cakes, I feel I got the better deal. Sadly, I never got the recipes for these. I can say that the wontons were much more stuffed any any store ones, bursting with chicken and green onions and what not, vs. the more common "fried dough with some microparticles of meat".

Christmas was Christmas, insofar as atheists have a tree and gifts, though we also did some Hanukah stuff out of some cultural reflex of my mothers. Dreidel, yarmulke, kid me lighting candles and reciting Hebrew I didn't understand or believe in. Eventually that just stopped. Later my father refused to drag a Christmas tree home by foot or bus anymore; my mother was sad but I supported him. We still had gifts and possibly even fruitcake... I don't remember what Christmas meal was, I'd guess roast beef and vegetables most often.

Icon appropriateness: hi

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She-Ra tech

The Evil Horde has tanks but no radio.

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missing WB song memory

A DW friend got nostalgic about Smallville and its "Save Me" theme. I looked it up on Youtube and it's a total blank. I watched this show for at least a couple seasons!

Gilmore Girls, which also got at least a year if not 2 or 3, was mostly blank, though I recognize some lines (and visuals).

Dawson's Creek and Roswell did just fine. Granted I may have seen most of DC... don't recall if I followed it all the way through. I did Roswell but there wasn't as much of it.

I didn't try Charmed or Felicity which I didn't see much of, or the bizarre "Zoe" shows (or seasons?), which don't even rate a mention in the network Wikipedia article.

(The WB)

(Of course I remember Buffy and Angel, those were *important*. And rewatched. And I have fanvids of the openings.)

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qotd: fandom 'home'

[community profile] questionoftheday asks: Is there a fictional world that feels like your home away from home? What is it and why does it appeal so much to you?

My answer:

Strictly speaking, no, that is not a thought I have.

More loosely speaking, Nanoha. It has the most fanfic I have actually written down, not just cycled in my head, and I think the most characters whose POVs I've thought about, and my own OCs. Although these days I've been reading more elsewhere, especially Valinor and Silmarillion fics, Nanoha is like a mental home space for composition.

Why? I like the characters: their good will, determination, prettiness, and yuri subtext. I like the optimistic magical Starfleet full of second chances and adoption, struggling to survive in a post-post-apocalyptic universe. I like the second communication channel of mental telepathy (Madoka has this too, and some brave Macross Frontier fics) and the games you can play with that. I like that I can justify some of the characters being immortal. I like how the various artificial beings raise various issues of ethics and identity, like some SF, only with a more engaging milieu and set of characters than most transhumanist SF.

And on the reading side of things, it's had quite a bit of good (re-readable) fic: funny gen fic, interesting worldbuilding gen fic, hot (to me) smut fic. Though not enough of the stuff I most want. The one (gen) which I know has amused multiple people who knew nothing of the franchise is Ready, Sette, Go.

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Damien Sullivan

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