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Ask HN: What's a promising area to work on? | Hacker News
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22 hours ago by nhaliday
Linus's Law - Wikipedia
Linus's Law is a claim about software development, named in honor of Linus Torvalds and formulated by Eric S. Raymond in his essay and book The Cathedral and the Bazaar (1999).[1][2] The law states that "given enough eyeballs, all bugs are shallow";

--

In Facts and Fallacies about Software Engineering, Robert Glass refers to the law as a "mantra" of the open source movement, but calls it a fallacy due to the lack of supporting evidence and because research has indicated that the rate at which additional bugs are uncovered does not scale linearly with the number of reviewers; rather, there is a small maximum number of useful reviewers, between two and four, and additional reviewers above this number uncover bugs at a much lower rate.[4] While closed-source practitioners also promote stringent, independent code analysis during a software project's development, they focus on in-depth review by a few and not primarily the number of "eyeballs".[5][6]

Although detection of even deliberately inserted flaws[7][8] can be attributed to Raymond's claim, the persistence of the Heartbleed security bug in a critical piece of code for two years has been considered as a refutation of Raymond's dictum.[9][10][11][12] Larry Seltzer suspects that the availability of source code may cause some developers and researchers to perform less extensive tests than they would with closed source software, making it easier for bugs to remain.[12] In 2015, the Linux Foundation's executive director Jim Zemlin argued that the complexity of modern software has increased to such levels that specific resource allocation is desirable to improve its security. Regarding some of 2014's largest global open source software vulnerabilities, he says, "In these cases, the eyeballs weren't really looking".[11] Large scale experiments or peer-reviewed surveys to test how well the mantra holds in practice have not been performed.

Given enough eyeballs, all bugs are shallow? Revisiting Eric Raymond with bug bounty programs: https://academic.oup.com/cybersecurity/article/3/2/81/4524054

https://hbfs.wordpress.com/2009/03/31/how-many-eyeballs-to-make-a-bug-shallow/
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5 weeks ago by nhaliday
Mars Direct | West Hunter
Send Mr Bezos. He even looks like a Martian.
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Throw in Zuckerberg and it’s a deal…
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We could send twice as many people half-way to Mars.

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I don’t think that the space station has been worth anything at all.

As for a lunar base, many of the issues are difficult and one ( effects of low-gee) is probably impossible to solve.

I don’t think that there are real mysteries about what is needed for a kind-of self-sufficient base – it’s just too hard and there’s not much prospect of a payoff.

That said, there may be other ways of going about this that are more promising.

--

Venus is worth terraforming: no gravity problems. Doable.

--

It’s not impossible that Mars might harbor microbial life – with some luck, life with a different chemical basis. That might be very valuable: there are endless industrial processes that depend upon some kind of fermentation.
Why, without acetone fermentation, there might not be a state of Israel.
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If we used a reasonable approach, like Orion, I think that people would usefully supplement those robots.

https://westhunt.wordpress.com/2019/01/11/the-great-divorce/
Jeff Bezos isn’t my favorite guy, but he has ability and has built something useful. And an ugly, contested divorce would be harsh and unfair to the children, who have done nothing wrong.

But I don’t care. The thought of tens of billions of dollars being spent on lawyers and PIs offer the possibility of a spectacle that will live forever, far wilder than the antics of Nero or Caligula. It could make Suetonius look like Pilgrim’s Progress.

Have you ever wondered whether tens of thousands of divorce lawyers should be organized into legions or phalanxes? This is our chance to finally find out.
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8 weeks ago by nhaliday
Two Performance Aesthetics: Never Miss a Frame and Do Almost Nothing - Tristan Hume
I’ve noticed when I think about performance nowadays that I think in terms of two different aesthetics. One aesthetic, which I’ll call Never Miss a Frame, comes from the world of game development and is focused on writing code that has good worst case performance by making good use of the hardware. The other aesthetic, which I’ll call Do Almost Nothing comes from a more academic world and is focused on algorithmically minimizing the work that needs to be done to the extent that there’s barely any work left, paying attention to the performance at all scales.

[ed.: Neither of these exactly matches TCS performance PoV but latter is closer (the focus on diffs is kinda weird).]

...

Never Miss a Frame

In game development the most important performance criteria is that your game doesn’t miss frame deadlines. You have a target frame rate and if you miss the deadline for the screen to draw a new frame your users will notice the jank. This leads to focusing on the worst case scenario and often having fixed maximum limits for various quantities. This property can also be important in areas other than game development, like other graphical applications, real-time audio, safety-critical systems and many embedded systems. A similar dynamic occurs in distributed systems where one server needs to query 100 others and combine the results, you’ll wait for the slowest of the 100 every time so speeding up some of them doesn’t make the query faster, and queries occasionally taking longer (e.g because of garbage collection) will impact almost every request!

...

In this kind of domain you’ll often run into situations where in the worst case you can’t avoid processing a huge number of things. This means you need to focus your effort on making the best use of the hardware by writing code at a low level and paying attention to properties like cache size and memory bandwidth.

Projects with inviolable deadlines need to adjust different factors than speed if the code runs too slow. For example a game might decrease the size of a level or use a more efficient but less pretty rendering technique.

Aesthetically: Data should be tightly packed, fixed size, and linear. Transcoding data to and from different formats is wasteful. Strings and their variable lengths and inefficient operations must be avoided. Only use tools that allow you to work at a low level, even if they’re annoying, because that’s the only way you can avoid piles of fixed costs making everything slow. Understand the machine and what your code does to it.

Personally I identify this aesthetic most with Jonathan Blow. He has a very strong personality and I’ve watched enough of videos of him that I find imagining “What would Jonathan Blow say?” as a good way to tap into this aesthetic. My favourite articles about designs following this aesthetic are on the Our Machinery Blog.

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Do Almost Nothing

Sometimes, it’s important to be as fast as you can in all cases and not just orient around one deadline. The most common case is when you simply have to do something that’s going to take an amount of time noticeable to a human, and if you can make that time shorter in some situations that’s great. Alternatively each operation could be fast but you may run a server that runs tons of them and you’ll save on server costs if you can decrease the load of some requests. Another important case is when you care about power use, for example your text editor not rapidly draining a laptop’s battery, in this case you want to do the least work you possibly can.

A key technique for this approach is to never recompute something from scratch when it’s possible to re-use or patch an old result. This often involves caching: keeping a store of recent results in case the same computation is requested again.

The ultimate realization of this aesthetic is for the entire system to deal only in differences between the new state and the previous state, updating data structures with only the newly needed data and discarding data that’s no longer needed. This way each part of the system does almost no work because ideally the difference from the previous state is very small.

Aesthetically: Data must be in whatever structure scales best for the way it is accessed, lots of trees and hash maps. Computations are graphs of inputs and results so we can use all our favourite graph algorithms to optimize them! Designing optimal systems is hard so you should use whatever tools you can to make it easier, any fixed cost they incur will be made negligible when you optimize away all the work they need to do.

Personally I identify this aesthetic most with my friend Raph Levien and his articles about the design of the Xi text editor, although Raph also appreciates the other aesthetic and taps into it himself sometimes.

...

_I’m conflating the axes of deadline-oriented vs time-oriented and low-level vs algorithmic optimization, but part of my point is that while they are different, I think these axes are highly correlated._

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Text Editors

Sublime Text is a text editor that mostly follows the Never Miss a Frame approach. ...

The Xi Editor is designed to solve this problem by being designed from the ground up to grapple with the fact that some operations, especially those interacting with slow compilers written by other people, can’t be made instantaneous. It does this using a fancy asynchronous plugin model and lots of fancy data structures.
...

...

Compilers

Jonathan Blow’s Jai compiler is clearly designed with the Never Miss a Frame aesthetic. It’s written to be extremely fast at every level, and the language doesn’t have any features that necessarily lead to slow compiles. The LLVM backend wasn’t fast enough to hit his performance goals so he wrote an alternative backend that directly writes x86 code to a buffer without doing any optimizations. Jai compiles something like 100,000 lines of code per second. Designing both the language and compiler to not do anything slow lead to clean build performance 10-100x faster than other commonly-used compilers. Jai is so fast that its clean builds are faster than most compilers incremental builds on common project sizes, due to limitations in how incremental the other compilers are.

However, Jai’s compiler is still O(n) in the codebase size where incremental compilers can be O(n) in the size of the change. Some compilers like the work-in-progress rust-analyzer and I think also Roslyn for C# take a different approach and focus incredibly hard on making everything fully incremental. For small changes (the common case) this can let them beat Jai and respond in milliseconds on arbitrarily large projects, even if they’re slower on clean builds.

Conclusion
I find both of these aesthetics appealing, but I also think there’s real trade-offs that incentivize leaning one way or the other for a given project. I think people having different performance aesthetics, often because one aesthetic really is better suited for their domain, is the source of a lot of online arguments about making fast systems. The different aesthetics also require different bases of knowledge to pursue, like knowledge of data-oriented programming in C++ vs knowledge of abstractions for incrementality like Adapton, so different people may find that one approach seems way easier and better for them than the other.

I try to choose how to dedicate my effort to pursuing each aesthetics on a per project basis by trying to predict how effort in each direction would help. Some projects I know if I code it efficiently it will always hit the performance deadline, others I know a way to drastically cut down on work by investing time in algorithmic design, some projects need a mix of both. Personally I find it helpful to think of different programmers where I have a good sense of their aesthetic and ask myself how they’d solve the problem. One reason I like Rust is that it can do both low-level optimization and also has a good ecosystem and type system for algorithmic optimization, so I can more easily mix approaches in one project. In the end the best approach to follow depends not only on the task, but your skills or the skills of the team working on it, as well as how much time you have to work towards an ambitious design that may take longer for a better result.
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10 weeks ago by nhaliday
Unix philosophy - Wikipedia
1. Make each program do one thing well. To do a new job, build afresh rather than complicate old programs by adding new "features".
2. Expect the output of every program to become the input to another, as yet unknown, program. Don't clutter output with extraneous information. Avoid stringently columnar or binary input formats. Don't insist on interactive input.
3. Design and build software, even operating systems, to be tried early, ideally within weeks. Don't hesitate to throw away the clumsy parts and rebuild them.
4. Use tools in preference to unskilled help to lighten a programming task, even if you have to detour to build the tools and expect to throw some of them out after you've finished using them.
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12 weeks ago by nhaliday
The Existential Risk of Math Errors - Gwern.net
How big is this upper bound? Mathematicians have often made errors in proofs. But it’s rarer for ideas to be accepted for a long time and then rejected. But we can divide errors into 2 basic cases corresponding to type I and type II errors:

1. Mistakes where the theorem is still true, but the proof was incorrect (type I)
2. Mistakes where the theorem was false, and the proof was also necessarily incorrect (type II)

Before someone comes up with a final answer, a mathematician may have many levels of intuition in formulating & working on the problem, but we’ll consider the final end-product where the mathematician feels satisfied that he has solved it. Case 1 is perhaps the most common case, with innumerable examples; this is sometimes due to mistakes in the proof that anyone would accept is a mistake, but many of these cases are due to changing standards of proof. For example, when David Hilbert discovered errors in Euclid’s proofs which no one noticed before, the theorems were still true, and the gaps more due to Hilbert being a modern mathematician thinking in terms of formal systems (which of course Euclid did not think in). (David Hilbert himself turns out to be a useful example of the other kind of error: his famous list of 23 problems was accompanied by definite opinions on the outcome of each problem and sometimes timings, several of which were wrong or questionable5.) Similarly, early calculus used ‘infinitesimals’ which were sometimes treated as being 0 and sometimes treated as an indefinitely small non-zero number; this was incoherent and strictly speaking, practically all of the calculus results were wrong because they relied on an incoherent concept - but of course the results were some of the greatest mathematical work ever conducted6 and when later mathematicians put calculus on a more rigorous footing, they immediately re-derived those results (sometimes with important qualifications), and doubtless as modern math evolves other fields have sometimes needed to go back and clean up the foundations and will in the future.7

...

Isaac Newton, incidentally, gave two proofs of the same solution to a problem in probability, one via enumeration and the other more abstract; the enumeration was correct, but the other proof totally wrong and this was not noticed for a long time, leading Stigler to remark:

...

TYPE I > TYPE II?
“Lefschetz was a purely intuitive mathematician. It was said of him that he had never given a completely correct proof, but had never made a wrong guess either.”
- Gian-Carlo Rota13

Case 2 is disturbing, since it is a case in which we wind up with false beliefs and also false beliefs about our beliefs (we no longer know that we don’t know). Case 2 could lead to extinction.

...

Except, errors do not seem to be evenly & randomly distributed between case 1 and case 2. There seem to be far more case 1s than case 2s, as already mentioned in the early calculus example: far more than 50% of the early calculus results were correct when checked more rigorously. Richard Hamming attributes to Ralph Boas a comment that while editing Mathematical Reviews that “of the new results in the papers reviewed most are true but the corresponding proofs are perhaps half the time plain wrong”.

...

Gian-Carlo Rota gives us an example with Hilbert:

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Olga labored for three years; it turned out that all mistakes could be corrected without any major changes in the statement of the theorems. There was one exception, a paper Hilbert wrote in his old age, which could not be fixed; it was a purported proof of the continuum hypothesis, you will find it in a volume of the Mathematische Annalen of the early thirties.

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Leslie Lamport advocates for machine-checked proofs and a more rigorous style of proofs similar to natural deduction, noting a mathematician acquaintance guesses at a broad error rate of 1/329 and that he routinely found mistakes in his own proofs and, worse, believed false conjectures30.

[more on these "structured proofs":
https://academia.stackexchange.com/questions/52435/does-anyone-actually-publish-structured-proofs
https://mathoverflow.net/questions/35727/community-experiences-writing-lamports-structured-proofs
]

We can probably add software to that list: early software engineering work found that, dismayingly, bug rates seem to be simply a function of lines of code, and one would expect diseconomies of scale. So one would expect that in going from the ~4,000 lines of code of the Microsoft DOS operating system kernel to the ~50,000,000 lines of code in Windows Server 2003 (with full systems of applications and libraries being even larger: the comprehensive Debian repository in 2007 contained ~323,551,126 lines of code) that the number of active bugs at any time would be… fairly large. Mathematical software is hopefully better, but practitioners still run into issues (eg Durán et al 2014, Fonseca et al 2017) and I don’t know of any research pinning down how buggy key mathematical systems like Mathematica are or how much published mathematics may be erroneous due to bugs. This general problem led to predictions of doom and spurred much research into automated proof-checking, static analysis, and functional languages31.

[related:
https://mathoverflow.net/questions/11517/computer-algebra-errors
I don't know any interesting bugs in symbolic algebra packages but I know a true, enlightening and entertaining story about something that looked like a bug but wasn't.

Define sinc𝑥=(sin𝑥)/𝑥.

Someone found the following result in an algebra package: ∫∞0𝑑𝑥sinc𝑥=𝜋/2
They then found the following results:

...

So of course when they got:

∫∞0𝑑𝑥sinc𝑥sinc(𝑥/3)sinc(𝑥/5)⋯sinc(𝑥/15)=(467807924713440738696537864469/935615849440640907310521750000)𝜋

hmm:
Which means that nobody knows Fourier analysis nowdays. Very sad and discouraging story... – fedja Jan 29 '10 at 18:47

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Because the most popular systems are all commercial, they tend to guard their bug database rather closely -- making them public would seriously cut their sales. For example, for the open source project Sage (which is quite young), you can get a list of all the known bugs from this page. 1582 known issues on Feb.16th 2010 (which includes feature requests, problems with documentation, etc).

That is an order of magnitude less than the commercial systems. And it's not because it is better, it is because it is younger and smaller. It might be better, but until SAGE does a lot of analysis (about 40% of CAS bugs are there) and a fancy user interface (another 40%), it is too hard to compare.

I once ran a graduate course whose core topic was studying the fundamental disconnect between the algebraic nature of CAS and the analytic nature of the what it is mostly used for. There are issues of logic -- CASes work more or less in an intensional logic, while most of analysis is stated in a purely extensional fashion. There is no well-defined 'denotational semantics' for expressions-as-functions, which strongly contributes to the deeper bugs in CASes.]

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Should such widely-believed conjectures as P≠NP or the Riemann hypothesis turn out be false, then because they are assumed by so many existing proofs, a far larger math holocaust would ensue38 - and our previous estimates of error rates will turn out to have been substantial underestimates. But it may be a cloud with a silver lining, if it doesn’t come at a time of danger.

https://mathoverflow.net/questions/338607/why-doesnt-mathematics-collapse-down-even-though-humans-quite-often-make-mista

more on formal methods in programming:
https://www.quantamagazine.org/formal-verification-creates-hacker-proof-code-20160920/
https://intelligence.org/2014/03/02/bob-constable/

https://softwareengineering.stackexchange.com/questions/375342/what-are-the-barriers-that-prevent-widespread-adoption-of-formal-methods
Update: measured effort
In the October 2018 issue of Communications of the ACM there is an interesting article about Formally verified software in the real world with some estimates of the effort.

Interestingly (based on OS development for military equipment), it seems that producing formally proved software requires 3.3 times more effort than with traditional engineering techniques. So it's really costly.

On the other hand, it requires 2.3 times less effort to get high security software this way than with traditionally engineered software if you add the effort to make such software certified at a high security level (EAL 7). So if you have high reliability or security requirements there is definitively a business case for going formal.

WHY DON'T PEOPLE USE FORMAL METHODS?: https://www.hillelwayne.com/post/why-dont-people-use-formal-methods/
You can see examples of how all of these look at Let’s Prove Leftpad. HOL4 and Isabelle are good examples of “independent theorem” specs, SPARK and Dafny have “embedded assertion” specs, and Coq and Agda have “dependent type” specs.6

If you squint a bit it looks like these three forms of code spec map to the three main domains of automated correctness checking: tests, contracts, and types. This is not a coincidence. Correctness is a spectrum, and formal verification is one extreme of that spectrum. As we reduce the rigour (and effort) of our verification we get simpler and narrower checks, whether that means limiting the explored state space, using weaker types, or pushing verification to the runtime. Any means of total specification then becomes a means of partial specification, and vice versa: many consider Cleanroom a formal verification technique, which primarily works by pushing code review far beyond what’s humanly possible.

...

The question, then: “is 90/95/99% correct significantly cheaper than 100% correct?” The answer is very yes. We all are comfortable saying that a codebase we’ve well-tested and well-typed is mostly correct modulo a few fixes in prod, and we’re even writing more than four lines of code a day. In fact, the vast… [more]
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july 2019 by nhaliday
Lindy effect - Wikipedia
The Lindy effect is a theory that the future life expectancy of some non-perishable things like a technology or an idea is proportional to their current age, so that every additional period of survival implies a longer remaining life expectancy.[1] Where the Lindy effect applies, mortality rate decreases with time. In contrast, living creatures and mechanical things follow a bathtub curve where, after "childhood", the mortality rate increases with time. Because life expectancy is probabilistically derived, a thing may become extinct before its "expected" survival. In other words, one needs to gauge both the age and "health" of the thing to determine continued survival.
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june 2019 by nhaliday
Philip Guo - Research Design Patterns
List of ways to generate research directions. Some are pretty specific to applied CS.
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may 2019 by nhaliday
Reverse salients | West Hunter
Edison thought in terms of reverse salients and critical problems.

“Reverse salients are areas of research and development that are lagging in some obvious way behind the general line of advance. Critical problems are the research questions, cast in terms of the concrete particulars of currently available knowledge and technique and of specific exemplars or models that are solvable and whose solutions would eliminate the reverse salients. ”

What strikes you as as important current example of a reverse salient, and the associated critical problem or problems?
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may 2019 by nhaliday
Braves | West Hunter
If  Amerindians had a lot fewer serious infectious diseases than Old Worlders, something else had to limit population – and it wasn’t the Pill.

Surely there was more death by violence. In principle they could have sat down and quietly starved to death, but I doubt it. Better to burn out than fade away.
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may 2019 by nhaliday
Lateralization of brain function - Wikipedia
Language
Language functions such as grammar, vocabulary and literal meaning are typically lateralized to the left hemisphere, especially in right handed individuals.[3] While language production is left-lateralized in up to 90% of right-handers, it is more bilateral, or even right-lateralized, in approximately 50% of left-handers.[4]

Broca's area and Wernicke's area, two areas associated with the production of speech, are located in the left cerebral hemisphere for about 95% of right-handers, but about 70% of left-handers.[5]:69

Auditory and visual processing
The processing of visual and auditory stimuli, spatial manipulation, facial perception, and artistic ability are represented bilaterally.[4] Numerical estimation, comparison and online calculation depend on bilateral parietal regions[6][7] while exact calculation and fact retrieval are associated with left parietal regions, perhaps due to their ties to linguistic processing.[6][7]

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Depression is linked with a hyperactive right hemisphere, with evidence of selective involvement in "processing negative emotions, pessimistic thoughts and unconstructive thinking styles", as well as vigilance, arousal and self-reflection, and a relatively hypoactive left hemisphere, "specifically involved in processing pleasurable experiences" and "relatively more involved in decision-making processes".

Chaos and Order; the right and left hemispheres: https://orthosphere.wordpress.com/2018/05/23/chaos-and-order-the-right-and-left-hemispheres/
In The Master and His Emissary, Iain McGilchrist writes that a creature like a bird needs two types of consciousness simultaneously. It needs to be able to focus on something specific, such as pecking at food, while it also needs to keep an eye out for predators which requires a more general awareness of environment.

These are quite different activities. The Left Hemisphere (LH) is adapted for a narrow focus. The Right Hemisphere (RH) for the broad. The brains of human beings have the same division of function.

The LH governs the right side of the body, the RH, the left side. With birds, the left eye (RH) looks for predators, the right eye (LH) focuses on food and specifics. Since danger can take many forms and is unpredictable, the RH has to be very open-minded.

The LH is for narrow focus, the explicit, the familiar, the literal, tools, mechanism/machines and the man-made. The broad focus of the RH is necessarily more vague and intuitive and handles the anomalous, novel, metaphorical, the living and organic. The LH is high resolution but narrow, the RH low resolution but broad.

The LH exhibits unrealistic optimism and self-belief. The RH has a tendency towards depression and is much more realistic about a person’s own abilities. LH has trouble following narratives because it has a poor sense of “wholes.” In art it favors flatness, abstract and conceptual art, black and white rather than color, simple geometric shapes and multiple perspectives all shoved together, e.g., cubism. Particularly RH paintings emphasize vistas with great depth of field and thus space and time,[1] emotion, figurative painting and scenes related to the life world. In music, LH likes simple, repetitive rhythms. The RH favors melody, harmony and complex rhythms.

...

Schizophrenia is a disease of extreme LH emphasis. Since empathy is RH and the ability to notice emotional nuance facially, vocally and bodily expressed, schizophrenics tend to be paranoid and are often convinced that the real people they know have been replaced by robotic imposters. This is at least partly because they lose the ability to intuit what other people are thinking and feeling – hence they seem robotic and suspicious.

Oswald Spengler’s The Decline of the West as well as McGilchrist characterize the West as awash in phenomena associated with an extreme LH emphasis. Spengler argues that Western civilization was originally much more RH (to use McGilchrist’s categories) and that all its most significant artistic (in the broadest sense) achievements were triumphs of RH accentuation.

The RH is where novel experiences and the anomalous are processed and where mathematical, and other, problems are solved. The RH is involved with the natural, the unfamiliar, the unique, emotions, the embodied, music, humor, understanding intonation and emotional nuance of speech, the metaphorical, nuance, and social relations. It has very little speech, but the RH is necessary for processing all the nonlinguistic aspects of speaking, including body language. Understanding what someone means by vocal inflection and facial expressions is an intuitive RH process rather than explicit.

...

RH is very much the center of lived experience; of the life world with all its depth and richness. The RH is “the master” from the title of McGilchrist’s book. The LH ought to be no more than the emissary; the valued servant of the RH. However, in the last few centuries, the LH, which has tyrannical tendencies, has tried to become the master. The LH is where the ego is predominantly located. In split brain patients where the LH and the RH are surgically divided (this is done sometimes in the case of epileptic patients) one hand will sometimes fight with the other. In one man’s case, one hand would reach out to hug his wife while the other pushed her away. One hand reached for one shirt, the other another shirt. Or a patient will be driving a car and one hand will try to turn the steering wheel in the opposite direction. In these cases, the “naughty” hand is usually the left hand (RH), while the patient tends to identify herself with the right hand governed by the LH. The two hemispheres have quite different personalities.

The connection between LH and ego can also be seen in the fact that the LH is competitive, contentious, and agonistic. It wants to win. It is the part of you that hates to lose arguments.

Using the metaphor of Chaos and Order, the RH deals with Chaos – the unknown, the unfamiliar, the implicit, the emotional, the dark, danger, mystery. The LH is connected with Order – the known, the familiar, the rule-driven, the explicit, and light of day. Learning something means to take something unfamiliar and making it familiar. Since the RH deals with the novel, it is the problem-solving part. Once understood, the results are dealt with by the LH. When learning a new piece on the piano, the RH is involved. Once mastered, the result becomes a LH affair. The muscle memory developed by repetition is processed by the LH. If errors are made, the activity returns to the RH to figure out what went wrong; the activity is repeated until the correct muscle memory is developed in which case it becomes part of the familiar LH.

Science is an attempt to find Order. It would not be necessary if people lived in an entirely orderly, explicit, known world. The lived context of science implies Chaos. Theories are reductive and simplifying and help to pick out salient features of a phenomenon. They are always partial truths, though some are more partial than others. The alternative to a certain level of reductionism or partialness would be to simply reproduce the world which of course would be both impossible and unproductive. The test for whether a theory is sufficiently non-partial is whether it is fit for purpose and whether it contributes to human flourishing.

...

Analytic philosophers pride themselves on trying to do away with vagueness. To do so, they tend to jettison context which cannot be brought into fine focus. However, in order to understand things and discern their meaning, it is necessary to have the big picture, the overview, as well as the details. There is no point in having details if the subject does not know what they are details of. Such philosophers also tend to leave themselves out of the picture even when what they are thinking about has reflexive implications. John Locke, for instance, tried to banish the RH from reality. All phenomena having to do with subjective experience he deemed unreal and once remarked about metaphors, a RH phenomenon, that they are “perfect cheats.” Analytic philosophers tend to check the logic of the words on the page and not to think about what those words might say about them. The trick is for them to recognize that they and their theories, which exist in minds, are part of reality too.

The RH test for whether someone actually believes something can be found by examining his actions. If he finds that he must regard his own actions as free, and, in order to get along with other people, must also attribute free will to them and treat them as free agents, then he effectively believes in free will – no matter his LH theoretical commitments.

...

We do not know the origin of life. We do not know how or even if consciousness can emerge from matter. We do not know the nature of 96% of the matter of the universe. Clearly all these things exist. They can provide the subject matter of theories but they continue to exist as theorizing ceases or theories change. Not knowing how something is possible is irrelevant to its actual existence. An inability to explain something is ultimately neither here nor there.

If thought begins and ends with the LH, then thinking has no content – content being provided by experience (RH), and skepticism and nihilism ensue. The LH spins its wheels self-referentially, never referring back to experience. Theory assumes such primacy that it will simply outlaw experiences and data inconsistent with it; a profoundly wrong-headed approach.

...

Gödel’s Theorem proves that not everything true can be proven to be true. This means there is an ineradicable role for faith, hope and intuition in every moderately complex human intellectual endeavor. There is no one set of consistent axioms from which all other truths can be derived.

Alan Turing’s proof of the halting problem proves that there is no effective procedure for finding effective procedures. Without a mechanical decision procedure, (LH), when it comes to … [more]
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september 2018 by nhaliday
Society of Mind - Wikipedia
A core tenet of Minsky's philosophy is that "minds are what brains do". The society of mind theory views the human mind and any other naturally evolved cognitive systems as a vast society of individually simple processes known as agents. These processes are the fundamental thinking entities from which minds are built, and together produce the many abilities we attribute to minds. The great power in viewing a mind as a society of agents, as opposed to the consequence of some basic principle or some simple formal system, is that different agents can be based on different types of processes with different purposes, ways of representing knowledge, and methods for producing results.

This idea is perhaps best summarized by the following quote:

What magical trick makes us intelligent? The trick is that there is no trick. The power of intelligence stems from our vast diversity, not from any single, perfect principle. —Marvin Minsky, The Society of Mind, p. 308

https://en.wikipedia.org/wiki/Modularity_of_mind

The modular organization of human anatomical
brain networks: Accounting for the cost of wiring: https://www.mitpressjournals.org/doi/pdfplus/10.1162/NETN_a_00002
Brain networks are expected to be modular. However, existing techniques for estimating a network’s modules make it difficult to assess the influence of organizational principles such as wiring cost reduction on the detected modules. Here we present a modification of an existing module detection algorithm that allowed us to focus on connections that are unexpected under a cost-reduction wiring rule and to identify modules from among these connections. We applied this technique to anatomical brain networks and showed that the modules we detected differ from those detected using the standard technique. We demonstrated that these novel modules are spatially distributed, exhibit unique functional fingerprints, and overlap considerably with rich clubs, giving rise to an alternative and complementary interpretation of the functional roles of specific brain regions. Finally, we demonstrated that, using the modified module detection approach, we can detect modules in a developmental dataset that track normative patterns of maturation. Collectively, these findings support the hypothesis that brain networks are composed of modules and provide additional insight into the function of those modules.
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april 2018 by nhaliday
Eternity in six hours: intergalactic spreading of intelligent life and sharpening the Fermi paradox
We do this by demonstrating that traveling between galaxies – indeed even launching a colonisation project for the entire reachable universe – is a relatively simple task for a star-spanning civilization, requiring modest amounts of energy and resources. We start by demonstrating that humanity itself could likely accomplish such a colonisation project in the foreseeable future, should we want to, and then demonstrate that there are millions of galaxies that could have reached us by now, using similar methods. This results in a considerable sharpening of the Fermi paradox.
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march 2018 by nhaliday
Existential Risks: Analyzing Human Extinction Scenarios
https://twitter.com/robinhanson/status/981291048965087232
https://archive.is/dUTD5
Would you endorse choosing policy to max the expected duration of civilization, at least as a good first approximation?
Can anyone suggest a different first approximation that would get more votes?

https://twitter.com/robinhanson/status/981335898502545408
https://archive.is/RpygO
How useful would it be to agree on a relatively-simple first-approximation observable-after-the-fact metric for what we want from the future universe, such as total life years experienced, or civilization duration?

We're Underestimating the Risk of Human Extinction: https://www.theatlantic.com/technology/archive/2012/03/were-underestimating-the-risk-of-human-extinction/253821/
An Oxford philosopher argues that we are not adequately accounting for technology's risks—but his solution to the problem is not for Luddites.

Anderson: You have argued that we underrate existential risks because of a particular kind of bias called observation selection effect. Can you explain a bit more about that?

Bostrom: The idea of an observation selection effect is maybe best explained by first considering the simpler concept of a selection effect. Let's say you're trying to estimate how large the largest fish in a given pond is, and you use a net to catch a hundred fish and the biggest fish you find is three inches long. You might be tempted to infer that the biggest fish in this pond is not much bigger than three inches, because you've caught a hundred of them and none of them are bigger than three inches. But if it turns out that your net could only catch fish up to a certain length, then the measuring instrument that you used would introduce a selection effect: it would only select from a subset of the domain you were trying to sample.

Now that's a kind of standard fact of statistics, and there are methods for trying to correct for it and you obviously have to take that into account when considering the fish distribution in your pond. An observation selection effect is a selection effect introduced not by limitations in our measurement instrument, but rather by the fact that all observations require the existence of an observer. This becomes important, for instance, in evolutionary biology. For instance, we know that intelligent life evolved on Earth. Naively, one might think that this piece of evidence suggests that life is likely to evolve on most Earth-like planets. But that would be to overlook an observation selection effect. For no matter how small the proportion of all Earth-like planets that evolve intelligent life, we will find ourselves on a planet that did. Our data point-that intelligent life arose on our planet-is predicted equally well by the hypothesis that intelligent life is very improbable even on Earth-like planets as by the hypothesis that intelligent life is highly probable on Earth-like planets. When it comes to human extinction and existential risk, there are certain controversial ways that observation selection effects might be relevant.
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march 2018 by nhaliday
Prisoner's dilemma - Wikipedia
caveat to result below:
An extension of the IPD is an evolutionary stochastic IPD, in which the relative abundance of particular strategies is allowed to change, with more successful strategies relatively increasing. This process may be accomplished by having less successful players imitate the more successful strategies, or by eliminating less successful players from the game, while multiplying the more successful ones. It has been shown that unfair ZD strategies are not evolutionarily stable. The key intuition is that an evolutionarily stable strategy must not only be able to invade another population (which extortionary ZD strategies can do) but must also perform well against other players of the same type (which extortionary ZD players do poorly, because they reduce each other's surplus).[14]

Theory and simulations confirm that beyond a critical population size, ZD extortion loses out in evolutionary competition against more cooperative strategies, and as a result, the average payoff in the population increases when the population is bigger. In addition, there are some cases in which extortioners may even catalyze cooperation by helping to break out of a face-off between uniform defectors and win–stay, lose–switch agents.[8]

https://alfanl.com/2018/04/12/defection/
Nature boils down to a few simple concepts.

Haters will point out that I oversimplify. The haters are wrong. I am good at saying a lot with few words. Nature indeed boils down to a few simple concepts.

In life, you can either cooperate or defect.

Used to be that defection was the dominant strategy, say in the time when the Roman empire started to crumble. Everybody complained about everybody and in the end nothing got done. Then came Jesus, who told people to be loving and cooperative, and boom: 1800 years later we get the industrial revolution.

Because of Jesus we now find ourselves in a situation where cooperation is the dominant strategy. A normie engages in a ton of cooperation: with the tax collector who wants more and more of his money, with schools who want more and more of his kid’s time, with media who wants him to repeat more and more party lines, with the Zeitgeist of the Collective Spirit of the People’s Progress Towards a New Utopia. Essentially, our normie is cooperating himself into a crumbling Western empire.

Turns out that if everyone blindly cooperates, parasites sprout up like weeds until defection once again becomes the standard.

The point of a post-Christian religion is to once again create conditions for the kind of cooperation that led to the industrial revolution. This necessitates throwing out undead Christianity: you do not blindly cooperate. You cooperate with people that cooperate with you, you defect on people that defect on you. Christianity mixed with Darwinism. God and Gnon meet.

This also means we re-establish spiritual hierarchy, which, like regular hierarchy, is a prerequisite for cooperation. It is this hierarchical cooperation that turns a household into a force to be reckoned with, that allows a group of men to unite as a front against their enemies, that allows a tribe to conquer the world. Remember: Scientology bullied the Cathedral’s tax department into submission.

With a functioning hierarchy, men still gossip, lie and scheme, but they will do so in whispers behind closed doors. In your face they cooperate and contribute to the group’s wellbeing because incentives are thus that contributing to group wellbeing heightens status.

Without a functioning hierarchy, men gossip, lie and scheme, but they do so in your face, and they tell you that you are positively deluded for accusing them of gossiping, lying and scheming. Seeds will not sprout in such ground.

Spiritual dominance is established in the same way any sort of dominance is established: fought for, taken. But the fight is ritualistic. You can’t force spiritual dominance if no one listens, or if you are silenced the ritual is not allowed to happen.

If one of our priests is forbidden from establishing spiritual dominance, that is a sure sign an enemy priest is in better control and has vested interest in preventing you from establishing spiritual dominance..

They defect on you, you defect on them. Let them suffer the consequences of enemy priesthood, among others characterized by the annoying tendency that very little is said with very many words.

https://contingentnotarbitrary.com/2018/04/14/rederiving-christianity/
To recap, we started with a secular definition of Logos and noted that its telos is existence. Given human nature, game theory and the power of cooperation, the highest expression of that telos is freely chosen universal love, tempered by constant vigilance against defection while maintaining compassion for the defectors and forgiving those who repent. In addition, we must know the telos in order to fulfill it.

In Christian terms, looks like we got over half of the Ten Commandments (know Logos for the First, don’t defect or tempt yourself to defect for the rest), the importance of free will, the indestructibility of evil (group cooperation vs individual defection), loving the sinner and hating the sin (with defection as the sin), forgiveness (with conditions), and love and compassion toward all, assuming only secular knowledge and that it’s good to exist.

Iterated Prisoner's Dilemma is an Ultimatum Game: http://infoproc.blogspot.com/2012/07/iterated-prisoners-dilemma-is-ultimatum.html
The history of IPD shows that bounded cognition prevented the dominant strategies from being discovered for over over 60 years, despite significant attention from game theorists, computer scientists, economists, evolutionary biologists, etc. Press and Dyson have shown that IPD is effectively an ultimatum game, which is very different from the Tit for Tat stories told by generations of people who worked on IPD (Axelrod, Dawkins, etc., etc.).

...

For evolutionary biologists: Dyson clearly thinks this result has implications for multilevel (group vs individual selection):
... Cooperation loses and defection wins. The ZD strategies confirm this conclusion and make it sharper. ... The system evolved to give cooperative tribes an advantage over non-cooperative tribes, using punishment to give cooperation an evolutionary advantage within the tribe. This double selection of tribes and individuals goes way beyond the Prisoners' Dilemma model.

implications for fractionalized Europe vis-a-vis unified China?

and more broadly does this just imply we're doomed in the long run RE: cooperation, morality, the "good society", so on...? war and group-selection is the only way to get a non-crab bucket civilization?

Iterated Prisoner’s Dilemma contains strategies that dominate any evolutionary opponent:
http://www.pnas.org/content/109/26/10409.full
http://www.pnas.org/content/109/26/10409.full.pdf
https://www.edge.org/conversation/william_h_press-freeman_dyson-on-iterated-prisoners-dilemma-contains-strategies-that

https://en.wikipedia.org/wiki/Ultimatum_game

analogy for ultimatum game: the state gives the demos a bargain take-it-or-leave-it, and...if the demos refuses...violence?

The nature of human altruism: http://sci-hub.tw/https://www.nature.com/articles/nature02043
- Ernst Fehr & Urs Fischbacher

Some of the most fundamental questions concerning our evolutionary origins, our social relations, and the organization of society are centred around issues of altruism and selfishness. Experimental evidence indicates that human altruism is a powerful force and is unique in the animal world. However, there is much individual heterogeneity and the interaction between altruists and selfish individuals is vital to human cooperation. Depending on the environment, a minority of altruists can force a majority of selfish individuals to cooperate or, conversely, a few egoists can induce a large number of altruists to defect. Current gene-based evolutionary theories cannot explain important patterns of human altruism, pointing towards the importance of both theories of cultural evolution as well as gene–culture co-evolution.

...

Why are humans so unusual among animals in this respect? We propose that quantitatively, and probably even qualitatively, unique patterns of human altruism provide the answer to this question. Human altruism goes far beyond that which has been observed in the animal world. Among animals, fitness-reducing acts that confer fitness benefits on other individuals are largely restricted to kin groups; despite several decades of research, evidence for reciprocal altruism in pair-wise repeated encounters4,5 remains scarce6–8. Likewise, there is little evidence so far that individual reputation building affects cooperation in animals, which contrasts strongly with what we find in humans. If we randomly pick two human strangers from a modern society and give them the chance to engage in repeated anonymous exchanges in a laboratory experiment, there is a high probability that reciprocally altruistic behaviour will emerge spontaneously9,10.

However, human altruism extends far beyond reciprocal altruism and reputation-based cooperation, taking the form of strong reciprocity11,12. Strong reciprocity is a combination of altruistic rewarding, which is a predisposition to reward others for cooperative, norm-abiding behaviours, and altruistic punishment, which is a propensity to impose sanctions on others for norm violations. Strong reciprocators bear the cost of rewarding or punishing even if they gain no individual economic benefit whatsoever from their acts. In contrast, reciprocal altruists, as they have been defined in the biological literature4,5, reward and punish only if this is in their long-term self-interest. Strong reciprocity thus constitutes a powerful incentive for cooperation even in non-repeated interactions and when reputation gains are absent, because strong reciprocators will reward those who cooperate and punish those who defect.

...

We will show that the interaction between selfish and strongly reciprocal … [more]
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march 2018 by nhaliday
Fermi paradox - Wikipedia
Rare Earth hypothesis: https://en.wikipedia.org/wiki/Rare_Earth_hypothesis
Fine-tuned Universe: https://en.wikipedia.org/wiki/Fine-tuned_Universe
something to keep in mind:
Puddle theory is a term coined by Douglas Adams to satirize arguments that the universe is made for man.[54][55] As stated in Adams' book The Salmon of Doubt:[56]
Imagine a puddle waking up one morning and thinking, “This is an interesting world I find myself in, an interesting hole I find myself in, fits me rather neatly, doesn't it? In fact, it fits me staggeringly well, must have been made to have me in it!” This is such a powerful idea that as the sun rises in the sky and the air heats up and as, gradually, the puddle gets smaller and smaller, it's still frantically hanging on to the notion that everything's going to be all right, because this World was meant to have him in it, was built to have him in it; so the moment he disappears catches him rather by surprise. I think this may be something we need to be on the watch out for.
article  concept  paradox  wiki  reference  fermi  anthropic  space  xenobio  roots  speculation  ideas  risk  threat-modeling  civilization  nihil  🔬  deep-materialism  new-religion  futurism  frontier  technology  communication  simulation  intelligence  eden  war  nuclear  deterrence  identity  questions  multi  explanans  physics  theos  philosophy  religion  chemistry  bio  hmm  idk  degrees-of-freedom  lol  troll  existence 
january 2018 by nhaliday
Quis custodiet ipsos custodes? - Wikipedia
Quis custodiet ipsos custodes? is a Latin phrase found in the work of the Roman poet Juvenal from his Satires (Satire VI, lines 347–348). It is literally translated as "Who will guard the guards themselves?", though it is also known by variant translations.

The original context deals with the problem of ensuring marital fidelity, though it is now commonly used more generally to refer to the problem of controlling the actions of persons in positions of power, an issue discussed by Plato in the Republic. It is not clear whether the phrase was written by Juvenal, or whether the passage in which it appears was interpolated into his works.

...

This phrase is used generally to consider the embodiment of the philosophical question as to how power can be held to account. It is sometimes incorrectly attributed as a direct quotation from Plato's Republic in both popular media and academic contexts.[3] There is no exact parallel in the Republic, but it is used by modern authors to express Socrates' concerns about the guardians, _the solution to which is to properly train their souls_. Several 19th century examples of the association with Plato can be found, often dropping "ipsos".[4][5] John Stuart Mill quotes it thus in Considerations on Representative Government (1861), though without reference to Plato. Plato's Republic though was hardly ever referenced by classical Latin authors like Juvenal, and it has been noted that it simply disappeared from literary awareness for a thousand years except for traces in the writings of Cicero and St. Augustine.[6] In the Republic, a putatively perfect society is described by Socrates, the main character in this Socratic dialogue. Socrates proposed a guardian class to protect that society, and the custodes (watchmen) from the Satires are often interpreted as being parallel to the Platonic guardians (phylakes in Greek). Socrates' answer to the problem is, in essence, that _the guardians will be manipulated to guard themselves against themselves via a deception often called the "noble lie" in English_.[7] As Leonid Hurwicz pointed out in his 2007 lecture on accepting the Nobel Memorial Prize in Economic Sciences, one of Socrates' interlocutors in the Republic, Glaucon, even goes so far as to say "it would be absurd that a guardian should need a guard."[8] But Socrates returns to this point at 590d, where he says that _the best person "has a divine ruler within himself," and that "it is better for everyone to be ruled by divine reason, preferably within himself and his own, otherwise imposed from without."_[9]
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january 2018 by nhaliday
Books 2017 | West Hunter
Arabian Sands
The Aryans
The Big Show
The Camel and the Wheel
Civil War on Western Waters
Company Commander
Double-edged Secrets
The Forgotten Soldier
Genes in Conflict
Hive Mind
The horse, the wheel, and language
The Penguin Atlas of Medieval History
Habitable Planets for Man
The genetical theory of natural selection
The Rise of the Greeks
To Lose a Battle
The Jewish War
Tropical Gangsters
The Forgotten Revolution
Egil’s Saga
Shapers
Time Patrol

Russo: https://westhunt.wordpress.com/2017/12/14/books-2017/#comment-98568
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december 2017 by nhaliday
Use and Interpretation of LD Score Regression
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies: https://sci-hub.bz/10.1038/ng.3211
- Po-Ru Loh, Nick Patterson, et al.

https://www.biorxiv.org/content/biorxiv/early/2014/02/21/002931.full.pdf

Both polygenicity (i.e. many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield inflated distributions of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from bias and true signal from polygenicity. We have developed an approach that quantifies the contributions of each by examining the relationship between test statistics and linkage disequilibrium (LD). We term this approach LD Score regression. LD Score regression provides an upper bound on the contribution of confounding bias to the observed inflation in test statistics and can be used to estimate a more powerful correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of test statistic inflation in many GWAS of large sample size.

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n3/extref/ng.3211-S1.pdf

An atlas of genetic correlations across human diseases
and traits: https://sci-hub.bz/10.1038/ng.3406

https://www.biorxiv.org/content/early/2015/01/27/014498.full.pdf

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n11/extref/ng.3406-S1.pdf

https://github.com/bulik/ldsc
ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
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november 2017 by nhaliday
Lynn Margulis | West Hunter
Margulis went on to theorize that symbiotic relationships between organisms are the dominant driving force of evolution. There certainly are important examples of this: as far as I know, every complex organism that digests cellulose manages it thru a symbiosis with various prokaryotes. Many organisms with a restricted diet have symbiotic bacteria that provide essential nutrients – aphids, for example. Tall fescue, a popular turf grass on golf courses, carries an endosymbiotic fungus. And so on, and on on.

She went on to oppose neodarwinism, particularly rejecting inter-organismal competition (and population genetics itself). From Wiki: [ She also believed that proponents of the standard theory “wallow in their zoological, capitalistic, competitive, cost-benefit interpretation of Darwin – having mistaken him… Neo-Darwinism, which insists on [the slow accrual of mutations by gene-level natural selection], is in a complete funk.”[8] ‘

...

You might think that Lynn Margulis is an example of someone that could think outside the box because she’d never even been able to find it in the first place – but that’s more true of autistic types [like Dirac or Turing], which I doubt she was in any way. I’d say that some traditional prejudices [dislike of capitalism and individual competition], combined with the sort of general looniness that leaves one open to unconventional ideas, drove her in a direction that bore fruit, more or less by coincidence. A successful creative scientist does not have to be right about everything, or indeed about much of anything: they need to contribute at least one new, true, and interesting thing.

https://westhunt.wordpress.com/2017/11/25/lynn-margulis/#comment-98174
“A successful creative scientist does not have to be right about everything, or indeed about much of anything: they need to contribute at least one new, true, and interesting thing.” Yes – it’s like old bands. As long as they have just one song in heavy rotation on the classic rock stations, they can tour endlessly – it doesn’t matter that they have only one or even no original members performing. A scientific example of this phenomena is Kary Mullins. He’ll always have PCR, even if a glowing raccoon did greet him with the words, “Good evening, Doctor.”

Nobel Savage: https://www.lrb.co.uk/v21/n13/steven-shapin/nobel-savage
Dancing Naked in the Mind Field by Kary Mullis

jet fuel can't melt steel beams: https://westhunt.wordpress.com/2017/11/25/lynn-margulis/#comment-98201
You have to understand a subject extremely well to make arguments why something couldn’t have happened. The easiest cases involve some purported explanation violating a conservation law of physics: that wasn’t the case here.

Do I think you’re a hotshot, deeply knowledgeable about structural engineering, properties of materials, using computer models, etc? A priori, pretty unlikely. What are the odds that you know as much simple mechanics as I do? a priori, still pretty unlikely. Most likely, you’re talking through your hat.

Next, the conspiracy itself is unlikely: quite a few people would be involved – unlikely that none of them would talk. It’s not that easy to find people that would go along with such a thing, believe it or not. The Communists were pretty good at conspiracy, but people defected, people talked: not just Whittaker Chambers, not just Igor Gouzenko.
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november 2017 by nhaliday
ON THE ORIGIN OF STATES: STATIONARY BANDITS AND TAXATION IN EASTERN CONGO
As a foundation for this study, I organized the collection of village-level panel data on violent actors, managing teams of surveyors, village elders, and households in 380 war-torn areas of DRC. I introduce optimal taxation theory to the decision of violent actors to establish local monopolies of violence. The value of such decision hinges on their ability to tax the local population. A sharp rise in the global demand for coltan, a bulky commodity used in the electronics industry, leads violent actors to impose monopolies of violence and taxation in coltan sites, which persist even years after demand collapses. A similar rise in the demand for gold, easier to conceal and more difficult to tax, does not. However, the groups who nevertheless control gold sites are more likely to respond by undertaking investments in fiscal capacity, consistent with the difficulty to observe gold, and with well-documented trajectories of state formation in Europe (Ardant, 1975). The findings support the view that the expected revenue from taxation, determined in particular by tax base elasticity and costly investments in fiscal capacity, can explain the stages of state formation preceding the states as we recognize them today.
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november 2017 by nhaliday
Ancient Admixture in Human History
- Patterson, Reich et al., 2012
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.”
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november 2017 by nhaliday
What are the Laws of Biology?
The core finding of systems biology is that only a very small subset of possible network motifs is actually used and that these motifs recur in all kinds of different systems, from transcriptional to biochemical to neural networks. This is because only those arrangements of interactions effectively perform some useful operation, which underlies some necessary function at a cellular or organismal level. There are different arrangements for input summation, input comparison, integration over time, high-pass or low-pass filtering, negative auto-regulation, coincidence detection, periodic oscillation, bistability, rapid onset response, rapid offset response, turning a graded signal into a sharp pulse or boundary, and so on, and so on.

These are all familiar concepts and designs in engineering and computing, with well-known properties. In living organisms there is one other general property that the designs must satisfy: robustness. They have to work with noisy components, at a scale that’s highly susceptible to thermal noise and environmental perturbations. Of the subset of designs that perform some operation, only a much smaller subset will do it robustly enough to be useful in a living organism. That is, they can still perform their particular functions in the face of noisy or fluctuating inputs or variation in the number of components constituting the elements of the network itself.
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november 2017 by nhaliday
What Does a “Normal” Human Genome Look Like? | Science
So, what have our first glimpses of variation in the genomes of generally healthy people taught us? First, balancing selection, the evolutionary process that favors genetic diversification rather than the fixation of a single “best” variant, appears to play a minor role outside the immune system. Local adaptation, which accounts for variation in traits such as pigmentation, dietary specialization, and susceptibility to particular pathogens is also a second-tier player. What is on the top tier? Increasingly, the answer appears to be mutations that are “deleterious” by biochemical or standard evolutionary criteria. These mutations, as has long been appreciated, overwhelmingly make up the most abundant form of nonneutral variation in all genomes. A model for human genetic individuality is emerging in which there actually is a “wild-type” human genome—one in which most genes exist in an evolutionarily optimized form. There just are no “wild-type” humans: We each fall short of this Platonic ideal in our own distinctive ways.
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november 2017 by nhaliday
The Evil Dead | West Hunter
Someone asked me to go over a chapter he wrote, about the impact of certain customs on human health. One of them was the health advantages of quick burial: the problem is, usually there aren’t any.   People seem to think that the organisms causing decomposition are pathogenic, but they’re not.  People killed by trauma (earthquakes,  floods, bullets) are dead enough, but not a threat.  Sometimes, the body of someone that died of an infectious disease is contagious – smallpox scabs have been known to remain infectious for a long, long time – but most causative agents are unable to survive for long after the host’s death. Now if you’re dissecting someone,  especially if they’re fresh, you probably don’t want to nick yourself with the scalpel – but if you just walk past the corpse and refrain from playing with it, you’re usually OK.
west-hunter  scitariat  ideas  trivia  death  embodied  disease  parasites-microbiome  spreading  public-health  epidemiology  medicine  sanctity-degradation 
november 2017 by nhaliday
Bouncing Off the Bottom | West Hunter
Actually going extinct would seem to be a bad thing, but a close call can, in principle, be a good thing.

Pathogens can be a heavy burden on a species, worse than a 50-lb sack of cement. Lifting that burden can have a big effect: we know that many species flourish madly once they escape their typical parasites. That’s often the case with invasive species. It’s also a major strategy in agriculture: crops often do best in a country far away from their place of origin – where the climate is familiar, but most parasites have been left behind. For example, rubber trees originated in South America, but they’re a lot easier to grow in Liberia or Malaysia.

Consider a situation with a really burdensome pathogen – one that specializes in and depends on a single host species. That pathogen has to find new host individuals every so often in order to survive, and in order for that to happen, the host population has to exceed a certain number, usually called the critical community size. That size depends on the parasite’s persistence and mode of propagation: it can vary over a huge range. CCS is something like a quarter of a million for measles, ~300 for chickenpox, surely smaller than that for Epstein-Barr.

A brush with extinction- say from an asteroid strike – might well take a species below the CCS for a number of its pathogens. If those pathogens were limited to that species, they’d go extinct: no more burden. That alone might be enough to generate a rapid recovery from the population bottleneck. Or a single, highly virulent pathogen might cause a population crash that resulted in the extinction of several of that species’s major pathogens – quite possibly including the virulent pathogen itself. It’s a bottleneck in time, rather than one in space as you often see in colonization.

Such positive effects could last a long time – things need not go back to the old normal. The flea-unbitten species might be able to survive and prosper in ecological niches that it couldn’t before. You might see a range expansion. New evolutionary paths could open up. That brush with extinction could be the making of them.

When you add it all up, you begin to wonder if a population crash isn’t just what the doctor ordered. Sure, it wouldn’t be fun to be one of the billions of casualties, but just think how much better off the billions living after the bottleneck will be. Don’t be selfish.
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november 2017 by nhaliday
Darwinian medicine - Randolph Nesse
The Dawn of Darwinian Medicine: https://sci-hub.tw/https://www.jstor.org/stable/2830330
TABLE 1 Examples of the use of the theory of natural selection to predict the existence of phenomena otherwise unsuspected
TABLE 2 A classification of phenomena associated with infectious disease
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november 2017 by nhaliday
Fish on Friday | West Hunter
There are parts of Europe, Switzerland and Bavaria for example, that are seriously iodine deficient. This used to be a problem. I wonder if fish on Friday ameliorated it: A three-ounce serving size of cod provides your body with 99 micrograms of iodine, or 66% of the recommended amount per day.

Thinking further, it wasn’t just Fridays: there were ~130 days a years when the Catholic Church banned flesh.

Gwern on modern iodine-deficiency: https://westhunt.wordpress.com/2017/10/28/fish-on-friday/#comment-97137
population surveys indicate lots of people are iodine-insufficient even in the US or UK where the problem should’ve been permanently solved a century ago
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october 2017 by nhaliday
Measles and immunological amnesia | West Hunter
A new paper in Science , by Michael Mina et al,  strongly suggests that measles messes up your immunological defenses for two or three years. This is the likely explanation for the fact that measles inoculation causes much greater decreases in child morbidity and mortality than you’d expect from preventing the deaths directly due to measles infection. The thought is that measles whacks the cells that carry immunological memory, leaving the kid ripe for reinfections.  I think there can be a similar effect with anti-cancer chemotherapy.

If correct, this means that measles is much nastier than previously thought. It must have played a significant role in the demographic collapse of long-isolated peoples (such as the Amerindians). Its advent may have played a role in the population decrease associated with the decline of the Classical world.  Even though it is relatively new (having split off from rinderpest a couple of thousand years ago) strong selection for resistance may have  favored some fairly expensive genetic defenses (something like sickle-cell) in Eurasian populations.

We already know of quite a few complex side effects of infectious disease, such the different kind of immunosuppression we see with AIDs, Burkitt’s lymphoma hitting kids with severe Epstein-Barr infections followed by malaria, acute dengue fever that requires a previous infection by a different strain of dengue, etc: there may well be other important interactions and side effects, news of which has not yet come to Harvard.
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october 2017 by nhaliday
[1709.01149] Biotechnology and the lifetime of technical civilizations
The number of people able to end Earth's technical civilization has heretofore been small. Emerging dual-use technologies, such as biotechnology, may give similar power to thousands or millions of individuals. To quantitatively investigate the ramifications of such a marked shift on the survival of both terrestrial and extraterrestrial technical civilizations, this paper presents a two-parameter model for civilizational lifespans, i.e. the quantity L in Drake's equation for the number of communicating extraterrestrial civilizations. One parameter characterizes the population lethality of a civilization's biotechnology and the other characterizes the civilization's psychosociology. L is demonstrated to be less than the inverse of the product of these two parameters. Using empiric data from Pubmed to inform the biotechnology parameter, the model predicts human civilization's median survival time as decades to centuries, even with optimistic psychosociological parameter values, thereby positioning biotechnology as a proximate threat to human civilization. For an ensemble of civilizations having some median calculated survival time, the model predicts that, after 80 times that duration, only one in 1024 civilizations will survive -- a tempo and degree of winnowing compatible with Hanson's "Great Filter." Thus, assuming that civilizations universally develop advanced biotechnology, before they become vigorous interstellar colonizers, the model provides a resolution to the Fermi paradox.
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october 2017 by nhaliday
Biopolitics | West Hunter
I have said before that no currently popular ideology acknowledges well-established results of behavioral genetics, quantitative genetics, or psychometrics. Or evolutionary psychology.

What if some ideology or political tradition did? what could they do? What problems could they solve, what capabilities would they have?

Various past societies knew a few things along these lines. They knew that there were significant physical and behavioral differences between the sexes, which is forbidden knowledge in modern academia. Some knew that close inbreeding had negative consequences, which knowledge is on its way to the forbidden zone as I speak. Some cultures with wide enough geographical experience had realistic notions of average cognitive differences between populations. Some people had a rough idea about regression to the mean [ in dynasties], and the Ottomans came up with a highly unpleasant solution – the law of fratricide. The Romans, during the Principate, dealt with the same problem through imperial adoption. The Chinese exam system is in part aimed at the same problem.

...

At least some past societies avoided the social patterns leading to the nasty dysgenic trends we are experiencing today, but for the most part that is due to the anthropic principle: if they’d done something else you wouldn’t be reading this. Also to between-group competition: if you fuck your self up when others don’t, you may be well be replaced. Which is still the case.

If you were designing an ideology from scratch you could make use of all of these facts – not that thinking about genetics and selection hands you the solution to every problem, but you’d have more strings to your bow. And, off the top of your head, you’d understand certain trends that are behind the mountains of Estcarp, for our current ruling classes : invisible and unthinkable, That Which Must Not Be Named. .

https://westhunt.wordpress.com/2017/10/08/biopolitics/#comment-96613
“The closest…s the sort of libertarianism promulgated by Charles Murray”
Not very close..
A government that was fully aware of the implications and possibilities of human genetics, one that had the usual kind of state goals [ like persistence and increased power] , would not necessarily be particularly libertarian.

https://westhunt.wordpress.com/2017/10/08/biopolitics/#comment-96797
And giving tax breaks to college-educated liberals to have babies wouldn’t appeal much to Trump voters, methinks.

It might be worth making a reasonably comprehensive of the facts and preferences that a good liberal is supposed to embrace and seem to believe. You would have to be fairly quick about it, before it changes. Then you could evaluate about the social impact of having more of them.

Rise and Fall: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/
Every society selects for something: generally it looks as if the direction of selection pressue is more or less an accident. Although nations and empires in the past could have decided to select men for bravery or intelligence, there’s not much sign that anyone actually did this. I mean, they would have known how, if they’d wanted to, just as they knew how to select for destriers, coursers, and palfreys. It was still possible to know such things in the Middle Ages, because Harvard did not yet exist.

A rising empire needs quality human capital, which implies that at minimum that budding imperial society must not have been strongly dysgenic. At least not in the beginning. But winning changes many things, possibly including selective pressures. Imagine an empire with substantial urbanization, one in which talented guys routinely end up living in cities – cities that were demographic sinks. That might change things. Or try to imagine an empire in which survival challenges are greatly reduced, at least for elites, so that people have nothing to keep their minds off their minds and up worshiping Magna Mater. Imagine that an empire that conquers a rival with interesting local pathogens and brings some of them home. Or one that uses up a lot of its manpower conquering less-talented subjects and importing masses of those losers into the imperial heartland.

If any of those scenarios happened valid, they might eventually result in imperial decline – decline due to decreased biological capital.

Right now this is speculation. If we knew enough about the GWAS hits for intelligence, and had enough ancient DNA, we might be able to observe that rise and fall, just as we see dysgenic trends in contemporary populations. But that won’t happen for a long time. Say, a year.

hmm: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/#comment-100350
“Although nations and empires in the past could have decided to select men for bravery or intelligence, there’s not much sign that anyone actually did this.”

Maybe the Chinese imperial examination could effectively have been a selection for intelligence.
--
Nope. I’ve modelled it: the fraction of winners is far too small to have much effect, while there were likely fitness costs from the arduous preparation. Moreover, there’s a recent
paper [Detecting polygenic adaptation in admixture graphs] that looks for indications of when selection for IQ hit northeast Asia: quite a while ago. Obvious though, since Japan has similar scores without ever having had that kind of examination system.

decline of British Empire and utility of different components: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/#comment-100390
Once upon a time, India was a money maker for the British, mainly because they appropriate Bengali tax revenue, rather than trade. The rest of the Empire was not worth much: it didn’t materially boost British per-capita income or military potential. Silesia was worth more to Germany, conferred more war-making power, than Africa was to Britain.
--
If you get even a little local opposition, a colony won’t pay for itself. I seem to remember that there was some, in Palestine.
--
Angels from on high paid for the Boer War.

You know, someone in the 50’s asked for the numbers – how much various colonies cost and how much they paid.

Turned out that no one had ever asked. The Colonial Office had no idea.
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october 2017 by nhaliday
The Water-Crossers | West Hunter
One interesting and puzzling question is when and how humans developed the ability to make ocean crossings.

Baby Steps: https://westhunt.wordpress.com/2015/07/20/baby-steps/
west-hunter  scitariat  discussion  ideas  sapiens  migration  spreading  world  oceans  anglo  history  antiquity  time  multi  usa  discovery  innovation  roots  archaeology  speculation 
october 2017 by nhaliday
Post-Columbian Evolution – Holes | West Hunter
At this point, we have some decent examples of post-Columbian evolution, genetic changes in New World populations after 1492. There is evidence for selection for increased fertility in Quebec, along with increased mutational load due to relaxed selection. Something similar must have occurred in American colonial populations.

I think that the Amish are probably becoming plainer, thru the boiling-off process – which can’t be a common mechanism, because it requires very high fertility, enough to sustain a substantial defection rate.

HbS (sickle-cell) gene frequency has almost certainly decreased significantly among African-Americans – a simple model suggests by about half. There has probably been a decrease in other expensive malaria defenses.

...

In principle, if you had an immune gene that defended against an Old World pathogen that didn’t cross into America, Amerindians would have gradually accumulated nonfunctional variants, just from mutational pressure. the percentage of people with such mutations in any particular immune defense gene would not be very high (not in only 500 generations) but since there are many such genes, the fraction of Amerindians with at least one such hole in their immunological armor might have been significant. Probably this would have been more of a problem in the Caribbean islands, where the Taino seem to have just melted away… Presumably most such holes are gone now in surviving populations, but you might be able to identify them in pre-Columbian DNA.

I see where some Kraut is saying that we now know that human evolution is continuing. I think that’s been an obvious conclusion for almost 160 years.

https://westhunt.wordpress.com/2016/05/04/post-columbian-evolution-holes/#comment-78811
Sarazzin acknowledges it.

interesting guy: https://en.wikipedia.org/wiki/Thilo_Sarrazin
He became well-known worldwide after publishing a controversial book about Muslim immigrants in Germany in 2010.[3] In his book Deutschland schafft sich ab ("Germany abolishes itself"),[4] he denounces the failure of Germany's post-war immigration policy, sparking a nationwide controversy about the costs and benefits of multiculturalism.
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october 2017 by nhaliday
Inferior Faunas | West Hunter
I mentioned South American paleontologists defending the honor of their extinct animals, and pointed  out how stupid that is. There are many similar cases: Jefferson vs Buffon on the wimpiness of North American mammals (as a reader pointed out),  biologists defending the prowess of marsupials in Australia (a losing proposition) , etc.

So, we need to establish the relative competitive abilities of different faunas and settle this, once and for all.

Basically, the smaller and more isolated, the less competitive.  Pretty much true for both plants and animals.

Islands do poorly. Not just dodos: Hawaiian species, for example, are generally losers: everything from outside is a threat.

something hidden: https://westhunt.wordpress.com/2014/12/01/something-hidden/
I’m wondering of any of the Meridiungulata lineages did survive, unnoticed because they’re passing for insectivores or rats or whatever, just as tenrecs and golden moles did. . Obviously the big ones are extinct, probably the others as well, but until we’ve looked at the DNA of every little mammal in South America, the possibility exists.
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october 2017 by nhaliday
New Theory Cracks Open the Black Box of Deep Learning | Quanta Magazine
A new idea called the “information bottleneck” is helping to explain the puzzling success of today’s artificial-intelligence algorithms — and might also explain how human brains learn.

sounds like he's just talking about autoencoders?
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september 2017 by nhaliday
WLGR: The Julian marriage laws (nos. 120-123, etc.)
In 18 B.C., the Emperor Augustus turned his attention to social problems at Rome. Extravagance and adultery were widespread. Among the upper classes, marriage was increasingly infrequent and, many couples who did marry failed to produce offspring. Augustus, who hoped thereby to elevate both the morals and the numbers of the upper classes in Rome, and to increase the population of native Italians in Italy, enacted laws to encourage marriage and having children (lex Julia de maritandis ordinibus), including provisions establishing adultery as a crime.

Jus trium liberorum: https://en.wikipedia.org/wiki/Jus_trium_liberorum
The ius trium liberorum, meaning “the right of three children” in Latin,[1] was a privilege rewarded to Roman citizens who had borne at least three children or freedmen who had borne at least four children.[2] It was a direct result of the Lex Iulia and the Lex Papia Poppaea, bodies of legislation introduced by Augustus in 18 BC and 9 AD, respectively.[3] These bodies of legislation were conceived to grow the dwindling population of the Roman upper classes. The intent of the jus trium liberorum has caused scholars to interpret it as eugenic legislation.[4] Men who had received the jus trium liberorum were excused from munera. Women with jus trium liberorum were no longer submitted to tutela mulierum and could receive inheritances otherwise bequest to their children.[5] The public reaction to the jus trium liberorum was largely to find loopholes, however. The prospect of having a large family was still not appealing.[6] A person who caught a citizen in violation in this law was entitled to a portion of the inheritance involved, creating a lucrative business for professional spies.[7] The spies became so pervasive that the reward was reduced to a quarter of its previous size.[8] As time went on the ius trium liberorum was granted to those by consuls as rewards for general good deeds, holding important professions or as personal favors, not just prolific propagation.[9] Eventually the ius trium liberorum was repealed in 534 AD by Justinian.[10]

The Purpose of the Lex Iulia et Papia Poppaea: https://sci-hub.tw/https://www.jstor.org/stable/3292043

Roman Monogamy: http://laurabetzig.org/pdf/RomanMonogamy.pdf
- Laura Betzig

Mating in Rome was polygynous; marriage was monogamous. In the years 18BC and AD 9 the first Roman emperor, Augustus, backed the lex Julia and the lex Papia Poppaea, his “moral” legislation. It rewarded members of the senatorial aristocracy who married and had children; and it punished celibacy and childlessness, which were common. To many historians, that suggests Romans were reluctant to reproduce. To me, it suggests they kept the number of their legitimate children small to keep the number of their illegitimate children large. Marriage in Rome shares these features with marriage in other empires with highly polygynous mating: inheritances were raised by inbreeding; relatedness to heirs was raised by marrying virgins, praising and enforcing chastity in married women, and discouraging widow remarriage; heirs were limited— and inheritances concentrated—by monogamous marriage, patriliny, and primogeniture; and back-up heirs were got by divorce and remarriage, concubinage, and adoption. The “moral” legislation interfered with each of these. Among other things, it diverted inheritances by making widows remarry; it lowered relatedness to heirs by making adultery subject to public, rather than private, sanctions; and it dispersed estates by making younger sons and daughters take legitimate spouses and make legitimate heirs. Augustus' “moral” legislation, like canon law in Europe later on, was not, as it first appears, an act of reproductive altruism. It was, in fact, a form of reproductive competition.

Did moral decay destroy the ancient world?: http://www.roger-pearse.com/weblog/2014/01/17/did-moral-decay-destroy-the-ancient-world/

hmmm...:
https://www.thenation.com/article/im-a-marxist-feminist-slut-how-do-i-find-an-open-relationship/
https://www.indy100.com/article/worst-decision-you-can-ever-make-have-a-child-science-research-parent-sleep-sex-money-video-7960906

https://twitter.com/tcjfs/status/913087174224044033
https://archive.is/LRpzH
Cato the Elder speaks on proposed repeal of the Oppian Law (https://en.wikipedia.org/wiki/Lex_Oppia) - from Livy's History of Rome, Book 34

"What pretext in the least degree respectable is put forward for this female insurrection? 'That we may shine,' they say."

The Crisis of the Third Century as Seen by Contemporaries: https://grbs.library.duke.edu/article/viewFile/9021/4625
"COMPLAINTS OF EVIL TIMES are to be found in all centuries which
have left a literature behind them. But in the Roman Empire
the decline is acknowledged in a manner which leaves no
room for doubt."

Morals, Politics, and the Fall of the Roman Republic: https://sci-hub.tw/https://www.jstor.org/stable/642930

https://en.wikipedia.org/wiki/Roman_historiography#Livy
The purpose of writing Ab Urbe Condita was twofold: the first was to memorialize history and the second was to challenge his generation to rise to that same level. He was preoccupied with morality, using history as a moral essay. He connects a nation’s success with its high level of morality, and conversely a nation’s failure with its moral decline. Livy believed that there had been a moral decline in Rome, and he lacked the confidence that Augustus could reverse it. Though he shared Augustus’ ideals, he was not a “spokesman for the regime”. He believed that Augustus was necessary, but only as a short term measure.

Livy and Roman Historiography: http://www.wheelockslatin.com/answerkeys/handouts/ch7_Livy_and_Roman_Historiography.pdf

Imperial Expansion and Moral Decline in the Roman Republic: https://sci-hub.tw/https://www.jstor.org/stable/4435293
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september 2017 by nhaliday
Europa, Enceladus, Moon Miranda | West Hunter
A lot of ice moons seem to have interior oceans, warmed by tidal flexing and possibly radioactivity.  But they’re lousy candidates for life, because you need free energy; and there’s very little in the interior oceans of such system.

It is possible that NASA is institutionally poor at pointing this out.
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september 2017 by nhaliday
Caught in the act | West Hunter
The fossil record is sparse. Let me try to explain that. We have at most a few hundred Neanderthal skeletons, most in pretty poor shape. How many Neanderthals ever lived? I think their population varied in size quite a bit – lowest during glacial maxima, probably highest in interglacials. Their degree of genetic diversity suggests an effective population size of ~1000, but that would be dominated by the low points (harmonic average). So let’s say 50,000 on average, over their whole range (Europe, central Asia, the Levant, perhaps more). Say they were around for 300,000 years, with a generation time of 30 years – 10,000 generations, for a total of five hundred million Neanderthals over all time. So one in a million Neanderthals ends up in a museum: one every 20 generations. Low time resolution!

So if anatomically modern humans rapidly wiped out Neanderthals, we probably couldn’t tell. In much the same way, you don’t expect to find the remains of many dinosaurs killed by the Cretaceous meteor impact (at most one millionth of one generation, right?), or of Columbian mammoths killed by a wave of Amerindian hunters. Sometimes invaders leave a bigger footprint: a bunch of cities burning down with no rebuilding tells you something. But even when you know that population A completely replaced population B, it can be hard to prove that just how it happened. After all, population A could have all committed suicide just before B showed up. Stranger things have happened – but not often.
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september 2017 by nhaliday
Second Bananas | West Hunter
Still thinking about domestication. Mostly,  the wild ancestors of domesticate animals were social: presumably, such behavioral tendencies were preadaptations that helped the domesticates come to bond with or at least tolerate people.   Social animals can have adaptive personality variation – difference behavioral strategies.  Sometimes those strategies are facultative, sometimes genetic, sometimes a mix.

I would guess that those wild individuals that account for most of the ancestry of f a domesticated species didn’t have a representative mix of personality types. Probably they were more likely to be followers rather than leaders – not the alphas of the pack, not the most aggressive stallions.  Sidekicks.  With dogs, we can probably check this hypothesis fairly easily, since wolves are still around.

https://westhunt.wordpress.com/2013/04/03/wyld-stallyns/
A few years ago, I was thinking about genetic male morphs. Turns out that you find qualitatively different forms of males in many species: Barry Sinervos’s lizards, Shuster’s isopods, Lank’s ruffs, jack salmon, etc. Logically, the Y chromosome would be the best place for a such a genetic switch, since that would avoid negative side effects in females. The problem is that the Y carries very few genes.

Alternate strategies don’t have to to be as complicated as they are in ruffs or Uta stansburiana. Different levels of aggressiveness, or different points on the cad/dad axis, would have different selective payoffs in different environments. If a new environment favored lower (or higher) aggressiveness in males , a Y-chromosome that induced lower (or higher) aggressiveness would take off. And since different Y chromosomes do indeed affect the level of aggressiveness in mice [which I just found out], possibly by affecting testosterone production – this mechanism is plausible.

This could explain a funny genetic pattern in the domestication of horses. There’s a fair amount of diversity in horse mtDNA: it looks as if many different mares were domesticated. On the other hand, it looks as if only one stallion was ever domesticated. All living stallions today are his descendants.

Stallions are pretty aggressive, and must have been hard to tame. Maybe one was genetically unusual – wimpier. Tameable.

Fortunately for all concerned, the selective value of aggressiveness, etc. has been the same for all human populations forever and ever, before and after the development of agriculture. Otherwise you might see weirdly rapid expansions of particular Y-chromosome haplogroups – common, yet only a few thousand years old.

https://westhunt.wordpress.com/2018/04/18/wyld-stallyns-part-deux/
A while ago, I wondered if modern stallions are a male morph adapted to domestication, one in which the strategy is mediated via the Y chromosome.

Looks as if I was right*. Check out “Decline of genetic diversity in ancient domestic stallions in Europe”.

Selection favored one particular kind of Y-chromosome. This had to be based on phenotype, not genealogy. Most likely it was favored under the new environment of domestication. Somehow, these stallions performed better, or were easier to get along with (my bet).

We already knew that Y-chromosomes could do things: Haplogroup I increases the risk of heart disease by about 50%, while the particular variant of Y chromosome influences aggression in mice.

Which means you have to re-examine the starburst phylogeny of R1b and R1a: it’s probably biology, rather than history, that drove those expansions. Some kind of selective advantage. Possibly one reason that those particular Y chromosomes far outraced steppe autosomal contributions. Most likely, R1a and R1b induce specific morphs – their carriers are somehow different. Maybe they’re born to be mild, or born to be princes of the universe. Maybe an R1b guy just finds it easier to cooperate with other R1b guys… Or maybe they’re resistant to typhoid.

* correct predictions mean nothing in biology. Ask any biologist.
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september 2017 by nhaliday
House O’Rats | West Hunter
Not content with our simple selection experiment, we also install complicated mazes with flaming hoops that the rats have to jump through in order to get extra food and mates: we want rats with different brains, and eventually we get them. They’re maze-bright and flaming-hoop-bright. We install treadmills and feed the rats according to their work output, and eventually they produce more work per amount of food eaten. They’ve maximized efficiency rather than surge power, which was more useful back when they were wild and free. Not only that, they eventually come to like being on the treadmill, almost as if it’s some sort of race.

There are other silos – one full of rice and another full of maize. They have different mazes and flaming hoops, built at different times: and there are still wild rats, too, although not as many as in the silos.

But no matter how much they change, they’re still just a bunch of rats.
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september 2017 by nhaliday
Of Mice and Men | West Hunter
It’s not always easy figuring out how a pathogen causes disease. There is an example in mice for which the solution was very difficult, so difficult that we would probably have failed to discover the cause of a similarly obscure infectious disease in humans.

Mycoplasma pulmonis causes a chronic obstructive lung disease in mice, but it wasn’t easy to show this. The disease was first described in 1915, and by 1940, people began to suspect Mycoplasma pulmonis might be the cause. But then again, maybe not. It was often found in mice that seemed healthy. Pure cultures of this organism did not consistently produce lung disease – which means that it didn’t satisfy Koch’s postulates, in particular postulate 1 (The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.) and postulate 3 (The cultured microorganism should cause disease when introduced into a healthy organism.).

Well, those postulates are not logic itself, but rather a useful heuristic. Koch knew that, even if lots of other people don’t.

This respiratory disease of mice is long-lasting, but slow to begin. It can take half a lifetime – a mouse lifetime, that is – and that made finding the cause harder. It required patience, which means I certainly couldn’t have done it.

Here’s how they solved it. You can raise germ-free mice. In the early 1970s, researchers injected various candidate pathogens into different groups of germ-free mice and waited to see which, if any, developed this chronic lung disease. It was Mycoplasma pulmonis , all right, but it had taken 60 years to find out.

It turned out that susceptibility differed between different mouse strains – genetic susceptibility was important. Co-infection with other pathogens affected the course of the disease. Microenvironmental details mattered – mainly ammonia in cages where the bedding wasn’t changed often enough. But it didn’t happen without that mycoplasma, which was a key causal link, something every engineer understands but many MDs don’t.

If there was a similarly obscure infectious disease of humans, say one that involved a fairly common bug found in both the just and the unjust, one that took decades for symptoms to manifest – would we have solved it? Probably not.

Cooties are everywhere.

gay germ search: https://westhunt.wordpress.com/2013/07/21/of-mice-and-men/#comment-15905
It’s hard to say, depends on how complicated the path of causation is. Assuming that I’m even right, of course. Some good autopsy studies might be fruitful – you’d look for microanatomical brain differences, as with nartcolepsy. Differences in gene expression, maybe. You could look for a pathogen – using the digital version of RDA (representational difference analysis), say on discordant twins. Do some old-fashioned epidemiology. Look for marker antibodies, signs of some sort of immunological event.

Do all of the above on gay rams – lots easier to get started, much less whining from those being vivisected.

Patrick Moore found the virus causing Kaposi’s sarcoma without any funding at all. I’m sure Peter Thiel could afford a serious try.
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september 2017 by nhaliday
Medicine as a pseudoscience | West Hunter
The idea that venesection was a good thing, or at least not so bad, on the grounds that one in a few hundred people have hemochromatosis (in Northern Europe) reminds me of the people who don’t wear a seatbelt, since it would keep them from being thrown out of their convertible into a waiting haystack, complete with nubile farmer’s daughter. Daughters. It could happen. But it’s not the way to bet.

Back in the good old days, Charles II, age 53, had a fit one Sunday evening, while fondling two of his mistresses.

Monday they bled him (cupping and scarifying) of eight ounces of blood. Followed by an antimony emetic, vitriol in peony water, purgative pills, and a clyster. Followed by another clyster after two hours. Then syrup of blackthorn, more antimony, and rock salt. Next, more laxatives, white hellebore root up the nostrils. Powdered cowslip flowers. More purgatives. Then Spanish Fly. They shaved his head and stuck blistering plasters all over it, plastered the soles of his feet with tar and pigeon-dung, then said good-night.

...

Friday. The king was worse. He tells them not to let poor Nelly starve. They try the Oriental Bezoar Stone, and more bleeding. Dies at noon.

Most people didn’t suffer this kind of problem with doctors, since they never saw one. Charles had six. Now Bach and Handel saw the same eye surgeon, John Taylor – who blinded both of them. Not everyone can put that on his resume!

You may wonder how medicine continued to exist, if it had a negative effect, on the whole. There’s always the placebo effect – at least there would be, if it existed. Any real placebo effect is very small: I’d guess exactly zero. But there is regression to the mean. You see the doctor when you’re feeling worse than average – and afterwards, if he doesn’t kill you outright, you’re likely to feel better. Which would have happened whether you’d seen him or not, but they didn’t often do RCTs back in the day – I think James Lind was the first (1747).

Back in the late 19th century, Christian Scientists did better than others when sick, because they didn’t believe in medicine. For reasons I think mistaken, because Mary Baker Eddy rejected the reality of the entire material world, but hey, it worked. Parenthetically, what triggered all that New Age nonsense in 19th century New England? Hash?

This did not change until fairly recently. Sometime in the early 20th medicine, clinical medicine, what doctors do, hit break-even. Now we can’t do without it. I wonder if there are, or will be, other examples of such a pile of crap turning (mostly) into a real science.

good tweet: https://twitter.com/bowmanthebard/status/897146294191390720
The brilliant GP I've had for 35+ years has retired. How can I find another one who meets my requirements?

1 is overweight
2 drinks more than officially recommended amounts
3 has an amused, tolerant atitude to human failings
4 is well aware that we're all going to die anyway, & there are better or worse ways to die
5 has a healthy skeptical attitude to mainstream medical science
6 is wholly dismissive of "a|ternative” medicine
7 believes in evolution
8 thinks most diseases get better without intervention, & knows the dangers of false positives
9 understands the base rate fallacy

EconPapers: Was Civil War Surgery Effective?: http://econpapers.repec.org/paper/htrhcecon/444.htm
contra Greg Cochran:
To shed light on the subject, I analyze a data set created by Dr. Edmund Andrews, a Civil war surgeon with the 1st Illinois Light Artillery. Dr. Andrews’s data can be rendered into an observational data set on surgical intervention and recovery, with controls for wound location and severity. The data also admits instruments for the surgical decision. My analysis suggests that Civil War surgery was effective, and increased the probability of survival of the typical wounded soldier, with average treatment effect of 0.25-0.28.

Medical Prehistory: https://westhunt.wordpress.com/2016/03/14/medical-prehistory/
What ancient medical treatments worked?

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76878
In some very, very limited conditions, bleeding?
--
Bad for you 99% of the time.

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76947
Colchicine – used to treat gout – discovered by the Ancient Greeks.

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76973
Dracunculiasis (Guinea worm)
Wrap the emerging end of the worm around a stick and slowly pull it out.
(3,500 years later, this remains the standard treatment.)
https://en.wikipedia.org/wiki/Ebers_Papyrus

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76971
Some of the progress is from formal medicine, most is from civil engineering, better nutrition ( ag science and physical chemistry), less crowded housing.

Nurses vs doctors: https://westhunt.wordpress.com/2014/10/01/nurses-vs-doctors/
Medicine, the things that doctors do, was an ineffective pseudoscience until fairly recently. Until 1800 or so, they were wrong about almost everything. Bleeding, cupping, purging, the four humors – useless. In the 1800s, some began to realize that they were wrong, and became medical nihilists that improved outcomes by doing less. Some patients themselves came to this realization, as when Civil War casualties hid from the surgeons and had better outcomes. Sometime in the early 20th century, MDs reached break-even, and became an increasingly positive influence on human health. As Lewis Thomas said, medicine is the youngest science.

Nursing, on the other hand, has always been useful. Just making sure that a patient is warm and nourished when too sick to take care of himself has helped many survive. In fact, some of the truly crushing epidemics have been greatly exacerbated when there were too few healthy people to take care of the sick.

Nursing must be old, but it can’t have existed forever. Whenever it came into existence, it must have changed the selective forces acting on the human immune system. Before nursing, being sufficiently incapacitated would have been uniformly fatal – afterwards, immune responses that involved a period of incapacitation (with eventual recovery) could have been selectively favored.

when MDs broke even: https://westhunt.wordpress.com/2014/10/01/nurses-vs-doctors/#comment-58981
I’d guess the 1930s. Lewis Thomas thought that he was living through big changes. They had a working serum therapy for lobar pneumonia ( antibody-based). They had many new vaccines ( diphtheria in 1923, whopping cough in 1926, BCG and tetanus in 1927, yellow fever in 1935, typhus in 1937.) Vitamins had been mostly worked out. Insulin was discovered in 1929. Blood transfusions. The sulfa drugs, first broad-spectrum antibiotics, showed up in 1935.

DALYs per doctor: https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/
The disability-adjusted life year (DALY) is a measure of overall disease burden – the number of years lost. I’m wondering just much harm premodern medicine did, per doctor. How many healthy years of life did a typical doctor destroy (net) in past times?

...

It looks as if the average doctor (in Western medicine) killed a bunch of people over his career ( when contrasted with doing nothing). In the Charles Manson class.

Eventually the market saw through this illusion. Only took a couple of thousand years.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100741
That a very large part of healthcare spending is done for non-health reasons. He has a chapter on this in his new book, also check out his paper “Showing That You Care: The Evolution of Health Altruism” http://mason.gmu.edu/~rhanson/showcare.pdf
--
I ran into too much stupidity to finish the article. Hanson’s a loon. For example when he talks about the paradox of blacks being more sentenced on drug offenses than whites although they use drugs at similar rate. No paradox: guys go to the big house for dealing, not for using. Where does he live – Mars?

I had the same reaction when Hanson parroted some dipshit anthropologist arguing that the stupid things people do while drunk are due to social expectations, not really the alcohol.
Horseshit.

I don’t think that being totally unable to understand everybody around you necessarily leads to deep insights.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100744
What I’ve wondered is if there was anything that doctors did that actually was helpful and if perhaps that little bit of success helped them fool people into thinking the rest of it helped.
--
Setting bones. extracting arrows: spoon of Diocles. Colchicine for gout. Extracting the Guinea worm. Sometimes they got away with removing the stone. There must be others.
--
Quinine is relatively recent: post-1500. Obstetrical forceps also. Caesarean deliveries were almost always fatal to the mother until fairly recently.

Opium has been around for a long while : it works.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100839
If pre-modern medicine was indeed worse than useless – how do you explain no one noticing that patients who get expensive treatments are worse off than those who didn’t?
--
were worse off. People are kinda dumb – you’ve noticed?
--
My impression is that while people may be “kinda dumb”, ancient customs typically aren’t.
Even if we assume that all people who lived prior to the 19th century were too dumb to make the rational observation, wouldn’t you expect this ancient practice to be subject to selective pressure?
--
Your impression is wrong. Do you think that there some slick reason for Carthaginians incinerating their first-born?

Theodoric of York, bloodletting: https://www.youtube.com/watch?v=yvff3TViXmY

details on blood-letting and hemochromatosis: https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100746

Starting Over: https://westhunt.wordpress.com/2018/01/23/starting-over/
Looking back on it, human health would have … [more]
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august 2017 by nhaliday
Let George Do It | West Hunter
I was thinking about how people would have adapted to local differences in essential micronutrients, stuff like iodine, selenium, manganese, molybdenum, zinc, etc. Australia, for example,  hasn’t had much geological activity in ages and generally has mineral-poor soils. At first I thought that Aboriginals, who have lived in such places for a long time,  might have developed better transporters, etc – ways of eking out scarce trace elements.

Maybe they have, but on second thought, they may not have needed to.  Sure, the Aboriginals were exposed to these conditions for tens of thousands of years, but not nearly as long as kangaroos and wombats have been.  If those animals had effective ways of accumulating the necessary micronutrients,  hunter-gatherers could have solved their problems by consuming local fauna. Let George do it, and then eat George.

The real problems should occur in people who rely heavily on plant foods (European farmers) and in their livestock, which are generally not adapted to the mineral-poor environments. If I’m right, even in areas where sheep without selenium supplements get white muscle disease (nutritional muscular dystrophy), indigenous wildlife should not.
west-hunter  scitariat  discussion  ideas  speculation  sapiens  pop-diff  embodied  metabolic  nutrition  diet  food  farmers-and-foragers  agriculture  nature  tricks  direct-indirect 
august 2017 by nhaliday
Genetic Architectures | West Hunter
Dairy cattle eventually graduate to McDonalds, so there is some interest in the genetics of beef production in dairy breeds. There is course more interest in the genetics of beef production in beef breeds of cattle.

Usually you don’t find a single allele that makes a lot of difference, but in some beef breeds, there are myostatin mutations that result in a ridiculous-looking, ‘double-muscled’ beast. Homozygosity for myostatin mutations causes difficulties in birth, so it takes really strong selection for beef production to make a myostatin null common. I don’t think you ever see this in dairy breeds.

But, as it turns out, there is a deletion that is pretty common in some dairy breeds that significantly increases milk production while killing homozygotes before birth.

Breeds under weaker selection for single traits, your typical cow of the past, probably have neither.

The point is that the genetic architecture of a quantitative trait does not have to be the same in different populations of the same species. For example, I have the impression that height is not as highly polygenic in Pygmies as it is most other human populations. There’s a particular region on chromosome 3 that seems to influence height- you don’t see such a concentration in Europeans.
west-hunter  scitariat  discussion  ideas  speculation  sapiens  pop-diff  genetics  population-genetics  QTL  homo-hetero  analogy  agriculture  nature  food  comparison  embodied  archaics  africa  genomics 
august 2017 by nhaliday
Stolen generations | West Hunter
Someone was quoted as saying that if you adopted an Australian Aborigine kid and raised him in England, he’d do just fine. This is a standard prediction, or maybe really an assumption, of most social scientists: people are the same everywhere. Let me put it more precisely: If you adopted a random draw of such kids just after birth, and then treated them in the same way that local native kids were treated, they’d end up with the same adult IQ, on average. And the same rate of alcoholism, and so forth. Same with any other racial group, the prediction says.

But is this actually true? The same people would say that one-day-old babies from different groups ought to act the same, and that’s certainly not true.

I would think that there was a lot of adoption of Australian Aborigines going on in Australia, back in the day. What were the results?

https://westhunt.wordpress.com/2014/03/15/stolen-generations/#comment-23715
I don’t see how you could spend a lot of time on this (aboriginal education) and not see the pattern in front of you. But people do, certainly in the US as well. Here’s a fun quote: “There is no logical reason to expect that the number of minority students in gifted programs would not be proportional to their representation in the general population. ” (p. 498) Frasier 1997
Of course this never happens, never has happened, but still it’s gotta happen.

This is secondhand, but an interesting story. There was once a graduate student in anthropology at UNM who was very interested in Australian Aboriginal education. I believe that’s what he wanted to do when he got out. He did a lot of digging into the subject, including mimeographed stuff that never got published, and much against his will came to the conclusion that Aboriginals really were different from Europeans, really did have significantly lower intelligence. It drove him nuts – he actually had to be hospitalized. Dropped out of the program.

https://westhunt.wordpress.com/2014/03/15/stolen-generations/#comment-23811
It’s easier than you think. Just threaten the members of the IRB – they generally have no honor.

The long-term effects of American Indian boarding schools: http://marginalrevolution.com/marginalrevolution/2017/09/long-term-effects-american-indian-boarding-schools.html
http://www.sciencedirect.com/science/article/pii/S0304387817300664
Combining recent reservation-level census data and school enrollment data from 1911 to 1932, I find that reservations that sent a larger share of students to off-reservation boarding schools have higher high school graduation rates, higher per capita income, lower poverty rates, a greater proportion of exclusively English speakers, and smaller family sizes. These results are supported when distance to the nearest off-reservation boarding school that subsequently closed is used as an instrument for the proportion of past boarding school students. I conclude with a discussion of the possible reasons for this link.

...

Last, the link drawn here between higher boarding school share and assimilation should not be misinterpreted as an endorsement of coercive assimilation.
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august 2017 by nhaliday
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