nhaliday + bio   442

Comparing within- and between-family polygenic score prediction | bioRxiv
https://twitter.com/StuartJRitchie/status/1116074740475736066
https://archive.is/bQnjM
See this thread for our new study on polygenic scores within fraternal twin pairs! Main point: take extra care with polygenic scores for traits like IQ & education, because they're confounded by (what seem to be) socioeconomic status effects. Not so for traits like height & BMI.
The idea is that the parenting is caused by the parental genotype, so it gets (mis)classified as a genetic effect on the children. It's really another way of looking at "genetic nurture" - see the papers from last year.
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april 2019 by nhaliday
Manifold – man·i·fold /ˈmanəˌfōld/ many and various.
https://infoproc.blogspot.com/2019/01/a-grand-experiment.html
Silicon Valley (Big Tech and startups and VC)
Financial Markets
Academia (Good, Bad, and Ugly)
The View from Europe
The View from Asia (Life in PRC? Fear and Loathing of PRC?)
Frontiers of Science (AI, Genomics, Physics, ...)
Frontiers of Rationality
The Billionaire Life
MMA / UFC
What Millennials think us old folks don't understand
True things that you are not allowed to say
Bubbles that are ready to pop?
Under-appreciated Genius?
Overrated Crap and Frauds?
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march 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]

...

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
Reconsidering epistemological scepticism – Dividuals
I blogged before about how I consider an epistemological scepticism fully compatible with being conservative/reactionary. By epistemological scepticism I mean the worldview where concepts, categories, names, classes aren’t considered real, just useful ways to categorize phenomena, but entirely mental constructs, basically just tools. I think you can call this nominalism as well. The nominalism-realism debate was certainly about this. What follows is the pro-empirical worldview where logic and reasoning is considered highly fallible: hence you don’t think and don’t argue too much, you actually look and check things instead. You rely on experience, not reasoning.

...

Anyhow, the argument is that there are classes, which are indeed artificial, and there are kinds, which are products of natural forces, products of causality.

...

And the deeper – Darwinian – argument, unspoken but obvious, is that any being with a model of reality that does not conform to such real clumps, gets eaten by a grue.

This is impressive. It seems I have to extend my one-variable epistemology to a two-variable epistemology.

My former epistemology was that we generally categorize things according to their uses or dangers for us. So “chair” is – very roughly – defined as “anything we can sit on”. Similarly, we can categorize “predator” as “something that eats us or the animals that are useful for us”.

The unspoken argument against this is that the universe or the biosphere exists neither for us nor against us. A fox can eat your rabbits and a lion can eat you, but they don’t exist just for the sake of making your life difficult.

Hence, if you interpret phenomena only from the viewpoint of their uses or dangers for humans, you get only half the picture right. The other half is what it really is and where it came from.

Copying is everything: https://dividuals.wordpress.com/2015/12/14/copying-is-everything/
Philosophy professor Ruth Millikan’s insight that everything that gets copied from an ancestor has a proper function or teleofunction: it is whatever feature or function that made it and its ancestor selected for copying, in competition with all the other similar copiable things. This would mean Aristotelean teleology is correct within the field of copyable things, replicators, i.e. within biology, although in physics still obviously incorrect.

Darwinian Reactionary drew attention to it two years ago and I still don’t understand why didn’t it generate a bigger buzz. It is an extremely important insight.

I mean, this is what we were waiting for, a proper synthesis of science and philosophy, and a proper way to rescue Aristotelean teleology, which leads to so excellent common-sense predictions that intuitively it cannot be very wrong, yet modern philosophy always denied it.

The result from that is the briding of the fact-value gap and burying the naturalistic fallacy: we CAN derive values from facts: a thing is good if it is well suitable for its natural purpose, teleofunction or proper function, which is the purpose it was selected for and copied for, the purpose and the suitability for the purpose that made the ancestors of this thing selected for copying, instead of all the other potential, similar ancestors.

...

What was humankind selected for? I am afraid, the answer is kind of ugly.

Men were selected to compete between groups, the cooperate within groups largely for coordinating for the sake of this competition, and have a low-key competition inside the groups as well for status and leadership. I am afraid, intelligence is all about organizing elaborate tribal raids: “coalitionary arms races”. The most civilized case, least brutal but still expensive case is arms races in prestige status, not dominance status: when Ancient Athens buildt pretty buildings and modern France built the TGV and America sent a man to the Moon in order to gain “gloire” i.e. the prestige type respect and status amongst the nations, the larger groups of mankind. If you are the type who doesn’t like blood, you should probably focus on these kinds of civilized, prestige-project competitions.

Women were selected for bearing children, for having strong and intelligent sons therefore having these heritable traits themselves (HBD kind of contradicts the more radically anti-woman aspects of RedPillery: marry a weak and stupid but attractive silly-blondie type woman and your son’s won’t be that great either), for pleasuring men and in some rarer but existing cases, to be true companions and helpers of their husbands.

https://en.wikipedia.org/wiki/Four_causes
- Matter: a change or movement's material cause, is the aspect of the change or movement which is determined by the material that composes the moving or changing things. For a table, that might be wood; for a statue, that might be bronze or marble.
- Form: a change or movement's formal cause, is a change or movement caused by the arrangement, shape or appearance of the thing changing or moving. Aristotle says for example that the ratio 2:1, and number in general, is the cause of the octave.
- Agent: a change or movement's efficient or moving cause, consists of things apart from the thing being changed or moved, which interact so as to be an agency of the change or movement. For example, the efficient cause of a table is a carpenter, or a person working as one, and according to Aristotle the efficient cause of a boy is a father.
- End or purpose: a change or movement's final cause, is that for the sake of which a thing is what it is. For a seed, it might be an adult plant. For a sailboat, it might be sailing. For a ball at the top of a ramp, it might be coming to rest at the bottom.

https://en.wikipedia.org/wiki/Proximate_and_ultimate_causation
A proximate cause is an event which is closest to, or immediately responsible for causing, some observed result. This exists in contrast to a higher-level ultimate cause (or distal cause) which is usually thought of as the "real" reason something occurred.

...

- Ultimate causation explains traits in terms of evolutionary forces acting on them.
- Proximate causation explains biological function in terms of immediate physiological or environmental factors.
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july 2018 by nhaliday
WHO | Priority environment and health risks
also: http://www.who.int/heli/risks/vectors/vector/en/

Environmental factors are a root cause of a significant disease burden, particularly in developing countries. An estimated 25% of death and disease globally, and nearly 35% in regions such as sub-Saharan Africa, is linked to environmental hazards. Some key areas of risk include the following:

- Unsafe water, poor sanitation and hygiene kill an estimated 1.7 million people annually, particularly as a result of diarrhoeal disease.
- Indoor smoke from solid fuels kills an estimated 1.6 million people annually due to respiratory diseases.
- Malaria kills over 1.2 million people annually, mostly African children under the age of five. Poorly designed irrigation and water systems, inadequate housing, poor waste disposal and water storage, deforestation and loss of biodiversity, all may be contributing factors to the most common vector-borne diseases including malaria, dengue and leishmaniasis.
- Urban air pollution generated by vehicles, industries and energy production kills approximately 800 000 people annually.
- Unintentional acute poisonings kill 355 000 people globally each year. In developing countries, where two-thirds of these deaths occur, such poisonings are associated strongly with excessive exposure to, and inappropriate use of, toxic chemicals and pesticides present in occupational and/or domestic environments.
- Climate change impacts including more extreme weather events, changed patterns of disease and effects on agricultural production, are estimated to cause over 150 000 deaths annually.

ed.:
Note the high point at human origin (Africa, Middle East) and Asia. Low points in New World and Europe/Russia. Probably key factor in explaining human psychological variation (Haidt axes, individualism-collectivism, kinship structure, etc.). E.g., compare Islam/Judaism (circumcision, food preparation/hygiene rules) and Christianity (orthodoxy more than orthopraxy, no arbitrary practices for group-marking).

I wonder if the dietary and hygiene laws of Christianity get up-regulated in higher parasite load places (the US South, Middle Eastern Christianity, etc.)?

Also the reason for this variation probably basically boils down how long local microbes have had time to adapt to the human immune system.

obv. correlation: https://pinboard.in/u:nhaliday/b:074ecdf30c50

Tropical disease: https://en.wikipedia.org/wiki/Tropical_disease
Tropical diseases are diseases that are prevalent in or unique to tropical and subtropical regions.[1] The diseases are less prevalent in temperate climates, due in part to the occurrence of a cold season, which controls the insect population by forcing hibernation. However, many were present in northern Europe and northern America in the 17th and 18th centuries before modern understanding of disease causation. The initial impetus for tropical medicine was to protect the health of colonialists, notably in India under the British Raj.[2] Insects such as mosquitoes and flies are by far the most common disease carrier, or vector. These insects may carry a parasite, bacterium or virus that is infectious to humans and animals. Most often disease is transmitted by an insect "bite", which causes transmission of the infectious agent through subcutaneous blood exchange. Vaccines are not available for most of the diseases listed here, and many do not have cures.

cf. Galton: https://pinboard.in/u:nhaliday/b:f72f8e03e729
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july 2018 by nhaliday
Does left-handedness occur more in certain ethnic groups than others?
Yes. There are some aboriginal tribes in Australia who have about 70% of their population being left-handed. It’s also more than 50% for some South American tribes.

The reason is the same in both cases: a recent past of extreme aggression with other tribes. Left-handedness is caused by recessive genes, but being left-handed is a boost when in hand-to-hand combat with a right-handed guy (who usually has trained extensively with other right-handed guys, as this disposition is genetically dominant so right-handed are majority in most human populations, so lacks experience with a left-handed). Should a particular tribe enter too much war time periods, it’s proportion of left-handeds will naturally rise. As their enemy tribe’s proportion of left-handed people is rising as well, there’s a point at which the natural advantage they get in fighting disipates and can only climb higher should they continuously find new groups to fight with, who are also majority right-handed.

...

So the natural question is: given their advantages in 1-on-1 combat, why doesn’t the percentage grow all the way up to 50% or slightly higher? Because there are COSTS associated with being left-handed, as apparently our neural network is pre-wired towards right-handedness - showing as a reduced life expectancy for lefties. So a mathematical model was proposed to explain their distribution among different societies

THE FIGHTING HYPOTHESIS: STABILITY OF POLYMORPHISM IN HUMAN HANDEDNESS

http://gepv.univ-lille1.fr/downl...

Further, it appears the average left-handedness for humans (~10%) hasn’t changed in thousands of years (judging by the paintings of hands on caves)

Frequency-dependent maintenance of left handedness in humans.

Handedness frequency over more than 10,000 years

[ed.: Compare with Julius Evola's "left-hand path".]
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july 2018 by nhaliday
Theory of Self-Reproducing Automata - John von Neumann
Fourth Lecture: THE ROLE OF HIGH AND OF EXTREMELY HIGH COMPLICATION

Comparisons between computing machines and the nervous systems. Estimates of size for computing machines, present and near future.

Estimates for size for the human central nervous system. Excursus about the “mixed” character of living organisms. Analog and digital elements. Observations about the “mixed” character of all componentry, artificial as well as natural. Interpretation of the position to be taken with respect to these.

Evaluation of the discrepancy in size between artificial and natural automata. Interpretation of this discrepancy in terms of physical factors. Nature of the materials used.

The probability of the presence of other intellectual factors. The role of complication and the theoretical penetration that it requires.

Questions of reliability and errors reconsidered. Probability of individual errors and length of procedure. Typical lengths of procedure for computing machines and for living organisms--that is, for artificial and for natural automata. Upper limits on acceptable probability of error in individual operations. Compensation by checking and self-correcting features.

Differences of principle in the way in which errors are dealt with in artificial and in natural automata. The “single error” principle in artificial automata. Crudeness of our approach in this case, due to the lack of adequate theory. More sophisticated treatment of this problem in natural automata: The role of the autonomy of parts. Connections between this autonomy and evolution.

- 10^10 neurons in brain, 10^4 vacuum tubes in largest computer at time
- machines faster: 5 ms from neuron potential to neuron potential, 10^-3 ms for vacuum tubes

https://en.wikipedia.org/wiki/John_von_Neumann#Computing
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april 2018 by nhaliday
High male sexual investment as a driver of extinction in fossil ostracods | Nature
Sexual selection favours traits that confer advantages in the competition for mates. In many cases, such traits are costly to produce and maintain, because the costs help to enforce the honesty of these signals and cues1. Some evolutionary models predict that sexual selection also produces costs at the population level, which could limit the ability of populations to adapt to changing conditions and thus increase the risk of extinction2,3,4.
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april 2018 by nhaliday
Is the human brain analog or digital? - Quora
The brain is neither analog nor digital, but works using a signal processing paradigm that has some properties in common with both.
 
Unlike a digital computer, the brain does not use binary logic or binary addressable memory, and it does not perform binary arithmetic. Information in the brain is represented in terms of statistical approximations and estimations rather than exact values. The brain is also non-deterministic and cannot replay instruction sequences with error-free precision. So in all these ways, the brain is definitely not "digital".
 
At the same time, the signals sent around the brain are "either-or" states that are similar to binary. A neuron fires or it does not. These all-or-nothing pulses are the basic language of the brain. So in this sense, the brain is computing using something like binary signals. Instead of 1s and 0s, or "on" and "off", the brain uses "spike" or "no spike" (referring to the firing of a neuron).
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april 2018 by nhaliday
The first ethical revolution – Gene Expression
Fifty years ago Julian Jaynes published The Origin of Consciousness in the Breakdown of the Bicameral Mind. Seventy years ago Karl Jaspers introduced the concept of the Axial Age. Both point to the same dynamic historically.

Something happened in the centuries around 500 BCE all around the world. Great religions and philosophies arose. The Indian religious traditions, the Chinese philosophical-political ones, and the roots of what we can recognize as Judaism. In Greece, the precursors of many modern philosophical streams emerged formally, along with a variety of political systems.

The next few centuries saw some more innovation. Rabbinical Judaism transformed a ritualistic tribal religion into an ethical one, and Christianity universalized Jewish religious thought, as well as infusing it with Greek systematic concepts. Meanwhile, Indian and Chinese thought continued to evolve, often due to interactions each other (it is hard to imagine certain later developments in Confucianism without the Buddhist stimulus). Finally, in the 7th century, Islam emerges as the last great world religion.

...

Living in large complex societies with social stratification posed challenges. A religion such as Christianity was not a coincidence, something of its broad outlines may have been inevitable. Universal, portable, ethical, and infused with transcendence and coherency. Similarly, god-kings seem to have universally transformed themselves into the human who binds heaven to earth in some fashion.

The second wave of social-ethical transformation occurred in the early modern period, starting in Europe. My own opinion is that economic growth triggered by innovation and gains in productivity unleashed constraints which had dampened further transformations in the domain of ethics. But the new developments ultimately were simply extensions and modifications on the earlier “source code” (e.g., whereas for nearly two thousand years Christianity had had to make peace with the existence of slavery, in the 19th century anti-slavery activists began marshaling Christian language against the institution).
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april 2018 by nhaliday
Ultimate fate of the universe - Wikipedia
The fate of the universe is determined by its density. The preponderance of evidence to date, based on measurements of the rate of expansion and the mass density, favors a universe that will continue to expand indefinitely, resulting in the "Big Freeze" scenario below.[8] However, observations are not conclusive, and alternative models are still possible.[9]

Big Freeze or heat death
Main articles: Future of an expanding universe and Heat death of the universe
The Big Freeze is a scenario under which continued expansion results in a universe that asymptotically approaches absolute zero temperature.[10] This scenario, in combination with the Big Rip scenario, is currently gaining ground as the most important hypothesis.[11] It could, in the absence of dark energy, occur only under a flat or hyperbolic geometry. With a positive cosmological constant, it could also occur in a closed universe. In this scenario, stars are expected to form normally for 1012 to 1014 (1–100 trillion) years, but eventually the supply of gas needed for star formation will be exhausted. As existing stars run out of fuel and cease to shine, the universe will slowly and inexorably grow darker. Eventually black holes will dominate the universe, which themselves will disappear over time as they emit Hawking radiation.[12] Over infinite time, there would be a spontaneous entropy decrease by the Poincaré recurrence theorem, thermal fluctuations,[13][14] and the fluctuation theorem.[15][16]

A related scenario is heat death, which states that the universe goes to a state of maximum entropy in which everything is evenly distributed and there are no gradients—which are needed to sustain information processing, one form of which is life. The heat death scenario is compatible with any of the three spatial models, but requires that the universe reach an eventual temperature minimum.[17]
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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
Baldwin effect - Wikipedia
If animals entered a new environment—or their old environment rapidly changed—those that could flexibly respond by learning new behaviors or by ontogenetically adapting would be naturally preserved. This saved remnant would, over several generations, have the opportunity to exhibit spontaneously congenital variations similar to their acquired traits and have these variations naturally selected. It would look as though the acquired traits had sunk into the hereditary substance in a Lamarckian fashion, but the process would really be neo-Darwinian.

Selected offspring would tend to have an increased capacity for learning new skills rather than being confined to genetically coded, relatively fixed abilities. In effect, it places emphasis on the fact that the sustained behavior of a species or group can shape the evolution of that species. The "Baldwin effect" is better understood in evolutionary developmental biology literature as a scenario in which a character or trait change occurring in an organism as a result of its interaction with its environment becomes gradually assimilated into its developmental genetic or epigenetic repertoire (Simpson, 1953; Newman, 2002). In the words of Daniel Dennett,[2]

Thanks to the Baldwin effect, species can be said to pretest the efficacy of particular different designs by phenotypic (individual) exploration of the space of nearby possibilities. If a particularly winning setting is thereby discovered, this discovery will create a new selection pressure: organisms that are closer in the adaptive landscape to that discovery will have a clear advantage over those more distant.

An update to the Baldwin Effect was developed by Jean Piaget, Paul Weiss, and Conrad Waddington in the 1960s–1970s. This new version included an explicit role for the social in shaping subsequent natural change in humans (both evolutionary and developmental), with reference to alterations of selection pressures.[3]

...

Suppose a species is threatened by a new predator and there is a behavior that makes it more difficult for the predator to kill individuals of the species. Individuals who learn the behavior more quickly will obviously be at an advantage. As time goes on, the ability to learn the behavior will improve (by genetic selection), and at some point it will seem to be an instinct.
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march 2018 by nhaliday
Antinomia Imediata – experiments in a reaction from the left
https://antinomiaimediata.wordpress.com/lrx/
So, what is the Left Reaction? First of all, it’s reaction: opposition to the modern rationalist establishment, the Cathedral. It opposes the universalist Jacobin program of global government, favoring a fractured geopolitics organized through long-evolved complex systems. It’s profoundly anti-socialist and anti-communist, favoring market economy and individualism. It abhors tribalism and seeks a realistic plan for dismantling it (primarily informed by HBD and HBE). It looks at modernity as a degenerative ratchet, whose only way out is intensification (hence clinging to crypto-marxist market-driven acceleration).

How come can any of this still be in the *Left*? It defends equality of power, i.e. freedom. This radical understanding of liberty is deeply rooted in leftist tradition and has been consistently abhored by the Right. LRx is not democrat, is not socialist, is not progressist and is not even liberal (in its current, American use). But it defends equality of power. It’s utopia is individual sovereignty. It’s method is paleo-agorism. The anti-hierarchy of hunter-gatherer nomads is its understanding of the only realistic objective of equality.

...

In more cosmic terms, it seeks only to fulfill the Revolution’s side in the left-right intelligence pump: mutation or creation of paths. Proudhon’s antinomy is essentially about this: the collective force of the socius, evinced in moral standards and social organization vs the creative force of the individuals, that constantly revolutionize and disrupt the social body. The interplay of these forces create reality (it’s a metaphysics indeed): the Absolute (socius) builds so that the (individualistic) Revolution can destroy so that the Absolute may adapt, and then repeat. The good old formula of ‘solve et coagula’.

Ultimately, if the Neoreaction promises eternal hell, the LRx sneers “but Satan is with us”.

https://antinomiaimediata.wordpress.com/2016/12/16/a-statement-of-principles/
Liberty is to be understood as the ability and right of all sentient beings to dispose of their persons and the fruits of their labor, and nothing else, as they see fit. This stems from their self-awareness and their ability to control and choose the content of their actions.

...

Equality is to be understood as the state of no imbalance of power, that is, of no subjection to another sentient being. This stems from their universal ability for empathy, and from their equal ability for reason.

...

It is important to notice that, contrary to usual statements of these two principles, my standpoint is that Liberty and Equality here are not merely compatible, meaning they could coexist in some possible universe, but rather they are two sides of the same coin, complementary and interdependent. There can be NO Liberty where there is no Equality, for the imbalance of power, the state of subjection, will render sentient beings unable to dispose of their persons and the fruits of their labor[1], and it will limit their ability to choose over their rightful jurisdiction. Likewise, there can be NO Equality without Liberty, for restraining sentient beings’ ability to choose and dispose of their persons and fruits of labor will render some more powerful than the rest, and establish a state of subjection.

https://antinomiaimediata.wordpress.com/2017/04/18/flatness/
equality is the founding principle (and ultimately indistinguishable from) freedom. of course, it’s only in one specific sense of “equality” that this sentence is true.

to try and eliminate the bullshit, let’s turn to networks again:

any nodes’ degrees of freedom is the number of nodes they are connected to in a network. freedom is maximum when the network is symmetrically connected, i. e., when all nodes are connected to each other and thus there is no topographical hierarchy (middlemen) – in other words, flatness.

in this understanding, the maximization of freedom is the maximization of entropy production, that is, of intelligence. As Land puts it:

https://antinomiaimediata.wordpress.com/category/philosophy/mutualism/
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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
Altruism in a volatile world | Nature
The evolution of altruism—costly self-sacrifice in the service of others—has puzzled biologists1 since The Origin of Species. For half a century, attempts to understand altruism have developed around the concept that altruists may help relatives to have extra offspring in order to spread shared genes2. This theory—known as inclusive fitness—is founded on a simple inequality termed Hamilton’s rule2. However, explanations of altruism have typically not considered the stochasticity of natural environments, which will not necessarily favour genotypes that produce the greatest average reproductive success3,4. Moreover, empirical data across many taxa reveal associations between altruism and environmental stochasticity5,6,7,8, a pattern not predicted by standard interpretations of Hamilton’s rule. Here we derive Hamilton’s rule with explicit stochasticity, leading to new predictions about the evolution of altruism. We show that altruists can increase the long-term success of their genotype by reducing the temporal variability in the number of offspring produced by their relatives. Consequently, costly altruism can evolve even if it has a net negative effect on the average reproductive success of related recipients. The selective pressure on volatility-suppressing altruism is proportional to the coefficient of variation in population fitness, and is therefore diminished by its own success. Our results formalize the hitherto elusive link between bet-hedging and altruism4,9,10,11, and reveal missing fitness effects in the evolution of animal societies.
study  bio  evolution  altruism  kinship  stylized-facts  models  intricacy  random  signal-noise  time  order-disorder  org:nat  EGT  cooperate-defect  population-genetics  moments  expectancy  multiplicative  additive 
march 2018 by nhaliday
Plague of Frogs | West Hunter
For a few years the herpetologists were concerned yet happy. Concerned, because many frog populations were crashing and some were going extinct. Happy, because confused puppies in Washington were giving them money, something that hardly ever happens to frogmen. The theory was that amphibians were ‘canaries in a coal mine’, uniquely sensitive to environmental degradation.

...

It took some time for herpetologists to admit that this chytrid fungus is the main culprit – some are still resisting. First, it was a lot like how doctors resisted Semmelweiss’ discoveries about the cause of puerperal fever – since doctors were the main method of transmission. How did this fungus get to the cloud forests of Costa Rica? On the boots of herpetologists, of course.

The second problem is Occam’s butterknife: even though this chytrid fungus is the main culprit, it’s just got to be more complicated than that. Even if it isn’t. People in the life sciences – biology and medicine – routinely reject simple hypotheses that do a good job of explaining the data for more complex hypotheses that don’t. College taught them to think – unwisely.
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february 2018 by nhaliday
Why Sex? And why only in Pairs? - Marginal REVOLUTION
The core conclusion is that mutations continue to rise with the number of sex-participating partners, but in simple Red Queen models the limiting features of the genotypes is the same whether there are two, three, or more partners.

Men Are Animals: http://www.overcomingbias.com/2018/06/men-are-animals.html
I agree with all the comments citing motility/sessility.
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january 2018 by nhaliday
Anisogamy - Wikipedia
Anisogamy is a fundamental concept of sexual dimorphism that helps explain phenotypic differences between sexes.[3] In most species a male and female sex exist, both of which are optimized for reproductive potential. Due to their differently sized and shaped gametes, both males and females have developed physiological and behavioral differences that optimize the individual’s fecundity.[3] Since most egg laying females typically must bear the offspring and have a more limited reproductive cycle, this typically makes females a limiting factor in the reproductive success rate of males in a species. This process is also true for females selecting males, and assuming that males and females are selecting for different traits in partners, would result in phenotypic differences between the sexes over many generations. This hypothesis, known as the Bateman’s Principle, is used to understand the evolutionary pressures put on males and females due to anisogamy.[4] Although this assumption has criticism, it is a generally accepted model for sexual selection within anisogamous species. The selection for different traits depending on sex within the same species is known as sex-specific selection, and accounts for the differing phenotypes found between the sexes of the same species. This sex-specific selection between sexes over time also lead to the development of secondary sex characteristics, which assist males and females in reproductive success.

...

Since this process is very energy-demanding and time consuming for the female, mate choice is often integrated into the female’s behavior.[3] Females will often be very selective of the males they choose to reproduce with, for the phenotype of the male can be indicative of the male’s physical health and heritable traits. Females employ mate choice to pressure males into displaying their desirable traits to females through courtship, and if successful, the male gets to reproduce. This encourages males and females of specific species to invest in courtship behaviors as well as traits that can display physical health to a potential mate. This process, known as sexual selection,[3] results in the development of traits to ease reproductive success rather than individual survival, such as the inflated size of a termite queen. It is also important for females to select against potential mates that may have a sexually transmitted infection, for the disease could not only hurt the female’s reproductive ability, but also damage the resulting offspring.[7]

Although not uncommon in males, females are more associated with parental care.[8] Since females are on a more limited reproductive schedule than males, a female often invests more in protecting the offspring to sexual maturity than the male. Like mate choice, the level of parental care varies greatly between species, and is often dependent on the number of offspring produced per sexual encounter.[8]

...

Since females are often the limiting factor in a species reproductive success, males are often expected by the females to search and compete for the female, known as intraspecific competition.[4] This can be seen in organisms such as bean beetles, as the male that searches for females more frequently is often more successful at finding mates and reproducing. In species undergoing this form of selection, a fit male would be one that is fast, has more refined sensory organs, and spatial awareness.[4]

Darwinian sex roles confirmed across the animal kingdom: http://advances.sciencemag.org/content/2/2/e1500983.full
Since Darwin’s conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental factors or chance. We demonstrate that, across the animal kingdom, sexual selection, as captured by standard Bateman metrics, is indeed stronger in males than in females and that it is evolutionarily tied to sex biases in parental care and sexual dimorphism. Our findings provide the first comprehensive evidence that Darwin’s concept of conventional sex roles is accurate and refute recent criticism of sexual selection theory.

Coevolution of parental investment and sexually selected traits drives sex-role divergence: https://www.nature.com/articles/ncomms12517
Sex-role evolution theory attempts to explain the origin and direction of male–female differences. A fundamental question is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in subsequent parental care. Here we construct models to confirm predictions that individuals benefit less from caring when they face stronger sexual selection and/or lower certainty of parentage. However, we overturn the widely cited claim that a negative feedback between the operational sex ratio and the opportunity cost of care selects for egalitarian sex roles. We further argue that our model does not predict any effect of the adult sex ratio (ASR) that is independent of the source of ASR variation. Finally, to increase realism and unify earlier models, we allow for coevolution between parental investment and investment in sexually selected traits. Our model confirms that small initial differences in parental investment tend to increase due to positive evolutionary feedback, formally supporting long-standing, but unsubstantiated, verbal arguments.

Parental investment, sexual selection and sex ratios: http://www.kokkonuts.org/wp-content/uploads/Parental_investment_review.pdf
The second argument takes the reasonable premise that anisogamy produces a male-biased operational sex ratio (OSR) leading to males competing for mates. Male care is then predicted to be less likely to evolve as it consumes resources that could otherwise be used to increase competitiveness. However, given each offspring has precisely two genetic parents (the Fisher condition), a biased OSR generates frequency-dependent selection, analogous to Fisherian sex ratio selection, that favours increased parental investment by whichever sex faces more intense competition. Sex role divergence is therefore still an evolutionary conundrum. Here we review some possible solutions. Factors that promote conventional sex roles are sexual selection on males (but non-random variance in male mating success must be high to override the Fisher condition), loss of paternity because of female multiple mating or group spawning and patterns of mortality that generate female-biased adult sex ratios (ASR). We present an integrative model that shows how these factors interact to generate sex roles. We emphasize the need to distinguish between the ASR and the operational sex ratio (OSR). If mortality is higher when caring than competing this diminishes the likelihood of sex role divergence because this strongly limits the mating success of the earlier deserting sex. We illustrate this in a model where a change in relative mortality rates while caring and competing generates a shift from a mammalian type breeding system (female-only care, male-biased OSR and female-biased ASR) to an avian type system (biparental care and a male-biased OSR and ASR).

LATE FEMINISM: https://jacobitemag.com/2017/08/01/late-feminism/
Woman has had a good run. For 200,000 years humankind’s anisogamous better (and bigger) half has enjoyed a position of desirability and safety befitting a scarce commodity. She has also piloted the evolutionary destiny of our species, both as a sexual selector and an agitator during man’s Promethean journey. In terms of comfort and agency, the human female is uniquely privileged within the annals of terrestrial biology.

But the era of female privilege is ending, in a steady decline that began around 1572. Woman’s biological niche is being crowded out by capital.

...

Strictly speaking, the breadth of the coming changes extend beyond even civilizational dynamics. They will affect things that are prior. One of the oldest and most practical definitions for a biological species defines its boundary as the largest group of organisms where two individuals, via sexual reproduction, can produce fertile offspring together. The imminent arrival of new reproductive technologies will render the sexual reproduction criteria either irrelevant or massively expanded, depending upon one’s perspective. Fertility of the offspring is similarly of limited relevance, since the modification of gametes will be de rigueur in any case. What this looming technology heralds is less a social revolution than it is a full sympatric speciation event.

Accepting the inevitability of the coming bespoke reproductive revolution, consider a few questions & probable answers regarding our external-womb-grown ubermenschen:

Q: What traits will be selected for?

A: Ability to thrive in a global market economy (i.e. ability to generate value for capital.)

Q: What material substrate will generate the new genomes?

A: Capital equipment.

Q: Who will be making the selection?

A: People, at least initially, (and who coincidentally will be making decisions that map 1-to-1 to the interests of capital.)

_Replace any of the above instances of the word capital with women, and you would have accurate answers for most of our species’ history._

...

In terms of pure informational content, the supernova seen from earth can be represented in a singularly compressed way: a flash of light on a black field where there previously was none. A single photon in the cone of the eye, at the limit. Whether … [more]
biodet  deep-materialism  new-religion  evolution  eden  gender  gender-diff  concept  jargon  wiki  reference  bio  roots  explanans  🌞  ideas  EGT  sex  analysis  things  phalanges  matching  parenting  water  competition  egalitarianism-hierarchy  ranking  multi  study  org:nat  nature  meta-analysis  survey  solid-study  male-variability  darwinian  empirical  realness  sapiens  models  evopsych  legacy  investing  uncertainty  outcome-risk  decision-theory  pdf  life-history  chart  accelerationism  horror  capital  capitalism  similarity  analogy  land  gnon  🐸  europe  the-great-west-whale  industrial-revolution  science  kinship  n-factor  speculation  personality  creative  pop-diff  curiosity  altruism  cooperate-defect  anthropology  cultural-dynamics  civil-liberty  recent-selection  technocracy  frontier  futurism  prediction  quotes  aphorism  religion  theos  enhancement  biotech  revolution  insight  history  early-modern  gallic  philosophy  enlightenment-renaissance-restoration-reformation  ci 
january 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
Sacred text as cultural genome: an inheritance mechanism and method for studying cultural evolution: Religion, Brain & Behavior: Vol 7, No 3
Yasha M. Hartberg & David Sloan Wilson

Any process of evolution requires a mechanism of inheritance for the transmission of information across generations and the expression of phenotypes during each generation. Genetic inheritance mechanisms have been studied for over a century but mechanisms of inheritance for human cultural evolution are far less well understood. Sacred religious texts have the properties required for an inheritance system. They are replicated across generations with high fidelity and are transcribed into action every generation by the invocation and interpretation of selected passages. In this article we borrow concepts and methods from genetics and epigenetics to study the “expressed phenotypes” of six Christian churches that differ along a conservative–progressive axis. Their phenotypic differences, despite drawing upon the same sacred text, can be explained in part by differential expression of the sacred text. Since the invocation and interpretation of sacred texts are often well preserved, our methods allow the expressed phenotypes of religious groups to be studied at any time and place in history.
study  interdisciplinary  bio  sociology  cultural-dynamics  anthropology  religion  christianity  theos  protestant-catholic  politics  ideology  correlation  organizing  institutions  analogy  genetics  genomics  epigenetics  comparison  culture  pdf  piracy  density  flexibility  noble-lie  deep-materialism  new-religion  universalism-particularism  homo-hetero  hypocrisy  group-selection  models  coordination  info-dynamics  evolution  impact  left-wing  right-wing  time  tradition  spreading  sanctity-degradation  coalitions  trees  usa  social-capital  hari-seldon  wisdom  the-basilisk  frequency  sociality  ecology  analytical-holistic 
january 2018 by nhaliday
A genetic map of the world – Gene Expression
The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.
gnxp  scitariat  commentary  bio  preprint  study  summary  genetics  genomics  pic  data  maps  visualization  stock-flow  gene-flow  walls  world  africa  europe  MENA  india  asia  china  japan  korea  anglo  developing-world  russia  sapiens  gavisti  population-genetics  geography  🌞  mediterranean  britain  oceans  race  tribalism 
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
Open Thread, 11/26/2017 – Gene Expression
A few days ago there was a Twitter thing about top five books that have influenced you. It’s hard for me to name five, but I put three books down for three different reasons:

- Principles of Population Genetics, because it gives you a model for how to analyze and understand evolutionary processes. There are other books out there besides Principles of Population Genetics. But if you buy this book you don’t need to buy another (at SMBE this year I confused Andy Clark with Mike Lynch for a second when introducing myself. #awkward)
- The Fall of Rome. A lot of historical writing can be tendentious. I’ve also noticed an unfortunate tendency of historians dropping into contemporary arguments and pretty much lying through omission or elision to support their political side (it usually goes “actually, I’m a specialist in this topic and my side is 100% correct because of obscure-stuff where I’m shading the facts”). The Fall of Rome illustrates the solidity that an archaeological and materialist take can give the field. This sort of materialism isn’t the final word, but it needs to be the start of the conversation.
- From Dawn to Decadence: 1500 to the Present: 500 Years of Western Cultural Life. To know things is important in and of itself. My own personal experience is that the returns to knowing things in a particular domain or area do not exhibit a linear return. Rather, it exhibits a logistic curve. Initially, it’s hard to make sense of anything from the facts, but at some point comprehension and insight increase rapidly, until you reach the plateau of diminishing marginal returns.

If you haven’t, I recommend you subscribe to Patrick Wyman’s Tides of History podcast. I pretty much wait now for every new episode.
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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
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
SEXUAL DIMORPHISM, SEXUAL SELECTION, AND ADAPTATION IN POLYGENIC CHARACTERS - Lande - 1980 - Evolution - Wiley Online Library
https://twitter.com/gcochran99/status/970758341990367232
https://archive.is/mcKvr
Lol, that's nothing, my biology teacher in high school told me sex differences couldn't evolve since all of us inherit 50% of genes from parents of both sexes. Being a raucous hispanic kid I burst out laughing, she was not pleased
--
Sex differences actually evolve more slowly because of that: something like 80 times more slowly.
...
Doesn't have that number, but in the same ballpark.

Sexual Dimorphism, Sexual Selection, And Adaptation In Polygenic Characters

Russell Lande

https://twitter.com/gcochran99/status/999189778867208193
https://archive.is/AR8FY
I believe it, because sex differences [ in cases where the trait is not sex-limited ] evolve far more slowly than other things, on the order of 100 times more slowly. Lande 1980: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1980.tb04817.x

The deep past has a big vote in such cases.
...
as for the extent that women were voluntarily choosing mates 20k years ago, or 100k years ago - I surely don't know.

other time mentioned: https://pinboard.in/u:nhaliday/b:3a7c5b42dd50
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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.
article  essay  org:nat  🌞  bio  biodet  genetics  genomics  mutation  genetic-load  QTL  evolution  sapiens  survey  summary  coding-theory  enhancement  signal-noise  egalitarianism-hierarchy  selection  tradeoffs  immune  recent-selection  perturbation  nibble  ideas  forms-instances 
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.
west-hunter  scitariat  ideas  speculation  discussion  parasites-microbiome  spreading  disease  scale  population  density  bio  nature  long-short-run  nihil  equilibrium  death  unintended-consequences  red-queen  tradeoffs  cost-benefit  gedanken 
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
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
Genetics: CHROMOSOMAL MAPS AND MAPPING FUNCTIONS
Any particular gene has a specific location (its "locus") on a particular chromosome. For any two genes (or loci) alpha and beta, we can ask "What is the recombination frequency between them?" If the genes are on different chromosomes, the answer is 50% (independent assortment). If the two genes are on the same chromosome, the recombination frequency will be somewhere in the range from 0 to 50%. The "map unit" (1 cM) is the genetic map distance that corresponds to a recombination frequency of 1%. In large chromosomes, the cumulative map distance may be much greater than 50cM, but the maximum recombination frequency is 50%. Why? In large chromosomes, there is enough length to allow for multiple cross-overs, so we have to ask what result we expect for random multiple cross-overs.

1. How is it that random multiple cross-overs give the same result as independent assortment?

Figure 5.12 shows how the various double cross-over possibilities add up, resulting in gamete genotype percentages that are indistinguisable from independent assortment (50% parental type, 50% non-parental type). This is a very important figure. It provides the explanation for why genes that are far apart on a very large chromosome sort out in crosses just as if they were on separate chromosomes.

2. Is there a way to measure how close together two crossovers can occur involving the same two chromatids? That is, how could we measure whether there is spacial "interference"?

Figure 5.13 shows how a measurement of the gamete frequencies resulting from a "three point cross" can answer this question. If we would get a "lower than expected" occurrence of recombinant genotypes aCb and AcB, it would suggest that there is some hindrance to the two cross-overs occurring this close together. Crosses of this type in Drosophila have shown that, in this organism, double cross-overs do not occur at distances of less than about 10 cM between the two cross-over sites. ( Textbook, page 196. )

3. How does all of this lead to the "mapping function", the mathematical (graphical) relation between the observed recombination frequency (percent non-parental gametes) and the cumulative genetic distance in map units?

Figure 5.14 shows the result for the two extremes of "complete interference" and "no interference". The situation for real chromosomes in real organisms is somewhere between these extremes, such as the curve labelled "interference decreasing with distance".
org:junk  org:edu  explanation  faq  nibble  genetics  genomics  bio  ground-up  magnitude  data  flux-stasis  homo-hetero  measure  orders  metric-space  limits  measurement 
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
Testing the moderation of quantitative gene by environment interactions in unrelated individuals | bioRxiv
We use simulation to estimate the accuracy, power, and type I error rates of our method and to gauge its computational performance, and then apply this method to IQ data measured on 40,172 individuals with whole-genome SNP data from the UK Biobank. We found that the additive genetic variation of IQ tagged by SNPs increases as socioeconomic status (SES) decreases, opposite the direction found by several twin studies conducted in the U.S. on adolescents, but consistent with several studies from Europe and Australia on adults.
study  bio  preprint  biodet  behavioral-gen  genetics  GxE  class  iq  britain  environmental-effects  regularizer  variance-components  correlation  s-factor 
september 2017 by nhaliday
Accurate Genomic Prediction Of Human Height | bioRxiv
Stephen Hsu's compressed sensing application paper

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correlate ~0.65 with actual height; actual heights of most individuals in validation samples are within a few cm of the prediction.

https://infoproc.blogspot.com/2017/09/accurate-genomic-prediction-of-human.html

http://infoproc.blogspot.com/2017/11/23andme.html
I'm in Mountain View to give a talk at 23andMe. Their latest funding round was $250M on a (reported) valuation of $1.5B. If I just add up the Crunchbase numbers it looks like almost half a billion invested at this point...

Slides: Genomic Prediction of Complex Traits

Here's how people + robots handle your spit sample to produce a SNP genotype:

https://drive.google.com/file/d/1e_zuIPJr1hgQupYAxkcbgEVxmrDHAYRj/view
study  bio  preprint  GWAS  state-of-art  embodied  genetics  genomics  compressed-sensing  high-dimension  machine-learning  missing-heritability  hsu  scitariat  education  🌞  frontier  britain  regression  data  visualization  correlation  phase-transition  multi  commentary  summary  pdf  slides  brands  skunkworks  hard-tech  presentation  talks  methodology  intricacy  bioinformatics  scaling-up  stat-power  sparsity  norms  nibble  speedometer  stats  linear-models  2017  biodet 
september 2017 by nhaliday
Global determinants of navigation ability | bioRxiv
Using a mobile-based virtual reality navigation task, we measured spatial navigation ability in more than 2.5 million people globally. Using a clustering approach, we find that navigation ability is not smoothly distributed globally but clustered into five distinct yet geographically related groups of countries. Furthermore, the economic wealth of a nation (Gross Domestic Product per capita) was predictive of the average navigation ability of its inhabitants and gender inequality (Gender Gap Index) was predictive of the size of performance difference between males and females.

- Figure 1 has the meat
- gender gap larger in richer/better-performing countries
- Anglo and Nordic countries do best (Finnish supremacy wins the day again)
- surprised China doesn't do better, probably a matter of development
- Singapore is close behind the Anglo-Nords tho
- speculation that practice of orienteering (originally Swedish) may be related to Nords doing well
- somewhat weird pattern wrt age
study  bio  preprint  psychology  cog-psych  iq  psychometrics  spatial  navigation  pop-diff  gender  gender-diff  egalitarianism-hierarchy  correlation  wealth  wealth-of-nations  econ-metrics  data  visualization  maps  world  developing-world  marginal  europe  the-great-west-whale  nordic  britain  anglo  usa  anglosphere  china  asia  sinosphere  polis  demographics  age-generation  aging  EU  group-level  regional-scatter-plots  games  simulation 
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.
west-hunter  scitariat  discussion  ideas  rant  speculation  prediction  government  dirty-hands  space  xenobio  oceans  fluid  thermo  phys-energy  temperature  no-go  volo-avolo  physics  equilibrium  street-fighting  nibble  error  track-record  usa  bio  eden  cybernetics  complex-systems 
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.
west-hunter  scitariat  discussion  ideas  speculation  domestication  nature  egalitarianism-hierarchy  multi  genomics  recent-selection  genetics  biodet  behavioral-gen  ecology  EGT  strategy  gavisti  theory-practice  bio  paying-rent  being-right  elite  europe  antiquity  migration  conquest-empire  consilience  explanans 
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.
west-hunter  scitariat  discussion  ideas  reflection  analogy  model-organism  bio  disease  parasites-microbiome  medicine  epidemiology  heuristic  thick-thin  stories  experiment  track-record  intricacy  gotchas  low-hanging  🌞  patience  complex-systems  meta:medicine  multi  poast  methodology  red-queen  brain-scan  neuro  twin-study  immune  nature  gender  sex  sexuality  thiel  barons  gwern  stylized-facts  inference  apollonian-dionysian 
september 2017 by nhaliday
Mechanisms of microbial traversal of the blood–brain barrier
A journey into the brain: insight into how bacterial pathogens cross blood–brain barriers: http://sci-hub.tw/10.1038/nrmicro.2016.178
How do extracellular pathogens cross the blood-brain barrier?: https://www.ncbi.nlm.nih.gov/pubmed/11973156
Defense at the border: the blood–brain barrier versus bacterial foreigners: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589978/
study  bio  medicine  health  embodied  neuro  neuro-nitgrit  disease  parasites-microbiome  metabolic  🌞  pdf  piracy  org:nat  multi  red-queen  epidemiology 
september 2017 by nhaliday
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