Category: biology

A Pause in Attention

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I routinely take a pause in what I am doing to reflect on my goals and what I’ve learned. I’m sure you do too. I had been listening to the recorded works of Jean Sibelius and Carl Nielsen, but am now on to Sir Edward Elgar and Josef Suk. Billie Eilish and Vampire Weekend didn’t last long. I gave up on my deep learning startup to pursue another, less abstract technology. I revamped this site. I put trail running on pause and have been lifting weights more. I shifted writing efforts to a new series centered on manipulating animal physiologies for war and espionage.

These pauses feel like taking an expansive stretch after sitting still for a long period; a reset of the mental apparatus that repositions the mind for a new phase. For me, one take away from recent events, up to and including the great pause of the coronavirus pandemic, is a reconsideration of the amount of silly and pointless content we absorb. Just a few examples: The drama of Twitter feuds among the glitterati and the political class, cancel culture, and shaming. The endless technology, photography, audiophile, fashion, and food reporting and communal commenting that serves to channel our engagement with products and services. Even the lightweight philosophizing that goes with critiques of tradition or society has the same basic set of drivers.

What’s shared among them is the desire for attention, an intellectual posturing to attract and maintain the gaze of others. But it does have a counterpoint, I believe, in a grounding in facts, reason, and a careful attention to novelty. The latter may be a bit hard to pin down, though. It is easy to mistake randomness or chaos for novelty.… Read the rest

Pro-Individualism, Pro-Social, Anti-Cousin

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I tend towards the skeptical in the face of monocausal explanatory frameworks, especially for ideas as big as human history and the factors that shaped it. The risk of being wrong is far too high while the payoff in terms of anything more than cocktail banter is too low, be it as a shaper of modern policy or bearer of moral prerogatives.

So the widely covered discussion of Schulz, et. al.’s AAAS Science paper, “The Church, intensive kinship, and global psychological variation” (paywall) is a curiosity that admits to cautious reading at the very least. The hypothesis is that Catholic Church prohibitions on consanguine marriage that began in the medieval period in Western Europe explain globally unusual aspects of the psychology of the people of those regions. By banning cousin marriage even out to the 6th degree in many cases, the Church forced people away from tribal ideas and more towards neolocal family structures. That, in turn, led to pro-social attitudes based on social trust rather than family power, and towards more individualistic and independent psychologies overall.

The methodology of the study is fairly complex: look at the correlations between consanguine marriages patterns and psychological attitudes, then try to explain those correlations away with a wide range of alternative data patterns, like the availability of irrigation or proximity to Roman roads, and so forth. Data experiments that look at Eastern Orthodox versus Western Church differences, or even between northern and southern Italy are used to test the theory further.

In the end, or at least until other data supervenes, the hypothesis stands as showing that reducing cousin or similar marriages is a “causal channel” for these patterns of individualism and social trust.… Read the rest

Deep Learning with Quantum Decoherence

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Getting back to metaphors in science, Wojciech Zurek’s so-called Quantum Darwinism is in the news due to a series of experimental tests. In Quantum Darwinism (QD), the collapse of the wave function (more properly the “extinction” of states) is a result of decoherence from environmental entanglement. There is a kind of replication in QD, where pointer states are multiplied, and then a kind of environmental selection as well. There is no variation per se, however, though some might argue that the pointer states imprinted by the environment are variants of the originals. Still, it makes the metaphor a bit thin at the edges, but it is close enough for the core idea to fit most of the floor-plan of Darwinism. Indeed, some champion it as part of a more general model for everything. Even selection among viable multiverse bubbles has a similar feel to it: some survive while others perish.

I’ve been simultaneously studying quantum computing and complexity theories that are getting impressively well developed. Richard Cleve’s An Introduction to Quantum Complexity Theory and John Watrous’s Quantum Computational Complexity are notable in their bridging from traditional computational complexity to this newer world of quantum computing using qubits, wave functions, and even decoherence gates.

Decoherence sucks for quantum computing in general, but there may be a way to make use of it. For instance, an artificial neural network (ANN) also has some interesting Darwinian-like properties to it. The initial weight distribution in an ANN is typically a random real value. This is designed to simulate the relative strength of neural connections. Real neural connections are much more complex than this, doing interesting cyclic behavior, saturating and suppressing based on neurotransmitter availability, and so forth, but assuming just a straightforward pattern of connectivity has allowed for significant progress.… Read the rest

A Most Porous Barrier

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Whenever there is a scientific—or even a quasi-scientific—theory invented, there are those who take an expansive view of the theory, broadly applying it to other areas of thought. This is perhaps inherent in the metaphorical nature of these kinds of thought patterns. Thus we see Darwinian theory influenced by Adam Smith’s “invisible hand” of economic optimization. Then we get Spencer’s Social Darwinism arising from Darwin. And E.O. Wilson’s sociobiology leads to evolutionary psychology, immediately following an activist’s  pitcher of ice water.

The is-ought barrier tends towards porousness, allowing the smuggling of insights and metaphors lifted from the natural world as explanatory footwork for our complex social and political interactions. After all, we are as natural as we are social. But at the same time, we know that science is best when it is tentative and subject to infernal levels of revision and reconsideration. Decisions about social policy derived from science, and especially those that have significant human impact, should be cushioned by a tentative level of trust as well.

E.O. Wilson’s most recent book, Genesis: The Deep Origin of Societies, is a continuation of his late conversion to what is now referred to as “multi-level selection,” where natural selection is believed to operate at multiple levels, from genes to whole societies. It remains a controversial theory that has been under development and under siege since Darwin’s time, when the mechanism of inheritance was not understood.

The book is brief and does not provide much, if any, new material since his Social Conquest of Earth, which was significantly denser and contained notes derived from his controversial 2010 Nature paper that called into question whether kin selection was overstated as a gene-level explanation of altruism and sacrifice within eusocial species.… Read the rest

Doubt at the Limit

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I seem to have a central theme to many of the last posts that is related to the demarcation between science and non-science, and also to the limits of what rationality allows where we care about such limits. This is not purely abstract, though, as we can see in today’s anti-science movements, whether anti-vaccination, flat Earthers, climate change deniers, or intelligent design proponents. Just today, Ars Technica reports on the first of these. The speakers at the event, held in close proximity to a massive measles outbreak, ranged from a “disgraced former gastroenterologist” to an angry rabbi. Efforts to counter them, in the form of a letter from a county supervisor and another rabbi, may have had an impact on the broader community, but probably not the die-hards of the movement.

Meanwhile, Lee Mcyntire at Boston University suggests what we are missing in these engagements in a great piece in Newsweek. Mcyntire applies the same argument to flat Earthers that I have applied to climate change deniers: what we need to reinforce is the value and, importantly, the limits inherent in scientific reasoning. Insisting, for example, that climate change science is 100% squared away just fuels the micro-circuits in the so-called meta-cognitive strategies regions of the brains of climate change deniers. Instead, Mcyntire recommends science engages the public in thinking about the limits of science, showing how doubt and process lead us to useable conclusions about topics that are suddenly fashionably in dispute.

No one knows if this approach is superior to the alternatives like the letter-writing method by authorities in the vaccination seminar approach, and it certainly seems longer term in that it needs to build against entrenched ideas and opinions, but it at least argues for a new methodology.… Read the rest

Free Will and Algorithmic Information Theory (Part II)

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Bad monkey

So we get some mild form of source determinism out of Algorithmic Information Complexity (AIC), but we haven’t addressed the form of free will that deals with moral culpability at all. That free will requires that we, as moral agents, are capable of making choices that have moral consequences. Another way of saying it is that given the same circumstances we could have done otherwise. After all, all we have is a series of if/then statements that must be implemented in wetware and they still respond to known stimuli in deterministic ways. Just responding in model-predictable ways to new stimuli doesn’t amount directly to making choices.

Let’s expand the problem a bit, however. Instead of a lock-and-key recognition of integer “foodstuffs” we have uncertain patterns of foodstuffs and fallible recognition systems. Suddenly we have a probability problem with P(food|n) [or even P(food|q(n)) where q is some perception function] governed by Bayesian statistics. Clearly we expect evolution to optimize towards better models, though we know that all kinds of historical and physical contingencies may derail perfect optimization. Still, if we did have perfect optimization, we know what that would look like for certain types of statistical patterns.

What is an optimal induction machine? AIC and variants have been used to define that machine. First, we have Solomonoff induction from around 1960. But we also have Jorma Rissanen’s Minimum Description Length (MDL) theory from 1978 that casts the problem more in terms of continuous distributions. Variants are available, too, from Minimum Message Length, to Akaike’s Information Criterion (AIC, confusingly again), Bayesian Information Criterion (BIC), and on to Structural Risk Minimization via Vapnik-Chervonenkis learning theory.

All of these theories involve some kind of trade-off between model parameters, the relative complexity of model parameters, and the success of the model on the trained exemplars.… Read the rest

Hypersensitive Conspiracy Disorder

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I was once cornered in a bar in Suva, Fiji by an Indian man who wanted to unburden himself and complain a bit. He was convinced that the United States had orchestrated the coups of 1987 in which the ethnically Fijian-dominated military took control of the country. The theory went like this: ethnic Indians had too much power for the Americans to bear as we were losing Subic Bay as a deep water naval base in the South Pacific. Suva was the best, nearest alternative but the Indians, with their cultural and political ties to New Delhi, were too socialist for the Americans. Hence the easy solution was to replace the elected government with a more pro-American authoritarian regime. Yet another Cold War dirty tricks effort, like Mossaddegh or Allende, far enough away that the American people just shrugged our collective shoulders. My drinking friend’s core evidence was an alleged sighting of Oliver North by someone, sometime, chatting with government officials. Ollie was the 4D chess grandmaster of the late 80s.

It didn’t work out that way, of course, and the coups continued into the 2000s. More amazing still was that the Berlin Wall came down within weeks of that bar meetup and the entire engagement model for world orders slid into a brief decade of deconstruction and confusion. Even the economic dominance of Japan ebbed and dissipated around the same time.

But our collective penchant for conspiracy theories never waned. And with the growth of the internet and then social media, the speed and ease of disseminating fringe and conspiratorial ideas has only increased. In the past week there were a number of news articles about the role of conspiracy theories, from a so-called “QAnon” advocate meeting with Trump to manipulation of the government by Israel’s Black Cube group.… Read the rest

The Retiring Mind, Part IV: Phenology

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An unexpectedly quick move to Northern Arizona thrust my wife and me into fire and monsoon seasons. The latter term is debatable: monsoons typically involved a radical shift in winds in Southeast Asia. Here the westerlies keep a steady rhythm though the year. The U.S. desert southwest has also adopted the Arabic term “haboob” in recent decades to refer to massive dust storms. If there is a pattern to loanword adoption, it might be a matter of economy. Where a single, unique term can take the place of an elongated description, the loanword wins, even if the nuances of the original get discarded. This continues our child language acquisition tendencies to view different words as being, well, different, even if a strong claim of “one word per meaning” is likely unjustified. We search for replacement terms that provide economy and even relish in the inside knowledge brought by the new lexical entry.

So, as afternoon breaks out into short, heavy downpours we dart in and out of hardware stores getting electrical fishing poles, screw anchors, and #10 8/32nd microbolts to rectify an installation difficulty with a ceiling fan. We meet with contractors and painters who rush through the intermittent squalls. And we break all this up with exploring new restaurants and hitting the local galleries, debating the subterfuge of this or that sculptor in undermining expectations about contemporary trends in southwestern art.

But there is a stability to the forest and canyon around our new house. Deer wander through, but less so as the rain has filled the red rock canyons with watering holes, allowing them to avoid long sojourns to Oak Creek for water. A bobcat nestled for half a morning on our lower deck overlooking the canyon, quietly scanning for prey.… Read the rest

Fantastical Places and the Ethics of Architecture

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Lemuria was a hypothetical answer to the problem of lemurs in Madagascar and India. It was a connective tissue for the naturalism observed during the formative years of naturalism itself. Only a few years had passed since Darwin’s Origin of the Species came out and the patterns of observations that drove Darwin’s daring hypothesis were resonating throughout the European intellectual landscape. Years later, the Pangaea supercontinent would replace the temporary placeholder of Lemuria and the concept would be relegated to mythologized abstractions alongside Atlantis and, well, Hyperborea.

I’m in Lemuria right now, but it is a different fantastical place. In this case, I’m in the Lemuria Earthship Biotecture near Taos, New Mexico. I rented it out on a whim. I needed to travel to Colorado to drop off some birthday cards for our son and thought I might come by and observe this ongoing architectural experiment that I’ve been tracking for decades but never visited. I was surprised to find that I could rent a unit.

First, though, you have to get here, which involves crossing the Rio Grande Gorge:

Once I arrived, I encountered throngs of tourists, including an extended Finnish family that I had to eavesdrop on to guess the language they were speaking. The Earthship project has a long history, but it is always a history of trying to create sustainable, off-the-grid structures that maximize the use of disposable aspects of our society. So the walls are tires filled with dirt or cut wine bottles embedded in cement. Photovoltaics charge batteries and gray water (shower and washing water) is reused to flush toilets and grow food plants. Black water (toilet water) flows into leachfields that support landscape plants.… Read the rest

Less Dead

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I’m feeling less dead than I could be. Here’s the rattlesnake that struck and bounced off my running shoe this morning:

He started rattling after the initial strike, which seems like an evolutionary spandrel. At least he didn’t have a machine gun. I’ve named him Bartholomew and wish him the best on his future journeys. And here is the juvenile oryx who was laughing at the situation nearby:

… Read the rest