Category: biology

A Most Porous Barrier

Mark Davis2 Comments

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

Mark Davis1 Comment

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

Zebras with Machine Guns

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I was just rereading some of the literature on Plantinga’s Evolutionary Argument Against Naturalism (EAAN) as a distraction from trying to write too much on ¡Reconquista!, since it looks like I am on a much faster trajectory to finishing the book than I had thought. EAAN is a curious little argument that some have dismissed as a resurgent example of scholastic theology. It has some newer trappings that we see in modern historical method, however, especially in the use Bayes’ Theorem to establish the warrant of beliefs by trying to cast those warrants as probabilities.

A critical part of Plantinga’s argument hinges on the notion that evolutionary processes optimize against behavior and not necessarily belief. Therefore, it is plausible that an individual could hold false beliefs that are nonetheless adaptive. For instance, Plantinga gives the example of a man who desires to be eaten by tigers but always feels hopeless when confronted by a given tiger because he doesn’t feel worthy of that particular tiger, so he runs away and looks for another one. This may seem like a strange conjunction of beliefs and actions that happen to result in the man surviving, but we know from modern psychology that people can form elaborate justifications for perceived events and wild metaphysics to coordinate those justifications.

If that is the case, for Plantinga, the evolutionary consequence is that we should not trust our belief in our reasoning faculties because they are effectively arbitrary. There are dozens of responses to this argument that dissect it from many different dimensions. I’ve previously showcased Branden Fitelson and Elliot Sober’s Plantinga’s Probability Arguments Against Evolutionary Naturalism from 1997, which I think is one of the most complete examinations of the structure of the argument.… Read the rest

The Obsessive Dreyfus-Hawking Conundrum

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I’ve been obsessed lately. I was up at 5 A.M. yesterday and drove to Ruidoso to do some hiking (trails T93 to T92, if interested). The San Augustin Pass was desolate as the sun began breaking over, so I inched up into triple digit speeds in the M6. Because that is what the machine is made for. Booming across White Sands Missile Range, I recalled watching base police work with National Park Rangers to chase oryx down the highway while early F117s practiced touch-and-gos at Holloman in the background, and then driving my carpool truck out to the high energy laser site or desert ship to deliver documents.

I settled into Starbucks an hour and a half later and started writing on ¡Reconquista!, cranking out thousands of words before trying to track down the trailhead and starting on my hike. (I would have run the thing but wanted to go to lunch later and didn’t have access to a shower. Neither restaurant nor diners deserve an après-run moi.) And then I was on the trail and I kept stopping and taking plot and dialogue notes, revisiting little vignettes and annotating enhancements that I would later salt in to the main text over lunch. And I kept rummaging through the development of characters, refining and sifting the facts of their lives through different sets of sieves until they took on both a greater valence within the story arc and, often, more comedic value.

I was obsessed and remain so. It is a joyous thing to be in this state, comparable only to working on large-scale software systems when the hours melt away and meals slip as one cranks through problem after problem, building and modulating the subsystems until the units begin to sing together like a chorus.… Read the rest

Tweak, Memory

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Artificial Neural Networks (ANNs) were, from early on in their formulation as Threshold Logic Units (TLUs) or Perceptrons, mostly focused on non-sequential decision-making tasks. With the invention of back-propagation training methods, the application to static presentations of data became somewhat fixed as a methodology. During the 90s Support Vector Machines became the rage and then Random Forests and other ensemble approaches held significant mindshare. ANNs receded into the distance as a quaint, historical approach that was fairly computationally expensive and opaque when compared to the other methods.

But Deep Learning has brought the ANN back through a combination of improvements, both minor and major. The most important enhancements include pre-training of the networks as auto-encoders prior to pursuing error-based training using back-propagation or  Contrastive Divergence with Gibbs Sampling. The critical other enhancement derives from Schmidhuber and others work in the 90s on managing temporal presentations to ANNs so the can effectively process sequences of signals. This latter development is critical for processing speech, written language, grammar, changes in video state, etc. Back-propagation without some form of recurrent network structure or memory management washes out the error signal that is needed for adjusting the weights of the networks. And it should be noted that increased compute fire-power using GPUs and custom chips has accelerated training performance enough that experimental cycles are within the range of doable.

Note that these are what might be called “computer science” issues rather than “brain science” issues. Researchers are drawing rough analogies between some observed properties of real neuronal systems (neurons fire and connect together) but then are pursuing a more abstract question as to how a very simple computational model of such neural networks can learn.… Read the rest