Category Archives: biology

Jun 28 2022
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biology, medical ethics, philosophy, politics, psychology

This again?

“Life! Don’t talk to me about life!”

Marvin the robot

My day began with a woman on the radio proclaiming a great victory for life. For the first time in a long time, a world in which no unborn child got murdered looked to her like a real possibility. Her statement contained a pile of red hot words, resting on one simple word: life. Let us be as clear as possible about the definition of life, because those who have adopted the label “pro-life” will not be. When they talk about life, they don’t mean to talk about biochemistry, they mean to talk about the soul. They mean to talk about all those little souls, bearing some indefinite relationship to little bundles of cells. Via that bond, the soul somehow sanctifies an embryo, while remaining completely uninvolved with biochemistry. What follows are the familiar discontents of substance dualism.

Like most of the pro-life crowd, the woman on the radio barged past the interaction problem and its implications with loud assertions. I got the sense that she may not have fully appreciated those implications herself, and so the rhetorical bum rush may have been a means of self defense as much as it was an offensive tactic.

Poor insight is no excuse though. She deserves the heap of scorn coming her way. Yet she doesn’t bear sole responsibility for her inconsistency. She no doubt labors under the influence of a defective definition of biology. In school, she probably learned a series of rhetorical tautologies (life is organism, organism is metabolism plus reproduction) in her biology classes which amounted to saying, “life is what biologists study”. Nor is biology unique in that regard. All of the sciences have backfilled their metaphysics.

Yet, the associated metaphysics is what really interests us. Though it is fantastic to know about the microscopic structure of the wood in the ship of Theseus, what we really want to know is not the composition of the planks, but the defining relationships of those boards in context. The planks are the ship of Theseus because they floated around the Aegean trod upon by Greek heroes, not simply because the boards consist of a cellulose polymer capable of floating around the Aegean while being trod upon by Greek heroes.

Life is not the Krebs cycle or the DNA in a blastocyst’s nucleus, and it is certainly not some vital substance wafting about, indefinable in principle, and opaque in its activity. Life is what sustains defining change across circumstances. In other words, it is the fulcrum of a dynamic equilibrium. Consider a bacterium in a nutrient broth. Energy from the broth translates into new molecules like the molecules which came before in the cell wall, ring chromosome, and cytoplasm of the bacterium. Having built up enough substrate, bacterium divides, relaying its balance point on through time and space. Then someone drops an antibiotic into the broth. Energy from the broth stops flowing into new substrate and shifts to the activation of efflux pumps. That’s life.

If the organism is overcome, it becomes adrift in its circumstances. Once its equilibrium gets tipped too far, it cannot make its way through the broth or the antibiotic exposure with its causal explanations intact.It’s molecules react with surrounding molecules based on ambient energy states. It cedes all its explanations to whatever is floating around with it in the broth. It is dead.

Beyond this stark boundary between life and death, lies an expansive liveliness. There is life that sails almost where it will (humans), life within life (Portuguese man of war, bees, lichen), and life explicable only in context (prions, chlamydia, embryos).

Embryos live strictly within the lives of their mothers. Embryo explanations require mothers. Embryo explanations do not require souls. Until someone comes up with an effective description of the soul and its relationship to a little ball of cells latched onto the endometrium, the soul remains an inert addition – an epiphenomenon at best. This is a problem which the pro-life fools can’t shout down or blow past. Because the problem with epiphenomena is that there is nothing really tying them down. They don’t do anything, so they can fill in wherever. The unknowable nature of the zygotic soul can justify whatever, from bombs to prayers. It’s a wonder that something so flimsy could ground a social movement of such size. The truth is though, it doesn’t.

The target of the pro-life movement has always been the women, as one might guess given the nature of trans placental relationship.

The vacuous nature of pro-life rhetoric needs exposure, so that we can get to the real purpose of that rhetoric, which is control. People in the pro-life movement are not really interested in the biology of human development, or even bioethics. Instead, they are interested in other people’s stories. Because their own narratives, jumbled as they are with souls, sins, and angels, are so weak, the pro-lifers see divergent narratives as invalidating. Accordingly, they try to curtail divergent narratives wherever they can.

That is the motivation behind the pro-life movement. I doubt that this motive is ever articulated within the ranks. I suspect it is held more as a feeling, which makes it even more dangerous. A stated policy can be confronted, criticized, and torn down. Opposition to a feeling is personal. Furthermore, feelings tend to take on lives of their own. Clarence Thomas is already telling us what comes of persistent, unleashed insecurity. Listen to him, and the rest, and then call them out.

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Sep 10 2021
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biology, Covid-19, medical ethics, medicine, philosophy, politics, psychology

The myth of the free range human

… Is a myth that I, as much as anyone, wish were true. My dream is to have a little place in the middle of nowhere, off the grid, with a couple of greenhouses, a composting toilet, a 12gauge loaded with rifled slugs, and a pair of vicious dogs. The truth is though, the only way to realize my dream involves relying on things made on the grid. Even after I am established, I’m going to need things from town – in other words, from other people – to maintain my little homestead.

One might argue that my situation is artificially contrived. Nobody asked me to begin in the middle of a civilization, I was just born here. I had no part in constructing it, and I am quite justified in feeling that the whole thing could’ve turned out a lot better than it did. But that would be wrong too. We are all stuck with something like what we’ve got. It’s inscribed in our genome. When my children were born, I did not have to give them any special instruction in speech and language. I simply talked to them, and soon enough, they began to speak. That’s because they have special structures in their brains which are receptive to language learning. We are social animals, and there’s no getting around that.

We are stuck with a duality. We are fully individual, but we can only realize our individuality by way of our social nature. There are no arts, sports, or academics without other people. And as social creatures, we direct our communal effort towards the full expression of individuality. From the isolated point of view of the collective, arts, sports, and academics are a waste of resources, yet we pursue such things as a group because of their benefits to the individual participants.

The dialectic of the social individual permeates all of our institutions, even medicine. Medical professionals treat patients one by one, but on the basis of the statistical effectiveness of each treatment. In fact, our most effective treatments – interventions involving nutrition, sanitation, and immunization – purely play collective odds to benefit an individual patient’s health.

By the same token, our best treatments are not things done to the patient by the physician. Our best interventions require the participation of the individual, and the exercise of individual virtues like patience, generosity, and courage. The current pandemic is a perfect example. Public health institutions aim to immunize the population, in the hopes of preventing individual tragedies.

Libertarians object to such collective efforts, in defense of individual integrity. But this is where the dialectic flips. To exercise individual virtues, and so maintain individual integrity, each person should participate in the treatment. The failure to do so does not demonstrate rugged individualism, but mean spirited cowardice.

In defense of individual integrity, our society allows meanness and cowardice. Nobody is going to hold someone else down and give them a shot. But neither is anyone obliged to give credence to all the excuses and objections expressed when measures are taken to mitigate the collective effect of failed individual character.

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Jul 25 2021
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biology, Covid-19, philosophy, psychology, theism

Revelations

In terms of what we know and how we know it, we are really no better off than scorpions, who are guided by shadows, cthonic vibrations and the fading scents of long gone passersby. For example, if I have a headache, I take some ibuprofen. I believe it will help me because I know how it works. I learned about the mechanism of action in my chemistry classes, and in subsequent review of the medical literature. But I have never seen the chemical do what those sources say it does. Nobody has seen ibuprofen at work, because the molecules are too small, and the reactions are too fast. However, there are ways to magnify the actions of the chemicals in question, so that those actions may be observed indirectly.

I have not even done that. I have read papers and listened to people who explained how they carried out those observations. Having compared their methods to the methods which I learned in chemistry classes and validated in the lab, I believed their report.

Therefore, I take the pills from the bottle labeled ibuprofen when I have a headache, and expect relief. As I choke down the maroon tablets, I act on a belief even more flimsy than the notion that ibuprofen will help my headache in the first place. I have no idea how the pills were made, and no way to know whether they contain ibuprofen at all. Within an hour, my headache is better.

I keep taking ibuprofen from those types of bottles, because it keeps making my headache go away. Maybe someday, I will unknowingly take a cyanide tablet instead. The risk is negligible though. The same biochemists, pharmacists, and physicians who taught my classes, and subsequently formed my beliefs about ibuprofen’s effect on pain, have declared their commitment to assuring the integrity of those maroon tablets in the bottle labeled ibuprofen on the drugstore shelf. The company that makes those pills has also committed to the recommendations of the biochemists, pharmacists, and physicians regarding the purity of the pills, and the company charges a price which reflects its commitment to giving me ibuprofen, the listed dose of ibuprofen, and nothing but ibuprofen in the bottle.

Philosophers have contended that knowledge is justified, true belief. It turns out though, that truth is probably too small for that purpose. Yet even without truth as a necessary condition, we know something. We go to sleep without fear of never waking again. We take one step after the other confidently, apparently certain of the ground’s persistent solidity. We move about justified by an interlocking network of constant correlations. Any single one of those correlations may be dubious, but taken as a consistent whole they support actionable beliefs – knowledge.

Like the scorpions’, our basics seem pretty janky. Nevertheless, though we are occasionally crushed by a boot or have to sting our way out of a situation, we survive for the most part, and even manage to snag an invigorating insect or two along the way.

It is possible to doubt a functional view of knowledge however. Anything less than absolute certainty merits some doubt. I think about that stray cyanide tablet now and again. Yet, I don’t doubt the justifying power of consistency built of constancy. I know that my pills are ibuprofen even though they might, in principle, be cyanide. Doubt in the method of justification itself invites fear, and fear is contagious.

Such doubt in our body of knowledge, driven by attendant fear, has spread in the populace recently. In place of functional knowledge – beliefs justified by their ties to a massive network of constant correlations – the afflicted strive to reclaim truth as their foundation for knowledge. They cast about the culture for a suitable candidate, what they find is revealed truth. Revealed truth has always lurked about in the cultural murk. Religion harbors it, but not the superstitious type of religion which one might reflexively suspect of such activities. The God of the Old Testament felt the need to carve a tablet, burn a bush, and drop some manna now and again. Revealed truth instead finds refuge with the more philosophical types. Think divine command theory or moral intuitionism.

Revealed truth acts something like Platonic form. Taken as a form, a circle is not a good model, it is the underlying reality which the flawed material of our world imperfectly represents. The circle itself is not the stuff of experience. Revealed truths differ from forms on that point, though. Revealed truths can be apprehended, and so blur the line between analytic and synthetic truths. The statement, “all unmarried men are bachelors”, is an analytic truth. The statement, “Bob is a bachelor”, is a synthetic truth. The statement, “Bob is an inherently unlovable person” is a revealed truth. On the same basis, what the Bible says is true because God wrote the Bible, which we know because it says so in the Bible. It is a truth by definition, but only in reference to a given assertion, in this case that an infallible God is the Bible’s author.

With revealed truth in hand, a person can know something with absolute certainty again. The result is appealing. We needn’t waste our time on the uncomfortable task of finding a date for Bob. We know what he is now.The problem with revealed truths should be obvious at this point. Such givens undercut justification. Consistency with the constancies does not matter anymore, only consistency with the given. If Bob actually gets married, we already know that the marriage is a sham. What remains is to discover the structure of the sham.

The justifying structures are easily built, and unassailable, since they have a given between themselves and any assault. The givens themselves are not beliefs, but natural conditions or kinds revealed by an authority, whether it be an intuition or the speech of a erstwhile prophet. Pick your definitive source; there are no limits.

This spoiled conception of knowledge has spread, generating Q anons, Antifas, and vaccine microchips. Similar epidemics have washed over us in the past. They never last, because eventually, the pragmatic view of knowledge outlasts them. Knowing the spells tucked in their jackets will protect them from bullets, a few of the participants in the Boxer Rebellion manage to avoid being shot. Most die. The scorpion who knows that he can wander around in the daytime because he feels the protective hand of God upon him will survive, for a while. The patient on the ventilator may know that Covid is a hoax because evil people lie, and evil people told him about Covid. He will still drown.

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Jul 07 2021
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biology, consciousness, philosophy, psychology

The Other Senses

We humans have a visual bias. Experiments have demonstrated our preference for sight, but there is no need for experiments. “The proof of the pudding is in the eating,” not the tasting, but “Seeing is believing,” they say. Whenever we want to illustrate something, well, we illustrate it. Our language and culture reify vision. Even our metaphysical discussions are rife with visual references: consider Mary the color scientist, spectrum inversions, and Gettier problems.

Our belief in seeing privileges our sense of sight relative to our other senses, and we are likely to take its instruction more seriously. We wave off any perceptual conundrums arising from our other senses as foibles of inferior organs. But we should take our nonvisual phenomena more seriously, for they have lessons for us if we do.

Those lessons start at the bottom, with our sense of smell. Though it is our crudest sense, and arguably the one sensory modality that we could most do without, the structure of smell has weighty implications. Olfactory neurons each bear a single kind of receptor. The odors we experience are mediated by activation of a set of receptors entirely. The number and distribution of that activation determines everything about a smell: its intensity, favorability, and motivational power. An odor is something which can be described, but not named. There is no equivalent to “red” in our odor palette. However, there are good and bad smells, and as with moral qualities (supposedly), smells are intrinsically motivating on the basis of their goodness and badness.

That motivational power lies in the smell itself. A chemical in a test tube which smells like a steaming pile, produces the same revulsion as the smell of a steaming pile itself. It is tempting to say that the odor of the chemical in the test tube is just an olfactory misrepresentation of crap. The common scent is supposed to smell just as it does, though. The smell is a conjunction linking an aversive mood, and things to be avoided. The smell and the mood are about a broad landscape, stretching over memory, history coded in our genetics and cultural instruction, all mediated by a particular pattern of receptor activation.

A similar sort of two-directional representation occurs in our auditory experience. The organ which generates auditory nerve signals, the cochlea, is tuned to the range of the human voice. The structures at the auditory end of the line are primed to respond directly to voices and music, and indirectly, to stimulate an emotional response to voices and music. As with smell, when hearing evokes a mood, it builds a memory of itself and its circumstances on a broad and sturdy base. A good framework improves the recollection’s relevance, and therefore its odds of survival. Here is another temptation. Fans of evolutionary psychology and divine teleology may see the beginnings of a good story in this structure. But those sorts of stories are unnecessary, and far beyond the point, which is: our hearing shapes the map of our experience in terms of words and music, as much as it recognizes musical and linguistic experiences.

The other senses break down the uni-directionality of representation, but even further, they blur the internal/external division itself. Taste receptors give us the sensations of sweet, salt, sour, bitter, and umami. Our conscious experience of taste locates those sensations on the tongue. But there are taste receptors for bitter and sweet in the pharynx, and sweet taste receptors throughout the intestinal tract. Those sweet receptors attach to neurons which do not reside in the central nervous system, but instead, lie in the intestinal tract itself, and the pancreas. Though these sense organs have no direct connections to the central nervous system, they still contribute to conscious experience. They simply do so via the adjacent somatosensory system.

Our somatic senses are a bit of a jumble. As a whole, they are the thing that represents our status. Though there are a few specialized sense organs in the system, it mostly relies on bare nerve endings and chemical signals built in to the tissues surrounding the nerve endings. This sense tells us where our limbs are, and what each appendage is doing. The somatosensory system lets us know when our gallbladder is on the fritz, and, indirectly, when we are hungry or full..

Though they are rarely the center of our conscious attention, our somatosensory experiences are always present in our conscious states. If I interrupt Dr. Penrose’s visualization of a 5 dimensional object, he will immediately be able to tell me whether he is standing or sitting, feeling hungry, feeling warm or cold, fit or tired. Somatosensory experience serves as the shade tree, grass, and sky in the painting of our phenomenal picnic.

Of all the senses, our somatic sense most effectively dissolves the boundary between what is internal and what is external. Because, our hunger is apparently our hunger. Our cold is our cold. These are things that seem to incorrigibly belong to us, just like our thoughts or our moods.

The thought that any of these things belong to us is a bit off anyway. Words and music, hunger, thought, and mood are constituents, but there is no separable “us” to which they may belong. We come by this error regarding identity via our most favored sense. Because we rely so heavily on vision, we confer an unmerited degree of independence to our visual experiences. We conceive of sight as purely received information, which given the limitations of the medium, naïvely represents an unconditioned reality. The plain truth gets transmitted through our optic nerves, into the dark room behind our eyes for the viewing pleasure of a little man in front of his little screen – the real us. Visual realism leads to other mistakes in its turn, regarding what is real and what is not. We begin to believe that numbers may be real because our eyes see objects as very discrete. Geometric shapes may seem real because we are able to depict them visually. A separate observer made up a separate stuff must sit behind our eyes to validate the reality of our visions. Our other senses beg to differ. They give as good as they get. Their contributions to our experience only make sense in reference to our global experience itself and do not rest on some outer, hard surface. Our world may be a ship sustained by the tension of its own spars, but it works for us – better than a brittle realism would.

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Jun 03 2021
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biology, consciousness, philosophy, psychology

The E-Word

Last night, the wife and I brewed up some nice Medicare mimosas (that’s orange Metamucil with a pinch of MiraLAX for those who don’t know, yet) and sat down to watch a documentary on the desktop. It was my night to choose, so we didn’t watch the National Geographic folks anthropomorphizing the animal of the week. Instead, we watched something interesting on PBS. It’s an old series imaginatively entitled “The Brain”. It’s really very good, except for one thing. Within the first few minutes, the narrator says the E word (emergence), and he just keeps saying it.

I’m prone to let this sort of thing go. Saying a property emerges in the subject of a micro structural description is often a means of stepping over a steaming pile of metaphysics in the path between discussion of the properties of an object’s components, and the properties of the object itself. I can forgive the use of shorthand..

The narrator initially uses this shorthand meaning of emergence. But as things go along, it becomes clear that he also endorses weak emergence. Then he offhandedly states that colors exist in the mind and not in reality, which indicates that he really does have things the wrong way around.

In defense of the narrator, he still isn’t advocating for strong emergence. Strong emergence is the idea that once some threshold condition is met among components of an object, the group of components comprising the object acquires a new property which then takes over the behavior of the object as a whole, and by extension, that object’s components.

This magical event effectively erases, at least temporarily, the properties of the object’s components. While they remain pieces of the whole, they participate in events according to the dictates of the new property. It is only when they fall off the bus, either accidentally, or via our purposeful examination, that they reacquire their individual properties once again.

For instance, neurons generate electrical impulses, regulate their membrane potentials, and secrete paracrine signals until they are gathered in a certain number and arranged in a certain pattern, at which point they exceed the threshold for becoming a mind and begin to do things like experience, think, and remember. As long as we look at the collection of neurons gathered in the threshold number and arrangement, we will see them exemplifying mental properties. If we pull one of the neurons out of the brain or touch a subthreshold group of them with an electrode probe, we see them revert to exemplifying neuronal properties.

Weak emergence differs from the claims above in that it takes those claims to be metaphorical. When we get to the threshold state for the components of an object, we don’t get an actual, new, causal force out of that last brick added to the structure. Instead, it just becomes more convenient to speak of the object as if it had developed such a new property.

In the case of the mind, that would mean that the threshold number and arrangement of neurons simply becomes too difficult to manage descriptively. It makes sense to begin to use mental terminology to describe their collective behavior rather than trying to persist in using neurologic terminology.

In the case of both strong and weak emergence, we generate additional mysteries to solve, and those mysteries appear to be unsolvable. We have no account of how or why threshold conditions are established or met. We have no idea how properties flip on and off in the components and in the designated objects composed by those subunits. The difference between the two positions is that, in weak emergence we have the above difficulties in explaining a metaphor rather than a mechanism.

The root problem however, is not flipping properties. The root problem is the non-relational account inherent in the treatment of objects and their components. We get another glimpse of this inverted view when the narrator of “The Brain” describes colors as constructs of the brain which are absent in reality. If we take the implied structure seriously, then there’s nothing to save neurons from a similar fate. The only difference might be that we have examples of people who live without colors, but no examples of people who live without neurons. However, we do have examples of people who seem happy to live without minds, from solipsists to eliminatrivists.

To clarify, minds are explained by brains which are explained by neurons which are explained by genes. Colors are explained by retinal pigment, neurons, cone cells, and wavelengths of light. The explanations begin with the object in question, and proceed down to the microstructure.

The microstructure doesn’t represent the object like the pieces of a jigsaw puzzle or a pile of little homunculi. Instead, the components provide a history of relationships and record of events situating the object of examination in the causal web of space and time.
A couple of examples, in the interest of de-spookifying the statement above. First, take the illustration that the documentary offers for neuronal activity generating consciousness. Our narrator gives the example of the unconscious brain during sleep. In deep sleep, the electrical activity generates a rudimentary waveform on EEG. In REM sleep, when the brain is ostensibly conscious, as well as during wakefulness, the EEG tracing shows a complex waveform. He compares this circumstance to a group of drummers, each initially drumming to their own rhythm. As they listen to each other and begin to coordinate their beats, music emerges.

If the implicit claim really held, John Coltrane wasn’t doing much of anything that any of the rest of us couldn’t do as long as we knew how to work the reed on a saxophone. The drummers can improvise a musical outcome because they understand the object (music) and the components’ (speed and timing of stick strikes on the drum head) relationship to the object composed. That relationship is a series of events involving hearing, drum making skills, proprioceptive experiences and the response of previous brains to frequencies of stick strikes on drum heads. This explains why we can’t play jazz like John Coltrane. We speak of him improvising, but he improvised off of an explanation that situated him in a most musical zone.

More to the point, we can look at the example of neurons and minds itself. Fully developed neurons can’t be placed in a bag, (to borrow from a more gruesome tale offered up by a substance dualist – they are disgusting people), and shaken up to make a brain, much less a mind. The neurons have to go through the developmental process to provide an adequate explanation for the supervening mind. By developmental process, I mean to say the whole history of neuronal development from primordial cells emitting chemical signals in response to changes in membrane polarization to cell migration during gestation, to sensory integration during early childhood. The neurons bear the history of events identified with mental events. The state of affairs is the same as the status of drumsticks and drum heads and drummers regarding music. Those components explain the music because they offer a narrative of events which situates music in the course of events overall. And those specific components pertain to the tune of the day because those components have specific, music related events explaining the components in their turn.

So that’s why I don’t like the E word. When it comes to minds, brains, and neurons, it perpetuates a mystery where there should be none. Worse, it dumbs things down generally, because it substitutes new properties for deep histories.
Problems remain. Dualisms will survive. The hard problem will still wake people in a cold sweat at night (go back to sleep, it’s epiphenomenal). People will still use their minds to insist that we don’t need minds.
Getting rid of the E word solve much.
But it’s a step in the right direction.

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May 30 2021
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biology, climate change, psychology

The Crematoria Runners’ Club

Late in the morning, I pass the same people trotting along the path. We are getting away with something. The sun is already over the mountains, and the temperature is rising rapidly. If we don’t get to shelter within the hour, we will burn up from the inside. The next day’s dawn walkers will find us bloating on the side of the trail, or worse, we will have to call for rescue. That is, if we have a phone. I never bring a phone.

I can only answer for why I run at this time of day.

My choice is pragmatic, partially. At some point in the central Arizona summer, it will not cool down at night. To continue to operate in the hottest months, the body must acclimate in preparation for that unrelenting heat.
But my choice also derives from a mild case of misanthropy. In the early hours of the morning, the dilettantes are about. Snowbirds walk their dogs along the trails at that time. Dieters who graduate from the contemplation stage to the action stage in their weight loss journey, turn out for their therapeutic rambles right after sunrise.

Dilettantes are friendly. It goes with the low commitment mentality. I don’t want to have to greet them or to detour around them on the trail. I don’t dislike them; I just don’t want to break my stride. So, I run when the heat has driven them away.

None of the other runners says hello in passing. Each makes a slight detour to pass the other on the trail. Everyone is concentrating. No one is smiling. Our club is not social. This is true to the extent that no one is following the same route, and when we pass each other, it is on the way to our own, individual paths.

My path leads up a wash sandwiched between two expensive housing developments. Preserved to prevent flash flooding in the communities, the wash now serves as a sort of terrarium for the exclusive houses which fence in the watercourse on either side.

I can hear the homeowners sometimes as I run, chatting as they enjoy a leisurely late breakfast on their back patios. The activities of their households echo in the wash as well – the sound of water filling their pools, the drone of leaf blowers wielded by landscape staff, the rumbling engines of their pickup trucks.

They don’t bother me, because they strictly ignore me. I share a status with the rattlesnakes, coyotes, javelina, and occasional bobcats who come down the wash. Though viewed with distaste, such creatures are tolerable as long as they stay in the terrarium.

As I run, more desirable fauna scatter before me. A few of these are rodents, (Western ground squirrels and desert rabbits), but most are birds. Flying from the tree branches are Rose finches and hummingbirds. On the ground, a roadrunner will occasionally dash across the trail. But mostly, California Quail break cover and run as I approach.

I like roadrunners. They are fast and agile. They have little fear and are driven by curiosity.

I despise the Quail. On this subject, my opinion is at odds with the majority judgment, which holds these birds in high esteem. However, the majority’s opinion is profoundly superficial at base.

The Quail have beautiful plumage, with very distinctive markings around their eyes and chest and a feather bobble which sprouts from the center of their head and hangs over between their eyes. Their calls are loud and emotive. They are handsome birds, but they are abject cowards

Despite excellent camouflage, they haven’t the gumption to hide. Even rabbits do better at freezing in the face of an oncoming threat. And once the quail lose their heads and flee, they flee in a pitiful fashion. They zigzag, but not with the head fakes and hard turns expected from an animal juking for its life. They change directions in a weak and indecisive pattern associated with sheer panic. They forget that they can fly, relying on whatever speed their stubby little legs can generate. Only when they would certainly be caught, does instinct takeover to deploy their wings. Worst of all, if chicks are trailing the adults during one of these stampedes, the adults will abandoned their offspring straightaway, either on foot or in the air.

Nor are the quail merely thralls to their fear. They are prone to indulge any impulse to its logical conclusion. There is a flock of quail which frequents the outdoor tables at the Desert Botanical Gardens snack bar. Their human admirers have fed these birds on scraps until the quail have lost all fear, and live only in anticipation of the next potato chip. They cluster around the chairs within easy reach of anyone with bad intent. They are so fat now, that they have lost the ability to fly.

By the time I reach the top of the wash, the quail, along with all the rest, have sought shelter in the underbrush as the desert simmers. The trail carries on up a steep hillside. I turn around at the top of the slope and start back. Now it grows hotter by the minute, but I cannot hurry or I will begin to generate more heat than I can dissipate. I don’t pass anything or anyone on the way back down. The club has disbanded.

They say that this will all end soon, because of the car that I drive to the trailhead and the heat pump that cools my hiding place from the furnace outside. Day by day it will just keep getting warmer until living in the valley becomes impossible.
Everyone that can will have to sell out and become a Snowbird. The rest will have to make do. Whatever else may follow, no one knows. The only sure thing is: drive, run, or fly, we are not going to get out of the terrarium.

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Apr 24 2021
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biology, climbing, philosophy, psychology

Body and Soul

“You can kill my body, but you cannot kill my spirit.”

 - Bo Diddley

I love that song. I play it on the way home from every big day, whether I have succeeded or failed.

Today I failed. I didn’t even make it to the crag. Something is happening to me, and I am not sure what it is. I shake. My back is in pain. My muscles lock up. All these things happen in the course of normal activity. If I can just get to the stone, and put my hands on the holds, everything gets better. I get back fluid movement.
But I can’t get to the stone. The course of normal activity is in my way.

I fear that I may end up like Fred Becky. He lived to climb, and did hundreds, if not thousands of first ascents in the Cascades, and all over the world. He continued to climb until he was in his 80s. In the final years, he made backcountry forays in mountain ranges all over the world. He often struggled to get to the base of climbs, and for the most part, he did not end up climbing. Nevertheless, he dragged his bones back to the mountains again and again. Video footage of some of these endeavors exists, and it is clear from the images that he was struggling, and suffering all the way.

I used to think that his efforts were heroic. Now, I think he exemplified an element of the human condition which our old poets referenced in the tales of Prometheus and Sisyphus.
Fred couldn’t help himself any more than those mythical figures could help themselves.
The problem, for Prometheus, Sisyphus, and Fred was, of course, that the spirit can die.

The eagle eating your liver isn’t the real issue. The real issue is that your liver keeps growing back. The rock rolling down the hill isn’t the truth. The truth is your own, inescapable compulsion to push it back up.

The spirit dies with each peck and each bound of the boulder. Unlike the body, it is easy to kill. It will die over almost nothing. The catch is: it keeps coming back. It snaps back in an instant and sends you back to the bottom of the hill and prepares you for the eagle’s next visit.

I will drive back home. I will wake up tomorrow morning without having asked for it. I will do some pull-ups and climb on plastic as if I were training for something. Some onlookers may think this is admirable, others may think it is sad. From the inside, it just is.
The religions are wrong about what we go through. There is no heaven. There is no hell. There is no samsara. Those are views from the outside.
Maybe next weekend, I will get my hands on those holds. But I will act just the same, between now and then, as long as I live.

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Aug 25 2020
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biology, Covid-19, medicine, politics, Trump

For Anyone

…who believes that, “we have more cases because we have more testing”.

Testing for an infectious disease is like counting the number of balloons in a dark room by tossing darts through the doorway. Say you throw 10 darts in the room and hear two pops. There is still a good chance that a number of balloons remain uncounted. But if you throw 40 darts in the room and hear two pops, the likelihood of a two-balloon scenario soars. When the rate of pops drops below a certain proportion, you can be sure that you have counted most of the balloons in the room. A low percentage of positive tests is what you’re after.
Once you have established the adequacy of your testing, you can sort out what the results reveal about containment. The raw numbers don’t tell you that much. In the case of national case counts, it is reasonable to expect a country with a large population to experience higher numbers than a country with a small population given similar degrees of disease containment. A true measure of containment is cases per population, or in our analogy, how crowded the room is with balloons.
So when a pinhead like Trump says that we have more cases because we have more testing, that standalone statement is pure bull shit. What’s worse, it’s a distraction from what really indicates the adequacy of our understanding of the outbreak’s extent and the effectiveness of our efforts to contain it: percent positive tests and infections per population.

How is the US doing?

Top of the heap with >15,000 cases/1 million persons (European Centers for Disease Control)

Percent positive tests: 7.9 (an adequate percentage is less than 5%)

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Apr 06 2020
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biology, Covid-19, medical ethics, medicine, politics, psychology, Trump

H plus or minus the A

Wee Donnie loves his Plaquenil. He says that hydroxychloroquine may be a game changer. He is not a doctor, and he is certainly not an academic, but he says that he has common sense to guide him. His common sense tells him that the drug might have some beneficial effect in Covid-19 infections, times are desperate, and so why not give it a go – what do you have to lose?

Of course, common sense is what tells us that the earth is flat and the sun goes around it. Shockingly, common sense is just as dependable when it comes to bio-statistics. Trump has no idea what he is talkiing about (as usual). Let me heap a fair helping of scorn on his contentions. To do that, Donnie’s argument has to be split into its two components; otherwise, the load would collapse the full-length argument before even a third of the deserved disparagement were dispensed.

Part one concerns the effectiveness of hydroxychlororquine for corona virus. There are a couple of observational studies from China suggesting that moderately ill people given the drug may have been less likely to progress to severe illness. There are also in vitro studies of viral replication which show hydroxychloroquine to be inhibitory. Finally, there is a study examining viral shedding in patients given the drug versus patients not given the drug. This last study is open label, not randomized, and examines a surrogate endpoint – what we want to know is whether the medicine makes people get better, not whether it makes their nasal swab get better.

All of this evidence generates a hypothesis (that hydroxychloroquine may improve clinical outcomes in coronavirus infection) but doesn’t yield any conclusions at all.  To illustrate how this can be so, witness research on the use of this very same drug for influenza treatment. Because, hydroxychloroquine inhibits replication of the influenza virus as well, in vitro. When given to patients in a randomized, controlled trial however, it didn’t make anybody any better, any faster.

But why let the perfect be the enemy of the good? We can go on hope and the possibilities implicit in the observational studies. The med is safe, right? Just give it. To clarify the consequences of such proposals, lets say that the putative cure for Covid-19 is not a Q/T – prolonging antimalarial. Let’s say, it’s a chocolate brownie. The instructions are: chocolate brownies cure corona. That’s it; that’s all we know.

Now, some people are going to take a tiny pinch of brownie, and secure in its protection, head off to the church picnic. They will get the virus and wind up in the ICU.

Other people will eat 5 brownies per day, sending their triglyceride levels through the roof. Those in this group who are also taking certain medications, will develop pancreatitis and wind up in the ICU (drug-drug interaction).

Some will go beyond the 5 brownie dose, to 7 per day. Among this lot are bound to be some latent diabetics who will subsequently land in the unit with hyperglycemic hyperosmolar non-ketotic coma (drug -disease interaction).

Finally, a few true believers will bump the dose to 10 brownies daily. They will experience nausea, vomiting, and diarrhea with subsequent dehydration and acute kidney injury, buying them an ICU bed right beside the Covid patients (adverse drug effect).

The point is: common sense sees no farther than its own nose and is blind to all these eventualities. Scientific method is not, largely because it admits that we can’t know all the eventualities. That’s why good clinical trials measure hard endpoints, like death or time to hospital discharge, and not surrogate markers, like the presence of virus on nasal swabs.

Don’t rely on that nitwit shyster Trump, his toadies, and their common sense. Rely on scientific method instead.

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Feb 18 2020
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atheism, biology, consciousness, philosophy, psychology, theism

The Other Minds

My dog loves me. Despite his creaking hips and back, he heaves himself up and comes to greet me when I return home each night, with his tail wagging. Yet I wonder if I am right about his feelings about me. After all, I am just interpreting his behavior as representative of mental and emotional states which I would have in similar circumstances. And, he has been bred over centuries to be a veritable human-pleasing machine which exhibits a set of behaviors that, among other things, is calculated to make me feel that he feels like I am the best thing since kibbles. Come to think of it, he does not wag his tail while he eats, and he never met a kibble he didn’t love.

If only he could tell me that he loves me, then I would know for sure. On second thought, I could not know for sure. I can’t even know for sure when another human reports their feelings or perceptions or any other personal, qualitative aspect of their experience to me. In any such case, the experience that I attribute to their report may be radically different from what they are actually experiencing. At least, that’s what the Inverted Spectrum teaches us.

The Inverted Spectrum is a thought experiment. It was not devised to tackle the problem of other minds. It was devised to demonstrate the ethereal nature of qualitative properties. But like any good thought experiment, it illustrates multiple aspects of the target issue.

Here’s how it goes: Imagine that you have a best friend named Fred, who you have known since you both could walk. Unbeknownst to you however, whenever you both look at something red, Fred does not see red, he sees green instead. This is not to say that Fred is color blind. On the contrary, he sees all the colors that you see, and he quite happily calls the red object “red”. He just sees it as green. The two of you could go through your entire lives discussing painting and picking out Granny Smiths instead of Red Delicious at the grocery store, without a hitch. The basic qualities “red” and “green” do not influence function; we happily operate the same way with the qualities flipped.

The implications of the Inverted Spectrum may seem bizarre, dramatic and disturbing, but closer examination may shrink the menace. If I assign you and Fred to sort red and green beads into separate boxes, the two of you will complete the task in no time with no mistakes. That’s because what we all call “red” designates the same set of beads, even though they produce in Fred what you or I would call a “green” experience. To take it a little further, if I assign the two of you to tell me the color of sour things, sweet things, hot things, dangerous things or growing things, you and Fred will give me the same answers in French, English, Fulani, or even just by pointing. All secondary associations are flipped along with the reds and greens.

The jolt from this thought experiment comes when we imagine our experience of Fred’s experience, with all of our secondary associations still in place. But that’s completely off base. What we have run down with this thought experiment is an account of Fred’s experience with all his own secondary associations attached. The point is that there is some irreducible personal element to it all. But then, where does that leave Fred’s “red” or his “green” or his any other what-it-is-like aspect of experience?

Having seen what it is like to see what it is like to experience what Fred sees from your viewpoint, you may have trouble explaining your horror to him. You will insist that the apple is red, as are hot things and dangerous things, and he will heartily agree. You can desperately insist that he is deluded and is pervasively mistaking red qualities for green ones. He will reply that he is not and will ask you to prove it, which, as the thought experiment demonstrates, you cannot. What remains to his personal, qualitative experience, stripped of all the secondary associations, is just its personalness.

If you were to truly step into Fred’s skin with all its secondary associations in place and your own secondary associations set aside, you would have to admit that Fred’s “red” is indeed red; it is just not your red.

My dog may be an automaton. He may be a human-pleasing machine who wags his tail on the basis of a genetic algorithm and just acts in a very convincing way, like he means it. But if so, as the Inverted Spectrum illustrates, he does mean it, just as Fred really means red when he says “red”. All the secondary associations are in place. I may rightly conjecture that what it may be like to be him may not be what it is like to be me, but I knew that before he wagged his tail. He loves me, as sure as I know what love is.

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