Category Archives: biology

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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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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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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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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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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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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A Bucket of Wings and a Pitcher of PBR with the Baby Jesus

The first time that the Baby Jesus talked to me was at YMCA Summer camp. I heard him on assignment, lying on my bunk in a group cabin while the cicadas droned outside. Us campers had been sent back to our quarters after an evening devotional to listen for a message from God. Around the campfire, our counselors had had admonished us to listen with humility. We had to silence all our selfish desires if we hoped to perceive a divine whisper. We even had to relinquish our hope to hear a whisper from the Lord, if we hoped to hear a whisper from the Lord.

As I lay with my eyes open in the darkness, I was having more trouble tuning out the insects than the cacophony of my selfish desires. The cicadas’ ballad seemed to come from the darkness itself. I had long practice ignoring the undulating buzz, having grown up in the South with no central air and therefore reliant upon open windows for enough cool to allow Summer sleep. With no clamor in my head, the bug song rose from the suppressed depths of my consciousness to make a noise again. I tried to block it out while not trying to block it out, or trying to try to block it out, and so on, until my attention became exhausted and let go of the sound.

Just then, something happened. A voice, or maybe just a feeling, told me not to worry. The speaker was there. Everything was going perfectly according to plan. I felt great. Maybe I even let go a few tears of joy that night. In any case, I soon fell asleep and when I woke the next morning, the world seemed to have a fresh scent, like it had been sprinkled with the lavender water of permeating divinity. The divine freshness lingered for a couple years, but from the moment of spritzing, it was doomed to fade. It could not be reconciled with events on the road to camp.

Our family had set out with a very aggressive vacationing agenda that year. We had left home two weeks prior on a mission to visit my grandmother and Disney World, both a day’s drive away. We would then loop back up to drop me at Summer camp, while my brother would go on to baseball camp, leaving my parents with a week of real vacation for themselves. The schedule was tight, and my father was not pleased when we pulled up behind a row of parked cars on a two lane road in the flatlands of North Florida. When we stepped out of the car, we could see an object blocking both lanes in the distance. Other people were getting out of their cars too, and it was quiet. We walked forward with all the rest.

On the opposite side of the road, about 30 yards up, a distraught elderly couple sat on the ground by their car. The car had a dent in the hood and its windshield was caved in. A few yards beyond lay a mangled bicycle. It was nice, or it had been. I had wanted a BMX bike like that for a couple of years, and I would have done with it what I imagined its rider was doing when the old folks hit him: jumping the banks on either side of the elevated roadway. The boy lay a dozen yards beyond his wrecked bike, diagonally across the lane lines. He was on his side with no apparent injury, from a distance, but with a puddle of blood around his upper body.

Standing over the boy, one could see that the blood was coming from his ears. His gaze fixed on something impossibly distant and his breaths came halting and deep. We circled around him as he died. Someone remarked that an ambulance was on its way, A nurse in the crowd screamed at the rest not to just stand there, but to run and get a blanket. She was upset to a degree beyond what the collective paralysis of the bystanders merited. She may have been wondering how Baby Jesus could allow such a thing. As a child, I knew that adults had their reasons and that those reasons were sometimes unfathomable. I just assumed that the same was true of the Baby Jesus.

I saw no injustice, but I saw his stare. Surely, the distant thing upon which the boy’s gaze fixed was his own death. Yet he would never get to that far place. If he just snuffed out, then he just snuffed out, like when the dentist gave me anesthesia to remove my wisdom teeth and asked me to count to ten as the drug took effect. I didn’t even fail to count to eight. I counted to seven and that was it; there was no experience of looking back on an unsuccessful effort to count to eight, only a memory of seven, then nothing. Likewise, if he saw a light at the end of a tunnel or rose into the ether to look down on his inert body, then he experienced a metamorphosis. He got yanked away from those final moments of physiologic cessation just like the anesthetic yanked me away from counting to eight.

If I had asked any of my fellow onlookers gathered around the body that day, I’m sure they would have spoken of death as a thing which might bear a scythe and a cowl. They would have named it an independent reality. But after that day on the road, I slowly came to see that they were wrong. I fantasized about what would happen if the boy could tell us about leaving his body. Jesus’ disciples were said to have had that very experience, when Jesus returned from the dead to speak to his inner circle. Yet they were only twelve meeting The One. I imagined a world where meetings with the dead were common. I imagined ghosts at first, but engaging in spectrology proved an unnecessary complication. The situation was the same if what happened to Jesus happened to everybody. Your bodily functions stopped. You went up into the clouds. You got a bit of a rebuild. You came back down.

If universal resurrection came to pass, the first generation affected might continue to speak of the Grim Reaper. But as the reportage of the pierced, crushed and disintegrated became commonplace, no one would refer to Death as a thing in itself. There would be misadventures and resurrections, and all would be properly seen as aspects of our total experience. Eventually, no one would even talk about Life anymore.

Though I did not appreciate it at the time, the considerations which began on that roadway in the Southern plains generated a frictional heat, which would finally evaporate the lavender water of permeating divinity. Over years, it dawned on me that Eau Divine had already transcended itself if we could put a name to it, even if we just spoke metaphorically. Like life and death, the scent arose from a great continuity of experience, which we could never look back upon from a discontinuous beyond. It was a slow drying out, and I did not even miss the scent until the next time Jesus spoke to me. That final time, I was sitting in a bar at lunch, far from Christian Summer camp, when the voice of the Lord came to me from a bucket of wings.

I don’t know why I ordered the wings. I was at a crossroads career-wise, so maybe I felt a little unstable and subject to whimsy. As I stared into the jumble of battered and fried appendages however, I recalled why I had become a de facto vegetarian. I felt sick as I imagined all the capabilities which those little wings had possessed in life, reduced to the mess before me on the plastic table cloth. But it was too late by then. I understood my place in the supply chain (having ordered) and besides, I could not leave food uneaten in my financial circumstances. Luckily, there was cheap beer on tap. I asked the bartender to bring me a pitcher.

I took a solid gulp of the rice-brew swill before having a second look at the wings. That’s when the voice, or maybe it was more like a feeling, came to me out of the bucket. It told me not to worry. Life had been given for life. It was all going according to plan. I could eat those chicken wings with a clear conscience, because that’s how it was meant to be. The essence of life got passed on, said the voice, and carried on from the poor little chickens to me. I stared at the crusty wings, and was not reassured. Those bits of bone and muscle that had been, could be taken for almost anything now. But they could not be taken out of circumstance or consequence, anymore than that boy on the road, Life and Death, plans both mortal and divine, or the voice of the Baby Jesus, coming, as it did, from the bucket, or the ether, or any other relatively distinguishable source.

I downed the remainder of the swill and pushed back from the table. Somebody else got the wings, and that was the last I heard from the Baby Jesus.

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No Clarence, You Do Not Have Clearance

Justice Thomas recently wrote a 20 page concurrence to a decision about an abortion law. Someday, this exposition will be renowned as the most extensive, inside-out examination of the genetic fallacy in history. Every textbook will cite it, eventually. To hasten its ascendance, I will make these observations on the Justice’s writing.

First some background. The law at issue is one which restricts abortion in a number of ways, only one of which really got the Judge going.

“This statute makes it illegal for an abortion provider to perform an abortion in Indiana when the provider knows that the mother is seeking the abortion solely because of the child’s race, sex, diagnosis of Down syndrome, disability, or related characteristics. §§16–34–4–1 to 16–34–4–8; see §16–34– 4–1(b) (excluding “lethal fetal anomal[ies]” from the definition of disability).”

We’ll get back to the “child” verbiage. What’s the upshot of this provision, the one which provoked such logorrhea from Thomas?

“Put differently, this law and other laws like it promote a State’s compelling interest in preventing abortion from becoming a tool of modern-day eugenics.2”

Wow, that is a big claim, and it is going to need a lot of support. But what he brings is: “Eugenicists are bad. Things Eugenicists like are bad. This is the sort of thing Eugenicists like, so it is bad.”

On the surface, his argument is just bad, mundane, and not even original. But he is a supreme court justice, so he digs deeper, and we get to see all the sub-strata of the genetic fallacy, and so why it, like all informal fallacies, merits its label.

The first purpose of the genetic fallacy is to shut down one’s opponents. By nature, it contains an accusation of guilt by association, not only for the position which it seeks to defame but for any advocates of that position as well.

Quite a bit of Thomas’ concurrence enumerates the deplorable sayings of Galton, Sanger, Stoddard, etc.. These are people to be reviled and feared. Galton originated the notion of social Darwinism – the survival of the fittest. Thomas provides this example of Stoddard’s toxicity:

Stoddard feared that without “artificial barriers,” the races “will increasingly mingle, and the inevitable result will be the supplanting or absorption of the higher by the lower types.”

But, wait a minute. If the higher types and lower types can’t keep it straight, then how are they ‘types’ at all? This kind of contradiction permeates eugenics, especially when it comes to the use of birth control to advance the cause. If a woman chooses to use birth control to give her children a better economic heritage, or to spare her child a brief and impoverished existence, she would seem to have met the superior-type criteria. Which brings us to the real problem with eugenics: It inevitably classifies on phenotype, with an assumption that the genotype follows. Furthermore, even their assessment of phenotype is hopelessly crude, because it includes social status as big part of the phenotype’s constitution. The blond hair and blue eyes come with a 3-piece suit.

It turns out that the eugenicists are just a bunch of crackpots who don’t really understand genetics, not the scary, evil geniuses referenced in Thomas’ argument. And that’s one problem with the genetic fallacy in general. To taint a position, the associated villains must have some potency to their poison – they must be right to some extent, or at least attractive – yet they must also be wrong, to discredit the position, and repugnant. In the end, you can’t have it both ways.

But the Justice does not stop in the upper layers of the genetic fallacy; he is digging for gold. Underlying every good deployment of this fallacy, there is a slippery slope argument as well. Usually the slippery slope remains implied. It risks being overlooked, in that case. Justice Thomas is not about to let that happen.

If “the masses” were given “practical education in Birth Control”—for which there was “almost universal demand”—then the “Eugenic educator” could use “Birth Control propaganda” to “direct a thorough education in Eugenics” and influence the reproductive decisions of the unfit. Propaganda 5. In this way, “the campaign for Birth Control [was] not merely of eugenic value, but [was] practically identical in ideal with the final aims of Eugenics.”

If you thought Sanger was bad, just wait. She was merely the vanguard. who aimed to soften us all up for the real assault.

And with today’s prenatal screening tests and other technologies, abortion can easily be used to eliminate children with unwanted characteristics. Indeed, the individualized nature of abortion gives it even more eugenic potential than birth control, which simply reduces the chance of conceiving any child. As petitioners and several amicus curiae briefs point out, moreover, abortion has proved to be a disturbingly effective tool for implementing the discriminatory preferences that undergird eugenics.

We are looking down a black diamond run. The last bit, however, brings us to the deeper reasons for rejecting genetic fallacies. In the course of his exposition, Justice Thomas reveals a profound misunderstanding of fetal anomalies, prenatal testing, and worst of all, Freakonomics (he must not have listened very carefully to the episode referenced on page 17). The genetic fallacy generally serves to smooth over such rough spots for its user. For Justice Thomas, it is a smoke bomb which he hopes will cover him while he slips past the implications of words like “child” tossed in to refer to – what? Does he mean zygote, blastocyst, embryo, fetus? What are the physiologic correlates of childhood? Or is it possession of a soul, and if so, just what the hell is a soul, and by what means do we know of it? He concludes:

Although the Court declines to wade into these issues today, we cannot avoid them forever. Having created the constitutional right to an abortion, this Court is dutybound to address its scope.

Indeed, you can’t hide forever.

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Knock Out Mouse Revolution

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Standing in the New Orleans convention center felt a little eerie. The interior was clean and neat. It looked like an airport. Still, I could not help but recall images of Katrina, when the huge edifice had become a beacon of false hope, luring the populace through its doors with the promise of aid, only to leave those who entered trapped like rats.

We had come to a conference to learn about endocrinology, which I had not considered too creepy before. I was wrong.

The proceedings began innocently. Hundreds of physician scientists, and I, filed quietly into a giant auditorium. I want to make clear my lack of qualifications relative to the rest of the group. I am no scientist, and barely a physician. I would much rather read philosophy books and climb around on crumbly sandstone towers than pipette solutions into a gel matrix.

But my job is mostly about helping people protect themselves from diabetes. Plus my wife had a poster to present. So, there I was, attending as an imposter.

The keynote speaker got a prolonged introduction. He deserved it. He was an important person with important research credentials. It was the kind of introduction where a name is never mentioned, for dramatic effect, and because everybody already knows exactly who the subject is. It is a an effective strategy for generating anticipation in the majority who are already quite familiar with the speaker, as well as in those who have never heard of him. It works for everyone, except my wife. She is honest to a fault, and that means that she is a real subject-object-verb kind of person. When presented with a dramatic, obscure speech, her attention lapses. As the speaker walked onstage to the sound of his name, she asked me who this Francis Collins person was.

After a long moment’s reflection, I told her that Francis Collins was a bad philosopher. She seemed to accept my summary, because she promptly settled back in her theater chair to nap through the rest of the lecture. I could not sleep, though I was feeling a little jet lag as well. The lecture was fascinating. Dr. Collins had been right in the middle of genetic research since the beginning of the human genome project, and he took the audience on a trip through the whole endeavor, right up to the current moment: the Big Data revolution.

The Big Data revolution referred to the use of advanced mathematical and computing techniques to sort through scads of data for druggable targets in endocrine diseases. The special techniques had become necessary because the database had exploded. Dr. Collins and his compatriots had deciphered the genomic book of life, but when they sat down to read it, they discovered that they needed a lamp, reading glasses, bookmarks, and indeed, the semantics of the language. The genes turned out to be active in the context of all sorts of transcription factors, promotors, coactivators, corepressors, etc. There was layer upon layer of conditionals which gave meaning to the genetics.

The source of the Big Data revelation was the knockout mouse. The knockout mouse and its cousins, the knockin mouse and the humanized mouse, were what happened when researchers turned to their traditional test subjects with gene manipulation techniques learned in dissecting the genome. By studying mice with selectively induced genetic defects, the researchers had produced the dense pile of data on gene regulation which advanced computing methods might sort out for us.

By the end of the keynote address, I had mouse fever. I wanted to hear all about the things which these creatures could do, and it turned out that I had come to the right place. Over the next few days, I would hear about mutant mice who could run on a treadmill off the couch like they had trained for months. Mice who developed diabetes. Mice who could turn on their brown fat to alter their metabolism. And many of these mice could serve as their own experimental controls. They had mechanisms inserted in their genomes which could turn their genetic defects on and off in response to substances in their mouse chow.

I’ll admit, when I heard about designer mice and their custom mouse chow, I got a little side-tracked. I had been eager to get out of medicine for a while. It all seemed so futile, and even a bit of a sham. Knockout mice might have been the ticket.

Two incidents elevated that thought to conscious consideration. The first was sighting a booth devoted to mouse chow in the exhibit hall.

To understand the significance of the chow booth, one must understand what the exhibit hall is all about. There is an exhibit hall at every conference. They are huge and opulent sometimes, sometimes modest, but always staffed by beautiful, shiny people and stocked with treats, from lattes to foam-model pancreases. Brands like Coach or Louis V. would feel at home amongst the booths.

Giant pharmaceutical companies ruled the hall, and the mouse kibble guys were right there in the mix. If mouse chow could buy an exhibit booth, the mice themselves must be golden.

The second incident was a conversation overheard in the poster hall.

The poster hall is a huge open space with row upon row of cork boards. Researchers pin up posters with summaries of their investigations on the boards, and attendees walk up and down the rows soaking in the knowledge. Usually there is a clearing in the middle with a nest of round banquet tables where everyone can go to take a break, chat and have a cup of pharma coffee. That’s where I sat while my wife presented her poster. I did not sit randomly.

As I walked up on the tables, I spotted a fat man in a plaid shirt and a yarmulke leaning in to say something to a thin, swarthy, bearded companion wearing a dark olive sport coat and a gold medallion. I needed in on that conversation, so I settled in the chair next to them, and swirled my coffee thoughtfully. Imagine my surprise as I picked up on the subject of their conspiracy.

“Yes,” said the fat man, ” I have been trying to find some of those mice. I need them to finish my work, but you can’t find them anywhere.”

“Yes,” echoed his friend, “those mice are nowhere to be found.”

“The closest I came,” the fat man continued, “was this Korean lady in San Fransisco. She said she had some, even said she would send me a few. But she never came through, and now I can’t get a hold of her anymore.”

The mice must be golden.

But my dreams of becoming a mouse Baron were short-lived. Upon further investigation, I found that genetically altered mice did not thrive. It was hard enough to get them past the embryonic stage. Once they could breathe on their own, they often required special conditions and diets just to survive. Worst of all, most of the really good mice had been patented. You bought the limited rights to a strain of mice when you bought the animals themselves. The patent system was the impetus for the black market discussion in the poster hall. You could trade for mice underground and avoid some costs, at the risk of incurring the wrath of the mouse factory lawyers after publication.

Despite the disappointment on economic grounds, I left the conference optimistic. I still had the image of all those colored bars from Dr. Collins’ slide in my head. Each one was a gene which a mouse model could exemplify, and therefore each one was potentially a druggable target. We had this. It was just a matter of time, and mice.

On my way to work, I have some time to think, though not too deeply. I leave early to beat the traffic, but I never do. Most commutes demand constant attention to collision avoidance. The situation is unfortunate, because the commute is the only time to think. Once work starts, I am behind. Someone constantly needs something from me to satisfy someone else who needs something from them, etc.. My workplace is carefully structured to facilitate this cycle. If I need to communicate with someone, odds are that I can lean over to one side and speak to them directly. Otherwise, my computer contains a messaging system which will pop in on whoever I need to inform or interrogate. Patient rooms cluster around my workstation, so I never need to walk more than 6 steps. However, patient contact occupies only a minor portion of my time. Most of the day is passed on the computer and the phone, addressing questions, requests and lab results. At the end of the day the freeway awaits again. By the time I get home, I am burned out and may or may not have it in me to do some physical training and watch television before retiring to get up and do it all again the next morning.

As luck would have it, traffic was light on the first day back from New Orleans. As I drove, I dreamed of druggable targets; Dr. Collins’ slides with the colored bars swam before me. Most of my patients were already on carefully targeted medications, but reaching down into the genome would ramp up medication effectiveness by orders of magnitude. Yet, not all my thoughts were so happy. Other images kept popping into my head, unbidden. I saw other colored slides, from another lecture by another renowned researcher. They were Dr. Brawley’s slides on the geographic and socioeconomic correlates of life expectancy and the epidemiology of conditions like obesity, cancer and diabetes. I could not banish those intrusive images, and by the time I was walking across the clinic parking lot, my mood had deteriorated.

I made it through the day, and finally got to resume my train of thought as I walked back to the car to drive home. I thought about gene targets and Dr. Brawley’s maps again. Then thoughts of one of the day’s patients joined the fray. She was very overweight, and had the metabolic problems that went with excess adipose tissue. She was on targeted therapy for her diabetes in the form of a monoclonal antibody directed at a counter-regulatory hormone receptor. It was the best science had to offer, but she often missed her doses. She had 2 jobs and no car, so she was up early and home late, and she simply forgot her meds sometimes. She set an alarm, but often could not attend to it, or forgot to reset it. We did not even discuss diet and exercise. She lived on a busy street with non-contiguous sidewalks, had no money for a gym, and no time to travel to a safe park. She could not cook, because she had grown up on packaged foods. In any case, she had grown too heavy by now. Her knees had given out under the weight. She could only mobilize fat stores in the face of severe calorie restriction. To reclaim  her life, assuming that was our aim, she would need two joint replacements and a gastric bypass.

I began to re-experience the rising panic which I had felt at the end of her appointment. Dr. Collins & Co. had let me down; I was not armed for this struggle, nor would I be. I stopped to take a breath and get my bearings. The parking lot was nearly empty. A bad smell rose from a nearby drainage grate, and a noise like water flowing.

I imagined that the noise might be something else. Maybe, instead of waste water, it was all those knockout mice, rising through the  sewers from the depths of the New Orleans convention center where the disappointments of Katrina had flowed down to bring the little fellows back, like a time-delayed Ghost Dance. The mice were coming with their little spectral incisors primed to clip down the cages, the labs, the chow booth, the convention center, and all the rest in a massive, surgical revision. I became convinced that the sound was the mice coming. It had to be. It was the only way that the knockout mice could save us.

mouse

 

 

 

 

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Imagine

…for a moment that you have been selected to participate in a groundbreaking experiment.

Neurobiologists have discovered a single neuron in the reticular activating system (RAS) which appears to be responsible for consciousness. In a rat model, when they hit this little cell with a pulse from an electrode, the rat stops and stares blankly. It will carry out reflexive acts, and even complex learned responses to stimulus. But when the electrode is hot, the questing nose and shifting eyes are still.

You will be the first human subject to undergo stimulation of the single consciousness neuron in the RAS. Well, at least one of the first human subjects, because I will undergo the procedure with you.

In the lab, we each have a tiny hole drilled in our skulls and a micro-wire inserted into the target neuron in our brains. Then, under video-EEG monitoring, I flip the switch that turns on your electrode.

Your EEG changes, but nothing seems to happen to you. You continue to chat with me and when I inquire as to the your status, you assure me that you are quite conscious.

But then I switch the current off.

You look surprised, and ask me, “How long was I out?”

I don’t know what to make of your behavior. Were you out? Was someone else in? Does the magic neuron just make you forget yourself for a bit?

There is only one way to find out. I tell you to flip the switch on my electrode.

I come to in the middle of a conversation, and report to you that I must have been unconscious while my electrode was hot. Your report of my behavior mirrors my report of yours: no change until the power goes off, and then the surprised “wake up”.

I still have no answer regarding anyone’s consciousness during the time when the RAS neuron is activated, nor will I get one. I may be able to make some guesses, if I gather loads of video-EEG data, or see what happens when I try to teach you something while the neuron is being stimulated. That behavioral information, in the brainwaves and in speech, may typically correlate with the presence or absence of a conscious state (in our experience).

The correlates can tell me nothing of the actual presence or absence of conscious experience, however. Consciousness occurs within a subject and won’t be found in the intersubjective. That state of affairs does not make consciousness particularly hard or mysterious – we all know all about it every day. It does require a subject to have it though, and it is always consciousness ‘of’. It is just ours and ours alone.

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