Category Archives: evolution

Knock Out Mouse Revolution

mighty-mouse-cartoon-clipart-16

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

 

 

 

 

Advertisements
Tagged , , , , , , , , , , , ,

The Simple Life

Life? Don’t talk to me about Life.

– Marvin the Robot

 

Life, living matter and, as such, matter that shows certain attributes that include responsiveness, growth, metabolism, energy transformation, and reproduction.

– Encyclopedia Brittanica

The javelina was dead, no doubt about it. By the looks (and odor) of the ruin which lay in the ditch, it had been several days since the animal had lived, as such.

Most likely, it had been hit on the nearby road and dragged itself to the protection of the ditch before collapsing. ‘Collapsing’ means: it ceased to respond as a javelina. Certain nerve cells lost their flow of metabolic substrate, could no longer transform energy in covalent bonds into electrical potential across cell membranes, and so could no longer respond as nerve cells.

The javelina behaved as a javelina if and only if those nerve cells behaved as nerve cells: no more nerve behaviors, no more javelina behaviors. Yet the remainder of the organism ticked along for quite a while after its defining brain functions ceased. Less sensitive tissues took minutes, or even hours to stop responding, growing, reproducing, etc.

Even after the last of the body’s eukaryotic cells ceased to do all those life-defining things, the prokaryotic components of the javelina carried on. Many of the bacteria which had worked with its other cells to keep the animal alive and healthy before it came to lie still in the ditch, continued to grow, metabolize, reproduce, etc.

At the other end of the javelina’s timeline, we see a similar situation. Before its mother could conceive, the environmental circumstances had to be right for piglets. Furthermore, its mother and father had to be right for the circumstances. They had to have a set of characteristics which led to survival and relative prosperity in their particular living conditions.

Within those proper circumstances, gamete membranes met and fused, DNA recombined, placental syncytium formed, organogenesis took place, the piglet began to exhibit its own physiology, and the little  javelina emerged from the amnion to take its first breath.  From some fairly basic biochemical reactions to the defining processes of biology itself, the animal faded into life, much as it faded into death.

Many people find this picture disconcerting. They yearn for the simple life, where our definitions are definitive and what’s real is real in and of itself. But that’s not what we have. The simple life, and its decadent certainty, are not available to us.

 

 

Tagged , , , , , ,

Is a Virus Alive?

life, living matter and, as such, matter that shows certain attributes that include responsiveness, growth, metabolism, energy transformation, and reproduction. – Encyclopedia Brittanica

Close enough, and encompassing the generally accepted criteria: responsiveness, reproduction, metabolism and adaptation. My older son asked the question about viruses the other day. I have been looking forward to this question. It means that he is prepared to understand some things about life which are important. It is a tricky question if considered from the wrong viewpoint. A virus displays some of the characteristics which define a living organism. It can respond to stimuli, attaching to the proper cells and injecting its genetic material through the cell membrane when it makes contact. It can replicate. It can adapt to avoid a host immune response. But it does not have the capacity to metabolize. It cannot, in other words, run its own show. It is entirely dependent on its host organism in that respect. Nor is the virus alone on the gray borders of life. Certain families of bacteria lack some essential metabolic processes which would make them autonomous. They must live inside another cell, and depend on their host’s metabolism to survive. Yet, they too can reproduce, adapt, and respond to stimuli in their environment. Because they have a membrane which is active, biologists are prone to give obligate intracellular bacteria, like mycoplasma and Rickettsia, a break. Most biologists are less charitable when it comes to prions. Prions are mis-folded proteins which replicate by somehow inducing their own conformal change in normally folded proteins with which they come in contact. Prions can reproduce, but they cannot metabolize. They cannot adapt much (although they have managed to pass from cows to humans), but they can respond to their environment, albeit in a very limited way. Still, the difference between the prion and the obligate intracellular bacterium would seem to be one of magnitude rather than quality. Differences in their classification reflect a little bit of membrane chauvinism on the part of biologists. The same prejudice is evident in the gray zone at the other end of the complexity scale. By our criteria for life, is a male angler fish alive? The fish can survive for a short period of time independently, but it cannot carry on its own metabolic processes independently for the long-term. It must rely on a female angler fish. It must quickly sniff out a female and attach itself to her, permanently. The male fish spends most of its existence as a tissue of the female angler fish’s body; its brief, free swimming existence is a transitional aberration. Its ability to adapt is extremely limited. Its existence can be mapped on an algorithm only barely more complex than the one which describes a prion’s lifestyle. So what does differentiate the male angler fish from a mycoplasma bacterium, a virus, or even a prion? A few extra membranes make the only difference. Even our own status as living things is at risk if we apply our criteria strictly. We can certainly reproduce, just like the viruses, obligate intracellular bacteria, prions, and angler fish. But it is questionable whether or not we can independently metabolize. We actually rely on hereditary intracellular symbionts for our primary metabolic process. Without these symbionts, our mitochondria, we could live only minutes on the metabolic processes encoded by our own genetic material. So, we can hardly be blamed for fudging our criteria. We certainly want to call ourselves alive. Since it looks and acts alive, we want to call the male angler fish alive. For practical purposes, we also want to call Rickettsia and mycoplasma alive, as well as viruses from time to time. As for the prions, it is often more convenient to view them as sophisticated toxins rather than living things. And that’s the upshot of my son’s question. The issue of whether or not a virus is alive is only confusing if we consider “life” an actual, efficacious thing. But life is just a category. When we look out across the terrible landscape of things, we see phenomena which cluster about each other by dint of their shared heritage. Our account of our cluster is biology, and our criteria for life provide the outline for our biological stories. This is correct viewpoint on the question of life, and what is alive. But this is not the popular viewpoint. The popular viewpoint attempts to preserve life as a thing, as vital essence or emergent property. Unfortunately, the popular viewpoint is not feasible. It leads inexorably back to the original question rephrased, “where is the life in a thing to be found?” In the end, we find that the essence or the emergent property is explained by the operational mechanisms and properties of the thing in question, but it in turn, explains nothing about the thing; it just notes where that particular thing lies on the vast, terrible landscape of things. Despite its glaring inadequacy, the popular viewpoint remains popular because it seems to save us from losing an idea that we don’t feel comfortable losing. But we don’t need to worry, becoming a category doesn’t vitiate life. We have the things which the category marks clustered around us after all, even if it’s only according to our viewpoint. We can’t escape life anymore than we can climb out of our skins. So, the answer to the question? Sure, a virus is alive – as long as you can explain why.

Tagged , , , , , , ,

Is Intelligent Design Distinguishable from Creation Science?

Yes, as horse shit is distinguishable from bull shit. ID is a deductive argument from analogy and teleology. As such, it is neither valid nor scientific. Both Creation Science and ID are based in the politics of religion, a genre which degrades both politics and religion, but ID is an attempt at subterfuge whereas Creation Science is at least an honest effort to advance an agenda.
Both are like unwanted attention from a belligerent drunk, but where Creation Science is like a shove, ID is like the question, ” What are you looking at?”. As with the shove or the question, one response is in order.

Tagged , , ,

Blip! Intelligent Design Is Done Before It Gets Going…

I’m republishing this because I think it bears repeating in light of the ongoing activities of intelligent design advocates, and because I realized that I was wrong about something right at the beginning. The core errors in ID do power the evolution-bashing arm of creationism. I’ve noticed that the error of de-contextualization which characterizes the positive argument for ID forms the core of many people’s arguments against evolution. Obviously, I think that this is no accident. To many creationists, evolution is one rationalizing story among many. This would be true, provided one considered the theory of evolution out of historical context. But remember, the hypothesis was derived from observations of biological variation across environments. Then came the archeological evidence predicted, and later the genetic evidence predicted. That historical evolution is the difference between all proper scientific theories and mere rationalizing stories. So, one more time – I swore I wouldn’t get into this anymore. The intelligent design crowd keeps pushing this crap, though, and I have kids who are at risk. Beyond that, I suppose intelligent design’s sort of dishonesty just galls me. Don’t say I didn’t warn you.

I am about to give an argument by analogy. I do so with trepidation, because analogies are always in danger of going off in the wrong direction and have no deductive validity in the first place. However, I think this form is the only fair tool for the subject since I’m going to use this argument by analogy to critique another argument by analogy: intelligent design (ID). Rather, I’m going to critique the positive arm of the intelligent design argument. This is the withered limb compared to the evolution-bashing arm, but it is necessary to the whole and the negative argument is a morass. Since scientific knowledge is never complete, critics have available to them an endless list of objections. The positive side of the ID case is more a philosophical than a scientific argument, so it can be settled on that level.

The positive ID argument is as follows: when humans start with a purpose (a problem to solve) and devise a tool to serve that purpose, the end product looks a certain way. Biological structures have a similar appearance, so biological systems must result from the same sort of process. An immediate problem arises at this point. Since proponents wish the analogy between man-made objects and biological structures to be precise the argument commits the fallacy of the undistributed middle (Designed structures look like X, Biological structures look like X, therefore Biological structures are Designed structures).

The proponents of ID subsequently introduce a number of modifiers to try to alleviate this situation. Complex specified information is not only used to portray designed and biological structures as essentially similar, it is also used to try to pare down the middle by saying it is statistically negligible. Appeals to abductive reasoning serve the same purpose, suggesting that design is so far and away the “best guess” that there’s no need to worry about the logic. There are deeper problems than the modifiers and the middle but those are the simplest things to consider, so let’s go there first. Let me tell you how I built my son a mountain bike.

The bike came in a big box in a bunch of pieces with a couple dozen pages of instructions. The instructions were complex and very specific. In fact, if you read the instructions through, you would know that a mountain bike and nothing but a mountain bike would result from following those instructions, even without actually building a bike to find out. But, I didn’t read the instructions. I know how bike parts work, so I just eyeballed the problem and figured it out. So, even though the Complex Specified Information (CSI) in the instructions has all the qualities that the advocates of biological CSI wish it to have, it doesn’t have the necessary relationship to the endpoint that those advocates want from it. There are multiple paths through the middle to the mountain bike. There is still a way out for ID, though. I must have picked up on the CSI contained in the parts themselves. It’s true. When I looked at the parts, they fit together in certain configurations and orders of assembly best, as I expected. My expectations were key, too. Over the years, bike designers had shaped those expectations, in effect teaching me to read the information they put in the parts so I could use my abductive reasoning to make a really good guess about how the parts should go together.

I use this “best guess” faculty all the time, because it is a great shortcut and pretty reliable in familiar circumstance. Notice I said ‘pretty reliable’. Also note that I said I didn’t use the instructions, but I didn’t say I threw them away. Sometimes the bike makers come up with an innovation and then my abductive reasoning is worthless and I have to rely on the instructions again to tell me what to do about the new part. I get in trouble if I try to rely on that ‘best guess’ shortcut in clinical medicine, too. The causal history of a manufactured bike is well-defined because people decided to make it that way. If the causal history of a patient’s symptoms is well-defined for me, it’s because I have decided so. Used outside of a situation with known prior constraints on the variables, the ‘good guess’ becomes confirmation bias. So, the problem is with the complex specified information. In biological structures, to achieve ‘specification’ and thus make the ‘best guess’ inference to design, the causal history has to be constrained after the fact. Anything less leaves open those pesky intermediate paths through the middle. ID imposes that constraint by assigning purpose to all biological structures it considers. Assigning purpose is easy for us humans and we like to do it because it lets us use shortcuts like guessing. Attributions of purpose (intent) are so appealing that we have trouble keeping them in the realm of human behavior where they belong (and not even there without some confirmatory process to check the attributions). Who hasn’t said their car “worked hard” to get up a steep hill? It’s just as easy to say that E. coli intends to swim to new food sources with its flagellum. In fact, it takes just that sort of presumption of intent to wrangle an object’s causal history into CSI, resulting in a bit of a Cartesian circle (if the flagellum is made for swimming, then it has a complex history treading a narrow path to that endpoint, which shows that the flagellum was made for swimming). Still, we should be able to safely use this attribution of intent after the fact in limited circumstances, as long as we’re careful, right? For instance, it is surely accurate to say that the guys who designed my son’s bike did so from an original purpose. However, even that presumption of intent from the endpoint is not accurate, and the problem with the retrospective attribution of purpose/intent in such a case leads us back to the problem with intelligent design that predates any attempt to distribute or minimize the middle.

What do we know about design? We really just know what we do and what we do requires an agent (us), a purpose, and means. The problem is that the relationship between those three factors is not linear, nor is it even hierarchical. When considering bike design, for instance, we could go back to the origin of the means via the agent and examine the influence the means then had on the agent’s intent and subsequent development of further means. We could track back to the origin of the wheel in geometry, which is in turn based on observed properties of materials, which are in turn based on some basic laws of physics, all of which humans bothered to investigate and remember in the first place because, if you are a tool-maker, it’s easier to investigate and remember than to, um, ‘reinvent the wheel’. We could trace bicycle history back to the wheel and beyond, but let’s keep it brief and just consider the design of mountain bikes.

Mountain biking started when some California bike racers moved to the country. Their new environment confronted them with the problem of riding, and of course racing, on gravel roads. Their road bikes’ narrow tires were too unstable for that purpose, so they found some preexisting cruiser bikes with wide tires that would at least be ridable on the fire roads near their homes. The cruiser bikes were not perfect. They were heavy and hard to pedal, so the riders raced them downhill. Even that compromise lead to problems though. The brakes and bearings on the cruisers couldn’t survive that kind of abuse. The riders replaced the brakes and bearings with motorcycle and road bike components. The riders soon found that the revised cruisers, now possessing cassettes of gears with the road bike bearings, were capable of riding on rough trails as well as fire roads. Trail riding prompted further modifications to the bikes. These guys in rural California invented the mountain bike, but not all at once and not out of the blue. They worked through a progressive series of problems, each leading to the next, until they arrived at a relatively stable final design that did something very different from the structure they started with. The mountain bike evolved. Of course, this is microevolution; the mountain bike is just a tweaked cruiser bike. Neither the mountain bike nor the cruiser looks anything like an old penny-farthing with the giant wheel in front. The lineage is clear though, and bike development has proceeded by the same basic process from the wheel to the velocipede to the mountain bike. Moreover, the agents in this process acted as selective forces and were acted upon by selective forces – and not just physically. As designers altered the bikes, the bikes’ new capabilities altered their conception of where and why they might ride a bike and thus their purpose in the next set of modifications.

To fingerprint design as the ID scheme misrepresents it, we really must close that Cartesian Circle by presuming intent for any and all endpoints we wish to examine. Then the history of that point is seen separated from any branches or external contingencies. If the mountain bike comes from a mountain bike factory, surely the mountain bike factory holds the entire explanation for its structure. When defined after the fact like this, the history of a structure looks irreducibly complex; if you take away one part it is rendered meaningless because it is its own context. ID’s analogy between designed structures and biological structures not only fails to distribute the middle, it doesn’t even accurately depict design processes as we undertake them. People, the source of everything we know about design, don’t start cold from an undetermined purpose and design toward that purpose in an implacable, irreducibly complex chain of events. Replication may work a bit like that, but not design.

What this method really does is provide for a hierarchical relationship between presumed intent and biological structures, where the intent causes the structure. Such a relationship seems to allow for a supernatural cause. This is why ID’s advocates have gone through such contortions to make it work (or at least look like it might) – see the Wedge Document. Yet the intelligent Design model fails even as a portal for the supernatural. It offers no solution to the interaction problem in dualism. This is a real problem because, as far as I can tell, one tenant of ID is that the design process in nature is ongoing. To drag a spiritual being into the material world and have it start doing things, one has to explain how it does so without being in some way beholden to the same laws, and thus part of the same causal history, as the rest of matter. If there is no good explanation, then the spiritual being from another realm is just a bizarre, unexpected new part of nature. Though this may seem an obscure technicality at first glance, here is an example of just how sticky the problem really is.

Descartes tried to defend the independence of the mind from brain processes. He offered the analogy of a virtuoso violinist asked to play on a broken instrument. The listener would have no clue as to his true skill. Likewise the damaged, diseased, or intoxicated brain may just be a broken instrument unable to give voice to the intact mind which plays upon it. Unfortunately, this analogy raises the question: May the virtuoso be a virtuoso without a violin? Study of music theory or any other purely mental operation is insufficient. He must play a physical violin. Yet the skill he gains is a mental faculty which is subject to his creativity, religious concepts, and emotion. The brain and its adjuncts affect the mind. There is no escape from this problem in a world of two supposedly separate substances in active contact. Deism or a strict idealism offer the only outs (and Deism may just push the problem back in time). Either of these scenarios keeps the supernatural supernatural, but thereby makes it irrelevant to any practical understanding of nature/matter. This is why it is best for religion that science adhere to methodological naturalism. This is why intelligent design is insidious as well as invalid, for all concerned. It robs religion of any hope of philosophical integrity, just as it misrepresents biology. Reason enough for everyone to drop this bullshit for good.

The Dry Cat Food Paradox

So close, yet so far...the Tetons

So close, yet so far…the Tetons

I’ve recently had the privilege of attending a continuing education conference in Jackson, Wyoming. As a climber who thinks of himself as primarily an alpinist headed to the Tetons, I should have felt like the proverbial cat who ate the canary. Instead, I left my gear in the basement. It wouldn’t have fit in the car with all the ski equipment and clothes anyway (the whole family of four was signed up for the trip). It wouldn’t have done me any good even if it did fit. Four months out of the year, those mountains are shut down due to a horrendous snowpack. When conditions allow, the climbing is still high up and far back.

It turns out that it is almost as hard for a climber to subsist on Teton routes as it is for a cat to live on hunted birds. Signs of compensation for these difficulties were everywhere in Jackson. Right around the corner from the conference center, was a sign for the “Teton Ice Park”. When the first morning of lectures ended, I walked up to take a look. What I saw was the result of  a noble effort, but one obviously born of desperation. An enterprising guide service had run a few hoses over a 40 ft. retaining wall to produce about five, moderately-angled chunks of ice. The ice park rented gear, but I decided to utilize a different compensatory facility – the climbing gym just outside of town. It turned out to be quite nice.

CIMG4000

Back in the conference center that evening, I was mulling over the dissonance of indoor climbing in the Tetons when the next set of lectures began. Maybe I should have been paying better attention to the speakers. However, it was a series about nutrition, and though the subject is interesting, the hard science behind it could be covered in about fifteen minutes rather than the three hours allotted  As I considered my Teton climbing experience, I kept coming back to the viewpoint which kept me in the Black Hills for all these years: alpine climbing is more about training than actually climbing. Adaptation to harder routes in the mountains paradoxically required less time climbing mountains. Living in a place like Jackson resulted in strong legs and weak skills. Unless a climber availed himself of  an artificial training facility, the volume of technical climbing needed to improve was just not accessible, at least to anyone with a job. My mind wandered back to the lecturer. He was talking about the Paleo Diet and I found it strangely relevant to the contradictions involved in trying to be a good alpine climber.

Guide service storefront.

Guide service storefront.

This diet is supposed represent our nutritional heritage. It encompasses the type and mix of foodstuffs our hunter-gatherer ancestors adapted to eat. Therefore, runs the logic of the diet’s proponents, it is the mix of foods that we ought to eat to  maximize our health and longevity. On the menu is lots of meat and a few plants. Grains and legumes are out. We should eat more like cats than cows, the speaker admonished. To back up his assertion, he flashed a slide on the screen with a picture of a cat at the top and a chart favorably comparing the body compositions of hunter-gatherers with those of cats.

The picture looked a little like my cat, but my cat thrives on dry cat food. I say “thrives”, because I have a dietary comparison-state for her. She was a stray who showed up in our garage when the weather got cold. Before coming to live in our house, she had, in fact, been subsisting on the cat version of the Paleo Diet – fresh, free-range mouse and bird meat. She wasn’t doing so well. She was thin and listless. After a few weeks living inside and dining on kibbles, however, she was tearing around the house like a maniac, destroying rolls of toilet paper and climbing the curtains.

Here are the first four ingredients listed on her cat food label: chicken by-product meal, corn grits, chicken fat, tuna, brewer’s rice. One would expect a wild cat to catch birds, but I doubt one ever took down a tuna, much less an ear of corn or rice. Still, a cat’s ability to live a long and active life eating nothing but rock-hard brown morsels shouldn’t surprise us. Evolution makes the most  of things, not necessarily the best of things. Wild cats developed the capacity to survive on mice and birds. Cats are therefore well suited to that diet. That doesn’t mean that there isn’t a diet better suited to cats. Perhaps humans are much the same.

A subsequent  slide showed a Kung! tribesman butchering an antelope with a stone tool, and then a chart with cholesterol levels and heart disease rates demonstrating the sterling health of various modern hunter-gatherers. Unfortunately, the health data for the Tarahumara, a group of indigenous people living in Mexico and renowned for their feats of long-distance running, look just as good. The Tarahumara subsist primarily on corn, beans, chiles, and beer.The answer to this dietary conundrum is not found in the diet, but what comes with the diet. Both the Kung! and the Tarahumara are incredibly active, and they do not suffer from surplus. The Paleo diet is not the answer to our health problems. No such simple answer exists.

Of course, there are limits imposed by natural adaptation and on artificial adaptation. Artificial answers are also incomplete. To be a good alpinist, one must climb a certain number of big routes in the mountains. But plate after plate of summits will limit a climber’s potential in the end. Though it isn’t complete in itself, some artifice is required as well. Likewise, when my cat came to live in the house, she didn’t just get dry food, she got a warm, stress-free place to sleep, immunizations, and anti-parasitic medicine. I’m sure she would not be so healthy if we limited our involvement with her to setting out a plate of kibbles on the driveway.

Of the billions of humans alive now, most are suffering from the short-comings of an agricultural, and subsequently an industrial, society and a few are suffering from its excesses. As the most realize the economic, social and technological benefits which drove the move to agriculture in the first place, they no longer get the grace period which the few enjoyed. The harms of excess come right along with the initial development. We can’t simply go back, though. Solutions will require some artifice, and may have an unsatisfying appearance – less like grass-fed beef  and more like a bowl of dry cat food or an indoor climbing gym in the Tetons.

Tagged , , , , ,

You Eyeballin’ Me?

ATTENTION

ATTENTION

An older gentleman lay on the gurney. His son had brought him in from the ranch suffering from abdominal pain. I pushed on his liver.

“Does that hurt?”, I asked.

“Well,” he replied after a moment’s reflection, “it ain’t sore, but it is a little tender.”

Attention

Attention

Tender, not sore. Twelve years and I still don’t know what the hell that means. A former colleague grew up in Wyoming, and since she habitually spoke more than three words in a day (not including ‘Yep’ and Nope’) I asked her a couple of times to explain it to me. She just looked annoyed and said it didn’t matter. I finally understood that she was right. The difference between sore and tender is clinically irrelevant.

attention

attention

‘Tender’ does not have any distinct denotative value, only a connotative one. It still bothers me not to understand its meaning. I’d like to think language can give me a working knowledge of other people’s thoughts and feelings. My expectation of understanding is not realistic. Symbols and their associated concepts just approximate the sets of unique experiences that constitute our shared mental universe. It’s all a big analogy of me to you, words or no. While imprecise, the analogy has one great advantage: it is durable. I may not be able to compare my experience of tenderness to the rancher’s to any good effect, but I can achieve a dialog with the dogs.

Attn.

Attn.

I can even predict the salamander’s response to me looking at it and it can anticipate my response to it clawing at the glass. All of us know our perceptions of each other are about something, which allows us to form these relationships, however vague and riddled with projection they may be (though the salamander does not beg food from people who are not looking at it or objects moving outside the glass, it does respond to the cat staring at it and she is surely looking in with a different intent than it understands).

Attention

Attention

I’m pretty sure I share an extensive mutual understanding with the mammals in the house, even the ones with ear-buds. I’m less confident about what passes between myself and the slimy monsters in the terrarium, but after a day of contemplating human tenderness with all its consequences and deficiencies, an amphibian’s intentional stare is the most reassuring.

Tagged ,

Beetle Battle

The Cathedral Spires after the beetles

The mountain pine beetle is a native son of the Black Hills, but nobody around here is very proud of the little guy. I like him. He’s tiny and a weak flyer. A victim of his own reproductive tactics, he’s a bit like the Lemming – doomed to population booms and busts that make him look stupid. Nevertheless, this little insect has thwarted the will of the baddest mammal on the planet.

For the most part, the life cycle of the pine beetle is typical, boring high school biology. It’s one of those egg-larvae-adult-egg affairs that fits well in a circle of arrows on the textbook’s margin. In late summer, adult beetles emerge from trees infested the year before and fly to new trees, where they burrow into the bark and lay eggs. The eggs hatch quickly into grub-like larvae which begin to eat the tender, inner layers of the bark. After a Winter’s break, the larvae finish their meal, metamorphose into adults and the cycle begins again.Within this staid tale, there are a few interesting details that, under the right conditions, conspire to make the smoldering, little endemic population of beetles into a conflagration.

First, there’s that Winter dormancy. To prepare for the cold, the larvae produce antifreeze. If cold weather strikes before they are ready, many will die. If they are ready, though, they can survive temperatures down to thirty below zero, Fahrenheit. Besides allowing more larvae to survive, adequate preparation means the larvae are further along in their development when they wake up in the Spring. Sometimes, they are far enough along to complete two generations in one year.

Second, the trees don’t just stand there and take it. They have an immune response to the beetles. As the insects dig into the inner bark, the injury prompts the tree to force resin upwards.  Sap spills out of the defect in the bark, smothering the beetles. If the beetles are few enough, and the tree is strong enough, the immune system can prevail. In turn, the beetles have adapted to overcome the trees’ defenses. They produce a pheromone which calls other beetles to a tree under attack, giving them the opportunity to exhaust the tree’s immunity with sheer numbers.

Blue stain fungus

The beetles have also developed a symbiotic relationship with a fungus that weakens the trees. The ‘blue stain’ fungus thrives in the core wood of pine trees, where it interferes with water transport to the crown. Beetles carry fungal spores on their bodies as they breach the outer layers of bark which normally bar the fungus entry.

Under usual conditions, things work out so a few trees die and a few beetles survive. However, if the weather is right and the trees are already weak, a positive feedback loop ensues and the beetle population explodes. Usually these excursions amount to little bursts, limited by the availability of suitable trees.  But presently, due to a lucky convergence of human and beetle preferences, there is no limit to the availability of suitable trees.

The forest that we have cultivated is made of trees which are just the species and size that the beetles prefer. Plus, we’ve made a dense forest, so even the mountain pine beetles’ weak flying skills carry them easily from trunk to trunk. Our relationship with the pine forest has unwittingly, coincidentally helped turn the little pops in beetle numbers into a boom. Modern human activity on the land, from fire suppression to agriculture to habitation, has attenuated a kind of herd immunity inherent in the age, size and density of the trees.

Cuttin’ & Chunkin’

Now, we are trying to stand in for that herd immunity. We want our forest back the way it was. It gave us logs, shelter and aesthetic satisfaction. So, we try to cut infected trees before the beetles can emerge. We try to trick the beetles with pheromones (the insects actually release a repellant pheromone when their host tree harbors too many beetles). We even spray neurotoxins on the trees in ‘high value’ areas, like Mt. Rushmore.

Beetle-thinned forest

Close up, our efforts look pretty smart, like a beetle attack on an individual tree looks smart, with its chemical communications, antifreeze equipped larvae, and fungal force multiplier. But just as the beetles are already doomed to population collapse by the time they start to thrive, we have already ensured that we won’t have the forest back the way we like it, simply because we liked it that way so much in the first place.

It will work out in the end. Preservation is a fool’s errand anyway. We pursue it for sentimentality’s sake, and because it makes us feel like we may be able to avoid our own eventual extinction. When the beetle epidemic is over, we will learn to like the new forest and maybe we will recognize the beetle battle as a farce. For at a proper distance, our interaction with the habitat is indistinguishable from that of the beetles. Like them, and the Lemmings, we’re condemned to a lifestyle that allows us to survive in spite of a built-in vulnerability to chaos.

Tagged , ,

Blip!

I swore I wouldn’t get into this anymore. The intelligent design crowd keeps pushing this crap, though, and I have kids who are at risk. Beyond that, I suppose intelligent design’s sort of dishonesty just galls me. Don’t say I didn’t warn you.

I am about to give an argument by analogy. I do so with trepidation, because analogies are always in danger of going off in the wrong direction and have no deductive validity in the first place. However, I think this form is the only fair tool for the subject since I’m going to use this argument by analogy to critique another argument by analogy: intelligent design (ID). Rather, I’m going to critique the positive arm of the intelligent design argument. This is the withered limb compared to the evolution-bashing arm, but it is necessary to the whole and the negative argument is a morass. Since scientific knowledge is never complete, critics have available to them an endless list of objections. The positive side of the ID case is more a philosophical than a scientific argument, so it can be settled on that level.

The positive ID argument is as follows: when humans start with a purpose (a problem to solve) and devise a tool to serve that purpose, the end product looks a certain way. Biological structures have a similar appearance, so biological systems must result from the same sort of process. An immediate problem arises at this point. Since proponents wish the analogy between man-made objects and biological structures to be precise the argument commits the fallacy of the undistributed middle (Designed structures look like X, Biological structures look like X, therefore Biological structures are Designed structures).

The proponents of ID subsequently introduce a number of modifiers to try to alleviate this situation. Complex specified information is not only used to portray designed and biological structures as essentially similar, it is also used to try to pare down the middle by saying it is statistically negligible. Appeals to abductive reasoning serve the same purpose, suggesting that design is so far and away the “best guess” that there’s no need to worry about the logic. There are deeper problems than the modifiers and the middle but those are the simplest things to consider, so let’s go there first. Let me tell you how I built my son a mountain bike.

The bike came in a big box in a bunch of pieces with a couple dozen pages of instructions. The instructions were complex and very specific. In fact, if you read the instructions through, you would know that a mountain bike and nothing but a mountain bike would result from following those instructions, even without actually building a bike to find out. But, I didn’t read the instructions. I know how bike parts work, so I just eyeballed the problem and figured it out. So, even though the Complex Specified Information (CSI) in the instructions has all the qualities that the advocates of biological CSI wish it to have, it doesn’t have the necessary relationship to the endpoint that those advocates want from it. There are multiple paths through the middle to the mountain bike. There is still a way out for ID, though. I must have picked up on the CSI contained in the parts themselves. It’s true. When I looked at the parts, they fit together in certain configurations and orders of assembly best, as I expected. My expectations were key, too. Over the years, bike designers had shaped those expectations, in effect teaching me to read the information they put in the parts so I could use my abductive reasoning to make a really good guess about how the parts should go together.

I use this “best guess” faculty all the time, because it is a great shortcut and pretty reliable in familiar circumstance. Notice I said ‘pretty reliable’. Also note that I said I didn’t use the instructions, but I didn’t say I threw them away. Sometimes the bike makers come up with an innovation and then my abductive reasoning is worthless and I have to rely on the instructions again to tell me what to do about the new part. I get in trouble if I try to rely on that ‘best guess’ shortcut in clinical medicine, too. The causal history of a manufactured bike is well-defined because people decided to make it that way. If the causal history of a patient’s symptoms is well-defined for me, it’s because I have decided so. Used outside of a situation with known prior constraints on the variables, the ‘good guess’ becomes confirmation bias. So, the problem is with the complex specified information. In biological structures, to achieve ‘specification’ and thus make the ‘best guess’ inference to design, the causal history has to be constrained after the fact. Anything less leaves open those pesky intermediate paths through the middle. ID imposes that constraint by assigning purpose to all biological structures it considers. Assigning purpose is easy for us humans and we like to do it because it lets us use shortcuts like guessing. Attributions of purpose (intent) are so appealing that we have trouble keeping them in the realm of human behavior where they belong (and not even there without some confirmatory process to check the attributions). Who hasn’t said their car “worked hard” to get up a steep hill? It’s just as easy to say that E. coli intends to swim to new food sources with its flagellum. In fact, it takes just that sort of presumption of intent to wrangle an object’s causal history into CSI, resulting in a bit of a Cartesian circle (if the flagellum is made for swimming, then it has a complex history treading a narrow path to that endpoint, which shows that the flagellum was made for swimming). Still, we should be able to safely use this attribution of intent after the fact in limited circumstances, as long as we’re careful, right? For instance, it is surely accurate to say that the guys who designed my son’s bike did so from an original purpose. However, even that presumption of intent from the endpoint is not accurate, and the problem with the retrospective attribution of purpose/intent in such a case leads us back to the problem with intelligent design that predates any attempt to distribute or minimize the middle.

What do we know about design? We really just know what we do and what we do requires an agent (us), a purpose, and means. The problem is that the relationship between those three factors is not linear, nor is it even hierarchical. When considering bike design, for instance, we could go back to the origin of the means via the agent and examine the influence the means then had on the agent’s intent and subsequent development of further means. We could track back to the origin of the wheel in geometry, which is in turn based on observed properties of materials, which are in turn based on some basic laws of physics, all of which humans bothered to investigate and remember in the first place because, if you are a tool-maker, it’s easier to investigate and remember than to, um, ‘reinvent the wheel’. We could trace bicycle history back to the wheel and beyond, but let’s keep it brief and just consider the design of mountain bikes.

Mountain biking started when some California bike racers moved to the country. Their new environment confronted them with the problem of riding, and of course racing, on gravel roads. Their road bikes’ narrow tires were too unstable for that purpose, so they found some preexisting cruiser bikes with wide tires that would at least be ridable on the fire roads near their homes. The cruiser bikes were not perfect. They were heavy and hard to pedal, so the riders raced them downhill. Even that compromise lead to problems though. The brakes and bearings on the cruisers couldn’t survive that kind of abuse. The riders replaced the brakes and bearings with motorcycle and road bike components. The riders soon found that the revised cruisers, now possessing cassettes of gears with the road bike bearings, were capable of riding on rough trails as well as fire roads. Trail riding prompted further modifications to the bikes. These guys in rural California invented the mountain bike, but not all at once and not out of the blue. They worked through a progressive series of problems, each leading to the next, until they arrived at a relatively stable final design that did something very different from the structure they started with. The mountain bike evolved. Of course, this is microevolution; the mountain bike is just a tweaked cruiser bike. Neither the mountain bike nor the cruiser looks anything like an old penny-farthing with the giant wheel in front. The lineage is clear though, and bike development has proceeded by the same basic process from the wheel to the velocipede to the mountain bike. Moreover, the agents in this process acted as selective forces and were acted upon by selective forces – and not just physically. As designers altered the bikes, the bikes’ new capabilities altered their conception of where and why they might ride a bike and thus their purpose in the next set of modifications.

To fingerprint design as the ID scheme misrepresents it, we really must close that Cartesian Circle by presuming intent for any and all endpoints we wish to examine. Then the history of that point is seen separated from any branches or external contingencies. If the mountain bike comes from a mountain bike factory, surely the mountain bike factory holds the entire explanation for its structure. When defined after the fact like this, the history of a structure looks irreducibly complex; if you take away one part it is rendered meaningless because it is its own context. ID’s analogy between designed structures and biological structures not only fails to distribute the middle, it doesn’t even accurately depict design processes as we undertake them. People, the source of everything we know about design, don’t start cold from an undetermined purpose and design toward that purpose in an implacable, irreducibly complex chain of events. Replication may work a bit like that, but not design.

What this method really does is provide for a hierarchical relationship between presumed intent and biological structures, where the intent causes the structure. Such a relationship seems to allow for a supernatural cause. This is why ID’s advocates have gone through such contortions to make it work (or at least look like it might). Yet the intelligent design model fails even as a portal for the supernatural. It offers no solution to the interaction problem in dualism. This is a real problem because, as far as I can tell, one tenant of ID is that the design process in nature is ongoing. To drag a spiritual being into the material world and have it start doing things, one has to explain how it does so without being in some way beholden to the same laws, and thus part of the same causal history, as the rest of matter. If there is no good explanation, then the spiritual being from another realm is just a bizarre, unexpected new part of nature. Though this may seem an obscure technicality at first glance, here is an example of just how sticky the problem really is.

Descartes tried to defend the independence of the mind from brain processes. He offered the analogy of a virtuoso violinist asked to play on a broken instrument. The listener would have no clue as to his true skill. Likewise the damaged, diseased, or intoxicated brain may just be a broken instrument unable to give voice to the intact mind which plays upon it. Unfortunately, this analogy raises the question: May the virtuoso be a virtuoso without a violin? Study of music theory or any other purely mental operation is insufficient. He must play a physical violin. Yet the skill he gains is a mental faculty which is subject to his creativity, religious concepts, and emotion. The brain and its adjuncts affect the mind. There is no escape from this problem in a world of two supposedly separate substances in active contact. Deism or a strict idealism offer the only outs (and Deism may just push the problem back in time). Either of these scenarios keeps the supernatural supernatural, but thereby makes it irrelevant to any practical understanding of nature/matter. This is why it is best for religion that science adhere to methodological naturalism. This is why intelligent design is insidious as well as invalid, for all concerned. It robs religion of any hope of philosophical integrity, just as it misrepresents biology. Reason enough for everyone to drop this bullshit for good.

Tagged , , , ,
Advertisements