Philosophy of Science, or Philosophy vs Science?

A review of "Theory and Reality", by Peter Godfrey Smith, touching on a few criticisms and issues in the philosophy of science.

The philosophy "of" science has been fraught for decades, if not centuries. The usurpation of the theological explanation certainly rubbed many religious thinkers the wrong way, and modern philosophy has, perhaps unconsciously, carried on that rather adversarial tradition. A 2003 book by Stanford professor Peter G. Smith recounts the more recent back and forths in a judicious fashion. The modern story starts with the logical positivists of the inter-war Vienna Circle. They wanted to put science on a firmer footing by describing a logical basis for the scientific method. While scientists were groping in the dark, they, with their logical powers as philosophers, were going to straighten out the whole field. Never mind that, at the very same time, Gödel and others were showing that even logical systems have their limits, quite apart from the details of how they are applied to what we (so naively!) call reality.

A logical positivist.

The logical positivists were a little like the behaviorists- they tried their best to ignore invisible abstractions and hidden causes. They were obsessed by language and clarity, attempting to make of scientific language something purely empirical, linked at every point to directly observable entities and tests. This language was also supposed to be comprehensive and simple, hopefully mathematical in nature. And everything "scientific" would then end up being proven and lock-tight. However there were many problems, some inspired by the arch-skeptic, David Hume.

One was the problem of induction. While the sun has come up over 4 billion times, and reliably in our personal observation, there is still no guarantee that it will rise tomorrow. Such a prediction, premised on the inductive logic that since the sun has always come up, it will ever do so, can never be "proven". It can only be a matter of probability, confounded by the next black hole to come sailing through the solar system. The positivists and others trying to put the routine scientific logic of explanation and induction on a footing of certainty could not do so, however hard they tried. Even calling our most regular and elegant findings "natural laws" doesn't help. They remain founded on the clay of repeated observation and probabalistic extrapolation, not gold-plated logic (except for relations that are actually mathematical, like the symmetry laws of Emmy Noether; yet these rely on other observables for their premises, so ultimately rest on contingent properties of the universe). There was a sort of mathematics envy going on, as philosophers obsessed with making sense of physics yearned to make everything provable.

But that is not possible. Our findings about the world, however carefully observed, elegantly abstracted, and powerfully predictive, are necessarily probabilistic generalizations. Late in Smith's book, he delves into Bayesian logic and its stong attractions to philosophers as a way to represent probabilistic representations of the claims of science. Smith is dubious, and hopes for another solution, but it is important to point out that Bayes' theorem is not just a technical innovation to parameterize our belief and doubt. It is a solution for the whole problem of induction, which is to say that our expectations for certainty (whereby it is called inductive logic) need to be fundamentally tempered. An earlier breakthrough along these lines happened from Karl Popper, who offered disproof as the coin of the scientific realm. Perhaps, since nothing could be inductively proven, scientists could just work in disproving bad hypotheses, and leave it at that. But that is not how science works either. More on that below.

There were many other problems with the logical positivist program, such as an inability to make of language a pure, clean, perfectly observation-based mode of expression. No, languages of any kind presuppose large networks of meaning that have to be learned, and imply ontologies (unseen and abstract, no less) which model some version of reality, including hidden aspects. The whole positivist program is now a historical curiosity, (though its empiricist aspects are far from dead), but it paved the way for other, sometimes even more extreme approaches.

The most devastating critique was a social one. The 60's and 70's brought philosophers who looked more closely at what scientists did, and found that, far from following the dictates of the logical positivists, or at least those of Popper, they were behaving a lot like humans, with pet theories, a mania to prove themselves right, and petty squabbles over elaborate theories and the credit for them. Thomas Kuhn led the way, with an altogether nuanced and sophisticated picutre of the scientific process. Kuhn is probably the hero of Smith's book, and is rehabilitated in several respects. Kuhn devoted most of his main work to the process of "normal science", which goes forth within an over-arching paradigm that is largely uncontested, is inculcated by lengthy training (not to say indoctrination!), and digs ever deeper into the secrets of its field. Kuhn then followed with a description of the crisis phase of science. This is when paradigms change, and old verities no longer hold. He noted dryly that this is when scientists tend to become interested in philosophy! The clearest example is the quantum and relativistic revolutions in physics, which upended the stable, indeed Euclidean, Newtonian world.

To step out of the story briefly, it is imporatant to note here that, while Kuhn's story has given us the impression that such paradigm shifts are a necessary and continuing part of science, thus that nothing we know now is really stable or "true", that would be misleading. The Newtonian world lives on as a first approximation of reality- it was not discarded in any complete way. Equally important, some fields have really come to a final picture of their subjects. Molecular biology is an example. New things continue to be found and we have very far to go to unravel all the molecular networks that touch on health, not to mention consciousness, but the basic picture of DNA and its core processes are not going to change. Biology after Darwin could have been upended by the new technologies of genetics, microscopy, crystallography, and then of DNA. But it has not been- far from. Each innovation has only provided deeper and more detailed explanations of the theory of natural selection, in all its ramifications.

While Kuhn was very measured in his portrayal, his successors in social constructivist and postmodern philosophy let it all hang out, generating a decades-long body of work that, at its fringes, claimed that science was entirely socially constructed, and had no more say about the nature of reality than did the science of voodoo, which was at least the province of an oppressed and thus virtuous and authentic society. This fed on the age-old obsession of philosophy- what is reality? If observation is theory-driven, which everyone now agrees on, (in contrast to the logical positivists), how does reality enter our models of it? Obviously, there is a cycle (one might even call it a dialectic!) going on, of hypothesis, observation, evaluation, problem, and re-hypothesis. Our minds excel in making models, which then inform our observations, which then feed back (if we are paying attention) to those models. But a sufficiently motivated philosopher with a sufficiently narrow and uncharitable view of what is going on in science can come to a different conclusion. Smith provides a valedictory about this phase of his field:

"A lot of work in these fields has been organized around the desire to oppose a particular Bad View that is seen as completely wrong. The Bad View holds that reality determines thought by stamping itself on a passive mind; reality acts on scientific belief with 'unmediated compulsory force'. That picture is to be avoided at all costs; it is often seen as not only false but even politically harmful, because it suggests a passive, inactive view of human thought. Many traditional philosophical theories are interpreted as implicitly committed to this Bad View. This is one source for descriptions of logical positivism as reactionary, helpful to oppressors, and so on. 

What results from this is a tendency for people to go as far as possible away from the Bad View. This encourages people to asset simple reversals of the Bad View's realtionship between the mind and world. Thus we reach the idea that theories construct reality. 

Some explicitly embrace the idea of an 'inversion' of the traditional picture, while others leave things more ambiguous. But there is little pressure within the field [Science studies, particularly] to discourage people from going too far in these statements. Indeed, those who express more moderate denials of the Bad View leave themselves vulnerable to criticism from within the field. The result is a literature in which one error - the veiw that reality stamps itself on the passive mind - is exchanged for another error, the view that thought or theory constructs reality."

One author comes in for extra discussion- Paul Feyerabend:

 "Feyerabend was not, as he is sometimes portrayed, an 'enemy of science'. He was an enemy of some kinds of science. In the seventeenth century, according to Feyerabend, science was the friend of freedom and creativity, and was heroically opposed to the stultifying grip of the Catholic church. ... But the science of Galileo is nto the science of today. Science, for Feyerabend, has gone from being an ally of freedom to being an enemy. Scientists are turning into 'human ants', entirely unable to think outside of their training. And the dominance of science in society threatens to turn man into a 'miserable, unfriendly, self-righteous mechanism without charm or humor.' In the closing pages of Againt Method, he delcares that society now has to be freed from the strangling hold of a domineering scientific establishment, just as it once had to be freed from the grip of the One True Religion."

One can see how this ties in with the anti-intellectualism of the current Trumpian moment, and how the Evangelical movement sees its deepest interests in the construction and maintenance of an alternate reality that has been comprehensively threatened by intellect salvaged by a man like Trump, who shares their postmodern view about things like reality and its moral implications.

Smith spends the later parts of the book not on historical review, but on an effort to synthesize a more mature view of the field, taking a pluralistic view of what counts as evidence in science, and how the interaction with reality operates, ending up with a very reasonable view of the matter:

".. we might think of science as something like a strategy. In this sense science is the strategy of subjecting even the biggest theoretical ideas, questions, and disputes to testing by means of observation. This strategy is not dictated to us by the nature of human language, the fundamental rules of thought, or our biology; it is more like a choice. The choice can be made by an individual or a culture. The scientific strategy is to construe ideas, to embed them in surrounding frameworks, and to develop them, in such a way that exposure to experience is sought even in the case of the most general and ambitious hypotheses about the universe. That view of science is a kind of empiricism."

There are a couple more points that I would add to what Smith presents. First is about the role of criticism in science. This gets somewhat short shrift, I think, in favor of citation credit as the primary mode of motivation, yet plays a central role. Everyone is a critic- that is true in all walks of life and work. There is great power that accrues to scientists who brilliantly point out the flaws in others' work. This is why thesis committees exist, and peer review, grant review, group meetings, conferences, and much of the social apparatus of science, such as it is. Criticism, especially in public, inspires fear, which in turn inspires enormous efforts to address weaknesses in one's work. It is one of the primary motivations for scientists to make extra mental effort step outside their pet theories and obsessions- to strain to be "objective".

A second point is about another motivation in science, the ultimate one. This is not social at all, whether social approbation, credit, or fear, but is rather more spiritual: personal contact with reality. There really are eureka moments, in science as elsewhere, and they are tremendously fulfilling. All the care about details, the straining to be objective, and the acceptance of criticism, all function in the service of making contact with some new truth about the real world. Scientists are not Marines. They do not live and die for their band of brothers. They dedicate their lives to truth ... the pursuit we all share in some portion in our native curiosity to learn ever more about our world, but which, taken seriously, morally, and systematically, turns into the privilege of working full time to push forward knowledge about topics more or less obscure and useful, aka science.

It is an implicit recognition of the philosophical difficulties of dealing with and knowing about reality- this shadow world that we study incessantly, through our mental powers of modeling, but can never directly know. This is why students are given laboratory exercises, rote as they may be- to show that what seems so inert on the pages of their textbooks was once alive as a question which was answered by nature via a theory-driven and carefully constructed test. That the sought-after truth may be imperfect, tentative, and probabilistic is no matter. Any progress is better than none. And touching a new truth about how things work, which no one has witnessed before, after a lifetime spent feeding on the regurgitated knowledge of others, is truly addictive.

Smith's book finally shows a significant retreat from the glorious early aims of the queen of the sciences to rule over her dronish brethren. Philosophy may deal in big questions, but it is not very adept at answering them, or even posing them very constructively. Its lack of empirical engagement leaves it prone to the kind of appalling group-think that led the French constructivists and science studies acolytes so thoroughly off the rails. Its attitude towards science has been remarkably patronizing and counterproductive, not to say politicized and naive. Smith retreats to a far more humble descriptive, rather than normative, program of accepting pluralism in the methods and criteria of various sciences, and working, (one might say almost scientifically), to sort through and make sense of each of them in turn.

• Errol Morris blames Kuhn for postmodernism and scientific faith-ism ... which is unfair.
• Coming to terms with reality.
• Trumpire Putinesca. "Sater is the one who famously sent Cohen the email in 2015 that said 'I will get Putin on this program, and we will get Donald elected.'"
• Comey v McCabe.
• Pigs on Twitter.

mm-Hmmm ...

The critical elements of conversation that somehow didn't make it into the "language". A review of How We Talk, by N. J. Enfield.

Written language is a record of elision. The first written languages were hardly more than accounting symbols, and many early forms of writing lacked basic things like vowels and punctuation. The written forms are a shorthand, for those practiced in the art of spoken language to fill in the blanks, and they still hide a great deal today. For example, the same letter, such as "a" can stand for several vowel sounds, as in ate, art, ahh, am, awe. Another rich part of the language left on the editing room floor are completely unrecorded (except by authors of dialog looking for unusual verisimilitude) sounds, like um, ah, huh, mm-hmmm and the like. N. J. Enfield makes the case that, far from being uncouth interjections, these are critical parts of the language, indeed, part of an elaborate "conversation machine" which is one behavior that distinguishes humans from other animals.

Arabic, a language commonly written without vowels.

When we are in conversation, time is of the essence. We expect attentiveness and quick responses. It is a relationship with moral aspects- with obligations on each side. The speaker should repeat things when asked, not take up too much of the floor, provide clear endings to turns. Enfield describes a very disciplined timing system, where, at least in Japan, responses begin before the first speaker has stopped. Other cultures vary, but everyone responds within half a second. Otherwise, something is discernably wrong. One thing this schedule indicates is that there is a sing-song pattern within the speaker's production that signals the ending of a speaking turn well before it happens. The other is that there is an serious obligation to respond. Not doing so will draw a followup or even rebuke from the speaker. Waiting more time to respond is itself a signal, that the response is not what is desired.. perhaps a "no". It can also be softened by an "uh" or "er" kind of filler that again signals that the responder is 1. having some difficulty processing, and 2. paving the way for a negative response.

Likewise, "mm-Hmm" is a fully functional and honorable part of the language- the real one used in conversation. It is the encouraging sign that the listener is holding up her part of the bargain, paying attention to the speaker continuously. Failing to provide such signs leads the speaker to miss a necessary interaction, and interject.. "Are you listening?".

Finally, Enfield deals with "Huh?", a mechanism listeners use to seek repair of speech that was unclear or unexpected. When a response runs late, it may switch to "Huh?", in a bid to say that processing is incapable of making sense of what the speaker said, please repeat or clarify. But at the same time, if something of the original speech can be salvaged, listeners are much more likely to ask for specific missing information, like "Who?", or "where was that?" or the like. This again shows the moral engine at work, with each participant working as hard as they can to minimize the load on the other, and move the conversation forward in timely fashion.

Huh is also a human universal, one that Enfield supposes came about by functional, convergent evolution, due to its great ease of expression. When we are in a relaxed, listening state, this is the sound we can most easily throw out with a simple breath ... to tell the speaker that something went off track, and needs to be repeated. It is, aside from clearly onomatopoeic expressions, the only truly universal word among humans.

A conversation without words.

It is a more slender book than it seems, devoted to little more than the expressions "uh", "mmm-Hmmm", and "Huh?". Yet it is very interesting to regard conversation from this perspective as a cooperation machine, much more complex than those of other species, even those who are quite vocal, like birds and other apes. But it still leaves huge amounts of our face-to-face conversational engine in the unconscious shadows. For we talk with our hands, faces, and whole bodies as well. Even with clothes. And even more interesting is the nature of music in relation to all this. It is in speech and in our related vocal intimacies and performances that music first happens. Think of a story narration- it involves not only poetry of language, but richly modulated vocal performance that draws listeners along and, among much else, signals beginnings, climaxes, endings, sadness and happiness. This seems to be the language of tone that humans have lately transposed into the free-er realms of instrumental music and other music genres. Analyzing that language remains something of an uncharted frontier.

• Machines can do it too.
• Varieties of technoreligion.
• Monopoly is a thing.
• Appalling display of religious fundamentalism: The US ambassador to Israel refers to old testament and 3,000 year old rights of Israel. If other 3,000 year old land claims were to be honored, the US would be in substantial peril!
• In praise of Jimmy Carter.
• Collapse or innovation.. can we outrun the Malthusian treadmill?
• Truth and Rex Tillerson.
• Sunlight makes us feel better.
• We still have a public sector pension crisis.
• Economic graph of the week. Worker quit rates are slowly rising. Will that affect pay?

The Biology of Fluoride

Fluoride has no biological functions, other than the need to get rid of it.

Fluorine is the smallest and most reactive halogen, a relative of chlorine, bromine, and iodine. Chloride is ubiquitous in salts and in the ionic milieu of our bodies, and iodine has found a central role in metabolism in virtually all species. Even bromine has various biological roles, though mostly in microorganisms. Fluorine, however, has found no role at all, despite being relatively common- more abundant in rocks than chlorine, let alone bromine or iodine. Its only part to play is as a noxious ion to get rid of. And all organisms have ways to get rid of it, via both active and passive trasporters. More on that below.

Humans, in their wisdom, however, have found some remarkable uses for fluorine. Modern chemistry uses it a great deal, to make very tough chemicals like Teflon, Lipitor, and Lexapro. Virtually nothing displaces fluorine from carbon bonds, so its compounds, while very useful, also end up as rather persistent waste products. More interesting, however, is our practice of ingesting fluoride (the ionic form of fluorine) in small amounts for oral health. This has been a subject of tremendous controversy and conspiracy theorizing for decades. But the benefits couldn't be more clear- teeth are much tougher from trace topical exposure to fluorine, which works its way into the crystal structure of enamel.

However, ingesting fluoride is another matter. It is reputed to cause kidney problems at higher concentrations, but there is very little epidemiology to support claims that these risks start at low concentrations.. anywhere near the levels used in drinking water supplementation. Similar to observations of bone deformities and tooth fluorosis, the syndrome of too much fluoride common in geologic regions with excess fluoride, there would have been observations of rampant kidney or other disorders. But that doesn't seem to be the case, other than very sketchy reports. At any rate, the therapeutic dose of fluoride put in water supplies is about 30 micromolar, while the newest regulations in the US establish a conservative cap of about 100 micromolar, in light of the lack of any use for higher concentrations, and the occasional problems from higher natural exposure, top which the artificial amount adds.

So we can't do much with fluorine, biologically speaking. Indeed it is generally toxic, messing with the phosphate chemistry that is central to all life. How do we get rid of it? There are three mechanisms, overall. In animals, our kidneys take care of it, using clever ion transport to excrete excess fluoride. (Recall that the first step of the kidney's work is to remove all the small solutes from blood plasma, and then later to selectively bring back the important things we want, like sugar, some salts, lactate, water, etc. The remainder that is not actively re-absorbed includes such oddities as fluoride.)

But other organisms that live directly in the soup, i.e. microorganisms, all need to take specific and active measures on the cellular level against fluoride. An important point in this chemistry is that fluoride has a significant acid-base preference. HF forms at relatively high pH (pKa of 3.4, much higher than HCl, which stays ionic to pH 1 and below, an oddity of fluoride's chemistry), which means that in moderately acidic environments, external HF can easily form and diffuse into cells as an uncharged entity, and there, under more neutral conditions, dissociate and be trapped as F- ions. This leads to chronic over-loading of cells with F-, (up to 30X over external levels), which can be remedied by a protein channel (second mechanism) that lets these ions back out passively, while not letting out other ions such as the closely related chloride. The third mechanism, exclusively used by bacteria, is active antiport, (H+/F-), using the stored energy of the proton gradient (high outside, low inside) to drive F- excretion.

 

Structure of two copies of E. coli-derived Fluc, a passive fluoride channel/exporter. The proteins are blue and yellow, respectively, the membrane represented by black lines, and the fluoride ions are modeled as gray or red balls. Given the symmetry of the proteins and their passive role, the orientation (up/down) makes no difference. The channel is formed at the interfaces between the two proteins.

A recent paper described the simple passive transporters that are ubiquitously used for fluoride export in microbes. They are odd in that it takes two proteins to form a functional transporter. The channel through which the F- ion passes is on the surface between the two proteins, in a symmetric structure that forms two channels (above). In eukayotic microbes like yeast cells, two such genes have become fused to form one gene encoding a protein that retains dimeric symmetry, but one of whose channels has become non-functional / vestigial.

A close-up view of one of the channels, showing some of the key individual amino acids that coordinate / bind to the fluoride ion as it travels along. This close physical and electrostatic coordination insures that nothing that is not fluorine can get through. Notably, part of the job is done by uncharged phenylalanine residues, (blue and orange ring structures), which are usually regarded as hydrophobic, but have a slight face/edge polarization that can be exploited by strong ions

The channel is, understandably, very tight, with intensive coordination all along the way, particularly with uncharged phenylalanines which provide an unusual side-ways polar coordination that is proposed to make the channel particularly specific to F-, vs Cl-. And it is very selective- over 10,000-fold selective for F- vs Cl-. Replacing these phenylalanines with the hydrophobic amino acid isoleucine reduces F- transport to negligible levels. It would have been interesting to ask what a less bulky and less hydrophobic replacement like glycine or threonine does to the channel's activity, perhaps making it significantly less selective, while still functional.

• Unfit to serve on a sewer board, cont. Climate, shimate.
• Desperate US military and allies have lost ground.
• Antitrust should not be just about consumers.
• Property is monopoly.
• Tourism makes up 8% of carbon emissions.
• Lowdown on money laundering.
• Driving remains dangerous.
• Some non-profits are not so non-profitable.

Green Power

California's open political structure opens the opportunity for the Green party to create a revolution.

A recent op-ed in the local paper by a Republican party official complained about California's open primary system. This system runs primaries and general elections without regard to party affiliation. The top two finishers in the primary run against each other in the general election. In California, this has resulted in many state-wide races being contested between two Democrats. The Republican party no longer has a lock on one position on the general election ballot as they used to, and this naturally rankles. The editorialist complained pathetically about lack of diversity (of all things!), and how the choice between two Democrats was so limited. It was whining at its most exquisite.

California has frequently been in the political vanguard, whether in tax revolts or in progressive climate change policy. The 60s were headquartered here. California has put redistricting on a non-partisan basis. The open primary system has been a dramatic success, giving the best two candidates a hearing before the voters in the general election, and reducing partisanship and cronyism in the state. One side benefit is that voters can register with a minor party without the penalty of being locked out of the key primary races, which are no longer parochial, but open to all. This new political landscape (which was the beneficent and ironic gift of Arnold Schwartzenegger) could lead to another progressive advance, in the form of a revitalized Green party.

Trends in party affiliation in California. Greens come in at 0.62%- currently negligible.

The Democratic regime in California has not been a bad thing on the whole. Under Jerry Brown, who operates as a centrist, the drama surrounding budget battles and other fringe issues has been sharply reduced. Except for the pension crisis, the state has been quite well run, if inefficient. Advances in climate change regulation, marajuana legalization, gun control, and formal resistance to the Trump administration are generally appreciated. Trump is reviled. Education and infrastructure funding remain dreadful. There is little stomach in the state for a return of Republicans as the opposition, (they are now legislatively locked out of veto power), which would bring back endless bickering and corrupt dealing. There is, however, room for less corporatism and more progressivism, which is what a stronger Green party could provide.

The Green party currently is not much healthier than the Republican party, unfortunately. In California, it fields a grand total of 60 office holders, none of which are statewide. Its web sites and organization seem moribund. Due to the two-party structure at the national level, it is unthinkable to support it in presidential races, where it would be a spoiler to benefit Republicans. But with open primaries in California, the party could cultivate a state-wide program and candidates, while vowing to back the Democratic party (or whichever party is more aligned with Green objectives) in races that are significantly contested by Republicans, which is to say, effectively support the left. That would provide a solid platform for activism within the state, building the movement and the party.

Each non-presidential race would have to be carefully evaluated for whether the participation of a Green candidate would raise the chances of Republican / Conservative victory significantly. In primaries, this is likely be a negligible risk as things stand. At least one Democrat will always win in non-rural districts. For the general election, if a Green candidate is not running, Greens would support the Democratic candidate, or whichever one most agreed with the Green agenda. This would make for a sort of mature, parliamentary-style politics, where coalitions are assembled in response to conditions.

Oddly, however, the Green party is officially against the open primary system, mistakenly thinking that the loss of a coveted (though pointless) automatic spot on the general election ballot outweighs the decisive gain of flexibility for their voters and sympathizers in the primary election. They want something still better, like proportional representation, logic that to me seems maybe nice in theory, but self-defeating and irrelevant in practice. Worse, the national Green party is a disaster, indeed a toxic blight on the left, pushing its presidential candidate in the teeth of all logic and experience. That is no way to succeed.

The Republican editorialist bemoaned the lack of competing perspectives and arguments in California politics. But the voters have decisively rejected the Republican program of meanness, business cronyism, labor expoitation, environmental degradation, and xenophobia, which has only become more extreme and blatant on the national level. Maybe the discussion that voters in the state really want is one between Democrats and those who want progress to go even faster- toward single payer health care, faster de-carbonization of the economy, more effective business (and internet) regulation, and more balanced housing and transportation growth, among many other issues. The climate is shifting.

• Change your party registration right now!
• We are choking on zoning.
• CO2 is not only rising, but rising faster than ever.