On the mythology of natural selection. Part X: Finally: Traveling evolution's geodesics

Science recognizes Charles Darwin's contributions to knowledge because he was a deep thinker who largely transformed a whole area of human knowledge in ways that seem likely to be permanent.   One often refers to such inspirational figures by coining terms to acknowledge their views.  'Darwinism' is one.  To name a concept after him is entirely deserved (even his co-recognizer of the salient facts of life as an evolving history, Alfred Wallace, in 1889 referred to the idea with the very title of a book summarizing the field: Darwinism: An Exposition of the Theory of Natural Selection, with Some of Its Applications).

By greatly honoring his name, science and history recognize his contributions.  But his work is not to be read exegetically as a source of The Word.  He's respected, but not sanctified.  No scientist we know of  checks what Darwin said as a means of testing whether something is true or not. This is science; exegesis is for historians.

Charles Darwin would not want a halo!

Darwin would want it that way ("And get that halo off me, please!").  He was a brilliant, doggedly thorough and persistent gentleman scholar.  His works are a wonder to read, because he was a keen and incredibly patient observer and a master synthesizer of reams of data from various fields.  But he was human and lived in the times in which he lived and with the knowledge and technologies then available.  Even he, the developer of the selectionist 'law' of nature, mainly offered hand-waving assertion and circumstantial evidence, but definitely did not in the Origin of Species by Means of Natural Selection show that the origin of species was by means of natural selection.  If you doubt this, read the Origin yourself, especially Chapter IV.  But that's a topic for another day.

Nonetheless, we think that Darwin's view of natural selection as a universal determinative law to account for the evolution of the traits of organisms has become widely and without deep thought adopted as a given rather than a matter of science to be examined in the real world.  This is in many ways taken almost directly from Darwin's personal view, though most who use the term have done little if any actual reading of Darwin's voluminous works.  Such a worldview becomes dogma, or the assumption of a belief system, an ideology, rather than science, as we have tried to show in this series. That is the sense in which we discuss its mythology--the tales told and assumptions made about it that don't reflect what we actually know, and don't know.

The public and professional literature are awash in 'gene for' or 'evolved for' assertions that go largely unquestioned (thoughtful, pointed reviews of this season's recent pulp eugenics book excepted).  Such stories about genomic causation or reconstructions of evolutionary history are often expressed as if they explain traits in question, but by equating plausibility with truth in fact verge on tautology, and serve preconceptions rather than testing how the living world actually works.  The pervasive explanatory 'ether' that is invoked, is natural selection.  Most biologists probably don't quite realize how close they come to explanations that would be the same if God's will were used instead.  That universal acid or Darwin's 'dangerous idea', as one philosopher referred to it, is indeed dangerous both to human society and to science.

In this series, we have discussed various ways in which purely historical processes of proliferation and divergence from common ancestry can potentially account for aspects of the origin of complex traits within organisms, and by extension among organisms, that are not due, or not just due, to natural selection.

Our objective has not been to denigrate the idea of natural selection, but to show that there are other entirely natural processes that can lead to the evolution of complex traits.  Evolution and genomics are not just one-trick ponies.  As we have noted, how and when (or even whether) these processes are at work is a matter that can be studied by clever designs or choice of material--they are testable ideas.  In fact one of them suggests that natural evolutionary historical processes could generate complex traits without any involvement of force-like natural selection at all.  However, if one clings to a selectionist ideology, selection as an axiom rather than a scientific assertion, then of course one will never even ask the questions as to whether such ideas might be correct, much less test them.

We can, however, ask a far more fundamental question, which is how selection works when it does occur.  For this, and as elsewhere in this series, we suspend skepticism for the moment and take universal, Newtonian force-like natural selection as a given.  To try to make our point, an analogy to astrophysics might be instructive.

The 'spacetime geodesics' of evolution by natural selection
In cosmology--the real thing--travel in the universe is governed by relativistic spacetime.  An object at any time moves in a way that is determined by its motion at the time and the gravitation field--one might say the gravitational 'ecology' due to the physical objects in the area.  The bigger or closer another object, the more spacetime is curved.  But the net curvature is the total of these effects in this location in spacetime.  We use the term because on the cosmic scale, space and time are inseparably part of the nature of existence.  We can say that the past has existed and, from our vantage point, we can get a glimpse of it from the distribution of matter and energy at the present time.  In real cosmology, we can also 'see' the future to the extent that we can know and (in principle, at least) predict the state and location of the objects towards which our object is moving.  Any object in motion essentially integrates all of the forces acting upon it, and moves through spacetime accordingly.  Unless driven by some separate impulsive force, the path it follows is determined by these local spacetime properties, and is known as a geodesic, which one can think of as the shortest path between points spacetime.

SpaceTime trajectory real and imaginary (modified from GoogleImages)

If the object of our interest is affected by several small local objects in the area, it meanders geodesically past them.  If or when there is a large nearby object, it follows a more greatly affected curvature around it (blue inset).  At the end of a period of interest (which we call now), and if we knew the location of the point at our chosen starting time (then), and we're oblivious to what happened between then and now, we can always assert that what happened was that the object of our desire was shot by a specific force directly along that path (shown as dotted arrow).  

But that assertion is a fiction, and science is supposed to be about fact.  That fact is that our object got to now through a path that essentially had nothing to do with now--it was not aiming toward now, its movement at any time was locally determined, sometimes by major (one might say clear-cut) factors, often by a host of minor even seemingly trivially small ones, collectively setting up the position at the next major influence.  Note that in our cosmic analogy all of our object's meanderings are considered to be totally determined by the shape of gravitational spacetime--we assumed that no probabilities were involved.

This should be enough about spacetime geodesics in astrophysics.  The point of the analogy should hopefully be clear.   Even if the implicit complete determinism of Darwinian assumptions were true, the complex dynamic nature of earthly ecologies means that an evolutionary geodesic need not follow a retrospectively reconstructable path from then to now.  A species or trait need not have evolved 'for' its current use, not even in stages aimed in a particular direction, not with its various components evolving synchronously or even sympatrically.  Indeed, if and where ecologies are complex and dynamic, the meanderings of our object--a trait or species--may be essentially indistinguishable from random movement relative to any long-term 'purpose'.  

An organism is a collection of traits, often correlated by shared genomic mechanisms, that are continually being pulled every which-way by selection of various intensities for various reasons (the nearby gravitational objects).  These pulls are based on the local context, and that context (the 'stars' etc. in the area) change over time and space--over evolutionary 'spacetime'.  The position in the future may not be predictable from its local conditions at any given time: evolution has no 'momentum' by which the past actively propels species through the present--or if it does, we need a much-revised theory of its causal dynamics.

The shape of the head (something I've worked on with collaborators for years) is measurable in its many dimensions, and we can look at fossils and comparative species, some of whose evolutionary past history we shared through common ancestry.  But the head is not a unitary trait, perhaps not a very meaningful trait to ask about its evolutionary trajectory in selectionist terms. The length of the face, say, need not have evolved 'for' language, or reduced smell, or balance in upright posture, or change in diet, or forward-looking stereo vision, or.....  

These factors and their importance for 'fitness' need only be synchronized if they share genomic pathways, and otherwise need not be synchronous in time or space, and the 'same' trait can serve multiple or even changing functions.

As one zooms one's lens closer and closer, the picture dissolves into every more graininess. No two individuals have the identical trait or genotype. We don't see 'spandrels' or other states that set the stage for the trait as we see it today. We don't see a ladder of discrete improvements towards today. No punctuated equilibrium, saltations, and the like except as we choose to impose them on our observations. To the extent the picture given here is apt, each local point in evolutionary spacetime is so local, so dependent on its context at that instant in time, that it need not suggest the kind of longterm arrow from then to now that is so commonly explicit or explicit in our texts, papers, and so much of the rhetoric even in professional biology.

Realizing in this way how things are--or at least might be--under deterministic assumptions, it is now time to re-introduce the other complications discussed in this series, including chance in its many manifestations, at the scales of change that are relevant.  The 'geodesic' path of evolution meanders in no one direction, by no one cause.  Even if it is 'driven' by selection at every instant, it is a path whose determinants are problematic to identify in practice. Whatever is the truth, selection is not obviously simple in a force-like way. 

And here's something to think about:   Scientists often say that the simplest--the most 'parsimonious' explanation is the preferred one most likely to be true.   In the case of our cosmological analogy, I think it's right to say that the straight-arrow path from then to now is not the simplest explanation of the change!   In fact, it may be among the least simple explanations.  That's because the geodesic path is actually the simplest: it only involves the explanation that the path follows spacetime curvature (e.g., gravity). In that sense, that is the 'straight' path.  Given the complexity of space, you'd need a host of ad hoc reasons to try to account for the usual notion of a 'straight' path (like our dashed arrow).  

The same can be said of evolution.  The straightest path is that which follows the dynamic local 'pulls' of selection; to avoid following that path, as if somehow 'insisting' on a direct rather than geodesic path from then to now, it would have to resist the myriad local conditions to keep on that path--and that then becomes teleological!  Is that a suitable 'simpler' explanation?

As we navigate our search for truth, if we are not careful in our thinking we, like Odysseus, face the twin threats of Scylla and Charybdis:  the mesmerizing sirens of examples of strong recent or artificial selection that can lead us onto rocks of extrapolation to events on a slow, long time-scale, and there is a danger of being sucked into a whirlpool of complacency by taking criteria like DNA sequence conservation too casually.

Between Scylla and Charybdis; Wikimedia

Darwin's magnificent legacy

Darwin's realization that life today is the legacy of processes of descent with modification and differential proliferation, was profound and correct as far as anything we know.  (Somewhat separate from, but related to the effectiveness of selection, is that branching from common ancestry into distinct entities such as species that are isolated from each other was also part of the theory in Darwin's view, as it is of ours today.)  But none of this implies there is only one manner of differential proliferation nor that we cannot find and flesh out the basic concepts--even if there are no fundamentally different phenomena yet to be discovered.  For example, with organismal selection, genetic variation and its effects can be sorted out by the organisms in their various local areas, with no competitive differential reproduction required, and in that sense no nasty competition to the death, necessary.

There has been nothing spooky in our use of the analogy of an imaginary odyssey through evolutionary 'spacetime'.  We are not invoking heresies, that Darwin himself would not recognize. Indeed, what we have said may be imperfectly stated but is perfectly consistent with the long-standing insistence that evolution is locally contingent and not teleological.   But that in fact is inconsistent with the ubiquitous simplistic 'evolved for' and 'gene for' tales in the public as well as professional literature.

Just to be clear, with all of its nuances, including chance effects, evolution can be accounted for by historical, material processes; there is nothing that we know that requires any external force (as in religious arguments) to guide evolution. 

Just because a story is plausible does not make it either probable nor true.  Think of it this way:  The dashed arrow in our geodesic figure is the direct then-to-now path.  We can note that by comparing a fossil to its descendants we can always construct the usual simple, direct here's-how adaptation story. But not only is plausibility not the same as truth, but considering what we've tried to say in this series, perhaps such stories are least likely to be the truth!  Perhaps it's very naive to think, much less to assert, that such simplicity is what we should expect in our evolutionary tales.  Indeed, Darwin himself tacitly was led by temptation to make some similar assumptions, basically if implicitly and unintentionally teleological ones, in his books describing barnacle evolution.

What is important to us is the difference between a nuanced view, and the way people act and speak in practice (despite perhaps their being clever enough to include briefly-stated caveats).  One can always defend business-as-usual, the direct then-to-now Just-So story, by asserting that, "Yes, yes, all the details you mention are true, but they don't really matter in my example." But one should ask whether that's sincere rather than a dismissive acknowledgement-in-passing, a lazy excuse for clinging to a comfortable ideology--especially, but not only, when it comes to explaining human variation.  If so, the invocation of 'natural selection' is an exercise in mythology, in ideology.

Ideology assumes, science asks.

Anthropology's troublesome arguments

By Anne Buchanan and Ken Weiss

These last few months have been strange ones for anthropology.  So much linen being aired so prominently, dirty and otherwise.  First we had a best-selling book by science journalist Nicholas Wade that in effect defines the field as the science of genetically determined traits, declaring among other things that there are five human races and that anyone who doesn't accept the biological basis of race is motivated not by science but by politics -- unlike his own stance. Then we had two papers (here and here) in PNAS suggesting that one of the now extinct short people on the Indonesian island of Flores had Down syndrome. And now we have a paper, albeit in a less visible journal than PNAS, but nothing's invisible to Twitter, declaring that premenstrual syndrome evolved to keep women from staying with partners with whom they are infertile.

The Wade book, of course, has gotten a lot of press, both positive and negative, including a letter in the New York Times last week refuting Wade's use of population biology by a long list of population biologists, many of whom are authors of the work Wade cites in support of his own political views, although of course he doesn't see it that way.  The PNAS papers got huge amounts of publicity around the world, but very accepting, none that we saw questioning the hypothesis. The PMS hypothesis, on the other hand, has been critiqued as nicely as 140 characters allow (including by Holly, who red-inks it below (it's a Twitter thing), and blames PLS (pre labor syndrome) for any perceived snark).

Each of these publications happens to bring up deep and long-standing issues in anthropology.  The issues involve the usual scientific food fights, but over and above the specific details, there are problems, and it's these that we want to discuss today.

Troublesome arguments
We'll take these issues one at a time.  Enough has been written about Wade's book that there's no need to look at the specific arguments again.  It's a continuation of retailing Just-So stories and selective reporting and misreporting, that he's been doing for many years; it sells well and he serves a surreptitious audience that includes various shades of racist enmity, as well as readers who have no way to know better, including many anthropologists.

Fine.  What's interesting to us, in terms of the broader field of Anthropology, is that it has clarified how deeply politics affects what we all make of scientific 'facts'.  You've got your genetic determinists on the right and your gene/environment interactionists on the left, and if you know how someone feels about genetic determinism -- that what and who you are is basically set the moment you are conceived -- then you know a lot about how s/he feels about IQ, scientific racism, natural selection vs drift, the importance of adaptation in evolution, and indeed about immigration, Obama, economic inequality, and so much more.  Sociopolitical views are correlated with what one seeks, accepts, or promotes when it comes to science -- not just some purportedly objective truth.

Genetic determinism is an interesting hot button issue.  Too often, people believe either that it explains virtually all traits or explains none, but of course it's some of both.  Some diseases, e.g., are caused with high predictability by a genetic variant, some diseases are due to gene/environment interaction, and some 'causal' variants are fairly useless for disease prediction.  Even infectious diseases that can affect almost anyone, that is, almost any genotype, do so in concert with genes.  Genes contribute to every trait, directly or indirectly: without genes we would not be here, and genetic variation can affect almost anything.  But that is not the same as saying that they determine, or specify, every trait.

There are academics who have trouble accepting strongly genetic arguments, because they believe they are, as the phrase goes, 'politically incorrect'.  But behind the political incorrectness smear is of course a dark history of eugenics, lynchings, the slaughter of 11 million people during World War II, including Jews, homosexuals, disabled people, and more.  But further, even if all of genetic-deterministic arguments were fully supported by the science, and we all were to accept that, for example, 'race' is a clear-cut biologically determined category of humans, why would that justify unequal, and worse, treatment of groups we (those in decision-making positions) deem unequal to ourselves?  Unequal because science tells us so.  Science doesn't make value judgements -- people do.  That is why the assertion of such points, or even the funding of studies to find them, is itself a political act.

To the people whose politics are supported by the new 'genomic' version of scientific racism (the latter term, we think, was invented in pre-Nazi Germany), of course, those arguments are 'politically correct' and their generally left-leaning proponents are just idiotic know-nothings.  Not in science, but in scientific racism, it's perfectly fine to cherry-pick the data when making an argument -- and the argument is supported by white supremacists, people who see genes behind everything, people who believe that every trait is here because it was naturally selected, and so on.  Genetic determinism and other labels have become code for accepting inequality, for hording resources, for rationalizing us having and them not having, and this often goes hand-in-hand with racism and hate (often not openly stated, of course, but sometimes it is). It's hard to argue that's science, not politics.  And, the disagreement won't be solved by science.

The problem here is simply the facile telling of stories without anything close to a sufficient understanding of the available information, the mixing of how things are today with how they got here, the assumption that how they are today is driven by genes rather than by much stronger and more ephemeral cultural factors, and the simple assumption that everything simply must be simply explained by genetic natural selection above other evolutionary paths.  In these conditions, a measured discussion of the issues is not possible -- and by the conflicting parties with their agendas, perhaps not even desired.

Getting to now may have nothing to do with then
The PMS paper is interesting for a number of reasons.  First, the author is a biologist who, at least judging from his web page, works on genetic variation in non-human organisms.  Mostly not even mammals.  So it's curious that he's decided to, er, wade into the evo psych realm.  Evo psych can be troubling enough when the arguments are coherent, so this one is particularly troublesome. In "Were there evolutionary advantages to premenstrual syndrome?" Gillings repeats and then discounts a number of previous evolutionary arguments about PMS, and then argues that premenstrual syndrome or premenstrual dysphoric disorder are essentially universal and experienced by all women, so there must be an adaptive explanation for such a maladaptive trait.  And of course it has a genetic basis.

Ongoing bonding between humans is complex, depending on sexual and nonsexual behaviours, and on previous experience in the relationship. Where such relationships do not result in pregnancy, premenstrual hostility may cause varying degrees of rejection, both sexually and of the relationship in more general terms. It might then be conjectured that infertile pair bonds are more likely to break down, freeing both partners to pursue fertile mates (Morriss and Keverne 1974).

Women suffering from PMS are likely to direct their anger at current partners, Gillings suggests, but most often it is when they have no children, that is, when one of the pair is infertile (or the pair, together, is infertile), that this will result in the dissolution of the pairing.

So, PMS evolved to dissolve infertile couplings.  But Gillings then says that this wasn't a problem in hunter gatherer times because women then weren't cycling nearly as frequently as women today -- they were pregnant or lactating, or poorly enough nourished that they didn't menstruate.  In that case, it's hard to understand how this evolved.  Gillings argues, though, that modern cycling is maladaptive, and that it causes health problems, as well as disrupts family dynamics with this genetically driven monthly bearishness of women.  He goes on to suggest that women should consider using cycle-stopping contraception (rather than, say, suggesting men should offer chocolate and not take it so personally).

But wait a minute.  First, a trait can only be selected if it's visible to natural selection.  It has nothing to do with whether people are paired up or happy (unless these are requirements for reproductive success, and the former is, according to some widely held evo psych-type assumptions), and it must be based on genetic variation, not cultural patterns.  If women weren't cycling regularly, and there's a lot of evidence that they weren't until modern times, how could PMS adaptively evolve if it didn't exist in any significant form?  And second, as Ken pointed out in his series a few weeks ago on the mythology of natural selection, there are many other ways that traits can evolve, including a series of reasons we might have no ability to guess, and including by drift relative to any Just-So story we reconstruct as if we got here in a straight adaptive line from then to now.

Like Wade's book, this paper makes the all-too-frequent mistake, in evo psych yes, but in anthropology -- and increasingly in other fields as well -- of assuming that every trait is adaptive, is here because of natural selection, and is thus genetically determined.  And that if we can build a plausible argument, it must be true.  And that the way it functions today is the reason for its evolution.  But, let's call this the geodesic fallacy.

SpaceTime trajectory real and imaginary (modified from GoogleImages)

See Ken's final post on the mythology of natural selection for the details, but here's the gist:

Even if the implicit complete determinism of Darwinian assumptions were true, the complex dynamic nature of earthly ecologies means that an evolutionary geodesic need not follow a retrospectively reconstructable path from then to now. A species or trait need not have evolved 'for' its current use, not even in stages aimed in a particular direction, not with its various components evolving synchronously or even sympatrically. Indeed, if and where ecologies are complex and dynamic, the meanderings of our object--a trait or species--may be essentially indistinguishable from random movement relative to any long-term 'purpose'.

It's very easy to make up adaptive scenarios.  That's why they are called Just-So stories.  And they are seductive.  But elegance or cleverness doesn't make them right.  Indeed, most often we have no idea if they are right, or even how to test them.

Again, the problem here is simply the facile telling of stories without anything close to a sufficient understanding of the available information, the mixing of how things are today with how they got here, the assumption that how they are today is driven by genes rather than by much stronger and more ephemeral cultural factors, and the simple assumption that everything simply must be explained by genetic natural selection.

Lumpers and splitters
The Flores controversy, of course, well-known in anthropology, has been ongoing since the first report of the findings of bones in Liang Bua Cave on the Indonesian island of Flores ten years ago.  The bones were from individuals obviously much smaller than other known hominids of the time, prompting the discoverers to declare them to be representatives of a species of human new to science.  The authors of the current re-interpretive papers on Flores at the time argued that no, these bones didn't represent a new species, but instead at least the one intact skull that was found represented an individual with microcephaly.  Now, it's an individual with Down syndrome.

LB1 skull: Wikipedia
 (associated postcranial remains can be seen here)

However, the argument is based on assuming that it's possible to definitively diagnose Down syndrome in a skeleton (among the many possible skeletal indicators of Down syndrome, most are not found exclusively in people with DS)  and that the asymmetry in the skull was present before the individual died, and not the result of thousands of years of burial, that this individual reached adulthood, and without modern medical care, that's less likely, all at least questionable assumptions.

But suppose LB1 really did have Down syndrome, then what?  Then it is completely irrelevant to any population or evolutionary argument.  One can argue about the Down diagnosis, a subject best left to actual experts of which there are many, but it matters not to the issue of whether the population experienced the very commonly observed evolutionary phenomenon of island dwarfism.

Cave where the bones were found: Wikipedia

This then gets into a very long-standing argumentation between those who tend to name each new fossil with a separate species designation (often called 'splitters' in evolutionary biology), and those who see a range of variation within species and argue that what we have found in the fossil record are representations of that variation, not of different species.  The latter are the 'lumpers'.  The snide and over-puffed Flores papers seem to be at heart a jab at those who see the Flores specimens as representative of a different species from the southeast Asian mainland.

Of course, 'species' is itself a largely subjective subject.  Even the idea of reproductive isolation is very hard to prove.  How many matings does one need to try to show that they never produce fertile offspring?  Usually, of course, and certainly with fossils we cannot do that directly!  The species problem has been debated for more than a century.

Were Neanderthals and early 'modern' Homo sapiens separate species?  Many would say so.  Are the recently prominent 'Denisovans', fossils from a region in Northwest Asia, a separate species?  They have separate names, after all!  Yet because they are recent enough, and perished under fortuitously helpful conditions, we have DNA from them.  And to date, the evidence suggests admixture between them (with remnants of both in modern humans today).  So: separate species, or not?

The arguments are heated among anthropologists about these sorts of issues and the more-heat-than-light regarding the Flores material reflects that.  There is, after all, a whole lot of publicity in the media for stories that sell, like tales of human fossils.  Anthropologists, whose field is often not all that rigorous given the problems of reconstructing the past, are particularly vulnerable to promoting their finds as different, or blasting their peers for doing so.  The media circus loves anthropologists, and anthropologists love it!

In these areas, the controversy is stirred up by the journals and the media.  Every week outrageously poorly supported evolutionary stories appear in journals and are eaten up by media reporters who either don't know the science, don't probe as they should, or don't care to be informed because the objective is to sell copy, and to do that content must be found.

Whether we'll see a day when appropriately measured questions can be asked and discussed, even if they can't really be 'answered', isn't clear.  Probably not in our lifetimes.

Who speaks for the facts?

Everyone else is speculating on what happened to Malaysia Airlines Flight 370, so we don't have to. The one thing that most people agree on is that the plane met a tragic end, and we pause for a moment to recognize the pain and sorrow this has caused so many people. But, the wide range of hypotheses is fascinating, and we wanted to briefly consider why there are so many and what this might say about science.

We don't need to rehash the possibilities, which range from simple accident to malicious intent on the part of one or more passengers, or even the pilots.  Indeed, you can generate your own conspiracy theory right here.  E.g.:

But a new hypothesis is intriguing and puts the rest in stark relief -- a piece over at Wired, "A Startlingly Simple Theory About the Missing Malaysia Airlines Jet", written by a pilot named Chris Goodfellow, is a reminder that perspective is everything. Well, informed perspective.

Goodfellow says:

There has been a lot of speculation about Malaysia Airlines Flight 370. Terrorism, hijacking, meteors. I cannot believe the analysis on CNN; it’s almost disturbing. I tend to look for a simpler explanation, and I find it with the 13,000-foot runway at Pulau Langkawi.

He goes on to say that pilots are trained to always know where the closest, safest airport is if something were to happen to the airplane they are flying.  He says the pilot of Flight 370 must have landed at Pulau Langkawi many times, and that he must have realized that there was an emergency on board, and turned toward that airport, knowing it was the closest place he would be able to land.

What I think happened is the flight crew was overcome by smoke and the plane continued on the heading, probably on George (autopilot), until it ran out of fuel or the fire destroyed the control surfaces and it crashed. You will find it along that route–looking elsewhere is pointless.

Goodfellow says this fits all the data, from the loss of transponders to the turning of the aircraft.  He is appalled that people are considering the pilot to have had malicious intent, when in all likelihood -- in fact Goodfellow is certain -- instead he acted heroically.  See his post for the detailed explanation.

Our point here is not to explain what happened, because we have no idea, but to take a look at how hypotheses are made, and how they are evaluated.  Goodfellow is an old and experienced pilot.  He is evaluating the data from inside the pilot's head, and it turns out that his is probably the most parsimonious explanation.  And, as everyone knows, a parsimonious explanation is always the best explanation.  Occam's razor.  And add to that that 'experts' are assumed to have judgment as to what explanation is most parsimonious.

Fossils from the Cretaceous, found in Lebanon; Wikimedia

Except that parsimony is an arbitrary measure of the quality of data assessment.  The basic idea, and it certainly has much merit, is that when a simple explanation will do, adding other variables and explanations is not called for by the data and as a general principle we avoid making explanations more complex than they need to be to account for our data.  Which is not to say that parsimonious explanations can't be the best, just that parsimony itself isn't why they are the best.

Everyone is working with the same data on this airplane mystery.  But terrorism experts see evidence of terrorism, mechanics see sure signs of engine trouble, and so forth.  It's the pilot who can imagine himself in the pilot's seat who, at least to us, makes the most sense.  Not because of parsimony -- do we have good reason to think that the flight tragedy was due to one thing only?  An electrical failure or fire, or a hijacking, or sudden gain in altitude that knocked everyone, pilot and passenger, out cold?  Normally, in this case, we would not think that there was, say, a hijacking and then an on-board fire.  That would be complex compared to just one of those--but how would we know that more than one event didn't account for things?  The hijackers could have jerked on the controls and sent the plane too high, which knocked everyone out, etc.

Also, of the separate hypotheses, is there really at this stage a good reason based on parsimony to choose one over the other?  Each author has his own idea, or advocacy.  The pilot's explanation seems to make the most sense because he's a pilot, and can evaluate the evidence as if he'd been flying a troubled plane.

And in science
Everyone saw the same world Charles Darwin saw in the early to mid 1800's, too, and only he and Alfred Wallace made lasting order from the data, suggesting that the diversity of life is the result of descent with modification from a common ancestor via natural selection, and the fact of evolution is confirmed every day in biology labs around the world.  Alternative explanations for the origins of the diversity that everyone saw around them were many; then as now fundamentalists saw the hand of God and, fossils were thought to be 'sports of nature', not evidence of extinct species, because God wouldn't have made species that went extinct.  A case can be made that Darwin lost his faith after the death of his daughter, Annie, and a theory that didn't require a divine being was one he could readily accept.

One argument against the God argument is that God would have had to have a separate reason for making insects have 6 legs, but not spiders or lobsters, and vertebrates four, but not fish or birds, who have fins and wings.  That is, God made a separate, unique decision about each creature.  That is more complex than saying evolution and common ancestry generically account for what we see. 

Now evolution is different for every creature, just as God's choices would have been, and 'God's choice' is as parsimonious as 'evolution', so the criteria for what is the empirically simplest explanation does involve some subjective judgment.  If evolution is a true generic explanation for life and its diversity, and all the evidence suggests that it is, we tend to seek the simplest evolutionary explanation.  Still, nothing guarantees that an ad hoc phenomenon like evolution has to go from A to Z by the shortest path!

Indeed, there are even those who question the 'obvious' physics principle that radiation like light travels in 'straight' lines (here, modern physics might say 'geodesic' lines in spacetime).  However, some physicists say that energy takes infinite histories all at once, and that the straight-line path is not 'the' path but the average path taken by the radiation.  That puts a twist, so to speak, on parsimony ideas.

And in genetics, everyone has access to the same data, when GWAS results are reported, or genome sequences uploaded to GenBank, yet some geneticists see simple answers and some see complexity. And evolutionary psychologists see adaptive explanations where others might see genetic drift. And many look for one explanation -- this gene, or that bad lifestyle -- even when it is blatantly obvious that genes and lifestyles have effects only in their overall context.  So what is the most 'parsimonious' explanation is debatable and we have no real rigorous way to adjudicate in many instances -- even if we would all agree that we don't invoke a gene plus the tooth fairy plus raging storms on Jupiter to account for a case of cystic fibrosis.

Observations don't speak for themselves, in science or forensics.  It is through the mouths of subjective observers that they speak, observers with more and less credibility.  Who we choose to believe is in turn affected by our own subjective decisions, not usually an evaluation of which argument is more parsimonious.  Parsimony can be one criterion, but it may not be 'the' true explanation, or even the best one.  Life, due to its meandering and highly probabilistic pathways, may be one of the least parsimonious phenomena that science tries to understand.

Darwin the Newtonian. Part IV. What is 'natural selection'?

If, as I suggested yesterday, genetic drift is a rather unprovable or even metaphysical notion, then what is the epistemological standing of its opposite: not-drift?  That concept implies that the reproductive success of the alternative genotypes under consideration is not equal. But since we saw yesterday that showing that two things are exactly equal is something of a non-starter, how different is its negation?  

Before considering this, we might note that to most biologists, those who think and those who just invoke explanations, non-drift means natural selection.  That is what textbooks teach, even in biology departments (and in schools of medicine and public health, where simple-Simon is alive and well). But natural selection implies systematic, consistent favoring of one variant over others, and for the same reason.  That is by far the main rationale for the routine if unstated assumption that today's functions or adaptations are due to past selection for those same functions: we observe today and retroactively extrapolate to the past.  It's understandable that we do that, and it was a major indirect way (along with artificial selection) in which Darwin was able to reconstruct an evolutionary theory that didn't require divine ad hoc creation events.   But there are problems with this sort of thinking--and some of them have long been known, even if essentially stifled by what amounts to a selectionist ideology, that is, a rather unquestioning belief in a kind of single-cause worldview.

What does exactly not-zero mean?

I suggested yesterday that drift, meaning exactly no systematic difference between states (like genotypes) was so illusive as to be essentially philosophical.  But zero-difference is a very specific value and may thus be especially hard to prove.  But non-zero is essentially an open-ended concept and might thus be trivially easy to show.  But it's not!

One alternative to two things being not zero is simply that they have some difference.  But need that difference be specifiable or of a fixed amount?  Need it be constant or similar over instances of time and place?  If not, we are again in rather spooky territory, because not being identical is not much if any help in understanding.  One wants to know by how much, and why--and if it's consistent or a fluke of sample or local circumstance.  But this is not a fixed set of things to check.

Instead of just 'they're different', what is usually implicitly implied is that the genotypes being compared have some particular, specific fitness difference amount, not just that they differ. That is what asserting different functional effects of the variants largely implies, because otherwise one is left asserting that they are different....sort of, sometimes, and this isn't very satisfying or useful.  It would be normal, and sensible, to argue that the difference need not be precisely, deterministically constant, because there's always a luck component, and ecological conditions change.  But if the difference varies widely among circumstances, it is far more difficult to make persuasive 'why' explanations. For example, small differences favoring variant A over variant B in one sample or setting might actually favor B over A in other times or places.  Then selection is a kind of willy-nilly affair--which probably is true!--but much more difficult to infer in a neat way, because it really is not different from being zero on average (though 'on average' is also easier to say than to account for causally).  If a difference is 'not zero', there are an infinity of ways that might be so, especially if it is acknowledged to be variable, as every sensible evolutionary biologist would probably agree is the case.

But then looking for causes becomes very difficult because among all the variants in a population, and all the variation in individual organisms' experience means that there may be an open-ended  number of explanations one would have to test to account for an observed small fitness difference between A and B.  And that leads to serious issues about statistical 'significance' and inference criteria.  That's because most alleged fitness differences are essentially local and comparative.  In turn that means the variant is not inherently selected but is context-dependent: fitness doesn't have a universal value, like, say, G, the universal Newtonian gravitational constant in physics, and to me that means that even an implicitly Newtonian view of natural selection is mistaken as a generality about life. 

If selection were really force-like in that sense, rather than an ephemeral, context-specific statistical estimate, its amount (favoring A over B) should approach the force's parameter, analogous to G, asymptotically: the bigger the sample and greater the number of samples analyzed the closer the estimated value would get to the true value.  Clearly that is not the way life is, even in most well-controlled experimental settings.  Indeed, even Darwin's idea of a constant struggle for existence is incompatible with that idea.

There are clearly many instances in which selective explanations of the classical sort seem specifically or even generally credible.  Infectious disease and the evolution of resistance is an obvious example.  Parallel evolution, such as independent evolution of, say, flight or similar dog-like animals in Australia and Africa, may be taken to prove the general theory of adaptation to environments.  But what about all the not dogs in these places?  We are largely in ad hoc explanatory territory, and the best of evolutionary theory clearly recognizes that.

So, in what sense does natural selection actually exist?  Or neutrality?  If they are purely comparative, local, ad hoc phenomena largely demonstrable only by subjective statistical criteria, we have trouble asserting causation beyond constructing Just-So stories.  Even with a plausible mechanism, this will often be the case, because plausibility is not the same as necessity.  Just-So stories can, of course, be true....but usually hard to prove in any serious sense.

Additionally, in regard to adaptive traits within or between populations or species, if genetic causation is due to contributions of many genes, as typically seems to be the case, there is phenogenetic drift, so that even with natural selection working force-like on a trait, there may be little if any selection on specific variants in that mix: even if the trait is under selection, a given allelic variant may not be.

Some other slippery issues

Natural selection is somewhat strange.  It is conceptually a passive screen of variation, but often treated as if an inherent property of a genotype (or an allele), whose value is determined on what else is in the same locus in the population.  Yet it's also treated as if this is inherent and unchanging property of the genotype...until any competing genotypes disappear.  As the favored allele becomes more common, its amount of advantage will increasingly vary because, due to recombination and mutation, the many individuals carrying the variant will also vary in the rest of their genomes, which will introduce differences in fitness among them (likewise, early on most carriers of the favored 'A' variant will be heterozygotes, but later on more and more will be homozygotes).  When the A variant becomes very common in the population, its advantage will hardly be detectable since almost all its peers fellws will have the same genotype at that site.  Continued adaptation will have to shift to other genes, where there still is a difference.  Some AA carriers will have detrimental variants at another gene, say B, and hence reduced fitness. Relatively speaking, some A's, or eventually maybe all A's, will have become harmful, because even in classical Darwinian terms selection is only relative and local.  So, selection even in the force-like sense, is very non-Newtonian, because it is so thoroughly context-dependent.  

Another issue is somatic mutation.  The genotypes that survive to be transmitted to the next generation are in the germ line.  But every cell division induces some mutations, and depending on when and where during development or later life a mutation occurs, it could affect the traits of the individual.  Even if selection were a deterministic force, it screens on individuals and hence that includes any effects of somatic mutation in those individuals.  But somatic mutations aren't inherited, so even if the mechanism is genetic their effects will appear as drift in evolutionary terms.  

Most models of adaptive selection are trait-specific.  But species do not evolve one trait at a time, except perhaps occasionally when a really major stressor sweeps through (like an epidemic).  Generally, a population is always subject to a huge diversity of threats and opportunities, contexts and changes.  Every one of our biological systems is always being tested, of in many ways at once. Traits are also often correlated with one another, so pushing on one may be pulling on another.  That means that even if each trait were being screened for separate reasons, the net effect on any one of the must typically be very very small, even if it is Newtonian in its force-like nature.  

The result is something like a Japanese pachinko machine.  Pachinko is popular type of gambling in Japan. A flurry of small metal balls bounces down from the top more or less randomly through a jungle of pins and little wheels, before finally arriving at the bottom.  The balls bounce off each other on the way in basically random collisions. The payoff (we could say it's analogous to fitness) is based on the balls that, after all this apparent chaos, end up in a particular pocket at the bottom.  In biological analogy, each ball can represent a different trait or perhaps individuals in a population. They bounce around rather randomly, constrained only by the walls and objects there--nothing steers them specifically. What's in the pocket is the evolutionary result. 

Pachinko machine (from Google images)

 (you can easily find YouTube videos showing pachinkos in action)

All similes limp, and these collisions are probably in truth deterministic, even if far too too complex to predict the outcome.  Nonetheless, this sort of dynamics among individuals with their differing genes of varying and context-specific effects, in diverse and complex environments, suggests why in this dynamic complex, change related to a given trait will be a lot like drift; there are so many that if each were too strongly force-like extinction would be more likely the result.  Further, since most traits are affected by many parts of the genome, the intensity of selection on any one of them must be reduced to be close to the expectations of drift. Adaptive complexity is another reason to think that adaptive change must be glacially slow, as Darwin stressed many times, but also that selection is much less force-like, as a rule.  After the fact, seeing what managed to survive, it looks compatible with force-like, straight-line selection.

Here, the process seems to rest heavily on chance.  But as we discussed in a post in 2014 in a series on the modes and nature of natural selection, we likened the course that species take through time to the geodesic paths that objects take through spacetime, that is determined (and there it really does seem to be 'determined') by the splattered matter and energy in any point it passes through.

An overall view

This leaves us in something of a quandary.  We can easily construct criteria for making some inferences, in the stronger cases, and testing them in some experimental settings.  We can proffer imaginative scenarios to account for the presence of organized traits and adaptations.  But evolutionary explanations are often largely or wholly speculative.  This applies comparably to natural selection and to genetic drift as well, and these are not new discoveries although they seem to be in few peoples' interest to acknowledge them fully.

Darwin wanted to show by plausibility argument that life on earth was the result of natural processes, not ad hoc divine creation events.  He had scant concepts of chance or genetic drift, because his ideas of the mechanism of inheritance were totally wrong.  Concepts of probabilism and statistical testing and the like were still rather new and only in restricted use.  Darwin would have no trouble acknowledging a role for drift.  How he would respond to the elusiveness of these factors, and that they really are not 'forces', is hard to say--but he probably would vigorously try to defend systematic selection by arguing that what is must have gotten here by selection as a force. 

The causal explanation of life's diversity still falls far short of the kind of mathematical or deterministic rigor of the core physical sciences, and even of more historical physical sciences like geology, oceanography, and meteorology.  Until someone finds better ways (if they indeed are there to be found), much of evolutionary biology verges on metaphysical philosophy for reasons we've tried to argue in this series.  We should be honest about that fact, and clearly acknowledge it.

One can say that small values are at least real values, or that you can ignore small values, as in genetic drift.  Likewise one can say that small selective effects will vary from sample to sample because of chance and so on.  But such acknowledgments undermine the kinds of smooth inferences we naturally hunger for.  The assumption that what we see today is what was the case in the past is usually little more than an assumption. This is a main issue we should confront in trying to understand evolution--and it applies as well to the promises being made of 'precision' prediction of genomic causation in health and medicine.  The moving tide of innumerable genotypic ways to get similar traits, at any time, within or between populations, and over evolutionary time, needs to be taken seriously. 

It may be sufficient and correct to say, almost tautologically, that today's function evolved somehow, and we can certainly infer that it got here by some mix of evolutionary factors.  Our ancestors and their traits clearly were evolutionarily viable or we wouldn't be here.  So even if we can't really trace the history in specifics, we can usually be happy to say that, clearly, whales evolved to be able to live in the ocean.  Nobody can question that.  But the points I've tried to make in this series are serious ones worth thinking seriously about, if we really want to understand evolution, and the genetic causal mechanisms that it has produced.