What do ravens do?

"As behavioral ecologists, we try to reveal rules of behavior as though we were discovering truths.  In reality, the word 'rule' as applied to animal behavior is a verbal shortcut.  A 'rule' means nothing more than  a consistency of response.  It is not adherence to dictum.  Animals adhere no more to rules than we do by showing up at the beach when its 110 degrees but not when it's 30 degrees.  Rules are the sum of decisions made by individuals that are then exhibited by crowds, not vice versa.  Rules are thus a result.  They are the average behavior that we and many animals are programmed with, learn, or make up as we go along."

This is a cogent quote from Bernd Heinrich's book Mind of the Raven (1999, Ecco books), which I was given as a birthday gift.  The idea was that I would like to read about the various capabilities of ravens, relative to our informal and even formal ideas about what 'mind' or 'consciousness' mean and how we might know, and whether these interesting birds might have it, whatever it is.

However, the quote I've given is more than just the author's views on what ravens' internal experiences might be.  It applies to much that we have to deal with in science--at least, in biological and behavioral sciences themselves.  I've used it because I think the observation also applies to something I've been writing about in recent posts--related to what may seem to be a very different topic, whether life is parametric or not.

The physical world seems to be parametric, that is, driven ultimately by some universally true processes, like gravity, that are in turn reflections of underlying, universal, fixed parameters, or numerical values.  Of course, 'numerical values' refers to human-derived mathematics and science, and might, from some wholly different point of view, be differently perceived or characterized.

But to us, phenomena like the speed of light, c, and various quantum phenomena etc., have fixed, universal values.  The value is the same everywhere, even if its manifestation may be modified by local circumstances.  For example, c is specified as in a vacuum.  Whether or not there exists any true total vacuum, the idea--and the belief in its universality--are clear and important bedrock aspects of physics, chemistry, and cosmology.  In some other substance, rather than a vacuum, the speed of light is altered in an orderly way.

But what about life?
We can ask whether, while life is a physical and molecular phenomenon, it is part and parcel of the same parametric cosmos, or if it has exceptions at the level at which we want answers to our basic questions.  That would be analogous to physics adhering to a dictum, in the raven quote.  But maybe life is not analogous to a vacuum.  This, at least, is what I mean by asking whether life is a parametric phenomenon, and expression doubts that it could be so.

An a priori reason, in my mind, is that life is a molecular process of regular molecular activity (genes, proteins, and so on), but it evolves because the specifics are different--they vary.  Without that, there would be no evolution, and organismal complexity, and the underlying genetic and proteinic complexity by which life, and its interacting ecosystems have come about, would not be here.  In that sense, I think it is appropriate to suggest that life is not a parametric phenomenon.

This, to me, is not the same as saying that life is a kind of self-organized complexity. It certainly is that, but the phrase misses what I think is the underlying fact, which is that life is not parametric.  Complexities like the mandelbrot set (figure below) are parametric: they repeat the same phenomenon in an evermore complex but always rigorously.  This is a form of 'complexity' but it is very rigorously regular.  Life is, if anything, rigorously irregular, among individuals, populations, species, and the structures within each of those.

Mandelbrot set.  From Wikipedia entry

Many people have written about life's complexity with analogies to things like the Mandelbrot set and many others of the sort.  But while that sounds as if it acknowledges the complexity of life, it really is an implicit hunger for just the opposite: for regularity, tractability, and 'parametricity'.   I think that is at best an ad hoc approximation but theoretically fundamentally wrong.

The consequences are obvious: we can describe existing data by various statistical and even mathematical data-fitting procedures.  But we cannot make predictions or projections with known 'precision' and indeed that is why I think that rhetoric like 'precision genomic medicine' is strictly an advertising slogan, scientifically misleading (and culpably so), and misunderstood by most people even those who use it, and perhaps even by the NIH that proffer it as a funding or marketing ploy for its budgets.  It is a false promise, as stated (saying instead that we want funds for research to make medicine more precise by including genomic information would be honest and appropriate).

Heinrich's description of ravens' behavior seemed an apt way to make my point, as I see things at any rate, clear by an easily digested analogy.  Some ravens did what they were seen to do, but that was the net result of what some observed ravens did on some occasions, not what 'ravens do' in the parametric sense.  The ravens are not all following a rule and even the 'consistency' of their responses is not like that (different ravens do different things, as Heinrich's book makes clear).

We want rules that explain 'truth' in genetics and evolution.  We ought to be able to see that that may be a misleading way to view the nature of the living world.  And, seeing that, to change what we promise to the public and, as important as what we promise to them, to change how we think.

Or, as quoth the raven: nevermore!

Evolution as a pachinko history: what is 'random'?

We discussed a Japanese pachinko machine in an earlier post, a pinball machine, as an example of the difference between randomness and determinism, in an evolutionary context.   Here we want to use pachinko machine imagery in a different way.

The prevailing, often unstated but just-under-the-surface assumption is that every trait in life is here because of natural selection.  Of course, for a trait to be here at all, bearers of its ancestral states up to the present (or, at least, the recent past) were successful enough to have reproduced.  It would not be here if it were otherwise, unless, for example, it's itself harmful, or without function but connected to a much better, related trait since genes are usually used in many different bodily contexts and may be associated with both beneficial and harmful traits.  Most sensible evolutionary geneticists know that many or even most sites in genomes tolerate variation that has either no effect or effects so small that in realistic population sizes they change in frequency essentially by chance.

However, the widespread default assumption that there must be an adaptive explanation for every trait usually also tacitly assumes that probabilism doesn't make much difference.  Some alert evolutionary biologists will acknowledge that one version among contemporary but equivalent versions of a trait can evolve by chance relative to other versions.  But the insistence, tacit or expressed, is that natural selection, treated essentially as a force, is responsible.  The very typical view is that the trait arose because of selection 'for' it, and that's why it's here.  And speaking of 'here', here's where a pachinko analogy may be informative.

If a bevy of metal balls tumbles through the machine, each bouncing off the many pins, they will end up scattered across the bottom ledge of the machine (the gambling idea is to have them end up in a particular place, but that's not our point here).  So let's take a given ball and ask 'Why did it end up where it did?"

The obvious and clearly true answer is 'Gravity is responsible'.  That is the analogue of 'selection is responsible'.   But it is rather an empty answer.  One can always say that what's here must be here because it was favored (that is, not excluded) by fitness considerations: its ancestral bearers obviously reproduced!  We can define that as 'adaptation' and indeed in a sense that is what is done every day, almost thoughtlessly.

Gravity is, like the typical if tacit assumption about natural selection, a deterministic force for all practical purposes here.  But why did this ball end up in this particular place?  One obvious answer is that each starts out in a slightly different place at the top, and no two balls are absolutely identical. However, each ball makes a different path from the top to the bottom of the obstacle course it faces. Yes, it is gravity that determines that they go down (adapt), but not how they go down.

In fact, each ball takes a different path, zigging and zagging at each point based on what happens, essentially by chance, at that point.   This one might think of as local ecosystems on the evolutionary path of any organism, that are beyond its control.  So, in the end, even if the entire journey is deterministic, in the sense that every collision is, the result is not one that can, in practice, be understood except by following the path of each ball (each trait, in the biological analogy).  And this means that the trajectory cannot be predicted ahead of time. And in turn, this means that our interpretation of what a trait we see today was selected 'for' is often if not usually either basically just a guess or, more often, equates what the trait does today to what it was selected to be, expressed as if it were an express train from then to now.

And this doesn't consider another aspect of the chaotic and chance-affected nature of evolutionary adaptation: the interaction with the other balls bouncing around at the same time in such an obstacle course.  Collisions are in every meaningful sense in the game of life, if not pachinko, chance events that affect selective ones, even were we to assume that selection is simple, straightforward, and deterministic.

The famous argument by Gould and Lewontin that things useful for one purpose, such as 'spandrels' in cathedral roofs, are incidental traits that provide the options for future adaptations--life exploits today with what yesterday produced for whatever reason even if just by chance.  The analogy or metaphor has been questioned, but that is not important here.  What is important is that contingencies of this nature are chance events, relative to what builds on them.  Selectionism as a riposte to creationism is fine but hyper-selectionism becomes just another often thought-free dogma.  Darwin gave us inspiration and insight, but we should think for ourselves, not in 19th century terms.

A far humbler, and far less 'Darwinian' (but not anti-Darwinian!), explanation of life is called for if we really want to understand evolution as a subtle often noisy process, rather than as a faith.  Instead, even serious biologists freely invent--and that's an apt word for it--selective accounts, as if true explanations, for almost any trait one might mention. It's invented because some reason is imagined without any direct evidence other than present-day function, but then treated as if directly observed, which is rarely possible. Here is an interview that I just came across that in a different way makes some of the same points we are trying to make here.

Everything here today is 'adaptive' in the sense that it has worked up to now.  Everything here today is also a 4 billion year successful lineage, that all made its way through the pachinko pins.  But these are almost vacuous tautologies.  Understanding life requires understanding one's biases in trying to force simple solutions on complicated reality.

Is genetics still metaphysical? Part VI. What might lead to a transformative insight in biology today--if we need one

It's easy to complain about the state of the world, in this case, of the life sciences, and much harder to provide the Big New Insights one argues might be due.  Senioritis makes it even easier: when my career in genetics began, not very much was known.  Genes figuratively had 2 alleles, with measurable rates of recurrence by mutation.  Genetically tractable traits were caused by the proteins in these genes; quantitative traits were too complex to be considered seriously to be due to individual genes, so were tacitly assumed to be the additive result of an essentially infinite number of them.

How many genes there were was essentially unknowable, but using identified proteins as a gauge, widely thought to be around 100,000. The 'modern evolutionary synthesis' solved the problem, conceptually, by treating these largely metaphorical causal items as largely equivalent, if distinct, entities whose identities were essentially unknowable.  That is, at least, we didn't have to think about them as specific entities, only their collective actions.  Mendelian causal genes, evolving by natural selection was, even if metaphorical or even in a serious way metaphysical, a highly viable worldview in which to operate.  A whole science enterprise grew around this worldview.  But things have changed.

Over the course of my career, we've learned a lot about these metaphysical units.  Whether or not they are now more physical than metaphysical is the question I've tried to address in this series of posts, and I think there's not an easy answer--but what we have, or should have, understood is that they are not units!  If we have to have a word for them, perhaps it should be interactants.  But even that is misleading because the referents are not in fact unitary.  For example, many if not  most 'genes' are only active in context-dependent circumstances, are multiply spliced, may be post-trascriptionally edited, are chemically modified, and have function only when combined with other units (e.g., don't code for discretely functioning proteins), etc.

Because interaction is largely a trans phenomenon--between factors here and there, rather than just everything here, the current gene concept, and the panselectionistic view in which every trait has an adaptive purpose, whether tacit or explicit, is a serious or even fundamental impediment to a more synthetic understanding. I feel it's worth piling on at this point, and adding that the current science is also pan-statistical in ways that in my view are just as damaging.  The reason, to me, is that these methods are almost entirely generic, based on internal comparison among samples, using subjective decision-criteria (e.g., p-values) rather than testing data against a serious-level theory.

If this be so, then perhaps if the gene-centered view of life, or even the gene concept itself as life's fundamental 'atomic' unit, needs to be abandoned as a crude if once important approximation to the nature of life. I have no brilliant ideas, but will try here to present the sorts of known facts that might stimulate some original thinker's synthesizing insight--or, alternatively, might lead us to believe that no such thing is even needed, because we already understand the relevant nature of life: that as an evolutionary product it is inherently not 'regular' the way physics and chemistry are.  But if our understanding is already correct, then our public promises of precision medicine are culpably misleading slogans.

In part V of this series I mentioned several examples of deep science insight, that seemed to have shared at least one thing in common:  they were based on a synthesis that unified many seemingly disparate facts.  We have many facts confronting us.  How would or might we try to think differently about them?  One way might be to ask the following questions: What if biological causation is about difference, not replication?  What if 'the gene' is misleading, and we were to view life in terms of interactions rather than genes-as-things?  How would that change our view?

Here are some well-established facts that might be relevant to a new, synthetic rather than particulate view of life:

1. Evolution works by difference, not replication Since Newton or perhaps back to the Greek geometers, what we now call 'science' largely was about understanding the regularities of existence.  What became known as 'laws' of Nature were, initially for theological reasons, assumed to be the basis of existence.  The same conditions led to the same outcomes anywhere.  Two colliding billiard balls here on Earth or in any other galaxy, would react in identical ways (yes, I know, that one can never have exactly the same conditions--or billiard balls--but the idea is that the parts of the cosmos were exchangeable.)  But one aspect of life is that it is an evolved chemical phenomenon whose evolution occurred because elements were different rather than exchangeable.  Evolution and hence life, is about interactions or context-specific relative effects (e.g., genetic drift, natural selection). 

2.  Life is a phenomenon of nested (cladistic) tree-like relationships Life is not about separated, independent entities, but about entities that from the biosphere down (at least) to individual organisms are made of sets of variations of higher-level components.  Observation at one level, at least from cells up to organs to systems to individuals, populations, species and ecosystems, are reflections of the nested level(s) the observational level contains. 

3.  Much genetic variation works before birth or on a population level Change may arise by genetic mutation, but function is about interactions, and success--which in life means reproduction--depends on the nature of the interactions at all levels.  That is, Darwinian competition among individuals of different species is only one, and perhaps one of the weakest, kinds of such interaction.  Embryonic development is a much more direct, and stronger arena for filtering interactions, than competition (natural selection) among adults for limited resources.  In a similar way, some biological and even genetic factors work only in a population way (bees and ants are an obvious instance, as are bacterial microfilm and the life cycles of sponges or slime molds). 

4.  Homeostasis is one of the fundamental and essential ways that organisms interact Homeostasis as an obvious example of a trans phenomenon.  It's complexly trans because not only do gene-expression combinations change, but they are induced to change by extra-cellular and even extra-organismal factors both intra and inter-species.  The idea of a balance or stasis, as with organized and orchestrated combinatorial reaction surely cannot be read of in cis.  We have known about interactions and reactions and so on, so this is not to invoke some vague Gaia notions, but to point out the deep level of interactions, and these depend on many factors that themselves vary, etc. 

5. Environments include non-living factors as well as social/interaction ones No gene is an island, even if we could identify what a 'gene' was, and indeed that no gene stands alone is partly why we can't.  Environments are like the celestial spheres: from each point of view everything else is the 'environment', including the rest of a cell, organ, system, organism, population, ecosystem.  In humans and many other species, we must include behavioral or social kinds of interactions as 'environment'.  There is no absolute reference frame in life any more than in the cosmos.  Things may appear linear from one point of view, but not another.  The 'causal' effects of a protein code (a classical 'gene') depend on its context--and vice versa. 

6. The complexity of factors often implies weak or equivalent causation--and that's evolutionarily fundamental. Factors or 'forces' that are too strong on their own--that is, that appear as individually identifiable 'units'--are often lethal to evolutionary survival.  Most outcomes we (or evolution) care about are causally complex, and they are always simultaneously multiple: a species isn't adapting to just one selective factor at a time, for example.  Polygenic causation (using the term loosely to refer to complex multi-factoral causation) is the rule.  These facts mean that individually identified factors usually have weak effects and/or that there are alternative ways to achieve the same end, within or among individuals.  Selection, even of the classical kind, must be typically weak relative to any given involved factor. 

7. The definition of traits is often subjective and affects their 'cause' Who decides what 'obesity', 'intelligence', or 'diabetes' is?  In general, we might say that 'Nature' decides what is a 'trait', but in practice it is often we, via our language and our scientific framework, who try to divide up the living world into discrete categories and hence to search for discrete causal factors.  It is no surprise that what we find is rather arbitrary, and gives the impression of biological causation as packaged into separate items rather than being fundamentally about a 'fabric' of interactions.  But the shoehorn is often a major instrument in our causal explanations. 

8. The 'quantum mechanics' effect: interaction affects the interactors In many aspects of life, obviously but not exclusively applied to humans, when scientists ask a question or publicize a result, it affects the population in question.  This is much like the measurement effect in quantum mechanics.  Studying something affects it in ways relevant to the causal landscape we are studying.  Even in non-human life, the 'studying' of rabbits by foxes, or of forests by sunlight, affects what is being studied.  This is another way of pointing out the pervasive centrality of interaction.  Just like political polls, the science 'news' in our media, affect our behavior and it is almost impossible to measure the breadth and impact of this phenomenon.

All of these phenomena can be shoe-horned into the 'gene' concept or a gene-centered view of life or of biomedical 'precision'.  But it's forced: each case has to be treated differently, by statistical tests rather than a rigorous theory, and with all sorts of exceptions, involving things like those listed here, that have to be given post hoc explanations (if any). In this sense, the gene concept is outmoded and an overly particulate and atomized view of a phenomenon--life--whose basic nature is that it is not so particularized.

Take all of these facts, and many others like them, and try to view them as a whole, and as a whole that, nonetheless can evolve.  Yesterday's post on how I make doggerel was intended to suggest a similar kind of mental exercise.  There can be wholes, and they can evolve, but they do it as wholes. If there is a new synthesis to be found, my own hunch it would be in these sorts of thoughts.  As with the examples I discussed a few days ago (plate techtonics, evolution itself, and relativity), there was a wealth of facts that were not secret or special, and were well-known. But they hadn't been put together until someone thinking hard about them, who was also smart and lucky, managed it. Whether we have this in the offing for biology, or whether we even need it, is what I've tried to write about in this series of posts.

Of course, one shouldn't romanticize scientific 'revolutions'.  As I've also tried to say, these sorts of facts, which are ones I happen to have thought of to list, do not in any way prove that there is a grand new synthesis out there waiting to be discovered. It is perfectly plausible that this kind of ad hoc, chaotic view of life is what life is like.  But if that's the case, we should shed the particulate, gene-centered view we have and openly acknowledge the ad hoc, complex, fundamentally trans nature of life--and, therefore, of what we can promise in terms of health miracles.

Is genetics still metaphysical? Part V. Examples of conditions that lead to transformative insights

A commenter on this series asked what I thought that "a theory of biology should (realistically) aspire to predict?" The series (part 1 here) has discussed aspects of life sciences in which we don't currently seem to have the kind of unifying underlying theory found in other physical sciences. I'm not convinced that many people even recognize the problem.

I couched the issues in the context of asking whether the 'gene' concept was metaphysical or was more demonstrably or rigorously concrete.  I don't think it is concrete, and I do think many areas of the life sciences are based on internal generic statistical or sampling comparison of one sort of data against another (e.g., genetic variants found in cases vs controls in a search for genetic causes of disease), rather than comparing data against some prior specific theory of causation other than vacuously true assertions like 'genes may contribute to risk of disease'.  I don't think there's an obvious current answer to my view that we need a better theory of biology, nor of course that I have that answer.   

I did suggest in this series that perhaps we should not expect biology to have the same kind of theory found in physics, because our current understanding doesn't (or at least shouldn't) lead us to expect the same kind of cause-effect replicability.  Evolution--which was one of the sort of basic revolutionary insights in the history of science, and is about life, specifically asserts that life got the way it is by not being replicable (e.g., in one process, by natural selection among different--non-replicate--individuals).  But that's also a very vanilla comment.

I'll try to answer the commenter's question in this and the next post.  I'll do it in a kind of 'meta' or very generic way, through the device of presenting examples of the kind of knowledge landscape that has stimulated new, deeply synthesizing insight in various areas of science.

1.  Relativity
History generally credits Galileo for the first modern understanding that some aspects of motion appear differently from different points of view.  A classic case was of a ship gliding into the port of Genoa: if someone inside the ship dropped a ball it would land at his feet, just as it would for someone on land.  But someone on land watching the sailor through a window would see the ball move not just down but also along an angled path toward the port, the hypotenuse of a right triangle, which is longer than the straight-down distance.  But if the two observations of the same event were quantitatively different, which was 'true'?  Eventually, Einstein extended this question using images such as trains and railroad stations: a passenger who switched on two lightbulbs, one each at opposite ends of a train, would see both flashes at the same time.  But a person at a station the train was passing through would see the rearmost flash before the frontward one.  So what does this say about simultaneity?

These and many other examples showed that, unlike Isaac Newton's view of space and time as existing in an absolute sense, they depend on one's point of view, in the sense that if you adjust for that, all observers will see the same laws of Nature at work.  Einstein was working in the Swiss patent office and at the time there were problems inventors were trying to solve in keeping coordinated time--this affected European railroads, but also telecommunication, marine transport and so on. Thinking synthetically about various aspects of the problem led Einstein later to show that a similar answer applied to acceleration and a fundamentally different, viewpoint-dependent, understanding of gravity as curvature in space and time itself, a deeply powerfully deeper understanding of the inherent structure of the universe.  A relativisitic viewpoint helped account for the nature and speed of light, aspects of both motion and momentum, of electromagnetism, the relationship between matter and energy, the composition of 'space', the nature of gravity, of time and space as a unified matrix of existence, the dynamics of the cosmos, and so on, all essentially in one go.

The mathematics is very complex (and beyond my understanding!).   But the idea itself was mainly based on rather simple observations (or thought experiments), and did not require extensive data or exotically remote theory, though it has been shown to fit very diverse phenomena better than former non-relativisitc views, and are required for aspects of modern life, as well as our wish to understand the cosmos and our place in it.  That's how we should think of a unifying synthesis. 

The insight that led to relativity as a modern concept, and that there is no one 'true' viewpoint ('reference frame'), is a logically simple one, but that united many different well-known facts and observations that had not been accounted for by the same underlying aspect of Nature.

2.  Geology and Plate Techtonics (Continental Drift)
Physics is very precise from a mathematical point of view, but transformative synthesis in human thinking does not require that sort of precision.  Two evolutionary examples will show this, and that principles or 'laws' of Nature can take various forms.  

The prevailing western view until the last couple of centuries, even among scientists, was that the cosmos had a point Creation, basically in its present form, a few thousand years ago.  But the age of exploration occasioned by better seagoing technology and a spirit of global investigation, found oddities, such as sea shells at high elevations, and fossils.  The orderly geographical nature of coral atolls, Pacific island chains, volcanic and earthquake-prone regions was discovered.  Remnants of very different climates than present ones in some locations were found.  Similarly looking biological species (and fossils) were found in disjoint parts of the world, such as South Africa, South America, and eventually Antarctica.  These were given various local, ad hoc one-off explanations.  There were hints in previous work, but an influential author was Alfred Wegener who wrote (e.g., from 1912--see Wikipedia: Alfred Wegener) about the global map, showing evidence of continental drift, the continents being remnants of a separating jigsaw puzzle, as shown in the first image here; the second shows additional evidence of what were strange similarities in distantly separated lands.  This knowledge had accumulated by the many world collectors and travelers during the Age of Exploration. Better maps showed that continents seemed sometimes to be 'fitted' to each other like pieces of a jigsaw puzzle.  

Geological ages and continental movement (from Hallam, A Revolution in the Earth Sciences, 1973; see text)

Evidence for the continental jigsaw puzzle (source Wikipedia: Alfred Wegener, see text)

Also, if the world were young and static since some 'creation' event, these individual findings were hard to account for. This complemented ideas by early geologists like Hutton and Lyell around the turn of the 19th century. They noticed that deep time also was consistent with the idea of (pardon the pun) glacially slow observable changes in glaciers, river banks, and coastlines that had been documented since by geologists  Their idea of 'uniformitarianism' was that processes observable today occurred as well during the deep past, meaning that extrapolation was a valid way to make inferences.  Ad hoc isolated and unrelated explanations had generally been offered piecemeal for these sorts of facts.  Similar plants or animals on oceanically separated continents must have gotten there by rafting on detritus from rivers that had been borne to the sea.

Many very different kinds of evidence were then assembled and a profound insight was the result, which we today refer to by terms such as 'plate techtonics' or 'continental drift'.   There are now countless sources for the details, but one that I think is interesting is A Revolution in the Earth Sciences, by A. Hallam, published by Oxford Press in 1973, only a few years after what is basically the modern view had been convincingly accepted.  His account is interesting because we now know so much more that reinforces the idea, but it was as stunning a thought-change as was biological evolution in Darwin's time.  I was a graduate student at the time, and we experienced the Aha! realization that was taking place was that, before our very observational eyes so to speak, diverse facts were being fit under the same synthesizing explanation (even some of our faculty were still teaching old, forced, stable-earth explanations).

Among much else, magnetic orientation of geological formations, including symmetric stripes of magnetic reversals flanking the Mid-Atlantic Trench documented the sea-floor spreading that separated the broken-off continental fragments--the pieces of the jigsaw puzzle.  Mountain height and sea depth patterns gained new explanations on a geologic (and very deep time) scale, because the earth was accepted as being older than biblical accounts).  Atolls and the volcanic ring of fire are accounted for by continental motions.  

This was not a sudden one-factor brilliant finding, but rather the accumulation of centuries of slowly collected global data from the age of sail (corresponding to today's fervor for 'Big Data'?).  A key is that the local facts were not really accounted for by locally specific explanations, but were globally united as instances of the same general, globally underlying processes.  Coastlines, river gorges, mountain building, fossil-site locations, current evidence of very different past climates and so on were brought under the umbrella of one powerful, unifying theory.  It was the recognition of very disparate facts that could be synthesized that led to the general acceptance of the theory.  Indeed, subsequent and extensive global data, continue to this day to make the hypothesis of early advocates like Wegener pay off.

3.  Evolution itself
It is a 100% irrefutable explanation for life's diversity to say that God created all the species on Earth. But that is of no use in understanding the world, especially if we believe, as is quite obvious, that the world and the cosmos more broadly follows regular patterns or 'laws'.  Creationist views of life's diversity, of fossils, and so on, are all post hoc, special explanations for each instance. Each living species can be credited to a separate divine reason or event of creation.  But when world traveling became more common and practicable, many facts and patterns were observed that seemed to make such explanations lame and tautological at best.  For example, fossils resembled crude forms of species present today in the same area.  Groups of similar species are found living in a given region, with clusters of somewhat less similar species elsewhere. The structures of species, such as of vertebrates, or insects, showed similar organization, and one could extend this to deeper if more different patterns in other groups (e.g., that we now would call genera, phyla, and so on).  Basic aspects of inheritance seemed to apply to species, plant and animal alike.  If all species had been, say, on the same Ark, why were similar species so geographically clustered?

It dawned on investigators scanning the Victorian Age's global collections, and in particular Darwin and Wallace, that because offspring resemble their parents, though are not identical to them, and individuals and species have to feed on each other or compete for resources, that those that did better would proliferate more.  If they became isolated, they could diverge in form, and not only that but the traits of each species were suited to its circumstances, even if species fed off each other.  Over time this would also produce different, but related species in a given area.  New species were not seen directly to arise, but precedents from breeders' history showed the effects of selective reproduction, and geologists like Lyell had made biologists aware of the slow but steady nature of geological change.  If one accepted the idea that rather than the short history implied by biblical reading, life on earth instead had been here for a very long time, these otherwise very disparate facts about the nature of life and the reasons for its diversity might have a common 'uniformitarian' explanation--a real scientific explanation in terms of a shared causative process, rather than a series of unrelated creations: the synthesis of a world's worth of very diverse facts made the global pattern of life make causal and explanatory sense, in a way that it had never had before.

Of course the fact of evolution does not directly inform us about genetic causation, which has been the motivating topic of this series of posts.  We'll deal with this in our next post in the series.

Insight comes from facing a problem by synthesis related to pattern recognition
The common feature of these examples of scientific insight is that they involve synthesis derived from pattern recognition. There is a problem to be solved or something to be explained, and multiple facts that may not have seemed related and have been given local, ad hoc, one-off 'explanations'. Often the latter are forced or far-fetched, or 'lazy' (as in Creationism, because it required no understanding of the birds and the beasts). Or because the explanations are not based on any sort of real-world process, they cannot be tested and tempered, and improved.  And, unlike Creationist accounts, scientific accounts can be shown to be wrong, and hence our understanding improved.

In our examples of the conditions in which major scientific insights have occurred, someone or some few, looking at a wealth of disparate facts, or perhaps finding some new fact that is relevant to them, saw through the thicket of 'data', and found meaning.  The more a truly new idea strikes home, in each case, the more facts it incorporates, even facts not considered to be relevant.

Well!  If we don't have diverse, often seemingly disparate facts in genetics then nobody does!  But the situation now seems somewhat different from the above examples: indeed, with the precedents like those above, and several others including historic advances in chemistry, quantum physics, and astronomy, we seem to hasten to generalize, and claim our own synthesizing 'laws'.  But how well are we actually doing, and have we identified the right primary units of causation on which to do the same sort of synthesizing?  Or do we need to?

 I'll do my feeble best to offer some thoughts on this in the final part of this series.

Is genetics still metaphysical? Part III. Or could that be right after all?

In the two prior parts of this little series (I and II), we've discussed the way in which unknown, putatively causative entities were invoked to explain their purported consequences, even if the agent itself could not be seen or its essence characterized.  Atoms and an all-pervasive ether are examples. In the last two centuries, many scientists followed some of the principles laid down in the prior Enlightenment period, and were intensely empirical, to avoid untrammeled speculation.  Others followed long tradition and speculated about the underlying essentials of Nature that could account for the empiricists' observations. Of course, in reality I think most scientists, and even strongly religious people, believed that Nature was law-like: there were universally true underlying causative principles.  The idea of empiricism was to escape the unconstrained speculation that was the inheritance even from the classical times (and, of course, from dogmatic religious explanations of Nature).  Repeated observation was the key to finding Nature's patterns, which could only be understood indirectly.  I'm oversimplifying, but this was largely the situation in 19th and early 20th century physics and it became true of historical sciences like geology, and in biology during the same time.

At these stages in the sciences, free-wheeling speculation was denigrated as delving in metaphysics, because only systematic empiricism--actual data!--could reveal how Nature worked. I've used the term 'metaphysics' because in the post-Enlightenment era it has had and been used in a pejorative sense.  On the other hand, if one cannot make generalizations, that is, infer Nature's 'laws', then one cannot really turn retrospective observation into prospective prediction.

By the turn of the century, we had Darwin's attempt at Newtonian law-like invocation of natural selection as a universal force for change in life, and we had Mendel's legacy that said that causative elements, that were dubbed 'genes', underlay the traits of Nature's creatures.  But a 'gene' had never actually been 'seen', or directly identified until well into the 20th century. What, after all, was a 'gene'? Some sort of thing?  A particle?  An action?  How could 'it' account for traits as well as their evolution?  To many, the gene was a convenient concept that was perhaps casually and schematically useful, but not helpful in any direct way.  Much has changed, or at least seems to have changed since then!

Genetics is today considered a mainline science, well beyond the descriptive beetle-collecting style of the 19th century.  We now routinely claim to identify life's causative elements as distinct, discrete segments of DNA sequence, and a gene is routinely treated as causing purportedly 'precisely' understandable effects.  If raw Big Data empiricism is the Justification du Jour for open-ended mega-funding, the implicit justifying idea is that genomics is predictive the way gravity and relativity and electromagnetism are--if only we had enough data!  Only with Big Data can we identify these distinct, discrete causal entities, characterize their individual effects and use that for prediction, based on some implicit theory or law of biological causation.  It's real science, not metaphysics!

But even with today's knowledge, how true is that?

The inherent importance of context-dependency and alternative paths
It seems obvious that biological causation is essentially relative in nature: it fundamentally involves context and relationships.  Treating genes as individual, discrete causal agents really is a form of metaphysical reification, not least because it clearly ignores what we know about genetics itself. As we saw earlier, today there is no such thing as 'the' gene, much less one we can define as the discrete unit of biological function.  Biological function seems inherently about interactions.  The gene remains in that sense, to this day, a metaphysical concept--perhaps even in the pejorative sense, because we know better!

We do know what some 'genes' are: sequences coding for protein or mature RNA structure.  But we also know that much of DNA has function unrelated to the stereotypical gene.  A gene has multiple exons and often differently spliced (among many other things, including antisense RNA post-transcription regulation, and RNA editing), combined with other 'genes' to contribute to some function.  A given DNA coding sequence often is used in different contexts in which 'its' function depends on local context-specific combinations with other 'genes'.  There are regulatory DNA sequences, sequences related to the packaging and processing of DNA, and much more.  And this is just the tip of the current knowledge iceberg; that is, we know there's the rest of the iceberg not yet known to us.

Indeed, regardless of what is said and caveats offered here and there as escape clauses, in practice it is routinely assumed that genes are independent, discrete agents with additive functional effects, even though this additivity is a crude result of applying generic statistical rather than causal models, mostly to whole organisms rather than individual cells or gene products themselves.  Our methods of statistical inference are not causal models as a rule but really only indicate whether, more probably than not, in a given kind of sample and context a gene actually 'does' anything to what we've chosen to measure. Yes, Virginia, the gene concept really is to a great extent still metaphysical.

But isn't genomic empiricism enough?  Why bother with metaphysics (or whatever less pejorative-sounding term you prefer)? Isn't it enough to identify 'genes', however we do it, and estimate their functions empirically, regardless of what genes actually 'are'?  No, not at all.  As we noted yesterday, without an underlying theory, we may sometimes be able to make generic statistical 'fits' to retrospective data, but it is obvious, even in some of the clearest supposedly single-gene cases, that we do not have strong bases for extrapolating such findings in direct causal or predictive terms.  We may speak as if we know what we're talking about, but those who promise otherwise are sailing as close to the wind as possible.

That genetics today is still rather metaphysical, and rests heavily on fancifully phrased but basically plain empiricism, does not gainsay that fact that we are doing much more than just empiricism, in many areas, and we try to do that even in Big Promise biomedicine.  We do know a lot about functions of DNA segments.  We are making clear progress in understanding and combatting diseases and so on.  But we also know, as a general statement, that even in closely studied contexts, most organisms have alternative pathways to similar outcomes and the same mutation introduced into different backgrounds (in humans, because the causal probabilities vary greatly and are generally low, and in different strains of laboratory animals) often has different effects.  We already know from even the strongest kind of genetic effects (e.g., BRCA1 mutations and breast cancer) that extrapolation of future risk from retrospective data-fitting can be grossly inaccurate.  So our progress is typically a lot cruder than our claims about it.

An excuse that is implicit and sometimes explicit is that today's Big Data 'precision, personalized' medicine, and much of evolutionary inference, are for the same age-old argument good simply because they are based on facts, on pure empiricism, not resting on any fancy effete intellectual snobs' theorizing:  We know genes cause disease (and everything else) and we know natural selection causes our traits.  And those in Darwinian medicine know that everything can be explained by the 'force' of natural selection.  So just let us collect Big Data and invoke these 'theories' superficially as justification, and mint our predictions!

But--could it be that the empiricists are right, despite not realizing why?  Could it be that the idea that there is an underlying theory or law-like causal reality, of which Big Data empiricism provides only imperfect reflections, really is, in many ways, only a hope, but not a reality?

Or is life essentially empirical--without a continuous underlying causal fabric?
What if Einstein's dream of a True Nature, that doesn't play dice with causation, was a nightmare.  In biology, in particular, could it be that there isn't a single underlying, much less smooth and deterministic, natural law?  Maybe there isn't any causal element of the sort being invoked by terms like 'gene'.  If an essential aspect of life is its lack of law-like replicability, the living world may be essentially metaphysical in the usual sense of there being no 'true' laws or causative particles as such. Perhaps better stated, the natural laws of life may essentially be that life does not following any particular law, but is determined by universally unique local ad hoc conditions.  Life is, after all, the product of evolution and if our ideas about evolution are correct, it is a process of diversification rather than unity, of local ad hoc conditions rather than universal ones.

To the extent this is the reality, ideas like genes may be largely metaphysical in the common sense of the term.  Empiricism may in fact be the best way to see what's going on.  This isn't much solace, however, because if that's the case then promises of accurate predictability from existing data may be culpably misleading, even false in the sense that a proper understanding of life would be that such predictions won't work to a knowable extent.

I personally think that a major problem is our reliance on statistical analysis and its significance criteria, that we can easily apply but that have at best only very indirect relationship to any underlying causal fabric, and that 'indirect' means largely unknowably indirect. Statistics in this situation is essentially about probabilistic comparisons, and has little or often no basis in causal theory, that is, in the reason for observed differences.  Statistics work very well for inference when properly distributed factors, such as measurement errors, are laid upon some properly framed theoretically expected result.  But when we have no theory and must rely on internal comparisons and data fitting, as between cases and controls, then we often have no way to know what part of our results has to do with sampling etc. and where any underlying natural laws, might be in the empirical mix--if such laws even exist.

Given this situation, the promise of 'precision' can be seen starkly as a marketing ploy rather than knowledgeable science.  It's a distraction to the public but also to the science itself, and that is the worst thing that can happen to legitimate science.  For example, if we can't really predict based on any serious-level theory, we can't tell how erroneous future predictions will be relative to existing retrospective data-fitting so we can't, largely even in principle, know how much this Big Data romance will approximate any real risk truths, because true risks (of some disease or phenotype) may not exist as such or may depend on things, like environmental exposures and behavior, that cannot be known empirically (and perhaps not even in theory), again, even in principle.

Rethinking is necessary, but in our current System of careerism and funding, we're not really even trying to lay out a playing field that will stimulate the required innovation in thought.  Big Data advocates sometimes openly, without any sense of embarrassment, say that serendipity will lead those with Big Data actually to find something important.  But deep insight may not be stimulated as long as we aren't even aware that we're eschewing theory basically in favor of pure extrapolated empiricism--and that we have scant theory even to build on.

There are those of us who feel that a lot more attention and new kinds of thinking need to be paid to the deeper question of how living Nature 'is' rather than very shaky empiricism that is easy, if costly, to implement but whose implications are hard to evaluate. Again, based on current understanding, it is quite plausible that life, based on evolution which is in turn based on difference rather than replicability, simply is not a phenomenon that obeys natural law in the way oxygen atoms, gravity, and even particle entanglement do.

To the extent that is the case, we are still in a metaphysical age, and there may be no way out of it.

Is genetics still metaphysical? Part II. Is that wrong?

What is the role of theory vs empiricism in science?  How do these distinctions apply to genetics?

Yesterday, we discussed some of the history of contesting views on the subject.  Much of the division occurred before there was systematically theoretical biology.  In particular, when creationism, or divine creative acts rather than strictly material processes, was the main explanation for life and its diversity, the issues were contended in the burgeoning physical sciences, with its dramatic technological advances, and experimental settings, and where mathematics was a well-established part of the science and its measurement aspects.

Around the turn of the 20th century, Darwinian evolution was an hypothesis that not even all the leading biologists could accept.  Inheritance was fundamental to any evolutionary view, and inherited somethings seemed obviously to be responsible for the development of organisms from single cells (fertilized eggs). Mendel had shown examples of discretely inherited traits, but not all traits were like that.  Ideas about what the inherited units were (Darwin called them gemmules, Mendel called them Elements, and hereafter I'll use the modern term 'genes') were simply guesses (or just words).  They were stand-ins for what was assumed to exist, but in the absence of their direct identification they were, essentially, only metaphysical or hypothetical constructs.

The cloak of identity had serious implications.  For example, evolution is about inherited variation, but genes as known in Darwin's time and most of the later 19th century didn't seem to change over generations, except perhaps due to grotesquely nonviable effects called 'mutations'.  How could these 'genes', whatever they were, be related to evolution, which is inherently about change and relative positive effects leading to selection among organisms that carried them?

Many critics thought the gene was just a metaphysical concept, that is, used for something imagined, that could not in a serious way be related to the empirical facts about inherited traits. The data were real, but the alleged causal agent, the 'gene', was an unseen construct, yet there was a lot of dogma about genes.  Many felt that the life sciences should stick to what could be empirically shown, and shy away from metaphysical speculation.  As we saw yesterday, this contention between empiricism and theory was a serious part of the debate about fundamental physics at the time.

That was more than a century ago, however, and today almost everyone, including authors of textbooks and most biologists themselves, asserts that we definitely do know what a gene is, in great detail, and it is of course as real as rain and there's nothing 'metaphysical' about it.  To claim that genes are just imagined entities whose existential reality cannot be shown would today be held to be not just ignorant, but downright moronic.  After all, we spend billions of dollars each year studying genes and what they do!  We churn out a tsunami of papers about genes and their properties, and we are promised genetically based 'precision' medicine, and many other genetic miracles besides, that will be based on identifying 'genes for' traits and diseases, that is enumerable individual genes that cause almost any trait of interest, be it physical, developmental, or behavioral.  That's why we're plowing full budget ahead to collect all sorts of Big Data in genetics and related areas.  If we know what a gene is then the bigger the data the better, no?

Or could it be that much of this is marketing that invokes essentially metaphysical entities to cover what, despite good PR to the contrary, remains just empiricism?  And if it is just empiricism, why the 'just'?  Isn't it good that, whatever genes 'are', if we can measure them in some way we can predict what they do and live to ripe old ages with nary a health problem?  Can't we in fact make do with what is largely pure empiricism, without being distracted by any underlying law of biological causation, or the true nature of these causative entities--and deliver the miraculous promises? The answer might be a definitive no!

The metaphysical aspects of genes, still today
In essence, genes are not things, they are not always discrete DNA sequence entities with discrete functions, and they are not independently separable causative agents.  Instead, even the term 'gene' remains a vague, generically defined one.  We went through decades in the 20th century believing that a gene was a distinct bit of DNA sequence, carrying protein code. But it is not so simple.  Indeed, it is not simple at all. 

It is now recognized by those who want to pay attention to reality, that the concept of the 'gene' is still very problematic, and to the extent that assertions are made about 'genes' they are metaphysical assertions, no matter how clothed in the rhetoric of empiricism they may be.  For example, many DNA regions code for functional RNA rather than protein.  Much DNA function has to do with expression of these coding regions.  Many coding regions are used in different ways (for example, different exon splicing) in different circumstances.  Some DNA regions act only when they are chemically modified by non-DNA molecules (and gene expression works exclusively in that way). Some of 'our' DNA is in microbes that are colonizing us.  And 'traits' as we measure them are the result of many--often hundreds or more--DNA elements, and of interactions among cells.  Each cell's DNA is different at least in some details from that of its neighbors (due to somatic mutation, etc.).  And then there is 'the' environment!  This is central to our biological state but typically not accurately measurable.

Some discussion about these issues can be seen in a report of a conference on the gene concept in 2011 at the Santa Fe Institute.  Even earlier, in 2007 when it seemed we had really learned about genomes, hardly suspecting how much more there was (and is) still to be learned, a review in Genome Research was defined in an almost useless way as follows: 

Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes.

Really?!  Is that a definition or an academically couched but empty kicking of the can down the road while seeming to be knowledgeable and authoritative?  Or is it simply so empty as to be risible?

There are many now who advocate a 'Third Way' that in a rather generic sense of advocating less dogma and more integrative and indeed innovative or integrative approaches.  But even this doesn't say what the Third Way actually is, though one thing for sure is that it's every Third Way member's favorite way of coopting the concept of biological causation as his or her own.  I'm being cynical, and I'm associated with the Third Way myself and believe that serious rethinking about biological causation and evolution is in order, but that doesn't seem to be too unfair a way to characterize the Third Way's characterization of mainline genome-centered or perhaps genome-obsessed thinking. At least, it acknowledges that we don't just have 'genes' and 'environment', but that biological causality is based fundamentally on interactions of many different kinds. 

DNA is basically an inert molecule on its own

In genetic terminology, DNA is basically an inert molecule.  That is, whatever you want to call genes act in a context-specific way, and this goes beyond what is known as cis interactions among local DNA elements (like regulatory sequences flanking coding sequences) along a given strand. Instead, genetic function is largely a trans phenomenon, requiring interaction among many or even countless other parts of DNA on the different chromosomes in the cell.  And often if not typically, nothing happens until the coded product--RNA or protein--itself is modified by or interacts with other compounds in the cell (and responds to external things the cell detects).

Beyond even that complexity provides comparable evolutionary or physiological complexity.  There are many, perhaps often also countless alternative biological pathways to essentially the same empirical result (say, height or blood pressure or intelligence).  These causally equivalent combinations, if we can even use the term 'causal', are many and un-enumerated, and perhaps un-enumerable.  The alternatives may be biochemically different, but if it they confer essentially no difference in terms of natural selection, they are evolutionarily as well as physiologically equivalent. Indeed, the fact is that every cell, and hence every organism is different in regard to the 'causal' bases of traits.  We may be able to define and hence measure some result, such as blood pressure or reproductive fitness; but to speak of causes as if they are individually distinct or discrete entities is still essentially being metaphysical. Yet, for various sociocultural and economic reasons, we seem unwilling to acknowledge this.

You might object by saying that in fact most geneticists, from Francis Collins down to the peons who plead for his funding support, are being essentially empirical and not indulging in theory.  Yes, they drop words like 'gene' and 'epigenome' and 'microbiome' or 'network' or 'system', but this are on or over the edge of metaphysics (speculative guessing).  Many who feed at the NIH (and NSF) trough might proudly proclaim that they are in fact not dealing with airy-fairy theory, but simply delivering empirical and hence practical, useful results.  They do genomewide mapping because, or even proudly declaring, they have no causative theory for this disease or that behavioral trait.  Usually, however, they confound statistical significance with formal theory, even if they don't so declare explicitly.

For example, most studies of genotypes and genetic variation relative to traits like disease, are based on internal comparisons (cases vs control, tall vs short, smart vs not-smart, criminal vs non-criminal, addictive vs sober, etc.).  They don't rest on any sort of theory except that they do implicitly identify entities like 'genes'.  Often this is so metaphysical as to be rather useless, but it is only right to acknowledge that these results are occasionally supported by finding an indicated 'gene' (DNA sequence element), whose manipulation or variation can be shown to have molecular function relevant to the trait, at least under some experimental conditions.  But this causative involvement is usually quite statistical, providing only weak causative effects, rather than in any clear sense deterministic.  We are enabled by this largely pure empiricism to argue that the association we saw in our retrospective study is what we'll see prospectively as causation in the future.  And we now know enough to know that when it seems to work it is (as, indeed, in Mendel's own time) it's only the simplest tip of the causative iceberg.

We are tempted to believe, and to suggest, that this 'gene' (or genetic variant, an even cruder attempt at identifying a causative element) will be predictive of, say, a future disease at least in some above-average sense. That is, even if we don't know the exact amount of associated risk.  But even that is not always the case: the associated risks are usually small and data-specific and often vary hugely from study to study, over time, or among populations.  That means, for example, that people--typically by far most people--carrying the risk variant will not get the associated disease! It may often do nothing when put into, say, a transgenic mouse.  The reason has to be context, but we usually have scant idea about those contexts (even when they are environmental, where the story is very similar). That is a profound but far under-appreciated (or under-acknowledged) fact with very widespread empirical support!

Indeed, the defense of pure empiricism is one of convenience, funding-wise among other reasons; but perhaps with today's knowledge all we can do if we are wedded to Big Data science and public promises of 'precision' genomic prediction.  When or if we have a proper theory, a generalization about Nature, we can not only test our empirical data agains the theory's predictions, but also use the theory to predict new, future outcomes with a convincing level of, yes, precision. Prediction is our goal and the promises (and, notably, research funding) rest on prediction, not just description. So, as Einstein (and Darwin) felt, an underlying theory of Nature makes data make sense. Without it we are just making hopeful guesses.  Anyone who thinks we have such a theory based on all the public rhetoric by scientists is, like most of the scientists themselves, confusing empiricism with theory, and description with understanding. Those who are thoughtful know very well that they are doing this, but can't confess it publicly.  Retired people (like me) are often less inhibited!

Or could there perhaps be another way to think about this, in which genetics as currently understood remains largely metaphysical, that genetics is real but we simply don't yet have an adequate way of thinking that will unite empiricism to some underlying global reality, some theory in the proper scientific sense?

Tomorrow we'll address the possibility that genetics is inherently metaphysical in that there isn't any tractably useful universal natural law out there to be discovered.

This is the forest primeval: each tree an evolution

This is the forest primeval. 
The murmuring pines and the hemlocks,
Bearded with moss, and in garments green,
indistinct in the twilight,
Stand like Druids of old,
with voices sad and prophetic,
Stand like harpers hoar,
with beards that rest on their bosoms.
Loud from its rocky caverns,
the deep-voiced neighboring ocean Speaks,
and in accents disconsolate
answers the wail of the forest.

These famous lines, from Longfellow's 1847 epic poem Evangeline, spoke of a sad human tale in the days of early European settlement in the New World. The story was about people, but there is much to tell about the Druids of old, the lives and evolution of treest can be quite surprising.

This post was motivated by a recent trade book The Hidden Life of Trees, by Peter Wohlleben, a German forester, who described what his life in the woods has taught him about trees, their nature, evolution, and biology.  It's written at a pop sci level, and is often quite subjective and evocative, but it's laden with important facts when it comes to trying to understand the evolution of these terrestrial beasts. And, in a sense, these facts generalize in many ways.

The author discusses all sorts of observations that have been made about the responses of different parts of trees (bark, vessels, wood, leaves, roots) to their environment (sunlight, presence of trees of their own species, or of other species, of insect, fungal and other parasites), even going so far as to describe the sociology of trees and their responses to being isolated vs being in a forest of their friends and relatives. Trees interact with their own detected relatives, connected via communication through the air and underground via fungal networks, to the point that they even assist each other, when in trouble, with nutrients. It is a remarkable picture of interactions between organisms in organized, positively coordinated ecosystems.

The book is very selectionist, in that every trait is described as an adaptation to this or that condition, but trees that seem very similar can be different in these respects, so there is the assumption (very hard to prove, if even possible) that each trait evolved 'for' its current function. This is a more deterministically selectionist or even determinist viewpoint than we think is justified by actual fact, even if the functional aspects are as described (which we have no reason to doubt). Indeed, many examples are given of ways trees respond differently to different environments, and hence are not rigidly programmed to live in one particular way.

In any case, our point here aside from recommending an interesting and informative book, is to muse over some we think rather widely missed aspects of trees, their lives, and how they manage to survive and evolve.

While the author is a very strong selectionist when it comes to explaining who does what among trees or among woodsy species, I think he--and for all I know the vast majority of botanists--overlooks what is likely a very major aspect of arboreal evolution.

One major problem that seems to need to be more widely considered (maybe it is by botanists, but we haven't seen much that refers to this particular issue) relates to the implications of time scales (a matter that Wohlleben discusses in detail). Trees can live for decades, centuries, or even millennia.
Wohlleben very clearly and repeatedly stresses the fact that trees live on such a different time scale compared to us, that it can be hard for us to fathom how their lives evolve--and evolve is the appropriate word. If trees are, so to speak, rooted in their origins for hundreds or even thousands of years, while insects, fungi, and other plants and animals (not to mention microbes) have generations in years or even minutes, how can trees ever adapt or survive? By the time a tree has reached a venerable age, hasn't it been out-evolved by almost every other species that lives in or that is blown into its neighborhood?  By the time it dies, when any of its seeds germinate they must already be obsolete, ready to fight the last war-or the last war minus 10 or 100 or 1000.

One answer, in my view, is the largely overlooked fact of the evolution of tree--of each individual tree--during its lifetime.

The evolution of tree (not trees)
Unless my feeble knowledge of botany totally fails me, I think there is a lot going on even at the normal pace of things, within an individual tree. That is that each tree is a remarkable micro-example of evolution in itself.

Each tree starts life as a single fertilized egg (its seed). During its life, that little cell divides into billions, probably trillions, of descendant cells. These make up its roots and, important for us, its trunk, branches, leaves, and flowers. While there are various aspects of communication among these cells, they are essentially independent.

Each cell division along the way from the root tip to the branch tip (or 'meristem'), mutations will occur. This happens in humans, too; such mutations are called somatic because they don't occur in the individual's germ line (that is, the cell lineage that leads to sperm or egg), and hence while the mutation carried by the original cell and its descendants may affect the local tissue, the change isn't inherited by the next generation. Only mutations in the germ line are, and indeed that's where the idea of 'mutation' historically arose. Most somatic mutations will have no effect on the gene-usage of the cell involved, but if they do it might be negative and the cell will die or just misbehave in a way that has no consequences because it's surrounded by countless healthy cells. Sometimes, such as with cancer, somatic mutations can be devastating.

Trees are different. They have no separated somatic and germ lines. Mutations occurring from the seed to the roots and limbs may lead to dead cells, or do nothing, or they may be screened for their 'fitness', their ability to generate the bark, vascular, leave of other tissues in their local time and place. They are, relative to other cells in the tree, removed by what we could call a version of natural selection. Those mutations that survive will be passed down the line or, rather up the line as the trunk, branches, and leaves grow.

Here is a photo of an oak tree and (metaphorically) its single starting genome:

At the end of the countless stems in a tree, over its long lifetime, would be meristem cells each carrying a wide but individually unique variety of mutational differences from what was in the founding acorn. At the meristem, in the appropriate time of year, cells differentiate into pollen and ovule cells. These are many generations of selection away from their founding acorn, and on a given tree there must be a great variety of genotypes, whose sequences would form a tree (a phylogeny), much as we find when we compare DNA sequences from dog species, or from individual humans.

A single tree is a very large evolutionary 'experiment'. Branches affected by harmful mutation, simply aren't there, so to speak. They and their genomic lineage are 'extinct'. A single tree, and its lifetime, comprise such a large 'experiment' that they are comparable in numbers to whole species of shorter-lived, germ-line-dependent organisms.

Here is a photo of a tree from our yard that may illustrate the point. Why are only the leaves on this one branch turning to fall colors so much earlier than the others on the same tree? There may be local environmental reasons, such as different sunlight or water supply or parasite effects, but this seems rather unlikely because other branches in similar positions, even on this same tree, are still green.

And now here is another photo, of a different tree in our front yard that we think illustrates the points we're making. This red oak loses its leaves in the usual way....except for the one major branch shown. Its leaves do not fall until the following spring, but the remaining branches on this tree drop in fall as would be normal. This happens every year and is not a fluke of some particular season.

A forester might have a local explanation, that there is some connection between the location of roots supplying these particular branches, relative to the underground water or soil conditions, but one possible explanation is somatic mutation. That is, some mutational effect, arising when the branch was early in its formation, led to a difference in the abscission  layers of the leaves to be produced by that branch, that retained those leaves through the winter.   If the explanation is local physical conditions, of course, that means the tree cannot be predicted from its founding acorn's sequence. But it is rather difficult to believe that somatic mutation doesn't have at least the kinds of effects seen.  A good experiment would be to take an acorn from this part of the tree and plant it next to one from another part of the tree and see what happens. Unfortunately, the answer wouldn't be available for many years....

Our point here is that among the countless cells in a tree's life, between its origin as a single cell and the also countless generations of its own acorns from its founding genome through its long live, there simply must have been countless somatic mutations, occurring all along the roots and trunk and branches, cell division by cell division.  Their descendants, down the root network, and up the trunk and into the branches must have been screened for the viability of any phenotypic effects, which many must have had.  If insects or bacteria attack or animal predators or the climate change, parts of a tree may be better able to survive than others.  Cells in the trees' future lives will have the benefit of these changes.  They may be small, but they may accumulate over the decades.  The branches affected by less helpful changes would flower less, or lead to branches that die or fall to predators, and so on--ones we never see later on, when we look at the tree.  Among the countless meristems every generation will be a population of differing genotypes to be passed on to its season's thousands and thousands of seeds.

In this way, by working through meristems everywhere (above ground) on the tree are cells with new genotypes screened for suitability in its environment at each time during the tree's life.  A tree is not a single organism, but a population of descendants of a founder.  The acorn was primeval perhaps, but not the forest.  It is this kind of within-life evolution that may, or perhaps must, explain how a single, immobile organism can survive for so long in the dynamics of local ecosystems.

That is, it's the tree itself, in its ever-renewing parts from root to twig, not just its evolving population of annual seeds, that must be evolving.  Decades, centuries, or millennia must often encompass changes in the biota around each primeval individual, and would destroy it, if it, too, were not evolving.  Otherwise, it would seem like asking for doom to be fixed in a given location for hundreds or thousands of years, surrounded by junior, dynamically evolving predators and competitors.  

The forest is always primeval: Each individual tree, in this view, is an evolving population, always adapting in its unchanging location to its locally changing conditions.