Metaphysics in science, Part V: Is 'risk' real or metaphysical?

Metaphysical ideas imposed on the world as if they were derived from the world go against the nature of modern science and bear similarity to a long-standing but rejected idea about how we understand existence.  We've discussed some facets of these issues, from the point of view of modern evolutionary and genomic sciences as we see them, and to provoke thought (but not as professional philosophers or historians of science, to which we make no claim!).

Here we want to conclude by considering these issues related to an aspect of causation that we've dealt with in a previous series of posts, when causation and in applied areas the notion of 'risk', are probabilistic.  Are these metaphysical concepts in any important sense, or are they just plain-vanilla and not-misleading conveniences, like our use of the term 'the human genome' to represent something that really doesn't exist but helps us understand what does exist?

Plato's cave: Wikimedia Commons

Plato's concepts, from his analogy of the cave that we have referred to, were that abstract ideals actually exist, but all we can experience of them are shadowy, imperfect manifestations.  In genetics, we only observe instances of the human genome, but there is no such thing as 'the human genome'.  This doesn't bother us a bit because we understand the usefulness of an arbitrary (that is, agreed-on) reference to organize our discussions of human genetics.

Ideas like 'chair' or 'dog' may not have Platonic reality, but again are very useful without being misleading, relative to real chairs or dogs.  In the case of dogs or genes, we even have very good, wholly material, empirical theories of population, that account for the collection of real-world objects to which we apply terms like 'dog' or 'gene'.  The population concept does not require the existence of some 'ideal'.

Plato also dealt with more elusive examples, like 'good'.  This is much less clear: does 'good' exist out-there in the meta-world with some reality of its own, or do we just observe instances of 'good' in the physical world? It's less clear than 'gene' or 'dog' because we haven't got a way to agree what 'good' is an arbitrary reference for.  'Good' is not a specifiable population of things.

But what about probability, say as expressed in terms of the 'risk' of getting a given disease if you carry a specific instance of some named gene?

Statistical causation: what kind of reality?
As we outlined in our series of posts on probability, the concept isn't always clear. When we speak of the probability of a given variant, say one of the two copies of a gene that a person has, being transmitted to a given offspring, what do we mean?  We mean that in a long series of producing offspring, each copy will be transmitted to an offspring the same fraction of the time.  That's a frequency interpretation.  We have purely materialistic notions of how the molecules (DNA) randomly buzz around the nucleus of the sperm or egg precursor cell, and one of the two just happens to end up in a given sperm or egg cell.  Neither copy has an advantage--that's a functional interpretation of probability.

In these instances, all we actually see are manifestations of the transmission of genes from parent to offspring.  So in a sense, the 'probability' is a purely metaphysical concept: it exists in our heads whether or not anybody ever produces an actual offspring.  In some ways the functional or frequency interpretations don't really matter, but in other ways the metaphysical nature is troubling. That's because we can only test its reality by experience and experience--even if our very  notion of probability is correct--never precisely realizes the expected result!  For example, the probability of your transmitting variant A to your next child may be 50%, and that may be as 'true' as true can be.  But if you only have one child, it either received the A or it didn't.  Further, in some sense (e.g., diploid organisms) we believe that the Mendelian process is universal.  The cave-wall manifestations of shadows of metaphysical truths simply cannot tell you the truth!

So we have other ways to view probability concepts about the world.  One is called 'likelihood', and it's used to say if our metaphysical idea that there is a true probability of transmitting an A to any given child is right, then what do the actual data tell us is the most likely value of that probability?  Again, we're playing around with notions of truth.  But if we believe--and 'believe' is the right word here--that genetic transmission works this way, we can learn from experience about it.  This and other statistical ways of dealing with the probabilistic world reside largely in belief about what might be true in the world, rather than direct proof of what's true. But even in this case we believe that one of the alternatives we are considering is actually true!  But is that not itself a metaphysical statement?

There is a danger in this and it seems to relate to the reason metaphysics was strongly rejected in the age of modern science, beginning around 400 years ago.  The danger is that we can assume that ideas in our heads are real, yet nothing other than actual experience can tell us if we're right.  So, instead, the new scientific method said, why not rely entirely on experience?  Let experience show us what the truth is.  After all, we want our ideas to enable us to predict future experiences, things not yet observed.  That's what scientific theory is all about.  As long as our theory is actually about reality, rooted in experience, this seems to work rather well, at least in practical terms.

Let's look at another example that we referred to earlier in this series.  What is the 'probability' that a human with curly hair and agile thumbs will evolve from monkey stock?  This is not about frequency of events in any useful sense; it's about something-or-other regarding things that might have happened.  (We did, in fact, evolve, but we could ask the similar question, like "what is the probability that a  4-fingered, 6-toed language-speaking fully aquatic primate will evolve?")

These really are basically metaphysical questions.  What is the chance that human-like life exists on other planets (something we've discussed earlier, as well, in posts about 'infinity')?  Such questions seem to be about reality, but hardly are because the answer requires a numerical value ('chance', between 0 and 1) and there is no serious way of finding out the value, much less whether it's true, much less whether the idea that some such value there actually exists is itself correct.

As we've said in this series, metaphysics is vulnerable to beliefs not clearly shown by reality.  Religious assertions are often accused of this fundamental fallacy.  But scientific assertions clearly are also vulnerable in this way, because unlike religion, science is purported to be strictly about the real, material world.  Yet, we believed Isaac Newton--clearly a modern scientist--until Einstein came along.  So, when probabilistic causation is important, or seems to be the case, we are very vulnerable.  What should we 'believe'?

To bring things back to earth, so to speak, these issues arise in full dress when it comes to interpreting genomics and in inferring genetic causation today and in evolution.   The promises made of individual life-experience prediction from genomes sequenced at birth, or that GWAS or biobank whole genome sequence will do that, or enable all known human ills to disappear, are examples.  They are based not just on what are largely metaphysical notions about causation, and when this is admitted to be probabilistic, about predicted outcomes.  This is treated as if in the functional or frequency sense of probability, but the evidence is really clear that this is only mildly accurate.  The point is that while advocates freely admit that we're not there yet, they believe that accurate--indeed perfect?--prediction is possible in principle. 

When traits like the objects of GWAS and other 'omics are due not just to practicably countless contributing factors, some genetic and perhaps identifiable but others not known, but each of them somehow working only probabilistically, then we are more squarely in the metaphysical world.  The probabilities now are really not of the frequency or even functional sort, except very abstractly.  They are more of the belief sort.  The same statements apply to many aspects of inferences made about how evolution has worked, and in particular, stories offering adaptive genetic explanations for traits seen today.  Those, too, are probabilistic in the belief sense ("it seems likely that upright-walking hominids were able to compete to secure food from .....").

It is not just a belief that no immaterial forces intervene in genetic causation, say, of a disease.  It is that if we knew everything, everything could be predicted.  But there is no way to replicate unique events, like individual genomewide genotypes and all environmental experiences, we can never actually know how true this is.

Yet, and here is where we think people are dabbling in metaphysics when doing this kind of genetics: the belief system is so strong that it goes beyond an assertion that we just don't yet have adequate evidence, but actually goes against the evidence, which in the face of probabilistic complexity is already generally quite weak.  It becomes, as we have said, imposing metaphysics on the real world, rather than the other way around.  And this then can be very misleading to science and the distribution of limited resources we have to understand the world.  It again becomes an obeisance of belief, or the exact opposite of science--a form of denial: again, it is the zen of genomics, when No means Yes.

What is metaphysical?  What can we hope actually to know?
Metaphysics as we use the term in this series is the Platonic ideal that truth does exist somehow, and all we see is approximate manifestations of it.  Science claims to have rejected that notion.  We've seen examples where metaphysical abstractions still used in science are not particularly damaging. 
But in genomics we are seeing something that was predictable (and predicted) for the right reasons decades ago--complexity is the rule, but people still want traits to parse simply.  It is the investigator as an ostrich, hiding from the very truth he claims dedicated to find.  It is the assumption of higher-level truth, in some ways thumbing one's nose at the evidence.

Coming full circle: when is a finding a 'finding'?
We return to where we began in this series, the assertion that unless you find some hoped-for, dramatic, simple tractable result, you haven't made a 'finding'.  This attitude is such a shallow shadow of any semblance of an understanding of the nature of reality and our understanding of it, that we think it's not too much of a stretch to say that it poses a threat to society.  That's because overly Platonic views of the world are misleading, divert resources, can lead to awful conflicts, and so on, as history very clearly shows.

Again, Plato provided a metaphysical view of existence.  Ideas about things were real, and things themselves were, in some sense, not as real.  Philosophers have sliced and diced these ideas over the centuries, in many sophisticated ways.  Metaphysics grew from being rather central to humans (in western cultures, at least) trying to make sense of the world, to an airy-fairy world that scientists love to sneer at.  But do we not much more, and much more culpably, indulge in implicit Platonic metaphysics than we care to admit?

Many philosophers have dealt with the difference between the real, empirical world we can touch and smell, and the world our neurons construct within our heads.  From Aristotle and solipsists in classic times, to Kant and many others, the issue of how or whether our limited sensory apparatus and brain can actually and truly know anything other than itself has been an open one for philosophizing.  And of course there are the works of countless religious thinkers about the nature or even existence of  'things' and non-things.

Here, we're not dabbling in such ultimates, nor are we qualified even to summarize the centuries of sophisticated thought about those issues--nor, for that matter, the thoughts of poets and artists whose work deals directly with them.  We are simply assuming there is a reality 'out there', and that the interest of science is in how to understand it, both pragmatically and ultimately.  Our context is genetics and evolution, not whether neutrons outrace light or electrons exist in fixed locations and all that.

But life goes beyond ordinary physics in which, anywhere at all, every oxygen molecule is alike and all photons speed equally through vacuums.  Physics and chemistry are comfortable with concepts about collections of such identical things, as abstractions representing tractable realities whose collective behavior follows nice principles, or laws. Even when they are probabilistic, as in describing the pressure of a gas in a container, when this is due to random buzzing of huge numbers of identical objects.  Pressure is empirical as a pragmatic stand-in for practically assessable instances.  But it's metaphysical to the extent of the assertion that 'it', whatever it is, exists uniformly, eternally, and ubiquitously.

But evolution is not about the collective and eternal behavior of identical items, but instead is inherently about variable, ephemeral ones--from genes on up to ecosystems.  We cannot assert identity in the way a chemist does, because the entirety of the life sciences is in a meaningful sense about variation.

This means that elusive issues like emergence or statistical causation, by individually unique collections of elements, isn't really like physics (even if all the elements, like you and us and globin genes and genomes, ultimately follow physical and chemical principles).  It is the organization of life that's different in the sense we're considering.

One can argue that making assumptions about that organization, when it does not have specific, replicable instances, verges on Platonic metaphysics, and goes beyond convenient pragmatism.  It is like asking whether 'good' exists.  The danger is not that we have things we profoundly don't understand, even deep concepts like probability when we cannot confirm it in any actual way.  The danger is that we really do indulge in metaphysics in the guise of science, by being immune to the messages that the real world, when it is not just instances like shadows on a cave-wall, sends us.

In a way, that has always been the deepest problem with metaphysics: it is not sufficiently constrained by reality. Yet of all fields of human endeavor, science should try very hard to understand the real world, not the ideal world or the wished-for world.  Instead, of the current kind of metaphysics, we should be out in the sun where the truth, as well as is shadows can be seen.  But things can be more comfortingly simple in the cave--the cave of denial of evidence.  Like the original cavemen, perhaps we prefer the comfort of the dark.   At least, to a great extent, for convenience and self-interest, even some scientists are staying in the cave on purpose.

We may respect Plato, but we should not become neo-Cavemen!

A request for comments by those who know!
We have said many times in this series, that we are not professional historians or philosophers of science, and that we are using terms--especially, 'metaphysics'--in a particular restricted sense.  We also know of the existence of a vast literature over 2500 years on aspects of the subject.  But we've only read, or dabbled, really, in a tiny fraction of that literature.  So if there are any MT readers who are expert in these areas, we'd be happy to have commentary that constructively addressed the issues, as we have raised them, or to add to or modify what we've attempted to say.

Metaphysics in science, Part IV. When causation is complex, what is it? Real or metaphysical?

This series has dealt with what it means to be scientific but not metaphysical, whether in a sense science has not really abandoned its ages-long flirtation with ideas imposed on the world rather than the world determining our ideas.

In previous posts we dealt with metaphysical notions like 'the human genome' or 'the globin gene', which do not really imply the actual existence of Platonic ideals, and serve mainly as pragmatic guides for our understanding of the world and the practice of science.

We then addressed why, whether, and how failure of data to replicate a theory should lead us to abandon it.  If it doesn't, then the theory is in a way shown to be a Platonic ideal assumed to be true rather than the kind of empirical truth we supposedly are seeking in science.  We mentioned a couple of examples in which Darwin held to his theory, correctly believing the overall evidence overriding mistaken notions of genes, but also imposed his theory on data as in making what amounted to 'progressive' theories of evolution when he studied barnacles.

Then we asked why GWAS and related omics, that did not find the expected, and promised, high accounting for important diseases, has not led to an abandonment of the underlying theory about major-gene causation, and whether that showed that for whatever set of reasons, metaphysics was driving our material assessment of the world of genetics and evolution.  These are all real and, we think, important issues that are rarely addressed by scientists. 

However, there are other issues that are important and we'd like to comment on two of them.  They are complexity, and statistical causation.  Here, we discuss the first of these two issues. 

Complexity and emergence: what are they?
So far in this series, we've considered rather simple theories:  A gene exists.  It codes for protein or its regulation in cells.  Antibiotic resistance results from genetic variants rising in frequency if they help the organism surmount the lethal challenge.

We've seen that these don't really seem to pose any serious systematic or fundamental threat to the notion that we can express our understanding of  the world in such abstract terms.

But what about when the theory gets more complex, when, say, many different factors interact to contribute to a single net result?  The net result, like a building, is sometimes called an 'emergent' phenomenon relative to the contributing components (bricks and steel beams).  That is, enumerating the components, or even studying them even down to the level of the atom, won't tell you much at all about the building itself.  What shape will it take?  How many stories will it be?  (We could estimate that by counting the bricks and beams, yes, but that won't be very precise.)  What's it going to be used for?  Who will use it?  Will the roof leak? 

Let's apply this to disease genetics.  Let's say that diabetes is the building, and many different genes and environmental factors the bricks and mortar.  We can't easily go forward or backward from here -- we can't reliably predict diabetes from the genes, and we certainly can't predict future environments, nor can we retrodict genes or environment knowing someone has diabetes.  In this instance, what kind of truth is an emergent phenomenon, relative to a material theory of the world?  Is it metaphysical in any way that should concern us?

If the result can't be predicted from the components, then more is going on than a list of those components.  The net result may be given a name, but this becomes more metaphysical than physical in some causal senses.  It's causally not so strictly utilitarian in the way 'the globin gene' guides us to study the instances of globin genes in actual people.

If every case of diabetes is due to a different set of causal factors, working and interacting in different ways in each instance, then diabetes is a different kind of reality, a somewhat metaphysical notion that exists independent of its assumed ordinary causality.  These are not just abstract philosophical questions, but in fact underlie our decisions about how to approach causation.  When our assumptions are unstated, and we don't think about why we're asking the scientific questions we ask, and designing the studies we design, our understanding of complex traits can easily become ensnared by their complexity, and this all becomes even more problematic if we assume we're looking at a simple trait. Even iron-clad ideas about causation, or the most appropriate uses of metaphysical convenience, can lapse into metaphysical vapor.

These are things you have to think about to grasp them, perhaps.  At least,  we do! If every instance is causally different so that we cannot enumerate the causes (because, for example, we need large samples or replications to show that they are really causes), then the emergent thing verges on a metaphysical ideal:  the trait may seem real enough, in our heads, but causally elusive in the world.  It is an assumption that it is a causally unitary....what?  It is too easy to assume its reality and force that onto assuming that if we but have big enough studies, or whatnot, we will be able to treat it by the usual reductionist methods (enumerating its causal bricks), when that may not be its reality as far as the current scientific method is concerned.  That is the 'emergence' problem, and we're not very good at solving it.  Instead, we wish it away through metaphysical ideals.

One strongly problematic aspect of all of this is related to, but goes far beyond, complexity and arbitrary agreed-on working definitions.  It is how we view probabilistic 'causation', to which we turn next.