Wednesday, February 25, 2015

Survival of the safest: Darwinian conservatism, not derring-do

A mantra for many in life science is 'survival of the fittest'.  This phrase, one Darwin liked and used many times after he saw its use by Herbert Spencer, reflects Darwin's view of life as a relentlessly competitive phenomenon.  To Darwin, life was an unending struggle for survival (and reproduction) among individuals in every species all the time.  Natural selection, a relentless force like Newtonian gravity, always identified the 'fittest', weeding out the others.

Darwin's objective was to show how new characters could arise, that were suited--'fitted'--to their environment, without the intervention of God via special creation events.  Because organisms, all and always, were struggling against each other for limited resources, they 'tried' (via their inherited genomic drivers) to be better, different, more exploitive of environmental opportunities than their fellows.  Dare to be different!

But in perhaps fundamental ways, Darwin had it very wrong, perhaps inverted from what is really going on.  We know this from the analysis of genomes, the presumed source of all evolutionary evidence, since everything that's inherited goes back, at least indirectly and usually directly, to information carried in DNA.

When DNA sequences are compared within or between species, there are segments that are seen to have very little variation among the sequences, and segments with much more variation.  Now we have learned how to identify truly functional parts like coding exons, transcription start sites, introns, promoter and some regulatory regions, functional RNAs (like tRNA, rRNA and so on), telomeres, and so on.  And we have also identified many parts (the majority, actually) that has far less obvious or strong function, if indeed any function at all.  So what do we see?

The clear, consistent pattern is that the more strongly functional, the more highly conserved (there are a few exceptions, like sensory system genes in the olfactory and immune system, but even their variation proves the rule).  The less, or non-functional regions vary much more, both within and between species.
Herd of dairy goats, Polymeadows Farm; photo A Buchanan

This has been seen so consistently, that for many purposes (like the ENCODE project to characterize all DNA elements) sequence conservation is the very definition of biological function.  The reason is that evolution conserves function but doesn't care about bits that have no function.  One can quibble about the details, but the main gist of the message seems unequivocally correct.  But this now near-dogmatic principle has some little-digested implications.

Darwinian evolution
The problem Darwin wanted to solve was to explain the differences among species, and the way they were suited to their ways of life, in terms of historical processes rather than Divine creation.  He had a deep sense of geological change and biogeography from his trip on the Beagle, that showed the evidence of local relationships that suggested common ancestry.  And then he had an idea of a law of Nature, an ineluctable force-like process of adaptive change, the way gravity is a force, that would gradually form the kinds of differences that characterized species.

'Natural selection' was the name he gave to that force.  And because it was force, like the way gravity is a force, it could detect the tiniest differences among competing organisms and favor them to produce the next generation.

The idea is that species always over-reproduce relative to their resources (an idea that was already 'in the air' in Britain at the time), and struggle to obtain what become limited resources.  Because of inherited variation, the individuals with the best genotype (to use our term for it) reproduced, their poor lesser peers fell to what Tennyson would call 'Nature red in tooth and claw'.

Darwin's idea was that selection always favored the innovator.  Relentless striving to be different from the herd, to get the scarce food or mate supply.  As the late thinker Leigh Van Valen suggested, the Darwinian struggle was like the Red Queen in Alice and Wonderland--always running as fast as she could, but never getting ahead because the competition was always trying to out-do you with their own adaptations.

This is so entrenched in the biological and evolutionary literature, that it may be surprising to realize how different from what we see in the actual data--the genetic data, our most precise indicator--about how evolution works.

Or is this Darwinian?
What we actually see in the genetic data is not the kind of chaotic variation that an intense, force-like, relentless struggle to be better than your peers would lead us to expect.  Instead, what we see is what can only be called herd behavior at the genome level.  Our ancestors did, and our contemporaries do, their very best to stay with the herd.  The high conservation of functional DNA sequence suggests that mutational variation is mainly harmful to fitness, that what selection really favors is conformism. Don't be very different, or you'll get pruned away from your species' posterity!

Herd of flamingos, the Camargue, France; A Buchanan
Instead of 'survival of the fittest', what is by far mainly going on is 'survival of the safest'.  Stay with the mean.  Why is that?  A standard answer that is likely accurate, is that we today are the product of a long past in which the traits we bear were able to survive.  We're very complex organisms, so what evolution hath joined, let no one put asunder except at their peril!

Survival of the safest might suggest that there is no innovation, which is clearly not correct, since different species have different adaptations--fish swim, cats eat meat, bats fly, we write blog posts. So clearly differences do arise and have been favored regularly in the past.  However, that seems inconsistent with the high level of genomic conservatism that is so predictably identified.

One way, perhaps the major way, that these apparent contradictions are reconciled is this:  As Darwin stressed repeatedly, evolutionary change is very, creepingly slow.  That means that either there are occasional short bursts of rapid, major change, brought about by largely catastrophic changes in circumstances, or, only a very minor 'ooze' of the distribution of traits occurs in some favored direction from one generation to the next.  This is imperceptibly slow at any given time, because being near the mean is still the safest place to be.  Just be a tiny bit different.

Survival of the safest is Darwinian in that it is a form of natural selection.  Indeed, it is a lot more Darwinian than Darwin was himself.  Selection is more probabilistic and less force-like than he thought (he lived still in Newton's shadow), but it is always at work as he said it was.  It's just that it's mainly at work removing rather than favoring what is different.  Every geneticist knows this, but it is far from thoroughly integrated into the common view of evolution even by professionals.

If a trait were being strongly driven by selection in some new direction all the time, as in the more exclusive connotation of survival of the fittest, we might expect only a few variants with strong effect in the favored direction would be contributing to its newly adaptive instances.  Mapping the variation in the trait would perhaps yield a rather simple genetic causal picture as a result.

But if a trait is being roughly maintained, by survival of the safest, pruning away serious deviants, then any genotypes that are consistent with being somewhere near the average can stay around, with individual variants coming and going by chance (genetic drift).  Variants conferring trait values too far from the mean are pruned by selection.  But most variants can hang around.  Mapping would reveal very large numbers of contributing variants across the genome.  And there would not be precise predictability from genotype to phenotype.

This is what we see in biology.

Survival of the safest in daily life, too
'Survival of the safest' thus seems to be a better metaphor for adaptive biological evolution.  But if you think about it you'll see that we see much of the same regularly in most aspects of our society. We may say heady things like 'dare to be different!', but those who dare to be very different are quickly punished by being ignored or directly slapped down.  This is true through history. It's the general fact in religion, government, social behavior.  And it's true in science, too.  Business as usual is safe, real innovation is a threat to the established.  We see the press of society to claim to be different, but not really to be different.  Innovation mostly means incremental change trumpeted with exaggerated verbiage.  We may even think we want major, rapid change, but emotionally we shy from it, and feel too nervous about what it might mean for our own current state.

Organizations and sociocultural and political systems are very slow to change. or they change in herd-like fashion.  This is true even in realms, like the business world, where one often hears a rather self-satisfied pronouncement that allowing free-market Darwinian competition is the way to get innovation. Innovation is often claimed, but much less often really major.  It's true in science, too: everyone is playing grantsmanship, to seem different to draw attention or funds, in this case, but you dare to be very different at your peril, lest reviewers suspect, distrust, can't grasp, or are jealous of your idea.  Some rapid change may occur, but it's not so common relative to the inertia of survival of the safest.

That is what we see in society.


Palfreyman1414 said...

This sounds much like a reversion to Stephen Jay Gould, let alone Darwin.

1. Extending evolutionary theory to social ideas can be dodgy.

2. Survival of the safest is subsumed within fittest, whereas fittest allows for the innovations that do occur.

3. The problem with the genome analysis is that, in genomes we analyse, we are bound to see those that survived, whether or not they were genuinely innovative to begin with (within the earlier population in which they emerged).

4. Sexual selection, as far as we know, can genuinely favour the different and keep favouring it.

5. You are absolutely right that extreme variations will probably not survive, but that is part of the standard evolutionary analysis in any case.

So apart from coining a phrase (a possibly less rich one than the original), I am not sure why you make the points you do here.

Ken Weiss said...

Well, you don't have to think the points are important, or you can think they are already known. I think they are worth making. This is no reversion to Gould, and I don't care, per se, what he or others say, if the point is to think about biology and evolution. But if anything our point is a response to the widespread, even if just subliminal, view about selection. It is not we who extend the theory to social ideas; that is widespread, among anthropologists and among popular writers, and is seen all the time.

Your point 2 is of course true, but the pervasive idea that life is always striving mainly for innovation is what we are noting.

The point about genome analysis is that there is no reason, in very adaptationist evolutionary theory to think that the kinds of traits being mapped should be genomically simple or that somehow mappers are misunderstanding something basic in the complexity that is being found.

I don't agree about sexual selection if I understand your comment. I think sexual selection very strongly favors current 'fashion' (to use a human word for it). I think that traits, like human 'racial' traits, that are often attributed to sexual selection, show this conservatism--even (as we noted) if on occasional they can drift into some different direction. We didn't say that positive adaptive evolution didn't occur, just that the stress is misplaced in our view.

Finally, we didn't say anything that goes against
'standard' evolutionary theory, and we noted I think that even conservative evolution is a form of selection.

Personally, I think it is an important corrective to move away from the strong Darwinian phrase (not to mention the ambiguous word 'fittest').

Ken Weiss said...

Another couple of thoughts (responding to Palfreman). Gould himself, in his Structure of Evolutionary Theory megatome, said that his own career-defining contribution was 'punctuated equilibrium'. In fact, Darwin recognized the same thing, very clearly, in the 6th edition of the Origin of Species. Both were reflecting an interpretation of fossil data, both not considering what this might mean genomically (during their lifetimes perhaps not even Gould could have known enough).

But there are problems, in my view, even with that, just as there are problems with what I believe is the usual working assumption about life as relentless force-like selection. That is, it is difficult to see why, when, or how complex species traits can stay essentially the same for tens of millions of years or more, with little or no drift. It isn't enough to say generically that 'the environment didn't change'. And such conservatism is found for traits that we know can vary (because of related but variable species).

There are even potential problems with the assumption that sequence conservation is the sine qua non for function of a genome region. But that gets far beyond today's post.

Anne Buchanan said...

Perhaps some semantic issues here. As has been argued by many, natural selection is generally a conservative process, not a creative one, though 'innovation' implies otherwise. And "survival of the fittest" itself is not an accurate description because, clearly, many more than the 'fittest' survive. As we've often said, 'failure of the frail' is a better phrase. So, perhaps the problem here is disagreement about underlying assumptions about the evolutionary process.

Thanks for the derring do correction though, 'derring do' being itself an incorrect rendering of 'daring do,' but one that caught on. An error that now seems like an innovative linguistic step? Back mutations not allowed.

Palfreyman1414 said...

Thanks for your responses, Anne and Ken.

I appreciate that correctives sometimes need to be applied. My concern is that they frequently turn into popularisation/linguistic issues rather than genuine corrections of scientific issues.

I apologise if I sounded too strident in my first response.

Ken Weiss said...

Well, thank you right back. I agree with the danger of over-sloganizing if I can put it that way. I would argue that scientists are vulnerable to it, not just the reporters and TV producers etc. Most population geneticists and so on know these things, but they are far less well understood by the large biomedical (and I think, social science) worlds, who we feel live on cardboard caricatures of what is actually known, and this influences a lot of science that is done.

And while 'fittest' is an almost uselessly vague term (as is 'safest'!), in a sense I think we understand evolution better if we realize the reason for conservation and the uphill struggle that real biological innovation faces most of the time.

Or, put another way, if we think about DNA sequence variation and how traits are or can be maintained and how that should appear at the genome level, there are important subtleties that I think deserve a lot more attention. But subtleties don't generally get attention in our current science research environment.

Palfreyman1414 said...

Thanks again for that.

My point about sexual selection was that, given it sometimes appears to have an arbitrary nature in its phenotype expression, small genome changes that are not negatively selected for can result in (very quickly) huge morphological changes. Which is the opposite of conservatism.

Of course we would expect some of the core genetic features to be hugely conservative, those involved in early development, for instance. But if so, doesn't that, drift aside leave a lot of leeway for innovative change (sexually selected or otherwise)?

Last question: you speak of species lasting ten million years or possibly more. Can you give me any genetic examples of such long lived species. I'm guessing palaeontologists believe they have many, but then they're not working in population genetics.

I'm just intrigued by the notion that there might be a record "longest lasting species".

Ken Weiss said...

As to persistent species, the horseshoe crab is the classical example. But, really, many others like recently characterized Spinosaurus supposedly lasted, recognizably, for 150 million years. Or what about biofilms that seem, morphologically, unchanged for 3.5 billion years?

Of course, molecular clocks show that these species (or their descendants) are still evolving clocklike at putatively neutral sites. So selection of some sort must be keeping them from phenotypically drifting, and I think that's a serious issue to explain.

Sexual selection, if it is as quick and strong as is suggested, has some problems. Unless you accept the shifting-balance theory, there are problems in accounting for its quickness, given that it is largely based on some sort of mate-choice 'judgment' (conscious or otherwise).

If we could look at mapping data for such traits, what would we find? Single-gene changes making the main difference, and hence great mappability?

I think biomedical GWAS data are relevant. Even traits like stature, that have changed dramatically in just a few generations and should in that sense reflect responses to rapid changes in environmental factors, is very complex and so are other similar traits. This is like s sexual selection in that the environmental changes, whatever they are (probably diet, lower infection loads etc.) should be expected to single out a few major responder-genes. But that's not what is being found. It's not genetically 'conservative' in that sense, at least.

As to developmental conservation, I agree, and that goes back at least to Waddington. It isn't Darwinian selection, though. It has to do with lack of molecular 'cooperation' (as we have stressed in our book), not struggle for limited resources, and so it is not 'Darwinian' selection. But it probably explains a lot, if not even the bulk, of conservation at the genome level.

Giancarlo said...

Has IQ been selected for in particular populations? Have the genes behind IQ as discovered through the GWAS and GCTA been reliably replicated and found to be result of a positive selections?

Ken Weiss said...

My answer is that IQ is a vague measure with various problems. I don't think any seriously manageable set of genes whose normal variation (that is, not associated with real mental impairment) affects 'IQ' have been consistently found. Whatever 'IQ' is, of course it will vary and some of this (roughly, proportional to the estimated heritability) will be affected by genetic variation interacting with environmental conditions. That fraction seems to be modest in terms of individually identifiable effects, and even with people with the same IQ the genotypes will be different.

Different groups from any local population will sample the same gene pool differently and so will differ in the details and the average trait value. That doesn't mean the average difference will be very great--it's a purely empirical question and it has clearly been proven to be very difficult and there's no real consensus about the details.

The more widely separated (in population history) two groups have been, the more they'll differ in the genomic variants that affect IQ and there will, as always, be some difference in mean and variance, as always happens with sampling and evolutionary history (a different form of sampling).

Again, whether the average differences among groups are 'important' or major is controversial, because IQ is so heavily affected by environment. There are temptations to make racist interpretations, with historically (and currently) socially discriminatory consequences, which is why categorical statements about group differences (that usually ignore the majority of the distributions which overlap between groups) are so controversial and should be made with great reservation. Since that rarely happens, and since environmental effects can maximize potential, and so on, I think this is a subject that is dangerous to deal with and, from a genetic point of view except for truly pathogenic variants, shouldn't be.

Giancarlo said...

Hello and thanks for answer. I am personally seeing some problems with your arguments about IQ. I agree there are many, including you, who make the argument that IQ is not necessarily a measure of intelligence. That there is problems with heritability, or twin studies, or GWAS, and so on. I want to counter such arguments, first with this paper by Plomin on IQ: and this link by some good Biosocial researchers on heritability:

Perhaps you can read these and tell me what you think. I think you are already agreeing with me that group differences in IQ can be genetically affected, and importantly, be a result of evolution. This argument is not necessarily popular, but it would seem that the data backs it up.

Ken Weiss said...

Robert Plomin has a career long interest in the genetic contribution to intelligence and related traits. I would interpret things rather differently and I think the tendency is to treat intelligence and inheritance as far more deterministic than I think they are, and also there is a subjectivity to what one chooses to measure and/or to name it.

Because it is so loaded with sociocultural uses and misuses, I think the subject should be treated with far more circumspection than it receives, and I believe it is a proven excuse for racist or other sociocultural discriminatory attitudes or policies.

'Intelligence' is a cultural, subjective, also inescapably sociopolitical characteristic. That doesn't mean 'it', whatever it is, or whether it is a well-posed trait, has no genetic influences. Everything does. The issues have to do with its degree of determinism, what it actually means in a given cultural context, why it is being measured as it has been chosen to measure it, and so on. And whether saying it is 'genetic' is code for some other agenda, as history proves it has often been.

Group differences always exist, and there will always be genomic influences (in terms both of development and variation); that's always related to evolutionary history; it's the nature of the kinds of processes, sampling, and measurement that are involved that there will be group differences. That is separate from questions about 'importance', which is subjective. Heritability is a notorious problematic metric, widely misunderstood.

But if you're so determined to stress the genetic/evolutionary side, ask yourself why. I don't particularly want to know the answer, because this subject rarely gets anywhere. So we can end this exchange, and make our own judgments about things.

Giancarlo said...

OK. Thanks for the kind and informative responses. I will agree definitely that science and practice of scientific research through the ages has been stricken with biases and political partisanship. We are of no exception, of course. I think we should as a result stick to what's largely agreed upon and obvious. When we say "intelligence" then of course it comes off as arbitrarily defined concept or very ideologically and culturally loaded. That is where, I think, things like IQ, and the g factor come in to clear things up. Fact is that these measures correlate very well to things like success in education, income, and so on. I think national differences in IQ and other group differences reflect that as well. But I agree that you may disagree with this. In fact, I am interested in the fundamental disagreement between us. For example, I would personally agree with a statement like "IQ is heritable." I think it's informative and obviously backed up by decades of research and output in the journals. But the way I interpret it is obviously much different than you, and I am only assuming, but I think you probably disagree that that statement really says much of use. If that is so, I am interested to hear why?


Giancarlo Piceno

Ken Weiss said...

These factors are defined in some way based on what we (basically, professors) decide is a good measure for statistical stability and correlation with various things. Let us assume it is so fixed that it (the measure and its correlates) don't change with time. Do they predict (say) skill at basketball or fishing or any number of things we don't associate with career success and so on? I think that we should not call it 'intelligence', and I've read that test scores often do not correlate with job success much of the time (i.e., the correlation is week). And remember that heritability is a relative, not absolute, measure and that many investigators say that IQ scores have been changing rapidly (if they have to keep up with the cultural times, then what's being measured is not some absolute trait).

The ratio nature of heritability, and its definition by western science, are why comparison among groups is problematic.

But any different groups will be different in mean (and probably variance and kurtosis etc) on almost anything and the issue then has to do with 'significance' and 'importance', and these are subjective judgments.

Using these subjective criteria is what leads to societal issues and policy. There is the tendency, that no one can really deny with a straight face, that the almost immediate tendency is to treat group mean differences as if everyone in the group had its average IQ. Could you doubt that this is almost perceptably a major reason for compairing groups? Well, go to Excel and plot a curve of two Gaussian distributions whose mean difference is about 1/2 a standard deviation (I think that is as much, or more, than careful, environmentally controlled studies find). What you'll see is the massive amount of overlap and the relatively useless value of the means.

Also, if we agree, as we must, that even if just because of sampling variation group means will differ, and if what we care about is individual opportunity, or distribution of educational resources, etc., then we need not geneticize these things: we just need to give achieved ability tests and see who's good at what, who needs what sort of assistance, etc.

And do we need to consider, say, 'race' unless we clearly use it as a stand-in for socioeconomic circumstances etc., since not everyone of the 'same' race has the same continental ancestry distribution. There's so much eagerness to map 'race and IQ', but hardly have I ever heard one ask for studies of the IQ distribution of Catholics or Buddhists. They may ask for that for Jews, or Arabs, or Africans....where biological category is what they're after. The subject is never far away from racism of one form or another, and one needs to ask why that is. It's often transparently about resource acquisition and societal status,

We know of many genes in which mutations can lead to serious cognitive impairment (these don't stand out, or are even found as 'hits' in Plomin-like gene mapping studies. Why not?

If you read our posts over the years on GWAS and the issues about what the findings are, and the ephemeral nature of individual genome location contributions, you'll see that the gene-trait connection is far more elusive than most would like to acknowledge.

OK, whether or not we agree, I think it gets nowhere to belabor these points.

Ken Weiss said...

If IQ is so inherently biological, then why is the score changing? Here's a current BBC News story:

It's an elusive subject. And who can write about it without having some agenda openly or covertly part of what they write? If this were so simple we would not still be having the same discussion decade after decade (and I don't even here cite the eugenics era literature)

Giancarlo said...

IQ may not be too inherently biological, but what needs explaining is why the popular environmental explanations have so much biological influence? One recent paper is this: