Do scientists increasingly doubt the truth of evolution?

Do scientists increasingly doubt the truth of evolution?

[ 16/April/21 ]

No.

I know of no scientists (as I accept the definition of scientist), who has any significant doubts about evolution.

And that requires understanding the definition of scientist.

I have met many people who have PhDs who are employed as what most would consider science roles, who do not meet my definition of a scientist.

To be a scientist, one must be able to consider many different possible interpretive schema, to look for sets of conditions that might falsify some and not others, and to design reliable tests in reality, then do those tests, and let the results (not one’s pre-conceived notions) determine which of the schema one then continues to use in practice.

If one looks at human beings and at the logic of the systems that allow us to learn and to build models, then it becomes clear that all models, all understandings, are necessarily simplifications of the complexity present in reality.

Sometimes the demands of reality for rapid response demand that we use simple models that usually give survivable results. That reality seems to explain most of “culture”.

And some systems are very complex, and have no simple model that delivers reliable results. So sometimes we need to create very complex models.

The modern synthesis of evolution is such a very complex suite of models. I have been studying it for over 50 years, and should I live the rest of eternity I would fully expect to find new and interesting things to study within it, it does in fact seem to be that complex.

So if people are look for simple answers that always work in science – sorry, that does not seem to be the sort of reality we exist in – it seems to be more complex and uncomfortable than that, demanding far greater levels of effort and responsibility from all of us than any simple adherence to any set of stories from the past can possible deliver (and that is not saying that all stories from the past are without value – some of the stories from the past encode deep levels of lessons which we ignore at our peril – those stories that have stood the test of time need to be given due respect and consideration, but not necessarily belief as any sort of ultimate truth, rather more of deeply useful lessons and pointers).

So no – I have not met anyone that is sufficiently free of all forms of dogma that they meet my definition of scientist who has any significant doubt about the reality of evolution. And all real scientists deal in uncertainty, always, all contexts of reality. In science the idea of truth is often misleading, and I prefer not to use it. Real science is always a balance of probabilities – it always has uncertainties in any particular context, even if in many contexts those uncertainties are so small that we ignore them in practice.

[followed by Brett Passmore replied …”But there certainly are geneticists, microbiologists, zoologists etc who rejects common ancestry beliefs”…]

Not in my experience.

I have never met one that didn’t have such a firm and unquestionable belief before they started to study science. I have not met anyone who was actually able to consider reasonably complex sets of evidence and strategic systems who has come to such a conclusion.

I have met more than a few who were unable to consider uncertainty, who hold such dogma – but to me, such people do not meet the test of being a scientist, even if they have PhDs. But in every case it is belief denying evidence, not evidence directing belief.

[followed by Brett replied “You haven’t met a true Scotsman but that doesn’t mean there aren’t any. For example geneticist John Sanford.”..]

I have met many a Scotsman (and woman). I have some Scottish ancestry.

There is no evidence for such a belief.

Sorry if that offends some set of beliefs you have.

Biology is deeply complex.

I was 19 when I completed my undergraduate studies in biochemistry, and I was top of the class in many of the tests (even as I was the youngest in the class). The biochemistry of genetics is deeply complex, and very few people understand it well. Most people who pass tests do so by some form of wrote learning, rather than by derivation from first principles derived from probability analysis of evidence sets.

Few people appreciate probability.

Very few have taken the time to examine both the evidence sets and the logic of the schema applied, to all of the assumption sets and schema that they use.

Fewer still have a reasonable grasp of quantum mechanics, and that demands being able to work with non-binary logic – being able consider reality having more states than true or false (not many can do that – our neural networks are so heavily biased to deliver true/false answers).

Both are demanded if one wants to build a reasonable understanding of modern genetics.

So I fully understand that there are many people employed in roles in the field of genetics who do not fit my definition of a scientist, who do indeed subscribe to the dogma you propose.

And I restate the assertion that I made, in a slightly different form:
Of the many thousands of people with whom I have discussed the subject of evolution over the last 50+ years, I have not met any who in my estimation had looked sufficiently broadly across the breadth of fields required to build a reasonable model of the modern synthesis, that did so with an open mind to the evidence from the best available interpretations of the evidence sets available, who have any significant doubt about the reality of the evolutionary relatedness of all life forms on earth. And that is the most complex thing I have studied – more complex by many orders of magnitude than any computer system yet existing (and that gap is rapidly narrowing).

[Followed by]

Sorry – all examples you give are just wrong.

They demonstrate that you do not understand.

The manner of your reply demonstrates no knowledge of or interest in the actual evidence.

The difference between science and dogma is that science relies upon evidence from tests designed to distinguish between different possible explanatory frameworks.

There are many people employed in what most people consider scientific pursuits who have not made the effort to rigorously apply that principle across all of the beliefs they use.

I give up, as clearly you have no real knowledge of the evidence or the interpretive schema. Your claims are all either false or irrelevant straw men.

How much time have you actually spent reviewing scientific papers?

How much time have you spent designing and performing experiments?

Have you actually read Darwin, or Dawkins, or any papers on biochemistry (my text book when I was doing undergrad was White Handler and Smith “Principles of Biochemistry” – brand new in 1973. I read it cover to cover. Along with everything written by Darwin and Dawkins, and many many others (and the bible, and many other cultural texts). A lot of reading, a lot of time in labs, a lot of mistakes, a lot of learning, Delving deeply into the mathematics of matter, to get an idea of what makes chemistry work, what allows for complexity to emerge in some very special sorts of contexts. Delving into probability. Slowly developing models of just how complex systems interact and operate. There is a kind of profound beauty in it, and it is a beauty and simplicity that can only emerge after one has pushed through the complexity – over and over again.

It isn’t easy, It wasn’t easy for me, and I have many unusual attributes, including an ability to do math that few possess.

Simplifying complexity is an essential part of learning, and at some point one has to accept that some things are sufficiently complex that there is no reliable simplification, and one simply has to deal with the complexity that exists.

That is why few people have much real idea about the modern synthesis of evolution, because it is seriously complex.

Of course simple models fail if you push them too hard.

And some things deliver just overwhelming evidence, like the fact that the same embryological gene expression codes for eye formation in all animals. All eyes, from those in worms, to those in squid, to those in insects, to those in us, clearly share a common developmental linkage. All those different life forms, all those very different types of eyes, all clearly share a common ancestor that had a very simple kind of eye – little more than a spot of light sensitive pigment – but a particular chemical trick that initiates its formation that is so unusual that everything since uses it. The biochemistry of that is just so clear, yet it takes a lot of work to get to.

And I am reasonably certain that you have not made a similar level of study, and thus, rather than using evidence you have examined yourself, you are using dogma to attack a straw man argument; rather than make the effort yourself to seriously examine the evidence.

So it seems very likely that you are not able at this point to conceive of the modern synthesis of evolution, because it contradicts a treasured dogma that is foundational to your understanding.
I can understand and accept that in a sense.

At the same time you need to accept that you have no real idea what the modern synthesis of evolution is.

[followed by 17 Apr 21]

OK.

First – let us look at the figure of 100 million nucleotide changes between us and chimps, which is what I assume you are referring to.

Of that figure, about 35 million are single nucleotide changes, and the rest are made up of insertions and deletions (bulk changes, so not part of the average drift process – so I will not go into details about those processes, and they are well characterized if you want to dive into the detail yourself).

Our likely common ancestor was about 7 million years ago, so that is 14 million years of mutations (7 million on each lineage – the one leading to us, and the one leading to chimps).

Let us just consider single nucleotide change.

It is not a straight forward thing, it varies a lot between different areas of the chromosomes, and different environments, but if we just stick with the averages we can observe and measure today.

The average change we see today is about 70 changes per generation, and even there it can vary quite a bit depending on a large number of factors, but if we use the average, with a generation being 20 years (3.5 per year), then it is easy to see how the single nucleotide portion of the difference is accounted for within the random drift we see right now (3.5 x 14 gives 50 roughly, allow for a bit of selection pressure and there is the observed 35).

And there is nothing simple about differential survival of variants.

Some few areas of the chromosome are very highly conserved. Areas that code for the active sites of key protein catalysts tend not to survive even minor mutations. Such eggs or sperm don’t survive, and less critical changes the embryos tend not to complete gestation.

Other areas of the chromosome can be mutated with little or no negative effects. What is a negative vs a positive effect will vary a great deal with the specific context in most situations. Environments are not steady state things.

So it gets really complex exactly how you measure mutation, and exactly where the filtering of damaging mutations occurs, as to how one looks very closely at the mutation rates over time between lineages.

It is not a subject for a 10 minute conversation. The conversation can take several days assuming that both parties are already familiar with complex math.

The empirical evidence is clear.

If you were actually interested you would have been aware of it. But instead you create an overly simplistic straw man argument, and then burn it.

So clearly you are not interested in details.

Clearly you are looking for anything that might be used to substantiate dogma – which is not how science works.

As to the development of eyes, no, I was not referring to opsin, but to the Hox family of genes involved in the embryology of eye development. If you take the time to get into the details the systemic structure of that whole family of genes is just beautiful; and what seems very probably to have been its emergence from a series of chromosomal doublings from the homeobox gene cluster of earlier life forms. It is a truly fascinating aspect if you take the time to follow it, and build up an understanding of all the levels of patterns and systems and probabilities involved (but it took me a few years to really start to understand it).

And if you get seriously into biology, then it is all probabilities, not certainties. All quantum mechanical processes are probability based, all enzyme action. And in some contexts those probabilities can sum to things that very closely approximate classical causality (which is a great thing for the emergence of complex pattern), but not all (which is the hard bit for most minds to accept – we are so strongly biased towards simple models – we tend to ignore the exceptions, and one cannot make sense of biology if one does that).

So every one of the objections that you raised are not actually objections based on understanding of the complexity present, but come from using overly simplistic models. They are objections from ignorance.

And of course there is a sense in which we are all ignorant, necessarily, as one doesn’t need to do a lot of math to realize that the complexity surrounding us is more complex than any computational entity can deal with in real time. So we must all work with some degree of simplification and ignorance (that gets really complex once you see what all perceptions are already simplified models).

Part of understanding is accepting that, and getting out of the habit of being confident through willful ignorance, rather than doing the work required to step into uncertainty with degrees of confidence and with associated eternal uncertainty. And that is hard, because our brains are so heavily biased to be “right” (for the simple fast answer). Certainty is like candy to the brain. In times of real stress, real urgency, it can be very helpful, but most of the time it is not. Most of the time reality is far more complex and uncertain than our brains are comfortable with, so we all have very strong tendencies to accept simple models that do not require us to deal with uncertainty. Seeing that for the evolved tendency that it is, is a necessary step on the path to real science. So it is easy to understand why most do not take that step – it is hard and uncomfortable at multiple levels. That is why most involved in science are not what I classify as scientists, but are some form of dogmatists involved in scientific activities; and why there is a degree of truth in the saying that science progresses one funeral at a time. It doesn’t have to be that way, and it very often is.

[Followed by 19 Apr 21]

Sorry Brett – but yet again your overly simple model leads to erroneous conclusions.

Most of the DNA of interest codes for proteins.

Most of the proteins of interest are catalysts of various types, but some are structural or perform other roles (often multiple overlapping roles).

If you look at the active site of a catalyst, then most mutations (changes – the words mean the same) have serious negative consequences. Most changes in the active areas of the protein are selected out before conception, the egg or sperm simply die. Such seriously negative changes do not take a generation to get selected out, they never make it into a generation.

The further along the chain a change is, the smaller its impact. Most changes that manage to make it through conception and gestation tend to be of this minor kind. Thus the vast bulk of changes (mutations) that make it into a generation have little or no effect. This is in fact what we observe. Very few mutations that seriously impact function at the cellular level make it through gestation (some, but not many).

The observed rate of change is about 70 per generation in humans (with quite a bit of variation from a wide variety of factors).

That is what we can actually measure – happening.

There is in fact variation in every generation – not just in humans but in every species.

That only changes when you have events like Toba some 70,000 years ago, which reduced the entire population of humans on the planet to a few thousand. Things like that happened from time to time in our past (not just to humans, but to all species).

When something like that happens, variation can be drastically reduced. The populations start to build up again, and diversity increases again when that happens. (Estimates are that the Toba winter lasted about 6 years). That seems to be the most recent major reset on human genetic variation, and there were almost certainly many more before that.

There is absolutely no evidence whatever – zero – for any sort of biblical creation event – none!

You are not arguing from evidence, you are twisting evidence to suit dogma. And it seems very likely that you have no intention of doing anything else. I doubt that you have ever seriously considered a position that you consider wrong. It is hard to suspend judgement, and consider another’s argument.

To try and argue young earth creationism, as you are, from genetic evidence, you have to ignore way over 90% of the evidence and focus only on a very tiny portion that from a simple interpretation seems to lend some weight to the argument. Sorry – but it doesn’t.

In going back 7 million years, then forward 7 million years – I am not doubling the amount of mutations, just doubling the time available for them to occur. The difference between us and chimps is still the same, but our common ancestor was probably somewhere near half way between us (at least in terms of single nucleotide mutations). That shows a failure to check even the most basic of math.

I don’t know how you can claim that J F Crow supported your hypothesis when he published papers like this that clearly refute what you claimed:
Mid-Century Controversies in Population Genetics (https://www.annualreviews.org/doi/10.1146/annurev.genet.42.110807.091612)

Another case of picking one aspect of an argument, simplifying it, and paying no attention to everything else.

Pay attention to the evidence – all of it!

[followed 20 Apr 21]

Brett,

If you pay attention to the evidence, all of it, then some things are very clear.

The evidence from geology is clear that the earth is about 4 billion years old.

The evidence from the fossils in rocks is that for about half of that time such life as existed was single celled.

The evidence from fossils is that we see changes in the makeup over time, with some periods of mass extinction (which we now have reasonable sets of evidence for the causes of and the timing of – to within a few million years for the older stuff – all measurement has uncertainty).

If you go to the evidence in the biochemistry of the life forms we see present today then it is fascinating, and multiple levels of evidence of slow genetic drift (of exactly the sort we see between us and chimps from our last common ancestor) is overwhelming.

I have not met anyone who is capable of doing the probability landscape analysis who has examined such evidence in depth who has any reasonable doubt about the long term nature of the evolution of those systems.

If seems beyond reasonable doubt that the earliest version of RNA life used a doublet codon for protein formation that only used the 4 most common amino acids; but understanding that requires a whole other level of sets of abstractions and data. And having had a reasonable examination of those datasets the issue is settled with 95%+ confidence in my mind.

Having read the bible cover to cover I can see a lot of wisdom encoded in the stories within it, and also a lot of mythology (like the creation myths) that simply do not stand up to modern evidence. And that is entirely what one would expect of such an evolving system of awareness and understanding.

So the evidence really is overwhelming, if one is prepared to seriously look at it, and examine the systems.

Yes mutations happen.

Yes some of those mutations have some deleterious effects.

And most of the serious negative effects are removed by levels of selection at the level of single cells (in eggs and sperm) long before a fully formed human is born. Most selection happens at that level – invisible to our naked eyes.

Only the tiny fraction that survive that vast selective pressure get to grow into children, and then on into adults.

When you have expanding populations then necessarily there is expanding diversity. That is a necessary part of how the system works.

It is a form of random search across the space of available variants for those that can survive the harsher periods.

One of the strategies our species can explore is that of reducing the harshness and frequency of the harsher periods, and thus allowing the survival of a far greater range of diversity.

This, clearly, is the system we exist within.

Sure there is some great wisdom in some of the stories of the bible, and there is a lot that is not relevant to our modern understanding, but does make sense in terms of the evolution of stories over time.

If you look at all evidence, across all sprectra, then there is no reasonable doubt.

[Followed by 21/Apr/21]

Brett,

There is no evidence for a young earth.

If you look at evidence of physics, and geology, all of it – then it makes sense only with an old earth.

Very clearly you have no interest in evidence – you really want to believe in a dogma and will ignore any and all evidence that contradicts your favoured dogma. That is not unusual, it is a reasonably common human response; and there are evolutionary reasons why such behaviours tend to persist in populations, and you really are fooling yourself if you think you are being evidence based. You are not.

[followed by different sub thread – in response to Mark H Smit – 19 Apr]

I don’t understand the claim you made that “Self-assembly is a logical impossibility” – I would like you to flesh that out a bit.

To me it seems entirely probable that life initially evolved in a very unusual context – probably a “white smoker” (an alkaline undersea hydrothermal vent) that provided sufficient hydrogen ions to power the initial processes of replication prior to the emergence of more complex metabolism. And we are unlikely to ever have any direct evidence of exactly how and when life emerged, and this does seem to me (on balance of probabilities across the dozen or so contenders I have investigated) to be the most likely (and I have been known to make mistakes – quite a few of them, as I have spent a lot of my life pushing various levels of boundaries of the known and understood).

So to me, self assembly – as in complex pattern emerging in a context containing a reliable energy gradient, is entirely possible – even probable.

To me, life seems to be about survival of pattern across varying domains of context over time; and often the class of pattern that survives best is very context sensitive. Thus the type of context present is often the major determinant of the general classes of life form that emerge in that class of context(s). When one explores that notion at sufficient levels of abstraction then it becomes clear that the existence of both complexity and freedom are predicated on levels of cooperation that can only survive in contexts with levels of abundance (sufficiency). That is something that existing economic theory is not doing a great job of acknowledging.

When one starts to seriously look at the classes of context that have existed in the not too distant past, then it becomes clear that we need some major new classes of risk mitigation technologies, and those demand entirely new levels of cooperation if they are to be of more benefit than risk. It does get really complex!!!

[followed by 20 Apr 21]

Hi Mark,

Self assembly only works in a very tiny range of contexts.

It seems very probable that it only happened once, in the entire history of life on earth (that qualifies as a very tiny set of contexts).

In terms of obeying the second law of thermodynamics, of increasing entropy (greater disorder overall) then life has to obey that, and it does so via metabolism. In order to maintain the order embodied, life has to take energy and order from one system, and leave the systems as a whole in a more chaotic state than the amount of order preserved in the living part of the system.

These days plants are responsible for most of that, taking the higher energy photons of light from the sun and converting them into bonds in carbohydrate molecules, and low energy photons.

To maintain the order of life there must be low grade heat as waste product. Managing that, and a lot of other environmental factors, are always issues for life forms.

Finding an environment with sufficient available energy, and sufficient reliability and sufficient stability for the random aspects of all such systems to deliver the first replicating system is a very special sort of context, and the most likely of the candidates proposed to my way of thinking is that of white smokers.

And we are unlikely to ever have any direct evidence. It is highly unlikely that any alien species was around with some sort of molecular level “video camera”, taking a tourist shot to show the family, at the precise time that the first replicating system that included metabolism got under way. And very likely that first system could only exist in that specific white smoker for a very long time, before any variants emerged that were sufficiently stable that they could drift around until they found another environment that they could grow in. Any way you look at it, it had to be a very uncertain start, and the evidence strongly suggests that it had to have happened, somewhere, somehow, in some way that is something like this general sort of picture.

The details of the processes present in the details of the chemistry of life are very strongly suggestive of classes of pattern; and they are fairly abstract topologies.

About Ted Howard NZ

Seems like I might be a cancer survivor. Thinking about the systemic incentives within the world we find ourselves in, and how we might adjust them to provide an environment that supports everyone (no exceptions) - see www.tedhowardnz.com/money
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