Does Evolutionary Theory Need a Rethink?

[Argon]

Sy, I really don’t see it that way. What I see are self-promoting statements about how a ‘new’ approach, ‘previously ignored’ will revolutionize a ‘moribund’ science of evolutionary biology. It’s a old, rhetorical technique of trying to play up the contrast between old and new. An extension seldom generates excitement like ‘the new’ or ‘the revolutionary’, but much of the hype is provided with an incorrect context of actual history. People like Larry Moran frequently skewer such pronouncements.

Aside:
The human genome project was also sold with a goodly amount of self-promotion and hyperbolic claims. Scientifically, the project was definitely useful but not nearly to the extent many participants said. And to be realistic, the early genome projects were done more because they were easy and could be readily accomplished, not because they were the best way for achieving groundbreaking science. Most biologists knew that the work would only start with the sequences, just providing one step along the long haul.

Still, as moon-shots go, it was probably more generally useful than many of the ‘omics’ initiatives since.

Epigenetics:
Epigenetics is the the spotlight now because initial measurements are also becoming easy. We have the technology. I suspect the field is also being oversold but we will still characterize epigenetic modification sites and mechanisms because it’s another step along the way that will produce some useful insights.

I don’t see these advancements as revolutionary but incremental. Perhaps because I favor the phagocytosis model for describing most of science.

Neo-Lamarkian:
Now, what really gets me seeing red is the term ‘Lamarckian’. I think that’s sad because the mechanisms currently proposed as “Lamarkian”-like are but a pale shadow of the theory Lamarck proposed. For instance, I’d like to see a biologically feasible, feedback mechanism of Lamarckian use/disuse that would account for the evolution of a giraffe’s neck. I think what counts as ‘Lamarckian’ under ‘new’ biology is piddling in comparison and I suspect these examples will cover a small set of special cases rather than be main drivers, especially in life with split germ and somatic cell lines. So, for those who want to claim that neo-Larmarckian mechanisms are wide-spread and generally applicable in evolution, I’d really like them to list the sort of feedback mechanisms, underlying functions and specificity required to support such mechanisms on a broad scale. Early estimates from genetics suggested an upper limit to the number of genes an organism could maintain against drift and decay. Those estimates seem to have been reasonably close to what we see. I suspect there are also very real limits to the additional number of components required to support a general-purpose, neo-Lamarkian system.

Regarding popularizations missing many details:
Here is my favorite quote – “Evolution is so simple, almost anyone can misunderstand it” by the late philosopher of science, David Hull

I doubt that many scientists in the field thought evolution was ever a simple, linear process. We hope it’s simple and there certainly are the rare, simple cases, but overall, biology rarely is easy.

I look at the advances from a technological view:

• Early on, ‘genes’ were something one could study and thus genes were modeled. This was necessarily incomplete and most scientists in that field knew it.
• Later, recombination and crossing-over were studied and the linear model of genomes added model refinements. This was necessarily incomplete and most scientists in that field knew it.
• DNA and its replication machinery were characterized and we refined models with traits as products of that machinery. This was necessarily incomplete and most scientists in that field knew it.
• DNA & protein sequences yielded snapshots for comparative studies at the molecular level. This technology was used to refine evolutionary models. This was necessarily incomplete and most scientists in that field knew it.
• And so on.

Despite the shortcomings at each step, we did learn something about the nature and mode of evolution. Variation and selection are real phenomena. Taxonomy was combined with sequence data, cementing the overall pattern of common descent. Human and chimp variation fell well within the range of known molecular mechanisms, further proving relatedness. We learned that genomes constantly shift while many gross physical characteristics may persist. Changes in regulation generally occur faster than changes in structural proteins.

[Sy_Garte]

@Argon

What I see are self-promoting statements about how a ‘new’ approach, ‘previously ignored’ will revolutionize a ‘moribund’ science of evolutionary biology.

Argon

If we remove the word self promoting (I trust you will agree that self promotion is a common occupational hazard of many scientists) and the quotes, I totally agree with this sentence.

Evolutionary biology itself has never been exactly moribund, but neither had it been terribly interesting in the mainstream. I think of the EES as what it says it is - an extension. There has been some degree of overblown rhetoric, (Shapiro is an example) but Wagner an Rosenberg and Laland are not claiming to be revolutionaries, they are just doing good research. I am aware of Moran’s skewering, and that is exactly the point. The fact that he, and his colleague Coyne bother to skewer efforts to expand evolutionary theory is exactly the reason that there is in fact a sense that this is a new, and controversial approach.

. To me there is no question that current evolutionary theory is incomplete. Dawkins disagrees. So do many others who feel that we dont need to find any further mechanisms for dramatic and rapid alterations in body plans other than the adaptationist paradigm (as Gould brilliantly wrote about).

We cannot say simultaneously that the EES is nothing new or different from SET, and that it is also wrong. So which is it? My own view is that neither are correct. I do expect a great deal of what is now found on the Third Way website will turn out to simply be wrong, as is the norm in science. But some of it has gone a long way to being well established. What counts now is not simply a recognition that the data imply a great deal more complexity than has been accepted previously, but that all of this must be incorporated into some useful theoretical framework within Darwinian theory. I think that is a very worthwhile endeavor, although I will not attempt to convince you further.

[GJDS]

Paradox is an odd term when discussing any scientific theory - what makes ToE so different that it can be discussed seamlessly as paradoxical. I should think a scientist would use semantics that either admitted the inadequacy of ToE in light of such an a paradox, or try to remove the paradox (some may argue that humanity contradicts ToE, but I am not looking for an endless exchange, so paradox will do).

[Swamidass (Peaceful Science)]

@GJDS

Paradox is an odd term when discussing any scientific theory - what makes ToE so different that it can be discussed seamlessly as paradoxical. I should think a scientist would use semantics that either admitted the inadequacy of ToE in light of such an a paradox, or try to remove the paradox (some may argue that humanity contradicts ToE, but I am not looking for an endless exchange, so paradox will do).

Science is full of paradox. Its not just evolution that works this way, but the whole endeavor. Paradox lies at the foundation. This shouldn’t be a surprise. Many early scientists were Lutheran after all =).

[GJDS]

I am not sure I understand you - the foundation of science is based on first principles, and from these we endeavour to understand the various disciplines. Your paradox is hardly in this area of science - we all admit that the human species is vastly different from any other species, as ~7 billion souls would show, with cities, vast tracks of land for food, the sky and ocean at the “mercy” of humanity, wars that can exterminate vast tracks of the earth and its inhabitants, magnificent animal close to extinction, environments and eco-systems all but exhausted or destroyed - the list goes on. How can evolutionary biologists claim that this is merely the work of a clever ape?

[Swamidass (Peaceful Science)]

@GJDS

I am not sure I understand you - the foundation of science is based on first principles, and from these we endeavour to understand the various disciplines. Your paradox is hardly in this area of science - we all admit that the human species is vastly different from any other species, as ~7 billion souls would show, with cities, vast tracks of land for food, the sky and ocean at the “mercy” of humanity, wars that can exterminate vast tracks of the earth and its inhabitants, magnificent animal close to extinction, environments and eco-systems all but exhausted or destroyed - the list goes on. How can evolutionary biologists claim that this is merely the work of a clever ape?

We are clever apes, but we aren’t just apes. We are not merely clever apes. So where else do we see paradox in science? Frankly, almost everywhere. Consider embryology…

@Swamidass

We see evolution the same way you probably see embryology. Science has a description of how babies are made that includes only natural laws and randomness. Scientifically speaking, this is description entirely excludes God. Yet, we also, at the same time hold that God “knits us together in our mother’s womb” and that He “knew us from before the foundations of the earth were laid.” These things are true too, and not in the scientific description.

Also consider general relativity and quantum mechanics. We hold both theories to be “correct” in important and salient ways, even though they produce entirely contradictory predictions in important questions (e.g. dark energy). So we have, here, two mutually exclusive theories that we simultaneously hold to be provisionally correct.

If non-contradiction was science’s highest value, this would be impossible. Rather, it isn’t. Science holds mutually contradictory theories simultaneously if they both have strong explanatory power. This is almost exactly the definition of a paradox.

Also see how science thinks about truth…

theories in science are never accepted as absolutely true. During hypothesis testing, only two results are possible: the scientist can reject the hypothesis if it did not make an accurate prediction, or the scientists can fail to reject the hypothesis if it did make an accurate prediction. The important point is that the scientist cannot accept the hypothesis.
From the Archives: Evolution as a Scientific Theory | The BioLogos Forum

This again is a paradox. We place high confidence in “provisional truth,” in fact science ignores absolute truth to focus just on absolute truth. There is paradox here, because we place high confidence in scientific theories, even as we simultaneously admit that they are not correct. They are simultaneously true and untrue.

I could go on and on from here. Another great example is emergent phenomenon (complexity arising from simple systems) and also consciousness. Regularly, here, simultaneously “true” theories contradict one another. Science works so well because it doesn’t care. Non-contradiction is not the most important guiding principle of science. It embraces the paradox.

Paradox is everywhere in science.

[GJDS]

The first point in this discussion is that paradox and contradiction are often interchanged - I have tried to follow your reasoning and I must confess that you are mixing paradox/contradiction with speculation. Scientists indeed speculate, but, eg, dark matter, is stated specifically as a “stop-gap” measure because there is NO scientific theory nor maths that can provide scientific understanding.

I want to avoid a lengthy exchange as most of the salient points in your response can be covered by a reasonable philosophy of science text book. My point may be better understood if I made it in the following manner:

1. your claim is that common descent is scientifically proven and is the foundation of ToE.
2. I point out an immense amount of clearly observable data that shows humans have very little in common with primates.
3. You imply now point (2) may be paradoxical
4. I state that no scientific theory would accept so much contradictory data by claiming some type of paradox - nor is QM a “way out” of this type of reasoning - for example, just look at the fantastic accuracy that QM computations provide. My work on DFT molecular models provides bond lengths that agree (at a high level of computation) to three decimal points with experimentally measured ones. This is a clear demonstration that QM is an accurate scientific theory as applied to molecular compounds - I would never contemplate a paradox with this.

Finally, emergence is not a scientific theory but an appeal to the difficulties experienced when faced by complex systems. Consciousness is the study of psychology - we do not doubt that we are conscious - we are examining it - we do not claim that consciousness is paradoxical - this would be absurd.

[Relates (Roger A. Sawtelle)]

@Swamidass

Regularly, here, simultaneously “true” theories contradict one another. Science works so well because it doesn’t care. Non-contradiction is not the most important guiding principle of science. It embraces the paradox.

Paradox is everywhere in science.

@Swamidass

In some sense you are right. Science doesn’t care, but people care. Indeed it is those contradictions which lead scientists like Einstein to new discoveries.

Also people are not just scientific beings, they are also philosophical and theological beings. This impels them to go beyond the contradictions to find the Truth. This is why there are New Atheists as well as YEC Christians.

Paradoxes and contradictions are enables by Western dualism. However Western dualism does not stand up to Einstein’s Relativity, which is based on a Relational universe. We need to go beyond Western dualism to relational world view to better understand the paradoxes of science.

[Swamidass (Peaceful Science)]

@GJDS

Scientists indeed speculate, but, eg, dark matter, is stated specifically as a “stop-gap” measure because there is NO scientific theory nor maths that can provide scientific understanding.

I was referencing dark energy, not dark matter. Cosmological constant - Wikipedia Quoting wikipedia…

If the universe is described by an effective local quantum field theory down to the Planck scale, then we would expect a cosmological constant of the order of {\displaystyle M_{\rm {pl}}^{4}} M_{{{\rm {pl}}}}^{4}. As noted above, the measured cosmological constant is smaller than this by a factor of 10−120. This discrepancy has been called “the worst theoretical prediction in the history of physics!”.

@Relates

In some sense you are right. Science doesn’t care, but people care.

Very true. Which is why paradox is a helpful framework, rooted in Christian theology.

@GJDS

1. your claim is that common descent is scientifically proven and is the foundation of ToE.2) I point out an immense amount of clearly observable data that shows humans have very little in common with primates.

Not really. I say that our best “provisional” understanding of biology is common descent. It explains almost everything we see at a genetic level, and resolves many puzzles we see at the phenotype level. This is true.

Phenotypically in humans, however, there is a big step change. At this level, nothing quite like this has happened before. Something emergent is going on here where the sum trancends the parts. This doesn’t render common descent false, but it does make it incomplete.

@GJDS

Finally, emergence is not a scientific theory but an appeal to the difficulties experienced when faced by complex systems.

This, I feel, is not true. In physics, many scientists resist the notion of emergence, however, is on key place where their is strong agreement of emergence Phase transition - Wikipedia.

At a basic level in biology, the properties of biopolymers (e.g. proteins) are emergent. We understand the monomers in exquisite detail, but we struggle to understand even the most basic properties of proteins. But these properties, on a protein leve, are where the most important “action” is happening. So we have to, essentially, move away from first principles to model emerge properties directly to have any hope of understanding biology. While atomistic models of proteins are more “correct,” they are much less useful make different predictions than less “correct” emergent models of protein behavior.

I know there is a strong reductionist trend in physics, but biology counters this. Biology is all about emergence.

[Swamidass (Peaceful Science)]

@GJDS

Scientists indeed speculate, but, eg, dark matter, is stated specifically as a “stop-gap” measure because there is NO scientific theory nor maths that can provide scientific understanding.

This also, I think, is incorrect. There are several maths and scientific theories that can explain dark matter (e.g. WIMPS or Axions). We just do not know which one is correct.

So on one hand, we have data that clearly contradicts our best theory of everything (Dark matter - Wikipedia), yet we resist revising it without further proof. Also, we do not entirely reject our best theory (even though it is in a sense falsified) because it successful explains so much.

Any how, I know you didn’t want a protracted argument, but I think evolutionary theory is going through the same progress as all theories. It is correctly explains a great deal of data, with no other alternative in sight, but it doesn’t explain everything. We slowly revise and improve and extend it, so it explains more (without loosing explanatory ability on what we already know).

I think this article is helpful…

Even theories change - Understanding Science

[GJDS]

I think you may concede that a great deal of the subject matter in these exchanges can be classified as speculation (and paradox would not be my preferred term). Speculation, questions, even educated guesses are part of the rich matrix we call scientific research and I cannot imagine it to be otherwise. My interest in participating on this blog from time to time, is mainly to point out the difference(s) between speculation from science (and other fields) and the tenets of the Christian faith. Central to this is the nature of human beings, which Christ took on Himself, to show us how we may be saved though faith in Him and by God’s grace. In this context, I do not share the enthusiasm for ToE displayed by some (well meaning) Christians who post here.

[Jay313 (Jay Johnson)]

@Swamidass

Both these seemingly contradictory narratives appear to be true. We are simultaneously “from the dust” and “image-bearers”. We are simultaneously “creatures” and in “communion.” We are simultaneously exceptional and non-exceptional. We are both a “tiny step” from our ancestors, and “a great leap.” This is the paradox. Both are true.

Our very faith rests in the Son of God, a paradox if ever there was one.

Ah, the greatness and wretchedness of man! A favorite theme of Pascal: “The greatness and the wretchedness of man are so evident that the true religion must necessarily teach us both that there is in man some great source of greatness, and a great source of wretchedness. It must then give us a reason for these astonishing contradictions. … ‘It is in vain, O men, that you seek within yourselves the remedy for your ills. All your light can only reach the knowledge that not in yourselves will you find truth or good. The philosophers have promised you that, and have been unable to do it. They neither know what is your true good, nor what is your true state. How could they have given remedies for your ills, when they did not even know them? Your chief maladies are pride, which takes you away from God, and lust, which binds you to earth; and they have done nothing else but cherish one or other of these diseases. If they gave you God as an end, it was only to administer to your pride; they made you think that you are by nature like Him, and conformed to Him. And those who saw the absurdity of this claim put you on another precipice, by making you understand that your nature was like that of the brutes, and led you to seek your good in the lusts which are shared by the animals. This is not the way to cure you of your unrighteousness, which these wise men never knew. I alone can make you understand who you are’… Adam, Jesus Christ.”

@Eddie

I think the ID people, in criticizing certain “neo-Darwinian” writers on evolution, have been alerting the public to the fact that evolution isn’t thought by the most advanced theorists to be nearly so simple and linear a process. And maybe most of the post-doctoral researchers knew that already, but the general public doesn’t. I would guess that the average reader of popular science is much more aware of the qualifications that quantum theory and relativity brought to physics than of the qualifications that evo-devo and self-reorganization of the genome have brought to evolutionary theory. For some reason, the biological establishment seems content to let a simplified version of “evolution” dominate the popular mind, whereas physicists, cosmologists, etc. seem to go out of their way to disseminate newer conceptions to the public as soon as possible.

A true observation, but it helps the physicists that a large chunk of the popular audience isn’t religiously committed to denying the results of their research. Many, many people only read the authors who already agree with them, so only half of the story is getting out there.

[Jay313 (Jay Johnson)]

@Eddie

Maybe it’s time that a real, full-time, active, professional evolutionary biologist shoved aside all these non-specialist or retired or virtually retired popularizers (Miller, Dawkins, Coyne, etc.) and wrote a good, up-to-date, popular presentation of evolution. Someone like Gunter Wagner could do it, if he put his mind to it.

It’s long overdue. They could do it as “Evolution for Dummies!” in Barnes & Noble, and re-brand it “Evolution for Christians!” in Family Christian Stores. (Joke! Joke!)

[aleo (Albert Leo)]

@Swamidass
First, I want to thank you for the lengthy and cogent reply to my earlier post and for the link to the discussion with Dr Varki on Veritas.org. (I missed it earlier, because I needed to update my Adobe Reader. Small world: A very close colleague of mine and Prof. Corwin Hansch’s, Prof. Cynthia Sellassie, worked on the early QSAR research a a post-doc. She is a Christian and emigrated from the same part of India as you and Prof. Varki did. She has served on the Grants Review Board of the NIH, and is highly respected in the field of computer prediction of bioactivity including toxicity and enzyme inhibition.

@Swamidass

The notion that we need a new epigenetic mechanisms is, in my opinion, “so much tommyrot.” Evolution by natural mechanisms explains how we got here; in at least our material origins, as far as can currently tell.

@Swamidass )
This is precisely my point! Am I the only one that appreciates the importance of this fact when it comes to discussing the relationship between science and religion?? Our Material Nature is essentially animal. Displayed graphically, we are just an unassuming twig on a symmetrical bush. But we know that is not so. As you so aptly put it: "humans are truly exceptional and unique. Something very special and beautiful has happened in our origins." Obviously it is the human Mind that has enabled us to become Masters of the Planet. (Perhaps to the chagrin and regret of Gaia–tongue in cheek.) What biological mechanism(s) could have converted a primate brain into mind? Just size? More neural circuits? The evidence is against it. Elephants and many cetaceans have larger brains. Our brains and our computers have much in common; so why not examine some similes?

The 1,400 cc brain of Homo sapiens has (I am told) more potential circuits than the IBM Watson computer. But how is this “hardware” directed and managed? What (who?) provided the operating system and programming that directs it? Current evidence suggests that apoptosis plays and important role: use it or lose it. [quote=“Swamidass, post:35, topic:5494”]
And with the human mind comes explosive cultural evolution,
[/quote]
Teilhard de Chardin prophetically called this the birth of the Noosphere. Once the Noosphere existed, any human baby (but not chimps) born into it will have its brain ‘programmed’ (certain neural circuits established) so that it becomes truly human. Once a certain level of programming has been reached, many brain cells are, in a sense, redundant. You can check on the internet under ‘adult hydrocephalus’ and see the brain scan of a modern Frenchman coping with today’s society but possessing less than 10% of normal brain matter–less than the famous Lucy, the Australopithicus afarensis who lived some 3 million years ago.

I maintain that Noogenic evolution is at least as important to human future as bio-evolution. And whatever brain changes occur as the result of exposure to the Noosphere (human culture if you prefer), these changes can be passed on to future generations and are thus Lamarkian. The Noosphere is where evolution can be purposeful. I believe this hypothesis is worth following in future research into brain function.
Al Leo

[aleo (Albert Leo)]

@Argon

Neo-Lamarkian:Now, what really gets me seeing red is the term ‘Lamarckian’.

I should probably plead guilty here. I should have used the term: “Neo-Lamarkian”, but even that would upset you if you did not realize that I was NOT applying it to biological evolution. I have proposed that there is a real, operational evolution in the Noosphere (modern human culture, if you object to Chardin’s term). And Noospheric evolution is directed by lived experience, and to that extent is neo-Lamarkian.
Al Leo

[Jay313 (Jay Johnson)]

I think a popular summary of the current state of evolutionary theory would do very well, particularly if it stayed above the fray. If any potential publishers happen to be listening in, I hereby volunteer to serve as Gunter’s ghost writer. (Volunteer for a fee, of course!)

[Sy_Garte]

@Eddie
@Jay313

The other Wagner, Andreas, has a good book called “The Arrival of the Fittest”. Worth looking at.

[Jay313 (Jay Johnson)]

@Sy_Garte

The Arrival of the Fittest

That does sound interesting. It was always my gut feeling that even a 4+ billion year time span wasn’t long enough to produce the results we observe today. From the reviews, it sounds like Wagner set out to explain why and how that was possible.