Evolution without accidents and also no intelligence?

Leading evolutionary biologist James Shapiro has written a new very interesting but still basically wrong thinking article in Aeon, Evolution without accidents - Why Did Darwin's 20th Century Followers Get Evolution So Wrong, at https://aeon.co/essays/why-did-darwins-2...n-so-wrong .

Shapiro starts by pointing out how Barbara McClintock's discovery of genetic transposable elements (TEs) should have shown how incomplete the prevailing New Synthesis Darwinism was in that it claims that the only source of genetic variation is random mutations, in the semi-random walk process of RM + NS.

"My own belief is that the reason for this willful neglect lies in the basic philosophical foundations of mainstream thinking about evolution, which requires a purely physical explanation for all evolutionary processes. The fact that TEs respond to stress indicates that they are regulated biological entities that play a sensory-guided role in survival and reproduction. The notion of controlled biological processes at the core of organic evolution is plainly incompatible with a purely physicalist explanation, such as random mutations plus natural selection.
................................................

Genome modifications by transposable elements may be the best-known examples of evolutionary processes that have nothing to do with the gradual accumulation of random mutations, but genome sequencing has revealed many others, equally important. They include the symbiotic cell fusion about 2 billion years ago that introduced the bacterial ancestor of mitochondria into the eukaryote progenitor cell from which all forms of complex life would eventually evolve. They include instances in which fully evolved adaptations were acquired by horizontal DNA transfers across taxonomic boundaries, rather than through vertical inheritance directly from ancestors. They also include the evolution of Lego-like proteins, in which specific regions or ‘domains’ in a protein’s chain structure can migrate between molecules and add new functionalities to the recipient proteins. Finally, they include the recent and actively growing field investigating the multifarious functions of non-coding RNA (ncRNA) molecules transcribed in part from TEs and other repetitive DNA elements.
.................................................
Like horizontal DNA transfer, ‘domain shuffling’ involves inserting extended segments of protein-coding DNA in various locations in the genome. This means that cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’."

This is at least some progress, but nowhere near enough. Shapiro and other new wave evolutionists still cling to the traditional naturalistic aversion to any form of outside conscious intelligence being involved in evolution. Though it is obvious, he ignores the fact that intelligent design exists in nature, design that can't possibly be ascribed to the unconscious cellular gene-modification processes he goes into. Unlike random mutations, these processes can respond to immediate environmental pressures, but they do not have the needed foresight and imagination and other aspects of a true designing intelligence. You just can't squeeze intelligence with foresight out of basically mechanical processes like transposable elements, symbiosis, and horizontal DNA transfers. 

The relatively simple bacterial flagellum is a perfect example, where the overall mechanism (including the reproduction subsystem) is irreducibly complex, meaning that if any part is removed the thing will not work - all the parts have to be present in the required arrangement or the thing is useless. A system that can't look ahead, and only adaptively responds to immediate stress, just couldn't build the flagellum and its various reproductive support subsystems. Some sort of mind with foresight had to visualize the overall requirements and the structures and processes needed to fulfill them. Shapiro can make a lot of generalizations but would be severely challenged if he was required to actually plot out how the flagellum could have come about through his various basically mechanical gene-modification processes.

Shapiro actually is rather vague and ambiguous in that he refers to "regulated biological entities" somehow generating complexly adaptive designs, without defining what these "entities" are and how they themselves came about.

Leading evolutionary biologist James Shapiro has written a new very interesting but still basically wrong thinking article


This is at least some progress, but nowhere near enough. Shapiro and other new wave evolutionists still cling to the traditional naturalistic aversion to any form of outside conscious intelligence being involved in evolution. Though it is obvious, he ignores the fact that intelligent design exists in nature,

When are you going to give up on arrogant assertions like these.  You might believe these things, and that is fine, but to make definite statements that they are just so and that scientists  who have had theses rigorously tested in order to get their PHDs are definitely wrong tells me a lot about your assumptions of how right your own thinking is.  I, myself believe that the universe was intelligently designed but I cannot, in all honesty, make the definite claims that you do.  Telling scientists that their work isn't enough because it doesn't match with your beliefs???

Shapiro does mention ID in the comments:

A number of the comments accuse me of giving comfort to Intelliegent Design creationists. Clay Farris Naff wrote “ This appears to invite creationism to the table…Given the unfortunate history of creationist propaganda, Prof. Shapiro’s statement strikes me as irresponsible.” Chris Weiss added, “There is a reason the Discovery Institute considers him a ‘friend.’” And Gerald Carey opined, “Creationist will love to quote-mine this line: ‘Species do not emerge from an accumulation of random genetic changes.’”

My response to these assertions is that, In my opinion, the strongest argument for Intelligent Design (ID) is to insist upon an outmoded and inadequate account of the evolutionary process (Shapiro 2021). Criticizing the inadequacies of out-of-date explanations is the way science should proceed. Evolution by stress-activated natural genetic engineering is currently the best way we have to address the origins of the complex systems which ID advocates claim neo-Darwinism cannot explain. Scientists who want to show that natural explanations exist for the evolution of intricate biological systems should embrace every advance in our understanding of the evolutionary process that molecular biology brings us. The fact that the new science of evolution includes organismal cognition and biological agency in originating adaptive novelties is the best counter we have to the criticisms of those like Michael Behe who claim that the origins of astonishingly sophisticated organic adaptations require supernatural intervention. Science is continuously self-renewing, and it cannot accept supernatural arguments. The discovery of so many unanticipated insights into living organisms –e.g., transposable elements, the existence of Archaea, discontinuous multi-coding genetic determinants, sophisticated operations involving non-coding ncRNAs – encourages us to be confident that natural solutions will be found where they currently do not exist. Those who circle the wagons and defend outmoded orthodoxy are the ones who have given up on the scientific process.

As for Erin Giglio, he chided me ‘Where is the discussion of punctuated equilibrium, which would have been a thriving center of the field during the time Prof. Shapiro was last reading?” I accept responsibility for not mentioning that the active organismal view of evolutionary change predicts a punctuated historical record rather than the gradual changes predicted by the Modern Synthesis.

REFERENCES

Shapiro, J. A. 2021. “Why the Third Way of Evolution Is Necessary.” Theor Biol Forum 114(2):13-26.

Scientists who want to show that natural explanations exist for the evolution of intricate biological systems should embrace every advance in our understanding of the evolutionary process that molecular biology brings us. The fact that the new science of evolution includes organismal cognition and biological agency in originating adaptive novelties is the best counter we have to the criticisms of those like Michael Behe who claim that the origins of astonishingly sophisticated organic adaptations require supernatural intervention. Science is continuously self-renewing, and it cannot accept supernatural arguments. The discovery of so many unanticipated insights into living organisms –e.g., transposable elements, the existence of Archaea, discontinuous multi-coding genetic determinants, sophisticated operations involving non-coding ncRNAs – encourages us to be confident that natural solutions will be found where they currently do not exist. Those who circle the wagons and defend outmoded orthodoxy are the ones who have given up on the scientific process.

While I applaud Shapiro's courage in face of live, materialist/reductionist fire; the wrongheadedness of his statements still confound me.

What are 'natural explanations' and why is intelligence excluded from this solution set?

Define 'supernatural'? If intelligence is part of the driving force (or perhaps THE driving force?) behind life and its evolution is that 'supernatural'?  Or is it only the source of the intelligence itself that creates the problem?  (i.e., a/the 'God' perhaps?)

And why these constraints on the advancement of science?  Why must science fit or be limited by statements such as 'cannot accept supernatural arguments'?  Why doesn't this apply to non-testables such as string theory, etc?  Who's the arbiter of what is or is not 'supernatural'?

They're so twisted up in the fight against religious fundamentalists (which I understand) so as to have become mostly nonsensical in what they're saying.

Shapiro does mention ID in the comments:

.....................
"Science is continuously self-renewing, and it cannot accept supernatural arguments."

"The discovery of so many unanticipated insights into living organisms –e.g., transposable elements, the existence of Archaea, discontinuous multi-coding genetic determinants, sophisticated operations involving non-coding ncRNAs – encourages us to be confident that natural solutions will be found where they currently do not exist."
.....................

First, a clear statement of closed-minded reductionist materialism, excluding in principle any intelligent intervention in evolution.
 
Then, an inherent grudging admittal that the various non-mutational mechanisms of biological gene self-modification that have recently been found are, despite looking promising, not sufficient to explain complex sudden adaptations such as the Cambrian explosion (such major innovative and geologically sudden development of complex innovative new biological designs is the primary area where New Synthesis Darwinism fails). 

Finally, a weak assurance of promissory materialism, that though these mechanisms are insufficient to solve the problem, he is confident that they will somehow be found in the future.

Good luck.

First, a clear statement of closed-minded reductionist materialism, excluding in principle any intelligent intervention in evolution.

But in the essay he says physicalist explanations are inadequate?

I do agree it's confusing what his position is exactly, though it seems he thinks there is an emergent level at biology that is not reducible to physics.

When are you going to give up on arrogant assertions like these.  You might believe these things, and that is fine, but to make definite statements that they are just so and that scientists  who have had theses rigorously tested in order to get their PHDs are definitely wrong tells me a lot about your assumptions of how right your own thinking is.  I, myself believe that the universe was intelligently designed but I cannot, in all honesty, make the definite claims that you do.  Telling scientists that their work isn't enough because it doesn't match with your beliefs???

I'll show you some real arrogance: how about Neil deGrasse Tyson, Richard Dawkins, Brian Cox, and William Provine? As usual your response is angry and vituperative, and without much substance. Concerning the irreducibly complex bacterial flagellum that I mentioned, how about an actual plausible argument that it still came about unintelligently either from random mutations plus natural selection, or DNA self-modifications generated in the organisms themselves or others by various mechanisms like horizontal gene transfer and genetic transposable elements? Silence hit it on the nose better than I could, in post #4.

[Ninshub]

When are you going to give up on arrogant assertions like these.  You might believe these things, and that is fine, but to make definite statements that they are just so and that scientists  who have had theses rigorously tested in order to get their PHDs are definitely wrong tells me a lot about your assumptions of how right your own thinking is.  I, myself believe that the universe was intelligently designed but I cannot, in all honesty, make the definite claims that you do.  Telling scientists that their work isn't enough because it doesn't match with your beliefs???

Mod here.

This is veering close to a personal attack, Brian, so I'd advise you to re-read our forum rule regarding respect. Members here don't have to share your own approach about making or not "definite claims" - if they express their viewpoint with confidence or even absolute certainty, that's their right. No need to castigate them as arrogant or to sermonize them about how they approach matters on this forum. Debate the argument, not the person.

Why must science fit or be limited by statements such as 'cannot accept supernatural arguments'?

Exactly! Why should we expect science to work under constraints like that?

Twisting his statement around, we can conclude that if life - or indeed the entire universe - was created by means of intelligence, science will never give us that truth - even if it is starkly obvious - which it is!

I, myself believe that the universe was intelligently designed but I cannot, in all honesty, make the definite claims that you do.

Remember that ultimately there are no proofs in science - only in maths. Scientists have to use their judgement.

Those who study the problem of evolution have to use their judgement too, and if they make statements like the one I quoted, you must ask yourself why you trust their judgement.

David

Twisting his statement around, we can conclude that if life - or indeed the entire universe - was created by means of intelligence, science will never give us that truth - even if it is starkly obvious - which it is!

I really like what you did here David.  Rather profound as I read it and wonder how the more thoughtful scientists themselves might react to such a statement.