A Fundamentally New Synthesis in Biology?

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Some fundamentally new thinking in biology. A monumental attempt at a new synthesis - a new paradigm. Time will tell whether it really explains consciousness as "serial pre-adaptations based on cell–cell communication" (I think highly unlikely - consider the Hard Problem), and the intricate designs of life not as due to some form of ID, but as the result of "collaborative natural cellular engineering" (I also think highly unlikely). We don't know whether it will go somewhere. 

The work is: "Cellular-Molecular Mechanisms in Epigenetic Evolutionary Biology", John Torday and William Miller Jr., at https://link.springer.com/content/pdf/bf...-2%2F1.pdf .

Chapter 1  Introduction
        2  Darwin, the Modern Synthesis, and a New Biology
        3  Cognition and the Living Condition
        4  What is Consciousness? An Evolutionary Perspective
        5  Networking from the Cell to Quantum Mechanics as Consciousness
        6  The Nature of Information and Its Cmmunication
        7  The Information Cycle and Biological Information Management
        8  Communication and the Accumulation of Genetic Information
        9  Non-Genic Means of Information Reception and Exchange
      10  The Primacy of the Unicellular State
      11  Phenotype, Niche Construction, and Natural Cellular Engineering
      12  Holobionts
      13  Four Domains: Cognition-Based Evolution
      14  Reconciling Physics and Biology
      15  Conclusion

A few highlights:

Chapter 4: What is Consciousness? An Evolutionary Perspective

The nature of consciousness has been debated for thousands of years. The perspective on evolution taken in this book, that it is serial pre-adaptations based on cell–cell communication, offers the opportunity to see consciousness as the sum total of our awareness of our physiology.

Chapter 8: Communication and Accumulation of Genetic Information

The genome is no longer considered a sacrosanct blueprint of the living form. Instead, a pluralistic approach through epigenetics and exogenetics is increasingly emphasized. The genome is now considered to be one consequential aspect of the informational interactome of the cell and its crucial cell–cell communications rather than a controlling agency. Transposable elements are substantial components of all modern genomes. They are one of the chief contributors to this informational interactome. Consequently, genetic material can now be assessed as (just) part of a common language of information transfer and communication among the cellular domains.

Chapter 11: Phenotype, Niche Construction, and Natural Cellular Engineering

In Darwinism, phenotype is a product of selection that emerges from random genetic variations. In cellular–molecular epigenetic evolution, the phenotype is the means by which the unicellular zygote acquires contemporary environmental information. That information becomes part of the cellular information cycle, which is expressed as the phenotype through collaborative natural cellular engineering and niche construction.

Chapter 15: What Does This Mean for Evolution?

Decades of debate have exposed numerous deficiencies in the standard Neo-Darwinian evolutionary narrative. In comparison, cognition-based evolution begins from the new vantage point of the primacy of the self-referential cognition embodied in all cells. It proceeds through self-referential cellular collaboration as natural cellular engineering and niche construction. It yields multicellular organisms that are really holobionts - combinations of personal cells and trillions of codependent, cooperative, and mutually competitive microorganisms - as collective life forms. Genes can now be properly understood as just part of the system - problem-solving tools of the cell. Selection is not an evolutionary driver, but serves an essential function as a consistent filter of cellular problem-solving to assure biological conformity with the environment.

Chapter 16: Conclusion

All biological and evolutionary development is governed by cellular faculties, limitations, and boundaries. Therefore, holobionic life can only be properly understood through its perpetual connection to its unicellular roots. Cellular–molecular evolution rests upon twin pillars of universal cellular cognition and continuous cell–cell communication among the four domains that constitute all life on the planet. The environment reciprocates in this elemental interplay through consistent epigenetic threads that assure life’s concordance with planetary realities.
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(2021-07-08, 10:12 PM)nbtruthman Wrote: Some fundamentally new thinking in biology. A monumental attempt at a new synthesis - a new paradigm. Time will tell whether it really explains consciousness as "serial pre-adaptations based on cell–cell communication" (I think highly unlikely - consider the Hard Problem), and the intricate designs of life not as due to some form of ID, but as the result of "collaborative natural cellular engineering" (I also think highly unlikely). We don't know whether it will go somewhere. 

The work is: "Cellular-Molecular Mechanisms in Epigenetic Evolutionary Biology", John Torday and William Miller Jr., at https://link.springer.com/content/pdf/bf...-2%2F1.pdf .


      13  Four Domains: Cognition-Based Evolution
      14  Reconciling Physics and Biology
    
Chapter 15: What Does This Mean for Evolution?

Genes can now be properly understood as just part of the system - problem-solving tools of the cell. Selection is not an evolutionary driver, but serves an essential function as a consistent filter of cellular problem-solving to assure biological conformity with the environment.

Chapter 16: Conclusion
 Cellular–molecular evolution rests upon twin pillars of universal cellular cognition and continuous cell–cell communication among the four domains that constitute all life on the planet. The environment reciprocates in this elemental interplay through consistent epigenetic threads that assure life’s concordance with planetary realities.
Just reading the most recent list of scientists declaring themselves on the Third Way website.  I was there after reading more from the Miller/Torday book.  The citations in it include many by Third Way leadership.  (Shapiro, Nobel, Jablonka, etc) 

The listing has tripled in the last year or two!  https://www.thethirdwayofevolution.com/people

The book abstract that knocked me out was Chapter 15.  It is so professionally written and so confident!!  The ending is perfect.

Quote:In 2010, the evolutionary biologist, mathematician, and geneticist, Richard Lewontin noted that the standard narrative of evolution by natural selection does not explain the actual forms of life that have evolved. He further contended that there is an immense amount of biology that is missing from neo-Darwinism. Other scientists also agree (Pigliucci 2007; Baluška 2009; Witzany 2010; Shapiro 2011; Torday 2015a, b; Miller 2016b, 2017; Miller and Torday 2018). 

Therefore, it can be defended that the central tenets of the modern synthesis should be questioned. Of these areas of inquiry, the most pertinent is the exact role and limits of natural selection in any evolutionary process. If selection has primacy in evolutionary development, does it proceed according to strict gene frequencies? Is it propelled by random genetic mutations? Is Crick’s central dogma that asserts a unilateral direction of the flow of biological information from DNA to RNA still applicable in the twenty-first century? 

Certainly, there is no requirement that the correct answers have to be any exact antipode of prior beliefs. Nor must any contradictions be absolute. Therefore, even a substantial reformulation of evolutionary development need not be an unyielding negation of the past. Instead, it is tasked to incorporate the weighty thoughts of prior generations of scientists and direct them toward a fuller understanding of this complicated issue.

When you see the day won, you don't gloat, you take over all the spoils still had by the defeated as your own.  And act like they should like it.

I am still smirking at the phrasing of "substantial reformulation" and questioning whether central dogma is "still applicable".

science trash-talk and throwdown?
(This post was last modified: 2021-07-09, 02:58 PM by stephenw.)
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Are you reading this book, nbtruthman?

I am wondering where it falls in relation to the discussions we have been having in the bugs in evolution thread? Do you think it has any really new approach?

Unfortunately, it seems to me that it is always possible to extract yet more complexity from biological systems, but my hunch is that this can't solve the problem regarding the source of the necessary information.
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I find the precis of the book incredibly frustrating to read. I mean, consider this:

Quote:In the twenti-
eth  century,  evolutionary  biology  was  ruled  by  Darwinian  metaphors.  Recent 
advances  in  molecular  biology,  microbiology,  and  metagenomics  permit  a  new 
cohesive cellular–molecular alternative approach to evolutionary biology. Through
a  growing  understanding  of  the  complete  range  of  non-random  epigenetic  influ-
ences on genetic expression and a fuller understanding of the complexities of cel-
lular  cognition  and  cell–cell  communication,  biology  can  be  transformed  into  a 
predictive science.

What exactly is it saying? It doesn't quite manage to say that Darwinian theory was wrong ..... or right. Furthermore, my understanding of epigenetic phenomena is that they use labels attached to DNA which affects the  extent to which that DNA is transcribed. Sometimes these can get passed to the next generation, but ultimately they fall off - so no long term genetic changes take place. In merging epigenetics into evolutionary theory, is he saying there is more to the story than that .... or not?

Then consider this quote:
Quote:The nature of consciousness has been debated for thousands of years.
The  perspective  on  evolution  taken  in  this  book,  that  it  is  serial  pre-adaptations 
based  on  cell–cell  communication,  offers  the  opportunity  to  see  consciousness  as 
the sum total of our awareness of our physiology.

This is either saying something big - that consciousness can exist without a brain to support it ..... or it isn't - I'm honestly not sure.

Likewise, "pre-adaptions" sounds very interesting, because it seems to imply step by step design .... but if you want to say that, why not be clear?

The consciousness that would be needed here would have to be pretty damn powerful. It would have to have a deep understanding of the way proteins fold and interact with other chemicals.

I suspect that this is all about trying to evade the stranglehold that Darwinism still has over biology, but writing in riddles just gets tedious.

David
(This post was last modified: 2021-07-29, 09:44 AM by David001.)
(2021-07-26, 09:27 PM)David001 Wrote: Are you reading this book, nbtruthman?

I am wondering where it falls in relation to the discussions we have been having in the bugs in evolution thread? Do you think it has any really new approach?

Unfortunately, it seems to me that it is always possible to extract yet more complexity from biological systems, but my hunch is that this can't solve the problem regarding the source of the necessary information.

I post on articles or other writings primarily because on initial examination they look interesting in some way or other. I posted on this book when I found that the furnished summaries of the chapters were somewhat interesting, but it turned out that only the preface containing summaries of the chapters, and the abstracts of the chapters, are available free. The text of this book is behind a prohibitive paywall (each chapter costs $29.95). For what it's worth I think that some of this thinking at least as it is described is probably either fundamentally wrong, or fundamentally too vague to characterize.

Also, if the text is as formidably technical and specialized as some of the abstracts, it would be very difficult to follow for a layperson. Accordingly, because of these problems I've not considered attempting a reading of the text. The less technical summaries of the chapters in the preface will have to do. I think they are at least worth perusing.

Apologies if I caused any frustration or confusion by not checking all this first before doing the post.

Abstract of the chapter (4) on consciousness:


Quote:"The Singularity/Big Bang is believed to have instantiated the Universe 13.8 billion years ago, giving rise to everything in the cosmos, including the Earth and its biosphere (Hawking 1998). From this unitary beginning, a path opens from the first primitive unicell to consciousness as one continuous process of dualities (matter and energy existing as two complimentary parts) formed after the Big Bang (Gionti 2015), culminating in the vital mechanism of homeostasis (Torday and Rehan 2012). By regarding the narrative of the cosmos and consciousness as having common origins and epistemology, predictions emerge that can illuminate aspects of biology that have previously been considered dogmatic or enigmatic."

Summary of Chapter 4 in the Preface:

Quote:"The nature of consciousness has been debated for thousands of years. The perspective on evolution taken in this book, that it is serial pre-adaptations based on cell–cell communication, offers the opportunity to see consciousness as the sum total of our awareness of our physiology."

As can be seen, this is unimpressive - it doesn't solve much of anything, certainly not the Hard Problem, since it seems just to assume "awareness" to be an expected emergent property of cellular existence without expaining what this mysterious "emergence" process really is. 

Some of the ideas in the book are certainly creative and provocative. For instance Chapter 11, Phenotype, Niche Construction, and Natural Cellular Engineering. This new thinking is a fundamental change to the concept of what evolution really is.

Summary of Chapter 11:


Quote:"In Darwinism, phenotype is a product of selection that emerges from random genetic variations. In cellular–molecular epigenetic evolution, the phenotype (adult multicellular organism) is the means by which the unicellular zygote acquires contemporary environmental information. That information becomes part of the cellular information cycle, which is expressed as the phenotype through collaborative natural cellular engineering and niche construction."

The abstract of this chapter is rather esoteric and technical and this is probably typical of the overall text:

Quote:"The conventional view of phenotype is that it is an epiphenomenon directly driven by selection. Instead, in a modern context based on the primacy of the unicellular form, phenotype can be re-appraised as a means toward obtaining contemporaneous genetic marks (Torday and Miller 2016c). When the evolutionary imperative is appropriately understood as the strategic derivation of epigenetic marks from the environment and their appropriate assortment through the EUC, its evolutionary meaning shifts away from the natural assumption that its impact necessarily relates to the direct survival advantage of the offspring (Wang et al. 2017). In part, this reflects that epigenetic effects need not be immediately apparent. Although the actual identity of the mechanism that determines the distribution of the epigenetic marks from germ cells to somatic cells is not completely known, it is clear that the unicellular recapitulation is the dominant governing phase, with further adjustments during embryogenesis (Gapp and Bohacek 2018; Wang et al. 2017). In this context, pleiotropy (the production by a single gene of two or more apparently unrelated effects) (Williams 1957), heterochrony (the developmental change in the timing or rate of events, leading to changes in size and shape of organisms) (Torday 2016a), and neoteny (the retention of juvenile features in the adult organism) (Skulachev et al. 2017; Godfrey and Sutherland 1996) can each be understood as mechanisms through which epigenetic inheritance might be governed."


Some creative new thinking:  Chapter 12, Holobionts.

Summary:

Quote:"All multicellular organisms are holobionts, and there are no exceptions. Such organisms are a combination of personal cells and trillions of codependent, cooperative, and mutually competitive microorganisms. Although these companion microbes have previously been considered mainly passive participants, it is now understood that all are intimate partners within holobionts as crucial coinhabitants of a complex form of life."


This is a new way of looking at the true inner nature of multicellular organisms. However, I have some skepticism - I think there is much to recommend the conventional view that the bacterial and viral loads are mainly parasitic and damaging to the organism, as indicated by the dedication of whole extremely complex and error prone body systems (like the immune system) to suppressing the invading microorganisms and viruses.

So it looks to me that this book is a mixed bag of good and fruitful new ideas, problematical ideas that may be or probably are mistaken, and vague or obscure writing that is hard to characterize. And it doesn't seem to answer the fundamental question of how simple cellular or multicellular organism intelligence can be the creator of immensely intricate and complex biological engineering designs, designs that seem very much to require a very high focused conscious intelligence.
(This post was last modified: 2021-07-29, 05:06 PM by nbtruthman.)
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(2021-07-29, 04:48 PM)nbtruthman Wrote: However, I have some skepticism - I think there is much to recommend the conventional view that the bacterial and viral loads are mainly parasitic and damaging to the organism, as indicated by the dedication of whole extremely complex and error prone body systems (like the immune system) to suppressing the invading microorganisms and viruses.
Don't forget that most of the bacteria are in the gut, where they certainly perform a vital role.

I found your review very interesting. There is no question in my mind that those pursuing the ID approach to this question write far more informative books for the 'intelligent layman', and at a reasonable price. For example Michael Behe's "Darwin Devolved".
(2021-07-29, 04:48 PM)nbtruthman Wrote: Summary of Chapter 11:

"In Darwinism, phenotype is a product of selection that emerges from random genetic variations. In cellular–molecular epigenetic evolution, the phenotype (adult multicellular organism) is the means by which the unicellular zygote acquires contemporary environmental information. That information becomes part of the cellular information cycle, which is expressed as the phenotype through collaborative natural cellular engineering and niche construction."

The abstract of this chapter is rather esoteric and technical and this is probably typical of the overall text.
First let me say, I support your call for these new ideas to be written in such a way so that a layperson can get the core meanings.  I apologize if I push you and others to experience the meanings, precisely because of this gap.

Unfortunately, my writing and organization skills are poor and no manner of good intentions are going to make my unpolished prose be anything but wordy and confusing.  Still, it does matter that Psi and recognition of mind in nature get heard in a science framework.  The history of the ideas helps.  The fight to cleave off mystical things from science is pragmatic and useful in getting to objective data.  For Psi to get taken seriously we cannot lose depth and soulfulness, but need to speak in the language of logic and math as well.

The term esoteric has a common meaning just as you use it.  But some will read it as the term - woo.  There is nothing woo-like in the Abstract's above wording.

(1) The first sentence sets the stage for a counter-argument in this chapter to RM + NS.
(2) The second sentence introduces Epigenetics as direct evidence against RM.  Those scientists that broke the data and process models are well represented as ThirdWay members.  The key concept is how information is communicated outside of RM and that information is connected (mutual information mathematically) to the greater environment.
(3) Is a sentence that if I had any expertise - I would like to write.  The term "information cycle" speaks to me of the separate level of processes that structure the information.  The term "niche construction" ties the information processing back to the environment, both the physical biology and the ecology.
(This post was last modified: 2021-07-30, 01:38 PM by stephenw.)
(2021-07-30, 01:36 PM)stephenw Wrote: First let me say, I support your call for these new ideas to be written in such a way so that a layperson can get the core meanings.  I apologize if I push you and others to experience the meanings, precisely because of this gap.
In a way we are all laypeople, and that is part of the trouble. The only people who are fully up to speed in all this are working in research labs. However, those people can wreck their whole career by stepping out of line about Darwinism. So those that want to, have to write in a very obscure way.
Quote:Unfortunately, my writing and organization skills are poor and no manner of good intentions are going to make my unpolished prose be anything but wordy and confusing.  Still, it does matter that Psi and recognition of mind in nature get heard in a science framework.  The history of the ideas helps.  The fight to cleave off mystical things from science is pragmatic and useful in getting to objective data.  For Psi to get taken seriously we cannot lose depth and soulfulness, but need to speak in the language of logic and math as well.
My feeling is that the only ideas we should cleave off from science are ideas that are wrong. I no longer think observations of psi phenomena are all wrong - though obviously some will be the result of mistakes or deception. Lab science has the same problems with mistakes and deception.
Quote:The term esoteric has a common meaning just as you use it.  But some will read it as the term - woo.  There is nothing woo-like in the Abstract's above wording.

(1) The first sentence sets the stage for a counter-argument in this chapter to RM + NS.
(2) The second sentence introduces Epigenetics as direct evidence against RM.  Those scientists that broke the data and process models are well represented as ThirdWay members.  The key concept is how information is communicated outside of RM and that information is connected (mutual information mathematically) to the greater environment.
(3) Is a sentence that if I had any expertise - I would like to write.  The term "information cycle" speaks to me of the separate level of processes that structure the information.  The term "niche construction" ties the information processing back to the environment, both the physical biology and the ecology.

I obviously do not think any of the Third Way scientists are fools. Some scientists manage to carry on that maybe aren't up to it, but they succeed by keeping their heads down and producing results that don't ruffle any feathers.

The third Way scientists don't just use technical terms, they play with words in a way that would be more appropriate for an artist of some sort - where sentences that have hidden meaning(s) are valued.

So if we are discussing the evolution of simple organisms, why have a section entitled, "Cognition and the Living Condition"? I mean if you are going to say that single celled organisms (say) have consciousness, why not damn well say it? There is in fact some published evidence for that:

http://www.basic.northwestern.edu/g-buehler/FRAME.HTM

It contradicts 'established' science enough that few people have followed up that line of enquiry, but surely it would make sense for the Third Way to gather evidence for that phenomenon rather than just sort of implying it in a discussion of evolution.

Rupert Sheldrake also quotes some research in which the lens of a newt's eye was removed. The lens re-grew but by a radically different mechanism - which strongly suggests that something intelligent saw what had happened and decided to fix it!

I would suggest you read one or two of Rupert Sheldrake's books. Yes, you will find some serious 'woo' in them, but he was a research biologist and his woo-like thoughts are grounded in his scientific experience. Of course he hasn't worked in a research lab for many years, at least partly because mainstream science would not have let him. He writes about profound questions in a clear, easy to understand way (the opposite of Floridi)
(This post was last modified: 2021-07-31, 12:00 PM by David001.)
(2021-07-31, 11:57 AM)David001 Wrote: I no longer think observations of psi phenomena are all wrong - though obviously some will be the result of mistakes or deception. Lab science has the same problems with mistakes and deception.

The third Way scientists don't just use technical terms, they play with words in a way that would be more appropriate for an artist of some sort - where sentences that have hidden meaning(s) are valued.

I would suggest you read one or two of Rupert Sheldrake's books. Yes, you will find some serious 'woo' in them, but he was a research biologist and his woo-like thoughts are grounded in his scientific experience. 
I do not respect your made-up vision of science and scientists.  I have read Sheldrake and found NO woo.

There are no hidden meanings, no special people and conspiracies.  Enough.

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