Darwin Unhinged: The Bugs in Evolution

I believe it is David B who often questions how proteins can spontaneously arise. Here's an article showing it does happen

Birth of a new protein

This new study from our laboratory provides the very first evidence that a protein evolved recently from scratch can in fact fold into a compact three-dimensional shape," said senior author Matthew Cordes, a UA associate professor of chemistry and biochemistry.

"What we've discovered doesn't come across as a completely developed biological molecule. It looks like what you'd think a newborn protein would look like—maybe a little clumsy or hazily formed," said Cordes, a member of the UA's BIO5 Institute. "But nonetheless, this protein folds into a three-dimensional structure and by a lot of measures it looks like proteins that evolved long ago.
https://m.phys.org/news/2017-10-birth-protein.html

I'd be interested to read some more about these things you mention: how living things design themselves and how consciousness intervenes. If only to give me an insight into how much evolution science appears to be moving away from the neo-darwinist model. I've read a few articles on epigenetics and I think I get the idea although I have not yet found a source indicating the role of consciousness (apart from Bruce Lipton, if I recall correctly).

The place to start is to follow the presentment of published works by the Third Way folks.  The 3 guys who formed the society each present their most relevant book aimed at the general public.  The first book listed is not by any of them, so its message can be inferred to be the most effective in their minds.

http://www.thethirdwayofevolution.com/books

 Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History
Author: Eva Jablonka, Marion J. Lamb
Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic (or non-DNA cellular transmission of traits), behavioral, and symbolic (transmission through language and other forms of symbolic communication). These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today. The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution...

Co-Founder, Raju Pookottil's, book is listed 7th:

 BEEM: Biological Emergence-based Evolutionary Mechanism: How Species Direct Their Own Evolution
Author: Raju Pookottil
In BEEM, author and engineer Raju Pookottil boldly diverges from the Darwinian theory of natural selection and offers a thought provoking counter-hypothesis for the evolution of all living organisms. He proposes that every species, be it single cells, plants or animals, are equipped with the fundamental mechanisms that allows them to generate intelligent and logical decisions that they could then utilize in directing their own evolution. Whereas natural selection depends on random mutations followed by selection, Pookottil argues that species are capable of deciding how to logically construct themselves to near perfection over many generations, making modifications to their own genes where necessary.
The principles of emergence, swarm intelligence and signal networks, which he proposes are available to all living organisms, could in fact be the real forces that cleverly and logically drive the evolution of every species on earth. Our brains work by exploiting these very same principles. It is proposed that the complex signal networks that exist between the millions of protein molecules in a cell, or the billions of cells that make up larger organisms, are also capable of generating intelligent solutions, albeit at a slower pace.
The hypothesis also argues that species are in control of their own genomes and that they are able to engineer their genetic codes where necessary in order to incorporate ‘design modifications’. Thus, species meaningfully assess their environment, create ingenious solutions, and crucially, pass them on to subsequent generations. Using observable examples, BEEM builds up a strong case supporting these arguments.

Perry Marshall, who is religious, but not a biblical creationist (nor, he says.  a supporter of ID), with his "Evolution 2.0" thesis, could be cited as someone who puts evolution down to intelligence at the cellular level. He's written a book about it, and I agree with a lot of what he has to say (though not his religious views), notably about how ridiculous it is to imagine that random mutations can account for evolution. If you have the time, you might care to check out a series of short videos on his website here or a single long video here. The latter video, by the way, is as good an introductory explanation of the absurd claims of Darwinists for random mutation as you're likely to come across.

He's not a third way person, but he shares some of their views e.g. on  epigenetics and horizontal gene transfer. Here's a summary of his thesis from his book:

• Neo-Darwinism says Random Mutation + Natural Selection + Time = Evolution.

• Random Mutation is noise. Noise destroys.

• Cells rearrange DNA according to precise rules (Transposition).

• Cells exchange DNA with other cells (Horizontal Gene Transfer).

• Cells communicate with each other and edit their own genomes with incredibly sophisticated language.

• Cells switch code on and off for themselves and their progeny (Epigenetics).

• Cells merge and cooperate (Symbiogenesis).

• Species 1 + Species 2 = New Species (Hybridization). We know organisms rapidly adapt because scientists producenew species in the lab every day.

• #Evolution in 140 characters or less: Genes switch on, switch off, rearrange, and exchange. Hybrids double; viruses hijack; cells merge; winners emerge.

• Adaptive Mutation + Natural Selection + Time = Evolution 2.0

• DNA is code. All codes whose origin we know are designed.

I must confess that I'm not entirely sure what his position is: does he think that cells possess intelligence? That biomolecules do? And though he doesn't self-identify as an ID person, he does draw on some of their ideas and seems ultimately to agree that in some shape or form intelligence comes into play in evolution.

According to him, as in the penultimate bullet point above, we can replace the concept of random mutation with adaptive mutation, i.e. some kind of intelligent or conscious capacity to change in response to the environment at the cellular level.

To me, this makes cells seem even more intelligent than human beings: for billions of years they have been doing things in a far more sophisticated manner than we can understand, even today. But does that make them intelligent in their own right? I have my doubts. I think that intelligence in some as yet unknown way lies behind cellular behaviour, but are cells/biomolecules in and of themselves intelligent?

Which brings me to the question of whether or not the ultimate source of intelligence can really be minutely controlling all cellular processes all the time. I don't think so, and the question may arise largely because of a tendency to think in a dualistic way. As soon as the ideas of a creator and creation arise, a conceptual divide is produced between the "spiritual" (a lousy descriptor) and the physical, which we think of in different ways.

Those who are dualists, such as theistic evolutionists (being simultaneously religionists and accepters of Darwinian evolution), somehow manage to square off the disparity. Monists fall into two broad categories: those who think everything is physical, and that consciousness/intelligence is emergent, maybe even an illusion; and those who think that consciousness is primal, with the physical being illusory. "Illusory" here doesn't mean unreal, so much as misinterpreted.

One guy whose work has struck me recently is Donald Hoffman, a cognitive scientist who seems to me to be someone who is entertaining the idea that consciousness is primal: this video outlines his ideas:



A somewhat longer video podcast explores his ideas in greater depth:



I love his desktop metaphor for how we perceive our environments, and other species theirs. I love the way he's trying to mathematise consciousness or "conscious agents"; has put forward the hypothesis that interactions between conscious agents lead to higher level conscious agents, ultimately culminating in the conscious agent that is the whole universe. I love his open mindedness and the way he's put forward things he'll have to prove if his hypothesis is correct. So far, he's derived de novo some of the equations of quantum mechanics.

I think he may rely a little too heavily on standard explanations of evolution (i.e. Darwinism), but he doesn't do that in too pushy a way, and concentrates more on natural selection than random mutation; I think he might grant that the source of variation may not primarily be random -- as appears to be Bernardo Kastrup's position on evolution. By the way, Hoffman isn't a panpsychist: he describes his philosophy as Conscious Realism, dealt with in his paper here.

I'll include one last recent (Sept. 17 2017) podcast with Hoffman, which asks questions (and gets answers) not entirely covered in the previous videos:




I find it interesting how thinking about evolution inevitably leads one to questions about consciousness; it seems that the two are inextricably linked, and that solving the one will provide the solution for the other.

The place to start is to follow the presentment of published works by the Third Way folks.  The 3 guys who formed the society each present their most relevant book aimed at the general public.  The first book listed is not by any of them, so its message can be inferred to be the most effective in their minds.

http://www.thethirdwayofevolution.com/books


Co-Founder, Raju Pookottil's, book is listed 7th:

Thanks for furnishing examples of the latest thinking in the Third Way group. For now, I have a few thoughts on Pookottil's BEEM: Biological Emergence-based Evolutionary Mechanism: How Species Direct Their Own Evolution.

From a review:

"When the network of billions of neurons in our brain passes simple signals between them, it generates intelligent solutions. Emergence and swarm intelligence are the fundamental principles that allow such signal networks to generate intelligence. BEEM argues that the complex signal networks that exist between the millions of protein molecules in a cell or the billions of cells that make up larger organisms are also capable of generating such intelligent solutions, albeit at a much slower pace. 

It is proposed that species, whether single cells, plants or animals, are able to meaningfully assess their environment, design clever solutions and, most importantly, pass them on to the next generation. The hypothesis argues that organisms are in control of their own genes and that they are able to manipulate and modify their genetic codes so as to incorporate any intelligently generated design modifications. In effect, species design themselves to near perfection over hundreds or thousands of generations. Using observable examples, BEEM builds up a strong case supporting these arguments."

Another review:

"The hypothesis essentially is that living organisms possess emergent intelligence at multiple levels, from the cellular to the societal, that this intelligence can generate gene mutations, that mutations are tested for fitness, and that the new genes can be passed on to subsequent generations. This chain of processes is set out with admirable clarity, the structure of the argument is well thought out, and a wealth of scientific studies is cited.

Pookottil is quite clear that he is attempting to overturn the central dogma of evolution's modern synthesis. He does not see DNA as the controller of the cell, but rather as a library created by the cell to store information. The cell's millions of molecules form a data network, each complying with very simple rules, but because of their large numbers, creating complex behaviour, in much the same manner as social insects do. This networking may occur between cells and tissues, as well as between individual organisms. The selfish gene of Dawkins is apparently a delusion.

While Pookottil's breadth of knowledge is impressive, the evidence cited is necessarily selective. He relies particularly heavily on Edward J Steele's Lamarck's Signature, which reviews the evidence for soma to germ line gene transfer. Neither author denies that natural selection occurs, but they doubt that it is the major driver of evolution. There is always a danger that enthusiasm for a new idea can trigger bias when assessing evidence, and this is exemplified by Pookottil's repeated references to a single study, which purports to show that Arabidopsis thaliana can replace a knocked out gene. As the author quite fairly points out, the study has not been replicated by other researchers.

Although it would be interesting to see a critique of BEEM by experts in molecular and evolutionary biology, overall I am most uncomfortable with Pookottil's rejection of parsimony. His explanation for evolution is many orders of magnitude more complex than natural selection, and relies on complexity if it is going to work. Descriptions of networks at various levels may sound plausible, but how they might be vertically integrated – i.e. from cells to tissues to whole organisms – is even more obscure. Nevertheless, it is important that the established consensus on any aspect of science is open to challenge, and for that reason the book is worth reading."


Comment:

The only source we know of through observation for the origin of complex specified information in the form of intricate irreducibly complex mechanisms is human sentient intelligence. Such creativity as exemplified to a very high degree in biology seems in our experience to require not just a high level of cognition, but also qualities like insight, imagination and an aesthetic sense. Biology in the form of living organisms even seems to exhibit the qualities of exuberance and sense of beauty. These characteristics seem to be that of conscious aware intelligence. 

Pookottil is hypothesizing that extended protein networks in numberless cells and multicellular organisms of a species somehow communicate as super networks to intelligently design innovative new biological solutions to current organismal problems. This intelligence is envisioned as an emergent property. I think that at present this is a rather nebulous concept. 

In theory of mind (at least as it applies to the human mind-brain problem), this emergence concept goes up against the so-called "hard problem" of qualia and the evident impossibility of mind, conscious awareness, being the result of mere data processing in either neuron/synapse networks of the brain or, presumably, any other sort of computational system. The notion of consciousness emerging from the operation and computation of complex networks has a lot of problems in philosophy and also empirically in the actual development of AI systems. In the interactive dualist theory of mind (which has a lot of evidence in paranormal phenomena), computational systems in themselves absolutely cannot exhibit awareness and consciousness. 

First, we would need empirical confirmation that cellular protein networks and/or networks of somatic cells can actually think and invent.

This thinking and inventing would have to extend not only to figuring out in detail how the body systems need to be modified, but also how to translate these functional requirements into specific actual DNA modifications, insertions, deletions, duplications, etc. in various genes, especially in developmental pathways. And even more importantly, this would have to lead to the creation of entirely new genes. This mapping function, starting with protein foldings and functions, is extremely intricate and is mostly way beyond any present knowledge in molecular biology. This high level of intentional cognition on the part of such networks would need to be demonstrated empirically.

Another area that would need to be fleshed out and empirically, experimentally demonstrated is the mechanism through which such extended intra- and inter-cellular networks actually insert their designed genetic changes into the cell. This would be some sort of mechanism through which the results of distributed creative cognition are transformed into actual physical genetic DNA changes in reproductive cells. It almost seems as if this would have to be the transforming of information at the level of conscious ideas into physical changes in physical structures. This gets into the mind-body problem again. Maybe it would have to involve some form of psi like telekinesis or psychokinesis.

Yet another area would be the mechanism of communication in the extended network - between separate somatic and reproductive cells in an organism and between separate animals or plants in the species. Would this have to be some form of psi or esp? 

Finally, a complete theory would need to somehow account for the origin of this extremely sophisticated system. It looks as if this would have to be some sort of monistic or panpsychist hypothesis, where mind just automatically emerges from complexity. 

Despite all the problems with it, this hypothesis has a lot of advantages. It seems to account for a lot of the observed characteristics of evolution, for instance its apparent indifference to the suffering often brought about by evolutionary creativity in parasitism, things like the Anopheles mosquito and malaria plasmodiums, and so on.

Perry Marshall, who is religious, but not a biblical creationist (nor, he says.  a supporter of ID), with his "Evolution 2.0" thesis, could be cited as someone who puts evolution down to intelligence at the cellular level. He's written a book about it, and I agree with a lot of what he has to say (though not his religious views), notably about how ridiculous it is to imagine that random mutations can account for evolution. If you have the time, you might care to check out a series of short videos on his website here or a single long video here. The latter video, by the way, is as good an introductory explanation of the absurd claims of Darwinists for random mutation as you're likely to come across.

I have come across Perry Marshall already and, indeed, posted a link to a podcast debate between him and Stephen Meyer earlier in this thread:

http://psiencequest.net/forums/thread-12...tml#pid745

I'm also not sure how the Third Way incorporates consciousness so I'll have to read some more following stephenw's links too. I see the mention of intelligence there but I'm not sure whether that is again the appearance of intelligence or conscious intelligence. In other words, are we talking about mind as the conscious agent.

The only source we know of through observation for the origin of complex specified information in the form of intricate irreducibly complex mechanisms is human sentient intelligence. Such creativity as exemplified to a high degree in biology seems in our experience to require not just a high level of cognition, but also qualities like insight, imagination and an aesthetic sense. Biology in the form of living organisms even seems to exhibit the qualities of exuberance and sense of beauty. These characterisics seem to be that of conscious aware intelligence. 

Pookottil is hypothesizing that extended protein networks in numberless cells and multicellular organisms of a species somehow communicate as super networks to intelligently design innovative new biological solutions to current organismal problems. I think that at present this is a rather nebulous concept. First, we would need empirical confirmation that cellular protein networks and/or networks of somatic cells can basically think and invent.

Despite all the problems with it, this hypothesis has a lot of advantages. It seems to account for a lot of the observed characteristics of evolution, for instance its apparent indifference to the suffering often brought about by evolutionary creativity in parasitism, things like the Anopheles mosquito and malaria plasmodiums, and so on.

Thanks for the the very thoughtful response.  I want to step out of an objective discussion and talk about my own personal context and ideas.

I was sympathetic to Ted (Edward) Steele when he was harassed and lost his academic job.  He is a serious scientist and he seemed to be encouraged by my simple emails of support.  It is never easy to be the first to promote counter-factual data on a hot-button subject.  Ted has been shown to be right. The early works of Corrado Spadaforra and James Shapiro were published soon after Lamarck's Signature, and I have followed their careers since .  Both are listed supporters of the ThirdWay and Shapiro is a founder.  Along with Lynn Caporale, they are the folks I was referring to, when I said I have followed the subject for decades.

I am not a fan of W. Dembski and take my definitions for "specified complexity" from Paul Davies and for irreducible complexity from standards in information theory.  I was active in ISCID and had a chance to directly question  Professor Dembski asking him about structured information.  He simply referred me to a chapter in his book "No Free Lunch", which I had already read and found lacking.  At the time I took it - that he had not considered the topic - which may be unfair.

 ISCID also hosted an online forum called Brainstorms and maintains a copyrighted online user-written Internetencyclopedia called the ISCID Encyclopedia of Science and Philosophy.[7] The society featured online chats with intelligent-design proponents and others sympathetic to the movement or interested in aspects of complex systems. Past chats included people such as Ray Kurzweil, David Chalmers, Stuart Kauffman, Christopher Michael Langan and Robert Wright.

I found these other "chats" outstanding, back then.

The structuring of informational relations into "information objects" is the root from which I understand a new worldview.  I don't think Dembski has ever addressed how information becomes structured, but I admit to not reading his latest book.

 But then what accounts for all the change that we see, the new things under the sun?   It is information, which is not conserved and has been increasing since the beginning of time.  - Bob Doyle

What is changing is the arrangement of the matter into what we can call information structures. What is emerging is new information. What idealists and holists see is that emergence of immaterial information.

Living things, you and I, are dynamic growing information structures, forms through which matter and energy continuously flow.   And it is information processing that controls those flows! -- Bob Doyle, The Information Philosopher 

http://www.informationphilosopher.com/

I'm still getting the impression that mind is being deliberately kept out of the picture. The intelligence being talked about seems to be described as an emergent property of complex networks of molecules, cells, swarms or neurons. As mentioned above, that seems to assume that intelligence will automatically appear out of complexity and ignores the subjective qualities of mind.

How does the control system in the body work? There seems to be a level of organisation a level above that of DNA in the cell. This appears to control how and where cells are deployed and how they develop. I have not been able to find, yet, a description of how that works. Perhaps I'm lacking in understanding of the technical details or I'm asking google the wrong questions.

Can I ask a completely ignorant question?

Is it possible to take a concrete example - for example the development of a particular biological structure - and make an estimate of the time that would be required for it to develop by random mutation, unassisted by any natural selection pressure, and then to compare that with the time actually taken, as estimated from the fossil record? Obviously the first estimate would depend on assumptions about population size and mutation rates and so on.

Or is the argument a purely qualitative one?

Why is it interesting to ask how long it would take if there was no selection pressure? In particular, let's say it accidently appears at time t. With no pressure, it could disappear at time t+1.

~~ Paul

Why is it interesting to ask how long it would take if there was no selection pressure? In particular, let's say it accidently appears at time t. With no pressure, it could disappear at time t+1.

I was thinking of a structure which was of benefit only when complete - so that selection pressure couldn't assist during its development. But once it was complete, selection pressure could come into play.

I have come across Perry Marshall already and, indeed, posted a link to a podcast debate between him and Stephen Meyer earlier in this thread:

http://psiencequest.net/forums/thread-12...tml#pid745

I'm also not sure how the Third Way incorporates consciousness so I'll have to read some more following stephenw's links too. I see the mention of intelligence there but I'm not sure whether that is again the appearance of intelligence or conscious intelligence. In other words, are we talking about mind as the conscious agent.

Yeah. Thanks. Hopefully my post adds some useful info about Marshall.

Near as I can tell, the third way people are avoiding "intelligence" lest they be perceived as tending towards creationism. Eva Jablonka, IIRC, was at pains to point out at the Royal Society conference on Evolution recently that the third way didn't imply God.

If third wayers are tending towards considering intelligence, I think they might be looking at it from the panpsychic viewpoint where consciousness is likely another property of matter rather than being fundamental, as Hoffman is postulating. I hope you can get a little time to read his paper (again, it's here) because, whilst he says he's not promulgating Idealism -- Conscious Realism being somewhat different -- he shares with Idealists the idea of consciousness being fundamental. Anyone who starts off with that axiom is someone I find interesting and take seriously.