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 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.

Having followed Shapiro for many years I can help with the ambiguity: "regulated biological entities" refers to all organisms from bacteria (his research focus) to primates.   The point of using this term is the emphasis on regulation and process control being essential for biological life.  These events are not magical chemistry, they are information processes active in the physical signals.

Regulation is not physically measurable, but in information science it can be simulated as an algorithm or program.  Regulatory activity can be functionally defined by its information flow.  Regulatory activity based on feed-back from the environment does learn from doing.  This is where the tiny steps of sub-conscious learning advance toward creative adaptation.  Not an answer in any religious sense, but an answer to a lot of the source behind instinctual cunning in nature.

 Shapiro’s work will generate extensive discussion throughout the biological community, and may significantly change your own thinking about how life has evolved. It also has major implications for evolutionary computation, information science, and the growing synthesis of the physical and biological sciences.

  bolding mine

 How Life Changes Itself: The Read-Write (RW) Genome
Physics of Life Reviews 10 (2013) 287–323

Abstract:

The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read–Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions.

If nature and humanity were made in God's image, wouldn't we find intelligence within the sub-conscious minds of living things, as well as without?  Believing, as I do, that life is helping to design itself --- in no way rules out external divine intelligence.

If nature and humanity were made in God's image, wouldn't we find intelligence within the sub-conscious minds of living things, as well as without?  Believing, as I do, that life is helping to design itself --- in no way rules out external divine intelligence.

I like that the discussion here can go this far but I would go further still. I prefer to think of that intelligence not as external nor divine but as one universal, interconnected matrix drawing from the same ground of consciousness. The diversity we see and experience is a magnificent manifestation of creativity which is constantly evolving and expanding.

I have just watched a fascinating discussion between Jo Rogan and Stephen Meyer. It is 3+ hours long, so it is best to absorb it in sections, but it is amazing. I watched it on Spotify, and I can't seem to rewind it, but if you GOOGLE their two names together that is what pops up.

Above all, I have always thought of SM as something of a Bible thumper, but near the end of the discussion, he really opens up and discusses all the things we discuss here.

Enjoy!

David

The bacterial flagellum, as a molecular machine, isn't something you would see in the fossil record directly. What you'd find is evidence of bacterial colonies, not the molecular machines that allow them to function. Our understanding of the evolution of complex cellular structures like the flagellum comes primarily from molecular biology and genetics, not paleontology.

The real problem with evolution by natural selection, is that most of "protein space" is populated by completely useless proteins. Thus to evolve from an existing protein to another one with a new function most of the evolutionary steps will be from one piece of junk to another piece of junk! Natural selection doesn't get a look in, because remember that the selection can't look ahead to what you might get if 50 more changes were made.

I would say Darwin's theory of evolution stopped making sense when it was realised that proteins were long specific sequences of amino acid residues, coded for by DNA. Think of 'evolving' one recipe into another just by changing it one letter at a time and trying to cook from the intermediate recipes!!

Molecular machines like the flagellum are just the most extreme example of this problem. Incidentally, I also find it fascinating that those things actually do rotate!

David

Having followed Shapiro for many years I can help with the ambiguity: "regulated biological entities" refers to all organisms from bacteria (his research focus) to primates.   The point of using this term is the emphasis on regulation and process control being essential for biological life.  These events are not magical chemistry, they are information processes active in the physical signals.

Regulation is not physically measurable, but in information science it can be simulated as an algorithm or program.  Regulatory activity can be functionally defined by its information flow.  Regulatory activity based on feed-back from the environment does learn from doing.  This is where the tiny steps of sub-conscious learning advance toward creative adaptation.  Not an answer in any religious sense, but an answer to a lot of the source behind instinctual cunning in nature.

  bolding mine


If nature and humanity were made in God's image, wouldn't we find intelligence within the sub-conscious minds of living things, as well as without?  Believing, as I do, that life is helping to design itself --- in no way rules out external divine intelligence.

I'm curious. How do you know that all living things have minds, much less subconscious minds? Faith? 

We have no idea how creative, designing intelligence can be anything but conscious intelligence (as actually exhibited by human beings, the only designing agents we know of from observation), and even though it is central to our existence we have no idea what consciousness is. So in all this ignorance, how can Shapiro confidently claim that even the tiniest of living organisms like bacteria can design themselves? 

I know from experience as an engineer and software designer that design or invention requires many conscious mental qualities like foresight, visualization, imagination and ingenuity. Do you or Shapiro seriously suggest that bacteria (or even primitive metazoan animals) have these capabilities?

OK Stephen, I have tried to avoid conversations with you for some time because somehow we don't seem to operate on the same wavelength. I'm going to try again.

Having followed Shapiro for many years I can help with the ambiguity: "regulated biological entities" refers to all organisms from bacteria (his research focus) to primates.   The point of using this term is the emphasis on regulation and process control being essential for biological life.  These events are not magical chemistry, they are information processes active in the physical signals.

It seems to me that Shapiro and the whole Third Way crowd are interested in researching the limitations of the traditional RM+NS paradigm. Explicitly contradicting Darwin's theory is deeply frowned on in academic science, and they seem to have come up with a formula that is just acceptable to orthodox biologists by using vague expressions like "information processes" (presumably meaning the same as "informational processes") without ever spelling out what these are.

I respect the Third Way because they are exploring phenomena that are inconsistent with orthodox biology - and getting away with it!

The point is that we on this forum generally don't feel the need to veil our thoughts to conform with orthodox biological ideas - so we don't need to use vague terms like "information processes".

Regulation is not physically measurable, but in information science it can be simulated as an algorithm or program. 
Regulatory activity can be functionally defined by its information flow. 

Flow between where and where? There is going to be some information flow when I finally post this reply, but it won't define anything!

This is just one example of slippery confusing terminology that the Third way use to obfuscate the fact that they are busy amassing facts to contradict Darwin's theory.

Regulatory activity based on feed-back from the environment does learn from doing. 

This is where the tiny steps of sub-conscious learning advance toward creative adaptation.  Not an answer in any religious sense, but an answer to a lot of the source behind instinctual cunning in nature.

If nature and humanity were made in God's image, wouldn't we find intelligence within the sub-conscious minds of living things, as well as without?  Believing, as I do, that life is helping to design itself --- in no way rules out external divine intelligence.

I don't think anyone here is arguing for a divine explanation of reality, though many of our ideas don't rule out such a possibility.

If by 'magical', you mean a process that depends on an external conscious agent (spirit or whatever you want to call it) then I am pretty much certain magical processes do exist. Take for example the morphic fields that Rupert Sheldrake postulates. One type of these fields - morphogenetic fields - seem to cover an entire species, and he has produced a lot of evidence to demonstrate that these are real. In one experiment that he quotes, a newt embryo's eye lens is removed using microsurgery. The embryo is then followed and it re-grows the lens by a completely different mechanism from that used naturally. This forces me to the conclusion that some intelligence outside of matter knows how a newt is designed, and figures out how to repair it on the fly!

David

I'm curious. How do you know that all living things have minds, much less subconscious minds? Faith? 

Maybe not great for debating, but in my worldview it is definitional.  Mind is an abstract term that defines actions within informational environments as detection of affordances.  Minds act on information objects and can detect and restructure their order to anticipate future states.  Picture the earth, or any planet in the known universe, as it cools down from geological formation, life is not active yet.  The Materialistic idea is of some "magic" chemical event starting life, life that will only have mind after achieving a certain level of physical complexity.  This is a just-so story.

The early earth would be characterized as deterministic to physical processes.  YET, as some stage of physical evolution of the planet, new shit starts to happen.  The informational environment grows as events have their information copied.  Mutual information, with early mind, interacts and then is structured into informational objects.  This activity is all happening as probability manipulation.  In the informational environment basic mind is active experiencing and altering the unfolding course of these real world probabilities.  With mind using just past and future probability it can realize new vectors for life and both physical and mental environments start changing in new ways.

Rather than faith, scientific observation has documented how information is real and causative.  It is science that is equal to physics and materials subject matter.  Mind experiences past, actual and future probabilities as the "stuff" and relates these in such a way as to change entropy of a local system.  Mind uses direct perception of probability waves to import mutual information.  Mind can organize real world probabilities into states of being where a local system of information activity can exert physical influence via states of being.

Rather than a definition based on Physicalism, mind in an informational environment is the means for making a measurable differences in the actual evolution of the world we inhabit.  Mind starts working and the compounds created in nature start to change.  Information objects like repeatable sequences and codes to communicate are part of mental evolution.

Sub-conscious mental activity is really well documented.  When a bacteria uses sophisticated communication tools - purposely - that is mental activity.  They make mutual information work - to help them maneuver, detect food and know when to consume.  It is solid science.

YET, as some stage of physical evolution of the planet, new shit starts to happen.  

Getting a bit technical here...

On a more serious note, it seems like you are saying Information is what shifts the physical over from deterministic processes...but isn't the best of our current scientific knowledge telling us QM is indeterministic?

As for "genetic knockout experiments" showing that some molecular machines are irreducibly complex, these experiments typically involve disabling genes to see the effect on the organism. While it's true that disabling certain genes can cause a system to stop functioning, this does not necessarily imply irreducible complexity. It may simply mean that the system has evolved to rely on all its components for optimal function, but it doesn't rule out that the system could have evolved incrementally.

You just can't prove a negative. Sure, there is always a "could have" option, no matter how improbable it is. For instance, there is indeed some exceedingly improbable but non-zero possibility that all the air molecules in this room will through their natural Brownian thermal motion, all jump in the same direction, creating some sort of explosion or other traumatic event. But we don't worry about this, since the probability is beyond microscopically small. 

In the case of the flagellum you need to work out exactly how (probably using "exaption" (that is, adapting an existing subsystem or molecular machine for a new use)), but as I point out, it needs to have at least some likelihood. You can hypothesize that the "stinger apparatus" of some bacteria was repurposed and extensively modified for use as a rotating propeller, but this idea needs to have some likelihood. Well, it turns out that the "stinger apparatus" appeared much later in evolution as actually a modification of the already existing flagellum. So this "stinger modification and re-use" hypothesis is invalid, with almost absolutely zero probability. Any other ideas?

There are no limits to the imagination, but the resulting hypotheses need to pass the likelihood test, where each step in the hypothesis is plausible probability wise, meaning it has to be simple (and therefore have some likelihood at all), generated by a process independent of reproductive fitness, and has to be exactly what is needed to build the next step of building a new biological subsystem (like the flagellum for instance). Other requirements for this hypothetical next step include that the new modified genetic structure needs to not result in significant survival disadvantage - that is, it needs to be either neutral or result in positive reproductive fitness change, or at least only very slightly adverse effect on reproductive fitness. 

Some sort of hypothesized process can always be worked out given the power of human ingenuity, but it is very hard to impossible to come up with something that has any practical degree of likelihood. 

But at that point the closed-minded ideological devotion to Darwinism of the orthodox scientific community steps in and the new gradualistic Darwinistic hypothesis is proclaimed to be the explanation for the existence of the irreducibly complex obviously designed biological system. Or (as is usually the case) the evolutionary biology community unanimously just assumes it must exist on ideological grounds, with no further comment. Instantly and automatically rejecting the intelligent design hypothesis as impossible because it contradicts materialism.

The real problem with evolution by natural selection, is that most of "protein space" is populated by completely useless proteins. Thus to evolve from an existing protein to another one with a new function most of the evolutionary steps will be from one piece of junk to another piece of junk! Natural selection doesn't get a look in, because remember that the selection can't look ahead to what you might get if 50 more changes were made.

I would say Darwin's theory of evolution stopped making sense when it was realised that proteins were long specific sequences of amino acid residues, coded for by DNA. Think of 'evolving' one recipe into another just by changing it one letter at a time and trying to cook from the intermediate recipes!!

Molecular machines like the flagellum are just the most extreme example of this problem. Incidentally, I also find it fascinating that those things actually do rotate!

David

Contrary to the assertion, not every single amino acid change results in a "piece of junk." Many mutations are neutral, having no effect on protein function. Some are deleterious and get selected against. But crucially, some confer new or improved functionality and get selected for. It's also worth noting that many proteins can tolerate a large number of sequence variations without loss of their primary function, offering a buffer for evolutionary innovation.