Darwin Unhinged: The Bugs in Evolution

Following on from my previous post, I'd just like to make it clear that I'm not particularly averse to the idea that there may be many universes. I just doubt that they are dead universes - especially if the only justification for proposing them is to increase the odds in favour of life-by-chance. If MAL wished to explore all possible avenues of physical experience then I don't doubt that all possible universes would be there for those experiences to take place.

Of course, I feel I need to repeat myself: all of this speculation is rendered moot if idealism is correct. If so, then the physical universe is a manifestation of mind: it is a mental entity with the appearance of being physical to those of us who experience it; who are within the illusion. What that mind is and how it came to be is beyond my ken and likely to remain so but perhaps the eastern religions got it right in saying that it is the eternal "uncreated". So the question of "who created the creator" is also moot.

It certainly may be that idealism is correct. However, two observations:

What does that have to do with evolution? Are we just going to assume it was poked at certain points by some sort of unspecified universal mind?

Why does everyone keep harping on the promissory nature of evolution when here you are noting that it may be beyond our understanding under idealism?

~~ Paul

It certainly may be that idealism is correct. However, two observations:

What does that have to do with evolution? Are we just going to assume it was poked at certain points by some sort of unspecified universal mind?

Why does everyone keep harping on the promissory nature of evolution when here you are noting that it may be beyond our understanding under idealism?

~~ Paul

"Are we just going to assume it was poked at certain points by some sort of unspecified universal mind?" 

That's rather shallow and simplistic isn't it? I'm not even sure what it has to do with an idealistic view. You talk as though evolution (on this planet) is pre-existing and being viewed and tinkered with by some external mind. That's completely missing the point of idealism which posits that there is only mind therefore the manifestation of the physical is happening within the mind. The physical laws are part of that manifestation as are the elements and the way chemicals react and bond, etc., etc. As a materialist, you might ask yourself how those laws came about and why they are so precise and finely tuned and I would suggest that it is only the visceral aversion to anything that might be construed as god-like that drives you to the desperation of the multiverse explanation.

A mind capable of such manifestation is certainly beyond my understanding but I'm not saying that people are not capable of investigating its nature where we can. Indeed, that is exactly what we should be doing but what people have done is to create a model of reality which excludes (and denies) anything beyond that which we can readily measure and account for. Furthermore, that model must be absolute and unchallenged. 

Idealism is my way of looking at the world and, of course, there are others here who are dualists but I think they and I would agree that materialism is falling short on the big and difficult questions. Invoking Many Worlds or the Multiverse is not answering those questions, it is avoiding them.

This is all very nice, but aren't we getting ahead of ourselves? Can you name an irreducibly complex biological mechanism that we can focus on?

The flagellum is not IC. Again, can we pick something that is?

Not according to Scott Minnich’s genetic knockout experiments on the E. coli flagellum. These experiments have shown that it fails to assemble or function properly if any one of its approximately 35 structural parts are missing. 

Excerpts from Minnich's sworn testimony at the Dover trial (article):

"I work on the bacterial flagellum, understanding the function of the bacterial flagellum for example by exposing cells to mutagenic compounds or agents, and then scoring for cells that have attenuated or lost motility. This is our phenotype. The cells can swim or they can’t. We mutagenize the cells, if we hit a gene that’s involved in function of the flagellum, they can’t swim, which is a scorable phenotype that we use. Reverse engineering is then employed to identify all these genes. We couple this with biochemistry to essentially rebuild the structure and understand what the function of each individual part is. Summary, it is the process more akin to design that propelled biology from a mere descriptive science to an experimental science in terms of employing these techniques.

[…]

So it was inoculated right here, and over about twelve hours it’s radiated out from that point of inoculant. Here is this same derived from that same parental clone, but we have a transposon, a jumping gene inserted into a rod protein, part of the drive shaft for the flagellum. It can’t swim. It’s stuck, all right? This one is a mutation in the U joint. Same phenotype. So we collect cells that have been mutagenized, we stick them in soft agar, we can screen a couple of thousand very easily with a few undergraduates, you know, in a day and look for whether or not they can swim.

[…]

We have a mutation in a drive shaft protein or the U joint, and they can’t swim. Now, to confirm that that’s the only part that we’ve affected, you know, is that we can identify this mutation, clone the gene from the wild type and reintroduce it by mechanism of genetic complementation. So this is, these cells up here are derived from this mutant where we have complemented with a good copy of the gene. One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We’ve done that with all 35 components of the flagellum, and we get the same effect."

(Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005)

During this testimony, Scott Minnich showed slides in the courtroom documenting his own research experiments, which performed knockout experiments on the flagellum, and experimentally found that the flagellum is irreducibly complex. 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/

This 2007 paper you cited documented research that investigated a number of alternate forms of flagella in different bacteria. It hardly refutes the irreducible complexity of the flagellum. They found a conserved core of flagellar proteins and corresponding basic structural components. They incorrectly claim that received opinion in the profession is that flagella arose from an early ancestral T3SS secretory system. 

Pallen and Matkze in their contemporaneous research paper (https://pdfs.semanticscholar.org/2a95/2f...6c3ee3.pdf) admit that “all (bacterial) flagella share a conserved core set of proteins,” numbering around 20 proteins, and they further concede that there is a common core of subsystems found in known bacterial flagella (See this article):

"Three modular molecular devices are at the heart of the bacterial flagellum: the rotor-stator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum."

Despite all the apparent diversity of flagella they admit that all bacterial flagella share a conserved core of about 20 proteins, and a common core (what could be called an irreducible core) of subsystems: a motor, a chemotaxis mechanism, and a secretion apparatus. It seems like the many diverse types of flagella are variations on a common thematic archetype. 

After claiming that the flagellar system initially evolved from an ancestral T3SS system (untenable because it almost certainly came at least a billion years after the flagellum) they concede that the flagellar apparatus in the various different bacteria still had a barrier to gradual evolution that they claim will ultimately be explained by exaptation. We're still waiting for the detailed testable model.

And we know this core is irreducibly complex (per Behe's definition) through Scott Minnich's research.

I won't worry about the rest of your post until we have picked an IC mechanism. But I will come back to it.

Also, could we decide on which definition of IC we're using? For example, is an IC mechanism one which, when reduced, does not maintain its original function or does not have any function? Here are four definitions:

http://www.asa3.org/ASA/education/origins/ic-cr.htm

"Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can't be produced directly, one can't definitively rule out the possibility of an indirect, circuitous route."
---Behe, 1996

~~ Paul

Michael Behe's original definition of irreducible complexity, in Darwin's Black Box, page 39, 1996: An irreducibly complex biological system is "...a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning." Perhaps this could be called functional irreducible complexity. However, as you noted, Behe conceded that even if a system is irreducibly complex in this way and thus could not have been produced directly except by a miracle, one cannot definitively rule out the possibility of an indirect, circuitous route of many steps using conceptual mechanisms like scaffolding, coevolution and co-option or exaptation. There is no strictly logical barrier against this. It's a matter of plausibility. As the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously.

The bacterial flagellum was identified by Behe as such a system.

"Are we just going to assume it was poked at certain points by some sort of unspecified universal mind?"

That's rather shallow and simplistic isn't it? I'm not even sure what it has to do with an idealistic view. You talk as though evolution (on this planet) is pre-existing and being viewed and tinkered with by some external mind. That's completely missing the point of idealism which posits that there is only mind therefore the manifestation of the physical is happening within the mind. The physical laws are part of that manifestation as are the elements and the way chemicals react and bond, etc., etc. As a materialist, you might ask yourself how those laws came about and why they are so precise and finely tuned and I would suggest that it is only the visceral aversion to anything that might be construed as god-like that drives you to the desperation of the multiverse explanation.

Hang on. The complaint so far is that the known laws are not sufficient to produce life on Earth as we know it and so some intelligent design is required. Yet you appear to suggest that the laws are sufficient but might have been devised by some idealistic mind. These are two different issues.

If the laws as we know them are not sufficient, then some poking was required. (Or possibly we haven't discovered all the laws yet.) On the other hand, if the laws are sufficient, then why is anyone arguing that they are not?

My visceral aversion notwithstanding.

A mind capable of such manifestation is certainly beyond my understanding but I'm not saying that people are not capable of investigating its nature where we can. Indeed, that is exactly what we should be doing but what people have done is to create a model of reality which excludes (and denies) anything beyond that which we can readily measure and account for. Furthermore, that model must be absolute and unchallenged.

Your use of the words "where we can" and "readily" demonstrate the problem. What we need to do is find ways of investigating the ideal that are consistent and reliable. If we can do that, then science can have a go at the investigation.

Idealism is my way of looking at the world and, of course, there are others here who are dualists but I think they and I would agree that materialism is falling short on the big and difficult questions. Invoking Many Worlds or the Multiverse is not answering those questions, it is avoiding them.

It may be falling short, but idealist/dualist science is even shorter.

If intelligent design is not amenable to scientific scrutiny, then the IDers should calm down. If it is, then they should bust their butts at it and (somewhat unfortunately) grow a thick skin about the complaints.

~~ Paul

Not according to Scott Minnich’s genetic knockout experiments on the E. coli flagellum. These experiments have shown that it fails to assemble or function properly if any one of its approximately 35 structural parts are missing.

Ah, okay, so we aren't talking about the flagellum as it stands, but about a "conserved core" of proteins. I'm happy to stipulate that if you remove all the proteins that aren't absolutely necessary, you will indeed end up with a subset that are necessary for motility. This would be true of all existing mechanisms, natural or human-designed. Water is irreducibly complex, as long as we are talking about original function.

This 2007 paper you cited documented research that investigated a number of alternate forms of flagella in different bacteria. It hardly refutes the irreducible complexity of the flagellum. They found a conserved core of flagellar proteins and corresponding basic structural components. They incorrectly claim that received opinion in the profession is that flagella arose from an early ancestral T3SS secretory system.

Actually, it does refute the IC of actual flagella. I agree that the jury is out on whether the flagella evolved from the T3SS or vice versa. However, note that the definitions of IC say nothing about evolutionary order. If old mechanism A reduces to new mechanism B, it's still reducible. So the flagellum reduces to the T3SS, although not perhaps exactly.

Michael Behe's original definition of irreducible complexity, in Darwin's Black Box, page 39, 1996: An irreducibly complex biological system is "...a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning." Perhaps this could be called functional irreducible complexity. However, as you noted, Behe conceded that even if a system is irreducibly complex in this way and thus could not have been produced directly except by a miracle, one cannot definitively rule out the possibility of an indirect, circuitous route of many steps using conceptual mechanisms like scaffolding, coevolution and co-option or exaptation. There is no strictly logical barrier against this. It's a matter of plausibility. As the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously.

You'll notice that Behe's original definition is not the one used today. To repost:

http://www.asa3.org/ASA/education/origins/ic-cr.htm

It was vague about whether a reduced IC mechanism would not perform its original function or not perform any function. Then Dembski offered a definition that talked about original function. Then Behe proposed a new definition that uses unselected steps as the criterion. Rusbult then reintroduces the idea of no function at all.

The problem with Behe's current definition is that it's impossible to test. How can we determine whether mechanism M evolved into M' by selected or unselected steps? And even if it did so with an unselected step, why is he apparently denying the process of genetic drift?

~~ Paul

Out of curiosity...I see people keep referring to RM+NS, as though that represents the theory of evolution, but does anybody working in the field of evolution actually hold that view? Everything I've seen refers to other means of genetic variation and non-genetic means of heredity, such as epigenetics and phenotypic plasticity.

Why refer to outdated ideas, rather than the state-of-the-art in the field?

Linda

Its a matter of context and applied logic.  If you believe in the mythos of blind evolution and like Paul, believe that there is no natural design before humans invented design, new add-ons to the base of bio-evolution like epigenentics - are fine and the theory is just gaining in complexity.

However, if you have data about how information from the environment is converted to adaptation, then the idea that evolution is proceeding by random events is nonsensical.  If living things adapt in a way that is correlated to changing information in their environment - then mind becomes the driver for change.  As said before - Darwin thought this to be the case.

Function, including bio-functionality requires processes to have mutual information between a living thing and its environment.  Mutual information is measurable - not in terms of meaning, but in structure.  There is "some group of encoded bits" that is a solid match for another group of bits. 

What makes functionality work is that the meaning of the groups of bits is available for organizing processes.  There is no doubt that living things sense their environment.  There is no doubt that the sensation event gains mutual information for use by any living thing.  The next step is to say that living things use this information to adapt at subconscious and also conscious levels.

If true - and is surely is - then the day-to-day work of minds of all living things (including single cell) are densely packed with mutual information stored up over billions of years.  Information drives functionality via instructions.  The genomes of living things are packed with the history of the intent to survive and from them design becomes apparent in the natural languages used in cells, organs and whole living beings.

Not a magical dispensation of qualities, not a blind watch assembly from luck - but adapted living things consuming and processing information into useful responses.  Our genomes express strategy in how they handle the information.  The data about about the genome and its ability to communicate is pouring in.  Let the myth die.

 Semiosis in nature:

Biosemiosis, the processes whereby living systems identify and interpret environmental states or events as signs - visual, olfacory, auditive etc. - using them to guide their activities, has become the focus of my research for the past 20 years. Little could I know as a young biochemist setting out to do research at the University of Copenhagen in 1968 that I would end up in such an unexpected field. But gradually I have come to see that there are no escape routes: Semiosis cannot be reduced to biochemistry - and yet semiosis is inseparable from biochemistry. Life appeared on Earth when complex systems acquired a capacity to use molecules as signs.  - Jesper Hoffmeyer

To say its all chemistry is like saying its all matter -- and energy is not that important.  There is no life without sign-based communication, no matter how simple.  Life didn't come from a bag of chemicals alone - it came when the bag of chemicals started asking - "what going on out there and how can I get me some of it in here?"

Hang on. The complaint so far is that the known laws are not sufficient to produce life on Earth as we know it and so some intelligent design is required. Yet you appear to suggest that the laws are sufficient but might have been devised by some idealistic mind. These are two different issues.

I'm saying that the whole thing is intelligent. Something similar to that stephenw is saying - information exchange (I'd call that intelligence) at every level. Not the traditional concept of a god-designer standing apart from his creation with an omniscient view and a known outcome but the kind of creation that is evolving towards something. An intelligence that is learning as it evolves. 

I read something about the distinction between laws and rules (physical laws and semiotic rules). Perhaps it was Pattee:

"The two great scientific disciplines of physics and evolution theory have traditionally been taught as disjoint subjects. Yet some billions of years ago, certain collections of physical molecules reached a level of complexity that began open-ended evolution by heritable (symbolic memory-based) variation and natural selection.

Von Neumann was the first to propose explicitly why this "threshold" of complexity requires description-based reproduction (taken for granted by biologists), but his argument was focused on the logical, not the physical requirements. He did not discuss the organizational requirements that would allow normal physical molecules to function as descriptions, nor was he clear about his logical distinction between "active" physical dynamics and "quiescent" symbolic descriptions. He did not mention the origin problem except to say it was "a miracle of the first magnitude."

Even if we still do not have a clear picture of the origin of life, the significance of this fundamental distinction between descriptions and constructions, that is, between semiotic processes (rules, codes, languages, information, control) and physical systems (laws, dynamics, energy, forces, matter) reaches to all levels of evolution. This is an essential distinction from the earliest genetic control of the synthesis of proteins, to the codes and languages of the brain, to the distinction between the mind and the brain (the knower and the known, the epistemic cut), and even to physical theory itself that requires a clear distinction between universal physical laws and the local semiotic process of measurement - an area in which there is still no consensus. This distinction between laws and semiosis, as well as how they are related, needs to be made more clearly at all levels if we are to fully understand evolution, physical laws, and the languages of the brain.

In biology, the basic physics and chemistry of elementary life processes as they exist on earth is well-developed. However, our knowledge of the semiotic controls and interactions within and between organisms and in some cases even in single cells is far from complete. In evolution theory it is still not clear that blind variation in a virtually infinite semiotic search space is adequate to explain so many successful species.

Howard H. Pattee

Its a matter of context and applied logic.  If you believe in the mythos of blind evolution and like Paul, believe that there is no natural design before humans invented design, new add-ons to the base of bio-evolution like epigenentics - are fine and the theory is just gaining in complexity.

Whether there is natural design depends entirely on your definition of design.

However, if you have data about how information from the environment is converted to adaptation, then the idea that evolution is proceeding by random events is nonsensical.  If living things adapt in a way that is correlated to changing information in their environment - then mind becomes the driver for change.  As said before - Darwin thought this to be the case.

The idea that it is proceeding entirely by random events is nonsensical anyway. Why is mind required for living things to evolve to adapt to the environment?

If true - and is surely is - then the day-to-day work of minds of all living things (including single cell) are densely packed with mutual information stored up over billions of years.  Information drives functionality via instructions.  The genomes of living things are packed with the history of the intent to survive and from them design becomes apparent in the natural languages used in cells, organs and whole living beings.

I have no idea what you're talking about here.

~~ Paul

Its a matter of context and applied logic.  If you believe in the mythos of blind evolution and like Paul, believe that there is no natural design before humans invented design, new add-ons to the base of bio-evolution like epigenentics - are fine and the theory is just gaining in complexity.

However, if you have data about how information from the environment is converted to adaptation, then the idea that evolution is proceeding by random events is nonsensical.  If living things adapt in a way that is correlated to changing information in their environment - then mind becomes the driver for change.  As said before - Darwin thought this to be the case.

Function, including bio-functionality requires processes to have mutual information between a living thing and its environment.  Mutual information is measurable - not in terms of meaning, but in structure.  There is "some group of encoded bits" that is a solid match for another group of bits. 

What makes functionality work is that the meaning of the groups of bits is available for organizing processes.  There is no doubt that living things sense their environment.  There is no doubt that the sensation event gains mutual information for use by any living thing.  The next step is to say that living things use this information to adapt at subconscious and also conscious levels.

If true - and is surely is - then the day-to-day work of minds of all living things (including single cell) are densely packed with mutual information stored up over billions of years.  Information drives functionality via instructions.  The genomes of living things are packed with the history of the intent to survive and from them design becomes apparent in the natural languages used in cells, organs and whole living beings.

Not a magical dispensation of qualities, not a blind watch assembly from luck - but adapted living things consuming and processing information into useful responses.  Our genomes express strategy in how they handle the information.  The data about about the genome and its ability to communicate is pouring in.  Let the myth die.


To say its all chemistry is like saying its all matter -- and energy is not that important.  There is no life without sign-based communication, no matter how simple.  Life didn't come from a bag of chemicals alone - it came when the bag of chemicals started asking - "what going on out there and how can I get me some of it in here?"

How does "mind" come in to this? I can agree with much of what you say (assuming I've understood it correctly), and I doubt most biologists would disagree with the idea that life involves a mutual, sometimes sign-based exchange of information. But none of that needs "mind". The production and reading of these "frozen-accident" signals is biochemical, not intelligent.

Linda