Darwin Unhinged: The Bugs in Evolution

Well I don't know if one can debunk exaptation simply by saying the parts are very complex and fit together very well? That seems to be the gist of Dodgen's argument, and without some elaboration it doesn't feel decisive against the claim of exaptation.

For example it seems the toxin delivery system bacteria - type III secretory system (TTSS) - use to kill host cells is possibly part of the flagellum yet serves a function on its own? ->


It is just hard for a layperson to know what argument is the right one here, whereas I can easily understand Cosmological Fine Tuning by reading a single article and seeing even the die-hard physicalists admit the constants are delicately set.

But as I've said before, I've no issue with design in principle. After all Fine Tuning in its original cosmological sense is quite persuasive when combined with arguments like Bernard Haisch's that an intelligence could provide the support for odd quantum behaviors like the 4:100 on average photons that reflect back off a thin glass.

And so I am ok with a designer who decided to fiddle around and make the flagellum while leaving a lot of other mutations around that didn't help their possessors pass on offspring...But as previously noted if you find a sandwich in my kitchen it's far more likely that I made it than God conjured it up. Meanwhile ID wants to hide this obvious point behind the supposed mystery, expecting us to believe that Yaweh - after creating the Universe, but before coming down as Jesus - decided to make the flagellum but never bother[ed] to rid us of pesky inheritable diseases like cancer.

For a group that bases its arguments on probabilistic reasoning it doesn't seem that hard to turn this same critical eye toward the possibl[e] identity of the designers?

I'm not sure where your argument or train of thought is leading. The sandwich in your kitchen is most likely one which you made yourself. Though there is a possibility that you bought it somewhere. Either way a human being made it. But, humans have only been around for a couple of million years or so. This wouldn't account for anything which happened aeons ago. Adding visitors from another planet or another galaxy doesn't get us very far. Just where are you heading in this line of reasoning?


I should add that the 'Yahweh' line to me is a bit of a distraction, it portrays things in the language and tradition of one human culture from a particular part of our world in a particular time. I think we need to spread our gaze somewhat wider than one tradition.

Well I don't know if one can debunk exaptation simply by saying the parts are very complex and fit together very well? That seems to be the gist of Dodgen's argument, and without some elaboration it doesn't feel decisive against the claim of exaptation.

For example it seems the toxin delivery system bacteria - type III secretory system (TTSS) - use to kill host cells is possibly part of the flagellum yet serves a function on its own? ->


It is just hard for a layperson to know what argument is the right one here, whereas I can easily understand Cosmological Fine Tuning by reading a single article and seeing even the die-hard physicalists admit the constants are delicately set.

But as I've said before, I've no issue with design in principle. After all Fine Tuning in its original cosmological sense is quite persuasive when combined with arguments like Bernard Haisch's that an intelligence could provide the support for odd quantum behaviors like the 4:100 on average photons that reflect back off a thin glass.

And so I am ok with a designer who decided to fiddle around and make the flagellum while leaving a lot of other mutations around that didn't help their possessors pass on offspring...But as previously noted if you find a sandwich in my kitchen it's far more likely that I made it than God conjured it up. Meanwhile ID wants to hide this obvious point behind the supposed mystery, expecting us to believe that Yaweh - after creating the Universe, but before coming down as Jesus - decided to make the flagellum but never bother[ed] to rid us of pesky inheritable diseases like cancer.

For a group that bases its arguments on probabilistic reasoning it doesn't seem that hard to turn this same critical eye toward the possibl[e] identity of the designers?

On the TTSS: the flagellum preceded the TTSS by more than a billion years in evolution and thus the TTSS represents a devolution from flagella rather than flagella being evolved from a TTSS. On top of this, the TTSS is itself irreducibly complex. This "explanation" is really no explanation.

(From PNAS summary): "Type III secretion systems (TTSS or secretons), are essential determinants of the interaction of many Gram-negative bacteria with animal or plant hosts, serve to translocate (inject) bacterial proteins into eukaryotic host cells to manipulate them during infection."

So: bacteria existed for over a billion and a half years before bacterial infection of eukaryotic host cells came along. The bacteria needed the flagella to simply find food and avoid noxious substances; then eukaryotes, and later insects, came along and with the endosymbiotic relationship established, the flagella no longer needed the other flagellar genes, and so, out of economy, eliminated them (this is one explanation for this "devolution"). Thus, the need to export proteins via the TTSS arose after the flagella had formed, not as a step on the way to the formation of the flagella.

As for using the Yahweh and Jesus card in attacking ID, this is becoming tiresome. The usual invalid debating tactic. Attack the science of ID not the faith of many of it's founders and scientific workers.

"Co-option is a demonstrably fantastic story made up out of whole cloth, with absolutely no basis in evidence. And it doesn’t withstand even the most trivial analytical scrutiny. There is not a shred of evidence that this process ever took place, or that it even could have taken place. Worst of all, it requires blind acceptance of the clearly miraculous." - Gil Dodgen

Are the minds of living things miraculous or did they develop mental capabilities by exploring the informational environment?  I surely see natural mind as causing phenomenal outcomes in bio-evolution called co-option.  Minds explore the informational possibilities and select future target states.

The manifestation of mind - as information processing - may still need a miracle to describe its very origin, but I stand sure that once mind is working - it can drive selection in the face of changes in the physical environment.

Ok - here is one of my (hopefully simple) arguments for using the widening the perspective of information science to promote mind and its function of understanding: 

All selection, including the phrase, "natural selection" is made by the action of mind changing real world probabilities. By design, science includes only natural data and causes.  Labeling the class of outcomes where mental choices exerts influence "natural", is redundant.  NS has a special meaning in narratives about how the past unfolded.  But if science is brought to bear, the selection processes should be modeled as (1) physical outcomes (2) informational outcomes.

(3) Ethical, artistic, literary selections are part of reality, but not directly subject to scientific method.

So, co-option in evolution, in light of (2) informational outcomes, seems a logical way for the mental processes of living things to respond to its environments.  https://physoc.onlinelibrary.wiley.com/d...012.071134

 Conclusions
We are privileged to live at a time of a major change in the conceptual foundations of biology. That change is set to bring the physiological study of function right back into centre stage......

The available evidence not only suggests an intimate interplay between genetic and epigenetic inheritance, but also that this interplay may involve communication between the soma and the germline. This idea contravenes the so‐called Weismann barrier, sometimes referred to as Biology's Second Law, which is based on flimsy evidence and a desire to distance Darwinian evolution from Lamarckian inheritance at the time of the Modern Evolutionary Synthesis. However, the belief that the soma and germline do not communicate is patently incorrect.

The only parts of this statement that I would change are, first, to remind readers, as I noted earlier in this article, that Darwin himself did not exclude the inheritance of acquired characteristics and, second, to remind us that Lamarck himself did not invent ‘Lamarckism’ (Noble, 2010). As we move on beyond the unnecessary restrictions of the Modern Synthesis we move back towards a more genuinely ‘Darwinian’ viewpoint and we also move towards a long‐overdue rehabilitation of Lamarck. Of course, neither Darwinism nor Lamarckism remains unchanged. Neither could have anticipated the work of the 21st century. But we can now see the Modern Synthesis as too restrictive and that it dominated biological science for far too long.

Are the minds of living things miraculous or did they develop mental capabilities by exploring the informational environment?  I surely see natural mind as causing phenomenal outcomes in bio-evolution called co-option.  Minds explore the informational possibilities and select future target states.

The manifestation of mind - as information processing - may still need a miracle to describe its very origin, but I stand sure that once mind is working - it can drive selection in the face of changes in the physical environment.

Ok - here is one of my (hopefully simple) arguments for using the widening the perspective of information science to promote mind and its function of understanding: 

All selection, including the phrase, "natural selection" is made by the action of mind changing real world probabilities. By design, science includes only natural data and causes.  Labeling the class of outcomes where mental choices exerts influence "natural", is redundant.  NS has a special meaning in narratives about how the past unfolded.  But if science is brought to bear, the selection processes should be modeled as (1) physical outcomes (2) informational outcomes.

(3) Ethical, artistic, literary selections are part of reality, but not directly subject to scientific method.

So, co-option in evolution, in light of (2) informational outcomes, seems a logical way for the mental processes of living things to respond to its environments.  https://physoc.onlinelibrary.wiley.com/d...012.071134

Yes, but only given the huge assumption that relatively simple life forms such as bacteria individually or collectively can exhibit "mental processes" - analytical mind. The huge assumption that consciousness - subjectivity - and therefore "mental processes" of some kind (which as exemplified by the Hard Problem are fundamentally different, higher and apart existentially from from processes or mechanisms) can be exhibited by relatively simple living organisms like bacteria. The informational processing so far observed in such organisms is very far from demonstrating this, and I would venture the view that evidence of actual consciousness will never be demonstrated in bacteria.

This capacity in the case of the flagellum example would have to be embodied in mental processes like the insight, imagination, foresight, etc. required to realize that in order to move in the watery environment the bacteria need not just some sort of proto-propeller or oar but also a hub and bearing assembly and motor, but also an assembly system, plus overall detailed requirements for interface compatibility between the parts, and then following that realization with separate design mental processes to come up with the designs of the individual parts. This is how I would define "mental processes" in this context. Do you have any alternative that is merely data processing and mechanism?

I'm not sure where your argument or train of thought is leading. The sandwich in your kitchen is most likely one which you made yourself. Though there is a possibility that you bought it somewhere. Either way a human being made it. But, humans have only been around for a couple of million years or so. This wouldn't account for anything which happened aeons ago. Adding visitors from another planet or another galaxy doesn't get us very far. Just where are you heading in this line of reasoning?


I should add that the 'Yahweh' line to me is a bit of a distraction, it portrays things in the language and tradition of one human culture from a particular part of our world in a particular time. I think we need to spread our gaze somewhat wider than one tradition.

If something small is done in the long series of deaths in the evolutionary change to a microscopic organisms, we have varied potential explanations for that.

Perhaps it's a spirit, perhaps it's some combination of Jim Carpenter's First Sight and Sheldrake's Morphic Fields so the organism is capable of making changes to its own species down the line.

As for aliens, they don't need to be visitors from another planet - Vallee suspects they've been around, here with us, since our earliest days.

My point is ID can't be a fully considered a serious science until it confronts the obvious question of rationally considering who the designer is. That doesn't even get into the questionable probability calculations and ideas of complexity that even some theists reject or see as clearly not adequate for showing the hand of God.

As for using the Yahweh and Jesus card in attacking ID, this is becoming tiresome. The usual invalid debating tactic. Attack the science of ID not the faith of many of it's founders and scientific workers.

Except this very criticism comes from Edward Feser, a Traditionalist Catholic ->

....Of course God can cause artifacts to exist miraculously, he can cause a voice to be heard from the sky or from a burning bush, and for that matter he could also cause “Made by Yahweh” to appear in every human cell.  And of course he can, and has, revealed himself via miraculous actions like some of these.  I don’t think it has ever occurred to any Thomist to dispute any of that.  It simply isn’t what is at issue.

What is at issue is the context in which such events could be known to be divine revelations -- and, in particular, whether such events could by themselves constitute evidence for the existence of God for someone who didn’t already know that God exists.  For there are different sorts of miracles, and different sorts of context in which they might be interpreted.  Suppose God miraculously caused the English words “I, God, exist” to be written in the dust on a certain car’s windshield -- but that the car was parked on a small side street in a neighborhood where most people spoke Mandarin, nobody was particularly religious, and the words appeared in the middle of the night when no one was around to see them.  This would, needless to say, be a pretty ineffective way of revealing himself.  There would be nothing about the evidence that those who come across it would be at all likely to see as miraculous.  It would just seem to be a silly prank, unworthy of a moment’s attention.  And pointing this out has nothing to do with arrogantly imposing idiosyncratic Aristotelian metaphysical limits on what God might do to reveal himself.

Consider something more dramatic, such as God miraculously causing a voice from the sky shouting “God loves you!” above a crowd all of whom spoke English -- but where this happened at Universal Studios or Disneyland in the course of a typically busy day there.  Almost certainly, no one would think that God was acting in a special way to reassure these people of his love.  Even if they were churchgoers, they’d think it was just some goofy prank by an employee with access to the requisite equipment.  Even if the context was a more unlikely one for such an event-- a quiet neighborhood, or the desert -- these days they might just as well wonder if the CIA or extraterrestrials were responsible. 

Contrast the sorts of contexts we find with biblical miracles like the burning bush or the voice from the sky at Christ’s baptism...

Here's another set of criticisms from the Christian physicist Howard Van Till ->

The Intelligent Design movement argues that it can point to specific biological systems that exhibit what ID’s chief theorist William A. Dembski calls “specified complexity.” Furthermore, Dembski claims to have demonstrated that natural causation is unable to generate this specified complexity and that the assembling of these biological systems must, therefore, have required the aid of a non-natural action called “intelligent design.” In his book, No Free Lunch, Dembski presents the bacterial flagellum as the premier example of a biological system that, because he judges it to be both complex and specified, must have been actualized by the form-conferring action of an unembodied intelligent agent. However, a critical examination of Dembski’s case reveals that, 1) it is built on unorthodox and inconsistently applied definitions of both “complex” and “specified,” 2) it employs a concept of the flagellum’s assembly that is radically out of touch with contemporary genetics and cell biology, and 3) it fails to demonstrate that the flagellum is either “complex” or “specified” in the manner required to make his case. If the case for Intelligent Design is dependent on the bacterial flagellum, then ID is a failure.

Now of course there could be a counter point, and I'm sure Van Till would have a counter point to that, but there's probably a counter^3 point.... So maybe Van Till isn't ultimately correct.

But again, contrast this with Cosmological Fine Tuning where the evidence isn't in question, just the interpretation. The constants are delicately set. You even have some Physicalists running to their precious Multiverse, a clear sign of defeat / excuse-making on their part. I even just posted an argument from a Christian that the laws of probability are an argument for God, and Fine Tuning can obviously also be the evidential side of that philosophical argument.

As I've already said I can appreciate ID for challenging materialism but I cannot be certain there's a clear challenge at all. Their dancing around the obvious issue of proximal causation and rationality of supposing God Himself decided to make the flagellum but leave in the genetic potential for varied illnesses doesn't do them any favors either.

Yes, but only given the huge assumption that relatively simple life forms such as bacteria individually or collectively can exhibit "mental processes" - analytical mind. 

"Analytical mind" includes advanced levels of understanding that took a long road in mental evolution to appear.  Information processes, such as the selection of a target future state  need go all the way down to a root level of life.  Intent, as a TFS, is there with the basic efferent instructions: to go, consume, retreat, reproduce and stop/refocus.  Just like a Turing machine reading a tape, living things exhibit, logical, functional and goal-state behavior in dealing with their environments.

Immune systems need not be aware of their own mental work to detect bacteria and respond with an array of defenses.  All of the detection and selected response are instinctual and subconscious.  Simulations of the information processes employed in the health and regulation of the simplest organisms are masterworks in command and control.

Evidence for abstract analysis is maybe, a few million years old.  Encoded instructions for ontogenetic development and self-regulation in hostile environments are billions of years old.  From the start, living things have explored the informational environment - and have used every trick in physics and computing to get here with their talents so gained.

Mental evolution has yet to break through as a field of defined research.   Bioinformatics has.  The science is clear now --- that mutations are not random to fitness.  That the important part of natural selection is not the magic of nature.  It is how mental selections change real-world probabilities that enforce intent and purposeful functioning by living beings.  Selections based on simple understanding of affordances are the mechanisms for exporting mental decisions into the local information environment.

Except this very criticism comes from Edward Feser, a Traditionalist Catholic ->


Here's another set of criticisms from the Christian physicist Howard Van Till ->


Now of course there could be a counter point, and I'm sure Van Till would have a counter point to that, but there's probably a counter^3 point.... So maybe Van Till isn't ultimately correct.

But again, contrast this with Cosmological Fine Tuning where the evidence isn't in question, just the interpretation. The constants are delicately set. You even have some Physicalists running to their precious Multiverse, a clear sign of defeat / excuse-making on their part. I even just posted an argument from a Christian that the laws of probability are an argument for God, and Fine Tuning can obviously also be the evidential side of that philosophical argument.

As I've already said I can appreciate ID for challenging materialism but I cannot be certain there's a clear challenge at all. Their dancing around the obvious issue of proximal causation and rationality of supposing God Himself decided to make the flagellum but leave in the genetic potential for varied illnesses doesn't do them any favors either.

There are a lot of Christian apologists who so greatly want to be legitimate in the eyes of science rather than espousing the heretical throwback to ancient superstition they assume ID is, that they twist themselves into rhetorical knots to try to reconcile Christian theology with Darwinism. Good luck to them.  

The following (once more) is leading Darwinist spokesman William Provine on the ultimate significance of Darwinism for the picture of man and his place in the universe:

"Let me summarize my views on what modern evolutionary biology tells us loud and clear — and these are basically Darwin’s views. There are no gods, no purposes, and no goal-directed forces of any kind. There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end of me. There is no ultimate foundation for ethics, no ultimate meaning in life, and no free will for humans, either. What an unintelligible idea."

All these consequences are clear implications of the true nature of human existence if Darwinism is true and that it of course applies also to the evolution of Homo Sapiens.

So be careful in espousing Darwinism because you're skeptical of the theory of ID, and because many of the people in the ID movement are Christians who adhere to a theology you heartily dislike.

If you disagree that these are the clear implications, please explain.

"Analytical mind" includes advanced levels of understanding that took a long road in mental evolution to appear.  Information processes, such as the selection of a target future state  need go all the way down to a root level of life.  Intent, as a TFS, is there with the basic efferent instructions: to go, consume, retreat, reproduce and stop/refocus.  Just like a Turing machine reading a tape, living things exhibit, logical, functional and goal-state behavior in dealing with their environments.

Immune systems need not be aware of their own mental work to detect bacteria and respond with an array of defenses.  All of the detection and selected response are instinctual and subconscious.  Simulations of the information processes employed in the health and regulation of the simplest organisms are masterworks in command and control.

Evidence for abstract analysis is maybe, a few million years old.  Encoded instructions for ontogenetic development and self-regulation in hostile environments are billions of years old.  From the start, living things have explored the informational environment - and have used every trick in physics and computing to get here with their talents so gained.

Mental evolution has yet to break through as a field of defined research.   Bioinformatics has.  The science is clear now --- that mutations are not random to fitness.  That the important part of natural selection is not the magic of nature.  It is how mental selections change real-world probabilities that enforce intent and purposeful functioning by living beings.  Selections based on simple understanding of affordances are the mechanisms for exporting mental decisions into the local information environment.

"Selection of a target future state" has many implications, when it comes down to the details of what is involved in an actual design problem like that of the bacterial flagellum. Say it's at the initial stage of design. The bacterium has no consciousness, therefore has no insight into the problem. It literally knows nothing, because to "know" implies consciousness. That means it doesn't and can't know that a propeller, a hub/bearing through the cell wall, a motor, and an assembly machine are all necessary. Since it has no consciousness it is fundamentally incapable of either envisioning or knowing or desiring the future state of being able to move via a new cellular organelle with certain basic components. I disagree that there can possibly be intent in this simple organism - intent clearly implies consciousness, which the bacterium simply doesn't have. The word "mental" simply doesn't apply to this organism.

So be careful in espousing Darwinism because you're skeptical of the theory of ID, and many of the people in the ID movement are Christians who adhere to a theology you heartily dislike.

The bold is a spurious charge. Look back to my posts - I'm the person who most advocated for Christian philosophers like Feser, Swineburne, Bonnette, on Skeptiko and here. I don't even think anyone had posted about Christian Apologetics on Skeptiko until I showed up?

The only religion [outside the Physicalist faith] I can think of that I've actively criticized is Hinduism, and only then insofar as the caste system is concerned.

ID being a half-at-best science, with its practitioners holding to the claim that there's nothing to be said scientifically about who the maker of the flagellum is, has nothing to do with disliking Christianity. It has to do with IDers not presenting a compelling enough argument even for other Christians to take it seriously, and then putting blinders on regarding the reality that their field is a branch of parapsychology.

This isn't to say it's all garbage, there are hints of design like that grasshopper having gears in its legs and other evolutionary oddities like the 3d optical illusion on this moth's back. And as Kastrup notes there's no way to be certain mutations in the past were just random. And much of our mental existence, such as our capacity for rationality and aboutness-of-thought, cannot be explained in evolutionary terms.

So perhaps someday IDers will have something that is rock solid, but I'm not convinced that day has come.