Darwin Unhinged: The Bugs in Evolution

My view is very naïve and I am a poor writer.  But sure.

https://philosophy.nd.edu/people/emeritu...eth-sayre/

https://philpapers.org/rec/FLOIR

Cool. I can start by making an Information Realism thread, giving what I think is going on, and you can offer elucidation and correction.

I figure this might help make the concepts clearer. And I apologize in advance for the inevitable repetition as I know I'll ask about things that you've gone over before.

Ah I still need to make the Information Realism thread, re-reading the NPR blog of biologist Stuart Kauffman partially for this reason. He also has some criticism of ID that vary on the quality of argument scale ->

Intelligent Design, No. Darwinian 'Exaptations' and More. Yes.

How do biologists explain "irreducible complexity" such as the flagellar motor? Largely by our now well discussed Darwinian "exaptations". Other bacteria have been found, and presented in the Dover trial, that have parts of the flagellar motor. In these other bacteria, the parts of the flagellar motor play entirely different functional roles, unrelated to swimming via the flagellar motor. The transition, we believe, to the flagellar motor arose, like the swim bladder from the lungs of lung fish, via Darwinian exapatations. The flagellar motor was never selected for directly and ab initio. It arose by a succession of exaptations, like the three bones of our middle ears from three adjacent bones of an early fish. Furthermore, as I've described before, we can have no probability measure for the evolution of the biosphere into its Adjacent Possible, since we do not know all the possibilities, hence we do not know the sample space of the process, so cannot construct a probability measure. Therefore, the calculations of improbability that the ID proponents make are vacuous.

If ID were taken to be a science, it would make one prediction: Darwinian exaptations do not occur, hence cannot offer an explanation for "irreducible complexity". But exaptations arise in evolution all the time. The one testable prediction of ID that I can think of is false.

He also says some stuff about how evolution is the foundation of morality...one only has to look those wasps that cut off the heads of bees or animals that target the infants/eggs of other animals to negate this. There is no *ought* from *is* as Hume famously noted.

I also don't know if one can say ID is vacuous if it makes no predictions save for the claim other explanations will fail to explain something. I admit this criticism does seem like it might have some teeth at first glance...

But, OTOH, can the study of dinosaurs yield any predictions in the sense of a physics theory? Isn't a scientific study of the past always limited by its subject matter when it comes to saying something about the future? Even someone as critical of ID as I am doesn't think it can be easily dismissed as not qualifying as a scientific pursuit. [However I do think Kauffman makes a point about the probabilities inherent to ID...can these be calculated in a rational manner?]

Regarding exaptations, here's some elaboration from Kauffman in another blog post ->

Darwin had a further important idea: A property of an organism, say wiggling water in the pericardial sac, of no selective use in the current environment, might become of use in a different selective environment, so be selected.

Typically a new function arises in the biosphere. These are called Darwinian "exaptations".

First case: Some fish have swim bladders, where the level of air and water in the bladder adjusts neutral buoyancy in the water column. Paleontologists believe that swim bladders arose from lung fish. Water got into some lungs, now there was a sac partly filled with air, partly with water, poised to be selected to be a swim bladder. Let's assume the paleontologists are right.

Second case: We have three middle ear bones. These derived by exaptations from three adjacent jaw bones of an early fish.

Now, I ask you three questions. First, did a new function come to exist in the biosphere? Sure, neutral buoyancy in the water column, and hearing. Second, did this new function change the future evolution of the biosphere? Of course, new species evolved, new proteins evolved, new niches came into existence.

From the BBC website
New light shed on Charles Darwin's 'abominable mystery'

A scientist has shed new light on the origins of Charles Darwin's "abominable mystery".

The famous naturalist was haunted by the question of how the first flowering plants evolved.

Darwin feared this inexplicable puzzle would undermine his theories of evolution, says Prof Richard Buggs.

Forgotten historical documents show a rival scientist was arguing for divine intervention in the rise of the flowering plants.

This greatly vexed Darwin in his final months, says the evolutionary biologist at Queen Mary, University of London.

And is the mystery solved?

In short, no. "One hundred and forty years later, the mystery's still unsolved," says Prof Buggs.

Ah I still need to make the Information Realism thread, re-reading the NPR blog of biologist Stuart Kauffman partially for this reason. He also has some criticism of ID that vary on the quality of argument scale ->

Intelligent Design, No. Darwinian 'Exaptations' and More. Yes.




He also says some stuff about how evolution is the foundation of morality...one only has to look those wasps that cut off the heads of bees or animals that target the infants/eggs of other animals to negate this. There is no *ought* from *is* as Hume famously noted.

I also don't know if one can say ID is vacuous if it makes no predictions save for the claim other explanations will fail to explain something. I admit this criticism does seem like it might have some teeth at first glance...

But, OTOH, can the study of dinosaurs yield any predictions in the sense of a physics theory? Isn't a scientific study of the past always limited by its subject matter when it comes to saying something about the future? Even someone as critical of ID as I am doesn't think it can be easily dismissed as not qualifying as a scientific pursuit. [However I do think Kauffman makes a point about the probabilities inherent to ID...can these be calculated in a rational manner?]

Regarding exaptations, here's some elaboration from Kauffman in another blog post ->

Oh well, Gil Dodgen on the miracle of exaptations (aka "co-option"):

"This claim of the refutation of IC by co-option is so ubiquitous that some people are actually starting to believe it. I therefore feel that it is my civic duty to refute this “refutation” of IC, which turns out to be a trivial exercise.

1) In order for co-option to produce a bacterial flagellum (for example) all of the component parts must have been present at the same time and in roughly the same place, and all of them must have had other naturally-selectable, useful functions. There is no evidence whatsoever that this ever was the case, or that it ever even could have been the case.

2) The components would have to have been compatible with each other functionally. A bolt that is too large, too small, or that has threads that are too fine or too coarse to match those of a nut, cannot be combined with the nut to make a fastener. There is absolutely no evidence that this interface compatibility ever existed (between all those imaginary co-opted component parts), or that it even could have existed.

3) Even if all the parts are available at the same time and in the same place, and are functionally compatible, one can’t just put them in a bag, shake them up, and have a motor fall out. An assembly mechanism is required, and that mechanism must be complete in every detail, otherwise incomplete or improper assembly will result, and no naturally-selectable function will be produced. The assembly mechanism thus represents yet another irreducibly complex hurdle.

4) Last, and perhaps most importantly, assembly instructions are required. Assembly must be timed and coordinated properly. And the assembly instructions must be complete in every detail, otherwise no function will result. This represents an additional irreducibly complex hurdle.

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.

There is a great irony here. This verifiably ridiculous co-option fantasy is presented as “science,” while a straightforward and reasonable inference to design is labeled pseudoscience. The real state of affairs is precisely the reverse."

Oh well, Gil Dodgen on the miracle of exaptations (aka "co-option"):

So the ID/IC argument is that some designer intervened directly to make the flagellum?

From the BBC website
New light shed on Charles Darwin's 'abominable mystery'

Unfortunately the link doesn't work.

So the ID/IC argument is that some designer intervened directly to make the flagellum?

I notice that you don't attempt to debunk the arguments against the viability of the "exaptation" theory. If it wasn't co-option or some other undirected quasi-Darwinian mechanism, logically it must have been something else. The ID/IC argument is that there is a massive amount of evidence that it wasn't an undirected mechanism involving random mutations and selection (or "exaptations"). The only alternative to an undirected Darwinian mechanism that comes to the imagination is intelligence of some sort. Any other ideas?  Further speculation is beyond ID's purview. Of course, you don't accept that limitation and claim that ID in order to be a legitimate science has to identify this intelligence. I disagree.

I notice that you don't attempt to debunk the arguments against the viability of the "exaptation" theory. If it wasn't co-option or some other undirected quasi-Darwinian mechanism, logically it must have been something else. The ID/IC argument is that there is a massive amount of evidence that it wasn't an undirected mechanism involving random mutations and selection (or "exaptations"). The only alternative to an undirected Darwinian mechanism that comes to the imagination is intelligence of some sort. Any other ideas?  Further speculation is beyond ID's purview. Of course, you don't accept that limitation and claim that ID in order to be a legitimate science has to identify this intelligence. I disagree.

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? ->

Stated directly, the TTSS does its dirty work using a handful of proteins from the base of the flagellum. From the evolutionary point of view, this relationship is hardly surprising. In fact, it's to be expected that the opportunism of evolutionary processes would mix and match proteins to produce new and novel functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains "by definition nonfunctional." Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum. The TTSS may be bad news for us, but for the bacteria that possess it, it is a truly valuable biochemical machine.

The existence of the TTSS in a wide variety of bacteria demonstrates that a small portion of the "irreducibly complex" flagellum can indeed carry out an important biological function. Since such a function is clearly favored by natural selection, the contention that the flagellum must be fully-assembled before any of its component parts can be useful is obviously incorrect. What this means is that the argument for intelligent design of the flagellum has failed.

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?

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.

A counter point to the above ->

Ironically, Behe's flagellum was used to publicly flog (let the Latin reader understand the pun) him and ID theory during the Dover School Board case. But once again, the evidence turned against the whip hand. The materialists argued that the flagellum of a paramecium is similar to a less complex version of the organelle called a Type 3 secretion needle system. Therefore, the court was told, needle secretion systems can evolve into flagella. Except that the needle system is still extremely complex so where did it come from? Except that what use would a paralyzing stinger be to a paramecium which has not evolved some kind of venom production and storage and hydraulic pressure system? Except that according to established Darwinian scholarship, the stinger is later in evolutionary history then the flagellum it is alleged to have evolved into. So, in that case, if there is a process of evolution from random mutation and natural selection, it is downward in complexity. An outboard motor turning into a hypodermic needle is hardly a proof of information creation through random processes.

But I am also confident I can go out and find a counter-counter point, and then a counter-counter-counter point...

OTOH Cosmological Fine Tuning is such a strong argument that atheists like Neil Degrasse Tyson are in some sense co-opting it for their own belief in a Simulation Hypothesis, which really is nothing but Design w/out God.

Unfortunately the link doesn't work.

Thank you. I fixed the post now. This is the correct link:
https://www.bbc.co.uk/news/science-environment-55769269