Evolution without accidents and also no intelligence?

Thought you all might find my two question (so far) dialogue with ChatGPT interesting.

First question: Is the bacterial flagellum irreducibly complex?

ChatGPT's response is below:

The concept of irreducible complexity was introduced by biochemist Michael Behe in his book "Darwin's Black Box" published in 1996. He argued that certain biological systems, like the bacterial flagellum, are composed of several interacting parts, and the removal of any one of these parts would cause the system to cease functioning, making it irreducibly complex and challenging to explain through gradual evolution.

The bacterial flagellum is a whip-like appendage used by some bacteria for movement. It consists of multiple components, including a filament, hook, basal body, and motor proteins. Behe argued that removing any of these components would result in a non-functional flagellum, implying that it could not have evolved gradually.

However, Behe's concept of irreducible complexity has been heavily debated and criticized within the scientific community. Critics argue that his argument rests on the assumption that the components of a complex system have no other functions or intermediates, which is often not the case. Many biological structures that were once considered irreducibly complex have been shown to have precursor functions or intermediate stages that could have evolved through natural selection.

Over time, research in molecular biology, genetics, and evolutionary biology has provided plausible explanations for the evolutionary origins of complex structures like the bacterial flagellum. There is evidence of simpler systems with partially functional flagella-like structures in other organisms, suggesting that the flagellum may have evolved through step-by-step modifications and adaptations.

In conclusion, while the bacterial flagellum was once proposed as an example of irreducible complexity, the concept has been widely criticized and lacks broad acceptance within the scientific community. The current consensus among scientists is that biological complexity can arise through natural evolutionary processes, and ongoing research continues to shed light on the evolution of complex structures.

My follow-up question: What evidence has been offered to counter the idea that a bacterial flagellum is irreducibly complex?

ChatGPT's response is below:

Several lines of evidence and research have been presented to counter the idea that the bacterial flagellum is irreducibly complex. Some of the key points include:

1. Homologous structures: Homology refers to similarities in structures or genes between different organisms due to shared ancestry. Researchers have identified homologous components of the bacterial flagellum in other bacterial systems, as well as in non-motile systems. For example, the type III secretion system (TTSS) found in various bacteria shares many components with the flagellum, suggesting that the flagellum might have evolved from a simpler structure like the TTSS.

2. Intermediate structures: Studies have identified intermediary forms of flagella-like structures in various organisms. Some bacteria possess partial flagella or components that resemble the flagellum but serve different functions. These intermediate structures suggest a step-by-step evolution of the flagellum, with each stage providing some selective advantage.

3. Functional redundancy: While removal of certain components from the flagellum may result in impaired motility, it doesn't necessarily mean the entire system becomes non-functional. Some parts of the flagellum can be redundant, and other mechanisms may compensate for the loss, allowing the bacteria to remain viable and continue evolving.

4. Computational modeling: Computer simulations and mathematical models have shown how complex structures like the flagellum could have arisen through small, incremental changes over time. These models demonstrate how selection for improved motility could drive the evolution of the flagellum.

5. Laboratory evolution experiments: Scientists have conducted laboratory evolution experiments with bacteria, subjecting them to selective pressure for improved motility. These experiments have shown that bacteria can evolve more efficient flagella-like structures within a relatively short time frame, supporting the idea that the flagellum could have evolved through natural selection.

6. Genetic and genomic evidence: Comparative genomic studies have revealed the presence of genes related to the flagellum in diverse organisms, suggesting that the genetic toolkit for building flagella-like structures exists in various lineages.

7. Fossil evidence: Although the bacterial flagellum itself doesn't fossilize, evidence from ancient rocks and sedimentary deposits has provided insights into the early evolution of microbial life and the emergence of motility-related structures.

It's essential to note that scientific understanding is continually evolving, and researchers are continuously exploring and testing hypotheses related to the evolution of complex structures like the bacterial flagellum. While the concept of irreducible complexity has been challenged by the evidence presented above, the scientific community remains open to new data and perspectives to further our understanding of evolutionary processes.

Several lines of evidence and research have been presented to counter the idea that the bacterial flagellum is irreducibly complex. Some of the key points include:

1. Homologous structures: Homology refers to similarities in structures or genes between different organisms due to shared ancestry. Researchers have identified homologous components of the bacterial flagellum in other bacterial systems, as well as in non-motile systems. For example, the type III secretion system (TTSS) found in various bacteria shares many components with the flagellum, suggesting that the flagellum might have evolved from a simpler structure like the TTSS.

I believe the ID crowd argue that the type III secretion system (whatever that is) developed AFTER the flagellum.

We are really talking about taking a fragment of something and using it for another purpose. I would argue that in general that becomes harder and harder the more complex the system is. Early electronics enthusiasts used to buy scrap electronic circuits and re-use their parts, but modern electronic circuits are more or less scrap.

2. Intermediate structures: Studies have identified intermediary forms of flagella-like structures in various organisms. Some bacteria possess partial flagella or components that resemble the flagellum but serve different functions. These intermediate structures suggest a step-by-step evolution of the flagellum, with each stage providing some selective advantage.

3. Functional redundancy: While removal of certain components from the flagellum may result in impaired motility, it doesn't necessarily mean the entire system becomes non-functional. Some parts of the flagellum can be redundant, and other mechanisms may compensate for the loss, allowing the bacteria to remain viable and continue evolving.

4. Computational modeling: Computer simulations and mathematical models have shown how complex structures like the flagellum could have arisen through small, incremental changes over time. These models demonstrate how selection for improved motility could drive the evolution of the flagellum.

I don't trust computer models of anything. The code is written and is then debugged so it doesn't crash. Then it is further debugged until it gives the expected answer.

5. Laboratory evolution experiments: Scientists have conducted laboratory evolution experiments with bacteria, subjecting them to selective pressure for improved motility. These experiments have shown that bacteria can evolve more efficient flagella-like structures within a relatively short time frame, supporting the idea that the flagellum could have evolved through natural selection.

If evolution doesn't happen by RM+NS, it happens some other way - presumably non-materialist ways, such as Rupert Sheldrake's morphogenetic fields.

6. Genetic and genomic evidence: Comparative genomic studies have revealed the presence of genes related to the flagellum in diverse organisms, suggesting that the genetic toolkit for building flagella-like structures exists in various lineages.

I suspect that the designer(s) have a bank of good protein solutions to a whole range of problems, and maybe to parts of problems. This is just like chip designers - they don't always design chips from scratch (maybe they never do by now) they use all sorts of existing modules (stored inside their computers) - simply adding them to the system they are designing.

There is a concept in evolution known as 'convergent evolution'. This describes a situation in which two or more distinct lineages come to the same 'decision as to how something is to be constructed. For example, our type of eye, with a lens can adjust its focal length etc. has been 'invented' multiple times. The official explanation is that this happens because there is no other effective solution. A simpler solution is to assume that the designer(s) pop that design into a drawer and pull it out again when they are working on another creature that needs to see!

David

I believe the ID crowd argue that the type III secretion system (whatever that is) developed AFTER the flagellum.

We are really talking about taking a fragment of something and using it for another purpose. I would argue that in general that becomes harder and harder the more complex the system is. Early electronics enthusiasts used to buy scrap electronic circuits and re-use their parts, but modern electronic circuits are more or less scrap.
I don't trust computer models of anything. The code is written and is then debugged so it doesn't crash. Then it is further debugged until it gives the expected answer.
If evolution doesn't happen by RM+NS, it happens some other way - presumably non-materialist ways, such as Rupert Sheldrake's morphogenetic fields.

I suspect that the designer(s) have a bank of good protein solutions to a whole range of problems, and maybe to parts of problems. This is just like chip designers - they don't always design chips from scratch (maybe they never do by now) they use all sorts of existing modules (stored inside their computers) - simply adding them to the system they are designing.

David

I hope you don't take this the wrong way, but your responses certainly aren't of a knock-down quality.  This isn't necessarily the thread for going over the defense of Behe's irreducible complexity argument anyway, but I am curious what Behe might provide in a more technical manner to the ChatGPT-offered counter points.

I did find the very last sentence of the second response from ChatGPT to be REALLY interesting:

While the concept of irreducible complexity has been challenged by the evidence presented above, the scientific community remains open to new data and perspectives to further our understanding of evolutionary processes.

I wonder what the source data it used to come up with the 'scientific community remains open' regarding irreducible complexity.  I realize I'm parsing the sentence in a way the bot may not have intended, but it struck me as a charitable thought.

Thought you all might find my two question (so far) dialogue with ChatGPT interesting.

First question: Is the bacterial flagellum irreducibly complex?

ChatGPT's response is below:



My follow-up question: What evidence has been offered to counter the idea that a bacterial flagellum is irreducibly complex?

ChatGPT's response is below:

Because of the propensity of AIs like ChatGPT to "hallucinate" and invent corroborating details, I am reluctant to respond, but the arguments seem mostly to be taken from available sources on the Internet including Wiki.  

Even if a separate function could be found for a sub-system or sub-part, that would not refute the irreducible complexity of the whole, nor would it demonstrate the evolvability of that entire system.

According to Darwin himself, Darwinian evolution requires that a system be functional along each small step of its evolution. One could find a sub-part that could be useful outside of the final system, yet the total system would still face many points and stretches over its “evolutionary pathway” where the total system could not remain functional through “numerous, successive, slight modifications.” Behe focuses on the (in)ability of the entire system to assemble in a stepwise fashion, even if sub-parts can have functions outside of the final system.

An internal combustion piston engine is still irreducibly complex despite the fact that many parts have other uses in other machines - the simplest parts being various size bolts, nuts and washers. A system does not become “reducibly complex” simply because one part remains functional outside of the final system; the latter is a straw man argument.

Scott Minnich’s genetic knockout experiments on the E. coli flagellum have shown that it fails to assemble or function properly if any one of its approximately 35 structural parts are missing. That’s prima facie evidence that it’s irreducibly complex.

Concerning the idea the T3SS "injectisome" used by some parasitic bacteria is a precursor of the flagellum, this is very unlikely for a lot of reasons, especially because of the timing involved. From https://www.discovery.org/a/24481/ :

"....it’s doubtful that the T3SS is useful at all in explaining the origin of the flagellum. The injectisome is found in a small subset of gram-negative bacteria that have a symbiotic or parasitic association with eukaryotes. The injectisome bacteria use their "injector" T3SS structure to attack the eukaryotic cells. Since eukaryotes evolved over a billion years after bacteria, this suggests that the injectisome arose after eukaryotes. However, flagella are found across the range of bacteria, and the need for chemotaxis and motility (i.e., using the flagellum to find food) precede the need for parasitism. In other words, we’d expect that the flagellum long predates the injectisome. And indeed, given the narrow distribution of injectisome-bearing bacteria, and the very wide distribution of bacteria with flagella, parsimony suggests the flagellum long predates injectisome rather than the reverse."

And the T3SS is just a pump that can move proteins across the cell membrane. It doesn’t in any way explain how the flagellum motor and its core propulsion function arose.

The skeptic can say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor could have evolved into the motorcycle. Perhaps, but not without intelligent design. Common observation is that multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. That doesn't affect the irreducible complexity of the more complex machine.

For a lot of complicated technical molecular biological details that refute the claims of the Darwinists re. the bacterial flagellum, see the article at https://evolutionnews.org/2011/03/michae...en_refute/ .

I hope you don't take this the wrong way, but your responses certainly aren't of a knock-down quality.  This isn't necessarily the thread for going over the defense of Behe's irreducible complexity argument anyway, but I am curious what Behe might provide in a more technical manner to the ChatGPT-offered counter points.

I did find the very last sentence of the second response from ChatGPT to be REALLY interesting:


I wonder what the source data it used to come up with the 'scientific community remains open' regarding irreducible complexity.  I realize I'm parsing the sentence in a way the bot may not have intended, but it struck me as a charitable thought.

Dr. Behe answered the main objections to the irreducible complexity of the bacterial flagellum in this podcast : https://idthefuture.com/1651/ .

Well like everyone here, we read ideas and pass ideas on, hopefully with some insight of our own! Thus inevitably you do speak TTW because that is what you read! All I am saying, is you need to think what exactly it means.

I find it fascinating that the science establishment is so invested with the concept of RM+NS, and particularly with the idea of evolution, that it is corrupting the whole logic of science.

I used to 'believe' in evolution by natural selection even while becoming interested in non-materilistic ideas in other contexts. I remember it was Lone Shaman on Skeptiko who converted me when that website was at its best. We had a number of intense discussions that changed my mind.

My earlier post took a tiny bit of TTW speak and challenged you to figure out what exactly it means.

David

I am sure of the meaning as it is a decades long quest for me.  The meaning of TTW group world-view is that the RM+NS debate is over -- it lost to better science.  I can appreciate your wanting to push ID.  But pragmatically in the environment of experts, it is peer-reviewed research, publication and applied practice that is important.  Great data have leverage!  Science has established new pathways documenting novel evolutionary outcomes.  Oh, and Spadafora is working on curing cancer.  

Here he is throwing a pie in the face of Neo-Darwinism.  In a paper just published, Spadafora is calmly, factually stating -- that RM+NS is not needed for evolution and there are pathways that need neither!!!!! 

https://www.researchgate.net/publication..._evolution

 a variety of biological tools favouring the emergence of evolutionarily significant phenotypic novelties driven by RNA information. Under this light, neither random genomic mutations, nor the sieving role of natural selection are required, as the sperm-delivered RNA cargo conveys specific information and acts as "phenotypic-inducer" of defined environmentally acquired traits. - https://www.researchgate.net/profile/Corrado-Spadafora 

Where is the horror from Dawkins and "Darwinists?  Is P.Z. Meyers going to respond?   No   It's over.  Myers precious darling, his award winning website doesn't even talk about bio-evolution anymore.  https://freethoughtblogs.com/pharyngula/...haryngula/

I am sure of the meaning as it is a decades long quest for me.  The meaning of TTW group world-view is that the RM+NS debate is over -- it lost to better science.  I can appreciate your wanting to push ID.  But pragmatically in the environment of experts, it is peer-reviewed research, publication and applied practice that is important.  Great data have leverage!  Science has established new pathways documenting novel evolutionary outcomes.  Oh, and Spadafora is working on curing cancer.  

Here he is throwing a pie in the face of Neo-Darwinism.  In a paper just published, Spadafora is calmly, factually stating -- that RM+NS is not needed for evolution and there are pathways that need neither!!!!! 

https://www.researchgate.net/publication..._evolution

Where is the horror from Dawkins and "Darwinists?  Is P.Z. Meyers going to respond?   No   It's over.  Myers precious darling, his award winning website doesn't even talk about bio-evolution anymore.  https://freethoughtblogs.com/pharyngula/...haryngula/

Back in post #88 (https://psiencequest.net/forums/thread-e...8#pid53938), I stated my impression of the deliberately ambiguous "TTW-speak" that David referred to. I used an earlier example quoted by you. I demonstrated that a high level of conscious mind must be behind design in evolution, and concluded with the following:

"Do the "Third Way" people recognize that this level of mind has to be conscious and self-aware, and that what they seem to be proposing is that this level of mind is exhibited by relatively simple bacterial cells? They never get down to brass tacks and call a spade a spade. I know this is probably because they know that to do so would probably terminate their careers. But the result to date is a lot of talk that doesn't make much sense."

Rather than responding, you have simply reiterated your position, using another "TTW-speak" utterance, this one by Spadafora. He refers to "...emergence of evolutionarily significant phenotypic novelties driven by RNA information..." What does this really mean? He doesn't seem to be aware that this phrase is ambiguous and makes a lot of built-in assumptions. "Emergence" is a very controversial and probably invalid concept, "driven by RNA information" doesn't address the key requirement for conscious intelligent agency in design. And finally, "information" or information processing are not the essence of mind - the essence of mind is subjective awareness, consciousness. If information processing was the key to design, our present supercomputers would be being used to profitably generate multiple patents for new inventions.

I almost have the impression that TTW-speak is motivated by the Third Way scientists liking the sound of their own voices, in lyrical prose having little meaning.

Because of the propensity of AIs like ChatGPT to "hallucinate" and invent corroborating details, I am reluctant to respond, but the arguments seem mostly to be taken from available sources on the Internet including Wiki.  

Indeed, we know wikipedia is unreliable because it contains sceptical bias and omits or misrepresents counter-arguments. In the case of AIs like ChatGPT there is an even more difficult obstacle, 'hallucination', inventions and fiction presented in a style which might appear convincing. That means everything has to be double and triple checked, before even beginning to consider whether it is coherent or representing a legitimate argument.

In mundane topics AI may be useful, in controversial areas I suspect it can only muddy the waters.

I am sure of the meaning as it is a decades long quest for me.  The meaning of TTW group world-view is that the RM+NS debate is over -- it lost to better science.  I can appreciate your wanting to push ID.  But pragmatically in the environment of experts, it is peer-reviewed research, publication and applied practice that is important.  Great data have leverage!  Science has established new pathways documenting novel evolutionary outcomes.  Oh, and Spadafora is working on curing cancer.  

Here he is throwing a pie in the face of Neo-Darwinism.  In a paper just published, Spadafora is calmly, factually stating -- that RM+NS is not needed for evolution and there are pathways that need neither!!!!! 

Well I think there is a vague analogy between TTW science and the people who collected more and more data to fit to the epicyclic model of the solar system. I don't suppose any of them were fools, but the only way they could publish their data was by sticking to the idea that the planets go around the Earth in circles, but there are also smaller circular motions to add to their orbit, and still smaller circular motions to add to that..... Their data collection was good, but their overall model was constrained by the church and was just daft.

Paradoxically the same situation applies now except that the church isn't ruling things, but the incredible reluctance of science to indulge anything that even smells vaguely of the church is. Individual bits of science produced by the TTW may be useful, but their TTW-speak (I like Nbtruthman's phrase) is unreadable as science.

Both Nbtruthman and I (and hopefully others here too) accept that the TTW couch their theoretical ideas in such a vague language that it is difficult to determine what alternative to RM+NS they are offering - if any.

I mean let me remind you. A long time ago in this thread, you quoted Shapiro

Evolution by stress-activated natural genetic engineering is currently the best way we have to address the origins of the complex systems which ID advocates claim neo-Darwinism cannot explain.

To this I pointed out that

I mean " Evolution by stress-activated natural genetic engineering" sounds great until you remember that engineering - genetic or otherwise - is done by (surprise, surprise) human engineers! As far as I can see, there simply isn't any materialistic alternative explanation!

I mean given that, wouldn't it be better for Shapiro to re-phrase his remark to acknowledge that " Evolution by stress-activated natural genetic engineering" implies an engineer, which in turn implies intelligent design?

David