Irreducible complexity in biology

[David Bailey]

I think this video puts the case for Intelligent Design (or at least the case that Darwin's theory doesn't cut it) very clearly.

Discuss!

David

 

[Silence]

Is there a thoughtful rebuttal?

 

[gabriel]

The video shows the overwhelming desire of institutional science to hang on to a body of knowledge for reasons that are not scientific. Not being a molecular biologist, I have no idea whether the graphics and voiceover authentically reflect the revolution that's implied, but I know for certain the responses to it are not driven by a studied unpicking of the theory, but a desire to lash out at the implications with any tool at hand.

I dislike the term ID because it suggests Superman, someone like ourselves but much smarter, mind at large that's settled for engineering programmes as a specialist discipline. I think God is more subtle than the geek ID suggests, but can see why irreducible complexity gets the right people's pants on fire.

 

[malf]

I dislike the term ID because it suggests Superman, someone like ourselves but much smarter, mind at large that's settled for engineering programmes as a specialist discipline.

With a curious penchant for bugs

https://www.si.edu/spotlight/buginfo/bugnos

There are a lot of assumptions in ID, the major one that evolution had a predetermined end-point in mind.

So is ID or traditional evolution more correct? It seems that one (maybe both) underestimates the magic and mystery of matter itself.

 

[Bart V]

Before we can even say we recognize 'design' in evolution, shouldn't we discuss what design actually is?
If, as i think, design is very much an evolutionary process itself, are we then not saying we recognize evolution in evolution?

Think about it, even the most genius inventions never happen in a vacuum. Technical advances so often happen independently in different places at roughly the same time.
Just like scientific discoveries that are 'in the air'. At a certain time, all the elements simply are there. A true genius may advance things a bit sooner, but a caveman is not going to get to a power drill coming from stone tools in one generation.

Human design never goes beyond the design elements that are available at the time. Even in human design, irreducible complexity is an empty concept.

Though there are obvious, and significant, differences between natural and cultural evolution.
For instance, if we compare genetic evolution with memetic (cultural) evolution, we see that memes have an almost limitless ability for horizontal meme transfer.

Thinking about design problems, is virtually recombining of existing design elements, allowing for countless generations of virtual design, and therefore being much faster than any possible genetic evolution.

In this we are helped by an ability to envision a point we want to get to. In an other way though, this is also a limiting factor.
Genetic evolution, not hindered by fantasy, will follow paths we would never think of, and get to places we did not know existed.
That is probably why memetic evolution is not afraid to borrow from genetic evolution.

To summarize my question to ID proponents.
Before we go looking for design in evolution, should we not first be looking for evolution in design?

 

[David Bailey]

I dislike the term ID because it suggests Superman, someone like ourselves but much smarter, mind at large that's settled for engineering programmes as a specialist discipline. I think God is more subtle than the geek ID suggests, but can see why irreducible complexity gets the right people's pants on fire.

Agreed, and I don't really imagine Yaweh as a biochemical nerd! I think the intelligence would be more like Rupert Sheldrake's morphic fields, which as far as I can see, have to be intelligent!

There are a lot of assumptions in ID, the major one that evolution had a predetermined end-point in mind.

That just isn't true. The crucial point is that irreducibly complex systems, are systems that can't really do anything useful with parts missing. This is the crucial point - evolution by natural selection needs to work one step at a time, and for each step to provide an advantage.

I have no idea whether the graphics and voiceover authentically reflect the revolution that's implied, but I know for certain the responses to it are not driven by a studied unpicking of the theory, but a desire to lash out at the implications with any tool at hand.

I think the point is that the other side in this debate simply claimed that a small part of the flagellum was used for something else. However,

1) Every part would need to be useful in some way in order to get created by NS.

2) Apparently the simpler device that could be made from some parts of the flagellum, came on the scene after the flagellum, not before.

There are a slew of books coming out from almost mainstream biologists questioning Darwinian evolution. On the face of it, they want to put some other materialist mechanism in its place, but I have a suspicion that all materialist evolutionary mechanisms probably degenerate into NS if you look hard enough! The one possible exception might be epi-genetics, because it enables offspring to inherit some adaptions made by the parent - e.g. to shortage of food. However, in the standard scheme the epi-genetic annotations of the DNA ultimately drop off.

David

 

[gabriel]

Agreed, and I don't really imagine Yaweh as a biochemical nerd! I think the intelligence would be more like Rupert Sheldrake's morphic fields, which as far as I can see, have to be intelligent!

I gave the film my full attention, my concern was the graphics made the bacterium look like a machine and labelled the parts stator, propeller and so on. I've no reason to doubt the validity of the comparison, and I got that a system can be sophisticated and indivisible. It's the design aspect that's coy, with the earnestness the term implies. I prefer created and not just because it makes some people self ignite.

My unsophisticated doubts about Darwinism come from the oft stated claim that given enough time and biological variables, an elephant, a human and a fruit fly are inevitable. I just don't think they are. I don't think throwing a thousand dice for a hundred, a hundred thousand, or a billion years will see every one come up six (I'll ignore infinity as its beyond my imagination). And some of the claims for nature's betting shop make the diceman seem a dead cert. I mean there's no test for such astronomical coincidence, even running super computers at lightning speed don't match those odds. Yet the claim is repeated unproblematically so the rest of the story fits. I think mind of a subtle and embedded kind is more likely than the Darwinian crap shoot.

 

[Silence]

Before we go looking for design in evolution, should we not first be looking for evolution in design?

I haven't studied this, but what struck me about the video is the irreducible complexity argument.

I would much prefer to analyze the supposed problem this presents for evolution via random mutation/natural selection first.

Let's leave God, religion, dogma, bias, out of it. Is there a sufficient scientific explanation for the flagella through Darwinian evolution? If not, what is the implication?

 

[malf]

I haven't studied this, but what struck me about the video is the irreducible complexity argument.

I would much prefer to analyze the supposed problem this presents for evolution via random mutation/natural selection first.

Let's leave God, religion, dogma, bias, out of it. Is there a sufficient scientific explanation for the flagella through Darwinian evolution? If not, what is the implication?

https://www.google.co.nz/amp/s/www....cterial-flagellum-is-irreducibly-complex/amp/

 

[Bart V]

I think the point is that the other side in this debate simply claimed that a small part of the flagellum was used for something else. However,

1) Every part would need to be useful in some way in order to get created by NS.

Which, i believe is plausibly shown to be so

2) Apparently the simpler device that could be made from some parts of the flagellum, came on the scene after the flagellum, not before.

From wiki:

Dembski has argued that phylogenetically, the TTSS is found in a narrow range of bacteria which makes it seem to him to be a late innovation, whereas flagella are widespread throughout many bacterial groups, and he argues that it was an early innovation.[83][84] Against Dembski's argument, different flagella use completely different mechanisms, and publications show a plausible path in which bacterial flagella could have evolved from a secretion system.[85]

Besides that, to me the concept of irreducible complexity has a fatal logical/philosophical problem, it is based on a lack of knowledge, and therefore becomes an argument from ignorance, or a "design of the gaps" argument.

If we take the flagellum, we seem to be able to give a reasonable explanation for every step in it's evolution, and the functions these intermediate steps fulfilled, despite what the Discoverites may say.

But we do not, and can not, know everything. So it is conceivable that at some time, someone will find a molecular biological process that is both complex, and not fully explained with current knowledge.

Does irreducible complexity then suddenly become viable again?, what if we find a possible explanation for half of the process? Is irreducible complexity then suddenly half possible?
A bit later we find another part of the puzzle, irreducible complexity is only 25% of a concept?

So if the viability of this concept lives in the gaps of our scientific understanding, it can only get even less viable as science progresses.

 

[gabriel]

I haven't studied this, but what struck me about the video is the irreducible complexity argument.

I would much prefer to analyze the supposed problem this presents for evolution via random mutation/natural selection first.

Let's leave God, religion, dogma, bias, out of it. Is there a sufficient scientific explanation for the flagella through Darwinian evolution? If not, what is the implication?

The argument suggests we wouldn't know how to distinguish design from non-design. If that's true, we wouldn't be able to recognise anything, and certainly would not be able to attribute something to natural selection. If you adopt the same approach to language there should be millions of variation of not only spoken language, but sonic and written variation. Human language isn't that diverse. If you adopt the same approach to Darwinism, memes might get as far a primitive jelly fish as a genetic constant, but why they should leave the sea, light fire and write poetry?

It seems you have to be a fundamentalist believer in the absence of mind as an active agent for the rest to make sense. And as you're using a mind that shows none of its working out as it goes along to get to that conclusion, the denial of recondite motivation is too presumptuous.

 

[Bart V]

I haven't studied this, but what struck me about the video is the irreducible complexity argument.

I would much prefer to analyze the supposed problem this presents for evolution via random mutation/natural selection first.

What problem? every form of complexity is reducible to it's parts. What can be missing, is the explanation for how we got to these parts.
For irreducible complexity to make sense, it does not only have to show that an explanation is impossible at this moment, but it also has to show that any potential explanation through evolution is not possible.

Let's leave God, religion, dogma, bias, out of it.

That horse has bolted, the video is a product of the Discovery Institute, a dogmatic, religious, very biased organization that has literally vowed to replace science with religion.

Is there a sufficient scientific explanation for the flagella through Darwinian evolution?

Yes, but that is the wrong question, the burden of evidence is on those who claim something like irreducible complexity is actually possible.
Even Behe had to admit that irreducible complexity is not a scientific concept

While testifying during the 2005 Kitzmiller v. Dover Area School District trial, Behe conceded that there are no peer-reviewed papers supporting his claims that complex molecular systems, like the bacterial flagellum, the blood-clotting cascade, and the immune system, were intelligently designed nor are there any peer-reviewed articles supporting his argument that certain complex molecular structures are "irreducibly complex."[111]

 

[David Bailey]

I haven't studied this, but what struck me about the video is the irreducible complexity argument.

I would much prefer to analyze the supposed problem this presents for evolution via random mutation/natural selection first.

Yes - I think this is key to the modern ID argument .I mean, if you went to the moon and came across a cache of components for making an alien spacecraft, you would obviously know that these had been made and collected by an intelligent being, or perhaps some sort of robot which had itself been designed by an intelligent being.

The argument behind natural selection relies on there being a chain of creatures, A, B, C, D, E, F...... where each is more 'fit' than its predecessor, and where the last member has some new feature that the first did not.

Thus a bacterium with a flagellum is presumably going to do better than one without a flagellum. The problem is those intermediate states, representing the acquisition of all the various parts of the flagellum motor. If you need all the parts to make anything useful, then there is no advantage in acquiring just one or two of them.

Not only that, but each individual part will require a whole string of DNA to specify it. The DNA will itself involve many micro-changes to create it, and at no point will there be any selective advantage to getting that DNA string right.

Finally remember that the flagellum is only one 'gadget' inside a cell - there are plenty more. Consider the mechanism that reads DNA and makes RNA, and the one that reads RNA three bases at a time and makes a protein.

The more I think about it, the evolution by natural selection theory became invalid as soon as the DNA code was discovered.

David

 

[nbtruthman]

Which, i believe is plausibly shown to be so


From wiki:
......publications show a plausible path in which bacterial flagella could have evolved from a secretion system.[85]

Besides that, to me the concept of irreducible complexity has a fatal logical/philosophical problem, it is based on a lack of knowledge, and therefore becomes an argument from ignorance, or a "design of the gaps" argument.

If we take the flagellum, we seem to be able to give a reasonable explanation for every step in it's evolution, and the functions these intermediate steps fulfilled, despite what the Discoverites may say.

But we do not, and can not, know everything. So it is conceivable that at some time, someone will find a molecular biological process that is both complex, and not fully explained with current knowledge.

Does irreducible complexity then suddenly become viable again?, what if we find a possible explanation for half of the process? Is irreducible complexity then suddenly half possible?
A bit later we find another part of the puzzle, irreducible complexity is only 25% of a concept?

So if the viability of this concept lives in the gaps of our scientific understanding, it can only get even less viable as science progresses.

Michael Behe hasn't been debunked on the irreducible complexity of the bacterial flagellum, as claimed in the Wiki link to the Talkorigins website. This sort of just-so story scenario of flagellum evolution from the T3SS system just doesn't work. It reminds me of the elaborate fanciful stories now-discredited Freudian psychoanalysts were trained to come up with during analysis of a patient: it is mainly the informed imagination of the therapist.

The time sequence is wrong, for one thing. The T3SS system is the "injectisome" used by pathogenic parasitic bacteria to kill eukaryotic animal and plant cells. The Talkorigins scenario claims it was the ancestor of the flagellum, but it actually came much later. See the research paper "The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems", at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459982/.

This is explained here. This article contains detailed refutations of various Darwinist debunkings of the irreducible complexity of the bacterial flagellum:

"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. 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 needs 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. As one paper observes:

Based on patchy taxonomic distribution of the T3SS compared to that of the flagellum, widespread in bacterial phyla, previous phylogenetic analyses proposed that T3SS derived from a flagellar ancestor and spread through lateral gene transfers. (Sophie S. Abby and Eduardo P.C. Rocha, “An Evolutionary Analysis of the Type III Secretion System” (2012).)

Likewise, New Scientist reported:

"One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later,” says biochemist Howard Ochman at the University of Arizona in Tucson."​

The professional received opinion is that the results of phylogenetic analysis are that the T3SS probably came from the flagellar system, not the reverse: "The broad distribution of flagella across all bacterial clades and the much more limited distribution of T3SS favours the evolutionary derivation of the T3SS from the flagellar system (Hueck, 1998; Troisfontaines and Cornelis, 2005, Vangijsegem et al., 1995)." From the textbook Plant Pathogenic Bacteria: Genomics and Molecular Biology, edited by Robert W. Jackson.

And that Talkorigins claimed scenario is based on a sadly oversimplified model of the actual bacterial flagellar system. In particular it doesn't even try to address one of its most complex subsystems (which is itself irreducibly complex) - the very complicated machine that self-assembles the flagellar apparatus. An even more detailed refutation of the Talkorigins sort of debunking is here:

"The synthesis of the bacterial flagellum requires the orchestrated expression of more than 60 gene products. Its biosynthesis within the cell is orchestrated by genes which are organised into a tightly ordered cascade in which expression of one gene at a given level requires the prior expression of another gene at a higher level."​

 

[David Bailey]

Nbtruthman,

Given what you have written, do you think there is any possibility of finding a materialist explanation for evolution, as the group known as "The Third Way" seem to think:

http://www.thethirdwayofevolution.com/

It seems to me that arguments regarding irreducible complexity are very general, and therefore very interesting.

David

 

[nbtruthman]

Nbtruthman,

Given what you have written, do you think there is any possibility of finding a materialist explanation for evolution, as the group known as "The Third Way" seem to think:

http://www.thethirdwayofevolution.com/

It seems to me that arguments regarding irreducible complexity are very general, and therefore very interesting.

David

At this point, I don't think so. It seems to me the "Third Way" credo merely expands the number of reductive materialist ways that genetic variation can occur; they are all mechanisms that still result in genetic changes that are mostly random with respect to fitness. Suggestions that the intracellular machinery incorporates mechanisms that "purposefully" modify parts of the genome in just the right ways needed in response to particular stresses, etc. just push the problem down the road a little. Then it has to be explained how such what must be intricate mechanisms originally came about, and so on.

From the linked website:

"Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications.

.....................................

The DNA record does not support the assertion that small random mutations are the main source of new and useful variations. We now know that the many different processes of variation involve well regulated cell action on DNA molecules.

Genomes merge, shrink and grow, acquire new DNA components, and modify their structures by well-documented cellular and biochemical processes."​

I have found one unfortunately to me ultimately unconvincing approach to, rather than throwing it out altogether (which seems untenable), instead expanding the understanding of neo-Darwinistic RM + NS evolution. This is Federico Faggin's wide-ranging speculation about the nature and role of consciousness in the universe, in particular his speculation about the need for participation of consciousness in furnishing the genetic variations of a basically Darwinistic process, at http://www.fagginfoundation.org/articles-2/consciousness-and-matter-co-evolve/ :

"However, if the pool of variations that need to be selected contains a much higher percentage of potentially successful variations, then the selection process can succeed in a far shorter time than what’s needed for purely random variations. This concentration of potentially successful variations can be achieved only if such variations are due to choices based on the understanding, or self-knowing, achieved by the co-evolving consciousness. Only in this way is it possible to climb the probability mountain to the hugely improbable peaks that we observe in nature, within a time frame commensurate with the time scale of environmental changes that require adaptation."​

He doesn't try to explain how "co-evolving consciousness" designs and implants such purposeful genetic changes, but I do think that he at least points in the right direction. Of course this concept is decidedly a violation of reductionist materialist taboos and would be rejected by most scientists.

 

[Baccarat]

[Besides that, to me the concept of irreducible complexity has a fatal logical/philosophical problem, it is based on a lack of knowledge, and therefore becomes an argument from ignorance, or a "design of the gaps" argument./QUOTE]

The irony evolution, big band are arguments from ignorance and "designs of the gaps"

 

[David Bailey]

At this point, I don't think so. It seems to me the "Third Way" credo merely expands the number of reductive materialist ways that genetic variation can occur; they are all mechanisms that still result in genetic changes that are mostly random with respect to fitness. Suggestions that the intracellular machinery incorporates mechanisms that "purposefully" modify parts of the genome in just the right ways needed in response to particular stresses, etc. just push the problem down the road a little. Then it has to be explained how such what must be intricate mechanisms originally came about, and so on.

This is my feeling too - the extra complexity makes combinatorial arguments a lot less easy to make, but there is no reason to expect the result to provide a shortcut to fitness. It may just supply endless fuel for hand waiving!

Even epi-genetics, doesn't seem to have much creative power - I mean that tags that get put on chromosomes operate at the level of whole genes, or longer stretches of DNA, so they don't really help to explain how it evolves!

"However, if the pool of variations that need to be selected contains a much higher percentage of potentially successful variations, then the selection process can succeed in a far shorter time than what’s needed for purely random variations. This concentration of potentially successful variations can be achieved only if such variations are due to choices based on the understanding, or self-knowing, achieved by the co-evolving consciousness. Only in this way is it possible to climb the probability mountain to the hugely improbable peaks that we observe in nature, within a time frame commensurate with the time scale of environmental changes that require adaptation."

Does he explain, even in outline, how those choices could be made? I mean, given that changes in the structure of DNA often result in different folding of the resulting protein, I doubt if the best protein chemists would do well at this job!

David

 

[nbtruthman]

Does he explain, even in outline, how those choices could be made? I mean, given that changes in the structure of DNA often result in different folding of the resulting protein, I doubt if the best protein chemists would do well at this job!

David

Not even in outline. It is evident that generating the precise and intricately designed DNA changes necessary to achieve particular adaptive changes to body structure and organismal development, or even just particular different adaptive protein structures like enzymes would require a very powerful focused sentient superintelligence. Faggin just vaguely envisions a proto-consciousness slowly developing self-awareness through some sort of undefined pseudo-Darwinian process during which this proto-consciousness slowly creates and embodies into matter. All quite lyrically and elegantly described, but too vague in the details to get much of a handle on it.

 

[nbtruthman]

Besides that, to me the concept of irreducible complexity has a fatal logical/philosophical problem, it is based on a lack of knowledge, and therefore becomes an argument from ignorance, or a "design of the gaps" argument./QUOTE]

The irony evolution, big band are arguments from ignorance and "designs of the gaps"

It's a little complicated. Irreducible complexity is not fundamentally based on a negative, namely that there is no evidence for a naturalistic pathway (even though in fact no evidence, no plausible pathway involving a long series of intermediate forms each of which providentially had a certain alternate function, has been found in cases like the bacterial flagellum, despite much theorizing by Darwinists). Actually most theorizing has been restricted to handwaving, sequence similarities, etc. Anyway, rather than an argument from ignorance, it makes a positive claim, which can in principle be falsified, that is based on (a) gene knockouts, (b) reverse engineering, (c) examining homologous systems, and (d) sequencing the genome of the biochemical structure.

From Darwin's Doubt, Stephen Meyer:

"...the argument takes the following form:​

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and bodyparts, and even of animals and plants, aka moths and flowers, for example."​

From Michael Behe's article:

"....scientific reviewers have objected that an appeal to intelligent design is tantamount to “giving up.” For example, in the Forward Emory University evolutionary biologist Marc Lipsitch remarks:

"Behe] correctly suggests that a complete theory of evolution would include an account of how the intricate chemical systems inside our bodies arose (or might have arisen) from inanimate molecules, one step at a time. Mr. Behe’s question is a fair one, but instead of suggesting a series of experiments that could address the question, he throws up his hands. (Lipsitch 1996)"
​

Unfortunately, the point is made with circular logic: it depends on the presupposition that life is not designed, which is the point at issue. If life is not designed then, yes, a theory of intelligent design is ultimately a blind alley (if not quite “giving up”). However, if aspects of life are indeed designed, then the search for the putative unintelligent mechanisms that built them is the blind alley. But how do we decide ahead of time which is correct?"

We can’t decide the correct answer ahead of time. Science can only follow the data where they lead, as they become available."
​

Also, a logician and philosopher weighs in: "In some circumstances it can be safely assumed that if a certain event had occurred, evidence of it could be discovered by qualified investigators. In such circumstances it is perfectly reasonable to take the absence of proof of its occurrence as positive proof of its non-occurrence." (Copi 1953, Introduction to logic, Macmillan: New York).

Comment: Where has the data led, in this case? No plausible evidence of the supposed train of intermediates either theoretical or actual despite much looking and theorizing, so irreducible complexity becomes more and more certain.