Darwin Unhinged: The Bugs in Evolution

Neo-Darwinians claim to debunk the extreme unlikelihood of the gradualistic evolution of the irreducibly complex bacterial flagellum through Darwinian processes, through inventing a scenario in which the flagellum is imagined to have been derived from the T3SS system. 

The T3SS system is the "injectisome" used by pathogenic parasitic bacteria to kill eukaryotic animal and plant cells. This 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/. There is certainly no reason not to suspect that a simplified system may have arisen from a much more complicated system  - such a process involves a drastic reduction in complex specified information, not a drastic increase of it.    

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 claimed T3SS scenario is based on a sadly oversimplified model of the actual bacterial flagellar system. It trivializes the sheer complexity and sophistication of the flagellar system — its functional apparatus, state-of-the-art design motif, and assembly apparatus. 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 flagellum. An even more detailed refutation of this 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."


Michael Behe on irreducible complexity:
  
"One needs to relax Darwin’s criterion from this (his own words): “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” to something like this:

If a complex organ exists which seems very unlikely to have been produced by numerous, successive, slight modifications, and if no experiments have shown that it or comparable structures can be so produced, then maybe we are barking up the wrong tree."

The Darwinist critics need to remember that mere remote possibility is not an adequate basis for asserting scientific plausibility. They can’t claim to have explained the evolutionary origin of irreducible complexity when their “explanations” are in fact little more than wishful thinking and wild speculation.

How about a Biblical refresher course? The creationist idea originates from the Biblical story of Genesis. The Bible is an article of faith not a science book. Now that this remedial lesson is over, shame on you for not acknowledging the creationist position is the epitome of wishful thinking.

How about a Biblical refresher course? The creationist idea originates from the Biblical story of Genesis. The Bible is an article of faith not a science book. Now that this remedial lesson is over, shame on you for not acknowledging the creationist position is the epitome of wishful thinking.

Oh really, if that is the best, most considered contribution to this discussion you can come up with then you really should consider stowing your keyboard and taking a break. I doubt that anyone with half a brain, skeptic or proponent, would think that comment appropriate.

How about a Biblical refresher course? The creationist idea originates from the Biblical story of Genesis. The Bible is an article of faith not a science book. Now that this remedial lesson is over, shame on you for not acknowledging the creationist position is the epitome of wishful thinking.

Is this the best you can do? Rather than engaging with the arguments regarding irreducible complexity, you choose to merely attack me as a Creationist, which I am obviously not. Where's the Ignore button.

[Laird]

A longtime ago perhaps back in the 90's I watched Sheldrake do a demonstration using pigeons and a movable pigeon coop. The assumption of course was the pigeons form a morphogenic bond with it.  The experiment took place on what appeared to be a hillside with a wide river below. In the first demo he let the pigeons stay at  the coop overnight. In the morning he loaded up the pigeons and move them to a distant location and released them. Sure as water is wet they returned to the coop. He did this several more times each time though he moved the coop. Eventually he moved it onto the river. No matter how far he moved it the pigeons flew to it. On the last move Sheldrake moved the coop behind a very large bluff which put the coop out of sight. Can you guess what happened? If you guessed they flew to it you would be wrong. What Sheldrake demonstrated is those pigeons were using sight to find the coop and we hen the coop was out of sight they were lost. Over the years I've attempted to find that demonstration without luck.

The best I've found is an excerpt from a roundtable discussion in 1993 (? An alternative video lists the date as 1992). Rupert describes his experiments to that point at about 7:37 (link goes to that location): https://www.youtube.com/watch?v=MU4O_luJnEU&t=7m37s

He goes on to say that the experiments were at that time incomplete. I'm not sure whether he later completed them, and that's what you saw, Steve, but based on what he describes in that talk, he hadn't yet encountered any failures.

Huh. So, really, there's no such thing as homing pigeons? Fascinating.

That dumb comment was the unfortunate result of posting after a few too many "cleansing ales". Apologies - I completely missed the point.

Oh really, if that is the best, most considered contribution to this discussion you can come up with then you really should consider stowing your keyboard and taking a break. I doubt that anyone with half a brain, skeptic or proponent, would think that comment appropriate.

Is this the best you can do? Rather than engaging with the arguments regarding irreducible complexity, you choose to merely attack me as a Creationist, which I am obviously not. Where's the Ignore button.

I could post numerous counter arguments why specific creationists are wrong but what good would that do? You just find something else. Then when that is rebutted you'd find something else and so on and so on. I chose to get to the heart of your opposition to evolutionary theory.  Whether you agree or not, both of you hold to a faith based position.

The best I've found is an excerpt from a roundtable discussion in 1993 (? An alternative video lists the date as 1992). Rupert describes his experiments to that point at about 7:37 (link goes to that location): https://www.youtube.com/watch?v=MU4O_luJnEU&t=7m37s

He goes on to say that the experiments were at that time incomplete. I'm not sure whether he later completed them, and that's what you saw, Steve, but based on what he describes in that talk, he hadn't yet encountered any failures.


That dumb comment was the unfortunate result of posting after a few too many "cleansing ales". Apologies - I completely missed the point.

I'm glad you found that vid; I've not seen it in a longtime. Well, he did fail. Right now I'm recalling all of the dead deer laying on the side of the road. Why do we need to warn very yound children not to touch the hot stove. The point I'm  making is if morphogenic fields are a real thing then both the deer and children should to look before choosing the road and children should know not to touch the hot stove. How many examples can you think of where moronic resonance should assert itself but does not? Sheldrake's thoughts. https://www.sheldrake.org/research/morph...troduction

P.S. We're good.

I could post numerous counter arguments why specific creationists are wrong but what good would that do? You just find something else. Then when that is rebutted you'd find something else and so on and so on. I chose to get to the heart of your opposition to evolutionary theory.  Whether you agree or not, both of you hold to a faith based position.

Do you understand the term straw man? 

And I very much doubt that you have a clue about evolutionary theory. You are so clearly out of your depth that you need to resort to creationist jibes.

This thread has been a total joy to read - thank you to everybody participating for your lucid and fascinating contributions.

As Chris admits of himself, I, too, am very ignorant on all of this, although from what I've read/watched I am very skeptical that neo-Darwinism can adequately explain (the evolution of) life, and tend towards believing in the need for "intelligent design" in some form - and not only because of the philosophical argument I affirmed earlier related to that of nbtruthman (based on the implications of interactionist dualism), but also because of what (little) I understand of the implausibility arguments against neo-Darwinism.

All of that said, there seems to me to be an issue that hasn't been addressed very much in this thread: the extent to which the biology of living organisms is subject to genetic determinism. It seems to me that to a large extent, most of the discussion in this thread has been predicated on some sort of genetic determinism. I'm interested then to know what folks think of ideas such as Rupert Sheldrake's "morphic resonance", or, generally, ideas along the lines that whilst genes provide helpful "recipes" for building proteins, their role in the development of a fully-functional adult being from conception is far less prominent, if relevant at all.

I have had thoughts along these lines. I looked into it a little.

The human genome consists of 20,000-25,000 protein-coding genes and contains a total of about 2.9 billion DNA base pairs. Molecular biologists have found that most of the genome DNA doesn't code for proteins, it apparently codes for a lot of complicated gene regulation mechanisms that are involved in developmental pathways. A study found that the figure was 98% for the mouse genome. This seems reasonable, since multicellular structural complexity and developmental complexity must require much more encoding data than the amount required to encode all the different proteins.

But there seems to be some doubt that even the total of the DNA base pairs are the source of all the actual information building bodies and brains. 

"Organismal complexity is thus the result of much more than the sheer number of nucleotides that compose a genome and the number of coding sequences in that genome. Not only may one coding sequence encode a large number of separate protein products via alternative splicing, but many genomes are also rich with noncoding RNA sequences that work to coordinate gene expression. When one combines these elements with other regulatory elements, such as enhancers and promoters, as well as with potential sequences that remain uncharacterized, it becomes clear that while size is one component of organismal complexity, its contribution to that complexity is small." (from https://www.nature.com/scitable/topicpag...lexity-437 )

Of course conservative mainstream opinion printed in textbooks claims that all that is required is the 2.9 billion-3 billion base pairs, but the actual scientists conducting cutting edge research seem to disagree. My impression is that there is a realization that a lot of the structural and presumably behavioral complexity especially of large complicated animals like humans is encoded in extra-DNA structures that have only partially been uncovered. All the developmental pathways and how they are encoded are not understood. 

One estimate calculates that the human genome of approximately 3 billion base pairs is equivalent in information to 1.5 Gigabytes, about 2 CDs worth of data. (from https://bitesizebio.com/8378/how-much-in...an-genome/) I have not found any estimate of the total information equivalent for a human body, but just the incredibly complex brain's memory capacity has been estimated to be equivalent to four terabytes. The DNA doesn't seem nearly enough. 

The actual huge amount of data must be encoded somewhere.  Extra-DNA structures seem to be heavily involved. J. Scott Turner has speculated that intra-and distributed cellular intelligence may be a function of the cell's membranes, microtubule organizing centers and cytoskeletons. Others have speculated that maybe these structures encode much of the huge data base required to build the body. There are Rupert Sheldrake's morphogenetic fields. But these ideas have a lot of problems. We just don't know.

[Laird]

Right now I'm recalling all of the dead deer laying on the side of the road. Why do we need to warn very yound children not to touch the hot stove. The point I'm  making is if morphogenic fields are a real thing then both the deer and children should to look before choosing the road and children should know not to touch the hot stove.

I'm not intimately familiar with Rupert's theory, having not read either of his books on it, but from what I understand, it doesn't anyway make the coarse claim that young children will have implicitly learnt via morphic resonance never to touch a hot stove, nor that deer will have implicitly learnt via morphic resonance never to remain on the road when there is oncoming traffic, but that, as time goes on, these learnt behaviours in both species will improve. I'm not sure that anybody has gathered data on either of these cases to test that prediction. And I doubt that anybody will. But there have been other tests of the general hypothesis of morphic resonance.

[Laird]

Thanks for your response, nbtruthman.

Molecular biologists have found that most of the genome DNA doesn't code for proteins, it apparently codes for a lot of complicated gene regulation mechanisms that are involved in developmental pathways.

Very interesting. I wasn't aware of this.

The actual huge amount of data must be encoded somewhere.  Extra-DNA structures seem to be heavily involved. J. Scott Turner has speculated that intra-and distributed cellular intelligence may be a function of the cell's membranes, microtubule organizing centers and cytoskeletons. Others have speculated that maybe these structures encode much of the huge data base required to build the body. There are Rupert Sheldrake's morphogenetic fields. But these ideas have a lot of problems. We just don't know.

OK, thanks, interesting again. I'd be curious to know though how these extra-DNA structures are passed on from generation to generation (other than morphogenetic fields, since those have their own explanation).