Darwin Unhinged: The Bugs in Evolution

I am uncertain about this. epi-genetics means that tags on DNA (methyl or acetyl groups) can be passed down to a child. These effects definitely seem to be real:
https://www.amazon.co.uk/dp/B00JFVOLZK/r...TF8&btkr=1
The problem is that ultimately these tags fall off, and no permanent genetic changes result - but maybe there is a way to make these changes permanent - even so they only affect the frequency of expression of the gene in question.

Good article:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207041/

~~ Paul

An irreducibly complex machine is a system which is composed of a number of interacting parts, where the removal of any one of the parts causes the system to cease functioning.

That is one of the definitions, an older one. Here are three more:

http://www.asa3.org/ASA/education/origins/ic-cr.htm

In particular, why define it as ceasing function rather than simply not having its original function? And why ignore the possibility of scaffolding (see video below)?

These systems exist in organisms. The origins of such systems in biology are very hard for Darwinian mechanisms to account for, especially for the separate complicated developmental pathways. The unevolvability of such systems by Darwinian mechanisms is a probability argument - it might be remotely possible, but only through various tenuous and speculative stories of indirect evolution involving things like cooption, opportune alternate functions of intermediaries, etc., which would have to be specified for each small step of the neo-Darwinistic evolution of the system for the story to work. In other words, wildly speculative and unfalsifiable scenarios. In most cases no detailed sequences have been proposed.

It's certainly difficult to account for if you think that an IC mechanism had absolutely no function until it was fully formed. But no one thinks this. The evolution of the eye is a good example. And the flagellum versus the Type III secretion system is a great example of reduced complexity having a different function.

Suppose for arguments sake that some irreducibly complex systems didn't evolve by long series of small steps via Darwinian mechanisms. This problem for Darwinian mechanisms is one of the underlying motivations for most of the various proposed neo-Lamarckian and other schemes going beyond neo-Darwinism. Then it must have been some sort of act or acts of intelligence of some sort (not specifying the form of that intelligence). From basic engineering design and implementation theory (as applied to living organisms), it seems to me that this process must necessarily have either explicitly or implicitly involved the three steps described, regardless of the form of the intelligence involved.

You're okay with this even though above you said "In other words, wildly speculative and unfalsifiable scenarios"?

~~ Paul

P.S. I call your attention to this video:

https://www.youtube.com/watch?v=BQJtV_YLuNE

 
An irreducibly complex machine is a system which is composed of a number of interacting parts, where the removal of any one of the parts causes the system to cease functioning. These systems exist in organisms. The origins of such systems in biology are very hard for Darwinian mechanisms to account for, especially for the separate complicated developmental pathways. The unevolvability of such systems by Darwinian mechanisms is a probability argument - it might be remotely possible, but only through various tenuous and speculative stories of indirect evolution involving things like cooption, opportune alternate functions of intermediaries, etc., which would have to be specified for each small step of the neo-Darwinistic evolution of the system for the story to work. In other words, wildly speculative and unfalsifiable scenarios. In most cases no detailed sequences have been proposed. This problem for Darwinian mechanisms is one of the underlying motivations for most of the various proposed neo-Lamarckian and other schemes going beyond neo-Darwinism. 

Suppose for arguments sake that some irreducibly complex systems didn't evolve by long series of small steps via Darwinian mechanisms. Then it must have been some sort of act or acts of intelligence of some sort (not specifying the form of that intelligence). From basic engineering design and implementation theory (as applied to living organisms), it seems to me that this process must necessarily have either explicitly or implicitly involved the three steps described, regardless of the form of the intelligence involved.  

The process must necessarily start with analysis of the engineering requirements - defining what is the problem, perhaps doing a tradeoff study of different envisioned possible structural solutions to the problem. This stage, at least, seems to require engineering insight, especially with irreducibly complex machines. Then going on to the implementation part, which in biology is a reverse mapping of the envisioned new structure (functional change requirements) back into the corresponding genetic changes. Then, finally, implementing the change by going on to the actual physical modification of the genes or other extra-DNA elements. That's the way engineering works.

Suppose  for arguments sake that some irreducibly complex systems didn't evolve by long series of small steps via Darwinian mechanisms. Then it must have been some sort of act or acts of intelligence of some sort (not specifying the form of that

Why should we suppose when to my knowledge no irreducible biological systems have ever been found?

Why should we suppose when to my knowledge no irreducible biological systems have ever been found?

This is exactly why, I'm glad you're here.
Thank you Steve 001. You made my day.

[Laird]

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.

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.

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.

Sheldrakes belief in morphogenic fields is at it's heart a philosophical position and as we have all seen not one philosopher ever empirically demonstrated a philosophical position to be absolutely true. My suggestion is if one wants the truth never use philosophy as a foundation from which to argue.

[Laird]

[The] pigeons were using sight to find the coop and we hen the coop was out of sight they were lost

Huh. So, really, there's no such thing as homing pigeons? Fascinating. (With apologies for the sarcasm, Steve - you're a big boy, you can handle it)

Sheldrakes belief in morphogenic fields is at it's heart a philosophical position

No, he has proposed falsifiable scientific tests of his hypothesis, some of which have been conducted and found not to falsify but rather to confirm his hypothesis.

Huh. So, really, there's no such thing as homing pigeons? Fascinating. (With apologies for the sarcasm, Steve - you're a big boy, you can handle it)



No, he has proposed falsifiable scientific tests of his hypothesis, some of which have been conducted and found not to falsify but rather to confirm his hypothesis.

Even though they were homing pidgeons they still were expected to find the coop not by sight but via the morphogenic field, they did not. He falsified his own idea with that one demonstration. 

 How do you know the truth when experiments both validate and falsify? Your position is belief is enough to know the truth. As with all beliefs it's ok to hold these ideas as personal truths, but that is as far as it should go. It goes to far when these ideas are claimed to be universal truth without evidence.

And the flagellum versus the Type III secretion system is a great example of reduced complexity having a different function.

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.