Evolution without accidents and also no intelligence?

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.

That sounds a lot more like what you hear from me, except my prose sucks.  You seem to think that their speech in reports of findings should be geared to the general public.  I , as a member of the public would love that.  Of course, their writing and vocabulary has to do with the conversations they have with academic colleagues.  And are using the technical terms that focus the conversation on repeatable results.

Please let me know what you think of my claim that the RM+NS debate is academically changed to the degree that it is no longer heated? 

Please let me see recent papers refuting the claims of Denis Nobel, Shapiro, C. Spadafora, Lynn Margulis and Barbara McClintock.  Who are the leading scientists on the subject.  Mind is not their subject.  Bio-function is.

  Barbara McClintock
The Nobel Prize in Physiology or Medicine 1983

Born: 16 June 1902, Hartford, CT, USA

Died: 2 September 1992, Huntington, NY, USA

Affiliation at the time of the award: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

Prize motivation: “for her discovery of mobile genetic elements” 

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.

Someone I work with tried to include an F# library suggested by ChatGPT...that doesn't exist...

That sounds a lot more like what you hear from me, except my prose sucks.  You seem to think that their speech in reports of findings should be geared to the general public.  I , as a member of the public would love that. 

Other scientists, such as Michael Behe, write clearly and their books are easy to read. Honestly, I think the TTW crowd don't want their ideas to be understood, because in truth I don't think they have anything to offer that does not boil down to RM+NS.

Possibly they know things that would be too controversial to repeat outside their circle

Don't worry Stephen, the TTW literature is meant to confuse,
[QUOTE]

RM+NS is a specific mechanism that once seemed a plausible driver of evolution. The problem is, it is extremely hard to conceive of a better alternative. If there were another mechanism consistent with materialism, I think conventional biology would have seized it long ago.

Epigenetics is at least interesting - the fact that DNA can be chemically modified - typically by adding methyl groups - that make the corresponding gene more or less likely to be transcribed and so as to produce the corresponding protein. This DNA can even be handed down to offspring, but the modification is only temporary as far as I understand it. Even if it can be made permanent, this is not a way to evolve a new gene to express a new function.

The core problem is, even if an organism were to make mutations to try to achieve some goal, how would it 'know' what to do?

I do agree with you that it would be interesting to read a clear description of how they see evolution working!

I'm glad we are discussing Intelligent Design because unless there is a much more effective alternative to RM+NS there is a gaping hole in our understanding of our place in the world!

David

That sounds a lot more like what you hear from me, except my prose sucks.  You seem to think that their speech in reports of findings should be geared to the general public.  I , as a member of the public would love that.  Of course, their writing and vocabulary has to do with the conversations they have with academic colleagues.  And are using the technical terms that focus the conversation on repeatable results.

Please let me know what you think of my claim that the RM+NS debate is academically changed to the degree that it is no longer heated? 

Please let me see recent papers refuting the claims of Denis Nobel, Shapiro, C. Spadafora, Lynn Margulis and Barbara McClintock.  Who are the leading scientists on the subject.  Mind is not their subject.  Bio-function is.

An illuminating article in Evolution News by Casey Luskin effectively and comprehensively took apart James Shapiro's ideas (as of 2011) re. a natural self-generated and non-ID alternative to Darwinistic RM + NS, at https://evolutionnews.org/2011/08/james_...ion_a_vie/ . The article is a review of Shapiro's book, "Evolution: A View from the 21st Century".  

The following quote is long but worthwhile, and I think Luskin's analysis demolishes Shapiro's concepts, at least as they had developed by that time. Question 3 is by far the most telling and important one.

"There are three questions that Shapiro’s model must face:

(1) Does Shapiro’s model really reject Darwinian evolution and random variation?
(2) Can we explain the origin of these “self-modification” mechanisms?
(3) Can these “self-modification” mechanisms explain observed biological complexity?
Let’s briefly look at these questions.

Question 1: Does Shapiro’s Model Completely Reject Darwinian Evolution and Random Variation?
According to Shapiro, since certain environmental stresses or triggers can induce mutations in organisms, mutations are not “random.” By ‘not random,’ he means that he disagrees with the classical Darwinian view that variation arises blindly, without regard to the needs of the organism. I see two problems:

First, in an important sense, even within Shapiro’s model some of these mechanisms of change still have a random element. Some of his examples show mutations being induced at non-random times. While these mutations are not completely random, in an important sense, their effects may still be “random” with respect to the needs of the organism. For example, in the transposon example above, bacteria increase the rate of transposon-mediated events in response to stress. As Shapiro notes, some transposons have targets that are “virtually ubiquitous throughout the genome” (p. 48). In another case he notes what he calls “indiscriminate LINE-mediated integration” (p. 52). The hope is that some will do something helpful and stick. But in an important sense this is still very much like a trial and error process of Darwinian selection, where not all change is adaptive. This becomes very clear when he writes that under his model:

The role of selection is to eliminate evolutionary novelties that prove to be non-functional and interfere with adaptive needs. (p.144)

While he notes that many of the mechanisms he cites provide a higher “probability of success” (p. 130) than mere point mutations, we’re still dealing with a trial and error process where variation arises, in an important sense, randomly without regard to the needs of the organism. The hope is that some of those changes will stick.

Some of the mechanisms he cites are like having monkeys sitting next to typewriters — they aren’t always typing but they are on standby, ready to start typing at a moment’s notice. The typewriting monkeys might be nonrandomly “switched on” at the right moment when you might need a letter, but there’s no guarantee that their random banging on the keyboard will produce a useful letter.

Second, though Shapiro doesn’t directly address this specific question, his model would seem to still require conventional random mutation and natural selection to explain how the “capacity to change” itself arose in the first place.

Shapiro argues convincingly that “the capacity to change is itself adaptive,” and thus the capacity to change is a selectable trait. But his argument implies that at some level, Darwinian evolution and random change must be invoked to explain the origin of the capacity to change. After all, he cannot invoke mechanisms of directed change to explain how those same mechanisms of directed change arose; those mechanisms could not have produced themselves, and had to come from something else. Under Shapiro’s model, at various points the capacity to change must have arisen by chance, and was preserved by natural selection. In Shapiro’s undesigned world, there is no way to ultimately divorce the evolutionary process from randomness, because at some point, “the capacity to change” arose randomly and blindly, without regard to the needs of the organism.

Here, Shapiro would seem to be confronted with a difficulty: He doesn’t want to rely on blind and random mechanisms for evolution because biological systems simply appear too complex to have arisen in such a fashion. However, if he doesn’t rely on blind and random mechanisms for at some point along the process, then he’s forced into the realm of intelligent design — which is exactly where he doesn’t want to go. In a sense, Shapiro’s thesis is no different from neo-Darwinism because he just pushes the selected trait back to the “capacity to change” rather than the “change itself.”

Question 2: Can we explain the origin of these “self-modification” mechanisms?
If the final complex “goal-directed” (p. 138) systems require non-random “genetic engineering” processes to form, does it make sense to believe that the processes which created those systems have a completely random and undirected origin?

Shapiro is very cognizant of this question, for he writes:

"The phrase natural genetic engineering has proven troublesome to many scientists because they believe it supports the Intelligent Design argument. As one Nobel Laureate put it after a seminar, “If there is natural genetic engineering, that means there has to be an engineer.” This empirically derived concept seems to many scientists to violate the principles of naturalism that exclude any role for a guiding intelligence outside of nature." (p. 134)

Clearly the specter of intelligent design is haunting Shapiro as he makes his case to other scientists. But his explanation for why ID isn’t needed is to simply assert that natural genetic engineering principles would provide a “distinct evolutionary advantage.” (p. 135) Here, Shapiro ignores his own advice.

While the capacity to change might be advantageous and “selectable,” as Shapiro reminds us at the opening of his book, that’s not enough to explain how something arose. Thus, as we saw above, Shapiro emphasizes that selection can only preserve the novelty provided by mutations. But Shapiro does not even attempt to explain how complex capacities to change — which he claims amount to a system of “cognitive networks and cellular functions for self-modification” could be produced by random mutations for selection to preserve.

It’s a truism to observe that there were no “natural genetic engineering” mechanisms in existence before “natural genetic engineering” mechanisms evolved. Thus, presumably he must rely upon more primitive and less dramatic Darwinian evolutionary mechanisms to explain how these mechanisms gained the capability to do things like “insert cis-regulatory signals and swap exons … simultaneously on more than one genetic locus encoding functionally related proteins.” (p. 135) Sure, the ability to do that precisely might sometimes provide a selective advantage, but Shapiro hasn’t established that the ability to effect such complex natural genetic engineering could evolve through step-by-step blind and unguided evolution.

Shapiro’s model goes partway in recognizing that biological systems operate in a “goal-oriented” (p. 138)–even “teleological” (p. 137) manner. Ultimately, however, Shapiro cannot escape from one vexing problem: goal-oriented processes don’t arise from random processes; goal-directed biological systems would seem to require a goal directed cause from the very start.

Question 3: Can these “self-modification” mechanisms explain observed biological complexity?
Shapiro’s excellent summaries of the mechanisms of non-random genetic and epigenetic biological change are entirely consistent with an ID view. For example, consider this claim from Shapiro:

"It is generally necessary to integrate the expression of different regions of the genome in a coordinated fashion to execute a particular phenotypic trait. This regulatory integration is often achieved by reusing the same binding sites at multiple locations." (p. 31)

But how these binding sites come to be reused in multiple locations?

In Shapiro’s materialist view, the very existence of these coordinated systems is taken as evidence that transcriptional regulatory circuitry “can be formed and taken apart easily.” But if multiple different regions of the genome must be coordinated to produce such new traits, doesn’t that imply it’s actually quite complicate to form such features? Are the “self-modification” mechanisms Shapiro cites always up to the tasks he assigns them, or is he taking their mere existence as evidence that they must be able to build observed features?

Let me put the question another way: Shapiro prefers to describe the evolutionary process as “engineering” rather than “tinkering,” but is that because he has observed and demonstrated material mechanisms that truly can “engineer” the genome, or because he has observed features in biology that require engineering to arise?

After all, many of the “natural genetic engineering rearrangements” he cites entail observations like “LINE-1 elements associated with deletions in human genome variation” or “Many inversions associated with L1 repeats.” (pp. 122-123) No doubt those are accurate observations, but is that evidence that some complex mutational mechanism can produce (and has produced) new traits by coordinating multiple regions of the genome?

Shapiro’s ideas are certainly interesting, but his claim that these complex mutational mechanisms like “horizontal transfers and the movement of transposable elements through chromosome rearrangements [and] whole genome duplications and cell fusions” (p. 128) can spontaneously produce radically complex traits is not conclusively established. Much here is speculative, and much is inadequate: “domain swapping” (p. 130) cannot explain the origin of domains in the first place."

Some of the mechanisms he cites are like having monkeys sitting next to typewriters — they aren’t always typing but they are on standby, ready to start typing at a moment’s notice. The typewriting monkeys might be nonrandomly “switched on” at the right moment when you might need a letter, but there’s no guarantee that their random banging on the keyboard will produce a useful letter.

That is a lovely quote!

Your piece also illustrates (for any who need persuasion) that Intelligent Design science is not done by invoking the Bible, it is done by analysing the alternatives that might avoid the need for design. Also, nothing in that analysis requires that the designer be Yahweh, or that the process was done by a supreme being.

David

Thanks for opening up a bit, because it is hard to respond well to short quips.


I suppose the real value of ID is to shake up the thinking process. Generations of kids have been brought up on Darwin, DNA, and natural selection. If this explanation is wrong, it is time people knew about it!

Whether the true explanation is as you suggest, or that some entities designed life on earth, is almost a secondary consideration, and the two concepts might even merge into one, since immaterial designers still need to impress their ideas into physical matter at some point.

OK first just a quick review of what we are talking about. A modest protein consisting of a chain of 100 amino acid residues can have

20^100, or
12676506002282294014967032053760000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000

possibilities. For comparison, the number of protons in the universe has been estimated as

10^80, or

100000000000000000000000000000000000000000000000000000000000000000000000000000000

Protein space is absolutely VAST. Talking about genetic variants floating about in individual microbes doesn't really cut it, unless effective proteins are actually fairly common.

For RM+NS to find one of these things is basically absurd unless useful proteins are really quite common, even if we allow that some activity might exist when we get within one or two steps of the end product.

On top of that, nobody seems to discuss the fact that many important enzymes - such as the proteases - would be deadly to a cell unless additional control machinery was available. This means that natural selection would operate against the adoption of such a protein just when it had finally evolved!

….

David

While there's a vast universe of potential protein sequences, only a fraction leads to stable, functional proteins. Both experimental studies and theoretical insights affirm this notion. Given billions of years, the interplay of natural selection, incremental improvements and constraints on the possible stable sequences in protein space has shaped the evolution of the vast and intricate protein landscape we see in life today.

Given billions of years, the interplay of natural selection, incremental improvements and constraints on the possible stable sequences in protein space has shaped the evolution of the vast and intricate protein landscape we see in life today.

That's certainly the mainstream consensus thinking.  Massive sample size = anything can happen.

Yet, I think that's being challenged as has been talked about/linked in this thread.  It seems some are suggesting the sample size in question for life on earth is insufficient as an explanatory force.

That's certainly the mainstream consensus thinking.  Massive sample size = anything can happen.

Yet, I think that's being challenged as has been talked about/linked in this thread.  It seems some are suggesting the sample size in question for life on earth is insufficient as an explanatory force.

While it may seem implausible, attributing evolution to an intelligent creator isn't science—it's religion. Our intuition often fails to accurately represent the complexities of the physical world, as evidenced by concepts like Quantum Mechanics.

While there's a vast universe of potential protein sequences, only a fraction leads to stable, functional proteins. Both experimental studies and theoretical insights affirm this notion.

That is right, and the 'problem' is that there is no way of sequencing through the potentially useful proteins without ploughing through the junk. Using RM+NS for example, random changes are made to amino acid residues one at a time.

I'm not sure if we know of any other way to search this space.

Given billions of years, the interplay of natural selection, incremental improvements and constraints on the possible stable sequences in protein space has shaped the evolution of the vast and intricate protein landscape we see in life today.

That is sliding back into TTW-speak. The vast intricate protein landscape is part of what we see around us - sure - but that is basically the problem that we are trying to solve. I increasingly think it got here because of some sort of non-materialist intelligence. If the intelligence were materialist then it would once again assume what it is trying to explain.

TTW-speak is quite seductive because it is just vague enough to keep people interested, without delivering any definite answers.

David

While it may seem implausible, attributing evolution to an intelligent creator isn't science—it's religion. Our intuition often fails to accurately represent the complexities of the physical world, as evidenced by concepts like Quantum Mechanics.

First of all, you erect the usual straw man argument by presuming that ID is a religious movement, rather than what it really is, the scientific pursuit of powerful evidence that life on Earth has by and large been designed by some form of high intelligence, where the exact form or identit(ies) of these intelligent agents is deliberately not attempted to be investigated.

Second, what is really the religious movement here is reductionist materialist scientism - the religion of science, where practitioners have such a deep faith in "mind from muck" neo- or new synthesis Darwinism, that they closed-mindedly and complacently say "I don't care about your "evidence" - it just had to happen that way" when challenged by ID scientists with powerful arguments for the total inadequacy of Darwinism to explain many aspects and features of Life. 

I notice that you have not responded much to all the ID arguments so far presented in the thread.