https://www.quantamagazine.org/solution-evolutionary-math-and-just-so-stories-20180907/

"How much stock should we put in mathematical models of evolution that have not been validated by rigorous empirical data?

***

"Such models can stimulate discussion and further research and may eventually lead to a deeper understanding of the evolutionary process. But as nonspecialists who follow cutting-edge scientific research, how much stock should we put in mathematical models of evolution that have not been validated by rigorous empirical data? Here is a partial list of caveats worth applying to all evolutionary claims. I am sure that evolutionary biologists could add many more.

"The conclusions of purely theoretical models, whether qualitative or mathematical, should be treated as plausible and interesting speculations. Evolution is a contingent, historical process. That something could possibly happen does not mean that it did happen.

"Any attempt to generalize the model beyond its restricted domain must be carefully and skeptically examined. The conclusions may be true but may apply only in circumstances so unusual as to have had no historical importance in evolution.

"Conditions under which evolution took place should be shown to be effective in the “environment of evolutionary adaptation,” not under conditions as they are now. Environmental conditions change, and the contribution to fitness by a given trait or mutation will vary over time, as Mark Pearson commented.

"Our minds are naturally drawn toward simple single-cause explanations as we discussed in a previous Insights puzzle column. We should resist the lure of Occam’s razor in subjects as complex as evolutionary biology. Rather, every theoretical model should be treated as a plausible contributor to the actual evolutionary story, which is likely to involve the sum total of many diverse and sometimes contradictory scenarios. Empirical research in evolution should try to assess the degree to which each model contributes to the picture.

"Only rigorous empirical work that shows consistent and mutually supporting results in empirical fields such as paleontology, field biology, biochemistry and genetics can establish the true course of evolution.

"Finally, conclusions about the evolution of traits should apply universally to all or almost all members of a species. This is especially true in elucidating the evolution of human traits. If the traits or their mechanism of evolution are not found across most or all ethnic populations, they may be the results of culture rather than biology. It is worthwhile to try to find exceptions or opposite practices somewhere within the world’s diversity of cultures and figure out why the hypothesized pattern or mechanism was not successful.

***

“'Evolutionary stories like the grandmother hypothesis are easy to construct from mathematical models, but how well do they reflect reality?” Realist commented, “About as well as physics hypotheses constructed from mathematical models do.” I beg to differ. I think single-cause models have a far greater chance of succeeding in physics than in the complicated process of biological evolution. The “soft sciences” are soft because nonlinearity and multifactorial causation run rampant in them, far more so than in the hard sciences."

Comment: Evolution, as a science, is extremely soft. This cautionary article should be taken to heart. All math studies are soft theoretically as they start with some suppositions at the start in the arena of evolution, a process we have not observed and try to deduce from existing evidence which is at the end point of the process.

Tony: Comment: What I have always asserted: Variation within tightly controlled pre-defined constraints.

David: My point all along about bacteria. Algorithmic control and pre-programming fit exactly. Information running the show but no innate intelligence.

Note this entry about penicillin:

https://cosmosmagazine.com/chemistry/turbocharged-vancomycin-1000-times-more-powerful-t...

"Since the discovery of penicillin began the antibiotic revolution in 1928, we have lived in a golden age of relative safety from infection. But the bacteria are catching up: they are able to develop resistance to antibiotic drugs quicker than we are able to invent new medicines. The rise of drug-resistant bacteria is one of the greatest threats to public health in the 21st century, according to the World Health Organisation.

"The tide might finally be turning, however, with the development of a new triple-threat drug that aims to outsmart bacterial evolution.

***

"Most new antibiotic drugs start to lose their effectiveness just a few years after release into the marketplace. For example, penicillin resistance was observed even before the drug was released as a therapeutic. (my bold)

"However, one drug that has proven itself over time is vancomycin. Itself produced by a non-hazardous soil bacteria, it is lethal against most of the bacteria that invade mammals. It has been widely used since the 1950s, and has only recently begun to lose its potency."

Comment: this article is on a different point but it shows that bacteria had automatic defenses in nature long before we found antibiotics. Note the bold.

QUOTE: In other words, the neo-Darwinian mechanism of mutation and natural selection lacks the creative power to generate the novel anatomical traits and forms of life that have arisen during the history of life. Yet, as Müller noted, neo-Darwinian theory continues to be presented to the public via textbooks as the canonical understanding of how new living forms arose — reflecting precisely the tension between the perceived, and actual, status of the theory. (David’s bold)
DAVID’s comment: If the Royal Society had no tentative answers and my bolded statement is noted, all that is left of the theory is common descent. Not much of a theory.

They are simply saying what we have both said over and over again, that the problem is innovation. Common descent is a tremendous theory which many of us now take for granted (Tony opposes it), and it caused a furore at the time because it contradicted the established view of separate creation. Although Darwin was far from being the originator of the theory, it was he who persuaded the world to accept it (while insisting that it did not preclude the existence of God). He himself regarded his book as a starting-point, not a conclusion, and how very right he was.

TONY: Common descent is actually inclusive in this issue. Having 'no theory of the generative' means that common descent stands no chance at all of having happened because 'new' features or traits have no means of occurring and causing speciation.

Again, innovation is indeed the great problem. David’s theory that his God preprogrammed the new features or intervened to “dabble” is perfectly in line with common descent, because in all cases the changes would have taken place in existing organisms. My own hypothesis of cell communities using their (perhaps God-given) intelligence to cooperate in producing new features also explains how common descent might work.

QUOTE: "James Shapiro’s talk, clearly one of the most interesting of the conference, highlighted this difficulty in its most fundamental form. Shapiro presented fascinating evidence showing, contra neo-Darwinism, the non-random nature of many mutational processes – processes that allow organisms to respond to various environmental challenges or stresses. The evidence he presented suggests that many organisms possess a kind of pre-programmed adaptive capacity – a capacity that Shapiro has elsewhere described as operating under “algorithmic control.” Yet, neither Shapiro, nor anyone else at the conference, attempted to explain how the information inherent in such algorithmic control or pre-programmed capacity might have originated."

dhw: Shapiro is a champion of cellular intelligence, and so I don’t know why he doesn’t go the whole hog and offer it as an explanation for innovation. Perhaps, though, it’s a bit too radical to present to the Royal Society, and it would probably be far too radical for them to countenance anyone allowing for the existence of God as the possible originator of cellular intelligence or a “pre-programmed capacity”.

Your paragraph above is an interesting and incorrect interpretation of the quote. What it states is Algorithmic control runs bacteria, and that is exactly my point about bacteria. They contain information to run the algorithms and are preprogrammed. They contain programs to turn on re-writes of their DNA ahd respond in that way.

David:

Comment: If the Royal Society had no tentative answers and my bolded statement is noted, all that is left of the theory is common descent. Not much of a theory.

"James Shapiro’s talk, clearly one of the most interesting of the conference, highlighted this difficulty in its most fundamental form. Shapiro presented fascinating evidence showing, contra neo-Darwinism, the non-random nature of many mutational processes – processes that allow organisms to respond to various environmental challenges or stresses. The evidence he presented suggests that many organisms possess a kind of pre-programmed adaptive capacity – a capacity that Shapiro has elsewhere described as operating under “algorithmic control.” Yet, neither Shapiro, nor anyone else at the conference, attempted to explain how the information inherent in such algorithmic control or pre-programmed capacity might have originated."

Tony: Comment: What I have always asserted: Variation within tightly controlled pre-defined constraints.

My point all along about bacteria. Algorithmic control and pre-programming fit exactly. Information running the show but no innate intelligence.

They are simply saying what we have both said over and over again, that the problem is innovation. Common descent is a tremendous theory which many of us now take for granted (Tony opposes it), and it caused a furore at the time because it contradicted the established view of separate creation. Although Darwin was far from being the originator of the theory, it was he who persuaded the world to accept it (while insisting that it did not preclude the existence of God). He himself regarded his book as a starting-point, not a conclusion, and how very right he was.

TONY: Common descent is actually inclusive in this issue. Having 'no theory of the generative' means that common descent stands no chance at all of having happened because 'new' features or traits have no means of occurring and causing speciation.

Again, innovation is indeed the great problem. David’s theory that his God preprogrammed the new features or intervened to “dabble” is perfectly in line with common descent, because in all cases the changes would have taken place in existing organisms. My own hypothesis of cell communities using their (perhaps God-given) intelligence to cooperate in producing new features also explains how common descent might work.

QUOTE: "James Shapiro’s talk, clearly one of the most interesting of the conference, highlighted this difficulty in its most fundamental form. Shapiro presented fascinating evidence showing, contra neo-Darwinism, the non-random nature of many mutational processes – processes that allow organisms to respond to various environmental challenges or stresses. The evidence he presented suggests that many organisms possess a kind of pre-programmed adaptive capacity – a capacity that Shapiro has elsewhere described as operating under “algorithmic control.” Yet, neither Shapiro, nor anyone else at the conference, attempted to explain how the information inherent in such algorithmic control or pre-programmed capacity might have originated."

Shapiro is a champion of cellular intelligence, and so I don’t know why he doesn’t go the whole hog and offer it as an explanation for innovation. Perhaps, though, it’s a bit too radical to present to the Royal Society, and it would probably be far too radical for them to countenance anyone allowing for the existence of God as the possible originator of cellular intelligence or a “pre-programmed capacity”.

******

Please note: I may struggle over the next few days to keep up with this stream of posts, but I will do my best!

Comment: If the Royal Society had no tentative answers and my bolded statement is noted, all that is left of the theory is common descent. Not much of a theory.

"James Shapiro’s talk, clearly one of the most interesting of the conference, highlighted this difficulty in its most fundamental form. Shapiro presented fascinating evidence showing, contra neo-Darwinism, the non-random nature of many mutational processes – processes that allow organisms to respond to various environmental challenges or stresses. The evidence he presented suggests that many organisms possess a kind of pre-programmed adaptive capacity – a capacity that Shapiro has elsewhere described as operating under “algorithmic control.” Yet, neither Shapiro, nor anyone else at the conference, attempted to explain how the information inherent in such algorithmic control or pre-programmed capacity might have originated."

Comment: What I have always asserted: Variation within tightly controlled pre-defined constraints.

"As Müller has explained in previously published work (with Stuart Newman), although “the neo-Darwinian paradigm still represents the central explanatory framework of evolution, as represented by recent textbooks” it “has no theory of the generative.” In other words, the neo-Darwinian mechanism of mutation and natural selection lacks the creative power to generate the novel anatomical traits and forms of life that have arisen during the history of life. Yet, as Müller noted, neo-Darwinian theory continues to be presented to the public via textbooks as the canonical understanding of how new living forms arose — reflecting precisely the tension between the perceived, and actual, status of the theory. (my bold)

Comment: If the Royal Society had no tentative answers and my bolded statement is noted, all that is left of the theory is common descent. Not much of a theory.

Common descent is actually inclusive in this issue. Having 'no theory of the generative' means that common descent stands no chance at all of having happened because 'new' features or traits have no means of occurring and causing speciation.

https://www.evolutionnews.org/2017/05/haunted-by-intelligent-design-an-organizer-report...

"The opening presentation at the Royal Society conference by one of those world-class biologists, Austrian evolutionary theorist Gerd Müller, underscored [ tne problems.]

"Müller opened the meeting by discussing several of the fundamental “explanatory deficits” of “the modern synthesis,” that is, textbook neo-Darwinian theory. According to Müller, the as yet unsolved problems include those of explaining:

"Phenotypic complexity (the origin of eyes, ears, body plans, i.e., the anatomical and structural features of living creatures);

"Phenotypic novelty, i.e., the origin of new forms throughout the history of life (for example, the mammalian radiation some 66 million years ago, in which the major orders of mammals, such as cetaceans, bats, carnivores, enter the fossil record, or even more dramatically, the Cambrian explosion, with most animal body plans appearing more or less without antecedents);

"Non-gradual forms or modes of transition, where you see abrupt discontinuities in the fossil record between different types.

"As Müller has explained in previously published work (with Stuart Newman), although “the neo-Darwinian paradigm still represents the central explanatory framework of evolution, as represented by recent textbooks” it “has no theory of the generative.” In other words, the neo-Darwinian mechanism of mutation and natural selection lacks the creative power to generate the novel anatomical traits and forms of life that have arisen during the history of life. Yet, as Müller noted, neo-Darwinian theory continues to be presented to the public via textbooks as the canonical understanding of how new living forms arose — reflecting precisely the tension between the perceived, and actual, status of the theory. (my bold)

Comment: If the Royal Society had no tentative answers and my bolded statement is noted, all that is left of the theory is common descent. Not much of a theory.

DAVID: Our problem is I don't see a dichotomy starting with the position that humans are the goal of evolution as God conducts it.

DHW: I pointed out to you that if God is all-powerful, and can dabble at any time, and his only goal was to create humans, it did not make sense that he would personally design millions of other life forms, lifestyles and natural wonders in order to do so (e.g. the weaverbird’s nest, monarch’s lifestyle, fly’s compound eye). Your response was “Guess what? It doesn’t make sense to me either”, and the only explanation you could come up with was that your God might be limited. I offered you experimentation as a "clear explanation", and you rejected it. You are currently backtracking on the limited God hypothesis because you can’t come up with any limitation you can accept as feasible. And so you are left where you started, with two hypotheses which, put together, don’t make sense to you. That is the dichotomy.

Tony: Ok, let's see if we can sort this statetement.

A) God did NOT have to create the endless variety, but he DID need to create sufficient variety to meet the requirements of sustaining a livable ecosystem.

B) The act of making the required resources beautiful, complex, interesting and wondrous is an expression of God's love for his creations.

Thank you. With my background I accept A, but am not sure of B

DAVID: Our problem is I don't see a dichotomy starting with the position that humans are the goal of evolution as God conducts it.

DHW: I pointed out to you that if God is all-powerful, and can dabble at any time, and his only goal was to create humans, it did not make sense that he would personally design millions of other life forms, lifestyles and natural wonders in order to do so (e.g. the weaverbird’s nest, monarch’s lifestyle, fly’s compound eye). Your response was “Guess what? It doesn’t make sense to me either”, and the only explanation you could come up with was that your God might be limited. I offered you experimentation as a "clear explanation", and you rejected it. You are currently backtracking on the limited God hypothesis because you can’t come up with any limitation you can accept as feasible. And so you are left where you started, with two hypotheses which, put together, don’t make sense to you. That is the dichotomy.

Ok, let's see if we can sort this statetement.

A) God did NOT have to create the endless variety, but he DID need to create sufficient variety to meet the requirements of sustaining a livable ecosystem.

B) The act of making the required resources beautiful, complex, interesting and wondrous is an expression of God's love for his creations.

DAVID: Our problem is I don't see a dichotomy starting with the position that humans are the goal of evolution as God conducts it.

dhw:I pointed out to you that if God is all-powerful, and can dabble at any time, and his only goal was to create humans, it did not make sense that he would personally design millions of other life forms, lifestyles and natural wonders in order to do so (e.g. the weaverbird’s nest, monarch’s lifestyle, fly’s compound eye). Your response was “Guess what? It doesn’t make sense to me either”, and the only explanation you could come up with was that your God might be limited.

I have explained that my comments are at the moment remarks and responses to your questions. Remember they are not set in stone as I've stated. I am ruminating out in public. You then pick up an at-the-moment thought and stick with it in responding to me. I don't settle on one thought or approach. My thoughts remaim fluid. I'm trying to understand the history as much as you are. You have not allowed yourself to make choices among the possible final decisions about what to believe.

dhw: I offered you experimentation as a "clear explanation", and you rejected it. You are currently backtracking on the limited God hypothesis because you can’t come up with any limitation you can accept as feasible. And so you are left where you started, with two hypotheses which, put together, don’t make sense to you. That is the dichotomy.

Again, no dichotomy. Main point, God's goal is to create humans. Time to do it is a human concept, not God's. He is timeless. Limitations or not are human thinking, not God's. Is He limited, probably not, but it remains a possibility. Is He all-powerful. More probable. Can I be absolutely positive about either thought? No. As for experimentation, all of the intricate examples of complexity in the genome and biologic functions reprised yesterday deny that possibility. They all strongly suggest immediate saltation of immediately active processes, nothing stepwise as would be the case with experimentation.

dhw: Of course I accept that position. As I keep repeating ad nauseam, nobody KNOWS if their beliefs are factually real, whether that relates to the existence of God, the purpose of God, or the nature of God. What I cannot accept is your insistence that (a) God had only one purpose (to create humans), and (b) everything else (e.g. the weaverbird's nest) is related to that purpose. Nor can I accept your refusal – despite your admission that the dichotomy between these two hypotheses leaves you without a “clear explanation” – to even consider any other possible purpose for his creation of life on the grounds that we mustn’t humanize your God (though you actually believe he has characteristics in common with humans) or that we cannot KNOW the truth.

DAVID: Our problem is I don't see a dichotomy starting with the position that humans are the goal of evolution as God conducts it.

I pointed out to you that if God is all-powerful, and can dabble at any time, and his only goal was to create humans, it did not make sense that he would personally design millions of other life forms, lifestyles and natural wonders in order to do so (e.g. the weaverbird’s nest, monarch’s lifestyle, fly’s compound eye). Your response was “Guess what? It doesn’t make sense to me either”, and the only explanation you could come up with was that your God might be limited. I offered you experimentation as a "clear explanation", and you rejected it. You are currently backtracking on the limited God hypothesis because you can’t come up with any limitation you can accept as feasible. And so you are left where you started, with two hypotheses which, put together, don’t make sense to you. That is the dichotomy.

D

DAVID: I do not understand why you cannot accept my position that I may attribute human characteristics to God in my position of faith, but intellectually admit that I cannot know those characteristics are factually real.

dhw: Of course I accept that position. As I keep repeating ad nauseam, nobody KNOWS if their beliefs are factually real, whether that relates to the existence of God, the purpose of God, or the nature of God. What I cannot accept is your insistence that (a) God had only one purpose (to create humans), and (b) everything else (e.g. the weaverbird's nest) is related to that purpose. Nor can I accept your refusal – despite your admission that the dichotomy between these two hypotheses leaves you without a “clear explanation” – to even consider any other possible purpose for his creation of life on the grounds that we mustn’t humanize your God (though you actually believe he has characteristics in common with humans) or that we cannot KNOW the truth.

Our problem is I don't see a dichotomy starting with the position that humans are the goal of evolution as God conducts it.

Of course I accept that position. As I keep repeating ad nauseam, nobody KNOWS if their beliefs are factually real, whether that relates to the existence of God, the purpose of God, or the nature of God. What I cannot accept is your insistence that (a) God had only one purpose (to create humans), and (b) everything else (e.g. the weaverbird's nest) is related to that purpose. Nor can I accept your refusal – despite your admission that the dichotomy between these two hypotheses leaves you without a “clear explanation” – to even consider any other possible purpose for his creation of life on the grounds that we mustn’t humanize your God (though you actually believe he has characteristics in common with humans) or that we cannot KNOW the truth.

DAVID: Your question answers itself. What I believe and what I 'know' are the difference between faith and no faith. I believe He has some/many of the attributes you listed, but I cannot 'know that.

dhw: And you cannot even know that God exists. All we can do is study life and either draw conclusions or not draw conclusions. It therefore seems to me perfectly reasonable to discuss the issue of God’s existence AND his purpose AND his nature, and it is not unreasonable to base our discussions on the possibility that he has many of the attributes I have listed, unless you regard your own beliefs as unreasonable. Nor is it unreasonable to assume that if he exists, there will be a clear explanation for his actions, and this may well be connected with the human attributes you believe he has. Of course you have every right to dismiss all the different hypotheses I have proposed on the grounds that we cannot know the truth – but that applies equally to your own anthropocentric interpretation of life’s history, which you cling to despite the fact that you cannot find a "clear explanation" for the dichotomy I have again outlined under “God and evolution”.

i
I do not understand why you cannot accept my position that I may attribute human characteristics to God in my position of faith, but intellectually admit that
I cannot know those characteristics are factually real.

DAVID: Your question answers itself. What I believe and what I 'know' are the difference between faith and no faith. I believe He has some/many of the attributes you listed, but I cannot 'know that.

And you cannot even know that God exists. All we can do is study life and either draw conclusions or not draw conclusions. It therefore seems to me perfectly reasonable to discuss the issue of God’s existence AND his purpose AND his nature, and it is not unreasonable to base our discussions on the possibility that he has many of the attributes I have listed, unless you regard your own beliefs as unreasonable. Nor is it unreasonable to assume that if he exists, there will be a clear explanation for his actions, and this may well be connected with the human attributes you believe he has. Of course you have every right to dismiss all the different hypotheses I have proposed on the grounds that we cannot know the truth – but that applies equally to your own anthropocentric interpretation of life’s history, which you cling to despite the fact that you cannot find a "clear explanation" for the dichotomy I have again outlined under “God and evolution”.

dhw: Of course, to anticipate your favourite response, we cannot “know” his characteristics – as Tony says, we can only infer them – but that applies equally to the argument that he has none. It is all a matter of what you believe. Do you actually believe he has none of the above attributes? If so, are they all the inventions of his creations?

Your question answers itself. What I believe and what I 'know' are the difference between faith and no faith. I believe He has some/many of the attributes you listed, but I cannot 'know that.

DAVID: Exactly as I do it, and the Quran agrees.

Dhw: David, I thought you prided yourself on not inferring ANY of your God’s characteristics, as that means humanizing him.

DAVID: If you read my comment, it clearly said 'to each his own': "Each of us can then shape the designer's characteristics as each of us wills". The word characteristics can obviously mean no human aspects.

Characteristic: “distinguishing quality, attribute or trait” (Encarta). By studying your God’s creations, have you therefore reached the conclusion that he definitely has no quality, attribute or trait in common with humans? Or do you think he might just possibly have such attributes as loneliness, boredom, curiosity, interestedness, humour, love, dislike, aesthetic pleasure etc., all of which I must confess I think I have noticed in his creations (I am wearing my theist hat). Of course, to anticipate your favourite response, we cannot “know” his characteristics – as Tony says, we can only infer them – but that applies equally to the argument that he has none. It is all a matter of what you believe. Do you actually believe he has none of the above attributes? If so, are they all the inventions of his creations?

TONY: I prefer to infer his characteristics by the examination of his creation. A preference which is supported in the biblewhen it stays that all that can be known the creator can be learned by studying his creation
DAVID: Exactly as I do it, and the Quran agrees.

dhw: Me too, if I put on my theist’s hat. And what do I see when I examine his creation? Wondrous beauty, love, compassion, inventiveness, mixed with appalling ugliness, selfishness, cruelty, suffering.

Two further observations:
David, I thought you prided yourself on not inferring ANY of your God’s characteristics, as that means humanizing him.
Tony, in anticipation of a possible reply from you: (a) my second list existed long before humans came on the scene, and (b) I am not objecting to the mixture here but am merely inferring your God’s possible characteristics by examining his creation.

If you read my comment, it clearly said 'to each his own': "Each of us can then shape the designer's characteristics as each of us wills". The word characteristics can obviously mean no human aspects.

dhw: In true agnostic fashion I would phrase it slightly differently: science leads us to the point where there may be something beyond the realm of science, because all of the 'natural' laws that we know break down, and what's left is currently inexplicable and may always remain so.
DAVID: If first cause is an accepted approach, we will reach the point where a 'designer' cannot be denied. Each of us can then shape the designer's characteristics as each of us wills.

I accept first cause as an approach, but deny that your single, causeless, conscious ‘designer’ mind cannot be denied. The alternative that I have suggested over and over again is energy and matter constantly interacting, and countless consciousnesses originating and evolving from that interaction. Design from bottom upwards, as opposed to design from top downwards. Of course I find both hypotheses equally difficult to believe, which is why I am an agnostic. What you would call an either/or.

TONY: I prefer to infer his characteristics by the examination of his creation. A preference which is supported in the biblewhen it stays that all that can be known the creator can be learned by studying his creation
DAVID: Exactly as I do it, and the Quran agrees.

Me too, if I put on my theist’s hat. And what do I see when I examine his creation? Wondrous beauty, love, compassion, inventiveness, mixed with appalling ugliness, selfishness, cruelty, suffering.

Two further observations:
David, I thought you prided yourself on not inferring ANY of your God’s characteristics, as that means humanizing him.
Tony, in anticipation of a possible reply from you: (a) my second list existed long before humans came on the scene, and (b) I am not objecting to the mixture here but am merely inferring your God’s possible characteristics by examining his creation.