I agree with you. Although Darwin's theory is based on scientific evidence, it is still not accepted by everyone. In particular, there is a discrepancy between scientific, religious and logical approaches to the issue. It is not impossible to identify this barrier and find a solution. I think that if we look at this theory in addition to scientific evidence, taking into account the life story formed on the basis of religious sources and the logical method applied by Aristotle, we can get more correct results. This may even lead to the formation of new theories in other areas.

Dear Orkhan Rajabli

This is the second discussion I’ve initiated on ResearchGate concerning evolutionary theory.

The first focused on the philosophical foundations of Darwinian evolution, particularly its roots in the empiricism and scepticism of David Hume. These philosophical ideas were so influential that several biologists prior to Darwin had already proposed evolution and evolution-like ideas, suggesting that the conceptual groundwork was in place well before Darwin's contributions.

This second discussion shifts the focus to what has happened after Darwin’s core theory—based on random variation and natural selection—was established. It explores how later discoveries (such as symbiosis, epigenetics, and horizontal gene transfer) have been retrofitted into the Darwinian framework, often without re-evaluating the philosophical and scientifical coherence of the theory as a whole.

To be clear, these discussions are not based on religious arguments. As explicitly stated in the first discussion, the critique is philosophical and scientific, questioning whether the explanatory role of “evolution” has at times become analogous to a god-of-the-gaps—an all-purpose answer invoked in place of detailed mechanisms.

https://www.researchgate.net/post/Is_Darwinian_Evolution_a_Scientific_Theory?

The short answer is: no.

The long answer will require a discussion needing time that I haven't to be complete.

My suggestion to you is to read some of the books written by the late Stephen J. Gould, who explained much better than I can do why your view of the evolutionary theory is a strawman.

Please let the religions out of this discussion, since science uses different tools and deals with different topics.

Dear Cesare Andrea Papazzoni

Thank you for your comments. However, I noticed that you did not engage with the core philosophical and scientific issues I raised concerning evolutionary biology. Instead, you referred me to the works of Stephen Jay Gould for further reading. May I ask whether you personally endorse his view of evolution, particularly the theory of Punctuated Equilibria, which he developed alongside Niles Eldredge?

Also, it seems that you may have missed some of my earlier clarifications. I have done my best, both in this discussion and in the first one1 I initiated, to make it clear that my arguments are not based on religious reasoning. In fact, I have uploaded my thoughts on the subject of religion to ResearchGate, which can easily be verified by the title of the uploaded article2.

I would very much appreciate a deeper engagement with the philosophical and theoretical questions I’ve posed, rather than general references or assumptions about the motivation behind them.

[1] https://www.researchgate.net/post/Is_Darwinian_Evolution_a_Scientific_Theory?

[2]

Preprint Religion-The Triumph of Deceit

Dear Ziaedin Shafiei

about religion, I referred to the answer of Orkhan Rajabli who mentioned religious sources.

As regards your first statements, you referred to the evolutionary theory of Charles Darwin and told that later scientific achievements expanded it including mechanisms that are out of the core of natural selection. This is obviously true but the natural selection has been demonstrated since then as the main driver of changes during time. Of course we now know a lot of new phenomena such as horizontal gene transfer, epigenetic mechanisms, etc. Nobody question them, evolution is more than natural selection, and again Darwin was right about how to explain most of the changes we observe. So, which is your point to say that "rather than revising the theory fundamentally, these discoveries are retrofitted into the existing framework"? No scientists did this. They simply extended the original Darwinian theory, so that we are currently speaking of Neodarwinian theory.

And, since science is work-in-progress, I would expect new achievements and new changes to encompass the progress in our knowledge of the life beings. I don't know if this is phylosophically inconsistent but this is how science works.

My impression is that you need the evolutionary theory to be something like a physical law, which could not be as life is a very complex issue and cannot be reduced to simple "laws" as more fundamental phenomena.

As regards the falsification, S. J. Gould explained several times how the just-so-stories using adaptationist "explanations" are not scientific at all. This is the reason I made reference to him.

Finally, to answer to your question about the punctuated equilibria theory I think it is again an expansion of the evolutionary theory which in my experience is sometimes useful and sometimes not. I am grateful to Gould and Eldredge for their great contribution and of course I am also happy that paleontologists intervened to clarify the actual history of the evolutionary transitions.

Hoping that my thoughts are now a little bit clearer, I thank you for this discussion.

Dear Cesare Andrea Papazzoni

I appreciate you taking the time to contribute your valuable input to this discussion.

The Neo-Darwinian synthesis underscores that the original Darwinian theory rested largely on two pillars: the concept of artificial selection and a significant lack of knowledge about life’s inner workings. This raises a fundamental question: how can a theory born out of such limited understanding continue to be treated as a nearly definitive scientific explanation for more than a century? The modern synthesis arguably compounded the issue by redefining "random change" as random genetic error - essentially, mutations as mistakes in replication. But can random mistakes truly serve as a foundational mechanism in a rigorous scientific theory? That seems philosophically questionable, if not scientifically unsound.

Over time, many crucial biological mechanisms, such as symbiosis, the neutral theory of molecular evolution, epigenetics, and horizontal gene transfer, were initially met with scepticism or outright dismissal by evolutionary biologists. Yet, as evidence mounted, these once-ridiculed ideas were gradually incorporated into the broader narrative. The case of symbiosis is particularly striking: initially marginalized, it is now recognized as a fundamental force in the evolution of complex life. In contrast, theories like punctuated equilibrium have remained on the margins, possibly because they diverge too far from the core Darwinian framework.

You rightly point out that life is profoundly complex. Given this, why should we continue to revere a theory formulated in the absence of modern biological insight? Why insist on maintaining random mutation and natural selection as exhaustive explanations, when they likely represent only fragments of a much deeper and still-unfolding story?

Rather than prematurely declaring evolution a settled triumph of science, perhaps we should acknowledge our current state more humbly - as one of dark biology, akin to astronomy before the invention of the telescope. Otherwise, we risk mistaking the tusk for the elephant - and calling it science.

Dear Orkhan Rajabli

Thank you for your comment.

What I have tried to convey in both discussions is that Darwinism, both in its original and modern forms, is not fundamentally grounded in scientific evidence. Rather, it gained credibility largely because it successfully challenged religious and folkloric explanations of life. This opposition, however important, does not necessarily make it a robust scientific theory.

We all have a responsibility to engage critically with established ideas, without hesitation, and to hold them to rigorous scientific standards. Constructive critique is not opposition to science; it is a vital part of its progress.

If you have time, I would appreciate it if you could read the presentation linked below, which outlines my understanding of the current state of both theoretical physics and evolutionary biology. I would greatly value your feedback.

Presentation God: Valid Scientific Conclusion

Thank you for your detailed explanation. This theory is indeed more debated than any other. I think people only understand it the way they want to, and this leads to misunderstandings. I am very disappointed that science is a victim of conflict. I would like to explore this theory in more detail in the near future. I will also interpret it from the perspective of cosmology and geology.

Thank you again for your feedback and for providing valuable information.

Hello! The thing is, Darwin's theory as we understand it now, based on the idea which is not really biological. Something that doesn't fit - is eliminated. Something that fit - keeps growing (until it grows too much). It's just a negative feedback. This principle works everywhere. It forms shapes of mountains, lakes, stars and star systems etc. It works when you hit your pinky or got a splinter in your foot. Darwin showed how this principle work for life creatures. And we appreciate it a lot. But as long as this principle is universal, It is not really biological evolution. Evolution theory is more about mechanisms which drive changes in life forms and ways to process them. Selection is one of many ways. Yeah, we do can explain almost everything with appropriate model and abuse it sometimes. It's quite difficult to reveal underlying mechanisms in every separate case though. But no worries - we keep gathering info and discover tendencies.

https://doi.org/10.1016/j.biosystems.2023.105031

Regards ...

Dear Marko Vitas

Thank you for sharing the reference to your paper. Unfortunately, it appears to be only partially accessible to those without institutional access. As ResearchGate members, we generally expect scientific discussions to remain open and freely accessible, especially when part of an ongoing exchange. For that reason, I would appreciate it if you could engage directly with the points raised here in the thread.

Your paper notes that Darwinian selection can sometimes act as a retrograde force. However, you present this not as a refutation of Darwinian principles, but rather as a reinterpretation grounded in empirical observations. This clearly illustrates my broader point: we continue to add contrasting or even contradictory layers to a theory originally built on a limited foundation, and then present that accumulation as a sign of its robustness.

You also reference Karl Popper's view of Darwinian evolution as unfalsifiable. It’s worth noting that Popper later modified his stance, acknowledging that certain aspects of evolutionary biology—particularly when combined with population genetics, palaeontology, and molecular biology, can indeed be tested.

The purpose of this discussion is not to reject evolution nor to promote any ideology, but to foster a thoughtful and critical examination of its foundations and extensions. Constructive scrutiny is vital for scientific advancement, and I hope we can continue in that spirit.

Dear Roman P Gorbunov

Thank you for your valuable input. You are absolutely right in noting that the original Darwinian theory introduced only a very slow feedback system. Influenced by geologist Charles Lyell, Darwin strongly embraced the principle of gradualism, the idea that both geological and biological changes occur slowly and incrementally over long periods. This commitment to gradualism limited his ability to recognize that evolution might also proceed in rapid bursts, a notion that was ironically contradicted by his own observations of the Galápagos finches.

Neo-Darwinism inherited this framework and initially had little choice but to remain within its boundaries. Yet today, the scientific consensus acknowledges that the feedback system can be both gradual and rapid. Despite this expanded view, many evolutionary biologists continue to maintain that Darwin’s original insights were fundamentally correct.

Dear Ziaedin Shafiei,

I was reading the discussion opened by Cesare Andrea Papazzoni with you. If I can, I want to add some of my following thoughts.

I notice a kind of rejection toward Darwin and his mechanism for explaining the evolution of species through selection. Also, it strikes me that Alfred Russell Wallace was left out of the discussion. Like any person, both had successes and failures in their understanding of biological processes; both were influenced by the society in which they developed. That somehow determined the way they understood how nature works. Ultimately, this is the purpose of many people who study biology. However, the "enchantment" of their proposal rests on its simplicity.

I understand that we now know more about nature. And I agree that the endosymbiotic theory was initially rejected as an explanation for the evolution of eukaryotic cells. But like other proposals in science, the weight of evidence showed its power to explain a biological process that proved crucial in the history of life on this planet, to the point of changing the atmosphere's composition.

Like the endosymbiotic theory, the theory of evolution by selection is part of a larger puzzle, of which we are only just beginning to glimpse a small part. And following its reasoning, how could we explain biological adaptations without resorting to selection? This does not refer to the sense established by the adaptationist program, but rather to understanding the evolution of reproductive systems in plants and animals or morphological differences between the sexes. Is there any other adequate explanation? What is that other option?

As Jacques Monod states in his book Chance and Necessity, objects and living beings in the universe can be explained from basic principles, the laws of physics, but they cannot be predicted from particular objects.

Best,

No, Darwinian evolution is not a "God-of-the-gaps." Unlike invoking God to explain unknowns, evolution is a scientific theory supported by extensive evidence from genetics, fossils, and observed natural selection. It explains known mechanisms, not gaps in knowledge.

I am not sure that I see the point of any of this. Darwin’s theory is actually quite simple. Organisms contain variation. In any given environment some variants will live longer and reproduce more than others. If the variants that are responsible for the greater reproductive success are heritable, individuals with these variants will increase in number in subsequent generations. He explicitly pointed out that all of this assumed that there was a mechanism of heredity. He did not know what this was or how it worked. But he theorized that it must exist and admitted that if such a mechanism did not exist his entire theory would collapse. He was not aware of the work of Gregor Mendel which contributed the final missing piece. When Mendel’s work was combined with Darwin in the Modern Synthesis it only served to provide additional evidence to support Darwin’s theory. In the years since we have learned a great deal. But all of them fit within Darwin’s theory. Probably the most important discovery is the impact of genetic drift (random chance events) on the process of evolution. But at the end of the day the environment (the agent of Natural Selection) still favors some variants over others. Endosymbiosis, horizontal gene transfer, mutation etc. are simply ways that create new variants. So far Darwin’s theory persists as the only scientific explanation for the diversity of life we see around us.

Dear Sergio López

You are absolutely right that Darwin was not the only person to propose what we now call Darwinian evolution. Alfred Russel Wallace, and even earlier, Patrick Matthew, independently formulated similar ideas. But that’s not the main issue here. What we are trying to assess is whether the idea of evolution by natural selection was genuinely based on scientific principles—which was your initial concern.

SL remarked, "I notice a kind of rejection toward Darwin and his mechanism for explaining the evolution of species through selection."

The crucial point here is that none of the early proponents of evolutionary theory had a scientifically accurate understanding of the mechanism of variation, which is essential for any theory of evolution to be complete.

We know that Darwin attempted to explain variation through his pangenesis hypothesis, but this was speculative and lacked empirical support. In fact, it was essentially guesswork. Later, Darwin introduced sexual selection as an additional mechanism alongside natural selection, but again, this did not solve the core problem of explaining how variations arise and are inherited.

Please let me know if I have overlooked anything so far. I would also like to refer you to another RG discussion, which examined the philosophical foundations of evolutionary theory.

https://www.researchgate.net/post/Is_Darwinian_Evolution_a_Scientific_Theory?

For a more detailed version of my argument, please see the article below.

Preprint SCIENCE IN THE SHADOW OF METAPHYSICS Part 1 -Gods of Science!?

Dear James Bonacum

Many thanks for your comment.

There are many simple theories that sound reasonable on the surface. For instance, consider the world of car manufacturing. Numerous companies produce different types of cars. Those that are durable and reliable become more desirable, and the companies behind them tend to thrive. In contrast, those that produce poor-quality vehicles eventually go out of business. This simple model of competition and survival makes sense—but it doesn't explain how a car is actually made.

We often fall into the trap of thinking that once we have such a basic explanatory framework, the rest is just a matter of trivial details. But that’s precisely the issue. There are other "simple" evolutionary theories, such as punctuated equilibrium, which likewise offer a broad outline but not necessarily the full picture. They are simply surface-level explanation.

Now, imagine someone claiming that all these cars were produced simply by the agitation of matter over a long period of time. That’s also a simple theory, but clearly a wrong one. And yet, we have accepted a similarly reductionist view of the world, heavily influenced by philosophical thinkers like David Hume, who treated complex order as something that might emerge from chance and time alone.

Mr. Shafiei,

Thank you for your response to my post. I am afraid though that I am still at a loss to understand what you are trying to say. Once the Modern Synthesis took place in the early 20th century, evolutionary biology became a true experimental science. Now as I constantly remind my students, scientists never “prove” anything. But we can disprove things and as far as I am aware Darwin’s theory has never been disproven and remains the only scientific explanation that is available to explain the diversification of life. Since Darwin published The Origin of Species in 1859 we have learned a great deal about the process of evolution. Yet there are still areas where further study is required. But no other explanation has been proposed to date that disproves what Darwin said.

You mention punctuated equilibrium and say it is only a simple surface level explanation. I disagree with this characterization. It simply describes how the rate at which evolution proceeds can vary. It does not disprove anything or provide an alternate explanation to the basic questions, although it does provide additional details that help to fill out our understanding. I am also afraid that I do not find your analogy about the manufacturing of automobiles appropriate. Let me explain. There are countless explanations for any natural phenomena but only some are valid. The way we evaluate an explanation is by subjecting it to the scientific method. Explanations that cannot be tested in this fashion (e.g. invoking supernatural causes) are not considered as they are outside of the purview of science. While it is a matter of some debate as to whether such explanations are possible scientists do not engage with them as they cannot be subjected to experimental testing. So while you are free to propose that automobiles are spontaneously assembled unless you could support this with some sort of empirical evidence it would not be considered to be a scientific explanation. In contrast, there are mountains of evidence to support evolution. Now is it possible that a better explanation might exist? Certainly. But until someone comes up with it, Darwin is our best explanation for the origin and diversity of life.

Dear James Bonacum

Many thanks for continuing this important discussion, and please accept my apologies for the length of my response.

One point on which we seem to agree is that Darwinian evolution is, at its core, a simple theory, constructed using the logic of artificial selection and Lyellian gradualism. As I’ve previously illustrated, it's comparable to the car manufacturing analogy:

"Over time, those who build reliable, long-lasting vehicles thrive, while those producing low-quality cars go out of business. It’s a straightforward model of competition and survival."

In this view, evolution is a filter, not a builder. Darwin and his contemporaries had virtually no knowledge of the molecular or developmental mechanisms behind variation or complexity. What they did have was a philosophical scaffolding rooted in Humean scepticism and a growing faith in time and chance as creative forces.

That was then. In earlier thread1, I tried to initiate a discussion precisely on this foundational framework—before Darwin’s theory emerged—highlighting how deeply it shaped the formulation and reception of evolutionary ideas.

Now, the problem is this: evolutionary biology has, over time, elevated this simple and incomplete model to the status of a totalizing explanation. The oft-quoted mantra that "Nothing in biology makes sense except in the light of evolution" reflects the field’s widespread belief that Darwinian evolution provides a full and sufficient account of life. As a result, when new ideas have emerged—such as punctuated equilibrium, the neutral theory of molecular evolution, symbiogenesis, epigenetics, and others—they were not welcomed as refinements, but rather resisted, ridiculed, and sometimes actively suppressed.

As I noted earlier, evolutionary biologists have clung to the “elephant” described by Darwin without truly revisiting the limitations of that original framework. Yes, many of these new theories have been reluctantly integrated into the evolutionary synthesis, but often without full engagement. Take punctuated equilibrium, for instance: besides the contributions of N. Eldredge and S. J. Gould, there has been no single-author monograph thoroughly developing the theory within a biological framework. That absence speaks volumes.

This pattern reveals how ideological forces can stifle new perspectives. Evolutionary biology has, at times, treated its own fellow scientists not with open-minded curiosity but with gatekeeping and suppression. And if this is how scientific insiders such as Margulis and Eldredge are treated, one must wonder: what other important insights or models might have been lost along the way?

I am not denying that science progresses. But we must also acknowledge that this progress is not always smooth or impartial. The rhetorical claim that Darwinian evolution has faced no serious challenge, and that all alternative ideas have been “naturally” accepted or rejected by evidence, is simply historically false.

In light of this, I find it increasingly reasonable to see Darwinian evolution as a kind of "god-of-the-gaps"—not in the theistic sense, but as an explanatory placeholder that persists because of what we don't yet understand, rather than what we do. It's a system that has filled in the gaps of our ignorance with a conceptually elegant but mechanistically vague process, often protected more by philosophical loyalty than empirical sufficiency.

At the very least, I ask that we do not deny the reality of resistance and suppression within evolutionary biology. To do so is to forget the very human side of science—a side that can cling to orthodoxy, resist change, and protect its intellectual boundaries, even when those boundaries need to be redrawn.

[1]

https://www.researchgate.net/post/Is_Darwinian_Evolution_a_Scientific_Theory?

Dear Ziaedin Shafiei,

I have not much time to answer to all your statements.

Just three points:

1) It seems you have not a comprehensive view of the theory of punctuated equilibria, which is a definitely Darwinian theory, as reaffirmed several times by the late S.J. Gould. He repeatedly celebrated the genius of Darwin, who worked without knowledge of the mechanisms of transmission of the characters to the offspring nor the one under the variation. S.J. Gould wrote a big book on evolution (The structure of evolutionary theory, 2002) explaining in detail his view.

2) The theory of Darwin was not "constructed using the logic of artificial selection and Lyellian gradualism", this is a strawman and reasoning on this ground is not acceptable. The parallel with car builders is completely out of target, I refuse to debate about it.

3) As well-explained by James Bonacum science goes on by testing hypothesis, and the Neo-Darwinian theory has been tested and found to explain the evolution of the organisms. As many before you, you are claiming natural selection to be wrong without any evidence. Darwin worked his entire life to find the evidence of his hypothesis, and nobody succeeded to disprove it. Find the evidence and you'll be remembered as the one who destroyed the natural selection.

Dr. Shafiel,

As an evolutionary biologist I must take issue with your description of the state of the field. It is quite broad and my work is confined to a small part of it, systematics which is concerned with understanding the evolutionary history of life. And I can testify that systematists can be a cantankerous lot, especially with regard to the philosophical underpinnings of the techniques that are used in various studies. But this is no different than the sorts of debates that occur in all fields of science. History shows us that scientific knowledge can become dogmatic and certain concepts that become widely accepted are rarely challenged, and new ideas are often scorned at first. But the benefit of the scientific method is that it is self-correcting. When an extraordinary new claim or theory is proposed, it is subjected to rigorous scrutiny and debate. But if there is sufficient evidence to support it, eventually it becomes the new dogma. This is how our understanding of the universe proceeds. We agree that we don’t know everything, and we only accept things that are supported by empirical evidence. And even then, we are open to changing our understanding of things we believe to be true if subsequent studies contradict our prior results.

You point out that Darwin’s theory is a filter, not a builder, and I agree with that. As I tell my students, evolution especially natural selection is not a conscious force that set out to build anything in particular. It is simply the interaction between environmental conditions like temperature, moisture levels and available nutrients and the organisms that are present at any given time. It only explains why individual organisms persist while others go extinct. The principles it is based upon can be used to speculate on how life originated but that is a question that I doubt will ever be completely answered. There are many ideas about this and as far as I know all of them are rooted in Darwinian thinking. They propose that at some point molecules created by random natural processes acquired the ability to replicate themselves. These molecules became enclosed within a membrane and the entire structure was able to replicate itself. Additional random effects allowed these primitive organisms to become more and more complex eventually leading to the current diversity of life. But because we don’t know how or where life originated it is only speculation. And even if someone was able to create a living cell through artificial means in a laboratory it still would not answer the original question as it could be quite different than the methods used in the lab. But our study of evolution has shown that even though it is more complex than Darwin imagined, it has yet to disprove his theory. You say that punctuated equilibrium, the neutral theory of molecular evolution, epigenetics and symbiogenesis were ridiculed and suppressed. I have never seen any evidence of that whatsoever beyond the usual vigorous debates that surround all new ideas. I suggest that you review any of the current textbooks used to teach about evolution in American universities. I think that you will find that all of these topics are included and discussed. We freely admit that we don’t know everything and we are willing to change our views if sufficient evidence is presented to require it. But so far no one has contradicted Darwin.

Dear Cesare Andrea Papazzoni

Here are my responses to your three comments. I have also added a fourth point, which I believe is the most important and deserves careful consideration.

1. I believe I made it clear in my previous response that the issue is not whether scientists like Gould, Eldredge, or Margulis considered themselves evolutionary biologists. They did. The problem lies in the fact that their ideas were rejected by other evolutionary biologists because they directly challenged the core assumptions of the Darwinian model, particularly the notion of slow, gradual change. These challenges were not philosophical abstractions but based on empirical evidence, such as the patterns seen in the fossil record (punctuated equilibrium) or the structure and origin of eukaryotic cells (symbiogenesis).

2. To continue this conversation meaningfully, could you please clarify: what exactly was Darwin's original theory of evolution, before Neo-Darwinism was formulated? Darwin had no concept of genetics, mutation, or molecular biology. His mechanism for variation, pangenesis, was speculative and ultimately discredited. So, what remained was a broad framework of natural selection acting on unknown variations over deep time. While this was a ground breaking insight, it was not a fully developed scientific theory in the modern sense.

3. In light of that, I believe it's fair to say that most, if not all, of the major new evolutionary theories that were initially rejected by the evolutionary biology establishment, whether punctuated equilibrium, neutral theory, or endosymbiosis, were introduced during the dominance of Neo-Darwinism. This is significant. If we are to take science seriously as a method based on falsifiability, prediction, and openness to revision, then even one well-supported, contrasting theory should have triggered a major reassessment of the dominant paradigm.

Instead, what we have seen is a pattern: each new theory is resisted, then gradually absorbed into the broader evolutionary framework without fundamentally rethinking Darwinism itself. This trend suggests that Darwinian evolution functions less like a falsifiable scientific theory and more like a flexible explanatory narrative, expanding to accommodate any new insight, even those it once excluded.

This process is telling. It is not I who am challenging Darwinism, it is the history of evolutionary biology itself that shows the theory being repeatedly challenged, rejected, and then retrofitted to include what it once opposed. This pattern reveals not just intellectual flexibility, but also a kind of conceptual elasticity that weakens its scientific integrity.

If the repeated rejection of new, evidence-based theories by evolutionary biologists, only to later accept them without fundamentally adjusting the core framework, is not evidence of a flawed scientific model, then what is? If we refuse to consider that such a model may be incomplete or overstretched, then we risk turning it into something more akin to an article of faith than a scientific theory.

4. To put this in perspective, consider Newtonian mechanics—one of the most successful scientific frameworks in history. It was abandoned only when it failed to predict the orbital motion of Mercury. A single anomaly, when confirmed, was enough to force a major scientific shift.

In contrast, Darwinian evolution has weathered multiple fundamental challenges, from genetics to development to palaeontology, yet its conceptual core has remained largely untouched. Instead of being revised or replaced, it has been stretched to accommodate even the ideas it originally excluded.

So, I leave it to you to decide: Is Darwinian evolution functioning as a scientific theory, open to revision and replacement? Or has it become something more akin to a cultural or intellectual habit, what one might call a "praying for rain" syndrome, where success is always assumed, explanations are always adjusted, and falsification is quietly deflected?

Dear James Bonacum

Thank you for your candid points. I believe I’ve already shared my main response in my reply to Cesare Andrea Papazzoni. However, to keep the tone a little light-hearted, I would like to add a few anecdotes that illustrate the early resistance faced by some now-prominent evolutionary theories.

I remember that critics of punctuated equilibrium jokingly referred to it as “evolution by jerks.” In response, Eldredge and Gould quipped back with “evolution by creeps,” poking fun at the gradualism of the Neo-Darwinists. Even the term “punk eek” was coined partly in jest, but it also reflects the strong and often hostile reception the theory received in its early years,particularly from committed Neo-Darwinists who viewed it as a challenge to the gradualist orthodoxy.

Similarly, Lynn Margulis reported that her ground breaking 1967 paper on symbiogenesis was rejected more than a dozen times, with one reviewer bluntly calling it “crap.” She also recalled that her colleagues literally laughed at her ideas, dismissing the notion that organelles like mitochondria could have evolved through symbiosis as fringe speculation.

With best wishes

Dear Ziaedin Shafiei,

I try to answer to all four points:

1. Your reconstruction is partly uncorrect, because the core of the original Darwinian model is not the slow, gradual change but the natural selection. Of course today we do not retain the gradualism as a totem, even if I can ensure you that we have plenty of gradual, slow transitions in the fossil record. To clarify, I would like to underline that George G. Simpson treated the different speeds of evolution in his "Tempo and mode in evolution" in 1944, so contributing to the Neo-Darwinian model, which is therefore encompassing also rapid transitions, always under control of natural selection.

2. It is of course true that Darwin had no knowledge of the mechanisms of variation; indeed he observed the variation in the natural environment as well as in the domestic animals and this was sufficient to state that variation occurs and on this variation natural selection acts. He could not go further but we can, and nobody found that the mechanisms of variation are in some way hampering the action of natural selection (by the way, the original manuscript before the Origin was named by Darwin "Natural Selection"!). He also accepted, even if only to a limited extent, the inheritance of acquired characteristics ("lamarckism"). You contest that natural selection in deep time is not a theory but this is only your opinion. Of course nobody today uses the original theory of 19th century but, I repeat it, nobody disproved it since now. For this reason we are in debt with C. Darwin for pointing out natural selection as the main mechanism of evolution. Neither punctuated equilibria nor symbiosis are in contrast with natural selection.

3. You are also right in saying that all modifications to the original theory were contrasted when presented. Welcome to the real science, where this is the normal reaction to any new proposal.

However, here you give a negative accession also to the inclusion of new mechanisms to the neo-darwinian theory. You seem not aware of the specificity of biology, which is not physics, having to do with complex phenomena which are not reducible to simple laws. What is really amazing, in my opinion, is that the core of Darwin's hypothesis is still intact after nearly 200 years from its first proposal.

I reject firmly your statement that "This pattern reveals not just intellectual flexibility, but also a kind of conceptual elasticity that weakens its scientific integrity". Please, explain for which reason a modification to a model should be a threaten to scientific integrity because I cannot see it.

In my experience, a "flawed scientific model" is rejected as some data and alternative explanations are demolishing it. I wait for both.

4. The Newtonian theory has not been completely abandoned, since it works fine for several phenomena which are far from the conditions where the Einstein's theory is applied. For most cases we can use Newton's laws as an approximation of the correct Einstein's laws. And we are dealing with fundamental "simple" phenomena, not with complex ones. By the way, the explanations of Einstein were firstly not accepted, than tested and found "true" (working); only after a certain time they were accepted and, funny, they enclosed the Newtonian mechanics!

The Neo-Darwinian theory (not the Darwinian original one, of course) is open to revision and replacement. The problem is, you have to find data and alternative explanation, and convince other scientists that you are right. This is not at all easy, you'll agree.

Dear Cesare Andrea Papazzoni

Thank you for taking the time to respond to my comments. I will try to go through your points one by one, as the discussion is growing in depth and length.

Regarding your first argument, I believe there is little room for debate: Darwin clearly stated what he meant, and we should not be selective or revisionist about his words. Across his works, there are numerous references to “slow” and “extremely slow” modification, and this gradualism was central to his theory.

To support this, I have quoted a few representative passages from On the Origin of Species (both the 1st and 6th editions). I hope these references clarify Darwin’s position on gradual change and contribute constructively to our discussion.

Ch. IV

“Natural selection acts only by the preservation and accumulation of (infinitesimally 1st Ed.) small inherited modifications, each profitable to the preserved being… it can act only by very short and slow steps.”

Ch. VI

“As natural selection acts solely by accumulating slight, successive, favorable variations, it can produce no great or sudden modification; it can act only by very short and slow steps.”

Ch. IX

On the sudden appearance of whole groups of Allied Species.—The abrupt manner in which whole groups of species suddenly appear in certain formations, has been urged by several palæontologists, for instance, by Agassiz, Pictet, and by none more forcibly than by Professor Sedgwick, as a fatal objection to the belief in the transmutation of species. If numerous species, belonging to the same genera or families, have really started into life all at once, the fact would be fatal to the theory of descent with slow modification through natural selection. For the development of a group of forms, all of which have descended from some one progenitor, must have been an extremely slow process; and the progenitors must have lived long ages before their modified descendants.

Ch. X

The process of modification must be extremely slow.

Also “Nature does not make leaps.” is repeated throughout Darwin’s work, in line with the principle “natura non facit saltum”.

There are many more such references, but I’ve limited myself to just a few for brevity. You can access digital versions of Darwin’s works, including the full first and sixth editions of On the Origin of Species, via Project Gutenberg.

I hope this helps ground our discussion in Darwin’s actual writings.

Ziaedin Shafiei

Gradualism:

"Darwinism, like most comprehensive and complex concepts, defies easy definition." (Gould, 2002)

See the same book for the three meanings of "gradualism" that Gould retrieved in Darwin's and subsequent scientists' view. Of course Gould refuses Darwin's gradualism in strict sense, and I agree with him.

But Gould also told us that gradualism as "insensibility of intermediacy" (p. 150 of Gould, 2002, his second meaning of the term) is retained: he wrote "Darwinian theory would require some adjustments and compromises—particularly a toning down of assertions about the isotropy of variation, and a more vigorous study of internal constraint in genetics and development (see Chapter 10 for advocacy of this theoretical shift)—but natural selection would still enjoy a status far higher than that of a mere executioner."

As far as I know, nobody contests this point, and as I wrote in my previous intervention we are not dealing with Darwinian theory but with Neo-Darwinian one, which is far more rich and complex, having his roots in the original thought of Darwin but being substantially different in several details.

Just to mention something I am familiar with, in geology we debate about the plate tectonics theory, not Wegener's continental drift, even if we recognize that Wegener laid the foundations for the modern theory.

Dear Cesare Andrea Papazzoni

We need to stay focused on the subject of the thread. My question was not about Gould’s views on Darwinism. The core issue here is quite clear.

Darwin proposed a theory of evolution, and in light of new knowledge, particularly genetics, it had to be revised into what became known as Neo-Darwinism. This revision introduced only a mechanism for modification (random mutation), while retaining the principles of gradual change and natural selection. The fact that a new name was adopted reflects broad agreement among biologists that the original and revised theories were not identical.

Now, my point is this: Neo-Darwinism itself has been challenged and revised repeatedly by new discoveries, data, and theoretical developments. These include theories such as punctuated equilibrium, symbiogenesis, epigenetics, and neutral theory, many of which were initially rejected by the evolutionary mainstream. These challenges have not only questioned the pace of evolution (gradualism), but also the randomness and sufficiency of mutation as a source of novelty.

All of this is well documented and unfolding before our eyes. It no longer seems tenable to maintain that the theoretical framework has remained unchanged. To do so — and I must emphasize this again — is like a rain priest urging his congregation to keep praying, despite the repeated failure of those prayers to bring rain. Science must remain open to correction, not shielded by allegiance to a prevailing narrative.

Apologies if my words sound too direct.

Warmest regards,

Dear James Bonacum

JB "There are countless explanations for any natural phenomena but only some are valid. The way we evaluate an explanation is by subjecting it to the scientific method. Explanations that cannot be tested in this fashion (e.g. invoking supernatural causes) are not considered as they are outside of the purview of science."

JB "They propose that at some point molecules created by random natural processes acquired the ability to replicate themselves. These molecules became enclosed within a membrane and the entire structure was able to replicate itself. Additional random effects allowed these primitive organisms to become more and more complex eventually leading to the current diversity of life. But because we don’t know how or where life originated it is only speculation."

In light of the above comments, I would like to raise a broader question:

Why are only certain types of speculation permitted in scientific discussions about the origin and evolution of life?

Some widely accepted scientific models rely on the assumption that random agitation of matter—both non-organic and organic—over vast stretches of time is sufficient to account for the emergence of order, complexity, and even life itself. This idea is seldom challenged. Philosophically, it can be traced back to David Hume, who proposed that order might arise by chance given enough time. Darwin himself echoed Hume’s reasoning, at times almost verbatim, particularly in his speculative comments on the origin of life.

In this framework, “chance” and “time” have become modern gods-of-the-gaps, invoked not only to explain the origin and evolution of life, but also the emergence of the universe itself. These forces are granted extraordinary creative capacity, yet such speculation is considered scientific, mainly because it avoids references to intelligence or design, and by extension, avoids association with religion.

But here is the key question:

If we are allowed to attribute such immense, unobservable creative power to time and chance, why are we not allowed to even entertain the possibility of some form of intelligence, within, or behind, the universe? Why must we restrict “intelligence” to known biological forms, ignoring the potential for non-human or non-local forms of intelligence?

This is not a call for mysticism or religious doctrine, but rather a plea for epistemic balance. If highly speculative mechanisms like self-organizing molecules or multiverse cosmologies are afforded space in scientific discourse, then surely the possibility of intelligence as a causal principle, not necessarily supernatural, deserves to be considered among the available explanatory models.

Shouldn’t science be open to all plausible explanations, especially in areas where empirical testing is inherently limited or unavailable (e.g., the deep origin of life)? If not, we are forced to ask whether what we are defending is still science, or simply a philosophical framework rooted in materialism, regardless of explanatory adequacy.

In my view, we remain, perhaps unknowingly, religiously minded, in the sense that we often assume we already have the correct overarching framework. Once that framework is taken as given, it becomes easy to classify which questions are “legitimate” and which are “out of bounds,” even before the evidence is in. And that, I would argue, is a difficult mindset to overcome.

I’ve tried to explore these ideas more fully in the following presentation and article, which I invite you to consider.

Presentation God: Valid Scientific Conclusion

Preprint SCIENCE IN THE SHADOW OF METAPHYSICS Part 1 -Gods of Science!?

Dr. Shafei,

I believe that I have already answered your question in the first passage of mine that you quoted in your previous posting. I stated that explanations which cannot be subjected to testing in an experimental fashion remain outside of the purview of science. By this I simply mean that we cannot apply the tools of science to every question, especially ones that enter into the domain of metaphysics.

Many years ago I saw a film called, “Hannah and Her Sisters” which I liked very much. It was written and directed by Woody Allen who also stars in it. If you are familiar with his films you will not be surprised to learn that it has a number of metaphysical themes. Part of the plot turns on a visit he makes to his doctor who is concerned about some of his symptoms. The doctor schedules him for some follow up tests, and because his character is a neurotic hypochondriac he immediately assumes the worst and that after the test results come back he will learn that he only has a short time left to live. Fortunately, the test results rule out any sort of serious problem and his first reaction is joyous relief. But the experience has had a profound effect on him, and he begins to question the reason he exists. He also tries a variety of religions hoping that they will set his anxious mind at ease. His father who is Jewish asks him why he is suddenly exploring other religions and why he has not returned to the religion he was raised in. Woody asks his father, “If God exists why did he allow the Nazis to exist?” His father replies, “How should I know why there were Nazis? I don’t even know how the toaster works!” When questioned about the afterlife he once again says he doesn’t know but he will worry about it when he dies.

The reason that I mentioned this is that it reflects my own attitudes to metaphysical questions. If there is an intelligence as you suggest it raises any number of questions, but I cannot imagine how one could conduct an experiment to answer them. This reminds me of the difference between ontological and methodological naturalism. Ontological naturalists believe that everything in the universe is the result of some sort of natural cause. It denies the existence of any sort of supernatural cause. Methodological naturalists have similar views, but the difference is they believe that it may be possible for supernatural causes to exist. But at the end of the day it really does not solve our problems or provide us with any answers. On the question of the existence of God, my training as a scientist only allows me one answer. I don’t know. There is no conclusive evidence to bring to bear for or against His existence. Yet it is a question we all must grapple with. This is why scientists simply refuse to consider the existence of any sort of intelligent designer. Sure, it is possible that one might exist, but no one has yet to provide any convincing evidence for one. The problem with the argument for one is that it does not provide a scientific explanation. And if we are scientists we are confined by our methodology so our point of view on the question is that it is not worthy of consideration in a scientific context. But I am sure that there are any number of philosophers and theologians who would be happy to discuss it.

Oh my apologies. I am looking forward to reading your paper. As you may have gathered I do have some interest in these sorts of things, but I should warn you that I am rather set in my ways on this sort of stuff. But perhaps if i can read your paper it will provide me with some new ideas.

Dear Ziaedin Shafiei,

I wrote a detailed answer to your last message and I accidentally deleted it.

I try here to re-write the main points:

1. It seems you are complaining about the theory which is named Neo-Darwinism which is not retaining the original details; we can solve this issue by changing its name but this will not have any effect on its content, so I do not see any real problem.

2. By answering to James Bonacum you refer to something that, according to your presentation "God: Valid Scientific Conclusion" is the concept of "an intelligent universe". Sorry, I don't think such a concept is different from a (respectable) religious position, since it is equally out of the scientific field being non-testable.

Dear James Bonacum and Cesare Andrea Papazzoni

The boxing ring in this thread has now been widened, and hopefully made fairer, by bringing “intelligence” into the conversation. The discussion is no longer limited to critiques of Darwinism or Hume’s influence; it now includes deeper questions that apply to all perspectives, including my own. That, in itself, is a healthy development. After all, the goal here is not to defend personal positions, but to collectively explore what lies at the root of this complex and consequential debate.

I have long believed that religion has left humanity with a deeply ingrained and misleading worldview. Despite personal efforts to de-religionize my thinking, it would be naive to claim complete immunity from that legacy. One way to move beyond it is to rely as strictly as possible on science; to make it the standard for examining reality and separating knowledge from inherited belief.

Here’s how I see the core issue, as concisely as possible:

Either we accept intelligence (God, for the sake of reference), or we accept a collection of speculative placeholders, what I call gods-of-the-gaps, to fill in our current explanatory deficits. In the case of life’s origin and evolution, the two leading deities are chance and time. These are invoked to explain phenomena for which we have little or no empirical mechanism, and yet their creative power is rarely questioned.

It’s important to realize that gods are not only ancient constructs; we continue to create them, out of the natural human impulse to explain the unknown. These days, they may appear in more polished, scientific language, but they still serve the same function: to give form to our ignorance and relieve us from having to say, "we don’t know."

Now, contrast that with the idea of God-as-intelligence, which is not simply a religious default, but a product of inductive reasoning, the very method Hume tried to dismantle, along with causation. Ironically, both induction and causation are essential to scientific inquiry. Without them, there’s no basis for experimentation, prediction, or progress.

So let me frame my position in scientific terms:

If an experiment can demonstrate that a citric acid cycle, a self-replicating molecule, or even a simple red Lego brick can arise purely by chance, without guidance or intent, then the hypothesis of God, or intelligent causation, is falsified.

This is a statement of falsifiability, which lies at the heart of scientific integrity.

In the end, it seems we are still religious-minded creatures, not necessarily in the theological sense, but in the sense that we continue to assume we already have the framework. And from within that framework, we feel justified in deciding which ideas are legitimate and which are off-limits. This, more than anything, is the challenge we must overcome.

Dear Ziaedin Shafiei

I'm quite perplexed by the entirety of this most recent post.

The claim that "Either we accept intelligence (God, for the sake of reference), or we accept a collection of speculative placeholders, what I call gods-of-the-gaps, to fill in our current explanatory deficits." is a strawman of the entirety of our scientific understanding. First, the idea that we must choose one or the other is wrong, because saying "I don't know" is fine. As a matter of fact, it is a way for us to find what to explore next. Second, framing a well established theory with literally tons of research to support it as "speculative placeholders" is a blatantly dishonest, as this make it seem as though there is no evidence to back up the claims contained within the theory.

I'm also shocked that a scientist would say that "It’s important to realize that gods are not only ancient constructs; we continue to create them, out of the natural human impulse to explain the unknown. These days, they may appear in more polished, scientific language, but they still serve the same function: to give form to our ignorance and relieve us from having to say, we don’t know". In natural sciences, we make an observation, we formulate a falsifiable hypothesis which directly tests some aspect of the observation, and then we run an experiment which addresses the claim. If the hypothesis is false, then we move on to the next experiment, if we hypothesis is true, then we continue to develop it from there. In some cases, a hypothesis is only partially true, in which case we continue to work on those portions. This is what happened with Darwinian evolution, the gradualism component was not entirely true (but not entirely false either) and the natural selection component was verified by experiment, and based on 200 years of research, many of the components of the original theory still hold.

My next issue is that I don't think you have demonstrated that an "intelligence" is even a candid explanation, as no observation or foundation for this claim is made. You state that God-as-intelligence is reached by inductive reasoning, but that has not been shown throughout this exchange.

Now lets get to your position:

If an experiment can demonstrate that a citric acid cycle, a self-replicating molecule, or even a simple red Lego brick can arise purely by chance, without guidance or intent, then the hypothesis of God, or intelligent causation, is falsified.

First, the Lego is not a naturally forming object, so asking us to demonstrate how an unnatural object formed naturally is dishonest. If I were similarly dishonest, then I could say "human are natural and we made the Lego", so lets try and keep the subject matter to natural components please.

Second, we have multiple experiments demonstrating self replicating molecules without the influence of living organisms, making this position false. Here are some relevant papers, one demonstrating the formation of polymers and one demonstrating autocatalytic amplification of prebiotic RNA enzymes:

Article Montmorillonite Catalysis of 30-50 Mer Oligonucleotides: Lab...

Article Self-Sustained Replication of an RNA Enzyme

And if you want a demonstration of molecules following evolutionary principles, here is a paper discussing that:

Article Niche partitioning in the coevolution of 2 distinct RNA enzymes

There is some research related to the evolution of the Krebs cycle as well, but as I don't understand it I will not include it here.

To conclude, I don't find it rational or reasonable to assume that an intelligence exists without demonstrating it as a possibility first. I also find it unreasonable to claim that our knowledge of something is flawed because we have developed an old paradigm to include new components.

Dear Curt Knott

Thank you for your comment.

As you know, Darwin, and many biologists after him, did not simply say “we do not know,” which is the more cautious approach I suggested earlier in this thread. Instead, they attempted to provide a theory. For instance, Darwin did not refrain from speculating on the origin of life; he famously proposed that it may have emerged from a “warm little pond.” This, I believe, reflects an appeal to chance and time, the very point I am trying to highlight.

In Darwinian evolution, we rely on chance variation and, arguably, chance-based selection (though often misrepresented as a deterministic process). What I’m suggesting is that between the two explanatory frameworks, intelligence and gods-of-the-gaps, Darwinism has chosen the latter.

Regarding the red Lego brick, my question is: Why is it fundamentally different from a product of nature? We have never observed a Lego brick erupting naturally, but neither have we observed a living cell doing so. If we do not expect a Lego brick to form spontaneously, why should we treat a living cell, arguably far more complex, as if it could? Perhaps the difference lies in feasibility: a Lego brick can be manufactured at will, while a truly simple living cell remains beyond our current scientific and technological capabilities. This gap often leads us to default to time and chance as placeholders for explanation, and that, I believe, is the problem.

(just to clarify, by self-replicating molecule, I was referring to a simple living cell, as Darwin envisioned it arising from that warm pool. Apologies for the confusion.)

Dear Ziaedin Shafiei

Once again you are setting up a strawman. What is the god-in-the-gap? We know that mutations are random, and therefore it could be said that they are ”based on chance”, but do you think that the evolutionary biologists just throw up their hands and say “welp is random so that’s that”? No, we track mutations genetically, what the mutation was, what if any other mutation are present, and from this information we derived a nested hierarchical structure showing common ancestery. We try to explain what mechanisms caused those mutations and how they propagate through time. So no, we are not committing a god-of-the-gaps fallacy. If you are talking about Darwin’s musings, I would agree that they are simply speculation, but that is not the same as a god-of-the-gaps.

Next regarding your Lego comment. It is unreasonable to expect an explination using natural mechanisms to produce a man-made object, as they are categorically different. Man did not make nature, man did make Lego, quite simple.

As for origin of life research, we have several plausible pathways leading to protocells. For example, amino acids has been observed on meteorites, nucleotide assembly via dehydration reactions has been demonstrated, and so forth. We of course don’t know the whole story, and may never know which pathway occurred. However, with life already established consuming available resources, it would be essentially impossible to see life forming spontaneously again on this planet barring some large extinction event.

What I find the most telling is that you shifted the goalposts after your “falsifiability criteria” were met. I demonstrated one of them to be false, and the other one to be unreasonable. So since you pivoted to the origin of life, why do you reference Darwinian evolution? That theory explains the diversity of life, not it’s origin. That’s a completely different field of study, so your position from this post is irrelevant, as evolution does not address that question. To me it seems like you are the one making the god-of-the-gaps fallacy, as you are saying “we can‘t explain this (origin of life, in this case) so an intelligence must have done it”.

Finally, you have yet to defend the position of intelligence as a candid explination. I said this in my previous comment. How do you demonstrate that intelligence is even a possibility in the context you are describing?

Dear Curt Knott

Many thanks for your comments. Allow me to respond to your various points.

• You are absolutely right to say that my goal here is to critique what I view as a strawman framework, but one not constructed by me. It was laid down by philosophers like David Hume, later reinforced by Darwin, and sustained across generations of biologists who, for example, initially resisted the paleontological findings of Eldredge and Gould, the molecular challenges posed by the neutral theory, or Margulis’s work on symbiosis. I fully acknowledge the depth and sophistication of ongoing scientific inquiry. My concern is not with the data or the rigor of individual studies, but with a theoretical architecture that relies so heavily on chance, error, and time as explanatory agents.
• As I understand it, and I welcome correction, the prevailing view holds that mutations are largely random, mostly neutral or deleterious, with a small minority being beneficial. Coupled with deep time, this model asserts that such mutations, filtered by natural selection, are sufficient to explain life’s full complexity. In this narrative, chance and time function as de facto gods-of-the-gaps: abstract forces invoked precisely where detailed understanding falters, cloaked in scientific respectability but carrying the same explanatory ambiguity as mythological deities.
• You also noted that humans did not create nature, and of course that is true. But the question remains: What is the fundamental difference between a manufactured object and a living organism? For centuries, shaped by religious metaphysics, we have now cordoned off “life” into a special, untouchable category. Yet functionally, our own technological systems arise through design, iteration, error correction, and modular integration. Given that even the simplest cell dwarfs any human-made object in complexity and coordination, why should we not consider the possibility of intelligence, non-human, non-local, as part of the explanatory landscape?
• To clarify: this is not goalpost-shifting. We are still within the domain of explaining life’s origin and transformation, just as Darwin sought to do. If there’s a misconception there, I’m more than open to being corrected. But let us not forget that the most-cited origin-of-life studies rely on laboratory-crafted conditions, often using pre-synthesized components like 10-mer primers; sophisticated, engineered starting points that would be vanishingly improbable under real prebiotic conditions.
• You are also entirely correct that the origin of life and its evolution are conceptually distinct. However, the point is that Darwin and Neo-Darwinists conflate them by relying on the same explanatory machinery, chance and time, to account for both. This conflation reveals a deeper philosophical dependency: whenever detailed mechanisms are lacking, abstract placeholders step in.
• In the end, whether it is a machine, a book, or a vaccine, complex functionality emerges only through specification, design, design validation, quality control, and reproducibility. We have yet to demonstrate that similar levels of coordination and information can arise from undirected forces. That, I believe, is the intellectual legacy of Hume and Darwin: not in what they resolved, but in the way their frameworks have licensed the use of undefined creative forces masquerading as mechanistic explanations.
• Given this asymmetry, and drawing upon inference from known causes, it seems more reasonable to consider intelligence not merely a speculative idea, but a legitimate hypothesis and potentially even a theoretical framework in its own right.

Dear Ziaedin Shafiei

Let's analyze your intelligence claim. If intelligence is driving evolution, then you would need to demonstrate that the development of organisms follows a directed path towards some goal defined by this intelligence. How could this be the case when we know mutations are random and that an overwhelming majority of them are either harmful or benign? This does not seem "intelligent" to me.

If you are saying time is a "gap" then you would need to demonstrate that your "intelligence" removes that gap, or at a minimum is able to explain it. Do you think that this "Intelligence" makes species after a single round of mutations? Or do you think that the intelligence is able to direct the mutations? You would need to demonstrate that either of these are the case is you have an issue with time.

Now lets look at how it is currently explained. Mutations are random, with some being beneficial and some being harmful. The harmful ones die out, while beneficial ones propagate more readily until the mutation is fixed in a population. After enough successive mutation, one population may become distinct from its parent population due to different mutations. Through this mechanism all species are related through common ancestry. This theory is able to explains why harmful mutations occur, as well as why it takes time. The time it takes for species to evolve has been measured in many species through radiometric dating, and these ages have also been run through molecular clocks and tend to show good concordance with the radiometric ages. Therefore the time "gap" is not a gap at all, but rather a experimentally robust and theoretically sound way of explaining how mutations accumulate in a species.

Article Dating the Time of Origin of Major Clades: Molecular Clocks ...

Now lets go to the "what is the fundamental difference between a manufactured object and a living organism" question. The fundamental difference is that life is not made with a purpose in mind, meaning that it does things "good enough" so to speak. Manufactured objects are constructed "top down", with specific purposes in mind. This makes the fundamental way these two things from entirely different. In evolution the process is "bottom up". This is why I reject the idea that we can use man made objects as an analogy to life.

I reject your claim outright that you are not moving the goalposts. I would go as far as saying your "warm little pond" comment is a quote mine. Darwin did look into the origin of life, but he did NOT claim that his evolutionary theory was the way to do it. He said

"it is often said that all the conditions for the first production of a living being are now present, which could ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sort of ammonia and phosphoric salts,—light, heat, electricity present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present such matter would be instantly devoured, or absorbed, which would not have been the case before living creatures were formed...".

Therefore, your claim of "...Darwin and Neo-Darwinists conflate them by relying on the same explanatory machinery..." is wrong. Just because one theory uses time and chance does not mean the mechanism or reasoning are the same. What Darwin is saying is that the formation of life through some chemical means MAY be possible. He even confirms what I told you previously about how we would not be able to see it happen in the world today with life already established. As further evidence that he did not think evolutionary theory would work for the origin of life, he was quoted as saying:

"...it is no valid objection that science as yet throws no light on the far higher problem of the essence or origin of life"

"…it is mere rubbish thinking, at present, of origin of life; one might as well think of origin of matter".

He was even criticized for this limitation of his theory by other contemporary scientists. So please don't pretend like the two are being conflates, because they definitely are not, and especially not today by modern biologists and chemists.

Article Charles Darwin and the Origin of Life

As for origin of life research, the researchers are looking into possible mechanisms through which a protocell can be formed. This process is obviously extremely complex, and trying to perform all the necessary steps in one experiment is simply not possible. So they break the steps apart and work on one step at a time. Are you suggesting that we should throw basic elements into a bucket and let it sit until life forms, without adjusting for the available mineral surfaces, interactive environments, temperature and atmospheric conditions? Even if such an experiment were possible, it took over 500 million years for the first evidence of life to arise on our planet. Origin of life researchers use materials that would be expected to be available at the time to try and develop our understanding from there. Some researcher even use field analogs for their studies, like David Deamer, who has some preliminary results from reactions using hot spring water, as well as a long form rationale for how to perform these kinds of experiments in hot spring analogs.

Article The Hot Spring Hypothesis for an Origin of Life

Article Amphiphilic Compounds Assemble into Membranous Vesicles in H...

"In the end, whether it is a machine, a book, or a vaccine, complex functionality emerges only through specification, design, design validation, quality control, and reproducibility". How are you determining function, and what differentiating them? I could argue that a snowflake is complex and has function and they form spontaneously with beautiful patters which are semi-predictable, but they definitely didn't go though those steps. That is a completely ridiculous position, as their complexity is easily explained without the need to appeal to an intelligence. And, once again, life did not form "top down" it developed "bottom up", so the analogy with man made objects is wrong.

Here is my challenge to the intelligence position:

1, If we are Intelligently designed, then why are there harmful or even benign mutations? Neither of these are make sense if an "intelligence" is causing them.

2, Why do we see organisms evolve predictably with changing environment? If an Intelligence has a plan for these organisms, why wouldn't he continue developing those intentions?

3, If everything was designed, why have a majority of animal families gone extinct?

4, How does this intelligence mechanistically modify the genes or structure of an organism? Note that saying a mutations is not an answer, I'm asking HOW he does this.

5, Demonstrate that intelligence, as you describe it, is POSSIBLE. This is the third time I've asked for this, and I have yet to hear an answer.

Dear Curt Knott

Thank you for raising several important challenges to the idea of intelligence in the emergence and evolution of life. Let me address them point by point.

First, I would like to clarify two important points:

1 - Orgel’s Second Law and the Problem of Bad Design

Orgel’s Second Law, "Evolution is cleverer than you are", was introduced at a time when Darwinian evolution was widely considered the sole scientific framework for understanding life. Some evolutionary biologists hastily dismissed certain biological structures, such as the appendix, the pineal gland, or non-coding DNA, as useless or vestigial.

Orgel's law was a cautionary reminder that a lack of understanding does not imply a lack of function. What may appear to be a flaw or evolutionary leftover could turn out to be ingeniously functional once fully understood. This principle was supported even by ardent Darwinists like Daniel Dennett.

Despite this, the lesson is still not widely heeded. For instance, the recurrent laryngeal nerve in giraffes is now commonly cited as an example of "bad design". In [1], I address such claims and argue that the less we know, the bolder we become in proclaiming “bad design” or evolutionary leftovers. The fact that more than 98% of the genome was once labelled as “junk” underscores the danger of proclaiming final judgments in the face of deep ignorance.

2 - De-religionizing Our Epistemology

As argued in [2], the historical entanglement of religion with philosophy has often constrained critical thought. I advocate for a dereligionized worldview, one that avoids assuming that we already possess the "theory of everything" and “knowledge of everything” as well as imprinting dualistic assumptions that linger even in ostensibly secular contexts. A clear example: when we consider a malfunctioning car, we do not deny it was designed just because it breaks down. Nor do we argue that poor design eliminates the fact of design altogether. The same logic should apply to biology. Design can fail, but failure does not negate design.

Mutation and forethought for Error Correction

Your point about harmful mutations is appreciated. Mutations can be caused by various factors, mutagens, replication errors, or environmental stressors. However, life is not passive: it comes equipped with intricate systems of repair, error correction, and cell-cycle control, including proofreading enzymes and apoptosis when damage is too severe. In fact, these mechanisms are strikingly analogous to practices in software engineering, albeit more autonomous. And while both biological and digital systems strive to maintain integrity, the biological ones are far more self-regulating and adaptive, an insight worth reflecting on when considering the origin of such complexity.

Time as a God-of-the-Gaps

I did not say time is a gap, I said it has become a kind of god-of-the-gaps, invoked whenever we face explanatory dead ends in the origin and diversification of life. The same applies to "chance." These are not mechanisms; they are conceptual placeholders, filling our ignorance with the illusion of understanding. Also, instead of speculating or demanding a complete explanation of how a designer might have created life and enabled its evolution, it would be more constructive to support the hard empirical work of evolutionary biologists and palaeontologists, such as Gould and Eldredge, whose contributions were long marginalized, not due to lack of evidence, but because they challenged prevailing scientific dogmas. Please remember that even within the Earth-centred system, it was still possible to predict solar and lunar eclipses. The key issue is not predictive success, but the need to remove ideological barriers to better understanding.

Beneficial Mutations and Software Analogy

Yes, most mutations are deleterious or neutral. Beneficial mutations are often cited as the driver of complexity in evolution. However, this idea emerged before we understood the complexity of cellular machinery. Today, it seems implausible that random, undirected changes can lead to increasing functionality in such a precise system.

In software development, randomly modifying code is almost always catastrophic, thus, we never allow random, blind edits to our codebase. Any change, especially one intended to be beneficial, requires deep knowledge and precise intervention. Even robust software with built-in redundancy cannot evolve through random alteration. Why should life, which is orders of magnitude more complex, be any different? To invoke randomness as a creative force in biology, without clarifying the informational framework within which it operates, is to make a claim that would be laughed out of the engineering world.

Origin of Life

You are absolutely right, though Darwin mentioned the “warm little pond” only in a private letter and with great caution, the idea profoundly influenced 20th-century origin-of-life research. It inspired Oparin’s “primordial soup” theory and the famous Miller–Urey and dozens of follow up experiments. Multiple reanalyses of the original samples have also been conducted using modern analytical techniques. Even NASA along with other institutions have published standardized protocols for conducting Miller–Urey-type experiments, enabling researchers to explore a wide range of planetary conditions. These experiments support my claim that the issue is not merely about Darwin’s cautious speculation. Rather, the idea has been taken seriously and actively investigated for over a century. Today, the concept persists in hypotheses involving shallow pools, hydrothermal vents, and chemically rich settings. Yes, despite its speculative origins, Darwin’s image provided a naturalistic framework for explaining life’s emergence, perfectly aligning with the materialist shift in biology and the broader goal of avoiding supernatural explanations. In contrast, I view Darwin’s remark as an uninformed conjecture and therefore reject the idea that life arose purely by chance over hundreds of millions of years, a scenario that, to me, seems even less plausible than expecting a simple red Lego brick to assemble itself through random processes.

The Lego Brick Analogy

I see no compelling reason to separate the origin and evolution of life from the question of purpose or design. To claim that life arose without intent, while we still lack the means to replicate even its most basic forms, seems less like scientific humility and more like metaphysical presumption. We should not pretend we know more than we do, especially regarding something as staggeringly complex as the cell. The burden of proof does not lie with those proposing intelligence, but with those insisting that pure chemistry, unaided, created the conditions for replication and metabolism. If we have never observed a cell emerge from non-living matter, and we don't presume that a Lego brick can self-assemble, then attributing life's origin solely to chance and time seems ideologically driven rather than empirically justified.

Shifting goalpost

As I previously pointed out, it is well documented that many prebiotic experiments begin with pre-synthesized components, such as 10-mer RNA primers, which are intelligently designed and do not arise spontaneously in nature. My original point can only be refuted if there exists an experiment in which such primers are not used and the conditions are not intelligently controlled. Therefore, I do not believe my argument has been adequately addressed. Even if the discussion has evolved, extending the inquiry to deeper questions is not a case of goalpost-shifting in bad faith, but rather a natural and necessary progression of scientific investigation.

Snowflakes and Complexity

Using snowflake formation to refute biological design seems misguided. Snowflakes are low-information patterns governed by simple crystallographic rules, often reproducible under known lab conditions. A wheelbarrow, or a ribosome, is another matter entirely. The analogy breaks when functional complexity enters the picture. We invoke snowflakes only because we have already decided life is like them. But life has self-repair, adaptation, and information encoding, features snowflakes do not share. Equating the two is a categorical error, driven by ideological commitment to naturalism rather than a fair analysis of complexity.

Your Numbered Challenges

Extinction: Extinction does not disprove design; designed products also go extinct when they no longer serve a purpose or conditions change.

Gene modification: The fact that we do not know how intelligence could modify life does not invalidate the hypothesis. Scientific history is filled with questions we could not initially answer.

Possibility of intelligence: You asked me to demonstrate the possibility of the type of intelligence I propose. That assumes we already know the limits of what is possible in the universe. This is again a kind of epistemic arrogance. I do not claim to know, but argue that this is a legitimate avenue of inquiry. I would argue, as I have done in [3], that this demand for total and unscientific explanation blocks productive investigation.

Design, whether in biology or engineering, is not disproved by error, failure, or ignorance. It is identified by pattern, purpose, and interdependence of parts. We should not let ideology replace inquiry, especially when dealing with questions as profound as the origin and evolution of life.

[1]

Preprint SCIENCE IN THE SHADOW OF METAPHYSICS Part 1 -Gods of Science!?

[2]

Presentation God: Valid Scientific Conclusion

[3]

Preprint SCIENCE IN THE SHADOW OF METAPHYSICS Part 2 -The Issue of Existence

I warmly thank Curt Knott for his point-by-point answer to Ziaedin Shafiei.

I did not make any new intervention because I do not see any real debate here. Ziaedin Shafiei is explaining his point of view without giving any evidence supporting it. He apparently did not publish anything on scientific journals: we are waiting for this to start a debate.

Anyway, I would like to spend a few words to defend Gould and Eldredge, who have been put in this discussion without a clear understanding of their thought. Please, let them out of this.

Dear Cesare Andrea Papazzoni

I also warmly thank you for your comments. I appreciate your engagement, even though we may differ in our interpretations.

While you suggest that no real debate is taking place, I am content to have participated in this discussion having advised that we should

• not follow Darwin’s conjectures on the origin of life simply because he was Darwin
• strive to dereligionize our thinking; for example, by avoiding assumptions of omniscience and rejecting dualistic thinking
• be cautious not to rely on “gods-of-the-gaps”, such as chance and time, to explain complexity, design, and the continuous emergence of life and its evolution.

I also pointed out that these gods-of-the-gaps stem from the philosophical legacy of Hume, who rejected causation and inductive reasoning, the very foundations of scientific inquiry.

If this message sparks further reflection, then the conversation has been worthwhile.

I thank Cesare Andrea Papazzoni for the encouragement. I think it is important to call out opinions which are not based on evidence, especially when they are formulated in such a way as to erroniously degrade well established scientific understanding. This kind of thinking can be damaging, especially when disseminated to the public.

Dear Ziaedin Shafiei

This will likely be my final response because based on our previous exchanges, you will not be reasoned with. You contradict the scientific consensus that evolution is a "bottom up" approach and continue to use man made "top down" objects as analogies. You shift the goalposts to defend your assertions and claimed that the origin of life researchers were not doing research pertinent to your falsification criteria. You have also brought up several quotes and laws which have been misrepresented or are completely inaccurate. Based on this I'm convinced you are deliberately trying to deceive to me.

I will respond to the comment from each of the sections you laid out.

1 - Orgel's Second Law

This law states, as you said "evolution is smarter than you". This axiom was formulated as a reminder that no matter how complex a biological structure, evolution is able to bring it about, and whether or not we can explain it right now does not change that. It has NOTHING to do with "bad design" or vestigial organs in any way. As a matter of fact, the development of vestigial structure would be one of the evolutionary explanations for certain organs. This is one of several quotes and laws you have brought up during these past few exchanges to mislead the conversation. The paper below provides a good explanation of what the second law was meant to represent.

Article The genetic code has a 'shift' key

2 - De-religionizing Our Epistemology

I find this title to be dishonest, and the argument of "De-religionizing" is contradicted by your appeal to intelligence. Religion is defined as "the belief in and worship of a superhuman power or powers, especially a God or gods" or "A particular system of faith and worship". Neither of these apply to the rigor of scientific inquiry. The second of these definitions is particularly harmful as faith is defined as "strong belief in the doctrines of a religion, based on spiritual conviction rather than evidence". In science, we follow the evidence where it leads, and ones feelings don't matter. Nothing is sacred. If you managed to demonstrate or prove that this "intelligence" is the cause, you won't just be praised, you would win the Nobel prize. There is nothing to De-religionefy here.

3 - Mutation and forethought for correction error

Your claim about error correction mechanisms is irrelevant. In your worldview, these mutations are being caused by the "intelligence", and if he gets by this correction mechanism then it doesn't matter that they exist. Similarly, in the evolutionary paradigm, genetic errors arise because this correction doesn't work 100% of the time. Your appeal to a computer code is inaccurate as evolution does not have a specific function in mind, random changes occur and then they are selected for.

4 - Time as a God-of-the-gaps

For the 3rd time, this is wrong. Mutations are random, we know this. It takes time for beneficial mutations to accumulate within a population, we know this. We do not say "we don't know, therefore time". They are not "conceptual placeholders", they are facts. When you say "Also, instead of speculating or demanding a complete explanation of how a designer..." Did you not read what I said? I asked "demonstrate that this intelligence is a candid explanation", meaning I just wanted some observation or parallel which indicates your position, not a complete explanation. There is no "ideological barrier", demonstrate the possibility of your position, then we'll talk.

5 - Beneficial Mutations and Software Analogy

Your claim in this section is entirely voided by Orgel's Second Law which you brought up earlier. Irrespective how unlikely it seems, evolution is able to produce any observed biological structures. Using the discovery institute computer program analogy is not applicable, as, once again, computer code is made with a specific purpose in mind, biological organisms are not.

"To invoke randomness as a creative force in biology, without clarifying the informational framework within which it operates, is to make a claim that would be laughed out of the engineering world.". Really? Because computer programmers have used a form of "evolutionary computation" to improve their existing programs for decades. When this is done, the code improves based on a simple set of rules and then is modified based on input data. So your claim is wrong. Here is an overview evolutionary computation explicitly stating that the pathway used is "bottom up" like in biological processes, further proving that your "top down" approach is false.

Article Evolutionary Computation: An Overview

6 - Origin of Life

Based on your comments in this section, you seem to think that Miller-Urey type experiments are invalid. Why? We know the conditions and the possible material which would have been available during the early earth. These experiments were formulated to test the prediction that organic molecules can be formed from inorganic ones in early earth conditions. The fact that time and change are involved is irrelevant. They made a prediction, tested the prediction, and the prediction was vindicated.

"Yes, despite its speculative origins, Darwin’s image provided a naturalistic framework for explaining life’s emergence, perfectly aligning with the materialist shift in biology and the broader goal of avoiding supernatural explanations." Are you implying that the shift to naturalism was wrong? The term supernatural is defined as "(of a manifestation or event) attributed to some force beyond scientific understanding or the laws of nature". So, by definition, appealing to the supernatural is not an explanation, and should be dismissed at face value. If it can be demonstrated, then it is no longer supernatural, and we can work on developing our understanding from there.

7 - Lego Brick Analogy

Your lack of understanding and refusal to see the difference between "bottom up" and "top down" creation is the fundamental issue. Your claim of "we lack the means of creating even its most basic forms" is also wrong. We know how to get from inorganic molecules to organic molecules, we know how to form amino acids from those organic molecules, we have a good idea of the first protocell membrane, and and we have several hypotheses investigating the remaining steps. So we know many of the steps, but are still missing some. You are correct, the burden of proof is on us to demonstrate that these processes can lead to life. You are wrong however, saying that you don't have a burden of proof for demonstrating intelligent design. Both sides are making positive claims, both sides have the burden of proof, and unlike you, scientists are actively working on gathering that proof.

"If we have never observed a cell emerge from non-living matter, and we don't presume that a Lego brick can self-assemble, then attributing life's origin solely to chance and time seems ideologically driven rather than empirically justified." The only ideology being expressed is naturalism, as science is only able to evaluate the natural world. From what you have said, can I reasonable say that you think that if we don't know precisely how life originated we can claim that god did it? I'm pretty sure that is the textbook definition of a god-of-the-gaps.

8 - Shifting Goalposts

In this section you are claiming that the evidence provided by the experiments I gave you were "influenced by intelligence" and therefore not pertinent to your falsifiability criteria. What kind of experiment would you propose that isn't "intelligently designed"? You said that the Miller-Urey type experiments are invalid above, even though those experiments have virtually no involvement after the setup and can run for decades. Since you don't accept that a cumulative set of experiments is sufficient, and that you won't even acknowledge that these researchers are making some progress towards that goal, tells me that you probably wont yield to any experiment I show you. I suspect the only thing that would convince you is if we throw a bunch of elements in a bucket and wait for it to produce a protocell. I explained in the previous post why this is a ludicrous position to hold, as it took over 500 million years for the first signs of life to appear on earth. Additionally, it would be impossible to have an experimental setup which is able to consider all possible conditions and environments from which the building blocks of life arose, such as tide pools, hydrothermal vents, meteor impacts and lightning strikes. Even if this were possible, the size of the vessel would reduce the number of chemcial interactions, exponentially increase the amount of time needed for life to form.

"Even if the discussion has evolved, extending the inquiry to deeper questions is not a case of goalpost-shifting in bad faith, but rather a natural and necessary progression of scientific investigation." I completely disagree. When there is a proposed position, like the one you said originally regarding how to falsify your "intelligence" position, you moved the goalpost with the intention of not acknowledging the refutation. I don't believe you when you say "not a case of goalpost-shifting in bad faith", because otherwise you would have acknowledged what I said and talked about those points with reference to your criteria. We discuss a topic to completion, then we continue, we don't jump around becuase its convenient for you.

9 - Snowflakes and Complexity

Your basic claim in this section is "people design things with complex function, therefore life must have been designed because it seems to have a complex function". This is a ridiculous position, as, once again, we know certain aspect of life arose by chance. The snowflake analogy was there to show that complexity can arise naturally. If you want something with a "complex function" what about the water cycle? It formed spontaneously, is far more complex than your wheelbarrow or you computer code, and performs a myriad of functions. So yes, it is possible for complex systems to form spontaneously.

10 - My Challenges

Extinction: Your response does not address the challenge. If an intelligence is guiding evolution with a goal in mind, then why would they allow large scale death of their creations, especially when they can guide the evolutionary process to preserve those species.

Gene Modification: While you are correct to say that not knowing how something works does not invalidate a hypothesis, I don't think you have proposed a testable hypothesis about "intelligence" and gene modification to be falsified. As a reminder, such a hypothesis would be in the form of "if god were to cause mutations then we would observe XX in the experiment". NOT "You need to show XX for god to be disproven".

Possibility of intelligence: "That assumes we already know the limits of what is possible in the universe. This is again a kind of epistemic arrogance." No, I don't assume we know the necessary limits of what is possible in the universe. I just want some parallel or observation which would indicate that your position is possible. For example, dark energy was proposed in response to the observed acceleration of the expanding universe. Do we know what it is? No. Do we know all of its properties? No. Is there an indication that its there? Absolutely. If this is a legitimate avenue of inquiry, then you should be able to at least tell me the indication of why its legitimate.

"I would argue, as I have done in [3], that this demand for total and unscientific explanation blocks productive investigation." This is not applicable to evolution/origin of life research, but it is applicable to your "Intelligence". As I showed before, appealing to the supernatural is, by definition, not an explanation, and thousands of papers from thousands of researchers aligning with a position is scientific evidence.

I would also argue it is more arrogant to assume you are correct without any evidence to support your position, or to project the flaws of ones position onto someone else assuming they are just as bad as you. That's the reason I decided to respond at all. Your god-of-the-gaps claim calls the diligence and integrity of thousands of scientists into question. I think it is reprehensible that someone as ideologically bound as you would have the gall to post this and waste the time of respectable scientists for no other reason than to project and misinform.

In the end, you failed to meet the basic criteria for something to be considered, which is evidence. As Hitchens's razor states "That which is asserted without evidence may be dismissed without evidence". I hope in the future you can drop the dogma and engage with the evidence honestly, and if some actionable suggestions or improvements arise, we can discuss and improve the theory with these new ideas.

Dear Curt Knott and Cesare Andrea Papazzoni

Thank you for your comments. I understand they were offered with conviction, though they included elements of personal accusation, prescriptive advice, and a tendency to sidestep some of the core points I’ve raised. From my experience, this is not uncommon in discussions around evolutionary biology.

The central issue, as I see it, is the assumption within Darwinian evolution that life is fundamentally different because it supposedly arises through a purely bottom-up process. This dichotomy, between bottom-up and top-down origins, is often taken for granted. But I ask sincerely: is it truly impossible for life to originate through a top-down process? This is the key question I believe deserves honest scrutiny.

To support the bottom-up view, a broader philosophical framework is often invoked, consciously or not. David Hume’s rejection of causation and inductive reasoning, which are foundations of scientific inquiry, opened the door to explaining order through nothing more than matter in motion over time. This idea, inherited by Darwin and others, laid the groundwork for attributing biological complexity to random mutations and long spans of time.

Yet when this process is challenged; when we ask, for example, why we cannot observe even the chance assembly of something as simple as a red Lego brick, the response is often that the process simply takes millions of years. This is why I refer to “chance and time” as gods-of-the-gaps: explanatory placeholders perched high atop the modern Tower of Babel. If I understand correctly, your position is that a Lego brick cannot arise by chance because it is a “top-down” artifact, whereas life, being “bottom-up,” is categorically different. Please confirm if this is indeed your position.

Dear Curt Knott

CK "This kind of thinking can be damaging, especially when disseminated to the public."

I understand and share your concern that my argument could be misused by others, particularly for ideological or religious purposes. I have done what I can to make it clear that I strongly reject religious frameworks as explanatory models for the natural world [1].

That said, I still find it troubling that many scientists continue to defend a theory that, in my view, can be meaningfully challenged with just a few pointed questions. Why must we maintain allegiance to a model so fragile that it risks collapsing under modest scrutiny? Why, in this modern age, do we continue to invoke what feels like a new version of the rain god, now clothed in scientific language?

If science is truly self-correcting, then we should be willing to acknowledge when we have begun from the wrong footing, and be open to rethinking the framework accordingly.

[1] Preprint Religion-The Triumph of Deceit

I am compelled to write one last intervention.

I started to answer to Ziaedin Shafiei because I was convinced there were some flaws in his reasoning, naively thinking to contribute to adjust his misconceptions about the evolutionary theory. Unfortunately, after following the discussion with some colleagues among which James Bonacum and Curt Knott (many thanks again to both) I have to admit that I see in the author of this post no real willing to debate, only a desperate try to maintain a position which is allegedly new but really refuted repeatedly in the last >150 years. No evidences supporting this so-called "intelligence" are brought to us to start a scientific discussion, whereas the countless counter-evidences are simply neglected.

Finally, since I am a paleontologist, I was especially sad to see the misuse of what S.J. Gould and N. Eldredge wrote over time. I would like to underline that it is simply not true that their proposals are discarded by scientists. Instead, they were seeds for a fruitful scientific debate both on the relative importance of the "rapid" evolutionary transitions and on the hierarchical levels on which evolution occurs, just to mention a few main points.

I hope that on this precious space for debate there will be better chances to exchange ideas on a common scientific ground. Best regards to everybody.

Dear Cesare Andrea Papazzoni

Thank you for your response.

It seems, unfortunately, that rather than addressing the core question I posed, whether life must arise through a purely bottom-up process, the reply has turned more personal. This is a central issue in our discussion, and one I believe deserves a direct and thoughtful answer. My full line of reasoning, explaining why I reject both religion and Darwinism as correct explanatory frameworks for life, is publicly available in my presentation [1] and its references here on RG.

Regarding your objection to my references to figures such as Gould and Eldredge: as respected scientists, their ideas belong to the broader scientific discourse. Of course, anyone is welcome to correct a misrepresentation of their work, and I would genuinely appreciate any such clarification. But suggesting that I should not invoke their names risks echoing the kind of gatekeeping that science has worked hard to move beyond.

I welcome open, evidence-based discussion, not appeals to authority or exclusion.

[1]

Presentation God: Valid Scientific Conclusion

Ziaedin Shafiei,

it seems as we are not understanding each other. I guess my words were not clear, so I try to better explain my points:

1. to move the discussion from the evolutionary process (which has been repeatedly tested and on which the knowledge is quite established) to the big issue of the origin of life (which instead is much less established and on which science says "we don't know" for several key points) is an old trick to avoid facing with the tested Neodarwinian model. Anyway, as repeatedly written in this thread, you do not suggest any alternative testable model, so there is nothing to discuss on.

2. You are of course free to support or discard or discuss the Gould and Eldredge statements, but you are not free to distort them, and to state that they are ostracized by other scientist, which is simply not true. This is not an appeal to authority, it is a plea to correctly represent the position in scientific debate.

3. Therefore, there is nothing personal as long as you correctly report the facts and the opinions. If in some way I was wrong, please tell me exactly where and why I did.

Dear Cesare Andrea Papazzoni

Thank you for your response.

I would like to begin by emphasizing that I have no intention to mislead or “trick” anyone. My questions and objections are sincere and rooted in a critical examination of Darwinian and Neo-Darwinian frameworks. My concern lies specifically with the philosophical foundations that support these theories, particularly the reliance on chance and deep time as explanatory mechanisms for both the origin and evolution of life.

Neo-Darwinism, in many of its formulations, has extended Darwin’s speculative remark about life originating in a “warm little pond” into serious hypotheses like the primordial soup model. Therefore, I consider the role of chance and time, especially when invoked without sufficient empirical constraints, a continuation of Humean scepticism, which dismissed causality and inductive reasoning. I believe science should challenge, rather than absorb, such philosophical roots, especially when they are used to frame foundational biological claims.

Regarding the reception of punctuated equilibrium, I want to be clear that I never claimed that Gould and Eldredge were formally ostracized. Rather, I pointed out that their theory was met with strong resistance from within the evolutionary biology community. This is well-documented, not only in terms of initial dismissal of their ideas, but also through personal attacks and ridicule. Describing Gould as “something of an intellectual fraud” and mockingly referring to the theory as “evolution by jerks” are just a couple of examples.

My mention of the lack of single-authored monographs supporting punctuated equilibrium (aside from those by Gould and Eldredge) was intended to highlight a broader institutional reluctance to fully engage with or develop the theory further, despite its empirical grounding in the fossil record.

Thank you again for engaging in this discussion. I believe constructive debate, especially when conducted respectfully, is essential for scientific progress.

Warm regards.

CK 06July25 "I think it is important to call out opinions which are not based on evidence, especially when they are formulated in such a way as to erroneously degrade well established scientific understanding. This kind of thinking can be damaging, especially when disseminated to the public."

Scientists often emphasize that science evolves through self-correction, unlike religion. However, the case of Darwinism challenges this claim. Critics like CK seem to dismiss the principle of falsifiability, treating legitimate questioning as off-limits. Unfortunately, the historical tension between science and religion has compromised the integrity of science itself. In resisting religious influence, we must not abandon scientific rigor. Darwinism, rooted in Hume’s notion of chance creation over deep time, lacks the empirical and methodological foundation expected of a scientific theory.