Do patterns of phylogenesis show evolution?

[Difflugia]

Question for debate: Are the patterns seen in molecular phylogenies sufficient to show that biological evolution occurred?

For reference and easier Googling, the science of generating evolutionary trees is known as cladistics or phylogenetic systematics. Using DNA sequence data to generate the trees is molecular phylogeny.

The standard of evidence I'll be discussing is reasonable doubt. Even that's pretty broad, but if your argument hinges on "possible," you should be able to at least quantify that.

I've generated phylogenies using online tools previously and discussed them in this post. I tried to start a tutorial in this thread. If someone wants to discuss how to actually use the tools and data, feel free to ask questions in the tutorial thread and I'll pick it back up.

This debate question is a response to this comment.

[Difflugia]

I want to clarify again that Im not redefining intelligence arbitrarily.

I disagree.

When I refer to intelligence, I mean the capacity to solve problems, optimize systems, or generate complexity in ways that are adaptive and functional.

OK, those can be considered features of intelligence, but you've already expressed an interest in broadening the definition to include things we don't normally include in intelligence. If that's the discussion you'd like to have, then let's come up with a different word or phrase for what you're talking about.

This isnt about invoking supernatural consciousness or intentits about recognizing traits we associate with intelligence in natural systems like evolution and ecosystems. These phenomena are observable, testable, and well-documented.

But they're not intelligence, even if some of the emergent properties you see are sometimes associated with intelligence.

I think its important to consider that many accepted definitions of intelligence are rooted in human-centric idealism. These definitions often reflect how humans perceive intelligence through our own lens of cognition, creativity, and intent. This focus might cause us to overlook clear evidence of intelligence in non-human contexts simply because it doesnt match the way humans exhibit or recognize it in themselves.

That's now a third topic.

For example, we might dismiss the problem-solving capacity of evolution or the self-organizing resilience of ecosystems as non-intelligent because they dont involve conscious human thought. But these processes demonstrate characteristics we traditionally associate with intelligence: optimization, adaptation, and complexity.

What does "problem-solving capacity" mean in a context that isn't human-centric? You're still fuzzy on your definition while, at the same time, you're trying to argue that whatever you're talking about is important to evolution in a way that's meaningful.

When rocks roll downhill and seek local minima in terms of gravity and potential energy, that can be seen as a kind of sorting. Is that nature solving a problem? Is that intelligence? If it is, then we can already say that "intelligent design" is too broad to be meaningful to the discussion that we're having now.

Ignoring this could be a form of cognitive bias. By focusing solely on human-like cognition, we risk ignoring evidence of intelligent outcomes in processes like evolution and self-organization, which science actively studies.

Maybe, but we can't know until you've defined what we're talking about. I suspect that ignoring this evidence is eliminating something that is simply not germane to the discussion.

Ive pointed to specific examplesfine-tuning, emergent complexity, convergence, and consciousnessthat exhibit traits we often associate with intelligence. These are not speculative claims but phenomena actively studied by science. If you disagree that these processes reflect problem-solving or optimization, Id love to hear how you interpret them.

You're making the leap from "traits we often associate with intelligence" to "intelligence." Since you are reluctant to discuss more narrow definitions, I suspect that later equivocation is important to your argument, whether you realize it or not.

My argument isnt that evolution requires intelligence in a mystical sense (consciousness remains enigmatic and not fully understooda phenomenon we continue to study and explore scientifically) but that it demonstrates characteristicslike iterative refinement and optimizationthat align with broader definitions of intelligence.

And those broader definitions of intelligence stray into areas that aren't normally considered intelligence, but you still want the concept of intelligence to be meaningful to the discussion.

This perspective doesnt replace evolutionary science but offers a complementary way to explore its remarkable outcomes.

Are they? Define them and we'll decide if those are complementary or simply a distraction.

Lets move past the debate over definitions and focus on the actual processes. For instance, how do you interpret the repeated, efficient solutions seen in convergent evolution?

Similar niches necessarily have similar local minima in terms of ecology. That offers insight into the process and has a certain predictive power, but it's not intelligent as we normally define the term.

Do you think theres a deeper principle behind these patterns,

Again, this is extremely vague and I've had enough discussions with you to suspect that "deeper principle" is about to move in a mystical direction.

or are they entirely reducible to environmental pressures?

By the definitions we use within ecology and evolution, yes.

[William]

[Replying to Difflugia in post #41]

I think there are a few areas where our discussion might benefit from clarification and focus. Id like to address some recurring issues in your response and point out where I feel some of my arguments might have been misunderstood or prematurely dismissed.

1. Clarifying My Position on Intelligence:
You suggested that I am redefining intelligence arbitrarily or making an unwarranted "leap" from traits associated with intelligence to calling these processes intelligent. However, I have consistently defined intelligence in this context as the capacity to solve problems, optimize systems, or generate complexity in adaptive ways. This is not an arbitrary redefinition but an attempt to broaden the framework in a scientifically meaningful wayone that aligns with observable patterns in natural systems.

By labeling this a "leap" or "equivocation," you seem to have mischaracterized my argument (a strawman fallacy). I am not anthropomorphizing natural systems or invoking supernatural forces but suggesting that certain traits we associate with intelligence are evident in evolutionary processes themselves. Could we discuss this specific point rather than reframing it as something I havent claimed?

2. Moving the Goalposts on Definitions:
You asked for a clear definition of intelligence and argued that the term might be too broad for this discussion. Yet Ive already defined intelligence and provided examples of fine-tuning, emergent complexity, and convergence to illustrate my point. By continually dismissing these examples as "vague" or requiring an entirely different term, it feels as though the criteria for engaging with my argument keep shifting (moving the goalposts).

If theres a specific aspect of my definition or examples you find inadequate, Id appreciate if you could point that out explicitly so I can address it.

3. Addressing Fine-Tuning and Consciousness:
I noticed that two key points I raisedfine-tuning of physical laws and the emergence of consciousnesswere not directly addressed in your response. These are significant aspects of my argument and deserve discussion. For instance:

Fine-Tuning: The precision of physical constants and conditions enabling life is a well-documented phenomenon. How do you interpret this in the context of evolutionary theory? Does it suggest a deeper principle, or is it entirely coincidental?

Consciousness: Evolution has led to self-aware beings capable of reflection and abstract thought. This is arguably one of the most remarkable outcomes of evolutionary processes. Do you see this as merely another byproduct of environmental pressures, or might it point to something more?

Your feedback on these specific points would help clarify your stance and deepen our discussion.

4. False Dichotomy in Defining Intelligence:
You suggested that if we expand the definition of intelligence beyond human-like cognition, we need to "come up with a different word." This creates a false dichotomy between rigidly adhering to conventional definitions of intelligence and discarding the term entirely. The broader definitions I propose are not meant to replace the conventional understanding of intelligence but to explore its application in contexts of evolution and natural systems.

Can we agree that intelligence might be exhibited in ways that differ from human cognition without losing its meaning entirely?

5. Avoiding Assumptions About Mysticism:
You speculated that my reference to "deeper principles" might lead to mysticism, which seems to be an appeal to ignorancedismissing the argument based on assumptions about where it might lead rather than engaging with its content. I have explicitly stated that my perspective does not invoke supernatural forces but aims to integrate observable phenomena with broader philosophical inquiry. Lets focus on what Ive actually presented rather than assuming where my argument might go.

6. Convergence and Predictive Power:
You argued that convergent evolution is reducible to ecological pressures and local minima, which provides predictive power. I agree that environmental pressures shape evolution, but the repeated emergence of similar solutions across seemingly unrelated lineages hints at something worth exploring. Is it possible that these patterns reflect underlying principles that go beyond the immediate pressures of specific environments? If not, why do we see such consistent optimization across these seemingly diverse contexts?

Final Thoughts:
Id like to re-emphasize that my perspective is not about discarding evolutionary science but complementing it with a broader framework that includes traits associated with intelligence. I hope we can move past definitional debates and engage more directly with the specific phenomena Ive highlighted: fine-tuning, emergent complexity, convergence, and consciousness. These are observable, scientifically studied aspects of the natural world that invite deeper inquiry.

I look forward to hearing your thoughts, particularly on the fine-tuning of physical laws and the emergence of consciousness, which were not addressed in your previous reply.

[William]

[Replying to benchwarmer in post #38]

Ummm, I hope I'm wrong and apologize profusely if I am, but it seems Difflugia might be debating with AI generated content here....

No shade William, but the tone and content is smelling awfully AI like. Again, if I'm wrong, apologies. Carry on.

Hi benchwarmer.

Scientific tools are there to use.
See.

COLLABORATIVE SENTIENCE



Cheers.
William

[Difflugia]

I've created a new topic.

[1213]

Question for debate: Are the patterns seen in molecular phylogenies sufficient to show that biological evolution occurred?
...

Wikipedia says:
Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, these analyses have important limitations. Most importantly, the trees that they generate are not necessarily correct they do not necessarily accurately represent the evolutionary history of the included taxa.
https://en.wikipedia.org/wiki/Phylogenetic_tree

I understand that means, no, it is not sufficient. Is Wikipedia wrong?

[William]

[Replying to Difflugia in post #44]

I think there are a few areas where our discussion might benefit from clarification and focus.

That's exactly what I've been telling you.

You suggested that I am redefining intelligence arbitrarily or making an unwarranted "leap" from traits associated with intelligence to calling these processes intelligent. However, I have consistently defined intelligence in this context as the capacity to solve problems, optimize systems, or generate complexity in adaptive ways.

That's not a sufficient definition of intelligence. For now, let's just use the long form. Make your argument about the capacity to solve problems (whatever that means in context), the ability to optimize systems (whatever "system" and "optimal" mean in context), and generate complexity (however one might measure complexity in context). Calling any of those "intelligence" will invariably lead to confusion because they broaden the concept of intelligence far beyond what is useful.

This is not an arbitrary redefinition

It's arbitrary because it's your own personal definition, regardless of how you arrived at it.

but an attempt to broaden the framework in a scientifically meaningful wayone that aligns with observable patterns in natural systems.

This just seems to be word salad. What is scientifically meaningful about broadening the concept of intelligence? What does it mean for your definition to be aligned with observable patterns in nature?

By labeling this a "leap" or "equivocation," you seem to have mischaracterized my argument (a strawman fallacy).

Describing the flaws in your approach isn't the same as changing your claim. Ask ChatGPT what a straw man actually is.

I am not anthropomorphizing natural systems or invoking supernatural forces but suggesting that certain traits we associate with intelligence are evident in evolutionary processes themselves.

That's not what you said. You said that intelligence is evident in evolutionary processes. If you want to discuss specific traits or patterns, I may discuss those with you.

Could we discuss this specific point rather than reframing it as something I havent claimed?

Here's your claim:

However, the evidence overall does not discount intelligent designing involved. How something unfolds intelligently can be overlooked and denied as fervently as those who deny overall evolution in favour of instantly manifested design.

When I said that there's no evidence of intelligence or intelligent design within the evolutionary data, you wanted to change the definition of intelligence.

Since then, our discussion has been about whether or not it's useful to redefine intelligence. You're the one losing sight of the progression of the discussion, not me.

You asked for a clear definition of intelligence

At the time I asked for it, you hadn't defined it.

and argued that the term might be too broad for this discussion.

The term itself is fine. Your attempted redefinition is too broad to be useful. If you need to redefine intelligence for the discussion, then I'm not going to have it with you because I will find the discussion confusing.

I noticed that two key points I raisedfine-tuning of physical laws and the emergence of consciousnesswere not directly addressed in your response. These are significant aspects of my argument and deserve discussion.

If you insist.

Fine-Tuning: The precision of physical constants and conditions enabling life is a well-documented phenomenon. How do you interpret this in the context of evolutionary theory? Does it suggest a deeper principle,

No.

I'm not going to make your argument for you. If you have a claim and evidence to go along with it, I'ld love to hear it.

or is it entirely coincidental?

As far as we can tell, yes.

Consciousness: Evolution has led to self-aware beings capable of reflection and abstract thought. This is arguably one of the most remarkable outcomes of evolutionary processes. Do you see this as merely another byproduct of environmental pressures,

Yes.

or might it point to something more?

No.

You suggested that if we expand the definition of intelligence beyond human-like cognition, we need to "come up with a different word." This creates a false dichotomy between rigidly adhering to conventional definitions of intelligence and discarding the term entirely.

Creating a new term is the opposite of the dichotomy that you imagine. If we retain the standard definition of intelligence and you use another word or phrase, then we can discuss both intelligence and your concept at the same time with less danger of confusing or conflating the two.

The broader definitions I propose are not meant to replace the conventional understanding of intelligence but to explore its application in contexts of evolution and natural systems.

Then discussions will be confusing. It will be like a Christian and pantheist trying to have discussions about God.

Can we agree that intelligence might be exhibited in ways that differ from human cognition without losing its meaning entirely?

Yes. You haven't described anything that I would agree is intelligence, but I agree that it's possible and you might yet do so.

You speculated that my reference to "deeper principles" might lead to mysticism, which seems to be an appeal to ignorance

Since that's not an appeal to ignorance and is the third named fallacy that invoked incorrectly, I can only assume that you're pulling these out of your hat.

dismissing the argument based on assumptions about where it might lead rather than engaging with its content.

Fine. Rephrase what you mean by "deeper principles." Deeper than what? In what nonmystical way?

I have explicitly stated that my perspective does not invoke supernatural forces but aims to integrate observable phenomena with broader philosophical inquiry. Lets focus on what Ive actually presented rather than assuming where my argument might go.

What you've presented is extraordinarily open-ended and requires a lot of subjective interpretation on my part before even answering your questions. As I said, I'm not crafting you argument for you. Present a claim and evidence to support it.

You argued that convergent evolution is reducible to ecological pressures and local minima, which provides predictive power. I agree that environmental pressures shape evolution, but the repeated emergence of similar solutions across seemingly unrelated lineages hints at something worth exploring.

Does it? It doesn't to me. Maybe you can change my mind if you can quantify terms like "repeated" and "seemingly unrelated," then explain why those quantities are unlikely to be due to the combination of environmental pressures and chance.

Is it possible that these patterns reflect underlying principles that go beyond the immediate pressures of specific environments?

Sure. It's possible. I see no evidence that they do, but I invite you to share any you have.

If not, why do we see such consistent optimization across these seemingly diverse contexts?

What do you mean by "consistent optimization across these seemingly diverse contexts" and why is whatever you mean unlikely without something beyond environmental pressure and chance?

Id like to re-emphasize that my perspective is not about discarding evolutionary science but complementing it with a broader framework that includes traits associated with intelligence. I hope we can move past definitional debates and engage more directly with the specific phenomena Ive highlighted: fine-tuning, emergent complexity, convergence, and consciousness. These are observable, scientifically studied aspects of the natural world that invite deeper inquiry.

That's fine. Formulate an argument and defend it instead of asking rhetorical questions.

Its become clear at this stage that our ways of viewing the universe are fundamentally different, and the gap between our perspectives is too wide to find mutual ground for a productive discussion. While I appreciate the opportunity to exchange ideas, it seems our approaches to these questions lead us in divergent directions, making it difficult to engage meaningfully.

Thank you for sharing your thoughtsI wish you well with any exploration of these fascinating topics.

[William]

[Replying to 1213 in post #45]

The Wikipedia quote you referenced accurately points out that phylogenetic trees are tools with inherent limitations. Scientists know these tools arent perfectthey rely on assumptions and models that can sometimes lead to errors in reconstructing specific evolutionary relationships. However, this doesnt mean molecular phylogenies are insufficient evidence for evolution.

Patterns seen in molecular phylogenieslike nested hierarchies and shared genetic sequencesare overwhelmingly consistent with the theory of evolution. These patterns provide strong evidence of common ancestry, even if individual phylogenetic trees occasionally need refinement.

So, no, Wikipedia isnt wrong, but the limitations it mentions dont undermine the conclusion that biological evolution has occurred. They simply highlight the complexity of reconstructing evolutionary history with perfect precision.

[Bible_Student]

It is indisputable that all living organisms share genetic information.

In my view, interpreting this fact as proof of the evolution of species is nothing more than wishful thinking. Just because a banana and a human share genes does not mean they are "related."

To a "creationist," the genetic likeness among organisms serves as evidence of the immense wisdom of our God, who fashioned all beings. From straightforward mechanisms, He crafted such diversity, much like a skilled mathematical programmer develops thousands of unique algorithms using the same foundational commands.

DNA is far more extensive document than any book found in a library. These intricate instructions are cleverly embedded within every cell, detailing how to create a new organism or mend the existing one. But, who wrote these documents in the first place?

[Difflugia]

Wikipedia says:
Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, these analyses have important limitations. Most importantly, the trees that they generate are not necessarily correct they do not necessarily accurately represent the evolutionary history of the included taxa.
https://en.wikipedia.org/wiki/Phylogenetic_tree

I understand that means, no, it is not sufficient. Is Wikipedia wrong?

More meaningless than wrong. That paragraph and the ones following it can be summed up as, "make sure you have sufficient data." I note two things. First, the section isn't up to Wikipedia's citation standards:



Second, it's clear in the talk page for that entry that they've had problems with creationists and edit wars. I'm guessing that section underwent a number of revisions until it was just true enough to keep. The section lists a number of ways that particular kinds of data can result in trees that don't always match expectations, but none of them undermine the method. It's like saying that clinical trials can sometimes be inaccurate because self-reporting of symptoms is unreliable and small sample sizes result in noisy data. Those are true as far as they go, but proper trial design will address them.

You'll note that when I discussed this previously, I said some of the same things:

The competing factor is "noise," which is essentially anything that obscures the exact number of mutations between those sequences. If a point mutation occurs changing one nucleotide into another, but then a second point mutation occurs at the same locus, that's "noisy" because it looks like only one mutation occurred, but it was actually two. Similarly, if one branch experiences a mutation and a neighboring branch happens to experience the same mutation, then the data are noisy because once again, what looks like one mutation was actually two.

I also suggested data standards to help overcome the problem:

The goal is to select data that have enough signal to overcome the noise. If one is working with close lineages, then unconserved sequences are preferable. If the organisms are related closely enough, then even junk DNA can be considered homologous by virtue of being at the same chromosomal location, for example. If enough shared sequence still exists to infer a reasonably accurate mutation rate, then resolution in such cases can be very high. On the other hand, more highly conserved sequences allow comparison between more distantly related organisms. The problem there is not as often the presence of noise, but the absence of signal. Longer sequences are often necessary to make statistical inferences.

The biggest strength of molecular techniques is the sheer volume of data. While every single problem listed in that "Limitations" section can be an issue, all of them are overcome by using a sufficiently large data set.

If you want to talk about particular limitations, I'm happy to, but I'll expect you to put in enough work to understand what's going on. If your response is that you just don't believe it, you're not going to get very far.

[Difflugia]

It is indisputable that all living organisms share genetic information.

In my view, interpreting this fact as proof of the evolution of species is nothing more than wishful thinking.

If "this fact" were all we had, you'd be right. Phylogenetic techniques allow us to go far, far beyond that one fact, however, and actually quantify that sharing.

Just because a banana and a human share genes does not mean they are "related."

The ability to painstakingly show each tiny step in that overall relationship, however, does mean that they're "related."

To a "creationist," the genetic likeness among organisms serves as evidence of the immense wisdom of our God, who fashioned all beings. From straightforward mechanisms, He crafted such diversity, much like a skilled mathematical programmer develops thousands of unique algorithms using the same foundational commands.

If your god did that, then it did it in a way that is utterly indistinguishable from evolution. This includes details that make no sense from the point of view of a skilled craftsman, but do make sense as the result of descent with modification.

I've mentioned before that we see the same evolutionary patterns in mitochondrial genes, which do the same things in all eukaryotes, as we do in the nuclear genes responsible for traits that we can more easily see. If a designer simply took the same gene and used it unaltered in different designs, why would that gene show patterns of genetic drift that match the patterns of functional differences between organisms? The respiratory electron transport chain works exactly the same way in all oxygen breathers, for example. The enzymes invoved show differences between them that show the same patterns of evolution, but they still do exactly the same thing between organisms. While there's no conceivable design reason for that, the accumulation of neutral changes due to drift explains it. That's why I often use one of the enzymes involved in that reaction, Cytochrome C oxidase, when I generate phylogenetic trees for creationists.

DNA is far more extensive document than any book found in a library. These intricate instructions are cleverly embedded within every cell, detailing how to create a new organism or mend the existing one. But, who wrote these documents in the first place?

That's like asking, "who made the sky," or, "who put the sand on the beaches?" A question being grammatically correct doesn't somehow confer meaning to it.

We have a pretty detailed understanding of the processes involved in germline changes to individuals and the ways that those changes accumulate in populations over time. Before positing a "who" to be involved, you'll first have to find a plausible reason that the impersonal processes are insufficient.