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.

[Jose Fly]

I have a lifetime degree, in the observance of animals producing what they are, not what they aren't.

That's all the education I need.

About how many different taxa have you studied? How long have you studied each of them? What were your methods?

Behe argues that while evolution can produce changes within species, there is a limit to the ability of evolution to generate diversity, and this limit (the "edge of evolution") is somewhere between species and orders. On this basis, he says that known evolutionary mechanisms cannot be responsible for all the observed diversification from the last universal ancestor and the intervention of an intelligent designer can adequately account for much of the diversity of life. It is Behe's second intelligent design book, his first being Darwin's Black Box.

https://en.m.wikipedia.org/wiki/The_Edge_of_Evolution

That's all I need to see, which matches what I observe.

Behe believes that common descent, including humans and primates, is true. He just believes evolutionary mechanisms can't do it themselves and God had to intervene in the process. So it's a form of theistic evolution.

Even if those guys I mentioned believe in theistic evolution, I would vehemently disagree with them.

Then I guess you have to cross Behe off your list of creationists you agree with.

You keep talking about jobs...if how they do their jobs don't line up with observation, experiment, and prediction, then they aren't doing science.

I'm a biologist. How do you know what I do every day at work?

[SiNcE_1985]

About how many different taxa have you studied? How long have you studied each of them? What were your methods?

My method: Observe the results of animal birth.

Observe the never-failing pattern of animal mothers giving birth to offspring of the same kind as she.

Observe the results of the many, selective breeding experiments, and seeing the same results every time.

No matter what, the mother will always produce what she is, not what she isn't.

That is my method.

I can care less about any bio-babble theories you want to expound upon.

Behe believes that common descent, including humans and primates, is true. He just believes evolutionary mechanisms can't do it themselves and God had to intervene in the process. So it's a form of theistic evolution.

Then Behe and I disagree on the human/primate common descent.

But we agree that if it is true, then God had to intervene.

Ain't nothing happening without God's hand in the mix...if at all.

Then I guess you have to cross Behe off your list of creationists you agree with.

I am open to theistic evolution.

I'm a biologist. How do you know what I do every day at work?

Once you tell me that you've never observed any reptile-bird transformations in nature, what you do at work is reduced to irrelevancy...at least as far as this topic is concerned.

[Jose Fly]

My method: Observe the results of animal birth.

Observe the never-failing pattern of animal mothers giving birth to offspring of the same kind as she.

Observe the results of the many, selective breeding experiments, and seeing the same results every time.

No matter what, the mother will always produce what she is, not what she isn't.

That is my method.

I can care less about any bio-babble theories you want to expound upon.

How many births have you studied? From how many different taxa? What data did you collect? How did you analyze it?

Once you tell me that you've never observed any reptile-bird transformations in nature, what you do a work is reduced to irrelevancy.

So you have no idea what I do at work or how I do it, correct?

[SiNcE_1985]

How many births have you studied? From how many different taxa? What data did you collect? How did you analyze it?

All babies that I see, from mammals, reptiles, to insects...all of the babies that I see tend to look like their parents.

When I went to the farm as a kid, I saw baby pigs next to their mother pigs.

When I watch wildlife and nature shows, I see animals either giving birth, or gave birth to babies of the same kind.

When I'm at the pet store, I see baby animals next to their mothers, of the same kind.

I never see any reptile-bird stuff going on.

And why you are asking me this, I don't know, as if I am saying something that goes against the grain.

You know full well that this is all that takes place in nature.

I'm not answering any more of these time wasting questions.

These questions are red herrings...all to take away from the fact that you've got nothing of substance to say against anything I'm saying.

So you have no idea what I do at work or how I do it, correct?

I can care less.

[Jose Fly]

How many births have you studied? From how many different taxa? What data did you collect? How did you analyze it?

All babies that I see, from mammals, reptiles, to insects...all of the babies that I see tend to look like their parents.

When I went to the farm as a kid, I saw baby pigs next to their mother pigs.

When I watch wildlife and nature shows, I see animals either giving birth, or gave birth to babies of the same kind.

When I'm at the pet store, I see baby animals next to their mothers, of the same kind.

I never see any reptile-bird stuff going on.

And why you are asking me this, I don't know, as if I am saying something that goes against the grain.

You know full well that this is all that takes place in nature.

I'm not answering any more of these time wasting questions.

These questions are red herrings...all to take away from the fact that you've got nothing of substance to say against anything I'm saying.

So you have no idea what I do at work or how I do it, correct?

I can care less.

Here's the point....

You claim that you know biology better than biologists and more about how they do their work than they do, despite the fact that:

• You have no education in biology
• You have no experience working in biology
• You don't read biology journals
• You've never attended a biology conference or other event
• You have no idea what biologists do at their jobs
• You have no idea how they do their jobs

Your sole qualifications to make those claims are:

• You've watched animals in farms, pet stores, and nature documentaries and you've never seen a reptile give birth to a bird
• You've watched some debates with creationists

So the point is, your claims are just plain ridiculous and it's an insult to people's intelligence to expect them to take it seriously.

[SiNcE_1985]

Here's the point....

You claim that you know biology better than biologists and more about how they do their work than they do, despite the fact that:

• You have no education in biology
• You have no experience working in biology
• You don't read biology journals
• You've never attended a biology conference or other event
• You have no idea what biologists do at their jobs
• You have no idea how they do their jobs

Your sole qualifications to make those claims are:

• You've watched animals in farms, pet stores, and nature documentaries and you've never seen a reptile give birth to a bird
• You've watched some debates with creationists

So the point is, your claims are just plain ridiculous and it's an insult to people's intelligence to expect them to take it seriously.

And, when you tell me that a reptile evolved into a bird, that is an insult to my intelligence, which is why I refuse to take the theory as a serious, viable explanation.

[Jose Fly]

Here's the point....

You claim that you know biology better than biologists and more about how they do their work than they do, despite the fact that:

• You have no education in biology
• You have no experience working in biology
• You don't read biology journals
• You've never attended a biology conference or other event
• You have no idea what biologists do at their jobs
• You have no idea how they do their jobs

Your sole qualifications to make those claims are:

• You've watched animals in farms, pet stores, and nature documentaries and you've never seen a reptile give birth to a bird
• You've watched some debates with creationists

So the point is, your claims are just plain ridiculous and it's an insult to people's intelligence to expect them to take it seriously.

And, when you tell me that a reptile evolved into a bird, that is an insult to my intelligence, which is why I refuse to take the theory as a serious, viable explanation.

The difference is, lots of people care what scientists think about the history of life on earth, whereas no one cares what you think about biology or how biologists do their jobs.

[SiNcE_1985]

The difference is, lots of people care what scientists think about the history of life on earth

So do I....but I'm under no obligation to take what they say as infallible or "Gospel truth".

, whereas no one cares what you think about biology or how biologists do their jobs.

The feeling is mutual.

[marke]

The coelacanth has been promoted as proof of evolution but there are reasons the claim is highly debatable.

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The 'living fossil' coelacanth fish left behind by evolution ...
Coelacanths are considered "living fossils" because they look very similar to their fossil relatives from 300 million years ago. However, the coelacanth's evolutionary history is controversial, with multiple competing hypotheses.
Evidence for coelacanth evolution

This is why you shouldn't depend on AI. It just cobbles together stuff from the net. "I saw it on the internet; it has to be true!" well, no it doesn't.

First the two species of coelacanth living today are from two genera not found in the fossil record. They have evolved from relatively small, freshwater fish to large, deep water marine species. They look somewhat like ancient sarcoptergians, but they aren't the same. In fact, there were four known species of sarcoptergians known before the two species of coelacanth were found. And as you just learned, genetics has cleared up the questions about their relationship to tetrapods. Although they have limb bones, the same ones as tetrapods, it turns out that lungfish are more closely related to tetrapods. Why they should be anatomically and genetically so closely related to tetrapods is a complete mystery to creationists. But it make perfect sense in terms of biology.

Another debatable evolution claim concerns the tiktaalik:

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Critics of the Tiktaalik as a "missing link"

They got that wrong. It's "missing lynx." And we've found it:
https://en.wikipedia.org/wiki/Lynx_issiodorensis

in evolution argue that its fossil features, while interesting, do not definitively show it could fully support its body weight on land, meaning it might not have been capable of true walking, and that other fossil discoveries, like footprints from Poland, indicate creatures were already walking on land before Tiktaalik existed, undermining its position as a transitional species between fish and land animals;

Perhaps you don't know what a "transitional species" is. It doesn't mean the precise species that gave rise to new taxa. Read this so you don't make the same goof again...
A fossil that shows an intermediate state between an ancestral trait and that of its later descendants is said to bear a transitional feature. The fossil record includes many examples of transitional features, providing an abundance of evidence for evolutionary change over time.
https://evolution.berkeley.edu/lines-of ... -features/

Maybe AI will get better in the future. For now, it's going to be a very frail reed to lean on.

Yes, I see that Answers in Genesis made the same goof you did. You might want to copy that definition down; it could prevent a lot of embarrassment in the future.

No matter what source reports the facts, there is no scientific hard evidence that demands assumptions that fish evolved into land animals.

Even honest and knowledgeable YE creationists admit that there is. No point in denial.

I have no doubt that there are many Christians who erroneously believe evolution happened, but I am not one of them.

Those people don't believe common descent happened; they are just honest enough to admit that the evidence shows that it did.

Those who believe in evolutionary common descent have been fooled by those who claim certain aspects of nature demand assumptions of common descent rather than simply suggest the possibility of common descent.

[Clownboat]

If you see me wrestling with a bear, help the bear.

Ok, something about pride and falling comes to mind...

For the sake of debate, we could grant the idea that the Christian God is what initially started life on this planet and then go on to discuss evolution.

Sure, and that is the only way that I could ever even begin to believe that evolution is even remotely, in even in the slightest bit, true.

I know this, which is why I said 'for the sake of debate' because you are closed off to any explanation that isn't your god. Therefore, by granting you the idea that your preferred god created first life, I was hoping we could then have an actual discussion about how populations of animals change over time.

Abiogenesis can be false and maybe even is

No maybes, it is false.

Readers, ask yourselves if you believe this person when they claim to know that abiogenesis is false. How could such a thing be known? It seems like someone is playing pretend.

No one is denying that changes exist...the question is, the scale.

The Theory of Evolution best explains the changes we see and the new species that have emerged. If you disagree, please provide the mechanism that better explains not only the animals we see now on earth, but also in the fossil record so we can compare that to the ToE.

Please, I beg you to show that this is true.
Do you now understand how evolution has NOTHING to do with any claim about how life arose?

I understand that, without God, life cannot arise naturally from nonliving material.

False. You do not understand such a thing. You believe such a thing because of faith. Readers will notice if you are replying with honesty or not.

So, without God, life cannot originate...and if it can't originate, then it can't evolve.

We all hear your faith based claims loud and clear and we are not even on a street corner. What really matter is if you can show that you speak the truth about your claim. Making false claims about evolution is NOT to provide evidence for your own claims. Please provide evidence for the claims you are making and not against some false understanding of abiogenesis and evolution.

My argument is AGAINST the religion of atheism....not necessarily that of theistic evolution, although I disagree with that concept as well.

Then your entire point is a fools errand. Atheism is to be without religion. A (without) theist (religion). You will be taken more seriously if you correct yourself here in place of a weak attempt to level the playing field (calling atheism a religion).

If you want to postulate a scenario where God did it, then fine...but you are undermining your own atheistic belief system...

See what I mean? You are hard to take seriously when you spout such nonsense.
I'm open to the idea of a God creating life and possibly even using evolution to get to where we are now, but atheism is a lack of belief, not some belief system. Please amend your thinking on this matter.

meanwhile, I can be wrong in my Christian theistic belief system, because the belief in evolution doesn't necessarily effect the Gospel, as far as I'm concerned.

I agree that you can be wrong and also agree that evolution doesn't affect the Gospels. Any idea why you needed to include such a statement? I fear I have missed something.

Your preferred god concept could be what started life on this planet and the Theory of Evolution could still be valid. Do you understand this or not? It's crucial in this discussion.

If we are talking God did it, then this would turn into a theological discussion...one of which I am willing to compromise with.

Derp! That is the exact scenario I proposed! See above in bold. How are you missing this?
Once again, let's grant the idea that your preferred god created life on this planet for the sake of debate. Is not evolution the best explanation for what we see on earth? If not, for the love of all that is holy, please explain the better mechanism.

Without God, no, no compromise.

It is clear that it is your god belief that is inhibiting your understanding, which is why I'm trying to allow for your preferred god as being the cause in hopes that we can then have a fruitful discussion. I'm trying very hard to work with you here and your stubbornness is being noted.