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.

[SiNcE_1985]

I'm curious....do you think the world's biologists, geneticists, paleontologists, geologists, etc. are really, really terrible at their jobs?

Depends on what you mean by "terrible".

They are good scientists, but poor philosophers.

Do you think you know more about their fields of science than they do?

I am reminded of an interview I saw with former POTUS Barack Obama.

It was a small excerpt, so I didn't catch the full context..but he said, in a nutshell..

"People from the outside looking in, they think that world leaders are so smart and intelligent...but let tell you, from someone that has been in those meetings, and conferences...nothing can be further from the truth. I soon began to realize, that there was nothing special about any of them". They weren't as bright as I thought they were or was perceived to be.

I am paraphrasing, but that was the gist of what he was saying.

And I am using that response to answer your question.

Or do you think they've been engaging in a massive conspiracy for the last 150 years? Or do you think they're under some sort of Satanic spell?

Most of them are atheists/naturalists/materialists.

And evolution is the "Gospel" truth to them.

Yes, I believe Satan is part of the influential equation.

You take what God did, distort it, pass it off as truth, and mislead others with it.

That is Satan's playbook...and is exactly what I think is going on here with evolution.

[Jose Fly]

Depends on what you mean by "terrible".

Terrible:

1: extremely bad: such as
a: notably unattractive or objectionable
b: of very poor quality

They are good scientists, but poor philosophers.

What do you base that on?

I am reminded of an interview I saw with former POTUS Barack Obama.

Your dodge of the question is noted. I always find it fascinating how evasive creationists tend to be. One would think if y'all were really on the correct side of things you wouldn't need to resort to such tactics.

Most of them are atheists/naturalists/materialists.

And evolution is the "Gospel" truth to them.

Yes, I believe Satan is part of the influential equation.

You take what God did, distort it, pass it off as truth, and mislead others with it.

That is Satan's playbook...and is exactly what I think is going on here with evolution.

So to be clear, you think when scientists go to work they come under the influence of Satan. Is that all scientists? If not, which ones? And are they under this influence to "distort" things in other areas of their lives, or just while at work?

[SiNcE_1985]

Show me anyone who has seen a mountain range erode down from high peaks to low hills.

First of all, I am unfamiliar with particular claims as it relates to this, and if something isn't adding up with this, then I'll reject it as well...the same way I do with evolutionary claims.

Nothing is immune to being rejected as false, even certain theistic claims.

Second, it isn't just the fact that I find the evidence presented for evolution to be lacking and unpersuasive, but I also have evidence AGAINST it.

So the TOE is losing battles on two different fronts...doubling the reason for my disbelief.

This is the last defense of the YE creationist, when he realizes all the evidence is arrayed against his modern revision of scripture. "No one ever lived long enough to see ... (whatever millions of years evolution)"

So, if someone said that nature has a way of giving your family X amount of money every so often.

This concept is called "Moneylution".

You ask for the money, and you are told "It has already given your ancestors the money, centuries ago".

You ask, well, when will my current, living family get the money?

And you are told, "It doesn't work like that. You just don't understand how moneylution works. Your family will get the money in a future tomorrow".

Sounds crazy, right? That's how evolution sounds.



Ridiculous, is what it is.

Do you honestly think any rational person finds that excuse to be compelling? Seriously?

I don't think any rational person finds the entire theory to be compelling.

But to address your question more deeply, tell me what feature of birds is not also found in other dinosaurs. We can then look at the issue rationally, determining what evidence there is for evolution of that trait. What do you have?

Woww, that is deep.

So, let me get this straight, you mean to tell me that since..

1. A Boeing 747 airplane has 18 wheels, a steering wheel, and an engine.

And..

2. A typical semi truck with trailer also has 18 wheels, a steering wheel, and an engine.

3. Conclusion: That since they both have similar features, that therefore, one clearly evolved from the other!!!

Wowww, that is some deep stuff!! I'm amazed!!

Ya know, this evolution stuff actually makes sense after all, especially when you can take the same concept and apply it to other existent objects as well.

I was a fool for ever doubting evolution!!

This is officially my Paul's Road to Damascus experience!!

I was once an unbelieving, persecuter of evolution and evolutionists, but now I'm a believer, and I owe it all to you!!

Thank you!!

Wolves and dogs are in the same family. Canidae. Just like humans, chimpanzees, gorillas, and bonobos are all in the same family Hominidae. So by your revision of "microevolution", the common descent of humans and other apes is "microevolution." You sure you want to do that? I would think you'd want to stay with the actual definition of the word.

Rock and hard place.

I would take humans out of the equation...it contradicts scripture...but you've been doing that for a while now.

Sorry, you're wrong. As you just realized, your man-made belief in "kinds" puts humans and chimpanzees and gorillas in the same "kind."

That is exactly what I'm not saying.

Miacids. Most likely M. cognitus or a closely related species. On of the few miacids showing adaptation of modern carnivores.

I cant rock with that.

God says it is. I believe Him. You should, too.

You deny abiogenesis, which God tells us is the way He created living things in the beginning. You deny evolution which is observed going on in all living populations.
Why not just accept it His way?

Still conflating a concept that is by definition, supposed to happen without God (abiogenesis), with a concept that takes occurs with God (creation).

Shamefully funny.

Well, since you brought that up, let's ask one of the guys who invented the concept of "intelligent design":
"it is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science - that the cosmos is a seamless unity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school". According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world - that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies."
IDer, and Discovery Institute Fellow Michael Denton Nature's Destiny (page xvii-xviii).

I won't respond to this until I have a lawyer present.

Nice try. But the "days" of creation can't be normal days, because you can't have mornings and evenings without a sun to have them. Once again, you've added things to scripture to make it more acceptable to you.

No, God was already distinguishing night from day, as early as Gen 1:3-4, and this was before the sun was created.

So, regardless of how/what you perceive a day to be, God was doing his own thing, not caring about what his creation (you) would think.

Perhaps it would benefit you to actually read it.

If you obsess on these things, you miss the entire message of Genesis. Not that you'll go to hell for being a YE creationist. But if you'd be willing to accept all of His word as it is, you'd have a better relationship with Him. Instead, you're trying to fit a dumb, manmade theory into the Bible, is what have you lost...and it is insulting to God.

Sounds familiar.

[SiNcE_1985]

Depends on what you mean by "terrible".

Terrible:

1: extremely bad: such as
a: notably unattractive or objectionable
b: of very poor quality

Then yes, they terrible. How about that?

What do you base that on?

For example, most scientists in cosmology refuse to engage the infinite regress problem, which would discredit and/or contradict any of their presented past eternal scenarios.

They are poor at correlating the two, despite such obvious and glaring problems.

In the same fashion, biologists do the same thing...but the infinite regression problem in cosmology, would be the abiogenesis problem in biology.

Biologists are poor are correlating the two...which is why the (now predictable) response is always..

"Abiogenesis doesn't have anything to do with evolution".

That statement is FALSE, on naturalism, which is their position.

If they were logical thinkers (putting on their philosophical thinking caps on), they would know this.

Your dodge of the question is noted.

Your question assumed that scientists are smarter than I.

My answer is, they aren't as smart as they portray themselves to be, and I just explained why.

I always find it fascinating how evasive creationists tend to be. One would think if y'all were really on the correct side of things you wouldn't need to resort to such tactics.

You guys are spreading lies with false teachings, and yet we are the ones resorting to questionable tactics?

So to be clear, you think when scientists go to work they come under the influence of Satan. Is that all scientists? If not, which ones? And are they under this influence to "distort" things in other areas of their lives, or just while at work?

Evil, period, is all influenced by Satan.

Doesn't matter if you are at home, at work, in the water, or in the air.

[benchwarmer]

So you've been in a biology lab to observe what the science says? Somehow I doubt that given your misunderstanding of the actual science.

I'm not going by what you claim the science says.

I'm going by what I can..

1. Observe: I observe animals producing what they are, not what they aren't.


2. Test/experiment: Throughout millions upon millions of selective breeding measures, all reproductive experiments have only lead to the results of #1^.

3. Predictions: Based on #1 and #2, I have no reasons to conclude anything contrary, and I predict that millions more of #1 and #2 will produce the same results.

That, is science.

So the answer to my question is "No". Got it. You haven't bothered to observe what scientists have, just what you can see out your window into your backyard.

You explain that science involves observation, predictions, and tests (fixed the order for you) correctly, but fail to believe what the experts in the field have published under peer review using observation, prediction, and tests. All because you didn't see it in your backyard. LOL!

So no. You think just looking at animals is the extent of possible observation. Got it.

Yeah, and it is really that simple.

I'm glad you are not involved in science then. We would get nowhere with this kind of laziness and lack of curiosity. Thankfully science and scientists have moved far beyond staring in the backyard.

This again? Every time this topic comes up, you say that as if that renders the science of evolution wrong. Evolution predicts EXACTLY that. We tell you this every time. You seem to forget every time.

You are going beyond dogs produce dogs, though.

Are we? You are imagining we are. We aren't. Whatever classification a life form has, all it's progeny will have the same classification and possibly some new subclassification. You clearly (yet again) don't understand what the science says. You prefer to make something up and then proceed to hack away at that.

Saying whales were once land dwelling animals that migrated to the sea, that is going far beyond dogs produce dogs.

What was the classification of the organisms that were once land dwelling and moved to the sea? Answer that and you may find a clue.

Spoiler alert, while the descendants are eventually gifted a new species name, they will still belong to the higher level classification. We've been over this before, you keep pretending (or purposely ignoring) all of it and keep spouting AiG nonsense or wherever you get your info from.

That is going into fantasy land.

Oh the irony.....

Ok, so you are saying that you will NEVER believe something you can't directly observe right?

Good.

Please stop preaching about anything to do with Jesus then. You haven't observed Jesus or anything he may or may not have done. You are not allowed to rely on anything other than your direct observation. Maybe he will show up in your backyard, alley, farm, or zoo and then you can resume telling anyone what you know about Jesus. Deal?

Not so fast.

Cue special pleading in 3... 2... 1...

I know you think you just made this grandeur point..but in reality, you didn't.

You see, my belief in Jesus isn't based on observation, experiment, and prediction (science)...my belief in Jesus is based on the historical method, which is a completely different methodology compared to the scientific method.

And the historical method relies on what? Imagining things out of thin air? Or maybe does it actually involve science like archeology, textual analysis, comparison of artifacts, etc? i.e. Observation, prediction, and experiments. We observe these texts. We predict we will find artifacts in this area that corroborate this story. We dig and find (or don't find) what we expected. Yup, no science here.

So, try again.

Sadly your rebuttal failed unless you think history involves just making up stories. Maybe you don't understand the historical method either?

At least in science we now have two separate lines of data to observe what has happened in the past. Paleontology and genetics.

And Im not convinced of the claims, using either line.

And we all know for a fact you have neither researched or understood any of it beyond parroting what you found on AiG or some other creationist website. Go take some university level biology courses, do some lab work, and then get back to us.

You have what exactly? Some documents that were collected together.

Documents are important, when using the historical method, especially with claims dealing with antiquity.

You apparently didn't know that.

So, no charge for the lesson.

Apparently you didn't know that simply having documents is not the end of the historical method. I guess you might learn something?

Feel free to visit a university campus with a large biology program and go take some courses. You can observe evolution in the lab if you can manage to learn enough to understand the experiments and data.

Or, I can go to a pet store or zoo, and when I see baby animals, I'll just assume that they came from their parents of the same kind.

Yup, can't be bothered to go do the hard work, happy to visit the pet store in the mall and think you have seen it all. Such convincing debate you are putting forth.

[Jose Fly]

Depends on what you mean by "terrible".

Terrible:

1: extremely bad: such as
a: notably unattractive or objectionable
b: of very poor quality

Then yes, they terrible. How about that?

What do you base that on?

For example, most scientists in cosmology refuse to engage the infinite regress problem, which would discredit and/or contradict any of their presented past eternal scenarios.

They are poor at correlating the two, despite such obvious and glaring problems.

In the same fashion, biologists do the same thing...but the infinite regression problem in cosmology, would be the abiogenesis problem in biology.

Biologists are poor are correlating the two...which is why the (now predictable) response is always..

"Abiogenesis doesn't have anything to do with evolution".

That statement is FALSE, on naturalism, which is their position.

If they were logical thinkers (putting on their philosophical thinking caps on), they would know this.

Your dodge of the question is noted.

Your question assumed that scientists are smarter than I.

My answer is, they aren't as smart as they portray themselves to be, and I just explained why.

I always find it fascinating how evasive creationists tend to be. One would think if y'all were really on the correct side of things you wouldn't need to resort to such tactics.

You guys are spreading lies with false teachings, and yet we are the ones resorting to questionable tactics?

So to be clear, you think when scientists go to work they come under the influence of Satan. Is that all scientists? If not, which ones? And are they under this influence to "distort" things in other areas of their lives, or just while at work?

Evil, period, is all influenced by Satan.

Doesn't matter if you are at home, at work, in the water, or in the air.

So you believe biologists are all bad at their jobs, you know their field better than they do, and they're agents of Satan (perhaps unwittingly).

What's your education level in biology? What classes have you taken? What biology journals do you read? Have you ever attended a biology conference or symposium?

IOW, how specifically did you acquire your knowledge of how biologists do their jobs?

[SiNcE_1985]

So you believe biologists are all bad at their jobs

, you know their field better than they do, and they're agents of Satan (perhaps unwittingly).

Sure, let's go with that.

What's your education level in biology? What classes have you taken? What biology journals do you read? Have you ever attended a biology conference or symposium?

IOW, how specifically did you acquire your knowledge of how biologists do their jobs?

Kent Hovind, Ken Ham, Jonathan Wells, Michael Behe, Stephen Meyers.

3 of whom are biologists, and two of whom know enough about the subject to debate some of the greatest minds in the subject.

They all have extensive knowledge on the subject, all the things you question against me...they've been to those prestigious conferences, taught the subject, and wrote in journals..and guess what, they still ain't buying it..and neither am I.

Next..

[SiNcE_1985]

So the answer to my question is "No". Got it. You haven't bothered to observe what scientists have,

Genetic similarities, and fossils.

That is the extent of what scientists have, with their interpretations of the data completely dubious.

just what you can see out your window into your backyard.

Yeah and you can see an awful lot, just by observing.

You explain that science involves observation, predictions, and tests (fixed the order for you) correctly

Um, no. I had it right the first time.

Predictions is last (#3), based on the prediction of future events, whichever way the evidence from your observation and experiment leads you.

I wasn't using prediction in the context of a hypothesis..as you are.

The hypothesis is embedded in the experiment (#2).

So again, thanks, but no thanks on your assistance...it just wasn't needed.

I got this.

, but fail to believe what the experts in the field have published under peer review using observation, prediction, and tests. All because you didn't see it in your backyard. LOL!

You have your experts, and I have mines.

I'm glad you are not involved in science then. We would get nowhere with this kind of laziness and lack of curiosity. Thankfully science and scientists have moved far beyond staring in the backyard.

The main, fundamental part of evolution is reproduction (no reproduction, no evolution), yet I am being ridiculed for seeking evidence from reproduction?

Wow.

Are we? You are imagining we are. We aren't. Whatever classification a life form has, all it's progeny will have the same classification and possibly some new subclassification. You clearly (yet again) don't understand what the science says. You prefer to make something up and then proceed to hack away at that.

If you view a reptile and bird as part of the same classification, then you are in fantasyland.

What was the classification of the organisms that were once land dwelling and moved to the sea? Answer that and you may find a clue.

You can classify them however you like, that doesn't mean that whatever is going on in your brain actually reflects what has happened, and what naturally can happen.

Spoiler alert, while the descendants are eventually gifted a new species name, they will still belong to the higher level classification. We've been over this before, you keep pretending (or purposely ignoring) all of it and keep spouting AiG nonsense or wherever you get your info from.

I'm not ignoring it. I am hearing it, considering it, and rejecting it.

Kinda like the same thing you do with the Gospel.

And the historical method relies on what? Imagining things out of thin air? Or maybe does it actually involve science like archeology, textual analysis, comparison of artifacts, etc? i.e. Observation, prediction, and experiments. We observe these texts. We predict we will find artifacts in this area that corroborate this story. We dig and find (or don't find) what we expected. Yup, no science here.

Not so fast.

A person can only live and die one time (all things equal), so if you are going to historically prove the existence of a specific person of antiquity, you can only rely on things from the past to corroborate the claim..as you just did.

However, with YOUR claims about evolution, no, we dont have a time machine to go back in time to witness these fanciful, voodoo claims in nature..but we do have millions of OBSERVATIONAL evidences from live births of which no single birth ever witnessed, have ever come remotely close to resembling any of these macro levels changes that you claimed occurred eons ago.

If it happened in real time back then (when no one was conveniently around to witness it), then it should be happening in real time now.

Or is it like the "If a tree falls in the woods, and no one was around to see it fall, would it make noise?" paradox?

Sadly your rebuttal failed unless you think history involves just making up stories. Maybe you don't understand the historical method either?

There have been more people who've claimed to see the risen Jesus, than of those who've claimed to see any of those voodoo macro changes you believe occurred in nature.

Maybe you don't understand that there is more evidence for the resurrected Jesus, than your reptile-to-bird fantasy?

And we all know for a fact you have neither researched or understood any of it beyond parroting what you found on AiG or some other creationist website. Go take some university level biology courses, do some lab work, and then get back to us.

3rd time you've spewed something about AiG..funny, because I don't even use that website as a source...although I acknowledge Ken Ham a BEAST.

I am more of a Kent Hovind guy.

I also like what Kent said about Ken Ham.

"Ken Ham and I, we don't agree on everything, but I support what he does".

Game recognizes game.

Apparently you didn't know that simply having documents is not the end of the historical method. I guess you might learn something?

That would obviously depend on the historical claims being made, wouldn't it?

Yup, can't be bothered to go do the hard work, happy to visit the pet store in the mall and think you have seen it all. Such convincing debate you are putting forth.

Yeah, I'll see whether any of those reptile arms are gradually turning into wings.

Oh, I forgot, it doesn't work like that.

[Jose Fly]

Kent Hovind, Ken Ham, Jonathan Wells, Michael Behe, Stephen Meyers.

3 of whom are biologists, and two of whom know enough about the subject to debate some of the greatest minds in the subject.

They all have extensive knowledge on the subject, all the things you question against me...they've been to those prestigious conferences, taught the subject, and wrote in journals..and guess what, they still ain't buying it..and neither am I.

Next..

So to be clear, you've never taken a course in biology, you've never read a biology journal, and you've never attended a biology conference. IOW, you have zero education, training, or professional experience in biology.

Nevertheless, you believe you know how biologists do their jobs better than they do because you've watched and read material from 5 creationists, 3 of whom are not biologists, and one of those agrees with universal common ancestry including human/primates (Behe).

Is that really the position you're putting forth here?

And exactly how did those creationists inform you about how biologists do their jobs?

[SiNcE_1985]

So to be clear, you've never taken a course in biology, you've never read a biology journal, and you've never attended a biology conference. IOW, you have zero education, training, or professional experience in biology.

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.

Nevertheless, you believe you know how biologists do their jobs better than they do because you've watched and read material from 5 creationists, 3 of whom are not biologists

Those aren't the only 3, those are just the 3 at the more popular end of the spectrum.

, and one of those agrees with universal common ancestry including human/primates (Behe).

Hmm..

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.

Is that really the position you're putting forth here? And exactly how did those creationists inform you about how biologists do their jobs?

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

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.