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.

[benchwarmer]

It's not the weak and the strong. You're falling back into Kent's imaginary ideas of evolution. Why not take a little time to learn what it is? Could save you a lot of embarrassment.

Go ahead, embarrass me.

No need really. You are doing that all on your own by your constant misrepresentation of what the science actually says.

You keep repeating the same things and fail to learn. I can't imagine how you think that is a convincing debate strategy. Though at this point it seems you aren't really here to debate, but simply to preach your misunderstandings.

[Difflugia]

What is lacking in molecular phylogenetics?

It's lacking the explanatory power, to rule out what we can call the common designer theory.

You're confused about what explanatory power is, but that's not a big deal. The mechanism, descent with modification via mutation and natural selection, has the explanatory power to explain how evolution happened.

Molecular phylogenetics demonstrates that descent with modification is overwhelmingly more likely than any other process, including common design. One of the features of cytochrome c is that the molecule does exactly the same thing in the mitochondria of all eukaryotes. All plants, animals, fungi, and protists are eukaryotes. With that being the case, your common designer should have used the same cytochrome c molecule for every eukaryotic species. Instead, the exact amino acid sequence drifts a bit as species diverge in a pattern that matches the divergence pattern of nuclear genes. Note this quote from the Wikipedia article, describing a biochemistry experiment: "For example, human cytochrome oxidase reacted with wheat cytochrome c, in vitro; which held true for all pairs of species tested."

This rules out a common designer, or at least the one put forth by Christian apologists. The apologetic argument is that organisms are similar because a designer reused components. Mitochondria, however, do exactly the same thing, but show genetic drift in a pattern that implies evolution. If the argument for a common designer is logically sound, then phylogenies based on mitochondrial genes rule out that common designer.

Pay close attention to what I'm about to say, because I don't want us talking past each other.

Edge of my seat.

I will explain my position.

Now my position is, abiogenesis is IMPOSSIBLE.

I believe water is impossible, but I somehow managed to take a shower this morning. It's a miracle.

According to common design theory, the reason there are similarities in DNA, cells, molecules, etc...is because the Designer used the same stuff to create all living things.

Except when he Didn't.

Now, all that being said, there is NO logical way, that you can be an atheist, and completely hop, skip, and jump over abiogenesis, and land at "evolution is true".

I'm not the one that claims that it didn't happen.

Because on atheism, abiogenesis MUST be true...but that is precisely what ISN'T true (or at the very least, hasn't been shown to be true).

It has at the very least been shown to be plausible, unlike the various gods.

[SiNcE_1985]

The Barbarian is doing a great job of addressing your points.

Opinions.

I just want to expand on this to hopefully get you to a better understanding.

Unwarranted, not needed.

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

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.

Abiogenesis can be false and maybe even is

No maybes, it is false.

, but that has nothing to do with how populations of animals change once they exist. That's when evolution enters the discussion, not before.

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

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.

Point blank, PERIOD.

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

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

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

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.

Without God, no, no compromise.

[SiNcE_1985]

No. That's a common misconception among YE creationists, but it's false.

Macroevolution
Definition
noun, plural: macroevolutions
Evolution happening on a large scale, e.g. at or above the level of a species, over geologic time resulting in the divergence of taxonomic groups.

And then...
As creationists, we must frequently remind detractors that we do not deny that species vary, change, and even appear over time.
...
Before the time of Charles Darwin, a false idea had crept into the churchthe belief in the "fixity" or "immutability" of species. According to this view, each species was created in precisely the same form that we find it today. The Bible nowhere teaches that species are fixed and unchanging.
https://answersingenesis.org/natural-se ... EWhVx5vis8

Occasionally, we see a new species evolve. Macroevolutionary change.

Show me any large scale reptile-to-bird type of evolution that we've seen.

You keep requesting to show me...well, show me that.

All 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.

Um, no. Where did Canidae come from? Lets go. Lets extrapolate back into time, shall we?

Show me where did the original, first Canidae come from, and lets see how much different it looked that what it became.

If you'll admit that much, why not just accept the way He did it?
Why not just accept it God's way?

Because, it aint God's way.

For example, 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?

Conflating intelligent design, with abiogenesis.

Tsk, tsk.

So you won't believe Him because He didn't give you a precise timeline?

There was a precise timeline...it is called the 6 day creation event.

Ever heard of 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.

Dogs produce dogs, cats/cats, fish/fish.

If there is anything in nature contrary to that, I aint seen it yet.

And still, as I said before, the theory of evolution contradicts the Genesis creation account.

Evolution: Death before sin.

Genesis: Sin before death.

Trying to fit a dumb, manmade theory into the Bible, is what have you lost...and it is insulting to God.

[SiNcE_1985]

No need really. You are doing that all on your own by your constant misrepresentation of what the science actually says.

What I believe occurs in nature, is constantly represented by what I observe in nature.

In any backyard.

Any alley.

Any farm.

Any zoo.

Any pet store.

All I see are animals producing their kind...I don't see anything remotely close to a reptile-to-bird process...or a land dwelling animal evolving and migrating to the sea process.

You talk about me misrepresenting what science actually says...well, your science is misrepresenting what millions of observations of animals giving birth tells us.

So, we are even.

You keep repeating the same things and fail to learn. I can't imagine how you think that is a convincing debate strategy. Though at this point it seems you aren't really here to debate, but simply to preach your misunderstandings.

Dogs produce dogs, benchwarmer.

I'm not gonna be gaslighted by people telling me that long ago, when no one was conveniently around to witness it...that the animals of yesterday was able to do things that the animals of today have NEVER been observed to do.

And not only that....but no one alive today will conveniently be alive to witness those macro changes as well.

No matter where you are on the timescale, you will always be told "it happened already"....or, "it will happen later"...but you will never actually see it.

It is a joke, a scam, and a deliberate deception by Satan to take what God has done, and misrepresent it....to take away God's glory and prestige.

Justice...is coming.

[SiNcE_1985]

You're confused about what explanatory power is, but that's not a big deal.

Nah, this is just an empty, baseless claim...more than likely acting as a filler.

Or, you can kindly explain to me exactly how I am confused about the phrase, within the context that I am using it.

I said what I said, and I stand by what I said...unless you can prove otherwise.

The mechanism, descent with modification via mutation and natural selection, has the explanatory power to explain how evolution happened.

Nonsense. Again, no one is denying mutation and natural selection. We can see it, we can observe it.

The problem is, you guys claim to know so much about evolution and how that stuff works, yet, the way you use "natural selection" within the context of evolution, goes to show that you actually don't have a clue as to what you are talking about after all.

Natural selection doesn't create...it selects.

No new genetic information was created....the animal with the "feather" gene (just an example), already had the feather gene within it...that feather gene was selected...and if the feather gene becomes dominate in the gene pool, that would give rise to a new population of animals from within that genus, with feathers.

But the genetic information was already there...it did not evolve nor was it created by some natural process.

Molecular phylogenetics demonstrates that descent with modification is overwhelmingly more likely than any other process, including common design. One of the features of cytochrome c is that the molecule does exactly the same thing in the mitochondria of all eukaryotes. All plants, animals, fungi, and protists are eukaryotes. With that being the case, your common designer should have used the same cytochrome c molecule for every eukaryotic species. Instead, the exact amino acid sequence drifts a bit as species diverge in a pattern that matches the divergence pattern of nuclear genes. Note this quote from the Wikipedia article, describing a biochemistry experiment: "For example, human cytochrome oxidase reacted with wheat cytochrome c, in vitro; which held true for all pairs of species tested."

This rules out a common designer, or at least the one put forth by Christian apologists. The apologetic argument is that organisms are similar because a designer reused components. Mitochondria, however, do exactly the same thing, but show genetic drift in a pattern that implies evolution. If the argument for a common designer is logically sound, then phylogenies based on mitochondrial genes rule out that common designer.

Either a common designer did it, or it didn't.

If you rule out a common designer, then that would mean that life originated from nonliving material...and this is naturally impossible.

Point blank, period.

You cannot use any biobabble concept to explain the origins of life, consciousness, or language.

That, followed by the fact, I'm sure the guys in my camp (Kent Hovind, Michael Behe, Johnathan Wells, and most of all, Stephen Meyer), are all aware of what you just said...and they aint buying it...they all remain intelligent design theorists...and so am I.

I believe water is impossible, but I somehow managed to take a shower this morning. It's a miracle.

Well, now you are a believer.

Except when he Didn't.

Opinions.

I'm not the one that claims that it didn't happen.

?

It has at the very least been shown to be plausible, unlike the various gods.

Dont' believe the hype.

[benchwarmer]

No need really. You are doing that all on your own by your constant misrepresentation of what the science actually says.

What I believe occurs in nature, is constantly represented by what I observe in nature.

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.

In any backyard.

Any alley.

Any farm.

Any zoo.

Any pet store.

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

All I see are animals producing their kind...I don't see anything remotely close to a reptile-to-bird process...or a land dwelling animal evolving and migrating to the sea process.

If you saw something like a lizard giving birth to a chicken we would think you were on drugs. At this point we simply think you are in denial of modern science. We've progressed far beyond looking in the backyard.

You talk about me misrepresenting what science actually says...well, your science is misrepresenting what millions of observations of animals giving birth tells us.

The science does not such thing. Your imagination and/or parroting pseudo science is doing that.

Dogs produce dogs, benchwarmer.

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.

I'm not gonna be gaslighted by people telling me that long ago, when no one was conveniently around to witness it...that the animals of yesterday was able to do things that the animals of today have NEVER been observed to do.

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?

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

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

And not only that....but no one alive today will conveniently be alive to witness those macro changes as well.

So again, if no one can witness it, it can't happen. You have just sunk your entire ability to talk about anything you haven't directly witnessed. Congratulations. I expect retractions in every debate thread from you about Jesus, God, beginning of the universe, etc. Looking forward to it.

No matter where you are on the timescale, you will always be told "it happened already"....or, "it will happen later"...but you will never actually see it.

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.

It is a joke, a scam, and a deliberate deception by Satan to take what God has done, and misrepresent it....to take away God's glory and prestige.

Good grief. A Christian if fully capable of understanding actual science and giving glory to their God if they assume this God is what created the processes we observe. You are arguing with one in this very thread. It seems it is you who have been taken in by scammers (devils) that would prefer that you blindly believe whatever they say rather than go actually learn and observe yourself. The irony is quite interesting.

Justice...is coming.

So after attempting to spread misinformation, a threat is your final word? Classic. You seem to be one of those angry Christians that hope everyone who doesn't believe exactly what you do will burn. Such a loving heart and humble character you display. Your Jesus would probably be so disappointed.

Can I suggest a Bible passage for you to pray on? It seems it would be beneficial for you.

https://www.biblegateway.com/passage/?s ... ersion=NIV

12 For those who exalt themselves will be humbled, and those who humble themselves will be exalted.

[The Barbarian]

No. That's a common misconception among YE creationists, but it's false.

Macroevolution
Definition
noun, plural: macroevolutions
Evolution happening on a large scale, e.g. at or above the level of a species, over geologic time resulting in the divergence of taxonomic groups.

And then...
As creationists, we must frequently remind detractors that we do not deny that species vary, change, and even appear over time.
...
Before the time of Charles Darwin, a false idea had crept into the churchthe belief in the "fixity" or "immutability" of species. According to this view, each species was created in precisely the same form that we find it today. The Bible nowhere teaches that species are fixed and unchanging.
https://answersingenesis.org/natural-se ... EWhVx5vis8

Occasionally, we see a new species evolve. Macroevolutionary change.

Show me any large scale reptile-to-bird type of evolution that we've seen.

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

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

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?

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.

Um, no.

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

Where did Canidae come from?

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

But let's continue to explore why your declaration of "kinds" puts humans and other apes in the same Biblical kind. Perhaps you're starting to realize why no scientists and even many creationists don't believe the stories you've been indoctrinated into. No bunny trails for you today. Let's focus on your "kinds" beliefs.

If you'll admit that much, why not just accept the way He did it?
Why not just accept it God's way?

Because, it aint God's way.

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? [/quote]

Conflating intelligent design, with abiogenesis.

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).

Tsk, tsk.

Indeed. You don't know much about Intelligent Design, either.

So you won't believe Him because He didn't give you a precise timeline?

There was a precise timeline...it is called the 6 day creation event

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.

Ever heard of it?

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.

[Jose Fly]

It is a joke, a scam, and a deliberate deception by Satan to take what God has done, and misrepresent it....to take away God's glory and prestige.

I'm curious....do you think the world's biologists, geneticists, paleontologists, geologists, etc. are really, really terrible at their jobs? Do you think you know more about their fields of science than they do? 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?

[SiNcE_1985]

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.

All of that other hocus pocus bio-wizard stuff is pure fantasy.

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

Yeah, and it is really that simple.

If you saw something like a lizard giving birth to a chicken we would think you were on drugs. At this point we simply think you are in denial of modern science. We've progressed far beyond looking in the backyard.

Backyard. Barn. Cage. Wilderness. Captivity.

Wherever.

Same thing.

The science does not such thing. Your imagination and/or parroting pseudo science is doing that.

You are right, the science ain't misleading people.

It is the scientists, that are guilty of such falsehoods.

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.

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

That is going into fantasy land.

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.

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.

So, try again.

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.

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.

So again, if no one can witness it, it can't happen. You have just sunk your entire ability to talk about anything you haven't directly witnessed. Congratulations. I expect retractions in every debate thread from you about Jesus, God, beginning of the universe, etc. Looking forward to it.

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.

Good grief. A Christian if fully capable of understanding actual science and giving glory to their God if they assume this God is what created the processes we observe. You are arguing with one in this very thread.

Christians disagree with each other all the time.

What else is new?

It seems it is you who have been taken in by scammers (devils) that would prefer that you blindly believe whatever they say rather than go actually learn and observe yourself. The irony is quite interesting.

I am under no obligation to believe what I don't find convincing evidence for.

So after attempting to spread misinformation, a threat is your final word? Classic. You seem to be one of those angry Christians that hope everyone who doesn't believe exactly what you do will burn. Such a loving heart and humble character you display. Your Jesus would probably be so disappointed.

Can I suggest a Bible passage for you to pray on? It seems it would be beneficial for you.

https://www.biblegateway.com/passage/?s ... ersion=NIV

12 For those who exalt themselves will be humbled, and those who humble themselves will be exalted.

God doesn't exist and neither does Hell, right?