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.

[Masterblaster]

Hello Difflugia
You have stopped being coherent to me ,at this stage.

You say -"This is exactly what we were discussing in the other thread."
You say -"It's not, but go ahead and answer in the other thread if you think it is"

Simple question ...it is or it isn't?????

[Difflugia]

Hello Difflugia
You have stopped being coherent to me ,at this stage.

Pretty sure it's not me.

You say -"This is exactly what we were discussing in the other thread."

Yes. We were discussing the scientific merit of evolution at that point in the thread.

You say -"It's not, but go ahead and answer in the other thread if you think it is"

It's not the same topic as the other thread, which is what you asked. The topic of the other thread is why (or even whether) some Christians don't like that other Christians understand evolution. The topic of this thread is whether the methodology and data behind molecular phylogeny are sufficient to establish evolution.

Simple question ...it is or it isn't?????

Are you trying to score rhetorical points because you don't want to address the science? How about we discuss the methods and data instead?

[Masterblaster]

Hello Difflugia

You say - " How about we discuss the methods and data instead?"

--
Ok! I am not doing much at the moment, so here goes! Nobody will see this anyway, we are in Debate Limbo, ( thanks to you )!

The methods and data of Evolution,you say. Just what I was reading about yesterday.

Charles Darwin was a truly amazing human being. His methodology and data-keeping was sincere and meticulous . One guy, of his time, looked at the obvious nature of his deductions and wondered as to why he didn't see the picture first. Genius will do that to you.

What spec of microscope did he use ,D?
What did he deduce from his many slides,D?
What was his general attitude towards the natural world, What were his ethics,D?

Did he announce Evolutionary Theory?

What did he announce?

Is Evolution an obvious extrapolation from his work,D?
Is that mouthful at the top of the page a further extrapolation, D?

What mileage will you extrapolate from this on a Religion site. Where is your science going, D?

I like method and data, D!

Thanks

[Difflugia]

Hello Difflugia

Hello Masterblaster.

You say - " How about we discuss the methods and data instead?"

--
Ok! I am not doing much at the moment, so here goes!

Excellent.

Nobody will see this anyway, we are in Debate Limbo, ( thanks to you )!

If you say so.

The methods and data of Evolution,you say. Just what I was reading about yesterday.

Excellent.

Is Evolution an obvious extrapolation from his work,D?

You've got it backwards. Scientists of the time had already noticed that evolution seemed to be a thing. They were trying to figure out why. Darwin's hypothesis was that small changes within populations that were selected for over a long time led because larger changes within the population. If those populations were separated in some way, they sometimes diverged into other species.



What Darwin didn't have are actual mechanisms for the transmission of genetic traits from one generation to the next that allowed the kinds of heritable changes that he hypothesized.

Is that mouthful at the top of the page a further extrapolation, D?

Again, you've got it backwards. The "mouthful at the top" would allow one to not only "extrapolate" Darwin's hypothesis, but provide a mechanism and suffient data to experimentally demonstrate that Darwin's basic idea is correct beyond any reasonable doubt.

What mileage will you extrapolate from this on a Religion site. Where is your science going, D?

I'm not sure what you're asking. You said that "rejecting the simple discovery of Darwin" is something other than denial. I've offered you a method and sufficient data to show beyond any reasonable doubt that the pattern of modern biodiversity is exactly the pattern expected by the theory of evolution. Furthermore, the dataset is so large, that if you can posit an alternate mechanism for the world's biodiversity that should result in a different pattern, we should be able to devise an experiment that would show it to us.

I like method and data, D!

Then by all means, let's start talking about them.

[Masterblaster]

[Replying to Difflugia in post #14]

Hello Difflugia

Life continues in the Outer Hebrides.

You say - "What Darwin didn't have are actual mechanisms for the transmission of genetic traits from one generation to the next that allowed the kinds of heritable changes that he hypothesized."

Did Darwin have a clue about genetics?
How much of a clue?
Did he understand D.N.A?

You say - " You said that "rejecting the simple discovery of Darwin" is something other than denial"

Question- Where did I say that???

Unanswered questions
What spec of microscope did he use ,D?
What did he deduce from his many slides,D?
What was his general attitude towards the natural world, What were his ethics,D?
Did he announce Evolutionary Theory?

Simple answers will suffice.

Why the big deal about Darwin ,you might ask, as a casual viewer. Difflugia introduces his OP, as a response to a comment of mine on this thread.

Why are Some Christians Upset that Other Theists Accept Darwin
Post 64 of that thread...

I said - "I will happily play devils advocate against Science, to my last breath as a theist"

Do you want to consider Posts 3 to 6 on this thread Difflugia. I'm easy, either way!
Thanks

[Masterblaster]

Hello Difflugia

You say - ". I've offered you a method and sufficient data to show beyond any reasonable doubt that the pattern of modern biodiversity is exactly the pattern expected by the theory of evolution"

-------

The problem with this statement is that people disagree with it. We have doubts and reservations. Scientific thought is fumbling just as much as theism is. The difference is that science continues to erase the natural world in a physical way. Its methodology is flawed and destructive. It is a folly.

1213 and I, expressed these reservations, many times. We probed with questions on the previous thread and we instantly became denialists and rejectionists. Now we are supposed to prove your scientific deduction wrong. Why?

At the risk of becoming tedious!
Did evolutionary theory predict modern human dominance?
Does Evolutionary Theory explain ageing and death.
Does evolutionary theory predict self-destruction.
Does evolutionary theory provide useful insight.
1213 wants to know why people are getting physically weaker and where does evolutionary theory suggest that this process will conclude.

If I discover that a stick will break , and my extrapolation is that a spear is better than a fruit tree, is that one giant leap for mankind. Should i exhort the art of desecrating fruit trees? Can you justify any conclusions that are unethically achieved? If you can then nuclear power is good. Is it? How much genetic research is based on animal experimentation, particularly ,on our genetic cousins,D?

Can you change your mind in science and graft your spear back on to the tree?. Unlikely, but that won't stop science having a go. Fixing what you break is the scientific modus.

Wear a coat on this shitake planet, D.(Eggman is coming back to Sonic 3...Great!)
Thanks

[Difflugia]

You say - "What Darwin didn't have are actual mechanisms for the transmission of genetic traits from one generation to the next that allowed the kinds of heritable changes that he hypothesized."

Did Darwin have a clue about genetics?
How much of a clue?

He hypothesized the idea of "heritable traits."

Did he understand D.N.A?

No.

You say - " You said that "rejecting the simple discovery of Darwin" is something other than denial"

Question- Where did I say that???

[Sigh]

Remember this?

Questions and reservations posed by 1213 and myself are 'denial'? The pitfalls of science are prompted at and we are, now, rejectionists??? We ask simple questions like, why do people age, why are people getting weaker and unhealthy and we are told to leave this for scientists to answer.1213 and I reject the scientific narrative. I reject that it has a control or a central morality to it and I summarized it's general influence as a dangerous folly. Science as a real answer, is dogma in so far as it is left unchallenged.
I extract more insight from Genesis 1 than I do from the blueprints of Boeing. We have been listening to scientific ....., on this site in the Christianity section for a long time now.

This often graduates into a high level of sophistication that excludes the non qualified. If a Muslim or Jew presented obscure, theological source material ,full of jargon and inference,they would likely be banned. Are these two situations not the same.
There is an exasperation, when you want to make it clear as a simple theists that you object to this 'high science.
You come along and wring your hands and ask how we could be rejecting the simple discovery of Darwin. That is not what I am doing. I am attacking the extrapolation (scientific deductions)(new science) (whatever) (small word and I too will be banned). Science builds on itself and it's hosts, like ivy. It dances to the tune of an evolving agenda that is usually self-serving in some way. How much science does our effective evolution as a species need? Are we science-dependant junkies , at this stage ? That is another discussion. It is fundamentally flawed and as such is false. Its cocktail of complicated truths add up to a big lie.That is another discussion.

When you're challenged to back up your denial with anything concrete, you retreat into "just asking questions" that are somewhere between rhetorical and an ungainly attempt at socratic discourse, either of which only works if you understand the topic in the first place.

Unanswered questions
What spec of microscope did he use ,D?
What did he deduce from his many slides,D?
What was his general attitude towards the natural world, What were his ethics,D?
Did he announce Evolutionary Theory?

I've no idea. This is your argument, so answer your questions and tell us what you imagine that the answers mean.

Skip the socratic nonsense and make your own claims.

Simple answers will suffice.

Why the big deal about Darwin ,you might ask, as a casual viewer.

My guess is that it's meant to be distracting in the hopes that you can avoid discussing scientific detail, but I'd love to be wrong.

Difflugia introduces his OP, as a response to a comment of mine on this thread.

Why are Some Christians Upset that Other Theists Accept Darwin
Post 64 of that thread...

I said - "I will happily play devils advocate against Science, to my last breath as a theist"

Do you want to consider Posts 3 to 6 on this thread Difflugia. I'm easy, either way!

No.

[Difflugia]

This is a discussion sub-forum. Please take the debate to one of our debate sub-forums.

This topic is where my response was sort of going, anyway.

They don’t misunderstand it. They go where the evidence leads.

Unlike 41% of the biologists, I guess.

The field of biology is governed by those who believe in evolution full stop.

"Governed?" Like this is some giant, monolithic conspiracy?

If you don’t publish, you perish. If you don’t promote evolution, you don’t publish. So honesty is not a virtue that is easily found. Conformity is demanded.

Where exactly is this dishonesty and demand for conformity? You realize that majority of scientists are just university professors, right? And professors are pretty much self-selected from students that like the subject matter so much that they're willing to turn academia itself into their career. How many people know about this grand conspiracy of dishonesty? Do biology undergrads know about it? Is it something that the professors tell prospective grad students during their orientations? How does this all come together in your head? Who are the ivory tower gatekeepers that are keeping all of the other frightened professors in line?

If your job is as academic, or at least academic-adjacent, as you let on, you should know this, but I'll explain it for everyone's benefit. There's an academic concept of tenure that is intended to guarantee academic freedom. The career goal of most professors is to land a tenure track position with a university that will ultimately result in the university granting them tenure. What that means is that the university is giving them a legally enforceable guarantee that they can't be removed from their position for mere academic disagreement. Someone who's granted tenure can pretty much run off the rails as much as they want as long as they continue to meet rather mundane job requirements. A tenured professor that's out of favor might end up teaching freshman classes or something, but would be difficult to silence, let alone straight-up remove as long as they don't do something outright illegal or unethical. Remember Michael Behe, the biochemistry professor that would shill for intelligent design? He was able to do that because he had been granted tenure. He's far from the only biology professor with tenure, so where are the rest? Are they all dishonest and trying to avoid rocking the boat? I want to know how you think this works.

The Intelligent Design side are able to follow where the science leads. The evolutionists follow where the scientists lead.

I want to know how you came to this conclusion. You keep claiming to be somehow connected to "research," but I'm not seeing it. What's your specialty?

If the data really supported intelligent design in any way, it would be obvious to someone that understands the underlying science. Here's a quick spoiler: they don't! If you think I'm wrong, pick one or three or ten studies and link them here. The evidence for evolution is the underlying pattern of relationships between biological organisms. If the data don't show that pattern, it will be obvious, even if some dishonest scientist says otherwise.

My day job is writing data collection and analysis software. I know what I'm looking at, I have the professional chops to evaluate it, and I'm convinced that the pattern is real. Do you think the biological establishment got to me and convinced me to lie to you? If not, the only question is what that pattern means. Creationists generally just deny that it exists, but it's robust enough in a mathematical sense that it's basically impossible that it's something like coincidence or the mathematical equivalent of pareidolia. The pattern that emerges is consistent across different sources of data: morphological characteristics of both fossils and living organisms, nuclear DNA sequences, mitochondral DNA sequences, and protein sequences. Are those data faked? Are the analyses faked? As I've mentioned before, the genetic sequences are in a database online and you can replicate the analyses yourself, or even perform new ones. Did your dishonest scientists fake the data so convincingly that analysis of any set of data from any combination of organisms will always show an evolutionary relationship, even if it's not really there?

You assert that the biologists are lying for some sort of benefit to their careers, but how do you think this actually happens in practice?

[Mae von H]

This is a discussion sub-forum. Please take the debate to one of our debate sub-forums.

This topic is where my response was sort of going, anyway.

They don’t misunderstand it. They go where the evidence leads.

Unlike 41% of the biologists, I guess.

The field of biology is governed by those who believe in evolution full stop.

"Governed?" Like this is some giant, monolithic conspiracy?

NOPE

If you don’t publish, you perish. If you don’t promote evolution, you don’t publish. So honesty is not a virtue that is easily found. Conformity is demanded.

Where exactly is this dishonesty and demand for conformity?

If you are unaware of the epidemic dishonesty in science, you won’t believe me. I work with scientists and they don’t trust each other. Now either you believe this or you prefer to think they’re a cut above other men ethically. In my experience it is a matter of wanting scientists to be truthful or wanting the truth.

You realize that majority of scientists are just university professors, right? And professors are pretty much self-selected from students that like the subject matter so much that they're willing to turn academia itself into their career.

You never heard of tenure? The head of Yale was a Professor of less than a year. Popularity among students didn’t save her. If no one selects a Professor, they are tenured and stay anyway. Why do you think it’s a popularity contest?

How many people know about this grand conspiracy of dishonesty?

Ask scientists if they completely trust other scientists?

Do biology undergrads know about it? Is it something that the professors tell prospective grad students during their orientations? How does this all come together in your head? Who are the ivory tower gatekeepers that are keeping all of the other frightened professors in line?

I give up. Trust the scientists. Trust the government. Take the shots, one after the other. Trust Big Pharma as they are completely free of profit motives.

If your job is as academic, or at least academic-adjacent, as you let on, you should know this, but I'll explain it for everyone's benefit. There's an academic concept of tenure that is intended to guarantee academic freedom. The career goal of most professors is to land a tenure track position with a university that will ultimately result in the university granting them tenure. What that means is that the university is giving them a legally enforceable guarantee that they can't be removed from their position for mere academic disagreement. Someone who's granted tenure can pretty much run off the rails as much as they want as long as they continue to meet rather mundane job requirements. A tenured professor that's out of favor might end up teaching freshman classes or something, but would be difficult to silence, let alone straight-up remove as long as they don't do something outright illegal or unethical. Remember Michael Behe, the biochemistry professor that would shill for intelligent design? He was able to do that because he had been granted tenure. He's far from the only biology professor with tenure, so where are the rest? Are they all dishonest and trying to avoid rocking the boat? I want to know how you think this works.

Yeah…tell that to Jordan Peterson. Tell that to the growing number of tenured university professors who don’t agree with woke. Shall I look for a list of tenured university professors who were fired for academic disagreement? It’s depressingly long.

The Intelligent Design side are able to follow where the science leads. The evolutionists follow where the scientists lead.

I want to know how you came to this conclusion. You keep claiming to be somehow connected to "research," but I'm not seeing it. What's your specialty?

Neuroimmunology. But you want to believe academia is pristine pure. There’s no hope. You certainly don’t work in science.

If the data really supported intelligent design in any way, it would be obvious to someone that understands the underlying science. Here's a quick spoiler: they don't! If you think I'm wrong, pick one or three or ten studies and link them here. The evidence for evolution is the underlying pattern of relationships between biological organisms. If the data don't show that pattern, it will be obvious, even if some dishonest scientist says otherwise.

My day job is writing data collection and analysis software. I know what I'm looking at, I have the professional chops to evaluate it, and I'm convinced that the pattern is real. Do you think the biological establishment got to me and convinced me to lie to you? If not, the only question is what that pattern means. Creationists generally just deny that it exists, but it's robust enough in a mathematical sense that it's basically impossible that it's something like coincidence or the mathematical equivalent of pareidolia. The pattern that emerges is consistent across different sources of data: morphological characteristics of both fossils and living organisms, nuclear DNA sequences, mitochondral DNA sequences, and protein sequences. Are those data faked? Are the analyses faked? As I've mentioned before, the genetic sequences are in a database online and you can replicate the analyses yourself, or even perform new ones. Did your dishonest scientists fake the data so convincingly that analysis of any set of data from any combination of organisms will always show an evolutionary relationship, even if it's not really there?

You assert that the biologists are lying for some sort of benefit to their careers, but how do you think this actually happens in practice?

You’re not a biologist. You don’t actually do research and I doubt you can scientifically evaluate papers. It’s pointless to argue with non-science majors. The background isn’t there. Believe those noble scientists working tireless for the good of mankind. The world is a nicer place for you and I really hope you never have a personal reason to think differently as that is despair beyond imagination.

[DrNoGods]

[Replying to Mae von H in post #19]

If you are unaware of the epidemic dishonesty in science, you won’t believe me. I work with scientists and they don’t trust each other.

Epidemic? If the level of dishonestly in science had reached that stage progress would slow or come to a halt. But there's no sign that this is happening. And if scientists as a whole did not trust each other then collaboration would stop and that isn't happening either.

Ask scientists if they completely trust other scientists?

Define "completely." I'm a scientist (Ph.D in Physical Chemistry) and mostly trust other scientists who have proven their ability to conduct science in their field productively and publish work in peer-reviewed journals, etc. Like all humans, there are bad apples and dishonest scientists, but as a group the incredible progress science has made over the last few centuries proves that it is a legitimate endeavor and benefits humankind tremendously in a wide range of disciplines.

Trust Big Pharma as they are completely free of profit motives.

In a capitalist economy like the U.S., big pharma are public companies who don't survive if they can't make a profit. But again, the medicines and treatments we have today are a testament to what science can accomplish, and this science has to be funded somehow. There are plenty of government research grants and programs that help, but internal R&D by "big pharma" is a major contributing factor in getting to the end results. They may be profit motivated as a business, but without them taking risks and making bets on what might be a profitable drug or treatment we wouldn't have a lot of the benefits we do have today. I don't think big pharma has any particular problems that other big companies don't have.

But you want to believe academia is pristine pure.

I don't see where Difflugia implied that,, but you seem to again be lumping all science and academia together as one bad thing. No field has to be "pristine pure" to be valuable, and with humans involved that won't be the case anyway. There are enough good, honest scientists and professors to ensure that the white hats are still winning over the black hats.

It’s pointless to argue with non-science majors. The background isn’t there.

What points are you making that require a science degree? It seems you are more into science bashing in general.