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.

[Mae von H]

[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.

Chemistry might be different. I can only speak to biology and medicine. I just listened today to a researcher in psychology discussing the leaked emails where a prominent scientist asked a junior to tweek the data fixing it and eliminating points that are not in favor of his thesis there by reducing the p value. I’ve worked with people who saw scientists steal another’s work. I’ve worked with scientists willing to throw out a coworkers previous samples. The list is depressing. I’ve asked PhDs if they trust other scientists and no joke, they laughed. Of course not. Keep all research under lock and key until published. I mean chemistry might be different. I cannot speak to that field.

[Difflugia]

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

NOPE

Then what? If that's not what's going on, then what does "governed" mean to you in this context?

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'm unaware of "epidemic dishonesty in science," but despite the poor attempt at poisoning the well, that's not why I don't believe you. I don't believe you because not only haven't you supported your claims and accusations, but you seem to be just guessing about how academia functions in the first place.

I work with scientists and they don’t trust each other.

Perhaps you work with particularly immoral or unethical scientists. I don't know. You've given me no way to know and, quite frankly, you've given me a number of reasons not to believe you.

Now either you believe this or you prefer to think they’re a cut above other men ethically.

That's both poisoning the well and a false dichotomy. Brava.

In my experience it is a matter of wanting scientists to be truthful or wanting the truth.

Yes. In my experience, the majority of scientists not only want that, but earnestly aspire to achieve that as a goal.

How many people know about this grand conspiracy of dishonesty?

Ask scientists if they completely trust other scientists?

I'm asking you. How many people know about this grand conspiracy of dishonesty?

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.

Or you could just answer the question.

For context, I'm the one that's repeatedly offered to help you learn to analyze the data yourself without having to take someone else's word for it, but you're telling me that I'm too credulous.

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.

That would definitely add a little support to your still unsupported assertions.

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.

Have any favorite neuroimmunology papers that would seem to suggest intelligent design rather than evolution? The conversation might range a bit above my pay grade, but I'll try to keep up.

But you want to believe academia is pristine pure.

A hyperbolic straw man, now? Have you really nothing else? Fine. "And you want to believe that magic is real."

There’s no hope. You certainly don’t work in science.

Certainly.

You’re not a biologist.

Biology was just my undergrad minor.

You don’t actually do research

Not published. I work in the private sector.

and I doubt you can scientifically evaluate papers.

I humbly suggest that reading through my posts might tell you otherwise.

It’s pointless to argue with non-science majors.

Not to mention embarrassing to argue with someone that calls your bluffs.

The background isn’t there.

I'll try to keep up.

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.

I think the key word here is imagination.

[Clownboat]

This is part of the Pantheon of false Gods in our modern world as it dances to a tune with Money, Folly and Greed.

It is my understanding that none of the available god concepts have been shown to be real concepts. Have I missed one? I ask because you allude to a 'pantheon of false gods' and it would seem to me that all the available god concept share equal footing when it comes to them existing or not.

[benchwarmer]

Ask scientists if they completely trust other scientists?

This question again raises a lot of doubt if you actually understand how science works. Perhaps it's just your wording. Of course scientists don't 'completely' trust other scientists. That's why they have a peer review process. However, that doesn't mean that scientists don't trust other scientists in general to do good work as long as they support their work with methodology and data so it can be repeated if necessary.

You seem to be painting science as some monolithic enterprise where everyone involved is backstabbing and ignoring the actual scientific method. I'm sure this plays to the narrative you wish to be true, but we know for a fact that science (and thereby scientists) in general are advancing human knowledge at an ever increasing pace. If all scientists were acting as how you are attempting to portray them, no progress would ever be made.

Are there some bad apples (like apparently the people you work with)? Sure, scientists are also humans and you are going to get some duds in every human endeavor.

Let's take this another way. If I can show you evidence of some extremely bad Christians, can we then (using your logic) assume all Christians, including yourself, must also be acting this way in general? You know I'm not afraid to use my vast Google powers and type 'church abuse scandals' and paste enough links to get the point across.

Back to the OP, what I find quite telling here is that no one seems to want to take Difflugia up on their kind offer of helping them work with the actual data. I'm wondering if the problem here is the typical conspiracy theory that scientists are all in league to 'destroy God' or 'attack the Bible' and therefore any data that can be found will be purposely made to look like evolution is true. I guess the other possibility is that no one really wants to face the actual data and have to deal with the cognitive dissonance that will follow when they realize what the data is actually showing.

[Mae von H]

Ask scientists if they completely trust other scientists?

This question again raises a lot of doubt if you actually understand how science works. Perhaps it's just your wording. Of course scientists don't 'completely' trust other scientists. That's why they have a peer review process. However, that doesn't mean that scientists don't trust other scientists in general to do good work as long as they support their work with methodology and data so it can be repeated if necessary.

You seem to be painting science as some monolithic enterprise where everyone involved is backstabbing and ignoring the actual scientific method. I'm sure this plays to the narrative you wish to be true, but we know for a fact that science (and thereby scientists) in general are advancing human knowledge at an ever increasing pace. If all scientists were acting as how you are attempting to portray them, no progress would ever be made.

Are there some bad apples (like apparently the people you work with)? Sure, scientists are also humans and you are going to get some duds in every human endeavor.

Let's take this another way. If I can show you evidence of some extremely bad Christians, can we then (using your logic) assume all Christians, including yourself, must also be acting this way in general? You know I'm not afraid to use my vast Google powers and type 'church abuse scandals' and paste enough links to get the point across.

Back to the OP, what I find quite telling here is that no one seems to want to take Difflugia up on their kind offer of helping them work with the actual data. I'm wondering if the problem here is the typical conspiracy theory that scientists are all in league to 'destroy God' or 'attack the Bible' and therefore any data that can be found will be purposely made to look like evolution is true. I guess the other possibility is that no one really wants to face the actual data and have to deal with the cognitive dissonance that will follow when they realize what the data is actually showing.

It’s clear to me I understand it better than you do. I’ve actually asked PhDs in research if they trust other scientists, taking a sampling as the good scientific practice prescribes. Something I doubt you’ve done.

My experience is those who elevate science and scientists as more morally noble than the rest don’t like that idol blasted. So I leave you with your admiration of those institutions in tact.

[benchwarmer]

It’s clear to me I understand it better than you do. I’ve actually asked PhDs in research if they trust other scientists, taking a sampling as the good scientific practice prescribes. Something I doubt you’ve done.

You're correct, I have not asked scientists if they trust each other. That doesn't effect my point at all. Is the field of science in general making progress? If so, even with your dim view of the entire enterprise, I guess it's still effective.

I also already said of course they don't trust each other 'completely' as you were arguing. That's a strange and useless question. In what large group of people does anyone trust all the others in the group 'completely'? Certainly not Christians. Nor atheists. Nor any other large group I can come up with. I look forward to your evidence there is such a group though.

My experience is those who elevate science and scientists as more morally noble than the rest don’t like that idol blasted. So I leave you with your admiration of those institutions in tact.

Who is "elevating science and scientists as more morally noble"? Link and quote please.

More morally noble than who? I already said that scientists are human and they will therefore have among them some who have the traits you describe. Does that mean all of them act like that as your sweeping assertion suggests? Readers will note yet again your complete lack of evidence for your claims. Hearsay is hardly useful. Congratulations, you asked a few scientists if they trust each other. Therefore all scientists distrust each other. Wow.

[Difflugia]

It’s clear to me I understand it better than you do. I’ve actually asked PhDs in research if they trust other scientists, taking a sampling as the good scientific practice prescribes. Something I doubt you’ve done.

So you keep claiming, without offering any sort of support or even plausible evidence of this better understanding. Your evidence is limited to private communication that is totally real, I swear, which you back up with nothing more than insults. Do you have anything even slightly more substantial?

[Mae von H]

. Congratulations, you asked a few scientists if they trust each other. Therefore all scientists distrust each other. Wow.

That’s not what I said. If you cannot refrain from misrepresenting what I said, discussion on this point is useless. Or alternatively, if your understanding of science is so weak that you think TENDENCIES or even POSSIBILITIES mean EVERYONE, then I definitely know more about science than you do. Shall I post links on the increasing cases of scientific fraud? Will that suffice as evidence? Don’t you want to find out if there’s an epidemic of scientific fraud? The head of Stanford had to step down because academic fraud was uncovered. He’s not the only one. Do you think it’s just me making this up rather than admit it’s true?

[benchwarmer]

. Congratulations, you asked a few scientists if they trust each other. Therefore all scientists distrust each other. Wow.

That’s not what I said. If you cannot refrain from misrepresenting what I said, discussion on this point is useless.

I apologize if I have misrepresented you, but I honestly fail to see how.

Have you not been telling us that scientists don't trust each other? Yes or no.

If yes, then I'm not sure how I've misrepresented you.

If no, then please be more clear and provide some evidence for exactly what you are trying to convey.

Or alternatively, if your understanding of science is so weak that you think TENDENCIES or even POSSIBILITIES mean EVERYONE, then I definitely know more about science than you do.

I can only go by what you have posted. You are free to clarify with quotes, evidence, etc.

I'm happy to admit when I'm wrong. Your continued going on about how you know more about science than others it tiring. I think everyone following along has a pretty good handle on who understands how science works and who doesn't. Readers are free to decide who is making the better case. I'm not trying to convince you of anything.

Shall I post links on the increasing cases of scientific fraud? Will that suffice as evidence? Don’t you want to find out if there’s an epidemic of scientific fraud? The head of Stanford had to step down because academic fraud was uncovered. He’s not the only one. Do you think it’s just me making this up rather than admit it’s true?

It would be quite refreshing if you would start backing up your claims.

I already know, as I've stated a couple times now, that there are bad apples in science. So? What exactly are you trying to convey to readers with that information? You've already implied you think we 'elevate' scientists as 'morally noble'. That's demonstrably false as I've already admitted. Scientists are people (I know - knowledge bomb there) and are obviously no better because they are in one discipline or another.

What exactly is it you are trying to argue? I mean, I know, but I can't piece together your logic.

1) Claim the scientific theory of evolution is wrong
2) Tell us scientists don't trust each other (to whatever degree you want to now explain to us)
3) Bring up the fact that there are bad scientists
4) ????
5) Therefore you are correct based on the above.

That seems to be your chain of logic, but please, I'm happy to be corrected and for you to lay out the chain of logic for everyone.

[Clownboat]

. Congratulations, you asked a few scientists if they trust each other. Therefore all scientists distrust each other. Wow.

That’s not what I said. If you cannot refrain from misrepresenting what I said, discussion on this point is useless. Or alternatively, if your understanding of science is so weak that you think TENDENCIES or even POSSIBILITIES mean EVERYONE, then I definitely know more about science than you do. Shall I post links on the increasing cases of scientific fraud? Will that suffice as evidence? Don’t you want to find out if there’s an epidemic of scientific fraud? The head of Stanford had to step down because academic fraud was uncovered. He’s not the only one. Do you think it’s just me making this up rather than admit it’s true?

Do you acknowledge that the scientific method is the best method humans have at arriving at truths, or do you argue that there is a better method humans should be using in place of the scientific method?

I'm trying to figure out what you are complaining about and why. It's like acknowledging that the ThrustSSC is the fastest land vehicle, but it just isn't fast enough. Such a complaint would seem misplaced don't you think?