Scientific Evidence for Universal Common Descent

[YoursTrue]

Yep. Do you think those ideas are still deserving of respect after they've been proven wrong?

Obviously in some cases (such as spontaneous generation of maggots from meat), they're wrong. In other cases it could be said that only some of the original idea was wrong, or at best incomplete. And of course, the idea that Pluto was definitely (and I mean definitely and certainly) considered a planet until recently is discarded now, isn't it?

 

[Jose Fly]

I already did that.

No you didn't.

In post #1479, you cited the Larget et al. paper as an example of "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

In post #1491 I asked you to specify where you saw anything like that in the paper.

In post #1497 you quoted a couple of introductory sentences from the abstract, with no explanation of how they constituted "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

In post #1511 I let you know that your post 1497 made no sense to me.

In post #1521 you responded "That’s okay. I want to say again that I’m grateful for your thoughtful and generous responses to my questions and comments. This turned out to be a lot more educational and fun for me than I would have thought."

And that's where it ended.

So I'm again asking you to explain how the Larget et al. paper is an example of "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

 

[Jose Fly]

The italicized words in this post.

To repeat, all you did was quote a couple of sentences from the abstract, with no explanation at all of how they are examples of "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

 

[YoursTrue]

I suppose one day a creationist can explain how Yahweh made bio-organic molecules from silicates (dust of the ground) by speaking. (yes, I laughed).

It's possible but not necessary to explain how God did it all. Because it may never be revealed by God to humans.

 

[Jose Fly]

Obviously in some cases (such as spontaneous generation of maggots from meat), they're wrong. In other cases it could be said that only some of the original idea was wrong, or at best incomplete. And of course, the idea that Pluto was definitely (and I mean definitely and certainly) considered a planet until recently is discarded now, isn't it?

You didn't answer the question. Are ideas deserving of respect after they've been shown to be wrong?

 

[Polymath257]

Obviously in some cases (such as spontaneous generation of maggots from meat), they're wrong. In other cases it could be said that only some of the original idea was wrong, or at best incomplete. And of course, the idea that Pluto was definitely (and I mean definitely and certainly) considered a planet until recently is discarded now, isn't it?

That is primarily because we changed the definition of the term 'planet'. Pluto is still out there orbiting the sun. It still has all the physical properties it had before. The only difference is in our classification scheme. It wasn't even in our understanding of Pluto.

 

[Polymath257]

It's possible but not necessary to explain how God did it all. Because it may never be revealed by God to humans.

If we rely on revelation, then no actual science can be done. We want testable ideas, not ones that can be use to explain *anything*.

Ultimately, that is because if an idea is so flexible that it is consistent with *everything*, then it has no explanatory ability whatsoever.

 

[Jim]

@Jose Fly In a post addressed to usfan, I said:

@usfan I’m beginning to see what you’re talking about here. The more I read about evolution research, the more that some of it looks like an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship.

You asked:

Where specifically do you see that?

I said:

Here for example:
Statistical evidence for common ancestry: New tests of universal ancestry

You asked:

So where exactly in that paper do you see "a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship"?

Please be specific.

I quoted from the article with the words italicized that looked that way to me. I will bold them here:

“While there is no doubt among evolutionary biologists that all living species, or merely all living species within a particular group (e.g., animals), share descent from a common ancestor, formal statistical methods for evaluating common ancestry from aligned DNA sequence data have received criticism ... We present a new statistical framework to test separate ancestry versus common ancestry that avoids this pitfall.

What I said originally, that you were questioning, was addressed to usfan, describing how it looks to me. You asked for an example of what looks like that to me, and I gave you one. I’m not trying to convince anyone. The way it looks to me could be all wrong.

 

[Polymath257]

@Jose Fly In a post addressed to usfan, I said:

You asked:

I said:

You asked:

I quoted from the article with the words italicized that looked that way to me. I will bold them here:

What I said originally, that you were questioning, was addressed to usfan, describing how it looks to me. You asked for an example of what looks like that to me, and I gave you one. I’m not trying to convince anyone. The way it looks to me could be all wrong.

Actually, this sort of criticism and modification is very common. For example, in the investigations of Bell's inequalities in quantum mechanics, the original experiment by Aspect verifying the violations was criticized for not dealing with some special cases. Subsequent experiments did deal with those. NOBODY really expected the results to be different than they were, but intellectual honesty required the criticism and the new experiments.

In this case, the previous models were criticized. New models were developed to test that criticism and the end results surprised nobody. But the test was important to do simply because *if* it had come out differently, our understanding would have to change.

 

[Jose Fly]

I quoted from the article with the words italicized that looked that way to me.

Exactly. All you did was quote a couple of benign sentences from the abstract, with no explanation at all of how they constituted "a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

What I said originally, that you were questioning, was addressed to usfan, describing how it looks to me. You asked for an example of what looks like that to me, and I gave you one. I’m not trying to convince anyone. The way it looks to me could be all wrong.

You're still not making any sense at all. You see, when you first cited that paper as an example of "a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship", I figured you were talking about the actual work the paper was about. But then all you did was quote a couple of generalized introductory sentences with no explanation.

So do you believe their work is solid and just take issue with those two introductory sentences?

 

[ratiocinator]

What I said originally, that you were questioning, was addressed to usfan, describing how it looks to me. You asked for an example of what looks like that to me, and I gave you one. I’m not trying to convince anyone. The way it looks to me could be all wrong.

I'm at a total loss to understand why you would think doing extra tests on a conclusion that is already widely accepted, due to extensive existing evidence, can be seen as a "desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

 

[Polymath257]

I'd also point out that the criticisms leading to new models or new experiments are *crucial* for the development of science. Sometimes it *does* happen that the new experiments don't turn out as everyone expects. Sometimes the new models *don't* give the answer everyone has thought they would.

A very good example was the Michelson-Morley experiment testing the theory of the ether. At the time, this explanation for the propagation of light was considered incredibly solid and *nobody* expected the result of the experiment to say anything different than this theory predicted.

Well, of course, the result *didn't* go as expected. That ultimately caused a radical re-thinking of our ideas of how light propagates and the development of special relativity by Einstein.

So, one of the *jobs* of a research scientist is to point out leaps of logic others have committed (or that they themselves have) and find ways to *test* to see whether those leaps actually are over holes. In the vast majority of cases, they are not, of course. But every once in a while, something turns out that requires us to do more work.

Such times actually will make the career of the person who pointed out the flaw and the person who verified it. This is how scientific revolutions are born.

But what never happens is that we go back to the *old* explanation, the one prior to the current one, because that one was rejected because it failed to match observations. This is why the basics of evolution and common descent aren't going to go away. There is simply too much that has been verified.

I might point out that, even after the Michelson-Morley experiment, the *equations* that describe the propagation of light remained the same. What changed was our understanding of what those equations said and meant.

 

[Jim]

So do you believe their work is solid

I’m not sure what you mean by “solid.” I don’t believe that it was done honestly and responsibly, if that’s what you mean, but I could be wrong.

... and just take issue with those two introductory sentences?

I don’t know what you mean by “take issue.” I wasn’t questioning it as a description of what the researchers did and why. It was the easiest example for me to find, of what I saw, that looked to me like a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship. Not that I think it’s really going to sink. I was just describing what some of the behavior of researchers looks like to me.

 

[Jose Fly]

I’m not sure what you mean by “solid.” I don’t believe that it was done honestly and responsibly, if that’s what you mean, but I could be wrong.

Wow....you're actually accusing the authors of that paper of being dishonest and irresponsible. You realize that's a very serious accusation, right? So hopefully you have something of substance to back it up.

I don’t know what you mean by “take issue.” I wasn’t questioning it as a description of what the researchers did and why. It was the easiest example for me to find, of what I saw, that looked to me like a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship. Not that I think it’s really going to sink. I was just describing what some of the behavior of researchers looks like to me.

All you've done is repeat yourself, again without explaining. So....

Do you see problems and/or errors in their methodology? In their analyses? In their conclusions?

And where specifically do you see them being dishonest and irresponsible?

 

[Polymath257]

I’m not sure what you mean by “solid.” I don’t believe that it was done honestly and responsibly, if that’s what you mean, but I could be wrong.

I'm going to challenge this. They did *exactly* what they were supposed to do to be honest and responsible. They considered a potential hole in previous results, investigated it, and closed it.

I don’t know what you mean by “take issue.” I wasn’t questioning it as a description of what the researchers did and why. It was the easiest example for me to find, of what I saw, that looked to me like a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship. Not that I think it’s really going to sink. I was just describing what some of the behavior of researchers looks like to me.

Your description of it as desperate is unwarranted. What they did is look at a potential hole in previous logic, considered how to deal with that hole, did the analysis and reported their results. This is exactly what is required of intellectual honesty. Yes, everyone fully expected the results to be what came out, but that is not the point. They didn't sweep the issue under the rug, but addressed it directly. Far from being 'desperate', it is what needed to be done to close a potential loophole.

You see, results in science are never completely settled. There is always the possibility that someone will point out a special case that hasn't been thought through. And, even if everyone expects that special case to not really be special, they still have to consider it and figure out just how special it is. This is precisely what was done in that paper.

 

[Jim]

@Polymath257 @Jose Fly @Dan From Smithville I’m not a person who could have any influence on any decision making or policy making even if I wanted to, and I won’t be trying. The way it looks to me could be all wrong, but all you’re doing is confirming it for me. I’ll consider what could possibly change my mind about it, and look for that.

 

[Subduction Zone]

Obviously in some cases (such as spontaneous generation of maggots from meat), they're wrong. In other cases it could be said that only some of the original idea was wrong, or at best incomplete. And of course, the idea that Pluto was definitely (and I mean definitely and certainly) considered a planet until recently is discarded now, isn't it?

Pluto was reclassified. That does not change any of what is known about it. And spontaneous generation never was a scientific theory. Science has improved its methodology over the years. In fact it was application of the scientific method that refuted spontaneous generation.

Quite often those that deny science do not have a very good grasp of the concept. The scientific method is rather simple. One observes a phenomenon, asks questions about it, and then tries to answer them. That is done by constructing testable models and trying to disprove them. It is not enough to find correlation. One must think of a reasonable test that could show one's idea to be wrong and test it with that in mind. Passing such a test does not"prove" the theory,but it does give one more confidence that it is correct.

 

[Jose Fly]

@Polymath257 @Jose Fly @Dan From Smithville I’m not a person who could have any influence on any decision making or policy making even if I wanted to, and I won’t be trying. The way it looks to me could be all wrong, but all you’re doing is confirming it for me. I’ll consider what could possibly change my mind about it, and look for that.

Jim, I'll be perfectly honest with you.....the above looks to me like a cop out. You made an accusation, got called on it, and now that you can't back it up you're just trying to weasel out of the situation.

Is it not possible for you to say something like "My accusation against the authors of that paper was mistaken and hastily made, so I retract it and apologize"? Is your pride preventing you from doing that?

 

[Jim]

Jim, I'll be perfectly honest with you.....the above looks to me like a cop out. You made an accusation, got called on it, and now that you can't back it up you're just trying to weasel out of the situation.

False.

Is it not possible for you to say something like "My accusation against the authors of that paper was mistaken and hastily made, so I retract it and apologize"?

That would not be possible for me because it would be dishonest for me to say that.

Is your pride preventing you from doing that?

No. What’s preventing from doing that is that it isn’t what I think.

 

[Jose Fly]

False.

That would not be possible for me because it would be dishonest for me to say that.

No. What’s preventing from doing that is that it isn’t what I think.

Okay then, you still need to substantiate your accusation that the authors of the paper were dishonest and irresponsible.