It may also be worth mentioning that molecular phylogenies produce gene trees that may not always reflect the true structure of the populations involved. One obvious reason is incomplete lineage sorting. For example, 30% of human genes are more closely related to gorilla genes than chimp genes, and a small percentage of human genes are more closely related orangutan genes than either chimp or gorilla genes. Like many methods in science, you need to account for both the signal and the noise.
What is an example of a software program that you use to create a phylogenetic tree? That software has as input a set of sequences from which it creates a tree diagram? What does a sample sequence look like?
Well, there are many, but my favorite is PAUP. You might try this book, Phylogenetic Trees Made Easy, for a fairly simple explanation of how these things work. It’s on Amazon.
Yes. Or a set of characters of any sort, from any source. It will work on made up data, if that’s what you’re getting at.
You know, just a series of A’s, G’s, C’s, and T’s. Surely you have seen these before. What are you really asking?
I am asking whether that series of A’s, G’s, C’s, and T’s has to come from some actual DNA/RNA from an actual organism. Could you sneak in some sequences that you just made up?
You appear to think that the only source of such a sequence would be from an actual organism.
As opposed to some sequences that you just made up, for example.
Are you at least beginning to see that from that fact that you can construct a phylogenetic tree it does not follow that it is evidence for common descent? It could be entirely fictional.
Yes, that is what I was getting at.
What part of " Or a set of characters of any sort, from any source. It will work on made up data, if that’s what you’re getting at." was unclear? Still searching for some kind of point here. Perhaps you could just tell me what your point is.
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Wouldn’t that be true of every single scientific experiment and scientific theory? What you seem to be arguing against is the reliability of the scientific method itself.
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No.
It would help if you expanded on that comment.
Why not?
The theory of evolution predicts that we should see a statistically significant phylogenetic signal. Why wouldn’t it be evidence for common descent if we observe the very thing that the theory predicts we should see?
You also claim that data is being faked, which is quite an accusation.
You could say the same thing about every single experiment ever done. You could say that the people at the LHC faked the data so that it would fit the prediction of extra photons at certain energies. Even more, you could argue that just because they really did see the expected excess of photons it doesn’t mean anything, even though it matches predictions.
Do you see the problem?
As far as DNA sequences go, the organisms are still out there in the wild. PCR is easy to do, and sequencing is dirt cheap (for 1,000 base pairs or less). It would be exceedingly easy to spot check any reported sequence. So why would scientists risk their entire careers to fake DNA sequence data that could easily be exposed?
Could you point out where I stated that data is being faked. That’s quite an accusation! 
From here, unless I am missing some context:
He hasn’t claimed that so far. But he also hasn’t explained where he was going with that line of thought. We may never know.
Mung, when I read that post, I knew that you would be misunderstood. Even though you posed it as a question, most readers will assume that it is a question with an agenda and one meant to make a very pointed statement.
So please allow me to make a suggestion for rewording that type of hypothetical so that readers are much less likely to misinterpret you:
Suppose some mischievous gremlin decided to sneak in some arbitrary sequences that he made up in order to play games with the scientists. Would the gremlin’s mischief be readily recognized for what it was?
Even though I don’t agree with your reasoning on this part of the thread, I think that the kind of re-wording I’m recommending can help readers understand what you are saying. (After all, most readers will recognize that you don’t actually believe that little unseen gremlins routinely manipulate DNA just to drive scientists crazy. It helps underscore the “what if” scenario you are imagining just for the sake of argument and questioning.)
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To restate my point even more clearly:
In other words, @Mung, it is always safer to blame such purely hypothetical manipulation on mischievous gremlins than to even subtly imply that scientists are routinely planting false data in their published studies!
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The first way you said it was better.
I did not “subtly imply that scientists are routinely planting false data in their published studies.” I simply cannot prevent people from taking what I write and reading it in the worst possible light. I could use the words you suggest and they would still think i was using the words mischievous gremlins to cover up what I “really” think, which is that evolutionary scientists are planting false data in their published studies.
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I see your point.
I should have written even more carefully (in my revised version): "to even appear to risk subtly implying_ that scientists are routinely planting false data in their published studies!
Yes, avoiding misunderstandings can take some very careful wording. Even meticulous wording—though some will certainly miss even that.
Agreed. No doubt we always take that risk on a public forum when real human beings are involved in any way. It is one of the reasons why I no doubt frustrate some people when I ask them to define particular words and to clarify various points before replying to their question. I’ve learned from experience that my interpretations of their meanings can be very wrong, no matter how carefully I’ve read their post.
And these are all among the reasons why on Peaceful Science we try as best we can to (1) give people the benefit of the doubt, (2) question and clarify when they or we are unclear, and (3) be gracious and forgiving when misunderstandings arise. Of course, as humans we will fall short in meeting these goals at times.
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The best way to counter this is to tell us all what you were trying to get at without making us keep guessing. What were you trying to get at?
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Mung, as you can see in our exchange above, even as I tried to explain how you could make your point with less risk of being misunderstood, you rightly explained how my explanation of your post could be misunderstood! This is far more common in human communications than people sometimes pause to consider. Even as native speakers we can easily misinterpret.
I emphasize this point while thinking of those who claim that the Bible should always be read for “the simple, obvious, and natural reading of the Biblical text.” They fail to see and acknowledge just how complicated Bible translation and hermeneutics (interpretation) can be.
That said, what line of evidence is strongest for evolution?
I agree with this one @Mung. Your posts are often like ink blot tests. In a context full of contentious arguments and distrust, this is an ineffective strategy. People should ask you what you mean. The terse one liners you often drop, however, are just asking to be misinterpreted.
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To be a bit less charitable, he should say what he means, the first time, without having to be asked.
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Perhaps one of the moderators could split this off into another 'Mung Misunderstood While … " thread.