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Author Topic:   Discussion of Phylogenetic Methods
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 170 of 288 (796049)
12-21-2016 2:03 PM
Reply to: Message 168 by caffeine
12-21-2016 1:38 PM


Re: The purpose of phylogenetics
I have no idea what point you're trying to make.
Well he can speak for himself, but surely from context by "lack of data" he doesn't mean to imply that we have no genes to work with, he just means that there's a lot of noise and no signal.

This message is a reply to:
 Message 168 by caffeine, posted 12-21-2016 1:38 PM caffeine has replied

Replies to this message:
 Message 173 by caffeine, posted 12-21-2016 4:19 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 175 of 288 (796057)
12-21-2016 4:38 PM
Reply to: Message 173 by caffeine
12-21-2016 4:19 PM


Re: The purpose of phylogenetics
No, no, he said "A result with low statistical significance indicates a lack of phylogenetic signal. This can be due to a lack of data or a lack of common ancestry and evolution." As concessions go, this is a fairly mild one. A lack of common ancestry could produce that, or indeed anything else so far as we know.
(It is, however, plain, I think, that a strong and "wrong" signal would be a major anomaly. Consider, for example, if in bits of the genome that don't affect anatomy (cytochrome of any flavor, ERVs, etc) there was a strong signal putting bats with birds or whales with fish ...)

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 Message 173 by caffeine, posted 12-21-2016 4:19 PM caffeine has replied

Replies to this message:
 Message 178 by caffeine, posted 12-21-2016 5:04 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 179 of 288 (796061)
12-21-2016 5:05 PM
Reply to: Message 176 by vaporwave
12-21-2016 4:43 PM


Re: The purpose of science
Crude example: start with a vertebrate template, and from a vertebrate template generate a vertebrate-tetrapod template and a vertebrate-fish template, and so on.
So that there would in fact be common ancestry and descent with modification, but of designs rather than organisms?

This message is a reply to:
 Message 176 by vaporwave, posted 12-21-2016 4:43 PM vaporwave has replied

Replies to this message:
 Message 186 by vaporwave, posted 12-21-2016 5:36 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 181 of 288 (796063)
12-21-2016 5:09 PM
Reply to: Message 178 by caffeine
12-21-2016 5:04 PM


Re: The purpose of phylogenetics
Well, if you take individual bits of the genome you get all sorts of odd results ...
When I said "bits of the genome" I meant collectively. Obviously size matters.
If 'anything else' could produce that, then it's not evidence of anything.
No, I meant a lack of common ancestry could produce anything else. Because of "evolution is wrong" not being a specific hypothesis.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 183 of 288 (796065)
12-21-2016 5:16 PM
Reply to: Message 182 by vaporwave
12-21-2016 5:12 PM


Re: The purpose of science
f you set this fallibility aside then my point still stands, a dominant "evolutionary" pattern emerges.
No.
No ... just ... no. I don't know where you're getting this idea from, but it can't be familiarity with the actual business of producing software.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(4)
Message 192 of 288 (796077)
12-21-2016 7:47 PM
Reply to: Message 186 by vaporwave
12-21-2016 5:36 PM


Re: The purpose of science
Sure, depending on how ambiguous you want to get with those terms you could also say a wood furniture set is made up of modified descendants of a common ancestral oak tree.
Bu suppose that I do not want to be ambiguous at all, but wish to describe your idea: "Crude example: start with a vertebrate template, and from a vertebrate template generate a vertebrate-tetrapod template and a vertebrate-fish template, and so on."
Now, this is not the same as making furniture out of a tree, is it? A chair made out of an oak tree is not both a chair and an oak tree. But a tetrapod derived from a vertebrate is both a tetrapod and a vertebrate.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 186 by vaporwave, posted 12-21-2016 5:36 PM vaporwave has replied

Replies to this message:
 Message 202 by vaporwave, posted 12-22-2016 7:24 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 193 of 288 (796078)
12-21-2016 7:50 PM
Reply to: Message 185 by vaporwave
12-21-2016 5:28 PM


Re: The purpose of science
I think it's pretty much a rule at this point, if you're looking for a philosophical presentation on deities or intelligent design, just ask an evolutionist to make his scientific case for common ancestry.
No, for that you need a creationist to join the discussion. At this point even if he himself is too embarrassed to talk about his magical beliefs, it is almost certain that someone else will start mocking them.
You brought the subject up, vaporwave, you don't get a free pass.
Edited by Dr Adequate, : No reason given.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 194 of 288 (796079)
12-21-2016 7:54 PM
Reply to: Message 185 by vaporwave
12-21-2016 5:28 PM


Re: The purpose of science
d.p.
Edited by Dr Adequate, : No reason given.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 203 of 288 (796098)
12-22-2016 8:29 AM
Reply to: Message 202 by vaporwave
12-22-2016 7:24 AM


Re: The purpose of science
Yes, but nothing in that statement necessitates evolutionary history.
I never said it did. We were discussing the nearest you've come to proposing an alternate hypothesis, remember?
So your idea is that instead of organisms copying themselves with variation and branching in an evolutionary tree, designs were copied with variation and branched in a non-evolutionary tree? Is that it?
That's just the way you automatically think about traits when you assume evolution is true.
Have you ever noticed how every time you tell me what I'm thinking you turn out to be talking complete shit?
Maybe you should let me tell you what I'm thinking, as this is a topic on which I am the world's greatest and indeed only expert.
Edited by Dr Adequate, : No reason given.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 204 of 288 (796099)
12-22-2016 8:34 AM
Reply to: Message 201 by vaporwave
12-22-2016 6:58 AM


Re: The purpose of science
So when sequence data reinforces a preferred evolutionary relationship you assume it was well-conserved.
And when the sequence data contradicts a preferred evolutionary relationship, you assume it was not well-conserved.
Then when making your case to laypeople, of course be sure to only focus on the "well-conserved" sequences, because they make evolution look better.
Is that about right?
"So when you can see Saturn's rings you assume you're looking through a telescope.
And when you can't see Saturn's rings you assume you're not looking through a telescope.
Then when making your case to laypeople that Saturn has rings, of course be sure to only focus on the observations "made through a telescope", because they make astronomy look better.
Is that about right?"
No, that's not about right.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 201 by vaporwave, posted 12-22-2016 6:58 AM vaporwave has replied

Replies to this message:
 Message 215 by vaporwave, posted 12-22-2016 4:12 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 217 of 288 (796120)
12-22-2016 4:46 PM
Reply to: Message 215 by vaporwave
12-22-2016 4:12 PM


Re: The purpose of science
Poor analogy. You don't have to assume or infer that the thing actually being observed through a telescope or microscope exists.
Good analogy because you don't have to assume that the telescope exists, which was my point.
And in fact, to address your point ... yeah, you kind of do. Some Ptolemaians did in fact object to Galileo's discoveries by proposing that the moons of Jupiter etc were illusions caused by his telescope, that he was not seeing a thing but only an illusion of a thing, and was erroneously assuming that the thing he was observing actually existed. The option of doing this sort of thing always stands open for anyone who wants to deny the significance of the data.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 218 of 288 (796121)
12-22-2016 5:06 PM
Reply to: Message 216 by vaporwave
12-22-2016 4:41 PM


Re: The purpose of science
Why are you obfuscating? You know very well it is much more than the direct observation.
In evolutionary terminology, stating that a genetic sequence is 'conserved' is to make a claim about evolutionary relationships.
"Conservation across species indicates that a sequence has been maintained by evolution despite speciation. A highly conserved sequence is one that has remained unchanged far back up the phylogenetic tree, and hence far back in geological time."
Now you're being dishonest again. That is certainly what conservation indicates, just as the article says, but it is not how it is defined or recognized, as you must know because the article says, right at the top: "conserved sequences are similar or identical sequences in nucleic acids (DNA and RNA), proteins, or polysaccharides across species (orthologous sequences) or within different molecules produced by the same organism (paralogous sequences)".
You should stop bullshitting us. It doesn't deceive anyone, it just makes you look dishonest.

This message is a reply to:
 Message 216 by vaporwave, posted 12-22-2016 4:41 PM vaporwave has replied

Replies to this message:
 Message 220 by vaporwave, posted 12-22-2016 5:41 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 223 of 288 (796128)
12-22-2016 11:12 PM
Reply to: Message 220 by vaporwave
12-22-2016 5:41 PM


Re: The purpose of science
Oh, I see... so the term isn't recognized as what it typically indicates in the literature?
You should probably think your comments through a little more instead of just kicking up dust and making noise every time I post.
Well, that was gibberish.
A red light indicates that you should stop. But it is recognized and defined by its color.
A fever indicates an infection. But it is recognized and defined by the patient's temperature.
A conserved gene indicates that a sequence has been maintained by evolution, but it is recognized and defined by having similar or identical sequences across species.
I shall not speculate on whether this is more of your dishonesty or whether you are genuinely so stupid you need to have this explained to you.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 228 of 288 (796141)
12-23-2016 9:55 AM
Reply to: Message 224 by vaporwave
12-23-2016 7:23 AM


Re: templates and peripheral features
On the other hand, if the genetic organization of the gliding membrane is the same or similar in both groups, then those particular gene sequences were inherited from a common mammalian ancestor and driven by natural selection to be recruited for a common function in different species.
Evolution would accommodate both observations in this case, just like design.
But it can't. Gliding is not in fact an ancestral characteristic of mammals, and if it was then the genes would be found throughout the mammal class if only as pseudogenes. If they weren't there, that would destroy any such hypothesis.
Unlike "design"/magic, evolution is testable.
You mean a more complex explanation than "natural selection did it" ?
You should really find out what the theory of evolution is, it's fascinating.
An alternative hypothesis doesn't necessarily have to be complex. If you like it could be as simple as the theory of evolution or even as simple as the theory of gravity. What we should require of it is first that it should actually exist, second, that it should be predictive, third, that its predictions should be correct. If it does better than the theory of evolution, we'll adopt it.
So far you're stuck on not even having anything with enough content to qualify as a hypothesis. Let us know.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 224 by vaporwave, posted 12-23-2016 7:23 AM vaporwave has replied

Replies to this message:
 Message 230 by vaporwave, posted 12-23-2016 1:21 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 232 of 288 (796156)
12-23-2016 1:30 PM
Reply to: Message 230 by vaporwave
12-23-2016 1:21 PM


Re: templates and peripheral features
That's how evolution could accommodate similar genetic organization of gliding membranes in marsupials and eutherians. It would not disprove common ancestry.
Your excuse might be somewhat plausible if they were just vaguely similar, but not if they were the same. And either way or your excuse to hold water the gene (or pseudogene) would have to be spread throughout the clade.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 230 by vaporwave, posted 12-23-2016 1:21 PM vaporwave has replied

Replies to this message:
 Message 234 by vaporwave, posted 12-23-2016 3:57 PM Dr Adequate has replied

  
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