Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
6 online now:
Newest Member: popoi
Post Volume: Total: 915,815 Year: 3,072/9,624 Month: 917/1,588 Week: 100/223 Day: 11/17 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Discussion of Phylogenetic Methods
JonF
Member (Idle past 168 days)
Posts: 6174
Joined: 06-23-2003


Message 196 of 288 (796081)
12-21-2016 8:05 PM
Reply to: Message 195 by Granny Magda
12-21-2016 7:59 PM


Re: The purpose of science
It's almost as if you don't realise that the stuff you write is available to check
I've found that trait to be fairly common among creationists. Yet this was a particularly egregious example.

This message is a reply to:
 Message 195 by Granny Magda, posted 12-21-2016 7:59 PM Granny Magda has not replied

Replies to this message:
 Message 197 by Coyote, posted 12-21-2016 9:33 PM JonF has not replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 197 of 288 (796083)
12-21-2016 9:33 PM
Reply to: Message 196 by JonF
12-21-2016 8:05 PM


Re: The purpose of science
JonF writes:
Granny writes:
It's almost as if you don't realise that the stuff you write is available to check
I've found that trait to be fairly common among creationists. Yet this was a particularly egregious example.
Creationists work from belief, which is not amenable to fact checking--its belief, after all. That's their approach, and if a particular sect has a major disagreement within its ranks there is most likely going to be a split, resulting in still another sect! They have to split, as there is no way to evaluate the evidence.
Not surprisingly they bring that approach to websites such as this, inhabited by many folks who do science and whose livelihood depends on fact checking! To be wrong in a publication is, for STEM scientists, a major embarrassment, and to be wrong several times could end a career.
Yet when creationists show up here they expect their belief-based approach, usually accompanied by little knowledge of science and way too much reliance on scripture and dogma, to convince everyone else that they have the one and only TRVTH.
And the "magic bullet" that is going to slay the evil evolution dragon is almost certainly one that has been tried unsuccessfully many times before. Some of them have been tried so often that they are considered PRATTs, or Points Refuted a Thousand Times. The Index to Creationist Claims has even numbered and organized the failed creationist claims by subject matter!
So, no. We are not likely to be impressed by the latest "magic bullet" to make the rounds of the interwebs...

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.

This message is a reply to:
 Message 196 by JonF, posted 12-21-2016 8:05 PM JonF has not replied

  
jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 198 of 288 (796085)
12-21-2016 9:41 PM


The facts remain. We win.
We have the fossils and the fossils refute the Biblical Creation myths. We win.
We have the natural causes. We win.
We have the designers. We win.
Creationism has absolutely nothing, not even a single creation myth. Even the Bible has two mutually exclusive creation myths. If one were true the other must be false. We win.

My Sister's Website: Rose Hill Studios My Website: My Website

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 199 of 288 (796087)
12-22-2016 12:48 AM
Reply to: Message 189 by vaporwave
12-21-2016 6:57 PM


Re: The purpose of science
I assume whatever you're driving at is universal to all phylogenies, right?
It is significantly widespread among phylogenies constructed from well-conserved, non-saturated nucleic acid sequence sites -- and this is the data set that's relevant.
Why might this be the case? My explanation is evolutionary descent. And that's a robust explanation, too.
What's your explanation?

This message is a reply to:
 Message 189 by vaporwave, posted 12-21-2016 6:57 PM vaporwave has replied

Replies to this message:
 Message 200 by AZPaul3, posted 12-22-2016 1:50 AM Genomicus has not replied
 Message 201 by vaporwave, posted 12-22-2016 6:58 AM Genomicus has not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 200 of 288 (796089)
12-22-2016 1:50 AM
Reply to: Message 199 by Genomicus
12-22-2016 12:48 AM


Re: The purpose of science
What's your explanation?
Probably...


This message is a reply to:
 Message 199 by Genomicus, posted 12-22-2016 12:48 AM Genomicus has not replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 201 of 288 (796094)
12-22-2016 6:58 AM
Reply to: Message 199 by Genomicus
12-22-2016 12:48 AM


Re: The purpose of science
It is significantly widespread among phylogenies constructed from well-conserved, non-saturated nucleic acid sequence sites -- and this is the data set that's relevant.
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?

This message is a reply to:
 Message 199 by Genomicus, posted 12-22-2016 12:48 AM Genomicus has not replied

Replies to this message:
 Message 204 by Dr Adequate, posted 12-22-2016 8:34 AM vaporwave has replied
 Message 207 by Taq, posted 12-22-2016 11:48 AM vaporwave has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 202 of 288 (796095)
12-22-2016 7:24 AM
Reply to: Message 192 by Dr Adequate
12-21-2016 7:47 PM


Re: The purpose of science
But a tetrapod derived from a vertebrate is both a tetrapod and a vertebrate.
Yes, but nothing in that statement necessitates evolutionary history.
That's just the way you automatically think about traits when you assume evolution is true.

This message is a reply to:
 Message 192 by Dr Adequate, posted 12-21-2016 7:47 PM Dr Adequate has replied

Replies to this message:
 Message 203 by Dr Adequate, posted 12-22-2016 8:29 AM vaporwave has not replied
 Message 208 by Taq, posted 12-22-2016 11:50 AM vaporwave has replied

  
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.

This message is a reply to:
 Message 202 by vaporwave, posted 12-22-2016 7:24 AM vaporwave has not replied

  
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

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 205 of 288 (796101)
12-22-2016 9:35 AM
Reply to: Message 176 by vaporwave
12-21-2016 4:43 PM


templates and peripheral features
Isn't that the impression you have been pushing all along? If a designer can mix and match design units freely, then creationism should not produce a nested hierarchy.
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 then you generate a vertebrate-tetrapod-eutherian template that is used to generate a squirrel template that is used to generate a flying squirrel template ...
... and you generate a vertebrate-tetrapod-metatherian template that is used to generate a possum template that is used to generate a sugar glider template ...
I'm not sure what your obsession is with this hypothetical mix-and-match scenario. ...
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same?
I thought this would be obvious. If a coder wants to design, say, a hundred variations of a web browser program, he would probably work off some sort of common coding base for the basic program and then add/remove/tweak various peripheral features in order to generate variety.
Or is it one of the "peripheral features in order to generate variety" that is added to both templates?
Inquiring minds want to know.
Perhaps the same "peripheral feature" was used for the colugo (flying lemur)
quote:
Recent molecular phylogenetic studies have demonstrated that colugos belong to the clade Euarchonta along with the treeshrews (order Scandentia) and the primates, with the colugos more closely related to primates. ...
Or even for Wallace's Frog
quote:
Wallace's flying frog or the Abah River flying frog (Rhacophorus nigropalmatus) is a moss frog found at least from the Malay Peninsula into western Indonesia. It is named for the biologist, Alfred R. Wallace, who collected the first specimen to be formally identified.
Help us understand how these traits are generated without evolution.
Enjoy
Edited by RAZD, : .

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

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 224 by vaporwave, posted 12-23-2016 7:23 AM RAZD has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 206 of 288 (796104)
12-22-2016 11:07 AM
Reply to: Message 166 by caffeine
12-21-2016 12:58 PM


Re: The purpose of phylogenetics
caffeine writes:
The issue here is not missing data - we have a lot of genes to work with.
Do we? For those frogs, what percentage of their genomes have been sequenced? How much phylogenetic coverage is there? If the divergence is ancient and you don't have lots of sister taxa coverage, then you might not have enough data. The deeper the node the more difficult it is to preserve a phylogenetic signal without sufficient coverage (at least from what I have read).
I have never seen anyone argue that an absence of phylogenetic signal implies that the organisms being studied are unrelated
To use an analogy, even though no one has found Jimmy Hoffa's body no one believes he was snagged by aliens and transported to another galaxy. We are pretty sure that humans are involved. In the same vein, we are extremely confident that these frogs evolved from a common ancestor.

This message is a reply to:
 Message 166 by caffeine, posted 12-21-2016 12:58 PM caffeine has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 207 of 288 (796106)
12-22-2016 11:48 AM
Reply to: Message 201 by vaporwave
12-22-2016 6:58 AM


Re: The purpose of science
vaporwave writes:
So when sequence data reinforces a preferred evolutionary relationship you assume it was well-conserved.
We OBSERVE that it is well conserved due to the number of shared bases. There are no assumptions. It is a direct observation.

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 216 by vaporwave, posted 12-22-2016 4:41 PM Taq has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 208 of 288 (796108)
12-22-2016 11:50 AM
Reply to: Message 202 by vaporwave
12-22-2016 7:24 AM


Re: The purpose of science
vaporwave writes:
Yes, but nothing in that statement necessitates evolutionary history.
It is evidence for an evolutionary history. Also, your inability to explain this data using creationism further reinforces this conclusion.
That's just the way you automatically think about traits when you assume evolution is true.
Linnaeus did not assume evolution in the 1700's, and he came to the same conclusion. The nested hierarchy is an observation, and creationism can't explain it. Evolution can.

This message is a reply to:
 Message 202 by vaporwave, posted 12-22-2016 7:24 AM vaporwave has replied

Replies to this message:
 Message 214 by RAZD, posted 12-22-2016 3:15 PM Taq has not replied
 Message 219 by vaporwave, posted 12-22-2016 5:25 PM Taq has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 209 of 288 (796109)
12-22-2016 11:53 AM
Reply to: Message 182 by vaporwave
12-21-2016 5:12 PM


Re: The purpose of science
vaporwave writes:
I don't think you should take the analogy quite so literally. Human programmers change design scope on the fly and obviously screw things up all the time, usually like you say, not anticipating what kind of effect a new feature will have on the rest of the program.
If you set this fallibility aside then my point still stands, a dominant "evolutionary" pattern emerges.
What "dominant evolutionary pattern"? Why would a single programmer build several programs in a way that they would form an evolutionary pattern?

This message is a reply to:
 Message 182 by vaporwave, posted 12-21-2016 5:12 PM vaporwave has not replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 210 of 288 (796111)
12-22-2016 12:11 PM
Reply to: Message 176 by vaporwave
12-21-2016 4:43 PM


Re: The purpose of science
vaporwave writes:
If a coder wants to design, say, a hundred variations of a web browser program, he would probably work off some sort of common coding base for the basic program and then add/remove/tweak various peripheral features in order to generate variety.
Such a collection of programs would easily fall into a nested hierarchy, and would have the effect of a phylogenetic signal similar to evolution.
Why would it fall into a nested hierarchy?
Let's say there are 5 different peripherals, A through E. A programmer could create these 5 programs with 2 peripherals each:
1. A, C
2. B, E
3. A, B
4. A, E
5. B, C
I can almost guarantee that those programs would not produce a nested hierarchy. There is absolutely no reason why a programmer would produce code that falls into a nested hierarchy because that programmer is able to mix and match peripherals in a manner that easily violates a nested hierarchy.
Not necessarily. Evolutionists might simply argue the species are still closely related but the genes were not conserved in their lineages.
Do you not understand what conservation of sequence is? You line up the sequences and see how many positions in the gene have the same base. It is an observation, not a conclusion.
Phylogenies are not objective. For example, subjective weighting of characters as either homologous or independent convergences is a huge issue in systematics.
You can't subjectively weigh a DNA base.
Yes, if you assume common ancestry is true, then that's exactly what phylogenies do.
A phylogeny is evidence that common ancestry is true. It isn't an assumption.
Do you have to assume that a suspect is guilty in order to get a DNA match? No. The DNA match is what evidences guilt. The same process works with phylogenies and common ancestry. The phylogeny is evidence of common ancestry.
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.
I'm not sure what your obsession is with this hypothetical mix-and-match scenario. I may as well be disparaging the common ancestry assumption because evolution could potentially have evolved different lifeforms at different times and it didn't.
Why not a vertebrate-cephalopod template? Why not a mammal-bird template? Why not a fish-jellyfish template?
All of these would violate a nested hierarchy, but there is nothing stopping a designer from making them.
Well then you have problems because you don't have an objective phylogeny.
"The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991). "
29+ Evidences for Macroevolution: Part 1

This message is a reply to:
 Message 176 by vaporwave, posted 12-21-2016 4:43 PM vaporwave has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024