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


Message 235 of 288 (796166)
12-23-2016 4:22 PM
Reply to: Message 234 by vaporwave
12-23-2016 3:57 PM


Re: templates and peripheral features
Just curious, why is this necessarily so?
Well, the clade that includes flying squirrels and sugar gliders would in fact be theria, i.e. all the mammals that aren't monotremes. If, then, the flying squirrels and sugar gliders inherited a gene from a common ancestor, it would also be the common ancestor of all the other theria.
It would simply mean re-positioning the animal on the tree of life.
Which animal, where on the tree of life?

This message is a reply to:
 Message 234 by vaporwave, posted 12-23-2016 3:57 PM vaporwave has replied

Replies to this message:
 Message 236 by vaporwave, posted 12-23-2016 5:35 PM Dr Adequate has replied

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


Message 237 of 288 (796168)
12-23-2016 6:14 PM
Reply to: Message 236 by vaporwave
12-23-2016 5:35 PM


Re: templates and peripheral features
Assuming the Theria clade is correct and doesn't need to be revised.
Revised how? By putting a marsupial next to a squirrel? What do you have in mind? 'Cos that wouldn't work either.
This clade has since been rejected but that it was seriously proposed highlights how resistant common ancestry is to being falsified by contradictory data.
In what sense was that "contradictory data"?
Phylogenetics is not testing common ancestry.
Assertion is not argument.
---
Are you going to answer my question? "Which animal, where on the tree of life?"
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 236 by vaporwave, posted 12-23-2016 5:35 PM vaporwave has replied

Replies to this message:
 Message 238 by Tangle, posted 12-24-2016 3:35 AM Dr Adequate has not replied
 Message 239 by vaporwave, posted 12-24-2016 5:11 AM Dr Adequate has replied

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


Message 243 of 288 (796182)
12-24-2016 9:31 AM
Reply to: Message 239 by vaporwave
12-24-2016 5:11 AM


Re: templates and peripheral features
One phylogeny has odd-toed and even-toed ungulates united
One phylogeny has odd-toed ungulates more closely related to bats
These phylogenies heavily contradict each other and tell totally different stories about the evolution of ungulate traits, yet common ancestry could potentially accommodate either one.
'Cos neither phylogeny contradicts common ancestry.
Do you understand now? This is not that complicated...
Yeah, I should have figured out for myself that you were just blathering on about irrelevancies, but foolishly I tried to interpret your post is though it was relevant to the point under discussion, silly of me.
---
Are you going to answer my question? "Which animal, where on the tree of life?"
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 239 by vaporwave, posted 12-24-2016 5:11 AM vaporwave has not replied

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


(1)
Message 248 of 288 (796254)
12-26-2016 10:43 PM
Reply to: Message 246 by vaporwave
12-26-2016 3:50 PM


Re: templates and peripheral features
I note from your latest inane ramblings that you still don't know what a conserved sequence is and that we can tell whether a gene is well-conserved by looking at it.
While concepts as simple as this escape you, you should not be lecturing us on any aspect of genetics, evolution, or biology.

This message is a reply to:
 Message 246 by vaporwave, posted 12-26-2016 3:50 PM vaporwave has not replied

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


(2)
Message 255 of 288 (796290)
12-28-2016 10:54 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Pointing to the strength of current phylogenies is irrelevant.
Evolution did not predict those phylogenies.
Evolution could have occurred an infinite number of ways, producing a near infinite number of potential phylogenies.
And if biology was not constrained by evolution, there would be a still greater number of non-phylogenies.
Your argument is like saying that the theory of gravity isn't supported by observing the dynamics of the solar system, because we can imagine an infinite number of alternate solar systems with different planets at different distances from the sun which also obeyed the theory of gravity.
Well, this is true, the theory of gravity doesn't predict the number of the planets, or their distance from the sun, or their sizes. But it does predict, for example, that they will obey Kepler's laws --- and we can imagine many more solar systems that don't.
We put a theory to the test by testing the things it does predict; it is irrelevant to note that there are features of the solar system that it doesn't predict, that could be changed and still be compatible with the theory.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has not replied

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


Message 256 of 288 (796291)
12-28-2016 10:55 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
d.p.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has not replied

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


(1)
Message 264 of 288 (796378)
12-29-2016 11:36 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Actually this wouldn't really bother me except evolutionists are constantly showing off cherry-picked examples of the former while concealing the latter ...
How do you know what they're concealing? Are you dressing up in evolutionist robes and infiltrating their secret conclaves? Or are they in fact not concealing it?
But nested hierarchies themselves are not evidence for evolution. They may be a requirement of evolution, but that doesn't mean they explicitly point to evolution.
Once more you are raising an objection which if taken seriously would destroy the whole of science and the scientific method.

This message is a reply to:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM vaporwave has not replied

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


(1)
Message 272 of 288 (796464)
12-30-2016 10:19 AM
Reply to: Message 271 by vaporwave
12-30-2016 8:57 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
For example, an animal group with an even mix of bird and mammal traits would not necessarily violate a nested hierarchy, it would only require modeling the branches of the tree of life accordingly. Mammals and birds would now be placed much closer.
But you can't do that and still have a tree.
Their relationship to dinosaurs would also likely be changed.
But you couldn't change the genetic distance between birds and crocodiles.
---
You over-estimate your capacity for ignoring and fudging the data. It might win you the admiration of creationists, but this sort of sloppy nonsense wouldn't fly in scientific circles.

This message is a reply to:
 Message 271 by vaporwave, posted 12-30-2016 8:57 AM vaporwave has not replied

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


(1)
Message 273 of 288 (796465)
12-30-2016 10:20 AM
Reply to: Message 267 by vaporwave
12-30-2016 7:08 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Another invocation of the hypothetical 'random-creature-generator' - (If not evolution, then we should expect the pattern of life to look like spaghetti thrown against the wall)
If that's the bizarre comparison you need to draw to make common ancestry seem more likely, then have at it.
Once more you are raising an objection which if taken seriously would destroy the whole of science and the scientific method.

This message is a reply to:
 Message 267 by vaporwave, posted 12-30-2016 7:08 AM vaporwave has not replied

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


(1)
Message 275 of 288 (796472)
12-30-2016 11:26 AM
Reply to: Message 274 by vaporwave
12-30-2016 11:22 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Nested hierarchies are an artifact of design. Human designers create nested hierarchies constantly without even thinking about it.
IIRC, you have given only one example of this, which turned out to be bollocks. Would you like to try again?
Cos if you can't think of a single valid example of this happening then you should probably stop pretending that it happens "constantly". Leaving aside for now the moral issue that it's wrong to tell lies, there's also the consideration that you're not fooling anyone.

This message is a reply to:
 Message 274 by vaporwave, posted 12-30-2016 11:22 AM vaporwave has not replied

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


(2)
Message 280 of 288 (796494)
12-30-2016 1:36 PM
Reply to: Message 279 by vaporwave
12-30-2016 1:06 PM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
So what.. for argument's sake let's say you find "cross-pollinated" violations, it's still true that designed traits tend to fall into nested hierarchies, especially models that are based off small variations of a basic design.
Maybe only 90% of the traits can be arranged in this hierarchy. That's still a dominant pattern of nested groupings.
Thus, nested hierarchies are a proven signal of design, whether you want to accept it or not.
So, still no examples?
If we needed any confirmation that you're bullshitting, this would be it.

This message is a reply to:
 Message 279 by vaporwave, posted 12-30-2016 1:06 PM vaporwave has not replied

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


(7)
Message 282 of 288 (796526)
12-30-2016 5:30 PM
Reply to: Message 279 by vaporwave
12-30-2016 1:06 PM


What Design Actually Looks Like
While we're waiting for vaporwave to think of a single example of the thing he says happens "constantly", let's look at a counterexample.
A quick look round on google shows me that there are cars having any of the following traits independently:
* 2 door / 4 door
* Gas / diesel
* Front-wheel drive / rear-wheel drive
* Manual / automatic
That gives us sixteen possibilities, every single one of which has been realized. And I would bet a reasonable sum that the same range of options exists in the UK and suchlike countries, meaning that having the steering wheel on the left or on the right is another independent trait.
(What's more, it often happens that many of these options are available in the same range of cars. If I liked, I could have two Mercedes, one with manual transmission and a diesel engine, the other with automatic transmission and a regular engine, and otherwise absolutely identical down to the last button on the dashboard and stitch on the seat upholstery. As though you saw what looked like two identical twins, but when you X-rayed them only one was human on the inside and the other had the lungs and heart of a reptile.)
Designed things do not form an nested hierarchy.
And the same, of course, can be said of any kind of consumer good that comes in varieties. Do you want your cigarettes full-strength or light, mentholated or plain, king-size or 100s? Pick any of those options independently, and someone makes what you want. Would you like your wine sweet or dry, red, white, or ros , sparkling or still? Those options are independent, so that's twelve kinds of wine. You're thinking of buying software to store your commercial information? Were you thinking of a spreadsheet or a database? For PC or Mac? Using the Roman or Cyrillic alphabet? You got it. Would you like your sandwich on white bread, wheat bread, rye? With or without mustard? With or without mayo? American cheese or Swiss? Pickle or no pickle? Let's build a house. How many stories would you like? Brick, wood, concrete, stone? How about the roof? Gable, hip, gambrel, mansard? How do you feel about dormers? Would you like pilasters with that? Should your windows be bay, bow, casement, picture, awning, double-hung? If you have no sense of aesthetic taste, why not one of each?
That's design for you. And it precludes the sorting of designed objects into nested hierarchies, because traits can freely vary independently of one another.
And now by contrast let's pick an animal. You want it to lactate? Right then. In that case --- no arguing, I'm telling you how it's going to be --- it will be endothermic, endoskeletal and featherless, it will have three bones in its inner ear and one in its lower jaw; it will have no sclerotic rings and no gastralia; it will have a four-chambered heart; its red blood cells will lack nuclei; it will have no renal portal system; its teeth will have prismatic enamel ...
Etc, etc. You don't get to mix and match. That's evolution for you. 'Cos it produces nested hierarchies.

This message is a reply to:
 Message 279 by vaporwave, posted 12-30-2016 1:06 PM vaporwave has not replied

Replies to this message:
 Message 283 by herebedragons, posted 12-31-2016 9:34 AM Dr Adequate has not replied

  
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