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Author Topic:   Discussion of Phylogenetic Methods
Taq
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Posts: 6461
Joined: 03-06-2009
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(1)
Message 211 of 288 (796113)
12-22-2016 12:35 PM


What Is Sequence Conservation?
There seems to be some confusion over what sequence conservation is. I will be using protein sequences here, since they are a 3rd the length of DNA sequences.

Here is a comparison of human and chimp cytochrome B:


355/379(94%)
Query 1 MTPMRKTNPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDAS 60
MTP RK NPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDAS
Sbjct 1 MTPTRKINPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDAS 60

Query 61 TAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYSETWNIGIILL 120
TAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLY ETWNIGIILL
Sbjct 61 TAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYLETWNIGIILL 120

Query 121 LATMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFFT 180
L TMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQW+WGGYSVDSPTLTRFFT
Sbjct 121 LTTMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWVWGGYSVDSPTLTRFFT 180

Query 181 FHFILPfiiaalatlhllflhETGSNNPLGITSHSDKITFHPYYTIKDAlglllfllslm 240
FHFILPFII AL TLHLLFLHETGSNNPLGITSHSDKITFHPYYTIKD LGL LFLL LM
Sbjct 181 FHFILPFIITALTTLHLLFLHETGSNNPLGITSHSDKITFHPYYTIKDILGLFLFLLILM 240

Query 241 tltlfsPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRSVPNKLGGVlalllsili 300
TLTLFSP LLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRS+PNKLGGVLALLLSILI
Sbjct 241 TLTLFSPGLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRSIPNKLGGVLALLLSILI 300

Query 301 lamipilHMSKQQSMMFRPLSQSlywllaadlliltwiGGQPVSYPFTIIGQVASVLYFT 360
L IP+LH SKQQSMMFRPLSQ LYWLLA DLLILTWIGGQPVSYPF IGQ+ASVLYFT
Sbjct 301 LTAIPVLHTSKQQSMMFRPLSQLLYWLLATDLLILTWIGGQPVSYPFITIGQMASVLYFT 360

Query 361 TILILMPTISLIENKMLKW 379
TILILMP SLIENKML+W
Sbjct 361 TILILMPIASLIENKMLEW 379

Here is a comparison of human and chimpanzee cytochrome c (somatic)


105/105(100%)
Query 1 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW 60
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
Sbjct 1 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW 60

Query 61 GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
Sbjct 61 GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105

Human and chimp cytochrome B is 95% conserved. Human and chimp cytochrome C is 100% conserved. We get these numbers by directly comparing the sequences. We say that cytochrome C is more conserved because 100% is greater than 95%. We do not change these values based on phylogenetic data.

Any questions?


  
Taq
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Posts: 6461
Joined: 03-06-2009
Member Rating: 4.2


Message 212 of 288 (796115)
12-22-2016 1:01 PM
Reply to: Message 172 by caffeine
12-21-2016 4:13 PM


Re: The purpose of phylogenetics
caffeine writes:

I'm taking issue with the point I've seen Taq and others make more than once on these forums, that phylogenetics by itself is a test of common ancestry. Since we don't reject common ancestry when we cannot produce a well supported phylogeny, it seems dishonest to say we're testing evolution this way.

But we do produce well supported phylogenies all over the place. I have already cited the cytochrome c example.


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Modulous
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Posts: 7407
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 3.6


(1)
Message 213 of 288 (796116)
12-22-2016 2:08 PM
Reply to: Message 176 by vaporwave
12-21-2016 4:43 PM


assumptions are vital to knowledge
Such a collection of programs would easily fall into a nested hierarchy, and would have the effect of a phylogenetic signal similar to evolution.

Seems like an own goal to me. You are saying that in a hypothetical scenario where we know that the current code was copied and modified over successive generations that that we could create a nested hierarchy of sorts. This being the case, we know that this would be an example of common descent.

If you want to say that nested hierarchies can be generated through descent with modification I'm fine with that, but it kind of undermines your thesis somewhat.

Yes, if you assume common ancestry is true, then that's exactly what phylogenies do

Yes, that's what science does. To quote Feynman who was discussing science in general, but from a physics background:

quote:
First, we guess it (audience laughter), no, don’t laugh, that’s really true. Then we compute the consequences of the guess, to see what, if this is right, if this law we guess is right, to see what it would imply and then we compare the computation results to nature, or we say compare to experiment or experience, compare it directly with observations to see if it works.

Assumptions / guesses are vital in science. The entire point is to say 'if the theory is true, then we should see x'. If you don't see x but you see something quite close to x you say 'oh that's interesting' and you try to guess why it's close but not right, modify your theory and try it again on a novel data set.

Evolutionary theory is the best guess we have, and it has proven very successful. From paternity to species ancestry, it works. What's your guess?

Nobody ever had to assume that people leave physical markings where they've traveled

Actually they do. We deny people liberty, and sometimes life, on the basis of the assumption that fingerprints are left by finger-havers and the assumption that all fingerprints are unique to each finger in existence.


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RAZD
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Posts: 18472
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


Message 214 of 288 (796117)
12-22-2016 3:15 PM
Reply to: Message 208 by Taq
12-22-2016 11:50 AM


fixed it
... Also, your inability to explain this data using creationism any other hypothesis/theory further reinforces this conclusion. ...

There, fixed it.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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vaporwave
Member (Idle past 56 days)
Posts: 66
Joined: 12-17-2016


Message 215 of 288 (796118)
12-22-2016 4:12 PM
Reply to: Message 204 by Dr Adequate
12-22-2016 8:34 AM


Re: The purpose of science
"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.

Poor analogy. You don't have to assume or infer that the thing actually being observed through a telescope or microscope exists.

Evolutionists observe character traits and sequence data and have to make evolutionary assumptions or inferences about them, at times resulting in a great deal of controversy between themselves.

Edited by vaporwave, : No reason given.


This message is a reply to:
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vaporwave
Member (Idle past 56 days)
Posts: 66
Joined: 12-17-2016


Message 216 of 288 (796119)
12-22-2016 4:41 PM
Reply to: Message 207 by Taq
12-22-2016 11:48 AM


Re: The purpose of science
We OBSERVE that it is well conserved due to the number of shared bases. There are no assumptions. It is a direct observation.

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."
https://en.wikipedia.org/wiki/Conserved_sequence

You don't observe geologic time in a genetic sequence. You observe the sequence and make inferences.

And so back to my last point:

Conflicting sequences can be accommodated into a preferred evolutionary narrative by simply assuming they were more or less conserved over deep time.

This is followed up by the usual circular reasoning whereby the conservation inference is considered self-evident because you *know* evolution is true.


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Dr Adequate
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Posts: 15929
Joined: 07-20-2006
Member Rating: 3.8


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.


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Dr Adequate
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Posts: 15929
Joined: 07-20-2006
Member Rating: 3.8


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.


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Replies to this message:
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vaporwave
Member (Idle past 56 days)
Posts: 66
Joined: 12-17-2016


Message 219 of 288 (796122)
12-22-2016 5:25 PM
Reply to: Message 208 by Taq
12-22-2016 11:50 AM


Re: The purpose of science
Linnaeus did not assume evolution in the 1700's, and he came to the same conclusion. The nested hierarchy is an observation

And a nested hierarchy is not evidence of evolutionary relationships unless you assume common ancestry.

You can't subjectively weigh a DNA base.

You can't subjectively measure a bone either. You make subjective inferences about why it looks the way it does.

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.

Oh that is just sad. You can be a bit more sophisticated than this I think.

Why not a vertebrate-cephalopod template? Why not a mammal-bird template? Why not a fish-jellyfish template?

Why didn't different types of animals evolve?

All of these would violate a nested hierarchy

Not necessarily. If there was a paleontological record of totally different types of animals, then it may have simply produced a different common ancestry narrative by those evolutionists studying them.

"Natural selection did it" is a surprisingly malleable explanatory device to wind a story around.

The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified.

There may be an objective data-set, but finding an animal's position within it is far from objective. (e.g. Evolutionists still can't decide whether or not birds nest in Theropoda. )


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vaporwave
Member (Idle past 56 days)
Posts: 66
Joined: 12-17-2016


Message 220 of 288 (796123)
12-22-2016 5:41 PM
Reply to: Message 218 by Dr Adequate
12-22-2016 5:06 PM


Re: The purpose of science
That is certainly what conservation indicates, just as the article says, but it is not how it is defined or recognized

Oh, I see... so the term isn't recognized as what it typically indicates in the literature? Is that really your argument?

You should probably think your comments through a little more instead of just kicking up dust and making noise every time I post.


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jar
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From: Texas!!
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Member Rating: 3.0


Message 221 of 288 (796124)
12-22-2016 6:33 PM
Reply to: Message 220 by vaporwave
12-22-2016 5:41 PM


Does vaporwave even have a position to offer?
vapor writes:

You should probably think your comments through a little more instead of just kicking up dust and making noise every time I post.

Maybe you might think about actually presenting something, anything, that might support your position if in fact you actually have a position and are not just kicking up dust and making noise.

As it stands we have the fossils. We win.

We have the natural causes. We win.

We have the designers. We win.

And we have the Theory. We win.

It really is that simple.

Edited by jar, : fix sub-title


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

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Coyote
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(2)
Message 222 of 288 (796126)
12-22-2016 9:19 PM
Reply to: Message 215 by vaporwave
12-22-2016 4:12 PM


Re: The purpose of science
Evolutionists observe character traits and sequence data and have to make evolutionary assumptions or inferences about them, at times resulting in a great deal of controversy between themselves.

The theory of evolution is a theory, rather than an assumption, hypothesis, or guess, because it fits the definition of a theory: it is the single best explanation for a given set of facts, it is not contradicted by any relevant facts, and it has withstood the test of time and made successful predictions.

When scientists (not evolutionists*) observe things that fit with the theory of evolution, they would be remarkably poor scientists if they jumped, out of the blue, to some other assumption, hypothesis or guess--as you presumably would have them do. When the theory of evolution explains the facts, why try to bring in creationism? (Answer--belief gets in the way of learning.)

* Whenever a poster on one of these websites starts discussing "evolutionists" we know he's a full-blown creationist. We can generally assume 1) a lack of scientific training and rigor, and 2) beliefs are favored over evidence.


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.


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Dr Adequate
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Posts: 15929
Joined: 07-20-2006
Member Rating: 3.8


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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vaporwave
Member (Idle past 56 days)
Posts: 66
Joined: 12-17-2016


Message 224 of 288 (796129)
12-23-2016 7:23 AM
Reply to: Message 205 by RAZD
12-22-2016 9:35 AM


Re: templates and peripheral features
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same?

Depends. I suppose it could but I wouldn't necessarily expect it because those animals have very different underlying anatomy which may promote unique design decisions.

Evolution would say, if the genetic organization of the gliding membrane is different between both groups, then it independently evolved in eutheria and marsupialia.

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.

Help us understand how these traits are generated without evolution.

You mean a more complex explanation than "natural selection did it" ?


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RAZD
Member
Posts: 18472
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


Message 225 of 288 (796131)
12-23-2016 8:36 AM
Reply to: Message 26 by vaporwave
12-18-2016 12:12 PM


metaphysics and morphology and macroevolution
Evolutionists fall back on a strange sort of metaphysics... they work off the assumption that if common descent were false, the pattern of morphology and DNA would necessarily be in discord. This assumption cannot be demonstrated or tested in any way of course.

The typical rebuttal here has the evolutionist quickly retreating to teleological territory and he begins rambling about how a Creator could do X or Y, etc....

Okay, then instead of our talking about creationism or what creators can or cannot seem to do, how about we just talk about alternate explanations -- ie - that in fact no alternate hypothesis or theory provides the detail explanation for the observed objective empirical evidence that evolution theory provides. No alternative hypothesis\theory has made testable predictions that don't falsify them, or they have failed entirely to make testable predictions.

Nested hierarchies descendant from a common ancestor (population) are observed:

(2) Speciation is the process whereby parent populations are divided into two or more reproductively isolated, independently evolving, daughter populations.

The reduction or loss of interbreeding (gene flow, sharing of mutations) between the sub-populations results in different evolutionary responses within the separated sub-populations, each then responds independently to their different ecological challenges and opportunities, and this leads to divergence of hereditary traits between the subpopulations and the frequency of their distributions within the sub-populations.

Over generations, these different responses accumulate into differences between the hereditary traits available within each of the daughter populations, and when these differences have reached a critical level, such that interbreeding no longer occurs, then the formation of new species is deemed to have occurred. After this "event" each daughter population evolves independently of the other/s.

An additional observable result of speciation is a branching of the genealogical history for the species involved, where two or more offspring species are each independently descended from the same common pool of the ancestor parent species. At this point a clade has been formed, consisting of the common ancestor species and all of their descendants.

With multiple speciation events, a pattern is formed that looks like a branching bush or tree: the tree of descent from common ancestor populations. Each branching point is a node for a clade of the parent species at the node point and all their descendants, and with multiple speciation events we see a pattern form of clades branching from parent ancestor species and nesting within larger clades branching from older parent ancestor species.

               |                 
|
^ c
/ \
/ \
/ ^ b
a ^ / \
/ \ / \

Where "^" represents a node or common ancestor species of a clade that includes the common ancestor species and all their descendents: "a" and below form a clade that is part of the "c" clade, "b" and below form a clade that is also part of the "c" clade, but "a" is not part of the "b" clade.

Speciation, the subsequent divergence of daughter populations, and the formation of nested clades, is an observed, known objective fact, and not an untested hypothesis.

The process of speciation with the subsequent formation of a branching genealogy of descent from common ancestor populations (also called "macro-evolution" in biology) is an observed, known objective fact, and not an untested hypothesis.

Enjoy


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) • • •

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