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Author Topic:   Discussion of Phylogenetic Methods
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 166 of 288 (796045)
12-21-2016 12:58 PM
Reply to: Message 115 by Taq
12-20-2016 10:38 AM


Re: The purpose of phylogenetics
So many posts, no wonder creationists feel overwhelmed!
From my understanding, that simply isn't true. Phylogenetics is a test for common ancestry and evolution through vertical inheritance. The various methods for detecting phylogenies return values that measure the phylogenetic signal. 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.
This is precisely the kind of reasoning I was questioning; for the simple reason that it leads us to odd conclusions. Consider these chaps:
I think we can all safely agree that these are all frogs. And yet I chose these because they represent one of the branches of the tree of life where we lack any sort of consensus phylogeny. These are all natatanuran frogs (not a great name, but the other names proposed for this clade are worse); and the interrelationships between natatanuran families are something of a mystery. Different studies produce wildly different phylogenies; none of which habve significant statistical support.
The issue here is not issing data - we have a lot of genes to work with. The issue is that these do not carry much phylogenetic signal in this case. As with other similar cases, it is usually argued to be the result of a rapid radiation at the origin of the extant families.
I have never seen anyone argue that an absence of phylogenetic signal implies that the organisms being studied are unrelated; so this is not clearly never used as a test of common ancestry. We already know that ranoid frogs are all related - to suggest otherwise would be laughable - and so researchers seek other loci or other techniques that might be more informative instead. Common ancestry was a well-established fact before anyone started doing cladistics.

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 Message 115 by Taq, posted 12-20-2016 10:38 AM Taq has replied

Replies to this message:
 Message 167 by Dr Adequate, posted 12-21-2016 1:23 PM caffeine has replied
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 167 of 288 (796046)
12-21-2016 1:23 PM
Reply to: Message 166 by caffeine
12-21-2016 12:58 PM


Re: The purpose of phylogenetics
I think you're over-interpreting what he meant by "lack of data".

This message is a reply to:
 Message 166 by caffeine, posted 12-21-2016 12:58 PM caffeine has replied

Replies to this message:
 Message 168 by caffeine, posted 12-21-2016 1:38 PM Dr Adequate has replied

  
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 168 of 288 (796047)
12-21-2016 1:38 PM
Reply to: Message 167 by Dr Adequate
12-21-2016 1:23 PM


Re: The purpose of phylogenetics
I think you're over-interpreting what he meant by "lack of data".
I have no idea what point you're trying to make.

This message is a reply to:
 Message 167 by Dr Adequate, posted 12-21-2016 1:23 PM Dr Adequate has replied

Replies to this message:
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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 169 of 288 (796048)
12-21-2016 2:01 PM
Reply to: Message 166 by caffeine
12-21-2016 12:58 PM


Re: The purpose of phylogenetics
I think that your point is a little pedantic.
To set it in context before somebody tries to make it much more than it is:
First, confused phylogenetic information is hardly the worst case for evolution, even if it were general (and if it was general I think we would have a rather different version of evolutionary theory).
Second, given that this confusion only gives one group of species it has relatively little weight compared with the overall pattern anyway.
Now if the genetic data showed a pattern inconsistent with evolution altogether then things would be very different.
As it is, I think we can say that there are things that can confuse genetic phylogenies, such as horizontal transfer, hybridisation and rapid radiations. But only the first could even conceivably pose a threat to evolution - and then only if the rate required to explain the genetic data was well above reasonable expectations (and to the best of my knowledge it is not)

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 Message 166 by caffeine, posted 12-21-2016 12:58 PM caffeine has replied

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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

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 171 of 288 (796051)
12-21-2016 2:45 PM
Reply to: Message 147 by vaporwave
12-21-2016 7:25 AM


cytB
This is why evolutionists, when trying to make their case, always focus on cytochrome C instead.
Here is a 'paper' I wrote, peer reviewed by a doctor in bioinformatics, specifically about cytochrome b, 10 years ago (not published of course, its too trivial):


Define the problem

It is said that genetic similarities can be used to demonstrate the relatedness of various organisms. For example, humans and chimpanzees are very similar genetically as a mice and rats. The contrary position to this is that since genetics determines an organism’s appearance, organisms that look similar are going to have similar genomes.
To overcome this initial hurdle proved to be quite straightforward, we can split mammals into three groupings: Placental, Marsupial and Monotreme. As the names imply, placental mammals are like ourselves and are the most common mammal type, we give birth to live young who are surrounded by a tissue known as the placenta. The most famous marsupial is the kangaroo, which has a pouch; monotremes are now rare, they are mammals that lay eggs like the platypus.

What to measure

The divide of Placental and Marsupial mammals appears in the fossil record about 125 million years ago. If the genetic method of relatedness is an accurate method it can be tested by finding a placental mammal which looks largely similar to a marsupial mammal and comparing their genes. Then we would compare at least two placental mammals that appear to very dissimilar, and do likewise with marsupial mammals.
Comparing genes is a little ambitious for a home project, so to simplify the issue I will compare protein codes, specifically the cytochrome proteins. The cytochrome class of proteins are essential for organisms since they are required in cell respiration. This means that the mammals we plan to look at will all use the cytochrome proteins.
To create a protein a string of amino acids is required, which amino acids to use and in which order are defined by the DNA sequences. Cytochrome proteins can be made up in an enormous variety of ways and different DNA sequences can yield the same amino acid sequences. There are trillions of ways to make cytochrome from DNA instructions. It would appear that the strongest reason why two organisms would make cytochrome in a comparable manner would be relatedness.
As an example, the genetic sequence GAG produces the same amino acid as the sequence GAA. Each protein can be made of hundreds of these amino acids.
I will be comparing the amino acid sequences of cytochrome b. I will also compare the actual DNA sequences, but will not reproduce them here, since they are each over a thousand characters long.

The Data

Each letter represents one amino acid; the entire string represents the full protein. The strings do differ slightly in their length: this represents incomplete sampling of the proteins in the scientific literature.
RED KANGAROO:
MTNLRKTHPLIKIVNHSFIDLPAPSNISAWWNFGSLLGACLIIQILTGLFLAMHYT
ADTLTAFSSVAHICRDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKE
TWNIGVILLLTVMATAFVGYVLPWGQMSFWGATVITNLLSAIPYIGTTLVEWIW
GGFSVDKATLTRFFAFHFILPFIITALVLVHLLFLHETGSNNPSGINPDSDKIPFHPY
YTIKDALGFMLMLLILLTLALFSPDMLGDPDNFSPAKPTEHSSHIKPEWYFLFAYAI
LRSIPNKLGGVLALLASILILLIIPLLHTSKQRSLMFRPISQTLFWILTANLITLTWIG
GQPVEQPYIIIGQVASISYFLLIIVLMPLAGLFENYMLEPKW
HUMAN:
MTPMRKINPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYS
PDASTAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYSET
WNIGIILLLATMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWIWG
GYSVDSPTLTRFFTFHFILPFIIAALAALHLLFLHETGSNNPLGITSHSDKITFHPYY
TIKDALGLLLFLLSLMTLTLFSPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTIL
RSVPNKLGGVLALLLSILILAMIPILHMSKQQSMMFRPLSQSLYWLLAADLLILTW
IGGQPVSYPFTIIGQVASVLYFTTILILMPTISLIENKMLK
CHIMPANZEE:
MTPXRKINPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYS
PDASTAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYLET
WNIGIILLLTTMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWVWG
GYSVDSPTLTRFFTFHFILPFIITALTTLHLLFLHETGSNNPLGITSHSDKITFHPYYT
IKDILGLFLFLLILMTLTLFSPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRS
IPNKLGGVLALLLSILILAAIPVLHTSKQQSMMFRPLSQLLYWLLATDLLILTW
MISSISSIPPI ALIGATOR:
MTHQLRKSHPIIKLINRSLIDLPTPSNISAWWNFGSLLGLTLLIQILTGFFLMMHFS
SSDTLAFSSVSYTSREVWFGWLIRNLHTNGASLFFMFIFLHIGRGLYYTSYLHEST
WNIGVIMLLLLMATAFMGYVLPWGQMSFWGATVITNLLSATPYVGSTVVPWIW
GGPSVDNATLTRFTALHFLLPFALLASLITHLIFLHERGSFNPLGISPNADKIPFHPY
FTMKDALGAALAASSLLILALYLPALLGDPENFTPANSMITPTHIKPEWYFLFAYAI
LRSIPNKLGGVLAMFSSILVLFLMPALHTAKQQPMSMRPMSQLLFWALTLDFLLLT
WIGGQPVNPPYILIGQTASLFYFIIILILMPMAGLLENKMVEPTYVTPK
PLACENTAL MOUSE:
MTNIRKTHPLFKIINHSFIDLPAPSNISSWWNFGSLLGICLMIQIITGLFLAMHYTS
DTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHVGRGMYYGSYTFME
TWNIGVILLFAVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTTLVEWIW
GGFSVDKATLTRFFAFHFILPFIITALVIVHLLFLHETGSNNPTGLNSDSDKIPFHPY
YTIKDILGVILMIMFLMTLVLFFPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAI
LRSIPNKLGGVLALILSIMVLMLLPFLHTSKLRSLMFRPITQTLYWILVANLLVLTW
IGGQPVEHPFIIIGQLASISYFSIILIFMPIAGIIEDSLLKFD
MARSUPIAL MOUSE:
MINLRKTHPLMKIINHSFIDLPAPSNISAWWNFGSLLGICLVIQILTGLFLAMHYT
SDTLTAFSSVAHICRDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKE
TWNIGVILLLTVMATAFVGYVLPWGQMSFWGATVITNLLSAIPYIGTTLAEWIW
GGFAVDKATLTRFFAFHFILPFIIMALVIVHLLFLHETGSNNPSGINPDSDKIPFHPH
YTIKDALGWMLLLLVLLFLALFSPDSLGDPDNFSPANPLNTPPHIKPEWYFLFAYA
ILRSIPNKLGGVLALLASILILLIIPLLHTANQRSMMFRPVSQTLFWILTANLMTLT
WIGGQPVEQPFIIIGQLASILYFSLILILMPLAGMFENYMLEPKR
Example comparison:
The first few characters of the Kangaroo and the Human:
MTNLRKTHPLI K
MTPMRKIN PLMK
The bolded letters represent where the amino acid sequence differs.

Prediction

If genetics can determine relatedness we should see that the chimpanzee and the human are very closely matched. The important thing to look for will be the marsupial mouse and the placental mouse. The prediction is that the placental mouse should more genetically similar to the human and the chimpanzee than it is to the marsupial mouse. Conversely, the marsupial mouse should be closer to the kangaroo than the placental mouse. Finally, the alligator should be distant from all of them.

Method

To compare the long strings of amino acids, rather than do it by hand, a program called ClustalW was used, this can be found online at http://align.genome.jp/ {now retired} Also used was a piece of software called, JalView from the University of Dundee which can also be found online at Jalview Home Page - Jalview

Results

The following is a table that shows the full sequences and how they match up.
The percentage similarities can be found in this table:
Human

Chimpanzee

95.25

Kangaroo

Marsupial Mouse

90.81

Marsupial Mouse

Placental Mouse

81.84

Kangaroo

Placental Mouse

81.05

Chimpanzee

Placental Mouse

78.34

Chimpanzee

Kangaroo

78.34

Chimpanzee

Marsupial Mouse

77.74

Human

Marsupial Mouse

76.46

Human

Placental Mouse

76.19

Human

Kangaroo

75.93

Marsupial Mouse

Alligator

67.45

Kangaroo

Alligator

67.02

Chimpanzee

Alligator

65.38

Human

Alligator

64.91

Placental Mouse

Alligator

64.3

We can compile this rather clunky table into something a little more readable, a tree:

Conclusions

Whilst some unexpected results came of it, the placental mouse seemed to be closer related to the marsupial mouse than it is humans, they are not entirely surprising due to the highly variable nature of cytochrome b, the incomplete sampling, the small data set and so on. A significant correlation was found in the fact that the marsupial mouse is more genetically similar to the kangaroo than it is to the placental mouse. This means that external morphology (what the organism physically looks like) does not necessarily mean that the organisms are going to share commonality in the genome.
In the course of investigating this phenomenon, which required learning an awful lot about genetics, I came across science papers that use this technique, and more advanced forms of it. My short bibliography includes an interesting paper that provides further reading for the interested reader.

Bibliography

http://www.nmsr.org/round1a.htm
David E. Thomas
- An interesting look at how and why this comparative technique is so powerful.
A molecular timescale for vertebrate evolution - By calibrating a genetic clock, Kumar & Hedges are able to show with good accuracy a time scale for evolutionary divergence
Sudhir Kumar & S. Blair Hedges
Bioinformatics Tools for Multiple Sequence Alignment < EMBL-EBI
Julie D. Thompson, Desmond G.Higgins, Toby J. Gibson
- Discusses the ClustalW program
National Centre for Biological Information
- This is where the protein sequences were found

Here's how we differ. I went and did hours and hours of gruntwork to see the truth for myself. You just want the truth to be a certain way and use words words words.
Edited by Modulous, : No reason given.
Edited by Modulous, : No reason given.

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caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 172 of 288 (796054)
12-21-2016 4:13 PM
Reply to: Message 169 by PaulK
12-21-2016 2:01 PM


Re: The purpose of phylogenetics
I think that your point is a little pedantic.
To set it in context before somebody tries to make it much more than it is:
First, confused phylogenetic information is hardly the worst case for evolution, even if it were general (and if it was general I think we would have a rather different version of evolutionary theory).
My point is not that the problems in phylogenetics are a problem for evolutionary theory. They can often be iluminating, since the most problematic and controversial parts of phylogeny are not arbitrarily distributed. If you look at vertebrate phylogeny, the bits that are most difficult to resolve make sense within our understanding of history (usually). They are often the results of explosive radiations - like that of Neoaves and percomorph fishes after the end-Cretaceous extinction.
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.
I think that your point is a little pedantic.
If you don't approve of pedantry, what are you doing on an internet forum?
Edited by caffeine, : Correct (my own) confusion over nomenclature

This message is a reply to:
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caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 173 of 288 (796055)
12-21-2016 4:19 PM
Reply to: Message 170 by Dr Adequate
12-21-2016 2:03 PM


Re: The purpose of phylogenetics
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.
His whole point (as I understood it) was that an absence of signal would imply a lack of common ancestry, but we know that there are parts of the phylogeny where signal is swamped by noise. In this case, we cannot claim that presence or absence of signal can be used as a test of common ancestry.

This message is a reply to:
 Message 170 by Dr Adequate, posted 12-21-2016 2:03 PM Dr Adequate has replied

Replies to this message:
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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 174 of 288 (796056)
12-21-2016 4:37 PM
Reply to: Message 172 by caffeine
12-21-2016 4:13 PM


Re: The purpose of phylogenetics
As I said I was setting it in context - and suggesting that someone other than you might (quite possibly wilfully) misrepresent your point as a challenge to evolution.
But it is not a challenge to evolution because it does support common ancestry, and it need not do so. We could find, for instance, that cytochrome C variations did not follow the pattern expected for evolution. If creationism were true, all the original kinds might have been created with the same cytochrome C and all differences are due to subsequent drift (which would not be very great in a YEC scenario)
I think it is something of a parody of phylogeny to say that common ancestry is simply assumed. It is certainly possble in principle for the data to be inconsistent with any likely ancestry - indeed the only reason common ancestry is assumed now is because it has already been established beyond reasonable doubt - in large part by the evidence used to establish phylogeny.

This message is a reply to:
 Message 172 by caffeine, posted 12-21-2016 4:13 PM caffeine has replied

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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 ...)

This message is a reply to:
 Message 173 by caffeine, posted 12-21-2016 4:19 PM caffeine has replied

Replies to this message:
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vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 176 of 288 (796058)
12-21-2016 4:43 PM
Reply to: Message 160 by Taq
12-21-2016 10:41 AM


Re: The purpose of science
How so? Why would an individual coder produce code so that it falls into a nested hierarchy?
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.
Such a collection of programs would easily fall into a nested hierarchy, and would have the effect of a phylogenetic signal similar to evolution.
No, it doesn't. It means a loss of phylogenetic signal for distantly related species.
Not necessarily. Evolutionists might simply argue the species are still closely related but the genes were not conserved in their lineages.
There is just a bit of ad-hoc maneuvering here.
If the genetic signal does not reflect a preferred narrative of how closely or distantly related particular species are, then evolutionists will simply argue that the genes in question were either more conserved or less conserved, thus accommodating the discordant data.
The pattern of shared derived characteristics (i.e. an objective phylogeny)
Phylogenies are not objective. For example, subjective weighting of characters as either homologous or independent convergences is a huge issue in systematics.
... do show us that they share a common ancestor in the same way that a fingerprint shows us that someone touched a surface.
Yes, if you assume common ancestry is true, then that's exactly what phylogenies do. Nobody ever had to assume that people leave physical markings where they've traveled. To be honest that was a ridiculous analogy.
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.
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.
We are saying that only common ancestry is able to explain why shared derived characteristics found in biological species form an objective phylogeny. Creationism can't explain it.
Well then you have problems because you don't have an objective phylogeny.

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Replies to this message:
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caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 177 of 288 (796059)
12-21-2016 4:53 PM
Reply to: Message 174 by PaulK
12-21-2016 4:37 PM


Re: The purpose of phylogenetics
I think it is something of a parody of phylogeny to say that common ancestry is simply assumed. It is certainly possble in principle for the data to be inconsistent with any likely ancestry - indeed the only reason common ancestry is assumed now is because it has already been established beyond reasonable doubt - in large part by the evidence used to establish phylogeny.
I don't see it as a parody. It seems to me you have to assume common ancestry in order to research phylogeny. All the techniques we have for building a phylogeny assume there is actually one there to discover. I don't understand how a falsification of common ancestry is supposed to differ from an unresolvable polytomy like that amongst Natatanuran families.
I understand what you mean that people may misrepresent what I say as a challenge to evolution; but it's precisely the fear of misrepresentation that makes me wary of the idea of presenting phylogenetics as evidence for evolution. This is probably because I spend a lot more time reading about the difficult bits than the easy bits. If nothing else I think it's a tactical error in arguing with am honest creationist, since the difficult bits are of course those focused on by researchers. If a curious creationist heads over to the literature on phyogenetics; he's going to find lots of arguments about the complicated radiations we cannot resolve and the problematic taxa that jump around the tree from one analysis to another.

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caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 178 of 288 (796060)
12-21-2016 5:04 PM
Reply to: Message 175 by Dr Adequate
12-21-2016 4:38 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 ...)
Well, if you take individual bits of the genome you get all sorts of odd results - results which I have seen creationists get very excited about. Over on EvolutionFairyTale there was a thread about one regulatory gene which, taken in isolation, produced trees in which teleosts were sister to all other vertebrates.
A lack of common ancestry could produce that, or indeed anything else so far as we know.
If 'anything else' could produce that, then it's not evidence of anything.

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 Message 175 by Dr Adequate, posted 12-21-2016 4:38 PM Dr Adequate has replied

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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?

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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 180 of 288 (796062)
12-21-2016 5:08 PM
Reply to: Message 177 by caffeine
12-21-2016 4:53 PM


Re: The purpose of phylogenetics
quote:
I don't see it as a parody. It seems to me you have to assume common ancestry in order to research phylogeny. All the techniques we have for building a phylogeny assume there is actually one there to discover. I don't understand how a falsification of common ancestry is supposed to differ from an unresolvable polytomy like that amongst Natatanuran families
As I said, a confused phylogeny is far from the worst case. And a phylogeny that is confused in parts is even less of a problem. We have evidence that the frogs are related, it just fails to make the distinctions we need to work out the details. There is no reason in principle why the genetic evidence could not tell us that some of the frogs were not closely related and did not belong in the Natatanuran family at all.
Seriously if you admit that the evidence says that they are related - then you are saying that there is strong evidence of common ancestry.
quote:
I understand what you mean that people may misrepresent what I say as a challenge to evolution; but it's precisely the fear of misrepresentation that makes me wary of the idea of presenting phylogenetics as evidence for evolution. This is probably because I spend a lot more time reading about the difficult bits than the easy bits. If nothing else I think it's a tactical error in arguing with am honest creationist, since the difficult bits are of course those focused on by researchers
I wouldn't want to hide the problems, but claiming that the findings of phylogenetic research is not evidence for evolution is going well beyond that. The evidence for common ancestry is the same as the evidence for any phylogeny we can work out. Additional data has caused revisions to phylogenies, but none so drastic or far reaching as to call common ancestry in doubt. This IS evidence for evolution.

This message is a reply to:
 Message 177 by caffeine, posted 12-21-2016 4:53 PM caffeine has not replied

  
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