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Author Topic:   Discussion of Phylogenetic Methods
Modulous
Member (Idle past 360 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 25 of 288 (795847)
12-18-2016 10:33 AM
Reply to: Message 24 by vaporwave
12-18-2016 9:47 AM


Re: Introduction
I guess the idea is that if you present enough numbers, data matrices, complex diagrams, etc. then it will intimidate the opposition into silence. As I mentioned before, this all works off the implied evolutionist bluff that such diagrams would be impossible to generate if common ancestry were false.

Of course, this doesn't explain how we can create those trees from morphology and from DNA evidence and come to very similar answers. This strongly suggests common descent is indeed correct.


This message is a reply to:
 Message 24 by vaporwave, posted 12-18-2016 9:47 AM vaporwave has responded

Replies to this message:
 Message 26 by vaporwave, posted 12-18-2016 12:12 PM Modulous has responded

  
Modulous
Member (Idle past 360 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 28 of 288 (795853)
12-18-2016 12:27 PM
Reply to: Message 26 by vaporwave
12-18-2016 12:12 PM


Re: Introduction
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.

Nope. I'll just say the theory of evolution explains this phenomena. No proposed alternative has.

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....

Unless you provide a coherent theory of the Creator I cannot do this.

Furthermore, back to phylogenetics... when DNA and morphological traits actually are in conflict, evolutionists simply say the morphology evolved twice or more, significantly insulating the theory from potential falsification.

I dispute this. Now you get to provide your evidence!

Ask an evolutionist what the evolutionary limits are to "Convergent Evolution", with regards to morphology.

There must not be a large path of reduced fitness through morphspace that can be achieved through incremental changes to the genome.

They won't be able to give you any kind of specific answer

Boy, is the egg on your face!


This message is a reply to:
 Message 26 by vaporwave, posted 12-18-2016 12:12 PM vaporwave has responded

Replies to this message:
 Message 33 by vaporwave, posted 12-18-2016 1:07 PM Modulous has responded

  
Modulous
Member (Idle past 360 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 38 of 288 (795866)
12-18-2016 1:41 PM
Reply to: Message 33 by vaporwave
12-18-2016 1:07 PM


Re: Introduction
But you didn't answer the question. Specifically, what level of morphological complexity (edit: **the traits themselves** not supposed evolutionary pathways) would be impossible for convergent evolution and why?

I answered the question you asked; you didn't ask this question.

This question is ill-formed and cannot be answered. What is a 'level of morphological complexity (or a trait itself)'? What does it mean for something to be 'possible' 'for convergent evolution'? The best answer I can give you, without any further information is 'the only limit to complexity is set by the amount of time, energy and resources available', but this isn't 'for convergent evolution' since this is meaningless.

I suggest you have attempted to run before you learned how to crawl. Try starting from simpler beginnings and maybe you will be illuminated.

So, when identifying a convergent trait, you just have to assume evolution did not take such a pathway. Simple enough.

This, for instance, is backwards. You don't assume evolution did not take a pathway, but if you can identify that evolution must have taken such a pathway you have demonstrated it is impossible (or rather, you can identify certain probabilities, and you can pre-define certain probabilities as essentially 'impossible').


This message is a reply to:
 Message 33 by vaporwave, posted 12-18-2016 1:07 PM vaporwave has responded

Replies to this message:
 Message 46 by vaporwave, posted 12-18-2016 3:38 PM Modulous has responded

  
Modulous
Member (Idle past 360 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(3)
Message 47 of 288 (795878)
12-18-2016 3:42 PM
Reply to: Message 46 by vaporwave
12-18-2016 3:38 PM


Theory, not isms
Well, if a particular evolutionary pathway is deemed impossible, then obviously the evolutionist will not assume it.

If a pathway is known to be impossible, it will be ruled out. What on earth are you trying to say?

The evolutionist will assume whatever he needs in order to reconcile the theory.

'The evolutionist'? This is ridiculous. Talk theory, not your prejudices about people.

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 46 by vaporwave, posted 12-18-2016 3:38 PM vaporwave has responded

Replies to this message:
 Message 49 by vaporwave, posted 12-18-2016 3:58 PM Modulous has responded

  
Modulous
Member (Idle past 360 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 52 of 288 (795883)
12-18-2016 4:17 PM
Reply to: Message 49 by vaporwave
12-18-2016 3:58 PM


Re: Theory, not isms
If an interpretation of the data leads to a conclusion that Common Descent did not take place, then the evolutionists will obviously dismiss this interpretation.

Again, let's talk theory and data, not what 'evolutionists' will or won't do. Or are you only here to complain about some group of people you don't like? I'm here for philosophy and science. If you have some specific interpretation of some data you want to discuss, or some example of someone dismissing an interpretation for reasons you find problematic then present it. I'm not interested in your gripes against ill-defined people doing non-specified things.

Bringing it back to your example, an evolutionist would simply never assume a large path of reduced fitness through morphospace in order to explain the existence of a character trait. By definition of being an Evolutionist he can't assume this.

So fuck the evolutionists! Let's talk actual science, not people. Are you so obsessed with your personal dislikes?

The theory of evolution is the best explanation of the data we have. If you disagree, please provide actual details with specific examples. Not innuendo. Thank you.

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 49 by vaporwave, posted 12-18-2016 3:58 PM vaporwave has not yet responded

  
Modulous
Member (Idle past 360 days)
Posts: 7789
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 http://www.jalview.org/

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

http://www.ebi.ac.uk/clustalw/clustalw_detail.html
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.


This message is a reply to:
 Message 147 by vaporwave, posted 12-21-2016 7:25 AM vaporwave has not yet responded

  
Modulous
Member (Idle past 360 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(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.


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

  
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