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Author Topic:   Discussion of Phylogenetic Methods
Taq
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Message 9 of 288 (775845)
01-05-2016 5:38 PM
Reply to: Message 3 by Admin
01-01-2016 2:07 PM


Re: Introduction
"Nucleotide characters" means groups of three nucleotides that program for amino acids? Or do just mean individual nucleotides?

It might be helpful to mention that non-coding DNA can also be used for constructing phylogenies. Obviously, non-coding DNA is never translated into a peptide, so there are no 3 base codons in non-coding DNA.

However, I would be interested to see if the Maximum Likelihood method takes advantage of synonymous vs. non-synonymous mutations. From the description above:

"Using an evolutionary model that defines the probability of different nucleotide substitutions (such as what is the probability of an A --> T or a C --> G, etc.), the probability for a site is the sum of the probabilities of every possible reconstruction of ancestral states."

Substitutions in the first two bases of a codon are much more likely to cause a detrimental mutation and be selected against. Mutations in the 3rd base may not change the amino acid sequence at all.

The question I have for HBD is if synonymous and non-synonymous mutations are weighted differently in this method.


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Taq
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Posts: 8010
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Member Rating: 4.5


Message 12 of 288 (775883)
01-06-2016 12:03 PM
Reply to: Message 11 by herebedragons
01-06-2016 12:49 AM


Re: Introduction
I am not aware of an alignment program that weighs the third codon differently. However, what they do is convert the codons to amino acids and then align the amino acids. A matrix is used to weight the amino acid substitutions where synonymous substitutions would have high scores and non-synonymous substitutions would have low scores (the alignment algorithm would try to maximize the alignment score). Below is an example of such a matrix (BLOSUM62).

Perhaps I am being overly critical or getting the terminology wrong, but in my understanding a synonymous mutation is one that results in the same amino acid. What your chart seems to be using is groupings based on charge and hydrophobicity. A substitution that replaces a polar amino acid with a hydrophobic amino acid is weighted less than a substitution with another polar amino acid of similar charge.


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Taq
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Posts: 8010
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Member Rating: 4.5


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Message 115 of 288 (795974)
12-20-2016 10:38 AM
Reply to: Message 76 by caffeine
12-19-2016 4:20 PM


Re: The purpose of phylogenetics
caffeine writes:

Phylogenetics is precisely what he says. Phylogenetic methods are means of calculating the most probable tree topologies given that a group of organisms share a common ancestor. These are not techniques to establish that evolution occured, but rather the means to figure how it did once we've taken that for granted.

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.

For example, you could list the physical characteristics of cars and measure the phylogenetic signal (which should be low). You don't have to assume common ancestry or evolution. People have also measured the phylogenetic signal for groups of languages and found a strong phylogenetic signal, as would be expected since many languages evolve much like biological species.

From the classic 29+ Evidences for Macroevolution Talkorigins page:

quote:
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).

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Taq
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Posts: 8010
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Member Rating: 4.5


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Message 116 of 288 (795976)
12-20-2016 10:49 AM
Reply to: Message 110 by Dr Adequate
12-20-2016 9:59 AM


Re: The purpose of phylogenetics
Dr Adequate writes:

Consider for example the gene for cytochrome c. This does nothing to control anatomical development, is not even nuclear, but mitochondrial, and does exactly the same thing in every organism, functioning as part of the electron transport chain in mitochondria.

To help drive this point home, for 30 taxa there are over 1 x 10^38 possible trees. That is over 10^38 different ways to organize 30 taxa into a branching tree. When you organize 30 different taxa by morphology and by cytochrome c you get a perfect match between them:

quote:
So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the "twin nested hierarchy". This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.
http://www.talkorigins.org/...1.html#independent_consilience

There is absolutely no reason that a creator would be forced to match cytochrome c sequences to morphology. None. As you mention, the function of cytochrome c has nothing to do with having fur, gills, feathers, or eyes. To stress this again, out of 10^38 possible ways that cytochrome c could have been arranged in a phylogeny, we see the single tree out of those 10^38 that we would expect to see from evolution.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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Replies to this message:
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Taq
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Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


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Message 118 of 288 (795981)
12-20-2016 11:00 AM
Reply to: Message 114 by Tangle
12-20-2016 10:31 AM


Re: The purpose of phylogenetics
Tangle writes:

But uracil also pairs with adenine, so why not use that combo in, say cows and only cows, just for a laugh. That'll screw those evil evolutionist up.

Or better yet, why not change the codon tables for each species? You could produce the same exact proteins but with completely different DNA sequences. I am not going to do the math here, but I would strongly suspect there are more than enough possible combinations between codons and amino acids to go around, even with 3rd base wobble. In fact, why not have some species where they have 1st base wobble, or 2nd base wobble? That would greatly increase the number of combinations.

For an all powerful and all knowing deity with unlimited time and resources, this would be child's play. I have always found it fascinating that creationists insist that God would have to reuse designs. They claim that humans reuse designs, so it would make sense that God would too. What they don't seem to realize is that humans reuse designs because we are not all powerful, not all knowing, and are limited in both time and resources. What they are saying is that God is as limited as human beings, which makes sense to atheists since we have long suspected that God was invented by humans.


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Taq
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Posts: 8010
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Member Rating: 4.5


(2)
Message 119 of 288 (795982)
12-20-2016 11:19 AM
Reply to: Message 112 by RAZD
12-20-2016 10:17 AM


More Fun With Cytochrome C
RAZD writes:

Being neither selected for nor selected against, they would be neutral mutations, and the fact that they are shared by some (humans, chimps) but not all primates (humans, chimps, rhesus monkeys) would imply descent from an ancestor (for chimps and humans) that first had the altered DNA.

Continuing with the cytochrome c theme . . .

There is another feature of cladistics that is called genetic equidistance. Here is a model phylogeny to work from:

In this phylogeny we can see that A and B share a recent common ancestor. A and B also share the SAME common ancestor with C. When you trace the phylogeny to where B and C meet it is the same node where A and C meet. Therefore, the genetic (i.e. evolutionary) distance between A and C is the same as that for B and C. A and B are genetically equidistant from C. We should see this equidistance in genetic data if evolution is true.

Using cytochrome c as our model gene, here are the pairwise alignment scores for human, mouse, and chicken DNA (from Homologene at NCBI, don't know if that link will work or not)

H.sapiens vs. Mouse = 90.5%
H. sapiens vs. Chicken = 81.6%

Humans and mice are the A and B in our model. Chickens are the C. Therefore, we should see similar genetic distance between humans and chickens as we see for mice and chickens. So do we? We sure do:

Chicken vs. Mouse = 81.9%

They are just 0.3% off. We see nearly the same genetic distance between humans and chickens as we see between mice and chickens. I have yet to find a single creationist who can explain this. Only evolution can explain this.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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Replies to this message:
 Message 122 by jar, posted 12-20-2016 11:50 AM Taq has responded
 Message 133 by RAZD, posted 12-20-2016 4:39 PM Taq has responded

  
Taq
Member
Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


Message 120 of 288 (795983)
12-20-2016 11:39 AM
Reply to: Message 66 by vaporwave
12-19-2016 7:33 AM


Re: Introduction
vaporwave writes:

But you are the one guilty of this so far. You've claimed to hold insight into the probabilities of how life would look if common ancestry were false.

We can directly observe what common ancestry, vertical inheritiance, and evolution would look like because we can watch it in real time. It produces a phylogenetic signal.

"Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains."
https://www.ncbi.nlm.nih.gov/pubmed/1948030

The ancestral history of these lab strains of mice are known. We know exactly how each strain is related to another, and they have been kept separate from one another. When we look at the phylogeny based on their DNA, it almost exactly matches the known relationships. We know what evidence common ancestry and evolution produces because we can directly observe it.

Earlier here you stated that genetic/morphological concordance of life would be "accidental" if not for evolution. I'm still waiting for you to explain how you got this knowledge.

We are still waiting for you to explain why an omnipotent and omniscient creator would be forced to fit DNA and morphology into the same nested hierarchies.


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Taq
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Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


(2)
Message 121 of 288 (795984)
12-20-2016 11:45 AM
Reply to: Message 35 by vaporwave
12-18-2016 1:26 PM


Re: Introduction
vaprowave writes:

Dogs and cats remain more similar to each other than either is to a jellyfish or a reptile. Surprise surprise...

Here is a mouse that, for one gene, is more similar to a jellyfish than any other vertebrate:

This mouse carries an exact copy of the jellyfish gene GFP (green fluorescent protein). How did it get there? These mice were DESIGNED by humans. We put the jellyfish gene in the mouse genome. If we can so easily violate a nested hierarchy, why couldn't God? Is God less powerful than humans?


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Replies to this message:
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Taq
Member
Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


Message 123 of 288 (795986)
12-20-2016 12:09 PM
Reply to: Message 26 by vaporwave
12-18-2016 12:12 PM


Re: Introduction
vaporwave writes:

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.

That isn't the case.

The theory of evolution is the only theory which specifically predicts that we should see a strong correlation between phylogenies based on morphology and DNA. When a theory is able to predict these types of relationships between independent observations, then that is the theory we go with.

Creationism, on the other hand, makes no such prediction. It can't explain why we see a phylogenetic signal at all. It can't explain why wild type mice don't have exact copies of jellyfish genes. We already know that designers can mix and match genes as they see fit, because humans can do it. We know that other designs made by intelligent beings don't form statistically significant phylogenetic signals as we see with things such as cars, paintings, and buildings.

Creationism can not explain the most fundamental observations in biology, observations that go back to Linnaeus in the 18th century. Evolution can explain these observations perfectly.

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....

We can simply point to the fact that no creationist can explain why we see a nested hierarchy instead of a different pattern of shared features.


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Taq
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Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


(1)
Message 124 of 288 (795987)
12-20-2016 12:15 PM
Reply to: Message 122 by jar
12-20-2016 11:50 AM


Re: More Fun With evidence
jar writes:

The fact and reality is that Creationism explains absolutely nothing and so has absolutely no value.

Creationism has no value as a scientific theory, that much is true. Perhaps it has value as a dogmatic religious belief, but not as a scientific theory.

Creationists often accuse scientists of refusing to even consider creationism. The real problem is that Creationists haven't offered any scientific explanations to consider. They haven't offered testable predictions or mechanisms. They haven't produced testable and falsifiable explanations for the data we do have. They can't even explain the nested hierarchy that Linnaeus discovered in the 1700's.


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Taq
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Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


Message 125 of 288 (795988)
12-20-2016 12:31 PM
Reply to: Message 101 by vaporwave
12-20-2016 8:31 AM


Re: The purpose of science
vaporwave writes:

I think even if molecular researchers had no concept of common ancestry they could have made similar predictions based off the simple idea that beings of similar anatomical properties are going to be more similar to each other in additional ways than not.

Google Chrome on the PC and Mac look almost exactly the same from the outside, yet the machine code underneath is entirely different.

Why wouldn't we think the same of different species? Why couldn't we see very different DNA even if their morphology is similar?

And why do we see areas of genomes that are more similar than others if creationism is true? Why should we see more similarities in exons than in introns when we compare the cat and dog genomes? How does creationism explain that?


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 Message 101 by vaporwave, posted 12-20-2016 8:31 AM vaporwave has responded

Replies to this message:
 Message 128 by vaporwave, posted 12-20-2016 2:56 PM Taq has responded

  
Taq
Member
Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


Message 127 of 288 (795990)
12-20-2016 2:48 PM
Reply to: Message 126 by vaporwave
12-20-2016 2:37 PM


Re: The purpose of phylogenetics
vaporwave writes:

Do you get a perfect match with cytochrome b ?

Do you even care?

Okay, what's your point? There's no reason evolution would be forced to give rise to eukaryotes.

My point is that creationism can't explain the observations. Evolution can.


This message is a reply to:
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Replies to this message:
 Message 129 by vaporwave, posted 12-20-2016 2:58 PM Taq has responded

  
Taq
Member
Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


Message 130 of 288 (795993)
12-20-2016 3:02 PM
Reply to: Message 128 by vaporwave
12-20-2016 2:56 PM


Re: The purpose of science
vaporwave writes:

Was the code for each version written by different people?

The same person would have to write completely different codes due to the difference in operating systems and hardware.

The whole point is that there are nearly infinite methods for writing computer code to produce an identical looking web browser. The same applies to biological organisms. There are nearly infinite options for making a human with DNA, protein, and RNA. Changing the codon table is just one idea. You could change almost every third base in exons and still get the same protein. You could probably find pigments other than melanin to darken skin and hair. I could go on for days listing how a specific morphology does not require a specific DNA sequence.

vaporwave writes:

Why expect this? If a particular template works, why change it?

There are millions and billions of other templates that would work, so why reuse the same one?


This message is a reply to:
 Message 128 by vaporwave, posted 12-20-2016 2:56 PM vaporwave has responded

Replies to this message:
 Message 142 by vaporwave, posted 12-20-2016 6:41 PM Taq has responded

  
Taq
Member
Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


(1)
Message 132 of 288 (795995)
12-20-2016 3:14 PM
Reply to: Message 129 by vaporwave
12-20-2016 2:58 PM


Re: The purpose of phylogenetics
I just wonder why evolutionists always bring up cytochrome C but never cytochrome B. Is there a reason for that?

Probably for the reason that cytochrome c is somatic while cytochrome b is mitochondrial. This is from Wikipedia:

"Cytochrome c is a highly conserved protein across the spectrum of species, found in plants, animals, and many unicellular organisms. This, along with its small size (molecular weight about 12,000 daltons),[6] makes it useful in studies of cladistics.[7]"

Added in edit . . .

This is also from Wikipedia:

"Cytochrome b is commonly used as a region of mitochondrial DNA for determining phylogenetic relationships between organisms, due to its sequence variability. It is considered to be most useful in determining relationships within families and genera. "

Variation in cytB is higher than cytC, making cytC the choice for comparing more distantly related organisms.

Edited by Taq, : No reason given.


This message is a reply to:
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Replies to this message:
 Message 136 by vaporwave, posted 12-20-2016 6:04 PM Taq has responded

  
Taq
Member
Posts: 8010
Joined: 03-06-2009
Member Rating: 4.5


(2)
Message 134 of 288 (795999)
12-20-2016 5:02 PM
Reply to: Message 133 by RAZD
12-20-2016 4:39 PM


Re: More Fun With Cytochrome C
RAZD writes:

And we should see the same genetic distance from chimp to rhesus monkey as from human to rhesus monkey?

Yes, although the differences aren't as dramatic.

You can do the same for any other species trio at Homologene:

https://www.ncbi.nlm.nih.gov/homologene?cmd=Retrieve&dopt...

(I don't know if this link works for anyone, let me know if you get sent to a weird page)

It has all of the possible comparisons between their model organisms if you scroll down. We could look at human, chicken, and fruit fly.

human v. chicken = 81.6%
human v. fruit fly = 71.9%
chicken v. fruit fly = 71.6%

As expected, we see the same difference between human and fruit fly as we do between chicken and fruit fly since both chickens and humans share the same common ancestor with fruit flies (as do all vertebrates). Other fun trios on that list are cows:frogs:round worms and dogs:rats:yeast.


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