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Author Topic:   Discussion of Phylogenetic Methods
RAZD
Member (Idle past 1404 days)
Posts: 20714
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Joined: 03-14-2004


Message 133 of 288 (795996)
12-20-2016 4:39 PM
Reply to: Message 119 by Taq
12-20-2016 11:19 AM


Re: More Fun With Cytochrome C
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.
In other words, we can test the genetic phylogenies to see whether they match this prediction or no.
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:
And we should see the same genetic distance from chimp to rhesus monkey as from human to rhesus monkey?

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This message is a reply to:
 Message 119 by Taq, posted 12-20-2016 11:19 AM Taq has replied

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 135 of 288 (796001)
12-20-2016 5:17 PM
Reply to: Message 128 by vaporwave
12-20-2016 2:56 PM


pro template and con template
Why wouldn't we think the same of different species? Why couldn't we see very different DNA even if their morphology is similar?
Why expect this? If a particular template works, why change it?
Let me introduce you to a couple of little cuties for the purpose of this discussion:
The Great Creationist Fossil Failure, Message 1121: Curiously, I have argued that the concept of clades is the closest parallel in evolutionary terminology to the creationist concept of kinds -- each reproduce after their own kind. A member of the wolf clade will always be a member of the wolf clade and not become a member of another clade via evolution. This is generally viewed by creationists as "micro" evolution.
quote:
Analogy: Squirrels and Sugar Gliders
Beyond being cute and cuddly, flying squirrels and sugar gliders have many striking similarities: big eyes, a white belly, and a thin piece of skin stretched between their arms and legs, a trait which helps them "glide" and remain stable when leaping from high places.
But sugar gliders and flying squirrels also have some key differences. Most importantly, they reproduce and bear their babies in fundamentally different ways:
Flying squirrels and sugar gliders are only distantly related. So why do they look so similar then? Their gliding "wings" and big eyes are analogous structures. Natural selection independently adapted both lineages for similar lifestyles: leaping from treetops (hence, the gliding "wings") and foraging at night (hence, the big eyes).

So while Diportodontia is a different clade from Rodentia, and it is a member of the marsupial mammal clade and not the placental mammal clade they both are members of the mammal clade ... there IS a common ancestor population they evolved from, (and we can go back further) ... BUT while each have not evolved "out of their (Diportodontia, Rodentia) clades" they have arrived at a similar point through selection and mutations.
Message 1140 in the same thread details the phylogeny from common ancestor to Metatheria to Diprotodontia to Petauridae ...
The sugar glider (Petaurus breviceps) is a small, omnivorous, arboreal, and nocturnal gliding possum belonging to the marsupial infraclass. ...
And it details the phylogeny from the common ancestor to Eutheria to Sciuridae to Pteromyini ...
Flying squirrels (scientifically known as Pteromyini or Petauristini) are a tribe of 44 species of squirrels in the family Sciuridae. ...
Did the squirrel become a possum or did the possum become a squirrel?
Message 101 (this thread): 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.
Here we have very similar outward appearances but a phylogeny that says their common ancestor was very distant. Sugar gliders have more in common with kangaroos than Flying Squirrels, and Flying Squirrels have more in common with giraffes than Sugar Gliders.
Why expect this? If a particular template works, why change it?
Let's see if this answers your question:
The Great Creationist Fossil Failure, Message 1143: Convergent evolution disproves two common creationist concepts:
  1. that there is a limit to what microevolution can accomplish (dogs will always be dogs and not some other critter),
    Because starting from two entirely different lineages very similar species are developed via mutation and selection,
    and
  2. special creation, that each new species is created fully formed rather than descendant from other nearby species,
    When confronted with closely related species and shown the degree of similarity, the creationist claim is that god/s reused a template they had already developed.
    This argument is contradicted by and invalidated by convergent evolution, where these "templates" were NOT used, ... with no explanation for this failure.
When we look deeper we see that the differences outweigh the similarities, and that those differences are linked by homologies to ancestor populations that were more different between the two lineages until you get back to their common ancestor population, as demonstrated in Message 1140 in detail.
So the same "template" was not used for two very similar critters, but it was used for species that are not as similar appearing ...
... while evolution explains both cases with no difficulty.
Enjoy

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

Replies to this message:
 Message 138 by vaporwave, posted 12-20-2016 6:20 PM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 145 of 288 (796015)
12-20-2016 10:19 PM
Reply to: Message 138 by vaporwave
12-20-2016 6:20 PM


Re: pro template and con template
So the same "template" was not used for two very similar critters
So the "template" would be inferred as features uniting Marsupials or features uniting Eutherians.
You mean the features that show hereditary traits from parent to descendant that evolution predicts. Again you put yourself in the bind that your god is mimicking evolution when it isn't necessary, unless that is all he can do. Seems more like like Loki to me.
You didn't answer my question though:
"Did the squirrel become a possum or did the possum become a squirrel?"
I once asked a creationist "How would a dog descendant not be a dog?" and he replied "When it looks like something else." Seems to me that we have that case here, where one looks like the other ... would you agree?
Note that you have gone from having a template that accounts for the small difference between sister species to one that applies to whole classes. That's the kind of thing that happens when an argument falls apart.
Cladistics actually works just fine without assuming common ancestry.
This seems to me to be a very curious argument for a creationist position, where one of the bulwarks of their argument is that all life reproduces after their own kind and are descendant from the original kind -- ie descendant from the original common ancestors.
Cladistics actually works just fine without assuming common ancestry.
Curiously, I'd like to know how that works ... would you care to enlighten me? Is it just random grouping based on whim? What is your paradigm for organizing those groups?
Additionally, I find it just a little awkward to have a "template" that takes care of wombats, kangaroos, koalas, thylacines, etc, ... all without traits of sugar gliders that match the flying squirrels ... to make sugar gliders, and how do all the different traits come about in Metatheria?
... and at the same time one that takes care of giraffes, badgers, elephants, rhinoceros, whales, tigers, wolves, bears, etc, ... all without traits of flying squirrels that match the sugar gliders ... to make flying squirrels, and how do all the different traits come about in Eutheria?
How are all those different Metatheria and Eutheria traits generated from the templates?
... and how do those matching traits between flying squirrel and sugar glider come about?
... how does your 'non-hereditary cladistic system' or your template explain both the different features and similar features for the sugar gliders and the flying squirrels?
Inquiring minds want to know.
Enjoy
Edited by RAZD, : ,

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This message is a reply to:
 Message 138 by vaporwave, posted 12-20-2016 6:20 PM vaporwave has replied

Replies to this message:
 Message 149 by vaporwave, posted 12-21-2016 7:56 AM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 151 of 288 (796027)
12-21-2016 8:44 AM
Reply to: Message 147 by vaporwave
12-21-2016 7:25 AM


cytochrome b
Higher variation = increased deviation from a phylogenetic signal or pattern.
But it doesn't mean that the work is not being done nor that it does not support the phylogenetics. From the first hit on the search on cytochrome b phylogenetic:
quote:
The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes.
The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement with the well-established phylogeny of cichlid fish.
bold added for emphasis.
Even a quick check with wikipedia shows it's usage:
quote:
Cytochrome b
Cytochrome b is a protein found in the mitochondria of eukaryotic cells. It functions as part of the electron transport chain and is the main subunit of transmembrane cytochrome bc1 and b6f complexes.[1][2]
So it would not be useful for prokaryotic cells which don't have mitochondria ... further:
quote:
Use in phylogenetics
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. Comparative studies involving cytochrome b have resulted in new classification schemes and have been used to assign newly described species to a genus as well as to deepen the understanding of evolutionary relationships.[6]
bold again for emphasis.
This is essentially an admission that cytochrome B data does not reinforce the preferred evolutionary relationships very well, or at least would not look as convincing when making a case to the public.
Except that this is a false conclusion you have reached based on your opinion instead of checking easily found facts. Sadly, for you, opinion has demonstrated a very poor record of affecting reality in any way shape or form.
This is why evolutionists, when trying to make their case, always focus on cytochrome C instead.
Or the reason is a simple matter of more universal applicability:
quote:
Cytochrome C
Cytochrome c is a highly conserved ~12 kDa protein consisting of a single 104 amino acid peptide with a single heme group, which is covalently attached to Cys14 and Cys17. Because of its ubiquitous nature and sequence homology, cytochrome c has been used as a model protein for molecular evolution.1
and bold again for emphasis.
So in summary, cytochrome b is useful in eukaryotes (with mitochondria) and cytochrome c is useful in eukaryotes and prokaryotes. In both cases the phylogenetic trees reinforce and fine-tune the previous derived trees.
Higher variation = increased deviation from a phylogenetic signal or pattern.
Or because there is more variation in cyt-b that it is better for fine detail within family and genus while cyt-c is better for larger scale detail ... ie cyt-c does not vary within a family or genus, so it cannot detail those branches, but cyt-b does vary and can be used to provide that detail.
I don't use a microscope to identify craters on the moon, and I don't use a telescope to identify moon dust.
Enjoy
Edited by RAZD, : .
Edited by RAZD, : .
Edited by RAZD, : added end
Edited by RAZD, : end analogy

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 156 of 288 (796032)
12-21-2016 10:29 AM
Reply to: Message 149 by vaporwave
12-21-2016 7:56 AM


Re: pro template and con template and taxon arguments
Only if you assume shared traits are the product of common inheritance. The traits themselves don't show you that.
It's what we observe happening in every species known. You have traits your parents had (and some they didn't). You have the same DNA for those shared traits. You get your DNA from your parents in the process of reproduction. Thus we know from observation that they are inherited.
What we hypothesis is that this pattern of inherited traits holds for all life, from the fossil record, the historic record and the genetic record.
That's how science works -- it observes objective empirical evidence and then posits an explanation for how the evidence came to be, then it tests that hypothesis.
"Did the squirrel become a possum or did the possum become a squirrel?"
Honestly I have no idea what you're talking about.
The argument was: dogs will always be dogs (descendants will still be dogs), so when will "macro"evolution be observed? -- when they no longer look like dogs, but look like something else; flying squirrels look like sugar gliders (and vice-versa), therefore "macro"evolution (by this creationist mis-definition) has occurred, agreed? So:
Has the flying squirrel become a look-alike to the sugar glider possum ... or has the sugar glider possum become a look-alike to the flying squirrel? (Or do they both look like something new?)
Are you under the impression that templates can only be used exclusively of each other? You can't use more than one when building something? That would be a bizarre thing to assume from a design perspective.
And now your argument is totally bizarre and useless. You can't predict a single thing from it, not sister species similarities (the original purpose of this creationist concept) nor the differences between sequoia trees slime molds and elephants. There is no time or location restriction on their use. Rabbits in the cambrian or on the moon, it's all good ... except it's just hand-waving, and it's denial of the strong evidence for evolution of inherited traits.
I haven't said anything about creationist models, but it sounds like you're suggesting that one cannot group objects by shared traits (cladistics) unless those objects are related via common ancestry. Is that really what you're saying?
Again, the definition of cladistics is that you start with a breeding population and then all the descendants are members of that parent population clade. By definition you start with a common ancestor for all the descendants:
quote:
Clade
A clade (from Ancient Greek: κλάδος, klados, "branch") is a group of organisms that consists of a common ancestor and all its lineal descendants, and represents a single "branch" on the "tree of life".[1]
Definitions
A clade is by definition monophyletic, meaning that it contains one ancestor (which can be an organism, a population, or a species) and all its descendants.[note 1][7][8] The ancestor can be known or unknown; any and all members of a clade can be extant or extinct.
If you are going to use a science term, you need to use it the way it is defined in the science and not for something else -- that's how you communicate without confusion.
You can't do cladistics without a common ancestor BY DEFINITION.
Perhaps you should use the old term taxon instead of clade
quote:
Taxon
In biology, a taxon (plural taxa; back-formation from taxonomy) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. ...
Although preceded by Linnaeus's system in Systema Naturae (10th edition, 1758)[1] and unpublished work by Bernard and Antoine Laurent de Jussieu, the notion of a unit-based "natural system" of biological classification was first made widely available in 1805 ...
Definition
A taxonomic unit, whether named or not: i.e. a population, or group of populations of organisms which are usually inferred to be phylogenetically related and which have characters in common which differentiate (q.v.) the unit (e.g. a geographic population, a genus, a family, an order) from other such units. A taxon encompasses all included taxa of lower rank (q.v.) and individual organisms. [...]"
ie -- that's the way we used to do it, then it was discovered that cladistics and the nested hierarchies from common ancestors was a better predictor of actual phylogenetic relationships.
But hey, go back to the 1850's if that whets your whistle.
... you're suggesting that one cannot group objects by shared traits ...
Like the shared traits between sugar gliders and flying squirrels, which you have previously rejected in favor of the hereditary traits of metatherians and eutherians?
See, this is the kind of mistaken relationships that the old taxonomy system tended to make. This is where phylogenetics based on cyt-c and cyt-b help to strengthen the cladistic relationships.
Are you under the impression that templates can only be used exclusively of each other? ...
The only "template" that we have any objective empirical evidence for is DNA, inherited from parents and modified by mutations. These individual "templates" are exclusive to, and guide the development of, each and every organism. We have observed it happen. We don't need multiple templates to explain the diversity of life as we know it, from the fossil record, to the historic record, from the genetic record to the record of life today.
Enjoy

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 164 of 288 (796043)
12-21-2016 11:41 AM
Reply to: Message 161 by Taq
12-21-2016 10:47 AM


levels of observation
This is why strongly conserved sequences of DNA are used for phylogenetic reconstruction of species that share a distant common ancestor. For more closely related species, the phylogenetic signal in the cytB gene is still there. For more distantly related species, the phylogenetic signal in cytC is still there.
We don't use a microscope to identify craters on the moon, and we don't use a telescope to identify the moon dust in the craters.
Enjoy

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This message is a reply to:
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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 205 of 288 (796101)
12-22-2016 9:35 AM
Reply to: Message 176 by vaporwave
12-21-2016 4:43 PM


templates and peripheral features
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.
So then you generate a vertebrate-tetrapod-eutherian template that is used to generate a squirrel template that is used to generate a flying squirrel template ...
... and you generate a vertebrate-tetrapod-metatherian template that is used to generate a possum template that is used to generate a sugar glider template ...
I'm not sure what your obsession is with this hypothetical mix-and-match scenario. ...
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same?
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.
Or is it one of the "peripheral features in order to generate variety" that is added to both templates?
Inquiring minds want to know.
Perhaps the same "peripheral feature" was used for the colugo (flying lemur)
quote:
Recent molecular phylogenetic studies have demonstrated that colugos belong to the clade Euarchonta along with the treeshrews (order Scandentia) and the primates, with the colugos more closely related to primates. ...
Or even for Wallace's Frog
quote:
Wallace's flying frog or the Abah River flying frog (Rhacophorus nigropalmatus) is a moss frog found at least from the Malay Peninsula into western Indonesia. It is named for the biologist, Alfred R. Wallace, who collected the first specimen to be formally identified.
Help us understand how these traits are generated without evolution.
Enjoy
Edited by RAZD, : .

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This message is a reply to:
 Message 176 by vaporwave, posted 12-21-2016 4:43 PM vaporwave has replied

Replies to this message:
 Message 224 by vaporwave, posted 12-23-2016 7:23 AM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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

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This message is a reply to:
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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 229 of 288 (796145)
12-23-2016 10:42 AM
Reply to: Message 224 by vaporwave
12-23-2016 7:23 AM


Re: templates and peripheral features
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same?
Depends. ...
On what? Whim? We're looking for a theory that can be tested and one that makes predictions, not one that depends on some arbitrary application of an untested concept.
... 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.
We are talking about flaps of skin, not internal structure.
Or is this why the skin flaps on the frog are just between toes? Because the internal anatomy of flying frogs is so different from the mammals?
Can those internal differences predict which template causes this group of frogs to grow membranes between toes or not?
quote:
Or even for Wallace's Frog
quote:
Wallace's flying frog or the Abah River flying frog (Rhacophorus nigropalmatus) is a moss frog found at least from the Malay Peninsula into western Indonesia. It is named for the biologist, Alfred R. Wallace, who collected the first specimen to be formally identified.
Help us understand how these traits are generated without evolution.
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same? And is it the same for the colugo and the flying frog?
Is the template for webbed frog feet also used to generate webbed feet in Newfoundland and some other dogs?
quote:
5 Dog Breeds With Webbed Feet
This black wooly giant of a dog was bred to help Newfoundland fishermen work in the cold waters of Canada. Nearly every one of their traits is perfectly suited to make them experts at that duty. Their thick fur is water resistant, their muscular build lets them haul in fishing nets and carts, and their size and loyalty make them perfect for lifesaving should a man fall overboard. And, of course, they have thick, webbed paws and the longest toes of any breed that let them tear through the water. They also use those paws to swim in a unique way, with a down-and-out motion, rather than an ordinary dog paddle. This lets them power through waves and surf. They’re so good at being water companions that a Newfoundland named Seaman accompanied Lewis and Clark as they explored and mapped the rivers of the American frontier.
Or the webbed feet of ducks? the platypus?
people?
Is that from the same template as the flying squirrel and sugar glider?
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 ...
Except that the membranes did not occur in older ancestors, and so would not expect them to be a conserved DNA section.
You mean a more complex explanation than "natural selection did it" ?
It is a common mistake of creationists to equal natural selection with evolution, and anyone saying this just demonstrates ignorance of how evolution actually works (and has been observed to work).
Remember this?
(1) The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.
and this?
Evolution is a two-step feedback response system that is repeated in each generation, like walking on first one foot and then the next.
Each generation builds on the generation before to adapt to their ecological challenges and opportunities.
Evolution would accommodate both observations in this case, just like design.
Evolution does indeed accommodate observed objective empirical evidence, that is the nature of science. It also makes testable predictions.
So far I have not seen any predictions from your nested templates concept, you haven't shown how it is activated or instigated, and you can't even decide whether or not one is used for both the webbed membranes of sugar gliders and flying squirrels. It's appears more like waving hands than providing a usable concept.
So I'm still trying to understand how these traits are generated by templates without evolution.
Enjoy

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This message is a reply to:
 Message 224 by vaporwave, posted 12-23-2016 7:23 AM vaporwave has replied

Replies to this message:
 Message 231 by vaporwave, posted 12-23-2016 1:28 PM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 241 of 288 (796180)
12-24-2016 8:35 AM
Reply to: Message 231 by vaporwave
12-23-2016 1:28 PM


Re: templates and peripheral features
Except that the membranes did not occur in older ancestors, and so would not expect them to be a conserved DNA section.
Unless the genes were conserved for some other function in the mammal line and later independently recruited for development of gliding membranes in the separate branches, because of similar selection pressures.
Let's break this down:
  • "the genes were conserved" -- from what source? theria? or some other totally unknown and unevidenced gliding ancestor?
  • "for some other function" -- would this be the same function in possums and squirrels (eg - homologous genes)? or just somewhere in the DNA?
  • "later independently recruited for development of gliding membranes" -- by what process? mutation? or some other totally unknown unevidenced process
  • "because of similar selection pressures" -- ie - natural selection ... or some other unknown unevidenced process?
Because it sure looks to me like you are saying "independently evolved from existing DNA from their common therian ancestor by mutation and selection" while trying desperately to make it sound like not-evolution.
Why is the membrane development in the Colugo different?
Enjoy

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This message is a reply to:
 Message 231 by vaporwave, posted 12-23-2016 1:28 PM vaporwave has replied

Replies to this message:
 Message 242 by herebedragons, posted 12-24-2016 8:55 AM RAZD has seen this message but not replied
 Message 244 by vaporwave, posted 12-26-2016 4:58 AM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 245 of 288 (796231)
12-26-2016 7:43 AM
Reply to: Message 244 by vaporwave
12-26-2016 4:58 AM


Re: templates and peripheral features
Yes, that was my entire point and it sounds like you forgot the case you were making. ...
The one where I'm asking you to explain how your templates work? The one which has observed your explanation evolve to nested templates but where you won't commit to whether or not the templates for gliding membranes are the same or different? The one that has led you into a position of mirroring evolutionary processes with your use of templates? Seems to me I'm right on target, and now that you are in a box you try to pretend I'm arguing something else?
Sorry, that won't work.
... You act like such discoveries (e.g. the gliding membrane example) would blow evolution out of the water and falsify it immediately, but then actually it wouldn't.
Curiously I'm the expert on what my argument is about, so like Dr A, I'll ask you to let me decide what my argument actually is.
You could of course use actual quotes instead of false claims ... if you can find them.
The story of common ancestry is far too pliable to be tested by phylogenetics.
Unlike your story of nested templates, which is scientifically completely useless for several reasons:
  1. they don't exist, there is no evidence for them
  2. there is no known process to apply them
  3. they provide no testable predictions
  4. doesn't provide any explanation that is not identical to evolution
  5. doesn't explain anything new that evolution does not explain
Nor does it matter what your opinion is regarding the pliability of phylogenetics, what matters is that it works. It has been observed, it has provided predictions, it has been tested.
It shows that the platypus are not closely related to ducks, and are only related by very distant non-duck billed common ancestors. It shows that the sugar gliders, and flying squirrels are not closely related, and are only distantly related by non gliding membrane common ancestors.
Enjoy
Edited by RAZD, : .

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This message is a reply to:
 Message 244 by vaporwave, posted 12-26-2016 4:58 AM vaporwave has replied

Replies to this message:
 Message 246 by vaporwave, posted 12-26-2016 3:50 PM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 247 of 288 (796253)
12-26-2016 10:11 PM
Reply to: Message 246 by vaporwave
12-26-2016 3:50 PM


we have motive (survival) means (evolution) and opportunity (proximity)
Unlike your story of nested templates, which is scientifically completely useless for several reasons:
It's not something I'm committed to. I only brought it up in the first place because evolutionists here insisted on driving the discussion towards creation/design.
That said, the nested design template idea does not seem significantly more ad-hoc than common ancestry. ...
Except that templates are pure imagination with ad hoc peripheral features added to fit special cases, each time differently. It is useless.
Common ancestry does have evidence both of mechanism and observed occurrences. That is the difference between scientific hypothesis and theory from imaginary ad hoc fantasies.
... It's not something I'm committed to.
Obviously.
Nor does it matter what your opinion is regarding the pliability of phylogenetics,
Well... this is a public discussion thread on phylogenetics.... I don't know where else I'd share my opinion on it.
You have every right to express your opinion, but you do not have the right to have it considered as anything other than ad hoc fantasy unless and until you provide objective empirical evidence to support your opinion. Opinion, historically, as a very poor record of altering reality in any way shape or form.
what matters is that it works.
Sure, common ancestry "works" in that it's a flexible backdrop to work against. The very fact that it is so open-ended, and accommodating to diverse and contradictory narratives is what makes the idea work so well.
A claim you have failed to substantiate in any way. There are a couple of examples that other people have brought up showing some small difficulty in determining lineage, as in the frogs above, and the reasons for those difficulties are also documented - their evolution was too rapid to show up in the markers.
Your argument is that this invalidates all the rest of the phylogeny where no such problems exist. It doesn't, and it doesn't even bring the methodology into question.
There are millions of species arranged in quantifiably strong phylogenies, so a handful of indeterminates is not surprising nor unexpected -- because that's science in the real world.
It isn't a willy nilly ad hoc arrangement either, as the evidence has to fit the requirement to be near in time and space ... there has to be motive (survival) means (evolution) and opportunity (proximity ... there had to be contact).
For example in Pelycodus we see
quote:
A Smooth Fossil Transition: Pelycodus, a primate
The dashed lines show the overall trend. The species at the bottom is Pelycodus ralstoni, but at the top we find two species, Notharctus nunienus and Notharctus venticolus. The two species later became even more distinct, and the descendants of nunienus are now labeled as genus Smilodectes instead of genus Notharctus.
As you look from bottom to top, you will see that each group has some overlap with what came before. There are no major breaks or sudden jumps. And the form of the creatures was changing steadily.
There is the evidence of generation by generation of evolution from common ancestor populations to younger populations, and the division at the top into two reproductively isolated daughter species.
From a common ancestor population, Pelycodus jarrovii.
It has been observed
Universal common ancestry, i.e. that all mammals share a common ancestor, that all vertebrates share a common ancestor, etc. has not been observed... obviously....
And yet we have the fossils that show the appropriate evolutionary changes at the appropriate times and in the appropriate locations ... we have motive (survival) means (evolution) and opportunity (proximity).
And we have the evidence that what is observed in the world today, and what is supported by the fossil evidence like Pelycodus (and others) provide is sufficient to explain the rest of the fossil record using the same processes. We don't have to invent any new or different process to explain the vast record of natural life on earth.
it has provided predictions,
Common ancestry has provided tons of predictions. ...
Agreed.
... It also has tons of excuses for when predictions fail. (e.g. well it must have evolved a lot sooner than we thought.... well those genes must not have been well-conserved....
Two very strong reasons why genetic phylogenies are innaccurate in a small number of cases ... ones we can test in the lab.
AND last time I checked two <<<<< tons.
... well we'll have to move that node somewhere else on the tree of life... etc.)
And curiously this is the scientific process when new information becomes available. This happens in ALL science.
, it has been tested.
Not really. Common ancestry is mostly ad-hoc.
Repeating your fallacious opinion doesn't make it any more correct.
If it were ad hoc, then two different groups would arrive at two different conclusions almost every time. Clearly that does not happen.
Enjoy
Edited by RAZD, : proximity

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This message is a reply to:
 Message 246 by vaporwave, posted 12-26-2016 3:50 PM vaporwave has replied

Replies to this message:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 251 of 288 (796285)
12-28-2016 10:07 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
For any one of these supposed "trends" you show me I could a fossil sequence that is out of order. One of the more interesting examples is advanced tetrapod footprints appearing in rocks roughly 20 million years older than the 'fishapods' that were supposed to just be starting to develop proto-limbs to walk on.
You mean this?
quote:
Oldest Land-Walker Tracks Found--Pushes Back Evolution
An undetermined species of tetrapod (illustrated) created tracks in what's now a Polish quarry (bottom), a new study says.
The first vertebrates to walk the Earth emerged from the sea almost 20 million years earlier than previously thought, say scientists who have discovered footprints from an 8-foot-long (2.4-meter-long) prehistoric creature.
Discovered in an abandoned mountain quarry, the tracks suggest that tetrapods were traipsing the planet 18 million years earlier than previously indicated by the fossil record.
Dozens of the 395-million-year-old fossil footprints were recently discovered on a former marine tidal flat or lagoon in southeastern Poland (prehistoric time line).
The tracks are also ten million years older than the oldest known fossils of lobe-finned fishes called elpistostegids, which are widely considered to be transitional forms between fish and tetrapods.
The age of the newfound tracks suggest that "these transitional fish continued to exist alongside the tetrapods for quite some period of time," said Per Ahlberg, a paleontologist at Uppsala University in Sweden, who led the new research.
It's not so strange for one type of animal to live alongside its evolutionary successors, Ahlberg noted. Several feathered dinosaurs, for example, "continued to exist alongside the birds for millions of years."
Please note that this is ~18 million years older than previous tetrapod finds, not the transitional "fishapods" -- that difference is ~10 million years.
Curiously, that is not so much "out of order" as it is that the "order" (sequence) is not fully determined, because evidence is lacking.
Pointing to the strength of current phylogenies is irrelevant.
Pointing to small numbers of seeming anomalies out of thousands and thousands of non-anomalous phylogenies is irrelevant.
Evolution could have occurred an infinite number of ways, producing a near infinite number of potential phylogenies.
And your templates could have produced fire breathing flying dragons and an infinite number of fantasies. After all they produced over 99% of the beasts whose only record is the fossils they left behind ... were they designed\created just to fill voids in rocks?
However, reality cares not a whit for how evolution could occur, and that is irrelevant to what did occur. Fossils are the record of what did occur, and evolution with nested hierarchies explain the evidence better than any other theory or hypothesis.
Evolution does not mean that anything that could be imagined would occur, only what survives and reproduces and evolves from ancestors that provide the base for modification and adaptation. Evolution cannot create wings without adapting an existing structure and modifying it to suit.
If the traits of animals happened to be different than what we see today, then we'd simply have a different story of common descent.
Let me fix that for you:
If the traits of animals had evolved to be different than what we see today, then we'd simply have a different story of common descent.
Correct. And it would still show the patterns of evolution and nested hierarchies ... because the mechanisms and processes that cause these are well known, observed and documented, and no other process that has been suggested explains the evidence any where near as well.
For example in Pelycodus we see
This is a good example of cherry-picking data. Fossils do not typically follow such a trend, and even this one I bet is questionable.
No, it is an example of the fossil evidence available, one that shows the development of a nested hierarchy by common descent from ancestor populations.
Another example is foraminifera:
quote:
A Classic Tale of Transition
Drs. Tony Arnold (Ph.D., Harvard) and Bill Parker (Ph.D., Chicago) are the developers of what reportedly is the largest, most complete set of data ever compiled on the evolutionary history of an organism. The two scientists have painstakingly pieced together a virtually unbroken fossil record that shows in stunning detail how a single-celled marine organism has evolved during the past 66 million years. Apparently, it's the only fossil record known to science that has no obvious gaps -- no "missing links."
"It's all here -- a complete record," says Arnold. "There are other good examples, but this is by far the best. We're seeing the whole picture of how this organism has changed throughout most of its existence on Earth."
The pattern is exactly what Arnold and Parker have found in the forams. It is but one of a number of observations that the FSU team has made thus far about what arguably is nature's crowning achievement -- the act of speciation itself.
"We've literally seen hundreds of speciation events," Arnold added. "This allows us to check for patterns, to determine what exactly is going on. We can quickly tell whether something is a recurring phenomenon -- a pattern -- or whether it's just an anomaly.
That's 66 million years of continuous evolution documented in the fossil record and hundreds of speciation events that form nested hierarchies.
... This is a good example of cherry-picking data. Fossils do not typically follow such a trend, ...
This level of detail is not always available, but whenever the detailed evidence exists, it shows the same patterns of evolution and the formation of nested hierarchies from common ancestor populations.
So .. we have the evidence (fossils), motive (survival) means (evolution) and opportunity (proximity).
Enjoy
Edited by RAZD, : .

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This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has replied

Replies to this message:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM RAZD has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 263 of 288 (796371)
12-29-2016 10:47 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
So when fossil "transitions" lie in geologic order, then it is evidence for evolution and when the inferred transition is out of geological order then it is simply "not fully determined because evidence is lacking" ... seems convenient.
In this case we have two pieces of evidence -- the footprints and tiktaalik. That is hardly a plethora of evidence.
We also have evidence of transitional species existing long after their developed offspring began existing, so an overlap is not out of the ordinary. I could point to coelacanth existing today, 65 million years after first appearing in the fossil record. Does that make today's specimens out of order? Yes they are different species (coelacanth is a family level clade), but we also don't know if the same is true of tiktaalik.
Actually this wouldn't really bother me except evolutionists are constantly showing off cherry-picked examples of the former while concealing the latter, (providing they are not ignorant of it themselves.)
Or they are just presenting the evidence that is easiest to understand. Perhaps you could give us an example of evidence being concealed? Obviously tiktaalik and the footprints are not concealed.
But the evolutionists in this discussion seem quite concerned about what 'could' occur, since your arguments continually circle back to how a designer 'could' create life, and why you claim this weakens the argument from design.
No. That is not to say evolutionists are concerned at all about what 'could' occur, just that they are putting it in contrast to other concepts.
We could as easily talk about Lamarkism to evaluate what could occur vs what does occur. Lamarkism would not necessarily produce nested hierarchies.
All I'm doing is applying the same standard to common ancestry.
No, you are cherry picking a small number of unresolved cases and claiming that it throws the whole concept of common ancestry out the window. It doesn't.
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.
They are what we expect\predict from evolution; we see evidence in life today, in the DNA and in the fossil record of it happening. That is a test that validates the expectation\prediction.
We do NOT see non-nested hierarchies, such as feathers on bats or whales with gills, ... except in very limited cases of horizontal gene transfer between bacteria.
And if common ancestry could potentially explain trillions of different nested hierarchies, then how strong of a theory is it really that it can explain one of them?
I think you meant "can't explain one of them?"
As I said above:
No, you are cherry picking a small number of unresolved cases and claiming that it throws the whole concept of common ancestry out the window. It doesn't.
Still very strong, as in high confidence that it will continue to apply to those trillions of situations, because the inability to explain a certain small number of situations where not all the facts are known is quite different from having something that actually invalidates the concept of common ancestry. Any system that models evidence with >99.99% accuracy is considered very accurate.
In science we expect to see anomalies rather than wholesale compliance, because that's the way reality works. Usually they are sought out to see if some new idea can be developed (a new way to detect phylogenies in rapidly evolving species, more evidence around the dates of the footprints and tiktallik, etc) as this is where names are made.
It is said that the verbal sign of a new discovery is not "eureka" but "that's curious ... "
Enjoy
Edited by RAZD, : .
Edited by RAZD, : .

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