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Author Topic:   Extent of Mutational Capability
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(2)
Message 91 of 279 (793243)
10-24-2016 2:10 PM
Reply to: Message 82 by RAZD
10-24-2016 11:06 AM


Re: Parentless Clades
Cladistics does not make that assumption, rather it is evidence that shows whether or not clades have ancestors. Thus whether or not there is a previous ancestor is a testable hypothesis, ie a scientific theory, not an assumption.
I have to correct you on this, RAZD; someone else also said something similar a few messages back, but it is not really correct. Cladistic analyses have three basic assumptions:
1. The groups being studied are related by descent from a common ancestor
2. The pattern of cladogenesis is bifurcating
3. Changes in character state occur in lineages over time
See: http://www.ucmp.berkeley.edu/clad/clad1.html
A cladistic analysis will always create a bifurcating tree where all organism being studied are related. So cladistics does not test to determine IF they are related but rather HOW they are related. This cladogram is then the hypothesis as to how the organisms are related and possibly how a particular character has evolved.
ABE: The congruence of independent cladograms is the strongest evidence for common ancestry /ABE
I like your definition of a "kind" though, which would be a clade without an ancestor. I don't think cladistics would be able to directly determine if a clade did not have an ancestor, but we could hypothesize about relationships between unrelated clades and use distantly related clades to test those hypotheses and then see if we see those types of patterns when testing larger groups.
I haven't given the idea of looking for clades without an ancestor much thought, though... understandably. It seems as if there would be a obvious signature of "kinds," but no one is really looking for it. I would need to give it some more thought as to what that signature would actually look like. But as far as I know, there is no test to determine IF a group has an ancestor, only what that ancestor might be.
ABE: Perhaps clades without an ancestor would not provide consistent results through different phylogenic reconstructions, at least in relation to other groups. Although I don't know that this would be a slam dunk. /ABE
HBD
Edited by herebedragons, : Additional thoughts
Edited by herebedragons, : No reason given.

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 82 by RAZD, posted 10-24-2016 11:06 AM RAZD has replied

Replies to this message:
 Message 93 by PaulK, posted 10-24-2016 2:41 PM herebedragons has replied
 Message 95 by Taq, posted 10-24-2016 3:09 PM herebedragons has replied
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 92 of 279 (793244)
10-24-2016 2:33 PM
Reply to: Message 89 by Taq
10-24-2016 1:33 PM


Re: Proposition: Another Angle
Quite so. And one should emphasize that not only does that mean that humans are closer to chimps than they are to anything else (after all, we have to be closest to something) but also chimps are closer to humans than anything else (e.g. gorillas).

This message is a reply to:
 Message 89 by Taq, posted 10-24-2016 1:33 PM Taq has replied

Replies to this message:
 Message 94 by Taq, posted 10-24-2016 3:03 PM Dr Adequate has replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.3


Message 93 of 279 (793245)
10-24-2016 2:41 PM
Reply to: Message 91 by herebedragons
10-24-2016 2:10 PM


Re: Parentless Clades
I think that to call common ancestry an assumption is at best an oversimplification. For a start, isn't the use of outgroups a test of that assumption ? And on a less formal level, why should cladistics produce a nested hierarchy if it is dealing with disjoint groups ? And surely there are characters - not to mention the genetic evidence - which are naturally explained in terms of common descent.

This message is a reply to:
 Message 91 by herebedragons, posted 10-24-2016 2:10 PM herebedragons has replied

Replies to this message:
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 Message 129 by herebedragons, posted 10-29-2016 10:37 AM PaulK has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(1)
Message 94 of 279 (793247)
10-24-2016 3:03 PM
Reply to: Message 92 by Dr Adequate
10-24-2016 2:33 PM


Re: Proposition: Another Angle
Dr Adequate writes:
Quite so. And one should emphasize that not only does that mean that humans are closer to chimps than they are to anything else (after all, we have to be closest to something) but also chimps are closer to humans than anything else (e.g. gorillas).
Here is the thing. We don't have to be closer to one species (as determined by statistical significance). As a lineage changes over time it does not become more like another lineage over time. If humans and apes had a separate common ancestor then humans should be diverging by the same amount as compared to all other ape species. What we should see is the same genetic distance between humans and all other ape species.
"The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity."
The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates - PMC
The only reason that humans should be more like one ape species than another is if humans share a more recent common ancestor with one ape species, as compared to all other ape species.
In the ape phylogeny illustrated in the previous post, the genetic distance between orangutans and gorillas is the same as the genetic distance between orangutans and humans. However, gorillas and humans are closer than gorillas and orangutans. It is this pattern of differences and equidistance that allows us to construct phylogenies and evidence shared ancestry.
It is actually fun to play around with genetic equidistance at Homologene. For example, we can look at cytochrome c:
HomoloGene - NCBI
If you click on the "Show Pairwise Alignment Scores" on the left hand side of the page, you get this comparison between model organisms:
HomoloGene - NCBI
For the DNA results you get:
Human v. Mouse: 90.5%
Human v. Chicken: 81.6%
Mouse v. Chicken: 81.9%
You get nearly the same distance between mouse and chicken as you see between human and chicken, exactly what you should see if evolution and common ancestry are true.
I
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 92 by Dr Adequate, posted 10-24-2016 2:33 PM Dr Adequate has replied

Replies to this message:
 Message 97 by Dr Adequate, posted 10-24-2016 4:18 PM Taq has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 95 of 279 (793248)
10-24-2016 3:09 PM
Reply to: Message 91 by herebedragons
10-24-2016 2:10 PM


Re: Parentless Clades
herebedragons writes:
I have to correct you on this, RAZD; someone else also said something similar a few messages back, but it is not really correct. Cladistic analyses have three basic assumptions:
1. The groups being studied are related by descent from a common ancestor
2. The pattern of cladogenesis is bifurcating
3. Changes in character state occur in lineages over time
See: Introduction to Cladistics
A cladistic analysis will always create a bifurcating tree where all organism being studied are related. So cladistics does not test to determine IF they are related but rather HOW they are related. This cladogram is then the hypothesis as to how the organisms are related and possibly how a particular character has evolved.
That is simply false. Do you have to assume the defendant is guilty in order to do a DNA fingerprinting test? Of course not. Cladistics analysis is no different. If there are many trees supported by the data then you will get a low statistical score from cladistics methods. Only real common ancestry (or highly improbable chance processes) produces objective and statistically significant results when using these methods.
"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). "
29+ Evidences for Macroevolution: Part 1
Cladistic analysis is a test for the hypothesis that species share a common ancestor, just as a DNA fingerprinting method is used to test they hypothesis of guilt.

This message is a reply to:
 Message 91 by herebedragons, posted 10-24-2016 2:10 PM herebedragons has replied

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 96 of 279 (793249)
10-24-2016 3:13 PM
Reply to: Message 93 by PaulK
10-24-2016 2:41 PM


Re: Parentless Clades
PaulK writes:
I think that to call common ancestry an assumption is at best an oversimplification. For a start, isn't the use of outgroups a test of that assumption ?
Absolutely, as discussed in the post above.
And on a less formal level, why should cladistics produce a nested hierarchy if it is dealing with disjoint groups ? And surely there are characters - not to mention the genetic evidence - which are naturally explained in terms of common descent.
It is a trivial matter to organize any group of objects or species in to a clade. The test is how many possible trees are there, and how well supported are they.
For example, we could organize automobiles into a clade. However, there are many, many possible trees that are all equal. Do we order them by make? By model? By number of cylinders? By drive train? There are billions of possible trees when organizing automobiles, all equally supported. Not so with life.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 97 of 279 (793253)
10-24-2016 4:18 PM
Reply to: Message 94 by Taq
10-24-2016 3:03 PM


Re: Proposition: Another Angle
Here is the thing. We don't have to be closer to one species ...
It's true that we don't have to be closest to one species, but we do have to be closest to something, be it a genus, a family, or whatever. (Aren't chimps in fact a genus, what with the bonobos?)
So you kind of miss my point, which is that the theory of evolution implies that because of the branching nature of evolution, such relationships should be reciprocal. If we are significantly closer to chimps than we are to anything else, then the chimps should be significantly closer to us than to anything else.
It's true that we can imagine a phylogeny where the split between humans and the other apes was the oldest and deepest, and we would be equally close to all of them, but given that we have closest relatives in the chimps, we must also be the chimps' closest relatives: and that is a special prediction of the theory of evolution.

This message is a reply to:
 Message 94 by Taq, posted 10-24-2016 3:03 PM Taq has replied

Replies to this message:
 Message 98 by Taq, posted 10-24-2016 4:23 PM Dr Adequate has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 98 of 279 (793254)
10-24-2016 4:23 PM
Reply to: Message 97 by Dr Adequate
10-24-2016 4:18 PM


Re: Proposition: Another Angle
Dr Adequate writes:
It's true that we don't have to be closest to one species, but we do have to be closest to something, be it a genus, a family, or whatever. (Aren't chimps in fact a genus, what with the bonobos?)
So you kind of miss my point, which is that the theory of evolution implies that because of the branching nature of evolution, such relationships should be reciprocal. If we are significantly closer to chimps than we are to anything else, then the chimps should be significantly closer to us than to anything else.
Your first paragraph holds the seeds of falsification for your second paragraph. If we consider Pan paniscus and Pan troglodytes as separate species then your second paragraph is false. The closest species to humans is chimps. However, the closest species to chimps is bonobos. It isn't reciprocal.

This message is a reply to:
 Message 97 by Dr Adequate, posted 10-24-2016 4:18 PM Dr Adequate has replied

Replies to this message:
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 99 of 279 (793271)
10-24-2016 7:25 PM
Reply to: Message 98 by Taq
10-24-2016 4:23 PM


Re: Proposition: Another Angle
Your first paragraph holds the seeds of falsification for your second paragraph. If we consider Pan paniscus and Pan troglodytes as separate species then your second paragraph is false. The closest species to humans is chimps.
And bonobos. And the thing we are closest to is the genus Pan, not one particular species in it.

This message is a reply to:
 Message 98 by Taq, posted 10-24-2016 4:23 PM Taq has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 100 of 279 (793276)
10-24-2016 9:46 PM
Reply to: Message 98 by Taq
10-24-2016 4:23 PM


Clades
Formally: for any living organisms belonging to a clade X there will be a smallest distance to living organisms outside of that clade. Those living organisms which are (approximately, not to the very last base of DNA) that distance from X will also constitute all the living members of a clade (prediction #1) which we may call the "sister clade" of X. Then (prediction #2) the relationship of being a sister clade will be symmetric: if Y is the sister clade of X then X is the sister clade of Y.
(So for example Pan troglodytes is the sister clade of Pan paniscus, and vice versa; but Homo sapiens is the sister clade of the genus Pan and vice versa.)
Now, there's no reason why this should be so if not for evolution, and it seems to me that it is this sort of relationship that makes molecular phylogeny really convincing. If (for example) you tell a creationist that birds are closer to crocodilians than to anything else, then he might with some justice reply that they have to be closer to something than anything else. But if you add that also crocodilians are closer to birds than they are to anything else, closer than they are to lizards or Komodo dragons or what-have-you, then this is a rather more remarkable fact and harder to shrug off.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

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 Message 98 by Taq, posted 10-24-2016 4:23 PM Taq has not replied

Replies to this message:
 Message 104 by RAZD, posted 10-25-2016 7:42 AM Dr Adequate has replied

  
dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 101 of 279 (793281)
10-25-2016 1:37 AM
Reply to: Message 54 by CRR
10-21-2016 8:51 PM


Re: What is a "kind"?
From Message 28:
CRR writes:
Indeed there is considerable variation possible within the dog kind. Similarly from hybrids we can infer that all cats, from tabby to tiger, are all part of the cat kind. However we have never observed evolution from one kind into another.
Looks suspiciously like you are arguing that your idea of "evolution" requires that at some point a dog would have to "evolve" into a cat, or vice versa. But just to be sure, we ask you were talking about and specifically what you meant by "kind". Eventually, you finally told us in Message 54:
CRR writes:
The definition I favour is "those animals/plants that could interbreed immediately following creation". There has been much speciation and differentiation since then and it is often difficult to precisely define boundaries between kinds. For example there is good evidence from hybridization within the cats that all from tabby to tiger are one kind. However further research could show differently; that the big cats are separate from the other cats.
Uh, OK. Three days and five hours before you posted that, I posted in Message 9:
DWise1 writes:
But it also proves macroevolution. In the "basic canid kind", a lot of canids, especially the wolf-like ones, are very compatible genetically and can freely interbreed. However, two types of jackel cannot. And other canids, such as South American canids, true foxes, bat-eared foxes, or raccoon dogs, also cannot interbreed with wolf-like canids. True reproductive barriers had evolved within the "basic canid kind." Macroevolution happened! See https://en.wikipedia.org/...id_hybrid#Genetic_considerations.
The same holds true of the "basic felid kind" -- see felid hybrid. That "baramin" consists of two branches: Pantherinae (tiger, lion, jaguar, leopard, snow leopard and clouded leopards) and Felinae (including all the non-pantherine cats). A lot of hybridization can occur within the Pantherinae branch and a lot within the Felinae branch, but none across the genetic divide between the two branches. Yet again, true genetic reproductive barriers evolved with a "basic created kind". Macroevolution happened!
Tabby to Lion hybrids? Where? Tabby? That is all within Felinae, but does not cross over into Pantherinae. From Leo? Across Pantherinae, but not into Felinae. All within the same "basic created kind."
What about the "basic worm kind"? What about the "basic insect kind"? What about the "basic fish kind"? What about the "basic bird kind"? Genetically-based reproductive barriers all over the place.
And among hybrids, what about the different kinds of hybrids? What about fertile hybrids and infertile hybrids? What's the difference? Why should there be a difference?
Evolution answers those questions. Your misrepresentation of evolution does not.

BTW:
Using a "quote-block" just to separate other information from this forum-usage message:
quote:
BTW, CRR (and Greg, too), in order to see how we perform our mark-up magic, simply go to the applicable message and click on the peek button. That will open a window that displays the raw marked-up text of the message. There is also a help page somewhere on this site which gives a more complete explanation of the mark-up features, but it's been so long that I forget how to find it again. Also, for the mid=..., look at the (exempli gratia) "Message 54 of 100" and right after it you will see a dim "(793144)". That is the message ID, which is what I used in the mid=793144. There is also an analogous tid=19287 for inserting topic names and links. Look in your web browser's URL for t=19287 to get the topic's ID.
To play with any of this, go to any message and click a reply button and write your "reply". At any point, click on the Preview button to see what your "reply" would look like. As long as you do not click on the Submit Reply button, your "reply" will not be sent. Then simply close that tab in your browser (or the browser itself) and your practice piece will go away.
The very basic syntax is very similar to HTML, only with square brackets instead of angle brackets. And some of the keywords are different. It should not be hard to work with once you have acquainted yourself with the basics.
Oh, and we can also use HTML, like with the HR I did above. Though sometimes HTML can "go stupid" here, such as usually happens to me with HTML tables.

This message is a reply to:
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dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 102 of 279 (793282)
10-25-2016 2:04 AM
Reply to: Message 48 by Gregory Rogers
10-21-2016 11:31 AM


Re: Greg, Please Don't Give Up Yet!
Waiting for answers to your questions is not a reason for refraining from participation.
My own religious orientation is Unitarian-Universalist (UUs). A buzz-word we hear often is "To question is the answer." If we were the KKK, people would wake up to find a burning question mark on their front yard. Our dual UU history is filled with many progressives who have all supported our modern world, without whom we would have been entirely and infinitely worse people. Here's a hint: Twilight Zone's Rod Serling was a Unitarian-Univeralist -- just where did you think his morality stories came from?.
A buzz-word slogan from UU is, "To question is the answer." Remember that burning question mark on your front yawn? As I understand it, that slogan came from the Vietnam War and was a call for everybody to question the Establishment. And yet that basic question applies to all theology. Since all theology is fallible Man-made ideas.

This message is a reply to:
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Pressie
Member
Posts: 2103
From: Pretoria, SA
Joined: 06-18-2010


Message 103 of 279 (793286)
10-25-2016 6:52 AM
Reply to: Message 48 by Gregory Rogers
10-21-2016 11:31 AM


Re: Greg, Please Don't Give Up Yet!
Gregory Rogers writes:
....although, by now I certainly have my answer, at least from a Darwinist perspective....
What the heck is a Darwinist perspective on DNA? Did you make it up?

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 104 of 279 (793292)
10-25-2016 7:42 AM
Reply to: Message 100 by Dr Adequate
10-24-2016 9:46 PM


Re: Clades
(So for example Pan troglodytes is the sister clade of Pan paniscus, and vice versa; but Homo sapiens is the sister clade of the genus Pan and vice versa.)
You can also throw Homo neanderthalus in the mix as sister species in clade Homo, closer to H.sapiens than the Pan clade.
Enjoy

we are limited in our ability to understand
by our ability to understand
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This message is a reply to:
 Message 100 by Dr Adequate, posted 10-24-2016 9:46 PM Dr Adequate has replied

Replies to this message:
 Message 108 by Tangle, posted 10-25-2016 10:45 AM RAZD 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


Message 105 of 279 (793294)
10-25-2016 8:07 AM
Reply to: Message 48 by Gregory Rogers
10-21-2016 11:31 AM


the ID/Creationist view ... sort of ...
In short, apart from rebuttals to existing posts, at this stage I would like to hear the ID/Creationist view on the extent and 'elasticity' of genetic mutations. If not, however, then perhaps this thread can suffer the 'coup de grace'; and I will duly go on to my next question in a new thread.
Well I can't answer for Christian IDologist, but I can answer as a Deist (the original ID faith): I see the universe as created to evolve life, and we just happen to be a part of that ongoing process. Learning how it works via science is a way to understand it.
... I was hoping for a more 'iron sharpens iron' experience, where posts could be tested from both sides.
Do we have to choose sides to investigate the inner workings of the universe and life as we know it? Surely what we are interested is the validity of the knowledge more than whether or not it fits a religious dogma or someone's opinion.
The "iron" to test such beliefs and opinions against is the empirical evidence that either supports it, is neutral to it, or invalidates it.
... the extent and 'elasticity' of genetic mutations. ...
What the evidence shows is that there does not appear to be any barrier to mutations, other than what survives and reproduces from generation to generation, and that given the accumulation of mutations over time through various selection pressures changes to species does occur, new species arise and old species become extinct.
Our world and the diversity of life currently on it is but a snap-shot of an on-going process that will continue, with results we cannot imagine.
Enjoy

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

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