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Scientific Evidence for Universal Common Descent

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tas8831

Well-Known Member
. And of course, the idea that Pluto was definitely (and I mean definitely and certainly) considered a planet until recently is discarded now, isn't it?
Did you get that from one of the "10 lies you were taught in high school" click bait articles?

Amazingly, with technological advances, Pluto's size and 'behavior' could be more accurately assessed, and it is now considered to be a "dwarf planet".

Of course, at one point the earth was was definitely (and I mean definitely and certainly) considered to be 6000 years old, until such silliness was discarded by facts and evidence. Well, at least by the educated and sensible.
 
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tas8831

Well-Known Member
No you didn't.

In post #1479, you cited the Larget et al. paper as an example of "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

In post #1491 I asked you to specify where you saw anything like that in the paper.

In post #1497 you quoted a couple of introductory sentences from the abstract, with no explanation of how they constituted "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".

In post #1511 I let you know that your post 1497 made no sense to me.

In post #1521 you responded "That’s okay. I want to say again that I’m grateful for your thoughtful and generous responses to my questions and comments. This turned out to be a lot more educational and fun for me than I would have thought."

And that's where it ended.

So I'm again asking you to explain how the Larget et al. paper is an example of "an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship".
Trolls gotta troll.
 

tas8831

Well-Known Member
See? That's what I'm saying. From the article, "And the institute believes that the 1,000 plus scientists who have signed the statement represent the tip of a massive iceberg. “While that number surely represents a scientific minority, it also no doubt vastly understates the number of Darwin-doubting PhD scientists,” wrote Discovery Institute Senior Fellow David Klinghoffer at Evolution News."
So who is lying here?
Among the signatories - "scientists" - there are lawyers, orthodontists, a guy from Moscow that believes water has memory, a nutritionist, engineers, mathematicians, etc. Very few biologists/biochemists. Virtually none that do any relevant research. Several that got degrees for the sole purpose of making their creationist claims seem more legitimate (like Jon Wells). Creationists, of one sort or another, all.
And Stanley Salthe, the one (supposed) non-creationist.
And then there were the several that signed on not knowing what the political goals of the DI are (Christian Reconstructionism).

And then there is the Project Steve List - a far more precise statement regarding the validity of evolution, signed only by people with the name "Steve" or a derivative thereof, which numbers ~1400, more than half of whom are biologists, and includes 2 Nobel Laureates.

And this David Klinghoffer - what kind of "fellow" is he? What is his scientific background?
Weird - it is apparently impossible to find out. The DI's links for him have no bio available. Wiki just says he 'attended Brown University in the 1980s.'
Best I could find was:

Education: Brown University, A.B. (magna cum laude), 1987; also attended the Jewish Theological Seminary.

Don;lt know what "A.B." means, but I am assuming that it is not relevant to his ranting about evolution.
 

tas8831

Well-Known Member
@Polymath257 @Jose Fly @Dan From Smithville I’m not a person who could have any influence on any decision making or policy making even if I wanted to, and I won’t be trying. The way it looks to me could be all wrong, but all you’re doing is confirming it for me. I’ll consider what could possibly change my mind about it, and look for that.


Cool belief system you operate under - almost identical to your buddy usfan.

You spew an unfounded, condescending, accusatory assertion.
After some tooth-pulling, you finally provide 'evidence' for you assertion.
2 or 3 people explain that you were wrong - people that, unlike you, by your own admission, have backgrounds in the relevant sciences.
You reject the corrections, and double-down on your unwarranted, unsupported, ignorant accusations.

Troll.
 

tas8831

Well-Known Member
It depends, doesn't it?
Ok - what about these claims by the originator of this thread:

1. there is a 'marker' in the human mtGenome called the "Eve gene"
2. only humans have it
3. only female humans have it

1. It is shown - in the very link that the thread originator later used to 'prove' a related point - that "eve gene" is just a simpleton's way to refer to the whole mitochondrial genome.
2. all eukaryotes have mitochondria.
3. all male animals have mitochondrial genomes.

The thread originator sort of tried to imply that he 'knew it all along', yet has still mentioned this fake "Eve gene" and has actively engaged in a campaign of dodging and whining to avoid the harsh truth about his position.

Shall those false claims - now essentially being lied about - be 'respected'?
 

tas8831

Well-Known Member
Yes, and his contract was not renewed. The university would probably have won in court. The only thing going against them was the comment of one employee of the university about not allowing him to spread his religious nonsense. They were probably worried by that a bit. Not by the fact that what he was spread was religious nonsense, but that the statement of the one university employee could look prejudicial.
Most annoying how right-wing/religious media describe it as he "won" in court. Even more annoying is the fact that these same sorts of outlets see settlements when their heroes are the defendants (e.g., Trump's many civil suits) as victories.


Can't wait - will he mention Caroline Crocker next? LOL!
 
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tas8831

Well-Known Member
In fact, when interviewed after signing the statement, many of the scientists who signed it revealed that they did accept common descent and evolutionary theory.
SOURCE: Doubting Darwinism through Creative License

On top of this, many of the signatories weren't actually scientists or didn't have PhD's in relevant fields.
SOURCE: AAUP: Wedging Creationism into the Academy

The petition is now widely considered little more than a dishonest joke.
By the educated and honest, yes.

That is why the DI and sundry creationists still refer to it and defend it. They have a worldview to 'defend' with their dissembling and distortions. Seems that such a "true" worldview should be able to stand without such shenanigans.
 

tas8831

Well-Known Member
There are other points, too, that should be examined with closer scrutiny. The mitochondrial clock, the mt-MRCA, the e.coli study, the canidae study.. all of these have significant facts that have major implications for this theory of origins.
If you say so, Dr.Evegene...
I've already debunked your Canidae study:

part 1
1. The ancestor of wolves, coyotes, dogs, and other canidae is unknown, appears suddenly, and contained all the genetic information for each haplotype. the origin of the huge morphological diversity that led Darwin to his speculation remains largely unknown
Your interpretation does not follow from the quote (nor the context).

Here is the quote in context:

In The Origin of Species, Darwin (1859) suggested that “several wild species of Canidae have been tamed and that their blood, in some cases mingled together, flows in the veins of our domestic [dog] breeds”. We now know that dogs (Canis familiaris) are entirely derived from the domestication of wolves (Canis lupus) (Vilà et al. 1997); however, the origin of the huge morphological diversity that led Darwin to his speculation remains largely unknown (Sutter and Ostrander 2004). The domestic dog is the most phenotypically diverse mammal on earth. The large differences in size, conformation, behavior, and physiology between dog breeds exceed the differences among species in the dog family, Canidae (Coppinger and Coppinger 2001; Wayne 2001). Recent studies show that the origin of most dog breeds may derive from very recent selective breeding practices and are probably <200 yr old (Parker et al. 2004). However, selection acts upon existing variability. It is remarkable that the potential for such large diversification existed in the ancestral wolf population from where the domestication process was initiated. Furthermore, the time since domestication (at least 14,000 yr; Vilà et al. 1997; Sablin and Khlopachev 2002; Savolainen et al. 2002) seems insufficient to generate substantial additional genetic diversity. What is the origin of this diversity? We hypothesize that changes in the living conditions of dogs as a result of domestication resulted in the release of selective constraint allowing a faster accumulation of functional (non-silent) genetic diversity in a large array of genes.​

Further, nothing in the paper indicates that the origins of wolves, etc., are "unknown." That is your editorializing.

This more recent paper (2017) indicates:

Abstract
There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development resolving long standing questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and by inference, transfer of trait and disease alleles among dog breeds.

and

Previous studies have addressed the genomic makeup of a limited number of breeds, demonstrating that dogs from the same breed share common alleles and can be grouped using measures of population structure (Irion et al., 2003; Koskinen, 2003; Parker et al., 2004), and breeds that possess similar form and function often share similar allelic patterns (Parker et al., 2004; Parker et al., 2007; Vonholdt et al., 2010). However, none of these studies have effectively accounted for the variety of mechanisms through which modern breeds may have developed, such as geographic separation and immigration; the role of hybridization in the history of the breeds; and the time-line of the formation of breeds. In this study we overcome these barriers by presenting an expansive dataset including pure-breeds sampled from multiple sections of the globe and genotyped on a dense scale. By applying both phylogenetic methods as well as a genome-wide analysis of recent haplotype sharing, we have unraveled common population confounders for many breeds leading us to propose a two-step process of breed creation beginning with ancient separation by functional employment followed by recent selection for physical attributes. These data and analyses provide a basis for understanding which and why numerous, sometimes deleterious, mutations are shared across seemingly unrelated breeds.​


And regarding the origin of the Canidae ("The ancestor of wolves, coyotes, dogs, and other canidae is unknown, appears suddenly"), well, you are way wrong:

Carnivora

Man's Best Friend
"Domestic dogs, wild dogs, and wolves all belong to the Family Canidae, which also contains jackals, coyotes, and foxes. Canidae is contained within the group caniformia which is contained within the Order Carnivora, one of the eighteen current groups of Eutherians, or placental mammals. A full list of the groups contained in Canidae is provided below.

Within the Canidae are 14 groups, or genera. Contained within those 14 genera are at least 34 species and two subspecies (a chart showing all members in the Canidae is provided below). The genus Canis contains dogs, jackals, and wolves. The gray wolf, Canis lupus, is among 7 species of canids and also related to two subspecies, Canis lupus dingo and Canis lupus familiaris, which are known commonly as the dingo and the domestic dog, respectively."

Some relevant references (follow link for refs)​

Parts 2 and 3 followed - if the reader is interested in seeing usfan's Canidae claims refuted in toto, follow the link to part 1 and scroll down.



Then ask him why he keeps making the same claims re: Canidae when his take on the paper has been refuted and supplanted with a more recent paper using more data.

I'm predicting that you will be called a heckler as a pretense for ignoring you, also.
 

tas8831

Well-Known Member
A deliberate, systematic examination is what i have called for, and examining each point thoroughly is appropriate.

If you have examined evolution as deliberately and systematically as you read the Bradshaw Foundation website wherein you got your "Eve gene" information*, then I am not surprised that your understanding of evolution is on par with a hyperactive 8th grader.



*the site clearly explains that there is no such thing as an "Eve gene", and that this term is just a "popular" [sic] term referring to the entire mitochondrial genome. This was in the 2nd paragraph on the page that usfan linked to to 'prove' that there is a thing called the Eve gene, that only humans had it, and that it was a 'flag' that proved humans are unique.
 

Jim

Nets of Wonder
That's a very serious accusation. Do you have any evidence that Larget et al. dishonestly manipulated the data?
Did you read the blog post by one of the authors, about how and why the study was done? It includes some correspondence with the editors of the Journal “Evolution.” Here is part of that correspondence:
It has been my understanding throughout that your group's development of tests for common ancestry is motivated by the need for such tests to address hypotheses of current scientific interest, of which special creation is not one. This response from you indicates otherwise, and this makes me think I misunderstood. If refuting the doctrine of special creation is the sole or even a primary motivation for this development, as your email suggests, then I seriously question whether it should appear in Evolution.
The paper was published in a peer-reviewed journal.
Where can I see that it was published in a peer-reviewed journal? Are you saying that the paper itself was peer reviewed? Where can I see that it was?
They specifically accounted for similarity = common descent (hint: that's what the phrase "functional constraints" refers to).
Where can I see that in the criticisms, “functional constraints” refers to similarity = common descent?
 

Jose Fly

Fisker of men
Did you read the blog post by one of the authors, about how and why the study was done?
Yes, it's how I came across the paper in the first place.

It includes some correspondence with the editors of the Journal “Evolution.” Here is part of that correspondence:

It has been my understanding throughout that your group's development of tests for common ancestry is motivated by the need for such tests to address hypotheses of current scientific interest, of which special creation is not one. This response from you indicates otherwise, and this makes me think I misunderstood. If refuting the doctrine of special creation is the sole or even a primary motivation for this development, as your email suggests, then I seriously question whether it should appear in Evolution.

Okay.

Where can I see that it was published in a peer-reviewed journal? Are you saying that the paper itself was peer reviewed? Where can I see that it was?
Dude, come on, seriously? The paper was published in the journal "Evolution". I mean....that's what the blog post you just quoted from is talking about! Sheesh....:facepalm:

Where can I see that in the criticisms, “functional constraints” refers to similarity = common descent?
Read the paper. If you're truly interested in it, take some time to actually read through it at least twice.
 

Jose Fly

Fisker of men
Are you saying that the authors did quote from peer reviews? Can you give an example?
No, I'm noting that the paper obviously was peer-reviewed (since it's published in a peer-reviewed journal....duh). And it's not at all common practice for a paper to include "quotes from peer reviewers" in the paper. That's why usfan's comment was ignorant nonsense.
 

Jim

Nets of Wonder
The paper was published in the journal "Evolution".
I didn’t see anything in the blog post saying that it was published in “Evolution.” I searched on the Web site of “Evolution,” and didn’t find any reference to that article.
 

Jim

Nets of Wonder
No, I'm noting that the paper obviously was peer-reviewed (since it's published in a peer-reviewed journal....duh). And it's not at all common practice for a paper to include "quotes from peer reviewers" in the paper. That's why usfan's comment was ignorant nonsense.
I didn’t find any reference to the paper on the “Evolution” website. The only place where I’ve been able to find the paper is on the bioRxiv site, where it says “This article is a preprint and has not been peer-reviewed.”
 

Jim

Nets of Wonder
In a post addressed to @usfan , I said:
The more I read about evolution research, the more that some of it looks like an endless, desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship.
Jose asked:
Where specifically do you see that?
The easiest example for me to find was:
That link was to the paper posted on the bioRxiv website, not to the revised paper Statistical evidence for common ancestry: Application to primates on the “Revolution” website.
So where exactly in that paper do you see "a desperate search for evidence for a foregone conclusion, and to find ways to plug holes in a sinking ship"?
I posted this from the abstract, with some words italicized which here are bolded:
While there is no doubt among evolutionary biologists that all living species, or merely all living species within a particular group (e.g., animals), share descent from a common ancestor, formal statistical methods for evaluating common ancestry from aligned DNA sequence data have received criticism ... We present a new statistical framework to test separate ancestry versus common ancestry that avoids this pitfall.
The words of the authors that I bolded, in their own description of what they did, are what led me to think that it was not done honestly and responsibly. Now the blog post by the lead author, describing how and why the research was done, has confirmed that suspicion for me.

What I said originally about the study was based on the abstract at the bioRxiv website, and not the abstract at the “Revolution” website, where it has been re-written, without the words in the first abstract that aroused my suspicions.
 
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