@GJDS @benkirk You are both out of line. Stop the personal jabs.
The remarks I made, go along with the abstract that I posted, which is from this paper:
Philosophy of science in an age of neo-Darwinian apologetics, Steve Fuller
It is available on academia.com (or .edu).
My remarks on universal common ancestor are from a paper that speculates on the topic - I do not have the time to hunt for it and I am sure a lit search can provide it to you.
My remarks are constantly twisted to obtain an irrational argument from some. If you find this paper (and if I happen to find it also), I would urge you to find any maths that would deal with the numerous postulated species in such a scheme.
Like this one?
A formal test of the theory of universal common ancestry
Douglas L. Theobald
Nature 465, 219–222 (13 May 2010) doi:10.1038/nature09014 Received 28 August 2009 Accepted 17 March 2010 Brief Communication Arising (December, 2010)
“Universal common ancestry (UCA) is a central pillar of modern evolutionary theory1. As first suggested by Darwin2, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past3, 4, 5, 6. The classic evidence for UCA, although massive, is largely restricted to ‘local’ common ancestry—for example, of specific phyla rather than the entirety of life—and has yet to fully integrate the recent advances from modern phylogenetics and probability theory.”
“Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing7, 8, 9, 10, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope1, 5, 8, 9, 11, 12, 13, 14, 15. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life11, 14, 15.”
" Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory5, 16, 17 to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous."
“Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.”
http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html#access
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This book specifically treats this article by Theobald:
The Mathematics of Life
By Ian Stewart
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But this is an article that opposes Theobald:
FYI-FTR: But, Wiki and Theobald’s 29+ evidences prove evolution is the best explanation of life and its branching tree pattern! — NOT
November 5, 2014 Posted by kairosfocus under Atheism, Cambrian explosion, Darwinist rhetorical tactics, Evolutionary biology, Functionally Specified Complex Information & Organization, FYI-FTR, ID Foundations, Origin Of Life, Science, worldview issues/foundations and society, UD’s Pro-Darwinism essay Challenge
Comments off
Darwin-ToL-Smithsonian400
The Tree of Life as presented by the Smithsonian
In recent exchanges in and around UD on origins and the tree of life, Theobald’s 29 evidences claims (and by implication the sort of summary presented by Wikipedia in its articles on Abiogenesis and Evolution) have come up. [NB: to carry forward discussions, I suggest here on. I intend to do a for reference in support of discussion here in this FTR post.]
That leads me to point out the case of the UD pro-darwinism essay challenge and the strange absence of and reluctance to provide a guest essay here at UD over the course of a full year, Sept/Oct 2012 – Sept/Oct 2013. The big issue seemed to be that in my challenge as explained, I required tackling the whole tree of life from its root in OOL on up (on grounds that this is the heart of the common origin of FSCO/I challenge).
[text truncated here; more at the link]
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I am trying to download the article in Nature - once I do I will read it with great interest.
EDIT Before I spend the time reading this paper, can you tell me if you have read it and have substantive comments to offer - I would hate to spend time that I need to spend on other work, just to get into another useless exchange.
Steve Fuller isn’t a scientist. He doesn’t even know what most 14-year-olds do: DNA, not protein, is the genetic material, as quoted and cited in my comment above. As a chemist, you should know how incredibly basic that is.
[quote=“GJDS, post:253, topic:35756”]
My remarks on universal common ancestor are from a paper that speculates on the topic - I do not have the time to hunt for it and I am sure a lit search can provide it to you.[/quote]
What terms would one use in that search to get the results down to the single paper that you read?
[quote]My remarks are constantly twisted to obtain an irrational argument from some. If you find this paper (and if I happen to find it also), I would urge you to find any maths that would deal with the numerous postulated species in such a scheme.
[/quote]What if the math is in other papers?
@GJDS, I have only had time to find the link. I’m not sure I can actually access the article. But perhaps there are some already here who can do have access and can read it promptly - - if they haven’t already read it!
Please consider my effort to find the link as a gesture of good will . 
I suggest that as moderator you ensure that remarks such as “any 14 year old knows…” be discouraged, especially when the remark is so outrageous as to constitute outright deceit. I have re-read the paper by Fuller, searched for the following “DNA” “protein” “genetic” “genetic material” and looked phrases that may provide some clue on what this person has in mind. None of my searches found anything to support his banal comment.
George (@gbrooks9) and George (@GJDS), and anyone else, I’ve acquired PDFs of the articles “A formal test of the theory of universal common ancestry” and “Philosophy of science in an age of neo-darwinin apologetics”. I’m not sure how much I’ll read, but happy to supply the library service 
Just send me a message with your email address and I will send the articles to you.
Consider it officially discouraged. Forbidden even.(And not just because I taught high school freshman for a number of years and I guarantee most people would be surprised by what they know and don’t know.) I thought about editing a bunch of posts last night, but I had other things to do. I’m trusting you all to raise the level of discourse without active babysitting, because I know you all know better. 
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If you scroll back up to comment 231 of this thread you will see the quote. It appears to be from the comment section rather than the article.
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Wow… talk about a brand new thread title!
“Does biology need the theory that all life shares a common ancestor?”
That phrase “all life” seems to be the controlling one in this situation. Is this really a fair question to be asking?
Isn’t this like asking: “Does Science really need the idea that the Universe is less than 14 billion years old?”
On first blush, I would have to answer “no”. So do we close up shop and go home now? Isn’t the point of all this to “Find out what is true” … rather than to find out what we can live without?
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To use an analogy, the theory of gravity does not need Mercury orbiting around the Sun. It just so happens that Mercury does orbit around the Sun. The same for universal common ancestry. If there were multiple origins of life that gave rise to unrelated groups of species then that would be part of the theory. As it turns out, all of the evidence points to a single universal common ancestor, so that is what the scientists conclude.[quote=“GJDS, post:241, topic:35756”]
I asked before, if anyone can show a direct connection between the genotype (and all such similarity in DNA) and the phenotype (the species we observe) and I have yet to find a straightforward answer.
[/quote]
There are plenty of association studies that link specific genotypes to specific phenotypes. For example, mutations in the MCR1 gene in humans correlates with skin color. Sickle cell traits are another perfect example. It does take a lot of work to directly link a phenotype to a specific genotype through study of function, so you won’t find info for every gene.[quote=“GJDS, post:241, topic:35756”]
One consequence of this
syndrome in the case of Neo-Darwinism is that the theory has become rife with
internal interpretive tensions, which philosophers have tolerated by loosening
their own criteria for a good scientific theory. This shift in philosophical
standards probably reflects the strong cultural standing of Neo-Darwinism.
Intelligent design theory, in its quest to achieve intellectual respectability as an
opponent to Neo-Darwinism, has somewhat mimicked its opponent by adopting
a conception of ‘intelligent designer’ just as open as that of the Neo-Darwinist
conception of ‘evolution’."
[/quote]
The problem is that there is a small minority among scientists who try to create controversy by purposefully muddying up what evolution means. They have little more than a semantic argument at the end of the day.
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Click the link, then scroll down to comment #60.
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I suggest that you ensure that what you put between quotation marks is what was actually written.
What was outrageous about me pointing out that Fuller doesn’t know the difference between protein and DNA (in a historical context that Fuller chose, no less) in response to your touting him as a philosopher of science?
Remarks on this forum may have some value if people took the time to read Fuller’s paper and deal with his reasoning - it is more than ironic that those who shout loudest about published material appear to be guilty of the very thing they accuse others. Scientists and philosophers have raised serious points that, for those interested, should require serious thinking.
Hi George -
I just read Fuller’s paper. It’s a hot mess, as we say in my region of the States.
Fuller was already vastly lagging in his reading of the biological literature at the time he wrote his essay. His only mention of mathematics in biology was molecular clock calculations, but at the time of his publication stochastic modeling and the calculation of phylogenies (nested hierarchies) from DNA sequences had been long practiced in the field. He is entirely unaware, it seems, of the burgeoning field of computational biology, which was quite advanced already at the time of his essay.
In addition, he characterizes various themes/mechanisms in evolutionary theory as discordant. This would be quite akin to stating that the field of chemistry is rife with contradiction because some chemists model theories of organic chemistry, while others model ionic bonds, while others model covalent bonds… You would rightly state about chemistry that those models do not contradict one another; well, neither do the various perspectives of evolution contradict one another. That said, any scientific domain will always have some controversies being worked out, of course, and biology is no exception.
In short, Fuller is a very poor source with regard to anything at all in the field of biology. I am not surprised that you have been critical of the lack of mathematics in biology, given that you have been relying on such an ill-informed source as Fuller. I know biology is not your field of expertise, so please do not think I am being harsh toward you personally. Fuller presented himself as having expertise, and you simply believed him. The fault lies with Fuller, not with you.
And yes, Fuller’s failure to understand the rudimentary facts about DNA (as cited by his comments to a blog post mentioned by @benkirk) illustrate how badly he understands biology.
I would also fault Fuller’s concluding remarks on intelligent design, but that would take this thread in an orthogonal direction, so I will refrain.
Grace and peace,
Chris Falter
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As for the Theobold paper (2010), here’s an interesting summary I found:
Theobald’s (2010) results show that the UCA [Univeral Common Ancestry] hypothesis is at least 102860 times more probable than the closest competing hypothesis and at least 106000 times more probable than the idea that humans are independent of all the domains of life.
A formal test of the theory of universal common ancestry article. Available from: https://www.researchgate.net/publication/282636358_A_formal_test_of_the_theory_of_universal_common_ancestry_article [accessed Jun 13, 2017].
Based on my reading of Theobold’s abstract and his follow-up paper, I find his Bayesian analysis to be scientifically compelling.
Grace and peace,
Chris Falter
The article that opposes Theobald’s conclusions does not challenge his mathematical analysis in any way, shape, or form. Instead, it’s a “greatest hits of ID” article, with an emphasis on irreducible complexity and the Cambrian explosion. As far as I can tell, the only reason Theobald’s work is cited is to make this run-of-the-mill pro-ID article show up in Google searches related to Theobald’s research.
Grace and peace,
Chris Falter
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