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Scientific Evidence for Universal Common Descent

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wellwisher

Well-Known Member
Since this statistical analysis of monkey/human amino acid sequences seems to be such 'compelling evidence!', for common descent devotees, I'll repeat a few points, if anyone wishes to rebut them in a systematic manner.

The Statistical based sciences have a major conceptual problem. A statistical analysis is a powerful mathematical approach. What makes it powerful is the same basic method can be applied to almost anything, and therefore works apart from the unique details of the application.

For example, if you were doing quality control on a complex machine, with a lot of variables, you would measure the input and outputs, and you can predict trends. It is not necessary to know how the complex machine works. You could employ a mathematician, who is not necessarily a mechanical engineer. The machine is placed in a black box by the mathematician. The value of the black box is this same basic math analysis can be used, by a mathematician on any machine, since the math approach is not fundamentally dependent on any particular machine theory.

The black box approach also means the math results exist independent of any theory use to explain the operation inside the black box. In other words, if my theory was the machine's black box function is based on the squirrels who run the treadmill that drives the machine, and/or the worms that crawl in the circuitry to make connections, the math and black box will still produce the same results.

Many aspects of Science has fooled itself into believing theory can be proven by statistical methods, even though the statistical methods can produce the same results independent of the theory of the black box. I am not anti science but anti-scam science.

I remember doing a development project which had political consequences for upper level management; good and/or bad. I am a rationalist and had invented and defined the science needed for an emergency process, and was 99% confident of a successful field test. Management was a little nervous since I did this so quickly. They decided to hire a statistician to parallel me. He would give them regulatory wiggle room if the worse case scenario was to happen. I did not need him, but had no choice.

I was surprised that my assigned mathematician did not need to know the exact chemical process but could nevertheless set up his math model around my process and black box the rest. He was operating independent of my theory. In the end, the process was 100% successful, with the statistical results similar, even though done independently of my reasoning and working theory.

That experience has stuck with me and recently made me realize how easy it would be to create theory illusions, using statistical results, and the black box. Irrational theory could work just as well as rational theory since statistics does not care what is in the black box. This approach is done during political polling season, and appears to be done even in modern science.

I can accept the basics of evolution, but the statistical approach makes me suspect of many of the assumptions; black box theory is not needed by statistics. However, if you use prestige to push a theory and attach this to sound statistical results, you can do a magic trick.

For example, nothing in life, down to the smallest scale, will work without water, nor can water be replaced by any other solvent. This makes water as important as the organics of life, since neither work without the other. Yet the black box theory of biology does not make water and organics co-partners. It does not have to, since it does not matter what is in the black box, if statistics is used. It can defies common sense and get away with it, theory is not critical to statistics. Evolution has similar problems. These can be corrected, if we detach statistics and require a rational theory with no black box fudge room for illusions.
 

tas8831

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


"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."


So much insight, and you failed to see that this refutes your initial (and continued) biased and uninformed assessment.

It is almost as if you think this is the only paper ever published on the subject.

Or something spectacularly stupid like that. It is hard to tell, with all your coy dissembling and such.
 

tas8831

Well-Known Member
usfan said:
No peer reviews for this obscure study were quoted ...
Jose Fly said:
???????? Nonsensical.
Are you saying that the authors did quote from peer reviews? Can you give an example?


Are you and usfan serious????

Have neither of you ever read a grown-up, adult, professional scientific publication?

You silly boys are upset because no QUOTES were used in the Abstract?

Here you go, fellows - the REFERENCES of the paper neither of you seem competent to discuss or understand:

References
  1. Baum, D. A., C. Ané, B. Larget, C. SolíS-Lemus, L. S. T. Ho, P. Boone, C. Drummond, M. Bontrager, S. Hunter, and B. Saucier. 2015. Statistical evidence for common ancestry: Application to primates.
  2. Bontrager, M., B. Larget, C. Ané, and D. A. Baum. 2015. Statistical evidence for common ancestry: Testing for signal in silent sites.
  3. Coyne, J. A. 2009. Why Evolution is True. Viking Penguin, New York.
  4. Darwin, C. 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London.
  5. De Oliveira Martins, L. and D. Posada. 2014. Testing for universal common ancestry. Systematic Biology 63:838–842.
  6. Efron, B. and R. J. Tibshirani. 1993. An Introduction to the Bootstrap, volume 57 of Monographs on Statistics and Applied Probability, chapter 16. Chapman and Hall, New York.
  7. Eugene V. Koonin, Y. I. W. 2010. The common ancestry of life. Biology Direct 5.
  8. Groves, C. P. 1991. A Theory of Human and Primate Evolution. Clarendon Press, Oxford.
  9. Hill, W. C. O. 1966. Primates Comparative Anatomy and Taxonomy VI Catarrhini Cercopithecoidea Cercopithecinae. Edinburgh University Press, Edinburgh.
  10. Nielsen, R. 2002. Mapping mutations on phylogenies. Systematic Biology 51:729–739.
  11. Paradis, E., J. Claude, and K. Strimmer. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290.
  12. Penny, D., L. R. Foulds, and M. D. Hendy. 1982. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297:197–200.
  13. Penny, D., M. D. Hendy, and A. M. Poole. 2003. Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology 223:377–385.
  14. Perelman, P., W. E. Johnson, C. Roos, H. N. Seuénez, J. E. Horvath, M. A. M. Moreira, B. Kessing, J. Pontius, M. Roelke, Y. Rumpler, M. P. C. Schneider, A. Silva, S. J. Obrien, and J. Pecon-Slattery. 2011. A molecular phylogeny of living primates. PLoS Genetics 7. E1001342.
  15. R Core Team. 2013. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
  16. Schliep, K. P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics 27:592–593.
  17. Sober, E. and M. Steel. 2002. Testing the hypothesis of common ancestry. Journal of Theoretical Biology 218:395–408.
  18. Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313.
  19. Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
  20. Theobald, D. L. 2010a. A formal test of the theory of universal common ancestry. Nature 465:219–222. Doi:10.1038/nature09014.
  21. Theobald, D. L. 2010b. Theobald reply. Nature 468. Article ID E10.
  22. W. Timothy J. White, D. P., Bojian Zhong. 2013. Beyond reasonable doubt: Evolution from DNA sequences. PLoS ONE 8. E69924.
  23. Yonezawa, T. and M. Hasegawa. 2010. Was the universal common ancestry proved? Nature 468. Article ID E9.
  24. Yonezawa, T. and M. Hasegawa. 2012. Some problems in proving the existence of the universal common ancestor of life on earth. The Scientific World Journal 2012. Article ID 479824, 5 pages doi:10.1100/2012/479824.
 

tas8831

Well-Known Member
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.

It is standard practice in creationist propaganda to use quotes, usually out of context, often altered, sometimes fabricated.
It is all they have, and it is largely a dishonest, lazy tactic. But as it is all they have, and they know it is dishonest, they project their own shallowness and dishonesty onto all others.
It is really something.
 

tas8831

Well-Known Member
Even though the abstract for Statistical evidence for common ancestry: New tests of universal ancestry was re-written for the revised version, without the words that originally aroused my suspicions, the motivation is still clear in the revised abstract.

From the blog post by the lead author, it looks to me like the research is part of a personal crusade against creation doctrine, and not what I would call serious, responsible research. Also the correspondence with “Evolution” confirms my suspicions about his dishonesty.

Do you think that this paper is the only paper on evolution? It sure seems that way.

If this paper is 100% bogus, do you really think that would be an issue for the Theory of Evolution?
Or are you just trolling some more?
 

tas8831

Well-Known Member
The whole idea of similarities on any level as proof of common ancestry looks fallacious to me.

So this is your level of understanding of the evidence for evolution?That it entails 'similarity', and that is all?.
 

tas8831

Well-Known Member
triggered True Believers
jihadist zeal.
you have a vivid imagination

Assertions and outrage
Progressive indoctrinees
lash out in unscientific, hysterical outrage
Hypocrite much?
Seldom has anyone addressed my rebuttals, and NEVER on this chimp/human computer statistics study.
When you use whiny snowflakey dodges to get out of admitting your dishonesty and ignorance of the material, I guess you can pretend to be super smart and on point.
Mostly i get jeering and ridicule, or indignation...
It is the essence of ad hominem, to direct your comments 'to the man', instead of to the topic.
triggered True Believers
jihadist zeal.
you have a vivid imagination
Assertions and outrage
Progressive indoctrinees
lash out in unscientific, hysterical outrage
My offer stands. If you wish to debate the science, and ditch the ad hom. I'm willing to do a 'reset', and start anew. But i have little hope of that either, as my offer usually falls on deaf ears, that prefer the joys of fallacy, to the mundane practice of reason.

TRANSLATION:
I will continue to hide behind whining phony martrydom so I can keep pretending my 40 years of "study and debate" wasn't wasted, and that my archaic beliefs are totally TRUE!'
 

tas8831

Well-Known Member
No peer reviews for this obscure study were quoted, just the self aggrandizing conclusions of the authors.
This is a hilarious example of what I and others have been saying for 90 pages - when you do not understand the science, or even the process of science, you write really really naive, silly things like usfan just did.

All his self-aggrandizing bombast, and claims of 4 decades of debate, and this guy actually thinks because there were no 'quotes' in a paper that something is suspicious????

I won't even mention his lies about nobody dealing with his other laughably naive claims. Dishonesty seem to be a primary motivating factor for many creationists.

How sad.
 
Last edited:

tas8831

Well-Known Member
Interesting phenomenon - I was reminded of of a 'debate' I had with another creationist about a year ago on the general subject of phylogenetics (his claim to scientific fame was that he has relatives who are scientists, therefore, he knows science), and in perusing those exchanges, I noticed that he, too, believed that the 'trees' in phylogenetic trees are actually just drawn first, and then some kind of rationalization is provided.
Lots of creationists seem to think this for some reason.
Why is that? There must be some source for this lie.
 

usfan

Well-Known Member
The Statistical based sciences have a major conceptual problem. A statistical analysis is a powerful mathematical approach. What makes it powerful is the same basic method can be applied to almost anything, and therefore works apart from the unique details of the application.

For example, if you were doing quality control on a complex machine, with a lot of variables, you would measure the input and outputs, and you can predict trends. It is not necessary to know how the complex machine works. You could employ a mathematician, who is not necessarily a mechanical engineer. The machine is placed in a black box by the mathematician. The value of the black box is this same basic math analysis can be used, by a mathematician on any machine, since the math approach is not fundamentally dependent on any particular machine theory.

The black box approach also means the math results exist independent of any theory use to explain the operation inside the black box. In other words, if my theory was the machine's black box function is based on the squirrels who run the treadmill that drives the machine, and/or the worms that crawl in the circuitry to make connections, the math and black box will still produce the same results.

Many aspects of Science has fooled itself into believing theory can be proven by statistical methods, even though the statistical methods can produce the same results independent of the theory of the black box. I am not anti science but anti-scam science.

I remember doing a development project which had political consequences for upper level management; good and/or bad. I am a rationalist and had invented and defined the science needed for an emergency process, and was 99% confident of a successful field test. Management was a little nervous since I did this so quickly. They decided to hire a statistician to parallel me. He would give them regulatory wiggle room if the worse case scenario was to happen. I did not need him, but had no choice.

I was surprised that my assigned mathematician did not need to know the exact chemical process but could nevertheless set up his math model around my process and black box the rest. He was operating independent of my theory. In the end, the process was 100% successful, with the statistical results similar, even though done independently of my reasoning and working theory.

That experience has stuck with me and recently made me realize how easy it would be to create theory illusions, using statistical results, and the black box. Irrational theory could work just as well as rational theory since statistics does not care what is in the black box. This approach is done during political polling season, and appears to be done even in modern science.

I can accept the basics of evolution, but the statistical approach makes me suspect of many of the assumptions; black box theory is not needed by statistics. However, if you use prestige to push a theory and attach this to sound statistical results, you can do a magic trick.

For example, nothing in life, down to the smallest scale, will work without water, nor can water be replaced by any other solvent. This makes water as important as the organics of life, since neither work without the other. Yet the black box theory of biology does not make water and organics co-partners. It does not have to, since it does not matter what is in the black box, if statistics is used. It can defies common sense and get away with it, theory is not critical to statistics. Evolution has similar problems. These can be corrected, if we detach statistics and require a rational theory with no black box fudge room for illusions.
Then you can appreciate the quote by Disraeli:

There are three kinds of lies: lies, damned lies, and statistics. ~Benjamin Disraeli

;)
 

Polymath257

Think & Care
Staff member
Premium Member
Interesting phenomenon - I was reminded of of a 'debate' I had with another creationist about a year ago on the general subject of phylogenetics (his claim to scientific fame was that he has relatives who are scientists, therefore, he knows science), and in perusing those exchanges, I noticed that he, too, believed that the 'trees' in phylogenetic trees are actually just drawn first, and then some kind of rationalization is provided.
Lots of creationists seem to think this for some reason.
Why is that? There must be some source for this lie.


I think part of it is that they really don't understand how it could be possible to use the data to create such a tree. It's almost like they cannot hold more than a certain amount of information (or a certain length of argument) in their heads at one time.

Now, to be fair, part of the training for the sciences (and even more for math) is learning how to do exactly this. It is common for a proof in math to go on for several pages with tight logic along the way. And being able to hold, say, the Kreb cycle in your head takes some practice.
 

tas8831

Well-Known Member
Then you can appreciate the quote by Disraeli:

There are three kinds of lies: lies, damned lies, and statistics. ~Benjamin Disraeli

;)
:facepalm:
triggered True Believers
jihadist zeal.
you have a vivid imagination
Assertions and outrage
Progressive indoctrinees
lash out in unscientific, hysterical outrage
 

tas8831

Well-Known Member
I think part of it is that they really don't understand how it could be possible to use the data to create such a tree. It's almost like they cannot hold more than a certain amount of information (or a certain length of argument) in their heads at one time.

Now, to be fair, part of the training for the sciences (and even more for math) is learning how to do exactly this. It is common for a proof in math to go on for several pages with tight logic along the way. And being able to hold, say, the Kreb cycle in your head takes some practice.

Ya...

Maybe if we wrote this:

image5.gif


like this:

(C(A,B))

they wouldn't complain?

Of course, that gets pretty cumbersome when trying to depict this:

Phylogeny-of-canid-speciesThe-phylogenetic-tree-is-based-on-15-kb-of-exon-and-intron.png


using a bunch of parentheses....
 

usfan

Well-Known Member
I think part of it is that they really don't understand how it could be possible to use the data to create such a tree. It's almost like they cannot hold more than a certain amount of information (or a certain length of argument) in their heads at one time.

Now, to be fair, part of the training for the sciences (and even more for math) is learning how to do exactly this. It is common for a proof in math to go on for several pages with tight logic along the way. And being able to hold, say, the Kreb cycle in your head takes some practice.
Is this a rebuttal for my points about the Study? If it is in reply to an ignored heckler, i cannot see the context, and don't see how, or if, it applies..
Unless, of course, that is the intent.

There is more to calling statistical analysis 'evidence!', than just declaring it so. Scientific methodology must question the data, assumptions, and methods, AND, the conclusions must be compelled by the data, not just asserted or plausibly inferred.

I am disappointed that you requested my review of The Study, yet have not considered my reply.
 

tas8831

Well-Known Member
So precious - the 4 decades of study superstar - Dr.Eve gene, ignores those whose refutations he cannot deal with.

The Broflakery is strong among creationists.

I wonder if he knows that I am still refuting his naive assertions and still pointing out his errors and fabrications, and that everyone else can see them???

:tonguewink::tonguewink::tonguewink:
 

Jose Fly

Fisker of men
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.

From the blog post by the lead author, it looks to me like the research is part of a personal crusade against creation doctrine, and not what I would call serious, responsible research. Also the correspondence with “Evolution” confirms my suspicions about his dishonesty.
Again Jim, you're not making any sense. On one hand you lament that no one is testing separate ancestry, but now that you've been given an example of scientists testing separate ancestry, you're complaining about it and calling it a dishonest crusade against separate ancestry. Weird.

Is this simply about the results, and how they're not what you would've liked? If it's not, then you need to show specifically where they were dishonest in their work.
 

Jose Fly

Fisker of men
What I would expect to see, in a research environment uncorrupted by factional feuding, would be various lines of evolution research, some with a premise of common ancestry and some not, with all the researchers valuing that diversity, encouraging and supporting each other and learning from each other. I’m still not sure that it isn’t already happening, out of public view. It might only be a few who are using evolution theory as a battleground for factional feuding, and of course that would be all we would hear about in media stories and Internet flame wars.
Why in the world would evolutionary biologists value and support research into separate ancestry, when it's been shown to be completely inconsistent with the data and useless?
 

Jose Fly

Fisker of men
Ad hom and deflection, not scientific analysis, is all that is offered.
Yes, you are indeed guilty of that.

Has anyone presented, examined, or scrutinized the CLAIMS of this study? Only me.
Again, your posts about this paper have been 100% wrong on how the work was carried out.

Has anyone pointed out the facts, and methodology that compels the conclusions of the abstract? No. Only me. ALL of the devotees to CA just sing the prsises of their priests, and parrot the CONCLUSIONS. NOBODY even mentions the actual science, data, or methodology.
Again, 100% incorrect. I pointed out the flaws in your "response". You have absolutely failed to address those flaws.

And, there IS NO peer review, mentioned, referenced, or quoted. As Jim noted, the abstract was 'pre published, NOT peer reviewed', so the claims that this study has ANY SIGNIFICANCE to the scientific community is absurd, and a bluff, to try to prop up the very shaky 'evidence!', that is not being presented.
The paper was published in the journal "Evolution" in 2016. So once again, you are completely wrong.

This paper is pseudo science bluff
Given the number of egregious errors you've made regarding this paper, your opinion on it is meaningless.

With NO EXAMINATION, of this (and other) studies, you stoop to attacking me, personally, for daring to question the assumptions, facts, and methodology of this obscure 'study', trumpeted by the faithful, as 'Proof of Evolution!!'
From what I can tell, the only ones here who haven't examined the paper are you and @Jim . All you've referred to is the abstract, with nothing at all posted about or from the body of the paper.

This study is a fraud.
Again, given that everything you've said about it has been completely wrong, plus that you appear to have only read the abstract, your opinion is meaningless.
 

Jose Fly

Fisker of men
You have claimed that the theory of common ancestry has produced multiple failures - that's not a claim of experience, that's just a claim. I'm asking you to provide examples of this claim. Can you do that?
@Jim has been doing this throughout the thread. He makes rather grand claims and then gets all folksy and deflects when challenged to substantiate those claims.
 
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