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derwood

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I wrote this up a few years ago...

***

"We look at the same data, just not under the same metaphysic as you."
“It’s all metaphysics, and my metaphysic is the best one!”

So the argument goes in this ‘debate’ – the evolution accepter, beholden as they are to the ‘metaphysic’ of Naturalistic materialism, cannot see how the creationist metaphysic – supernaturalistic antimaterialism, is far superior. It is, after all, premised on Scripture, and Scripture is Inspired.
And so, if one views evidence, in the words of Henry Morris, “the right way” – that is, through the eyes of the creationist metaphysic – one will see the Truth of the creationist claims.

Well, let’s take a look at this creationist metaphysic in action. I will let the objective, rational reader determine if this metaphysic is the superior one when dealing with issues scientific…
When I was a graduate student working on molecular phylogenetics, I discovered a series of articles in the Creationist peer-reviewed literature * dealing with the same subject.
The authors of these articles were applying computer algorithms to molecular data to determine the relationships between creatures that descended from the ‘kinds’ that were Created and were later allowed to live on the ark.
These and other papers lay out the creationist version of systematics, called Baraminology (or Discontinuity Systematics), which utilize standard computer programs and reproducible analyses using molecular data. These ‘baraminologists’ have set up an entire field of study, complete with its own bible-based terminology and concepts.

The first paper, “A Mitochondrial DNA Analysis of the Testudine Apobaramin,” 1997, DA Robinson, CRSQ 33:4 p. 262-272, examines the relationships between turtles, and establishes or at least lays out some important criteria for establishing affinity of species (baramina) – patterns of mutation bias, gaps between ingroup and outgroups, topological congruence of cladograms using differing parameters and analyses, and strong bootstrap support for the arrangements. The author was able to determine using these methods – which are essentially the same as those used by systematists – that all turtles are related via descent from a created kind, but could not resolve lower-level relationships.

The third paper dealt with cat phylogeny, and just expanded on earlier ‘proof of concept’ papers.

But the second paper was of great interest to me.

“A Quantitative Approach to Baraminology With Examples from the Catarrhine Primates,” 1998, D. Ashley Robinson and David P. Cavanaugh, CRSQ 34:4 p. 196-208, was the very subject I was working on.

Much of the paper consists of quoting/referring to Scripture, which is odd for a scientific paper but not, I assume, for a scientific paper premised on the supernaturalistic metaphysic, and outlining their justification for their “baraminic distance” criterion. This takes up about the first 4 pages. The baraminic distance is essentially equivalent to the materialistic genetic distance measure, it is just called something else.

Those pages are, save for the references to Scripture, well written and exhibit a great deal of thought. The paper gets interesting, however, when we get to the Materials and Methods section on p. 201. The title of the paper and several sentences in the introductory portion indicate that the interest here is in the Old World monkeys, not the human-ape question. Indeed, they discount that question altogether:
“Since Scriptures clearly imply that humans were specially created (Genesis 1:26-272 , 22), and thus phylogenetically distinct from other organisms, we utilize the human-nonhuman primate relationship as a control.”
This will be of interest later.
Their data consisted of 12s rRNA gene sequences, chromosomal characters, morphological characters, and ecological characters. The data were analyzed individually and as a total evidence dataset using standard phylogenetic analysis software.
It is the results and discussion in which the metaphysic of supernaturalism comes into play.

For those of you that do not know, when you set up a data matrix for analysis you utilize what is called an outgroup – a taxon that is not closely related to the group under study – for use as a ‘yardstick’ of sorts. For example, when analyzing primates you might use rabbit as an outgroup. Interestingly, as quoted above, the baraminologists use human as the outgroup in their analyses.
Outgroups must be designated prior to running the analysis, or the results will appear strange. If you designate the wrong taxon as the outgroup, your results will be strange indeed (you can, of course, run analyses without an outgroup, but these analyses were not utilized by the baraminologists).
So, when the baraminologists ran neighbor joining analyses on the data, they used human as the outgroup. NJ methods assume a constant rate of evolution, which is not indicated by either fossil or molecular evidence and so has fallen out of favor. Though they do not specifically state that they designated human as outgroup, this is what must have happened. This is because the order of the taxa in the dataset can influence the arrangement produced in NJ analyses. For example, I analyzed one of my datasets and I got an arrangement similar to the one seen in the CRSQ paper. Human is first in that dataset, so I cut and pasted it last, re-ran the analysis, and Human got stuck somewhere in the middle of the cluster (however, when I ran a bootstrap analysis, human grouped with chimp). However, when I designated a new world monkey as outgroup, I got the ‘accepted’ arrangement – human + chimp. Making human the outgroup produces an arrangement similar to the one in the CRSQ paper – NJ analyses by default use the first taxon as the outgroup unless designated otherwise.
And what follows from that is the production of weakly supported topologies, since they tried to force the data to conform to a ‘non-natural’ topology. The node linking chimps and gorillas was supported with only 53% bootstrap support. That is fairly low. In a paper not constrained by the antimaterialism metaphysic, in which human is not the outgroup, chimps join gorilla with 96-100% support, depending on the data used. Forcing the data to fit a preconceived notion based on a metaphysic produces statistically significant error.
They mention in the abstract “We have found that baraminic distances based on hemoglobin amino acid sequences, 12S-rRNA sequences, and chromosomal data were largely ineffective for identifying the Human holobaramin. Baraminic distances based on ecological and morphological characters, however, were quite reliable for distinguishing humans from nonhuman primates.”

The description of the morphological analysis sounds impressive – 43 characters. The morphological characters, however, I believe, were specifically selected to produce the desired results. Why do I say this? Because this paper:
Mol Phylogenet Evol. 1996 Feb; 5(1): 102-54. Primate phylogeny: morphological vs. molecular results. Shoshani J, Groves CP, Simons EL, Gunnell GF.**
Was known to the authors. It contained an analysis of not 43 characters, but 264, and this analysis grouped human with chimp.
The other data, ecological data, is the most subjective and should produce no surprise when it was this data that provided the baraminologists their ‘strongest evidence' for a separate human baramin. And what were some of these data? Things like percent foliage in diet, monogamy, population group size and density, home range size, etc. It looks to me like these data too were chosen to produce a desired outcome, for what exactly does “monogamy” have to do with descent?

Indeed, the authors state in their Discussion section:
“Character selection, not the method of analysis, is expected to be the primary factor affecting baraminic hypotheses. False conclusions can be reached unless baraminically informative data has been sampled. Since we have no a priori knowledge regarding which characters are more reliable for identifying holobaramins, it is important to evaluate the reliability of a wide variety of biological data for inferring baraminic relationships.”

And later:

“it is interesting to note that the ecological and morphological criteria were the most adept at distinguishing humans and the most highly correlated, indicating that the datasets in the strongest agreement were the most reliable.”

Yes, that is interesting – the most subjective and limited criteria are the most reliable for giving the creationist the arrangement they want…

That is, they have to pick data that give them the results they want – those that conform to Scripture.

Creationism’s metaphysic in action…
What I did not mention is this, from the section on selecting characters:
“With the exception of the Scriptural criterion no single data set is sufficient to define the holobaramin.”

Translation: Scripture gives us the answers, we need to find the data that will conform to these answers.
The ‘superior’ metaphysic in action.

*I had contacted the authors of this paper in 1999 asking for reprints and neither replied to my requests. I had to buy the issues from CRSQ. Later, after reading in the paper that the data sets were available from the authors on request, I sent an IM to DA Robinson while online one day. First he pretended not to know what I was talking about. After he acknowledged co-authoring the paper, he said something that astounded me – he said that he didn’t think the data sets even existed anymore!



-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 09:52 AM on April 14, 2009 | IP
orion

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Derwood-
I had contacted the authors of this paper in 1999 asking for reprints and neither replied to my requests. I had to buy the issues from CRSQ. Later, after reading in the paper that the data sets were available from the authors on request, I sent an IM to DA Robinson while online one day. First he pretended not to know what I was talking about. After he acknowledged co-authoring the paper, he said something that astounded me – he said that he didn’t think the data sets even existed anymore!


CRSQ - Creation Research Society Quarterly.  Hmmm, I never heard of it.  But these are the points it makes on its home page:


- Published continuously since 1964
- Peer-reviewed by degreed scientists
- World-wide circulation
- Scholarly articles representing the major scientific disciplines
- Fresh perspectives on science and society as impacted by origins
- Emphasis on scientific evidence supporting: intelligent design, a recent creation, and a catastrophic worldwide flood


Sounds authoritative.  

Derwood - you should have told him you were a fellow Creationist researcher.  Then maybe he would have given you a copy of the data.
 


Posts: 1460 | Posted: 3:19 PM on April 14, 2009 | IP
derwood

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But that would have made me as dishonest and misrepresentative as them...


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 08:31 AM on April 15, 2009 | IP
orion

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Quote from derwood at 08:31 AM on April 15, 2009 :
But that would have made me as dishonest and misrepresentative as them...


Derwood - I thought you would say that.  I agree.  I'm glad you didn't.  Integrity and honesty have to be among the qualities of any good scientist.

You presented a very interesting example of why Creationism is NOT a science.  The Bible is not a science book.  It's not even an accurate history book.  



 


Posts: 1460 | Posted: 10:30 AM on April 15, 2009 | IP
wisp

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Or a good moral guide.


-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 2:05 PM on April 15, 2009 | IP
orion

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Quote from wisp at 2:05 PM on April 15, 2009 :
Or a good moral guide.


Excellent point, Wisp.  The God depicted in the Bible, especially in the OT, always bothers me.  Its as though the writers of the OT wanted to put the fear of the wrath of God into people so they could be cowed into obedience.  



 


Posts: 1460 | Posted: 2:46 PM on April 15, 2009 | IP
wisp

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Sometimes i think it bothers them too.

They know Yahweh was very ugly sometimes.

If they gave it any thought, they know they don't use the Bible as a moral guide. That they wouldn't stone a person to death for doing something in the sabbath.

Even if they managed to believe that Jesus abolished the old law they know that they don't pay attention to Jesus either.

They care for tomorrow. They don't love their enemies. They don't withhold their judgments. They bury their dead.

Well, i'm talking about all christians now.

Perhaps creos sometimes hate to have to defend the ark. And the vegan lions and spiders.



-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 12:30 AM on April 17, 2009 | IP
wisp

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"Peer reviewed", haha!

examines the relationships between turtles, and establishes or at least lays out some important criteria for establishing affinity of species (baramina) – patterns of mutation bias, gaps between ingroup and outgroups, topological congruence of cladograms using differing parameters and analyses, and strong bootstrap support for the arrangements.
What's "bootstrap"?

“A Quantitative Approach to Baraminology With Examples from the Catarrhine Primates,”
THAT seems interesting!

It would be interesting with examples from many "kinds", but well.

Much of the paper consists of quoting/referring to Scripture, which is odd for a scientific paper but not, I assume, for a scientific paper premised on the supernaturalistic metaphysic, and outlining their justification for their “baraminic distance” criterion.
Oh... No attempt for some objective determination of the baraminic distance? How disappointing...

Even if it was conventional i'd like to know about that distance.
Do you remember what it was? Some whimsical percentage of DNA or what?

Those pages are, save for the references to Scripture, well written and exhibit a great deal of thought.
I confess i'm surprised.
I guess you smell dishonesty when you see thought AND creationism, right?
The paper gets interesting, however, when we get to the Materials and Methods section on p. 201. The title of the paper and several sentences in the introductory portion indicate that the interest here is in the Old World monkeys, not the human-ape question.
How convenient...
Indeed, they discount that question altogether:
How scientific...
“Since Scriptures clearly imply that humans were specially created (Genesis 1:26-272 , 22), and thus phylogenetically distinct from other organisms, we utilize the human-nonhuman primate relationship as a control.”
Get out of here!!! They even used the discarded human as a control???
This will be of interest later.
I already see where that's going. The results will be a mess.

But shouldn't they show the primates as LESS related to each other if the human acts as a control?
I know nothing about the methods you're describing, but it sounds like if you take a random primate as a control for measuring distances between primates... Oh, i think i get it...
Some will seem to be too close and some will seem to be too far?
I'm sorry, i'm sleepy. I don't trust my reasoning much.
Could you explain it?

Their data consisted of 12s rRNA gene sequences, chromosomal characters, morphological characters, and ecological characters.
Ecological??? Hum... Sounds like an easy way to discard the already discarded human ape.

-Let's make an objective ecological analysis. How many of these species build houses? How many of them live close to a TV set?

For those of you that do not know, when you set up a data matrix for analysis you utilize what is called an outgroup – a taxon that is not closely related to the group under study – for use as a ‘yardstick’ of sorts.
I didn't know.
Where did you write this? For whom?
For example, when analyzing primates you might use rabbit as an outgroup. Interestingly, as quoted above, the baraminologists use human as the outgroup in their analyses.
Knowing very little about such tests, i can see that the results will be a mess.
Outgroups must be designated prior to running the analysis, or the results will appear strange.
I don't understand that. Where can i learn more about this subject?
Though they do not specifically state that they designated human as outgroup, this is what must have happened.
Oh... I thought you knew...
This is because the order of the taxa in the dataset can influence the arrangement produced in NJ analyses. For example, I analyzed one of my datasets and I got an arrangement similar to the one seen in the CRSQ paper. Human is first in that dataset, so I cut and pasted it last, re-ran the analysis, and Human got stuck somewhere in the middle of the cluster (however, when I ran a bootstrap analysis, human grouped with chimp).
Way over my head.
However, when I designated a new world monkey as outgroup, I got the ‘accepted’ arrangement – human + chimp. Making human the outgroup produces an arrangement similar to the one in the CRSQ paper
Hum... I half get it...
Well, perhaps i don't reach a half.
Forcing the data to fit a preconceived notion based on a metaphysic produces statistically significant error.
In variable directions?
They mention in the abstract “We have found that baraminic distances based on hemoglobin amino acid sequences, 12S-rRNA sequences, and chromosomal data were largely ineffective for identifying the Human holobaramin. Baraminic distances based on ecological and morphological characters, however, were quite reliable for distinguishing humans from nonhuman primates.”
Haha! Yeah, feel free to take whatever helps your cause.

The description of the morphological analysis sounds impressive – 43 characters. The morphological characters, however, I believe, were specifically selected to produce the desired results. Why do I say this? Because this paper:
Mol Phylogenet Evol. 1996 Feb; 5(1): 102-54. Primate phylogeny: morphological vs. molecular results. Shoshani J, Groves CP, Simons EL, Gunnell GF.**
Was known to the authors. It contained an analysis of not 43 characters, but 264, and this analysis grouped human with chimp.
Very revealing.
But how did you know they knew that paper? Did they mention it in their own paper?

The other data, ecological data, is the most subjective and should produce no surprise when it was this data that provided the baraminologists their ‘strongest evidence' for a separate human baramin. And what were some of these data? Things like percent foliage in diet,
HAHAHAHAHAHA!!!
Why not "percentage of pizza in diet", right?
monogamy,
Rate of divorces...
population group size and density,
Presence in theaters...



-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 01:11 AM on April 17, 2009 | IP
wisp

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Hum... Bootstrap as in... Cross reference?


-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 01:14 AM on April 17, 2009 | IP
derwood

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Quote from wisp at 01:14 AM on April 17, 2009 :
Hum... Bootstrap as in... Cross reference?


No, as in a statistical algorithm that employs deletion and replacement of data blocks followed by re-anaylsis.



-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 08:20 AM on April 17, 2009 | IP
wisp

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Forcing the data to fit a preconceived notion based on a metaphysic produces statistically significant error.
In variable directions?
I mean, if you put a close animal as an outgroup control you get errors in both directions?
(More and less related than they actually are?)



-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 11:37 PM on April 17, 2009 | IP
derwood

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IDcreationists?


-------
Lester:

"I said I have a doctorate and a university background in anatomy, physiology, biochemistry, physics, chemistry, pathology etc. ..."
 


Posts: 1646 | Posted: 11:54 AM on April 30, 2009 | IP
wisp

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This would be a good moment to say: "Yeah, those guys are frauds. Nevermind them, look at these other remarkable examples of research being conducted by creationists, and these revealing results."
If there was any serious research worth mentioning, that is.



-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 09:34 AM on May 4, 2009 | IP
wisp

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Hello?


-------
Quote from Lester10 at 2:51 PM on September 21, 2010 in the thread
Scientists assert (by Lester):

Ha Ha. (...) I've told you people endlessly about my evidence but you don't want to show me yours - you just assert.
porkchop
Would we see a mammal by the water's edge "suddenly" start breathing underwater(w/camera effect of course)?
Contact me at youdebate.1wr@gishpuppy.com
 


Posts: 3037 | Posted: 7:34 PM on May 20, 2010 | IP
    
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