Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)

Monday, February 06, 2006

crevo and the baraminologists

This is in response to Crevo's reply in this thread.

I have now read the paper. And, again, you are confusing the assumption and the conclusion. _Nowhere_ in the paper does it say that "therefore humans and chimps are separately created kinds". That is not a conclusion of the paper. It is an _assumption_ of the paper.

It is an assumption that is "tested" in the paper. Actually, it is more of a pre-conclusion, and when the data analyses do not support their pre-conclusion, they dismiss the relevance of the data. If it is an assumption, it is an unwarranted one. For, as they indicate, only the Scriptural criterion can give the true answer. If the Scriptural criterion is above falsifiability, then it is not science at all.
Can any reader imagine the fuss that would be made if evolutionary biologists rejected data anaylses because the results did not conform to the Origin of Species/Darwinian criterion?
I am confusing nothing. I know that the baraminologists started with their conclusions then rejected data analyses that did not fit. If it were merely an assumption, why then did they justify their rejection of objective data analyses because it did not support their "assumption"? Is that how leguitimate science is performed?

Let's look at it this way. Let's say that you were friends with an artist. Let's say that artist told you, "I have made several paintings using different styles. In the 80s I used one style, in the 90s I used another, and now I am embarking on a brand new style of painting. For instance, here are two paintings I have recently completed, and here are two that I did in the 90s". Now let's say that you are tasked with determining, for each of the artists paintings, which one was painted in what decade. The best thing to do is to look at the paintings that you _know_ to be from different decades, and try and conclude what characteristics are decade-dependent, and which characteristics are not. The paintings from the current decade may be very different from each other. However, the artist himself has told you that he uses a consistent style, and it is different from a style he used to use. Therefore, it is reasonable that, if I want to know which aspects of the artists paintings differentiate them stylistically, I should compare two that are known to be different in style. In fact, it would be even better if I had a painting of the same subject done by two different styles. That would show best of all which features were stylistically important. And that is precisely what this paper does.

So, you are constructing a silly analogy to justify fruadulent science? In actual science, one does not start with THE ANSWER. There is no 'artist' that told us that humans are special creations, seperate form all other animals and that therefore, any evidence indicating otherwise is false. Even when the same data can be used to show other things are related. Special pleading and equivocation are the tools of the Apologist, not the scientist.

The Author has said that humanity is a unique root of ancestry (being formed "from the dust"). Physically, we are most similar to other primates than other animals. Therefore, if we are to know which characters are most important in defining a baramin, it would be useful to examine humans vs chimps and determine which traits are baraminically important.This is not cherry-picking data -- that would only be the case if they then turned around and said "and therefore we can be sure that the Bible is correct", which they do not do.

Right - they do something totally different:

"With the exception of the Scriptural criterion no single data set is sufficient to define the holobaramin....

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 data sets in strongest
agreement were the most reliable."

Morphological criteria that were cherry-picked and subjective and largely irrelevant ecological data are better at giving them the results they know are true based on Scripture than are objective molecular data...

True, they do not write that "therefore, the bible is true." Instead, they declare the bible true at the outset, then assume that data analyses that do not coincide with Scripture are simply unreliable.

Yup. Totally different.

There is a good case for humans and chimps being from different ancestors, but this paper is not it nor does it claim to be.

Not in the least. But I do wonder about this "good case" - what is it?

Only if it claimed to be such a paper would the objection of cherry-picking make sense.

"Crevo accepts that things like where a creature lives is more important than their genetic make-up in determining their ancestral and descendant
Why would you think that genetic make-up is necessarily good at determining ancestral relationships? Have you ever written a program? Ever used design patterns? How, specifically, would you differentiate a genomic pattern that was based on common descent versus common design (creationists have a hypothesis,
which I will get to).

Ah - the old "I am a computer guy, and therefore my insight trumps all" routine. I was wondering when that hackneyed distraction was going to make an appearance. Well, try this on: Have you ever sequenced DNA and analyzed the reults? Have you ever compared sequence alignments?
Here is how I know that genetic make-up is good at determining ancestral relationships:

Science. 1991 Oct 25;254(5031):554-8.
Gene trees and the origins of inbred strains of mice.

Atchley WR, Fitch WM.
Department of Genetics, North Carolina State University, Raleigh 27695.

Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities.

Science. 1992 Jan 31;255(5044):589-92.

Experimental phylogenetics: generation of a known phylogeny.

Hillis DM, Bull JJ, White ME, Badgett MR, Molineux IJ.

Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

among others.
Using testable and tested methodologies is a good way to know that your results are valid, for starters. How could I tell evolution from design? Well, if patterns of nuckleotide substitution were haphazard and analyses of the same produced random trees, regardless of the liocus or amount of data, then descent would be in trouble.
Of course, design would not be. No matter what the outcome. Observable patterns of nucleotide substitution that coincide with evolution-based hypotheses? Design!
No 0bservable pattern of nucleotide substitution?
Also Design!

Also, my own data shows it clearly.
The patterns are unmistakable.
And one need not be a computer programmer to see them.

"There is a major difference here, that Crevo is glossing over. The “assumption” of human-chimp ancestry is actually a conclusion based on multiple lines of empirical evidence, while the assumption that humans are special creations separate from all other animals is premised solely on Scripture."
This isn't quite correct. You are implying that there is no evidence for the common ancestry of humans and chimps, which is incorrect.
Ummm... Actually I am saying that there IS evidence for the common ancestry of humans and apes.
So, what - other than Scripture - is the evidence that runs counter to human-ape ancestry?

Scripture is _sufficient_ reason for creationists to doubt the common ancestry of humans and chimps, but it is not the only reason, and many (including myself) think that the problems in assigning common ancestry for both groups are sufficient to doubt that such ancestry exists even in absence of scriptural authority.

Well, don't keep me guessing! What IS this amazing evidence that only you and your fellow creationosts seem to know about, and why would you keep it a secret? And how is it scientific again for a religious text to trump data analyses?

"Further, the goal of the Nachman and Crowell paper is not to ‘prove’ or support human evolution, rather it is to examine mutation rates. The baraminology paper, on the other hand, presents it’s rigged findings to support their assumptions." This is a false statement. The point of this paper has nothing at all to do with proving different ancestry. It is about finding which characters are important in determining ancestral relationships from a Biblical perspective, not in proving that such multiple roots occur.

It is not false at all. I understand that you are engaging in fellow-creationist protection here so I will not take umbrage.
As creationists like analogies, consider this one:

I think that humans and rabbits are not closely related. I produce a DNA sequence alignment which includes humans and rabbits and other mammals. I designate rabbit as the outgroup of my analyis , meaning that I tell the analysis software that humans and rabbits are not closely related. I run my analyses and, amazingly, the results show that humans and rabbits are distantly related! I then write up a paper in which I declare that my assumptions were borne out.

I understand what the stated goal of the paper is. I also understand the stated implications. I do not require explicit statements from the authors to know what they are up to.

"The authors start with Scripture, they then essentially discard the analytical results that do not conform to their assumptions."

They don't _discard_ anything. The question is, which characters are baraminically important? How better to do that than examine creatures which are close but known to be in different baramins and see which types of characters can reliably represent the difference?

And you give away the farm.

"...known to be in different baramins "

How are apes and humans "known" to be in different baramina? Why, Scripture says so! And which criterion is the only TRUE criterion by which to determine ancestor-descendant relationships? Why, the Scriptural one. The circle is complete.

As with the artist example mentioned above, how is that invalid, given the assumptions?

It is invalid for a number of reasons, among them the fact that there is no scientific reason to adopt the stated assumption.

It would only be invalid if that data were turned around and used as proof of the assumption, which it is not."No, my criticism stems from the fact that they cherry-picked data to get the results they “knew” were correct."

They did not at the outset of the study know which characters were going to be baraminically important, now they do.

Yes, those that are the most subjective and irrelevant to ancestry. Of course, those OTHER criteria - genetic data and the like - are still OK for use in non-human analyses...

What they knew beforehand was the separate ancestry of chimps and humans.

And how did they "know" this? Scripture. And Scripture cannot be incorrect, according to creationists. Therefore, when data analyses were insufficient to prop up their interpretation of Scripture, those data had to go.

I cannot understand why this is so difficult to see.

What they did not know was what characters are most important for determining

TRANSLATION: What they wanted to find were data that could be construed to prop up their Scriptural criterion.

They used what they knew beforehand to find out what they didn't. Isn't that the
whole point of analytical studies?

Typically, a legitimate researcher starts with a question, gathers data, analyzes the data, then sees if the question is answered. The baraminologists start with an answer, then seek out data and analyses that will support that.

When I do a sequence analyses my question is always "Will the patterns of nucleotide substitutions support my hypothese/hypotheses?" It has NEVER been "Which of these data sets can I use to lend credence to my assumption/conclusion/answer and which shall I disregard?"

Again, this is the same line of reasoning used in "Estimate of the Mutation Rate per Nucleotide in Humans". They used a assumption to determine an unknown fact. The difference is that in the case of the "Estimates" paper, the assumption was common ancestry, while in the paper under discussion it was separate ancestry.
Neither paper attempts to prove the assumption. Both papers use their assumption to make a conclusion. The difference is with which assumption you agree with.

This is a false statement. As I explained before, the 'Estimate...' paper assumed common descent not premised on an ancient text, but on multiple lines of evidence. There are NO lines of evidence indicating a seperate creation for apes and humans. One assumption is justified. One assumption - that is treated not as a tentative position as in science, but as a firm unyielding cconclusion - is not.

"It is true that establishing the separate baramin for humans was not a stated goal of the paper, yet it was stated clearly in their conclusions (and in the abstract) that this was a result."

This is a false statement. I will reproduce the abstract below to prove it.

Your declaration that my statement is false is itself false.

"We have found that baraminic distances based on hemoglobin amino acid sequences, 12srRNA 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."

So, their subjective data and analyses were "quite reliable" at telling what they already "know", that the human holobaramin is 'established', i.e., delineated by 'scientific' analyses.

"In reality, the baraminologists accept descent, they just place arbitrary (i.e., premised on Scripture) limits on it."

(a) scripture is not arbitrary(b) scripture is not the only measuring stick for determining descent (though, for creationists, where it lists separate descent is a sufficient reason for believing so)

Please do not misrepresent me. I did not say scripture is arbitrary, I said that the authors arbitrarily use Scripture as a source for their limitations on what can and cannot be the product of common descent.

I have written some of my own thoughts on some of the problems with universal common descent from an information science perspective here.

It will be interested to read yet another creationist trying to address biological issues from a non-biological perspective. I shall read and rebut it in time. One of the common problems with information theory mongers is that they do not seem to be able to duiscuss the manner in a way that is relevant to biology. It is usually via some silly contrived analogy to english language sentences or computer code with no acknowledgement that genes really do not work the same way computer code or english language sentences do. We shall see how Crevo deals with it...

Todd Wood has hypothesized that, genetically, mobile elements within the genome will be the most important in defining baramins. This makes sense from a semantic perspective, as mobile elements are basically collections of entities which have semantic meaning. They would have to be different (as a group at least, though not necessarily each individual one) when applied in a different semantic environment. See Todd Wood's The AGE-ing Process: Rapid Post-Flood Intrabaraminic Diversification Caused by Altruistic Genetic Elements (AGEs).

It was quite entertaining, to say the least. Wood, like ReMine, Wells, Bergman, et al., can write an awful lot of words while saying very little and producing no original science.

"If the baraminologists are not bound by descent, why on earth are they even trying to determine baraminological relationships? If God can just poof into (and out of) existence anything He wishes, isn’t trying to define these groups and their ancestral-descendant relationships a futile effort?"

Often times people who believe in God are criticized because God, theoretically, can do anything. However, Christians don't believe in any God, they believe in Yahweh. Yahweh has made His acts and His ways known to us (at least partially), therefore, any comment about something that God did or could have done is constrained by what is in the character of Yahweh to do. In fact, modern science is premised on many of Yahweh's characteristics, specifically that He made the universe understandable to man. And cosmologists have shown over and over again that this is true in a major way.

(searches for the 'rolleyes' emoticon...)

And so what, for the baramionologist/creationist, would/could falsify their Scripture-bound descent hypothesis?

If I answer for you and say "Absolutely nothing," would I be incorrect?


Doppelganger said...

I am hoping that Crevo will reply to his claims re: 'ReMine's dilemma'.

Anonymous said...

Guess he's not interested.

Better to stick to making uninformed proclamations at his own site.