Monthly Archives: February 2005

End of the Season

This past weekend was the last of the upland bird season for falconry. So we headed north to see if the hawks and dogs might find something to chase and perhaps catch.

Genie Scott’s friends Ira and Shirley Lee have vineyards and graciously allowed us to come and see what the hawks might find there. We drove up on Sunday morning and prepared Rusty and Glamdring for an outing. After a little bit of visiting with Genie, Ira, and Shirley, we started off on a walk around and through the vineyards.

Rusty weathering at the Lee\'s

Ira, Glamdring, Shirley, and Diane

Genie and Glamdring

Because this was vineyards, we didn’t use the backpack frame perch for the hawks. There were plenty of perches available. The dogs found a couple of jackrabbits, and the hawks chased one for a bit, but no connection was made.

Rusty and Glamdring in the vineyard


Glamdring near creek

Rusty near creek

Diane, Ritka, and Farli

There was a pond with ducks on it. Ritka and Farli each did some swimming in the pond, with Ritka trying to close in on a duck without success.

Ritka in pond

We had a bit of a visit with Ira and Shirley afterward, and they opened up a a very nice bottle of Saintsbury Pinot Noir produced from their grapes.

Ira with Pinot Noir

I’m hoping that this next year will see an improvement in our ability to provide slips for the hawks. While they got some outings this hunting season, my surgeries and health issues put a real crimp in our ability to get out.

Wired for Sound: A Q&A Concerning Dolphin Brains

I took preliminary exams for my Ph.D. back in 1997. One of my committee members was Sam H. Ridgway Senior Scientist at the US Navy Marine Mammal Program. About half of the questions he asked had to do with neural organization in the bottlenose dolphin and modelling it. “DarkSyde” asked in comments about such things, so I thought I would post my answers to those pre-lim questions.

1. Discuss afferent and efferent routes between the ear and brain.

For my particular interests, the goal would be to determine a “wiring diagram” of the neural structure, including feedback loops and other possible control structures. This does not appear to have been done yet for any mammal. From the descriptions that I have read, either the overall coherence of path of activation has not been a major issue, or I am missing some important underlying background that has been assumed to be known by any reader. I tend to favor personal ignorance as a working hypothesis. I will give my understanding of my reading thus far, with the caveat that in several circumstances I suspect that some intermediary neurons or structures have been elided from the description.

Major sources:

[1] Iurato, S & MD Bari. 1974. Efferent innervation of the cochlea. In: WD Keidel & WD Neff (eds.), Handbook of Sensory Physiology (Vol. 1). Springer-Verlag, pp. 261-282.

[2] Harrison, JM & EM Howe. 1974. Anatomy of the afferent auditory nervous system of mammals. In: WD Keidel & WD Neff (eds.), Handbook of Sensory Physiology (Vol. 1). Springer-Verlag, pp. 283- 336.


Neural activity begins with the transduction of acoustic waves into electrochemical communication in the hair cells of the basilar membrane. Synaptic connections stimulate activity in sensory neurons. Apical, intermediate, and basal neurons of the cochlea innervate the cochlear nucleus. The cochlear nucleus gives rise to a variety of connections. Ipsilaterally, these connections are to the medial superior olive, the lateral superior olive (absent or reduced in dolphins and bats), the lateral nucleus of the trapezoid body, lateral pre-olivary nucleus, and dorsal and ventral nucleus of lateral lemniscus. Contralaterally, these connections of the cochlear nucleus are to the medial trapezoidal body, medial superior olive, medial pre-olivary nucleus, and dorsal and ventral nuclei of the lateral lemniscus. The medial trapezoidal body innervates the lateral superior olive of the same side. [2, pp. 284-294]

Afferent innervation of the retro-olivary group is laminar, and may indicate a tonotopic arrangement [1, p. 261].

Further connections of the cochlear nucleus include contralateral connections to the inferior colliculus. The medial superior olive makes only an ipsilateral connection to the inferior colliculus. In organisms with lateral superior olive, both ipsilateral and contralateral connections to the inferior colliculus exist. The inferior colliculus connects to both ipsilateral and contralateral medial geniculate bodies.

The medial geniculate body makes ipsilateral connection to the auditory cortex.

(Here is a good diagram of these connections in the human brain.)


The “olivo-cochlear bundle” of the cochlear nerve is efferent and has been described in man, cat, rat, opossum, pigeon, and caiman [1, p. 261]. Given the broad range of taxa, the assumption that it also exists in cetaceans seems fairly safe.

These connections originate both ipsilaterally and contralaterally. The descriptions vary with the subject animal and the researcher publishing the description.

The contralateral connections stem from an area near the accessory olive, the retro-olivary group of neurons and trapezoidal body nucleus. The ipsilateral connections stem either from the S-shaped olivary segment or the pre-olivary nuclei for one bundle, and the reticular formation of the pons and medulla for the other. The reticulo-cochlear bundle is described from rodents. [1, pp. 261-263]

The two separate sources of fibers form a single bundle near the point of exit from the brain. In the inner ear, the bundle separates into various fasciculi, joining the cochlear nerve and also the intraganglionic spiral bundle [1, pp. 263-264].

In man, acetylcholinesterase containing fibers are found in the cochlear nerve trunk, suggesting yet more links to efferent fibers [1, p. 264].

2. How have efferent fibers been identified?

The histological tool of choice seems to be the use of injected horseradish peroxidase. Ketten has discussed HRP and another technique suitable when a subject will be sacrificed, but indicates that she mainly has to rely upon a technique applicable to fixed specimens, which only allows the elucidation of one fiber per specimen, and still takes six months or so in preparation time. According to Ketten, there is no mammalian auditory system which has had the efferent pathways completely mapped out. Acetylcholinesterase is selectively stained or tagged in order to identify efferent fibers.

Degenerative studies compare normal histological specimens with those where lesions or surgery destroys certain areas of the neural system. Loss of normally seen connections at the periphery indicates that the missing fibers were efferent.

A physiological study stimulated the crossed OCB at the floor of the fourth ventricle, and found activity only at the pre-olivary nuclei [1].

3. How could efferent input be considered in designing a neural network model of dolphin hearing?

Until more neuroanatomical work is done on dolphin auditory efferent pathways, some cues will still have to be taken from work done in other species. This is a hazardous step, since neuroanatomical work in bats shows large variations in efferent wiring across genera (Bishop & Henson 1988). Some speculation is unavoidable, but this is precisely where model generation should be able to contribute to biological research, by identifying the likely areas of interest and suggesting mechanisms of testing model predictions.

In the Bishop & Henson study mentioned above, some species of bat have systematic multiple efferent synapses on the outer hair cells.

Physiological work in some species has not shown any change in absolute thresholds when the efferent fibers to the auditory system are cut. However, there does appear to be a loss in frequency discrimination capability and also in raising the required signal-to-noise ratio for threshold of hearing (Iurato & Bari 1974). Models of the auditory system should attempt to produce a mechanism for the role of the efferent fibers in refining frequency discrimination and identification of signal in noise.

AL Bishop & OW Henson, Jr. 1988. The efferent auditory system in doppler-shift compensating bats. In: PE Nachtigall & PWB Moore, Animal Sonar: Processes and Performance. Plenum Press.

Iurato, S & MD Bari. 1974. Efferent innervation of the cochlea. In: WD Keidel & WD Neff (eds.), Handbook of Sensory Physiology (Vol. 1). Springer-Verlag, pp. 261-282.


inward direction of neural impulses, toward the central nervous system
basilar membrane
a membrane in the cochlea or inner ear dividing the cochlea and supporting the auditory sensory structure
on the other side
toward the top
outward direction of neural impulses, from the central nervous system toward the periphery
supply nerves to
on the same side
organized in ordered layers
a spatial arrangement that provides a “mapping” function
toward the bottom

The Transitional Fossil Existence Challenge (2005/02/24)

First, have a look at the following text:

This gradualism insisted upon by Darwin has proved increasingly embarrassing to modern scientists. If evolution occurred at an excruciatingly slow rate, then why can’t we find transitional forms in the fossil record? There should be literally millions of instances where a fossil manifests many of the characteristics of a reptile, but some of the characteristics of a bird (or vice versa)—where are those fossils? Darwin dodged this lack of evidential support for his theory by claiming that scientists had seen only a small portion of the fossil record, and it was spotty at best. Modern scientists have a much more complete picture of the fossil record—but, tragically, still no transitional forms. [Emphasis added — WRE]

This lack of evidence—confessed by committed evolutionists like Stephen Jay Gould—drove Gould to concoct the theory of “punctuated equilibrium.” We obviously don’t have space to discuss punctuated equilibrium here (for an excellent discussion, see the work of Bryan College professor Dr. Kurt Wise), but briefly this theory kicks neo-Darwinism into hyper-drive. Darwin’s gradualism must be discarded in order to save evolution! More to the point, Darwin’s theory must be re-interpreted to account for the lack of evidence precisely where Darwin told us we should expect to find evidence.

When we read Darwin himself, rather than modern textbooks about Darwin, we find what the scientific community has known for awhile: Darwin, and theories of evolution in general, are on shaky ground.

(Jeff Baldwin on “Worldview Blog”)

No, Jeff, evolutionary biology is doing just fine. Modern evolutionary biology textbooks are not “about Darwin”; they are about a branch of science that has gone a long way past where Darwin left off.

The text above has plenty of egregious errors. There’s the typical antievolutionist take on “punctuated equilibria”. I explain why several antievolutionist claims about PE are ill-founded in this essay. There’s the common error of saying that Darwin predicted that we should find “millions” of transitional forms, but that’s not what falls out when one applies some numbers to what Charles Darwin actually wrote.

But the claim that I would like to concentrate on here is the one I highlighted in bold above, that the fossil record has no transitional fossil sequences in it at all. This is hardly the first time that I’ve seen such a claim. It had been fairly common throughout my time online discussing these matters going back to the late 1980s. But around 1994 I decided to start documenting the claims made and the response to a challenge. If the claim is so good, I figured that the claimant would have no trouble at all explaining why real paleontological evidence should be set aside as not showing transitional sequences. This led to my development and deployment of the “Transitional Fossil Existence Challenge”.

Transitional Fossil Existence Challenge

Last Updated: 2005/02/24

The Claim:

Anti-evolutionists often make a claim that the fossil record contains no transitional fossils. This runs counter to the claims of many researchers in paleontology.

The Challenge:

This challenge is to show just how much familiarity the anti-evolutionist making the claim of no transitional fossil sequences has with the actual evidence of the fossil record. By making a universal claim concerning transitional fossils, the anti-evolutionist should be prepared to back up the claim with extended technical discussion of the reasons why all sequences that others believe to be transitional in nature really are not transitional. Because there have been many such sequences put forward by various researchers, this challenge focusses upon one case at a time. The first such case is found in:

Pearson, P.N.; Shackleton, N.J.; and Hall, M.A., 1997. Stable isotopic evidence for the sympatric divergence of _Globigerinoides_trilobus_ and _Orbulina_universa_ (planktonic foraminifera). Journal of the Geological Society, London, v.154, p.295-302.

Now, it is up to you to show why the fossil sequence described therein fails to show transitional fossils. After you outline your objections to this sequence, I have another 100 or so citations of sequences that are said to show fine grained transitions ready to go, one at a time, until either you demonstrate that none are actually transitional, or you give up your claim.

Consider yourself challenged.

Andrew MacRae pointed out the citation listed above. Other bibliographic entries come from the examples in Tables 1 & 2 in Roger Cuffey’s excellent paper, Paleontologic evidence and organic evolution, which can be found in Montagu’s “Science and Creationism” or the Journal of the American Scientific Affiliation 24(4), just in case you want to get a jump-start on the rest of the entries.

Please note that unfamiliarity with the reference above is a failure of the claim of absence of transitional sequences — the claim requires *complete* knowledge of fossil sequences, and unfamiliarity with any is prima facie evidence that the claimant doesn’t have the basis for the claim.

Andrew Macrae’s commentary on the cited paper:

In the example I cite above, it is a transition between two species that are assigned to separate genera. Furthermore, there are 4 other species “between” them, 3 of which are assigned to yet another genus. It could always be argued that the genera have been “oversplit” in the foraminifera, but that does not change the obvious morphologic pattern or the fact that one morphology incrementally diverged into two that remained subsequently distinct.

[End quote — A. Macrae, Message-ID <5prq71$d91$>]

Figures from the Pearson et al. paper are now on the WWW at

Evidentiary and Non-Evidentiary Responses to Challenges

There are two main ways in which respondents can deal with the Transitional Fossil Existence Challenge. The intellectually honest and appropriate way is with specific discussion of the fossil evidence as described and discussed in the primary literature. This is by far the least common approach taken by those who have been given the TFEC, and typically only follows after a long period of non-response, the elapsed time apparently serving as an index of the claimant’s unfamiliarity with the specific evidence.

The other category of approach is to ignore, so far as possible, any mention or discussion of actual fossil evidence. These varied strategies are what I term “non-evidentiary” responses, since they are completely independent of empirical data. There are many routes to achieving this end. The simplest is non-response. The challenged person may decide that not saying anything further is the best option, sometimes in the hope that there will be no long-term penalty for this behavior, and that eventually few, if any, persons will remember the abandonment of the original claim. Another common non-evidentiary response is digression. Bringing up a different topic as if it held some relevance to the TFEC allows someone to give a semblance of a reply, even though few will be fooled by it. Yet another strategy is to discuss theoretical issues as if theory did away with the need to actually look at the empirical data. A variant of the theory strategy is the quote-mining of those people who expound theory. Usually, though, quotes reveal nothing about the specific data at hand, and often come from sources whose opposition to anti-evolutionary action is otherwise well-known. Still another variant upon the theory strategy is the definition game. One can construct connotations of “transitional” such that no real-world evidence can satisfy all the piled-on conditions. It is useful to know when an anti-evolutionist simply defines evidence out of existence, though. Another possible tactic is to dismiss the taxonomic category from which the cited example comes. A respondent can claim that they really meant no transitional fossils in some other taxonomic hierarchy, but they often seem to forget that this means that the “no transitional fossils” claim is then self-admittedly false. A particularly brazen non-evidentiary response is to play an “even if” game, as in, “Even if this is true, it doesn’t mean anything.” That ignores that if the cited sequence does contain transitional fossils, it at least means that the claim of no transitional fossils is false.

The following is a short form for response to the TFEC, if a challenged person wishes to ignore the evidence and simply adopt one of the non-evidentiary tactics for their own. Simply indicate which one or more of the following Non-Evidentiary Response Items (NERI) fits what would otherwise involve a bunch of redundant typing.

Non-Evidentiary Response Items:

A. You have your faith; I have mine.

B. I meant that no vertebrate transitional fossils exist.

C. I meant that no transitional fossils above taxonomic rank ____________ (fill in the blank) exist.

D. I have quotes from _______________ (give list of names) that say that no transitional fossils exist.

E. My understanding of ________________ theory (fill in blank) is that transitional fossils cannot exist.

F. My connotation of “transitional fossils” is ____________ (fill in blank), which means that none can exist.

G. I have a cool rebuttal of ___________ (fill in blank). What were you saying about transitional fossils?

H. Even if the cited example does show transitional fossils, it doesn’t mean anything.

I. I cannot be bothered to support my claim, so I will not be giving you a reply.

J. I promise to support my claim Real Soon Now. I will be in touch. My reply will be devastating to you and completely and utterly convincing to everyone. Just you wait. It’s in the mail.

K. Provide the fossils for the transition from X to Y, which will let me ignore these fossils that actually exist. (Courtesy of “edwin voltaire” aka “evossler” 20030210.)

L. Person X says this challenge is bogus, therefore I don’t have to provide any response to actual evidence of transitional forms.

The Challenged:

The people whose names appear below all made a claim or implication of absence of transitional sequences, and were served up with a version of the Transitional Fossil Existence Challenge. This is a roster of who they were, when they were challenged, where they were, and how they responded to the challenge.

It should be noted that the TFEC may be issued to “trolls”, people who assert nonsensical claims in an annoying fashion in a bid for attention. It is unfortunately quite difficult to distinguish a “troll” post from the usual antievolution effort.

Date Name Forum/Source Response

19940228 Bruce Willis CONTROV Disappeared

19940309 Michael Funk CONTROV None

19940510 Johnnie Odom CONTROV None

19940714 Andrew Cummins Evolution “Prove all biologists accept it”

19940717 Ras Mikael Enoch t.o. None

19940718 Jim Pattison CONTROV “Can’t find the reference”

19940816 Charles Edward Evolution None

19940917 Davey Jones Evolution None

19941002 Lane P. Lester Evolution None

19941030 John Shirey t.o. None

19941129 Kevin Clark Evolution None

19941208 Doug Wagner Evolution None

19941214 Jim Loucks t.o. None

19950312 Mark Russell None

19950322 Ross Wolfle t.o. Implied recantation

19950401 Scott Brian Allen t.o. None

19950404 B. Schweig (?) t.o. “No time to do research”

19950407 Lawrence Free Email “I only meant vertebrate transitions”

19950514 Arthur Biele t.o.
Irrelevant re-posted criticisms of Hunt’s FAQ (19961116)
Irrelevant re-re-posted criticisms of Hunt’s FAQ (19990305)
First mention of Barnard’s paper (19990306)
Misquoted Barnard (19990306, M-ID
Misrepresented Barnard (19990306, M-ID
Claims differences are due to temperature or environment (19990306)
See for
my rebuttal (19990309)
Some further highly selective commentary on Barnard has been posted
by Biele, in which he misrepresents Barnard as disputing any
change at the species level or higher.

19950610 Tony Ermie Evolution None

19960408 Jahnu Das Email “I am really not qualified to discuss
evolution on a technical level.”

19960506 David Markwordt Evolution None

19960520 Ted Holden t.o. None

19960828 David Ford t.o. DF actually looked up the article, quoted
Barnard saying that he had transitionals across genera, but did not
admit existence of transitionals. Has since engaged in a great deal
of rhetorical excess, none of which disestablishes Barnard’s examples.

19961027 Steve Sorenson t.o. “You’ve got your faith; I’ve got mine.”

19961109 Tim Harwood t.o. None

19961230 Karl Crawford t.o. None

19970125 Herman Reimann t.o. None

19970224 Darren Serhal t.o. None

19970324 Eldridge t.o. “Put the paper on a WWW page.”

19970412 Joe Potter t.o. None

19970421 RevMike t.o. None

19970423 Larry Cavender t.o. “Do you believe the Bible?”

19970603 Yehuda Silver t.o. None

19970701 A Pagano t.o. Didn’t understand the logic behind the challenge;
failed to address the evidence for over three years.
2001/01/29: Whined that the Pearson citation was in a journal other
than “Science”; admitted that he was ignorant of the evidence
discussed by Pearson et alia.
2001/03/01: Posted a response saying that the Pearson et alia 1997
sequence didn’t show “nascent structures” and “increasing diversity”,
neither of which appeared in Pagano’s 1997 claim.
2001/08/04: Repost of the 2001/03/01 post, with some additional
comments about the lack of a reply from me (I’ve been writing up
my dissertation; Pagano is welcome to disagree with my assignment
of priorities.)
2002/01/08: Pagano posted claiming that I had never addressed six
specific issues he had raised. I posted on 2002/01/14 showing how
each of those topics were addressed by me in previous posts.
Further posts by Pagano have shown no reduction in his ignorance and
a considerable decline in his courtesy. It seems that each new
issuance of the TFEC results in a flurry of re-postings of old
refuted arguments by Pagano.

19970816 Jonathon O’Quinn t.o. None

19980717 Publius t.o. None

19981006 Alal t.o. None

19981110 t.o. None

19990107 Teno Groppi
“These figments of imagination are renewed constantly. It
used to be Archaoepteryx and the Equuine series. One they
were disproved, it was something else. Once that was
debunked it was another. Now this. How much you wanna bet
this is replaced by another wild claim next year?” (19990108)
“They are not transitions FROM anything, they are not
transitions TO anything. The entire claim is totally bogus and
a figment of your imagination. […] When did I agree to a
wager? Was that as one groundless as your alleged
transition?” (19990114)

19990224 Steve Sorenson (again) t.o. None

19990225 Mark Allison t.o “Worst case scenario (for me): all 100
of your examples are at least possible scenarios to prove you
completely correct. But… here are three reasons why this wouldn’t
prove ANYTHING:” No discussion of Barnard or the fossil evidence (19990304)

19990309 Katy Moffitt atl.general None

19990417 Rhett alt.religion.christian.roman-catholic None

19990421 Brad Clark alt.christnet None

19990505 MS Goodrich None

20000202 JerryG None

20000217 Todd None

20000815 Erik “Sorry, your challenge, as
written, is impossible. Trying to prove a negative is
impossible. The burden of proof lies on you to prove a
positive.” (2000/08/16)
Erik wasn’t asked to prove his entire claim all at once.
Erik was asked why the specific evidence cited should not
be considered transitional. Erik did not address the
existing evidence.

20001107 “Pastor Dave” Raymond alt.christnet Original
statement: “The fact remains, that there are no
transitional fossil records.”
Response to TFEC (2000/11/28): “Another faulty and false tactic.
It is never up to me to prove a negative. It is up to the ones
making the claim that something is the way they say it is, to
prove that it is. The fact remains, there are no transitional
Pastor Dave completely ignored the evidence of the fossils
and gave no reason to discount the cited example as
documenting a transitional fossil sequence.
2003/01: Pastor Dave has gone from asserting that there are
no species-to-species transitions to saying that there are
no kind-to-kind transitional fossils. What you hear is ratchet
noise from Dave’s furious backpedalling.

20010116 Ed Finn alt.politics.bush Original statement:
“The most shocking fact is that the fossil record has
absolutely no transitional forms between species.”
Response: None.

20010118 ‘d ocean’ Original statement:
“there are NO transitional fossils, and there is NO proof
that the fossil record confirms macro-evolution.”
Response: None.

20010120 John B. Williston Original
statement: “What would be nice would be a clear,
consistent and slowly gradual record of even *one* species’
transition. And to date, there is none to be had.”
Response: “More specifically, I should not have said that
*no* evidence for transitional forms exists; rather, I
should have said only that there is a startling *dearth* of
evidence.” (20010121)

20020320 “Amy Lynn” Original statement:
“There have been no transitional species. The fossil record
only shows fossils of different kinds. Noone can prove
definitively that those fossils were some kind of transitional
creature.” (20020320)
Response: None.

20021212 “Doug Matulis” Original statement:
“Transitional forms should be prolific. There are none.
Some have dreamed them up, but they are either non-existent
or far from conclusive.” (20021212)
“First, I am sure you know this is an unfair challenge, throw a
highly technical paper, loaded with terms I have not idea the
definitions of and expect a lay person develop and rebuttal.
I will give it a shot and post my response under a new
subject.” (20021216)
“Dana, your points are well taken and will be acted upon.”
(20021219 response to Dana Tweedy, who pointed out that Doug’s
original claim was based upon ignorance.)
(No further responses.)

20030206 “” Original statement:
“But yet, evolution is STILL a theory and there are still no
in-transition fossils. How do you explain that?” (20030206)
“Sending a BS, trick survey is not equivilent to
procurring a in-transition fossil. If you have so much
evidence of these changes, show me a fossil of the
in-transit form between archeoptriches(sp) and whatever
dinso-form it came from.” (20030210)

20030408 “Suzanne” Original statement:
“Because we still have one celled organisms. They are
plentiful. We still have living uncomplicated lifeforms.
And, the question is, where are the fossils, indeed. There
are no living examples, and there are no dead ones
either. Yet there are fossils of life abundant. But in the
fossil record, there are not any transitionals. How can it
be that the solid lifeforms lasted in the record, yet the
transitionals all disappeared, if they ever existed, that
is.” (20030408)
Response: None.

20040103 “Roy Jose Lorr” or.politics Original statement:
“I repeat: ‘No one has shown anything close to what
you claim… no “transitional fossils” and no evidence that
“speciation” is compatible with “evolution theory”.'”
Response: None.

20040104 “Laurie AppIeton” Original statement:
“Out of the millions of fossils in the world, not one
transitional form has been found. All known species show up
abruptly in the fossil record, without intermediate forms,
thus contributing to the fact of special creation.”
Response: None.

20050224 “Jeff Baldwin”
Original statement: “This gradualism insisted upon by Darwin has
proved increasingly embarrassing to modern scientists. If evolution
occurred at an excruciatingly slow rate, then why can.t we find
transitional forms in the fossil record? There should be literally
millions of instances where a fossil manifests many of the
characteristics of a reptile, but some of the characteristics of a
bird (or vice versa).where are those fossils? Darwin dodged this lack
of evidential support for his theory by claiming that scientists had
seen only a small portion of the fossil record, and it was spotty at
best. Modern scientists have a much more complete picture of the
fossil record.but, tragically, still no transitional forms.
Response: Pending.

No *evidentiary* response within a month causes the “Pending” to be changed to “None”. A “None” response can be changed to something else if an *evidentiary* response is eventually made, or a particularly revealing non-evidentiary response is made. Responses sent via non-public channels confer an irrevocable right of publication to Wesley R. Elsberry. I can’t have unquotable responses showing up in my incoming email or snailmail. I plan to create a web page that includes every follow-up made to the TFEC, whether the contents are relevant or not, for public documentation of all claims and counterclaims, arguments and rebuttals.

Mice with Second Sight

A news item reports that researchers at the Schepens Eye Institute have succeeded in regenerating an optic nerve in mice.

The research reached that stage by producing strains of mice that were genetically manipulated to not turn on a nerve growth inhibiting gene and also with reduced glial cell activity in the brain. So this is nowhere close to being made into a treatment for people, but it does give some information for directing lines of research toward that end.

Trying out the new plugin…

Just tried installing a plugin that will let me add formatted math stuff…

[tex]\displaystyle Joules = \sum _{i=1}^{n-1} {\frac {P_i + P_{i+1}} {2} * A [/tex]

This is the LatexRender plugin, which is nice if your server can handle [tex]\displaystyle \LaTeX[/tex] and ImageMagick.

Blog upgrade

I’ve upgraded the blog software to WordPress 1.5 from 1.2.1. With version 1.5 comes themes, which means I’ll need to do some tweaking to suit. It also brings improved “spam” comment handling, “pages”, and various other cool features.

One annoying thing that I’ll try to tweak is how the right hand column appears and disappears willy-nilly in IE 6 depending on how wide one sets the IE browsers.

Update: Shifting to the “Shaded Grey” theme seemed to work wonders with rendering under IE. The theme needs its own set of tweaks, but that will hopefully come as time goes by.

“whatcha readin’?” meme

From Profgrrrrl via Pharyngula:

1. Grab the nearest book.
2. Open the book to page 123.
3. Find the fifth sentence.
4. Post the text of the sentence in your journal along with these instructions.
5. Don’t search around and look for the “coolest”� book you can find. Do what’s actually next to you.

Well, this morning I would have had Terry Pratchett’s Feet of Clay Discworld book at hand, but since I finished it, I’m left with the nearest book on the reference shelf, Grier and Burk’s Biology of Animal Behavior. P. 123 is the start of Chapter 5, “The Evolution of Behavior: An Introduction”, and the fifth sentence is:

Other, more advanced evolutionary topics, such as evolutionarily stable strategies (ESSs, Chapter 14), are presented in other chapters, where appropriate.

Other books that are next to it on the reference shelf: Zar’s Biostatistics and the Chemical Rubber Company’s Standard Math Tables.

And I’m sorry to burst coturnix’s prediction on Pharyngula concerning the single quote that would be produced by Christian bloggers.

Good News, Bad News

In a good news item, The European Union rejected a bill to establish “software patents”. They were trying to call it “computer-implemented invention”, and it did not fly. Basically, the “software patent” issue pits businesses who want to claim patent protection for things like, oh, particular types of widgets in graphical forms, not just esoteric algorithms for data processing, against the open source community. Such patents, say the open source developers, elevate trivialities to protected status and inhibit the development of open source software systems. And I agree with the open source people. Patent offices have a poor track record on distinguishing between trivial developments that are simply things that most programmers would be capable of producing from genuine pieces of coding worthy of the name “invention”. When patents are afforded to the former, the result is a bunch of corporate bean-counters dictating terms to application developers for including particular shaped buttons on forms and the like. Since the basic idea of patenting items is to reward placing intellectual property in the public domain with a period of corporate monopoly, trivial “software patents” are a form of theft: they can provide a period of corporate monopoly for ideas that are simply part of the usual and normal development of the field, not ideas that significantly advance the state of the art.

In a bad news item, scientists have come up with even more evidence that (1) global warming is real and (2) global warming is accelerated by human-made greenhouse gasses. The reaction is typical:

But a spokesman for the Bush administration — which has been criticized for not taking global warming seriously — was unfazed by the latest news.

“Our position has been the same for a long time,” said Bill Holbrook, spokesman for the White House Council on Environmental Quality. “The science of global climate change is uncertain.”

Well, yes, science is uncertain in its findings, but what the White House spokesman is saying is that the sort of uncertainty generated by climate change studies is such that all the results may be safely ignored. This looks like further bad news on top of the original bad news. I think that it is not at all uncertain that there will be changes that affect day-to-day life for humans across the planet, even in the USA, if no effort is made to modify human contributions to greenhouse gasses.

Flu fading…

I’m happy to report that my flu symptoms have been diminishing over the course of Thursday. Now I just need to figure out getting to sleep. There was something making noise in the yard, so I had to check that out. It’s a bit foggy out. I didn’t find the proximate noise-maker, but away off to the west I could clearly hear the yips and howls of coyotes over on the Naval Weapons Test Station grounds. It’s a bit eerie standing in the dark and listening to that.

Diane tells me that she had a bit of a turn with coyotes this past weekend. She had Rusty and Glamdring out flying, and Farli and Ritka nosing around. There was a swampy area where she couldn’t see Ritka, but she could hear coyotes — and what sounded like a canid in distress. She said that this went on for about five very long minutes. Ritka then turned up, looking her usual happy self.

The Flu

OK, now I know why people took their chances of dying of exposure in lines last fall trying to get the flu vaccine. I didn’t get the vaccine then, and I came down with the flu this past Sunday.

In my case, I started off with a pounding headache, soon joined by fever. After two days of continuous headache, nausea and vomiting joined in. Today I got diarrhea, too.

I’ve only been able to take looking at the computer for a few minutes at a time. When the headache pain increases a notch, I know it is time to rest and relax, so far as I can.

This evening, I spent some time in between sleep and waking, where my brain noted, “Thinking in dreamworld — no pain. Thinking in reality — pain.” This week is turning out to be pretty unproductive.

That is, other than a couple of email messages I sent to Vincent Cassone at Texas A&M last Saturday, listing various online resources to get him better acquainted with the work of Michael Behe, whom he debated at A&M on Tuesday. See the Battalion article on the debate. It sounds like Cassone held his own with Behe, and I hope that what I sent helped him in part to prepare. Otherwise, I think this week is a write-off.

At the Week’s End

I am conducting an experiment in this post. I am pointing to an MP3 encoded sound file where I discuss some of the events of my week just past. (Sorry to those who tried to get this early on Saturday; I had messed up the URL for the file. It is fixed now.) Topics include my health, a talk I gave at UC Berkeley, news in the world of antievolution, computers and content management systems, and Diane’s outing with the hawks on the first weekend in February.

Here are some URLs to go along with the audio…

Where I work:

Ted Cranford’s page:

Georgia House Bill 179:

Links to non-Christian antievolution that Georgia House Bill 179 opens the door to:

General antievolution and the law:

PostNuke CMS:
CivicSpace CMS:
Moodle Courseware CMS:
LogiCampus CMS:

Rusty, Glamdring, and Orcrist flying:

Fisher and Falsehood

You might think with the title above I’m going to criticize something from noted 20th century evolutionary biologist and statistician Sir Ronald Fisher. You would be wrong. This time, I’m looking at an op-ed piece by Larry Fisher in the Searcy, Arkansas Daily Record. This Fisher is a justice of the peace in Beebe, Arkansas who supports the idea of adding an antievolution disclaimer to biology textbooks.

Now, Fisher’s article has an assortment of appeals to the authority of such luminaries as “[q]ualified scientists at” and “300 or more scientists with credentials from secular universities and employed as scientists or in teaching positions”. In the former case, those folks are pushing often refuted creationist claims, and in the latter it simply is not the case that all the signatories are either practicing scientists or teachers. The affiliations listed are simply the more impressive of either where the signatory works now or where they got a degree. David DeWitt, for example, is not a practicing scientific researcher in the field of neuroscience despite the listing of his affiliation with Case Western University. That’s where DeWitt got his degree. He now works for Falwell’s Liberty University and is an unabashed young-earth creationist. His last published neuroscience research article was dated 1998 (although he lists one on his CV as being “in progress”). While DeWitt may be teaching at Liberty University, the “Scientific Dissent from Darwinism” list misleads by implying DeWitt is active in neuroscience. Some of those signing the statement also had no problem with the idea of common descent, which is counter to the general antievolution message that Fisher wishes to deliver. I got into disputing the claims made by antievolutionists precisely because the promulgation of falsehood was antithetical to the Christian principles I grew up with. This means that I find myself arguing against shady tactics practiced by my fellow Christians a lot, since the sheer volume of problematic statements in antievolution material is just enormous. (I don’t hold back on problematic statements made by people simply because they are also anti-antievolution as well; there are a number of exchanges on the former Evolution Echo and on the newsgroup that show this as well.) The above case of the DI statement goes to the matter of shading what is true to puff it up a bit, to make it look more impressive than it is to someone who has all the relevant information to hand. This isn’t something that people whose motivation is to restore moral behavior should be doing.

But that’s just some of the usual flapdoodle one gets from antievolution advocates. Fisher manages to transcend that state with another falsehood…

It is interesting that when people are exposed to alternative scientific models they may actually see a better way to explain the data. This is what has recently happened with Antony Flew. He has been called the most influential atheist philosopher in the world with his arguments against the existence of God being found in many college textbooks and anthologies.

Mr. Flew read Michael Behe’s “Darwin’s Black Box” and called it an “incredible book.” As a result of Flew’s exposure to Intelligent Design theory and the “irreducible complexity” examples in Behe’s book, he has become a deist. He has concluded that the information content of DNA is unexplainable without postulating an intelligent mind behind it all.

This assertion of Fisher’s isn’t simply a falsehood, it isn’t just mildly off the mark; it is oriented precisely 180 degrees away from the truth. I asked James Lippard about this assertion by Fisher, and he sent Fisher the following email (posted with Lippard’s permission):

Mr. Fisher:

I read your recent column at,
where you write:

    It is interesting that when people are exposed to alternative scientific models they may actually see a better way to explain the data. This is what has recently happened with Antony Flew. He has been called the most influential atheist philosopher in the world with his arguments against the existence of God being found in many college textbooks and anthologies.

    Mr. Flew read Michael Behe’s “Darwin’s Black Box” and called it an “incredible book.” As a result of Flew’s exposure to Intelligent Design theory and the “irreducible complexity” examples in Behe’s book, he has become a deist. He has concluded that the information content of DNA is uexplainable without postulating an intelligent mind behind it all.

This is incorrect. Flew’s deism was not a result of Behe’s book, but because of Gerald Schroeder’s _The Hidden Face of God_–and Flew has been inconsistent of late about what his views actually are, or whether he finds Schroeder plausible.

Flew was initially impressed with Behe’s book, but concluded that it was incorrect after reading Kenneth Miller’s _Finding Darwin’s God_:

    To illustrate these points about confirmations of antecedent beliefs I recommend a book recommended to me by Richard Dawkins for its total discrediting of Michael J Behe’s Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Simon and Schuster, 1996). That book is Kenneth Miller’s Finding Darwin’s God (New York: Harper Collins, 1999). Miller is a cradle Catholic, but that does not prevent him from destroying Behe’s argument point by point, and making scathing comments on Behe’s failure to attend to recent relevant research findings in what is after all Behe’s own field.

This is the concluding paragraph of a review, by Flew, of a book by Kai Nielsen. The full review may be found here:

For more information about Flew’s current rather confused state of mind (he keeps changing his position even about whether or not he has changed his position), see:

It’s amazing how sleazy and dishonest Christians have been in taking advantage of Flew’s deteriorating mental condition.

James Lippard

Birdbrains – The Smart Kind

Scientists: ‘Birdbrained’ doesn’t mean stupid

Jarvis, who studies how birds learn vocalizations such as songbird songs and imitated speech in parrots, said their behavior can be surprisingly complex.

They can use tools, they can use songs and imitate human language to communicate and they can count.

The article doesn’t mention the groundbreaking work of Irene Pepperberg in demonstrating the conceptual capabilities of parrot cognition using human language for communication.

There are times when I definitely feel that Rusty and Glamdring, the Harris’s hawks, have gotten the better of me, and raptors aren’t particularly noted for avian intelligence.

There was another interesting passage in the news article:

The names scientists use to describe a bird’s brain structure date back 100 years to a German scientist, Ludwig Edinger, who is considered the founder of comparative neuroanatomy.

“A lot went into trying to support the idea of a human’s place in the evolutionary scheme of animals. They didn’t follow Darwin’s view that evolution was a tree,” Jarvis said.

They tried to link it to religion — a linear system where god created one creature, not good enough, then created another creature, not good enough and then created human — perfect,” he added.

“It was beautiful story but it wasn’t true.”

I’d prefer to have a look at Edinger’s work myself before blithely accepting this construction of events. However, if this is correct in its broad outlines, we would have an example of what Darwin himself referred to as the unwholesome power of a false fact:

False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for every one takes a salutary pleasure in proving their falseness.

End of the Week

This was my first part-time back to work week since I went on disability following surgery last October. I commuted to the office three days this week. All in all, things were OK. I’m more tired in the evenings, but that is only to be expected.

The dogs are being left out while I’m at work. Farli gets a bit barky during the day, which can make it a bit harder to rest after arriving home. We’ll see how things develop.

Gonzales is In…

Alberto Gonzales has been confirmed and sworn in as our new Attorney General of the United States of America. And so the denial of any sort of conscience concerning the wholesale violation of human rights that our once-proud country now engages in continues. Having started with the presidential election of 2004, we now confirm and embrace the architect of the policies that have ruled at Guantanamo Bay and at Abu Ghraib.

We’ve sent a message to the rest of the world, loud and clear: the practice of democracy in the USA is too weak, too insecure, to both retain its principles and also meet the challenge posed by motley groups of barely-organized thugs.

Congratulations, thugs, you have humbled the USA in a way that I could not have believed would come to pass within my lifetime. You may not get us to change our foreign policy or capitulate to any of your demands, but you did get us to give up the practice of recognizing innate human rights as a matter of course, to reverse centuries of jurisprudence and consider people guilty until proved innocent, and to deny certain liberties even to our own citizens. Ah, well, the society we built and nurtured up until a few years ago was a nice experiment while it lasted.

The Rude Pundit held forth on the peculiar position of Senator John McCain who voted to confirm Gonzales, and is also the only member of the Senate known to have himself undergone treatment that we used to call “torture” before Gonzales helped redefine the term. While I generally don’t go in for the profanity that marks the Rude Pundit’s posts, the content is on the money in this one.