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Date: 2002/05/28 19:50:34, Link
Author: rafe gutman
am i to understand that dembski thinks that all proteins interact with the same binding affinity?  that's a pretty ridiculously wrong assumption.

also, does dembski think that all proteins are expressed at equal concentrations in the bacterium at any given time?  that is also fabulously wrong.

i also noticed that dembski does not factor in the volume of the cell in his calculation.  his formula would give the same value for the flagellar components expressed in the bacterium at physiological concentrations as it would for 4900 individual proteins floating around a pool.

i noticed a distinct similarity between dembski's formula and a common situation used in probability questions in introductory statistics.  a box is filled with pieces of paper with numbers written on them.  the student is asked to calculate the probability of a certain outcome when one or more pieces of paper are removed from the box, with replacement.  by "replacement", i mean that each time a piece is drawn, it is put back into the box before the next piece is drawn.  does dembski really believe that a cell behaves in this manner?  that the bacterium will "draw" 250 proteins from a pool at random (with replacement), test the entire combination for flagellar formation, then if it fails put them all back and start over again?

how can anyone take this seriously?

Date: 2002/06/03 21:54:07, Link
Author: rafe gutman
IDists like to complain that they are being treated unfairly, that their ideas are being dismissed without being considered or discussed.  that may be a fair complaint, but when these very same IDists abuse any display of open-mindedness made by members of the scientific community, they absolve their right to complain.  i'd like this thread to be a place where ID critics can post examples of IDists confusing open-mindedness with support.

one example of this is when IDists use book sales as an indicator of the success of ID.  considering that an individual has to first buy the book in order to read it, it doesn't necessarily mean that they will then agree with the arguments presented within.  on that note, it is interesting what IDists consider to be an endorsement of their work.  consider this one, which is printed on the dust jacket of no free lunch:
I disagree strongly with the position taken by William Dembski. But I do think that he argues strongly and that those of us who do not accept his conclusions should read his book and form our own opinions and counter-arguments. He should not be ignored.

Michael Ruse, Lucyle T. Werkmeister Professor of Philosophy, Florida State University; editor of Biology and Philosophy; author of Monad to Man and many other books on Darwinism

IDists have even tried to spin disagreement in their favor:
"If we're generating such strong, visceral responses, we must be doing something right." william dembski

so even if a scientist disagrees with ID, they interpret that to mean that ID is taken seriously.

i'd like to keep this thread open to more quotes and examples of how IDists have preyed upon the open-mindedness of scientists and perverted their comments to support ID.

Date: 2002/09/24 13:45:26, Link
Author: rafe gutman
have you ever heard behe (or more recently dembski) imply that subsets of IC systems have no function?  i certainly have.  however, in a recent internet discussion over on ISCID, dembski clearly stated that that was false, and that ID critics were misrepresenting their opinion.  in his own words,
You've charged me with moving the goalposts and adjusting the definition of irreducible complexity because I require of evolutionary biologists to "connect the dots" in a causally convincing way. The dots here are functional precursors that could conceivably have evolved into the final system of interest. You state that previously I claimed that the dots couldn't exist because they wouldn't be functional. Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right. The point is not whether subsystems can be functional on their own but whether they can exhibit the same function in the same manner as the system in question. You misrepresent our position.

then later, when presented with quotes implying such (which will be given later):
I wrote, "Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right." Both Behe and I have always defined IC with reference to the basic function of the system in question (if we've not said it explicitly -- and I have in NFL -- then a charitable reading would have granted that -- neither Behe nor I are that stupid). We therefore left open the possibility of subsystems having function in their own right. You and Yersinia charge us with a denial.

one of the key arguments of irreducible complexity being a roadblock to evolution is the lack of "functional intermediates" for selection to act upon.  if a purportedly IC system has 20 components, and homologues to all 20 are observed in 20 separate systems, then an IDist might propose that all 20 components had to come together in one step in order for the IC system to evolve.  of course, to say this is to deny that 3, or 5, or 10 components could have a function all to their own (whether it be the IC function or something else).  i'd like this thread to serve as a place where ID critics could post quotes of behe or dembski, or any other IDist where they propagate this myth.  please indicate the source of the quote in your post.  i'll post my initial contributions below.

Date: 2002/09/24 14:05:49, Link
Author: rafe gutman
michael behe's original definition of irreducible complexity:
"a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.  an irreducibly complex biological system, if there is such a thing, would be a powerful challenge to darwinian evolution.  since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." (DBB page 39)

dembski's definition of IC, NFL:
"A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system." (page 285)

"a flagellum without its full complement of protein parts does not function at all. Behe therefore concludes that if the Darwinian mechanism is going to produce the flagellum, it will have to do so in one generation." (page 251)

"To achieve an irreducibly complex system, the Darwinian mechanism has but two options. First, it can try to achieve the system in one fell swoop. But if an irreducibly complex system's core consists of numerous and diverse parts, that option is decisively precluded. The only other option for the Darwinian mechanism then is to try to achieve the system gradually by exploiting functional intermediates. But this option can only work so long as the system admits substantial simplifications. The second condition [that the irreducible core of the system is at the minimal level of complexity needed to perform its function] blocks this other option. Let me stress that there is no false dilemma here-it is not as though there are other options that I have conveniently ignored but that the Darwinian mechanism has at its disposal." (page 287)

by john bracht in a metanexus article entitled: Knotty Pine and Corroding Coins
"In order for the fitness function to have smoothly sloped sides rather than sharp cliffs, there must be a way to gradually build a flagellum with fitness increases at each step as parts of the system are added. It is common for biologists to do mutation experiments in which they destroy some component of a molecular system and see whether it still works; with the flagellum they have found that all the components are required for function. In other words, the intermediates are non-functional and thus convey no selective advantage."

and also:
"In contrast to the coin-flipping machines in which a sequence has progressively greater selective value the more heads it contains, there is no advantage in having a nearly complete flagellum."

from washington times article entitled: Challenging Darwin by jen waters:
"Mr. Behe argues that cells are full of "molecular machines." All the parts must be there at once for the "molecular machines" to work correctly. (In the same way, all the pieces of a mousetrap must be present for it to operate properly.) Taking away parts from the molecular machines of a cell would make them stop working, which is why Mr. Behe believes life appears to be designed."

does anyone have any more examples?  also, if you have examples where behe or dembski acknowledge that subsets of IC systems can be functional, let me know.  so far, i've found no such acknowledgement in any of their popular writings.

Date: 2002/12/05 17:13:26, Link
Author: rafe gutman
allen orr recently wrote a review of dembski's "no free lunch" in the boston review.  dembski wrote a response to it, and orr responded to that:

this article is currently being discussed on several intelligent design fora (such as ARN and ISCID), but considering the intense moderation/censorship of those sites, i thought i would bring the topic here for discussion.  those critics of ID who are concerned that their comments will be censored can post them here.

here is the intro:
Allen Orr wrote an extended critical review (over 6000 words) of my book No Free Lunch for the Boston Review this summer ( The Boston Review subsequently contacted me and asked for a 1000 word response. I wrote a response of that length focusing on what I took to be the fundamental flaw in Orr's review (and indeed in Darwinian thinking generally, namely, conflating the realistically possible with the merely conceivable). What I didn't know (though I should have expected it) is that Orr would have the last word and that the Boston Review would give him 1000 words to reply to my response (see the exchange in the current issue at

In his reply Orr takes me to task for not responding to the many particular objections he raised against my work in his original review, suggesting that this was the result of bewilderment on my part and intelligent design running out of steam and not, as was the case, for lack of space. This sort of rule-rigging by Orr and the Boston Review -- give the respondent a little space, and then let the original author crow about winning -- is to be expected. I actually find it encouraging, taking it as an indication of intelligent design's progress. Orr's review and follow-up hardly spell the death-knell for intelligent design or for my work in this area. Sooner or later (and probably sooner) Orr will find himself in a forum on intelligent design where the rules of engagement are not rigged in his favor. I look forward to his performance then.

Date: 2002/12/17 18:45:01, Link
Author: rafe gutman
i'd like to use this thread to collect references to articles and research relevant to the evolution of the immune system.  i imagine that i'll be the only one contributing to this, but others are certainly welcome.  i included several references in my posts in an ISCID thread on the topic, and i'll probably copy my posts from there to here.

there are also some good references here.

Date: 2002/12/17 18:58:06, Link
Author: rafe gutman
from the ISCID thread:

martin poenie:  Again Inlay refers to ITAMs in a tunicate gene. This is a reference to a protein called A74 that has no similarity to any other known protein. So what are ITAMs? ITAMs are an arrangement of two tyrosines in a peptide with a certain spacing between them. Tyrosines are widely used in cell signaling. When phosphorylated, they can become ligands for proteins with SH2 domains. What makes ITAMs special is that there are proteins such as ZAP70 that contain dual SH2 domains and bind to the ITAM phosphorylated tyrosines as a unit. At present, no such protein has been identified in tunicates. The ITAM motif is based on four residues. It is possible that these are ordinary SH2 binding sites and that no dual SH2 domain-containing will be found. Until and unless one does find such a protein this is not a compelling argument. If proteins with these dual SH2 domains are found in tunicates, then it becomes a good argument.

rafe:  i'm not an expert on signal transduction, but it seems pretty clear that A74 is involved in immune-related signal transduction, and that tyrosine phosphorylation of the ITAM is part of it. as for the SH2-containing proteins, i should point out that homologues for syk and ZAP70 have been discovered in organisms as distant as hydra [1], and as similar (to tunicates) as sea urchin [2]. additionally, a CD45 homologue, which can augment signaling through ITAMs, was found in hagfish [3]. so while we don't have a tunicate syk-family homologue, many of the other pieces are already in place. it's not unreasonable to think that the downstream targets of A74 will be identified soon, i guess we can reserve judgement til then. do you think it will be homologous to syk/ZAP70?

[1] Steele RE, Stover NA, Sakaguchi M.
Appearance and disappearance of Syk family protein-tyrosine kinase genes during
metazoan evolution.
Gene. 1999 Oct 18;239(1):91-7.

[2] Sakuma M, Onodera H, Suyemitsu T, Yamasu K.
The protein tyrosine kinases of the sea urchin Anthocidaris crassispina.
Zoolog Sci. 1997 Dec;14(6):941-6.

[3]Nagata T, Suzuki T, Ohta Y, Flajnik MF, Kasahara M.
The leukocyte common antigen (CD45) of the Pacific hagfish, Eptatretus stoutii:
implications for the primordial function of CD45.
Immunogenetics. 2002 Jul;54(4):286-91.

i should also note, in reference to dr. poenie's argument, that the genome of a tunicate has been sequenced and dozens of zap-70/syk homologues have been found.  i'm not sure what the best way to search through it is, but i entered "syk" into the search engine for the tunicate genome and found a bunch of hits.  here's one

Date: 2002/12/17 22:17:31, Link
Author: rafe gutman
although it doesn't reference anything, i came across a post of mine where i present a model for the origin of the adaptive immune system.  since it's original material (the wording, that is, the model itself has been around for awhile), i thought i'd post it here as well:

here's a run down of the general details of this model

1. the RAG genes and RSSs were originally a transposon, and the RAG proteins had transposase activity.
2. a gene existed in the ancestor to the jawed vertebrates that encoded a receptor with at least one immunoglobulin domain
3. this gene was only expressed in a somatic lineage, like hemocytes
4. the receptor could activate a pathway somehow involved in immune-related function
5. the RAG transposon integrated into the receptor near the binding site-coding region.
6. once inserted, the transposase
would be under the receptor's transcriptional control.
7. the RAG's ability to reassemble the receptor gene once activated was sloppy, and made slight sequence changes upon reassembly.
8. those changes were beneficial to the host

and the evidence supporting it:

1. there seems to be ample evidence suggesting that the RAG genes were once transposases, do you dispute this? the fact that they have transposase activity (in vitro) basically says it all.

2. the immunoglobulin domain is well-represented in nearly all organisms (even prokaryotes, i think). because its structure is so stable, a large portion of cell-surface molecules possess it, even some related to immunity (outside of the jawed vertebrates). however, no direct homologue to the antibody proteins have been found. so here is a prediction of the model: a non-rearranging receptor with an immunoglobulin domain existed in the ancestor to the jawed vertebrates. of course, this ancestral gene may no longer exist, but if it is ever discovered, that would fill in a major hole.

3. a lot of genes have tissue specific expression. as for the extant antibody genes, they are heavily regulated by enhancers (because of the need to prevent premature recombination, or recombination on both alleles). there's no reason to think that the enhancer wasn't there in the ancestral receptor (such as, if it was located between the V and J segments).

4. see 2.

5. this is the only step that appeals to chance. as yersinia said, there could have been many integrations by transposons (our genome is littered with remnants of retrotransposons). all it takes is one to be beneficial, and it will become fixed into the population.

6. a common molecular technique is transgenics, where whole genes are inserted into the chromosome randomly. one of the main problems with this approach is the lack of consistency in transgene expression. this is because the transgene becomes subject to the local transcription control. unless the transgene has a really powerful promoter, it's uncertain whether or not it will be expressed correctly.

7. the current mechanism of RAG-mediated recombination is sloppy. one of the reason is through the generation of hairpin loops at the two exposed ends. this is intrinsic to the activity of the RAG and is common to transposases (in fact, this is one of the observations that led scientists into thinking the RAGs were originally transposons).

8. here the evidence may never be to your satisfaction, but it's very reasonable to suppose that a high rate of mutation would benefit immune receptors. why do you think new flu vaccines come out every season? because the influenza's receptors can mutate very rapidly to avoid host recognition. furthermore, they don't need to mutate drastically and change the total structure of their receptors, only just enough to hamper the host's receptor's binding ability. if during tthe lifetime of the first RAG-integrated organism, one of the thousands to millions of hemocytes alive at the time form a receptor beneficial to the host, this will increase the host's chances for survival and the nature will have something to select upon.

maybe this requires more evidence to convince you, but is it really that unreasonable?

Date: 2002/12/17 22:24:04, Link
Author: rafe gutman
here's a link to a recent article on the discovery of lymphocytes in lamprey:

another post i found on ISCID:

a couple of interesting papers on the immune system have popped up recently:

1.  Mayer WE, Uinuk-Ool T, Tichy H, Gartland LA, Klein J, Cooper MD.
Isolation and characterization of lymphocyte-like cells from a lamprey.
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14350-5.

this paper presents evidence for the existence of lymphocytes (cells intimately involved in the adaptive immune response) in lampreys, which don't have an adaptive immune system.  previously, one could have argued that rearranging antigen receptors and lymphocytes were irreducible.  now it doesn't look like that is the case.

2.  Uinuk-Ool T, Mayer WE, Sato A, Dongak R, Cooper MD, Klein J.
Lamprey lymphocyte-like cells express homologs of genes involved in
immunologically relevant activities of mammalian lymphocytes.

Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14356-61.

this article, the complement to the previous article, shows that the lamprey lymphocytes express genes similar to ones expressed in mammalian lymphocytes.  these genes are also involved in the adaptive immune response in mammals, so it's strange that they are present in lamprey.  incidently, both these articles are freely accessible online.

3.  Dodds AW.
Which came first, the lectin/classical pathway or the alternative pathway of
Immunobiology. 2002 Sep;205(4-5):340-54.

this article provides a model for the evolution of the complement system.  if paul wants to call the author's model "storytelling", he's free to do so, but now it's not just some random internet poster's idea.

i won't quote his model (it spans 2 pages), but he does say this about the model:

"the scheme outlined in figures 5 and 6 involves a stepwise increase in effectiveness of the system, each step giving benefit to the species involved."

since the time this thread began, probably a dozen articles have been published that support the notion that the immune system evolved.  has ID advanced in any way since then?

Date: 2002/12/17 22:32:20, Link
Author: rafe gutman
here's an extremely important article from nature immunology:

Nat Immunol 2002 Dec;3(12):1200-7
Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate.

Cannon JP, Haire RN, Litman GW.

[1] Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA. [2] All Children's Hospital, 801 Sixth Street South, St. Petersburg, FL 33701, USA.

The evolutionary origin of adaptive immune receptors is not understood below the phylogenetic level of the jawed vertebrates. We describe here a strategy for the selective cloning of cDNAs encoding secreted or transmembrane proteins that uses a bacterial plasmid (Amptrap) with a defective beta-lactamase gene. This method requires knowledge of only a single target motif that corresponds to as few as three amino acids; it was validated with major histocompatibility complex genes from a cartilaginous fish. Using this approach, we identified families of genes encoding secreted proteins with two diversified immunoglobulin-like variable (V) domains and a chitin-binding domain in amphioxus, a protochordate. Thus, multigenic families encoding diversified V regions exist in a species lacking an adaptive immune response.

pubmed link

link to article

incidently, i did a blast search of one of these genes on the recently-sequenced ciona intestinalis (tunicate) genome, and got a hit.

Date: 2002/12/17 22:38:08, Link
Author: rafe gutman
last one for now:

pubmed link

Immunobiology 2002 Sep;205(4-5):467-75

The biological functions of MBL-associated serine proteases (MASPs).

Hajela K, Kojima M, Ambrus G, Wong KH, Moffatt BE, Ferluga J, Hajela S, Gal P, Sim RB.

Department of Biochemistry, University of Oxford, UK.

The Mannose-binding lectin-associated serine proteases (MASPs) have been the subject of intensive research particularly over the past 10 years. First one, then two, and currently 3 MASPs have been characterized. Initially it was thought likely that the MBL + MASPs system would resemble very closely the C1 complex of the complement classical pathway, and that MASP1 and MASP2 would have similar activities to their classical pathway homologues C1r and C1s. MASP2 does certainly have similar activities to C1s, but MASP1 does not have the activities of either C1r or C1s. MASP1 has been thought to act on the complement system by cleaving C3 directly, but work with recombinant and purified native MASP1 shows that direct C3 cleavage by this protease is very slow, and may not be biologically significant. MASP1 and MASP2 appear not to have such a narrow specificity as C1r and C1s, and may have significant substrates other than complement proteins. As an example, MASP1 does cleave fibrinogen, releasing fibrinopeptide B (a chemotactic factor) and also cleaves and activates plasma transglutaminase (Factor XIII). These reactions are also relevant to defence against microorganisms, and may represent a biologically significant action of MASP1.

this is a review article that mentions an interesting finding, that a serine protease exists that has substrates in two functionally different pathways, the blood-clotting system and the complement system.  i looked up the reference, but the article it mentions hasn't been published yet.  i guess we'll have to wait til then to see the details.

Date: 2002/12/18 18:13:47, Link
Author: rafe gutman
from nature science update:

Back two bases

Stripped down genetic code provides candidates for first molecules of life.

Chemists in the United States have constructed the simplest possible genetic language. Like Morse or binary code, it has only two letters - but it can orchestrate some of the basic molecular reactions needed for life to evolve.

This stripped-down genetic scheme might provide clues about how life began in the chemical soup of the early Earth, say its developers John Reader and Gerald Joyce of the Scripps Research Institute in La Jolla, California1.

Today, the recipes for life - RNA and DNA - are normally written in a four-letter molecular alphabet: the bases adenine (A), guanine (G) and cytosine ©, together with thymine (T) in DNA or uracil (U) in RNA. Each gene in DNA is a sequence of A's, G's, C's and T's.

But these bases aren't easy to make from the chemical constituents of the early Earth, point out Reader and Joyce. So they may not have been available to build molecules capable of carrying out the basic chemical processes of life, such as replication and catalysis.

A simpler two-base molecule might have stood a better chance, argue the duo. They have made a two-letter ribozyme - a molecule that helps another to stick to it. These catalysed link-ups are necessary to construct the molecular chains of the genetic molecules DNA and RNA.

Most biological catalysts, or enzymes, are proteins. But ribozymes are made from RNA. Because they can both catalyse reactions and hold and transmit genetic information, RNAs could have provided the molecular basis of life before proteins and DNA evolved.

Pair bonding

Using just two bases, Reader and Joyce mimicked the R3 ligase ribozyme, a stretch of RNA that latches onto another RNA molecule.

Part of the R3 ribozyme has a base sequence that matches that on its RNA target molecule. The researchers constructed this binding sequence and target from A and U bases alone.

Then, for technical reasons, they replaced the A's with a non-natural base called diaminopurine (D). The resultant ribozyme can be copied without the need for G or C bases. Copying is a necessary part of the process of finding a two-letter mimic.

The researchers then eliminated all of the G's that they could from the R3 molecule while still retaining some of its catalytic behaviour (it can manage without C's). All but three could go; if the researchers took any of those out, the molecule was no longer catalytic.

To get further, the researchers abandoned rational design and turned to in vitro evolution. They replaced the remaining G's at random with U or D, while shuffling a few of the other U's and D's in the molecule.

None of the products made this way is a particularly stunning catalyst. But they work. The best, containing just U and D, links to the RNA target 36,000 times faster than in the absence of any catalyst at all. In other words, a two-letter ribozyme is a lot better than nothing.

D isn't too difficult to create from the kind of ingredients that were probably available on the early Earth, say Reader and Joyce. They also point out the advantage of an RNA-like molecule that contains no C: cytosine decomposes quite quickly if it gets warm.

Date: 2002/12/18 18:24:29, Link
Author: rafe gutman
here's a good recent discussion of the implications of the finding of a proto-immunoglobulin in amphioxus, branchiostoma floridae:

(in nature immunology)

The origins of the adaptive immune system: whatever next?

The discovery of a V-like Ig multigene family in the protochordate amphioxus provides new insights into the evolution of the adaptive immune response.

Diversity is at the same time the essential product of evolution and the essential substrate on which it must act. Although diversity can be the result of many different pressures and mechanisms, it is particularly evident and rapidly evolving in the responses of hosts to pathogens and parasites. Of the many defense systems described from the simplest single-celled bacteria to the most complicated plants and animals, none has been more intensively studied than the mammalian adaptive immune system. It has only recently become apparent that the adaptive immune system arose in the jawed vertebrates, but little is known about the deeper origins of this system or the relationship with other defense systems in nonvertebrate organisms. In this issue of Nature Immunology, Litman and colleagues describe a set of newly identified sequences from the protochordate amphioxus (Fig. 1), which make up a diversified multigene family and could hold some clues to the emergence of the adaptive immune system.

for the rest of the article, follow the link at the top.

Date: 2003/03/21 16:20:56, Link
Author: rafe gutman
it's been known for several years now that the RAG proteins can mediate transposition in vitro, providing pretty strong evidence for the theory that the RAG genes evolved from an ancient transposase (though not the only evidence).  skeptics of the theory claim that the ability to catalyze a reaction in vitro does not necessarily mean that it does so in vivo, or more to the point, that it did so.  there is some basis to this argument.  additionally, it has been theorized that RAG-mediated transposition in vivo could be a source of mutation.  the paper below not only demonstrates that RAG proteins can act as transposases, but also that the activity is possibly tumorigenic:

In vivo transposition mediated by V(D)J recombinase in human T lymphocytes

Terri L. Messier, J.Patrick O’Neill, Sai-Mei Hou, Janice A. Nicklas and Barry A. Finette

The rearrangement of immunoglobulin (Ig) and T-cell receptor (TCR) genes in lymphocytes by V(D)J recombinase is essential for immunological diversity in humans. These DNA rearrangements involve cleavage by the RAG1 and RAG2 (RAG1/2) recombinase enzymes at recombination signal sequences (RSS). This reaction generates two products, cleaved signal ends and coding ends. Coding ends are ligated by non-homologous end-joining proteins to form a functional Ig or TCR gene product, while the signal ends form a signal joint. In vitro studies have demonstrated that RAG1/2 are capable of mediating the transposition of cleaved signal ends into non-specific sites of a target DNA molecule. However, to date, in vivo transposition of signal ends has not been demonstrated. We present evidence of in vivo inter-chromosomal transposition in humans mediated by V(D)J recombinase. T-cell isolates were shown to contain TCR(alpha) signal ends from chromosome 14 inserted into the X-linked hypo xanthine–guanine phosphoribosyl transferase locus, resulting in gene inactivation. These findings implicate V(D)J recombinase-mediated transposition as a mutagenic mechanism capable of deleterious genetic rearrangements in humans.

(emphasis mine)

Date: 2003/04/05 16:47:32, Link
Author: rafe gutman
this is more of a reminder to myself to read this article, since it is now freely available online:


Roth DB.
From lymphocytes to sharks: V(D)J recombinase moves to the germline.
Genome Biol. 2000;1(2):REVIEWS1014. Review.

The antigen-receptor genes of vertebrates are rearranged by a specialized somatic recombination mechanism in developing lymphocytes - and, unexpectedly, also in the germline of cartilaginous fishes. The recombination system that carries out these DNA rearrangements may thus be a significant evolutionary force, perhaps not limited to rearrangements at antigen-receptor loci.

Date: 2003/04/07 19:43:22, Link
Author: rafe gutman
here's a group that has found functional homologues for some human TCR beta V pseudogenes in chimpanzees. check it out

Analysis of the TCR(beta) Variable Gene Repertoire in Chimpanzees: Identification of Functional Homologs to Human Pseudogenes

Dirk Meyer-Olson*, Kristen W. Brady*, Jason T. Blackard, Todd M. Allen*, Sabina Islam*, Naglaa H. Shoukry, Kelly Hartman*, Christopher M. Walker and Spyros A. Kalams2

The Journal of Immunology, 2003, 170: 4161-4169.

Chimpanzees are used for a variety of disease models such as hepatitis C virus (HCV) infection, where Ag-specific T cells are thought to be critical for resolution of infection. The variable segments of the TCR(alpha/beta)  genes are polymorphic and contain putative binding sites for MHC class I and II molecules. In this study, we performed a comprehensive analysis of genes that comprise the TCR  variable gene (TCRBV) repertoire of the common chimpanzee Pan troglodytes. We identified 42 P. troglodytes TCRBV sequences representative of 25 known human TCRBV families. BV5, BV6, and BV7 are multigene TCRBV families in humans and homologs of most family members were found in the chimpanzee TCRBV repertoire. Some of the chimpanzee TCRBV sequences were identical with their human counterparts at the amino acid level. Notably four successfully rearranged TCRBV sequences in the chimpanzees corresponded to human pseudogenes. One of these TCR sequences was used by a cell line directed against a viral CTL epitope in an HCV-infected animal indicating the functionality of this V region in the context of immune defense against pathogens. These data indicate that some TCRBV genes maintained in the chimpanzee have been lost in humans within a brief evolutionary time frame despite remarkable conservation of the chimpanzee and human TCRBV repertoires. Our results predict that the diversity of TCR clonotypes responding to pathogens like HCV will be very similar in both species and will facilitate a molecular dissection of the immune response in chimpanzee models of human diseases.

Date: 2003/04/18 17:33:22, Link
Author: rafe gutman
Flajnik MF.
Comparative analyses of immunoglobulin genes: surprises and portents.
Nat Rev Immunol. 2002 Sep;2(9):688-98. Review.


The study of immunoglobulin genes in non-mouse and non-human models has shown that different vertebrate groups have evolved distinct methods of generating antibody diversity. By contrast, the development of T cells in the thymus is quite similar in all of the species that have been examined. The three mechanisms by which B cells uniquely modify their immunoglobulin genes -- somatic hypermutation, gene conversion and class switching -- are increasingly believed to share some fundamental mechanisms, which studies in different vertebrate groups have helped (and will continue to help) to resolve. When these mechanisms are better understood, we should be able to look to the constitutive pathways from which they have evolved and perhaps determine whether the rearrangement of variable, diversity and joining antibody gene segments -- V(D)J recombination -- was superimposed on an existing adaptive immune system.

Date: 2003/07/29 19:04:36, Link
Author: rafe gutman
more stuff:

Sci Prog 2001;84(Pt 2):125-36

The serpins: nature's molecular mousetraps.

                 Huntington JA, Carrell RW.

University of Cambridge, Department of Haematology, Wellcome Trust Centre for Molecular Mechanisms in
Disease, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK.

A special family of inhibitors, known as the serpins, has evolved an extraordinary mechanism to enable the
control of the proteolytic pathways essential to life. The serpins undergo a profound change in conformation to
entrap their target protease in an irreversible complex. The solving of the structure of this complex now
completes a video depiction of the changes involved. The serpin, just like a mousetrap, is seen to change with
a spring-like movement from an initial metastable state to a final hyperstable form. The structure shows how
this conformational shift not only inhibits the protease but also destroys it. A bonus from these structural
insights is the realisation that a number of diseases, as diverse as thrombosis, cirrhosis and dementia, all share
a common mechanism arising from similar mutations of different serpins.

                 PMID: 11525014 [PubMed - indexed for MEDLINE]

IUBMB Life 2002 Jul;54(1):1-7
                 Serpins: finely balanced conformational traps.

                 Pike RN, Bottomley SP, Irving JA, Bird PI, Whisstock JC.

Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia.

Serine protease inhibitors (serpins) play very important roles in the maintenance of various physiologically
important systems. As knowledge of the workings of proteins of this family grows, new understanding is
gained of the mechanisms by which they inhibit target proteases, using conformational changes for which the
structure of serpins is uniquely adapted. This finely balanced system is utilized to healthy benefit in the control
of serpin function by modulators, arguably the most striking examples of which occur in the control of
proteolytic cascades, such as the coagulation system. Serpins also play very important intracellular roles: one
example is the protection of immune cells from their own cytotoxic proteases. The finely balanced serpin
mechanism also means that it is prone to disastrous consequences if mutations should occur in vital positions
in the serpin structure. Many examples of disease-associated mutations have been shown, which has the dual
effect of highlighting how important these molecules are in the maintenance of health and the fine balance that
must be maintained in order to preserve their active, inhibitory conformation.

                 PMID: 12387568 [PubMed - in process]
Curr Opin Struct Biol 2001 Dec;11(6):740-5
                 Serpins and other covalent protease inhibitors.

                 Ye S, Goldsmith EJ.

Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry
                 Hines Boulevard, Dallas, Texas 75390, USA.

Serpins are irreversible covalent 'suicide' protease inhibitors. In the past two years, important advances in the
structural biology of serpins have been forthcoming with the crystal structures of a covalent complex between
trypsin and alpha1-antitrypsin, and of a Michaelis encounter complex between trypsin S195A and serpin 1B
from Manduca sexta. These structures have helped elucidate many aspects of the mechanism of action of
serpins. Also, the crystal structure of the cysteine protease caspase-8 in complex with the inhibitor p35 has
revealed a new family of suicide protease inhibitors.

                 Publication Types:
                     Review, Tutorial

                 PMID: 11751056 [PubMed - indexed for MEDLINE]

Bioessays 1993 Jul;15(7):461-7

                 The role of conformational change in serpin structure and function.

                 Gettins P, Patston PA, Schapira M.
Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee.

 Serpins are members of a family of structurally related protein inhibitors of serine proteinases, with molecular
masses between 40 and 100kDa. In contrast to other, simpler, proteinase inhibitors, they may interact with
proteinases as inhibitors, as substrates, or as both. They undergo conformational interconversions upon
complex formation with proteinase, upon binding of some members to heparin, upon proteolytic cleavage at
the reactive center, and under mild denaturing conditions. These conformational changes appear to be critical
in determining the properties of the serpin. The structures and stabilities of these various forms may differ
significantly. Although the detailed structural changes required for inhibition of proteinase have yet to be
worked out, it is clear that the serpin does undergo a major conformational change. This is in contrast to other,
simpler, families of protein inhibitors of serine proteinases, which bind in a substrate-like or product-like
manner. Proteolytic cleavage of the serpin can result in a much more stable protein with new biological
properties such as chemo-attractant behaviour. These structural transformations in serpins provide
opportunities for regulation of the activity and properties of the inhibitor and are likely be important in vivo,
where serpins are involved in blood coagulation, fibrinolysis, complement activation and inflammation.

                 Publication Types:
                     Review, Tutorial

                 PMID: 8379949 [PubMed - indexed for MEDLINE]

J Biol Chem. 2003 Jul 7 [Epub ahead of print].
                                                                         Related Articles, Links                  
Conserved Ser residues, the shutter region, and speciation in serpin evolution.

Krem MM, Di Cera E.

Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO 63110.

The suicide inhibitory mechanism of serine protease inhibitors of the serpin superfamily depends heavily on
their structural flexibility, which is controlled in large part by the breach and shutter regions of the central
Ab-sheet. We examined codon usage by the highly conserved residues Ser53 and Ser56 of the shutter region
and found a TCN-AGY usage dichotomy for Ser56 that, remarkably, is linked to the
protostome-deuterostome split. Our results suggest that serpin evolution was driven by phylogenetic speciation
and not pressure to fulfill new physiologic functions, mitigating against coevolution with the family of serine
proteases they inhibit.

PMID: 12847097 [PubMed - as supplied by publisher]
J Biol Chem 2002 Oct 25;277(43):40260-4
                                                                                    Related Articles, Links

                 Ser(214) is crucial for substrate binding to serine proteases.

                 Krem MM, Prasad S, Di Cera E.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis,
                 MO 63110, USA.

Highly conserved amino acids that form crucial structural elements of the catalytic apparatus can be used to
account for the evolutionary history of serine proteases and the cascades into which they are organized. One
such evolutionary marker in chymotrypsin-like proteases is Ser(214), located adjacent to the active site and
forming part of the primary specificity pocket. Here we report the mutation of Ser(214) in thrombin to Ala,
Thr, Cys, Asp, Glu, and Lys. None of the mutants seriously compromises active site catalytic function as
measured by the kinetic parameter k(cat). However, the least conservative mutations result in large increases
in K(m) because of lower rates of substrate diffusion into the active site. Therefore, the role of Ser(214) is to
promote the productive formation of the enzyme-substrate complex. The S214C mutant is catalytically
inactive, which suggests that during evolution the TCN-->AGY codon transitions for Ser(214) occurred
through Thr intermediates.

PMID: 12181318 [PubMed - indexed for MEDLINE]
Trends Biochem Sci 2002 Feb;27(2):67-74
                                                                                    Related Articles, Links

Evolution of enzyme cascades from embryonic development to blood coagulation.

                 Krem MM, Cera ED.

                 Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box
                 8231, St Louis, MO 63110-1093, USA.

Recent delineation of the serine protease cascade controlling dorsal-ventral patterning during Drosophila
embryogenesis allows this cascade to be compared with those controlling clotting and complement in
vertebrates and invertebrates. The identification of discrete markers of serine protease evolution has made it
possible to reconstruct the probable chronology of enzyme evolution and to gain new insights into functional
linkages among the cascades. Here, it is proposed that a single ancestral developmental/immunity cascade gave
rise to the protostome and deuterostome developmental, clotting and complement cascades. Extensive
similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and
from similar macromolecular building blocks.

                 Publication Types:
                     Review, Tutorial
PMID: 11852243 [PubMed - indexed for MEDLINE]


J Biol Chem. 2002 May 31;277(22):19243-6. Epub 2002 Mar 29.
                                               Related Articles, Links
Substrate recognition drives the evolution of serine proteases.

Rose T, Di Cera E.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis,
Missouri 63110, USA.

A method is introduced to identify amino acid residues that dictate the functional diversity acquired during
evolution in a protein family. Using over 80 enzymes of the chymotrypsin family, we demonstrate that the
general organization of the phylogenetic tree and its functional branch points are fully accounted for by a
limited number of residues that cluster around the active site of the protein and define the contact region with
the P1-P4 residues of substrate.

PMID: 11925426 [PubMed - indexed for MEDLINE]
Trends Microbiol 2000 May;8(5):238-44
  The eukaryotic-like Ser/Thr protein kinases of Mycobacterium tuberculosis.

                 Av-Gay Y, Everett M.

                 Divn of Infectious Diseases, University of British Columbia, 2733 Heather St, Vancouver, BC, Canada.

In bacteria, extracellular signals are generally transduced into cellular responses via a two-component system.
However, genome sequence data have now revealed the presence of 'eukaryotic-like' protein kinases and
phosphatases. Mycobacterium tuberculosis appears to be unique among bacteria in that its genome contains 11
members of a newly identified protein kinase family. These M. tuberculosis eukaryotic-like protein kinases
could be key regulators of metabolic processes, including transcription, cell development and interactions with
host cells.

   Publication Types:
                     Review, Tutorial

   PMID: 10785641 [PubMed - indexed for MEDLINE]
EMBO J 2002 Dec 1;21(23):6330-6337
                                                                                    Related Articles, Links
A serpin mutant links Toll activation to melanization in the host defence of Drosophila.

Ligoxygakis P, Pelte N, Ji C, Leclerc V, Duvic B, Belvin M, Jiang H, Hoffmann JA, Reichhart JM.

                  Corresponding author e-mail:
P.Ligoxygakis and N.Pelte contributed equally to this work

A prominent response during the Drosophila host defence is the induction of proteolytic cascades, some of
which lead to localized melanization of pathogen surfaces, while others activate one of the major players in the
systemic antimicrobial response, the Toll pathway. Despite the fact that gain-of-function mutations in the Toll
receptor gene result in melanization, a clear link between Toll activation and the melanization reaction has not
been firmly established. Here, we present evidence for the coordination of hemolymph-borne melanization
with activation of the Toll pathway in the Drosophila host defence. The melanization reaction requires Toll
pathway activation and depends on the removal of the Drosophila serine protease inhibitor Serpin27A. Flies
deficient for this serpin exhibit spontaneous melanization in larvae and adults. Microbial challenge induces its
removal from the hemolymph through Toll-dependent transcription of an acute phase immune reaction

  PMID: 12456640 [PubMed - as supplied by publisher]

Int J Biochem Cell Biol. 2003 Nov;35(11):1536-47.
Serpins: structure, function and molecular evolution.

van Gent D, Sharp P, Morgan K, Kalsheker N.

Division of Clinical Chemistry, Institute of Genetics, Queen's Medical Centre, University of Nottingham, NG7
2UH, Nottingham, UK

The superfamily of serine proteinase inhibitors (serpins) are involved in a number of fundamental biological
processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and
tumor suppression and are expressed in a cell-specific manner. The average protein size of a serpin family
member is 350-400 amino acids, but gene structure varies in terms of number and size of exons and introns.
Previous studies of all known serpins identified 16 clades and 10 orphan sequences. Vertebrate serpins can be
conveniently classified into six sub-groups.We provide additional data that updates the phylogenetic analysis in
the context of structural and functional properties of the proteins. From these, we can conclude that the
functional classification of serpins relies on their protein structure and not on sequence similarity.

PMID: 12824063 [PubMed - in process]
J Thromb Haemost. 2003 Jul;1(7):1535-49.
Mechanisms of glycosaminoglycan activation of the serpins in hemostasis.

Huntington JA.

Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge,

Serpins are the predominant protease inhibitors in the higher organisms and are responsible, in humans, for the
control of many highly regulated processes including blood coagulation and fibrinolysis. The serpin inhibitory
mechanism has recently been revealed by the solution of a crystallographic structure of the final
serpin-protease complex. The serpin mechanism, in contrast to the classical lock-and-key mechanism, involves
dramatic conformational change in both the inhibitor and the inhibited protein. The final result is a stable
covalent complex in which the properties of each component are altered so as to allow clearance from the
circulation. Several serpins are involved in hemostasis: antithrombin (AT) inhibits many coagulation proteases,
most importantly factor Xa and thrombin; heparin cofactor II (HCII) inhibits thrombin; protein C inhibitor
(PCI) inhibits activated protein C and thrombin bound to thrombomodulin; plasminogen activator inhibitor 1
inhibits tissue plasminogen activator; and alpha2-antiplasmin inhibits plasmin. Nearly all of these reactions are
accelerated through interactions with glycosaminoglycans (GAGs) such as heparin or heparan sulfate. Recent
structures of AT, HCII and PCI have revealed how in each case the serpin mechanism has been fine-tuned by
evolution to bring about high levels of regulatory control, and how seemingly disparate mechanisms of GAG
binding and activation can share critical elements. By considering the serpins involved in hemostasis together it
is possible to develop a deeper understanding of their complex individual roles.

PMID: 12871289 [PubMed - in process]

J Thromb Haemost. 2003 Jul;1(7):1343-8.
Inflammation and thrombosis.

Esmon CT.

Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation; Departments of
Pathology, and Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center; and
Howard Hughes Medical Institute, Oklahoma City, Oklahoma, USA.

Systemic inflammation is a potent prothrombotic stimulus. Inflammatory mechanisms upregulate procoagulant
factors, downregulate natural anticoagulants and inhibit fibrinolytic activity. In addition to modulating plasma
coagulation mechanisms, inflammatory mediators appear to increase platelet reactivity. In vivo, however,
natural anticoagulants not only prevent thrombosis, but they also dampen inflammatory activity. Some insights
into the evolution and linkages between inflammatory mechanisms and the coagulation/anticoagulation
mechanisms have become evident from recent structural studies. This review will summarize the interactions
between inflammation and coagulation.

PMID: 12871267 [PubMed - in process]

Date: 2004/02/07 16:49:12, Link
Author: rafe gutman
advocates of Intelligent Design often hold seminars and conferences to present their arguments to the public.  some of these seminars are held in churches or community centers, but a sizeable number of them take place in well-respected research institutions.  this does not require the endorsement of the institution itself (or i think even their knowledge of what the event is about), as any university club can book a room on campus for their events.  however, through clever word play, IDists can give the appearance that their position is officially acknowledged.

for example, this announcement was posted on ARN, under the title, "Dembski at UC-Davis":
William Dembski
Lecture: "Detecting Design in Biological Systems"

Friday, 16 January 2004
7:30 PM
194 Chemistry Building
University of California, Davis

as is, it seems pretty innocuous, although the choice to present it in a building named after an entire field of science, and the title of his talk, leave the impression that somehow this talk is affiliated with the chemistry department of UC davis.  however, there's no overt deception here.

but who is sponsoring the talk?  not the chemistry or biology departments, but the grace valley christian center under the "faith and reason" seminar series whose express purpose is to:
The Faith and Reason series seeks to bring eminent scientists, logicians, and theologians to Davis to
speak on issues regarding the proper relationship between human reason and vital Christian faith.

The purpose of this series is to demonstrate that the Christian worldview correctly defines ultimate
reality and is consistent with all that is known about the world through the proper application of
logic and the scientific method.

although i think it would have been fairer had the poster of this event mentioned who was sponsoring it, i don't think he was trying to be deceptive.  but when an ID critic did mention who the sponsor was, they were immediately accused of trying to dismiss the talk as religiously-motivated.  look how one IDist responded:

I suppose that in your perspective there's no overlap between the 'scientific' and 'religious'. So by saying the talk has a 'religious goal', it's automatically not a scientific goal or a scientific talk, even though given in a science department of a major university.

and so now we see the strategy come full circle.  while there was no attempt by the original poster (or the sponsors of the talk) to imply that the talk was endorsed by either UC davis or its biology or chemistry departments, the net effect is that people come away with the impression that the talk is endorsed by those groups.

i'd like this thread to be a place where people can cut and paste examples like these.  so if you see a flyer or website for an ID-related event at a university, where the language implies that the university endorses ID, feel free to post it here.  i'd also like to see examples where IDists post comments like the one above, mistakenly interpreting the location of an ID event at a university for the university's endorsement of it.

Date: 2004/02/07 16:57:31, Link
Author: rafe gutman
here is another example:  in this ARN thread, an IDist, when challenged to provide examples of actual ID teaching material, responded:

Since you've been begging for a lesson plan, here is one that got taught at the University of Minnesota.

[omitted picture of professor under the following title]
Distinguished Professor of Chemistry

Chris Macosko who taught an ID seminar at the University of Minnesota

WHAT! AN ID SEMINAR AT A SECULAR UNIVERSITY!!!! Oh no, he succumbed to Wedgie indoctrination. Creationisms Trojan Horse deluded a real scientist, a distinguised professor. Forrest and Gross are right, the sky is falling and the IDers are making credible arguments. What's this world coming to.

however, an ID critic responded:
for the record Macosko's lecture was not "taught at the University of Minnesota" - it was presented at the Darwin, Design, and Democracy conference (DDD4) sponsored by the Intelligent Design network and the MacLaurin Institute, "A Christian study center at the University of Minnesota: Bringing God into the marketplace of ideas by communicating the Christian worldview with its transforming potential."

DDD4 was held on the University of Minnesota campus, but it was not an academic event held under the auspices of the university itself.

Date: 2004/02/07 17:17:33, Link
Author: rafe gutman
okay, one more for now.  

UCSD's IDEA club (intelligent design education and awareness) had a guest speaker come give an alternative theory of human evolution.  while i have no problem with the flier that advertised the event, on the IDEA club website the following screen shot, taken from UCSD's homepage, was displayed:

the red markings on the screen shot were from the IDEA club.

Date: 2004/02/11 16:32:01, Link
Author: rafe gutman
Accuracy demands a clarification of the Chris Macosko seminar alluded to by the ARN respondent. Macosko may have given a DDD4 lecture, but this is possibly not what the ARNie meant. According to Forrest & Gross (p.302-303) Chris Macosko taught a freshman honors colloquium titled "Origins: by chance or design?" in 1999 and 2001. This was a for-credit course, although it was outside the bounds of the normal curriculum programming.

my mistake.  i found the link that refers to the colloquium.  i recant that example.

interestingly, in the kiosk article that discusses the class, there's no mention of intelligent design at all.  i wonder if ID was even discussed in the class.  if so, i'd like to see what material they actually taught.  

(i'll keep the example up so people will know what the heck we're talking about)

p.s.  you're right about the title.  when i figure out how to edit titles i'll change it.  serves me right for writing this over lunch.

Date: 2004/02/19 20:11:18, Link
Author: rafe gutman
here is the body of an email i sent to several board of education members on 2/13/04:

I am a recent graduate of the Ph.D. Biology program at the University of California, San Diego, and have been following the Intelligent Design (ID) movement for several years now.  I’ve watched the advocates of ID go from state to state, trying to insert their ideology into high school science classrooms, and held my breath each time.  As someone who has spent the last six years completely engrossed in biology, I’m always amazed at how bad their arguments are against evolution or for intelligent design.  Their writings display a lack of understanding of biology, and of the nature of evidence. However, I realize now that they are not trying to convince me, or the scientific community, that evolution is indeed a theory in crisis.  They only have to convince you.  Ultimately, it is not the scientific community that holds the power over what high school students are taught, you do.  So ID dvocates start with an innocuous proposal, that students should learn both the scientific evidence for and against evolution.  Then they present distortions and half-truths and claim it as "scientific" evidence against evolution.  They know that it doesn’t have to be accurate, or based on sound logic.  It doesn’t actually have to *be* scientific evidence, it just has to look like it.  It doesn’t even matter if members of the scientific community challenge them and expose the flaws in their arguments.  If the public doesn’t understand the evidence, then how do they know who’s right?  I guess that’s the big question here.  How do non-biologists gauge biological evidence?  To me, the answer is simple.  If it’s an issue of science, then listen to the scientific community.  When asked whether they thought there was any scientific evidence that challenges the fundamental principles of the theory of evolution, 93% of Ohio scientists said no [1].  When asked whether they thought students should be tested on Intelligent Design, 90% of Ohio scientists said no [1].  What I’ve found most disturbing in these latest incidents is not the actions of the IDists, but in the lack of trust displayed by boards of education toward their state’s own university scientists.  Examining the lesson plan entitled “Critical Analysis of Evolution”, in the “five aspects of evolution” in attachment A, the brief challenging sample answers read just like stock creationist responses [2].  By adopting such material, the board is tacitly endorsing such fallacious arguments.  Surely the Board must have seen the letter signed by the Presidents of Ohio's public universities. Surely the board must have seen the poll of Ohio scientists demonstrating their resounding support for the teaching of evolution.  If any of the board members do not understand why those “challenging” sample answers are erroneous, then please, ask one of your own scientists to explain it.  It all comes down to an issue of trust.  Who can the Ohio board of education trust if not the consensus of Ohio’s own scientists?

[2] (pages 326-328)