Saturday, September 30, 2006

Kansas Guild of Bloggers!

astersIt's fall now, and it looks like Kansas bloggers are spending a lot of time outside and not so much time blogging. So I had to do some serious digging to grub up some posts for this week, but there is still plenty of life and diversity in the Kansas portion of the noosphere and I tried to reflect that diversity in my selections this week.

Politics and religion are on the mind of a lot of Kansas bloggers lately so first up from Pat Hayes over at Red State Rabble is a report on events related to Judge Jones's recent appearance at the University of Kansas. Judge Jones is the judge who rendered the decision that intelligent design is not science in the Dover Pennsylvania case.

Next up Josh Rosenau, who hosted the last KGB carnival, worries about the recent votes in Congress to increase presidential powers to hold citizens without Habeas Corpus in terrorism cases.

A very different take on the same issue is at another Kansas Blog:

Over at Evolution-next step, j.d. wonders if government is going too far in terms of requiring felons to register on a list. He reports on a proposal to require convicted meth dealers to be on a registry just like sex offenders.

A Christian reflection about the Middle East and the events happening there comes from Phil Dillon over at his blog, Another Man's Meat. He has an interesting meditation on Armageddon. He seems to think that maybe Armageddon is coming but he cautions Christians:
... It seems to me that this is not the time to be self centered. Christians, of all people, should be focusing on more than just themselves, as if GodÂ’s sole purpose is to bring them to some mystical state of self-actualization.

A quite different perspective is at The Science Ethicist, an unabashedly anti religious blog where Aerik at the believes that fellow atheist PZ Myers is wrong when he says that other people's beliefs are not any of his business.

Continuing our set of articles dealing with religion and government we have a post from John at Blog Meridian, who has been a regular host for Kansas Guild of Bloggers. John discusses the relevance of Henry David Thoreau's essay on civil disobedience to today's world situation and the policies of our government.

Here is one more post from Josh at Thoughts from Kansas who takes umbrage at the phrase "citizen journalist"

Josh observes that with respect to himself and his blogging that:

"I have spent time talking to sources, and there are people in Congress and in campaigns who take my calls. That makes me a journalist. And having done that work, I know that it's serious work, hard work, that deserves to be taken seriously."

I saw Josh at work the other year blogging the evolution hearings at the Kansas Board of Education and he certainly does work hard. Also j.d. has an entry on the same subject wich ought to be read along with Josh's.

On the lighter side
, another article submitted by John at Blog Meridian takes a not very serious look at T.S. Eliot's most famous poem in "The Love Song of J. Alfred Poprocks" (excerpts)"

Kansas is an innovative state and since I am a chocolate fiend, I could not resist highlighting Lady Gunn's post introducing us to a new type of chocolate over at

I wonder if I can talk my dentist into using gaseous chocolate along with laughing gas.

Speaking of food, KS cowboy discusses the merits of old style coffee makers in a post that elicits fond memories for those of us who grew up in households where thepercolatorr was always on the stove.

Finally since this is fall, I thought I would end with a poem, originally written for Poetry Thursday's weekly prompt. Of course the poem is not really about fall or Katydids. Be sure to read the associated commentary.

I hope I have properly reflected the diversity of Kansas bloggers. If I missed one of your posts about Kansas, make sure you submit your entry to the kgb's submission page! Next week's kgb carnival will be probably be back to Blog Meridian.

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Kansas Guild of Bloggers..repent the deadline is nigh!

Kansas Guild of Bloggers will be featured here on Monday. Looks like Kansas bloggers are too busy enjoying the great fall weather we are having, as have I will probably have to tear myself away from this great Kansas weather and prowl around the noosphere to grub up some great Kansas blogging.

Photo credits:
photo by:Edward C. Robinson III

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Sunday, September 24, 2006

Intersex Children

A fascinating article was just brought to my attention from the Trans-Academics group on Google. The article from today's health section of the NY Times (What if it's (sort of) a Boy and (sort of) a Girl?) has to do with whether or not intersexed children should be assigned a gender at birth. This may seem like something out of Jerry Springer to some folks, but the incidence of intersexuality is quite high somewhere between 1 in 2,000 and 1 in 4,500, so this is likely to be a condition a pediatrician will encounter at some point during his or her practice. The usual strategy has been to assign a gender and also surgically alter the genitalia to match. The article discusses the crusade of intersexed people to change this usual practice, focusing on Cheryl Chase of the Intersex Society of North America. Chase and other advocates for the intersexed, such as Alice Dreger, whom I have mentioned before, believe the best strategy is to rear the child in what seems to be the best gender for the child based on the medical evidence at birth-but not to rush into surgery.

The article reports:

She contends that the most important thing is for a child to feel loved by her parents, despite her difference. An operation, she says, should not be done to assuage parental embarrassment or anxiety; it should be chosen, if it is chosen at all, by an intersex individual who is old enough to make her own decision and give proper consent.

But getting families and Doctors to be open to letting the person make his or her own decision will be difficult even in today's social climate. The thought is that the problems the child might face growing up with ambiguous genitalia in some cases might be less than the need to correct an erroneous guess at the child's final gender identity.

Some of the medical guidelines are, well arbitrary. For instance babies with phallic structure (that's penises and clitorises) must be at least 2.5cm long on boys and shorter than 1.0 cm for girls. Since it is easier to make a vagina than reconstruct a penis those "phallic structures" in between are typically altered to be female in form.

The article notes that children seem to be able to determine what gender they are in one case studied by William Reiner, the article reports that a child assigned as female at birth, though she had been born male, leapt at the chance to identify as a boy saying:

Mom, I've been telling you: I'm a boy, and boys have short hair, so I cut off my hair.

Other links:

Creighton, Sarah. Surgery for Intersex J R Soc Med. 2001 May; 94(5): 218-220

Another take on the NY Times article is at Jen Burke's Blog Transcending Gender:

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Kansas Guild of Bloggers

The Kansas Guild of Bloggers (kgb) is over at Josh Rosenau's blog, Thoughts from Kansas. Next week the kgb will be here at the force that through...

Josh is taking submissions through tonight...almost forgot to send one in myself. So if you have a Kansas related post, send it via the kgb's submission page.

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Discovery Institute's major new publication?

Well they probably think so if quote on a Starbuck's coffee cup counts as a peer reviewed article. See for more details!

Tip of the antennae to Karl over at Inoculated Mind for uncovering this report.

The quote reads:

"The morality of the 21st century will depend on how we respond to this simple but profound question: Does every human life have equal moral value simply and merely because it is human? Answer yes, and we have a chance of achieving universal human rights. Answer no, and it means that we are merely another animal in the forest.
Wesley Smith senior fellow with the Discovery Institute "

Sounds harmless right? Just a little new age fluff, eh? Well think again about the assumptions here. First does every human life have equal moral value? If yes, why do we have the death penalty? Why are conservatives so opposed to equal protections for same sex couples. Why is torture without oversight OK?

On the other side what is wrong with being an animal in the forest? Are we not animals? Does the discovery Institute really think that the fact that we are animals and evolved from other animals mean that there is no rational basis for morality? Of course that is exactly what they think. This quote is reactionary politics disguised as new age fluff, something the Discovery Institute and it's PR spinners are real good at. Shame on Starbucks for not seeing this quote for what it is.

Hmmm I wonder if this counts as a major milestone in the Discovery Institute's Wedge Strategy. Certainly they are pretty excited about this!

Maybe Starbucks ought to put the last paragraph from Origin of the Species on a cup. Society would be better served.

" It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. "

But then, most great ideas well explained probably don't fit well on a coffee cup.

Other links:

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Tuesday, September 19, 2006


9/19/06 It was cool this evening which enabled me to get this nice Katydid in my garden.

A poem and commentary follow for Poetry Thursday.



The evenings are cooling now
And on the Heliopsis in my garden
Rests at sunset a katydid,
Her antennae slowly caressing
The space around her.
She is so still that I can reach
My slim fingers out to the bloom
And pull her closer if I wish
Or run inside, return
With the camera to pull the moment
Closer, this moment close to the equinox
When everything runs together
Slowly coalescing into this instant.
The cool air is on my cheek;
soft fall its hands on my breasts
As the insect is being there
In her green skeleton
Wrapped in the pink light.
And what am I but an equinox child
Soft and pink and new
Wrapped for now in what people
Expect to see, middle aged and grey
Taking pictures of a bug.

Paul Decelles 9/20/06

This week's Poetry Thursday is all about finding our authentic selves, to "Peel away the layers and see what you discover. Then let that voice speak. " Implicit here seems to be the idea that we have some core which is somehow our essence. I know what Liz over at Poetry Thursday is getting at, but for me it is hard to get to that authentic self because I am not sure which self that is. After all I don't believe that the authentic self is an essence in the sense of some intrinsic nature. Rather it is a continuity of existence and experience. Getting at that authentic self is perhaps getting beyond what other people expect to see and perhaps even what you expect that authentic self to be. The authentic self may even involve a dream or wish of what you want to be, once you strip away all the external epectations, because are not dreams and wishes part of existence?

My submission is inspired by a confluence of events. First today, the 20th, is my birthday. Plus I have the first line of my blog entry on the Katydid. So I already knew there was a poem here. But then while coming in with my car pool partner, she remarked that I am an almost equinox baby.

Once I had those things, the poem unfolded itself while I was waiting for my first class to assemble.

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Sunday, September 17, 2006

Beetle Blogging

This weekend my son and I decided to go out for one of our occasional rambles to Lawrence's Baker Wetlands, he looking for snakes and me for some good insect blogging.

Late summer to me is a great time for biology because so insects and other critters are mating. At times it seems almost a frenzy of genetic recombination and good old fashioned Darwinian Natural Selection and you might enjoy a side trip to a more poetical view of the season.

We had completely forgotten about Monarch Watch doing their monarch butterfly tagging so we stopped in to see "Chip" Taylor and chatted a bit. He had quite a crew of volunteers out there tagging monarchs to track their migration and mortality and he and his colleagues have put to together a great model for how scientists can enlist non scientists to help in important scientific work.

But I was mainly interested in checking out the insects and other arthropods on fall composites such as golden rod and sunflower and relatives because I think that these insects are among the most spectacular we have and yet often overlooked by the average person. One common critter is this soldier beetle(Cantharidae) in the genus Chauliognathus. These are extremely common and familiar beetles that make very nice experimental organisms for field studies.


Click most of the images for a larger view on my photostream.

Often times Cantharids are confused with blister beetles, family Meloidae which we also saw at the wetlands. One of the most famous confusions is with 'Spanish Fly' a concoction of ground up Meloid once used as an aphrodisiac. The active ingredient, cantharidin is highly toxic as pointed out by Tom Eisner in his book For Love of Insects, so don't get any ideas that cantharidin might be a cheap substitute for Viagra. Dr. Eisner points out that Cantharidin is a potent insect defensive compound. So the irony of course is that Cantharidin is not produced by Cantharids at all!


As pointed out by Dr. Eisner, certain male insects from a wide range of groups sequester Cantharidin from Meloids and present it to females during mating. Apparently the cantharidin ends up in the eggs providing protection from predators. Insects that do this are attracted to pure cantharidin, a phenomenon called cantharidiphilia. How do these cantharidiphiles get the cantharidin?

Probably one way is because when Meloids are attacked by predators they release cantharidin rich "blood" via reflex bleeding in which the blood is released at the joints of the insect. Here is an interesting report of just such a case from Bugguide:


Dr. Eisner also has a picture of anthicid beetles licking the surface of a dead Meloid apparently to take up cantharidin. As Dr. Eisner observes, there is still a lot to be learned about cantharidiphilia.

Why the initial confusion between Meloids and Cantharids? I really don't know. Cantharids are mainly predacious:


whereas adult Meloids are herbivores. Both are somewhat soft bodied beetles and I suppose could be confused with each other.

Meloids have a very interesting life cycle because the larvae transform into radically different stages during metamorphosis, a process called hypermetamorphosis ( This handsome black Meloid, probably Epicauta pennsylvanica, is very common on golden rod.


I have always loved crab spiders and they are quite abundant right now including this one on thistle and crab spiders (Thomisidae) are common on other composites.


Crab spiders seem to like moths and flies and often take bees


a fact I rediscovered to my dismay as a graduate student when I was trying to rear some Augochlorella bees in a bee room. I accidentally introduced some crab spiders in some flowers out in the room for the bees. The only result was some very well fed spiders. One might suspect these spiders would take Cantharids, but they don't seem to bother with them.

We were fortunate this weekend to spot a yellow crab spider (Misumena?) on a composite along with a Cantharid and decided to see how they would interact. Several times the spider would seem to touch the beetle with it's long pair of legs and then withdraw to its part of the flower. The beetle did not seem to react to the spider's presence.


This image shows the crab spider touching the beetle with its legs. The spider then drew back. The spider touched the beetle several times before the beetle flew off. The two flower petals curled over the spider were actually held together by a small number of silk threads.


Another shot of the spider after the beetle flew off.

What is going on here? Fortunately there is a nice but hardly exhaustive database, called perfuse, of insect chemicals and a query for Cantharide shows that beetles of the genus Chauliognathus do have a potent allomone called (Z)-8-Deca-4,6-diynoic acid which is an "anti-feedent" or feeding deterrent to spiders-at least jumping spiders. Whether this same compound is a deterrent for crab spiders is not clear, but certainly this is a reasonable hypothesis.

Eisner, T., Hill, D., Goetz, M., Jain, S., Alsop, D., Camazine, S., and Meinwald, J. 1981. Antifeedant action of Z-dihydromatricaria acid from soldier beetles (Chauliognathus spp.). J. Chem. Ecol. 7:1149-1158. (abstract)

So we have another irony. These spiders which can take on bees, including honeybees may be deterred by a compound produced by these relatively soft bodied beetles that ought to be a great food source for the spiders. I am sure there is a lot more to this story. For instance it is not clear how the compound serves to deter feeding. Is it irritating to the spider? Do inexperienced spiders need to learn to avoid the beetles? Is the compound even a defensive compound or do we perhaps have the chemical equivalent of warning coloration and the defensive compound is something else?

Each creature, whether the charismatic monarch butterfly, or the somewhat more mundane beetles discussed here all have wonderful coevolutionary adaptations to predators, and wonderfully complex stories yet to unravel.

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Friday, September 15, 2006

Today's Chuckle

I am sure every one has seen a big SUV with a God is my copilot sticker. Well if you find that sort of thing annoying, and the height of hubris, then here is a cartoon for you courtesy of Jay Sennett over at Jaywalking: cartoons about a way of life. Click on the image for a hi-res version.

Tip of the Antennae to Jay and to Jamie Ward for this. Jay has lots of other quirky cartoons at his site. Personally I hope he tackles the rapture soon.

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Mendel's Garden #6 is out!

Mendel's Garden #6 is out at the The Voltage Gate ! Jeremy Bruno presents us with a genetic tour of his school. But you can learn something about genetics without paying any sort of tuition.

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Tuesday, September 12, 2006

Grokking the Products of the Insulin Gene


As part of getting their feet wet in bioinformatics, I have my students search for information about various bioinformatics topics using the tools available through the NCBI portal. One of the things I decided to have them find is the sequence of amino acids in human insulin, which in its active form, has two chains joined by disulphide linkages . A reasonable place to start is to search for protein amino acid sequences, since insulin is a protein.

But when my students did this they found a record that starts out:

LOCUS AAH05255 110 aa linear PRI 23-JUN-2006
DEFINITION Insulin [Homo sapiens].
VERSION AAH05255.1 GI:13528924
DBSOURCE accession BC005255.1
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.

and ends with the amino acid sequence:

1 malwmrllpl lallalwgpd paaafvnqhl cgshlvealy lvcgergffy tpktrreaed
61 lqvgqvelgg gpgagslqpl alegslqkrg iveqcctsic slyqlenycn

Each of the letters is an abbreviation for one of the 20 standard amino acids.
For instance m = methionine; a alanine and so forth.

Now some of my students knew from other sources that human insulin actually has 51 amino acids. So, they asked,what's going on? How come the record we pulled up has 110 amino acid residues, not 51? My short answer to them was that insulin is produced in an inactive form, proinsulin, that has to be processed post translation. This is basically correct but as we will see we can get a much deeper understanding of what's going on by carefully exploring the data base records. There are other ways to do this I am sure, but rather than blindly searching lets take a careful look at some of the protein data base records avaialble through NCBI, beginning with the original record my students were finding with the 110 amino acid long polypeptide.

I don't pretend to be bioinformatics expert, but let's go exploring.

Near the top of the record is the line:
DBSOURCE    accession BC005255.1
Opening the database source link, BC005255.1, gives you the information about the source of the protein sequence and you can see that it is predicted from a cDNA sequence made from a mature mRNA. Toward the end of this record is both the cDNA and the amino acid sequence for the protein.

But let's see what else we can glean from the original record. The reference provided near the start of the record is:

AUTHORS Strausberg,R.L., Feingold,E.A et al
CONSRTM Mammalian Gene Collection Program Team
TITLE Generation and initial analysis of more than 15,000 full-length
human and mouse cDNA sequences
JOURNAL Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002)
PUBMED 12477932

Pulling up the reference, via its pubmed number 1247792, using the above link takes to the abstract of the paper and pdf files for free download-always a nice thing to have. But the first sentence in the abstract gives a clue as to what's going on:

"The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene."

So what do we have here? An open reading frame is the actual amino acid coding region of a gene. That's also where the cDNA comes in because cDNA basically is a DNA sequence for the gene with all the introns stripped out producing using mature mRNA and reverse transcriptase. Basically we have the predicted amino acid sequence for proinsulin from the mRNA.

The record provides us with yet more information.

After a list of references to different regions of the protein, which we will return to later, is a set of annotations after the heading Features.

One of these annotations for the 29th to the 109 amino acid residue reads:

Region 29..109
/note="Insulin / insulin-like growth factor / relaxin
family; insulin family of proteins; groups a number of
active peptides which are evolutionary related including
insulin, relaxin, insulin-like growth factors I and II,
mammalian Leydig cell-specific insulin-like peptide (gene
INSL3), and early placenta insulin-like peptide (ELIP)
(gene INSL4), insect prothoracicotropic hormone
(bombyxin), locust insulin-related peptide (LIRP),
molluscan insulin-related peptides 1 to 5 (MIP), and C;

The little note in this case is telling you that region starting from amino acid 29 through 109 is evolutionarily related to a number of different proteins such as insulin, a protein called relaxin, several growth factors, and interestingly, several insect hormones and even a molluscan peptide.

So we have learned a lot about insulin without even finding the actual 51 amino acid sequence!

But wait there's more!

Just before the amino acid sequence for the predicted amino acid sequence from the open reading frame is this series of lines:

CDS 1..110

CDS stands for CoDing Sequence and clicking on the CDS link give the sequence of nucleotides including start and stop codons along with the amino acid sequence. Here is a sample record that shows what's in these sorts or records.

CDD stands for Conserved Domain Database and opening the CDD link can tell one a lot about what's going on. In this case our protein has two conserved domains and is part of a large family of proteins called IlGF. The little summary tells us that:

"Typically, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the "A" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the "B" chain. This alignment contains both chains plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds."

There still yet is more!

The section of our original record has a link to the INS gene, /db_xref="GeneID:3630".

Opening this link gives access to further information about the INS gene, first showing this screen:

Official Symbol: INS and Name: insulin [Homo sapiens]
Other Designations: proinsulin
Chromosome: 11; Location: 11p15.5
MIM: 176730
GeneID: 3630
Note the little tidbit that the INS gene is on chromosome 11 in the upper or P arm.

Open the GeneID link, and look for the various links on the right hand side of that data screen. Open the one labeled "links" and select proteins from the choices. When you do that, you get a whole series of records including one(you may have to scroll down) that says P01308. This particular record is a Swiss Prot record, and it looked like a fairly complete record related to the proinsulin protein.

Opening P01308 yields another data record with a wealth of information about the INS gene and the regions of the protein. At the top of this record is a link that says Features. Clicking on that link provides a series of annotations that starts out like the image to the left.

As part of the Feature various regions are annotated. If you have the P01308 record open and scroll down you will find a region
that says:

Region 1..24
/experiment="experimental evidence, no additional details

Click on the Region link, select sequence at the top shows the signalling sequence as:
1 malwmrllpl lallalwgpd paaa

Since the initial product of tranlation includes the signalling sequence, what I have trmed proinsulin is better termed preproinsulin.

Scrolling just a bit farther down in the P01308 record, brings you to:

Region 25..54
/region_name="Processed active peptide"
/experiment="experimental evidence, no additional details
/note="Insulin B chain. /FTId=PRO_0000015819."

This is telling you that residues 25 through 54 are the insulin B chain. This chain is 30 amino acids long. Opening this Region link and clicking on Sequence at the top of this record shows you the residues as:

1 fvnqhlcgsh lvealylvcg ergffytpkt

Going back to the P01308 link and doing a bit more scrolling brings you to

Region 90..110
/region_name="Processed active peptide"
/experiment="experimental evidence, no additional details

which tells you where the insulin A chain is, namely amino acids 90..110 of our original product from the INS gene.

That region has the amino acid sequence:
1 giveqcctsi cslyqlenyc n.

If you look at the Features, there is a lot more to warm the hearts of your favorite protein chemist about the details of proinsulin's structure!

So getting back to our original protein product from the INS gene we have that:

Residues 1 through 24 is a signalling sequence, residues 25..54 are the B chain; residues 90..110 are the A chain and the remaining part of the protein is a linking region.

Let's see if what we have makes sense with the original amino acid sequence (in red) from way back when:

1 malwmrllpllallalwgpdpaaafvnqhlcgshlvealylvcgergffytpktrreaed
1 malwmrllpllallalwgpdpaaafvnqhlcgshlvealylvcgergffytpkt_____
61 lqvgqvelgggpgagslqplalegslqkrgiveqcctsicslyqlenycn

I did this manually with blue, the signalling region, black the B chain and green the A chain. We still have this linking region to look at:

rreaedlqvgqvelgggpgagslqplalegslqkr which comprises amino acids 55-90.

In the record scrolling up to the references there is the following two entries:
REFERENCE 10 (residues 1 to 110)
AUTHORS Oyer,P.E., Cho,S., Peterson,J.D. and Steiner,D.F.
TITLE Studies on human proinsulin. Isolation and amino acid sequence of
the human pancreatic C-peptide
JOURNAL J. Biol. Chem. 246 (5), 1375-1386 (1971)
PUBMED 5101771
REFERENCE 11 (residues 1 to 110)
AUTHORS Ko,A.S., Smyth,D.G., Marktussen,J. and Sundby,F.
TITLE The amino acid sequence of the C-peptide of human proinsulin
JOURNAL Eur. J. Biochem. 20 (2), 190-199 (1971)
PUBMED 5560404
These entries refer to a C-peptide. Scrolling down in the record reveals a series of links to regions and the one for C-peptide give the following sequence of amino acids for the C-peptide:


Thus we have mapped out the proinsulin protein as consisting of these regions as before with the C-peptide shown in purple:

1 malwmrllpllallalwgpdpaaafvnqhlcgshlvealylvcgergffytpktrreaed
1 malwmrllpllallalwgpdpaaafvnqhlcgshlvealylvcgergffytpkt**ead
61 lqvgqvelgggpgagslqplalegslqkrgiveqcctsicslyqlenycn

So it looks like the INS gene not only codes for the A and B chains of insulin but also for another polypetide. Looking at the first reference gives the primary structure for this peptide, but what does this peptide do?

At one time it was thought that C-peptide was not biologically active. Indeed some diabetes related sites still talk about it in this way, for instance this one from Perkinelmer. However, this peptide seems to have a number of effects. For instance a recent paper in Diabetes/Metabolism Research and Review (abstract) suggests that C-peptide reduces apoptosis of pancreatic islet cells. Another paper in Diabetes/metabolism research and reviews (2003 Sep-Oct;19(5):345-7., abstract calls attention to what appear to a number of different biological effects of C-peptide. In some cases the C-peptide clearly works along with insulin. C-peptide seems to increase dilation of arteoles in skeletal muscle in conjunction with insulin as discussed here. This makes sense since skeletal muscle is a target for insulin. Further there is some evidence that administration of C peptide improves blood flow in the skin of patients with insulin dependent diabetes.

By the way the C-peptide has diagnostic value since one C-peptide molecule is released per insulin molecule. Monitering the level of C-peptide can tell doctors about how much insulin the pancreas of a person taking insulin shots is producing.

So what have we got here? The INS gene not only codes for the two insulin chains that are activated later to make insulin, but also codes for another peptide in another violation of the old idea of one gene coding for one polypeptide.

At this point here are some questions that we can investigate:

1. Do the other members of the IlGF also have C-peptides as part of their structure? Doing a quick protein blast of the various protein databases is not particularly illuminating here. So we may have to BLASTn the corresponding nucleotide sequence from the INS gene record.

2. Where did the C-peptide come from evolutionarily? Are there homologous proteins of this type separate from the INS gene? If so ,looking at their function might give insight into other possible functions of the C-peptide. Again the protein databases are not particularly useful here. Maybe the fact that there are no conserved domains, and no apparent C-peptide proteins except for mammals suggest that this protein evolved maybe from a short sequence that got elaborated over time, coevolving with the insulin chains.

3. Many members of the IlGF family are growth factors, what is the tie in between the function of a growth factor and insulin? Looks like a classic case of evolution using material at hand for a new function, but can we infer anything about how that happened?

4. What about other proteins with mutliple chains? Are there analogous peptides to the C-peptide that work along with the multple chained protein? Maybe the one polypeptide product, several protein system from one gene simultaneously is more common than we think.

We are getting into the sorts of areas where more powerful tools such as BLAST and looking at conserved domains can help us with, now that we have dissected the protein product of the INS gene. Now we could have gone to Google and come up with this reference,; but there is something satsfying with getting down with the data.

Other links:

Insulin and Insulin Resistance.
Wilcox G.
Clin Biochem Rev. 2005 May; 26(2): 19-39.

Specific binding of proinsulin C-peptide to human cell membranes.
Rigler R, Pramanik A, Jonasson P, Kratz G, Jansson OT, Nygren PÅ, Ståhl S, Ekberg K, Johansson BL, Uhlén S, Uhlén M, Jörnvall H, Wahren J.
Proc Natl Acad Sci U S A. 1999 Nov 9; 96(23): 13318-13323.
PMCID: 23945

Biological activity of C-peptide on the skin microcirculation in patients with insulin-dependent diabetes mellitus.
Forst T, Kunt T, Pohlmann T, Goitom K, Engelbach M, Beyer J, Pfützner A.
J Clin Invest. 1998 May 15; 101(10): 2036-2041.
PMCID: 508791

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Sunday, September 10, 2006

Getting it on in the Universe:Firestorm over Miller's talk.

The reaction to Ken Miller's talk at KU has been quite interesting to watch...and it looks like maybe he has succeeded in shifting the focus from evolution to whether or not evolution naturally leads to what he called anti-theistic. I just hope that once we get beyond the name calling stuff we get a reasoned exchange of viewpoints.

For a taste of this reaction take a look at PZ Myers over at Pharygula:

I believe religious people have to admit that evolution is not going away, that ID is sterile, and that if you think logically, the fact that evolution upsets people and even might lead to atheism, is no reason to reject evolution. Evolution is just the natural explanation how much of the biological world works. But I think that some of the atheist and agnostic response is needlessly strident.

I am a theist of sorts, and reading Darwin's God and listening to Miller's speech I find myself thinking that he is trying to find a niche where religious people can feel comfortable with evolution and maintain how they like to relate subjectively to the Universe. Likewise, when I read Dennett-Darwin's Dangerous Ideas I got the sense that Dennett is thinking the same thing but from the atheist perspective- namely how can people best forge connections with each other and the universe. If you buy into the notion that the religious impulse is some sort of evolutionary adaptation that arose through natural selection then has that impulse really lost it's adaptive significance because the logical framework and the surface doctrines of religion? How can that void be filled?

For instance, Catholic theistic evolutionists may augment their understanding of science with the mystery of transubstantiation, or maybe sacred music; Committed atheists such as Richard Dawkins seems to get his connection through science itself.

Dawkin's says for instance answering a common criticism of science that science will some how drain all the mystery of life away as we learn more about the universe:

"I wish I could meet Keats or Blake to persuade them that mysteries don't lose their poetry because they are solved. Quite the contrary. The solution often turns out more beautiful than the puzzle, and anyway the solution uncovers deeper mystery. The rainbow's dissection into light of different wavelengths leads on to Maxwell's equations, and eventually to special relativity."

I doubt there is just one way to forge that sort of deep connection is seems we crave. One of my biologist atheist friends, whose quite militant by the way, surprised me one day by saying that he didn't like organized religions because they get in the way of spirituality. What I think in retrospect he was getting at, is that the haggling over doctrine, and who is doing what to whom gets in the way of how we connect with the Universe and each other on a basic level. Maybe this is where the discussion needs to be focused on. Maybe then the question of whether or not science is necessarily anti-theistic will become irrelevant to the job of getting it on in the Universe.

Other links:
Ken Miller Creationist?

Other reports on the Miller talk and sound files have been posted by Jack Krebs:

Jon Voisey has a very detailed two part report:

Pat Hayes at Red State Rabble's report that got PZ Myers at Pharyngula going!

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Father Coyne speaks out...

Anthony Dick at the National Review Online did a radical thing: he e-mailed Father Coyne and asked him about what happened. Read excerpts from Father Coyne's response here. The upshot is that the media over reacted and that stepping down was Father Coyne's idea.

Tip of the Antennae, to Bill Tammeus at 'Faith Matters' for picking this tidbit out of the noosphere.

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Saturday, September 09, 2006

More on Ken Miller's KU talk...

Is posted by Jack Krebs over at Panda's Thumb:

including some sound files.

Thanks Jack!

Also check out

Friday, September 08, 2006

What is consciousness?

In a great illustration of how scientific knowledge changes and upsets our preconceptions, an investigation reported in the Chicago Tribune into the so called vegetative state, suggests that at least some vegetative state patients may show higher brain functions characteristic of consciousness. The patient in the study, had been in a coma but then later progressed to a vegetative state. This means, she was awake and not aware of her surroundings and with no obvious "conscious volition."

But MRI studies of her brain activity showed that her brain centers were activated in response to questions and requests in a way very similar to a conscious person.

" 'I was absolutely stunned,' Adrian Owen, a British neurologist who led the research team, told the Washington Post. 'We had no idea whether she would understand our instructions. But this showed that she is aware.' "

So is this patient conscious and totally unable to communicate? Or is awareness not really the same thing as consciousness? At the very least, the study suggests that MRI's may be an important tool in assessing brain states for patients in a vegetative state.

As pointed out in the article, this patient is not comparable to Terri Schiavo, since Ms Schiavo was much more seriously injured.

A tip of the antennae to Jack Krebs for this find.

Other links

Association for the Scientific Study of Consciousness:

Links from Science to more background material:

Consciousness: Entry from the Encyclopedia of Philosophy:

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Thursday, September 07, 2006

Catholicism and Evolution Take 2.

Ken Miller spoke tonight at the University of Kansas as part of KU's Difficult Dialogues at The Commons series. As noted earlier Dr. Miller is a Catholic and a theistic evolutionist who sees no conflict between religion and science. There was a lot in his talk; he reviewed some of the recent evolution controversies such as Kansas and the recent Dover PA court case and had some really amusing things to say about certain intelligent design advocates such as Michael Behe. The big take home message was that the anti evolution movement is nationwide and world wide. He pointed out that acceptance of evolution is not that much different in England than in the United States.

He says we should draw two lessons from the results of the Dover case: first that intelligent design has collapsed as any sort of scientific theory and second, that intelligent design is really a religious doctrine. He noted for instance that the infamous creationist text Panda's and People was repackaged as an intelligent design text when the Supreme Court ruled the teaching of Creationism in public schools to be unconstitutional. He illustrated the collapse of intelligent design with numerous examples of the power of evolutionary thinking and how it contradicts notions of intelligent design.

Then he discussed the definition of science and noted that in cross examination in the Dover trial, Michael Behe was forced to concede that any definition of science that included intelligent design also would render astrology a scientific subject. He pointed out that the change in the definition of science to eliminate natural explanations in Kansas was in some sense quite radical.

He then examined why evolution is under attack. His assertion is the attack is due to the belief that evolution is seen as the foundation for anything that is wrong with our society. The key weapon of the antievolutionists is the notion that evolution is antitheistic, a notion reinforced by evolutionists such as Richard Dawkins and Daniel Dennett. Miller very boldly I think claimed that saying science can lead us to a deep understanding of the purpose of existence has no more standing scientific than faith based statements. Neither are testable.

Miller next argued that religious people make a mistake when they attack evolution when what they should do is argue against the notion that evolution necessarily leads to an antitheistic interpretation of evolution. This is a really interesting idea and Miller believes that a discussion of this may lead to some sort of peace between science and religion. Science has limitations in that it doesn't carry people "as deep into the mysteries of life as we want to go". At the same time, following St. Augustine's "On the Literal Meaning of Genesis", Miller argued that using scripture to interpret science is a mistake as well.

Faith and reason in Miller's view are both gifts from God and should complement each other. Indeed he argues that faith gives reason to pursue science because it provides at least in Abrahamic religions the notion that nature can be understood. Faith after all has to be grounded in reason. In an analysis very similar to Stanley Jaki's Savior of Science he noted that science is also a child of faith because science require the human being to step back from nature, a notion quite different from the notion in Eastern religions that man and nature are one. I asked him about this after the talk and he was no familiar with Jaki's arguments about the origin of science.

Ken Miller's the handsome one on the left. On the right is some local Kansas Blogger.

A questioner asked if all faiths are equally valid and can science help us choose. Miller's answer was quite interesting. No all faiths are not equal. Saying that they are implies "a failure to choose." At the same time science is not much help either and since we are "severely limited" in our ability to comprehend the world we are required to respect the choices of others.

Most of the audience was friendly but I did catch the infamous Tom Willis who was active in drafting the Kansas 1999 creationist designed 'science' standards. Here he is smoozing with a reporter. One can only wonder what spin he is going to put on Miller's talk.

Update! Additional insight into Miller's talk is at Red State Rabble.

Transcript of Dover case-recommended by Miller.

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Wednesday, September 06, 2006

No Change in Church Position.

According to an article in Catholic News, there will probably not be any shift in Church teaching about evolution. According to Father Joseph Fessio, a participant in the seminar, intelligent design did not come up as a topic. Sounds like we can expect a clarification of the Church's current position according to other participants at the Pope's seminar. The article reports that the published minutes will show that theologins see no conflict between divine creation and evolution.

See also:

Interesting article about Fr. Fessio:

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A Catholic Creationist

From time to time in Catholic circles the name Dominque Tassot crops up as being an influence on Pope Benedict's thinking about evolution. John Allen at the National Catholic Reporter has a revealing interview with this behind the scenes player in the development of Benedict's thinking about evolution.

Key points:

1. Tassot is a creationist-he denies it saying that he is not a creationist because he is not "committed" to a literal interpretation of the Bible. But like many creationists he does not accept macroevolution claiming that there is no scientific basis for it or for the concept of geological time.

For instance, about the principle of Superposition Tassot says:

"But if you think about it, the question of what's on top and what's on bottom doesn't necessarilyhave anything to do with comparative ages. If you pour mercury, oil and water into a glass, the mercury will end up on the bottom, and not because it's older. Physical principles operate. Density is the causal factor that determines position; chronology has nothing to do with it. The same thing applies to the different strata of sedimentary remains. The strata have been deposited where they are, and it's not necessarily the case that the oldest material is on the bottom. That's akin to thinking that the sediments basically fell from the sky. "

2. Tassot defines macroevolution as "the appearence of an organ in the offspring that did not exist in the parent". Clearly he has absolutely no concept of how evolution operates, and his arguement sounds a lot like the old canard that evolution can't lead to novel structure, just expressed very badly.

3. He parts company with the intelligent design crowd by claiming that the designer can be known through religion, and so at least he doesn't pretend that ID is somehow scientific.

So Tassot is more akin to a young Earth creationist in that he doesn't accept the scientific basis for geological time and does not accept macro-evolution. He concludes the interview with a little speculation as to what the Pope will do. He thinks that the Pope will issue a statement about evolution basically through Cardinal Schonborn since they know each other well.

I just pray that the Pope get's exposed to someone who really understands evolution.

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Tuesday, September 05, 2006

Catholicism and Evolution

Ken Miller a prominent theistic evolutionist, who by the way will be at the University of Kansas this week has posted a good commentary on Catholics and Evolution in the Guardian. Miller correctly points out that the Church's problem is not so much with evolution but with the false "nihilistic" philosophies that are incorrectly attached to evolution, sometimes I might point out by proponents but also by opponents to evolution.

Update! Brief summary of Miller's KU talk is here.

Addressing the current concern about the outcome of Pope Benedict's evolution seminar, Miller says:

"Far from reducing humanity to the random result of pointless molecular collisions, evolution unites us with every living being in a fabric of life and change in which our emergence, and the continuing creative power of our universe, is the product of the Creator's will and love. There is indeed a design to life - and the name of that design is evolution. Look deeply enough, and I am sure that the Holy Father and his students will come to the same conclusion."

I hope Miller is right!

A tip of the antennae to Pat Hayes over at Red State Rabble for pointing the Miller article out. See his commentary here.

On another note apparently the Pope will publish a chat, actually minutes of the recent Papal Seminar on evolution according to a story in the Register. The article quotes Father Joseph Fessio as saying the conclusion that God created the universe is philosophical not scientific and that:

"There's a controversy in the United States because there is a lack of awareness of a thing called philosophy. Evangelicals and creationists generally lack it and Catholics have it."

Ouch! Of course some Catholics are creationists as well, so I guess they are not aware of philosophy either. I can buy that!

The Force will be covering Dr. Miller's talk on Thursday as will several other Kansas Bloggers I am sure!

Other links:

Open Letter to Pope Benedict

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Monday, September 04, 2006

Bee excitement at School

No Killer bees, but last Friday I was prowling around campus looking for something to blog on and found a wonderful patch of bright blue Salvia that had been just planted by our landscaping staff. So I wondered over to see what insects were visiting and was excited to find the plants being visited what for a second I thought were yellow jackets that turned out to be these wonderful yellow and black Anthidium bees, at least what I think is Anthidium.


The actual bee is a bit under 10mm long and quite fast so I was lucky to get these shots. At first I thought these were Anthidium manicatum, an introduced species from Europe, but I don't think so. Knowing the danger of trying to identify insects from pictures I wanted to catch one for keying out. Since I didn't have an insect net, I caught one in a plastic bag used to line a trash can and it only took me five tries to perfect the technique of catching a bee in a trash bag on a windy day all the time hoping I didn't get busted by campus security.

The bee is safely in my freezer awaiting a chance to key it out and maybe a visit to KU's bee collection to check my ID. The mint, according to our greenhouse people is Blue Victoria Sage, Salvia farinacea.

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Mendel's Garden # 5 is out!

My wife and I celebrated our anniversary with a little 2 day trip to a B&B in Missouri and I am glad to note the Mendel's Garden #5 is out at Evolgen. Rich has harvested a delightful sampling of genetics delights for us this week. Mendel's Garden #6 will be at The Voltage Gate on September 15.

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