USA Honors Two Biochemists and an Evolutionary Biologist

The United States has just honored two biochemists, an evolutionary biologist, and some other scientist by issuing stamps to commemorate their achievements [American Scientists (Forever)].

Melvin Calvin (1911-1997) is famous for working out an important pathway of carbon fixation known today as the Calvin cycle. This pathway is prominent in photosynthetic bacteria and in chloroplasts. It is often considered to be a fundamental part of photosynthesis, although some workers prefer to maintain the distinction. Calvin won the Nobel Prize in Chemistry in 1961.



Severo Ochoa (1905-1993) received the Nobel Prize in Physiology or Medicine in 1959 along with Arthur Kornberg. Ochoa demonstrated that RNA could be synthesized in vitro using purified RNA polymerase. Later on he helped create synthetic polynucleotides that helped crack the genetic code.

Asa Gray (1810-1888) is best known today as a friend of Charles Darwin and one of the early supporters of evolution in America. He was a botanist at Harvard for most of his career. The website says he "... became the principal American advocate of evolutionary theory in the mid-nineteenth century." I think it would be much more fair to say that Asa Gray was a strong supporter of evolution. He and Darwin had many discussions (by letter) on the mechanisms of evolution.

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Done!

The book is done! It's off to the printer and we should have copies by the end of August. Everyone who posts a comment will get a free copy.¹

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1. In some parallel universe.

The DNA Hall of Shame

Kalliopi Monoyios is a science illustrator who works at the University of Chicago. She's the artist behind Your Inner Fish and Why Evolution Is true. She has a blog called Symbiartic where she writes about the trials and tribulations of working with scientists making scientific illustrations.

I was especially interested in her recent article about The DNA Hall of Shame.

Confession time. Illustrators are people, too. And by that I mean they bring assumptions to the table at the outset of every project. There’s no avoiding it – no matter how educated and experienced you are, you can’t know it all. That is why it is so critical for researchers and editors to be intimately involved in every draft of the drawings they commission and publish. This may sound like a mega no-brainer, especially if you’re an editor or art director in a field other than in the sciences who is accustomed to working intimately with illustrators to get what you want. But in my experience illustrating two popular non-fiction science books, illustrations are treated as icing on the cake and are glossed over by fact checkers and editors who otherwise comb manuscripts for errors. Illustrating Your Inner Fish is a prime example. The manuscript went through four drafts of revisions with at least two specialized scientific editors. And yet this gaffe made it through:

I know exactly how she feels but even multiple expert reviewers won't save you. When we're writing a textbook we take care to review the text and figures together and we pay just as much attention to the figures as we do to the text. For the most recent edition—about to be sent to the printer—the pages were reviewed by me, my coauthor Marc Perry, our developmental editor Michael Sypes (University of Arizona), content reviewer Barry Ganong (Mansfield University), and accuracy reviewers Scott Lefler (Arizona State University) & Kathleen Nolta (University of Michigan). That's six pairs of expert eyes that look at every page.

All the previous editions went through the same intensive review. Nevertheless, the following incorrect figure—originally drawn by me back in 1992— has been published in four books. It wasn't until Barry Ganong looked at it a few months ago that he recognized the error. Can you spot it? It's subtle, and it may only be apparent to experts on DNA structure, but it's an error nevertheless.¹

I add it to The DNA Hall of Shame.

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1. I'll post the correct version in a few days.

MaRS Phase II

MaRS stands for "Medical and Related Sciences." It's a large complex of buildings kitty-corner from where I work, also known as the MaRS Discovery District. Work has now re-started on Phase II—the tallest building in the image below. That image is the view from my building. The Ontario legislature (Parliament Buildings) is just off to the left.

The new building will house dozens of tenants including some research labs associated with my department and our sister departments. The idea is to bring together various researchers in the university community with private companies who might benefit from their research.

When completed, the extra space will make Toronto one of the largest focused centers of medical research in the world. We have MaRS, the University of Toronto, and four major research hospitals within two blocks of one another. In my particular field of biochemistry and molecular biology there are over 200 active research labs with about 500 graduate students in four departments.

I just hope they have a nice cafeteria.

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The EES Newletter

Not yet available at the website above

Ancient Lives

Ancient Lives is a collaboration between a diverse collection of Oxford Papyrologists and Researchers, The Imaging Papyri Project, The Oxyrhynchus Papyri Project, the Egypt Exploration Society and the following institutions.

The papyri belong to the Egypt Exploration Society and their texts will eventually be published and numbered in Society's Greco-Roman Memoirs series in the volumes entitled The Oxyrhynchus Papyri.


BBC report

Join the Carnival!

The next Carnival of Evolution (#38) will be posted right here on Sandwalk. You have only one week to submit your best work on evolution—or recommend something you read that just has to be included!

The August 1st carnival is shaping up to be one of the best ever so get your submissions in right now so I can prepare the posting.

There's going to be a surprise category so watch this space next Monday.

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Worth Quoting

It often seems as though Cornelius Hunter can't read any news article about science without spinning it into an attack on evolution. His latest attempt is a misreading of an article in New Scientist that reminds us of the complexity of some modern bacterial species. According to Hunter this information refutes a major prodiction of evolution [New Scientist: Not so Simple—Bugs That Break all the Rules].

It seems that first born cell of evolution must have been quite complex, including a vast proteome of hundreds of different proteins. This is just one of many scientific falsifications of evolution’s prediction of simple beginnings.

Most intelligent people can see the flaws in Hunter's logic so I won't bother pointing them out. However, I would like to highlight the first comment on Hunter's blog. Thorton said ...

We know you hit the bottom of the barrel with your anti-science nonsense some time ago CH. Now we discover your barrel had a trap door.

Very clever. And very appropriate. Well said Thorton.

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Deaddog (Re-)Discovers Idiots

Back in the olden days of talk.origins there was a bright young student named "deaddog" who posted frequently. His speciality was The origin of life.

Deaddog became Professor Andy Ellington at the University of Texas at Austin and he's still interested in the origin of life [The Ellington Lab] and the creation of new life forms [Dr. Andy Ellington].

Deaddog (Andy) has testified before in front of the Texas board of education in an attempt to educate them about science. As you might imagine, given his interests, he concentrated on showing that Jonathan Wells and the IDiots are dead wrong about origin of life research. This is about as hard as shooting fish in a barrel but somebody has to do it.

Last week he was back at the meetings to testify in favor of adopting good biology textbooks. Here's what he said on Andy Ellington's Blog: On the Circus.

Today I’m at the State Board of Education hearings on textbook adoption. Or, in other words, the once every-so-often meeting that helps to determine whether or not Texas makes itself a laughingstock with respect to the teaching of evolution. I guess this is sort of my first “live blog,” which is just weird.

I continue my love / hate relationship with Texas. On the one hand, this board meeting is democracy in action (not necessarily a good thing in a Republic): every idiot gets their say. On the other, their say means very little. The larger forces at work will drive both curriculum and the impact of that curriculum.

This provoked a response from some of the main IDiots like Casey Luskin [University of Texas Evolutionary Biologist Andy Ellington Mocks Fellow Texans as "Idiots" and "Laughingstocks" for Doubting Darwin] and Denise O'Leary [Tax dollar alert: Who pays this Texas biology profs salary?]. Don't you just love it when the IDiots voluntarily supply us with evidence of their reasoning ability?

They should have been careful about who they tried to pick on. Here's Andy's response [On Idiocy].

The Discovery Institute, largely a spent force both intellectually and politically since Dover, has chosen to take issue with my comments at the State Board of Education. This is especially amusing as the original disputation of their idiocy came many years ago, and has been published via a NSCE publication for quite some time. Indeed, I refer to this publication in my previous testimony, which was and is available to the Discovery Institute. From this, we can conclude that the Discovery Institute is woefully behind the times not only in terms of science, but even in terms of their own shallow attempts to provide a revisionary context to science. Guys, this just can’t be good for your funding posture. Try to keep up.

...

So, when the DI has a vague, anonymous scientist (apparently the only kind that the DI employs) point out, as they do in their current idiot posting (please note the use of the word ‘idiot,’ as it absolutely applies to the DI for their complete lack of understanding of the extant scientific literature) ...

...

The DI claims this all as a teachable moment, saying that “What we see evidence of here is a scientific debate over the origin of life ….” No, actually, the problem with that claim is that science for the most part requires experimentation. You guys don’t do experiments. We do. You guys just carp about our experiments, and you don’t even do that very well.

...

Which would you rather see helping to set policies relating to teaching biology, literally millions of scientists who spend their entire careers doing experiments, or a handful of folks at a faith-based think tank whose jobs largely depend on trying to make inconvenient facts go away?

...

Well, Casey, I hope this gets your page hit count up somehow. God knows you need it. But really I don’t think that picking a fight about the facts is going to help you guys much in your further, currently grossly unsuccessful attempts to show your relevance. You didn’t even have boots on the ground at the Texas SBOE hearings this time, you just sent a 80 page screed that in the end didn’t change one word in one textbook up for consideration. Sad, really. But, there ya go. Happy trails.

I miss deaddog.

UPDATE: How many have heard that old saying about what you're supposed to do when you've dug yourself into a deep hole?¹ Here's a couple of examples of what you're NOT supposed to do. These postings attacked real science and they were the ones that provoked Andy's response. Why do so many non-scientist IDiots think they can successfully debate with an expert in the field?²

Casey Luskin, the lawyer, says Andy Ellington's Citation Bluffs and the Scientific Debate Over the Miller-Urey Experiment

Denyse O'Leary, the jounralist, says Texas school board hearings: Startling gains in the hard science of citation bluffing are now widely noted.

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1. Stop digging.

2. It's a rhetorical question. They are IDiots and that's exactly what IDiots do.

Stop the Press!!! Scientists Discover the 7th and 8th Bases of DNA!

Science Daily published a press release from the University of North Carolina School of Medicine: Researchers Identify Seventh and Eighth Bases of DNA. The news was so extraordinary that the article was copied on RichardDawkins.net. Here's the opening paragraphs from the press release ...

ScienceDaily (July 21, 2011) — For decades, scientists have known that DNA consists of four basic units -- adenine, guanine, thymine and cytosine. Those four bases have been taught in science textbooks and have formed the basis of the growing knowledge regarding how genes code for life. Yet in recent history, scientists have expanded that list from four to six.

Now, with a finding published online in the July 21, 2011, issue of the journal Science, researchers from the UNC School of Medicine have discovered the seventh and eighth bases of DNA.

These last two bases -- called 5-formylcytosine and 5 carboxylcytosine -- are actually versions of cytosine that have been modified by Tet proteins, molecular entities thought to play a role in DNA demethylation and stem cell reprogramming.

...

Much is known about the "fifth base," 5-methylcytosine, which arises when a chemical tag or methyl group is tacked onto a cytosine. This methylation is associated with gene silencing, as it causes the DNA's double helix to fold even tighter upon itself.

Last year, Zhang's group reported that Tet proteins can convert 5 methylC (the fifth base) to 5 hydroxymethylC (the sixth base) in the first of a four step reaction leading back to bare-boned cytosine.

Speaking of textbooks, this amazing discovery couldn't have come at a better time since I'm just wrapping up the final chapters of my introductory biochemistry book. I'd better review what I wrote to see if I can include the 7th and 8th bases. Here's what I've got so far ...

DNA and RNA contain a number of modified nucleotides. The ones present in transfer RNA are well known (Section 21.8B) but the modified nucleotides in DNA are just as important. Some of the more common modified bases in DNA are shown in Figure 18.17. Most of them are only found in a few species or in bacteriophage while others are more widespread.

We will encounter N6-methyladenine in the next chapter when we discuss restriction endonucleases. 5-Methylcytosine is a common modified base in mammalian DNA because it plays a role in chromatin assembly and the regulation of transcription. About 3% of all deoxycytidylate residues in mammalian DNA are modified to 5-methylcytidine.

Oh dear. Looks like I've made a serious mistake. I've shown bases #5, #6, #7, #8, #9, and #10 but everyone knows that up until yesterday only six bases were known.

Where did I go wrong? Can anyone help me out before I have to send this chapter to the printer?¹

(The original Science paper is Ito et al. (2011). The authors really do imply that there are only six known modified nucleotides but they add an important qualifier that seems to have been played down the press release.)

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1. One of my sources is Gomers-Apt and Borst (1995). In addition to the modified bases I've shown above they describe three forms of glycosylated hydroxymethyl cytosine (#11, #12, #13), uracil (#14), α-putrescinylthymine (#15), two different sugar substituted forms of 5-dihydroxypentyluracil (#16, #17), a-glutamylthymine (#18), 7-methylguanine (#19), N⁶-carbamoylmethyladenine (#20), N⁶-methylcytosine (#21), three versions of glycosylated 5-hydroxycytosine (#22, #23, #24) and β-D-hydroxymethyluracil (#25).

Gommers-Ampt, J.H. and Borst, A.P. (1995) Hypermodified bases in DNA. FASEB 9: 1034-1042 [FASEB]

Ito, S., Shen, L., Dai, Q., Wu, S.C., Collins, L.B., Swenberg, J.A., He, C., and Zhang, Y. (2011) Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine. Science Published Online 21 July 2011 [doi:10.1126/science.1210597]

F. Naether, Die Sortes Astrampsychi

FRANZISKA NAETHER

Die Sortes Astrampsychi

Problemlösungsstrategien durch Orakel im römischen Ägypten

"Du wirst deine Geliebte heiraten, aber es wird dir leid tun"; "Du wirst von deiner Frau erben, aber nicht als Alleinerbe". So spricht ein dem Pythagoras zugeschriebenes Orakel, das schon Alexander zur Weltherrschaft verholfen haben soll. Das Losbuch "Sortes Astrampsychi" ist auf römerzeitlichen Papyri und mittelalterlichen Handschriften in griechischer Sprache überliefert. Mit 92 vorformulierten Fragen und 1030 Antworten aus fast allen Lebensbereichen liegt eine ergiebige Quelle zur Sozialgeschichte Ägyptens vor - vom Überleben von Krankheiten über Geschäftsbeteiligungen hin zu Verhandlungstaktiken vor Gericht. Wichtige Fragestellungen dieses Kommentars zu den Sortes Astrampsychi zielen auf den Anwendungskontext und die Einordnung des Werks innerhalb der religiösen, divinatorischen und magischen Praktiken Ägyptens unter besonderer Berücksichtigung der "Ticket-Orakel" in demotischer, griechischer und koptischer Sprache.

NAETHER, FRANZISKA  Die Sortes Astrampsychi. Problemlösungsstrategien durch Orakel im römischen Ägypten
2010. XVIII, 491 pages.ORA 3

ISBN 978-3-16-150250-7

cloth € 109.00

English blurb

"You will marry your girlfriend, but you will be sorry." "You will inherit from your wife, but you will not be the sole heir." These are the words of an oracle attributed to Pythagoras which supposedly also helped Alexander gain world supremacy. The "Sortes Astrampsychi" were transmitted on papyri from the Roman period and medieval manuscripts in Greek. Consisting of 92 pre-formulated questions and 1030 matching answers from nearly all areas of daily life, the oracle represents an important source for the social history of Egypt, for example its demography, economy and jurisdiction. In this commentary on the "Sortes Astrampsychi," the author focuses on the background of its use in antiquity and the contextualization among the religious, divinatory and magical practices of Egypt, in particular the "ticket" oracles in Demotic, Greek and Coptic.


BMCR review
Franziska Naether, Die Sortes Astrampsychi: Problemlosungsstrategien durch Orakel im römischen Ägypten. Orientalische Religionen in der Antike 3.   Tübingen:  Mohr Siebeck, 2010.  Pp. 550.  ISBN 9783161502507.  $195.00.   

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Reviewed by Pieter W. van der Horst, Utrecht, The Netherlands (pwvdh@xs4all.nl)

Even though the text of the ancient lot oracle known as Sortes Astrampsychi is not one of central concern to classical scholarship, it has had its share of attention in recent years. The Teubner edition of the shorter version by G. M. Browne appeared in 1983, and in 2001 R. Stewart’s Teubner text of the longer version (the so-called ‘ecdosis altera’) came out;1 both scholars also published a series of valuable articles on this document. Stewart’s English translation of the text appeared in W. Hansen (ed.), Anthology of Ancient Greek Popular Literature (Bloomington: Indiana University Press, 1998) 285-324. In 2006 an edition of the Greek text with a German translation was published by K. Brodersen, Astrampsychos: Das Pythagoras-Orakel (Darmstadt: Wissenschaftliche Buchgesellschaft). And now we have the monumental and exhaustive study of the Sortes Astrampsychi by Franziska Naether, an immensely learned work that the author completed when she was only 29 years. The book is so densely packed with information on all possible aspects of the study of the Sortes Astrampsychi (and many related documents) that it is impossible to do justice to its contents in this short review. The book can best be characterized as a comprehensive contextualization of the Sortes Astrampsychi.

 etc. at BMCR

Happy Birthday from Google!

Google wishes happy birthday to ..... ?

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43. Ständige Ägyptologenkonferenz (SÄK), Leipzig, 22.-24. Juli, 2011

Registration information here

Freitag, 22.07. 2011

ab 12:00 Uhr Registration im Tagungsbüro (Seminargebäude, Raum S 204)

ab 13:00 Uhr Gelegenheit zur Besichtigung des 2010 neu eröffneten Ägyptischen Museums

14-16:00 Uhr Treffen der Studiengangsverantwortlichen (Thema: Flexibilisierung von BA und MA, Seminargebäude, Raum S 420)

14-16:00 Uhr „StudierendenSÄK“ (Thema: Studium – und danach?, Seminargebäude, Raum S 202)

16:00 Uhr Begrüßung in Hörsaal 9

Prof. Dr. Beate Schücking (Rektorin der Universität Leipzig)

Prof. Dr. Hans-W. Fischer-Elfert Prof. Dr. Pirmin Stekeler-Weithofer (Präsident der Sächsischen Akademie der Wissenschaften zu Leipzig)

Dr. Volker Rodekamp (Direktor des Stadtgeschichtlichen Museums Leipzig und Präsident des Deutschen Museumsbundes)

Dr. Mamdouh el-Damaty (Botschaft der Arabischen Republik Ägypten, Berlin)

16:30-max. 17:45 Uhr Berichte aus den Institutionen (über das INFO online hinausgehende Informationen)

Pause 

18:15-19:15 Uhr Festvortrag von Prof. Dr. Stefan Rebenich (Bern): 

Zwischen Verweigerung und Anpassung. Die Altertumswissenschaften im „Dritten Reich“

19:30-22:00 Uhr Empfang im Grassimuseum am Johannisplatz 

Samstag, 23.07. 2011

09:00-09:15 Uhr Einführende Worte

09:15-09:45 Die Ägyptologie im Nationalsozialismus: Umriss eines Forschungsgebietes

Thomas Schneider (Toronto; gelesen von Claus Jurman)

09:45-10:15 Das Deutsche Haus in Theben 1904 bis 1958 – ein Spiegel deutscher Politik in der ägyptischen Provinz

Daniel Polz (Kairo)

10:15-10:45 Ludwig Stern – ein Ägyptologe zwischen Keltologie und Bibliothek

Barbara Magen (Hildesheim)

10:45-11:15 KAFFEEPAUSE

11:15-11:45 Der lange Arm des Nationalsozialismus: Die politischen Einflüsse auf die Abteilung Kairo des DAI während der Amtszeit Hermann Junkers von 1929-1949

Susanne Voß (Kairo/Köln)

11:45-12:15 Hermann Junker – Ein deutsch-österreichisches Forscherleben zwischen Pyramiden, Kreuz und Hakenkreuz

Julia Budka (Berlin/Wien); Claus Jurman (Wien)

12:15-12:45 Das Institut für Ägyptologie der LMU München im Nationalsozialismus

Thomas Beckh (München)

12:45-14:45 MITTAGSPAUSE

14:45-15:15 Ludwig Borchardt und sein „Institut für ägyptische Bauforschung und Altertumskunde“ in Kairo – Ein Beitrag zur Urgeschichte des Schweizer Instituts Kairo

Cornelius von Pilgrim (Kairo)

15:15-15:45 Bissing – Küthmann – Hölscher: Ägyptologie und Bauforschung zwischen Den Haag, Hannover und Ägypten 1922-1951

Christian E. Loeben (Hannover)

15:45-16:15 Ein Ägyptologe in Königsberg. Zum Leben und Wirken Walter Wreszinskis

Alexander Schütze (Leipzig/München)

16:15-16:45 KAFFEEPAUSE

16:45-17:15 Erich Lüddeckens – ein Pfarrerssohn auf Abwegen

Heinz-Josef Thissen (Erftstadt)

17:15-17:45 Die deutsche Ägyptologie zwischen 1945 und 1949 im Spiegel der Autorenkorrespondenz des Leipziger Verlages J.C. Hinrichs

Anke Weber; Henning Franzmeier (Berlin)

17:45-18:15 Hedwig Fechheimers Plastik der Ägypter – Ägyptologie, Kunstwissenschaft und jüdisches Schicksal

Sylvia Peuckert (Berlin)

18:15-18:45 Steindorffs Brief an Wilson

Dietrich Raue (Leipzig)

18:45-19:15 Uhr Abschließende Diskussion

ab 19:30 Abendveranstaltung in der Moritzbastei Leipzig, Universitätsstraße 20:00 Uhr Eröffnung des Buffets

ab 22:30 Uhr nicht mehr geschlossene Veranstaltung (Discobetrieb „All you can dance“, freier Eintritt für SÄK-Besucher), www.moritzbastei.de

Sonntag, 24.07. 2011

09:30- 10:00 Bericht des Deutschen Archäologischen Instituts, Abt. Kairo (DAI)

Ulrike Fauerbach

10:00- 10:30 Bericht des Österreichischen Archäologischen Instituts, Zweigstelle Kairo (ÖAI)

Irene Forstner-Müller

10:30- 10:45 Bericht des Schweizerischen Instituts für Ägyptische Bauforschung und Altertumskunde in Kairo

Cornelius von Pilgrim

10:45- 11:00 KAFFEEPAUSE

11:00- 11:30 Bericht des Internationalen Ägyptologenverbands (IAE)

Ursula Verhoeven

11:30- 12:00 Bericht des Sondersammelgebiets Ägyptologie der UB Heidelberg, Propylaeum, INFO online

Nicole Kloth

12:00- 12:15 Situation ägyptischer Museen in kommunaler Trägerschaft

Katja Lembke, Christian E. Loeben

12:15- 12:30 Bericht des Treffens der Studiengangsverantwortlichen

Hans-W. Fischer-Elfert

12:30- 12:45 Bericht der Studierenden SÄK 

Juliane Seemann, Marc Brose

12:45- 13:00

Festlegung des nächsten Austragungsorts

NN

Horace Judson (1931 - 2011)

Horace Freeland Judson died on May 6, 2011. He is best known as the author of The Eighth Day of Creation first published in 1979 and later re-published in an expanded edition in 1996. This is a "must-read" book for all students of biochemistry and molecular biology.

Mark Ptashne has published an obituary in PLoS Biology [Horace Judson (1931 - 2011)]. Ptashne raises an issue that should be of concern to all biological scientists; namely, the fact that modern molecular biologists seem to be completely unaware of the history of their field and of all the fundamental work done with bacteria and bacteriophage. This was a problem that Judson tried hard to rectify before it was too late but it's beginning to look like he was not successful.

Here's Ptashne's take on it.

The Eighth Day, first published in 1979, is a gift that keeps on giving. It is not the completeness of his history, nor even the vivid prose that imparts its lasting effect. Rather, Judson had the drive and wit to probe until he understood not just who did what, and with what quirks of personality, but why they did it, and how they did it. At each stage he reveals what was at stake, what the crucial alternatives were, and how the problems were solved (or not, as the case may be). Who cares about this past, you might ask, we scientists being neither artists nor composers?

Could it be that—for scientists as well as composers and artists—the past can be a source of inspiration, and that we ignore it at our peril? Consider the question of how states of gene expression are conveyed from mother to daughters as cells divide. Are instructions passed along by regulatory proteins present in the cytoplasm (so-called “cytoplasmic determinants”), or is the information somehow built into, or attached to, the DNA and transferred along with it? Experiments performed by Francois Jacob and Jacques Monod and their colleagues at the Institut Pasteur in the 1960s distinguish between the models, strikingly supporting the first of these possibilities. These experiments (including the famous “zygotic induction” and “PaJaMa” experiments—see Judson's book) were, of course, performed with bacteria.

I recently spoke with an editor of a major journal that regularly publishes sensational papers on the question as it applies to higher organisms, and learned that s/he, like many of the journal's authors, had never heard of these bacterial experiments! You realize, reading Judson's book, that the challenge is to engage the thought processes of these French scientists, ponder their approaches and results, and design experiments of comparable power and clarity to confirm or refute their conclusions in a different setting. Without that engagement, the new answers are apt to be (and in my opinion usually are) baloney.

Shortly after I read this obituary I was browsing Biology News Net and came across this remarkable opening statement in a press release from Stowers Institute for Medical Research in Kansas City, Missouri, USA.

Look up “transcription”—the copying of a gene’s DNA into RNA intermediaries—in any old molecular biology text book, and it all seems very simple: RNA polymerase II, the enzyme that catalyzes the reaction, assembles at the start site and starts motoring down the strand, cranking out the RNA ribbon used to construct proteins. But researchers now know that RNA polymerase II often stalls on DNA strands where it was once assumed to just barrel down.

A report from the Conaway lab at the Stowers Institute for Medical Research in the July 8, 2011, edition of the journal Cell identifies a switch that allows RNA polymerase to shift gears from neutral into drive and start transcribing. This work sheds light on a process fundamental to all plant or animal cells and suggests how transcriptional anomalies could give rise to tumors.

This is a very misleading statement. Back in 1989 I wrote an extensive section on "RNA Polymerase Pauses While Transcribing Some Sequences" in my first textbook. I described the effects of sequence and secondary structure on the rate of elongation and explained how a protein component of the the transcription complex (NusA) promotes pausing in order to enhance transcription termination. The idea that rates of elongation were NOT constant was an important part of most molecular biology textbooks.

But this was in bacteria (E. coli), where most of these fundamental discoveries were first made. The press release refers specifically to eukaryotic RNA polymerase II. In the second edition of my textbook (1994) I talked about RNA polymerase II elongation factors (eukaryotes) and specifically mentioned that "TFIIS may play a role in pausing and transcription termination that is similar to the role of NusA in bacteria." The point is that older molecular biology textbooks were well aware of the fact that even the eukaryotic transcription elongation complexes did not move at a constant rate. The press release is quite incorrect.

The actual paper is not about transcription elongation but transcription initiation and how various factors assist in the transfer from the initiation complex to the elongation complex. All this was known for transcription in E. coli back in the 1970s. The old molecular biology textbooks explain abortive initiation and how RNA polymerase can stall at initiation sites until sigma factors are replaced by elongation factors. None of that is new in spite of what the press release implies.

How does this happen? I think it's because modern researchers are completely unaware of the history of their field. That's partly because the work on bacteria and bacteriophage—where the basic concepts were often discovered—is no longer taught in biochemistry and molecular biology courses. This leads to the false idea, as expressed in the press release, that all new discoveries in eukaryotes are truly new concepts that nobody ever thought of before.

The solution to this problem is to make all students read The Eighth Day of Creation.

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Insulting Religion by Pat Condell

The accommodationists aren't gonna like this ...

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Evolution According to the Canadian Society for Ecology and Evolution

The National (USA) Center for Science Education (NCSE) has just endorsed a four-year-old statement on teaching evolution from the Canadian Society for Ecology and Evolution [Canadian Society for Ecology and Evolution adds its voice for evolution]. Here's the text from the CSEE website [CSEE/SCEE President's Forum].

There is overwhelming evidence that life has evolved over thousands of millions of years. The ancestors of modern organisms, as well as whole groups that are now completely extinct, have been found in great abundance as fossils. The main processes responsible for evolutionary change, such as variation and natural selection, have been repeatedly observed and verified in natural populations and in laboratory experiments. All the features of living organisms, including those discovered in the recent advances in molecular biology, are readily explained by the principles of evolution. Any scientific theory that provides a clear mechanism, offers a broad explanation of natural phenomena, receives strong support from observation and experiment and that is never refuted by careful investigation is usually called a “fact”. The cell theory of organisms, the germ theory of infection, the gene theory of inheritance and the theory of evolution are all facts. Teaching alternative theories as though they had equivalent scientific status is a perversion of education that damages children’s ability to understand the natural world. In particular, creationism is a religious doctrine long since known to be a fallacious account of Earth history that has no scientific standing and cannot be represented as a credible alternative to evolution. Evolution is the single most important principle of modern biology and the foundation of any sound biology curriculum.

Graham Bell
President, Canadian Society for Ecology and Evolution

I don't like this statement because: (1) it implies that the "theory of evolution" is only about variation and natural selection, (2) it confuses evolutionary theory with the facts of evolution, and (3) it confuses creationism with Young Earth Creationism.

If you are going to claim that your version of evolutionary theory is correct then you would be well-advised to define it. And if you are going to claim that it's a fact then what's the point of calling it "evolutionary theory"? The "theory" part of evolution is an explanatory model that's used to understand and interpret various facts about the history of life.

With respect to point #3, one of the main threats to science these days comes from Intelligent Design Creationism and there are many IDiots who do not subscribe to an obviously "fallacious account of Earth's history."

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