Stockholm: Old Town

We visited Stockholm yesterday and toured the city with my cousin Sharon and her husband Dennis. (That’s them with Ms. Sandwalk in the third photo.) Here are some photos of the Old Town including one of the Swedish Academy where I tried to put in a good word for all my readers.

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45 Years Ago

We're celebrating our 45th wedding anniversary by taking a cruise in the Baltic. We were in Oslo, Norway on our anniversary day (August 9) where we met our friends Dag and Robin from graduate student days. They are als0 marride 45 years so we celebrated with champagne at their house. More about that later.

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University of Rostock

The University of Rostock was founded in 1419. It’s said to be the oldest university in the Baltic Sea area. The main university building is a prominent landmark in Rostock but I was more interested in the Zoology building off to the side.

Looks like I just missed an important conference. Does everyone know who Willi Hennig is?

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Warnemünde and Rostock

Yesterday our boat stopped at the habor in Warnemünde, Germany. There was a lot of activity of the quay in Warnemünde because a number of tall ships were in the harbor.

We took the train to the medieval town of Rostock—a key port in the Hansiatic League (Hansa=guilds). The architecture was similar to that in other leading cities of the Hansiatic League, notably Bruges.

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Cruising

We've been on this boat for three days and we'll be on it for another 8 days as we cruise the Baltic Sea. Internet access costs 70 cents ($0.75 US) per minute so posts will be short and infrequent.

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Copenhagen Canals

We were in Copenhagen a few days ago. Here are some pictures of the canals.

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Carnival of Evolution #62: The Whig History

The latest issue of Carnival of Evolution is hosted by Joachim D, an evolutionary ecologist who blogs at Ecology and Evolution Footnotes. Read: Carnival of Evolution 62: The Whig History .

When it comes to the history of evolutionary theory, a whiggish image could look something like [the figure below]

I leave it to the readers to come up with a female version (including, for example, Maria Sibylla Merian, Rosalind Franklin, Barbara McClintock, Christiane Nüsslein-Volhard).

Arranging July's posts that I found interesting or entertaining as well as the few submitted by others according to a Whig history of evolutionary theory in the following is purely ornamental and does, of course, not imply any whiggishness on the side of the contributors.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Carnival of Evolution #61: Crustie Lovin; Edition

I was out of town when the last two Carnivals of Evolution were published so I'm doing a bit of catchup. The July issue of Carnival of Evolution was hosted by Marc Srour at Teaching Biology. He's the only blogger I know who is based in Cyprus. (He may have just moved to Japan.) Read: Carnival of Evolution #61: Crustie Lovin; Edition.

Hello, and welcome to the Carnival of Evolution #61. For this edition, I’ve chosen to celebrate what I perceive as an inexplicably underappreciated group of animals: the Crustacea. Of the major arthropod groups, I notice that crustaceans often get the short end of the stick. Everyone can name insects and recognise spiders, but besides seafood, crustaceans seem to be a question mark with most people. Insects and spiders have movies and songs written about them; crabs are the logo for cancer, the vernacular name for an STD, and they are an astrological sign.

Insulting. Crustaceans are awesome. There may be over a million insect species, but crustaceans take the cake when it comes to disparity, or morphological diversity, a measure in which no other taxon can match them.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Carnival of Evolution #60: Party like it’s 1953

I was out of town when the last two Carnivals of Evolution were published so I'm doing a bit of catchup. The June issue of Carnival of Evolution was hosted by Zen Faulkes at NeuroDojo. He's a invertebrate neuroethologist, whatever that is. Read: Carnival of Evolution #60: Party like it’s 1953.

Ladies and gentlemen, this is a special edition of the Carnival of Evolution. It’s the big six oh!

In honor of that achievement, we shall share this carnival’s space with other events celebrating their sixtieth anniversary.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

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Monday's Molecule #212

Last week's molecule was a thymine dimer. The winners were Alex Ling and Matt McFarlane. [Monday's Molecule #211].

Today's molecule is an important part of a major pathway. Give the common name and identify the pathway. Explain briefly why this pathway is important.

Email your answers to me at: Monday's Molecule #212. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Dear Denyse, Stop Digging

You're not going to believe what Denyse O'Leary just posted on Uncommon Descent: Junk DNA: Just because information is never used, doesn’t mean it is junk.

Further to Cornelius Hunter’s “Evolutionist: We do not promote any ‘spiritual ideologies,’” (in which he recounts that recent findings about RNA structure conservation suggest that even more of the mammalian genome is functional than supposed, hence there is less “junk DNA”:

I’ve never clearly understood Darwin’s fans attachment to junk DNA. It makes a good “anti-God” statement, as long as you are certain that the stuff is not and never could be any use. But that is precisely what is now widely contested. And it was a trap they need not have fallen into.

But a simple illustration will show that even if most of the information in DNA were never used, it would still be valuable. Let us say I have a directory of members of a club I belong to. I never use most of the phone numbers. Many numbers may never be used by anyone.

Does lack of use make that proportion of the directory junk?

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Goodbye Dumpster

Jerry Coyne posted this video and I thought it was so funny I just had to put it on my website blog.

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What Would Jerry Coyne, Daniel Dennett, and Richard Dawkins Do at Ball State University?

I'm trying to understand how the rules announced by President Jo Ann Gora would work in practice.

Let's think about how they might affect three prominent atheists. Jerry Coyne is an evolutionary biology professor at the University of Chicago. He is a prominent atheist and he defends the position that science and religion are not compatible. He does not have to adhere to the Ball State University rules because the University of Chicago is a private school.

Daniel Dennett is a philosopher at Tufts University (private). He is a prominent atheist and no friend of religion.

Richard Dawkins was a professor and evolutionary biologist at Oxford University in the UK. He did not have to worry about following the Ball State University rules because they don't apply outside of the USA.

Let's imagine that all three became professors at Ball State University. They would have to pay attention to the rules outlined by President Jo Ann Gora. Here are the relevant passages from her recent message.

Creation science, intelligent design, and other worldviews that focus on speculation regarding the origins of life represent another important and relevant form of human inquiry that is appropriately studied in literature and social science courses. Such study, however, must include a diversity of worldviews representing a variety of religious and philosophical perspectives and must avoid privileging one view as more legitimate than others.

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As a public university, we have a constitutional obligation to maintain a clear separation between church and state. It is imperative that even when religious ideas are appropriately taught in humanities and social science courses, they must be discussed in comparison to each other, with no endorsement of one perspective over another.

All three professors have written extensively about religion and their views are widely known. They attend conferences and give public lectures. They do not pull any punches when they talk about the evils of religion. Nobody would ever say that they go out of their way to avoid endorsing one perspective over another. Academics have opinions and they are not afraid to express them.

Most professors have graduate students. They do not hide their opinions from their graduate students. Nor do they hide them from their colleagues or the administrators in their university.

These professors aren't shy about expressing their points of view on blogs, twitter, Facebook, newspapers and just any other means of communication.

Now let's imagine that they are teaching an undergraduate course about atheism and religion in a humanities department at Ball State University. How is that supposed to work? Are they supposed to go out of their way to avoid "privileging one view as more legitimate than others"? And if so, are any of the students going to be fooled? They can all access the internet.

It's clearly a ridiculous rule unless it also applies outside of the classroom. Does it mean that professors at a public university must avoid criticizing religion at all times?

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President of Ball State University Forbids Teaching Intelligent Design

A few months ago Jerry Coyne learned that an astronomy professor (Eric Hedin) at Ball State University (Indiana, USA) was advocating an intelligent design perspective in his course on "The Boundaries of Science." Jerry contacted the Chair of the department to request that the administration intervene to prevent this professor from expressing his personal opinion in class. Jerry also contacted the Freedom From Religion Foundation and the FFRF lawyers sent a letter to Ball State University threatening them with a lawsuit for exposing students to intelligent design creationism in science class. Jerry Coyne, FFRF, and a host of others, think this course is forbidden by the US Constitution.

The Junk DNA Controversy: John Mattick Defends Design

The failure to recognize the implications of the non-coding DNA will go down I think as the biggest mistakes in the history of molecular biology.

John Mattick
abc AustraliaJohn Mattick has just published a paper dealing with the controversy over the ENCODE results and junk DNA. As you might imagine, Mattick defends the idea that most of our genome is functional. He attempts to explain why most of the critics are wrong.

The title of the paper is "The extent of functionality in the human genome" (Mattick and Dinger, 2013). It's published in the HUGO Journal. Recall that HUGO (Human Genome Organization) gave Mattick a prestigious award for his contributions to genome research. (See The Dark Matter Rises for a discussion of these contributions.)

UPDATE: Mike White also discusses this paper at: Having your cake and eating it: more arguments over human genome function.

Mattick's paper begins by mentioning three of the papers that were critical of ENCODE results: Dan Graur's paper (Graur et al. 2013), Ford Doolittle's paper (Doolittle, 2013), and the paper by Niu and Jiang (2013).

He begins by addressing one of Dan Graur's points about conservation.