Wednesday, July 30, 2008

Improving evolution education at zoos and museums

Many zoo and museum exhibits go out of their way to avoid using the word "evolved" in the text describing the exhibits. Commonly used terms are "developed", "acquired" and "emerged". The text in the photo above mentions "one theory". I wonder what that theory might be? I guess they don't want to offend their more sensitive visitors.

Colin Purrington is trying to improve science education at zoos and museums. He has 12 suggestions to get evolution back into exhibit texts.

I like this idea: If you take your class on field trips to these places, design an exercise that charges your students with designing more interesting, evolution-based plaques. If you have a digital camera, you can take pictures of the existing plaques for use back in the classroom. Then get your students to send the ideas (slickly packaged) to the director of the place you visited. The students will enjoy being simultaneously engaged in both science and social change.

There is a lot of great stuff in Purrington's evolution outreach pages.

Sunday, July 27, 2008

All Theories Proven With One Graph

All Theories Proven With One Graph by Don Grace of Florence, Alabama. Winner: Funniest Graph Contest in Journal of Irreproducible Results.

Saturday, July 26, 2008

21 Congressmen are Nontheists

Today I went to a lecture by Lori Lipman Brown at the New York City Skeptics. Brown, a former state senator from Nevada, is director of the Secular Coalition For America and the first Congressional lobbyist expressly representing nontheistic Americans. In her lecture, Brown detailed her lobbying efforts on behalf of nontheists and emphasized the overlap between Secularists and Skeptics.

One of the more interesting facts that came up was that the Secular Coalition For America has asked 60 congressmen what their religious views were (it was a decidedly biased sample, i.e. they did not ask Senator Brownback). Of these senators and representatives, 21 professed to be nontheists, but requested that they not be named since on account that they feared they would not be reelected. To date, only one congressman has had the fortitude to stand up and state his true beliefs: Rep. Pete Stark of California.

Another highlight was buying (yet) another Darwin/Evolution t-shirt.
Afterwards, I headed downtown to the South Street Sea Port to check out Bodies: the Exhibition. The exhibit was fascinating (albeit a little creepy because all the cadavers were Chinese).

There is actually this disclaimer:

This exhibit displays human remains of Chinese citizens or residents which were originally received by the Chinese Bureau of Police. The Chinese Bureau of Police may receive bodies from Chinese prisons. Premier cannot independently verify that the human remains you are viewing are not those of persons who were incarcerated in Chinese prisons. This exhibit displays full body cadavers as well as human body parts, organs, fetuses and embryos that come from cadavers of Chinese citizens or residents. With respect to the human parts, organs, fetuses and embryos you are viewing, Premier relies solely on the representations of its Chinese partners and cannot independently verify that they do not belong to persons executed while incarcerated in Chinese prisons.

Nonetheless the exhibit was well done. Having butchered numerous amphibians in high school anatomy, I cannot imagine the effort it must have required to dissect these cadavers so exquisitely. Especially interesting was the blood vessel exhibit. Here a preservative was pumped into the vessels, and everything else was dissolved with a corrosive leaving jus the vessels. Kidneys and other important organs were amazingly dense nets of vessels. The exhibit is a little pricey (~$30), but hey you would spend that in one hour in any NYC bar.


My favorite blog is Small Things Considered. This week Elio provides an annotated list of past mini-essays for your reading convenience. Do your brain a favor and check it out!

Thursday, July 24, 2008

I've been tagged!

Jessica over at Bioephemera wants to know what books I've read from the following list.

Update: book meme is contagious.

I freely confess 99% of what I read these days is non-fiction, but in my (misbegotten) youth I frequently dabbled in the *gasp* humanities.

The rules: boldface the books on this list that you've read, and italicize books you started but never finished.

1 Pride and Prejudice - Jane Austen
2 The Lord of the Rings - JRR Tolkien (the trilogy actually)
3 Jane Eyre - Charlotte Bronte
4 Harry Potter series - JK Rowling (ugh)
5 To Kill a Mockingbird - Harper Lee
6 The Bible
7 Wuthering Heights - Emily Bronte
8 Nineteen Eighty Four - George Orwell
9 His Dark Materials - Philip Pullman
10 Great Expectations - Charles Dickens
11 Little Women - Louisa M Alcott
12 Tess of the D'Urbervilles - Thomas Hardy
13 Catch 22 - Joseph Heller (Hilarious)
14 Complete Works of Shakespeare
15 Rebecca - Daphne Du Maurier
16 The Hobbit - JRR Tolkien
17 Birdsong - Sebastian Faulks
18 Catcher in the Rye - JD Salinger
19 The Time Traveller's Wife - Audrey Niffenegger
20 Middlemarch - George Eliot
21 Gone With The Wind - Margaret Mitchell (Does the movie count?)
22 The Great Gatsby - F Scott Fitzgerald
23 Bleak House - Charles Dickens
24 War and Peace - Leo Tolstoy
25 The Hitch Hiker's Guide to the Galaxy - Douglas Adams (So long Doug and thanks for all the erm... books)
26 Brideshead Revisited - Evelyn Waugh
27 Crime and Punishment - Fyodor Dostoyevsky (Brothers Karamazov was better IMHO)
28 Grapes of Wrath - John Steinbeck
29 Alice in Wonderland - Lewis Carroll
30 The Wind in the Willows - Kenneth Grahame
31 Anna Karenina - Leo Tolstoy
32 David Copperfield - Charles Dickens
33 Chronicles of Narnia - CS Lewis
34 Emma - Jane Austen
35 Persuasion - Jane Austen
36 The Lion, The Witch and The Wardrobe - CS Lewis
37 The Kite Runner - Khaled Hosseini
38 Captain Corelli's Mandolin - Louis De Bernieres
39 Memoirs of a Geisha - Arthur Golden
40 Winnie the Pooh - AA Milne
41 Animal Farm - George Orwell
42 The Da Vinci Code - Dan Brown (regrettably)
43 One Hundred Years of Solitude - Gabriel Garcia Marquez
44 A Prayer for Owen Meany - John Irving
45 The Woman in White - Wilkie Collins
46 Anne of Green Gables - LM Montgomery
47 Far From The Madding Crowd - Thomas Hardy
48 The Handmaid's Tale - Margaret Atwood
49 Lord of the Flies - William Golding
50 Atonement - Ian McEwan
51 Life of Pi - Yann Martel
52 Dune - Frank Herbert (this might be a rare instance of the movie being better)
53 Cold Comfort Farm - Stella Gibbons
54 Sense and Sensibility - Jane Austen
55 A Suitable Boy - Vikram Seth
56 The Shadow of the Wind - Carlos Ruiz Zafon
57 A Tale Of Two Cities - Charles Dickens

58 Brave New World - Aldous Huxley
59 The Curious Incident of the Dog in the Night-time - Mark Haddon
60 Love In The Time Of Cholera - Gabriel Garcia Marquez
61 Of Mice and Men - John Steinbeck
62 Lolita - Vladimir Nabokov
63 The Secret History - Donna Tartt
64 The Lovely Bones - Alice Sebold

65 Count of Monte Cristo - Alexandre Dumas
66 On The Road - Jack Kerouac
67 Jude the Obscure - Thomas Hardy
68 Bridget Jones's Diary - Helen Fielding (This was a snap buy in an airport bookstore for a flight I was almost late for. I should have gone with David Sedaris)
69 Midnight's Children - Salman Rushdie
70 Moby Dick - Herman Melville (for a long time this was my favorite book)
71 Oliver Twist - Charles Dickens
72 Dracula - Bram Stoker
73 The Secret Garden - Frances Hodgson Burnett
74 Notes From A Small Island - Bill Bryson (I'm still pissed about A Walk In the Woods. You'd think someone who writes about hiking the Appalachian Trail would have actually hiked it)
75 Ulysses - James Joyce (has anyone ever finished?)
76 The Bell Jar - Sylvia Plath
77 Swallows and Amazons - Arthur Ransome
78 Germinal - Emile Zola
79 Vanity Fair - William Makepeace Thackeray

80 Possession - AS Byatt
81 A Christmas Carol - Charles Dickens
82 Cloud Atlas - David Mitchell
83 The Color Purple - Alice Walker
84 The Remains of the Day - Kazuo Ishiguro
85 Madame Bovary - Gustave Flaubert
86 A Fine Balance - Rohinton Mistry
87 Charlotte's Web - EB White
88 The Five People You Meet In Heaven - Mitch Albom
89 Adventures of Sherlock Holmes - Sir Arthur Conan Doyle
90 The Faraway Tree Collection
91 Heart of Darkness - Joseph Conrad
92 The Little Prince - Antoine De Saint-Exupery (I think I have read everything by Saint-Exupery I could get my hands on)
93 The Wasp Factory - Iain Banks
94 Watership Down - Richard Adams
95 A Confederacy of Dunces - John Kennedy Toole
96 A Town Like Alice - Nevil Shute
97 The Three Musketeers - Alexandre Dumas
98 Hamlet - William Shakespeare
99 Charlie and the Chocolate Factory - Roald Dahl (James and the Giant Peach was better)
100 Les Miserables - Victor Hugo

Drawing: Bookworm from Robert Hooke's Micrographia.

Friday, July 18, 2008

This Week's Citation Classic

Simberloff DS & Wilson E0. 1969. Experimental zoogeography of islands. The colonization of empty islands, Ecology 50:278-96.

This week's citation classic comes from Dan Simberloff and Ed Wilson, and in terms of scale, ranks of one of the most daunting ecological experiments every attempted. The pair was interested in the recolonization process following an extinction event. Specifically they wanted to test whether the number of species on an island existed in a dynamic equilibrium with present species going extinct being replaced by new immigrants.

The classic example of a major extinction event was the eruption of Krakatoa. When Krakatoa exploded in 1883, it exterminated every living organism on the island. When the first researchers reached the islands in May 1884, the only living thing they found was a spider in a crevice on the south side. However life quickly recolonized the island and today it supports a large ecosystem.

Krakatoa was a natural experiment. The question was, how to replicate Krakatoa on a controlled basis. Simberloff and Wilson hit upon the idea of fumigating entire mangrove islands by encasing the islands in a canopy of plastic sheeting and pumping in methyl bromide (which killed the bugs, but not the mangroves). Prior to and after fumigation, every single arthopod on the island was collected and identified. It was, needless to say, a massive endeavor.

Simberloff comments, "Even identifying the over 100 species that we found required us to enlist an army of systematists, and physical aspects of operating in the shallow, shark-infested waters of the Florida Keys put us one up on molecular biologists who always seemed engaged in momentous breakthroughs."

But it worked!

Simberloff and Wilson found that following defaunation, the number of species on islands recovered previous levels. What's more is that they showed substantial species composition changes over time indicating extinction and immigration.
In terms of sheer boldness, this is one of my favorite experiments. It's hard to imagine an established scientist attempting something of this magnitude with just a graduate student. But Ed Wilson was always a bold visionary.

Thursday, July 17, 2008

Nobel Video Games

Will our future Nobelists get their first taste of science from video games? The Nobel Prize organisation hopes so. They have available a series of educational games based on previous Nobel Prizes. My first run of malaria I was quickly killed by DDT =/ Then I thought (incorrectly) that I could obtain blood from a bird. I was quickly consumed. Then once I found a host, I took too long to draw blood and was swatted. It's hard out there for a mosquito!

Wednesday, July 9, 2008

This Week's Citation Classic: The Fluctuation Test

Luria S. and Delbruck M. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 8: 491.

This week's citation classic comes from Nobelists Salva Luria and Max Delbruck and is one of the most famous experiments in biology. Luria and Delbruck wondered about the nature of mutations. Are mutations spontaneous? Or do they occur in response to environmental conditions? The latter view, common to scientists of the day (e.g. Cyril Hinshelwood), was one of the last vestiges of Lamarckism in evolutionary biology.

Since the time of d'Herelle, it was known that a culture of bacteria exposed to bacteriophage would eventually become clear, as if all the bacteria in the culture were killed. However, eventually the culture would grow cloudy again. It was surmised that the bacteria acquired resistance to the phage, and were able to repopulate the culture. The question was, how can the system be used to demostrate the role of chance in mutations?

Luria struggled with the problem for several months, trying to devise a test to show that mutations were spontaneous. Then at a faculty dance at Indiana University, Luria had his eureka moment.

"During a pause in the music I found myself standing near a slot machine, watching a colleague putting dimes into it. Though losing most of the time he occasionally got a return. Not a gambler myself, I was teasing him about his inevitable losses, when he suddenly hit a jackpot... gave me a dirty look at walked away. Right then I began giving some thought to the actual numerology of slot machines; in doing so, it dawned on me that slot machines and bacterial mutations have something to teach each other." (From Luria's autobiography: A Slot Machine, A Broken Test Tube).

Luria returned to the lab and set up a large number of bacterial cultures containing just a small number of bacteria in each, to which he added some bacteriophage. Luria reasoned that if mutations were spontaneous, then their distribution would resemble jackpots. Here the number of surviving bacteria would be small in most cultures, but large in a handful. On the other hand, if mutations were directed as the Lamarckists supposed, then their payoffs would be evenly distributed. Each culture would contain a small number of mutants, as the figure here shows:

Luria and Delbruck's experiments showed unequivocally that mutations were spontaneous and emphasized the role of chance and historicity in evolutionary biology, thus putting the final nail in the coffin of Lamarckism. See Fig. 2 from L&D's paper where the number of jackpots (>9 resistant bacteria) far exceeds that expected by chance. The reason I selected the Fluctuation Test as this week's citation classic is because of a recent exchange between Rich Lenski and I, of which I reprint portions of here:

"I've always been fascinated by the tension between chance and necessity, between randomness and repeatability. As a kid, for example, I especially liked games with dice and cards that involved both luck and skill.

Then, when I was at Oberlin College, I took a wonderful course in which we used Gunther Stent's "Molecular Genetics: an Introductory Narrative" as a text. Unlike most science textbooks, it emphasized the history of who did what experiments and why. I remember reading about the "fluctuation test" performed by Salvador Luria and Max Delbruck, and trying to make sense of it, and then having that eureka moment when the whole point of the experiment hit me. It's my all-time favorite experiment and to this day, whenever I think about it, I'm struck not only by its elegance, but also by the subtlety of the interpretation and by an appreciation of why the problem had been so difficult until they did their experiment.

As you know, a main focus of the long-term evolution experiment with
E. coli has been to better understand the repeatability of evolution that arises from the tension between random mutation, on the one hand, and the systematic process of natural selection, on the other hand, that pushes populations toward greater fitness in the environments in which they live. So in a way, you might think of my long-term evolution experiment as a descendant of the fluctuation test, one that examines the role of random mutation in producing statistically quantifiable variation between replicate lineages, not in overnight cultures but across, now, more than 40,000 generations of evolution."

It is precisely this randomness of evolution that led to Lenski's and colleagues latest discovery that, after 33127 generations, a strain of E. coli evolved the ability to digest citrate. Carl Zimmer does a bang up job of covering that story.

Lenski also had a recent dustup with the IDiots, and his tolerant response is covered here.

Update:P Jonathan Eisen of Tree of Life also wrote about this paper here.

Photo: Max Delbruck, Salvador Luria, and Frank Exner at Cold Spring Harbor Laboratory from the National Library of Medicine.