Darwin – Jonathan Eisen's Lab

Evolution pumpkins – from Darwin to Woese

OK I know I am a geek, but I do think these came out pretty well …

“I think” in honor of Darwin

Woese Tree of Life

Art-Science Fusion and Darwin’s Face at Davis

ART/SCIENCE FUSION STUDENTS EXHIBIT PHOTOGRAPHY AND A CERAMIC MOSAIC MURAL, THE FACE OF DARWIN

The final student exhibition for “Photography: Bridging Art and Science,” a Science and Society Program class taught by Terry Nathan as a part of the Art/Science Fusion series at the University of California, Davis (UC Davis), will be held at the Buehler Alumni and Visitors Center on the University of California, Davis campus beginning June 3 and continuing through July 3. The exhibit features over 50 student photographs exploring the conceptual connections between art and science and the role of art and science on the UC Davis campus. The opening reception, which is free and open to the public, is June 4 from 3-5 p.m.

Also included in the exhibition is a ceramic mosaic mural, The Face of Darwin, created by students and community members in a special Freshman Seminar entitled, “The Face of Darwin: Exploring the Art/Science Borderland”. In recognition of Darwin’s 200^th birthday, students from majors across campus studied Darwin’s life and the observations that led him to propose evolution by natural selection. Darwin’s face is formed by selections from his secret notebooks and the images of those organisms that influenced him most. With a beard of peppered moths, hair of barnacles and a coat of iguanas, finches, orchids and a host of other creatures, this mosaic is a profound learning experience in and of itself. The seminar was led by Diane Ullman and Donna Billick (co-directors of the Art/Science Fusion Program).

(this came in an email to me and am posting here)

Lie to Me, Darwin

Hey – that looks like good old Charlie D. in the room of the lead character in Fox’s Lie to Me. Seems likely that it is, given that the show is advised by Paul Ekman from UCSF who is into Darwin. And of course, it really looks like some of the classic pics of Charlie. Good to see Fox TV is not too sold by the lame anti-evolution rhetoric sometimes spouted on Fox News.

Darwin in Davis

Since this is kind of a Davis thing too I am cross posting it from my work blog.

Well, this has been a good week for me in Davis in terms of things in which I am interested. First, the Tour of California started in Davis and then tonight we had a Darwin celebration (with cake and talks) in a movie theater in downtown. The three talks were by Rick Grosberg, who gave a good background on Darwin the person, Mau Stanton who talked about Evolution and Society and me, who talked about Uses of Evolution. The shindig was sponsored by the Center for Population Biology and funded by the Storer Endowment. And it was organized by Angus Chandler and Dena Grossenbacher and possibly some others. And the theater was packed to the gills. Food. Folks. And Fun. And I owe some thanks to folks who responded to my FriendFeed posting asking about other examples of Uses of Evolution.

Here are some pics …

http://picasaweb.google.com/s/c/bin/slideshow.swf

Also see

Charles Darwin relic hidden in the chimp and human genomes

So – in honor of Charles Darwin and as a follow up to my analysis of Sarah Palin’s name (which amazingly showed as a best hit a fungus called B. fuckeliana) I decided today to do some blast searches with old Charlie D.’s name. You see CHARLES DARWIN includes letters that all are abbreviations of amino acids that make up proteins, so you can compare his name, pretending it is a protein, to proteins from other organisms.

So I went to the NCBI blast page and did a BLASTP search. Blastp searches a peptide against a database of peptides and identifies in the database sequences if one or more have similar amino-acid sequences to the one used to search (which is known as the query) . To make this work, I had to adjust some of the default parameters to make it possible to better detect short matches (I raised the # of expected matches to 10000).

Alas, no good matches convincing matches to known or predicted proteins came up. So I was sad. Then I said, what if Darwin was hiden in the genome of some organism? So I did a “translational” blast search called tblastn which takes a peptide and searches it against a DNA database and translates the DNA into all possible peptides it could encode. When one does this, one can possibly find “hidden” proteins or relics of proteins in the DNA that may not have been labelled as proteins by whomever analzyed the DNA data.

And what did I find by this Tblastn search? A jackpot to make evolutionary biologists VERY happy. The best matches for CHARLESDARWIN the peptide? Pan troglodytes. AKA Chimps. And humans (the matches were equally strong).

So – hidden in the human and Chimp genomes is a relic of one Charles Darwin. Happy Birthday Charlie.

———————————————-

See search results below:

Score E
Sequences producing significant alignments: (Bits) Value

gb|AC199643.3| Pan troglodytes BAC clone CH251-444E8 from chr… 25.8 1930
gb|AC093749.3| Homo sapiens BAC clone RP11-30B7 from 4, compl… 25.8 1930
gb|AF250324.1|AF250324 Homo sapiens chromosome 4q35 BAC clone… 25.8 1930
gb|AC217674.3| Pan troglodytes BAC clone CH251-398H5 from chr… 25.0 3549
gb|AC195095.2| Pan troglodytes BAC clone CH251-577A14 from ch… 25.0 3549
gb|AC188794.3| Pan troglodytes BAC clone CH251-69H24 from chr… 25.0 3549
gb|AC183104.3| Pan troglodytes BAC clone CH251-567E15 from ch… 25.0 3549
gb|AF105153.3| Homo sapiens alpha-satellite centromere border… 25.0 3549
emb|AL353763.14| Human DNA sequence from clone RP11-87H9 on c… 25.0 3549
gb|AC116618.4| Homo sapiens BAC clone RP11-98L17 from 4, comp… 25.0 3549
emb|CR786580.6| Human DNA sequence from clone RP11-764K9 on c… 25.0 3549
emb|AL591385.7| Human DNA sequence from clone RP11-391M20 on … 25.0 3549
emb|AL445925.19| Human DNA sequence from clone RP11-403A15 on… 25.0 3549
emb|AL592183.10| Human DNA sequence from clone RP11-297D8 on … 25.0 3549
ref|XM_787798.2| PREDICTED: Strongylocentrotus purpuratus sim… 24.3 6861
ref|XM_001201471.1| PREDICTED: Strongylocentrotus purpuratus … 24.3 6861
gb|AC195625.1| Pan troglodytes BAC clone CH251-895L14 from ch… 23.9 7711
gb|AC175749.2| Pan troglodytes BAC clone CH251-1124N9 from ch… 23.9 7711

Pan troglodytes BAC clone CH251-444E8 from chromosome 7, complete sequence Length=155150
Score = 25.8 bits (55), Expect = 1930, Method: Composition-based stats. Identities = 8/13 (61%), Positives = 11/13 (84%), Gaps = 0/13 (0%) Frame = -2

Query 1 ____ CHARLESDARWIN 13
_____________CH RLE D+++IN
Sbjct 145762 CHVRLEQDSKYIN 145724

gb|AC093749.3| Homo sapiens BAC clone RP11-30B7 from 4, complete sequence Length=163102 Score = 25.8 bits (55), Expect = 1930, Method: Composition-based stats.
Identities = 8/13 (61%), Positives = 11/13 (84%), Gaps = 0/13 (0%) Frame = -3

Query 1 ___ CHARLESDARWIN 13
____________CH RLE D+++IN
Sbjct 31925 CHVRLEQDSKYIN 31887

10 simple ways to honor Charlie D (aka Darwin)

If you do not know, Thursday is a big day – Darwin Day 2009. A global celebration in honor of the 200th anniversary of Charles Darwin’s birth. Today I am making a suggestion of 10 simple things you can do to honor Darwin:

Read one of his books OTHER than Origin of Species (see Darwin online for some there). My favorite is the Voyage of the Beagle but there are many others.
Stop using the terms Darwinism and Darwinian evolution (see Safina for more on this – I thought this article was a bit of overkill but still has some important points).
Vote against anyone who says Intelligent Design should be taught in science class or that you should “teach the controversy.” Or at least endorse right thinking candidates.
Contribute to evolution education in some way – teaching, writing a book, releasing teaching materials, donate to a museum (e.g., California Academy) or other organization (e.g., NCSE) or even the cool HMS Beagle Project. Just help educate the world about the science of evolution.
Attend some Darwin Day celebration(s).
Get a cool evolution tattoo (see Zimmer for more) or display your support in some outward way.
Support the National Science Foundation (if you are in the US) as they are the strongest supporters of Evolution related research.
Name your kid or pet or boat or city after him.
Visit the Galapagos or at least check out the Darwin Station online.(see pics below …)
Insert your own here …..

Forget Lincoln-Douglas – How about a Lincoln-Darwin debate?

In case you did not see it – it is worth seeing the discussion of Lincoln vs. Darwin in Newsweek (How Darwin and Lincoln Shaped Us). They set up the discussion by pointing out that they had the same birthday. They say Lincoln was more important. Not going to argue but not sure they are right. My favorite section on this article:

This questioning spirit is one of the most appealing facets of Darwin’s character, particularly where it finds its way into his published work. Reading “The Origin of Species,” you feel as though he is addressing you as an equal. He is never autocratic, never bullying. Instead, he is always willing to admit what he does not know or understand, and when he poses a question, he is never rhetorical. He seems genuinely to want to know the answer. He’s also a good salesman. He knows that what he has to say will not only be troubling for a general reader to take but difficult to understand—so he works very hard not to lose his customer. The book opens not with theory but in the humblest place imaginable: the barnyard, as Darwin introduces us to the idea of species variation in a way we, or certainly his 19th-century audience, will easily grasp—the breeding of domestic animals. The quality of Darwin’s mind is in evidence everywhere in this book, but so is his character—generous, open-minded and always respectful of those who he knew would disagree with him, as you might expect of a man who was, after all, married to a creationist.