September 2012 Archives

Wallace Online

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The written works of Alfred Russel Wallace, co-discoverer with Darwin of the principle of natural selection, are now online. The Wallace Online project is directed by John van Wyhe, who also produced the Darwin Online project. Enjoy!

Via the BBC

Freshwater: The bait and switch laid out

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Freshwater aficionados will recall that I pointed to differences between Freshwater’s request to the Ohio Supreme Court to hear his case (his Memorandum in Support of Jurisdiction–MiS) and the subsequent Merit Brief (MB) in which he actually argued his case. The Court accepted his appeal on the basis of two Propositions of Law (I and II) described in the MiS, but in the actual argument of the Merit Brief those two Propositions changed into two quite different propositions. Now the Mt. Vernon Board of Education has filed a motion to strike the two Propositions–in effect, to strike the whole basis for the acceptance Freshwater’s appeal–because of that bait and switch.

More below the fold.

Selasphorus platycercus

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Photograph by David Young.

Ruby throated hummingbird at Aspen Highlands.jpg

Archilochus colubris Selasphorus platycercusruby-throated broad-tailed hummingbird, Aspen, Colorado.

The ENCODE delusion

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I can take it no more. I wanted to dig deeper into the good stuff done by the ENCODE consortium, and have been working my way through some of the papers (not an easy thing, either: I have a very high workload this term), but then I saw this declaration from the Electronic Frontier Foundation.

On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California's warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

An interactive brain atlas

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As one gets older one learns to ration one’s obsessions. I don’t play Angry Birds, stayed away from SimCity, and successfully avoided first-person shooters. However, there’s a web toy that’s about to capture me: The Allen Brain Atlas. I’ve only recently managed to fade out exploring synteny viewers, but I fear that wandering around gene expression networks will capture whatever leisure time that frees up.

Boavus idelmani

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IMG_2882_Boavus_idelmani_600.jpg

Boavus idelmani – extinct species of boa, middle Eocene, western South America, 48.6-37.2 million years ago. Denver Museum of Nature and Science; cast by American Museum of Natural History FR 3850.

The DI’s list of “Darwin doubters” analyzed

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On Facebook (yeah, I’ve got an account that I look at occasionally), Genie Scott calls attention to David Bailey’s analysis of the Disco ‘Tute’s list of “Scientific Dissent[ers] from Darwinism,” which is now up to 854 signators by my count. There were 840 names on the list when the analysis was performed last April. I quote from Bailey’s conclusion:

In short, no matter how one objectively compares these lists, it is a fair conclusion that several hundred times as many well-qualified professional scientists accept the main precepts of evolution as dissent from them.

Add to that the wishy-washy wording of the “Dissent,” and one has mush.

Where’s the DI’s (research) beef?

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The Sensuous Curmudgeon has obtained the Disco ‘Tute’s Form 990 for 2010. There are several interesting aspects of it, but I’ll mention just one. (See the linked post for more.) In the breakdown of funds, roughly $3m–75%–of the DI’s total budget was devoted to the Center for the Renewal of Science and Culture. However, just $220K, 7.3% of the CSC’s total, was devoted to actual scientific research (assuming that the BioLogic Institute does actual scientific research). Undoubtedly that number has grown since 2010, but I would be surprised to see it approach even a quarter of CSC’s revenue. Kind of sad for a purportedly scientific enterprise.

Badlands National Park

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Big and Crinkly, by Michael Klaas.

Photography contest, Honorable Mention.

Klaas.Big and Crinkly.jpg

Badlands Wall, Badlands National Park, South Dakota.

The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.

However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”. People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.

Anyway, I’d write more, but I’m jammed and Ryan Gregory has said everything I would say, except better: http://www.genomicron.evolverzone.c[…]encode-hype/

See also Larry Moran: http://sandwalk.blogspot.com/2012/0[…]-of-our.html, especially the rather wry comments.

Hashtag: #oniontest

Update, Sept 5, 2012: The answers have been posted, but the site cannot handle the traffic. Scientific American has posted the candidates’ answers here. I have not studied them yet, but according to a press release,

Notable highlights include a shift in Romney’s policy toward climate change away from his more recent position of “My view is we don’t know what’s causing climate change on this planet…” back toward his view in June of 2011 when announcing his run for president. However Romney’s ideas about what to do about the problem are not clear. They contrast with Obama’s, who says he has specifics plans and is taking specific steps such as doubling fuel economy standards, but who was unable to get a cap-and-trade bill through congress.

Shawn Otto, the founder of ScienceDebate, further adds, “Some of the questions aren’t fully answered when they become politically difficult and others could really benefit from followup discussion.…”

***

… but Congress refuses.* See here for the presidential edition and here for the congressional edition of the questions. The presidential campaigns’ responses will be published here. Science Debate is an “independent citizens’ initiative” sponsored by the American Association for the Advancement of Science, the National Academies, and others.

* Well, OK, Representatives Henry Waxman and Chris Van Hollen have responded to the questions, so 2/535 = 0.0037, or about 0.4 %, which is close enough to 0 for my taste. Besides, John Boehner refused outright.

Save Siccar Point!

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rocksdontlie.jpg I recently acquired the new book “The Rocks Don’t Lie: A Geologist Investigates Noah’s Flood” by David Montgomery. It’s a splendid read, and very much applicable to the readership of Panda’s Thumb. The book has some excellent pictures and discussions regarding Siccar Point in Scotland, “…celebrated as the place where Scottish farmer James Hutton discovered geologic time..” Siccar Point graces the cover of Montgomery’s book.

Just last Thursday, I cited Siccar Point in a lecture on the Flood for our new social studies class at New Mexico Tech in Socorro. (See slides 56-58). I have resolved to visit Siccar Point - it’s on my bucket list.

That’s why I found this announcement from the Facebook group “Save Siccar Point” to be quite disturbing. They are alarmed that developers are “ruining the geological mecca of Siccar Point, the location of Hutton’s unconformity.”

More info here:http://www.savesiccarpoint.co.uk/

From the site comes this urgent plea:

The deadline for objections has been extended to 23 September 2012 - the day before the application is considered. If you want to lodge an objection you have some time to do it. Please don’t forget!

It still not too late to object…keep them coming.

You can object by email if you want. Here’s how:

  1. In the Subject Line put “12/00929/FUL Objection Comment”
  2. Add your comment in the email body
  3. Send your email to [Enable javascript to see this email address.] or [Enable javascript to see this email address.]

If you want to CC anyone else into your email, you might want to consider:

  1. Scottish Natural Heritage: [Enable javascript to see this email address.]
  2. Scottish Environmental Protection Agency: [Enable javascript to see this email address.]
  3. Crown Estates: [Enable javascript to see this email address.]
  4. Dunglass Estate: [Enable javascript to see this email address.]

I have sent along my objections - will you?

(Don’t forget to be polite!)

Grand Canyon

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IMG_2987GrandCanyon_600.JPG

Grand Canyon. Digital photograph of a print taken on Kodak Plus-X film in 1964. Took several hours in a smelly darkroom to achieve what you can do in tens of minutes today.

Sequencing the Denisovan genome

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There has been a good deal of publicity recently about the sequencing of the Denisovan genome by Svante Pääbo’s group at the Max Plank Institute (see here and here for examples). Using brand new technology for sequencing single strands of DNA (single strands as opposed to the normal double-strand), the group was able to achieve a sequencing rate of 30x–every position in the genome was sequenced 30 times. That’s comparable to sequencing modern genomes.

While some of the coverage has focused on what can be inferred about the individual from whom the DNA was recovered (female, dark skin, brown eyes and hair) what is much more interesting are the relationships of the Denisovans to various modern human populations and to Neandertals. Also interesting is the identification of genetic changes that have occurred in modern humans, a number of the changes having to do with genes associated with brain function and nervous system development,

Since John Hawks has discussed the paper in some detail, I won’t, but will direct you to Hawks’ review of the research. One quotation from that piece–the final sentence–is worth repeating:

Evolution really is the fundamental principle of biology, but using evolution to learn about biology sometimes requires traveling through time. Ancient DNA gives us a time machine bringing new insights into reach.

I can hear the echo of Ken Ham’s minions mindlessly shouting “Were you there???” No, but this is the next best thing.

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