July 2013 Archives

Reverse evolution?

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When I bought my house, I inherited a weed (which some consider a ground cover) known as snow on the mountain (Aegopodium podagraria “variegatum”). The plant has a variegated leaf, and I assume it is a cultivar. It is very aggressive and propagates by rhizomes.

Photo Contest V: Finalists

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Note added Aug 3: Please vote! I plan to end the poll as soon as I can after noon MDT, Monday, August 5 – probably around 13:00. Your intrepid judges will announce the winner on Wednesday. We will display a Semi-Finalist each of the next 2 Mondays at noon.

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Here are the finalists of the 2013 photography contest. We received approximately 30 photographs from 17 photographers, about the same statistics as last year. Most of the pictures were excellent, and we practically had to roll the dice to limit the finalists to 6.

To choose the finalists, we considered what we thought were the scientific and pictorial qualities of the photographs, and also attempted to represent as many photographers and present as much variety as possible. The text was written by the photographers and lightly edited for consistency.

The finalists are given below the proverbial fold, in alphabetical order of last name. Please look through their photographs before voting for your favorite. You will have to be logged in to vote on the poll. We know it is possible to game these polls. Please be responsible and vote only once. If we think that the results are invalid, we will cancel the contest.

The winner will receive a copy of Unintelligent Design by our late colleague Mark Perakh. We dedicate this contest to his memory.

An interview with Francis Collins was published in yesterday’s New York Times Book Review. The most interesting quotations, from our point of view, were possibly,

What books might we be surprised to find on your shelves?

Considering my own stance on the satisfying harmony of science and faith, you might be surprised to find on my shelves nearly everything written by Richard Dawkins (including “The God Delusion”) and my late friend Christopher Hitchens (including “God Is Not Great”). One must dig deeply into opposing points of view in order to know whether your own position remains defensible. Iron sharpens iron.

What book has had the greatest impact on you?

As an atheist evolving to agnosticism, and seeking answers to whether or not belief in God is potentially rational, my life was turned upside down 35 years ago by reading C. S. Lewis’s “Mere Christianity.”

No further comment!

In May I encouraged everyone to think of how to explain their research using the most common 1000 words in American English. There were a lot of excellent submissions!

Now, take a look at this winning poster from a team of Penn State researchers entitled, “Powering Your Car with Sunlight”! The researchers were allowed one word in addition to the list of 1000 common words: energy.

by Steven Mahone

Bruce Chapman, the Big Cheese over at the Discovery Institute, is apparently feeling a bit threatened by an interview that Bill Nye (“The Science Guy”) recently did for the Seattle Times. Chapman wrote an article expressing concern that Bill’s straight talk about science literacy might somehow implicate his cherished “Intelligent Design” theory by lumping it in with young earth creationism, thereby leading some to conclude that ID is nothing more than the pseudo-scientific equivalent of those get-rich-working-from-home schemes so ubiquitous on the radio and Internet.

I’m working on an article discussing “Trends in Evolution”, to be written for a broad audience interested in science, but not experts.  I’ve already narrowed it down to a few sub-topics to focus on, but I would like some advice on figures.

I am working on figures to succinctly illustrate how evolution works, while also addressing common misconceptions. What do you think? How can I improve these? What have I unwittingly misrepresented? Which do you like best?

1. Evolution is the gradual change of populations over time, not distinct transitions between species.


Here, I’ve already received feedback that I should remove the word “gradual”. I agree that “gradual” is a relative term, and in many cases, evolution happens very quickly. Given that I work on long-lived species, I tend to use “gradual”, and like it for this example.

It’s bad enough that Kentucky has the Ark Park, but also subsidizes it - now its residents are complaining about the Next Generation Science Standards. The headline of the Courier-Journal article is “Critics: Kentucky science academic standards are ‘fascist,’ ‘atheistic,’” but that does not do justice to the sheer lunacy of some of the comments quoted in the article.

Here are two excerpts:

Sex chromosomes are fascinating, and we still have so much to learn about how they originate and change over time. This last week I had the pleasure of talking to one of the leaders in the field, Deborah Charlesworth, about explaining sex chromosome evolution and genetics. I hope she’ll forgive me for this simplification of a recent beautiful genetic analysis from her lab. 

I study sex chromosomes in mammals (X and Y), but lots of other wonderful species have evolved chromosomal sex determination (instead of, say, using temperature or environmental cues to determine males and females).

One of those species is a lovely plant called Silene latifolia, also called a White Campion.

Weiße Lichtnelke
The plant, Silene latifolia, with sex chromosomes

Prothero reviews Meyer’s Hopeless Monster

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Donald Prothero, paleontologist and author of Evolution: What the Fossils Say and Why It Matters, has reviewed Meyer’s “Darwin’s Doubt” monstrosity on Amazon. Money quote:

In short, Meyer has shown that his first disastrous book was not a fluke: he is capable of going into any field in which he has no training or research experience and botching it just as badly as he did molecular biology. As I’ve written before, if you are a complete amateur and don’t understand a subject, don’t demonstrate the Dunning-Kruger effect by writing a book about it and proving your ignorance to everyone else!

Via Larry Moran at Sandwalk.

Orthonevra nitida

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Photograph by Al Denelsbeck.

Denelsbeck.Orthonevra_nitida.jpg

Orthonevra nitida – syrphid fly or flower fly on a parsley flower. The fly is about 5 mm long. Mr. Denelsbeck is fascinated by the pattern on the eyes and asks, “I’ve only seen this tiny fly once … and couldn’t even make out the pattern of the eyes in the viewfinder. While I’ve identified it as Orthonevra nitida, no source has given the faintest idea how or why this eye pattern evolved, and I’m dying to know. Closely related species have different patterns, or virtually none at all.” Can any reader answer the question?

How many mutations?

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Tuuli Lappalainen tweeted a result presented by Daniel Wegmann:

Daniel Wegmann: Every non-lethal genome position is variable in the human population #bc2
– Tuuli Lappalainen (@tuuliel) July 4, 2013

Really?

There are 23 pairs of chromosomes in the human genome. If you counted the number of positions - A’s, T’s, G’s, and C’s - you would have approximately three billion positions across those 23 chromosomes. And because each chromosome is part of a pair, you can multiply that number by two, for a total of six billion places where a mutation can happen. Assuming there are not very many lethal positions, is it really possible to have a mutation at every site in at least one living human?


Yes!

In fact, we expect that across all humans, there are over 100 mutations at every single position in the human genome. And, here is the math to prove it:

The lying liars of the Disco ‘Tute

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(This is for the three people who don’t read Sandwalk.)

Every once in a while one sees a takedown so powerful that it makes one smile for days. One such is in the comment thread on a post on Sandwalk, Larry Moran’s blog. In the comments Diogenes eviscerates an anonymous poster on Evolution News and Views, an arm of the Disco ‘Tute, about a claim about ‘junk’ DNA. Read it and laugh at the ‘Tooters.

Hyla versicolor

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Photograph by Darren Garrison.

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Hyla versicolor – gray tree frog. Mr. Garrison writes, “BTW, the frog can change its skin color somewhat – they used to hang around my elephant ear plants a lot when I was drip-irrigating them (setting up a mini-biome.) I’d often look out and see one of the frogs clinging to the outside of a window. But sometimes they are dark colored like the one in the first photo, and sometimes white (but always with the yellow patches on the rear legs).”

Science reports today that Turkey’s main science-funding agency denied a grant to a workshop on the grounds that “evolution is a controversial subject.” The purpose of the workshop was “to expose Turkish biology students to population genetics, game theory, and evolutionary modeling.” The organizers of the workshop had asked for approximately $18,000 (US) to cover the cost of students’ lodging and speakers’ travel. The workshop will go on, with private donors contributing the $18,000.

Photography contest, V

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IMG_3406_Films_600.JPG

4 x 5 film holder (2 exposures), Tri-X film (24 exposures), SD memory card (>1000 exposures).

The fifth Panda’s Thumb photography contest, begins – now!

We will accept entries from July 8 through 22, inclusive.

We encourage entries in a single, general category, which includes pictures of just about anything of scientific interest: any object of experimentation or observation, from single-celled organisms, through nematodes, fruit flies, rats, chimpanzees, and undergraduates to volcanoes, stars, and galaxies. In order not to omit theoreticians, we will consider computer-generated pictures and also photographs of equipment. Photomicrographs and electron micrographs are likewise welcomed.

We dedicate this contest to the memory of our colleague Mark Perakh. First prize will be a copy of his book Unintelligent Design.

If we get enough entries, consistently with Rules 12 and 13, we may add categories and award additional prizes, presuming, of course, that we can find more prizes.

Intelligent-design creationist Guillermo Gonzalez has been appointed assistant professor of physics at Ball State University, according to an article in jconline.com. Gonzalez is the author of The Privileged Planet and was famously denied tenure at Iowa State University. Gonzalez will teach two introductory astronomy courses, The Sun and Stars, and The Solar System.

Ball State has also come under fire recently following reports that another professor, Eric Hedin, teaches a Boundaries of Science class whose curriculum allegedly includes intelligent-design creationism. The Star Press article, incidentally, notes that the university, not the professor, has the legal right to define the curriculum. Let us hope that they will watch Professors Gonzalez and Hedin closely.

Years ago, someone gave me a book on child-rearing, and I noticed afterward that it was on The New York Times bestseller list. I mentioned the fact to my father, an expert on child-rearing, and his only comment was, “That’s not why it is lousy.” My father would no doubt feel vindicated right about now: Stephen Meyer’s book, Darwin’s Doubt, will be on the Times‘s bestseller list this coming Sunday, July 7.

Acknowledgment. Thanks to Alert Reader for pointing out this depressing fact.

Update, July 5: As a commenter has pointed out, Darwin’s Doubt will not appear on the July 14 list. The book is evidently a flash in the pan—unless they moved it to the fiction section. Advance orders were evidently vigorously promoted, but no one is actually reading the book, which we may consider a blessing.

The folks at Uncommon Descent are accusing me of being a Nazi (“Nick Matzke - Book Burner?”, “Will Our Darwinist Friends Be Telling Us Next That ‘Arbeit Macht Frei’?”, It Gets Even Better) for using my free-speech rights to criticize the prestigious publisher Springer for publishing crypto-creationist/ID meeting held at Cornell (but not sponsored by Cornell) in 2011. They seem to think that I, single-handedly, with the mighty power of the Panda’s Thumb blog, crushed the otherwise inevitable publication by Springer.

junk_DNA_front.pngThe SMBE meeting is coming up next week in Chicago, and I am going for the first time, in part to present some of my work combining fossils and molecular data in Bayesian dating analyses*, and partially because I wanted to see the junk DNA symposium in person: http://smbe2013.org/2013/Scientific[…]ymposia.aspx

Buteo swainsoni jamaicensis

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Buteo jamaicensis – red-tailed hawk, Boulder Valley Ranch, Colorado. Eddie Boosey of Norfolk, England, tells me [apparently incorrectly], “It is Swainson’s buzzard, Buteo swainsoni. You can tell that it is a buzzard because it is called Buteo. In America, however, for some unknown reasons this, like your seven other buzzards, is called a hawk, so it is known as Swainson’s hawk.” Eddie and I are often separated by a common language.

Freshwater: Still waiting for the Ohio Supreme Court

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John Freshwater’s appeal of his termination as a middle school science teacher in the Mt. Vernon, Ohio, public schools is still hanging fire in the Ohio Supreme Court. Decisions normally are promulgated between three and six months following oral arguments, and it’s been four months since the February 27, 2013, arguments in this case. The Mount Vernon News had a story on it last week.

More below the fold.

Many times we utilize and study the products of evolution that result from species sharing a common history. For example, the reason we can use mice for studies of human diseases and medical treatments is that, because of shared ancestry, a mouse body and the set of mouse genes is similar enough to a human body and the set of human genes that both will develop similar diseases, and respond similarly to treatments.

There are other products of evolution that occurred independently, and are not the product of common ancestry.

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