Readers’ wildlife photographs

March 16, 2015 • 7:20 am

We have photos from two readers today: a new contributor and an old one. The first is reader Susan Heller, who sent birds and mammals on March 2:

This mourning dove [Zenaida macroura] nested just outside my backdoor: I got to watch from egg to fledgling, with the parents feeding these babies.

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Baby and mom Gray whale [Eschrichtius robustus] in Scammon’s Lagoon (Baja Mexico) two weeks ago. There were over 1000 whales present when I was there.

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Osprey [Pandion haliaetus] at Scammon’s Lagoon:

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   Brown pelican [Pelecanus occidentalis], Bahia de Los Angeles, Baja Mexico:

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Burrowing owl [Athene cunicularia] near the Salton Sea, California last week.  Went on a great bird watching trip — there are thousands of birds on the Salton Sea now, as it’s on a major flyway.

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And a regular with some new photos, Stephen Barnard from Idaho:

Bald Eagle (Haliaeetus leucocephalus) busy with home maintenance and repairs. The light was poor, but I think the behavior is interesting.

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Red-tailed Hawk (Buteo jamaicensis) doing a pole dance.

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Google Doodle celebrates Anna Atkins

March 16, 2015 • 6:55 am

This is my 9,970th post, which means that within the week we’ll get to post number 10,000. I’m still pondering the 172 comments on the thread following “The 10,000th post: what shall it be?“, in which readers suggested way to celebrate this landmark. If I decide to use one of those suggestions, that reader gets an autographed copy of WEIT with a cat drawn in it. Given that there will probably be nearly ten posts today, as there’s a lot to say, I expect the Big Day to be Thursday or Friday. Stay tuned.

Meanwhile, today’s Google Doodle (click on screenshot below to go there) celebrates Anna Atkins (1799-1871), a British botanist and photographer. Today would be her 216th birthday, and her distinction was to be the first person to publish any book that included photographs. In fact, she may have been the first woman to take a photograph. The Doodle gives an idea of what her photos looked like:

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Anna Atkins

Here’s the title page of that pathbreaking self-published book, which appeared in 1853 (the first commercially published book with photos, by William Henry Fox Talbot, appeared 8 months later). This and all photographs are taken from the British Library’s site.

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The captions were in her Atkins’s own handwriting, and the book went through three editions. According to Wikipedia, only 17 copies still exist, and they’re extremely valuable: one was auctioned off for £229,250 in 2004. But you can see the whole book for free, as the British Library has most of it scanned in (go here).

Here’s one of the pages from the table of contents, in Atkins’s handwriting:

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From Vox we have some information about the process she used (their text indented):

Early photographers struggled with a problem: they couldn’t easily develop their pictures because the existing techniques were slow, expensive, or required dangerous chemicals. Herschel came up with a solution: using an iron pigment called “Prussian blue,” he laid objects or photographic negatives onto chemically-treated paper, let them be exposed to sunlight for around 15 minutes, and then washed the paper. The remaining image revealed pale blue objects on a dark blue background. This was a cyanotype — a new way to print photographs permanently.

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Herschel primarily used cyanotypes to copy notes, but when Atkins heard about the opportunity, she leapt at it. Though she’d shown herself to be a capable artist, she realized instantly that cyanotypes were a better way to capture the intricacies of plant life and avoid the tedium — and error — involved with drawing. As importantly, her passion for botany allowed her to see a new application of the exciting technology.

So, in 1843, she began making a photographic book of algae.

Atkins’ British Algae was the definition of a labor of love. Published in piecemeal over a decade, from the 1840s to the 1850s, the book was made at home using her own materials. From what we know, she collected the algae with the help of her friend Anne Dixon and dried and pressed it, the same way you might press flowers. Then, she identified it using William Harvey’s Manual of British Algae. Finally, she made the cyanotype by laying each piece upon the paper (that’s why, technically, her pictures are called photograms, not photographs, because they didn’t use a camera). The book’s text appears in her own elegant cursive.

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The book wasn’t a profit-making enterprise for Atkins, but it was an important one. It stands as the first book illustrated with photographs, and it brought together photography and botany for the first time. Atkins took the most fleeting and unusual of subjects — British algae — and made it timeless.

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You have to really love algae to do something like this.

Monday: Hili dialogue

March 16, 2015 • 4:34 am

And so the week begins. What will it bring? Only one thing for sure: a week closer to The Big Nap.  But at least Hili is extra cute today!

Hili: Children and scientists are most similar to cats.
A: In what way?
Hili: Statistically, they are more likely to understand the significance of frivolousness.
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In Polish:
Hili: Dzieci i naukowcy są najbardziej podobni do kotów.
Ja: W jakim sensie.
Hili: Statystycznie częściej niż inni rozumieją doniosłość niepowagi.

 

Who’s a good d*g?

March 15, 2015 • 3:22 pm

This comes from Matthew, so blame it on him. He found it in a tw**t by Brian D. Earp:

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Apropos, Terry Pratchett on d*gs (from Men at Arms):

“Dogs are not like cats, who amusingly tolerate humans only until someone comes up with a tin opener that can be operated with a paw. Men made dogs, they took wolves and gave them human things–unnecessary intelligence, names, a desire to belong, and a twitching inferiority complex. All dogs dream wolf dreams, and know they’re dreaming of biting their Maker. Every dog knows, deep in his heart, that he is a Bad Dog…”

 

The splendid and assiduous beaver

March 15, 2015 • 2:30 pm

This National Geographic documentary on beavers (Castor canadensis) and their dams (the classic example of an “extended phenotype” as well as “niche construction”) is very good, and well worth watching if you have 45 minutes to spare. Why would anyone watch a reality t.v. show about the Kardashians if they can watch a reality show about beavers?

There are two named species of beavers—the other is the Eurasian beaver, Castor fiber, but I don’t know why they’re classified as separate species. Would they be reproductively isolated were they to live in the same area?

 

A writer for CNN debates whether Judas is in hell

March 15, 2015 • 12:40 pm

Bloody hell, just when you think the Cable News Network (CNN) may have some redeeming features, it publishes a piece of such mind-boggling stupidity that you scratch your head in wonderment. Such a piece is Craig Gross’s new Easter lucubration, “Is Judas in hell?” Read it—it’s short. And after you do, I’ll be you’ll wonder why CNN would not only publish such a thing, but even pay somebody to write it. (If Gross wasn’t remunerated, he was still paid too much!)

First, let’s identify Craig Gross. His CNN bio says this: “Craig Gross is the pastor and founder of XXXchurch.com. He has written seven books and speaks across the country on a range of topics.” (His longer and “official” bio is here.) And Wikipedia identifies XXXchurch.com as

“. . . a non-profit Christian website that aims to help those who struggle with pornography. It targets porn industry performers and consumers. The organization describes itself as “the #1 Christian porn site designed to bring awareness, openness and accountability to those affected by pornography.”

So, as Easter approaches, the supposedly respectable CNN hosts a self-debate on whether the apostle who betrayed Jesus is in hell! Actually, Gross doesn’t think that question is answerable, or even worth considering, since it demands a certainty he can’t find. He says this:

Recently, I asked on my Facebook page: “Is Judas in heaven or hell?”

The first response was:

Judas is in hell today. He has been there for 2,000 years and he will be there forever.

There is a button on Facebook that I have started to love. It is called “unfriend.” I won’t unfriend you because you believe differently than I do, I just don’t need more theologians as my friends on Facebook who speak with such confidence when it comes to someone’s place in eternity.

A debate continues on my Facebook wall. I love how everyone is so convinced they know whether Judas is in heaven or hell.

Yet Gross speaks with remarkable confidence about other Christian stuff. I find the following passage remarkable, especially in light of what he said above (emphasis is mine):

Let me tell you a little bit about what the Bible says about Judas:

He was personally chosen to be an apostle by Jesus.

He spent 3 1/2 years traveling with Jesus.

He saw all the miracles of Christ in person.

He watched as Christ healed the sick, raised the dead and cast out demons.

In terms of experience with Jesus, whatever you can say about Peter, James and John, you can say about Judas.

On top of all this, he handled the money, which is most of the time the most trusted one in the bunch. No one suspected that Judas would betray Jesus, which tells me he was a believer.

His life was changed.

He knew Jesus personally.

In a dark moment of his life, he made a mistake. A big one. He sold Jesus out for 30 silver coins or so. The moment he knew what he had done, he felt remorse, and he killed himself.

I am not here to debate theology. The facts are the facts.

Seriously? Those are facts? Who says so? Clearly, for Gross “facts” consist of “whatever the Gospels say.” But doesn’t CNN do fact-checking?  Is it a “fact” that Muhammad traveled from Mecca to Jerusalem and back on a flying horse? That’s a belief of Muslims that comes from the Qur’an. Is it a “fact” that there was a worldwide flood that destroyed all but eight humans? That’s in the Old Testament! Is it a “fact” that Jesus came to North America, and that Native Americans are of Middle Eastern ancestry? That’s in Mormon scripture? And is it a “fact” that Xenu stored millions of people in volcanoes and then blasted them with hydrogen bombs? That’s in Scientology scripture.

Gross also says this:

Do I believe in heaven and hell? Yes. I believe one is dark and one is light, and they both last forever.

What we have here is a credulous man who passes off the most ludicrous assertions of Bronze Age mythology as “fact”, and then unfriends people who “believe” that Judas is in hell. Well, he’s a Christian, and so he belongs in that asylum.

But if I were a Christian, the answer would seem clear to me. Without Judas’s betrayal, Jesus might not have been crucified, and his whole mission—to expiate the sins of humanity—would have been a dismal failure. Judas thus played a necessary role in saving all of us, and so he should find his reward in heaven. Even Gross sort of alludes to Judas’s critical role:

We all fall short and deserve death, but because of what Jesus did on the cross 2,000 years ago, we are able to have life. And I believe that where you end up, God only knows.

(Note that it should be “only God knows” in the final sentence.) Given this role, why should Judas be eternally immolated in molten sulfur! It was predetermined that he did what he did, and what he did saved all humanity from sin—at least if they believe in Jesus as their savior.

But the question of whether Judas is in hell is far less important than this question: Why did CNN publish such a ridiculous piece?

h/t: Chris

Francis Crick was a fricking genius—and Matthew’s new book

March 15, 2015 • 10:30 am

I am reading a pre-publication copy of Matthew Cobb’s new book about the genetic code, for he asked me if I could provide a blurb. Now, I never tout a book unless I’ve read the whole thing, but in this case it’s a labor of love. His book is called Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code. It will be published in the UK by Profile on June 11, and in the US by Basic Books on July 7 (links go to the respective Amazon sites where you can pre-order it).

Here’s the Amazon UK description:

Life’s Greatest Secret is the story of the discovery and cracking of the genetic code. This great scientific breakthrough has had far-reaching consequences for how we understand ourselves and our place in the natural world. The code forms the most striking proof of Darwin’s hypothesis that all organisms are related, holds tremendous promise for improving human well-being, and has transformed the way we think about life.

Matthew Cobb interweaves science, biography and anecdote in a book that mixes remarkable insights, theoretical dead-ends and ingenious experiments with the pace of a thriller. He describes cooperation and competition among some of the twentieth-century’s most outstanding and eccentric minds, moves between biology, physics and chemistry, and shows the part played by computing and cybernetics. The story spans the globe, from Cambridge MA to Cambridge UK, New York to Paris, London to Moscow. It is both thrilling science and a fascinating story about how science is done.

This is a pretty accurate take on the book. I’m about halfway through it (it’s 320 pages long), and it’s very good, on par with Horace Freeland Judson’s The Eighth Day of Creation (which everyone should read), itself a superb account of the revolution in molecular biology in the twentieth century. While there is some overlap between the two books, Matthew’s story concentrates on the deciphering of the genetic code itself:  how DNA can carry information that makes the molecule a blueprint for organisms’ bodies and behaviors.

Life’s Greatest Secret is a logical successor to Watson’s The Double Helix, and it would be a nice exercise to read them one after the other, though Watson’s is a memoir and Matthew’s a historical account. Most of us have read Watson’s book, but if you have you might not have realized that finding the structure of DNA was only the beginning of understanding how genes work. After Watson, Crick, Wilkins, and Franklin figured out that DNA was a double helix, and W&C elucidated its structure, geneticists still—as Hitchens might say—”had all their work before them.”  For the structure, while telling us how DNA maintains its specificity through meiosis and mitosis, and how mutations might happen, tells us nothing about how the structure is translated into organisms. That depends on understanding the genetic code.

It took more than a decade to fully understand that code, and that’s the subject of most of Matthew’s book (he also describes the earlier work by Avery et al. on how they figured out that DNA rather than protein was the genetic material, and recounts the work of the four DNA sleuths mentioned above). While we know now how it all works, back then it was a complete mystery, and people like George Gamow—a fierce and eccentric intellect—bruited about erroneous suggestions like protein sequences being determined by amino acids fitting into the interstices of the DNA molecule. People were truly casting about for ideas on how the whole thing fitted together. Nothing was known about messenger RNA, about transfer RNA, or about the whole apparatus whereby DNA ultimately produces proteins. Figuring it out was a formidable task, requiring both theoretical insights and difficult experimental work. That story is gripping, as the blurb above says, and, at least for this biologist, Matthew’s book is a page-turner. I occasionally had to stop reading to digest and marvel at the detective work involved in gleaning what is now routine knowledge for high-school biology students.

One of my strongest impressions so far is that, in all of this tale, Francis Crick was a fricking genius. Yes, both he and Watson collaborated fairly equally in elucidating the structure of DNA. But Crick went on to help solve the problem of “translation,” and in so doing produced remarkable insights available only to someone with a brain qualitatively different from those of other scientists.  I want to mention three of Crick’s intuitive leaps that were remarkably prescient, all turning out to be correct.

The first is the notion of transfer RNA: those small RNA molecules that latch onto amino acids and, moving to the ribosomes where the messenger RNA (the transcribed product of DNA) resides, assemble those amino acids into proteins. It was known that DNA remains in the nucleus, but that both RNA and proteins are found in the cytoplasm, the place where proteins appeared to be made. But it wasn’t obvious how an RNA product of DNA (and that product wasn’t known when Crick made his speculations) could get itself into the cytoplasm and act as a template for assembling proteins.

In 1957, only four years after he and Watson proposed the correct structure of DNA, and well before the genetic code was unraveled, Crick gave a lecture at University College London in which he speculated how DNA coded for proteins. In it, he took up the twin issues of how DNA was connected to RNA, and how RNA itself might help assemble proteins. His solution, which turned out to be right, was remarkably prescient. And here I’ll quote Matthew’s book (with permission):

In his lecture, Crick turned his brilliant mind to both these issues and publicly described the idea he had worked up with [Sydney] Brenner: there must be an unknown class of small molecule, which they called an adaptor, which would gather each of the twenty amino acids and take them to the ribosome, so that each protein could be assembled there. The most likely hypothesis was that there was one adaptor for each type of amino acid, and that it would contain a short stretch of nucleotides—a tiny bit of the genetic code that was able to bind to the RNA template in the ribosome, just like base pairing between the two strands of the DNA double helix. At the same time, on the other side of the Atlantic, Hoagland and Zamecnik were isolating what was later identified as Crick’s adaptor—eventually known as transfer RNA or tRNA—without knowing anything about Crick’s hypothesis.

Crick’s insight and Brenner’s contributions were remarkable, for at that time nobody knew about either messenger RNA or transfer RNA, much less how they worked. In all but trivial details—some amino acids can attach to more than a single tRNA molecule—Crick’s hypothesis was on the money. And yet it was a pure, blind stab in the dark.

Second, Crick realized, well before evolutionary biologists started even thinking about DNA and protein sequences, that these sequences could be of enormous value to our field. Here’s an excerpt Matthew gives from Crick’s 1957 talk—surely one of the most far-reaching scientific lectures of all time:

 “Biologists should realize that before long we shall have a subject which might be called ‘protein taxonomy’—the study of the amino acid sequences of the proteins of an organism and the comparison of them between species. It can be argued that these sequences are the most delicate expression possible of the phenotype of an organism and that vast amounts of evolutionary information may be hidden away within them.”

That is an amazingly far-sighted statement, especially coming from someone who wasn’t even close to being an evolutionary biologist. It misses the mark only in that Crick didn’t mention that if DNA coded for proteins, then perhaps we could have the same kind of taxonomy based on DNA as on protein sequences. But here Crick was seeing proteins as part of the organism’s phenotype, and the “evolutionary information” as the way different phenotypes arose from different proteins.

Finally, a year earlier, Crick had already formulated the idea of the “central dogma”: “DNA makes RNA makes protein,” and the notion that no information could flow from protein structure back to the DNA.  Below is Crick’s first recorded sketch of this idea in notes he made for himself. Note that Crick also allows both molecules to give information about themselves (i.e. the replication loops), as well as for information from RNA to be incorporated into DNA, which was later verified by the discovery of the enzyme reverse transcriptase.

Here are Crick’s notes from the NIH archive sketching the “central dogma,” which Crick called “The Doctrine of the Triad.” (See also the “Profiles in Science” page of The National Library of Medicine for information on lots of the principals in this story).

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This is remarkable, and makes my heart beat a bit faster. Those were the days of the giants on whose shoulders we stand, and Crick was the biggest of them all. I won’t go on, as there is a lot more to this story that you can read in Life’s Greatest Secret. I’ll add only that if you have any interest in the history of genetics, or about the most amazing and informative discovery in biology of our time, you should read Matthew’s book. Here’s the cover; note the clever use of nucleotide bases:

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Matthew also said that he’d be glad to answer readers’ questions about the book, or about the subject of the book, if you put them in the comments below.

Finally, here’s Francis Crick (1916-2004). Both he and Watson, by the way, were diehard atheists. Watson once told me that they were both partly driven to find the structure of DNA because showing that the “secret of life” was purely chemical would dispel notions that God had a hand in it:

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Michael Shermer responds to me: There’s no such thing as “the supernatural”

March 15, 2015 • 9:00 am

After Tanya Luhrmann published an egregious op-ed in the New York Times claiming that she melted a bicycle light with her mind (mentioning Michael Shermer’s experience with a dead radio that mysteriously played music on his wedding day), I first posted my own critique of Luhrmann’s woo and then wrote Shermer to let him know he was mentioned. Shermer, in turn, wrote a letter to the Times (“Unsolved, not supernatural”) criticizing Luhrmann and arguing that if there was no clear naturalistic explanation for the melted bicycle light—or other weird woo-ish phenomena mentioned by Luhrmann—we should simply suspend judgement until we find one.

Four days ago I called attention to Shermer’s letter, by and large agreeing with him on all but one point: I argued that there could indeed be supernatural phenomena—ones not explainable by the laws of physics but perhaps by divine action, though those phenomena could still be detected by natural means. (In fact, that’s the only way we could discover they existed.) Nevertheless, I contend that supernatural phenomena could arise by, say, God changing the speed of light, or moving stars about with his mind to spell out “I am a yam!” in the sky, and, at least in principle, those things could defy our understanding of the universe.

Shermer disagrees on that one point, and sent me a “response” which I’m glad to post here. You can be the judge of whether the term “supernatural” is useless, since there must be a natural explanation for phenomena we regard as spooky. That is, even if God moves stars around with his mind, he must do it in a way that we could understand through physical law. (I believe Sean Carroll has made this point before.) I am prepared to admit I’m wrong if readers can make a convincing case that Shermer is right—a case based not on semantics but physics.

The one point I’ll make before putting up Michael’s note is that even if God has to work through physical law, there could in theory still be a God, a personlike bodiless mind. And even if that god must work by using physical law in a way that, in principle, we can comprehend, this would still show that there are supernatural beings. But perhaps people disagree with that, even in principle.

At any rate, here’s his response to me:

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Response to Jerry Coyne

Michael Shermer 

When I say that “there is no such thing as the paranormal or the supernatural,” I mean that these words are just linguistic placeholders to talk about something for which we do not as yet have a normal or natural explanation. Analogously, when cosmologists talk about “dark energy” and “dark matter” they don’t mean those words to be an explanation, only linguistic place holders until they figure out what exactly is causing the as-yet unsolved mysteries (rotation of galaxies, accelerating expansion of the cosmos). But whereas cosmologists do not stop searching for the underlying mechanisms of the observed phenomena just because they have a label, religious believers and New Agers treat words like “paranormal” and “supernatural” (or “miracle”) as if they were causal explanations.

If it turned out that, say, people really could read other peoples’ minds and that they were able to do so because inside our neurons are tiny microtubules in which quantum effects happen that allow thoughts (patterns of neural firing) to be transferred from one skull to another at any distance (like “spooky action at a distance” effects that quantum physicists have measured in experiments), that would not be ESP or PSI, and we wouldn’t need to call it a “paranormal” effect because we would then know that the ability to read minds was due to the properties of neurons and atoms, and it would be subsumed under the sciences of neuroscience and/or quantum physics (quantum neuroscience?). (This is, by the way, an actual theory.)

As for the possibility that a God could be using other forces, “forces outside of nature to interact with the world” as Jerry says, if a God did that  (through intercessionary prayer, miracles, or whatever) in a way we could measure the effects of such interactions, wouldn’t that mean that God must be using forces measurable by our scientific instruments? Here I am reminded of the analogy drawn by the great British astronomer Sir Arthur Stanley Eddington in his classic 1958 book The Philosophy of Physical Science:

Let us suppose that an ichthyologist is exploring the life of the ocean. He casts a net into the water and brings up a fishy assortment. Surveying his catch, he proceeds in the usual manner of a scientist to systematize what it reveals. He arrives at two generalizations:

 (1) No sea-creature is less than two inches long.

(2) All sea-creatures have gills.

In applying this analogy, the catch stands for the body of knowledge which constitutes physical science, and the net for the sensory and intellectual equipment which we use in obtaining it. The casting of the net corresponds to observations.

An onlooker may object that the first generalization is wrong. “There are plenty of sea-creatures under two inches long, only your net is not adapted to catch them.” The ichthyologist dismisses this objection contemptuously. “Anything uncatchable by my net is ipso facto outside the scope of ichthyological knowledge, and is not part of the kingdom of fishes which has been defined as the theme of ichthyological knowledge. In short, what my net can’t catch isn’t fish.” (1958, p. 16)

Extending the analogy beyond the physical sciences to all fields, regardless of what forces a God may use outside of our universe, if he’s interacting with our universe in a way we can measure it, then he must be using forces measurable by scientific instruments or our senses, so by definition they must be natural. What our scientific nets catch are natural fish. If one were to argue that God’s forces are non-natural (or supernatural) and they can still effect the world but in a non-measurable way (because our scientific nets only catch natural fish), then what’s the difference between an invisible God and a nonexistent God?