Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Here are two items I encountered yesterday. The first is a bicycle with a cup holder affixed to the handlebars. Why someone would need a cup of liquid on their bicycle defies me. But perhaps it’s supposed to hold a water bottle, which isn’t much better.
The next item:
Now what are these? Looking up “alternative” in the Oxford English Dictionary, the closest adjectival form I’ve found is this:
Of one thing or set of things: available in place of another or others.
In other words, these cookies are available in the place of “real” cookies. But they’re not: they’re gluten-free, or organic, or whatever. “Alternative medicine” is disjunct from real medicine, and so these cookies should be disjunct from other cookies. But they’re not; they’re just a special type of cookie. An Oreo, for instance, could be considered an “alternative” cookie if you’re a Brit. So get off my lawn!
Since we’ve been discussing Christopher Hitchens’s discussions of religion with the faithful, Michael Shermer sent me a link to this 1.5-hour documentary about Hitchens’s interactions and debates with one Christian man. Michael’s description:
Along the lines of what I mentioned previously about how Hitch would often engage people “on the other side” in order to better understand their positions, this documentary, Collision, is worth watching as it follows Hitch on the road, in debates, in restaurants, elevators, taxis, homes, etc. with evangelical Christian Doug Wilson. Hitch was certainly not a one-dimensional man. His motives were complex, but mostly I think he loved being engaged with people to challenge them and learn from them, and of course to stir things up and get people thinking, including himself.
Click on the screenshot to go to the documentary; its description from the thoughtmaybe website is below:
Renowned political journalist and best-selling author Christopher Hitchens is pitted against fellow author, satirist and evangelical Christian Douglas Wilson, as they go on the road to exchange debate over the question: Is Christianity Good for the World? The two theologians argue, confide and even laugh together as they journey through three cities presenting the debate. This film documents the journey, bringing the sharp points together to provide a critical analysis of religion and its perpetuation.
There are some preliminary shots, and the film proper begins at 7:30:
I wonder if Hitch confessed to Wilson that he was thinking of embracing Christianity. 🙂
We’ll have two guest posts today, and the second comes from Greg Mayer, who’s been AWOL for a while (he’s now in Costa Rica).
by Greg Mayer
As WEIT readers know, Pulitzer Prize winning author and physician Siddharta Mukherjee has been in the news since he published an article in the New Yorker on “epigenetics”. Surprisingly for such an accomplished author, he presented a rather misleading view of the field of gene regulation, emphasizing what he called “epigenetics”. This has led to widespread criticism by the leading lights of molecular biology, and Jerry has provided rather full discussion of theses criticisms, including posting statements from a number of prominent molecular biologists (here, here, here, and here). Among those sharing thoughts and criticisms with Jerry were Mark Ptashne and Wally Gilbert. Such great molecular biologists may not be household names, so to put this in terms WEIT readers will readily comprehend, this is like having Darwin and Wallace criticize your article about evolution.
The article was sort of a teaser for Mukherjee’s new book, The Gene, and Jerry noted the New York Times‘ review of it in its weekday book review. Now, two more reviews have appeared this week in the Times, in the Sunday Book Review, and in the Tuesday Science section. Both are laudatory, the former including words such as “clarifying” and “definitive”. I was particularly struck by that reviewer’s statement that Mukherjee views his subject “panoptically”, which contrasts strongly with what Matthew wrote in his mixed review of the book for Nature:
Furthermore, because the book centres on medical genetics, anyone expecting an exploration of the state of genetics as a whole will be disappointed. Our Genes would have been a more appropriate title than The Gene.
While not quite myopic, this is far from panoptic. The reviewer does, however, mention Dawkins’ analogy of the DNA sequence as a “recipe”, which of course is much more apt than the common but misleading analogy of DNA as a “blueprint”.
Mukherjee’s book promotion continues apace: he has another Times piece about him forthcoming, and last Sunday I heard on the radio parts of an interview with him on “The New Yorker Radio Hour”. Based on what I heard, he really seems confused about the meaning of the word epigenetics. He seems to want it to mean any non-genetic (sensu-stricto) influence on development, but this usage is in fact close to C.H. Waddington’s (i.e., the traditional) definition of “epigenetics” which I prefer. Mukherjee has mixed up that correct usage (after all, development is epigenetic) with the new usage of the word by certain molecular biologists to mean anything weird: “all the weird and wonderful things that can’t be explained by genetics”, and so he mistakes the deeply important fact that development is epigenetic (in the traditional sense), with the importance of the molecular oddity du jour.
On a personal note, I was heartened to learn from the comments by leading molecular biologists that they too are unhappy with the appropriation and overuse of the word “epigenetics”. When I mentioned my unhappiness at this in an earlier post, a number of commenters thought it was too late to go back to the meaning based on epigenesis: “epigenetics” now firmly applied to the weird things, they wrote. So I’m glad to see that that’s not the case, at least among some of the leading molecular biologists. To understand the history of the word, the best place to go is still David Haig’s paper on the subject.
[JAC: I’ll have a few more words about The Atlantic‘s review of Mukherjee’s book tomorrow.]
Haig, D. 2004. The (dual) origin of epigenetics. Cold Spring Harbor Symposia on Quantitative Biology 69:1-4.
JAC: Melissa Chen is a doctoral candidate in genetics at MIT, and, like me, a moderator of the Global Secular Humanist Movement Facebook site. She recently went on a cool NASA-sponsored trip from Wood’s Hole, and when she volunteered to write about her adventures here, I of course said, “Sure.” Here they are. (By the way, Melissa’s alter ego is “Space Girl,” which she assumes, as you see below, by putting on a fake NASA helmet.)
The Adventures of Space Girl: What’s in a NAAMES?
by Melissa Chen
With Prof. Craig Carlson and Jason, both researchers on the NAAMES mission, about to embark on a 26-day journey to sea
Space Girl was invited by NASA for a “social” which was essentially a press junket for social media “influencers” to aid the agency in disseminating information and publicizing its research. In particular, this was an insider’s look into NAAMES (North Atlantic Aerosols and Marine Ecosystems Study), a 5-year study to understand processes that govern ocean ecosystems and their influence on atmospheric aerosols—which in turn affect clouds and Earth’s climate.
NASA’s scientific portfolio is usually dominated by the “sexy” space sciences which involves research about other planets, asteroids, galaxies and the fundamental nature of our universe. It conjures up enthralling images of space exploration, rocket launches and spacefaring missions that captivate the public mindset and stoke the flames of science-fiction fantasies. But what about our own planet, the pale blue dot that we call home? Probing outer space for an extraterrestrial sanctuary for our species seems prudent, but why not spend some resources to save the one we live on now? To do so, we’ll have to understand the problems that plague Earth first.
I arrived early at the NASA Social hosted at Woods Hole Oceanographic Institute. Check out all the NASA swag laid out for bloggers and guests!
This is exactly what NAAMES, the first earth-suborbital mission focused on studying the coupled ocean ecosystem and atmosphere, intends to do. Fortunately for us, NASA has an Earth Sciences division that is funded to the tune of USD$2 billion. Dr. Paula Bontempi spoke to us about this terrestrial niche, one that gets scant attention compared to the titillating and awe-inspiring space sciences. Further exacerbating this is the fact that the research they do, particularly in areas like ocean sciences and biogeochemistry, have been caught up in the culture wars of our time. There’s no question that the earth sciences tend to be held to a much higher and more rigorous standard due to the stubborn pervasiveness of climate-change denialism among some factions of the American public. Funding is scarce and press coverage virtually non-existent.
“Which is why Space Girl was here to save the day,” I mused to myself as I sat in the conference room on a warm spring morning at Woods Hole Oceanographic Institute.
Dance of the phytoplankton
The NAAMES mission is not only multi-disciplinary but also multi-modal, using ships, aircraft and satellites simultaneously. A C-130 Hercules airborne laboratory that deploys from St. Johns, Newfoundland will rendezvous with the R/V (research vessel) Atlantis which departs from Woods Hole, MA, along a route in the North Atlantic that takes it to the tip of Greenland.
One of the major biological events of the year is the phytoplankton bloom that takes place in the North Atlantic ocean. Below, you’ll notice the mesmerizing swirls of green biomass, reminiscent of a dreamy Van Gogh painting; they form the basis for the entire marine food chain. Satellites pick up the climax of blooms from April-May and were previously attributed to the same seasonal processes that cause terrestrial plants to flower in spring – namely, the gradually warming temperatures and increasing sunlight.
Under this hypothesis however, warmer oceans should produce larger phytoplankton blooms, which means more carbon-rich fuel for zooplankton and the other marine creatures that depend on them. That goes against what we observe, however.
According to Mike Behrenfeld from OSU (pictured below), a researcher in the NAAMES study, phytoplankton actually bloom when conditions are “worse” for growth, i.e., during the dead cold and stormy swells of winter in the North Atlantic. It follows that global warming would produce smaller and smaller blooms, reducing photosynthesis and drastically limiting the ocean’s food supply and the foundation for the entire ocean ecosystem.
How biology influences cloud science
Another way these phytoplankton blooms affect global climate is by affecting aerosols and hence cloud formation. Clouds are made up of many tiny droplets of water condense from water vapor onto microscopic particles floating in the Earth’s atmosphere. Plankton essentially help to provide clouds with these nuclei to form around by “aerosolizing” to form airborne particles. It’s akin to how crystallization of a supersaturated liquid requires a “seed.”
The more dissolved organic material in the ocean, the more particles get aerosolized in the atmosphere, which encourages cloud formation. Warming of the oceans could lead to decreased phytoplankton blooms, which, in turn, would decrease aerosols in the marine layer, thereby decreasing cloud formation. This further accelerates warming, resulting in a positive-feedback loop!
One of the NAAMES scientists showed us a neat demo which illustrates this point: holding a piping hot cup of tea on a particularly crisp cold day with minimal pollution (virtually no airborne particles), no ghostly streams of steam were detected emanating from his mug. When he blew onto the beverage surface or tried perturbing it with a lighter, hazy white ribbons of steam immediately formed.
In addition, large phytoplankton blooms are what causes the oceans to act as carbon sinks, since via photosynthesis, these micro plant cells convert CO2 to sugar that form the basis for all marine life.
R/V Atlantis: a floating laboratory
After the briefing, the participants were led on a tour of the R/V Atlantis, which was poised to embark on a 26-day mission the following day. This is no cruise – it’s a utilitarian research vessel that functions as a floating science laboratory, carrying 33 scientists and 26 crew.
There wasn’t an idle soul on board – everyone was industriously bustling about, tending to their respective duties or calibrating scientific instruments. We walked through the main lab space where we got a sense of what each group was studying, from the genomic sampling of the phytoplankton to the biogeochemistry of the oceans. It was clear to me that the only way to successfully carry out research on a ship that will, at times, be rocking quite violently, is to be fastidious and neurotic about securing everything with cable ties and rope.
Out on the deck, we had to be very careful as we moved around, for the floor of a research vessel is a booby trap for those who, like me, have two left feet. Rows of plastic incubators were being set up to see how phytoplankton respond to various conditions like osmotic shock or varying degrees of sunlight.
Biologists setting up a series of incubating tanks to learn more about the variables that affect phytoplankton growth. Check out that scientist’s (right) T-shirt!
Toward the bow of Atlantis, several modular ship containers (below) are perched side by side, each masquerading as mobile science laboratories. Inside, instruments like mass spectrometers and flow cytometers haphazardly corralled together from spare parts were whirring noisily as researchers were doing their final preparations.
The NAAMES study involves some really unique and expensive instruments to take measurements. The CTD “rosette” (left) is basically a glorified sample collection device with multiple cylinders. When it is carefully hauled back on deck, the scientists gather around it with their containers in a ritual that is known on board as “milking the cow.” Then there are the “floaters,” (right) which is a little bit of a misnomer because they actually sink quickly and slowly rise as they collect data about the water column and transmit the information back to the ship. Each of these costs USD$30,000 and are for single use only!
Off the ship, we saw the deep-sea sub named Alvin, who works with the R/V Atlantis for scientific research and exploration. He was in the dry dock because his ability to operate under immense pressures and total darkness was not needed for the NAAMES mission. Of his 4,400 dives, the most famous was probably the exploration of the wreckage of RMS #Titanic led by Dr. Robert Ballard in 1986.
Despite such an esteemed track record and illustrious career, Alvin is of course, still subject to what the internet does best – poking fun at things. Fittingly, he has been christened “Subby McSubface” (below) by an eager engineer wielding a label-maker.
Like the ocean ecosystem that the NAAMES researchers were studying, the entire ship and its inhabitants are a kind of ecosystem as well, each part of a teeming organism whose lifeblood is the desire to learn and discover. It was all quite beautiful, like a symphony in perfect harmony or a stage of dancers in exquisite synchronicity.
Theirs is a devotion to science on a level that I have never known despite having worked in wet labs in academia for many years: crammed sleeping quarters, narrow and dim hallways, and huge logistical challenges plaguing the most basic everyday routines. Scenes from disaster movies such as “The Perfect Storm” are not just fiction to those on board – the maniacal stirrings of the North Atlantic occasionally toss people and things around. Motion sickness notwithstanding, the crew has to also “do science” under these conditions! Because of the variable working (and funding) conditions, many of the NAAMES scientists have mastered the art of “MacGyvering,” one even repurposing an engine from a Dodge truck to power sea water ionization.
One of the NAAMES scientists was specifically looking out for Space Girl and wanted this photo. I told her that SHE was the real “celebrity” here!
The day ended with lunch at Captain Kidd’s next to WHOI where we were all still riding on the kind of high you can only get from being inspired by science. All this data from NAAMES will not only tell us so much about what processes trigger the yearly pattern of phytoplankton blooms, but also connect the dots between the blooms, aerosols and clouds. This information will in turn, help us to refine our climate models so that we can make better predictions on how marine ecosystems will be affected by climate change.
Thank you to NASA for inviting me. I met some amazing people like mega space dork Jason Major who’s a social media rockstar and blogs at lightsinthedark.com; Michael Finneran from NASA Langley Research Center; Nichole Estaphan, reporter from WCVB and a journalist who embedded with the NAAMES mission during its November mission. She wrote about her experience as a science journalist who spent her free days roughing it out on the rough sees on the Atlantis instead of kicking it back on vacation in the Carribean at journalistatsea.com. Why? To tell the stories of the men and women who put it all the line for the sake of knowledge and discovery.
I’ve held onto this story a while (there are usually three or four Caturday Felid drafts in different stages of production), but the March 8 New York Times had an article on “The Cat-Mayor of Carroll Gardens“. It’s about Petro, a 13-year-old Tom who was a Brooklyn house cat until a baby was born in his territory three years ago. Petro then took to the outdoors and became a “local celebrity”:
On nice days, Petro, his coat flecked with silver, patrols the block, from the corner of Clinton Street almost to the far end at Court Street. He delights children, greets strangers and friends, poses for photos, terrifies dogs (or imagines he does).
“He’ll sit in the middle of the sidewalk,” said Richard Fluker, who delivers parcels for the Postal Service. “You have no choice — you have to go around him. He’s not afraid of anyone.”
From Petro’s collar hangs an ID tag shaped like a fish. “We used to get four or five calls a week from people who ‘found’ him,” said Ms. Chi’s husband, Jason Glenn. “People wake you up at 1 in the morning holding your cat in the doorway. We felt like taping to the tag, ‘It’s all right for him to be outside.’”
For a short video of Petro, and more of the story, click on the first screenshot below:
When the weather is less agreeable, Petro makes house calls in his five-story brownstone.
“One time he somehow got into my apartment,” said Tommy Mulvoy, a teacher who lives on the top floor. “I turn around and this freaking cat is on the back of my couch. How my cat didn’t see him, I don’t know. He’s a sneaky dude.”
Petro started going outside after his owner Jennifer Chi had her second child. “He wasn’t getting enough attention anymore,” she said, “and he was jealous.”Credit: Christopher Lee for The New York Times
. . . downstairs neighbor David Sandholm came home. Petro slalomed between his legs and followed him inside.
“He’s the perfect pet for us,” said Mr. Sandholm’s wife, Carolyn. “We don’t have to clean out a litter box.”
The Sandholms have never met Petro’s owners.
Mr. Sandholm gave Petro some treats and sat on the couch with a sandwich. Petro got up on the coffee table to sniff it. After lunch, he took a nap on Mr. Sandholm’s computer keyboard.
Visiting a neighbor’s house one recent Monday, Petro napped on the man’s computer. Credit David Sandholm
Yes, I know that cats should be kept indoors, so you needn’t say that in the comments.
Russia’s Optina Monastery is an Orthodox Christian center located south of Moscow that dates back to at least the sixteenth century. The sacred spot has reportedly welcomed many notable guests during its long history — including writers Nikolay Gogol, Fyodor Dostoevsky and Leo Tolstoy.
. . . Optina uploaded a YouTube video on March 29 showing a band of cats following one of the center’s residents while he performed a ritual blessing.
In an email, one of the monks from Optina confirmed to The Huffington Post that the cats’ human leader was Sergey Kuzmich, a lay person who is living at the center. The monk said that the members of the community have an old tradition of walking around inside the center every day to bless the walls, gates and buildings with a cross. The monks take turns performing this task daily.
Kuzmich is the one who usually feeds the stray cats that appear at the hermitage. But this particular time, it seems that when it was their friend’s turn to do the blessing, the furry felines couldn’t resist jumping in.
“Cats know and love him and so they decided to take part in the whole procedure, though it wasn’t feeding time, which looked very touching and that’s why we filmed it and have shared this video on YouTube,” the monk wrote to The Huffington Post.
Last month, the staff at the museum thought it’d be funny to use Maray as a joke for April Fools’ day. They wrote his job application letter and sent a press release to local media saying they had accepted his application.
Here’s the letter. Anybody able to translate it?
Unfortunately, the media took the press release seriously and began contacting the museum for information about the employed cat.
So staff decided to make the appointment real, and declared him their official doorman. According to museum employee Nina Strelkova, Maray works from 9 to 5 each day with a break for lunch and a springtime walk. He even has a tent to sleep in at night.
Here’s a video of Marai:
And, of course, everyone loves him:
“All people who work in our museum love Maray. Many bring him food from home and take pictures with him. So he gets a little fat now,” she said. “And visitors love the cat too — lots of them taking selfies with him.”
Photo (and below): Serpukhov Historical and Art Museum
Don’t forget to keep those photos coming in. While I have a decent backlog, I can always use more good ones. And please, when you send them in, include descriptions of the species (and its Latin binomial) as well as a bit of information about the beast (or plant or landscape), where you photographed it, and so on.
We have some more photos of bird rescue, this time from Karen Bartelt:
Ruby-throated hummingbird (Archilochus colubris) that flew into the garage and couldn’t find its way out. It was near exhaustion when my husband snagged it with his butterfly net – one of the upsides of being married to an entomologist.
First, from Stephen Barnard:
Great Horned Owl (Bubo virginianus), Idaho. The robins were angry with this owl perching near their nest.
I shot this early in the morning right outside my house. The light was dim so I had to take full advantage of my camera’s excellent high ISO performance and image stabilization.
And I guess Stephen’s off fishing again, judging from this photo:
Sunrise on the Florida Gulf coast. Yesterday morning.
It’s Saturday, May 21, and we’re in for a lovely weekend (weatherwise) in Chicago. On this day in history, Charles Lindburgh landed in Paris (1927), completing the first nonstop flight across the Atlantic by a solo pilot. And, according to Wikipedia, in 1936 “Sada Abe is arrested after wandering the streets of Tokyo for days with her dead lover’s severed genitals in her handbag. Her story soon becomes one of Japan’s most notorious scandals.” She was sentenced to six years in prison and served four You may well have seen the movie based on this, “In the Realm of the Senses,” a mainstream film (and a pretty good one) with real sex scenes. Finally, on this day in 1992, Johnny Carson hosted his very last episode of The Tonight Show, with guests Bette Midler and Robin Williams.
Those born on this day include Mary Anning (1799), Henri Rousseau (1844), Andrei Sakharov (1921), and Al Franken (1951). Deaths on this day included Christopher Smart (1771), who wrote the best cat poem ever,Jane Addams (1935), and Twinkle (2015). Meanwhile in Dobrzyn, Hili and Cyrus are squabbling like brother and sister:
Cyrus: Take your paw off my nose.
Hili: First you take yours off mine.
In Polish:
Cyrus: Zabierz swoją łapkę z mojego nosa.
Hili: Ty zabierz najpierw swoją z mojego.L
Lagnaiappe 1: from George Takei’s FB page, courtesy of reader JSP, we get “the REAL Ceiling Cat.” (I’m not so sure.)
It’s Friday afternoon, and that means CAT TIME! This video was put up only 3 days ago, and already has nearly 1.8 million views. Such is the power of cats on the internet.
I’m not sure who Coyote Peterson is, and I’m dubious of a guy who takes the nickname of a d*g. I’m also worried that a “tame” wild ocelot (Leopardus pardalis) has the potential to be poached. But what a gorgeous creature this half-grown cat is! As reader Su mentioned when sending it to me, it’s a great pity this hasn’t happened to me during my travels.
