By Tom Spears, The Ottawa Citizen. You owe it to yourself to read the whole thing.
Ernest Small's research colleagues at Agriculture Canada had a
mystery. Peering at the cellular innards of a clover plant, they
wondered why nothing was behaving the way clover should.
They asked Small, a veteran scientist at the Central Experimental Farm, for help.
It didn't take him long to pinpoint the problem. Their clover was an alfalfa.
Protea obtusifolia in the De Hoop Nature Reserve, Western Cape, South Africa Photograph by Kent Holsinger Click on the image for a high-resolution image in a new window.
The Dimensions of Biodiversity project that Carl Schlichting, Cindi Jones, John Silander, Andrew Latimer, Justin Borevitz, and I are working on is featured in a recent Discovery article on the NSF website. Here are the first couple of paragraphs of the article:
Climate change is on your porch and in your backyard and living room--anywhere you bedeck with flowering plants.
Global warming affects favorite flowers of garden and vase. This is true of plants around the world, including the proteas and the pelargoniums native to South Africa.
Head over to the NSF site if you'd like to read the whole thing.
Much about James Franklin Crow, who died on 4 January two weeks short of
his 96th birthday, challenges our sense of scale. Over seven decades,
he contributed to an astonishing array of topics in genetics, and the
list of his students and postdocs reads like a who's who. One of them,
the pioneering geneticist Motoo Kimura, wrote that getting Crow as his
adviser after a period of uncertainty was such a joy it was like
"meeting Buddha in Hell". Crow also played the viola for 45 years with
the Madison Symphony Orchestra. He once performed with the great violin
soloist Yehudi Menuhin.
That's the opening paragraph of Alexey Kondrashov's wonderful piece remembering the life and work of James F. Crow. Please visit Nature and read the whole thing. Jim was a remarkable individual.
The #arseniclife saga may have opened a new chapter in the way science gets done, at least in the life sciences. For those of you who haven't been following the story over the last year, here's a quick recap.1
29 November 2010: NASA announces a press conference to discuss a finding that "will impact the search for evidence of extraterrestrial life".
2 December 2010: At the press conference, Felisa Wolfe-Simon and colleagues announce that a bacterium can substitute arsenic for phosphorous in proteins and DNA.
4 December 2010: Rosie Redfield makes a blog post questioning the claim.
7 December 2010: Carl Zimmer writes a piece for Slate explaining the skepticism many scientists have about the claim.
Through it all there was a lot of commentary on blogs and on Twitter. Wolfe-Simon and her colleagues did not engage in that debate. Science magazine, where the paper describing the results appeared, took the unusual step of publishing a series of comments on the paper simultaneously with the paper.2
There are a couple of interesting things about this article.
Rosie hasn't been able to replicate Wolfe-Simon's findings, in spite of her best efforts to do so. While there remains a slim possibility that Wolfe-Simon is right, "[o]ther researchers who published critiques of the arsenic-life paper say that Redfield and her collaborators have produced a reasonable refutation of its findings." #arseniclife appears to be dying, though it may be a slow death, and it may be awhile before it is completely dead.
"Redfield and her collaborators hope to submit their work to Science by the end of the month. She says that if Science refuses to publish the work because it has been discussed on blogs, it will become an important test case for open science." There may be good reasons for Science not to publish Rosie's paper. The details of the work are sufficiently technical and sufficiently far removed from my expertise that I wouldn't presume to judge that. But the wide-open discussion of her work on her blog should be seen as strengthening her work, not as a reason for rejecting it. Because she has worked in the open, documenting her successes and failures, accepting advice from colleagues, and debating approaches and protocols, the paper Science receives is likely to be far more thoroughly vetted than most they receive. The editors of Science should ask themselves this question if they have any doubts:
Would we refuse to publish the paper describing faster than light neutrinos just because an early version appeared in Arxiv?
You saw Drew Berry's TED talk a few days ago. Here's a video from the New York Times talking about how molecular visualizations can be used. You won't learn as much biology from this as from Drew Berry's talk, but it demonstrates a greater variety of applications. Enjoy!
Visualizing is a vital part of scientific discovery. Drew Berry starts with Galileo and Darwin before moving on to his work showing the dynamics of the molecular machinery in our own cells. Watch, be amazed, and understand something about DNA replication.
Carl Zimmer gets it just right (not surprisingly):
Berry's TEDx talk is more satisfying because it's a talk.
You look at the mesmerizing images, and Berry explains what you're
seeing. What's really interesting is how he-no doubt unconsciously-uses
words that switch on the mental eye. When he zooms in on a chromosome,
he points out structures passing through it that look "like whiskers,"
which act as the "scaffolding" for the cell (the microtubules). He then
zooms into the place where the chromosome and microtubule meet, the
kinetochore. What you see looks like a supercomputer's acid trip. But
you can make sense of what you see because Berry uses metaphors. He
calls it a "signal broadcasting system." Now all the molecules jittering
around aren't totally random. We can see how molecules come together to
make life possible.
There's no question that people like Berry are going to be making the
movies that fill our heads in our future when we think about what's
going on in our bodies. But those movies will need good soundtracks.
I was greatly saddened when I learned yesterday that James F. Crow died earlier this week. Jim was a link to everyone who had a hand in the development of genetics, from Mueller, Sturtevant, Fisher, Wright, and Haldane to Kimura and too many others to mention. I can't claim to know him well. Our paths crossed only a few times, but he was extraordinarily generous and kind. I was especially flattered that he came to a talk I gave last April when I visited the University of Wisconsin. He asked a difficult, incisive question and in his gentle way encouraged me to think more carefully about my results.
The January issue of Genetics began a series of articles, "Honoring Our Colleague James F. Crow, an Outstanding Gentleman, Citizen, and Scientist".
Why honor Jim? The answer is obvious to the many who have the privilege to know him: a gentleman and scholar of the highest order, he represents the best of our field. (source)
John Hawks sums up the feelings of those who knew him the best, his colleagues at the University of Wisconsin.
Several years ago, colleagues from several departments here at the University of Wisconsin-Madison succeeded in a long-time ambition of Jim's to found an Institute for the Study of Evolution. He had envisioned that the institute should be named for Sewall Wright, who had been important to Jim himself and forms a major part of the legacy of genetics and evolution. But the future institute's members insisted instead to name the new entity in honor of Jim. It is a fitting legacy for a great evolutionary geneticist.
Jim was a treasure, and he will be greatly missed.
If you want to find life forms that truly seem otherworldly, your local
forest is a much better place than your local cineplex. It is home to
creatures that are immensely old, fundamentally bizarre and capable of
startlingly sophisticated behavior. They are the slime molds. ("Can answers to evolution be found in slime?", by Carl Zimmer, The New York Times, 3 October 2011)
Carl Zimmer's piece in The New York Times on the wonderful world of slime molds is wonderful. And there is a superb photo gallery for Beauty and the Blob. From Dictyostelium to (my favorite) Metatrichia, it's a weird and marvelous world. Head over and see for yourself some things so strange that even Hollywood couldn't imagine them.
Today is the first day of Fall into Phenology. What's that? It's part of Project BudBurst at NEON, Inc. Still confused? Just head over to the website, register for Project BudBurst, pick a plant, make an observation, and report it.
Why would you want to do that?
Because scientists want to know when plants are losing their leaves, when they're flowering, and many other things. And we want to know it about as many different kinds of plants from as many different places as we can. There are too many plants and too many places for us to do it ourselves, so NEON is asking for your help. It will only take a few minutes, and your data will be very valuable. Please join in.
Maybe now things are starting to click. Let's see. Rosie Redfield, she was among the first to criticize the paper by Felisa Wolfe-Simon and colleagues1 claiming discovery of a bacterium that can substitute arsenic for phosphorous in biomolecules, including DNA. GFAJ-1 is the strain of bacteria claimed to have this ability. Now Rosie has cells of GFAJ-1 growing in her lab and can run her own experiments.
Leave aside whether or not Felisa Wolfe-Simon and her co-authors are shown to be wrong, as seems likely given my reading of the critiques,2 the #arseniclife episode illustrates something important about how science works, something that intelligent design proponents ignore. I pointed out last December that
Wolfe-Simon and her colleagues will give other scientists samples of the
bacterium that is claimed to have these extraordinary properties and
those scientists will have a chance to verify Wolfe-Simon's claims. If
Wolfe-Simon's claims turn out to be right, textbooks will be rewritten,
and all of us will have to think differently about the chemistry of
life. If her claims turn out to be wrong, only a few specialists will
remember that the paper was ever published.
Now those samples are in the hands of Wolfe-Simon's critics. Experiments, data, and analysis will now vindicate either Wolfe-Simon or her critics
Compare that lengthy,
tortuous process of debate and review among experts to the "debate"
that intelligent design creationists want to have in high school
textbooks. Which process do you think is most likely to help kids
understand their world?
