Chemistry’s Last Judgment

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The brilliant blues in Michaelangelo’s Last Judgment, which covers the western wall of the Sistine Chapel, come from ultramarine. The once rare and precious pigment has appeared on Western canvases since the 13th Century. The name comes from the Italian for “beyond the seas,” and the pigment itself is derived from the semi-precious stone lapis lazuli. And as it turns out, ultramarine fades over time.

A new collaborative study among the NYU Chemistry Department, the Pratt Institute, and the Metropolitan Museum of Art has established the chemical mechanism for the pigment’s slow change in color. Using nuclear magnetic resonance, the researchers found that ultramarine’s blueness comes from sulfur atoms trapped inside a lattice of aluminum and silicon; when the sulfur siggles free, ultramarine loses its blue. Armed with this knowledge, conservationists can now begin to develop means for preserving works.

On the visualziation side of things, I have to admit that I’d like to see a cartoon or rendering that shows the aluminum-silicon structure and how the sulfur atoms fit in. But if I have to settle for Michaelangelo (an image similar to the above appeared with the NYU press release), so be it.

In case this all sounds intriguing… Victoria Finlay’s brilliant book, Color: A Natural History of the Palette, has a chapter about blue that includes many intriguing details. The story of pigments used in art—and how those pigments and other chemicals interact and change over time—contains many fascinating twists and turns. Also, a couple of years ago, the American Folk Art Museum ran an exhibit about “blue” that examined some of the science behind pigmentation; I seem to recaall a catalog, but I can’t find any evidence for one.

Before There Were Sponges

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I lifted the above image from an article in today’s issue of Science, which you probably can’t read unless you’re logged in from a subscribing institution. That’s okay: take a look at the Reuters article instead, although it doesn’t have any accompanying pictures.

Which is too bad, because however abstract, I think the above image (depicting results of x-ray tomography on the specimen) communicates its ideas fairly clearly.

The caption in the Science article reads as follows… “Aberrant embryos. (A) Reflected-light photomicrograph of a 3-cell embryo (specimen DOU-25). (B) Exterior isosurface model. (C) Volume rendered and extracted cell models, with the left cell rendered transparent to show the only subcellular structure (shaded green) in this embryo.” Admittedly, you might want to rewrite that before putting it in a press release: “(A) Here’s a photo. (B) We can reconstruct what’s inside. (C) We can even figure out its constituent parts—going so far as to see inside the fossilized cells to see their interior structure.” Something like that.

Of further interest is a punchline that appears in the scientific publication but not in the popular re-interpretation. The very last sentence reads, “the combined observations suggest that the Doushantuo embryos are probably stem-group metazoans.” Which, translated from biologiese, means that these cells are precursors to metazoans—i.e., further down the trunk of the family tree that led to us. Such humble beginnings…

Little Day-Glo Orange Spot

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The above Hubble image, released back in April, is in the news again because the origin of the so-called “Little Red Spot” seems to be “the only survivor among three white-colored storms that merged together” in the last decade, resulting in a ruddy storm with wind speeds that rival its Great Red Sibling.

But I find this image slightly disturbing. The almost radioactive, day-glo red of the two spots (and excessive blue of the normally white bands) deserves greater attention than it receives in the picture’s caption. All we learn is that “two filters are shown in red/orange (F892N, near-IR strong methane band) and blue/cyan (F502N continuum/cyan light),” which I find less than satisfying. Is that “red/orange” and “blue/cyan” on top of a “true-color” image? I take it to be the case, but the verbiage leaves me guessing. (Certainly when you compare the above to another Hubble image of the same part of Jupiter, taken around the same time, the colors are quite different.)

This is a good place to spend a little time, in my opinion, explaining a bit of process. Mention something about “particular wavelengths of light” or “enhanced color” or something. Make it clear that we’re not seeing Jupiter as it would appear were one to put one’s eye up to Hubble’s eyepiece.

(Um, just in case… That last line was a joke. Hubble has no eyepiece. It’s in space. For more info on how Hubble images are made, please read the lovely “Behind the Pictures” page at the Hubble website.)

Bird Bucks Trend

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More critters today, albeit slightly larger than yesterday…

A Reuters story today tells the story of the Yariguies Brush-Finch, newly determined to be a new species residing “ in a Colombian cloud forest accessible only by helicopter.” The results were reported in the Bulletin of the British Ornithologists’ Club.

Interestingly, the above photo seems to be the only one readily available, courtesy of The National Ledger. In the Yahoo version of this story, the same image appears, albeit blown up and blobby. It’s the only image that crops up when one googles “Yariguies Brush-Finch” at the moment.

Now, this is all well and good, but for context, allow me to present the (complete) table of contents from the latest Bulletin of the British Ornithologists’ Club:

  • “Recent Avian Extinctions”
  • “New Zealand’s extinct giant eagle”
  • “Going or gone: defining ‘Possibly Extinct’ species to give a truer picture of recent extinctions”
  • “The rise and fall of wildfowl of the western Indian Ocean and Australasia”
  • “Recent avian extinctions on Réunion (Mascarene Islands) from paleontological and historical sources”
  • “Unpublished drawings of the Dodo Raphus cucullatus and notes on Dodo skin relics”
  • “How confident are we that a species is extinct? Quantitative inference of extinction from biological records”

    Seems like we’re missing part of the story here—i.e., discovering a new species bucks a bit of a trend in the biz. Didn’t this merit a line in the story? I can imagine one of the scientists saying, “In an era when we mostly report on the extinction of species, it gladdens one’s heart to discover a hitherto unknown species before it, too, goes the way of the dodo.” Soon photos (perhaps only low-quality versions from the web) are all we have left of such creatures.

    Hmmm. I think my inner eco-freak is showing.

    • Photocopier Art

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    An article in today’s Science Times (n.b. that you’ll have to pay to see it if you look after 17 October) describes Thomas Eisner’s use of a color photocopier to create compositions based in his admiration of natural forms.

    The image above appears in conjunction with the Science Times piece, even though it dates to an era before Eisner began using the photocopier as a means of expression. Instead, it represents an innovation in preserving specimens and then using a scanning electron microscope to create aesthetically interesting and highly informative images of the microscopic world. Eisner published an entire book’s worth of similar images (albeit mostly in color), although in fact he’s known in scientific circles for his seminal work in chemical ecology.

    Physically disabled by the onset of Parkinson’s disease, Eisner has started using photocopiers for artistic expression, now interpreting the natural world in a more subjective way. He claims that a color copier “can serve for the inventive generation of imagery, for composition of novel pictorial arrangements, and in that capacity find use in the expression of fantasy.”

    Eisner’s statements speak to the deeply aesthetic motivation that underlies many scientists’ work. The orientation toward imagery occurs particularly in astronomy and biology, it seems, but the underlying intellectual aesthetic pervades most disciplines. (Cf. the new collection of Carl Sagan’s “Gifford Lectures in Natural Theology” to be released next month.

    More Mapmaking

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    In honor of Indigenous People’s Day (still called “Columbus Day” here in New York), I thought I’d present an image from a non-Western culture that communicates an in idea we would dessribe as fundamentally “scientific.” Having previously discussed mapmaking on this blog, the above image of a Marshallese stick chart seemed appropriate.

    I recently ran across an image of a stick chart in the National Geographic volume Mapping the World, which includes maps from a variety of times and places. In the foreward, Allen Carroll, Chief Cartographer of the National Geographic Society, writes about the challenges of creating maps, then adds… “Reading maps is challenging, too: interpreting patterns, deriving locations and routes, understanding interrelationships, making the not insignificant mental leap from color, label, and symbol back to the original form—the surface of the Earth.”

    To my mind, the stick chart represents a perfect example of the kind of embedded visual language that goes into creating images intended to communicate concepts, particularly scientific concepts. Like a graph of the cosmic microwave background, the stick chart uses a specific visual vocabulary to convey essential properties of interest about its subject. Interconnecting sticks represent ocean currents and swells, although this rebbilib chart is more concerned with island positions in a broad view of the archipelago. The motivation is to communicate essential elements, much as a “map” of data into abstract cartesian space.

    You can learn more about Marshallese stick chart navigation on a website put together by the Marshall Islands Chamber of Commerce. I wouldn’t recommend setting sail without a little additional guidance, however.

    Orbiter Sees Rover

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    Too freakin’ kewl. The HiRISE camera aboard the Mars Reconnaissance Orbiter (MRO) captured the above image of the Opportunity rover. You can also take a look at a higher-resolution version of the image or a close-up portion of the image that shows the rover.

    Now compare it to what the Opportunity rover is looking at now. Coordinated observations! Yay!

    Now, if only we could get a high-res camera in orbit around the Moon in order to take pictures of Apollo landing gear! Oh, wait,
    that will happen eventually    , I guess. (Of course, people will still question the authenticity of such images, but… C’est la vie.)

    Flahback to the Cosmic Microwave Background

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    On the heels of the Nobel Prize committee announcing that John Mather and George Smoot had been awarded the 2006 Physics Prize “for their discovery of the blackbody form and anisotropy of the cosmic microwave background radiation,” I thought it might be nice to flash back briefly.

    I was in grad school when the Cosmic Background Explorer (COBE) results were first analyzed and announced, and the graph above was the first result I saw. For astrophysicists and cosmologists, the result confirmed expectations stunningly well. The solid, curved line in the graph depicts the blackbody spectrum predicted by theory; the dots and squares lying along the curve indicate actual data collected by the satellite (some of which have lines attached to them indicating uncertainty in the measurements). The match between data and theory rarely matches so precisely, and (as I remember) the astronomical community was quite impressed with itself.

    However, cosmologists expected some variation around this simple curved line—little squiggles, if you will, that would tell us about the structure of the early Universe. But as the COBE scientists dug deeper and deeper into their data, they didn’t find anything. Hubris turned to worry until fluctuations were discovered at the level of one part in 100,000! Tiny variations in this otherwise smooth curve. Depicting these variations as color differences in pink and purple led to the classic, garish COBE image depicting the entire sky as an oval.

    In the past few years, the Wilkinson Microwave Anisotropy Probe (WMAP) has refined these measurements and told us even more about the structure and origins of the Universe, bt as I recall, it all started with the graph you see above…

    Speaking Warmly of Saturn

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    Okay, this just proves I’m a whore for astronomy images. I’d already started writing something about PET scans in relation to today’s story about the long-term effects of chemotherapy on brain function, but then I saw the press release for the above image.

    In spite of the mediocre resolution (mostly because it’s a composite of infrared mapping spectrometer, which operates in a scanning, single-pixel-at-a-time mode), the image rather intuitively communicates the idea of seeing ”through” Saturn’s clouds.

    As described in the caption from JPL, we’re looking at a near-infrared image of Saturn, in which the shorter-wavelength light (shown as blue-to-green) is reflected off the cloudtops whereas the longer-wavelength emission (colored red) from Saturn’s warm interior shines through in shadowed regions, less obviously in the daylit regions. Because most people (stellar astronomers excluded) think of red as warm and blue as cool, this image capitalizes on people’s natural sensibilities. Always a good thing.

    This strikes me as a good image to talk about some of the confusing aspects of infrared light, which well-informed people typically perceive simply as “heat,” because that’s what they’ve been told. Of course, the problem with blackbody radiation is that there’s a big contrast issue: yeah, the lower layers of Saturn’s atmosphere may be warm, but their infrared glow gets blocked by clouds in the upper atmosphere, plus it has to compete with the bright, reflected glare of the Sun. The image above allows one to talk about those contrast issues while clearly conveying that infrared light allows us to see things we can’t in visible light. Also, the rings cut across the center of the image as a blue line, indicating that they reflect the short-wavelength infrared light but don’t emit much thermally—pretty much as one would expect from chilly rings made mostly of ice.

    Stunningly Incomprehensible

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    Words fail me on this one (well, not really). How incomprehensible is it? Let me count the ways.

    First off, we’re confronted with the somewhat cryptic information that we’re seeing the “cosmos” at a distance of 450 million light years. Mmmm hmmm. Then we have a color bar at the bottom, sans units, that tells us that the values range from –1.0 something to 4.3 something. Other labels appear scattered pell-mell across the image… “Fur-For”? “Per-Peg”? What is an Average Jane to make of these? (They’re short for “Further Fornax” and “Perseus-Pegasus,” BTW. I’ll even make the obnoxious grammarian observation that it should be “Farther Fornax” if anything.) And to add insult to injury, the red typeface blends right into the color scheme of the plot!

    What saddens me most about this image is that it represents a spectacular result poorly communicated. What you’re looking at, FYI, is a color-coded representation of matter density within a thin sliver of the Universe at an approximate distance of (you guessed it) 450 million light years. The press release correctly identifies this as “the largest full-sky, three-dimensional survey of galaxies ever conducted” (based on 2MASS data, just so you know). How kewl is that? You wouldn’t know from this picture.

    (If I were petty, I would note that the headings on the images don’t even match the captions provided in the press release from the Royal Astronomical Society, at least as it was emailed to me. For example, the caption for the image above reads, “The reconstructed density field, evaluated on a thin shell… at 45 million light years. The main overdensity, Shapley, is shown in red and green. Other overdensities are Rixos F231\526 (RIX), SC44, C19, Pisces (Pis), Perseus-Pegasus (Per-Peg), C25, C26, Hercules (Her), Abell S0757, C28, C29, C30, SC 43, Leo, Abell 3376, C27 and C21. The voids (blue) are V4, Further-Fornax (Fur-For) and V15.” Emphasis mine. But I’m not petty. Oh, and the picture is correctly labelled; the caption is wrong.)

    The academic paper presents the same images as black-and-white contour plots, so I can only assume that the researchers believed themselves to be translating their results into user-friendly format simply by adding garish color.

    Allow to digress for a moment to explain why I see this as such an egregious mistake. My two-bit definition of science visualization goes something like this… We make images from data (i.e., ones and zeros) for essentially one of three purposes: 1) communication to oneself in the form of data analysis, 2) communication to peers, often in the form of a graph or contour plot, and 3) communication to a general audience. The first two purposes depend heavily on well-developed visual language—for example, knowing what variables you’re plotting against one another, knowing what color-coding means, etc.—that often tend to be very specialized. Those of us who have been reading cartesian coordinates for most of our lives forget what it’s like not to be exposed to that visual vocabulary on a day-to-day basis. Needless to say, scientists tend to communicate via an extremely sophisticated visual language (that furthermore varies from discipline to discipline). The biggest problem occurs when scientists try to make the leap to the third form of visualization—communicating to the general public. It’s difficult to translate their complex visual language into a visual vernacular. (More details on my “personal paradigm” are available as part of my “What Is Viz?” PowerPoint, but be warned that you need to read the comments for each slide; otherwise, it’s just a bunch of pictures.)

    Thus, the fundamental issue I see here can be likened to a mistranslation. The image above uses a very specific vocabulary (e.g., false color, Aitoff projection of a sphere onto a plane) to describe a small part of the Universe. Without attempting to translate the truly challenging aspects of the image, the presentation of candy-colored data sans specific quantifying information in fact results in a terribly confusing message.

    Oddly enough, we have played with an earlier version of the 2MASS data as part of the Hayden Planetarium Digital Universe, so I’ve seen (in 3-D) the galaxy data upon which this is based. The data certainly lend themselves to a 3-D representation, and I can image a fly-through in which the matter distribution is represented by 3-D isosurfaces, or if a lot of rendering time were at one’s disposal, by volumetric rendering (similar to the manner in which some dark matter simulations are depicted.