Tangled Bank 72: What’s in a name?

Welcome to the 72nd installment of Tangled Bank, a blog carnival devoted “to science and medicine, broadly defined.”

A great many of the excellent submissions for this issue are articles dealing with biological classification, taxonomy and nomenclature. This focus on naming gives us our theme and a title for the carnival. For your navigation pleasure, our other categories are:

If you’re visiting Ouroboros for the first time: Greetings! The site is devoted to reviewing research literature in the biology of aging (e.g.), with occasional forays into the popular media (e.g.). Feel free to poke around and stay a while. If you like what you see, here is our RSS feed.

We’ve got a heck of a lot of entries, so let’s get going without further ado:

What’s in a name?.

In Unlocking the future of keys, Luigi Guarino at Agricultural Bioiversity Weblog describes software for the taxonomic identification of plants based on incomplete information, and contrasts these solutions to the less flexible hierarchical method of dichotomous keys (“#70. Is the fruit yellow? See line 71. Is the fruit a color other than yellow? See line 72. #71. Is the fruit the shape of a boomerang?” &c.).

Taxonomy itself is not fixed and unchanging, even for long-extinct species. Matthew Celeskey, curator of The Hairy Museum of Natural History, illustrates the way in which new data (or the re-examination of old data) can force paleontologists to reconsider prior classifications. In The Sinking of Seismosaurus, Matt describes vertiginous rise — and thunderous fall — of what was once thought to be a separate genus of sauropods.

Just what happens to obsolete terminology, anyway? Find out from SMC at The Big Room. Short answer: it sticks around.

A digression from taxonomy, since we’re on the subject of dinosaurs: Remember when dinosaurs used to be considered cold-blooded (ectotherms), but all of a sudden we were told that they were very likely to have been warm-blooded (endotherms)? Well, what happened to our beliefs also had to happen during evolution: energetic endotherms had to evolve from sluggish ectotherms. How did it happen? Jeremy Bruno of The Voltage Gate has some thoughts on the subject, in Dinosaurs and the Mystery of Body Temperature II: The Evolution of Endothermy.

Still digressing, but a slightly more recent note, on geological timescales at least: Check out this report at Living the Scientific Life a paleontological treasure trove found recently at Thylacoleo Caves in Australia. The finds, dating from 400,000 to 800,000 years ago, include a whopping 69 new vertebrate species — including Thylacoleo carnifex, a marsupial lion, for which the caves were named.

Which brings us back to naming: In addition to being dynamic, classification nomenclature can also be fun, even when the trait being described is “the state of being gray.” Over at 10,000 Birds (is that still only worth one picture?), birdbrain/word-hawk/jive turkey Mike Bergin asks us to Color Me Plumbeous. The title’s key word derives from the Latin plumbum, “lead,” the same word that gives us the elemental symbol Pb.

Sticking with the color theme for the moment, Mike Kaspari of the deeply ironically named blog Getting Things Done in Academia delves into the appetizing-sounding “brown food web.” No, he doesn’t mean chocolate but rather detritus, decomposers, and the lucky creatures who in turn feed upon them. Complete with detailed advice that begins “Step 1: Sit on your butt in the litter”, latent formicophile Mike sings in praise of litter ants.

More on color, or in this case, the lack thereof. Daniel Flück of Colblindor devotes a lengthy article to confusion lines, a method of quantifying chromaticity that dates all the way back to James Clerk Maxwell.

Sometimes an animal can give its name to a completely different sort of beast, as is the case with the quagga mussel, an invasive species currently working its way across the US. The menacing mollusc in question is named after the quagga, an animal that resembled the zebra and isunfortunately now extinct — but at least that stops us from confusing a bivalve for a quadruped. Jennifer Forman Orth at the Invasive Species Weblog tracks the shady shellfish on its westward march.

One animal whose territory is unfortunately not expanding is the Bactrian camel, whose fascinating traits and endangered status are detailed by exclamation point enthusiast Melinda Wenner, of She Blinded Me With Science!, in her article Camel Fever!. The news isn’t all bad: the Bactrian is one of the ten focal species of the EDGE of Existence, a conservation group that bases the need for action not only on a species’ extinction status (i.e., its numbers) but also on its level of evolutionary distinction.

Let’s move on from our theme to my own favorite subject: aging..

With an eye toward developing a conceptual model for regeneration of tissues, Attila Csordás asks the stem cell biologists and bioinformaticians in the audience a simple (ha!) question: How would you define the regenerative potential of a tissue/organ? Attila’s weblog PImm: Partial Immortalization is one of two aging-related blogs contributing to this issue of Tangled Bank.

Our other biogerontological contributor is Reason, Blogasaurus rex of the struggle against senescence, parent of Longevity Meme and Fight Aging! among other projects. In this issue’s contribution, Reason presents The Skeptical View of Cancer Stem Cell Research. Much recent work suggests that stem cells have a dark side, possibly playing a crucial role in the initiation and development of cancer — the ability to self-replenish indefinitely is, after all, something of a two-edged sword — raising the possibility of stem cell-directed cancer therapies. “However,” Reason points out, “it is worth airing the skeptical viewpoint – which starts with the observation that next to nothing in the world of biochemistry is as simple as we would like it to be.”

More skeptical thinking on a subject related to aging comes from neuroscience and psychology writer Orli Van Mourik of Neurontic, who asks a tough question about calorie restriction (CR) in her article The Quest for Long Life: “Is a life of such extreme deprivation worth living?” Find out her answer when you read the article; as a bonus, learn of her secret desire to wear air-conditioned leisure wear.

From aging itself we’ll move to a disease of aging — cancer — and thence to more general treatments of cell biology and microbiology.

Stem cells might be involved in cancer, but your Nokia isn’t. Erika Groth of Tur I Oturen (Swedish for “luck in the bad luck” or more loosely “a blessing in disguise”; she says the expression “describes the normal progress of my research”) shares the good news from a Danish study showing that cell phone use will not give you cancer.

In fact, electronics may be useful as cancer therapies, at least in the “treating the whole patient” sense: In addition to the vast pharmaceutical armamentarium, doctors have begun treating cancer with video games. Bertalan Meskó of ScienceRoll describes Re-Mission, a video game designed to help young cancer patients cope with their disease. The results so far suggest that real biological endpoints like retention of chemotherapeutic agents and positive response to antibiotics might actually improve as a result of playing the game.

While young leukemia patients shoot virtual bullets at cancer’s electronic avatars, flesh-and-blood genetic engineers are firing microscopic DNA-coated tungsten pellets in order to introduce new genes into plant cells. Other sorts of cells (bacterial, animal) are easier to transfect using chemical tricks to get the DNA inside the cell, but plants have a tough outer cell wall that’s extremely difficult to fool in those ways, so sterner measures are required. Fire!. The name of the technique: biolistics. Cody Cobb gets down to the little details at 90% True.

The cell isn’t simply for target practice, of course. Nor is it merely a bag of M&Ms floating around randomly, as Alex Palazzo takes pains to remind us in his tour of the dynamic networks of the cytoskeleton. How many can you name without peeking? Pencils down — check your answers at The Daily Transcript.

More on the difference between animal and plant cells — specifically, at the levels of their proteins — can be found at Lab Cat‘s Intro to Food Chemistry. A quick summary: Animals have to move, but plants don’t; hence animal proteins have to be strong (load-bearing) whereas plant proteins just have to be compact.

Cells don’t have to be from different kingdoms in order to differ, of course: The cells of a given species can vary wildly, even when those cells are involved in the same physiological process. The quintessential difference of this kind (or at least, the one I’m thinking of, so it seems to epitomize the general case) is the difference between male and female gametes, the technical term for which is anisogamy. Matt MacManes of the Behavioral Ecology Blog covers the evolution of anisogamy and its implication for distinct sexual strategies between the sexes.

Even more sperm are coming at you from Jake Young (man, that sounds dirty) over at Pure Pedantry. In his rousing tale of spermly solidarity, Swim Sperm, Swim Together, Swim Like The Wind!, he reviews evidence that the hooks on rodent sperm heads enable the cells to band together in clumps that can actually swim faster than individual spermatozoa. There’s even video. In Jake’s own words: “Hot.”

One of the things I was confused about when I first learned about human reproduction was about how the sperm get up in there in the first place — for some reason, this is one issue my mom and dad always avoided. Too bad I didn’t have Sandwalk‘s Larry Moran living down the street — judging from his no-punches-pulled biochemical breakdown of how Viagra works, I think he would have happily given me the scoop.

For those of you who love microbes of any description, please visit pretty much any entry at Small Things Considered, a blog devoted to share the author’s appreciation for the width and depth of the microbial activities on this planet. The author is Moselio Schaechter, formerly president of the American Society for Microbiology, so he knows what he’s talking about.

As science is a human endeavor, let’s now explore the sociology and history of science..

What does it take…to be a pioneering scientist? Sunil Laxman at ponders this question at balancing life, where he has compiled a list of traits necessary (if not sufficient) for success in our business. The list includes organization, memory, focus, passion, perseverance, a particular sort of hunger for acknowledgment, and stubbornness. Oh. Is that all?

The history of science is also represented today: Jim Cambias of Science Made Cool has penned a short biography of Sir Francis Bacon, on the occasion of his recent birthday (January 22nd, in case you forgot to send a card). From her article, I learned about Bacon’s contribution to observation-based science as we would recognize it today, as contrasted to the Aristotelian “science” of pure logic and extrapolation. How many teeth are in the mouth of a horse? Go count them. For his tremendous influence over the modern incarnation of our profession, Diane bestows upon Sir Francis yet another title: The Man Who Invented Science.

That’s right: science hasn’t always been the way it is today, and observation (the root of the modern scientific enterprise) hasn’t always tried to be neutral. Before the advent of modern science, there was no hard-and-fast delineation between the observation of nature, the admiration of desirable traits in non-human (or even fictional) beasts, and the artistic depiction of animals. We can see some of the beauty and mystery of early post-Roman European animal art in Martin Rundkvist’s article Migration Period Beast Noodles, now at his hilariously entitled blog Aardvarchaeology.

Whew. That’s a lot of information. But we’re just getting started. On to neurobiology and neuroscience, always a major component of any bioscience carnival:

Dave Munger (whose better half Greta rounds out the husband-and-wife blogging team at Cognitive Daily) discusses right-hemisphere involvement in language processing. Specifically, he addresses the neurological correlates of metaphor and irony, and how the process of detecting these two related forms of non-literal language differs at the level of brain activity. Brains can tell the difference between metaphor and irony — just one more feature allowing us to tell the difference between brains and Alanis Morissette.

Q: What’s the difference between fish and the Bush administration? A: Fish are capable of applying simple logic to dominance-related conflicts. M C, the brains behind Neurophilosophy and the organizer of the neuroscience blog carnival Encephalon, has the story: In a recent study, male African cichlids were shown to be able to figure out their own social status relative to other males by observing fights between those males. Strikingly, the fish could perform transitive inference: If A beats B and B beats C, cichlids can figure out that A beats C even if they’ve never seen that particular cage match happen. Simple, yet impressive. Now, if only we could get a fish into the Oval Office.

From piscine logic we turn to primate illogic (or perhaps it should be “non-logic”?): Ebonmuse of Daylight Atheism surveys some of the psychological studies demonstrating the important yet unsettling fact that apparently neutral information which we are exposed to can at least temporarily alter our behavior in dramatic ways. Find out more about how this works in Priming the Mind.

Primate illogic, especially in its human form, probably deserves a carnival in its own right. Greg Laden, in his article False Pearls, discusses the falsehoods and occasional idiocies that occur when the lay press reports on evolutionary biology…and goes on to explore a much longer, broader list of falsehoods about science and culture in general. His blog name says it all: Evolution…Not Just a Theory Anymore.

There’s more going on upstairs than logic (or lack thereof), of course: The brain (in particular the suprachiasmatic nucleus, or SCN) contains a pacemaker that sets the body’s biological clock. “Biological clock?” you say. “What’s that?” Bora Zivkovic is glad you asked, as he has just laid out a basic definition of a biological clock at his appropriately entitled website A Blog Around the Clock. Bora himself has been making use of every minute and keeping himself up all hours, organizing the Science Blogging Conference and editing The Open Laboratory, an anthology of the best science blog writing from 2006.

And finally: Miscellaneous. .

From time to timely: Our next story gets at the science behind one of the sadder news stories of the past month: At his home on the web Rhosgobel, the wizard and biology instructor Radagast describes the physiology of Death by water intake. Apparently it works more or less the same way regardless of whether you’re doing it to win a Wii.

More on how to mess yourself up with water: David Bradley of ScienceBase reviews the evidence that superheated water from a microwaved coffee cup can cause serious injury. Urban myth or genuine hazard? Read the article and find out.

Water isn’t all bad, though: it’s one of the principal ingredients in beer. At MicrobiologyBytes, AJ Cann tours a brewery and takes us on a tour of the magical transformation called the brewing process. Ah, that’s refreshing…our just reward for making it all the way through this carnival.

Er…almost. I did say up at the top that this blog carnival was devoted to science and medicine, didn’t I? Well then I’d better throw in an entry about medicine: Over at Drugs and Poisons, Captain Drudge reviews drugs that didn’t make it through the FDA. Which ones? Find out in Teh Rejects: Drugs that didn’t make the cut (and no, that’s not a typo; get with it).

The next Tangled Bank will be hosted by Lab Cat on Feb 14. This happens to be a very special date: Not only is it St Valentine’s Day, but it is also International Quirky Alone Day and two days after Charles Darwin‘s 192nd Birthday. So themes are already suggesting themselves to the Cat. Please put on your thinking caps and try to write to fit into these themes or any others that fall on or around that time. (And no, World Sound Healing Day may not be a theme.) Since the Science Blogging Challenge is being held during the next two weeks, Feb 5 -11, Lab Cat will only accept one post per blogger. So send her your best post by 5 pm Feb 13 at cgadavies [at] gmail [dot] com.



  1. Great work, Chris. I especially liked the different sections with different subjects. And, of course, thanks for including my post.

  2. A low methionine diet is provided to people with Homocystinuria (HCU)a herditary disorder of amino acid metabolism which leads to elevated blood levels of methionine. The diet must be low in methionine and so it is a low-protein diet. Vitaflo is a company which produces a low-methionine protein source.

  3. Well written, and chock full of sweet, sweet science reading. Thank you for the link! I kept on scrolling down through oodles of great stuff, hoping and hoping…and then there I was.

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