Peer Review on Science Blogs

Pouches, pockets and sacs in the heads, necks and chests of mammals, part VI: guttural pouches, false nostrils and preorbital fossae in horses, tapirs and rhinos [Tetrapod Zoology]

Darren Naish none@example.com — Mon, 06 Dec 2010 19:08:00 -0500

Back to the series on pouches, pockets and sacs (for previous articles see links below). The previous article finished by looking at the guttural pouches present in the Mongolian gazelle Procapra gutturosa. This links us nicely to the select group of mammals - perissodactyls, hyraxes, bats and rodents - that possess air-filled structures (called guttural pouches) located in the upper respiratory tract, pressed up close to the tympanic region at the back of the skull. In this article, I'm only going to deal with perissodactyls: the other groups can wait to later.

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Chiemgau Impact Hypothesis is Dead [Aardvarchaeology]

Martin R none@example.com — Mon, 06 Dec 2010 14:02:11 -0500

Back in August, I blogged about this dodgy paper that had been published in Antiquity. Subsequently, German geologists Robert Darga and Robert Huber and I got together and wrote a rebuttal, which we submitted to Antiquity. It got turned down for a pretty good reason: somebody else wrote a rebuttal featuring original results from the site in question that blows the whole idea of the original paper to bits. That work hasn't been published yet, and the authors of the dodgy paper have been busy promoting their freaky ideas, so the two Roberts and I have decided to publish our paper here on Aard. The title pretty much says it all:

The Site of Phaëton's Chariot Crash is Most Likely Illusory, as the Chiemgau Impact Hypothesis is Not Accepted by Geological Consensus.

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I, For One, Welcome Our Gammaproteobacterial Arsenic-Using Overlords: Why Old School Microbiology Still Matter [Mike the Mad Biologist]

Mike none@example.com — Mon, 06 Dec 2010 10:12:48 -0500

I don't see the need to redescribe the recent paper about the discovery of bacteria that ~~can~~ might replace, in extremis, phosphorus with arsenic, which was overhyped by NASA, was poorly covered by most journalists, and which has compromising methodological problems (for good coverage, read here, here, and here; and snark). But what the paper does demonstrate is the importance of culturing microorganisms, knowledge about which is becoming rapidly lost by younger scientists.

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[guest post: Alex Bradley, PhD] Arsenate-based DNA: a big idea with big holes [We Beasties]

Heather Olins none@example.com — Sun, 05 Dec 2010 14:58:40 -0500

In the wake of the NASA excitement over the new arsenic study, and my promise to give a detailed review of the paper itself, I have recruited a colleague with strong opinons about the work, a solid chemistry and microbiology background, and "Dr." in front of his name to share his analysis. I ~~will be posting~~ have posted my personal and less-technical take on the whole thing ~~soon, so stay tuned~~ as well.
Dr. Alex Bradley uses modern geochemistry and microbiology tools to study the evolution of life and Earth. He has the following to say about the paper.

There's been a lot of hype around the news of GFAJ-1, the microbe claimed to substitute arsenate for phosphate in its DNA. In the midst of all the excitement, one thing has been overlooked:

The claim is almost certainly wrong.

The study published in Science has a number of flaws. In particular, one subtle but critical piece of evidence has been overlooked, and it demonstrates that the DNA in question actually has a phosphate - not an arsenate -backbone.

To understand why, we need to back up a bit. One thing that everyone agrees on is that all things being equal, DNA with an arsenate backbone will hydrolyze quickly in water, while DNA with a phosphate backbone will not. Steve Benner has pointed out that the half-life of the hydrolysis reaction is about 10 minutes.

Wolfe-Simon et al. recognize this, but claim that the bacterium GFAJ-1 must have some unknown biological mechanism to compensate, and this prevents the DNA from falling apart in the cells. Let's assume for now that they are correct. It might be plausible - biology has all kinds of strange tricks and this idea can't be quickly dismissed, even if it seems radical.

But chemistry is much more predictable. Once DNA is out of the cell, pure chemical processes take over, and experiments have demonstrated that hydrolysis of arsenate links is fast. So you could do a simple experiment to test whether DNA had a phosphate or arsenate backbone: just remove DNA from the cell and put it in water for a few minutes. Then examine whether it hydrolyzes or not.

In an accidental way, Wolfe-Simon et al. performed precisely this experiment. The result indicates that the DNA of GFAJ-1 has a phosphate backbone.

The details are these: to isolate DNA, Wolfe-Simon et al. performed a phenol-chloroform extraction. In this technique, after cellular disruption, DNA and other cellular material were dissolved in water, and then the non-DNA material (such as lipids and proteins) were cleaned out of the mixture using phenol and chloroform. This is a pretty common laboratory procedure, and typically would take an hour or two. But here is the key point:

During this whole procedure, the DNA was in water.

Remember, proteins were removed from this mixture. Any cellular machinery that stabilized arsenate-DNA was removed. In the absence of biochemistry, pure chemistry takes over: any arsenate-DNA would have been quickly hydrolyzed in the water, breaking down into fragments of small size. Alternatively, phosphate-DNA would not hydrolyze quickly, and large-sized fragments might be recoverable.

So what size are the fragments of DNA extracted from GFAJ-1? They are large. Figure 1 shows a single strong band. This pattern is a bit unusual for a genomic DNA extract, but the important thing is that the fragments in this band have around 10,000 nucleotides between breaks in the DNA. These long chains of nucleotides did not hydrolyze in water. Yet it is precisely this DNA band that is claimed to have an arsenate backbone.

How can this be?

The answer is: it can't be. If this DNA did not hydrolyze in water during the long extraction process, then it doesn't have an arsenate backbone. It has a phosphate backbone. It is normal DNA.

So what accounts for the claim of arsenic in this DNA? Wolfe-Simon et al. used a technique called nanoSIMS to analyze elemental concentrations of the agarose gel at the location of the DNA band. They determined that the part of the gel containing DNA also contained both arsenic and phosphorus. But what did they really analyze?

The answer is that the nanoSIMS determined the concentration of arsenic in the gel - not specifically in the DNA. Arsenic was present in the gel at the location of the DNA band. But these data do not require that arsenic is part of the DNA, only that it is somehow associated with the DNA. So here is a more plausible explanation: arsenate sticks to stuff. When you grow bacteria in media containing lots of arsenate, cellular material gets covered in arsenate. If you analyze this material chemically, you see a high arsenic background. The arsenic background will remain even after you separate the cellular material into its constituent parts - DNA, lipids, and proteins - because the chemical separation is imperfect. You could imagine a parallel experiment: if you grew bacteria in seawater, a band of DNA extracted from these bacteria might show a high background of sodium and chloride. This would not be very surprising - and it certainly wouldn't imply that the DNA had a chloride backbone.

Wolfe-Simon and her colleagues might quibble with this, and claim that arsenate is not that 'sticky'. This should have been resolved by running a negative control. Grow some bacteria with phosphate-backboned DNA in media containing high concentrations of arsenate. Then extract the DNA, run a gel, and just demonstrate that the gel does not have a high arsenic concentration associated with the DNA band. That would be evidence that my explanation is wrong. But this simple control was not performed in study published in Science.

One objection to my claim might be: if the GFAJ-1 DNA contains phosphate, where did the phosphate come from? The researchers claim that there wasn't much phosphate in their growth media. In fact, they did a very good job of quantifying the background phosphate concentration: it was about 3 micromolar, which was certainly much lower than the arsenate concentrations (by a factor of about 10,000).

But here's the relevant question: Is 3 micromolar phosphate a lot? Or a little? One point of comparison is the Sargasso Sea, where plenty of microbes survive and make normal DNA. Here, the phosphate concentrations are less than 10 nanomolar - or 300 times less phosphate than the "phosphate-free" media in the GFAJ-1 experiment. At such low phosphate concentrations, some bacteria compensate by removing phosphorus from their lipids - but not from their DNA.

So the Sargasso Sea tells us that some bacteria are capable of making DNA at very low phosphate concentrations. The most plausible explanation is that the bacterium GFAJ-1 can make normal DNA at micromolar phosphate concentrations, and that it also has the ability to tolerate very high arsenate concentrations.

There are numerous other aspects of this study that don't make sense. Why would bacteria from Mono Lake need the ability to substitute arsenate for phosphate in their DNA? Yes, arsenic concentrations are high in Mono Lake. But so are phosphate concentrations, which approach 1 millimolar - or 100,000 times higher than in the Sargasso Sea. Mono Lake has more phosphate available than nearly any other environment on Earth. There is no selective pressure for the evolution of what would surely be a massively complex switch in nucleic acid chemistry from phosphate to arsenate. I can only begin to imagine the structural problems that would be imposed on DNA by this switch, which would change bond lengths between nucleotides, and cause secondary problems with transcription, etc. Then there is the radical suggestion that nucleotide chemistry is stable because might occur in a 'non-aqueous' environment. It's not clear how that could work.

Finally, there's a simple experiment that could resolve this debate: analyze the nucleotides directly. Show a mass spectrum of DNA sequences demonstrating that nucleotides contain arsenate instead of phosphate. This is a very simple experiment, and would be quite convincing - but it has not been performed.

This study lacks any real evidence for arsenate-based DNA; unfortunately these exciting claims are very very shaky.

Update (12/6/2010): Dr. Rosie Redfield has a quantitative discussion of why there's plenty of phosphorus here.

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.) PMID: 21127214

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Bilingual Brains: Reading in Hebrew and in English [The Thoughtful Animal]

Jason G. Goldman none@example.com — Sun, 05 Dec 2010 12:02:00 -0500

I've got an article that appeared in this week's Jewish Journal of Greater Los Angeles about recent research from Hadassah University on the neurobiology of bilingual (English-Hebrew) reading.

Is the English-reading brain somehow different from the Hebrew-reading brain? You might not expect any major differences; after all, both languages are alphabetic and are read more or less phonetically by breaking words into their constituent sounds. Compare English and Hebrew to a logographic language like Chinese or Japanese, and the similarity between the alphabetic languages becomes obvious. But new research by Hadassah University researchers Atira Bick and colleagues, published online in October in the Journal of Cognitive Neuroscience, found that despite their similarities, there are some key differences in the way the brain processes English and Hebrew words.

I'm particularly excited about this as its my first in-print article, but also because this is part of my ongoing effort to get science into publications where you wouldn't otherwise expect it (i.e. "push journalism"). It's a particularly tough (but fun) challenge to entice readers into reading an article about science if they're not already seeking it out.

Bick AS, Goelman G, & Frost R (2010). Hebrew Brain vs. English Brain: Language Modulates the Way It Is Processed. Journal of cognitive neuroscience PMID: 20961169

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Close up to Andrias, despite the smell and the teeth [Tetrapod Zoology]

Darren Naish none@example.com — Fri, 03 Dec 2010 07:44:00 -0500

Aww, look at that cute little face, those piggy little, opaque eyes, that wrinkled skin. I just know that you want a little refresher on giant salamanders, so - accompanied with new photos taken at the SMNK in Karlsruhe (by Markus Bühler; thanks) - here's a substantially augmented chunk of text that originally appeared here back in January 2008...

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It's not an arsenic-based life form [Pharyngula]

PZ Myers none@example.com — Thu, 02 Dec 2010 17:28:15 -0500

Oh, great. I get to be the wet blanket.

There's a lot of news going around right now about this NASA press release and paper in Science — before anyone had read the paper, there was some real crazy-eyed speculation out there. I was even sent some rather loony odds from a bookmaker that looked like this:

WHAT WILL NASA ANNOUNCE?

NASA HAS DISCOVERED A LIFE FORM ON MARS +200 33%
DISCOVERED EVIDENCE OF LIFE ON ONE OF SATURNS MOON +110 47%
ANNOUNCES A NEW MODEL FOR THE EXISTENCE OF LIFE -5000 98%
UNVEILS IMAGES OF A RECOVERED ALIEN SPACECRAFT +300 25%
CONFESSES THAT AREA 51 WAS USED FOR THE ALIEN STUDIES +500 16%

[The +/- Indicates the Return on the Wager. The percentage is the likelihood that response will occur. For Example: Betting on the candidate least likely to win would earn the most amount of money, should that happen.]

I think the bookie cleaned up on anyone goofy enough to make a bet on that.

Then the stories calmed down, and instead it was that they had discovered an earthly life form that used a radically different chemistry. I was dubious, even at that. And then I finally got the paper from Science, and I'm sorry to let you all down, but it's none of the above. It's an extremophile bacterium that can be coaxed into substiting arsenic for phosphorus in some of its basic biochemistry. It's perfectly reasonable and interesting work in its own right, but it's not radical, it's not particularly surprising, and it's especially not extraterrestrial. It's the kind of thing that will get a sentence or three in biochemistry textbooks in the future.

Here's the story. Life on earth uses six elements heavily in its chemistry: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur, also known as CHNOPS . There are other elements used in small amounts for specialized functions, too: zinc, for instance, is incorporated as a catalyst in certain enzymes. We also use significant quantities of some ions, specifically of sodium, potassium, calcium, and chloride, for osmotic balance and they also play a role in nervous system function and regulation; calcium, obviously, is heavily used in making the matrix of our skeletons. But for the most part, biochemistry is all about CHNOPS.

Here's part of the periodic table just to remind you of where these atoms are. You should recall from freshman chemistry that the table isn't just an arbitrary arrangement — it actually is ordered by the properties of the elements, and, for instance, atoms in a column exhibit similar properties. There's CHNOPS, and notice, just below phosphorous, there's another atom, arsenic. You'd predict just from looking at the table that arsenic ought to have some chemical similarities to phosphorus, and you'd be right. Arsenic can substitute for phosphorus in many chemical reactions.

This is, in fact, one of the reasons arsenic is toxic. It's similar, but not identical, to phosphorus, and can take its place in chemical reactions fundamental to life, for instance in the glycolytic pathway of basic metabolism. That it's not identical, though, means that it actually gums up the process and brings it to a halt, blocking respiration and killing the cell by starving it of ATP.

Got it? Arsenic already participates in earthly chemistry, badly. It's just off enough from phosphorus to bollix up the biology, so it's generally bad for us to have it around.

What did the NASA paper do? Scientists started out the project with extremophile bacteria from Mono Lake in California. This is not a pleasant place for most living creatures: it's an alkali lake with a pH of close to 10, and it also has high concentrations of arsenic (high being about 200 µM) dissolved in it. The bacteria living there were already adapted to tolerate the presence of arsenic, and the mechanism of that would be really interesting to know…but this work didn't address that.

Next, what they did was culture the bacteria in the lab, and artificially jacked up the arsenic concentration, replacing all the phosphate (PO₄^3-) with arsenate (AsO₄^3-). The cells weren't happy, growing at a much slower rate on arsenate than phosphate, but they still lived and they still grew. These are tough critters.

They also look different in these conditions. Below, the bacteria in (C) were grown on arsenate with no phosphate, while those in (D) grew on phosphate with no arsenate. The arsenate bacteria are bigger, but thin sections through them reveal that they are actually bloated with large vacuoles. What are they doing building up these fluid-filled spaces inside them? We don't know, but it may be because some arsenate-containing molecules are less stable in water than their phosphate analogs, so they're coping by generating internal partitions that exclude water.

What they also found, and this is the cool part, is that they incorporated the arsenate into familiar compounds^*. DNA has a backbone of sugars linked together by phosphate bonds, for instance; in these baceria, some of those phosphates were replaced by arsenate. Some amino acids, serine, tyrosine, and threonine, can be modified by phosphates, and arsenate was substituted there, too. What this tells us is that the machinery of these cells is tolerant enough of the differences between phosphate and arsenate that it can keep on working to some degree no matter which one is present.

So what does it all mean? It means that researchers have found that some earthly bacteria that live in literally poisonous environments are adapted to find the presence of arsenic dramatically less lethal, and that they can even incorporate arsenic into their routine, familiar chemistry.

It doesn't say a lot about evolutionary history, I'm afraid. These are derived forms of bacteria that are adapting to artificially stringent environmental conditions, and they were found in a geologically young lake — so no, this is not the bacterium primeval. This lake also happens to be on Earth, not Saturn, although maybe being in California gives them extra weirdness points, so I don't know that it can even say much about extraterrestrial life. It does say that life can survive in a surprisingly broad range of conditions, but we already knew that.

So it's nice work, a small piece of the story of life, but not quite the earthshaking news the bookmakers were predicting.

^*I've had it pointed out to me that they actually didn't fully demonstrate even this. What they showed was that, in the bacteria raised in arsenates, the proportion of arsenic rose and the proportion of phosphorus fell, which suggests indirectly that there could have been a replacement of the phosphorus by arsenic.

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PCW, Anbar AD, Oremland RS (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science DOI: 10.1126/science.1197258.

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Arsenic-Eating Bacteria May Not Redefine Life, But Could They Be Useful in Oil Spill Cleanup? [Dean's Corner]

Jeff none@example.com — Thu, 02 Dec 2010 15:44:58 -0500

Today's report of Arsenic-eating bacteria published in Science could have some unanticipated benefits: clean up and bioremediation after an oil spill. I may be off base, but here's my reasoning. Caveat: these newly discovered bacteria may not be useful in reducing arsenic levels after an oil spill if they are "fastidious" or too finicky to adapt to a marine environment. But then again, bacteria seem to always surprise us.

NASA Image Gulf Oil Spill
On May 24, 2010, the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite captured this false-color, high-resolution view of the very tip of the Mississippi River Delta. Ribbons and patches of oil that have leaked from the Deepwater Horizon well offshore are silver against the light blue color of the adjacent water. Vegetation is red.

Our oceans are generally resilient in the wake of contamination such as industrial waste, in part due to the highly effective filtration by deep sediments that can "bury" the toxins. Of course, there are limits. The BP Oil Spill is an alarming example. What happens when the ocean's filtration system, a delicate balance of sediments working together, are shut down?

Not surprisingly, wastewater generated from oil production can be quite toxic. An unappealing cocktail of toxins including heavy metals, this water contains high levels of mercury, lead, cadmium and arsenic. Of particular concern is arsenic: such waste can contain up to one hundred thousand times the safe limit in drinking water set by the Environmental Protection Agency. About two liquid ounces of contaminated wastewater consumed by a 150 pound person in one day corresponds to a lethal dose.

Fortunately, oil rig wastewater is not a beverage of choice and sediment filtration in our oceans can effectively "eliminate" the waste or least minimize any leaching.

British scientists recently conducted a study of the effect of crude oil on how ocean sediments can filter out toxic chemicals such as arsenic. They found that arsenic absorption within sediments is significantly reduced when exposed to oil. With the filtration system essentially shut down, arsenic can then be dispersed freely affecting the entire food chain, including us.

Potential dangers of arsenic-contaminated water are reminiscent of Bangladesh, with widespread reports of skin lesions and a higher incidence of cancer. Drinking water in Bangladesh is widely recognized as an environmental and public health nightmare, having poisoned up to 77 million residents, resulting from the widespread use of groundwater. Hand-pumped wells can access water containing extremely high levels of arsenic leached from rocks, not to mention contamination from mining and industrial production plants. Indeed, the World Health Organization has referred to this as "the largest mass poisoning of a population in history".

Lessons learned from Bangladesh should guide us in the event that arsenic-laced waters begin washing ashore in the Gulf. A number of technologies were specifically developed for arsenic removal.

I sincerely hope that relying on such lessons will be unnecessary, and that the study by these British scientists will simply give us one more reason to manage oil spills effectively using the best technologies and minds that this country has to offer.

A version of this article was published originally in OpEdNews.

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NASA's new organism, the meaning of life, and Darwin's Second Theory [Greg Laden's Blog]

Greg Laden none@example.com — Thu, 02 Dec 2010 15:34:17 -0500

In his highly readable book, One Long Argument, Ernst Mayr breaks down the body of thought often referred to as "Darwin's Theory" into five separate and distinct theories, the second of which being "common descent." Darwin's second evolutionary theory (second by Mayr's count, not Darwin's) is really a hypothesis that could be worded this way:

All life on earth descended from a single, original, primordial form that arose eons ago.

The evidence in favor of this hypothesis is strong, but the test of the hypothesis ... the means of disproving it, which is, after all, the point of stating it to begin with ... is difficult to define, but like pornography to a judge, one would know it when one sees it.

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Gratitude: Uniquely Human or Shared with Animals? [The Thoughtful Animal]

Jason G. Goldman none@example.com — Wed, 01 Dec 2010 12:30:00 -0500

"Two chimps had been shut out of their shelter by mistake during a cold rain storm. They were standing dejeted, water streaming down their shivering bodies, when Professor Köhler chanced to pass." Upon opening the door for the two chimps, Dr. James Leuba recounts, "instead of scampering in without more ado, as many a child would have done, each of them delayed entering the warm shelter long enough to throw its arms around his benefactor in a frenzy of satisfaction."

"Chimpanzees," primatologist Frans de Waal points out, "do not normally hug their caretakers for no reason." It's a compelling image, isn't it? The idea that at least some animals might be capable of feeling and communicating gratitude? If we wish to make an argument that some animals possess at least some sort of proto-gratitude, or the cognitive building blocks required for them to feel and express gratitude, we first have to decide what gratitude really means.

Impala are large antelopes native to Africa that groom eachother. Grooming exchanges among African impala are usually unsolicited: one individual grooms the neck of a second individual, and then the second individual returns the favor, and grooms the first individual for an equivalent amoung of time. Hart and Hart suggested that this mutual grooming behavior serves to remove ticks from parts of the body that an individual can't reach itself.

Vampire bats, as you might expect, survive only on blood, and most feed at least once every three days. And while adult vampire bats regularly miss meals, they need not worry, as other individuals will regurgitate blood to feed them.

While the impala and vampire bat examples are interesting, they can be explained by much a simpler mechanism than gratitude: symmetry-based reciprocity. That is, "if members of a species preferentially direct favors to close associates, the distribution of favors will automatically be reciprocal due to the symmetrical nature of association." In other words, the mutual back-scratching of the impala and blood-vomiting of the vampire bat could simply be correlational: individuals who hang out together will tend to engage in reciprocal interactions, but only because they tend to hang out together. These sorts of interactions do not require any sophisticated mental computation for directing repayment only at certain individuals or for keeping track of services received and rendered over time.

Perhaps it seems like your adopted dog or cat pays special attention to you, perhaps in gratitude for his or her rescue? Bonnie and de Waal write:

Even though we have all heard of (and the authors have personal experience with) pets adopted from a miserable stray existence into the comfort of modern homes, it is possible to tell if their greater-than-average appreciation (e.g. tail wagging, purring) of our care and food has anything to do with gratitude. The simpler alternative is that, after prolonged deprivation, there is a constrast effect that lasts a lifetime, making these animals show greater-than-average expressions of pleasure at receiving a full bowl of food. In humans, no one would confuse pleasure with gratitude. On the other hand, if the pleasure is expressed in a personal manner, aimed specifically at the individual who delivers it, are not we getting closer to gratitude?

De Waal observed the common exchange of food for grooming among chimpanzees in order to determine if the trade of food for grooming is simply the result of proximity (as in the impala or vampire bat), or good feelings (as in the adopted domestic dog), or if it is somehow more computationally intensive, such as requiring the ability to direct reciprocity at specific individuals.

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Using the immune system to fight cancer [We Beasties]

Kevin none@example.com — Tue, 30 Nov 2010 13:00:00 -0500

Cancer sucks. I'm sure I don't have to tell you that - it's one of the leading causes of death in developed countries, and our treatment options are pretty thin. Basically, it amounts to cutting out the tumors that can be seen, and then giving a controlled administration of poison in the hopes that the cancer cells die before you do. Don't get me wrong - advances in oncology have saved many lives, but it's no surprise that there's a lot of research happening to find better options.

One promising avenue of study is augmenting the immune system to fight cancer directly. It's known that the immune system already plays a role in protecting us from tumors (immunodeficient mice and humans are more prone to cancer), and we already know it's great at targeted destruction, so it seems like a no-brainer. Indeed, my weekly "immunology research" google news alert almost always has at least one article about a new study curing cancer with the immune system. Case in point:

The answer to curing cancer may lie in the capabilities of the human immune system as opposed to current chemical treatments, according to a new study published by researchers at Dartmouth-Hitchcock Medical Center. The study, published Nov. 15 in Clinical Cancer Research, used tumors found in cancer patients to develop individualized vaccines that induce immune responses to cancers.

This study is pretty great, but there's a caveat.

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Dinosaurs and Other Extinct Saurians: A Historical Perspective, the book [Tetrapod Zoology]

Darren Naish none@example.com — Mon, 29 Nov 2010 07:07:00 -0500

As you'll know if you have your fingers on the throbbing pulse of dinosaur-related publications, the massive, incredibly pricey volume published by the Geological Society of London, and resulting from the 2008 meeting History of Dinosaurs and Other Fossil Saurians, now exists in dead-tree form. It's titled Dinosaurs and Other Extinct Saurians: A Historical Perspective and (in my totally unbiased opinion) is a definite must-see* for anyone interested in the historical side of Mesozoic reptile research. Here are thoughts and comments on some of the contents.

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The toll due to secondhand smoke [Respectful Insolence]

Orac none@example.com — Mon, 29 Nov 2010 03:00:00 -0500

Given that I've dedicated my life to treating cancer and researching the biology of cancer, the ultimate goal being to use that knowledge of cancer biology to develop ever more effective treatments directed at the specific molecular derangements that lead to cancer, it's not surprising that I'm very much anti-tobacco. After all, arguably there is no known behavior that causes more cancer-related deaths than smoking tobacco. It's not just lung cancer, either. Smoking causes a wide variety of cancers, chronic obstructive pulmonary disease (COPD), and cardiovascular disease, all of which result in huge numbers of deaths among smokers each and every year. Clearly, smoking tobacco is so harmful due to a variety of health problems that it can cause that it is rare to find anyone who tries to argue otherwise. Unfortunately, there are estimated to be over 1 billion smokers in the world, and the toll of their addiction includes cancer, lung disease, and heart disease, and it's estimated that during the 20th century over 100 million people worldwide died due to tobacco-related diseases.

While it is clear that smoking tobacco is deadly to those who actually become addicted to it, what has also becoming increasingly clear is that secondhand smoke is also a health hazard. It turns out that I've dealth with this topic before, mostly in the context of dealing with those who would argue against the contention that secondhand cigarette smoke increases the risk of cardiovascular disease (and cardiac events in those with preexisting cardiac disease), chronic lung problems, and lung cancer. For instance, denialists like to try to argue that epidemiology can never demonstrate a relative risk less than two, a contention that no reputable epidemiology organization accepts and a contention that, if accepted, would force us to deny a whole range of health risks, including the relative risk of myocardial infarction due to, for example, Avandia. Indeed, six years ago Tim Lambert ably described the origin of the claim that epidemiology can't confirm a relative risk of a magnitude less than two. Not surprisingly, this claim originated with Philip Morris as a strategy to downplay the risk due to secondhand smoke.

I may have left my blog (mostly) inactive during the recent Thanksgiving holiday weekend, but there was a story describing a study that appeared on the Friday after Thanksgiving and tries to come up with an estimate of the death toll worldwide that can be attributed to secondhand tobacco smoke:

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Weekend Review: Sterile Inflammation [We Beasties]

Kevin none@example.com — Sun, 28 Nov 2010 21:00:00 -0500

If you've ever rolled your ankle (as I have many times), you have a visceral knowledge of inflammation. Clinically, inflammation is the redness, swelling, heat and pain that's associated with injury. From an immunologist's perspective, it's the set of molecular events that get the immune system going. All of the clinical systems associated with inflammation are due to increased vascular permeability, which is just a fancy way of saying leaky blood vessels. Actually, "leaky" implies that it's uncontrolled, when in fact there's a very orchestrated set of events that recruit immune cells and other helpful factors to the site of an injury.

I've talked a lot about inflammation in a lot contexts, but generally, I think of it as being triggered by the activation of a pattern recognition receptor (PRR) in response to a potential pathogen. When you get a cut, some bacteria are bound to get into it and set off the alarms - alarms that are triggered by "pathogen associated molecular patterns" (PAMPs). But in reality, there are a lot of things that trigger inflammation in the absence of bugs - the rolled ankle I mentioned above is a perfect example. Since there are no bugs involved, it's called sterile inflammation:

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Isopachys: worm-like skinks from Thailand and Myanmar [Tetrapod Zoology]

Darren Naish none@example.com — Sat, 27 Nov 2010 10:05:00 -0500

I've been ill, and pressing deadlines for book chapters and other projects have kept me busy. An inability to post stuff on Tet Zoo always frustrates me, as there's just so much Tet Zoo-relevant stuff to get through. And, on that note: I must have said on many occasions that there are whole tetrapod groups, consisting of hundreds or even thousands of species, that I've either never mentioned at all, or have only touched on in passing. I aim to get through as many as I can while the going's good, but there are just so many constraints and distractions. Anyway...

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The Social Cognition of Your Thanksgiving Dinner [The Thoughtful Animal]

Jason G. Goldman none@example.com — Wed, 24 Nov 2010 14:53:37 -0500

Even still, we tend to think of the turkey as a fairly unintelligent bird, skilled at little more than waddling around, emitting the occasional "gobble," and frying up golden-brown-and-delicious. But...what if I told you that the domestic turkey (Meleagris gallopavo) could actually be quite clever, at least when it comes to social cognition? Apocryphal or not, Ben Franklin may have been on to something with the "Bird of Courage."

Head on over to Scientific American to catch my latest contribution to their Guest Blog: Turkey talk: The social cognition of your Thanksgiving dinner

Buchwalder, T. (2003). A brief report on aggressive interactions within and between groups of domestic turkeys (Meleagris gallopavo) Applied Animal Behaviour Science, 84 (1), 75-80 DOI: 10.1016/S0168-1591(03)00149-7

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On Definitions: They Matter [We Beasties]

Kevin none@example.com — Mon, 22 Nov 2010 13:00:00 -0500

Most of my favorite long-standing discussions with friends and family tend to resolve around definitions. My good friend Paul and I have had hours upon hours of discussion about the nature of the universe - he calls his perception of the order of the universe "god," and I call myself an atheist (interestingly, that picture was taken by Paul), though in practical terms I don't think our beliefs are really that far apart. He says his definition allows him to engage with religious people, I say it just causes confusion.

In my first year of graduate school, I used to argue endlessly with my class-mates that viruses are alive. I did this not because I think viruses are alive (though I do), but because I think it's facinating the way we humans give an arbitrary definition of a word, "life," and then dogmatically exclude anything that doesn't fit into that definition. The real answer isn't that simple, viruses aren't the same as cellular organisms, but they're also not the same as unambiguously non-living things. Richard Dawkins (from A Devil's Chaplain):

This way of thinking characterises what I want to call the discontinuous mind. We would all agree that a six-foot woman is tall, and a five-foot woman is not. Words like 'tall' and 'short' tempt us to force the world into qualitative classes, but this doesn't mean that the world really is discontinuously distributed. Were you to tell me that a woman is five feet nine inches tall, and ask me to decide whether she should therefore be called tall or not, I'd shrug and say 'She's five foot nine, doesn't that tell you what you need to know?' But the discontinuous mind, to caricature it a little, would go to court (probably at great expense) to decide whether the woman was tall or short.

The use of language forces us to place boundaries on things. In order for words to have meaning, they must necessarily encompass some concepts and not others. Most of the time, it doesn't really matter - arguments about whether or not a couch is a chair or a machine gun is a robot can be entertaining, but not necessarily important or enlightening.

But this is a post about immunology. Enter NK cells:
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Pouches, pockets and sacs in the heads, necks and chests of mammals, part V: palatal (and other) pouches in camels and gazelles [Tetrapod Zoology]

Darren Naish none@example.com — Mon, 22 Nov 2010 05:42:00 -0500

Everybody knows that camels are weird. As you'll know if you've been keeping an eye on SV-POW! lately, we've recently been quite taken with their necks. But it's not just camel's necks that are weird. Here, we embark on another look at the sometimes bizarre pouches, pockets and sacs present in certain mammals, most of which are outgrowths of the respiratory system.

Relatively little known is that (some) camels possess an inflatable diverticulum on the palate, termed the dhula, dulaa, gulah, goola, qulla or pálu, and known technically as the vesica palatina or palatine diverticulum. It seems unique to the Dromedary Camelus dromedarius (where it's present in both adult males and females): people have looked for it in the Bactrian camel and Llama and have shown it to be absent [screen-captures above shows inflated dhula in an Australian dromedary, as seen in a memorable scene from BBC's Wild Down Under, © BBC].
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