Classic ecology in charmingly animated rhyme

Ecomotion Studios has been working with the Ecological Society of America to produce short animated films about some of the most influential papers of modern ecology — they’re calling it “The Animated Foundations of Ecology.” Here’s the film about Robert Paine’s famous experiment in removing the top predator of tidal pool communities, sea stars, which led to dramatically reduced diversity in the other species that shared the pools.

There’s a handful more, including on one of my favorite classic ecology papers, David Simberloff and EO Wilson’s experimental demonstration of the process by which species colonize new habitats. Go check ’em out!


Paine, R. T. 1966. Food web complexity and species diversity. American Naturalist, 65-75. doi: 10.1086/282400.

Simberloff, D. S., & Wilson, E. O. 1969. Experimental zoogeography of islands: the colonization of empty islands. Ecology, 278-296. 10.2307/1934856.

Stomach acid to pathogens: YOU SHALL NOT PASS

Did you know you’re walking around with a little vat of super acid in your belly? Human stomach acid registers 1.5 on the pH scale, making it more acidic than pure lemon juice. And we have to invest energy into not only making the powerful stuff, but then also into making sure we don’t accidentally kill ourselves with it. Why do we do that?

A recent paper by Beasley et al. (in open access PLOS ONE) hypothesizes stomach acid in vertebrates is used to protect our bodies from pathogens – and the more dangerous your diet, the more acidy your acid. “Obligate scavengers”, as defined in this paper, are animals that eat (and only eat) carrion – aka the decaying flesh of dead animals. Delicious? I guess they think so. But sanitary? Definitely not. These species should have the lowest stomach pHs because they need an acid “filter” to kill all the pathogens they’re ingesting with their diet. Herbivores, on the other hand, have plant-based diets with a much lower associated risk for pathogens. These species should have a higher stomach pH because they don’t need a “scorched earth” policy for their digestive tracts.

They further suspect that animals with a phylogenetically close diet might have a higher pathogen risk than animals that eat more phylogenetically distant organisms (and thus lower stomach pHs). The theory here is that eating something related to you means that their pathogens are potentially well-suited to also infect you.

Beasley et al. conducted a literature search and found pH data for 68 species of birds and mammals – which according to them was “far fewer than expected”, given its importance in digestion. They then categorized the species as “obligate scavenger”, “facultative scavenger”, “generalist carnivore”, “omnivore”, “specialist carnivore”, “hindgut herbivore” or “foregut herbivore”. The data show that obligate scavengers have the lowest pHs (average ~1.3) and foregut herbivores have the highest (average ~6.1, all seen in the very cool figure below from their paper). Omnivores and carnivores had the most variable stomach acid levels.

The authors conclude that these results are in line with their expectations – that organisms that eat “high risk” diets have lower stomach pHs. They leave room for the influence of other factors (like how much work it is to break down one’s diet once it’s been ingested) but note that all things being equal, a scavenger’s diet shouldn’t be more difficult to digest as a regular carnivore’s – the only difference being the – er – fact that it’s dead and rotting.

One note: humans have a stomach pH similar to carrion feeders, although we’re technically omnivores. Why would that be? Did we evolve eating a diet that contained more scavenging? (In practical terms, should the Paleo diet include roadkill?) Or does our relatively large number of “fecal-oral pathogens” favor a more acidic stomach? More data on other hominds would be illuminating here.

The paper finally discusses their expectation that when human stomach pH is raised more pathogens are able to become established. Elderly humans have a stomach pH of ~6.6 – a full 5 pH points higher than a healthy adult (wowza!); premature babies have a stomach acid of 4 or higher. Both of these groups suffer more bacterial infections than adults and children. Furthermore, gastric bypass patients have a stomach pH around 6 and may also suffer more bacterial infections. These facts seem to support their main hypothesis – that stomach acid acts as a barrier to pathogens as strong as the risk of infection – but statistical tests remain to be done.

It’s pretty interesting to me to contemplate why animals invest energy into the things that we do. But it seems at this point, stomach acid may be blocking the path of pathogens in the same way Gandalf stopped the Balrog: YOU SHALL NOT PASS. (And it occurs to me – if we stick with this analogy and the caves of Moria are a digestive tract – that would make the rest of the Fellowship that emerges from the caves…turds? Oh geez. I’m sorry, Tolkien…)

The Fellowship does not like being called turds.

Going Viral Against Cancer

We have heard of viruses causing cancer (HPV) or even cancers that act like viruses (devil facial tumor virus).

But now there is a virus that can fight cancer! An engineered herpevirus provokes an immune response against cancer. And after a long hard road, it has been approved to treat certain types of cancer by the FDA!

Read about it over at Nature!

Killer T cells (orange) are recruited to attack malignant cells (mauve) in the viral-based cancer therapy T-VEC.

Killer T cells (orange) are recruited to attack malignant cells (mauve) in the viral-based cancer therapy T-VEC.