pH in the body and ancient life

[Like New Horizons waking up for its arrival with Pluto, this blog is blinking back to life after a long hiatus.]

Our bodies are not in equilibrium with their surroundings, but energy and matter flux through them in a steady state, maintaining the structures and reactions that give us our form and movement. The human body keeps up a carefully controlled internal environment, watery and full of many dissolved compounds such as phosphate, chloride, and ions. It’s amazing how fundamental and far-reaching this idea of maintaining an internal environment (called homeostasis) is—it’s essential to life as we know it today and raises deep questions about the origins of life.

Some ions, like sodium, potassium, and many metals, come from ingesting common salts. Another type of ion in our body fluids is H+, the nucleus of hydrogen, also known as a proton. It’s an intrinsic component of watery environments and the chemical reactions that take place in those environments; its concentration is denoted by pH, a number scale where lower values signify higher H+ concentration, which means greater acidity.

pH is controlled very sensitively throughout the body because the right acid-base balance is essential for the structures, stabilities, and interactions of proteins, which comprise many structures of our bodies and control chemical reactions. From the scale of whole organ systems down to the scale of subcellular compartments, pH is regulated by robust and sophisticated mechanisms. Incidentally, appreciating this goes a long way toward explaining why the “alkaline diet” and other diets or products claiming to fix acid-base imbalances in our bodies are pseudoscience and wrong.

What are some of these mechanisms? As H+ levels in cells and in fluids outside of cells, including blood and interstitial fluid (tissue fluid), increase as a normal byproduct of metabolism, molecules such as carbonate can buffer, or “soak up”, the extra H+. Carbonate supply in the blood can be adjusted by changing breathing rate, metabolic rates, and by the filtering of carbonic acid (the product of carbonate soaking up H+) in the kidneys. The kidneys adjust H+ levels during other filtering steps, too, which are coupled with pumping sodium and other ions and compounds. In addition to the work done by kidneys, blood, and cell fluids, the body’s fluid volumes, ion concentrations, osmotic pressures, and pH are also being tightly controlled by the liver, endocrine system, and gut. The body keeps all these intertwined rates and processes calibrated constantly and automatically.

The turnover of H+ through normal metabolism is actually a huge quantity that dwarfs what could supposedly (in the pseudoscience claims) come in through diet. Those claims already seem to neglect that the stomach contents are extremely acidic (to facilitate digestion of proteins) and then get balanced by base in the small intestine. The point is that body pH is controlled internally and without interference from your diet. Your arterial blood will stay steady at pH 7.4; venous blood at 7.35.

According to biochemists’ and cell biologists’ best measurements to date, the pH of the bulk fluid in cells is about 6.85 (this, not pH 7, is neutral pH at body temperature). Not just kidney cells but all cells have ion transporter proteins to control the flow of H+. It’s vital for the integrity and function of proteins, for regulating the cell life cycle, and for establishing a chemical environment conducive to metabolism. In particular, the mitochondria, which are the cell’s subcompartments in which most metabolic reactions take place, have a double-membrane structure: very high pH (alkalinity) is maintained in the core of the mitochondria and low pH (acidity) is maintained between the membranes. This difference in H+ concentration is a form of energy and is the essence of metabolism: food energy is used to pump H+ into the intermembrane space, and then the gated flow of H+ back in powers the creation of ATP, which is the cell’s energy currency for many other reactions.


If this is so essential to life as we know it, did early cells also depend on pH control? Did they convert and store energy by coupling chemical reactions with proton pumping? There are good reasons to think they did.

This mechanism of energy transduction, called the chemiosmotic theory, seems to be the best solution to the problem of how to get the energy of certain chemical reactions (eg breaking down sugar) to drive other reactions (eg building proteins). It would actually be very difficult to meet the thermodynamic requirements of all sorts of biological reactions if all you had were a “primordial soup” and energy input from light; compartmentalization and ion (especially H+) flow are needed to get the thermodynamics right. The chemiosmotic solution to this problem is ubiquitous across the domains of life: all organisms on earth use an ATP synthase protein for energy transduction, meaning that they share a common ancestor that performed energy transduction with largely the same proteins and compounds we use today, with an overall architecture like that of the mitochondria described above—alkaline inside, acidic outside.

Oceanographers and geochemists discovered a geochemical analog to this architecture about a decade ago in the Lost City hydrothermal vent system at the Mid-Atlantic Ridge. Strongly alkaline and warm fluid, generated by reactions in the rock below, circulates through intricate pores in 60-meter towers made of calcium carbonate. The alkaline fluids, rich in hydrogen (H2 not H+) and methane, are separated from acidic ocean water by thin inorganic membranes around the pores, a natural setting for the chemiosmotic architecture required for life. The ATP synthase protein could have originated and evolved to take advantage of this geochemistry, with lipid membranes arising soon after to augment the inorganic membranes—it has been shown that hydrocarbons similar to those in our cells’ lipid membranes are formed by the hydrothermal vent chemistry.

It would be poetic to learn that our biology is the legacy of such a place—that our cells mirror the geology and chemistry at the bottom of Earth’s oceans. We would be “of this earth”. 


Cockerill, G., and Reed, S. (2011). Essential Fluid, Electrolyte and pH Homeostasis (Hoboken: Wiley).

Lane, N., Allen, J.F., and Martin, W. (2010). How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays 32, 271–280.

Madshus, I.H. (1988). Regulation of intracellular pH in eukaryotic cells. Biochem J 250, 1–8.

Watch the transit of Venus with us at Johns Hopkins

The Astrobiology Forum and Maryland Space Grant Observatory will host transit of Venus observing at the Bloomberg Center for Physics and Astronomy on the Hopkins Homewood campus, on June 5, 2012.

Event schedule:

5 pm – Short talks in the Schafler Auditorium, including one by Nobel Prize winner Adam Riess on the importance of transits in the history of astronomy and cosmology

6 pm to sunset – Observation of transit using Bloomberg’s Maryland Space Grant Observatory telescope (projecting onto paper)

…and using several personal, smaller telescopes set up on the Bloomberg roof

…and using a live feed from Hawaii (projecting in the Schafler Auditorium)

Contact me at richman[at]pha[dot]jhu[dot]edu if you have questions.

If you would like to bring your own telescope, please contact us at least one week before the event so we can make sure it is ok to use. We will have limited space for telescopes on the roof, so please get in touch with us early. See this for directions to the Bloomberg Center:

Two odd balls

The marvelous line of discoveries made by the Kepler mission continued last week with the announcement (article) of two planets orbiting a hot B subdwarf — a star way past its prime. Both planetary candidates are smaller than the Earth and are on very short orbits which is already exciting on its own.

What makes them special, however, is their unusual history. The authors suggest that these are the remnants (cores) of larger planets that have been immersed inside the star as it expanded to become a Red Giant — the inevitable fate of our own planet. The two probably proceeded into spiraling ever deeper inside the envelope of the gigantic star, losing mass and possibly even driving the evolution of the host itself.

This discovery adds yet another example of the wide variety of environments extrasolar planets can be found in. More importantly, it show how…stubborn…and resourceful planets are in the game of survival. But of course, nothing less is to be expected of the carriers of this most fascinating and robust thing called life.

Pyruvate: a key molecule in metabolism

I was just reading about pyruvate to build my biochemistry literacy (the molecule is relevant to an NMR project I’m helping out on). Wikipedia describes pyruvate, which is the product of breaking down glucose, as a key intersection in several metabolic pathways, aerobic and anaerobic. Being at the heart of the chemistry of metabolism makes a molecule a candidate for being a very old player in biochemistry. Here’s how the Pyruvate article puts the molecule in the context of the origin of life:

Main article: iron-sulfur world theory

Current evolutionary theory on the origin of life posits that the first organisms were anaerobic because the atmosphere of prebiotic Earth was, in theory, almost barren of diatomic oxygen. As such, requisite biochemical materials must have preceded life. In vitro, iron sulfide at sufficient pressure and temperature catalyzes the formation of pyruvate. Thus, argues Günter Wächtershäuser, the mixing of iron-rich crust with hydrothermal vent fluid is suspected of providing the fertile basis for the formation of life.

55 Cnc e: 0.74 day period, 8.57 Mearth, 1.63 Rearth, *11* g/cm^3!

The exoplanet 55 Cnc e may get its period and mass revised downward due to recent observations that support a paper from last year.

In short, we thought it had a period of 2.8 days and a minimum mass of 14 Mearth.  This is from radial velocity measurements.  The paper from last year, however, made the case that this period may be due to aliasing in the data.  If the planet has a period closer to 0.7 days, it could appear to have a 2.8 day period in radial velocity observations.  And if its period is 0.7 days, then there’s a really good chance that it could transit its star.

Which, it turns out it does.  These new observations confirm it has a 0.74 day orbit, and that it’s mass is much lower: 8.5 Mearth.  But because it’s transiting, we can much more accurately determine its radius: 1.63 Rearth.  This gives it an average density of 11 g cm^-3.  For comparison, that makes it twice as dense as the Earth or Mercury.  For further comparison, that iron meteorite we had at our Physics Fair table (just to the left of Veselin’s laptop in the picture) has a density of roughly 7.5 g cm^-3 and weighs 24.5 lbs.  It was roughly the size of a large dog’s head. If it were a chunk of 55 Cnc e, then it would weigh 36 lbs., roughly a third heavier.

Physics Fair 2011 Astrobiology Table. The iron meteorite in question is to the left of the laptop.

Detecting rings around exoplanets

Figure 2 from "Detectability of planetary rings around an extrasolar planet from reflected-light photometry"
Figure 2 from "Detectability of planetary rings around an extrasolar planet from reflected-light photometry"

Just saw this on Could Rings Exist Around Kepler “Warm Saturns”?

It’s a new paper on that follows a couple of older papers that try to pin down the detectability of rings around exoplanets.  In this case, the authors are focusing only on planets and candidate planets detected by Kepler.  Astrobites does a good job of summing up the paper, so I’ll just provide a couple of other quick-read papers and a book reference if you’re interested in learning more.

Transit Detectability of Ring Systems Around Extrasolar Giant Planets
Detectability of planetary rings around an extrasolar planet from reflected-light photometry
Planetary Rings

This latter reference, a book from the Cambridge Planetary Science series, is a good introduction to (Saturn’s) rings suitable for undergraduates.

New 365 Days of Astronomy podcast available!

Part 1 of the abridged version of an interview we did with Dr. Naomi Levin from the Earth & Planetary Science Department is now available on the 365 Days of Astronomy website.  This was a pretty long interview, so the site asked us to break it up into two parts.  The second part comes out on May 3rd.  In the meantime, here is the full interview With Dr. Levin.

Dark Matter And The Habitability of Planets

There’s a lot of weird and silly stuff on, but the idea behind this paper is two too weirds to pass up (that is, two orders of magnitude more “weird” than usual).

Dark Matter And The Habitability of Planets

In many models, dark matter particles can elastically scatter with nuclei in planets, causing those particles to become gravitationally bound. While the energy expected to be released through the subsequent annihilations of dark matter particles in the interior of the Earth is negligibly small (a few megawatts in the most optimistic models), larger planets that reside in regions with higher densities of slow moving dark matter could plausibly capture and annihilate dark matter at a rate high enough to maintain liquid water on their surfaces, even in the absence of additional energy from starlight or other sources. On these rare planets, it may be dark matter rather than light from a host star that makes it possible for life to emerge, evolve, and survive.

I came across this on the always-excellent site.

@ Johns Hopkins University