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Phlogiston, bloodletting, and the four humors

Phlogiston – You know, the stuff that’s in stuff. The burny stuff that’s released by fire?Screen Shot 2016-06-09 at 5.20.34 PM.png

Not familiar? Well, that’s because it’s isn’t a thing at all – anymore.

Screen Shot 2016-06-14 at 10.04.59 PMGeorg Ernst Stahl (1659–1734) lived in a complicated time for science. It was just being brought out of the dark ages in many ways and much of what he studied sounds completely foreign and backward to modern ears.

Primarily, Stahl studied the distinction between living and dead material. This vital force was supposedly the anima, or spirit, of a living thing, that gives it ‘agency.’ This was the same force, known as vitalism, that even Louis Pasteur believed was necessary for enzymatic reactions to proceed. Pasteur wasn’t wrong about much, but this one time he fell victim to the prevailing zeitgeist.

Stahl also proposed, in his De motu tonico vitali, that there was a ‘tonic motion’ in things that needed to be permitted for proper circulation of blood. When inflammation or other obstructions occurred, the problem was that this tonic motion was being blocked. One cure for these obstructions was the practice of bloodletting, which addressed the most easily managed of the four humors and was used to treat just about everything.

Although this may sound like a criticism of  Stahl, he was highly regarded as a professor and physician in his time and his work was critical in that it added an experimental element to scientific work. As a testimony to his reputation, he served as physician to both Duke Johann Ernst of Sachsen-Weimar and King Freiderich Wilhelm I of Prussia.

To get to the point here, he proposed the existance of a substance, Phlogiston, that was a component of many things that was released when that thing was burnt. Phlogiston was colorless, odorless, and weightless and it spoke to the question why something, once burnt, could not be burnt again. Ash, for example, was completely deflogistated matter. It contained no more phlogiston and was therefore impervious to further burning.

Additionally, air could fill with phlogiston, becoming saturated. When this happened, the principle of diffusion Screen Shot 2016-06-10 at 4.26.42 PMwould kick in to prevent further diffusion of phlogiston out of a substance. Recall that the basic principle of diffusion is that substances go from regions of high concentration to regions of low concentration (Actually, the random movement of particles will continue unendingly. The apparent result of this movement is that a non-random, concentrated source of particles becomes a random distribution that is effectively uniform. Actually, the particles are still moving, but the random distribution appears stable).

It sets up a simple equation for combustion of any (flamable) thing like this:

Phlogiston(s) + heat + something else –> Phlogiston(g) + ash + energy

Actually, it’s a great hypothesis. It does a servicable job in predicting the behavior of a combustible material in a simple system.  Imagine that phlogiston = carbon. This phlogiston / carbon exists in different forms around us: a waxy hydrocarbon chain in the candle, CO2 in the air, and as the backbone of sugars. However, it fails to recognize a couple of important things too: Mass doesn’t just disappear, the CO2 does have mass, of course, but it’s harder to appreciate. Also, flames don’t necessarily go out because of too much CO2 in the surrounding air, but because of a lack of something else, Oxygen.

However, it does fail to recognize a couple of important aspects. First, mass doesn’t just disappear during combustion. What remains as ash is lighter than the starting material.  CO2 is released and despit that fact that it is harder to appreciate, it does have mass. Second, flames don’t necessarily go out because of too much CO2 in the surrounding air, but because of a lack of something else.

preistly making o2It was by following in Stahl’s footsteps that Joseph Priestley discovered oxygen. Priestley had a knack for studying gasses. He was good at capturing and manipulating them in a controlled way. The figure to the left is an apparatus  of a type common to Priestly’s work, where a substance is heated (e.g., KClO3) to boil off a gas (e.g. O2) in a way that the gas displaces water in an inverted flask so that it may be captured in pure form.

Priestley found that oxygen purified in this way could refresh deflogistated (-perhaps, phlogistated?)26844_lg air allowing it to support combustion once more. It could also rescue an animal from suffocating in a bell jar (something that Preistley did enough that is sounds almost like a hobby of his.) The idea that air was composed of numerous components was a new one, and already Preistley was purifying these substances and demonstrating their requirement for life and for chemical reactions.

So, how does this change the way we needed to think about phlogiston?

It explains that mass doesn’t just disappear when burnt. It goes somewhere, it becomes something else (CO2). It changes the requirement for combustion from one considering the diffusion of matter out of one thing and into the air into a chemical conversion of something into something else.

Instead of the Phlogiston equation, we have the combustion reaction (either proceeding until completion or not):

Screen Shot 2016-06-12 at 8.51.00 PM

Phlogiston might still fit in as carbon if we are insistant, but now we see that something else is required as well: Oxygen.

Flames don’t necessarily go out because of too much Phlogiston (CO2) in the surrounding air, but because of a lack of something else, Oxygen.

The importance of Stahl’s work was not that he was right or wrong, but that Stahl was attempting to bring rigor and experimentation into science. In medicine and chemistry, Stahl believed in taking an empirical approach to his work. Ultimately, this was a stepping stone from the pseudoscience of alchemy to the real science of chemistry.

chemistry_alchemy

:istr makes a nucleophilic attack on chemy, resulting in the leaving group (Al) to leave and precipitate out.

 

 

 

 
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Posted by on June 14, 2016 in Uncategorized

 

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Photosynthesis: Turning CO2 into O2 – or maybe not.

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It’s so simple, right?

“The evolution of photosynthesis remade the Archaean Earth. Before photosynthesis, the air and oceans were anoxic. Now the air is a biological construction, a fifth of which is free molecular oxygen”  – Bendall et al. 2008cIt’s easy to mistakenly think that photosynthesis turns CO2 into O2, people have been doing it for years. In fact, you’d even be remiss not to initially think that it’s the case – it is, after all, a simple conclusion to make and William of Ockham tells us to always start with the simplest ideas.

How could we do this experiment now?

We could  use radiolabeled Oxygen in our CO2 and then look for that same radioactive O2 being produced as a waste from the plant. But if that experiment were done, we’d quickly see that this wasn’t the case. As we will see below, this experiment was eventually what was done and instead of labeled CO2 being produced, the leaves of the plant becoming radio labeled, while only ‘cold’ CO2 was being released. Vexing!

One complication in addressing this idea comes from the very notion of air as being something to begin with. So, what is air? – and what happens (to air) during photosynthesis?

The Dutch scientist and physician, Jan Baptista van Helmont (1579-1644), did some early experiments to understand the nature of photosynthesis. His experiment was to determine where the mass of the plant came from. He suspected that it would be from the soil it was growing in, and did a very simple experiment that refuted this hypothesis. He reasoned that if the mass of the plant came from the soil, then it was a simple conversion that he could observe happening over time as soil was depleted resulting in an equal growth in mass of the plant. His experiment used a potted willow tree planted in 200 lbs of soil. In five years, his 5 lb sprig grew to 169 lbs, using only 2 oz. of soil.

Clearly the mass was coming from somewhere else. Knowing that he watered his tree regularly, he speculated that this was the source of the tree’s growing mass.

Helmont’s experiment did nothing to answer the question directly, but it does introduce a new player into the mix: Water… H2O. There’s Oxygen in water too – another possibility?

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What could possibly have killed this mouse?

In 1771 Joseph Priestley came onto the scene with experiments examining the nature of air as something more than just “nothing.” He noticed that a flame tainted the air with a kind of pollutant that was not amenable to animal life. He called this pollutant, phlogiston. Phlogiston could be produced by burning a candle in a closed container until the candle put itself out. Then, any animal (he used a mouse), that was put in this phlogistated air would quickly die. Yet a sprig of mint could counter this effect and somehow clean up the phlogistated air.

What do we know now?

1. Air is not just ‘nothing.’

2. Air quality (composition) is affected by certain biologic and abiologic processes.

a. Candle flames pollute the air with something toxic to animals (at least mice)

b. A mint sprig is sufficient to neutralize or eliminate this pollutant

Another Dutchman, Ingenhousz determined that de-phlogistation by plants occurs only in the light and required he green parts of plants to accomplish this.

(Much of the above material can be found in the excellent History of Research Page)

How to observe these gasses more easily? Perhaps under water, where gas will appear as bubbles.

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A simple experimental setup to measure photosynthesis

“When a sprig [of Elodea] is placed upside down in a dilute solution of NaHCO3 (which serves as a source of CO2) and illuminated with a flood lamp, oxygen bubbles are soon given off from the cut portion of the stem. ” -from a History of Photosynthesis. Using this device (pictured below) as a readout, F.F. Blackman measured gas production under various conditions by observing the production of bubbles under a number of conditions.

Data from such an experiment looks like this:

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The data

From these data, Blackman concluded that photosynthesis occurred in several stages, the first was a ‘light-limited’ stage that hastened with increasing light intensity, the second did not increase with increasing light intensity and required the work of enzymes (accounting for the effect of heat speeding up the reaction).

The Dutch scientist, van Niel  first suggested the idea of Oxygen gas coming from H2O based on his observations of purple sulfur bacteria converting H2S to S2 and assuming a parallel reaction was occurring in green plants.

CO2 + 2H2S → (CH2O) + H2O + 2S             (observed in purple sulfur bacteria)

CO2 + 2H2O → (CH2O) + H2O + O2             (predicted in green plants)

The final proof of this did not come until Ruben and Kamen were able to use an isotope of Oxygen to trace its route through photosynthesis.

Using algae, given ‘heavy’ oxygen in the form of either water or carbon dioxide, it was found that the isotope given in H2O was invariably that found in the resulting O2. Their experimental procedure is outlined in the diagram as two parallel experiments:

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% 18O FOUND IN
H2O CO2 O2
START 0.85 0.20
FINISH 0.85 0.61* 0.86
START 0.20 0.68
FINISH 0.20 0.57 0.20

So, what we should be saying is not that plants turn carbon dioxide into oxygen, but that plants turn carbon dioxide into sugar, which is precisely why van Helmont was confused by a 169 lb. tree growing from only 2 oz. of soil. He probably never would have believed that all that tree was actually built out of thin air.

 
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Posted by on September 28, 2013 in Uncategorized

 

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More on Oxygen Binding

A reader brought up some interesting points and uncovered some details about Oxygen binding that I wanted to update. You can find the transcript of our discussion in the ‘Getting Oxygen Where It’s Needed’ post below.

What I wasn’t able to post there was a graph of an Oxygen dissociation curve comparing caucasians with Sherpas living at high altitude (+4000m) and those living at sea-level. Surprisingly, the advantage Sherpas have in binding Oxygen at low partial pressure is completely lost at sea level. (see below)

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Oxygen dissociation curve of the blood of (A) Sherpa living at high altitude, (B) Caucasians, (C) Sherpas living at low altitudes.

Presumably,  caucasian blood came from those living at sea level. It would have been great to have data on caucasians (or anyone, else for that matter) living at both high and low altitudes.

For those unfamiliar with data presented in this way, the horizontal axis starts at very low Oxygen concentration on the left and increases to the right. The vertical axis shows the amount of the subjects’ blood binding oxygen at each particular concentration. If the curve rises quickly on the left side, it means that the blood is picking up Oxygen even when it is present at relatively low concentrations in the air.

 

Data from:

Sherpas living permanently at high altitutde: a new pattern of adaptation.

 

 
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Posted by on July 10, 2013 in Uncategorized

 

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Getting Oxygen Where It’s Needed

Oxygen is required by many organisms for survival, luckily it is plentiful in the air, but how does it get into all the tiny cells all over the body?

periodicFirst, Oxygen is a highly electronegative atom. This means that it attracts electrons very well and can pull them away from other molecules. Only one other atom is more electronegative and that’s the most reactive element in the periodic table, Fluorine. Electronegativity becomes useful biologically because electrons are capable to storing energy that can be passed along from one molecule to the next. But , to do this, each molecule must be more electronegative than the last. Therefore, it is not surprising that Oxygen is used as the final electron acceptor in the electron transport chain of cellular respiration. This reaction is required by many organisms, and can be highly beneficial even to some organisms that can live without Oxygen. An electron transport chain is a process by which molecules in a membrane pass en electron down the line using its energy in a controlled way to extract even more energy from sugar.

But how does Oxygen get to the cells that need it? Two molecules account for much of this action, myoglobin and hemoglobin, both illustrated below:

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Hb- hemoglobin, Mb-myoglobin.

What this image also elegantly portrays is the amazing similarity between the molecules that belies their evolutionary relationship.

Each of these molecules is capable of binding Oxygen, but each occurs in a different tissue. ImageHemoglobin is present in Red Blood Cells, making them capable of transporting oxygen from the lungs to other tissues. Myoglobin occurs in these ‘other’ tissues, particularly muscle cells.

Despite the fact that they both bind oxygen, they do not bind it equally well under all conditions. While hemoglobin is just as good at binding Oxygen in high concentration environments (like the lung after inhalation), it is not as good at retaining oxygen when found in less Oxygen-rich environments (such as tissues like muscle).  Under these conditions, myoglobin is much better at binding Oxygen and can pull the molecules away from hemoglobin.

Recently, several groups have published new data about how subtle differences amongst proteins involved in Oxygen transport through blood and muscle result in different binding properties. In turn, the variability in these properties underlie the amazing diversity of lifestyles found in nature, from humans to birds to giant whales capable of holding their breath for up to an hour.

Image That brings us back to the electron transport chain and Oxygen’s electronegativity, where Ois used as a ‘magnet’ for the electron traveling down the pathway from one molecule to the next. As it goes it loses some of its energy, which is converted into a new form that the cell can use. Once the electron, now at a lower energy state, gets to O2, the Oxygen splits  and takes up a Hydrogen ion to form water.

So, electronegativity and binding affinity are the forces that both transport Oxygen through the body and pulls electrons from one molecule to another. Together, the movement of electrons, like that of water through a mill, powers processes that lead to the synthesis of ATP, the energy currency of the cell (see below).

 

electron-transport-chain-cpg-notes

Note the electron traveling down the chain (in pink)

Given what we’ve discussed here, how do you think a baby ever gets to pull the Oxygen away from its mother’s blood / hemoglobin?

 
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Posted by on June 26, 2013 in Uncategorized

 

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