Tuesday, June 29, 2021

True Protein, Fake Protein

An important question in scientific thinking is, how do you know which measurements to trust? Let me give an example regarding protein. I just posted a video about this.

For photosynthesis, leaves require both chlorophyll (to absorb the light) and an enzyme called rubisco (to absorb the carbon dioxide). All leaves require both, but a leaf down in the shade requires more chlorophyll, and a leaf out in full sun requires more rubisco. If a scientist is interested in measuring the amount of rubisco, it would seem to be easy enough: just measure the amount of carbon dioxide that the leaf absorbs.

But carbon absorption varies from moment to moment, based on temperature, light, and amount of carbon available to the leaf. What many scientists really want to know is, how much carbon absorption capacity does a leaf have? That is, how much has the leaf invested in carbon uptake? We expect leaves in full sunlight conditions to invest more in carbon uptake—that is, to make more rubisco. That’s what we really want to measure.

But measuring the amount of rubisco is difficult and expensive. Is there a simpler, and still valid, way of measuring rubisco indirectly? The measurement has to have construct validity—that is, it must give a realistic idea of how much rubisco is in the leaf.

It turns out that there is such a measurement. Instead of picking rubisco out from among the thousands of proteins in the leaf, just measure the total amount of protein. Total protein content is a valid estimate of rubisco content because, as it turns out, rubisco constitutes one quarter of all the protein in the leaf. It stands out from all the others. Total protein content is a realistic stand-in for rubisco content.

But even measuring protein is a complex process. There is an even simpler way. Most of the nitrogen in a leaf is inside of proteins. There are a few other kinds of nitrogen-containing molecules, such as DNA, but they are very rare in comparison. Thus, measuring the amount of nitrogen in a leaf is a pretty good stand-in for the amount of rubisco.

Measuring the nitrogen content of leaf tissue is fairly simple—not quite simple enough to do in your garage, but it doesn’t require a fancy lab. The Kjeldahl technique was developed over 100 years ago. You put the tissue in strong sulfuric acid, which pretty must blasts the organic molecules to smithereens. One of these smithereens is ammonia. Most of the nitrogen in the leaf ends up in the ammonia, which can be easily measured by titration. Thousands of articles have been published in which investigators measured rubisco in leaves indirectly by the Kjeldahl technique.

But the method is open to manipulation. It is a good measure of protein only if most of the nitrogen in the sample comes from protein. For a leaf, this is a good assumption. For milk, it is a good assumption. That is, unless a milk producer wants to lie about how much protein is in the milk. This is what happened in China in 2008. Milk producers tried to pass off low-protein milk as high-protein milk by adding melamine, which contains nitrogen atoms. Maybe nobody would ever have noticed, but Chinese babies started dying from kidney failure.

I suppose it is possible for botanists to adulterate their leaf tissue with melamine to bump up the estimate of rubisco content. But who would do that? The milk producers thought they could save millions of yuan by adulterating the milk. But, although crime pays, botany doesn’t. The cardinal rule of credibility in science, as in anything else, is to follow the money.

I give other examples of construct validity, and its everyday importance, in my book Scientifically Thinking.

Tuesday, June 15, 2021

Quiet and Close Observation: The Forest Unseen by David George Haskell

The Forest Unseen is a 2012 book by David George Haskell which I have only now gotten around to reading. This blog is your place to go for reviews of old books. Of course, maybe it is new to you, in which case I hope this review encourages you to read the book.

Haskell chose a square meter of area on the floor of an old growth forest in Tennessee. It was not out in the middle of a wilderness; there is no such place in the eastern United States. In fact, it was just downhill from a golf course. But it was as close to undisturbed nature as one could expect to find. Having chosen his spot, Haskell watched it for a year and wrote a book about what he saw.

Anybody could have done what Haskell did. It is true that he used his immense knowledge of nature to not only identify the organisms that he saw, but to draw the numerous connections between these organisms and the larger world of science. But anybody could have seen these things and figured out at least a little about what they were doing. That is the main impact of The Forest Unseen: wonders await us if we just sit quietly and look closely at the natural world. You don’t need a Ph.D. to do this.

The tiny world of fungi and arthropods and wildflowers is an exciting place. Haskell captures the immediacy of this excitement by usually writing in the present tense. You are there with him, seeing what he sees. You can’t just quickly glance at the world of nature. There is a photo on the cover of Haskell looking through a hand lens at the forest floor. Much of the excitement is on a tiny scale. At one point, he had to watch the soil for a half hour before he realized that what he was seeing was a horsehair worm rather than a bit of leaf litter.

Haskell used poetic language masterfully. As numerous reviewers have remarked, his descriptions are some of the most beautiful that have been written. For example, he described chickadees on a cold day as “four pennyweight furnaces” because of the immense amount of heat, relative to their size, that they produce. He referred to the “pheromone love poems” of invertebrates. Tiny mushrooms and other fungi are a “regatta” (he also says “flotilla”) of colors in a decomposing sea of leaf litter. He is the only writer I know, other than Edgar Allan Poe, to use the word tintinnabulation. This poetic language is exactly what his readers, amateur naturalists, need. Scientists would strongly object to some of his terms, for example when he called a fern gametophyte a little lily pad. It looks like one, but the description is misleading—but only misleading if you are taking a botany course. Maybe the university publishers rejected it for this reason. But the major commercial publisher that released it knew that this book was perfect for nature-lovers.

Haskell draws many fascinating connections between what he sees and the larger world of scientific (and other) knowledge. For example, when he describes a snowflake, he explains how the six-sided shape follows inevitably from the chemical characteristics of the water molecules, but also that each snowflake is different because its shape is determined by so many microscale processes, the little tiny differences in temperature, humidity, and wind as each snowflake forms. Thus each snowflake is the product of natural law and historical accident. This is a major scientific concept, but you can see it in a snowflake. He also explained that Johannes Kepler, in his study of snowflakes, drew some incorrect conclusions, but his observations laid the groundwork for scientists a few decades later to discover that everything was made of atoms—something Kepler did not believe.

Haskell even discusses theology when he describes ichneumon wasps, which he saw following a sunfleck on the forest floor. These wasps lay eggs in caterpillars. The eggs hatch, and the grubs eat the caterpillars from the inside. In the nineteenth century, scientists, philosophers, and theologians argued about whether this constituted cruelty that was contrary to the character of the creator God. I’ll bet that very few of Haskell’s readers knew anything about this controversy that directly involved Charles Darwin and his religious friend, the botanist Asa Gray. Wonderful!

I hope that this book continues to inspire all of us, even after we have finished reading it. I sat outside, reading it, and my two-and-a-half-year-old granddaughter saw the picture on the cover. I told her what Haskell was doing, and right away we got out a magnifying glass and started looking closely at the soil of our backyard. It is possible that this little act, especially if we continue to do it, will have changed by granddaughter’s life.

Richard Louv’s books encourage parents to let kids play in the wild—climb trees and all that. Such undirected play is extremely important. But it is also important for people of all ages to stop and watch the immediate environment carefully and quietly, as Haskell did. It may be hard to get kids to do this for very long, but even for the few moments that they will slow down and look will prove very important to their mental development.

Alas, I cannot do what Haskell did. I cannot go and find an undisturbed place and listen to nature. I don’t believe there is any such place in Oklahoma. Every square meter of Oklahoma is filled with human noise, as well as human garbage. One “natural area” near Tulsa is right near an airport where hundreds of amateur pilots fill the sky; you can usually see and hear three at a time. Another is near a quarry which has constant explosions. There is no place where one does not continually hear loud, fast pickup trucks. Down by the Arkansas River in Tulsa, and Lake Texoma on the state’s southern border, there are hundreds of pieces of garbage everywhere. Or, perhaps there is a quiet place without trash. That is what Black Mesa is like, out in the Panhandle, very near New Mexico. But to get there I have to drive almost nine hours (one way). Not only is silent watching of nature a rare gift that Haskell has, and the rest of us could have, but places to do it are even rarer.

Wednesday, June 2, 2021

Garbage in Oklahoma: Another Message from Fluff


Hi. This is Fluff, a female cottonwood tree in Tulsa (she/hers). My thoughts are being passed on to you by a botanist named Stan Rice (he/him/his), who is the only human who stops to talk with me.

Right at the base of my trunk, the City of Tulsa has designated an area in which volunteers can place bags of trash. The volunteers can pick up pieces of garbage from the banks of Joe Creek, which is a drainage ditch near where I am growing, put them into plastic bags, and leave them for the city to pick up.

Joe Creek certainly needs the trash pickup. The banks of the creek are thick with garbage, most of which has floated in from upstream. Stan has estimated the number of pieces of garbage along Joe Creek. It is approximately one thousand pieces of garbage per mile. There is a similar density of garbage along the banks of the Arkansas River.

Stan has made over a hundred estimates of the number of garbage items, easily visible from an automobile, along Oklahoma highways. The number ranges from ten to a thousand, with the average being about a hundred, per mile. This means that, on a typical 200-mile drive through Oklahoma, you are likely to see twenty thousand pieces of garbage. No wonder Oklahoma has such a bad reputation, completely apart from the political news of…don’t get me started. Since Stan made so many estimates, it is not likely that bias (which I discussed in an earlier message) accounts for the results: Stan did not just see a trashy place and count the pieces of garbage. He made a systematic, unbiased survey.

Every once in a while, you will find plastic bags of garbage along the roadside in which volunteers have picked up garbage for the highway department to pick up. Once Stan even saw a man actually picking up garbage. But, from month to month and year to year, such acts seem to make very little difference in the amount of garbage along the road. The reason is the huge number of people who throw litter on the roadsides. While most people do not litter, a very large number of people do, and do so in huge amounts. One of the most common ways is that people pile light garbage in their pickup truck beds and drive along the highway, pretending to not notice that the garbage blows out of the truck bed.

And nearly all this garbage is recyclable. Not that it makes any difference right now; the City of Tulsa recycling facility is shut down due to a fire. Recyclables, put into separate bins by many conscientious homeowners, now gets mixed in with the regular garbage.

But I told Stan about another source of garbage along Joe Creek. Thieves break into houses and grab stuff to take with them. Later, they hide under the bridge and sort through it to find anything of value to them, whether it is costly items or pieces of information they can use for identity theft. They simply dump the remainder into the creek bed. Since I stand by the creek all day and all night, I have seen this happen. In addition, the homeless people gather garbage with which they construct shanties in which to live along the creek. Much of the garbage problem is also a crime problem, and a poverty problem. And a sanitation problem. It is not at all uncommon to see piles of human excrement on the path. Designating a place under a cottonwood tree for volunteers to place bags of trash will not solve these problems.

In addition, I told Stan that it is nearly inevitable that people will start bringing bags of household garbage to leave at this spot. The people who live in apartments have large dumpsters for their garbage, but these dumpsters are frequently overfilled. And then there is the stuff too big for dumpsters. Stan once saw a semi-truck fuel tank left at a recycling depot. I told Stan that the spot at the base of my trunk will quickly become a pile of junk. The location is easily accessible by truck, including pickup trucks that will bring in big pieces of junk to dump them.

The problem is that you Americans get, use, and throw away too much stuff, almost all of it in large packaging. The creek bed in my shadow is thickly studded with Styrofoam fragments. You don’t need all that stuff to be happy. Of course, what would you expect a cottonwood tree to say?

I produce a lot of leaf litter each autumn. But unlike industrial human litter, my leaves decay rapidly and help to build up the soil.

The City of Tulsa sign, beside my trunk, has been out for a couple of days and is already covered with graffiti. The city officials have good intentions, but what can they do against the mass of human filth?

There is so much garbage along the creekside path, including broken glass, that Stan doesn’t like to walk there anymore. But I hope that he comes along to say hello to me once in a while. Until next time, farewell from Fluff, the cottonwood tree.