Photosynthesis (the best thing ever)

Note: This program first aired on May 14, 2016.

Every day this time of year the world gets more and more green. Over night it seems like lawns spring up lushly, and the light green fuzz that covers the deciduous forest asserts itself more strongly every day. All of that green is a result of the growth of the photosynthetic structures of plants, structures that are replacing the ones that died last fall in preparation for the cold and dry winter season, or are growing anew from last year’s seeds. The primary photosynthetic structure for land plants is the leaf, a structure that has a lot of surface area relative to its volume. The surface area is important, as the leaf’s main job is to absorb solar radiation, so surface area equals absorption potential.

You all learned (I hope) in school that plants take carbon dioxide and water and sunlight and make sugar and oxygen gas*. The energy from the sunlight, electromagnetic radiation, gets transformed into chemical energy as stored in the bonds between the carbons and the hydrogens in the glucose molecule that is formed. Something we can’t store gets turned into something we can. It sounds quite simple, and if you look at them chemical equation for this reaction, it even looks quite simple. The reality though is far different, as my biology students this spring learned. Photosynthesis is amazing, and beautiful, and a process that virtually all life depends on, but it is not simple.

Nor should it be. Plants execute a very tricky procedure in fixing the carbon from carbon dioxide in to a glucose molecule. It isn’t easy to transform and store energy. Photosynthesis starts with light and that light energy gets transferred to electrons, electrons that are hanging out on chlorophyll molecules in the chloroplasts of plant leaves. Chlorophyll is a pigment that absorbs light, mostly red and blue light, because those wavelengths are especially good at activating chlorophyll’s electrons. Green light incidentally, is not good at all at exciting chlorophyll’s electrons, so it isn’t absorbed, it is reflected instead, which is why plants look green. Those electrons go through a series of steps in processes imaginatively called photosystems I and II. The light bumps them up to a high energy state, and over the course of photosystem I and II they bump back down, releasing that energy along the way. The end results of photosystems I and II are a whole bunch of temporary energy storage molecules called ATP, and a few electron acceptor molecules. ATP is adenosine triphosphate and is the go to molecule for temporary chemical energy in cells. The phosphate part is what makes it good for holding energy, but is also what makes it only able to do it temporarily, as the phosphate is very unstable. So ATP isn’t a viable long term storage solution, but cells make ATP to then use the energy stored in ATP to do other cellular business. Photosystems I and II are the light dependent parts of photosynthesis, and where the water (a reactant in the reaction) is used and the oxygen (a product of the reaction) gets formed.  The water gets split, and is where the electrons that get moved around ultimately come from, and the oxygen is a byproduct of splitting the water. Notice, no where in this part of photosynthesis have we talked about carbon or glucose. Carbon doesn’t have anything to do with this part.

The other nearly entirely separate part of photosynthesis is the light independent reaction—called the Calvin cycle. This is where all that ATP gets used, and those electron acceptor molecules from the photosystems give their electrons back up. Carbon dioxide gets incorporated into several different intermediate molecules with names like PGA and G3P and RuBP, and after 6 full turns of the Calvin cycle, you end up with enough carbons being fixed to make one glucose molecule. That requires a lot of electrons , and even more ATP. When you study the Calvin cycle you gain an appreciation for just how much energy really goes into making glucose, the energy molecule of life.  And note here, in the Calvin cycle, this is where the carbon comes into play. The carbon dioxide is a reactant in the chemical equation, and the glucose is the product linked to it. The water and oxygen gas that appear right next to the carbon and glucose on paper aren’t really connected to them at all in the plant cell, except for a few electrons.

And what that also means, if you think about it, is that the material of glucose, the carbon that makes up the main backbone of the glucose molecule comes only from the carbon dioxide the plant inhales from the atmosphere. That means that plants make food out of air. The material portion of that food, the actual atoms that make up the sugar we all eat, came out of thin air. And that is something I can’t get over, every time I think about how amazing plants are that is what I come back to, plants make food out of air (specifically the carbon dioxide gas) and oxygen out of water. I only wish I could make that much of a difference in the world.

*Here’s that reaction equation: 6 CO₂ + 6 H₂O → C₆H₁₂O₆ + 6 O₂

References:

Look at any college level biology book and  you will find the basic mechanics of photosynthesis. I used Freeman’s Biological Science 5^th ed in my class this past year https://www.pearsonhighered.com/product/Freeman-Biological-Science-5th-Edition/9780321743671.html

Show your fall colors

Note: This program first aired on October 19, 2013.

This fall if you have been listening, you may have noticed I’ve been talking a lot about how it seems like everything in the world changes its behavior with the seasons, everything in the world except us, myself included. Yet I find that, as the end of October nears, my calendar is actually starting to clear, and for once I am in no rush to fill it. The signs of fall are all around us, flocks of sparrows and shore birds are arriving, resting a day or two as they migrate south for the winter. The golden rod and last of the asters have gone to seed, and the trees of course are turning color and gradually losing their leaves.

Leaves are green in spring and summer due to the photosynthetic pigment chlorophyll. Chlorophyll is the substance that allows plants to capture carbon dioxide and water and use the sun’s energy to recombine them into sugars and oxygen. Chlorophyll is what absorbs the sun’s energy and uses it to move electrons around in this process. Here’s the thing about the sun, its rays have a lot of energy, more than the plant can use, and some of it in wavelengths the plant can’t use. It is the same with us, many of us get a sunburn if we absorb too many of the sun’s rays. We stay in the shade or wear sunscreen to prevent over exposure to the sun, but plants can’t do that. They are, by evolutionary design, required to be in the sun as much as possible. Trees solve this problem by having other substances in their leaves that absorb some of the excess sun, and the harmful ultraviolet rays (the same ones that burn us). They have related substances that act as on board antioxidants, so that when sun damage does occur to the delicate chlorophyll molecule, it can be repaired as soon as possible. These substances are the carotenoids and xanthophylls, a group that includes over 60 different pigments. We are familiar with some of the better known carotenoids, beta carotene, the precursor molecule to Vitamin A is found in dark leafy greens and deep orange vegetables, and lycopene, the molecule found in tomatoes that is reported to offer cardiovascular benefits. We know these molecules to be beneficial to our health, and they play much the same role for the trees. Carotenoids also assist chlorophyll in the capture of light energy in photosynthesis.

When the season changes and the trees stop metabolically maintaining their leaves, as broad leaves are simply an energetic and hydration liability in the winter, the chlorophyll molecule breaks down rapidly. As the chlorophyll goes away, so does the green. The carotenoids don’t break down as fast and their yellow and orange color is revealed as the green chlorophyll decomposes. The yellow and orange were there all along, helping to protect the leaf as it did the important work of capturing and storing energy for the tree.

The red color of many a maple, as well as other trees, is a different group of substances called anthocyanins. They weren’t there all along, like the carotenoids. Anthocyanins appear to only form in the fall, and seem to play a role in helping the tree recapture the any remaining sugars or other nutrients that remain in the leaves before they fall off. It would be a tremendous waste to simply let all of that nutrition fall to the ground. They are powerful antioxidants, and this is at least in part an aspect of their role in the leaf in the fall.

So as the season changes productivity shifts from the external to the internal, resources are drawn in, and what is no longer needed is cast off. In the process we see a different side of the trees around us. The change in season provides an opportunity for us to show our other colors, and show appreciation for the hidden strengths and supports, be they friends, family, community that enable our fullest summer expressions. Enjoy this slow motion dive into fall, and take a moment to look at yourself, and see what hidden colors are now shining out of you.

References:

Fun site about Autumn for kids, from the Wisconsin Department of Natural Resources:
http://dnr.wi.gov/eek/veg/trees/treestruecolor.htm

Really nice info on the chemistry and roles of different leaf pigments, from the University of Georgia School of Forest Resources:
http://warnell.forestry.uga.edu/warnell/service/library/index.php3?docID=144

An authoritative voice, from the University of Illinois Extension service: http://web.extension.illinois.edu/forestry/fall_colors.html

Fall Equinox

Note: This program first aired on September 28, 2013.

It’s fall in Maine. We’ve just passed the autumnal equinox, that point in the Earth’s orbit where, mathematically we can think of the spin axis of the Earth as a tangent line on the orbital ellipse. What this means in practice is everywhere on Earth has a day of 12 hours of daylight, 12 hours of darkness, more or less. After that, at least here at our middling  northern hemisphere latitude, the darkness increases dramatically, making the light sensitive among us go into mourning, and the snow lovers among us optimistic.

I recently received a weather alert on my phone, telling me that frost and freeze advisories had been suspended for northern Maine, as they had officially reached the end of the growing season there. The alert added that frost and freeze warnings would continue in my neck of the woods, coastal Maine, until the official end of the growing season here, noted as October 10, or earlier if we received a hard freeze before then. It made me wonder, what exactly is the growing season? How is it calculated and what does it really mean? How do we know the exact date when it ends?

Here in Maine, midway between the equator and the north pole, there are three components to growing plants, which when we talk about the growing season, is what we mean. We need light, water and we need warm enough temperatures. The light aspect is very predictable, at least in terms of day length. We know to within seconds how much time the sun will be above the horizon on any given day of the year. Temperature, however, is harder to predict. We can look at averages over time; the date of the first frost for a region, averaged over a period of years for example. I suspect that is where the October 10 deadline came from. Water is, for the most part, not a significant issue here, as we usually have plenty of it, with one major exception. In winter, there may be lots of water around, but it is frozen, and thus not available for use by living plants.

Information for farmers about the growing season is all about mitigating the effects of cold temperatures, really, unless you want very powerful grow lights, temperature is the only aspect of the growing season we can control, and only on a small scale at that. When it comes to light, 10 hours seems to be the magic number. Below that amount of daylight, plants can simply not fix enough of the sun’s energy to meet their metabolic needs and grow. They may be able to maintain, but not get any bigger, or reproduce. For that reason winter is a time of dormancy, a holding period that plants simply wait through. Here in Maine, our true non growing season runs from the beginning of November until the beginning of February, based on that magic 10 hours of light. Wild plants obey the same rules as their domesticated cousins, if my observations are correct. Trees lose their leaves, annual grasses and forbs die back to their under ground roots, or over winter as seeds. Even the hardy ever green trees are limited in their abilities to photosynthesize over the dark, cold winter months by low light, cold slowed metabolism, and lack of available liquid water.

We are tropical animals, living in a temperate climate. Even in the tropics there are patterns of growth and rest, wet and dry, exuberance and senescence. As the calendar rolls towards October 10th, the last day they will bother to warn us about a possible frost, or the beginning of November, when the daylight dips below the 10 hour mark and stays there for three whole months, take heart that this time of year plays a valuable role in the yearly cycle of plants, and people. Take this time to show your other, hidden colors; draw in and hunker down. The dark provides our excuse, our opportunity, finally, after the excitement of summer, to simply stay home and regroup. So don’t fight it. Look around you, are the trees in your yard, the weeds in your garden, or the ferns in the woods arguing with the solstice? Neither should you. Happy fall everyone.

References:

Interesting info from Maine’s own Johnny’s Seed company http://www.johnnyseeds.com/t-catalog_extras_vegetables.aspx

A frost free dates for my neck of the woods, from the National Climatic Data Center, featured on a gardening website: http://davesgarden.com/guides/freeze-frost-dates/index.php?q=04676&submit=Go

The Baxter Flora Project

Note: This program first aired on August 24, 2013.

I recently spent a week in Baxter State Park, volunteering for the Baxter State Park Flora project, a multi year study to document and catalog all of the plants found in the park. We were based at Russell Pond, and made daily forays into various habitats, most of them wet, listing every plant we saw, and photographing the best specimens. Working from a hodge podge of older plant surveys, we had a functional list of plants that had been found somewhere in the park at some time.  The high point of any day was finding a plant not on the list, meaning we had found a plant new to the park.

To naturalists, nature geeks, botanists and all those who own dog eared copies of Newcomb’s Wild Flower Guide, this sounds like a terrific way to spend a week, botanizing in bogs, along streams, off trails and even from canoes. To many others though this may sound not so fun. The questions arise: “Who cares what plants grow in Baxter State Park? And why does it matter?”

Why do we name all the plants? Why do we identify everything we see? There are so many levels on which to answer these questions. Naming and identifying has a practical use, recognition and utility have been part of the human condition since before we were human; I can eat this plant, this one is a medicine, this one makes me sick. In the modern scientific tradition of Carl Linneaus and others the names of a plant are significant because they identify not only the plant itself but all its relations as well. Linneaus developed the conventions of naming and the system of taxonomy we still use today. Taxonomy starts with each individual type of plant, a species. Being able to correctly discern one species from another is the primary skill of botanizing, this is not the same as that. Species that are related to each other will share physical characteristics, and that relatedness will be reflected in a shared name at some taxonomic level. Botanists in Linneaus’s day did the hard work of classifying all the plants they found, essentially starting from ground zero. In modern times botanists who are also explorers may get lucky and find a novel species to identify, but everything most of us see around us on a daily basis has already been entered into the annals of science. No, modern botanists spend most of their time second guessing Linneaus, or perhaps more politely put, improving upon him. I said relatedness is based on physical characteristics, and modern technology allows us to assess these characteristics in greater and greater detail, all the way down to the genetic level. DNA analysis is the reason that, as any amateur botanist can tell you, the names of plants keep changing. There are over four type written, single spaced, pages of changes to names in Newcomb’s Wild Flower guide alone. As new genetic similarities and relationships are discovered, names have to change to reflect this. So to the outsider, the scientific names of plants look like an incomprehensible list of latin, to be drily memorized. To the naturalist, nature geek, and botanist plant taxonomy is no less than a vibrant and dynamic expression of our quest to understand evolution and the very nature of life on the planet.

And to the other question: Why does it matter what plants are found in Baxter State Park or anywhere else for that matter? It may come as a surprise to some listeners, but the truth is that not every plant lives everywhere. There is a community of plants that is distinct to Baxter State Park, and if we go in and figure out what comprises that community, we have set a base line from which we can measure change. Botanists today draw on the historical work of botanists from 100 or 200 years ago to document how plant communities respond to variability in environmental conditions and shift over time. So the Baxter plant survey is interesting for us now, but really it lays the ground work for some one else’s research in 100 or 200 years from now. We know that climate is changing in ways that are both predictable and uncertain. We also know that plants will respond to those changes, and we expect plant communities to shift. We can’t know how they shifted unless we know what was there to start. And that’s why we ask the question, and spend hours shin deep in bogs to answer it.

References:

From the Maine Natural History Observatory, the originators of the Baxter Flora Project: http://www.mainenaturalhistory.org/plants-baxter-state-park-project-0

From the University of California Berkley Museum of Paleontology’s terrific educational website, a brief history of Carl Linneaus: http://www.ucmp.berkeley.edu/history/linnaeus.html

Microbiome Part 4: Photosynthesis

Note: This program first aired on Saturday October 6, 2012.

If all the bacteria on Earth were suddenly to vanish, would you care? They are too small to be seen (unless of course, you’ve left something alone in the back of the refrigerator for way way too long), so would you even know it? In fact, some of you, without thinking it through fully, might think it would be a good thing if all the bacteria on earth were to vanish. But, I can say unequivocably that that would be an unmitigated disaster. They have an important job to do here on Earth, many jobs in fact. If all the bacteria on Earth were suddenly to vanish there are many ways we would miss them.

It is often said that bacteria are responsible for much of the oxygen we breathe. This may come as a surprise but many bacteria are indeed photosynthetic. The only source of the free oxygen gas we breathe is photosynthesis, it always has been. Before there was photosynthesis, there was essentially no free oxygen in the atmosphere, and all life (entirely prokaryotic) was anaerobic. The photosynthetic bacteria are the cyanobacteria (popularly known as blue green algae), the green and purple sulfur bacteria, and the purple non-sulfur bacteria.  In terms of oxygen production, the cyanobacteria are the heavy hitters here. The sulfur bacteria by the way, photosynthesize using  the energy of light from the sun to change CO2 into sugar the same way plants do, except that they use hydrogen sulfide instead of water in the chemical reaction. This sounds crazy until you look at the periodic table and see that oxygen and sulfur are in the same column (and thus behave the same way, so the difference between H2O and H2S actually isn’t that great).

We can attribute essentially all of the oxygen we breathe to bacteria if we recognize that the chloroplasts in plant cells—the grass on your lawn, the leaves on the trees around your house, the algae in the ocean—were originally bacteria. This is the theory of endosymbiosis. The original plant was probably a hungry single celled protist that engulfed a cyanobacteria, but then failed to digest it. The bacteria realized it had a good gig there inside the protist, surrounded by a soup of half digested food and all. The protist had a good deal going as well, now housing its own sugar making factory, which is all that chloroplasts do inside a any cell, they absorb light and use that energy to rearrange some commonly found chemicals and store the energy of the sun in the chemical bonds in the sugar they make. The oxygen we breathe is a byproduct, really a waste product, of that process (note, those sulfur bacteria that don’t use water?  They don’t make oxygen either, their waste product is, unsurprisingly, sulfur).

So, directly (through photosynthesizing mats of cyanobacteria), and indirectly (by being responsible for the existence of chloroplasts in plant cells), bacteria save the day and make life  as we know it possible.  And the best part is, that isn’t even half of all the good stuff they do here on Earth, but we’ll have to save that for next time.

References:The University of California Museum of Paleontology has a huge and amazing website devoted to education about evolution and the tree of life, as well as the geologic past:  http://www.ucmp.berkeley.edu/bacteria/bacterialh.html

See for yourself, Oxygen and Sulfur ARE in the same column! http://www.webelements.com/

“From Endotymbiosis to Synthetic Photosynthetic Life”, Andreas Weber and Katherine Osteryoung http://www.plantphysiol.org/content/154/2/593.full (full text available)