Tuesday, May 29, 2012

Interlude: Next Changes

I'm still reading my biology book but I'm not sure whether I'll continue this series, or when I will if I do.

Several things have been happening. The first is that I kept a copy of all the posts that I've written on a flashdrive that I kept in my pocket. Some of it was backed up, but there was much of it that wasn't. Then one day the flashdrive was missing. I still haven't found it and that's put a crimp in my desires to write lots of posts.

More importantly, about halfway through this first year of my latest community venture, I realized that it wasn't working. I'm not happy about this but I don't think that continuing on, as is, makes sense. Neither does starting over. I've done this several times and it hasn't worked. There comes a point where I need to pay attention and decide that it's time to go in a different direction.

In essence, instead of trying to create community (at least for now) I'm looking at trying to join an already functioning community. Part of the reason is to learn from what's working (as well as to perhaps help a community or two work even better) and part of it is to look for others with experience living in community. I will not (and this is a promise to myself) try again to start building a community alone or only with people who haven't done it before. I need to have others with experience to do this with--and, I think the way to find others with experience is to get active in the communities movement.

Unfortunately, this is a challenge, as I'm now sixty and starting over, especially since it will involve traveling and some short term community situations (a year or two, is what I'm thinking). It may involve more than one situation before I find the folks I'm looking for. This isn't exciting and it is risky, but I don't have any better ideas.

What I want to do is to build or live in community in New England, but the kind of community I want (simple, sustainable, communal, and egalitarian) doesn't exist here. What it looks like I'll be doing is leaving New England, hopefully not for too long and not going too, too far.

Meanwhile, my next post will be on what I see as one of the most hopeful developments in building this kind of community: communities of communities.

Quote of the Day: “Life is occupied in both perpetuating itself and in surpassing itself. If all it does is maintain itself, then living is only not dying.” - Simone de Beauvoir

Thursday, May 17, 2012

Biology 101: Photosynthesis

Biologists define us humans, as well as almost all other animals, fungi, and even many bacteria as heterotrophs--which means we can't make our own food. Plants, algae, and cyanobacteria, on the other hand, are defined as autotrophs, or more specifically, photoautotrophs, which means that they make their own food from carbon dioxide, water, and sunlight.

We get our nutrition from plants. Even extreme carnivores who might eat nothing but meat really get their nutrition from plants--it's just that they get it by eating animals who eat plants, or even animals who eat animals who eat plants. This is what's meant by eating lower on the food chain. At the base of that chain is plants (and algae, etc).

In my last post (Cellular Respiration, 5/10/12), I talked about why we need oxygen and ended with the question: 'where does the oxygen come from?' From plants, of course. Plants and algae and cyanobacteria.

It's believed that Earth's original atmosphere was mostly methane, and the first organisms were anaerobic. Cynobacteria came along and began giving off oxygen, which triggered what is sometimes called the 'Great Oxygenation Event' or the 'Oxygen Catastrophe'--where some of the oxygen caused rust and mineral formation, some of the oxygen combined with the methane to form carbon dioxide, and some of the oxygen stayed in free form. This killed off much of the aerobic population and allowed the formation of oxygen breathing creatures.

Plants (etc) keep oxygen in the atmosphere and, as I said, feed us as well. In my last post I gave the formula: C6H12O6 + 6 O2 → 6 CO2 + 6 H2O, which means we take in glucose (and other carbohydrates) and oxygen and break them down into carbon dioxide and water. Photosynthesis allows plants to do the opposite, to take carbon dioxide and water and using the energy from sunlight, make them into glucose and oxygen. The formula for photosynthesis is the reverse: 6 CO2 + 6 H2O → C6H12O6 + 6 O2.

Photosynthesis is a two part operation. First the plant collects light using the 'light-dependent reactions', then it feeds the generated energy into what's called the Calvin cycle or even the 'dark reactions' (because light isn't needed for this).

So here's another question, similar to why do we need oxygen and where does the oxygen come from: Why are plants green?

Light, as you may know, is made of a spectrum of colors. We see black when something absorbs the entire spectrum of light, and we see white when something rejects (or reflects) the full spectrum. The spectrum goes from red to blue and purple--and apparently the colors at either end have the most useful energy for the plants. The plants look green to us because that's what's in the middle and what the plants can't use. The chloroplasts of the plants are filled with pigments that pull in the red and the blue and reflect back green (chlorophyll), as well as pigments that pull in other parts of the spectrum and reflect back yellow (xanthophyll) or orange (carotene)--this is why, when the chlorophyll disappears in the fall, leaves turn yellow or orange.

All of these pigments collect photons from the light and pass them to a 'Reaction Center' which uses the energy to excite electrons from the hydrogen in water (H2O) to send along an electron transport chain (similar to what I talked about in my last post). The protons are sent through various pumps and the oxygen is given off as a waste product. (Yes, this is the oxygen we breathe.) It also uses the energy from the electron transport and the proton powered pumps to create ATP and NADPH--which, as I explained in my last post, are just ways of storing energy.
The Calvin Cycle is sort of like the Krebs cycle in reverse. It takes in carbon dioxide and the reconstituted hydrogen from the electron transport system (and the energy from the ATP and NADPH created by the system) and uses them all to form sugars.

All this happens in the chloroplasts of plants. It also happens in the chloroplasts of algae. Something similar happens in cyanobacteria, but they don't have chloroplasts--in fact, the theory is that cyanobacteria were absorbed by the ancestors of plants and algae and became the chloroplasts.

Again, plants take in carbon dioxide and water and give off oxygen as well as creating sugars, starches, proteins, etc. We breathe in the oxygen and eat the nutrients from plants and breathe out carbon dioxide and pee out water--which is what the plants can use. Photosynthesis and cellular respiration are connected in a cycle that basically keeps the whole planet alive. This is why I think learning this stuff is important. As I heard someone once say, every time you breathe, you should thank a plant.

Quote of the Day: "On a global scale, the collective productivity of the minute chloroplasts is prodigious; it is estimated that photosynthesis makes about 160 billion metric tons of carbohydrates per year... No other chemical process on the planet can match the output of photosynthesis. And no other process is more important than photosynthesis for the welfare of life on Earth." - Neil Campbell and Jane Reece

Thursday, May 10, 2012

Biology 101: Cellular Respiration

Take a deep breath. Now what just happened?

Okay, you took in air and the oxygen in it was absorbed by your lungs and travelled through your bloodstream to your cells. Now what? What do your cells want oxygen for?

Cells (as I put in my last post) are complex organisms, always in motion, always working. That work is powered by the mitochondia (also called 'the powerhouses of the cell'). The process of energy production that they do is called cellular respiration.

Cellular respiration is a process that converts a molecule of sugar (glucose)--or some other energy source: carbohydrate, protein, or fat--and six molecules of oxygen into six molecules of carbon dioxide and six molecules of water. (The chemical formula is C6H12O6 + 6 O2 → 6 CO2 + 6 H2O.) It actually consists of three processes: glycolysis, the citric acid cycle (aka the Krebs cycle), and something called oxidative phosphorylation (aka the electron transport chain).
Glycolysis is the process where glucose (or some other carbohydrate/protein/fat) is broken down into the chemical pyruvate. It takes place in the fluid of the cell (which is called the cytosol). This is done as a first step and is in itself a complex process that creates a small amount of energy in the form of molecules of ATP and NADH. Basically the cell uses these molecules as ways to store energy, sort of like little batteries that can be plugged in and used when energy is needed. Once glycolysis is complete a couple of things can happen.

The most likely (in our bodies, anyway) thing to happen next is that the pyruvate enters the citric acid cycle. This is a really complex circle of reactions that take the pyruvate and break it down into carbon dioxide and water. It takes place in the mitochondria in our cells and whether it happens or not is decided by whether there is oxygen available or not.

If there isn't oxygen available (either because this is happening in a muscle that can't get oxygen quickly enough or because we're talking about yeast or bacteria), alternatively cells can use fermentation, which creates a lot of waste products--lactic acid in the case of your muscles, and which is why they become sore after hard work, as well as what happens from the bacteria in yogurt, and alcohol in the case of yeast, and people drink the waste products.

Assuming that the citric acid cycle happens, a few more energy molecules (ATP, NADH, and FADH2) are created. But the real energy pay-off is from the third part of the respiration process. This is called oxidative phosphorylation which breaks down the hydrogen from the glucose (or whatever) into electrons and protons (which is all hydrogen is, an electron and a proton) and sends the electrons along an electron transport chain in the membrane of the mitochondrion (the singular of mitochonria) and pumps the protons back and forth through the membrane. The whole process of the electrons travelling along the transport system reminds me of electricity (ie, electrons flowing through a wire). And the process creates a whole lot of ATP, which is what powers all the work your cells do.

Now here's what keeps it going. At the end of that transport chain is a molecule of oxygen. Oxygen is, in this case, the electron acceptor--it's what attracts the electrons and keeps them flowing through the transport chain. I think of it almost like a magnet--it strongly attracts the electrons and keeps the whole thing running. When the electrons and protons arrive, they combine back to hydrogen and then combine with the oxygen to form water (H2O). Then you pee out the extra water (and breathe out the carbon dioxide created in the citric acid cycle).

I've quoted a couple of times the line that "you can only live 3 minutes without air, you can live 3 days without water, and you can live 3 weeks without food." (See Air, 5/7/09, and Water, 5/10/09.) We need water to keep everything fluid in our bodies. Here is why we need food and air. We need food for those molecules of glucose (etc) to start the process of cellular respiration. And we need air to supply the oxygen to finish the process of cellular respiration. And, as you can tell by the fact that we can make it three weeks without food, but only three minutes without air, we really need that oxygen.

So, now that you know why we need oxygen, another question is, where does the oxygen come from? That's the topic of my next post.

Quote of the Day: "...When your muscles are doing lots of work, they need lots of ATP. Your cells make ATP by doing cellular respiration. In order to make ATP, you need oxygen to accept electrons at your electron transport chain. So, as you use up your ATP in your muscles, you breathe faster to bring in more oxygen, so you can have more oxygen in you mitochondia to accept more electrons, to make more ATP. This is why you breathe.
"Everything you already knew about breathing, such as bringing oxygen to your lungs and having your red blood cells carry it around your body, is all true, but that's really more about how you get oxygen to your cells, not why your cells need it. The why is all about electron transport chains. Really. And if you're denied oxygen for some reason, you die because no oxygen = no final electron acceptor = no ATP = no cellular work = cells cease to function = death." - René Fester Kratz

Thursday, May 3, 2012

Biology 101: Cells

Cells are the basic unit of biology. All living things (except viruses, and it's debatable whether they're alive) are made of cells--or are cells themselves. Some creatures are unicellular (consisting of one cell--examples are bacteria, amoebas, and diatoms) and others are multicellular (such as plant and animals).

While the cell structure of some unicellular beings (such as bacteria) is fairly simple, the structure of the cells of protozoa, fungi, plants, and animals are very similar and very complex. When I first started learning about cell structure, I had trouble believing all those little things (called organelles) really existed.

The cell is basically a huge chemical factory, constantly busy, constantly in motion. It's filled with these organelles, such as the nucleus, the endoplasmic reticulum, the Golgi apparatus, mitochondria, and, in plants, chloroplasts.

One of the interesting things about these organelles, is where they came from; how did cells become so complex? One theory about some of the organelles--in particular, the mitochondria (the energy source for the cells) and chloroplasts (which contain the chlorophyll in plants)--is that they were originally bacteria that were taken in by cells. The mitochondria and chloroplasts even have their own separate DNA.

Besides organelles, cell have membranes that surround the cell and many of the organelles and, suprisingly (at least to me), they have their own skeleton. The membrane is particularly intriguing since it not only protects the cells (or organelles) but is also very involved in biochemical processes as well as regulating transport of materials across its boundary.

The mitochondria (and particularly the membrane of the mitochondria) and the chloroplasts are involved in two of the most important processes for all life on earth: cellular respiration and photosynthesis. I will talk about these in my next two posts.

I'm still trying to wrap my head around all this. Each of us is a walking conglomerate of millions of these cells. At this minute, they are all in action in your body. Think of it. Who you are is the sum of all these cells--the cells make up your organs and your organs make up the body you call you. All our thoughts are electrical impulses traveling through these cells. It makes me appreciate the Buddhist ideas of 'dependent origination' and having no separate, permanent self.

Quote of the Day: "Cells are the smallest living things and they have all the properties of life, including reproduction, response to environmental signals, a need for energy, and the release of waste products. ...
"All living things are made of cells. All cells are built out of the same materials and function in similar ways, showing the relationship of all life on Earth." - René Fester Kratz