Saturday, October 31, 2009

Eukaryotic Cells: Size Matters

Every living thing is either a cell or made up of cells. The fact is, every living thing starts life as a single cell. This divides and divides again as the body is constructed cell by cell.

Lewis Thomas in his famous essay “Lives of a Cell said: “ The uniformity of the earth's life, more astonishing than its diversity, is accountable by the high probability that we derived originally from a single cell.”

The cell is the basic building block of biology. It can be all there is to an organism as many creatures are single-celled, including all bacteria. For humans and other multi-celled creatures one cell can be a tiny fraction of our body, yet each and every cell in our bodies carries our entire genetic identity.

The cells of every living thing are unique. They all contain DNA molecules, the molecules of heredity, that are unique to that particular organism and nothing else. That's why my body can detect the cells of other organisms and produce antibodies that mark these alien cells for destruction by my immune system.

It was about two billion years ago I recall, when something very important happened and a new type of cell developed from bacterial cells. This new type of cell we call Eukaryotic.

If you are old enough to remember, at that time there were no plants, no animals, only microscopic critters called bacteria. Lots and lots of bacteria, many different kinds of bacteria: bacteria that ate iron sulphate and produced sulphur and bacteria that ate sulphur and produced hydrogen sulphide, bacteria that produced methane and bacteria that ate methane. And while there was great diversity in the different metabolic processes that bacteria could do there wasn't much diversity in the size and shape of bacteria.

Why would diversity of size and shape matter? Think about what a world of nothing but bacteria would look like... We're talking soup, slime, and ooze, and PU, what a smell. Enough to literally kill you - not a particularly attractive place to raise your kids. And that was what life on Earth was like for maybe three billion years. Until eukaryotic cells came along, that is.

OK, now what does life look like? There's grass, human beings, seaweed, eagles, redwood trees, moss, elephants, sharks and whales. There's microscopic single-celled sea creatures with fantastic glass houses called diatoms, there's turtles and squids and giant clams and periwinkles. Talk about different shapes and sizes and temperments. Better than 60 degrees of slime any day.

Eukaryotic cells, which is what plants, animals, fungi, and diatoms are made of, are bigger and more complex than prokaryotic (bacterial) cells. They have more parts than bacterial cells and much more DNA, 1000 times more. Eukaryotic cells have more membranes that separate and protect all the numerous parts of the cell.

Eukaryotic cells can do more things, they can specialize and link up to other cells forming organs and entire bodies. They have structures and scaffolding that allow the cells to move about like amoeba or link together like bones, skin, nerves and muscles or layers and fibers in a tree. They can secrete shells of calcium carbonates or silicates to surround and protect themselves.

Bacteria just don't have it in themselves to do any of these things. Their masters of the slime universe but what do they do besides consuming and polluting and exchanging genetic calling cards?

Let's not be disrespectful to our elders now. After all it was out of bacteria that the eukaryotic cell evolved. And that's the amazing thing that I'd like you to contemplate, because if we're looking at the “tree of life” then bacteria aren't in the branches and they aren't part of the trunk. They are in the roots.

Charles Darwin conceived of evolution as a tree with successive species as successively smaller branches, as old species went extinct and new species came into being. New species developed by inheriting new characteristics that eventually separated them from the old species.

Darwin saw the mechanism behind the generation of new species as the competitive struggle to survive. But note: the roots of a tree don't compete with each other. They each extract nutrients from the ground and send them into the tree.

Just so, the first eukaryotic cell evolved not from bacterial competition but from bacterial cooperation. That's something that Darwin didn't anticipate. Tune in next week as I describe how this symbiosis came about.

Thursday, October 22, 2009

May the Phosphorous be With You

Phosphorous burns with desire for Oxygen. To prove its love it will even burn under water. Carbon won't do that. So it is Phosphorous that makes Oxygen potential food rather than poison. Without Phosphorous Oxygen would have remained on the dark side of life. A deadly toxin that was killing off it's photosynthetic producers. We should be thankful for this intense love affair between Phosphorous and Oxygen, for without it we wouldn't exist.

Our brains require both sugar molecules and oxygen to remain conscious. Sugar is the product of photosynthesis. Oxygen is also the product of photosynthesis. Consciousness would not be possible without photosynthesis.

Imagine that. We think we are so independent, we can understand things not seen, see things that are no longer there, and predict things that haven't happened, yet we could not do any of these things without the existence of photosynthesizers.

Oxygen has great potential, electrically speaking. And molecules with phosphorous are the key to tapping its potential. Phosphorous is essential to bone formation and basic metabolism in most animals. It forms a part of ATP, otherwise known as Adenosine triphosphate and ADP, or Adenosine diphosphate. These are the molecules that are the workhorses of “ cellular respiration”

And DNA – the molecule of heredity, is non-functional without phosphorus. Maybe it's the power of love between Oxygen and Phosphorous that has really made it possible for life to endure longer than the mountains and the continents

In cellular respiration oxygen atoms are passed from one molecule to the next in a controlled stepwise process that extracts the maximum energy from an oxygen atom and makes it available to the cell for work. It is molecules of ATP and ADP that makes this possible.

Microbiologist Lynn Margulis is the scientist who first brought to our attention the idea that oxygen played a major role in shaping the direction of early evolution.

“Whereas fermentation typically produces two molecules of ATP for every sugar molecule broken down, the respiration of the same sugar molecule utilyzing oxygen can produce as many as thirty-six.”

“With greater quantities of energy available to them cyanobacteria exploded into hundreds of different forms. They spread into greater extremes of the environment, from cold marine waters to hot freshwater springs.”

“Cyanobacteria's continuing air pollution forced other organisms to acquire the ability to use oxygen too. This set off waves of speciation and the creation of elaborate forms and life cycles among them.”

“Growing, mutating and trading genes, some bacteria producing oxygen and others removing it, they maintained the oxygen balance of the entire planet.”

Oxygen has been twenty-one percent of the atmosphere for hundreds of millions of years. This is a sign of the endurance of the balance of nature. It shows that there has been a balance between photosynthesizers and respirers for at least that long.

If oxygen was much higher than 21% then all the plants on land would burn even if they were wet. But if there was much less oxygen than 21% then all animals, including humans would asphyxiate. So as animals that need to breathe and depend on plants for food we are lucky that there is just the right proportion of oxygen in the atmosphere.

How could this be? Some lovers of certainty think that there must be an intelligent designer behind it all. On the other hand, strict Darwinists, like Richard Dawkins can't explain this as anything but a coincidence. Neither considers that new properties can emerge from the ground up. In fact, living things maintain themselves. They sometimes adapt to change by changing the environment.

When too much oxygen was produced its dark side came into play. There was massive extinctions. When new forms of life evolved to take advantage of oxygen, the new form of energy, they quickly expanded in population. A new balance was created between the creatures that produce oxygen and the creatures, like us, that consume it. All this occurred over a time scale of millions of years.

There is a parallel between oxygen and oil. We humans have changed the face of the Earth much faster than any other creature. We discovered coal and oil in the ground and developed technologies like steam, diesel, and internal combustion engines to utilize the new form of energy. This occurred over a few hundred years.

Developing transportation, agricultural and extraction technologies based on machines that run on fossil fuels allowed the human population to grow rapidly because it gave us the ability to get more resources from the ground, to grow more food, and to provide more amenities for ourselves.

The greater population led to the greater utilization of fossil fuels which in turn is leading to a greater output of carbon dioxide. It is carbon dioxide that regulates global temperature and ocean acidity. Increasing the amount of carbon dioxide in the atmosphere along with other stresses on other life forms caused by increases in human population is leading to a new major extinction event.

Many creatures will go extinct. Carbon dioxide will stabilize at some higher level until millions of years from now new life forms evolve to fill the empty niches left behind by the mass extinctions and they draw down the amount of carbon dioxide in the atmosphere once again.

The balance of nature is a metaphor, but it represents a real process. In maintaining itself life uses energy and creates pollution. Pollution is toxic to many organisms and many of them die off. New life forms evolve to take advantage of the pollution creating a balance.

 The global combination of all living creatures may keep the content of oxygen and carbon dioxide in the atmosphere in stable proportions until a new creature, in this case one that adds huge amounts of carbon dioxide, tips the entire system over.

Thursday, October 15, 2009

Oxygen: Saviour

We're the blue planet. That's us. When you're talking planets - blue is associated with life. The blue colour comes from oxygen which makes up a large portion of the weight of a water molecule. And the blue sky also comes from the element oxygen. Oxygen comprises twenty-one percent of our atmosphere.

The colour red also has to do with oxygen. Rust, gets it's red colour because it is oxidized iron. Blood gets it's red colour from the iron and oxygen in hemoglobin. The planet Mars gets it's red colour from oxidized minerals which means that Mars used to have oxygen, probably in the form of water.

Oxygen, with it's all consuming hunger for electrons, has a lot of potential energy. But it is potential for good or ill. Free oxygen has the potential to destroy biological molecules. That's why we use bleach to get out stains. Bleaching is an oxidation process. Oxygen, by grabbing electrons from other elements, weakens covalent bonds in organic molecules leading to their disintegration.

Atmospheric oxygen is the source for ozone, a molecule made up of three oxygen atoms. Ozone is a toxic pollutant, an ingredient in automobile exhaust, but it also exists in the atmosphere where it protects life on Earth from ultraviolet rays. High up in the atmosphere a layer of ozone absorbs the ultraviolet light that would otherwise harm living creatures.

Not only does ultraviolet light harm living things but for time periods of billions of years it has even greater potential for harm. The high energy content of ultraviolet light means that it has the power to break the bonds of water molecules.

Once liberated from water, hydrogen can escape Earth's gravity into space. Without protection, over billions of years, the sun's ultraviolet rays could deplete the oceans of water.

There is evidence on Mars – the famous “Canals” - that there was once water there. Now there is no water and only a thin atmosphere of carbon dioxide. No oxygen in the atmosphere. No ozone to protect against ultraviolet light. No water anymore. And without water there is no life.

No life without water and no water without life. Earth has both. Mars had only one and now has none.

Twenty years ago there was an international treaty signed to protect the ozone layer from a man-made substance called freon. Freon was used as the main coolant in virtually all refrigerators and air conditioners. The problem was that when it was released into the air , which is what happens eventually when all fridges and air conditioners are discarded, it rose high into the atmosphere where it chemically reacting with ozone - destroying it.

Sometime during the 1990's Scientists discovered a “hole” in the Ozone in the southern hemisphere. The Ozone hole has gotten smaller since countries complied with the treaty and stopped manufacturing freon, but not before it took it's toll on Australia, where the incidence of skin cancer has increased considerably.

When bacteria first existed there was no oxygen so there was no ozone to protect living things from ultraviolet rays. It took millions of years for oxygen to reach a high enough percentage for the protective ozone layer to develop. We call that a “Time-lag. In that time bacteria were on their own to develop resistance to these deadly toxins: oxygen and ultraviolet light.

Life is autopoietic, but in maintaining itself life alters the chemistry of the Earth. And when that chemistry changed from zero free oxygen to twenty-one percent free oxygen, life developed in a radical new direction.

From photosynthesis, to – “respiration” – the utilization of oxygen to supply chemical energy to life, oxygen,which was first a pollutant and a toxin, became the basis for all new forms of life.

Tune in next week when we learn who helped Oxygen turn from the “dark side” and transform into a Creator.

Wednesday, October 7, 2009

Why Bacteria Invented Sex

Bacteria are the ultimate survivors. They've been around for three and a half billion years. Longer than the continents, and all the mountain ranges on Earth. In contrast, the animal kingdom has been here only a paltry six hundred million years – one sixth of that time.

Bacteria are the simplest of creatures being as they were the first of all creatures to exist. They are single-celled. They are so small,that they are invisible to the naked eye. But they are not solitary creatures and they live in huge communities that are sometimes visible in the form of coloured blobs of slime, the kind you might see in a petri dish or on rotting food. It's easy to look down on them as disgusting and smelly but without them we would not exist.

It is bacteria, more than any other creature that has altered the face of the Earth – breaking down it's rocks, and adding to it's atmosphere gases such as carbon dioxide - which is crucial to Earth's temperature regulation, methane, and oxygen – without which we animals could not survive.

The technical name for bacterial cells is “Prokaryotes” , which refers to the fact that bacteria don't have a nucleus. All “Eukaryotic cells” - the kind of cells that we have in our bodies – have a nucleus. The nucleus contains all our genetic material wound up like the rubber strands in a golf ball only way tighter – if the DNA in the nucleus of one of your cells was unwound it would stretch to the moon and back several times.

That extra genetic material and the protective membrane means that eukaryotic cells can do more things and make up more complex multicellular organisms like us.

In contrast bacteria don't have as much genetic material. And the genes are looser, not packed as tight because they are not surrounded by a nuclear membrane.

But, bacteria have an advantage over eukaryotic cells. Bacteria are the original party animals. They love to hang out in huge numbers, and they're not so particular that they have to hang out with their own species. They love to mix and when they mingle they can easily exchange genetic material with whoever they please. They have no shame and the whole thing is over in seconds. Which means that bacterial evolution has been fantastically quicker than the evolution of eukaryotes

This bacterial promiscuity is the basis for genetic engineering, by the way. Because it's so easy to get bacteria to take on different genetic material bacteria can be given genes that will manufacture just about anything we want. That kind of stuff is just not possible for eukaryotic cells, thank God.

Technically speaking, “sex” is the exchange of genetic material between different organisms. It isn't necessarily tied to reproduction the way it is for bigger eukaryotic creatures. Bacteria aren't male and female because they pre-date reproductive sex.

It's immaculate conception. Bacteria can split all by themselves, And go on making millions of exact copies of themselves. They don't need love. But they need protection from toxins.

Ultraviolet light coming from the sun is hazardous to life. It can damage biological molecules. It damages DNA molecules,the genetic material for all forms of life. In Microcosmos, Lynn Margulis and Dorion Sagan's book about microbial evolution, the authors hypothesize about this connection: “The pressure to patch up damaged DNA or die induced the development of DNA repair systems. Sometimes instead of using healthy copies of their own genetic material, crowded bacteria borrowed DNA from their neighbours.”

“By adapting to life under harsh light the microcosm had invented sex. Though this first sex was different from the kind of sex animals are involved in, it was sex all the same...”

This was probably their most important means of evolving rapidly in the face of environmental danger. We now know why it was so easy for bacteria to aquire resistance to deadly toxins like anti-biotics. Bacterial sex takes advantage of the natural variety in the population to provide resistance to new toxins.

It's easy enough to say that bacteria should have just kept away from the sun's dangerous rays, and then they would have survived. Because if that's all they ever did they would never have developed photosynthesis and then we wouldn't exist. It's autopoieses. Life maintains itself. And life that survives over time does so because it adapts to Earth's changing environment. In next week's article we will discover how life can also change the odds for itself in a positive direction by altering the environment.