Tag Archives: nature

Evolving photosynthesis


All photosynthetic machinery seems to have evolved from a single common ancestor, a bacterium. Nature has learned that when something works, one keeps it and uses it over and over.


Trees may now take less water from the ground and need less water to grow because of rising carbon dioxide levels in the air. Far out idea? Perhaps; but not quite. How might a changing climate change forests and the interwoven ecological systems that depend on them? Are such changes common during the history of the earth? The answer is yes.


Let’s suppose…


Imagine forests were to transport less water up to their leaves or needles while carbon dioxide in the atmosphere is rising.  With enough time, trees might evolve resilience to drought and higher temperatures. But there’s a downside.  The huge volume of water that trees pull from the ground enters the atmosphere as gas, condenses and returns to us as rain. Might trees transporting less water eventually lead to less rainfall and more desertification?


Studies suggest trees can partly close the pores in their leaves  (stomates) and still take in more carbon dioxide from the atmosphere than they did just ten years ago. Remember stomates control how much water passes to the atmosphere as well as how much carbon dioxide enters the leaves during photosynthesis.


Photosynthesis now and then


The photosynthesis we learn about in school is not the only photosynthesis on the planet. Photosynthesis is what pulls water through plants. In its current form, photosynthesis in higher plants converts energy from the sun (light) into chemical energy trapped in carbohydrates that plants and animals use for food. Photosynthesis in green plants today requires water, carbon dioxide and light. Photosynthesis also releases oxygen. But it didn’t always work like this. There was no atmospheric oxygen in the very beginning. As with many natural systems exposed to a changing planet over billions of years, photosynthesis has evolved along with the earth.


The evolution of photosynthesis began with the origins of life, and changed as the earth’s climate changed. Photosynthesis evolved continually along a complex crooked path from primitive Cyanobacteria or blue green algae into the many types of photosynthetic systems we have today.


The first Cyanobacteria


Earth formed about four and a half billion years ago. It took about a billion years for the first photosynthetic bacteria to form. Starting three and a half billion years ago, these bacteria absorbed low energy infra red light and trapped this energy in molecules that contained sulfur and not oxygen. The pigments in these bacteria that trapped the energy of red light are the simplest predecessors to today’s chlorophyll.


After another billion years, about two and a half billion years ago, the atmosphere changed. Rocks from back then show evidence that the earth now had oxygen in its atmosphere. Blue green cyanobacteria were now well developed, employing a mixture of pigments including several chlorophylls to capture light.


Cyanobacteria live in water and manufacture their own food. Although cyanobacteria are small and usually unicellular, many grow in colonies large enough to see. Cyanobacteria more than three and a half billion years old form one of the largest and most important groups of bacteria.


The first hard evidence for how early photosynthesis worked comes from stromatolites in warm shallow seas in western Australia. By trapping and cementing sand grains together, slimy films of microorganisms form these layered rocky masses that look like cauliflowers. From these structures we see how cyanobacteria live and work. (Fig)


To enjoy the beauties of cyanobacteria, (also called blue-green algae) you only have to look at that moist black film along the bottom of your shower curtain. (Fig) These primitive beauties are very old and need only moisture and very little light to live and reproduce. They have been found in fossil remains from more than 3.5 billion years ago.


Brown algae


The next changes came when red and brown marine algae (kelp and seaweed) evolved several new forms of chlorophyll about one and a half billion years ago. Brown algae could now use shorter, more energetic wavelengths of light than Cyanobacteria. (Remember, the shorter blue violet wavelengths of light carry more energy than the longer red-infra red wavelengths.) As chlorophyll evolved and became more complicated, more and more energy could be extracted from sunlight.


Green algae evolved in shallow water where green pigments can trap more energy than red or brown algae. In today’s tide pools on rocky coasts you can find red, brown and green algae.


About half a billion years ago mosses and liverworts evolved from green algae and invaded the land. Lacking vascular tissues as well as stems and roots, these simpler plants cannot grow tall. Only 0.4 billion years ago did we get ferns, grasses, cacti and trees. All these plants contain vascular tissues that provide support and let them rise above the earth and capture more light.




The earliest photosynthetic organisms did not make oxygen as a byproduct. The photosynthetic machinery and systems for capturing light and using its energy to build molecules has changed multiple times. Once bacteria learned how to capture light and make carbohydrates, new soon-to-be plant cells acquired these photosynthetic bacteria. First these bacteria inside cells evolved to become symbiotic inside the cells of green plants. These symbiotic bacteria grew more dependent on their hosts and evolved into our contemporary chloroplasts. Today’s chloroplasts are organelles derived from bacteria in the green parts of all plants.


This ability to produce oxygen, which thenaccumulated in the atmosphere, forever changed the Earth and permitted advanced life to develop and use oxygen efficiently during respiration to break down food and carbohydrates to get the energy to grow and reproduce.

A new study presents evidence that life on earth is four times as old as we thought.

2.2 billion years old, and extends almost half way back to earth’s formation. Fossils the size

of match heads, ( Diskagama) neither plants nor animals, resemble a modern soil organism (

Geosiphon) a fungus filled with cyanobacteria. Evidence in Sept issue of journal: Precambrian Research.

Published July 23, 2013



Zoonoses in West Marin?


A zoonosis  (plural zoonoses) is a pathogen that passes from animals to humans or from humans to animals. A vector or agent such as a tick or a mosquito can transport a zoonosis betweeh hosts. The vector uses one host to complete part of its own life cycle. One zoonosis we have in West Marin is Lyme disease; another is West Nile virus; another is rabies. Humans can get animal diseases when they’re bitten or scratched, or contact an animal’s waste, saliva or dander. Of greatest concern are young children whose immune systems are still developing, and some infections that might mildly sicken an adult can be more serious for children.


Pathogens from animals


What is a pathogen? A pathogen is a “germ.” Germ is a common word for a microorganism, usually a virus or a bacterium or a fungus. Pathogens cause disease. Of the almost fifteen hundred pathogens that infect people, over sixty percent, or around nine hundred, are zoonoses.  Why do such a large percentage of human diseases involve animals? Many of our diseases began as zoonotic infections, and once a part of humanity, they evolved with us. We have good evidence that measles, smallpox, HIV and diphtheria appeared first in animals, and that these pathogens have evolved their behavior in us.


Human history is repeated infections


Our earliest ancestors were hunter-gatherers who lived in small bands of a hundred people or so. They contacted many animals.  Each group wandered following food and weather, but because groups were so widely separated, people rarely came together.


When a pathogen jumps from an animal to people, and the group has no immunity, sick people can infect one another until the whole group is infected, and many people can die. You remember that many Native Americans died after early contact with Europeans. If people recover from their illness, their immune systems now carry records of prior exposure to the pathogen, so folks can make antibodies when next exposed and can now resist the next infection more easily.


Life as a pathogen


For a new zoonosis pathogen to survive and spread a disease, the pathogen must live long enough in a person to be able to infect that person and for that person to infect someone else.  It does a pathogen no good if it kills its new host too soon, so it cannot pass itself on.


Pathogens can also “live” outside people in an animal “reservoir” and remain ready to infect a person when the opportunity arises. Bats, foxes, raccoons and other carnivores carry rabies and act asreservoirs from which humans can contract rabies. Our West Marin examples are again Lyme disease, rabies and West Nile virus. If one of us gets infected with rabies, it is unlikely that that person will bite someone else. It is improbable that a person with Lyme disease will newly infect a deer tick that will transmit the Lyme disease to someone else.


Exposing the culprits


Often, susceptible people without prior contact with a new pathogen die without transmitting the pathogen to others. A new illness may kill many people, then burn itself out, and thus not become an epidemic.  Unexplained deaths in outlying areas make new zoonoses difficult to identify.


New zoonoses usually begin in rural areas where people live closely with vectors, but not always. West Nile virus carried by a mosquito from Africa came to New York in 1999, and because people travel widely and fast, West Nile moved throughout the country causing much new illness in 2002, just three years after arriving in the US. When a new zoonosis enters a human population, at first we don’t know what is making people sick. Mild and geographically dispersed cases go undetected, and doctors cannot suspect an illness they don’t know. After immunities develop, the frequency of new infections drops.


When a new disease appears, scientists at the Center for Disease control must ask: How do we know what this is? What do we do? Where does the bug come from? Where does it live in nature? Why does it show up now? How are people getting exposed? Is the pathogen evolving rapidly when it jumps to us? How long should the outbreak last? How far will the outbreak spread? As we know, animal to person infections occur frequently from bats, monkeys, chickens, ducks and hogs; pathogens can spill over to humans one time, or a spillover can happen over and over.


How do we catch new zoonoses?


The most efficient way is for people to increase their contact with wildlife and animals. When we destroy wilderness and settle in new places we expose ourselves to new infections. When wild or infected animals invade our towns we can get what they carry.  Raccoons enter houses through pet doors and can eat from our kitchens. Recall bird flu. Bird flu or SARS erupted in early 2003 but had ended by summer.


SARS (Severe Acute Respiratory Syndrome) emerged from the live animal markets in China’s Guangdon Province and made over eight thousand people ill, killing almost eight hundred. Health workers initially thought SARS came from civet cats sold live to people who killed them and ate them. Health workers killed many civet cats, but later traced the virus to horseshoe bats that had transferred the virus to civets.


We now have a new bird flu to contend with. Will H7N9 evolve to leap from not only birds to people, but from person to person? The international community has to cooperate each time a new infection appears to prevent it becoming a pandemic. When a disease springs up in geographically separated places, we must think of a stable reservoir or one that is easily transported, or that in the SARS case has wings.




Bats can transmit disease (vampires) directly to people or to other animals that can infect humans. But there are almost fifteen hundred species of bats with uniquely different lives. All reservoirs have unique ecologies. If animals are acting as the reservoir, how does this happen? Does an animal carrying the pathogen get sick? Do animals infect people by coughing? Or do they pass the pathogen in urine or feces, and infect people who clean up after them? Testing of a suspected animal may identify a species that can carry the pathogen, but will not immediately explain why the pathogen has suddenly entered people. The most common way that wildlife viruses make the jump into people is that we do things that bring our animals and ourselves into closer contact with wildlife.


The sleuths at the CDC have interesting work, and for me anyway, I’d like the challenge.

Published July 11, 2013


We Will, We Will Shock You!

627.1627.2In Tomales Bay we have an electric ray, Torpedo californica, whose specialty is what early scientists called animal electricity. If you find a Torpedo on the beach, don’t pick it up. Some of Torpedo’s muscles are electric organs that, like car batteries, hold an electrical charge. They’re primed to shock you. Electric fishes and eels use electricity to find prey in muddy water, to stun it before they eat it, and for defense

Small to large Torpedo rays look like this: (fig 1)

Most of the body looks like a flat, soft, flabby, rounded bluish, gray or black disc with both eyes on the topside and two wings. Torpedo’s snout is short. Its body has two dorsal fins, a short stout tail and a large tail fin. Torpedo lives on sandy bottoms, near rocky reefs, and in kelp beds to depths of 3 to 30 meters. Torpedo moves slowly as he’s the toughest guy around. He can discharge more than fifty volts at a pop. The wings of Torpedo contain layers of modified muscle cells stacked like batteries in a flashlight. Each cell, called an electrocyte or an electroplax, works like a very small battery. Stacks of these cells in Torpedo discharge together to make the electricity you can feel when you grasp him.


If an object like your hand is in the water and grasps the top and bottom of Torpedo your fingers complete the circuit, and current flows through your hand. The current is large enough to penetrate your skin and excite nerves and muscles in your hand. If the object is a hand or a small fish, and is large enough, it distorts the electric voltage around the body of Torpedo, so now Torpedo can sense your presence. He thinks you are prey, and ZAP.  Electric organs are useful for fishes living in murky water where vision is impaired. Eectric organs have evolved in several groups of fishes independently of each other.

Animal Electricity

In the mid-1780s, the Italian physician Luigi Galvani connected the nerves of a recently killed frog to a long metal wire and pointed the wire at the sky in a thunderstorm. With each lightning flash the frog’s legs twitched as if it were still alive. Galvani showed that intact muscle tissue responds to electricity. He reasoned the muscle twitch resembled the living frog’s movements, and that muscles and nerves use electricity to move the frog.


After touching exposed nerves to muscles or nerves to nerves, Galvani showed that the electricity came from the muscles and nerves themselves, because he got the same muscle contractions he got from lightening. He saw that no metals or external sources of electricity were needed for contractions.


Galvani inspired fellow Italian scientist Alessandro Volta, but he could not convince him. Volta in 1800 invented the first electrical battery—the voltaic pile. He soaked pieces of cardboard in brine then piled them up between disks of various metals. Volta was not convinced that the animal electricity came from the muscle tissue or nerve fibers themselves, but that animals reacted to electricity produced by two different metals used somewhere inside the frog that connected their nerves and muscles. Did Volta’s piles make him a biased observer? To see who was right and how Torpedo creates a battery and can shock you, we need to understand some basic electricity: charge separation, voltage, current and simple series circuits.

[Fig 2 ]

Charge separation and voltage


In nature, free electric charges of opposite sign, + and –, try to keep as close together as they can. Like an old couple, + and — move around holding on tightly to each other. Like an old couple, the closer the charges are to each other the more they hold on. Like an old couple, when you pull a pair apart they strain to stick together, but the further away one partner gets from the other, the less attraction each partner feels for the old charge left behind. How hard they pull on each other weakens with increased distance between them. Voltage measures the electrical force pulling separated charges together.


Voltage is strong if the charges are closely separated, but the voltage is weaker if the separated charges are held farther apart. Torpedo uses cellular energy from metabolism to separate ions. Potassium chloride (used as a salt substitute) breaks down to K+ and Cl—and table salt (what makes seawater salty) is Na+ and Cl—or sodium chloride. Each electrocyte cell keeps these ions separated by the thickness of the cell membrane. Torpedo uses both these salts in forming electrical potentials.

Stacked Electrocytes in series circuits form Torpedo’s batteries.

Remember those old Christmas tree lights: A string of bulbs with a plug for the wall socket? Do you also recall that when a single bulb went out, the whole line of bulbs went out? If you know how this string works, you know about series circuits. As an example, consider a very simple circuit consisting of four light bulbs and one battery.  (The battery and the wall socket are just sources of voltage or separated charges). If the wire joins the positive end of the battery to one bulb, to the next bulb, to the next bulb, to the next bulb, then back to the negative end of the battery, in one continuous loop, the bulbs are joined in a series circuit. Electricity passes along the string as current. Electrical current is like a river. It flows from a high point to a low point. With the four light bulbs connected in series, the same current runs through all of them, but the voltage drops across each bulb.  When the current re-enters the battery, the battery increases the voltage in the circuit from low to high. When one bulb goes out, the stream of current breaks, no current flows and all the bulbs go dark together.


From Bulbs to Batteries


Now do a thought experiment. We will make each light bulb in our series circuit a battery. Unlike a bulb that consumes electricity, so that each bulb next in the line receives less, if each bulb is a battery, each battery adds an additional voltage in the series. When bulbs are replaced by batteries, the voltage in the string can increase. Think of a flashlight where the batteries are in series. As you stack the batteries in the flashlight, one on top of another, the positive end of one battery contacts the negative end of the next in line. Each time you add a battery you get a brighter flashlight, because brightness is greater as the battery voltages add. Think of voltage as pressure that drives current. Now Torpedo uses batteries also to drive current through your hand.

Stacks of electrocytes are shocking.

Electrocytes are modified muscle cells that have lost their ability to contract.  Each electrocyte is a little battery, and each cell by itself produces a very small voltage. Electrocytes are stacked in piles, perhaps a thousand cells in each pile. The piles of cell batteries are oriented from top to bottom in the wing. Each Torpedo has five hundred to a thousand stacks of batteries lined up close together in each wing.  Five hundred to a thousand columns each, with about a thousand electrocyte cells stacked in each column, means that now when you grab TORPEDO….

Published June 27, 2014


Eating Metal in the Dark


Microbes are everywhere. They are almost as old as the earth. Before earth had oxygen, there were no plants and animals, only metals in the crust. Later when life learned to do photosynthesis by trapping the energy of light and using water to make carbohydrates and carbon dioxide, life became more efficient and spread into every niche. What microbes learned about eating metal in the earliest days got incorporated into the machinery for plants to make carbohydrates. How did metal eaters eat and get energy to live without any sunlight or oxygen? Note: we still have metal eaters in West Marin.

What are microbes?


Today’s microbes are bacteria, protozoa, fungi and algae. They live everywhere all over the earth and are crucial for decomposing and recycling nutrients through all ecosystems. Microbes inhabit soil, hot springs, the atmosphere, rocks throughout the earth’s crust, and geothermal vents in the oceans. These guys are not the same as those extant when the earth was very young.


Microbes Evolve


Single-celled microorganisms were the first living things on the earth. They evolved about three to four billion years ago. Remember the age of the earth is about four and a half billion years, so they were present early on. Microbes have been identified in petrified sap (amber) that is 220 or so million years old. From such fossils we learn that the shapes and parts of microorganisms have changed very little since the Triassic, 250 million years ago. Once they appeared, further evolution of microbes seems to have proceeded very slowly. In those primordial times, all living things were microscopic in size.


For most of its history on Earth, life took very small forms. Animals and plants had only one cell. Even way back, nothing much could live on dirt, as there was no cellular equipment to use sunlight to make carbohydrates. Slowly, single cells evolved these abilities. They could acquire energy and food, make proteins and carbohydrates, grow, reproduce, excrete and avoid extinction. Early microbes diverged into today’s bacteria, algae and fungi. Microbes, being so small and compact, can evolve very quickly and exploit new niches and sources of energy very rapidly, almost as soon as these become available. Later microbes could reproduce very rapidly. When conditions are right, adult microbes can exchange genes and materials among their neighbors. Borrowing a neighbor’s genetic stuff ensures maximum genetic variability and permits a quick fit to new environments.


Contemporary sheets of microbes destroy metal

Microbes often form mat-like layers over surfaces. To the untrained eye these films appear as soft carpets of mucus slimed over stones, plants, soil and other objects. Think of the bacterial film on your teeth your dentist wants you to brush away. Microbes are tenacious and live everywhere, even in your mouth, one of the “dirtiest” places on earth if we define dirty as full of microbes. The oldest complete fossils of a microbial mat are about three and a half billion years old.


Energy from metals


How do they do it? Take iron for example. Microbes can use several metals for energy, but iron is the most common metal on the planet. Iron forms much of the earth’s outer and inner cores and was readily available in the environments of the earliest microbes. Fresh metallic iron is gray, but when oxygen is available in the air, iron combines with oxygen to make iron oxides, or rust. Iron oxides take up more space than the iron metal itself, so as rust forms, the rust swells and flakes off the metal, making more of the naked metal available to continue rusting.

Life from rust

Rust is two iron oxides together: ferrous and ferric oxide. Ferrous iron dissolves in water. Microbes can use this iron to get energy. What’s left after microbes get energy is ferric iron, ferric oxide. Ferric iron is not soluble in water and is excreted by the bacteria as little grains that are rust colored. But chemistry is terrific. Only when oxygen is available will the ferric iron react spontaneously with oxygen and become soluble ferrous iron again.

Iron bacteria also are hard at work over two miles down in the Atlantic where light doesn’t penetrate. They are eating the Titanic. This “unsinkable ship” lies on the sea floor where it sank on April 15, 1912, killing over fifteen hundred people. The bacteria eat the wreck’s metal and leave rusticles. Rusticles are icicle-like deposits of ferric oxide, hanging from the railings. Bacteria make the rusticles as they excrete the ferric iron. Each rusticle appears to be built of rings, similar to growth rings in a tree. About thirty percent of a rusticle is salts of iron: oxides, carbonates and hydroxides with some sulfur and phosphorus, but about seventy percent of a rusticle is just the working microbes. Rusticles are delicate and disintegrate into fine powder if disturbed, so in 20 years or so the Titanic may be an unrecognizable rust pile. http://www.mnn.com/earth-matters/wilderness-resources/stories/bacteria-munching-on-titanic


Tube worms from metal eaters.


Figure tube worm


Deep in ocean fissures, magma touches cold seawater under enormous pressure. Dissolved metals and chemicals from the magma, including iron, support complex biological communities. Bacteria use the energy from the iron and chemicals to grow in complete darkness. Snails, copepods, shrimps, crabs, tube worms, fish and octopuses are a food chain of predators and prey that live ultimately on the bacteria. Because vents release so much energy, vent critters live in dense populations, 10,000 to 100,000 times larger than populations on the ocean floor far away from the vents. The largest animals are the giant tube worms. These giants can grow over 80 inches long. They have no mouth or digestive tract. Tube worms absorb the nutrients from the bacteria directly into their tissues. About 285 billion bacteria are in one ounce of tubeworm.




Iron eaters of West Marin



In West Marin we have iron-eating bacteria in our springs and streams. The bacteria live underground where there is little oxygen, and the bacteria can stain spring and well water and block pipes with rust colored slime. Look for rusty patches in shaded fresh water. Bacteria deep in the ground use the ferrous iron for energy. They excrete the insoluble ferric iron. When the ferric iron contacts oxygen in the air it gains energy and cycles back to ferrous iron the bacteria can eat again. Recycling works for the bacteria of West Marin too.