Tag: bacteria

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Nitrogen Fixation and Life

Nitrogen Fixation and Life

There are many chemical wonders in our world, but few are as important and complex as the chemistry of nitrogen. Nitrogen makes up 78% of our atmosphere. It combines with oxygen to form nitrates and with hydrogen to produce ammonia, both of which are essential for growing our food. Nitrogen fixation, which is how nitrogen gets from what we breathe to what we eat, is an amazing demonstration of design.

First, let us review a little high school chemistry. The atoms of all elements have electrons which give them their properties for forming compounds. The electrons are arranged in pairs with their magnetic poles designed so that in a stable arrangement, one electron’s north pole is matched with its neighboring electron’s south pole. The electrons have various orbitals with different energy levels. The atom is stable and chemically inert if an orbital is filled with all the paired electrons it can hold. For example, neon has 10 electrons. The first two orbitals each have two paired electrons, and the last orbital has six electrons in three pairs. This pairing of electrons makes neon an inert gas which does not combine chemically with other elements.

Nitrogen has an uneven number of seven electrons. So how does nitrogen become chemically stable? The answer is that two nitrogen atoms share three electrons, giving them stability. The two nitrogen atoms bond together to form a diatomic molecule that cannot be easily pulled apart to bond with other elements. How strong is the bonding? To break up a nitrogen molecule into two nitrogen atoms requires temperatures of 400 to 500 degrees Celsius and pressures of 200 atmospheres. So with nitrogen as the dominant element in our atmosphere, the atmospheric gases are stable and inert. Also, nitrogen is not a greenhouse gas that could threaten our temperatures on Earth. How then has God built a system that takes these stable nitrogen molecules and breaks their triple bonds to produce nitrates and ammonia?

If you think this isn’t an important subject, ask yourself where your food comes from? The answer is that 50% of the American diet is produced using artificial fertilizers containing nitrogen, which has been “fixed.” Nitrogen fixation combines that inert gas with oxygen and/or hydrogen to supply the soil with the chemical needed to grow the plants we eat, and which the livestock eat to provide us with meat.

Bacteria accomplish God’s method of nitrogen fixation. The bacteria turn nitrogen into ammonia, which is a nitrogen atom sharing electrons with three hydrogen atoms instead of with another nitrogen atom. Plants known as legumes such as soybeans and peas, as well as bayberry and alder trees, attract bacteria which concentrate in nodules on the plant’s roots. The bacteria turn nitrogen gas into ammonia and nitrates the plants can use. Cyanobacteria in the ocean and cycad plants on the land are also major nitrogen fixers. Scientists are also discovering tropical plants that contribute to the wealth of nitrogen compounds in the soil.

Most of our fertilizers have nitrogen fixed by a method called the Haber-Bosch process. It uses massive amounts of energy to break the triple bonds of nitrogen gas. Producing 500 degrees and 200 atmospheres is expensive, and that is why you pay so much for the fertilizer you use in your garden. God’s methods are free. Scientists are trying to figure out how to recreate God’s nitrogen fixation method to save energy and produce more food.

Many bacteria are beneficial in various ways, and nitrogen fixation is only one of them. This is a great apologetic for God’s wisdom and design in preparing the Earth to provide food for us to eat.

— John N. Clayton © 2020

An excellent article on this topic titled “Out of Thin Air” was published in Science News, April 12, 2008. It is available online at THIS LINK, but a subscription is required to read it.

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Origin of Our Microbiome

Origin of Our Microbiome during pregnancy

The microbiome consists of trillions of beneficial bacteria that support our bodies in many ways. Some bacteria play an essential role in digestion and in separating the waste and processing it so that it can be excreted. Other bacteria play a role in our reproductive system. When I was a student at Notre Dame, there was a germ-free laboratory on campus where researchers raised animals with no bacteria. One of the complications of doing that was that even rabbits could not conceive if they were germ-free. For years, scientists have debated the question of the origin of our microbiome.

One interesting discovery that has come from prenatal research is that pre-born babies have their own microbiome separate from their mothers. For the past century, medical experts believed that babies acquired their microbiome at or shortly after birth. Research like that done at Notre Dame was thought to support the” sterile womb paradigm” hypothesis. Recent research has suggested that the origin of our microbiome may be from small amounts of bacteria built into the placenta. Discover magazine (June 2020, page 16) reviews the debate over when babies get their microbiome. Part of the problem is that it is very easy for contamination to get into the research specimens creating confusion over whether the bacteria were natural or if they came from contamination.

Our interest in this subject is not so much about the origin of our microbiome as to look at the implications of the data. Everyone agrees that the baby does not have its mother’s microbiome. Some microbes like E. coli are so common that they are found in all microbiomes. Beyond those, there is a unique makeup to each person’s microbiome, including newborns and pre-born babies.

Maintaining that a baby is an extension of the mother and therefore has no rights is to ignore the evidence. Morning sickness is caused by the mother’s immune system not recognizing a foreign object, the baby, and going into defensive mode. The baby growing inside the mother is a unique person with its own genetic makeup, awareness, and microbiome.

The abortion issue ignores the evidence and attempts to create a new vocabulary to make it seem less brutal, but taking a baby out of the womb and killing it is still infanticide. As tough as this issue is, we need to not shield the vile nature of this process by ignoring the evidence. Instead, we should look for solutions that recognize the value of life and the worth of every human being.

— John N. Clayton © 2020

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Evolution Experiments and their Results

Evolution Experiments and their Results

What if we could speed up time to test the concept of evolution? A scientist can’t wait millions or billions of years to study the process of natural selection as it creates new creatures. With that in mind, science must devise evolution experiments to study many generations in a much shorter time.

More than thirty years ago, Richard Lenski, who teaches at Michigan State University, began a project to study the evolution of the bacteria Escherichia coli, commonly known as E. coli. The project is called the Long-Term Evolution Experiment (LTEE). The scientist and his assistants carefully track the naturally-occurring random mutations in succeeding generations of E. coli. The environment for the bacteria is optimized for these one-cell creatures to grow and reproduce. Mutations are often harmful, but sometimes beneficial mutations lead to an improvement in the bacteria’s reproductive ability. Natural selection removes the bacteria with harmful mutations while those with beneficial mutations become more fit and reproduce. It’s what we call survival of the fittest.

Since 1988, the evolution experiment has continued, and scientists have kept careful records of the changes. Since the generation period of these bacteria is much shorter than that of humans, the study has gone through 70,000 generations. That is equivalent to more than 1.75 million years of human generations.

Through thousands of generations, there have been billions of mutations. Beneficial mutations that have lasted and accumulated amount to dozens. It is interesting that as time passes, successful mutations become increasingly rare. What the scientists are looking for is what they call “historical contingency,” which means a succession of small, almost inconsequential changes that accumulate to create significant changes.

So how has the E. coli changed after the 70,000 generations in this evolution experiment? The latest generation of E. coli can reproduce 70% faster than their ancestors. They are still bacteria. In fact, they are still E. coli bacteria. They have not mutated into some more advanced form of life. Dr. Lenski wants to see funding made available to continue the experiment for another 30 or even 300 years in the hope of seeing more dramatic results.

The LTEE has inspired other scientists to conduct evolution experiments. There is one at Harvard experimenting with yeast. Other scientists have experimented with fruit flies (Drosophila) to study the evolution of multi-cell creatures. They have bombarded the fruit flies with radiation and chemicals, changing light levels, and changing temperatures. After thousands of generations, the result has been mutant fruit flies with extra eyes or wings that didn’t function. They were still fruit flies.

The bottom line is that multi-generation evolution experiments have not resulted in new creatures or even greatly improved old creatures. The changes resulting from mutations and natural selection are either harmful or insignificant. God created animals to adapt and change due to environmental forces. Humans can change and sometimes improve animals by selective breeding. We see that very clearly in the many and very different breeds of dogs. But the evidence seems to indicate that only God can make a Canine or a Drosophila or an Escherichia—or a human.

— Roland Earnst © 2019

You can read about the LTEE in the December 2019 issue of Discover magazine, page 49.

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You Are a Spaceship with a Full Crew

You Are a SpaceshipOne of the most interesting sites on the web is the “Astronomy Picture of the Day” produced by NASA. This website features a new picture every day, usually of objects in deep space with an explanation of the image. On August 18, 2019, there was a beautiful artistic rendition of a human with a star-filled background titled “Human as Spaceship.” (Because of copyright we can’t show you the picture, but you can see it HERE.) The opening line of the explanation is, “You are a spaceship soaring through the universe.”

The point of the presentation is that as we soar through the universe, we are not alone. We are the captains of our ships, our human bodies because we are not a singular living organism. There are a massive number of separate organisms that exist inside our bodies that do specific things for us. They help digest food, fight disease and infection, and carry vital materials on a liquid highway (your bloodstream) from one end of your body to the other. These organisms are the crew of this spaceship. They are bacteria, fungi, and archaea, and they actually outnumber your own cells. Science still doesn’t know what many of these organisms do, but they have their own DNA, and together they make up the human microbiome. You are a spaceship with a massive crew.

We sometimes seem to view God’s creation of the human body as a process similar to building a machine. To build a machine you would put together pre-manufactured parts in a prescribed way. To build a working and living human body requires a host of communities which do the jobs they were designed to do in ways that science is just beginning to understand.

David said it best in Psalms 139:14: “I am fearfully and wonderfully made: marvelous are your works.”
— John N. Clayton © 2019

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Romantic Get-Away Inside a Sponge

Venus flower basket
The Venus’ flower basket (Euplectella aspergillum) is a deep ocean sponge with fascinating properties and an unusual symbiotic relationship with a pair of crustaceans. We call it a romantic get-away inside a sponge.

The Venus’ flower basket is classified as a glass sponge because its body is made of silica, which is chemically the same as glass. The silica fibers are woven together to make a hollow, cylindrical vase-like structure. The fibers form a fine mesh which is rigid and strong enough to survive deep underwater. The picture shows a Venus’ flower basket more than 8400 feet (2572 meters) under the ocean’s surface.

Glassy fibers thin as a human hair but more flexible and sturdier than human-made optical fibers attach the sponge to the ocean floor. The sponge forms the fibers at ocean temperatures while human-made glass fibers require high-temperature furnaces to melt the glass. Human-made fibers are brittle while the sponge’s fibers are more flexible. Scientists are studying these sponges to find ways to make better fiber-optic cables.

We think it’s amazing that the Venus’ flower basket lights its fibers using bioluminescence to attract prey. Even more interesting to us is the symbiotic relationship these sponges have with some crustaceans called Stenopodidea. The Venus’ flower basket holds captive two of those small shrimp-like creatures, one male and one female, inside the sponge’s hollow mesh tube. The captive creatures clean the flower basket by eating the tiny organisms attracted by the sponge’s light and consume any waste the sponge leaves. The sponge provides the crustaceans with protection from predators.

As the crustaceans spawn, their offspring are small enough to escape from the basket and find their own sponge-home where they grow until they are trapped. Because a pair of crustaceans spend their lives together inside the sponge, Asian cultures sometimes use a dried Venus’ flower basket as a wedding gift to symbolize “till death do us part.”

The Venus’ flower basket and the crustaceans benefit each other by mutual cooperation, which we call symbiosis. One more thing, the bioluminescence comes from bacteria that the sponge collects. This amazing three-way partnership occurs deep under the ocean where humans have only recently explored. We think this romantic get-away inside a sponge is another evidence of Divine design, not chance mutations.
— Roland Earnst © 2019

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Biomass on Earth Measured

Biomass on Earth Mostly Plants
Biomass is the mass of living biological organisms. If you lumped all living things by category, what group of organisms do you think would have the greatest biomass on Earth? We aren’t talking about the number of individuals, but the mass of the different lifeforms.

The Proceedings of the National Academy of Sciences on May 21 published a study of the different areas of the world and what form of life dominates in those areas. (Click Here to read the full report.) Plants contribute the primary biomass in the terrestrial environment. Animals are primary in the marine environment. Bacteria and archaea (single-celled microorganisms) dominate the deep subsurface environment.

You may find the results surprising. The total biomass of Earth consists of 80% plants. Bacteria make up the second largest biomass at 15%. After that in descending order are fungi, archaea, protists (unicellular organisms that sometimes form colonies), animals (including humans), and viruses. Soil fungi, protists, soil archaea, arthropods, annelids, and livestock all exceed humans in their biomass. Only wild mammals, nematodes, and wild birds have smaller biomasses than humans. In the marine environment the biomass is much smaller than on land, and after animals, the greatest biomass is in protists, archaea, fungi, and finally bacteria. It is interesting that tiny Antarctic krill contribute about the same biomass as humans.

As you think about the biomass on Earth, it becomes evident that for human life to exist, we need a huge biomass of supporting life-forms. It becomes apparent that we must take care of all of the living things that support us. It is also obvious that before human life could exist on Earth enormous preparation was required.

We have to be reminded of the words of the psalmist in Psalms 8: “When I consider your heavens, the work of your fingers, the moon, the stars, which you have set in place, what is man that you are mindful of him, the son of man that you care for him… You have made him ruler over the works of your hands; you put everything under his feet: all flocks and herds, and the beast of the field, the birds of the air, and the fish of the sea, all that swim the paths of the sea.”
–John N. Clayton and Roland Earnst © 2018

Reference: Scientific American, August 2018, page 16.

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Extreme Animals

Bar-headed Goose
Bar-headed Goose

Much has been made of bacteria that live in extreme conditions. We have mentioned the forms that live in the geyser pools at Yellowstone National Park. Those bacteria use a chemical source to allow them to exist in high-temperature environments. They, in turn, provide the basis for other forms of life that use the Sun as their energy source. The British Broadcasting Corporation has had numerous features in which they have reported on other animals that function in extreme environments. Some of the examples that the BBC cites are:

The sperm whale feeds 2000 meters down in the ocean where the pressure “is the equivalent of carrying ten jumbo jets on your back.” The whales deflate their lungs to do this and then spend up to an hour using chemically-stored oxygen to supply their muscles while they are down there.

Polar bears spend seven months without eating or drinking and then give birth in an area where the temperatures can hit -60 Celsius and the winds can reach 160 km/hr.

The bar-headed geese that fly over the Himalayas at 10,000 feet by concentrating oxygen with their special lung design.

We have discussed some of these mechanisms in the past. Their design and construction are not well explained by chance hypothesis proposals. It would seem that a designer was involved in these intricate systems. God wanted all the earth to be inhabited, but to do that a variety of very specialized structures had to be built into living things. Romans 1:18-22 tells us that we can know there is a God by seeing this design in living things. Extreme animals, just like extreme bacteria, powerfully testify to the truth of that message.
–John N. Clayton © 2017

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Soil Studies Speak of God’s Preparation for Humans

Healthy Soil
There is an economy of language in the Hebrew descriptions of the Bible. In Genesis 2:8-9 for example, the Bible says: “Now the Lord God had planted a garden in the east, in Eden; and there he put the man he had formed. The Lord God made all kinds of trees to grow out of the ground…”

We can learn a lot from those verses. They tell us that the Lord planted something, he did not “zap” something into existence. Later the man was told to tend the garden (verse 15), suggesting that it needed care to continue to provide for the man’s needs and later for the woman’s needs. How long was it after God planted the trees before they began to produce fruit? What did Adam and Eve have to do to take care of the garden? How long was it before Adam and Eve sinned? What else did God need to do in the process of planting the trees?

This last question opens the door to a great deal of understanding that science has gained in recent years through the study of soil chemistry. Plants do not grow in sterile sand. For soil to nourish plants so that they can feed us, much careful science has to be applied. Modern soil scientists refer to “healthy soil” meaning that it is rich in organic material, is crumbly, and has the right chemical profile. To have these things, the soil must contain microbes including bacteria, fungi, nematodes, and protozoa. A teaspoon of healthy soil can hold more microorganisms than there are people on Earth.

We now know that there is a symbiotic relationship between plants and soil microbes. Plants use the sun’s energy to pull carbon dioxide from the air and create a carbon-rich nutrient packet to allow growth. Oxygen is released in that process. The plants also leak nutrients to the microbes, and the microbes supply plants with other nutrients they have extracted from the minerals in the soil. The fungi produce an underground network that brings water and carbon to the plants. When insects begin to feed on a plant, fungi filaments called hyphae help the plant bring tiny soil nematodes that feed on the insects.

When humans abuse the soil and interrupt this system, we have to artificially add chemicals to do what organisms in the soil were designed to do. The chemicals of modern farming could be reduced or eliminated if farmers worked on building healthy soils. The Garden of Eden was a place of healthy soil. God used incredible wisdom and intelligent design to build a system that would meet human needs. This was done in God’s time and was not a magic show, but a consciously built system that has sustained all living things for a very long time. Proverbs 8:22-31 tells us that wisdom was involved in all of this planning and design, and Romans 1:18-22 lets us know that all of this is a testimony to the existence of God.

There is a wonderful article in the April/May 2017 issue of National Wildlife page 35 (available online http://www.nwf.org/News-and-Magazines/National-Wildlife/Gardening/Archives/2017/Soil.aspx) that documents all of this and shows us the complexity of God’s soil science.
–John N. Clayton © 2017