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Life Lines

A scene from 'Breaking Away' was shot at the Empire limestone quarry in Bloomington, Indiana

By Elof Axel Carlson

Elof Axel Carlson

What do the Empire State Building, the Metropolitan Museum of Art, the Flat Iron Building and the Yankee Stadium all have in common? They are all made of Indiana limestone whose quarries are chiefly in Monroe County where Bloomington, Indiana, and Indiana University are located.

The limestone industry got its start when the Welsh founder of New Harmony, Indiana, a British millionaire by the name of Robert Owen, tried establishing a utopian community (it lasted less than five years). He returned to Great Britain but his two sons liked American culture. One became the president of Purdue University and the other became a geologist at Indiana University and promoted the virtues of the limestone he studied in the Bloomington area.

By the 1830s with the advent of railroads, limestone crushed into pebbles was widely used for railroad track construction. In the 1880s the era of skyscrapers in large cities began and Indiana limestone was favored because it was easily shaped and cut.

Limestone is calcium carbonate that was formed 330 million years ago when most of the Midwest was an inland sea. Most of life on Earth was in the sea. Ameba-like protozoa sometimes formed calcium carbonate shells. So did crinoids or sea lilies, which are related to echinoderms like starfishes. The limestone for buildings came from a region of the inland sea that had mostly protozoa raining down their external skeletons when they died, forming a fine silt dozens of feet thick.

The Empire limestone quarry in Bloomington, Indiana, now abandoned

When I was a graduate student getting my doctorate in genetics, I would sometimes go on field trips to visit the caves and limestone quarry holes. One of the delights was scooping water from a quarry hole and bringing it back to Indiana University to look at a very rare organism — Craspedacusta — a freshwater jellyfish. Most jellyfish are found in saltwater oceans. Craspedacusta are small, about a half inch in diameter, and they pulsate as they swim in water. During the summer when we have visits from family and friends, we like to take our guests to Lake Monroe and collect fossils, mostly crinoids, in the fractured limestone gravel along the lake’s beachfront.

The limestone industry has supplied courthouses throughout the United States, government buildings like the Pentagon, thousands of limestone war memorials, cemetery headstones and hundreds of skyscrapers around the world.

The quarry holes are not used as landfills for trash. They dot the south central hilly terrain of southern Indiana. Sometimes the homeless or runaways live in the caves that have been dug into the sides of the quarry hole. The land around them slowly turns green with new grasses and trees. Those who work in the stone trade are like a medieval guild, with stone cutters whose families have done this for three or more generations.

In the 1979 movie, “Breaking Away,” which portrayed the Little 500 IU Bicycle Race, the children of the stone workers called their team “the cutters” and many townspeople still wear T-shirts with the word “Cutters” as a mark of pride. We are often connected without knowing it. In my childhood and youth, I was unaware as a Yankee fan that the house that Ruth built was made of limestone that would make my future retirement home (whose façade is made of limestone). I did not know the magnificent paintings I looked at and studied at the Metropolitan Museum of Art were housed in limestone. I did not know that the Flat Iron Building and the Empire State Building that I saw hundreds of times in my youth were made from the same limestone quarries that would house the laboratory in Indiana University where I studied genetics.

Sometimes life imitates art where a skilled writer hopes that in a novel the reader will end up seeing everything connected to everything.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

One of the marvels of being a conscious organism is our capacity to interpret the things we do.

By Elof Axel Carlson

Elof Axel Carlson

Nedra had her right knee replaced on Sept. 13, 2017, and our daughter Christina and I waited in Indiana University’s General Hospital in Bloomington. She was groggy after some of the anesthesia wore off, and I was surprised that during the same day she was shown how to get out of bed and use a walker to get to the bathroom.

The next day she learned from an occupational therapist how to dress and undress. Also that second day she learned about 10 different exercises in bed to move her right leg. This included sliding her foot along the bed back and forth with her knee elevated and doing a half snow angel movement with her right leg.

I vaguely knew that the mechanics of body motion were first worked out by Giovanni Borelli (1608-1679). Borelli was taught by one of Galileo’s students and was skilled in mathematics, physics and medicine. He also used a microscope for his studies and discovered the stomata of plant leaves and the corpuscles in blood. He did experiments and claimed all body motion is caused by muscle contractions and he worked out the mathematics of animal motion, identifying where the limbs were in relation to the body’s center of gravity.

One of the marvels of being a conscious organism is our capacity to interpret the things we do. Many of those things — like walking, running, holding things or grooming our bodies — we do without a knowledge of the science that is involved in making them possible. We also assign other functions to body motions besides their pragmatic uses. Nedra and I both take Tai Chi for Arthritis at our local YMCA and the slow graceful motions provide exercise of all our joints. The “chi,” or vital energy, I equate in my mind with the same sensation as phantom limbs for amputees, which is neurologically based and not a psychiatric lament for the slow withdrawal of that feeling.

Body motion is paramount for those who dance, relating motion to music and the bonding and unbonding of partners as they go through a dance routine. Judo and tae kwan do are martial arts and can be used for aggressive or defensive activities among combatants. Yoga provides a spiritual aspect to body motion accompanied by meditation for those who practice it. Virtually all of us enjoy spectator sports whether watching baseball, football, basketball, tennis or the myriad of activities in winter or summer Olympic Games.

Anatomists today are well acquainted with the way muscles and bones and their tendons interact for any motion of our limbs, neck, head, hands, feet or other parts of our body. The one activity I did not include in this list is one that I find particularly appealing. The name given to it was by Thoreau who tells us in his Walden diaries that he enjoyed sauntering. It is walking with no direction or goal in mind, just wandering about in the woods or along a stream to take in the delights of nature and to stimulate thoughts for his writing.

When I was in high school and as an undergraduate, I loved solitary walks through Central Park in Manhattan, and my favorite discovery was a spot where I could sit and there were no buildings from Central Park West or Fifth Avenue visible to my eye. I thought of myself as an urban nature boy.

Nedra spent three days in the hospital and she then moved to a rehabilitation facility in a retirement community called Bell Trace. It is nice to see Nedra doing her exercises, converting pain into progress, and we look forward to her returning to our home which will be safety checked before she arrives to prevent slips and falls. For those coming days and weeks our daughter Erica, followed by two of our granddaughters and their husbands, will be out to enjoy Nedra’s progress to experience the confident walking by those with successful knee surgery enjoy.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

Oxford University, Gilman Hall

By Elof Axel Carlson

Elof Axel Carlson

If I had to praise a virtually unknown person as having had the greatest impact on our lives, I would choose Daniel Coit Gilman (1831–1908). Gilman attended Yale University and majored in geography. He became an administrator and founded the Sheffield School of Science at Yale, became the president of the University of California and in 1876 became the first president of Johns Hopkins University. He also helped set up the Carnegie Institution for Science in Washington, D.C.

In 1875 when he was asked to be president of Johns Hopkins University, he embarked on a tour of Europe. He liked the German university emphasis on scholarly research, the ideas of Thomas Huxley on liberal education, and came back with several European scholars who agreed to teach at Johns Hopkins, which opened its program in 1876.

Gilman started his university with a graduate school, then added an undergraduate program and eventually a medical school. He felt the German model was flawed by giving too much power to a single professor in a department who chose subordinates to teach or assist in research. Instead Gilman created departments with several professors committed to scholarship so they could stimulate their research and mentor graduate students who benefited from the multiple outlooks of the department.

By 1910 the success of the Johns Hopkins graduate program shifted the flow of scholars going from the United States to Germany, and after World War I the flow of scholars moved westward to American graduate schools. Gilman’s ideas led to the overwhelming success in Americans winning Nobel Prizes especially in physics, chemistry and the life sciences. It also flooded industries, hospitals and agencies with talented people applying their skills and creativity to their work.

I wish every science teacher would read T. H. Huxley’s “A Liberal Education and Where to Find It” and “On a Piece of Chalk.” They were published about 1868. The first essay shows how Huxley approached education as a way to connect the sciences, art and humanities, shifting knowledge away from an exclusive focus on Greek and Roman civilization as it was then in British schools and toward our connection to the universe in which we live.

Daniel Coit Gilman

The second is an example of good teaching. When I first read his essay when I was about 19 or 20, I could see him in my mind lecturing to the public and holding a piece of chalk in his hand and describing some shavings of it under the microscope revealing the miniature snail-like skeletons of plankton that dribbled down to build the chalk cliffs of Dover. I wanted to be like Huxley, creating lectures that would send shivers of surprise and delight at new knowledge that touched students’ lives.

I singled out Gilman as an educator who changed how knowledge can be learned and transmitted. Our Nobel Prizes and the esteem of rewards are showered on those who make wonderful contributions to knowledge. They are rarely given to founders of institutions that make new ways of learning possible. Both are necessary in our lives.

If I had to single out the one scientist who made the greatest contribution to humanity, I would give that honor to Louis Pasteur for introducing the germ theory of contagious diseases. His use of the microscope to investigate the spoilage of wines turning to vinegar showed that small round yeast cells were replaced by smaller rod-shaped bacteria. His experiments demonstrated numerous infectious diseases as stemming from specific bacteria. It led to vaccinations, public health programs, pasteurization of the milk children drink and the reduction of infant mortality, allowing mean life expectancy to rise from about 45 years at birth to about 80 years today.

New knowledge and inquisitive minds are what make civilization possible.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

By Elof Axel Carlson

Elof Axel Carlson

Why is the term race rarely used by geneticists? The term race is not a scientific one. It is largely cultural when applied to humans. It is too ambiguous a term for describing a population of any one species.

For example, suppose I were a breeder of dachshunds and I specialized in two varieties — one that had a black coat of fur and the other that had a tan coat of fur. I would not call them black or tan races. I would call them varieties of a specific breed called dachshunds of dogs who are described by biologists as the species Canis vulgaris.

The term race is vague. Is it the varietal difference? Is it the collection of traits that we use for dogs, cats, horses, cattle and other domesticated animals? If it is applied to the color of dachshunds, does that mean humans are divided into thousands of races if I were to use McKusick’s online reference work on Mendelian inheritance in humans?

That work describes thousands of genetic traits caused by single gene malfunctions. Geneticists use the term breed for genetically manipulated traits or collections of traits by human selection or breeding. They use the term varieties or naturally occurring variations in a population or for new varieties arising by mutation in a sperm or egg.

Racism is used to describe a social application of race to designate rights and to assign attributes to other races by members of a specific race. There is far more genetic variation within a single race than there is between any two races. The criteria for classifying human races are often arbitrary and are based on skin color, facial appearance, hair texture and other visually distinctive traits. Many of these traits involve quantitative factors (like skin color), and thus racial mixture quickly obliterates the sharp racial traits initially used to describe a person of a specific race.

Quite a few people who have considered themselves and their immediate family as white are surprised when they send off DNA to be analyzed and discover they have percentages of African, Asian, Hispanic, Native American or Jewish ancestry along with their majority Caucasian Western European ancestry.

Racism is particularly destructive in assigning behavioral traits (personality, intelligence and social failure or inadequacy) to race. Most of those traits are determined by how we are raised and not by a roll of genes in forming our parents’ sperm or eggs. If they were to follow their own criteria, racists would find that white Catholics and Protestants are inferior to Jews and Orientals in intelligence measured by intelligence tests or IQs.

The revival of racist ideology among groups like the KKK, neo-Nazis and white supremacy groups is not based on biology or genetics. It is based on prejudice passed down by people who feel victimized if people different from them are treated with justice, fairness and equal opportunity.

The Civil War was fought over slavery. Thousands of abolitionists participated to hide escaped slaves, write books and pamphlets denouncing slavery and demanded the freedom of all slaves. The Confederacy seceded from the U.S. and fought to keep its slaves, many slave owners justifying slavery on biblical grounds — that it was a divine punishment for the descendants of a son who laughed at his drunken naked father.

Most ministers and priests in the North denounced that interpretation. We are not born with a knowledge of our past history. It has to be learned and it has to be taught. It is easier to avoid talking about our past errors than to ignore them.

Germany made a special effort after World War II to teach the racism of its Nazi past to all its school children so that error would never again be repeated. Let us hope that we teach our youth that we are one living species, Homo sapiens, and in the Judeo-Christian tradition we all have one ancestor in common.

In the scientific tradition we also have one human species in recorded history and enormous genetic variation that is constantly changing as humans migrate around the world, settle down or move on to new areas of the Earth. Most of that variation is in Africa where our species first arose.

It is ironic that whites who enslaved or colonized Africa diminished, in their minds, this genetic variation and reduced it to racist formulas of a handful of physical or behavioral traits. I hope this revived racism will recede and our focus will shift to problems that can and should be solved by our elected representatives. Those problems are overwhelmingly caused by our social and economic conditions and not by our genes.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

By Elof Axel Carlson

Elof Axel Carlson

We tend to generalize in making judgments about ourselves and others. Some claim they are self-made and promote their work ethic as the reason for their success. Some claim they are victims of circumstances over which they had limited control. Examples exist of people who have moved from rags to riches, and no one would blame victims of racial prejudice or the Holocaust for the misery they or their family members experienced.

In my own life I can think of many such events that have either made my life possible or significantly influenced it. My father told my brother and me that when his father was on a business trip from Stockholm, Sweden, to Hamburg, Germany, he was walking down a street when a German officer was walking directly toward him.

It was the custom there to step in the gutter to let a military officer have the right of way. My grandfather felt no such sense of obligation and felt his side of the road was appropriate for continuing his walk. The officer pulled out his sword and slapped my father’s face with it. The insult made him a pacifist, and that outlook was passed on to my father and to me. It also made him shorten his trip, and he went to Normandy to visit friends and relatives who had a summer house near the Baltic Sea.

There he met the young woman he eventually married, my grandmother, Amanda, who lived near Göteborg. I can say that I owe my existence to a slap in the face. My parents, too, met in a strange circumstance.

My mother was selling key rings on Broadway in Manhattan on a cold winter day. She entered a hotel entrance on 75th street to warm up, and the doorman told her to go downstairs to warm up in the employee’s room. There she met a Swedish elevator operator who was changing out of his uniform to go home. He took her to dinner and that began the courtship of my parents. I could say I owe my existence to a sympathetic doorman who felt compassion on a woman down on her luck.

When I was a graduate student at Indiana University, I met my wife Nedra, also by a curious circumstance. I had written letters to my parents and friends and lacked 3-cent stamps to mail them. I asked around and was told there was a girl who may have stamps who was usually working in a laboratory the floor above me. I knocked on the door and met a nervous undergraduate who did have stamps and I invited her to tea. When she did not come, I brought the tea to her. That was our first day of courtship. I could say that I owe my marriage to Nedra to a 3-cent stamp.

I do not doubt that such chance events play major roles in our lives. But most of our lives are under our control and shaped by habits and circumstances. We do not choose our partners randomly. Assortative mating is influenced by religion, race, ethnicity, social class, education, looks, personality and many other features that steer us toward or away from possible partners. Before the 20th century most marriages were arranged or required parental approval.

But it is not just social factors that determine how we come into this world. Each act of intercourse involves tens of millions of sperm. The odds of the one that made you on a particular day were not predictable when that sperm was in a testis or when it made its initial way to the cervix of the uterus and eventually to the oviduct where it would meet the egg that formed you.

That is quite a contrast to the injection of single sperm into an egg during a form of in vitro fertilization (IVF) used by infertile couples where the sperm has problems wiggling its tail or having the right surface proteins to recognize it is encountering an egg. In that case we get the paradoxical conclusion that the child born by the IVF procedure owes its existence to the father being sterile!

Life is filled with rare events, the overwhelming number of them not even being recognized as significant in our lives. At the same time society is so organized that much of what we do is planned and anticipated and goes essentially as we hoped it would.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

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By Elof Axel Carlson

Elof Axel Carlson

Yeasts are single-celled organisms belonging to the eukaryotes. They have a nucleus with chromosomes and a surrounding cytoplasm with embedded organelles. There are 1,500 species of yeasts (in contrast to the small number of species of the genus Homo). Most of these yeast species reproduce by mitosis without a sexual phase.

Some species use a process of budding, with the dividing nucleus producing one nucleus entering a small bleb of cytoplasm at the surface and the other staying with the large mass of cytoplasm of the original cell.

The yeast that gives civilization a boost is Saccharomyces cerevisiae. It converts sugars into carbon dioxide and ethyl alcohol. Different strains of this species are used to make beer, wine, mead and other alcoholic beverages that prolonged life expectancy because the alcohol killed harmful bacteria in the water that humans needed. Other strains of this species lead to the rising of bread during baking and helped bring about the agricultural revolution that tamed humanity into cultural communities.

Beer making goes back to at least 6,000 years ago. In Africa a different species, S. pombe, was used to make a beer from millet.

There are also species of yeast that are harmful to humans. Some cause urinary tract and vaginal infections, especially Candida albicans. Yeast strains are also involved in babies’ mouths (thrush) or in toenail and fingernail infections.

The yeast cell has 16 distinct chromosomes and its DNA has 13 million base pairs. Its genes produce 5,800 different proteins. Its mitochondrial DNA has almost 86,000 base pairs and 35 genes.

Molecular biologists have used yeast as engineering systems for producing pharmaceutical products. Yeast chromosomes can be identified, and genes from other organisms can be inserted into them. The yeast genome can also be used for basic science, and each of its 5,800 protein products can be studied for function in the cell.

Yeasts are also being used to study synthetic genetics where genes and chromosomes are designed by scientists and inserted into one or more yeast chromosomes. Artificial yeast chromosomes are reliable for inserting one or more genes designed for commercial use.

Within 10 years scientists hope to have the first artificial nucleus with all the essential yeast genes needed to allow yeast cells to divide and grow and make alcohol. That nucleus will have 16 synthetic chromosomes made by putting together the nucleotide sequences of the genes in each chromosome without using a living system to do so. They will tag each chromosome with inserted genes that can serve as switches to make them machines capable of turning specific genes or groups of genes on or off. The switches will respond to temperature, pH or chemical signals to activate the switches.

No one knew what yeast was some 6,000 years ago. The cell theory did not come into our awareness until 1838. Brick yeast was not sold until 1867. Granulated yeasts (like the packets available in supermarkets) did not exist before 1872. Instead, bakers would save some of the raised dough and mix it into a fresh batch of flour and water.

Similarly, wine makers or beer makers would take samples from their fermenting kegs and use that to start a new batch of cereal mash or crushed fruits to start the fermentation process. Even if those were not available, there was usually a lot of naturally occurring yeast cells on the surface of grains or fruits to generate fermentation. Yeasts have been domesticated to make alcoholic beverages. Bacteria and other fungi have also been domesticated to make sour cream, yogurt and cheeses. Since the 1940s, fungi and bacteria have been used to make antibiotics that have saved millions of lives from pneumonia, gangrene, sepsis and other infections.

Diphtheria, anthrax, bubonic plague, typhoid fever and typhus are no longer threats to the lives of those in industrialized nations that have access to antibiotics, public health measures and sanitation. We owe to Pasteur and Koch in the last decades of the nineteenth century the knowledge of the microbial germ theory of infectious diseases. Their work explained what produces some foods we love through fermentation by microbes, the microbial basis of rotting or spoilage of food and the microbial basis of contagious diseases.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

By Elof Axel Carlson

Elof Axel Carlson

Science is a way of interpreting the universe in the era in which we live. One of the realities of our lives is that we do not know how much of the world we think we know is really incomplete.

Think of it this way — If you grew up when the American Revolutionary War was being fought, you would not know a lot. You would not know your body is composed of cells. You would not know that heredity is transmitted by genes located on chromosomes present in nuclei of cells because no one knew there were nuclei, chromosomes or genes.

You would also not know there are biochemical pathways that carry out your metabolism in cell organelles because no one then knew there was such a thing as metabolism, biochemical pathways or cell organelles. And you would not know that infectious diseases are associated with bacterial and viral infections nor would you know that your body is regulated by hormones. If you created a time line of scientific findings in the life sciences, the cell theory was introduced in 1838. Cells were named in 1665, but Robert Hooke thought they accounted for the buoyancy of cork bark. He drew them as empty boxes.

When Schleiden and Schwann described cells, they were filled with fluid; and Schwann thought nuclei were crystallizing baby cells being formed in a cell. The cell doctrine (all cells arise from pre-existing cells) did not come until Remak and Virchow presented evidence for it. Mitosis, or cell division, was not worked out until the late 1870s; and meiosis of reproductive cells (sperm and eggs) was not worked out until the 1990s.

Fertilization involving one sperm and one egg was first seen in 1876, while most cell organelles were worked out for their functions and structure after the invention of the electron microscope in the 1930s. There was no organic chemistry before Wöhler synthesized molecules like urea in 1823, and biochemical pathways were not worked out until the 1940s.

DNA was not known to be the chemical composition of genes until 1944, the structure of DNA was worked out in 1953, molecular biology was not named until 1938 and the germ theory was worked out in the 1870s and 1880s by Pasteur and by Koch, who both demonstrated bacteria specific for infectious diseases. Embryology was worked out in 1759 by Wolff, while hormones were first named and found in 1903 by Bayliss and Starling.

What the history of the life sciences reveals is how dependent science is on new tools to investigate life. Microscopes up to 30 power came from Hooke’s efforts in 1665. A better microscope by Leeuwenhoek distinguished living organisms (“animalcules”) at up to 500 power.

It was not until the 1830s that microscopes were able to overcome optical aberrations and not until the 1860s that a stain technology developed to see the contents of cells. This boosted observation to 2000 power. For the mid-20th century, cell fractionation made use of centrifuges and chromatography to separate organelles from their cells and work out their functions.

Experimental biology began in England with Harvey’s study in 1628 of the pumping action of the heart. Harvey was educated in Padua, Italy, where experimental science had been stressed by Galileo and his students who began applying it to the motion of the body relating bones and muscles to their functions. No one alive in 1750 (or earlier) could have predicted DNA, oxidative phosphorylation, the production of oxygen by plants, Mendel’s laws of heredity or the role of insulin in diabetes.

But what about the present? How complete is our knowledge of life processes? Are there major findings in the centuries to come that will make our present understanding look as quaint as reading the scientific literature in the 1700s?

We can describe what we would like to know based on our knowledge of the present and likely to be achievable. We cannot predict what may turn out to be new functions or structures in cells. At best (using what we do know) we can hope to create a synthetic cell that will be indistinguishable from the living cell from which it was chemically constructed. But that assumes the 300 or so genes in a synthetic cell will account for all the activities of the vague cytoplasm in which metabolism takes place.

For the level of viruses there are no such barriers and the polio virus has been synthesized artificially in cell-free test tubes in 2002 (an accomplishment of Eckard Wimmer at Stony Brook University).

Within a few years ongoing studies of bacteria and of yeast cells with artificial chromosomes, may resolve that question for the genome of a eukaryotic cell. I hope that an artificial cytoplasm will be worked out in that effort. That might be more of a challenge than presently assumed.

By Elof Axel Carlson

There are projects underway to test the feasibility of sequencing every species on Earth (including extinct species where their DNA is still available). The largest of these programs is in China, which is hoping to sequence the 1.5 million known named species of animals, plants and microbes.

Elof Axel Carlson

Phase one will sequence one species from each of 9,000 families (the taxonomic unit above the genus level). The second phase will sample one each of the 200,000 forms of life described as belonging to a genus. Phase three will look at all the species remaining.

It is a daunting amount of work. Think of it this way. There are 6.8 billion telephones on Earth. If you entered every telephone book into one computer site, you would have access to more than 90 percent of all living people.

Looking up a phone number would also give you information on the person’s name, country that person lives in and the home or business address. For perhaps one billion of them who are listed in Yellow Books, it would tell you what they do for a living.

But DNA sequences will do more than identify a species. The sequence of genes and their functions will classify the organism and tell us if it is a plant, animal or microbe, and what it does as a particular species. We would know its anatomy, physiology, metabolism, life cycle, mean life expectancy, where to find it on Earth, what it eats and how it lives.

For humans it would show how we are related to the 7 billion other humans on Earth. It would provide abundant information on how all of us are related in an evolutionary pathway of immense size. The Chinese company, BGI, located in Shenzhen, estimates it will take 10 years and cost about $5 billion to complete the project.

There are six other projects underway around the world. One is seeking to sequence all vertebrates, a second wants to do that for arthropods (mostly insects, spiders and crustaceans), a third is looking at marine invertebrates, a fourth is interested in the world’s ants, a fifth prefers to sequence the world’s birds, and the sixth is seeking to identify all African food crops.

As far as I know, no one is trying to do a genome sequencing of all human beings. The closest to doing that is the country of Iceland, which has asked its citizens to volunteer and give a sample of saliva for DNA sequencing. Half of Iceland’s people have done so. They are mostly descendants of Viking settlers and their DNA studies are immensely helpful for looking at genes involved in human disease risks (such as birth defects, Alzheimer syndrome, cancer, hypertension, risk of late-onset diabetes, heart disease and strokes).

The implications of this effort to gain knowledge of the world’s genomes are numerous. For evolutionary studies they are a remarkable resource. For medical diagnosis they are equally valuable. They will be a gold mine of rich ores for the pharmaceutical industry. Think of all the antibiotics that will be mined from the microbial genome data. Just as there are tens of thousands of projects engineers do for buildings, electronics, infrastructure and transportation so, in the coming decades, will thousands of projects emerge and new fields of science from applications of this immense resource of the all Earth genome project.

Will this also involve bad outcomes of new knowledge? Certainly. We did not abolish engineering because engineers have designed most of the weapons used in war. We did not abolish chemical industries because some of them gave us environmentally toxic or harmful agents like DDT, Agent Orange, gas in World War I or thalidomide. We do not condemn X-ray diagnosis because radiation can induce gene mutations. What we do is regulate our technological innovations.

Think of regulation in industry as something like criminal law in society. We punish those who break laws (embezzlement, theft, assault, rape, slander, robbery, kidnapping, extortion, bribery). Regulation addresses many issues only one of which is misconduct. Similarly, law addresses wrongs, not all of which are criminal (we call that noncriminal law civil law). Some politicians want to do away with regulation of industries.

Is not dumping wastes into rivers a criminal act? Is not choking a city with industrial gases a criminal act? Laws can be changed or even abolished, but loss of human life, damaged health, destruction of ecosystems and putting the brunt of waste disposal on those most vulnerable (the poor) should be regulated.

I am an optimist, not a Pollyanna, about the future of the all Earth genome projects. We need both new knowledge and new regulation.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

By Elof Axel Carlson

On March 20, 1997, I was happy to see my first Life Lines column in the Arts and Lifestyles section of publisher Leah Dunaief’s North Shore newspapers. Since then more than 400 Life Line columns have appeared for which I am grateful.

It has been my good fortune, since I was a teenager, to be a storyteller. I learned that the best way to understand something is to tell it out loud like a story. It worked in high school and it has been an asset in my teaching whether at the graduate level or for courses on science for nonmajors.

This column has been my connection to a largely unknown audience. When I was teaching at Stony Brook University, I regularly ran into strangers at the supermarket who would give me feedback. I learned from Editor Heidi Sutton that the online version of the TBR newspaper site has a substantial number of readers of this column.

To celebrate this anniversary, I will share with you the story of the newest field of the life sciences, synthetic genomics. A team of scientists led by Jef Boeke at NYU published an article in Science describing their success in making synthetic chromosomes for yeast cells. Yeast has 16 chromosomes and 6,275 genes. Those 16 chromosomes also contain 12,156,677 base pairs that make up its DNA.

The DNA sequence was worked out in 1996 so that knowledge goes back to the time I was writing the first batch of articles for this column. The NYU study has synthesized five of the 16 chromosomes and tested them in yeast cells to show that they function. They removed nonfunctional genes and inserted components that do not play a role in gene function or metabolism.

They also have created a 17th chromosome that contains a set of genetic tools. These include genes that repair mutations, genes that shuffle genes more effectively to speed up new mutation production when a desired type is sought, and genes that make new products or boost their production. Different strains of yeast cells make bread, beer and wine.

Boeke’s team hopes to complete the remaining chromosomes this year. For their long-range plans they hope the synthetic yeasts they make will produce antibiotics, vitamins, painkillers, hormones and other biological products for the pharmaceutical industry. They hope their synthetic yeasts will have a wide range of uses in making breads fortified with vitamins and proteins.

Think of having synthetic yeast-made varieties of food on a space journey to Mars where opportunities to grow plants are limited for a journey that might take months or years. They are following federal regulations to make sure their yeast is safe and they do not plan on making new species or new forms of life. But all new inventions of science lead to new outlets; so I will not be surprised years from now to see artificial life-forms made to do useful things like digesting industrial wastes and degrading them to harmless components.

Imagine if you could engineer a yeast cell to concentrate the gold from ocean water. Imagine a synthetic yeast that could pull the carbon dioxide from the air and turn it into gasoline or coal so that carbon dioxide levels are actually lowered while carbon-based fuels are made without mining for them.

I have never been a practical person and such applications, while easy for me to imagine, are not as satisfying as the knowledge that synthetic genomics can provide. Synthesizing the 16 chromosomes from off-the-shelf chemicals and forcing yeast cell cytoplasm to accept an artificial nucleus is not the same to me as finding out what that cytoplasmic material does and how it works.

Is it, as one geneticist remarked, a “playground for the genes?” Or will it turn out to house something so new to our field of biology that we can’t even imagine its components and functions? Will this too be synthesized once it is successfully tackled by a future generation of scientists?

I am not worried about applications to germ warfare. Most military planners know that germ warfare is a risky way to wage it because it is not easy to immunize your own nation’s citizens before you manufacture and launch new germ warfare agents against an enemy. There is also the war crimes risk for those involved if they are on the losing side of the war.

I am also not worried about runaway contagions as unexpected consequences of scientific studies. I strongly believe government regulations are essential to protect the public’s health and the NYU team is rigidly following those guidelines.

I celebrate this accomplishment because it is opening up a new field of science and some of the persons learning about this might be among the first to apply that new scientific knowledge to medicine, industry and our ever-changing conception of life and our stewardship for fostering it.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

'A trip to the American Museum of Natural History was my idea of being in heaven.' - Elof Carlson

By Elof Axel Carlson

The life sciences are vast in the number of specialties that exist for those pursuing a career as a biologist. A majority of college biology majors are premedical or seek some sort of health-related field. As much as possible they hope the biology they learn will find its way into the health field they seek to enter. Persons who want to be scholars in biology are often motivated by a desire to know as much about life as they can. I was one of those from early childhood when a trip to the American Museum of Natural History was my idea of being in heaven.

Elof Axel Carlson

I loved learning about evolution and the diversity of life. I knew I wanted to be a geneticist when I was in ninth grade and learned about Paul Müller’s Nobel Prize work on inducing mutations. Like a duckling, I felt imprinted and wanted to work with Müller someday.

Graduate work was different. As a teaching assistant I got to see about 90 different specimens each week for the various organ systems displayed by students. Unlike the textbook perfect illustrations, veins and arteries could be slightly off in the specimens I looked at. Their colors differed. Their texture differed.

I also learned how much we didn’t know about life. For my specialty of genetics (with Müller, as I had hoped) I felt steeped in experimental design, techniques and ways of thinking. Doing a Ph.D. allowed me to examine a gene using the tools of X-raying to produce mutations of a particular gene and subtle genetic design to combine pieces of a gene — taking it apart and combining pieces that were slightly different. It gave me an insight into that gene (dumpy, in fruit flies) that for a short time (until I published my work) I was the only person in the world that knew its structure.

In my career I have taught biology for majors, biology for nonscience majors, genetics, human genetics and the history of genetics. I have taught lower division and upper division courses, graduate courses and first-year medical classes. I learned that sharing new knowledge with students excited their imaginations. I learned that the human disorders I discussed led to office visits; and if I didn’t know the information they sought, I went with them to the medical library and we looked up articles in the Index Medicus and discussed their significance.

Often that student was married and had a child with a birth defect (born without a thyroid, having a family trait that might appear like cystic fibrosis). I would prepare a genetic pedigree and give it to the student to stick in a family bible for future generations to read. I also delighted in going to meetings to discuss genetics with colleagues whose work I had read.

I was pleased that I shared a body plan with other mammals. I liked comparative anatomy, which taught me how other body plans work (mollusks, arthropods, worms, coelenterates, echinoderms). As a graduate student taking a vertebrate biology course, I went into a cave and plucked hibernating bats from a ceiling.

The world under a microscope is very different. To see amoebas, ciliated protozoans, rotifers and other organisms invisible to the naked eye or as mere dust-like specks is a thrill. I can go back in time and imagine myself as a toddler, a newborn, an embryo in my mother’s uterus or an implanting blastocyst rolling out of her fallopian tube. I can imagine myself as a zygote, beginning my journey as a one-celled potential organism typing this article into a computer. I can go back in time to my prehistoric ancestors and trace my evolution back to the first cellular organism (bacteria-like) more than 3 billion years ago.

I learned, too, that I contain multitudes of ancestors who gave me one or more of their genes for the 20,000 I got from my father’s sperm and the matching 20,000 genes in my mother’s egg nucleus. I contain some 37 trillion (that is, 37,000,000,000,000) cells or 2 to the 45th power, which means some 45 mitotic cell divisions since I was a zygote. I know that the warmth of my body is largely a product of the mitochondrial organelles in my cells that using the oxygen from the air I breathe and converting small molecules of digested food to provide energy that runs the metabolism of my body and disposes carbon dioxide that eventually is expelled from my lungs. This knowledge makes me aware of my vulnerability at the cellular level, the chromosome level and the genetic level of my DNA to the agents around me that can lead to birth defects cancers, and a premature aging.

Knowing my biology allows me to know my risks as well as new ways to celebrate my life.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

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