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Planet Earth/7d. The Origin of Sex

Asexual Reproduction
Bacteria belong to a group of unicellular organisms, called the prokaryotes that exhibit a cellular membrane and wall that surrounds a free-floating circular DNA molecule held in a cytoplasm fluid with various proteins produced by ribosome RNA, and coded by the DNA molecule. The cellular membrane and wall are constructed by lipids and proteins, produced by RNA from amino acids and carbohydrates that most bacteria will consume from the outside environment. Some bacteria exhibit long, whip-like protrusions from their cellular wall that aids cellular locomotion, called flagella, while others are able to secrete calcium carbonate forming a hard-skeletal cellular wall. Prokaryotes mostly reproduced by asexual reproduction by binary fission, which is where the DNA molecule replicates a nearly identical functional copy and the cellular membrane pitches off into two cells (cytokinesis), each containing a DNA molecule. Most prokaryotes replicate by this simple process of asexual reproduction. Hence, a single cell can reproduce very quickly by doubling. As long as there is sufficient amino acids and carbohydrates in the environment and or proteins, bacteria can quickly reproduce to large numbers from a single cell. This doubling allows bacterial colonies to grow rapidly in population size.

Individual bacterial cells do eventually die, which is highly dependent on environment conditions. For example, if the environment becomes too harsh, such as in lacking nutrients, high-water temperatures, acidic or basic water pH, high salinity, short wave length electromagnetic radiation, nuclear radiation or high oxidation, the cells will perish. This means that early bacterial populations were held back by the conditions of the external environment and availability of nutrients vital for life, which early on were produced naturally from the Earth’s atmosphere and oceans, but in limited supply. If a large bacterial population faced a harsh environment, many of these single celled organisms would perish and die, leaving fresh sources of nutrients behind of complex organic molecules by their decaying cellular masses. If just a single living cell was able to survive this harsh environment, there was a great benefit to it, as there would be amble supply of nutrients for the survivors. The trait that makes a living organism better at surviving in an environment is called an adaptation. These adaptations likely originated by the randomization that is brought about during the replication of DNA in the cell. DNA is short for deoxyribonucleic acid a large organic molecule composed of two polynucleotide chains that coils around each other forming a double helix. Each molecule of DNA is unique as to each molecule, and carries very large strains of individual unique nucleotides, which are composed of one of four nucleobases (cytosine [C], guanine [G], adenine [A], and thymine [T]), each connected to deoxyribose and a phosphate group, that provides the sugar-phosphate backbone to DNA. The double helix strains are held together by weak hydrogen bonds between the nucleobases, with adenine [A] pairing with thymine [T], and cytosine [C] pairing with guanine [G]. These pairings are easily broken during the first step of replication of the DNA molecule, where the double helix is “unzipped,” using an enzyme called helicase. The two single loose strands of DNA will act as templates to make new copies. One strand is called the leading strand, which has a 3′ prime end capped with a terminal hydroxyl group, while the lagging strand has a 5’ prime end capped with a terminal phosphate group. Both will act as templates to build a copy of each side or strand of the original DNA. The leading strand will build onto this template using a primer RNA molecule that binds to the leading strand at the 3′ prime end and moves toward the 5’ prime end. DNA polymerase binds to the leading strand and moves down the template adding complementary nucleotide bases (A, C, G, and T) as it goes along the strand building a nearly identical copy of the original lagging strand of DNA. This is called continuous replication. It was often thought that the original lagging strand of DNA was built along the same fashion. We today know, that it does something different thanks to a brilliant woman from Japan. Tsuneko Okazaki (岡崎 恒子) was born in Japan in 1933, and witness the horror of the Second World War while in grade school, the lasting effects of which would haunt the rest of her life. In the aftermath of the devastating war, she enrolled in post-secondary school to study biology earning a PhD in Japan, during a time in which woman were first permitted to earn advanced degrees at a university. She loved working in the lab, studying the early cell division in frog and sea urchin eggs, and understanding how these early cells replicate and grow. She fell in love with Reiji Okazaki (岡崎 令治), a fellow scientist who also studied in the lab, Reiji Okazaki had experienced the death and destruction of war as well, having been exposed to the radiation fallout of the Hiroshima nuclear bombing as a child. The two married, moved to the United States to continue their research, and begin to focus on the common bacteria Escherichia coli, that lives in the intestine of many animals and humans. Their work demonstrated something unusual in how the lagging strand of DNA is copied. The lagging strand of DNA is built piecemeal from fragments that are added to the opposite side following the same direction as the leading strand, with the first parts built near the unzipping, and working down toward the 5’ prime end. These fragments (which are called Okazaki fragments) are added using RNA primers, which will need to be replaced. Once these fragments are placed next to their corresponding bases (A with T, C with G), an enzyme called exonuclease pulls out the temporary primers and fills the gaps with any missing nucleotides. This process is called discontinuous replication.

Once each side of the original DNA molecules has resulted in a new paired DNA molecule, the enzyme DNA ligase binds up the sequence and results in two new DNA molecules, each with one half of the original DNA molecule and one half with a copied DNA molecule. The process is complicated, and errors can be introduced during this delicate process of cellular replication. If exposed to nuclear radiation these processes of replication can stop, or mismatches can occur caused by the breakage of these delicate linkages inside each cell. In a bacterial colony, or in the living tissue of a human being, such mistakes can lead to abnormal cells. Most of these abnormal cells will fail, but some can become cancerous, copying abnormally until they replace healthy cells.

The high exposure of nuclear radiation of the Hiroshima bomb dramatical increased this risk to Reiji Okazaki, while the couple moved back to Japan, celebrated the birth of their two children, and success of their international research, Reiji was becoming ill. In 1975 he died of cancer, at the age of only 44, leaving behind his beloved wife and two small children. Tsuneko continued her research, and advocated for better resources for woman scientists in Japan, as she was suddenly thrust into the difficult life of raising two children alone and carrying out her intense scientific experiments. Nevertheless, she persevered, by making new discoveries in the field of genetics and how cells divide, and leading further research into more complex organisms.

The complexity of the replication of DNA always leads to the possibility that mistakes or differences will appear in the strands of the four possible nucleobases (cytosine [C], guanine [G], adenine [A], or thymine [T]). For example, where a cytosine might accidentally be replaced with a guanine, these mistakes introduce variation, which are called mutations. Mutations can be bad or in more rare cases they can be advantageous, allowing a cell to survive in a slightly harsher environment for example. In the early Earth, with only bacterial single cells replicating in such a way, any innovation only came from the random likelihood of a mistake turning out good. This process resulted in the continued trial and error method for any change or advancement within individual cells. Most cells would be near perfect copies or clones of the original cell. If the environment changed harshly, and the bacteria did not escape, the entire colony of cells would nearly all perish. Those that survived death could go on replicating.

The Advent of Sex
One of the greatest innovations in the evolution of life on planet Earth was the origin of sexual reproduction. Most bacteria reproduce by making copies, or clones of themselves that closely resemble the original cell, asexual reproduction. This allowed bacterial populations to grow in great numbers, but also die in great numbers when the conditions for life change. This is because each descendant cell is nearly identical to the original cell, and there is little genetic variation within the population. One of the most amazing abilities that bacteria developed was the ability to share genetic information between cells, either as fragments of RNA or DNA that could be used to communicate between individual cells. This process of reproduction is an early form of sexual reproduction. Modern bacteria do this through the use of a pilus (also called a sex pilus), which is a long tube-like appendage that can carry fragments of novel DNA or RNA and share this with surrounding cells. The pilus can also serve as an anchor point to bind bacteria to other cells, holding them in place, and likely used to provide genetic communication between cells. This additional DNA or RNA molecules can increase genetic diversity within a population of cells more quickly than simple random mutations.

One theory for the origin of viruses, suggests that these fragments of DNA or RNA which encode or alter the bacteria’s original DNA, mutated into forms that code for the replication of more viruses, instead. Indeed, this is very likely the origin of many viruses that exist today, and likely most viruses are miss-coded RNA or DNA strands that continue to infect cells, and altering them in the process. It is remarkable that the vast majority of differences between DNA molecules in a population of individual cells is likely do to the interaction of virial RNA or DNA infections that can change and alter the genetic code of these cells. Much of this information maybe excessive and non-informative for the production of proteins or the expression of traits within the cell, but it does enhance the probability of new and novel features that might appear with beneficial results.

If two colonies of bacteria are replicating, the colony that shares genetic information between cells will have a major advantage compared to the one that has to rely on the randomness of mutations and mistakes during replication. Such early networks of communication between cells became vitally important during the early stages of life on Earth, as cells begin to work as a network of individual cells, rather than individualistically. This type of sexual reproduction is fundamentally very different than that observed by more complex single celled organisms, as well as plants and animals, but both serve the purpose of increasing genetic variability within a population. The ability to share genetic information significantly improves the outcome of adaptive individuals that are able to survive changes to the environmental conditions.

The Origin of Complexity of Single Cells
In the laboratories at the University of Chicago, Stanley Miller’s experiments sparked in the corner of Harold Urey’s lab, a demonstration that the vital ingredients required for primitive lifeforms could be easily produced in the ancient atmosphere and ocean of Earth. These amino acids and carbohydrates would have allowed primitive early bacteria to thrive in this primordial world. However, with rising populations inevitably these rapidly reproducing bacteria would use up all of the limited input of these natural resources. As such, life was precious as it depended on the amount of nutrients provided by the natural processes, coupled with the harsh environment of an early Earth. It was no surprise that some cells during this time turned to feed on other cells. This was the origin of heterotrophic organisms, which take in organic substances from other living cells. In addition to the nutrients from natural occurring chemical reactions and other living or decaying organisms, many of these early microscopic single-celled lifeforms utilized the primordial atmospheric gasses for a type of respiration, or energy source, principally CO2, SO2 and NO2. These early cellular lifeforms are called the Archaea, or archaebacteria, from the Greek arkhaios meaning primitive. They thrive today in environments that lack free oxygen, and many are also often identified as extremophiles, which are bacteria that can exist in harsh environmental conditions, such as anoxic or euxinic waters, deep underground, hot sulfur springs, or extreme warm or cold climates that may have been more common during the Archean period. The three major types of archaebacteria lifeforms can be divided based on how they rely on chemosynthesis, the synthesis of organic compounds by living organisms using energy derived from reactions involving inorganic chemicals only, typically in the absence of sunlight.

First are the methanogenesis-based lifeforms that take advantage of carbon dioxide (CO2), by using it to produced methane CH4 and CO2, through a complex series of chemical reactions in the absence of oxygen. Methanogenesis requires some source of carbohydrates (larger organic molecules containing carbon, oxygen and hydrogen) as well as hydrogen, but these organisms produce methane (CH4) particularly in sediments on sea floor in the dark and deep regions of the oceans. Today they are also found in the guts of many animals. Second are the sulfate-reducing lifeforms that take advantage of sulfur in the form of sulfur dioxide (SO2), by using it to produce hydrogen sulfide (H2S). Sulfate-reducing life forms require a source of carbon, often in the form of methane (CH4) or other organic molecules produced naturally, such as amino acids, as well as sources of sulfur, typically near volcanic vents deep underwater. And finally, the nitrogen reducing lifeforms, which take advantage of nitrogen in the form of nitrogen dioxide (NO2) by using it to produce ammonia (NH4). Nitrogen-reducing life forms also require a source of carbon, often in the form of methane (CH4) or other organic molecules produced naturally (many of these bacterial organisms form a symbiotic relationship with plants). All three types of life-forms exhibit anaerobic respiration, or respiration that does not involve free atoms of oxygen. They all benefit from the input of naturally occurring amino acids, carbohydrates and other complex carbon-based molecules that the Urey-Miller experiment at the University of Chicago demonstrated could form naturally on a primordial Earth, but also taken in organic molecules from other single celled organisms.

Endosymbiosis

Two inquisitive love-struck teenagers were hanging out at the lab pondering the ramifications of the Urey-Miller experiment. Their names were Carl Sagan and Lynn Margulis. Sagan had blazed through high school graduating at the young age of 16, and had enrolled at the University of Chicago, where as an undergraduate he was working in the lab of Harold Urey as a young student. Lynn Margulis was a 15-year-old local high school student, interested in science, enrolled in the University of Chicago Laboratory School, when the two met in Chicago. At the end of their undergraduate college experience and dating, the two married in 1957, and had two sons (Dorion Sagan and Jeremy Sagan), while Carl dreamed of extraterrestrial life, switching his degree to astronomy and physics, and later popularized science with his television show. Lynn instead focused on how life became complicated and went on to study biology in graduate school at the University of Wisconsin. The couple struggled with the demands of academia and raising two boys while trying to conduct research and teaching. At the University of California Lynn Margulis focused on a deceptively simple organism for her doctoral research called Euglena, which is a Eukaryote. Eukaryotes are more complex organisms that have a cell or cells composed of a nucleus enclosed within a membrane that holds the genetic information of DNA (often as chromosomes), as well as a number of organelles within the cell that provide special functions to the cell. Euglena is unique in that it is a mobile type of algae that lives in pond water, swimming around with a flagellum, but also is able to photosynthesize like plants. Most species of Euglena have many photosynthesizing green chloroplasts within cell, which allows them to generate food and energy from carbon dioxide and sunlight. These single celled organisms are an example of an autotroph (also called a primary producer), a life form that can generate its own food from the surrounding inorganic environment.

Chloroplasts, and the advent of carbon dioxide breathers
Lynn Margulis realized that the advent of such organisms must have been a major breakthrough for early organisms in Earth’s history. The origin of chloroplasts, and ability for cells to photosynthesize must have completely altered the world. A major scientific discovery she personally made came about in wondering where these chloroplasts within the cells of Euglena came from. What allowed these creatures to be able to photosynthesize in the first place?

The origin of an organism that is able to take carbon dioxide gas and photons (in addition to traces of ammonia, phosphate, potassium and other nutrients) and build them into the needed raw ingredients (mostly carbohydrates) for food within the cell was a mystery. She searched around for other types of single celled algae that use photosynthesis, and she noticed that some forms of algae are in fact tiny prokaryotic organisms, classified in a group called the blue-green algae, or more appropriately named cyanobacteria. These are bacteria that are able to photosynthesis, often replicating in long strains of tiny cells, that live in the photic zone of the world’s oceans (but can survive nearly everywhere on Earth where there is sunlight).

The occurrence of cyanobacteria prokaryotic organisms with the ability to photosynthesize would completely alter Earth in extraordinary and profound ways. The early Earth when the Archean bacteria dwelled was significantly limited by the environmental conditions and availability of nutrients. The advent of photosynthesis unlocked a vast storage of carbon dioxide directly from Earth’s early atmosphere. Like Mars and Venus, the early atmosphere of Earth was composed of nearly 95% carbon dioxide, this carbon dioxide was the source of carbon in the natural development of organic molecules necessary for life. What this group of single celled prokaryotes acquired was the ability to directly take in carbon dioxide and produce carbohydrates necessary for growth. As long as there was carbon dioxide in the atmosphere the cyanobacteria could flourish and reproduce in vast numbers. Very quickly cyanobacteria became the dominate lifeform on Earth, the fossils of which are preserved because of a unique interaction this process has on the formation of calcium carbonate. Photosynthesis takes out the carbon from acidic waters in which carbon dioxide gas is dissolved in the ocean water as carbonic acid, and returns oxygen gas to the water. This raises the pH of the water (making it more basic) surrounding the cell, which results in the precipitation of calcium carbonate in marine and freshwater systems. These bacteria increase pH as a result of this photosynthetic activity and also produce extracellular sticky polysaccharide sugars, which act as binding sites for calcium and carbonate ions coating the cell in a protective skeleton. These cells when they die get buried in the subsurface and form calcium carbonate limestones. Ancient limestones and fossil algal mats called stromatolites preserve a record of the first appearance of these organisms during the Archean, about 3 billion years ago, and their steady increase over a great span of time. These cyanobacteria released oxygen, while drawing down carbon dioxide to lower and lower levels in the atmosphere and oceans.

Heterotrophic organisms benefited from these new organisms, as they had a source of nutrients in these rapidly growing populations of cyanobacteria, and they likely consumed them by evaginating their cells around these organisms, releasing their nutrients. The thick carbonate skeletons were an adaptation to protect these organisms from being consumed. As Lynn Margulis watched her study organism, Euglena, dance around under her microscope, with a cell filled with green chloroplast organelles, she wondered if these green chloroplast organelles were just cyanobacteria that instead of being consumed by the cell, were in fact just incorporated within the cellular structure. The advantage was clear, as keeping cyanobacteria alive would provide the whole cell a continued source of carbohydrates. Was this a form of symbiosis, in which each tiny squirming cell of Euglena in actuality a multicellular organism of various species of prokaryotic cells living together? Was eukaryote cells actually made up of multiple species of prokaryotic cells with different functions? This idea was a radically different view of biology, which is called endosymbiosis. She drafted a famed paper proposing the idea entitled “Evolutionary Criteria in Thallophytes: A Radical Alternative” Thallophytes is an abandoned term for primitive fungus and algae, and primitive plants, of which Euglena was a member of. The paper was rejected numerous times, as reviewers argued that she did not have the evidence to back such a radical idea, despite this she was able to persevere and got it published in Science gathering some amazing evidence for symbiotic relationships in all eukaryotic cells.

The full force of evidence backing her idea would come swiftly from the study of another organelle in eukaryotic cells, one that is found inside your own cells – mitochondria. Mitochondria are oval to rod shaped organelles found in most eukaryotic cells. They have a double membrane with an inner layer that forms pockets called cristae. The mitochondria serve an important function in the process of respiration and energy production for more complex eukaryotic cells.

Mitochondria, and the advent of the oxygen breathers
During the billions of years of the Archean the amount of available carbon dioxide for photosynthesis in the Earth’s atmosphere was used up by the highly successful cyanobacteria, reducing the Earth’s atmosphere of carbon dioxide being replaced with oxygen. The amount of input of new carbon dioxide was limited to the volcanic activity of the Earth, which was still much more active than today, as the accretionary heat was much greater early in Earth’s history, but still limited. This limited flow of carbon dioxide into the atmosphere meant that it would often get used up by photosynthesizing cyanobacteria in vast algae blooms following volcanic eruptions. The atmosphere was instead filling with a new dangerous gas – oxygen. For most Archaea bacteria, oxygen is a poisonous gas that causes harmful oxidation to the cells and reduces the ability for them to conduct chemosynthesis. What is worst, is that oxygen destroys methane, ammonia, and hydrogen sulfide from the atmosphere and oceans that these prokaryotic cells need to live. There was one group of prokaryotic organisms that developed the ability to derive energy from the free oxygen now in abundance in the atmosphere and ocean. These were the precursors to the mitochondria found in most eukaryotic cells. Mitochondria converts free oxygen and nutrients into adenosine triphosphate (abbreviated ATP). ATP is how cells store chemical energy that can be used in metabolic activities, such as growth, movement and cellular replication. This process (called aerobic respiration) works by taking free oxygen and using it to convert carbon-based molecules into ATP that can be used for energy later in the cell. This highly efficient method of energy storage allows these types of cells to survive longer in an oxygen-rich environment that was beginning to occur in the early Earth. These organisms, however, still had to find a source of carbon, which they did so by being a heterotrophic organism, that is feeding on other cells. These bacteria are the aerobic prokaryotes. Some examples include the infectious Staphylococcus, a type of bacteria that feeds on animal cells, and causes many bacterial diseases and infections. Staphylococcus is a facultative anaerobe which means that cells can make ATP in the presence of oxygen, but can still survive anoxic environments by switching to anaerobic respiration, which is less efficient. The common gut bacteria Escherichia coli is another example of a prokaryote that exhibits both aerobic and anaerobic respiration. These bacteria survived by taking in oxygen, and respiring carbon dioxide back into the environment. When Lynn Margulis looked through her microscope watching the tiny moving individual celled Euglena, she could see that they in addition to having chloroplasts, also had mitochondria. These little eukaryotic organisms were a community, each and every one of them like tiny ships carrying prokaryote passengers, some that could photosynthesize and make carbohydrates, while others produced ATP for energy. Inside the cells, these chloroplasts and mitochondria could reproduce asexually independent as these organelles where like a well crewed ship, each type of organelle with a unique beneficial purpose for the cell as a whole. The heart of the ship, was the nucleus, protected by a membrane with its own series of DNA, often paired into chromosomes as twisted treads of double helix strands of DNA. The nucleus was like the captain of these tiny ships. If true, that the individual organelles were individual cooperating prokaryotic crew members, they should have their own genetic information within each organelle. In the 1960s, Margit Nass-Edelson and her husband Sylvian looked at mitochondria organelles under a scanning electron microscope, and discovered they do indeed have DNA within them. Lynn Margulis also documented DNA within the chloroplast organelles. Eukaryotic organisms were a symbiotic group of organisms working together to provide energy and nutrients to the larger cell. The endosymbiosis theory revolutionized biology, demonstrating an important driver in the strength of a community of organisms even at the smallest scales of life, such as a single eukaryotic cell.

Your body is a multiple of millions of individual ships filled with tiny prokaryotic evolved organelles all working together to give you the consciousness to read these pages, to understand these thoughts. Every human is a planet of their own multitudes. Illness and sickness and the consistent battles that rage inside your cells play out, as do the armies of your multitudes, without your own acknowledgment. Keeping you breathing oxygen, transporting your blood, making you crave food and drink, and serving you and your survival. It is odd to think about, that we are not a single one, but multitudes and multitudes of individual cells.

title: Planet Earth/7d. The Origin of Sex


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Planet Earth/7e. Darwin and the Struggle for Existence

Natural Selection
A little tombstone sits in the graveyard in the town of Malvern near Worcestershire England. It reads “''Anne Elizabeth Darwin, Born March 2 1841 Died April 28 1851. A dear and good child''” The death of Charles Darwin’s eldest daughter at the age of 10 came at a time in his life when he was struggling both with his mental and physical health and as a scientist. Since returning from his grand voyage around world in 1836, where he served as a scientific investigator on board the research vessel H.M.S. Beagle, Darwin had been feverously working on scientific reports describing everything that he saw and collected, including the rocks, fossils and animals that he collected onboard the research vessel. He had sent many of his collections off to the experts of the time, Richard Owen (who coined the word dinosaur) wrote about the fossils he collected, George Waterhouse wrote about the mammals, John Gould and George Robert Gray wrote about the birds, Leonard Jenyns the fish, and Thomas Bell the reptiles, each naming new species and varieties discovered during the expedition. These reports were assembled into a large edited volume describing, with wonderment and rich and detailed illustrations, the wide variety of life on Planet Earth. When it was completed around 1844, Darwin was married with a growing family, including little Annie, a joyful little girl. And he was beginning to turn to new projects, including a detailed study of barnacles, and other shells he had collected during his trip.

It was during this time that Darwin read a short essay by the economist Thomas Robert Malthus entitled “Essay on the Principle of Population,” which had been written in 1798, but recently reprinted in 1826. In summary, Malthus wrote “the power of population is indefinitely greater than the power in the earth to produce subsistence for man,” in other words, population sizes will continue to grow exponentially, until the population runs out of resources, and then it will crash. What pertained to bacterial populations, also pertained to human populations. A growing population was limited by the availability of food.

For Darwin, this idea that population growth was limited by available natural resources was something he wondered about in trying to understand how so many varieties of plants and animals came to be on the Earth. His second key insight came from his life in the country and working with livestock, and learning of the ways in breeding cattle, sheep, horses, dogs, goats, chickens and pigeons, which each had been selected for by the various traits that they possessed by famers of the day, who would artificially select which pairs to mate.

In fact, when he bought Annie a pet canary, a little yellow bird with a beautiful song, he was introduced into the world of bird-fanciers and breeders, who selected for the best traits, such as singing, or weird feathers, or large body sizes or unique colors, and only allowing those individuals to breed together. He also bought his children ponies; small horses bred to be tiny for his children to learn to ride on. It was from these homelier observations that he started thinking about the origin of new forms of life in the natural world. In particular, how did a new species come to be? What was the cause of all this variety of life on Earth? Most of his ideas were kept in a notebook, and still not well defined, composed of simple and loose diagrams and observations from talking with animal breeders in the rural country and visiting local county fairs. He also enjoyed exploring the countryside making observations in his notebook about the animals and plants that he witnessed on these trips into nature, but also sharing conversations over a fence on local breeds of dairy cows.

In 1848, Darwin become gravely ill, spending nights vomiting, and struggling to eat. He grew weary and sick. He entrusted his unfinished notebook to his wife, Emma, and told her that if he were to die, she should publish the work it contained. Worried about his condition, the family traveled to Malvern Wells looking for a cure for his sudden illness, where they meet a doctor. His name was Dr. Cully. He had developed a series of homeopathic cures featuring the emersion of one’s body into cold waters and bathing, as well as hot saunas, but also was known to consult ghosts through seances and other unorthodox treatments that were in vogue during the middle 1800s. Darwin was very skeptical of the treatments, but after a few months, the routine at Malvern Wells improved his health and he was able to return home. Much of his health was likely restored from the long walks that were part of the treatment, which he continued to practice into old age. In the Autumn of 1850, Annie became ill on holiday with the family with a fever and the family took her home to nurse her to health. They consulted a local traditional doctor, who prescribed some medicine. Still ill later that winter, she took to spending the day with her father helping to organize his collection of barnacle shells in his study. In early December, Annie developed a horrible sounding cough, and the Darwin’s again visited the doctor in London, who gave them the grim news of her serious illness. This was in the days before antibiotics, and typhoid was a major cause of death at the time. Typhoid is caused by a bacterial infection of Salmonella typhi found in unclean water that leads to a high fever, diarrhea, and vomiting. It can be fatal, especially in children. The worried parents took Annie to Dr. Cully as a last resort, as he had helped with Charles Darwin’s ailment before and maybe the treatment would help his sick daughter. During the early Spring, while staying at Malvern there was some hope of her improvement, but on April 28th, she died. Her death devastated Charles Darwin, and he entered into a dark period of his life.

Filled with depression and sadness, Charles Darwin’s productivity decreased during the years after Annie’s death. He published his work on barnacles which was dragged out over a few years, but melancholy kept him from returning to his earlier ideas. He kept thinking about the fragility of life, and how with Annie’s death, it was not just the death of her, as painful as that was, but all her offspring. She would bear him no grandsons and no granddaughters— it was like a great chain of being had been cut off. Life was a struggle- a struggle for survival. Five years later, with a push from his scientific mentor and hero, Charles Lyell, Darwin started to formula his ideas into an actual book. Like the process of breeders selecting mating pairs by the traits they possess, nature can select for advantageous traits in that not all individuals are able to successfully reproduce and pass on those traits. Only those individuals that leave offspring for the next generation leave behind those traits. With enough time, new species can arise when populations become isolated and exposed to different selective forces, as over time the population will adapt and change to suit the environment. Those individuals in a population that survive are the ones that reproduce and pass on their traits to the next generation. This book became known as “The Origin of Species, by Means of Natural Selection.”

Just when Charles Darwin was about to publish his book, however a letter arrived from a man named Alfred Russel Wallace. Wallace was working on the other side of the world, in Singapore in the 1850s and had discovered the possible evolution by natural selection that Darwin had been working on. Wallace was collecting natural history specimens that he hoped to sell on his return to England and was busy collecting on the Island of Ternate in Indonesia at the time. Here in 1858, he came upon an idea for evolution in which species can become organized by progressive steps checked and balanced by the necessary conditions of life, which leads to an extraordinary modification of form between each generation.

The idea was nearly the same as that of Charles Darwin’s. Wallace had written to him, with the hopes that he would pass it on to Charles Lyell for publication for the Linnaean Society meetings. When Darwin showed the letter to Lyell, the two decided to write back, and mention that Darwin had come to the same conclusion, although Darwin explained his explanation was part of large book he was writing on the topic. Later that year, in 1858 both Darwin and Wallace’s short essay was read to the Linnaean Society meetings. Sadly, Charles Darwin was unable to read it himself, as his young infant son died of fever a few days before, and Charles Lyell presented in his place. While the essay did not garnish much interest, Darwin’s book, which came out the following year quickly becoming a best seller, and altered culture even into the modern age— Charles Darwin is likely the best-known name in the field of biology, as Einstein is in physics. But he is often mistakenly characterized in the modern realm of science.

Darwin knew nothing of genetics, chromosomes, heredity, DNA, or RNA. Instead his writings resulted in our modern understanding of how life adapts by its continued process of being selected by nature. Death removes all of life in the end, but it is only those individuals that survive to at least the stage in life to have offspring and reproduce that succeed in the long run with a new generation after their parent’s death. Each generation growing stronger by the natural selection of traits that make each generation slightly better adapted to the world it confronts. This adaptive process of trial and error is powerful, resulting in the amazing diversity of life on our planet. Evidence for Darwin’s theory of natural selection was powerfully vindicated by fossilized remains of transitional animals preserved in an orderly fashion in the stratigraphy of rocks on the Earth’s surface. Each generation of fossilized lifeforms working to perfect the act of surviving long enough, long enough for a brief moment on Earth, enough to leave its descendants and a new generation.

The Species Problem
Darwin left behind more questions than he answered. Darwin viewed that organisms were naturally selected by the harsh environments that they found themselves in, and the best fit individuals of that harsh environment would leave behind the next generation, with each generation overtime becoming better adapted to the environment. If the harsh environment was too harsh, and zero individuals survived, then the lineage or species would become extinct. This trial and error method of change was similar to the artificial selection that animal and plant breeders will employ in cultivating the traits that they personally find advantageous. It is one of the reasons why there are so many different breeds of dogs, and such variety, each lineage was selected for those particular traits that make each breed unique. Darwin viewed differences in shape (morphology) and characteristics of each variety as a unique species of lifeform, which changed as the environment changed, but his ideas did not truly explain what a species is and how they originate. This led biologists to try to define what is a species? And secondarily how do they appear in nature?

The Biological Species Concept
Much of our current understanding of what a species is comes from the work of a famous ornithologist by the name of Ernst Mayr. Mayr grew up in Germany, with a complete fascination of birds, which he fanatically catalogued and described from his numerous bird-watching trips into the mountains of southern Germany. He could easily identify most birds on the basis of color, shape, and song, with particular skill. He would use the nomenclature of paired genus and species scientific names developed by Carl Linnaeus in the 1600s, as well as the local German common names for birds. After his education, he worked in Berlin at the museum continuing to catalogue the occurrence of various birds in the country. In 1927, he was introduced to Walter Rothschild, an eccentric wealthy English aristocrat. Rothschild was the oldest son of the famous Rothschild banking family in London. Walter Rothschild struggled throughout his life with a stuttering speech, and found it difficult to make connections with fellow humans, both in communicating verbally as well as being socially awkward and self-conscious when he spoke. It was animals that he felt most comfortable being around, and from an early age dreamed of building a private zoo, and taking care of an assortment of animals. As he grew older, he had the finances to make it possible and founded a zoo and natural history collection in London. This private collection housed many living species of animals collected from around the world, including many cassowary birds (large flightless birds from New Guinea). Rothschild had described many of these birds as new species, with slight observable differences in the shape of their crests and skulls. Fascinated with these birds from New Guinea, Rothschild was eager to continue to collect bird specimens from the islands for his collections in England. Ernst Mayr seemed the best choice to send on an expedition to New Guinea to find more bird specimens. For Mayr this was a chance in a lifetime, and he was eager to spend a year or more collecting birds in the tropical islands of the South Pacific and Indonesia and getting paid all the while. The adventure lead to the collection of one of the largest museum bird collections ever made of the region, and quickly Mayr discovered the importance of geography in the occurrence of species. Using the colors and morphology (shape) of individual specimens to name species, Mayr also found that he could use other differences to distinguish individual birds, such as differences in mating calls or behaviors he observed. These traits were localized to particular geographic regions, likely representing interbreeding populations. These traits may not be demonstrated by differences in observable morphology or color on an individual specimen back at the museum. He wondered how such behaviors would affect the localized breeding populations and influence mating or breeding between pairs in the wild.

On returning from the trip, the collections were added to Rothschild’s museum and zoo, but a mysterious scandalous event occurred a few years later which would allow Mayr to study the collections again. Rothschild was being blackmailed, and to make the payment he sold the valuable collection of museum bird specimens to the American Museum in New York, where Mayr was working after his return from New Guinea. For Mayr, it meant that his collection of birds he had personally collected in the field was within his possession again. He could study all of these birds in more detail, and furthermore he knew exactly where each had been collected. It was during this period of cataloguing specimens that Mayr begin to develop a new concept for what defines a species. Rather than distinguishing species based on similarity of appearance, Mayr began to distinguished species based on their ability to interbreed in nature. He developed the modern idea of a species— the biological species concept.

The biological species concept defines a species as individual members of a population that actually or potentially interbreed in nature with viable offspring. Species are defined this way by their ability to share genetic information within a population over time, rather than their physical appearance. The biological species concept differs from the earlier morphological species concept, which simply groups individual organisms by their shared appearance. The biological species concept groups individuals based on their ability to interbreed with each other instead. This more reproductive definition is somewhat difficult to distinguish in practice, because not all individuals will interbreed within a population. It is much easier to compare differences and similarities within individuals, but recent developments in bioinformatics (the study of genetic similarities and differences of organisms) has allowed biological species to be defined based on shared generic information, rather than their appearance.

Species are the fundamental unit of evolution since they pass on information through heredity of specific traits. These traits allow species to recognize each other in the wild, and will restrict interbreeding between species. The concept of what truly defines a species is debated among biologists, but often takes into factors of viability of offspring, potential ability to interbreed in the wild and genetic similarities between individuals, rather than appearance. Although the general appearance of animals and plants can be more directly used by biologists to determine a species in practice in the field, often discoveries of new species rely on genetic information as well.

How Species Originate
Ernst Mayr’s work in cataloguing the large variety of birds from New Guinea highlighted something also observed by Charles Darwin, that geographic isolation was an important factor in the origination of new species and varieties of life. During Darwin’s expedition around the world he collected many new bird specimens as well, most notably finches from the Galapagos Islands. The collection of birds was studied by John Gould who realized that they were all closely related to each other (appearing to share traits with the species Geospiza magnirostris, the Galapagos Ground Finch), but differed depending on which island the bird was collected from. Each bird appeared to be adapted to the particular environment of the island it lived on. Some birds had larger beaks to break tough seeds, while others had narrow beaks to feed on small seeds, depending on the local plants that grew on each island. Ernst Mayr discovered that birds were also localized, but this regional environment influence was the source of new species. For example, if a group of individual birds of a particular species arrived at a new island, and survived for many generations in isolation they would be subjected to different natural selection processes, and could come to resemble a different species over time. If they later returned to the original geographic range, they may not be recognized as the same species, and would not interbreed with the general parent population. This process of complete geographic isolation is called peripatric speciation, which was first proposed by Ernst Mayr in 1954, which states that species originate from isolated portions of the general population, which change due to differences in the local environment. This is often cited, for example when a species originates on geographic isolated islands, but can also be applied to regions along the periphery of a species geographic range if the individual population become cut off from the main parent population center. This idea has led to the discovery that most species originate along the periphery of a species geographic range, or when the geographic range of a species becomes fragmented. Together this style of speciation is collectively called allopatric speciation, which is used whenever biological populations of the same species become geographically isolated from each other to an extent that it prevents or interferes with gene flow. The term parapatric speciation is used when an isolate population is restricted from the parent population, but may not be completely isolated geographically. There is some debate if new species can originate within the population without geographic isolation or restriction. The origin of species from within the parent population is called sympatric speciation. Ernst Mayr viewed that sympatric speciation was rare or impossible, and indeed over the years examples of sympatric speciation have proven elusive, indicating that geographic barriers or isolation is the main driver in the origin of new species on Earth. Down the long museum halls of the American Museum, where Ernst Mayr worked on his bird collection, an equally large collection of fossil trilobites is housed. Niles Eldridge happily studied these ancient fossils that exhibit a wide diversity of varieties and forms preserved in Paleozoic shales from around the world. Long extinct, these small fossils are highly sought after by collectors who have named and classified many species and forms. Eldridge noticed that the observed appearance of new varieties and species in the fossil record exhibited a pattern which appeared to be influenced by the mechanism of parapatric and peripatric speciation, where new species or forms appeared to change rapidly in the periphery of a species geographic range, within a small isolated population, then expand outward, colonizing larger regions. Since the fossil record is limited geographically, these periphery small populations were not preserved in the fossil record as frequently, but do appear when they expand their range and population size. The temporal pattern of evolution observed in the fossil record is one of rapid change (or colonization) followed by status. In 1972, Nile Eldridge authored with fellow paleontologist Stephen Jay Gould the idea of punctuated equilibrium. Punctuated equilibrium states that species appear suddenly in the fossil record, and exist over time in stable populations that show little morphological change. The pattern is a result of the observation that most species originate from small isolated or restricted populations separated from the parent population These regions are rarely sampled in the fossil record, although examples have been demonstrated. Simply stated, this idea of evolution views that the major driving force for the great variety of life on Planet Earth is a result of peripheral changes occurring along the edges or among isolated small populations, which if successful will sweep out adding new varieties of life, as accumulations of layer upon layer of growing biodiversity.

Geographic reproductive isolation is important for the origin of species within sexually reproducing organisms, but asexually reproducing organisms, like bacteria can also speciate into new forms through isolation as well, but relies on chance genetic mutations or sharing of genetic information between individual cells. This process is much slower, since genetic information is slower to change in frequency over time in these populations, through the lack of intermixing of mating pairs.

Darwin’s Dilemma
Charles Darwin struggled to define how heredity of traits worked between mated pairs and their offspring. He recognized, as most of us do, that traits are passed from the parents to the offspring, but the mechanism behind this heredity was a mystery to him. Darwin coined the long disused term pangenesis, for this out of date idea that traits were blended together from both parents, but this presented the problem. The problem is that overtime the diversity or frequency of novel traits would decrease. For example, if you can imagine a population of a single species of a reproducing population of individuals, each individual in this population exhibiting a variety of color, say red ones, blue ones, and yellow ones, and each time one pair would mate and produce offspring, the resulting colored offspring would be a mix or blend of the two parent colors, for example a yellow and red pair, would produce an orange offspring. With each generation the population would began to look a drab gray, as more and more colors would be mixed with each generation. Like mixing or blending all the colors of paint together will also result in a drab gray or brown color over time. How does a population retain its genetic diversity over time? This idea of Darwin’s blended inheritance of traits was clearly incorrect, heredity was not blended or mixed equally from each parent, but there must be some other mechanism behind the heredity of traits. The solution to Darwin’s dilemma would come from a contemporary of Darwin’s, but one a world away in the highly religious Augustinian Order of the St. Thomas Monastery in Brno in the Czech Republic.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Happiness/Freedom

"The secret to happiness is freedom and the secret to freedom is courage." - Thucydides

"Courage is magic that turns dream into reality." -Aster and Richter abend

Go out from the nest to enjoy the beauty and cruelty of the world. Take its experiences and life lessons until you reach happiness and success in the future. Choose freedom, let world see your efforts and happiness will come in its way, god promises that. Letting go gives freedom and freedom is the only condition for happiness. When you come to the point where you have no need to impress anybody, your freedom will begin.

"Freedom is never given, it is won. " -A. philip Randolph

Break the rules find your freedom live your life.

title: Happiness/Freedom


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Free Knowledge Culture Calendar/December 12

Today in 1984 Cisco was founded. It became a multi-billion dollar company based on the production of physical infrastructure for the Internet.


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Free Knowledge Culture Calendar/May 3

Today in 1978 the first spam email was sent, one of the first cases of online advertising. Email spam is estimated to have reached ~90% of global email traffic.

title: Free Knowledge Culture Calendar/May 3


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Free Knowledge Culture Calendar/October 9

 Today in 1971 was the first time an email was sent from one host computer to another. Email is the oldest popular Internet service.


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Free Knowledge Culture Calendar/April 3

Today in 2004 the first working meeting of Guifi.net took place. Six weeks later the first permanent connections were established.

title: Free Knowledge Culture Calendar/April 3


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Free Knowledge Culture Calendar/May 26

Today in 1995 Bill Gates sent the “Internet Tidal Wave” memorandum to Microsoft executives, in which he acknowledges the importance of the Internet and the Web. Microsoft then abandoned its own proprietary “Microsoft Network” and turned it into a portal on the open Web.

title: Free Knowledge Culture Calendar/May 26


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Free Knowledge Culture Calendar/December 18

Today in 1987 the Perl programming language was released. It was designed for administrators, with a focus on manipulating text. Its power and a shallow learning curve allowed for quick, satisfying hacks and contributed to its once immense popularity, especially for operating Internet services. It held hundreds of thousands of websites together. Problems included a lack of focus on code maintainability.


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Free Knowledge Culture Calendar/November 25

Today is Richard Greenblatt’s birthday. He was a key figure in the early hacker and Lisp communities and a member of the MIT AI Lab. He pioneered running a commercial IT company with a hacker-friendly environment and flat hierarchies.


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Free Knowledge Culture Calendar/April 17

Today in 1977 the first West Coast Computer Faire was concluded.


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User talk:Promoter Samaras

Promoter Samaras

title: User talk:Promoter Samaras


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Planet Earth/7f. Heredity: Gregor Mendel’s Game of Cards

The Father of Genetics
In 1849, the timid young friar named Gregor Mendel taught lessons in the small city of Znojmo, he was a popular teacher and enjoyed teaching nature and science subjects at the local school. Initially Gregor was training to be a priest, and run his own parish church, but the local abbot recognized his interests in nature and science, and encouraged him to teach at a local school, rather than serve at a parish. The teaching experience gave Mendel encouragement to study science more than previously allowed in the strict boarding school or Catholic monastery he attended. In 1849, however, a new law was passed that required that teachers at schools be certified in the subjects that they taught, and Mendel had to take a test to prove that he was qualified to teach science. The exam to get his certification was an intense examination, requiring written essays, oral questioning from university professors, and detailed reports written on subjects of science, including physics, chemistry, geology and biology. Mendel failed the exams, which were administered at the University of Vienna. The failure however came with an offer to study at the University of Vienna, and Mendel returned to school to pursue a degree in science. It was during his schooling that he enrolled in the botany courses offered by Franz Unger, who popularized the ideas of shared descent, and was particularly interested in the fossil record of plants, demonstrating in class how the Earth and its plants changed over time. Unger authored a popular book in 1851, entitled Die Urwelt in ihren verschiedenen Bildungsperioden (The Primitive World in its Various Transitional Periods), which feature lithographic reconstructions by Josef Kuwasseg and Leopold Rottman of ancient natural landscapes, as they may have looked like in Earth’s ancient past. These were primordial landscapes, featuring strange lizard-like creatures, and fern covered dense tropical forests. Mendel had never been introduced to these ideas from his religious Catholic teachings; ideas of a very old Earth and change over long spans of time featuring strange lifeforms that grew on Earth in the ancient past. This was all new and very exciting, and the botany course taught by Franz Unger excited his imagination regarding the study of plants. At the monastery, however, many of his superiors viewed his scholarly pursuits of science as too secular for the friar. There was talk of disbanding the St. Thomas Monastery for allowing too much freedom of its members. His schooling at the university was one contention frequently brought up in local discussions with the church. After attending courses and working hard however (and after encouragement from his friends, the abbot and fellow friars), Mendel was ready to take the certification exam again in 1856 at the University of Vienna. On arriving to take the exam, he was relieved to see the first question was an easy one, but then the second one was harder, and he started to panic. His hands started to shake, his stomach wanted to explode, and he felt feverous. He felt the need to vomit, and fled the room in devastation, embarrassed at his sudden illness and suffering a nervous breakdown. Back at the monastery he refused to leave his room, his family were called for, and Mendel realized that he had failed the exam once again. He would never teach in a classroom.

A Game of Cards
Devastated by his failures in school Mendel had during this time begun experimenting by growing peas, and carefully pollinating each flowering and recording the appearance of traits in the offspring. He was interested in studying how plants and animals inherit traits. He had begun the project by pollinating various garden peas so that they breed true in terms of a variable trait, like flower color. The expression of a variable trait in a population is referred to as a phenotype. Phenotype is the scientific term used for the observable characteristics or traits of an individual organism, as a result of genetic variability. Using these true breeding plants, for example plants that always produce pink flowers, and plants that always produce white flowers, he would cross pollinate the two with each other, and record the frequency in the offspring that resulted in pink and white flowers. He noticed that when he did the experiment the ratio of pink to white flowers remained nearly the same, about 25% of the flowers were white, while 75% were pink. None of the flowers appeared to be a blend of colors, rather they exhibited either pink or white. It was these ratios that made Mendel suspect that the inheritance of traits was not like blending paint together (as Darwin assumed), but more akin to a game of cards, for which he only knew the outcome of, and not the rules to the game.

Imagine a deck of cards containing only red or white cards. Two cards are each dealt to each offspring pea plant player (we will call this hand of cards genotype) that will be used to determine the peas unique flower color (called a phenotype). The color will always be red, if any of the cards dealt are red. However, if the pea has no red cards, just white cards, then the plant will be white.

In this first game of cards (see above), the probability of a red card showing up is 75%, since the hand of cards could be two red cards (called homozygous since they are the same), one red and one white card (heterozygous since they are different), or one white and one red card (also heterozygous). All these hands of cards (called genotype) would result in a red flower.

The only way a flower would be white would be if the cards were both white (also homozygous). Hence red cards trump white cards in this game, and we referred these types of traits as being dominate. While white cards are recessive, meaning that you need both cards to be white in order for that trait to manifest white flowers as the phenotype. Each parent contributes one half of its cards (scientist called these hypothetical cards alleles), but only dominate traits are manifested when the pairs do not match, in this case red. This allows the diversity of traits to remain in following generations. As a test, Mendel took pea plants of the first generation, white ones and pink ones, and self-fertilized them, so that they only drew alleles from themselves. The white peas only produced white flowers, because both cards were also white. However, pink peas produced both white and pink flowers in the subsequent generation, indicating that some offspring were heterozygous, containing both a pink and a white card (which again are called alleles, or heterozygous). Mendel did similar experiments with seven other traits with peas, ranging from the height of the plant, to seed shape and color, as well as pod shape and color. All appeared to be related to a key ratio or outcome that suggested a pairing of traits from unique alleles. Since inheritance appeared to be a probability distribution, variability within individuals can be preserved between generations, it is only the frequency of those traits that change. This discovery allowed the retention of variable traits that natural selection could work on. In 1863, Mendel read a German translation of Darwin’s Origin of Species book, which was all the discussion among a small group of scientists that regularly attended local meetings in Brno. Gregor Mendel in February and March of 1865 published his classic study, which he read before the Brno Natural History Society, and was published in 1866. The now classic study was never read by Darwin, and despite rumors of Mendel writing to Darwin during his lifetime, no evidence of correspondence exists between the two. Part of this lack of communication between the two scientists was likely a result of their differing languages, and the fact that Mendel was overly humble and fearful that his scientific experiments on peas would cast too much attention from those within the Catholic Church, who frowned upon his evolutionary experiments with plants. Mendel himself may have repressed his ambitions when he became abbot of the monastery in 1868, acknowledging his failures at the university, and avoiding attention to his scientific interests. Mendel’s ground-breaking research was to remain obscure to the greater scientific community, especially outside of Vienna, even among fellow botanists who could quickly understand the importance of his experiments.

Rediscovering Mendel’s Experiment
In 1886, the Dutch botanist Hugo de Vries collected primrose seeds and planted them in his garden, noticing the great variety of flowers that the seeds produced, it was from this observation that he speculated that the plants must exhibit spontaneous mutations between generations, with the continued introduction of new traits, or phenotypes. In fact, the word mutant was coined by de Vries himself. This idea, which helped to explain increased variation between generations, was built on an older idea that there was some mechanism that changes between generations. He termed this mechanism or unknown molecule, pangenes, from Darwin’s idea of pangenesis. Later scientists shortening this term to simply gene. Hence de Vries viewed that genes mutate between generations, which introduce variation between each generation, helping to solve Darwin’s dilemma with blended inheritance. The problem with this idea was that it contradicted the experiments conducted by Mendel on peas. Mendel’s experiments were also ignored by the Swiss botanist Carl Nägeli, who despite numerous correspondences with Gregor Mendel never mentioned his work in his own publications, however, one of his students, Carl Correns became aware of the experiments and retested them while at the University of Tübingen, his verification was published in 1900, using Gregor Mendel’s name in the title of his paper. Overnight Mendel’s experiment became well known in biology, revealing an apparent pattern in how traits are inherited from parent to offspring.

Chromosomes and the complexity of cellular division in Eukaryotes
Study of individual cells of eukaryotic organisms highlighted a complex process of cellular division, which invokes not only the copying of the nucleus of the cell, but also the many organelles within each cell. In bacteria, cellular division (called binary fission) is a simple process of DNA replication and cytokinesis, which divides the cell into two equal halves each containing a complete DNA molecule. In eukaryotic cells, cellular division is more complex, because the cell contains a nucleus in which sets of DNA are arranged into a series of chromosomes. Chromosomes in eukaryotes are held together by chromatin fibers, which prevent the long molecules from becoming entangled within the nucleus of the cell. Unlike prokaryotes, in which the DNA forms a ring or circle and floats in the cell freely, chromosomes in eukaryotes nucleus are extremely long tangles of DNA molecules paired into a series of rod-like chromosomes. During cellular replication in eukaryotes, the chromosomes condense such that they can be seen under a microscope, as tiny X shaped structures.

Mitosis
Most eukaryotic cells reproduce by mitosis. Mitosis is the cellular replication that results in two daughter cells each having the same number and kind of chromosomes as found in the parent nucleus. In multicellular organisms, mitosis cellular reproduction is responsible for ordinary tissue growth. Cells within a multicellular organism will continue to grow and be replaced through mitosis throughout the life of the organism, until all cells expire with death and no longer replicate. While mitosis in single celled eukaryote organisms produces two copies (or clones) of the cell, with nearly identical copies (asexual reproduction).

There are a number of stages in mitosis cellular division in eukaryotic cells, the end result of which is that each chromosome is paired up (Prophase,) hung on a mitotic spindle (Metaphase), and then pulled apart into individual chromatids (Anaphase), replicating the missing paired chromosome to form a new nucleus (Telophase), and finally the cell will pitch off in the middle (Cytokinesis) forming a new copy of the parent cell. This type of replication is occurring all the time in multicellular organisms, producing new tissue and growth over time. This cellular replication allows a multicellular organism to heal and repair itself, and is happening throughout your body right now. Single celled eukaryotic organisms mitosis is a method of asexual reproduction. Each cell produced during mitosis is said to be a diploid (meaning that each cell has two copies of each chromosome).

Meiosis
The other type of cellular reproduction is called meiosis. Meiosis is much rarer, and only occurs in sperm and egg cells, called gametes in multicellular organisms. These cells rather than being identical copies of the original parent cell, produce genetically unique cells. First the cells produce four genetically unique gamete cells, each with half the number of chromosomes as found in the parent cell (haploid cells). These cells then come together through sexual reproduction between individuals. This process shuffles the genes forming new pairs, one received from each parent gamete cell, producing recombinant chromosomes with unique genetic combinations.

The best way to think of meiosis is that it is like shuffling two decks of cards (one from each parent) and splitting each deck to make a total of four piles, and then combining two of the piles to make a new deck with the same number of cards. In many primitive multicellular plants (such as ferns and many alga), these gamete cells can form gametophytes, or multicellular individual plants that contain only haploid cells. This results in a strange life cycle that starts with meiosis by reducing the number of chromosomes in each cell by half to make abundant haploid spores. These spores are released to the environment and develop into a gametophyte. The mature gametophyte produces male or female gametes (or sometimes both) by mitosis. These male and female gametophytes then come together in the water to produces a complete diploid zygote/seed (a cell with paired chromosomes). The fertilized seed then develops into a new sporophyte that will produce haploid spores and start the process again. Most gametophytes are small and associated with only the reproductive stage of a life span. Spores on the other hand can be protected for long periods of time (such as dinoflagellate cysts), and only become active when conditions become ideal for the organism to reproduce. Such a life cycle is employed by dinoflagellates, which are single celled eukaryotic organisms that make up much of the Earth’s phytoplankton in the oceans. Dinoflagellates, when they bloom during ideal conditions can result in toxic red tides for fish and other animals in the oceans. These organisms have evolved these strategies to help them survive harsh natural conditions.

Genetics
The discovery of how variation is maintained in a population of individual life forms through the continued recombination of chromosomes has revolutionized science. Many diseases and traits are inherited through genetic material either directly by recessive traits or by incorrectly copying chromosomes (such as chromosome duplications), or by mistakes or mutations that result in maladapted cells during cellular reproduction, such as in cancer. A clear overview of genetics is beyond the goal of this class, but knowledge of its existence explains the wide variety of life on Earth.

The Importance of Population Size and Genetic Diversity
One of the important factors that leads to new varieties of life on Earth is something called the founder effect. The founder effect is the loss of genetic variation that occurs when small populations are isolated. These small samplings from the larger population will statistically be limited in their genetic variation. This will cause them to exhibit fixed states due to the random sampling of the original larger population. This can sometimes be caused by a population bottleneck, when populations drop to small numbers. These tiny populations may not genetically represent the original population by their characteristics, and over time become unique, with increased inbreeding, and low variation. These isolated populations might become new species, but they are also prone to extinction. New species often originate from such isolated pockets in a geographically distributed population.


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Free Knowledge Culture Calendar/May 4

 Today in 2000 the first Fórum Internacional de Software Livre (FISL) started in Porto Alegre, Brazil. It is one of the world's largest free software events and part of the strong free software scene in Brazil.

title: Free Knowledge Culture Calendar/May 4


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Free Knowledge Culture Calendar/September 2

 Linux 1.0

Unix für PCs

Deutsche Slackware LST DLD Quellcode & Anwendungen Today in 1992 the Gesellschaft für Software und Systementwicklung mbH was founded, which developed the influential german SuSE Linux distribution that got many people into Linux.


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Free Knowledge Culture Calendar/January 19

Today in 1983 the Lisa desktop computer was introduced by Apple Computer, Inc. It started the successful commercialization of the graphical user interface concepts they had stolen from the 1973 Xerox Alto system.


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Free Knowledge Culture Calendar/August 27

Today in 2006 the first edition of Linux Mint was released.


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Free Knowledge Culture Calendar/August 21

Today in 2018 the Valve corporation released Proton, a compatibility layer for running Windows games on Linux systems.


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LLVM Compiler/OpenMP Support

With the release of Clang 3.8.0, OpenMP 3.1 support is enabled in Clang by default, and the OpenMP runtime is therefore built as a normal part of the Clang build, and distributed with the binary distributions. You do not, therefore, need explicitly to check out this code, or build it out of tree; a normal Clang check out and build will automatically include building these runtime libraries.

https://openmp.llvm.org/

installation
cmake -G Ninja -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=$LLVM_PATH -DLLVM_ENABLE_PROJECTS="clang;clang-tools-extra;compiler-rt;openmp" -DCLANG_BUILD_EXAMPLES=1 $LLVM_SRC/llvm

ninja install -j8 -l8

Hello example
cat omp_hello.c
 * 1) include
 * 2) include

int main (int argc, char *argv[]) { int nthreads, tid;

{
 * 1) pragma omp parallel private(nthreads, tid)

tid = omp_get_thread_num; printf("Hello World from thread = %d\n", tid); }

} clang -fopenmp -S -O3 -emit-llvm omp_hello.c

cat omp_hello.ll 1 ; ModuleID = 'omp_hello.c' 2 source_filename = "omp_hello.c"  3 target datalayout = "e-m:e-p270:32:32-p271:32:32-p272:64:64-i64:64-f80:128-n8:16:32:64-S128" 4 target triple = "x86_64-unknown-linux-gnu" 5  6 %struct.ident_t = type { i32, i32, i32, i32, i8* } 7  8 @.str = private unnamed_addr constant [30 x i8] c"Hello World from thread = %d\0A\00", align 1 9 @.str.1 = private unnamed_addr constant [23 x i8] c";unknown;unknown;0;0;;\00", align 1 10 @0 = private unnamed_addr global %struct.ident_t { i32 0, i32 2, i32 0, i32 0, i8* getelementptr inbounds ([23 x i8], [23 x i8]* @.str.1, i32 0, i32 0) }, align 8 11 12 ; Function Attrs: nounwind uwtable 13 define dso_local i32 @main(i32 %argc, i8** nocapture readnone %argv) local_unnamed_addr #0 { 14 entry: 15  tail call void (%struct.ident_t*, i32, void (i32*, i32*, ...)*, ...) @__kmpc_fork_call(%struct.ident_t* nonnull @0, i32 0, void (i32*, i32*, ...)* bitcast (void (i32*,     i32*)* @.omp_outlined. to void (i32*, i32*, ...)*)) #4 16  ret i32 0 17 } 18 19 ; Function Attrs: norecurse nounwind uwtable 20 define internal void @.omp_outlined.(i32* noalias nocapture readnone %.global_tid., i32* noalias nocapture readnone %.bound_tid.) #1 { 21 entry: 22  %call = tail call i32 @omp_get_thread_num #4 23  %call1 = tail call i32 (i8*, ...) @printf(i8* nonnull dereferenceable(1) getelementptr inbounds ([30 x i8], [30 x i8]* @.str, i64 0, i64 0), i32 %call) 24  ret void 25 } 26 27 declare dso_local i32 @omp_get_thread_num local_unnamed_addr #2 28 29 ; Function Attrs: nofree nounwind 30 declare dso_local i32 @printf(i8* nocapture readonly, ...) local_unnamed_addr #3 31 32 declare !callback !2 dso_local void @__kmpc_fork_call(%struct.ident_t*, i32, void (i32*, i32*, ...)*, ...) local_unnamed_addr

offloading example

 * 1) include
 * 2) include

int main(void) { int isHost = 0;

{ isHost = omp_is_initial_device; }
 * 1) pragma omp target map(from: isHost)

if (isHost < 0) { printf("Runtime error, isHost=%d\n", isHost); }

// CHECK: Target region executed on the device printf("Target region executed on the %s\n", isHost ? "host" : "device");

return isHost; } clang -fopenmp -S -O3 -emit-llvm -fopenmp-targets=nvptx64-nvidia-cuda offloading_success.cpp

relevant source files
List
 * tests: clang/test/OpenMP
 * Clang CodeGen for OpenMP IR:
 * clang/lib/CodeGen/CGOpenMPRuntime.cpp
 * clang/lib/CodeGen/CGStmtOpenMP.cpp //This contains code to emit OpenMP nodes as LLVM code.
 * LLVM OMP IR Builder: llvm/lib/Frontend/OpenMP/OMPIRBuilder.cpp
 * Runtime support: openmp/runtime/src/kmp_csupport.cpp

How to Debug
First, use -v to show the actual command line used by the clang driver:

clang -v -fopenmp omp_hello.c clang version 10.0.1 (https://github.com/llvm/llvm-project d24d5c8e308e689dcd83cbafd2e8bd32aa845a15) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /home/ubuntu/install/llvm_install/bin Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/7 Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/7.5.0 Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/8 Selected GCC installation: /usr/lib/gcc/x86_64-linux-gnu/7.5.0 Candidate multilib: .;@m64 Selected multilib: .;@m64

/home/ubuntu/install/llvm_install/bin/clang-10 -cc1 -triple x86_64-unknown-linux-gnu -emit-obj -mrelax-all -disable-free -main-file-name omp_hello.c -mrelocation-model static -mthread-model posix -mframe-pointer=all -fmath-errno -fno-rounding-math -masm-verbose -mconstructor-aliases -munwind-tables -target-cpu x86-64 -dwarf-column-info -fno-split-dwarf-inlining -debugger-tuning=gdb -v -resource-dir /home/ubuntu/install/llvm_install/lib/clang/10.0.1 -internal-isystem /usr/local/include -internal-isystem /home/ubuntu/install/llvm_install/lib/clang/10.0.1/include -internal-externc-isystem /usr/include/x86_64-linux-gnu -internal-externc-isystem /include -internal-externc-isystem /usr/include -fdebug-compilation-dir /home/ubuntu -ferror-limit 19 -fmessage-length 0 -fopenmp -fgnuc-version=4.2.1 -fobjc-runtime=gcc -fdiagnostics-show-option -fcolor-diagnostics -faddrsig -o /tmp/omp_hello-c73985.o -x c omp_hello.c

clang -cc1 version 10.0.1 based upon LLVM 10.0.1 default target x86_64-unknown-linux-gnu ignoring nonexistent directory "/include" /usr/local/include /home/ubuntu/install/llvm_install/lib/clang/10.0.1/include /usr/include/x86_64-linux-gnu /usr/include End of search list. "/usr/bin/ld" -z relro --hash-style=gnu --eh-frame-hdr -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o a.out /usr/lib/gcc/x86_64-linux-gnu/7.5.0/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/7.5.0/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/7.5.0/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/7.5.0 -L/usr/lib/gcc/x86_64-linux-gnu/7.5.0/../../../x86_64-linux-gnu -L/lib/x86_64-linux-gnu -L/lib/../lib64 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/7.5.0/../../.. -L/home/ubuntu/install/llvm_install/bin/../lib -L/lib -L/usr/lib /tmp/omp_hello-c73985.o -lomp -lgcc --as-needed -lgcc_s --no-as-needed -lpthread -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-linux-gnu/7.5.0/crtend.o /usr/lib/gcc/x86_64-linux-gnu/7.5.0/../../../x86_64-linux-gnu/crtn.o
 * 1) include "..." search starts here:
 * 2) include <...> search starts here:

Next, use gdb to debug the actual executable with the full command line options

 * gdb -args /home/ubuntu/install/llvm_install/bin/clang-10 -cc1 -triple x86_64-unknown-linux-gnu -emit-obj -mrelax-all -disable-free -main-file-name omp_hello.c -mrelocation-model static -mthread-model posix -mframe-pointer=all -fmath-errno -fno-rounding-math -masm-verbose -mconstructor-aliases -munwind-tables -target-cpu x86-64 -dwarf-column-info -fno-split-dwarf-inlining -debugger-tuning=gdb -v -resource-dir /home/ubuntu/install/llvm_install/lib/clang/10.0.1 -internal-isystem /usr/local/include -internal-isystem /home/ubuntu/install/llvm_install/lib/clang/10.0.1/include -internal-externc-isystem /usr/include/x86_64-linux-gnu -internal-externc-isystem /include -internal-externc-isystem /usr/include -fdebug-compilation-dir /home/ubuntu -ferror-limit 19 -fmessage-length 0 -fopenmp -fgnuc-version=4.2.1 -fobjc-runtime=gcc -fdiagnostics-show-option -fcolor-diagnostics -faddrsig -o /tmp/omp_hello-c73985.o -x c omp_hello.c

Warmup run of the compiler within gdb
 * (gdb) r

Set a breakpoint at 1829 llvm::FunctionCallee CGOpenMPRuntime::createRuntimeFunction(unsigned Function)
 * b CGOpenMPRuntime.cpp:1829
 * r # run it

Now can check the backtrace/call stack Breakpoint 1, clang::CodeGen::CGOpenMPRuntime::createRuntimeFunction (this=0x555565d75fd0, Function=0) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGOpenMPRuntime.cpp:1829 1829	llvm::FunctionCallee CGOpenMPRuntime::createRuntimeFunction(unsigned Function) { (gdb) bt   at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGOpenMPRuntime.cpp:787 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGOpenMPRuntime.cpp:3145 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGStmtOpenMP.cpp:1329 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGStmtOpenMP.cpp:1439 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGStmt.cpp:193 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGStmt.cpp:444 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenFunction.cpp:1146 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenFunction.cpp:1311 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenModule.cpp:4474 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenModule.cpp:2864 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenModule.cpp:5279 at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/ModuleBuilder.cpp:170 MainAddr=0x555557d541aa ) at /home/ubuntu/source/llvm_src/clang/tools/driver/cc1_main.cpp:240
 * 1) 0 clang::CodeGen::CGOpenMPRuntime::createRuntimeFunction (this=0x555565d75fd0, Function=0) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGOpenMPRuntime.cpp:1829
 * 2) 1 0x000055555af54a62 in clang::CodeGen::CGOpenMPRuntime::::operator(clang::CodeGen::CodeGenFunction &, clang::CodeGen::PrePostActionTy &) const (__closure=0x7fffffff80a0, CGF=...) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGOpenMPRuntime.cpp:3109
 * 3) 2 0x000055555af89801 in clang::CodeGen::RegionCodeGenTy::CallbackFn, const clang::Expr*):: >(intptr_t, clang::CodeGen::CodeGenFunction &, clang::CodeGen::PrePostActionTy &) (CodeGen=140737488322720, CGF=..., Action=...) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CGOpenMPRuntime.h:76
 * 4) 3 0x000055555af45212 in clang::CodeGen::RegionCodeGenTy::operator (this=0x7fffffff8080, CGF=...)
 * 1) 4 0x000055555af55072 in clang::CodeGen::CGOpenMPRuntime::emitParallelCall (this=0x555565d75fd0, CGF=..., Loc=..., OutlinedFn=0x555565d0bf78, CapturedVars=..., IfCond=0x0)
 * 1) 5 0x000055555aabd108 in emitCommonOMPParallelDirective (CGF=..., S=..., InnermostKind=llvm::omp::Directive::OMPD_parallel, CodeGen=..., CodeGenBoundParameters=...)
 * 1) 6 0x000055555aabdbbf in clang::CodeGen::CodeGenFunction::EmitOMPParallelDirective (this=0x7fffffff8880, S=...)
 * 1) 7 0x000055555aa94671 in clang::CodeGen::CodeGenFunction::EmitStmt (this=0x7fffffff8880, S=0x555565e22980, Attrs=...)
 * 1) 8 0x000055555aa95392 in clang::CodeGen::CodeGenFunction::EmitCompoundStmtWithoutScope (this=0x7fffffff8880, S=..., GetLast=false, AggSlot=...)
 * 1) 9 0x000055555ab1ff79 in clang::CodeGen::CodeGenFunction::EmitFunctionBody (this=0x7fffffff8880, Body=0x555565e229b8)
 * 1) 10 0x000055555ab20be3 in clang::CodeGen::CodeGenFunction::GenerateCode (this=0x7fffffff8880, GD=..., Fn=0x555565d0bd38, FnInfo=...)
 * 1) 11 0x000055555ab498d0 in clang::CodeGen::CodeGenModule::EmitGlobalFunctionDefinition (this=0x555565d73210, GD=..., GV=0x555565d0bd38)
 * 1) 12 0x000055555ab42709 in clang::CodeGen::CodeGenModule::EmitGlobalDefinition (this=0x555565d73210, GD=..., GV=0x0)
 * 1) 13 0x000055555ab4123f in clang::CodeGen::CodeGenModule::EmitGlobal (this=0x555565d73210, GD=...) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenModule.cpp:2567
 * 2) 14 0x000055555ab4d9a0 in clang::CodeGen::CodeGenModule::EmitTopLevelDecl (this=0x555565d73210, D=0x555565e20f20)
 * 1) 15 0x000055555baa4537 in (anonymous namespace)::CodeGeneratorImpl::HandleTopLevelDecl (this=0x555565d72870, DG=...)
 * 1) 16 0x000055555ba9de7a in clang::BackendConsumer::HandleTopLevelDecl (this=0x555565d72690, D=...) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenAction.cpp:214
 * 2) 17 0x000055555cf95464 in clang::ParseAST (S=..., PrintStats=false, SkipFunctionBodies=false) at /home/ubuntu/source/llvm_src/clang/lib/Parse/ParseAST.cpp:162
 * 3) 18 0x000055555b1ba873 in clang::ASTFrontendAction::ExecuteAction (this=0x555565d52ac0) at /home/ubuntu/source/llvm_src/clang/lib/Frontend/FrontendAction.cpp:1043
 * 4) 19 0x000055555ba9bd46 in clang::CodeGenAction::ExecuteAction (this=0x555565d52ac0) at /home/ubuntu/source/llvm_src/clang/lib/CodeGen/CodeGenAction.cpp:1179
 * 5) 20 0x000055555b1ba1d4 in clang::FrontendAction::Execute (this=0x555565d52ac0) at /home/ubuntu/source/llvm_src/clang/lib/Frontend/FrontendAction.cpp:936
 * 6) 21 0x000055555b14eb74 in clang::CompilerInstance::ExecuteAction (this=0x555565d4f490, Act=...) at /home/ubuntu/source/llvm_src/clang/lib/Frontend/CompilerInstance.cpp:965
 * 7) 22 0x000055555b325e07 in clang::ExecuteCompilerInvocation (Clang=0x555565d4f490) at /home/ubuntu/source/llvm_src/clang/lib/FrontendTool/ExecuteCompilerInvocation.cpp:290
 * 8) 23 0x0000555557d60900 in cc1_main (Argv=..., Argv0=0x7fffffffe2fb "/home/ubuntu/install/llvm_install/bin/clang-10",
 * 1) 24 0x0000555557d55a4c in ExecuteCC1Tool (ArgV=...) at /home/ubuntu/source/llvm_src/clang/tools/driver/driver.cpp:329
 * 2) 25 0x0000555557d561ca in main (argc_=54, argv_=0x7fffffffdef8) at /home/ubuntu/source/llvm_src/clang/tools/driver/driver.cpp:403

title: LLVM Compiler/OpenMP Support