Saturday, April 2, 2016

Garden Creation Story

In the beginning God created heaven and earth. I do not believe the biblical creation story is a historical account of the beginning of life, but the myth of Adam and Eve still has deep meaning. Whenever I have to weed the garden I always think, “Cursed is the ground for thy sake… Thorns also and thistles shall bring forth to thee; and thou shalt eat the herb of the field; In the sweat of thy face shalt thou eat bread, till thou return unto the ground; for out of it wast thou taken: for dust thou art, and unto dust shalt thou return.“  The thorns and thistles that we are punished with are the little challenges of life. I’ve never heard a sermon on that but I like to think that is what it means. I kind of enjoy weeding the garden. Sometimes I like to think that Eve and Adam were quite bored in a garden that required no work. Imagine all the plants coming up by themselves like winning some sort of garden lottery without real appreciation for the work put in to the planting and caretaking. Gardening would be dull and unchallenging without weeds, thorns, bugs and sometimes bad weather. The weeds of life and the weeds of the garden work in the same way because they keep us challenged and distracted enough to keep us out of trouble.

Gardens are mentioned many times in the Bible. In the Song of Solomon, the woman’s body is compared to various plants. The Garden of Gethsemane literally means “oil press.” I’ve read that there are very old olive trees in that area that can be 900 years old. In the book of Esther the king’s gardens are mentioned quite a bit. In Ecclesiastes, Solomon talks about the beautiful gardens that he had planted. The city of Babylon is written about in the Bible, but I’m not sure that there is mention of the Hanging Gardens of Babylon. Historians are not sure if the Hanging Gardens were real or poetry. I like to think that the garden was real. There are people who have gardens with only plants that are mentioned in the Bible. I find that an interesting project and it would be a challenge.

Friday, April 1, 2016

The Smell of Soil

Pea plant wrapping itself around the previous year vine
Soil has a particular aroma but it is not the soil itself but an actinobacteria which produces geosmin. I like the earthy taste of freshly dug potatoes or carrots. There is a saying that a good farmer can know when to start planting by picking up a handful of soil and smelling it. This is a true statement considering the actinobacteria only thrives in warm soil. Since most seeds need a soil temperature between 50-77F which is optimum for the life cycle of the species of Streptomyces that I studied for a semester in microbiology. Below is an excerpt from my essay:   

Description of an actinobacterium isolate from soil sample taken in the vicinity of the Oconaluftee River, Great Smoky Mountains National Park
12 December 2012


There are over 500 recognized species of Streptomyces, which is a testament to how important the genus is to humans. Many Streptomyces species play important roles in the decomposition of organic matter and are ubiquitous in soil accounting for 106-107 per gram of soil. [10] The genus is an important source of antibiotics for both animals and plants. The genome of Streptomyces are typically large and that is attributed to the high number of genes required for antibiotic synthesis.[7] Chromosomes are linear, much like eukaryotes, and the chromosomal ends functions similar to the function of telomeres in eukaryotic cells. [11]

The isolated colony used for the study on the R2A agar was 1-2mm in size with an opaque consistency, circular appearance and curled edges. There was a zone of inhibition around the first colony which was undetectable with subsequent inoculated plates. The isolated colony appeared to change color from white to dark pink-purple with time, possibly due to nutrient depletion of the agar. The cause for the coloration of the colony is due to pigmented conidia and sporophores. [7] Depending on the composition of the medium, the colony can appear blue, gray, green, red, violet or yellow. [10] The life cycle of Streptomyces involves sporophores which form cross-walls in the multinucleate sporophores produce conidia also known as conidiospores or spores. [7] Conidiospores germinate to make substrate mycelium. [10] Dormant spores can readily be dispersed by air currents. [9] The colony had a particular earthy odor which was caused by a group of volatile organic compounds known as geosmins. [10]

Gram staining techniques showed the Streptomyces spp. to be gram-positive. Because gram-positive microorganism have cell walls a thicker layer of peptidoglycan, the crystal violet-iodine complex gets trapped in the cell wall making the cells appear dark purple. A negative staining technique was also performed to enable viewing the microorganism morphology and cellular arrangement. With the aid of a compound light microscope, the microorganism appeared filamentous with diameter sizes of approximately 1µm and a variable length size of up to 80µm. According to data collected about Streptomyces, the filament sizes are typically 0.5-1µm in diameter and indefinite in length. [7]    

Environmental parameter tests were performed to find the optimal environment which the microorganism could grow. The tests showed Streptomyces spp. to be a facultative anaerobe, but the growth was slower than aerobic environments. Temperature parameter testing was used to determine if the Streptomyces spp. could thrive with a range of temperatures. The results showed the species does not tolerate extreme temperatures of 4°C or 50°C and only two of the three streaks grew in 37°C. The microorganism thrived in the control condition of 25°C. A salt tolerance test was performed using concentrations of 0%, 5%, 10% and 15% NaCl. The Streptomyces spp. is halointolerant and only grew under the control conditions of 0% NaCl. A pH test also conducted and it was found the microorganism can tolerate a range of pH and growth occurring from pH 5-9. The pH test results show the growth of the microorganism in alkaline to neutral soils is more favorable than acidic.

Results from the environmental parameters test demonstrate the variable soil pH the Streptomyces can tolerate. Since the microorganism can tolerate lower oxygen levels as a facultative anaerobe, the depth at which the organism can grow varies. In one study Streptomyces was found in a three different locations of prairie soil at four depths. The study used variation in the 16S rDNA sequence to determine the genetic variation among the Streptomyces strains. There was little variation found in the genetic diversity from the isolates taken at differing soil depths. [5]  An extreme Streptomyces has been isolated from the hyper-arid Atacama Desert. Streptomyces desertai can grow in temperatures from 10°C to 35°C between pH 4 and 11 and in the presence of 4% NaCl. [12]

A modified catalase test was used to determine if the organism had the enzyme. Because the genus does not typically react with the standard amount used for a slide test, a modification of using more of the sample directly on the R2A plate was used. The Streptomyces spp. tested positive for catalase, which means the microorganism has the ability to convert hydrogen peroxide into water and gaseous oxygen. The microorganism does not have cytochrome c oxidase as a respiratory enzyme because it the results were negative for oxidase test. [1]

An Enterotube II was used to determine the metabolic characteristics of Streptomyces spp. The test included possible reactions with glucose, adonitol, lactose, arabinose, sorbitol and dulcitol fermentation, lysine and ornithine decarboxylation, sulfur reduction, indole production, acetin production from glucose fermentation, phenylalanine deamination, urea hydrolysis, or citrate utilization. The organism tested positive for the characteristic to ferment glucose and had a slow reaction with hydrolyzing urea.[1] The Streptomyces spp. uses the carbohydrate, glucose, as a sources of carbon and energy. A positive result for the enzyme urease means that the organism hydrolyzes urea to ammonia, CO2 and water. Despite the Streptomyces spp. inability to react with the majority of medium found in the Enterotube II, the microorganism has the ability to decompose biopolymers like lignocellulose, starch, chitin, pectin and latex. [8][10]

The rhizosphere zone in the soil profile is defined as the zone of soil that adheres to plant roots. Streptomyces thrive in the rhizosphere zone with the aerobic conditions and loose loamy soil. [9] With 106-107 Streptomyces per gram of soil, the microorganism is ubiquitous in the rhizosphere.[10]  Because of the filamentous mode of growth, the Streptomyces has a competitive advantage in colonizing around plant roots. Streptomyces decompose organic matter such as plant residues, but also benefit plants by growing in close associating with the root system where they protect the plant roots from potential invasion by fungal pathogens. Studies have shown with legumes, the Streptomyces assimilate iron from the soil and transfer it into root nodules where it is assimilated by bacteroids. [8] Streptomyces virginiae has been found to be beneficial in the prevention of tomato wilt caused by a soil-borne plant pathogen called, Ralstonia solanacearum. [3] The use of microorganisms to combat plant pathogens is only in the beginning stages, but using biocontrol microbes is considered to be a less invasive alternative to pesticides and fertilizers. The natural antibiotics produced in the rhizosphere are thought to cause less stress on the indigenous microbes when compared with chemical fungicides. Streptomyces can easily colonize the plant root surfaces because of the filamentous growth pattern, they can help protect roots against pathogens and can decompose organic matter. The spores can also be dried, packaged into powdered products making it a potential candidate for future commercial use. [8]

Within Actinobacteria there are many organisms that have antibacterial and antifungal characteristics. In a study involving fungus-growing termites, antibiotic screening has shown that most Actinobacteria throughout the termite nests produced molecules with antifungal activity. [6]

The zone of inhibition around the colony in the original first colony collected for this study demonstrated the antibiotic characteristics of the Streptomyces spp. It is interesting to note an organism is sensitive to the antibiotics made by other streptomycetes. The production of antibiotics is poorly understood, but it is linked with sporulation which may be a mechanism to inhibit the growth of nearby organisms competing for resources. There are over 500 distinct antibiotics produced by stretomycetes. [7] Over half of the commercially produced antibiotics originated from the genus. [10] Streptomycin and is often used in patients who are allergic to penicillin. The antibiotic Daptomycin is produced by Streptomyces and is used against pathogenic staphylococci and streptococci. Streptomyces platensis produces the antibiotic, platensimycin, which is effective against methicillin-resistant Staphylococcus aureaus and vancomycin resistant enterococci. The first treatment used against tuberculosis originated from Streptomyces griseus. [7] It is unclear if Streptomyces produce antibiotics in their natural habitat.[10]

A possible change to the study could involve using more cells for the metabolic tests. For example, by using more cells than usually needed for the catalase test, a positive reaction with hydrogen peroxide occurred. Using mediums other than those found in the Enterotube II may result in finding more metabolic characteristics of Streptomyces spp. Studying why the color of the colony changed with age would or possible advantages for the organism to have a variety of colors may be an interesting focus for future studies. Further studies may also include why humans are able to smell the compound and how it could have been useful to humans from an evolutionary perspective.

Sunday, March 27, 2016

First Day of Spring

Pear Buds
"Some people find fall depressing, others hate spring. I’ve always been a spring person myself. All that growth, you can feel Nature groaning, the old bitch; she doesn’t want to do it, not again, no, anything but that, but she has to. It’s a fucking torture rack, all that budding and pushing, the sap up the tree trunks, the weeds and the insects getting set to fight it out once again, the seeds trying to remember how the hell the DNA is supposed to go, all that competition for a little bit of nitrogen; Christ, it’s cruel." John Updike, The Witches of Eastwick

I have read several books by John Updike and I love his sensual somewhat erotic descriptions of otherwise mundane occurrences. In the brief quote above, he calls attention to sap, weeds and insects most people view those things as nuisances.

I’m a little late in writing this post… Easter is directly linked with the first day of spring because it is always the first Sunday, following the full moon, after the spring equinox.

In the northern hemisphere, the beginning of spring is considered to be the time when day and night are roughly equal. I was watching the news on the 1st of March and the weatherman called that day the first day of “meteorological spring” which I had never heard of the term before, but it means the months are divided into three months most closely related to temperature. The three warmest months are summer and the three coldest are winter. In other words, March, April and May are considered to be meteorological spring.
Blueberry Flowers

 I find it strange that many cultures do not view the spring and vernal  equinoxes as a significant time to divide the seasons. The Chinese  calendar and Celtic tradition place the first day of spring between the  winter solstice and spring equinox or around the beginning of  February. Imbolc refers to the Celtic spring with etymology possibly to  the old Irish world meaning “in the belly” linking to the lambing  season. There are several megaliths in Ireland aligned with the rising  sun during the time of Imbolc constructed during the Neolithic Age  (≈10,200-2000 BC). It’s interesting to note that Imbolc was also a time  for weather divination by watching to see if snakes and badgers came  out of their dens. Groundhog Day can almost be considered a type of  weather divination and is held roughly the same time as Imbolc.  Groundhogs are a little safer to watch than snakes and badgers but  native only to North America.

On researching spring, I came across an interesting Gaelic myth about Cailleach she is a weather, ancestor and creator deity. She is considered to be the Queen of Winter and gathers firewood on the Imbolc. If the weather is fair it means she can gather a lot of wood in preparation for creating a long winter. In contrast, if the weather is bad it means Cailleach is still asleep and not gathering firewood so the winter will be short. A specific day is used for weather divination for a season.      
Sugar Snap Pea Sprouts

 I included three photos of how the first day of  spring on March 20th looked this year. The pear  tree is usually tricked by the first warm spell and  blooms early in the season which usually results  in no pears because the last frost for where I live  is around the beginning of May. The individual  blueberry bush is rather early for flowers and  was the only one in bloom. Blueberries can  handle cold down to around 28°F, and I have yet  to have a year without blueberries so they should  be fine. Sugar snap peas are extremely cold tolerant and can tolerate quite a bit of snow I sowed the pea seeds on March 7th. Some people in western NC begin them as early as the end of February.  

Saturday, January 23, 2016

Social Media Distraction

Recent Snow Storm

I spend too much time on social media sites, at least six times a day I log on to fb. It's like I'm addicted to the lives of those around me. I think there is also the psychological need to feel important in other people's lives so sometimes I will post some photos about what I'm doing. I posted the picture above because it is informative to those who live where I do and are considering driving through town to get to work, but mostly anytime spent on social media is a distraction with a lot of visual noise. I have recently been keeping track of  my online time and it amounts to an average of about 25hrs a week of finding useless information. Occasionally I do find something that inspires me to write an article or expand an idea, but the vast majority of my online time is really just a waste and adds to a certain amount of frustration in my life. I often hear that we live in the information age but really I think we live in the age of distraction. What are we distracted from, though?   

Saturday, October 10, 2015

The Leech Place

The Leech Place
Murphy NC

Western NC is filled with Cherokee stories with almost every mountain, river, animal, plant and location having a story behind it. James Mooney’s “History, Myths, and Sacred Formulas of the Cherokee” is an excellent source of information about the area. I grew up living near the Cherokee Indian Reservation. My mother taught at the elementary school on the Reservation for a couple of decades and loved her job. She has a huge collection of Native American books. My childhood was surrounded by a combination of Cherokee folklore, Sundays with Bible stories and the living room bookshelf full of Norse myths.

I have come to realize that myths and legends make the most sense when one lives in the area they are being told. The environment where the story originated influenced the meaning behind it. We do things all the time that really are not connected to anything other than family tradition. For example, my family stands outside on New Year’s Eve and rings bells. We have cow bells and a huge dinner bell attached to the front porch. We are the only people in the neighborhood who perform this noisy tradition every year. It wasn’t until I spent a New Year’s Eve in Munich, Germany that our actions finally made sense because all of the church bells in the city ring in the New Year. My mother’s family came from Germany around 150 years ago and here we had been ringing bells ever since without the connection to the churches.

Recently I visited Murphy, NC which has its own Cherokee legend of a huge leech that lived in the bottom of a deep pool where the Hiwassee and Valley rivers join. Hiwassee is a Cherokee word for large meadow or savanna and according to Mooney, there is not a special story connected with the name other than it applied to two former settlements on the stream. The photo shows the remnants of a stone footbridge leading across the river and beneath that is where the “Great Leech” is said to live. The leech is described as having red and white stripes along its body and is as big as a house. On the one river bank is a steep rock cliff. The story goes that some men were walking on the trail above the pool and saw the leech roll and unroll on a rock and then crawl back down into the water out of sight, and the water then began to boil and foam until a huge column of water shot straight up in the air. According to the legend, the waterspout could be so strong as to carry a person down into the hole and that more than one person was found lying on the riverbank with their ears and nose eaten off. Another story is told of a man who wanted to hunt the leech and is said to have crossed the river halfway when a great wave overtook him and he was swept under never to be seen again.  

Written on a sign just above the river it mentions that there is a vein of red and white marble at the bottom of the pool which is visible with low amounts of sediment, so the location of the marble may have influenced the myth. We also have to realize that his river has been modified since the folklore behind the story originated. This river has been dammed and altered that I’m sure a few hundred years ago this was an extremely dangerous place to be and people actually drowned here.  

Tuesday, October 6, 2015

Der Schmied von Kochel

Der Schmied von Kochel

Yesterday I wrote about the strong men of myth and these stories exist throughout all cultures. Viking legends are filled with men who single handedly guarded a bridge or something similar and killed dozens of men. This is a statue of “Der Schmied von Kochel” I found him outside of a small church when I lived in Munich many years ago. I can’t remember which church the statue is near, but it is outside of tourist central so if you go to Munich you probably won’t find it. I miss going for long walks through Germany finding history and stories. 

My German is very bad and I can only find the story in German, so I’ll translate the best that I can. Der Schmied von Kochel means the Blacksmith of Kochel. He is a legendary figure for Munich. During the Sendlinger Mordweihnach or the Sendlinger Christmas Slaughter in 1705 he was the last man standing in a battle at the gate of Sendlinger where around 1,100 men died by the Austrian King Joseph I army. The blacksmith is described as a 70-year old and was of great stature and strength. According to Muenchenwiki he was not a real person but a legend. From another site it says his last words were, “lieber bayerisch sterben als kaiserlich verderben“ which means something like “Love for Bayern, death and ruin to the Kaiser.” He is a symbol for the love and honor to his homeland. There are still festivals and plays dedicated to him. If he didn’t exist there was a need to create him. I said in an earlier post all history somehow becomes myth. I hold myths in very high regard it doesn’t matter if they are true or not it only matters that they are told, and an important message is always hidden under the surface. In the German language the word Geschichte is the word for both history and story. 

Monday, October 5, 2015

Samson Summary

Many years ago I was a religious nutcase. I read the Bible obsessively and summarized most of it studying  an average of about three hours a day and I did it for a couple of years. During that time in my life I watched hundreds (perhaps thousands) of sermons, interviewed a Wiccan, studied the nearby Cherokee myths, attended humanist meetings and read some of the Quran.  Why I took on such an undertaking seems crazy to me now. I do love finding the commonality between completely different cultures through their myths and legends so that may have been much of my motivation.  

Below are some of my original writings from March 2010.

Samson is depicted as the strongest man in the Bible, and he is described by Wikipedia as having Herculean strength. I think that is a funny phrase that he had “Herculean strength” we all know what it means but it is strange to use Hercules as a comparative of Samson’s strength. Why don’t we say Samsonian strength instead? I’m writing a comparison of Thor, Hercules (Heracles in Greek) and Samson because they are all described as strong men. My favorite story involving Thor is when he wrestles with an old woman called Grandmother and he loses. It is later revealed that he was wrestling with old age and the myth represents growing old is a fight that no mortal can win.
Thomas Bulfinch wrote this in “The Age of Fable” about theories on where various Greek myths came from. “The Scriptural theory; according to which all mythological legends are derived from the narratives of Scriptures, though the real facts have been disguised and altered. Thus Deucalion is only another name for Noah, Hercules for Samson, Arion for Jonah, etc. Sir Walter Raleigh, in his “History of the World” says, “Jubal, Tubal, and Tubal-Cain were Mercury, Vulcan, and Apollo, inventors of Pasturage, Smithing and Music. The Dragon which kept the golden apples was the serpent that beguiled Eve. Nimrod’s tower was the attempt of the Giants against Heaven.” There are doubtless many curious coincidences like these, but the theory cannot without extravagance be pushed so far as to account for any great proportion of these stories.”

I read a little bit about Thomas Bulfinch (1796-1867) tonight, because he is a main source that I use when I read about Greek or Roman mythology. I found that I really like him as a person. He wrote this book in the 1850’s and he wanted to make myths available for everyone to be able to read and understand. Bulfinch was well educated but not rich. He worked as a bank clerk so he didn’t have a high social standing. He was a parishioner of King’s Chapel and a member of the Boston Society of Natural History. Writing and studying ancient literature were his hobbies not his job, and his room was described as having volumes of Latin, Italian, German and English classics piled on chairs. His first literary work was “Hebrew Lyrical History” where he rearranged Psalms so that they would be more of a narrative of Jewish history. In “The Age of Fable” he uses a similar method by connecting the myths in a logical way so they are easier to understand, but he doesn’t make them text-book fashion he keeps their charm and appeal. His goal was to make myths more accessible to the general public so that everyone could understand the symbolism used in British and American poetry.

Summary of Samson from March 2010 found in Judges 11-17.  

The Birth of Samson – Samson was of the tribe of Dan, and his father was named Manoah from Zorah. Samson’s mother is described as barren, but an angel came to her and said she would have a son. The angel told her not to drink wine or strong drinks and not to eat any unclean thing. She is told that no razor should touch his head because her son would be a Nazarite and would deliver Israel out of the hand of the Philistines. Remember the Nazarites? The ascetics mentioned in Numbers that any man or woman who makes the vow of a Nazarite should not drink, or eat kernels or shave his head. Manoah asked God to send the angel again to teach them what they should do when the child would be born. Then angel went to the mother in a field so she went to find her husband. Manoah asked the angel “How shall we order the child, and how shall we do unto him?” The angel told him the same thing that he said to his wife but he told Manoah to sacrifice a kid. During the sacrifice a flame went toward heaven and the angel ascended in the flame of the altar. That was the last time they saw the angel.
The Marriage of Samson – He saw a Philistine woman in Timnath that he wanted as a wife. Samson asked his parents if they would get her for him. His parents asked him if there were no women from his own people that he could marry instead of from the uncircumcised Philistines. Samson and his parents went to Timnath and to the vineyards when a young lion roared at them. Samson killed the lion as easily as he would have killed a baby goat with his bare hands. He then went to talk with the woman he desired to marry. When he returned home he saw the carcass of the lion had a swarm of bees in it. He took the honey and gave some to his mother and father but did not tell them he had gotten it out of a dead lion. Samson’s father went to find the woman and Samson made a feast for 30 of his wife’s people.  Samson gave a riddle to them that they had to figure out during the 7 days of the feast. He would give them a reward of 30 sheets and 30 garments. If they could not solve the riddle then they would have to give him 30 sheets and 30 garments. Here is the riddle, “Out of the eater came forth meat, and out of the strong came forth sweetness.” When they could not solve it in 3 days they told his wife that they would burn her and her father’s house if she could not entice Samson to tell her the answer. She cried to him but Samson said that he did not even tell his mother and father. He told her on the 7th day and she told her people. Samson was angry that she had told them and seems to refer to her as a heifer. He went down to Ashkelon and killed 30 men and took their garments and gave them to the men who had answered his riddle. Samson’s wife was given away by her father to a companion that he considered a friend.
The Revenge of Samson – Samson visited his wife with a baby goat as a sacrifice. Her father would not let him see her and told him that he had given her to his friend. The father says why don’t you take her younger prettier sister instead. Samson then went and caught 300 foxes and attached a fire to their tails, and he then let the foxes go through the fields of the Philistines. They knew Samson had set the fire because his wife was given to another so they went and burned the woman and her father to death. Samson then killed many Philistines and afterward he went to live on top of rock Etam. The Philistines went to find him and bind him. Three thousand men went to find him and tell him that they are his rulers. When they had carried Samson to Lehi and the spirit of God was in him and the cords were loosened. He found a jawbone of a donkey and killed a thousand men with it. Samson cried to God that he was thirsty and would die from it but God put water in the hollow of the jaw bone.
Samson and Delilah – Samson traveled to Gaza and saw a harlot. The Gazites had heard Samson was in the city so they waited for him at the gate of the city with the intention of killing him. Samson rose at midnight and took the doors of the gate and carried them up the hill near Hebron. He fell in love with a woman named Delilah who lived in the valley of Sorek. The Philistines told her to entice him and find where his strength laid. If she did that they would pay her a large sum of money. Delilah said to Samson, “Tell me, I pray thee, wherein thy great strength lieth, and wherewith thou mightiest be bound to afflict thee?” He told her that if he is bout with 7 green boughs then he would be as weak as other men. Samson had lied to her about this and broke the boughs. She then asks him again how he is weakened and he said with new ropes but he broke those as well. He then tells her that if she weaved 7 locks of his hair with a web but his strength was still with him so he had lied to her again. Finally he told her that if his head is shaved he would be weak. This time she saw that he was not lying. She told the Philistines who gave her money. When Samson was asleep with her holding him on her lap she called men to shave his head. He awoke and had not realized his strength was gone because his head was shaved so he went out to revenge the Philistines but they overpowered him and took his eyes out.
Samson’s Revenge and Death – The Philistines were grateful to their god, Dagon, that Samson was imprisoned. They were happy and wanted to make a sport of him. He was called and placed between pillars. Samson took one of the two middle pillars and broke it so that the roof of the building collapsed killing 3,000 people along with Samson.