aspark's blog

Google gains its credibility from being a well-known resource used by the vast majority of computer-users. The amount of information available on Google also contributes to its reliability; however, the reliability of Google can be questioned based on recent accusations against their bias for website order. The order of website results is affected by your location, history, etc. It's up to users to decide which websites available on Google are trustworthy or not. The fact that Wikipedia pops up on the side of the page when "ecology" is searched also lessens its credibility becasue Wikipedia is not considered a very trustworthy source. Google curates scientific literature in Google Scholar that is more credible and from established scientific journals. 

DNA extraction was performed in the laboratory today. Leaves from the plant Brachypodium distachyon were frozen in liquid nitrogen and placed inside a 2-mL round-bottom tube with two metal balls. A machine was used to shake the tubes vigorously, allowing the balls to grind up the frozen leaves inside into a fine powder. Detergent was added to the powder to break down the cell and nuclear membranes, and ethylenediaminetetraacetic acid was added to stop the cells’ enzymes from degrading the DNA. The tube was then incubated and chilled in ice. A potassium solution was then added to the tube, which caused the proteins and carbohydrates to precipitate. The tube was centrifuged, causing the precipitated contents to form a solid pellet. The supernatant containing the DNA was transferred to a new, clean 2-mL tube, and isopropanol was added to the solution, which caused the DNA to precipitate. The tube was centrifuged, causing the precipitated DNA to form a small, clear pellet at the bottom of the tube. The supernatant was extracted, and the DNA pellet was washed with 70% ethanol. Lastly, the DNA pellet was dissolved in a preservation solution.

Covalent bonds occur when atoms share electrons; however, becasue different atoms have different electronegativites, there is often an uneven distribution of electrons between the two that are covalently bonded. This results in polarity, where one atom is slightly positive, while the other atom is slightly negative. This can lead to interactions with other molecules that result in non-covalent bonds. Non-covalent bonds are electrostatic. This does not mean that they are only between fully charged molecules. Non-covalent bonds occur when two molecules have any sort of charge: partial or full or temporary or permanent. They can be intermolecular or intramolecular, meaning two parts of one molecule interact with each other. Noncovalent bonds are classified based on their magnitude and duration. Ionic bonds occur between opposite permanent, full charges. Meanwhile, van der Waals interactions occue between opposite temporary, partial charges. Dipole interactions describe any non-covalent bond in between. Dipole interactions can be dipole-dipole, ion-dipole, etc. A very important dipole-dipole interaction is the hydrogen bond. A hydrogen bond occurs when it is bound to a highly electronegative atom, usually nitrogen or oxygen. This causes the hydrogen atom to hold a permanent, partially positive charge. When it interacts with an atom with a permanent, partially negative charge, it forms a hydrogen bond. 

Today we quantified DNA that was extracted in an earlier lab session. A single sample of DNA was split into two, one being treated with RNase while the other was not. Each was measured using a spetrophotometer, which tests the absorbance of just one microliter of the sample, just enough to form a drop. The greater the absorbance, the more DNA in the sample. The sample treated with RNase is expected to have a lower absorbance because the RNA is degraded. It turns out that a lot of the "stuff" extracted was also RNA along with the DNA. Our absorbance for the RNase-treated sample was a bit lower than expected, meaning our DNA sample was not very pure. We then did gel electrophoresis with our samples. With each sample, both the RNase-treated and non-RNase-treated samples, we diluted some to 50%, which resulted in a total of four samples. Each of these four samples were treated with loading dye to allow it to sink when loaded into the gel and indicate the migration of the samples across the gel. We poured the gel with a dye added to it that will allow the samples to be visible under blue light. After the gel had solidified, we loaded a standardized DNA ladder into the first two wells. We then loaded five microliters of each sample into the next four wells. We ran the gel at 100 volts for 30 minutes, and we viewed the gel under blue light to illuminate the migrated samples. As expected, the samples treated with RNase only had one stripe, which the samples that weren't treated with RNase had two, one that represented the DNA and one that represented the RNA. The DNA was longer in length, so it did not migrate as far as the RNA, which formed a stripe much farther down the gel. Also as expected, the diluted samples had fainter stripes, showing that there was less DNA and RNA contained. 

The geese have mostly brown feathers on their backs while their undersides are mostly white. While the feathers on its torso are shorter, the featers at its tail are longer and fewer in number. There is a sudden shift in color at its neck, which is black up through its face and beak. Its cheeks remain a clean white. The geese float on the water, with only about a tenth of its body submerged in the water. Some geese lower their body and crane their necks out to peck at food floating on the surface of the water. One goose glides along the water with its neck perpendicular to the surface, looking like it is scoping the surface for any food. The necks of the geese are clearly very flexible. They can bend in a "U" shape before extending to reach for something. The baby geese are smaller, about one fifth the size of their parents. They are mostly brown in color, but it is a light brown that is much softer than the darker gray-brown feathers of the adults. The undersides of the young geese are still white, and the necks and face remain white and light brown. There is no traces of black in the feathers of the young geese, except for their small beaks. They have much shorter necks than the adults, making them resemble ducks more than geese. They too peck at the water for food, cocking back their head and lurching forward to grab anything. Occasionally the adult geese extend their necks straight into the air, although it is unknown why. As the geese move, they create ripples in the water. 

Today I performed DNA extraction in a labratory course. We took the leaves of a plant and ground it up using two metal balls inside the 2 mL roundbottom tube. The tube was attached to a machine that shook the tubes rapidly and rigorously for one minute. That was enought to crush the frozen leaves in a fine powder. Detergent and EDTA were added to the powder to break down the cell and nuclear membranes and stop enzymes from breaking down the DNA. The tube was heated and chilled. Next we added a potassium solution to the tubes to cause proteins and carbohydrates to precipitate, which they did. After centrifuging the tube, the supernatant containing the DNA was transferred to a new, clean 2 mL roundbottom tube. Isopronanol was then addded to the solution to cause the DNA precipitate, leaving behind lipids and remaining proteins and carbohydrates in the solution. The content was centrifuged once again, and this time, the pellet was what we wanted to keep, for it was the DNA. The resulting pellet was very small and almost clear. It appeared as a small, cloudy smudge on the bottom of the tube. We extracted the supernatant and washed the DNA pellet with 70% ethanol. The DNA pellet was then dissolved in a solution that would preserve the DNA to be able to be used far in the future. 

A jar of walnuts is turned to its side on the lawn. A squirrel propels off of the side of the tree and lurches toward it. It is gray with brown in its tail and face. It also has sprinkles of white fur. It has a bushy tail, bent in the middle so that the bottom half flaps in the air. It suddenly stops and darts in the opposite direction. It turns and hesitantly approaches the jar of nuts again. It darts to the jar and grabs a walnut. It jumps far from the jar and nibbles on the nut using both of its hands. With the nut in his mouth, it climbs back up the tree. Just then, a second squirrel approaches the jar in quick, sudden movements and reaches its arm inside to grab a walnut. It squats next to the jar and nibbles on the walnut, similarly to the first squirrel. It then darts away, across the lawn, with the nut in its mouth. The way it moves is that it jumps forward using its back legs and lands on its front arms. It's like taking little jumps forward. The squirrel scurries up the tree. 

The development of an embryo is a very unique and odd process when you really think about it. Two essentially halves of a cell come together to form a full cell with a full genome. This cell continues to divide, and along the way, these cells begin to differentiate and form different parts of the larger oganism that is being created. It's strange to think that cells that have organelles to regulate themselves and take care of themselves work together to form a greater being. They stop functioning for their own sake and begin to function for the survival and wellbeing of the larger organism it is a part of. Organs and different types of tissue are created, and these cells communicate using hormones and other cell signaling ligands. Eventually, a full human is formed that will continue to grow and develop outside of the womb. 

There is a single larva-like organism contained within a clear, plastic container. The larva's body is long, semented, and tan in color with a dark brown head at one end. There are also brown flecks along its side. The organism moves around the perimeter of the container using its many small appendages on its underside. Waves travel through its body from the back to the front, propeling the organism forward. The organism seems to want to leave the container, rearing the upper half of its body up onto the container walls and scratching the sides with its front six appendages. 

There's a larva-like organism in the small, clear container. The organism is off-white, almost tan, in color with brown flecks along its side. It has a small, brown and red face at oe end of its long, segmented body. The organism travels around the perimeter of the container on many small feet on its underside. Waves of motion starting from its back end propel the organism forward. Its face presses up against the sides of the container, and its stops to rear its front body up and scratch the walls with its front feet. These front six feet don't have much traction. The organism flips over easily when I tilt the container.