week 2 journal #2

Submitted by jiadam on Fri, 02/03/2017 - 17:05

DNA dictates the sequence of amino acids. When talking about protein, you can break the protein into different structures. The primary structure is the sequence of amino acids. The secondary structure shows alpha helices and beta sheets. Tertiary structure shows the 3D structure of a protein and not the protein as chain. This is the first instance where the interactions between the side chain r groups are important because they show they affect how the protein folds. The amino acids that have non polar hydrophobic side chains primarily stay in the interior of the protein. The polar hydrophilic amino side chains encompass the interior. The last structure of protein is quaternary structure where multiple protein subunits come together and interact as a protein complex.

week 2 journal

Submitted by jiadam on Fri, 02/03/2017 - 16:29

Proteins are very important organic molecule because they have a slew of function in our body and keep us alive and healthy. The protein monomers are amino acids and a chain of amino acids becomes a polypeptide (protein) where “poly” is more than one and “peptide” is the amino acid. A neat way to think about this is with legos. You have one lego which is a amino acid. With multiple legos, you can build something like a house. When you have a chain of amino acids, you have a functional protein. There are 20 essential amino acids and the only difference between all the amino acids is the side chain r group. An amino acids is made up of a central carbon, an amino group, a carboxyl group, and the individualized r-group.

Perfect Paragraph Week 2 - Vocalizations

Submitted by kngallant on Fri, 02/03/2017 - 14:53

          Few animals on Earth have the ability to learn vocalizations, for example songbirds, humans, and whales. Vocal learning happens when young individuals try to reproduce vocalizations heard from an adult of the same species. This behavior is seen when human toddlers try to recreate words they've heard their parents say, resulting in babbling. The same thing occurs in songbirds, which was discovered in a two-part experiment. First, researchers incubated songbird eggs until they hatched in captivity. The newborn birds had no exposure to songs from adults, and the result was they could not form proper vocalizations, as they would in a natural environment. Next, a second set of birds born in captivity were exposed to recordings of adults of their species singing a typical song. The baby birds were successfully able to reproduce the same song they heard on these recordings. This indicated that songbirds must “learn” the songs they sing, and that they are not simply an instinct that is inherited. These results can be helpful when studying how and why vocalizations occur in other species around the world.

Methods Project: Initial breakdown

Submitted by lcampion on Fri, 02/03/2017 - 13:55

Methods Project: a multi-panel scientific figure that includes three elements (below)

-multi-panel scientific figure- embedded in paper; Figure 1 A, B, and C 

-use Inkscape to create figure

-methods written to allow someone to complete the same figure as you did; have to be able to find moss, take a picture, and identify the parts, then find/use the same location photos;


1) A close-up photograph of a moss on campus with sporophytes and gametophytes

-Moss= phylum: Bryophyta; flowerless plants, lack well developed vasclar systems, nontracheophytes; alternating generations life cycle;

-Moss Sporophytes= diploid, characteristics: shoots projecting upwards from the gametophyte(sterotypical moss); "foot" looks like gametophyte, long stem-like structure that pertrudes upward and is called the seta, on the top of the seta is a calyptra, a capsule that holds spores;

-Moss Gametophytes= haploid, characteristics: leaves, stems, short root system, what you think of when you hear "moss"; usually grows on rocks, damp soil, tree bark, concrete, and other stable surfaces;

-Photograph of a moss sample must be labeled.

2) A photograph that shows the setting with the moss location labeled

3) A map or orthogonally-corrected air photo that shows the location of the moss on campus

-Use Google Earth Pro (downloaded from class page)


This will be a part of the final paper.


The methods portion:

-create a google doc on umass.edu account

-write methods portioin on there 

-not directions! description of what you did as an exposition not a narrative

-when finished makw sbrewer@umass.edu as the OWNER of the document


-Follow someone else's methods once received to recreate their scientific figure

-create it as a PNG file, add to course website, title=Author's last name and "-Duplicate"

-once your methods has been followed and an image has been posted, post the original figure to the class webpage as "Campion-Original"


-write the rest of your paper on the same google doc that contains the methods section, as each section is completed

-include both figures and write a consise caption for your figure that explains each element

Emerald Ash Borer

Submitted by eriklee on Fri, 02/03/2017 - 13:51

For the first few weeks in lab, I worked with Ryan, another Graduate student/technician, observing infected saplings. We used a saw to peel the top layers of bark to find Ash Borer larvae. After they hatch, they create “galleries”, which are tunnels that zig-zag through the bark. The saplings were collected from upstate New York, Canada, and Western Massachusetts where the Ash Borer infestation is dense. The goal was to find living or dead larvae samples and count how many we find in a set of logs. We took measurements of the diameter and length of the samples. If larvae were deceased, we characteristics in the log such as Woodpecker marks, other beetle larvae, or fungus/pathogen infections. These indicated possible causes of death. 

Emerald Ash Borer

Submitted by eriklee on Fri, 02/03/2017 - 13:47

I started in the Elkinton Resource and Conservation lab February. My first Graduate Research advisor was Theresa. She worked with the Emerald Ash Borer Beetle. This beetle is considered an invasive species from East Asia. From East Asia, these beetles were speculated to have been transported by contaminated shipments of wood. Their infestation began around the Greek Lakes region and spread through the Mid-Atlantic, and then up the East coast to Massachusetts. Western Massachusetts and upstate New York are the central areas of study for Theresa.

For the first few weeks in lab, I worked with Ryan, another Graduate student/technician. We used a saw to peel the top layers of bark on tree saplings. These saplings were collected from upstate New York, Canada, and Western Massachusetts where Ash Borer infestation is strong. The goal was to find living or dead larvae samples and count how many we find in a set of logs. If samples were deceased, we characteristics in the log such as Woodpecker marks, other beetle larvae, or fungus/pathogen infections. These indicated possible causes of death.

For the rest of the semester, Theresa had me measure bark thicknesses of infected trees. She wanted to know how deep these beetles would lay their eggs in the saplings. I took measurements of the entire bark thickness and the top layer of the bark. To distinguish the top, I looked at the lighter colored layer. On each piece, I took two measurements of the peaks and valleys for accuracy. These values were first recorded onto paper and then transferred to an excel spreadsheet. 

Perfect Paragraph 1

Submitted by mduque on Fri, 02/03/2017 - 13:11

In my Animal Communications class we are studying chimpanzee vocalizations. The study and analysis of the vocalizations of Gombe Chimpanzees (Pan troglodytes) from (1971-193) by Jane Goodall provided us with sufficient data to help determine which male chimpanzee would fulfill the top position of the dominance hierarchy.  We organized and separated the data in a way in which allowed us to find a correlation between frequency of pant hoots and dominance. Our predictions of relative social-rank were based on vocalizations such as pant-hoots, pant-grunts, and waa-barks, as well as other factors including the individual’s age, and response from group members.

Chimpanzees (Pan troglodytes) are our closest living relatives, sharing more than 95 percent of our DNA and are amongst the most intelligent animals on the planet (Britten 2002).  They travel in fission-fusion social groups, meaning that the troops in which chimps function in, are constantly fluctuating.  This occurs dynamically as new members may join the troop, while existing members may wander off and join a different troop or start one of their own.  These Sub-Saharan primates have evolved to incorporate a dominance hierarchy within these groups to establish social order.

The dominance hierarchy among male chimpanzees is fairly linear, ranging from the most submissive male in the group to the most dominant alpha male.  Although female chimps have their own, more complex social hierarchy, a male chimp always retains dominance over a female (regardless of the female’s social ranking).  In addition to determining social-standing, the male-dominance hierarchy is used to settle disputes and to determine possession of females as mates.  By adhering to the social order in-stated by the dominance hierarchy, male chimps are often able to resolve conflicts with the use of vocalizations and gestures rather than resorting to physical violence.

Several factors play a key-role in determining which male will fulfill the top position of the dominance hierarchy, including physical strength, aggressiveness, intelligence, and age (Sapolsky 2005).  The alpha-male of a troop typically falls within a range of 20 to 26 years of age.  Male chimps assert their dominance through a variety of social interactions, such as vocalizations, facial expressions, body gestures, and actions (Arcadi 2000).

One of the most commonly used vocal signals among chimpanzees is the pant-hoot, a four-part call used by both males and females.  Pant-hoots are used in a wide variety of situations, including expressing excitement, food-enjoyment, and announcing arrival.  Because each chimpanzee has its own distinct pant-hoot, this call can be used to determine an individual’s identity.  As a result of cultural evolution, pant-hoots generally vary between geographic populations and individuals (Whiten & Boesch 1999). This is very similar to human accents and our ability to recognize each individual voice.  

Another important vocalization is the pant-grunt, which also serves as an indicator of dominance ranking.  The pant-grunt is a unidirectional call, expressed as a sign of submission from a lower-ranking chimp to a higher-ranking individual, therefore the direction of this call can be used to discern the social hierarchy.


consciousness and the cortex

Submitted by jdantonio on Fri, 02/03/2017 - 13:05

The question of how human consciousness and cognition are created has been a topic of debate in neuroscience and psychology for many years but recent studies have begun to uncover the truth as to where are consciousness is derived. A recent paper published by Desmurget et al. on the initiation of human conscious intent to move provides evidence that human consciousness is derived from a physical region of the brain and not some intangible force such as the “soul” or the “self”.

In the study patients posterior parietal cortex as well as their premotor cortex were stimulated via direct electrical stimulation. The patient was then asked a series of questions to determine what there conscious experience of the stimulation was.  The results showed that when the posterior parietal cortex was stimulated patients reported a strong desire to move different parts of there body and when the intensity of stimulation was increased they even reported that they had in fact moved there body part, even though they had not actually moved. The authors of the paper termed this illusory movement and suggested that this could explain why amputees often experience “phantom limb syndrome”. Desmurget and his colleges also stimulated the premotor cortex of the patients and questioned them on their conscious experience of the treatment. When patients premotor cortexes were stimulated they reported no sensation of having moved but there was clear evidence of muscle activity through both EGM monitoring of muscle cell activity and through physical movement observed by the researchers.

The evidence brought forth in the paper suggests that our consciousness is created within certain regions of the cortex and that our perception and intent of physical action are separated from the actual physical activities themselves. This refutes the previously held scientific belief that muscle movement drove intent to move and perception of movement. This raises and interesting question, If intent to move and muscle movement are derived from separate regions of the brain and do not appear to directly stimulate each other how then is intent to move converted into the command to move a muscle by the brain.  The author of the desmurget et al. paper suggests the answer could lie in the SAM region of the brain. Previous studies of the brain have shown that SAM stimulation causes the felling of desire to move similar to the posterior parietal stimulation but also at high enough levels of stimulation actually causes muscle movement. It has been speculated that intent may be derived in the parietal cortex and then integrated and relayed to the motor cortex by the SAM region of the brain.

The subject of human consciousness is still a matter of debate in the neuroscience community with many questioning if all conscious intent can be linked to the brain and to what parts of the brain. As studies move forward new evidence will be brought to light and one day we may fully understand where consciousness comes from. 


Desmurget, M., Reilly, K. T., Richard, N., Szathmari, A., Mottolese, C., & Sirigu, A. (2009). Movement Intention After Parietal Cortex Stimulation in Humans. Science, 324(5928), 811-813. doi:10.1126/science.1169896

Fried, I., Katz, A., Macarthy, G., Sass, K., Williamson, P., Spencer, S., & Spencer, D. (1991). Functional organization of human supplementary motor cortex studied by electrical stimulation. Journal of Neuroscience, 11(11), 3656-3666. Retrieved February 3, 2017, from http://www.jneurosci.org/content/11/11/3656

Journal 3

Submitted by abnguyen on Fri, 02/03/2017 - 12:55

The world is becoming overpopulated.  As we are currently destroying natural habitats to put up settlements, our resources are dwindling.  Prisons are overflowing and new diseases are constantly spawning.  I believe that we should start using people who have little to no purpose.  The parasites of society should be used as lab rats for disease testing.  Criminals who have been given the death penalty should be shipped off to a research lab where they are injected with illnesses we have no cure for.  If they can be cured before they expire then it’s a good thing, we cracked the code to save more lives.  If the person dies, then oh well, they were given the death sentence/life in prison anyways.  Sometimes the life of hundreds outweigh the lives of a few people who have thrown away their humanity.  If at least one good person’s life can be saved, then the sacrifice of a handful of scum is worth it.

Journal 2

Submitted by abnguyen on Fri, 02/03/2017 - 12:54

            DNA is a double helix that holds the genetic information that will be passed down to the next generation.  Its shape was discovered in the 1900’s and Watson and Crick were given the bulk of the credit for the findings.  They are thought to have stolen the concept from Franklin, a woman who many think deserve the bulk of the credit.  Personally I think she deserves more credit but not the majority.  Watson and Crick were able to piece together a puzzle that stumped most people for decades.  Yes, franklin did play a crucial role in deciphering the shape but she was reluctant to help the two.  Instead of offering her help when Watson came to London, she pushed them aside and dismissed his ideas.  I believe that if Franklin aided Watson and Crick she would have been a more respected scientist.

            From the discovery of DNA, sprung a number of experiments and attempts to better understand and alter the structure.  Currently, the most known and easiest method to change DNA is CRISPR.  CRISPR can cut out a segment of DNA and then add in an entirely new segments that codes for something completely different.  With the power of CRISPR known genetic diseases can be overwritten saving thousands of lives.  Hopefully we can start human testing soon.  The idea that it’s immoral to test on humans first is an outdated idea.  It’s better to test on a subject that is abundant and overpopulated than on a series of lab mice.


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