Drafts

After reading these articles my stance on the problem of what we consider life is that we can consider all things that are able to self replicate as a form of life. When we are discussing life the main feature that people look for is the aspect of self replication. This aspect of life is found as too broad and includes things that people would be hesitant to call life. In the "Life is..." paper Carl Woese starts with the concept that life is just "an entity that can make a copy of itself from parts which are far simpler than itself" however later in the interview he goes back on this and questions this when the concept of a robots that could replicate is introduced. This hesitation makes sense since there is a numerous amount of vast differences between human made robot "life" and the life we know from studying our biology. This hesitation however is just from a naming perspective, classifying two things that are so different under the same umbrella. The question is where we decide to place this Umbrella of the term life for what and that determines what will fall under it and it has changed many times over the course of history as we learn more and more about how our world works. As brought up in the "Why life doesn't not really exist" the author points out the fact the living beings are also just a machine, just a much more complex one and therefore life does not actually exist. However there is a  distinction between the human machinery that we have created and the "life" we currently observe and that is the ability for self replication which I why i used it for my cut off point for my definition of life.

Regarding the carnivorans, the character #6, tail, has two character states. In this phylogenetic analysis, an elongated tail is the ancestral character state (scored with a 0) and a short tail is the derived character state (scored with a 1). In phylogeny A, a short tail is hypothesized to have evolved after the split between otters and the group of bears, sea lions, walrus, and seals. This proposes that a short tail is the synapomorphy for the monophyletic group of bears, sea lions, walrus, and seals. In phylogeny B, a short tail is hypothesized to have evolved twice. This is an example of homoplasy. For example, a short tail here is a derived trait for the seals, but it is also a shared derived trait for bears, sea lions, and walrus. However, there are a few separate divergences between seals and this group, and the common ancestor is hypothesized to have an elongated tail. In phylogeny C, a short tail is hypothesized to have evolved twice as well, but then lost in one lineage branch. For example, a short tail is a derived trait for the bears, but it also initially evolved as a shared derived trait for the sea lions, walrus, seals, civets, hyenas, and cats taxa. Cats, hyenas, and civets then lost this short tail trait. This is an example of an evolutionary reversal. In phylogeny D, a short tail evolved once in the lineage to include its monophyletic group branching from seals to dogs, but then this trait was lost later in the phylogeny in otters, raccoons, and dogs. This is another example of an evolutionary reversal. Based on this trait and the parsimony principle, phylogeny A is the most likely. The parsimony principle guides us to the evolutionary tree with the fewest character-state changes, and this is the one usually regarded as the best. In phylogeny A, the tail trait only evolved once in the lineage and was not lost at any point.

Our internal self is constantly fighting with the thoughts and opinions of others in trying to decide how impactful they are. However, sometimes people’s opinions can be beneficial to us(under certain circumstances). The idea here is that, you must recognize that whatever they say is their particular view or judgement. With that recognition, we are able to release ourselves from the belief that their judgement should matter the most. We’ll slowly be able to “free ourselves from fear and we no longer need to look outside for validation”(Formica, Michael J). We only look to others for some sort of validation to help support our self-esteem. A sense of validation from outside sources boosts our self-esteem ultimately “making us feel better as people”(Suval, Lauren). We shouldn’t have to rely on others to help us boost our self esteem, instead we should be completely satisfied with ourselves and not really need one’s intake of words.

Land birds and waterfowl maintain their directions at night by using the stars as their source of direction. Ornithologists also believe that birds use a geomagnetic map which is a map of horizontal space justs as gravity and barometric pressures and it gives information about vertical space. They also believe that birds use the Earth's magnetic field to orient them. 

Carbon dioxide can diffuse into the bloods plasma or into the blood stream. 7% of it dissolves into the plasma, 23% binds to hemoglobin, and 70% becomes bicarbonate. When carbon dioxide binds to hemoglobin it changes the shape of hemoglobin preventing it from binding to oxygen. When carbon dioxide in the blood stream reacts with water it forms bicarbonate and hydrogen ions. The hydrogen ions make the blood acidic. When the blood becomes highly acidic, it can disrupt the normal functions of a cell. Therefore, an increase in carbon dioxide in the blood can be dangerous. Carbon dioxide is constantly being filtered out of the body through the lungs. 

Monoamine neurotransmitter agonists are used to treat depression. Monoamineoxidase inhibitors (MAOIs) are use to inhibit enzymes that destroy monoamines. Monoaminesoxidase is an enzyme that destroys monoamine neurotransmitters in the synaptic cleft. So if the receptor was inhibited then neurotransmitters can stay in the synaptic cleft for longer. Tricyclics incresae the norepinephrine and serotonin by blocking reuptake. Reuptake is an ability of the presynaptic cleft to absorb any of the left over neurotransmitters back into the neuron. Having the neurotransmitters stay in the synaptic cleft for longer allows for more chances for the neurotransmitters to bind. Selective serotonin reuptake inhibitors (SSRIs) are used to increase serotonin within the synapse by blocking reuptake. Specifically it blocks the transporter on the presynaptic neuron. 

The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) was used as a homology-based method.  We performed a Standard Nucleotide BLAST of the RZW genomic DNA using the Highly Similar Sequences (megablast) program in the Expressed Sequence Tags (EST) database for Brachypodium distachyon (taxid: 15368).  All matches with greater than 95% Ident were saved. All of the saved ESTs were imported into the CAP3 software. CAP3 takes these and generated consensus contiguous sequences bases on the overlap between numerous ESTs.  To find a full length cDNA sequence for our gene, we performed a Standard Nucleotide BLAST of the RZW genomic DNA using the Highly Similar Sequences (megablast) program in the Nucleotide Collection (nr/nt) database for Brachypodium distachyon (taxid: 15368).  We found accession number XM_003562897.4, an mRNA sequence that is predicted to code for the Brachypodium distachyon G-type lectin S-receptor-like serine/threonine-protein kinase B120 (LOC100825184). The two contigs were aligned to the cDNA sequence using the NCBI BLAST.

For our project proposal my group had two different ideas. The first idea that we had was to monitor the behavior of ducks and geese on the campus pond. We would monitor many different things in order to create nine separate research projects that every group could complete. One thing that we would test is the correlation between the weather and how many geese or ducks would be on the pond. Another thing that we would try and measure is how many ducks and geese are on the pond at a specific time of the day. To do this a group would need to take measurements at multiple time periods throughout the day. Another thing we would try and measure is how the ducks and geese reacted when people were nearby. Did they leave the land to go in the pond during class transitions? Did they leave the pond all together? Were they inclined to come up to the people? Questions along those lines. Another key aspects of this question that we would try and test is the ratio between ducks and geese on the pond at any given moment and if anything changes to affect the ratio of them. To better understand this last aspect we must first find any correlations within the previously mentioned questions.

When a geneticist is given an unknown DNA sequence and is tasked with finding out its function, there are two approaches.  Ab initio, or “from the beginning” involves using programs that analyze the sequence for known trends in gene expression. These trends include translation initiation occuring at ATG, and intron boundaries being defined by GT at the beginning and AG at the end.  Stop codons include TAG, TAA, and TGA. Using these in combination with more complex trends of gene expression, ab initio programs can make a prediction about the coding sequence and protein sequence of a gene. The other method is homology based searches. These include comparing a query sequence to sequences of nucleic acids of a known origin. In this lab, we begin by building two predictions of the protein our gene encodes: one using ab initio methods and another using homology based methods.  For the ab initio method, we use the program FGENESH. For the homology based searches, we use Phytozome and NCBI BLAST. We compare the two predictions and proceed to research our gene of interest.  We then provide an assessment of function of our gene.