HIV Treatments

In chapter 1 I was interested by HIV treatments and what kind of things they are trying now besides the drug "cocktails." The textbook doesn't go into much detail besides the combination of drugs treatment and I figured I would see what other ways they may be trying to treat HIV. I found that there is actually one case where a patient was cured of HIV and no longer has to take antiretroviral drugs anymore either. The patient received a bone marrow transplant for his acute myeloid leukemia. The donor for the transplant had a genetic mutation that didn't allow HIV to enter the cell; the article didn't say what mutation it was but it could be the delta 32 mutation we learned about. That patient, who lives in Berlin, is the only one who was "cured" of the disease and was able to stop taking medication; however, there are two other cases where bone marrow transplants have reduced HIV to undetectable amounts. The two men received transplants trying to see if the HIV could be removed from their plasma, but the doctors were surprised to find that there were also no traces of the virus in their cells. These men still remain on antiretroviral medication and treatments and the doctors are still searching for traces of HIV in the patient's tissues.
The fact that bone marrow transplants have showed some positive outcomes is interesting, but a transplant like that is both difficult and dangerous. Luckily there are still other ways that people are looking to combat HIV. Another group of researchers are looking at histone deacetylase inhibitors (HDIs) and psycho-stimulant drugs like cocaine. These drugs and HDIs can both control gene expression by way of altering chromatin structure in DNA. The HDIs in a way force out dormant HIV viruses that can be hiding in the body. They believe that the psych-stimulant drugs can act the same way and ultimately the two can be used to possibly find a cure for HIV.
For more information regarding this check these sites out:
http://www.sciencedaily.com/releases/2012/09/120921124633.htm
http://www.sciencedaily.com/releases/2012/07/120726153945.htmhttp://articles.latimes.com/2012/jul/27/news/la-heb-hiv-cure-aids-meeting-20120727

Chapters 1-4

As much as I hate to read (I always have), I actually enjoyed reading chapters 1 through 4. I find evolution a fun and interesting topic, and learning about it is very exciting.
Chapter 1 mostly discussed the HIV and its continuing evolving pattern. What interested me the most about HIV was how its populations can resist to certain drugs or treatments. This occurs due to mutation, inheritance, and differences in survival to AZT for example, which results in a change in the composition of the population over time. HIV is one of the fastest evolving entities known. It reproduces sloppily, accumulating lots of mutations when it copies its genetic material. It also reproduces at a lightning-fast rate, a single virus can spawn billions of copies in just one day. To fight HIV, we must understand its evolution within the human body and then ultimately find a way to control its evolution. When all is said and done, there are 3.1 million AIDS related deaths per year ( as acquired from Yale AIDS watch), and I am hoping someone finds a cure ASAP.
Chapter 2 went more into detail of "decent from a common ancestor." There is numerous examples and evidence of this. The example that caught my attention was the observation by Louis Agassiz who observed the similarities of embryos. Figure 2.20 on page 55 shows that embryos from different vertebrates (from snakes to possums to humans) all have very similar traits, such as a tail and pharyngeal pouches in early stages.
Natural selection is broadly defined in chapter 3. A huge portion of this chapter discussed Darwin's 4 postulates, or components. These are:

1. Variation. Organisms within populations exhibit individual variation in appearance and behavior. These variations may involve body size, hair color, facial markings, voice properties, or number of offspring. On the other hand, some traits show little to no variation among individuals—for example, number of eyes in vertebrates. 
2. Inheritance. Some traits are consistently passed on from parent to offspring. Such traits are heritable, whereas other traits are strongly influenced by environmental conditions and show weak heritability.
3. High rate of population growth. Most populations have more offspring each year than local resources can support leading to a struggle for resources. Each generation experiences substantial mortality.
4. Differential survival and reproduction. In other words, survival and reproduction are NOT random. Individuals possessing traits well suited for the struggle for local resources will contribute more offspring to the next generation. 

The panda's thumb was pretty interesting. Figure 3.9 explains the modified wrist bone helps the panda grasp a bamboo stalk. This of course is an example of preadaptation.
I found learning about phylogenetic trees in chapter 4 fascinating. I had a little bit of this topic in general biology, but learning it more extensive was entertaining. A phylogenetic tree is defined (from our textbook) as a diagram or estimate of the relationship of ancestry and descent among a group of species or populations; in paleontological studies the ancestors may be known from fossils, whereas in studies of extant species the ancestor may be hypothetical constructs. That definition is quite extensive, and a bit confusing. This YouTube video helped me better understand a phylogenetic tree:

















For more information on these topics, check out these websites:

http://www.eou.edu/~jjohnson/Chapter%20Five%200909.pdf

http://onthehuman.org/2010/06/common-ancestry-and-natural-selection-in-darwin%E2%80%99s-origin/

http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956

Vestigial Traits

One aspect of evolution that has always interested me is vestigial traits. We are taught that every organ and bone in our body has a special and vital role in allowing our bodies to function. However, this is not the case. Certain traits called vestigial traits break this “everything has a vital purpose” rule. Vestigial traits can be an actual organism, a DNA sequence, or just an involuntary action. They are one of the above examples that have no immediate function or purpose in the species, but is vital to another, closely related species. Darwin was one of the first to realize that these traits were evidence of evolution. These traits were necessary for survival in one species, but as that population evolved the trait or body part was no longer needed. Instead of disappearing all together, the body part is found in the new species but doesn’t play a necessary role in function. Scientists have used these traits to link species together. It helps to prove that two species came from a common ancestor and evolved.

Vestigial traits can be seen in most species, including humans. One of the most famous vestigial organs is the appendix. It was once used by primates to help with the digestion of cellulose rich plants, but is now unused by humans. Often the appendix can become a nuisance and even deadly, in which case it is removed. We are able to function completely unharmed in absence of our appendix. Wisdom teeth are another example of a vestigial trait in humans. Kiwi's have tiny wings which are considered vestigial traits since the kiwi is a flightless bird. Animals that live in darkness or caves often have useless eyes. For example the blind mole rat has eyes that would be considered vestigial. 

http://www.colonista.com/my_weblog/2010/06/the-appendix-actually-is-important.html

Where your appendix is located

Other useful links: 

http://curiosity.discovery.com/question/what-vestigial-and-atavistic-traits

http://www.livescience.com/11317-top-10-useless-limbs-vestigial-organs.html

Reflection: Artificial Selection

When we were first introduced to Darwin's cousin and oh yeah future WIFE, Emma, he brings up the topic of artificial selection. He started talking about dogs, which are one of the most common examples of artificial selection. Campbell's Biology defines artificial selection as, "the selective breeding of domesticated plants and animals to encourage the occurrence of desirable plants." But what is a desirable trait? It can be anything, making fruit sweeter, making dogs shed less, or even making a plant less susceptible to insect activity. By looking at examples of selective breeding Darwin was able to solidify and eventually proposed the idea of natural selection to explain evolution. Artificial selection and its success was another source of explaining evolution because it shows how a collection of naturally occurring mutations can affect the appearance of an organism, when striving towards a certain trait.  If mutations were not allowed to occur, then the organism could not vary from others in its population and selection would be impossible.

Artificial and natural selection may seem very similar but there is one very important difference to note. Natural selection is based on the fact that in nature, not directly influenced by humans, individuals with certain inherited traits will have a higher fitness level. This means that this individual will survive longer to produce more viable offspring than its counterpart. Nature is the one that “chooses” which variation to favor. Artificial selection, on the other hand, is directly influenced by humans. Farmers have been performing a form of artificial selection before they even really knew what they were doing.  For example, a dairy farmer, he has many dairy cows but he notices that one in particular produces twice as much milk than his other cows. He would choose this dairy cow to mate, in hopes that she will give him a calf that produces the same high rate of milk as its mother. The same would happen with produce. The farmer notices that this stalk of corn is sweeter than the rest of his corn; next season he would use that corn’s seeds to plant with. Which would produce more stalks of sweeter corn.

Artificial selection has been used for many years, creating a better lifestyle in many cases. Some cases of artificial selection are solely for aesthetic purposes, while others are for more practical purposes. The following link shows two good examples of artificial selection through the use of pictures: http://evolution.berkeley.edu/evolibrary/search/imagedetail.php?id=382&topic_id=&keywords= 

From: http://evolution.berkeley.edu/evosite/evo101/IIIE4Evochange.shtml

This is a great link from an AP Biology website if you can get past the strange computer, monotone voices: http://www.youtube.com/watch?v=R19zY1kkuSY

Darwin's Dangerous Idea Reflection

In the movie Darwin’s Dangerous idea, It explains Darwin’s theory along with showing Darwin’s life and how it affected the way he thought about evolution. According to Merriam-Webster dictionary, evolution is a theory that the various types of animals and plants have their origin in other preexisting types and that the distinguishable differences are due to modifications in successive generations (Merriam-Webster Dictionary ). This is just one of the definitions.  The movie showed how his findings from South America really made him start thinking about the concept of evolution.  He found that all the birds brought back from his trip were from the same ancestor, the common ground finch, but all the birds had different characteristics that made them unique. He noticed that the beak sizes where different on all the birds that were found.  We can see this in today.  We see that species change or evolve over a certain time period.  These changes can be caused by many different factors ranging from the habit including the food source and environmental conditions and natural disasters such as drought and hurricanes.  The PBS website demonstrates how these various factors can play a role in evolution along with explaining Darwin’s dangerous idea of evolution. Another interesting point that was made in the movie is the Tree of Life.  This is that all living things on earth are related and are descendants of each other with modification. Even with all of the evidence that we have today, it is a really hard concept for people to accept.  People cannot see how humans could have ever evolved from say a single celled organism.  Another interesting thing within the movie was the religious conflict that Darwin faced with coming out with his theory.  We still have conflicts with religion and the concept of evolution.  I believe that the movie did a very good job at explaining Darwin’s idea and the different view about evolution.  It also showed where evolution stands in today’s society from a scientific stand point and from a religious stand point as well. 

http://www.merriam-webster.com/dictionary/evolution

http://www.pbs.org/wgbh/evolution/index.html

Reflections: Darwin's Dangerous Idea

The topic that caught my attention in Darwin's Dangerous Idea was the controversy between science and religion. This surprisingly is still a huge subject in today's society. A valid question is what events caused Darwin to become less religious? During the Beagle Voyage he had many opportunities to see how harsh slavery was and wondered how God could allow such inhumanity to exist. He could not accept that a kind God would allow humans to live in such a wretched state. Why would god allow such suffering in the world was an internal conflict Darwin could not resolve. Me being non-religious, I can see where Darwin is coming from, I'm sure we have all asked questions such as these before at least once in our lifetime. While I was doing research for this assignment, I came across something that surprised me: "Many church leaders do not believe their own book, the Bible. This plainly teaches that God created recently in six consecutive normal days, made things to reproduce ‘after their kind,’ and that death and suffering resulted from Adam’s sin. This is one reason why many Christians regard evolution as incompatible with Christianity" (as taken from creation.com).
In my opinion, I believe in the evolution theory. And I might be getting a bit off topic, but I believe that religions are nothing more than a piece of literature. Have you ever asked yourself who wrote the bible? Many say God did. The Hebrew say in the Old Testament that it came to them by "God's mandate." So sorry but I can't say that God has ever literally ever told me to do anything. My point is that it all makes no sense. And don't get me wrong, I respect all religious views. To me, as a future scientist, evolution theory makes sense. AND not to mention it can be proven, unlike many scriptures in the bible.
Although, science does have its limits. Science deals only with repeatable observable processes in the present. This has been very successful in understanding the world, and has led to many improvements in the quality of life. In contrast, evolution is a merely a speculation about the unobservable and unrepeatable past.
Howard Stern knows what he's talking about:

 

For more information on evolution vs religion visit:
http://creation.com/refuting-evolution-chapter-1-evolution-creation-science-religion-facts-bias

http://ncse.com/religion/scientific-perspectives?gclid=COffi5Ds77QCFQf0nAodaxsA_w

Reflections on Darwin's Dangerous Idea

I thought that the eye section of the film was very interesting. It was a key point in the Creationists' argument because they thought it was perfect and it actually has many imperfections, which Darwinian evolutionists talk about to argue the Creationists' theory. I wanted to know some more about the evolution of the eye and i found some interesting things.
People used to believe that the main contributing factor for eye size was when the animal species was most active either nocturnal or diurnal but an article on sciencedaily.com says that there is a correlation between eye size and maximum running speed. The theory was originally developed for birds and their flight speeds but these researchers and anthropologists used it to analyse mammals. They found that the size of the animal and their maximum speed "explain 89 percent of variation in eye sight among mammals" ( from sciencedaily.com). I also searched for more details on how the eye could have evolved and found information about how all of the stages of eye can still be seen today, and more remarkably all in one phylum, Mollusk. The video shows and explains how the eye could have evolved and gave examples of the varying complexity and organisms that have the different levels of the eye. I thought it was interesting that the ones with more complex eyes can move faster in the water and it seems like the maximum speed theory can be used to explain more than just mammals. I think its interesting that there has been so much emphasis on the evolution of the eye and that both sides of the argument use it as an example for their case. I also like that the speed correlation to the eye size is another selecting agent for how the evolution of the eye could have occurred to help give them an advantage in the competition among species.

More information can be found at:

http://www.sciencedaily.com/releases/2012/05/120502112606.htm

http://www.sciencedaily.com/articles/e/evolution_of_the_eye.htm

The video can be found at:

http://www.youtube.com/watch?v=7jEhzAn1hDc