Friday, February 22, 2013

One for All and All for One.

SNP research has always been a huge competition between the scientific community, as it was mentioned in the "Design by Numbers" presentation. The first to make a significant discovery, the first to publish, and the first to be given bragging rights. Of course, a healthy little competitive nature between scientists never hurt, as it can motivate them to work harder. However, as shown with the SNP research, too much of a competition can create friction between the community, and it eventually becomes every man for themselves. This corrupts the original purpose of scientific research, along with the corruption of their government and their own greed. With all this corruption around SNP research, it's no wonder the scientists are unwilling to collaborate with one another. Unfortunately, this results in a stunt in the growth of our society, as scientists are not willing to come together in order to break through their SNP research sooner.
Perhaps, if the scientists are willing, there should be a gathering every month to discuss the progress of their research so far. This will allow scientists to be with each other for as short of a time as possible since they do not trust each other. This gathering could even be done over the web with a livestream so that scientists from all over the world can participate. A specific time can be set so that all the scientists that contribute to SNP research will be able to join, no matter what time zone they are in.
Since the SNP research faces so much corruption already, there should be a neutral party involved in the collaboration as well. This third neutral party should have representatives from all countries involved in SNP research. All the scientists will be required to send in their individual findings to the neutral party, and altogether, they will gather them up, and redistribute them to the scientists so they obtain each others' research. If a scientist has not given in their findings, then they will not receive the findings of others.
During the collaboration, no one is allowed to publish individually, because they are all for the same goal, not for their own individual fame.
This could be a potential solution since it requires minimal collaboration from the scientists and their government. This will also make sure that the scientists are up to date with each others' research.
However, this plan can also give a huge amount of problems in the future if it were to be carried out.To begin with, there is a huge problem with communication if the scientists were to live stream with each other. Unless the scientists spoke a common language, they would probably need an interpreter. Unfortunately this gives room to vital information and pieces being lost in translation, as well as backhand schemes where the interpreter purposely gives wrong information. Another problem could be that the neutral party could be corrupt as well. Even though, given by their title, they are supposed to remain "neutral", they are only human and can definitely succumb to their personal greed and gains. Also, there will be a huge problem in convincing the government to fund such a party, as they more than likely believe that their country is superior, and thus it is not required of them to collaborate.

It is very possible that there will be a idea of collaboration that works sometime in the future, but until then, the corruption of the scientific community continues.

Wednesday, February 20, 2013

Translation

Translation can almost be looked at as the continuation of Transcription, where the mRNA is used as a template to make proteins. However, translation tends to differ quite a bit from transcription or replication since it is not making copies of genes, but rather converting genes into proteins. The process includes:

  • tRNA (transfer RNA) which includes the 3 nucleotide anticodons
  • mRNA, the finished product of Transcription, which includes the codons for tRNA to attach to
  • ribosomal subunits to help the process along
                                                               

Just like replication or transcription, Translation includes three processes: Initiation, Elongation and Termination.

Initiation:
  • Proteins known as initiation factors assemble all the molecules together for the production of proteins. First, a small ribosomal sub-unit will find the start codon (AUG) in the mRNA, and attach itself there. This will act as a signal for the tRNA.
  • After the tRNA has grabbed the corresponding amino acid to the mRNA codon from the cytoplasm, the tRNA comes over to the start codon, it will attach onto the mRNA with its anticodon, which includes the complementary base pair to AUG (UAC) and the corresponding amino acid for AUG, methionine.
  • Then, the large ribosomal sub-unit joins the group, gets the process kicking. With the large ribosomal sub-unit, there are three binding sides for the tRNAs: The P (peptide) site, the A (amino acid) site and the E (exit) site.

Elongation:
  • The mRNA is established as the reading frame, and the codons are read in sequence from the starting codon.
  • The amino acid on the initiator tRNA, methionine, is the beginning of the polypeptide chain. It occupies the P site in the large ribosomal sub-unit. Simutaneously there is another tRNA in the A site, with the complementary anticodon of the subsequent codon sequence on the mRNA, carrying the corresponding amino acid.
  • The amino acid of the initiator tRNA then forms a peptide bond with the amino acid in the A site, with the outcome of the a dipeptide attached to the tRNA at the A site.
  • Once the initiator tRNA is now robbed of its amino acid, it goes to the E site, where it exits the ribosomal sub-unit. This entire process repeats, as the ribosomes moves one sequence over, putting the tRNA with the amino acids in the P site, and giving room for a complementary tRNA to land in the S site.
                                            

Termination:
  • The process of elongation continues until it reaches the stop codon in the mRNA, signified with the codon sequences UGA, UAG or UAA.
  • When this happens, a protein will come called the release factor, and cut the polypeptide from the tRNA it is on. 
  • Then, the polypeptide is released, and set out to carry out its duties in the cell.

Transcription



When I learned about the transcription of RNA, I realized it was pretty similar to how DNA replicated, except with a few differences:
  • Tanscription of pre-RNA is single stranded instead of double stranded
  • Uracil replaces Thymine
  • ribose sugars are used instead of deoxyribose 
  • pre-RNA uses DNA as a template 
 

When looking at the bigger picture though, pre-RNA transcription also includes three major parts: Initiation, Elongation, and Termination.

Initiation:

  • The place where transcription happens is chosen on the DNA, based on a the location of the promoter (also known as the 'TATA' box) which signifies the beginning of transcription and the location of the terminator ('AAAUAAA' box) which signifies the end
  • Then, transcription factors recognize the location of the promoter region, and bind to the promoter. Since pre-RNA is single stranded, only one strand of the DNA is used as a template. The other strand, the coding strand, is used to help guide the pre-RNA when it matches the complementary bases.
  • The transcription factors are used to attract the RNA polymerase II, the enzyme used assemble the base pairs. Once the RNA polymerase II is tracked down,it begins to unwind the DNA helix.

Elongation:

  •  The polymerase II initiates the production at the promoter region, moving towards the terminator (going upstream and away from the promoter, then downstream and towards the terminator) as it synthesizes complementary bases to the DNA template, and matching the coding strand with the exception of T which is replaced with U.
  •  Just like DNA, pre-RNA grows in the direction of 5' to 3', attaching on to the 3' OH group, as it is the most reactive. Unlike DNA replication, however, the pre-RNA has no need for Okazaki fragments, since RNA is single stranded.
  •  As one RNA polymerase complex begins to move along the DNA, another RNA polymerase can bind to the promoter and begin synthesizing another strand of RNA simultaneously. This indicates that hundreds of RNA from the same DNA at one time.
  • Also, the RNA polymerase II seems to be a one-man army, as it does not need polymerase III to proofread its work. This is because RNA is only used to form protein molecules, not the genetic make up. Thus, the production of RNA is much less time time consuming than DNA.
 
Termination:

  • As the pre-RNA is being synthesized, the RNA polymerase II is also rewinding the double helix of the DNA at the same time, and the already made RNA detaches itself.
  • Once the pre-RNA is synthesize, it is capped at the 5' end with Guanine, as the structure itself is too unstable, while poly-A-tails are added to the 3' with Adenine. 
  • Once the pre-RNA is modified, then it is ready to be sent into the cytoplasm.


Tuesday, February 12, 2013

What is Perfection?

When I first read "Deaf by Design", my immediate thought was that being deaf was a disability, and it was completely unethical of the parents in the article to enforce deafness upon their child. This is because a majority of the world has the capability to hear, and therefore, the child would have a disadvantage over the others.
However, after watching the video "Sound and Fury", and really getting to understand more about Heather's parents along with their deaf community, I realized that perhaps it was me who has been unethical about the whole topic. Even though the word "disability" may have a by-the-book defintion, it can still be perceived differently by different people. That doesn't mean one person is more right than the other though. "One man's trash is another man's treasure". We are all entitled to our own opinions and beliefs. To the deaf community, deafness is not viewed as a disability, but rather, as a blessing. They see it as a means to preserve their deaf culture.
Disabilities are anything that gives you a disadvantage over others. However, what is seen as a disadvantage or advantage can only be determined by its survival in a given environment, as explained by Darwin in his theory of natural selection. Since the environment is constantly undergoing change, then the image we paint in our heads of "disabilities" should change as well. In Heather's case, she lives in an environment where deafness plays a huge role in her life. Her parents take pride in being deaf, and teach their children to sign, while Heather is always being exposed to the deaf community. In this environment, deafness to Heather, would not be a disadvantage. If Heather were deaf, then she would fit into her community, and be accepted amongst her friends and parents.  In fact, it would probably be more of a disadvantage if Heather was not deaf, since she would feel shut out of the society that her parents value so much, and would not understand or sympathize with her parents on their beliefs. For Heather to ensure her best survival in her own environment, it is better for her to remain deaf.
It is unfortunate that just because a majority of the society has a certain image of "perfection" that it automatically makes people think it is the "right" image. Although, just because it is the belief of the majority, does not necessarily indicate that it is the right belief. Therefore, if  we were to follow that logic, then deaf people aborting what the majority of society considers a "normal" child is not the wrong thing to do. It is just viewed as immoral by the majority of others because they live in an environment where it is more beneficial for a child to have hearing. Everyone has a right to their own opinion, and no one's opinion is ever really wrong if there is proper reasoning behind their thinking, and thus, deaf people have every right to abort a child who has normal hearing because in their minds, a deaf child is advantageous over a child who can hear.
Nevertheless, this whole controversy was brought to light was because of the ability to alter our genetic codes. Having the ability to alter our genetic codes is an amazing advancement in our society, but it doesn't come without consequences as well. Just as with every gift, comes a curse, altering genetic codes can easily be abused by the parents who hope for a "perfect" baby. Not only does this mold our society into something artificial and shallow, but it decreases the chance for genetic variation. When the genetic variety in our community decreases, we are more in danger of becoming extinct if there was a severe change to the environment. Even though the idea of altering genetic codes started off with good intentions, it became too easily abused, and thus, becoming more and more of a curse.

In summary, perfection is definitely in the eye of the beholder. We have become too corrupted by present day media as to what is "ideal beauty". This article has opened both our minds, and our hearts into accepted different kinds of beauty, and different ideals of what perfection is. Thus, from this, we can conclude that everyone is perfect, and everyone is beautiful :)!