Occurance of Natural Ribozymes

Shawn Hall

Interview Reflection

1. Describe your feelings about or response to the interview.

I was very impressed with the wealth of knowledge I was able to gain in the one interview. Our interviewee was extremely knowledgeable in his field, as well as molecular biology in general. After listening to him explain his approach to research, I was astounded by the conceptual understanding I now had of using biological molecules as tools in research. 

2. What changes occurred for you as a result of your interview?

After the interview, I was able to better understand the work of Ribozymes within endogenous organisms, and in vitro and in vivo experiments. I feel my understanding of the subject was elementary and needed clarification to its natural role in organisms in order to better understand its possibilities as a tool in scientific discoveries. 

3. Did anything about the interview disturb you?

I would not say anything about the interview was disturbing, but there was a moment of confusion and uncertainty in the interviewee that was unsettling. By discussing Ribozymes we ended up on the topic of RNA World. In talking about RNA World we ended up discussing the definition of life. Essentially, we were curious as to whether future discoveries of RNA catalyst elsewhere in the Universe, or more evidence for RNA World on other planets, that led to life would re-define life for us. As the interview delved into philosophical contemplation, and away from science, our interviewee seemed to draw blanks and become uncomfortable with the topic. Although he is paid to answer biological questions strictly from a scientific perspective, it was curious as to whether he ever considered deeper implications to the material he was publishing for the World. 

4. Describe the connections you found between the interview and your research & classwork.

The person we chose to interview was an understudy to the founder of Ribozymes, which was the topic of our research. During his time as a post-doctorate in the Ribozyme lab, our interviewee used Ribozymes as molecular tools, in biological research. His explanation for the role of this molecule as a tool in non-native, cellular environments to better understand the work of, and lack of work by, telomerase gave us a better understanding of the endogenous roles of Ribozymes and their primary functions.

Sierra West- Interview Reflection

1.      Describe your feelings about or response to the interview.

         The nature of the hypothesis for the RNA World had perhaps led to more philosophical questions on the nature of life itself.  I did not personally realize the difficulty in which we encountered in receiving responses from experts in the biological sciences.  Perhaps few are willing to stand by a hypothesis that can be considered untestable.  This is to say, no one was present in the time in which such events may have occurred.  Aside from hypothetical situations, I suppose that even the research of workers such as Cech cannot ultimately support one way or the other, that the pre-DNA material of life involved RNA and ribozymes.  Ultimately, we are faced with our own opinions and philosophy on how we define life and the origins of life itself.  Though much research, and the grid-computing project we became involved in, has provided many compelling arguments supporting the RNA World hypothesis, we may not fully understand the implications for the hypothesis in our modern view, known as the Central Dogma of Biology.  We may define life as an organism capable of self-replication, but it does not provide enough substance to hypotheses which posit that pre-DNA forms existed as RNA and ribozymes.  I may feel that there are few better explanations, but until our modes of inquiry improve concerning this subject, we may always refer to the RNA World view as a hypothesis.

2.      What changes occurred for you as a result of your interview?

         I feel that I now have a greater appreciation for the work of researchers in this field, and also for the impact that may be brought about for these scientists if they were to definitively conclude that the RNA World hypothesis is supported.  Perhaps, for some who we interviewed, it was a matter of their namesake not being attached to such an inquiry from biology majors on a topic which raises more questions than are answered.  In any case, I respect the views of these individuals and their organizations in promoting ideas which they can specifically support using their own research.  In the future, however, I would hope that views on understanding the origin of genetic material will relax as more information pours in to substantiate hypotheses on the RNA World.  In much the same way people refer to the Big Bang Theory as a theory, perhaps a day could come which provides more relevant evidence for the RNA World and becomes a theory as well.  A theory, in the scientific mode of inquiry, should always be substantiated with many years of data and independent analysis from well- qualified, authoritative individuals and organizations which dedicated the whole of their work to understanding and not merely hypothesizing.

3.      Did anything about the interview disturb you?

         Perhaps one implication that I did not have the foresight at the beginning of the semester on was how this hypothesis would ultimately meld together with philosophical beliefs on the origin of life, the nature of life and how we define life.  Scientists constantly struggle to find out how phenomena occur, how mechanisms of life processes occur.  But it is not often asked why.  Why would genetic material evolve into DNA if RNA had been sufficient, given that the RNA World hypothesis is accurate?  One may say that DNA is more stable than RNA and allows for greater complexity within an organism, but it still does not answer a more general question of why.  Furthermore, upon exploration into the possible origin of life on the Earth, we may find it relevant to consider whether life could or is evolving in a similar manner elsewhere in the universe.  Perhaps the best way to understand the origin of life on Earth is to actually investigate other planets similar to ours for even the smallest and simplest semblance of life imaginable. 

4.      Describe the connections you found between the interview and your research & classwork.

Within this study of the RNA World, it becomes ever more apparent the value of evolution as a mechanism of change in life forms on Earth.  There is no doubt that evolution and adaptation heavily influenced the outcome of life and how life replicates genetic material and subsequently produces the proteins that are the ultimate building blocks of life itself.  Within our class, we talked about many changes due to evolution, which itself is defined for our purposes as the change in allelic (and for some, genotypic) in a population over time.  HIV, for example, is a rapidly evolving virus that infects many humans all over the world.  Though, in a strict sense, viruses are not considered living because they depend on the machinery of a host cell in order to replicate its genetic material and ultimately produce more viruses.  But if you look at the genetic material of HIV, single stranded RNA, it becomes interesting as to why HIV would maintain RNA instead of having its genetic material converted to DNA for what might be considered as more efficient in the utilization of the host cell, which itself houses its genetic information as double stranded DNA. More questions like this may be raised as to how and, more importantly in my opinion, why organisms have evolved the way they are now and what exactly were the precursors to the current status of these organisms.  Also, these questions are all relevant to those more philosophical questions that are ultimately raised when one endeavors to research a topic and complex and hypothetical and the RNA World hypothesis.

I would also like to mention how much I appreciate the opportunity for our class to participate in grid-computing projects and to endeavor into biological topics that may not be otherwise covered in a class such as ours.  In the future I hope that more students push themselves to work diligently to find a biological topic of their own choosing.

Discovery of Ribozymes: Thomas Cech

Background information: Dr. Thomas Cech was born December 8, 1947 in Chicago. He would earn his Ph.D in 1975 at the University of California at Berkeley. In this video, Dr. Cech explains his experiment that would lead to his discovery of catalytic RNA in which he would win his Nobel Prize on in 1989.



Mini autobiography of Dr.Cech

An Introduction to: Grid Computing and RNA World

     Since the members of this blog are participating in a computing grid with RNA World, it would only be fair to explain the basics behind a computing grid is in order to understand the idea behind RNA World. A computing grid is a network of computers linked together by a program in order to compile, analyze, and store large amounts of information. A middleware program is needed to connect all of the computers on the network. The program allows for a central sever to relegate tasks to each computer on the grid and for the computers of the grid to communicate with one another; this information is then fed back into the central sever through the program and stored there until it is needed by another computer on the grid for analysis. Without the program, the computers would not be able to communicate with one another and utilize the processing power of all of the computers connected to the grid. Furthermore, the program determines how much of the processing power from each computer on the grid is dedicated to the network. The main computer sever also determines the task that each computer on the grid will run. Finally, the main computer server determines which computers can access the full power of the grid. This is done in part to keep the grid secure.

     In many regards, a computing grid is similar to a supercomputer. A supercomputer needs large processing power in order to compile and analyze large information on various subjects such as weather prediction, studies  of the Sun, simulations of nuclear explosions, and especially biological molecules such as proteins.  They can also cost a vast amount of money; this is where grid computing comes in handy because it can simulate the large processing power of a supercomputer for a relatively cheap amount of money; especially if one allows their grid to be a voluntary grid, meaning that an anonymous person can allow their computer to run the grid's program and donate processing power to the grid. Thus, a lot of research grids have sprung up in a variety of fields to utilize extra processing power. Furthermore, some non-scientific grids have appeared as well. There have also been recent strides to utilize grid computing in the educational field as well.

Courtesy of  ProQuest

            In conclusion, the ability of a grid to utilize small amounts of computing power from multiple computers to simulate the overall computing power of a supercomputer is quite remarkable. With improvements in Internet-based technology, who knows how grid computing will shape our lives?





For more information about grids:
Grid Cafè
How Stuff Works on Grid Computing
Grid Computation

Why ribozymes?
According to RNA World (http://www.rnaworld.de/rnaworld) , ribozymes are "non-coding RNA molecules that, like protein enzymes, catalyze chemical reactions". Originally discovered in 1982 (Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena), scientists have been studying ribozymes to see if other natural analogs exist in prokaryotes and eukaryotes. Many workers theorize that the earliest evolution of life could have begun with RNA molecules acting as both the primary information carrier and enzyme. These scientists refer to that time before modern DNA and protein formation as the "RNA World". The goal of this blog will be to inform those interested in the study of RNA and ribozymes of the latest discoveries and possible natural analogs for these molecules.  Furthermore, we would like to encourage you to join the computing grid RNA World (http://www.rnaworld.de/rnaworld) in order to contribute to the study of RNA.  With such a vast wealth of knowledge to be gained by these studies, it is imperative that all individuals be informed of the opportunity that presents itself.

Picture courtesy of Chris King of the University of Auckland, New Zealand (http://www.dhushara.com/book/bchtm/biocos.htm)