Introduction to Evolution
04.17.09 by Daniel Gaddy
February 12th, 2009 was Charles Darwin’s 200th birthday. That weekend, I had dinner with some friends, most of whom are scientists. I mentioned Darwin’s birthday and, being scientists, we raised our glasses and toasted Darwin. However, one of the ladies at the table, who is not a scientist, objected and said that evolution is just a theory and she doesn’t believe it. She was the only person at the table to hold this opinion, and much of the night was spent trying to convince her otherwise. Her primary stumbling block was her belief that evolution is an entirely random process, and she did not believe that ever-increasing complexity could arise by chance. There are a variety of things wrong with her idea of evolution, and what I quickly realized is that she simply did not understand evolution. Worse yet, I quickly learned that a table full of scientists could not do a sufficient job of explaining it to her! This led me to ask myself a couple of questions. First of all, how many people out there accept evolution without fully understanding it? Secondly, how many people do not believe in evolution because they simply do not understand it? Therefore, I decided to write this blog post as a simple introduction to evolution. Universities offer entire courses focused on explaining evolution. This post is not meant to substitute for a 4-month college class. Instead, I simply aim to address the basics of evolution and some of the common misconceptions.
In 1859, 150 years ago, Charles Darwin published On the Origin of Species, one of the most important and influential books ever written. In it, Darwin introduced his theory of evolution, which itself evolved over the course of Darwin’s 5 year journey around the world on the HMS Beagle, and in the subsequent years studying his notes from the journey. At its core, Darwin’s theory established a scientific explanation for diversity in nature. A minimal working definition of evolution is “a process that results in heritable changes in a population spread over many generations.”
Antibiotics that Don’t Kill Bacteria.
02.13.09 by David Vitrant
Antibiotics and drug resistant bacteria are a little talked about yet growing problem. I recently saw a well written and lay person oriented article about creating antibiotics that don’t kill bacteria. The article is here.
Ok. Now to the question everyone is probably asking by now: Why is that a good thing? Isn’t more bacteria around a bad thing ?
In order to answer that question I have to say a few general things about bacteria in general:
- Bacteria grow and reproduce very very quickly.
- It usually only takes one or a few bacteria to re-grow a complete colony.
- Most if not all therapies deal with inhibiting the bacteria and killing it off (usually while killing other types of bacteria as well)…
Gene Therapy for Type-1 Diabetes
02.11.09 by Daniel Gaddy
Introduction.
Type-1 diabetes is a chronic disease resulting from autoimmune-mediated destruction of insulin-producing pancreatic beta cells. Although progress has been made toward improving diabetes-associated pathologies and the quality of life for those living with diabetes, no therapy has been effective at eliminating disease manifestations or reversing disease progression. Therefore, novel therapeutic approaches are currently being sought. Among the approaches with the most promise is gene therapy.
Background on the Disease.
Type-1 diabetes (T1D), also known as insulin-dependent diabetes mellitus, is recognized as a rapidly growing health threat worldwide. The CDC estimates that 15,000 young people in the United States per year are diagnosed with T1D, with 19 new cases per 100,000 youth each year
Existing Therapies.
Gene Therapy for Rheumatoid Arthritis
11.14.08 by Daniel Gaddy
Introduction.
Gene therapy offers great possibilities for the treatment rheumatoid arthritis (RA). RA was the first orthopedic condition to be targeted by gene therapy. Initially, RA, a non-lethal disease that is not regulated by a single gene, may not have been an obvious target for gene therapy. However, while traditional surgical and pharmaceutical methods of treating RA have met with limited therapeutic success and have failed to produce a cure, the past several years have seen extensive progress toward development of gene therapy for arthritis. Numerous vectors and therapeutic genes have been investigated in animal models of arthritis, and the potential of gene therapy to treat or manage RA has been demonstrated in several clinical studies. Gene therapy offers the possibility of overcoming many of the limitations of current biologic therapies by providing long-term, high-level localized expression of therapeutic genes, potentially in as little as a single dose.
Gene therapy emerged as a novel strategy to treat arthritis in the early 1990s. Fundamentally, arthritis gene therapy involves the transfer of complementary DNA (cDNA) encoding antiarthritis gene products, which may be difficult to administer by more conventional methods. Gene therapy offers the promise of long-term expression of antiarthritis gene products, as well as targeted delivery to and expression in affected tissues, limiting potential systemic side effects.
Background on the Disease.
Arthritis is the leading cause of disability among adults in the United States, affecting approximately 21% (more than 46 million) adults. Rheumatoid arthritis (RA) affects approximately 1.3 million adults in the United States, and more than 60 million people worldwide [1]. RA is characterized by inflammation of the synovial lining and destruction of extraarticular bone and cartilage [2]. It is believed that arthritogenic peptides, either from foreign or self proteins, are presented to T cells preferentially by RA-associated MHC molecules on antigen-presenting cells [3]. Activated T cells produce a variety of proinflammatory cytokines, including TNF?, IL-1 and IL-6. The inflammatory response induced by these cytokines is directly responsible for the overt RA symptoms, including joint pain, swelling, effusion and stiffness.
The Lowly Fruit Fly Takes a Giant Swat!
10.29.08 by Syam Anand
by Syam Anand
Who would imagine that scientists are mindlessly wasting taxpayer dollars on stupid fruit flies? That too, not the money that came through the NIH after peer review, but from ear marks- those wasteful “pork-barrel” projects that help politicians channel money for projects in their pet constituencies! Is it not a shame that this has been going on behind our backs until the most popular governor in USA decided to bring out this activity into the open in her first major policy speech?
During her first major policy speech, she made fun of the lowly fruit fly and the researchers who are after it. Amazingly, she even managed to garner a few laughs from the audience.
Watch the portion of the speech for yourself here.
http://www.youtube.com/watch?v=HCXqKEs68Xk
Poor fruit flies! Also, those poor souls of scientists who worked and continue to work on them!
Outrageously ignorant- that is how I would summarize the fruit fly remarks.
This is what happens if you don’t believe in science. This is exactly what happens if you don’t understand how science works. This is what happens if you don’t know that “WHAT IS TRUE FOR E. COLI IS ALSO TRUE FOR THE ELEPHANT”. This is what happens if you don’t understand evolution (whether you believe in it or not and to what scale). The list is long. But since it starts sounding personal, I will get back to the point.
Bug’s Life
10.20.08 by Syam Anand
Bacteria are ubiquitous microorganisms (typically in the scale of a few micro meters; a micrometer is one ten thousandth of a centimeter) that are present in almost every habitable nook and corner of earth. Some of them have even specialized for surviving seemingly uninhabitable places such as hot water springs and extremely dry or acidic environments. In an era of high personal hygiene what would amaze most of us is that there is an abounding presence of these minute life-forms in our own bodies. It is estimated that in our own bodies they outnumber our cells nearly one to ten! Most of these harmless bacteria live on our skin and inside our digestive tract. Among the advantages of harboring these bacteria are nutritional and immune system-stimulatory functions. This suggests that they are useful to us in many ways than we previously thought plausible. However, under certain circumstances such as immune depletion, these harmless bacteria can become dangerous and even fatal to the host. One notorious example is Staphylococcus aureus, which lives on our skin. It is estimated by CDC (Centers for Disease Control and Prevention), USA that S. aureus causes more infections than AIDS! Worse, this bug seems to be able to develop resistance to any drug that is thrown at it from time to time. Thus we have Methicillin Resistant Staphylococcus aureus (MRSA) and Vancomycin Resistant Staphylococcus aureus (VRSA) among others that make a substantially long list.
Watch the following video to get a grasp on the “grapes of wrath”.
More information about MRSA and the challenges it pose, is available in the following video.
Scientist Who Discovered GFP Gene Left Out of Nobel Prize
10.11.08 by Daniel Gaddy
On October 8th, the Nobel Prize in Chemistry was awarded to 3 scientists for their work on green fluorescence protein (GFP), a protein that is now utilized by scientists around the world to label cells and proteins and to study a variety of conditions. Congratulations to these scientists, and their brilliant work that has contributed enormously to the work of so many other scientists, including myself. However, a story that has been under-reported is that of the scientist who originally discovered and cloned the gene that encodes GFP. The work of Osamu Shimomura, Martin Chalfie, and Roger Tsien, the 3 winners of the prize, would not have been possible with the previous work of Douglas Prasher. Prasher originally cloned GFP and had the vision to see what an important impact this protein could have.
Prasher’s GFP work was funded by the National Cancer Institute. In his grant he suggested that it should be possible to take the GFP gene out of the jellyfish cell and attach it to cancer cells so that they would be labeled with a fluorescent tag. Prasher managed to find the gene for GFP in Aequorea victoria and was able to express it in bacteria. In 1992 he published a paper in Gene; it reported the cloning of GFP and the sequence of the 238 amino acids in GFP, shown below. Sadly it was only a two year grant and the funding ran out before he could express the GFP clone he had produced in a manner that would result in a fluorescent GFP.
PCR without the PCR machine!
10.9.08 by Syam Anand
Sounds like fiction? Guess not. It is a distinct possibility now. This innovation is likely to revolutionize field applications of PCR and further expand its commercial potential.
For those of you, who are unfamiliar with PCR: PCR stands for Polymerase Chain Reaction. Since 1983, when the idea of PCR was first conceived by Kary Mullis, it has grown to be the method of choice for economically amplifying fragments of DNA or RNA over a billion times with the help of polymerases- enzymes that make more copies of nucleic acids such as DNA and RNA. Due to its ability to make more of the same from very less of the starting material, PCR is the backbone of both basic-science labs and application-oriented labs such as biotech and forensics. The expiration of the original PCR patent is bound to bring in more innovations and cheaper methods from competing players in the multi-million dollar PCR industry!
Watch the following movie, which explains the molecular basis of the reaction in layman’s terms. In essence the two strands of DNA act as molds for making more DNA molecules that contain the same coded sequence information.
http://www.youtube.com/watch?v=_YgXcJ4n-kQ
Until recently, the PCR machine was an indispensable part of PCR reaction as it drives the temperature cycles in the PCR. Recently, scientists have successfully attempted to replace the PCR machine with helicases to achieve amplification of DNA. Currently PCR uses three different temperatures that cycle multiple times to accomplish amplification. The first step of denaturation melts the DNA by increasing the temperature to 94°C. In nature however, molecular machines called helicases carry out DNA melting. Helicases melt double helical DNA by using chemical energy provided as ATP. They hydrolyze ATP and utilize the energy released for mechano-chemical cycles that help them to physically separate DNA strands in a stepwise manner. Inside living cells, helicase reactions support a variety of DNA and RNA transactions.
Biological processes: purpose or outcome?
09.26.08 by Syam Anand
Given below are dictionary meanings for three words, which are used routinely by biologists.
Purpose: the reason for which something is done or created or for which something exists.
Function: an activity or purpose natural to or intended for a person or thing.
Outcome: the way a thing turns out or the consequence.
Selfish DNA….hmmm, sounds like this kind of DNA has no purpose or objective in life other than some goal of its own! While other pieces of DNA are altruistic, providing coded information for the cell that harbors them, these selfish bits of DNA contribute nothing and at the same time ensure that they are passed on to future generations.
Selfish: lacking consideration for others. Concerned chiefly with one’s own profit or pleasure.
The questions I wanted to pose is the following: Is it right to use these kinds of expressions to explain the existence of a piece of a chemical because we don’t understand its function yet? Why not call it DNA of unknown function? Just like, genes in sequenced genomes with no apparent function are called FUN genes (FUN standing for function unknown). Does giving it any other name such as passenger DNA help? Are transposons more selfish than “selfish DNA’’? How selfish can DNA get? What is the scale for measuring selfishness in chemicals? Is Sodium chloride (common salt) also selfish? As sea water it got into my alimentary canal leaving a bad taste in the mouth and an upset stomach for my sensitive friends…all this to ensure that they get a free ride from Florida beach to Oakland, Pittsburgh doing nothing for me and my gang, when all other Sodium chloride molecules we ingested from the Cuban restaurant was making us feel good and also keeping our salt balance in the hot summer.
Presidential Candidates Answer Science Questions
09.17.08 by Daniel Gaddy
In the debates that took place during the Republican primaries earlier this year, some of the candidates for President proudly proclaimed that they did not believe in evolution. Many of us in the science world were aghast. Luckily, none of those candidates made it very far in the race, but it still raised an important issue: politicians of all stripes will pander to almost any group of people on almost any topic, but science is not one of them. With this in mind, Lawrence Krauss, a Case Western University professor of astrophysics, decided to try to do something about it. He joined with screenwriter/directer Matthew Chapman, journalist and author of The Republican War on Science Chris Mooney, and screenwriter Shawn Lawrence Otto to form a non-profit organization called Science Debate 2008. The primary purpose of this organization is to “elevate the visibility of science in the Presidential race,” with the hope of organizing science-oriented debates between candidates of both parties. More than 38,000 scientists, engineers, and other concerned Americans signed on and supported Science Debate 2008, including nearly every major American science organization, dozens of Nobel laureates, elected officials and business leaders, and the presidents of over 100 major American universities. More than 3400 questions were submitted for candidates to answer about science and the future of America.
Well, those debates never materialized, but Science Debate 2008 would not be defeated. Instead, they narrowed the list of 3400 questions down to the top 14 questions, addressing a broad range of topics including climate change, energy, health care, research, science education and American innovation. The questions were submitted to the candidates and, finally, the candidates decided these topics were important enough to address specifically.
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