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.
Does Open Source Apply to Science?
10.24.08 by Syam Anand
Release early, release often- the mantra of open source softwares- can it be applied to Fundscience?
By Syam Anand
I want to first introduce the mantra of open source softwares to the small minority of those who may not be aware of it. “Release early and release often” summarizes the philosophy of people who work and support open source softwares. Open source softwares thrive on the committed efforts of groups of people who work from different parts of the world. They put their brains together for a common goal- constant improvement based on feedback. They are not part of any real organization. But they always evolve into an organization of sorts that is governed by operating principles that co-evolve with them keeping in tune with changing priorities. The good thing about evolution is, it tests and selects the fittest. Being more flexible thus makes them more adaptable as an organization.
From a strategic perspective open source softwares thrive on “real” feedback and “real” solutions. People who actually uses these softwares work on it and to improve it and keeps on improving it. First, they don’t wait to come up with packages such as version x or version y and then try to sell it in a form that cannot be tinkered with (similar to a biology kit whose information in “proprietary” and you don’t have access to it, even if you own the kit!). Second, they don’t set the intervals with which they come up with updates, beforehand. They do it on a regular basis. If a software has a bug, it is explained in the open for possible solutions. When a solution is found, it is notified to everyone. As a practicing scientist, it seems very similar to what we do everyday for every aspect of laboratory life, except for funding. We regularly do experiments, we regularly improvise and find better ways to ask questions and get answers. But when it comes to funding, we can do it three times a year for NIH and once a year for the foundations. Of course, we regularly work towards getting funded!
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.
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.
Direct public funding of science
10.1.08 by Syam Anand
Currently, NIH funds the majority of biology research in USA using taxpayer dollars. The success of the NIH system and the adaptation of the scientific community to NIH have made this system stable and dependable. A significant amount of additional support for biology research, especially health related research, also comes from foundations. Some of them such as Bill&Melinda Gates foundation, and Howard Hughes Medical Institute provide substantial financial support far exceeding and often more attractive than what even NIH offers. A lot of good science have been done and fundamentally important discoveries been made by scientists who have been recipients of grants from all these sources. However, the success of NIH funding philosophy has influenced every major biological research funding operation that goes on in USA. Its impact is so widespread that the alternative funding options seem to be a product of inbreeding and incapable of providing new cultures or avenues that would complement the goals of NIH. As a result, the differences between most of these foundations that have clear independent goals are only superficial and all of them operate essentially on the same principles as NIH.
The NIH funding philosophy
NIH fellowships and grants come in different flavors with one underlying foundation, which is the provision of an efficient and goal-oriented institutionalized system that takes into account national priorities. This system makes sure that the available budget is prioritized and distributed between various sub-disciplines. Policy-makers arrive at these decisions through a systematic process, which tunes itself to changing demands from time to time. The institutionalized system makes sure that adequate resources are constantly available for the carrying out the funding process with a high efficiency by maintaining and providing trained pools of peer-reviewers (scientific colleagues) and program managers. The system of peer-review ensures that support is provided ONLY to scientists (or emerging scientists) who are likely to be successful. This is largely decided by three factors- 1) their prior success and pedigree 2) current environment of support and 3) the likely success of their research proposals based on preliminary evidence and arguments they provide in support thereof. The independent foundations that fund biology have also adopted the same principles and have not thought seriously outside the hat. So far, no one has argued with the success of NIH philosophy.
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.
End of the “restriction enzyme era” in molecular biology?
09.15.08 by Syam Anand
Restriction enzymes are the workhorses of modern recombinant DNA laboratories. They cut DNA at specified positions by recognizing specific sequences on DNA (such as the order of G, A, T and C).
http://www.youtube.com/watch?v=-sI5vy-cD2g
Presently, the methods to engineer recombinant DNA molecules with predictable coding specificities rely mostly on the ability of these enzymes to cut DNA into predictable fragments, which can be subsequently ‘pasted’ in specific ways using DNA ligases thus generating new coding information. In the classic work that first described the generation of recombinant DNA molecules in E. coli1 and since then, the term recombinant DNA meant mostly the generation and use of mostly artificial combinations of DNA fragments through the use of restriction enzymes. In nature, the ‘real’ DNA recombination reaction drives evolution in incremental steps and it’s products are subjected to selection pressure due to its tie up with cell viability. Until recently and even as we write, molecular biologists the world over, are stuck with restriction enzymes for generating recombinant DNA molecules.
The current spectrum of our understanding of basic cellular processes such as how the genetic material is replicated and segregated into daughter cells, how damaged DNA is recognized and repaired by the cellular machinery devoted for this cause, how intracellular localization and trafficking of molecules take place and how populations of different kinds of cells (such as in the immune system or during the spread of cancer cells during metastasis) localize to various parts of the body by whole body imaging, to name just a few, have been driven to a large extent by our ability to interrogate these processes in creative ways with the help of mutational DNA libraries and gene fusions of various kinds. The economic generation of recombinant DNA molecules to answer complex biological questions is however limited by our ability to identify, characterize and commercialize restriction enzymes with novel specificities, even though the currently available enzymes has allowed us to do wonders. Manipulating DNA molecules that had no cut sites for user-friendly restriction enzymes, large genomic fragments where the enzyme specificities are represented multiple times or where the sites are not at desirable positions seemed to be nearly insurmountable barriers for path-breaking discoveries. It appears that DNA recombination can overcome these barriers in order to generate recombinant DNA molecules in a practical and user-friendly way.
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