Those of you who are SFN members probably realize I’m not dead, for the rest of you, it might not be so obvious. I have 5 days of finals left for the semester, so that’s taking up most of my time.
I’m also, as a new Linux user, slowly trying to figure out how to debug Mandriva 2008.
That’s all for now… I’m off to take part in the “Midnight Scream”
What’s one of the first thing students learn in high school about nucleic acid molecules? It’s that DNA is double stranded and RNA is single stranded. Not only is this fundamentally incorrect, such type of “linear” thinking is, I would argue, a ‘dangerous’ line of thinking, that may be hard for students to escape from.
Any biochemistry student can tell you that, not only can certain types of RNA form secondary and tertiary structures, but that these structures are critical to understanding the catalytic activity of RNA. This has important revelations for evolution (the RNA-first world hypothesis) and for molecular biology.
Microbiology Bytes ran a segment on The shape of HIV RNA (see image below). The higher order, 3 dimensional structure of HIV RNA could play some important role in viral replication and pathogeneiss
This example serves to illustrate the important point that higher order RNA structure could more important in biology than we could have imagined. Therefore, if we keep giving students the impression that RNA (and other molecules) are linear and static, than they could carry with them a false veiw of biological models.
Coincidently, this also is another reason that computational and mathematical modeling in biology will become all important in the coming years. As it turns out, biochemical structures are just too complex to realistically model without computers (at least not easily).
And, as it turns out, even knowing three dimensional structures may not be enough. Carlos Simmerling from Stony Brook University does computational modeling of biomolecular systems (specifically proteins and nucleic acids) as dynamic entities. In other words, intra-interactions, as predicted by mechanics, cause molecules to “move and shake.” These molecular “vibrations” caused by electrostatic interactions could also greatly potentially affect reactivity of molecules in ways we could have never predicted without computer modeling. Simmerling also develops tools to view these molecules in their energetic states. Here’s a video from Simmerling’s group of the enzyme HIV Protease.
These developments stress the need for new scientists (yes, even biologists) to think mathematically and artistically. We need to be aware of all three dimensions (plus the time dimension) in order to work towards building accurate models of biological and biochemical systems.
‘Reduce, Reuse, Recycle’ is a wise waste management policy and words to live by. However, we also need to ‘Rethink’ our approaches to environmental policy and the role of government in its enforcement.
Government organizations, implemented by legislation or executive order, tend to be large and intrusive. The Environmental Protection Agency (EPA), for example, has largely been a positive motivator for environmental awareness; however, this large federal bureaucracy also uses its power to violate states rights. Back in February, the EPA blocked 16 states from raising fuel economy standards for new cars, with unreasonable justification. Presumably, EPA administrators were trying to shield the automakers from environmental responsibility.
Though, thankfully, this type of abuse of power is not too frequent, the fact that any federal agency not administrated by elected officials has this level of authority is worrisome. Furthermore, it is against the spirit of the Constitution to forbid states from making their own environmental policy, especially when that policy would tend to improve the environment.
The things rich people will do… No offense to cricket enthusiasts, but I can hardly imagine this being a solid investment.
Even though I didn’t get a chance to update my blog over the weekend (family is visiting for passover) somehow my page views increased to over 11 thousand from around 2 thousand. I think this is quite a feat for a couple days. I think this was mainly due this post: Why Objects are Blurry Underwater, which has been getting some love from StumbleUpon. So thanks to the stumbleupon community for taking an interest. Hopefully I’ll have more decent posts ahead of me that will draw even more traffic in the future.
So, hello to all stumblers. Be sure to check out my parent site: www.scienceforums.net for all your science forums needs.
And now the weather: cloudy with a small chance of a microbiology post sometime within the next 24 hours.
Update: now over 15500 page views… thanks stumblers!
What’s with the recent obsession with green tea for its alleged medicinal properties?
Every weekend I turn on the radio, and I’ll hear on at least 3 major stations, and all day long is people talking about how great green tea is. Here’s a short list of the supposed healing powers of green tea, courtesy of the Beauty Blog.
• promotes blood circulation
• increases the body’s natural resistance
• helps with oxygenation
• helps achieve “greater harmony”
• improves the body’s ability to handle the external physical and psycological [sic] pressures of life
• prevents tooth decay and maketeeth more resistant to acids
• promote digestion and cleanses the body internally
• tea drinkers say that they actually feel less tired and brightens their whole outlook
So anything this wonderful, of course makes me immediately suspicious. It sounds like alternative medicine to me, which I immediately wary of, because proponents almost invariably exaggerate the benefits, if there are any.
doing some quick poking around at scienceblogs, I found some mixed results. The Angry Toxicologist found some incorrect reporting in a major news outlet about green tea. Respectful Insolence found a study, the title of which was more enthusiastic than the results indicated.
On the other hand, this webpage from the University of Maryland lists some benefits and references, which I assume are relatively accurate (though I haven’t checked up on all them).
So, for now I conclude that we don’t yet know enough about green tea and the effects on the body to state anything overly positive or negative about it. I know that people who frequent places like the Green Tea blog and forum would like to believe that green tea is the magical mystery cure. However, just from my general experience with biology and medicine, there is rarely any single substance that is a cure all, and that even healthy substances should be rationed appropriately, balance and variety being key to a healthy diet. I also recommend sticking to reputable news sources, try to avoid those radio programs, and make sure to check the sources on all information. When it comes to health, you can afford to be skeptical about miracle elixirs and potions.
Ever open your eyes underwater without goggles? You probably noticed that objects are really blurry, a fact that has nothing to do with the chlorine, though that will cause them to sting after a while.
It has to do with the fact that a ray of light traveling through a medium refracts, or bends upon entering another medium. However, its not merely because water refracts light that makes underwater objects blurry. In fact, the refraction of light in water is the basis upon which human vision is based.
This is because our eye is filled with a fluid mostly consisting of water. We are adapted to light rays traveling from the air into the fluid in our eyes, which is refracted at a specific angle. Our eyes therefore focus incoming light in a specific way, which is projected on the back of the retina, and fine-focused with the lens. So we are adapted to a specific incoming angle of light, due to this refraction.
Under water, light travels from water into another water based media in the eye. Therefore the angle of refraction is fairly small. The eye cannot focus the light so the image appears blurry (the focal point is in the wrong place).
So, how to fix this problem?
Well you already know that goggles work. But, how they work is explained by Snell’s Law, the index of refraction (n) multiplied by the sine of the incident (incoming) angle is equal to the index of the refraction of the second medium times the sine of the angle of refraction. A light ray traveling through air into water will bend the same amount, though the opposite way, as a ray of light going from water to air. In other words, light coming from the water into the goggles will refract at a certain angle. When this light enter the eye, it will refract back to almost the original angle it was traveling in the water. So, by placing a layer of air over the eye via goggles refracts light, received from from objects underwater, in a way they would normally look in the air.
(PS - special thanks to klaynos for reviewing this post)
Swansont points out the physical/medical problems that come from blogging.
A few days ago, Bug Girl blogged about some legal implications. (her etymology blog is great, btw)
The above links are not the reason I haven’t been posting as much lately. I’ve just been really busy in real life… but hopefully that will change.
So what’s with academics infatuation with facial hair? I suppose its perhaps less common these days, but facial hair is certainly more commonly seen in universities than on the street. Jake Young’s theory (from Pure Pedantry) is that it extends from the necessary slovenliness that comes with being a grad student.
In any case, having a beard can pose problems, especially for those microbiologists, because beards happen to be an excellent substrate for microbes. It then becomes as issue of balancing wisdom vs. safety.
I don’t usually write about this type of thing, and I promise I won’t make it a habit. Mike the Mad Microbiogist brought up an interesting post the other day, related to the Jewish holiday of Purim, I felt I should share it with my readership.
Its essentially about the concept of free will and the unusual way (for a ‘Western’ religion) that Judaism deals with it.
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