April 29th, 2008 ecoli
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.
Posted in biochemistry, link out, microbiology, musings | 2 Comments »
April 29th, 2008 ecoli
you gotta love this one. (thanks BBC)
Posted in link out, news, politics | No Comments »
April 28th, 2008 ecoli
This is a correlation that I believe is nonetheless relevant. There is a certain link between people who have a fear of others with a different lifestyle, those who’s insecure belief system is threatened by objective research and people who enjoy their own ignorance.
Posted in link out, politics | No Comments »
April 28th, 2008 ecoli
I’m about a month late on this one, but I just stumbled on it. It’s a funny list.
Posted in humor, link out | No Comments »
April 24th, 2008 ecoli
The things rich people will do… No offense to cricket enthusiasts, but I can hardly imagine this being a solid investment.
Posted in link out, musings, news | 2 Comments »
April 23rd, 2008 ecoli
Microblogology shares a study by the Evanston Northwestern’s MRSA screening program that demonstrates that the most effective ways to control infectious diseases can also be the cheapest, and least ’scientific.’ To study epidemiology is to be smart about pathogens. Where are they coming from, how do they infect, what physical barriers can we set up to stop the spread of pathogens from patient to patient?
The study found that 8.5% of their patients carried MRSA into the hospital (carried, not necessarily infected with). By isolating these patients and taking special precautions, in terms of hygienic practices, the hospital was able to cut down hospital-acquired infections 70%.
This is a more cheaper way to control MRSA than drug development, and it doesn’t give the bacteria a chance to development new antibiotic resistance in the first place. Simple cleanliness and hygiene can probably to attributed to the lessening of the roles of infectious pathogens to the human death rate perhaps even more than antibiotics or vaccines. We seem to have forgotten this along the way; that chemicals and not efficient planning is the more effective method of preventing infections.
Posted in link out, medicine, microbiology, news | No Comments »
April 22nd, 2008 ecoli
Apparently, today is earth day.
Go grab an earth wallpaper for your desktop.
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April 16th, 2008 ecoli
From Adventures in Science and Ethics
Ultimately, what bugs me about this story is that it seems to boil down to a piece about a teenager who has done something unusual and become a minor celebrity because if it. Yet, there’s no critical examination of the something unusual that she’s done — in particular, of whether she’s done it in a way that holds up to scientific scrutiny — of what sorts of deeper motivations might be behind it, and of what the impacts of this project might be for the rest of us. To the extent that the “something unusual” this particular teenager is doing is presenting herself on the internet as a reliable source of scientific information, it feels to me like the critical analysis missing from this story is very important indeed.
From Respectful Insolence:
Sadly, the one thing that Kirsten could have used is a public smackdown on NPR from a climate science who really knows his or her stuff, someone who could demonstrate in excruciating detail just how thin her knowledge base really is… By doing the piece, though, NPR put itself in a no-win situation. If it criticized Kirsten’s denialist arguments, NPR would have looked as though it was making fun of a teenaged girl who’s clearly smart but not well trained in science or critical thinking. If it didn’t, well, the results are easy to see: A puff piece that portrays the plucky outsider taking on the scientists and apparently beating them at their own game.
Posted in link out, news | No Comments »
April 15th, 2008 ecoli
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.
Posted in link out, medicine, musings | 4 Comments »
April 14th, 2008 ecoli
This has been making the rounds on the blogs.
Ben Stein’s expelled movie is in hot water for using secondary party content without permission. Read science after sunclipse’s witty response.
Posted in creationism, link out, news | No Comments »
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