Why Arsenic-based life is cool, but not revolutionary

If you’ve been on the Internet the past couple days, particularly if you use any social media, you’ve invariably read something about the Arsenic-based life forms discovered in the bottom of Mono Lake in California.

The headlines have read with typical sensationalist flair:

From the sounds of the headline, one would think it was ET that we found, or that this discovery somehow turned our understanding of life and biology on its head. But not quite. Continue reading

My last undergraduate term paper EVAR.

Below is a copy of my term paper written for my Cell Biology course. I wrote it in a slightly less-formal style of scientific journalism, but didn’t spare on the technical details. Feedback, good or bad, is appreciated.


The Effects of the Consumption of Methylxanthines on the Adenosine Receptor System

Every year, humans around the world consume an estimated 10 to 20 billion pounds of coffee. (Gale) While some may drink it for the flavor, one can imagine it is probably the psychoactive stimulant, caffeine, that is the puppetmaster, beguiling we Americans to consume 200 mg (approx. 2 cups of coffee), and our northern European counterparts, up to 400 mg, every day. (ibid) For most people, it provides a useful mental edge: sharpening their focus and providing a subtle kick-in-the-pants of chemical motivation. Caffeinating over that sharpened-edge, however, can lead to disorders of sleep, anxiety, and even a jittery anxious quasi-hallucinatory state known as “caffeine intoxication”, all noted by the DSM-IV. (ibid) The other dark side is the silent escalation of tolerance to caffeine’s beneficial effects. Prolonged, regular exposure of caffeine can set up the consumer for an uncomfortable withdrawal period, ripe with headaches, myalgia, fatigue, and anxiety. (Ramkumar et al.) Continue reading

An Open Letter to Andrew Alexander, Ombudsman at the Washington Post

Subject:
Please start double-checking George Will’s facts when he talks about science
Body
I don’t know if you’ve been following Carl Zimmer’s blog, “The Loom,” and if you haven’t, you may want to read today’s post  – it covers the outline of the “saga”, as Zimmer calls it.

The fact checkers FAILED. Citing a blog in lieu of contacting the original source is *NOT* good fact checking; particularly when you are reporting something as a FACT rather than an INTERPRETATION. If Will had written “The DailyTech blog interprets the data from the Illinois center as….” that would warrant fact checking to the DailyTech blog — but that’s not what he did. And his fact-checkers neglected to contact the center for the study AT ALL.

As for the issue of ice — I don’t care what you or anyone thinks about Global Warming, Climate Change, whatever the spin doctors are calling it these days — Will is misrepresenting the issue by focusing on two discrete moments in time; some would call this “cherry picking”. Consider, for a moment, that I were to compare the amount of snow in Washington D.C. on February 1st 1979 to the amount on February 1st 2009 — can I reasonably draw ANY conclusions regarding overall trends of snow? Whether the snow is less, more, or the same, it is meaningless without a swath of aggregated data across the 30 year time-span. And yet, that’s exactly what Will did.

The Center that Will cited has a couple charts up that illustrate my point, see here:
http://arctic.atmos.uiuc.edu/cryosphere/IMAGES/current.anom.jpg
and here:
http://arctic.atmos.uiuc.edu/cryosphere/IMAGES/current.anom.south.jpg

The drastic ups and downs have an overall downward trend — but if you pick *JUST*  1979, at the low point, and compare it to the high point of 2009 — they are almost the same. But this totally misrepresents the data!

George Will may want to capitalize on the mock-troversy regarding Climate Change, and he apparently feels he knows the subject matter better than folks who study this professionally, but he is not doing humanity any favors by misrepresenting an issue simply so he can seem like a rebel.

Aaron Hill

Heroes, a science-geek critique

 

Ok, I just recently finished catching up on the “Heroes” television series. (Assuming there are no new episodes past the season finale of Chapter 3: Villains). I had originally watched most of the first season when it first aired, but for one reason or another, missed out on two and three. I have some complaints. Continue reading

Limonene, part 1

We’re starting a new lab in O-Chem this week: Extraction of a Volatile Oil from Orange Peels via Steam Distillation.

In layman’s terms: we’re taking the stuff that smells good out of the orange peels by boiling it off. 

The major compound responsible for the orange smell in peels is a volatile oil called “Limonene”, and is also found in lemons. Interestingly, the enantiomer (more on that in a minute) of this compound is not palatable at all (it has an odor similar to Turpentine).

Briefly, an Enantiomer is a mirror-image of a molecule. These 3-d arrangements behave differently (the case study always used is the Thalidomide tragedy) and thus interact differently with the smell receptors in our noses.

d-limonene l-limonene

The enantiomers of limonene, in stick structure form, are pictured to the left. 

They may not look like mirror images, but I just need you to trust me on this. (If you were to make up a MolyMod model of it, you’d see what I mean) You may think that they look identical except for that the left one has a thick black line towards the bottom and the right one has a dashed line. 

In organic stick structures, thick black lines like that indicate a bond whose subsitiuents are coming TOWARDS you, and dashed lines indicate a bond whose substituents are receding into the paper. So the left side one, imagine that the /\\ part at the bottom is coming towards you.

Side note: “d” and “l” indicate which enantiomer is being referred to, and are necessary for drawing the structure correctly. “d” is from the latin “dextrorotatory”, and “l” from the latin “laevorotatory”. [Read more]

If you’ve ever had a citrusy-flavored alcoholic beverage, you may have seen the  bartender “zest” the orange peel into the drink as a garnish. I always used to wonder why they would zest the PEEL instead of just squeezing some juice into it. 

As it turns out, the peel contains the highest concentration of d-Limonene in the orange, so zesting is the easiest / most effective way to get that volatile oil out. 

Also contained in the orange peel are the compounds “Octanol” (like “Octane” found in gasoline, except with a hydroxyl (-OH) group on the end of the chain, making it an alcohol), and “Carvone“, a compound derived from Limonene (via Oxidation).

Carvone is another interesting case like Limonene: its flavor depends on which enantiomer you consume. Fortunately, they are both non-toxic and (in my opinion) tasty. 

The “R” orientation (For the purposes of this blog post, “R” = “d” and “S” = “l” — pardon the confusion) is a major contributor to the flavor of spearmint oil, and the “S” orientation is a “principal constituent” of caraway seeds.

Through oxidation, we can produce Carvone from d-limonene. (If you compare the structures, you’ll notice that the only difference is that extra “O” doublebonded near the top of the molecule.) I suspect that leaving lemon or orange peel out in the open air will cause it to naturally oxidize (via an SN2 reaction), and we could certainly test for this by leaving the peels out and running an FTIR scan on the extract, looking for ketone peaks (that “O” double bond attached to a secondary carbon).

At this point, we are working on developing the procedure. I’m pretty sure that our lab group will be using a distillation apparatus (the big ol’ macro variety) to try and steam off some of the orange oil. The thing I found interesting was that all the sources I consulted (admittedly: all via google) said that orange oil has a boiling point of 176 C — we’re not going to get temperatures that high with our apparatus. I suspect that the heterogeneous mixture (the orange oil is non-polar, and we’ll be mixing it with water, a very polar solvent) may have a decreased boiling point, or that it will piggy back on over or something. We’ll see. 

If it works, we’ll see a thin film on the distillate beaker, if not, we’ll know to look into the short-flask. I’ve got lab again on Thursday afternoon, so we’ll see what happens!