Archive for January, 2011

DIY Spectro FAQ

Apparently a lot of people were interested in my spectrophotometry project! It was picked up by several websites including BoingBoing and HackADay. An update is long 0verdue [ed: HERE], but first some answers to questions I got. A few things I should have mentioned (the -photometer actually uses a transmission diffraction grating, which is what you see in those glasses that put rainbows on everything, [eg, these.] They work slightly differently but the principle is the same.) I also left a lot of detail out because I didn’t think people would be interested. Here’s the dirt:

What about the width of the light source? [BB#3; TO comment from James]

As it happens, the shape of the light source is one of the factors effecting the resolution of the device. When a beam of light hits the diffraction grating, ‘copies’ of it get reflected at different angles, and thus get projected to different locations. If the beam is thick, then the red copy of the beam will also be thick, and will overlap significantly with the orange copies. If the beam is very wide, there will be so much overlap that all colors overlap in the middle of the spectrum, and you get a white blur edged with red and blue.

The width of the light source limits the resolution of the device; a thinner light source gives a higher resolution, because there is less overlap between the 'projections' of each color. In extreme cases, there will be significant overlap of most of the spectrum, and the colors will recombine to form 'white' light everywhere except the red and violet edges. Of course, the smaller the slit, the less light gets through...

You reduce this overlap by making the beam thinner. I do in fact do this; it is unpictured but there is a beam-narrowing slit in front of the spectrophotometer, similar to the one in the spectroscope. The ideal setup is an infinitely bright light behind an infinitely thin slit, but this is difficult to accomplish on a DIY scale, though two razor blades can be a good approximation. I used double-layered electrical tape with a ~1.5mm slit cut in it, further narrowed with bits of aluminum. Also, although a smaller slit means higher resolution, it also lets less light through, which can lead to detector sensitivity issues.

You need to remove baseline detector response! [BB#5]

I did ;D What Anon is saying is that it doesn’t make sense to claim that these data are an absorption spectrum: Continue reading

A part of my John Everett series – read more: 0/I – II.0 – II.5 – II.75 –  III.0 – III.3 – IV.0 – IV.4 – IV.8 – V – VII – VIII – Full Report 

We’ve seen that Dr. Everett’s discussion of paleogeochemistry fails to consider both rates of change and the geological record of ocean acidification. There is one last talking point in this section which requires comment:

“From 50-600 million years ago, atmospheric CO2 levels were usually 2-20 times higher than at present. […] This included the age of the dinosaurs, when life was so prolific that we still use its carbon, limestone and chalk.”

Limestone and chalk, like corals and coccoliths, are made out of calcium carbonate. Many deposits of calcium carbonate occurred when there was much more carbon dioxide in the air. The Cretaceous is named after chalk deposits like the White Cliffs of Dover; CO2 levels during the Cretaceous were over 1000 ppm, compared to current levels around 390 ppm. If the ocean deposited calcium carbonate en masse during the high-CO2 Cretaceous, why should we expect it to become hostile to carbonates now?

The chalk cliffs of Dover, massive deposits of calcium carbonate from the high-CO2 Cretaceous. Is this a paradox? Not really. Click for sauce.

The answer lies, again, in time scales.

Over short time scales, like those on which acidification is currently occurring, the saturation state of calcium carbonate is determined by pH, which is controlled by CO2. However, on longer time scales, it’s controlled by another factor. As this article explains:

“Hence, the key, but rather counterintuitive result, is that on long time scales, ocean pH and atmospheric CO2 are decoupled from carbonate mineral saturation state, which is dictated primarily by weathering (in conjunction with the major cation [Ca2+, Mg2+] content of the ocean). Actually, saturation is not entirely decoupled geologically from pH and CO2, as all things being equal, at high CO2 (and a warmer climate), enhanced weathering requires higher carbonate burial and hence higher ocean saturation. Thus, the presence of “carbonate factories” with widespread CaCO3 production and burial is entirely consitent with a high CO2, low pH world. […] Only in significant and geologically “rapid” departures from steady-state carbon cycling will both pH and saturation fall together…” (my emphasis)

In other words, over a long timeline, it’s the calcium that determines calcium carbonate favorability. Over short timelines, it’s the pH- and CO2 emissions are altering the pH on a short timeline.

A part of my John Everett series – read more: 0/I – II.0 – II.5 – II.75 –  III.0 – III.3 – IV.0 – IV.4 – IV.8 – V – VII – VIII – Full Report 

Last time we looked at Dr. Everett’s testimony, we examined his claim that, because carbon dioxide levels have been higher in the past, increasing levels are not alarming now. His argument is flawed, because although CO2 levels have changed, they usually change only very slowly. Now, they’re changing abruptly. Graphs of Deep Time can be intuitively misleading, because they collapse time scales and it can be hard to compare the rates of change from one image to the next. For example, this next graph shows information that we have gathered from looking at  gasses trapped in Antarctic ice. It’s obvious that the climate changes over Deep Time- but is it obvious from this graph how historical rates of change compare to modern rates?

Paleoclimatic and paleogeochemical data gathered from the Vostok ice core. Temperature (red) and carbon dioxide (blue) go up and down on these time scales - but its the rate that really matters. Click for sauce.

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