Kitchen chemistry: fats and oils

Our previous kitchen chemistry post discussed esters. Fats and oils (triglycerides) are an important special case of esters. The alcohol in triglycerides is glycerol, a “triple alcohol” with three OH groups:

The glycerol combines with “fatty acids” (like the one on the right) which resemble acetic acid (left), but with a much longer hydrocarbon chain hanging off the COOH group:

      

The resulting triglyceride esters have three COO groups:

Fatty acids have important dietary implications, and they can be classified in dietary terms, but the most common classifications are chemical. The three main chemical classifications all refer to the presence of carbon-carbon double bonds:

One important classification is in terms of the number of carbon-carbon double bonds:

• Saturated fatty acids have no carbon-carbon double bonds (they are “saturated” in the sense of containing as much hydrogen as possible). Fats made from saturated fatty acids (“saturated fats”) tend to be solid at room temperature, because the straight-line molecules stick to each other. Saturated fats are usually of animal origin (although coconut oil and palm oil are also mostly saturated).
• Monounsaturated fatty acids have exactly one carbon-carbon double bond per molecule. Oleic acid (in e.g. olive oil) is an example.
• Polyunsaturated fatty acids have two or more carbon-carbon double bonds per molecule. Linoleic acid (in e.g. sunflower oil) is an example.

   

The position of carbon-carbon double bonds is also significant. A common classification counts the position of the first double bond, starting from the “omega” end of the molecule (the end furthest from the oxygen atoms). For example, there are omega-3, omega-6, and omega-9 fatty acids:

    

Finally, the orientation of double bonds is very important. In cis fatty acids, there are two hydrogen atoms on the same side of the double bond, giving a molecule with a “kink.” In trans fatty acids, the two hydrogen atoms are on the opposite sides of the double bond, giving a straight-line molecule (trans fats are usually synthetic, resulting from the partial hydrogenation of vegetable oils). Since the straight-line molecules tend to stick together, “trans fats” (made from trans fatty acids) tend to be solid at room temperature, while “cis fats” (made from cis fatty acids) tend to be liquid – that is, oils (such as olive oil) rather than fats:

   

Fatty acids can also be classified in dietary terms. The body needs fatty acids, but can manufacture most of them itself. Essential fatty acids are fatty acids that must be included in the diet. Both ALA and linoleic acid (found in vegetable oils) are essential. Adult men need about 13 grams of linoleic acid and 1.3 grams of ALA per day. Some omega-3 fatty acids from oily fish should also be included in the diet.

Fish oil capsules contain the omega-3 fatty acids EPA and DHA.

In contrast, trans fats are particularly unhealthy, and should be eliminated from the diet completely. This can be difficult in the USA, since pre-packaged foods there often contain trans fats (because of their long shelf life). Monounsaturated and polyunsaturated oils are also preferable to solid saturated fats.

Butter contains a large amount of saturated fat.

A new moth for 2014

A new moth, Sympistis forbesi, was reported earlier this year by Brigette Zacharczenko, David Wagner, and Mary Jane Hatfield (thanks also to them for the photos above). The moth feeds on horse gentian plants in the woodlands of eastern North America.

Reports like this are a reminder of the unexplored species diversity that exists, not only in distant and exotic locations, but in our own back yards.

Running NetLogo from R: a tutorial

In the previous NetLogo tutorial, I discussed running R inside NetLogo. In this post, we discuss the RNetLogo package for running NetLogo inside R (see also this article). We use a NetLogo implementation of Conway’s “Game of Life” similar to that in the previous NetLogo tutorial.

Running NetLogo inside R may be the best option for analytical purposes (the 32-bit version of R is usually necessary). The NLStart function starts NetLogo (with or without a GUI), while NLLoadModel loads the selected model. There are also functions to execute selected NetLogo commands or reporters (once, repeatedly, or until a condition becomes true). The following R function sets a parameter, runs setup, followed by go 100 times, and returns the NetLogo history list defined in the model:

library("RNetLogo")
NLStart ("C:\\Program Files (x86)\\NetLogo 5.0.3", gui=FALSE)
NLLoadModel ("Folder\\Life.nlogo")

run.life1 <- function (d) {
    NLCommand (paste("set average-density", d))
    NLCommand ("setup")
    NLDoCommand (100, "go")
    NLReport ("history")
}

h <- run.life1 (0.2)
plot (0:100, h, type="l", col="red", lwd=2, ylim=c(0, max(h)))

The plot shows how average density varies with time:

Since we can inspect the “inside” of the NetLogo model, and apply all the analytical power of R, many statistical tests can be performed, and many plots drawn.

The following function calculates the average endstate of a run, by taking the mean of the last 10 items in the history list:

run.life2 <- function (d) {
    h <- run.life1 (d)
    n <- length(h)
    mean (h[(n-9):n])
}

More useful is to average 100 calls to that function:

run.life <- function (d) {
    dd <- rep (d, 100)
    h <- sapply (dd, run.life2)
    mean (h)
}

xx <- (0:20)/20
yy <- sapply(xx, run.life)
plot(xx, yy, type="l", col="blue", lwd=2, ylim=c(0, max(yy)))

Plotting the calls to run.life shows how the final average density varies with the initial state. For example, an initial density of around 0.4 gives the highest average final density.

With multiple parameters, it may be best to use R’s optimisation capabilities to find the best parameter values. The parallel-execution features of R are also potentially useful.

The loopy surface of the sun

The Solar Dynamics Observatory has taken this wonderful video of the activity going on at the hellishly hot surface of the sun – showing coronal loops, in particular.

See also these other SDO videos.

Observational vs Historical Science?

The debate last February between creationist Ken Ham and science educator Bill Nye has been widely discussed (see also the video). Both sides were rather an embarrassment, but one interesting aspect was Ham’s distinction between “observational science” and “historical science.” This has been called an “inane and baseless fallacy” – but is it?

In fact, all watchers of the CSI franchise know that there is a clear distinction between (on the one hand) applying known science to the past – in order to decide who did what – and (on the other hand) developing new knowledge of scientific principles. There is, of course, an interplay between the two. For example, forensic entomology draws on experimental work in a specific aspect of insect ecology. Experimental work in ballistics (popularised by the MythBusters) is used to decide what conclusions can be drawn from bullets and bullet wounds.

Observational science tends to be restricted to the here-and-now, where confounding factors can be dealt with. NASA and ESA justifiably spend a lot of money sending probes around the solar system (e.g. the probe above) so that the reach of observational science can be extended to objects which humans cannot visit. Events which are outside the solar system, or are distant in time, are outside the scope of direct observation altogether, which means that some degree of inference is inevitable.

Of course, this does not mean that scientists throw up their hands in despair, and say “we’ll never know.” Astronomers routinely investigate the same phenomenon at multiple wavelengths (e.g. radio waves and visible light), in order to get a clearer picture of what’s been going on. The supernova of last April (see image below) is one example, having been investigated at gamma-ray and optical wavelengths.

Carbon dating involves several assumptions about the past – but from the very beginning those assumptions were cross-checked using other dating techniques, such as tree rings and historical methods (the diagram below is redrawn from the Arnold & Libby paper of 1949). In practice, carbon dating is adjusted for multiple confounding factors, and provides a moderately accurate dating method for carbon-containing objects with ages up to tens of thousands of years.

In summary, then, a distinction can indeed be drawn between “observational science” and “historical science.” The latter draws on the scientific principles established by the former. Scientists tackle the problem of not being able to directly observe the past by using multiple independent methods to infer what happened, and this can allow very solid conclusions to be drawn. That’s precisely what makes books, films, and television shows about forensic science so compelling.

Update: see also this 2008 post from the National Center for Science Education on the topic.

Monitoring space debris from Australia

The NASA Orbital Debris Program Office has long worked on monitoring and managing the serious problem of space debris.

Now, a new Australian Collaborative Research Centre (CRC) for Space Environment Management based at Mt Stromlo Observatory will add to this effort. It will bring together the expertise of two Australian universities and two companies, together with US and Japanese partners. The photo below of the Satellite Laser Ranging (SLR) facility at Mt Stromlo is by Ian Sutton.

Happy Pi Day!

It’s Pi Day again today (3/14 as a US-style date). The piday.org website has more information. Happy π day!

Kitchen chemistry: esters

Our previous kitchen chemistry post discussed acids, particularly the acetic acid in vinegar (and its reaction with sodium bicarbonate):

Acids like acetic acid, with a structure that looks like X–COOH, are also important because they react with alcohols (with a structure Y–OH) to form compounds called esters. The reaction is X–COOH + Y–OH → X–COO–Y + H₂O. For example:

Industrially, strong acids are often used to make this reaction happen, but biologically, enzymes do the job. The combination of acetic acid and ethanol is ethyl acetate (used in some nail polish removers), and the image below also shows isoamyl acetate and geranyl acetate. Each ester has the same X–COO–Y structure:

Esters have a “fruity” smell, and indeed the odour of fruit is largely a result of a mix of various esters (go on, sniff some fruit, and celebrate the complex odours that you smell!). Synthetic fruit flavours likewise use esters, but typically in a simpler mix that never smells quite like the real thing.

      

James Kennedy has produced this wonderful infographic of esters and their smells (click on the thumbnail to zoom):

Carbon dating: Science in the service of History

In 1949, Willard Libby proposed carbon dating, a method for dating carbon-containing objects (like wood, leather, or cloth) that exploits the radioactive decay of carbon-14. The diagram above [redrawn from J. R. Arnold & W. F. Libby, “Age Determinations by Radiocarbon Content: Checks with Samples of Known Age,” Science 110 (2869), 678–680, 23 Dec 1949] shows the decay curve for carbon-14, together with some comparison samples Libby used (including wood dated by tree rings and items from the tomb of Pharaoh Zoser, for whom the first of the pyramids was built). It’s a very good fit! Later tests of carbon-dating have used dendrochronology back to about 10,000 BC.

The carbon in plants contains about one part per trillion of carbon-14, which the plants absorb from the atmosphere. The same amount of carbon-14 is present in animals, which get their carbon by eating plants or other animals. All living things therefore contain about one part per trillion of carbon-14. In dead plants or animals, however, the carbon-14 decays with a half-life of 5,730 years. For practical dating purposes, measurements of carbon-14 are adjusted to match the tree-ring data, so as to compensate for small changes in the amount of atmospheric carbon-14 over time. Such calibrated dates are reported as “Before Present” (BP), where “Present” means 1 January 1950.

One of the most famous examples of carbon-dating has been the Shroud of Turin, purported to be the burial shroud of Jesus Christ, and shown below in a negative image from 1898. The Shroud has been carbon-dated to between 1260 and 1390 AD, which is consistent with its denunciation as a forgery by the Bishop of Troyes in 1389, shortly after it first appeared on the historical scene. For the dating story, see P. E. Damon et al., “Radiocarbon Dating of the Shroud of Turin,” Nature 337 (6208), 611–615, 16 Feb 1989.

Giant redwoods at Muir Woods

I love this 2006 photograph of giant redwoods (Sequoia sempervirens) at Muir Woods, California (which is a wonderful place to visit).