So you know how sometimes, you get a pile of work on your desk, and by the time you have a moment to stop and breathe, you realize it’s three weeks later than you hoped it was? Fun times, that. I’m hoping to be done this particular pile of work in a week or two — I’ve not abandoned ship a mere handful of posts in! In the mean time, have a clip of the hilarious (and scientifically literate) Dara O’Briain on the so-bad-it’s-hilarious movie 2012 (starts at 10:25, continues into next segment of the show).
Sometimes it seems like it’s only a matter of time before the hagfish comes up for discussion, though at least one person thinks that I may be, and I quote, “vastly over-estimating the market saturation of hagfish blogging.” Perhaps it’s a holdover from that one seminar talk I went to when I was in undergrad given by a professor who researched (among other things) the properties of hagfish slime. While he was talking my friend drew a quick sketch of Hagman, the hagfish superhero, and we all snickered loudly in the back row. Hagman then sporadically came up in conversation for weeks afterward, and still makes me snicker several years later.
Hagman fights for truth, justice, and the Stanley Cup.
There’s a good reason that hagfish are one of those creatures that gets a disproportionate amount of cultural presence, and that’s because they’re weird and gross. They’re marine invertebrates, living mostly at great depth in the ocean, burrowing into dead whale carcasses and other rotten corpses and eating their way out. They have no bones or jaws, but intimidating rings of scaly teeth. And when they’re attacked or startled, they produce a cloud of slime, tie themselves in a knot, shimmy out of the slime cloud that’s now engulfed the attacker, and escape.
That’s an impressive trick, disgusting table manners or no.
Hagfish slime is astounding. The mucus the hagfish produces is a milky white goo, and while it doesn’t produce much mucus at any one time, a small amount of mucus quickly turns a large container of water into a large mass of slime.
Hagfish slime contains three things: seawater, slime threads, and mucins. Mucins are proteins found in mucus of all sorts, including saliva and gastric juices, while slime threads are thin protein tendrils that are curled up when excreted by the hagfish and then unfold when in seawater. Both mucins and slime threads are produced by separate glands located all along the body of the hagfish. Given how thick and, er, slimy hagfish slime is, intuition would say that either the slime is made up principally (or at least significantly) of either threads or the mucins, but it seems that this is not the case. It appears that hagfish slime is about 99.996% seawater, 0.0015% slime threads, and 0.002% mucins.
So, given that hagfish slime is so cohesive, those threads and mucins must be pretty remarkable. The threads, when produced, are tightly curled or folded up, and unfold in water; mucin is produced in packets that swell with water, but do not burst. Mucin plays a critical role in the unfolding — threads will not form unless mucins are present in the solution. It’s thought that the mucin packets bind to the the threads somehow, almost like deep conditioner binds to hair, and in doing so make the thread unfold rapidly, but it’s unclear how exactly that works. But given proportion of the threads to mucins, the size of the threads (~15 cm long unstretched, ~3 um thick in the middle), and the mucin packets (~7um long, ~3um thick), there is enough room on the threads for the mucin packets to bind to and give good coverage.
Left: The slime thread tapers to the ends, and the ellipsoid mucins bond along its length. Right: The threads curl and tangle around each other, forming a network that traps water.
The threads, when unfolded and covered in water-swollen mucin packets, then form a network throughout the slime mass. The threads are long, and can span the entire slime mass (depending on how much slime the hagfish is producing, ie, how agitated the hagfish is). This means that the threads, which while thin and diffuse, are quite strong, form a mass of channels and chambers in the slime mass. The seawater gets trapped in these channels and chambers, and cannot flow freely anymore. It doesn’t form a chemical gel, that is, the water does not stop flowing, but it slows down sufficiently to form a coherent, slimy mass.
But how does the slime help them evade predators? Sure, it’s startling to suddenly have a mass of slime in your face, but is that enough of a deterrent to justify the energy costs to the hagfish? Slime may not only be startling, but it appears to be thick enough (and cohesive enough) that it clogs the gills of predator fish, which not only startles the attacker, but may suffocate them.
Unfortunately, the hagfish also has gills, and those gills can be clogged by its own slime. To avoid drowning, the hagfish uses its other unique trick: the ability to tie itself in an overhand knot, and wiggle the knot very quickly down the length of its body. This effectively peels the slime off itself, clearing its gills and avoiding suffocation. It’s also useful for escaping from dastardly researchers who’re holding them in midair:
But hagfish also have a nostril, to be able to sniff out dead whale carcasses and other food, and slime can get stuck in it too. To clear it out, hagfish sneeze. Hagfish are the only known type of fish that sneeze, though sadly, “hagfish sneezing” does not turn up any relevant videos.
At the end of September, a paper was published with the provocative conclusion that neutrinos had been measured to travel faster than the speed of light. It was big news, and was widely reported in the media as a reasonably established finding (when in reality it had been released on arXiv, an open-access physics portal, but was not yet peer reviewed, and was subject to much eyebrow raising from physicists at large). In the past week, news has come out that there were some systematic sources of error, and the results are not necessarily accurate.
a beam of neutrinos was generated at the Large Hadron Collider (LHC), and the beam was aimed through the Alps (ie, underground) to a detector in Italy called OPERA about 730 km away
the signal leaving the LHC is timestamped, using a highly accurate (and very carefully calibrated) GPS system
as the neutrinos leave the LHC, a light signal is sent to the same location in Italy via a fibre optic cable. This provides a time-of-flight for a light signal to compare to the time-of-flight for the neutrino signal.
when the light and neutrino signals are detected in Italy, they are timestamped using the GPS system, and the times of flight cane be compared
this repeated over and over again to reduce statistical errors in the measurements
The scientists reported that there was a difference in the times-of-flight of about 60 ns, with the neutrino beam reaching the detector before the light signal. Now, the scientists involved have found two sources of error, which, indicentally, mirror my hunch from when this first hit the news. First, the GPS equipment is operating far outside of its normal operating range, and so my not behave exactly as expected; this error is thought to produce a faster neutrino speed. But the second source of error is a loose connection for the fibre optic cable that carries the light signal, introducing a delay that may account for the difference in time elapsed for the two signals (light and neutrino).
I’m not at all surprised at this — when the paper was first put out, I thought it was only a matter of time before a systematic source of error was found. General relativity has held up spectacularly in every experimental test undertaken, and it would take a lot to upend all of that.
I was surprised that the group released their paper as early as they did, and without initial peer review, and I think that speaks to the authority that the scientific community confers on the CERN collaboration. If this exact paper had been written be a group at a small, less renowned institution (assuming they had all the equipment to do the experiment), would it have ever seen the light of day? Would a smaller group release very controversial results which naturally invite a huge amount of attention from popular media, without even subjecting them to peer review first? Would they ask for scrutiny from all and sundry, not just their peers?
I doubt it, because the stakes are too high. For a smaller, less authoritative group, the hit that their reputation could sustain could be devastating. No-one’s going to give CERN side-eye at everything they do from here on, because it’s CERN! They’ve done incredible work and have a very solid reputation. But if a group without that name backing did the same science and presented it that same way, there’s a good chance it’d be either ignored, chalked up to poor science or ineptitude, and probably wouldn’t be given much of a second look.
I bring this up not to cast aspersions at CERN — they do excellent work — but rather to highlight the weight that an authoritative name can carry in the scientific word. We like to think that science is objective and speaks for itself, and that good science will get the recognition it deserves regardless of who does it. This is not true — there’s plenty of excellent scientists who face all sorts of barriers (monetary, linguistic, social, etc) in their attempts to get their science visible. This isn’t to say that crackpots don’t exist — there’s plenty of people with a tenuous grasp of general relativity who insist that “Einstein was WRONG!”, though they are generally easily refuted — but this is a prime example of how having a big name collaboration helps people take a second look at your work, rather than just writing it off as an errant result.
I don’t think that this paper would’ve gotten as much attention from the scientific community (or the popular media, but they’re not the best arbiter of what’s new and important in science) had it not come from such an authoritative group. I think that, like me, most scientists would’ve said “there’s probably an error in the GPS or the cabling” and left it at that. An awful lot of scientists said that this time, but they typically said it after they’d read the paper; I doubt many of them would’ve bothered to read the paper had it not been from an authoritative collboration. It’s a disappointing realization, but it’s always good to have a reminder to check for our unconscious (or conscious) biases.
There’s been reams of digital ink spilled about the leak of a large quantity of documents from the Heartland Institute, which is a think-tank devoted to to anti-environmentalism. The leaked documents are available here on DeSmogBlog, and the contents aren’t especially surprising: there’s lists of donors, including big tobacco companies and pharmaceutical companies, there’s the names of people on their payroll, including Anthony Watts, and there’s some strategy documents which don’t have anything startlingly unexpected in them that I’ve seen. The added wrinkle is that the documents were collected by Peter Gleick, an American environmental scientist who worked, among other things, in ethics. He contacted the Institute with a false identity and got a hold of the documents, which was a deeply stupid move that demolishes Gleick’s credibility as an ethical scientist. While it’s nice to have these documents, as they confirm a lot of the tactics and participants that climate and environmental scientists thought were a part of anti-environmental movement, it’s not like there’s much that earthshattering in them.
I don’t have very much to say about the documents themselves, though I encourage you to have a look at them — primary sources are optimal! I do have a few words to say about how the documents were obtained and what that means for the scientific community as a whole, and a few other words about the strategy to dissuade teachers from teaching science, which is the bit from the documents that’s caused the most hubbub in the media.
Limnic explosions are really bizarre and not very well understood, since there’s only been two confirmed and documented events in recent history (Lake Monoun and Lake Nyos, both in Cameroon, in 1984 and 1986 respectively), and it’s difficult to study an exploding lake for what should be obvious reasons.
What happens is this: gas emitted from the lakebed dissolves into the lower depths of the lake water, creating a supersaturated solution. Solutions consist of who components: the solvent, or the liquid which forms the bulk of the solution, and the solute, which is the material dissolved in the solute. A solution is undersaturated when the quantity of solvent can dissolve more solute than is currently in solution, saturated when the critical amount of solute is dissolved in the solvent and no more can be added to the solution, and supersaturated if, under some circumstance, more solute than can normally be dissolved in the solvent is present in the solution. A supersaturated solution is generally unstable, and if the solution is jarred or disturbed, the compound dissolved in the water will suddenly precipitate out, releasing a lot of energy and heat. While this is commonly demonstrated in high school chemistry class by dropping a crystal of salt into a large flask of supersaturated salt water, the same basic principle can apply to a lake, too.
Three things are needed for a limnic eruption to be even remotely possible:
The lake must be tropical, so that it doesn’t overturn. Lakes in temperate regions (for example, the Great Lakes) overturn due to the seasonal fluctuation of the air temperature above the lake. As the air cools in winter, the surface water cools and sinks, pushing water from the depths up to replace it. This means that there is no consistent bottom layer of water that remains undisturbed for long periods of time.
The lake must be deep and very stably stratified, so that there is a bottom layer of water that is not disturbed for a long period of time and doesn’t interact with the surface or sunlight.
There must be a geophysical source of gas, usually CO2 or methane (CH4) at the bottom of the lake. This may be as a result of volcanic activity under the lake.
Top left: a tropical lake that does not over turn. Top right: a temperate lake overturns. Bottom left: a stratified lake Bottom right: a lake with a gas source in the lake bed.
Without all three of these ingredients, a limnic explosion is not possible, because there is no way to create a supersaturated bottom layer. If the first is lacking, the bottom layer of water interacts with the upper layers, and the dissolved gas will dissipate. If the fluid is not strongly stratified, the gas will easily diffuse upwards and out of the bottom layer. If there is no source of gas, there is nothing to explode. Lake Nyos is a very deep crater lake, which sits on top of a dormant volcano. It’s surrounded by tall hills, which shields it from strong winds (which can help stir lakes). It’s a perfect candidate for a limnic explosion.
What’s still very unclear is how a limnic explosion is set off. Some scientists suspect a small earthquake jiggled the lake and set it off, while others think that there was a change in the stability of the lake. If the stability of the lake changed, the stratification could weaken and an overturning circulation could form, bringing the bottom water to the surface where the sudden change in pressure could cause the gas to rapidly expand (and thus explode out of the water). Some scientists think that for some reason a plume of light water formed at the bottom of the lake and entrained the bottom layer water as it rose to the surface (ie, the light water dragged the denser water up to the surface with it) . There’s a theory that an unusually severe thunderstorm the night before the explosion deposited a layer of cold water at the surface, which then caused an overturning circulation to form and the gas, again, to reach the surface and expand rapidly. Another idea is that the inflow from rivers was colder than usual. The precise mechanism is still unclear, especially since it’s difficult to accurately analyze what cause the explosion after the fact, and before the fact it was an otherwise unremarkable lake in remote Cameroon.
What is clear is that the bottom water with the extremely high concentration of CO2 reached the surface, and the change in pressure caused the dissolved CO2 to explode out of the water and into the surrounding atmosphere. Carbon dioxide is heavier than air, so when all the gas exploded out of the lake, it sank and hugged the ground, and ran through the valleys in the hills surrounding the lake. The high concentration of CO2 in the cloud from the explosion asphyxiated nearly 1800 people, some as far away as 20 km from the lake, and countless animals. The victims appeared to die peacefully; eyewitness accounts from survivors tell a tale of people falling suddenly or quickly into a coma and never awakening, or people who were asleep (the explosion occurred at around 10 pm) never waking up.
In the wake of the explosion, scientists devised a way to degas the lake to prevent CO2 from building up in the lake again and thus decreasing the potential for another explosion. They have installed a pipe and a pump that vents the bottom layer of saturated water to the surface, allowing the CO2 to bubble off at a continuous rate that allows it to dissipate before it can form a lethal cloud. A similar structure is installed in Lake Monoun, though since the lake is smaller less pipes are needed. I’ve had a surprising amount of difficulty finding current information about the state of these degassing projects, unfortunately, and it’s unclear to me whether the projects were ever finished or if they’re still in operation.
The pipe connects the bottom fluid layers to the surface, allowing the gas to bubble off into the air. Initially the water must be pumped, but as the water becomes buoyant in the tube (due to the expanding gas), water from the bottom gets sucked up to replace the water in the pipe, and the pump is no longer needed.
Lake Kivu, which sits between the Democratic Republic of Congo and Rwanda, is the only other known lake that is at risk for a limnic explosion. Lake Kivu is about 2,000 times larger than Lake Nyos, and is not nearly as remote — about 2 million people live near its shores. Lake Kivu contains not only CO2, but also high concentrations of methane (CH4), which has lead to some engineering projects which attempt to retrieve the methane for use as fuel. This is doubly useful in that in the process of extracting the methane, some CO2 is also extracted. Fortunately, the gas concentrations in Lake Kivu are not nearly as high as those in Lake Nyos, and so it is probably less likely to explode, but the consequences (and death toll) from a limnic explosion at Lake Kivu are likely to be several orders of magnitude higher than from previous confirmed explosions. Considering that the effect of extracting the methane may not be enough to offset the natural build-up of gas, and also that the scientific community still knows very little about limnic explosions and what triggers them, Lake Kivu is possibly a ticking bomb.
Soap is ubiquitous in modern life, in many forms, from hand soap to laundry detergent to shampoo. Chemically, soaps are alkali salts of fatty acids, and are formed by taking a fat or oil and combining it, either at room temperature or at or around the boiling point of the fat, with a strong alkali compound like sodium hydroxide. (Alkali compoounds are chemicals that have a high pH; please see the post on the pH scale for reference.) The alkali compound used is usually a hydroxide, either sodium, potassium, or occasionally lithium. All these hydroxides are very reactive, which is useful for forming soap, but they are also very corrosive, and so soapmaking must be done very carefully to avoid accidents.
A triglyceride is a fatty acid with three branches. It reacts with NaOH to produce soap molecules with a hydrophobic tail and a hydrophilic head and a molecule of glycerol.
At the heart of soap’s effectiveness is that soap molecules have two distinct parts. One part is hydrophobic (ie, does not mix will with water) and grabs on to dirt (which typically is oil based, ie, also hydrophobic) while the other part is hydrophilic (ie, mixes well with water).
A bit of dirt gets covered in soap molecules, all with the hydrophobic end attached to the dirt, with the hydrophilic end trailing like a string away from the dirt. This structure is sometimes called a micelle, though the term is not just used for soap.
Lutefisk is made in a similar manner to soap, and it’s one of those things, like soy sauce, that I wonder how on earth someone figured out how to make it (and thought to try eating it). It’s a Nordic dish made by taking salted fish like cod, treating it with lye (ie, a very strong alkaline compound) for a couple of days, and then soaking it in water for several days to rinse out the caustic lye. Traditionally, the fish is treated with ash, which is alkaline but not nearly as strong as lye, and then buried for several months. Either way, the chemical reaction between the fats and oil in the fish and the lye needs to be stopped before all the fats saponify; though the whole point of making lutefisk is that some of the fats saponify, rendering the entire fish soap seems even more unsavory than only a partial rendering. The end result is a fish concoction that is somewhat gelatinous and falls apart easily, is either baked or broiled, and looks about as appetizing as you’d expect given how it’s made. I’ve never eaten it myself, but it’s got a reputation for smelling and tasting awful with a very unpleasant texture, but apparently some people genuinely enjoy it. While on description alone I can’t say as I’d recommend it, if you’re going to eat it, it seems especially prudent, given the chemistry involved in making it, to avoid the dented can on the discount shelf at the grocery store.
There’s a common line in soap commericals that goes something along the lines of “This soap is pH balanced, for soft, smooth skin.” The claim about the soft, smooth skin may or may not be accurate, but what does “pH balanced” mean?
The pH scale is a measurement of the acidity of an aqueous (ie, water-based) liquid compound. The capital H indicates that it’s a measurement of hydrogen ions (denoted H+ in chemical notation); the definitive meaning of the p is lost to the sands of time. A low pH value means that the solution is acidic, and has more H+ ions than OH- ions, while a high pH means the solution is basic (or alkaline — the two terms are interchangeable) and has more OH- ions than H+. The more extreme the inbalance (ie, the lower or higher the pH) the stronger the solution, and the more likely it is to eat through your skin if you spill it.
The fluid in the flask on the left is more acidic than the fluid in the beaker on the right is basic.
The precise value of the pH of a solution is given by the negative logarithm of the concentration of hydrogen ions in the solution, though there are compounds that can act as catalysts in specific solutions that will alter the measured pH. Logarithms are a useful way of describing quantities that vary of a wide range of scales. Mathematically, if x = b^y, y = log_b (x).
Logarithms are typically either in base 10 (ie, b=10) or base e (ie, b = e = 2.718…; these are also called natural logarithms). The most commonly known logarithmic scale is the Richter scale, which measures the strength of earthquakes. The Richter scale is a base 10 scale, so an earthquake of magnitude 6.0 is 10 times stronger than an earthquake of magnitude 5.0, and 1000 times (ie, 10^3 times) stronger than an earthquake of magnitude 3.0.
Similarly, the pH scale is a base 10 logarithmic scale. A solution of pH 4.0 is ten times more acidic than a solution of pH 5.0, and 10 times less acidic (ie, more alkaline) than a solution of pH 3.0. The scale runs from 0.0 to 14.0, (explain why zero can be reached due to catalytic reactions and whatnot)
Click to enlarge.
The pH of a solution can be tested using a variety of compounds called indicators that are known to change colour at specific pH values. Indicators do not generally interact with the solution, and so do not drastically alter the chemical mix in the solution. An indicator can be added to a solution, and then the solution can be titrated (ie, another solution is dripped slowly into the original solution to reach a desired pH) until the indicator changes colour. The colour change of the indicator indicates that the solution has reached a specific pH. Litmus paper is a crude indicator: it will indicate if a solution is acidic or basic, but does not determine exactly how acidic or basic the solution is.
In a general sense, then pH balanced, means that the solution in question has the same pH as its surroundings. Skin has a pH of around 5.5, so in the context of facial soap, the manufacturer may be using “pH balanced” to mean that the soap has a pH around 5.5, so the soap will not undergo an acid-base reaction with (and thus irritate) the user’s skin.
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