Using Plants to Turn Pollution into Profits

Once again, I may prove why I’m a poor writer, by burying a lede. But bear with me here, because this will come full circle and yield some fruit. You probably know that urban farming has become more popular over the last decade or so as local eating became trendy. As city dwellers started their own plots, people realized there might be a unique challenge to urban areas: avoiding lead poisoning. (Although a more recent study evidently suggests you’re getting less lead than people expected.) We used lead in lots of things throughout the 20th century, and it easily accumulated in the soil in areas exposed to high doses of some sources – so cities and areas by busy highways have lead from old gas emissions, old lots have lead from old paint, and even old lead pipes and batteries can leach lead into soils. There are other pollutants that can leach into soils in other places. Mercury and cadmium can build up in places where significant amounts of coal are burned, and many mining practices can result in a lot of the relevant metal leaking out into the environment.

Traditionally, the way to deal with polluted soil is to literally dig it all up. This has a major drawback, in that completely replacing a soil patch also means you throw out some nice perks of the little micro-ecosystem that was developed, like root systems that help prevent erosion or certain nutrient sources. Recently, a new technique called phytoremediation has caught on, and as the NYT article points out, it takes advantage of the fact that some plants are really good at absorbing these metals from the soil. We now know of so-called hyperaccumulators of a lot of different metals and a few other pollutants. These are nice because they concentrate the metals for us into parts of the plants we can easily dispose of, and they can help preserve aspects of the soil we like. (And roots can help prevent erosion of the soil into runoff to boot.) Of course, one drawback here is time. If you’re concerned that a plot with lead might end up leaching it into groundwater, you may not want to wait for a few harvests to go by to get rid of it.

But a second drawback seems like it could present an opportunity. A thing that bugged me when I first heard of hyperaccumulators was that disposing of them still seemed to pose lots of problems. You can burn the plants, but you would need to extract the metals from the fumes, or it just becomes like coal and gas emissions all over again. (Granted, it is a bit easier when you have it concentrated in one place.) Or you can just throw away the plants, but again, you need to make sure you’re doing it in a place that will safely keep the metals as the plants break down. When I got to meet someone who studies how metals accumulate in plants and animals last summer, I asked her if there was a way to do something productive with those plants that now had concentrated valuable metals. Dr. Pickering told me this is called “phytomining”, and that while people looked into it, economic methods still hadn’t been developed.

That looks like it may have changed last month, when a team from China reported making multiple nanomaterials from two common hyperaccumulators. The team studied Brassica juncea, which turns out to be mustard greens, and Sedum alfredii, which is a native herb, and both of which are known to accumulate copper and zinc. The plants were taken from a copper-zinc mine in Liaoning Province, China.  The plants were first dissolved in a mix of nitric and perchloric acid, but literally just heating the acid residue managed to make carbon nanotubes. Adding some ammonia to the acid residue formed zinc oxide nanoparticles in the Sedum, and zinc oxide with a little bit of copper in the mustard greens. What’s really interesting is that the structure and shape of the nanotubes seemed to correlate to the size of the vascular bundles (a plant equivalent to arteries/veins) in the different plants.


A nanotube grown from the mustard greens. Source.

But as Dr. Pickering said to me, people have been looking into to this for a while (indeed, the Chinese team has similar papers on this from 5 years ago). What’s needed for phytomining to take off is for it to be economical. And that’s where the end of the paper comes in. First, the individual materials are valuable. The nanotubes are strong and conductive and could have lots of uses. The zinc oxide particles already have some use in solar cells, and could be used in LEDs or as catalysts to help break down organic pollutants like fertilizers. The authors say they managed to make the nanotubes really cheaply compared to other methods: they claimed they could make a kilogram for $120 while bulk prices from commercial suppliers of similar nanotubes is about $600/kg. (And I can’t even find that, because looking at one of my common suppliers, I see multiwalled nanotubes selling on the order of $100 per gram.) What’s really interesting is they claim they can make a composite between the nanotubes and copper/zinc oxide particles that might be even more effective at breaking down pollutants.

I imagine there will be some unforeseen issue in attempting to scale this up (because it seems like there always is). But this is an incredibly cool result. Common plants can help clean up one kind of pollution and be turned into valuable materials to help clean up a second kind of pollution. That’s a win-win.

A non-biologist’s guide to not saying dumb things about biology

I’m not a biologist, but even I still can see when some people make strange claims about biology. But maybe not being an expert can help here because I don’t know enough to give a super detailed explanation.

  • Nature vs nurture is really complicated. I think to some people nurture has become almost synonymous to “choice”  because of the use of this phrase in discussions about child-rearing and personal development, like the debate over whether or not people are “born gay”. But nurture also encompasses stuff in the environment that no one may reasonably have control of, like exposure to certain hormones in the womb.


  • This also ties into genetic causes being hard to figure out. Many traits that are associated with a known gene aren’t completely controlled by it – it just may increase or decrease the odds of a person having it, because there are still environmental influences. The other issue is that many traits are influenced by multiple genes. For instance, 33 different parts of the human genome may be related to Alzheimer’s disease.
  • Being allergic to something doesn’t mean you are allergic to every molecule in it. This seems to come up a lot in debates on GMOs, when people raise concerns about people having allergies to novel genes. Those concerns are mostly legitimate, but it’s worth pointing out almost any new molecule we encounter could end up being an allergen. (Latex and nickel allergies  were probably surprising when they first started showing up in populations.) We could actually test if whatever a new gene expressed could cause an allergic reaction. For instance, this paper says most shellfish allergies seem to be in response to one protein. Or your may know people who are allergic to cow’s milk, but can still eat beef. And it makes sense, because a major piece of evidence supporting evolution is how similar many proteins are across different species – we share a lot proteins with all the other multicellular species on Earth.
  • One study doesn’t really prove anything. This applies to all science, but it seems to come up a lot in reactions to reporting about biology and medical studies. One study saying something about a specific effect of eating chocolate or finding a gene correlating to a disease doesn’t mean much. A hallmark of modern science is reproducibility, and so we should generally look at multiple studies before accepting things as “fact”.
  • Genetic engineering does not work like LEGOThe TV tropes link explains a lot. And the Analysis page on TV Tropes also explains how this actually works in relatively accessible detail. You won’t get wings by adding bird genes to your genome – even if you got the right Hox genes, you would also need to still ensure the right signals were sent to activate the genes to begin the appropriate limb formation.
  • Rates of change matter. When people are concerned over climate change or pollution or other impacts humans have on the environment, it’s not that ecosystems can’t adapt to any change. The issue is that if the environment changes too fast, it can outpace the speed at which organisms can adapt and cause a large number of extinctions.

Red Eye Take Warning – Our Strange, Cyclical Awareness of Pee in Pools

The news has been abuzz lately with a terrifying revelation: if you get red eye at the the pool, it’s not from the chlorine, it’s from urine. Or to put it more accurately, from the product of chlorine reacting with a chemical in the urine. In the water, chlorine easily reacts with uric acid, a chemical found in urine, and also in sweat, to form chloramines. It’s not surprising that this caught a lot of peoples’ eyes, especially since those product chemicals are linked to more than just eye irritation. But what’s really weird is what spurred this all on. It’s not a new study that finally proved this. It’s just the release of the CDC’s annual safe swimming guide and a survey from the National Swimming Pool Foundation. But this isn’t the first year the CDC mentioned this fact: an infographic from 2014’s Recreational Water Illness and Injury Prevention Week does and two different posters from 2013 do (the posters have had some slight tweaks, but the Internet Archive confirms they were there in 2013 and even 2012), and on a slightly related note, a poster from 2010 says that urine in the pool uses up the chlorine.

A young smiling boy is at the edge of a swimming pool, with goggles on his forehead.

My neighborhood swim coach probably could have convinced me to wear goggles a lot earlier if she told me it would have kept pee out of my eyes.

Here’s what I find even stranger. Last year there was a lot of publicity about a study suggesting the products of the chlorine-uric acid reaction might be linked to more severe harm than just red eye. But neither Bletchley, the leader of study, and none of the articles about it link the chemicals to red eye at all, or even mention urine’s role in red eye in the pool. Also, if you’re curious about the harm, but don’t want to read the articles, the conclusion is that it doesn’t even reach the dangerous limits for drinking water. According to The Atlantic, Bletchley is worried more that it might be easier for an event like a swimming competition to easily deplete the chlorine available for disinfecting a pool in only a short amount of time. This seems strange because it seems like a great time to bring up that eye irritation can be a decent personal marker for the quality of the pool as a way to empower people. If you’re at a pool and your eyes feel like they’re on fire or you’re hacking a lot without swallowing water, maybe that’s a good sign to tell the lifeguard they need to add more chlorine because most of it has probably formed chloramines by then.

Discussion of urine and red eye seems to phase in and out over time, and actually even the focus of whether its sweat or urine does too. In 2013, the same person from the CDC spoke with LiveScience and they mention that the pool smell and red eye is mainly caused by chloramines (and therefore urine and sweat), not chlorine. A piece from 2012 reacting to a radio host goes into detail on chloramines. During the 2012 Olympics, Huffington Post discussed the irritating effects of chloramines on your body, including red eye, and the depletion of chlorine for sterilization after many Olympic swimmers admitted to peeing in the pool. (Other pieces seem to ignore that this reaction happens and assume it’s fine since urine itself doesn’t have any compounds or microbes that would cause disease.) In 2009, CNN mentions that the chloramines cause both red eye and some respiratory irritation. The article is from around Memorial Day, suggesting it was just a typical awareness piece. Oh, and they also refer to a 2008 interview with Michael Phelps admitting that Olympians pee in the pool. The CDC also mentions chloramines as potential asthma triggers in poorly maintained and ventilated pools and as eye irritants in a web page and review study that year. In 2008, the same Purdue group published what seems like the first study to analyze these byproducts, because others had only looked at inorganic molecules. There the health concern is mainly about respiratory problems caused by poor indoor pool maintenance because these chemicals can start to build up. Nothing about red eye is mentioned there. In 2006, someone on the Straight Dope discussion boards refers to a recent local news article attributing red eye in the pool to chlorine bonding with pee or sweat. They ask whether or not that’s true. Someone on the board claims it’s actually because chlorine in the pool forms a small amount of hydrochloric acid that will always irritate your eyes. A later commenter links to a piece by Water Quality and Health Council pinning chloramine as the culprit. An article from the Australian Broadcasting Corporation talks about how nitrogen from urine and sweat is responsible for that “chlorine smell” at pools, but doesn’t mention it causing irritation or just using up chlorine that could go to sterilizing the pool.

Finally, I just decided to look up the earliest mention possible by restricting Google searches to earlier dates. Here is an article from the Chicago Tribune in 1996.

There is no smell when chlorine is added to a clean pool. The smell comes as the chlorine attacks all the waste in the pool. (That garbage is known as “organic load” to pool experts.) So some chlorine is in the water just waiting for dirt to come by. Other chlorine is busy attaching to that dirt, making something called combined chlorine. “It’s the combined chlorine that burns a kid’s eyes and all that fun stuff,” says chemist Dave Kierzkowski of Laporte Water Technology and Biochem, a Milwaukee company that makes pool chemicals.

We’ve known about this for nearly 20 years! We just seem to forget. Often. I realize part of this is the seasonal nature of swimming, and so most news outlets will do a piece on being safe at pools every year. But even then, it seems like every few years people are surprised that it is not chlorine that stings your eyes, but the product of its reaction with waste in the water. I’m curious if I can find older things from LexisNexis or journal searches I can do at school. (Google results for sites older than 1996 don’t make much sense, because it seems like the crawler is picking up more recent related stories that happen to show up as suggestions on older pages.) Also, I’m just curious about the distinction between Bletchley’s tests and pool supplies that measure “combined chlorine” and chloramine, which is discussed in this 2001 article as causing red eye. I imagine his is more precise, but Bletchley also says people don’t measure it, and I wonder why.

“Cosmos” is allowed to have a narrative

Neil deGrasse Tyson’s sequel/reboot to Carl Sagan’s Cosmos: A Personal Voyage, Cosmos: A Spacetime Odyssey, premiered last week on Fox and there’s a multitude of reactions to it. One of the most common negative reactions focuses on the episode’s relatively long segment on Giordano Bruno. If you really want to learn more about Bruno and the various other figures people relate him to and see one of the clearest criticisms and replies to defenses of the show, I suggest you look at the Renaissance Mathematicus’ post on the issue. (And if you want to learn REAL history of science, I highly suggest you check out the rest of his blog.)

A very religious friend posted concerns from Catholic commentators that Cosmos is attacking religion here. I argue that both just seem to be taking offense and ignore Tyson’s actual narration during and around this segment. At no point does Tyson criticize faith. If anything, it’s a critique of institutions which both blog posts seem to also acknowledge by saying that structures and actors in the Church may be bad, but that doesn’t mean Catholicism itself is bad. I’d argue the bigger takeaway is that Bruno thought others’ God was too small.

Several people have asked why mention Bruno at all in the show. Because the entire point of this first episode was to establish the scale of the Universe and our place in it. Bruno was one of the first Western thinkers to propose a Universe where humanity and Earth and the Sun are all small and not particularly unique with respect to the rest of the cosmos. though he was still off on how that actually worked out, as detailed in the Renaissance Mathematicus link above. To Bruno, that had immense philosophical implications and he was willing to die for them (and the host of other heterodox beliefs he held). Why should we just ignore that? Tyson (and Sagan!) are both big on the idea that science can inform metaphysics, and Western culture seems to have a fear that science will leave life without meaning. It seems perfectly reasonable for the show to mention a person whose cosmology inspired a lot of his own religious and spiritual thought. 

Hank Campbell, founder of Science 2.0 and one of the co-authors of Science Left Behind, has different criticisms than most about the first episode, saying “Science is cool. Should we care if it’s accurate?” I want to quickly respond to these points, and I’ll go in more depth later. 

  1. The greenhouse effect is in fact different from the idea of global warming, but the greenhouse effect does play a part in the latter.
  2. I kind of cringed too at the reference to a multiverse but considering the language the episode used, I’d say the phrase “many of us suspect [a multiverse]” was chosen precisely because it isn’t an accepted theory.
  3. The first time I watched the episode, I didn’t notice the external sounds in space separate from the soundtrack. It struck me as kind of funny because Tyson would typically destroy any show that did it. He should be held accountable on his own.
  4. The episode did not claim Bruno was more important than contemporary natural philosophers and empiricists and definitely pointed out that he wasn’t a scientist. Bruno’s ideas, though, do fit in well with the idea of understanding our place in the universe, which was the entire point of the first episode, as stated in like the first five minutes.
  5. The age of the universe as 13.8 billion years old was given multiple times, and the introduction to every major historical landmark on the calendar involved Tyson giving both its date on the calendar and a conversion to how many millions or billions of years ago it actually was.

There Might be Life in Space, but This Paper Didn’t Prove It

An article published in the Journal of Cosmology last month made headlines with its bold claim: alien life can be found in Earth’s atmosphere. The rest of the scientific community ins’t convinced. The Journal of Cosmology isn’t a “peer reviewed” journal, which is the gold standard for scientific work. This means papers the journal publishes aren’t really evaluated for quality or accuracy. In fact, it’s even been labelled “predatory” by one research librarian. As a general rule, it’s also really not a good sign when a paper making a bold claim mainly cites other papers by its authors.

The lack of peer review on the paper seems justified; there’s not much data.  The paper relies almost entirely on just microscope images . Virtually any structure that has a bend or fiber is declared evidence of life, for no clear reason. (This may be a trend, as PZ Myers basically made the same complaint of a previous Journal of Cosmology paper claiming to have found bacteria in meteorites)

If you can see four bacteria in this post, I will give you a prize*

If you can see four living things in this post, I will give you a prize*

This paper claims the images are of diatoms or diatom-like lifeforms, but they don’t show any as reference and their images aren’t magnified like most that try to show diatom structures.

A known diatom from Earth.

The authors also try really hard to link the alleged cells they see to alleged organisms responsible for the red rains in Kerala, India several years ago (those claims inspired similar controversy and seemed to rely on evidence that was only slightly more firm than what is offered here). If you’re going to make that connection, though, maybe you should show an image of that.

Aside from images, the only other data the paper mentions is a technique to measure the amount of elements in the sample. The paper only says the samples are high in carbon and oxygen, but don’t provide numbers.  They say that means what they’re looking at isn’t a mineral, but it’s worth pointing out there are in fact many meteoroids that are mostly carbon and oxygen so they might be looking at weird dust from those. That’s it; no attempt to extract any potential organic matter (though that’s also a dime a dozen in space, even without life).

The people at the Journal of Cosmology say other scientists are irrationally opposed to the idea that life on Earth may have originally come from outer space. While that’s not the dominant opinion in biology right now, it actually is something mainstream scientists are looking at. It’s just that, as Carl Sagan said, “extraordinary claims require extraordinary evidence”. And a bad SEM image is not the latter.

*The prize is my affection.

Wine Tasting 101

NPR’s blog about food and science, The Salt, has an amusing story on wine tasting this week. Part of it is pointing out the actual science in wine tasting, which has recently been a victim of fights on the Internet*. Basically, The Salt’s post focuses on the actual chemicals present in wines and wants to help wine newbies detect by saying where we can find them in other foods. So here’s the quick lowdown

  • Whites aren’t aged in oak as often as reds.
  • Wine aged in American oak picks up more vanillin from the word than wines aged in French oak. Evidently American oaks have a higher concentration of the lactones than the French oaks. (I can’t find an explanation why, but that’s interesting) Vanillin, of course, is the primary chemical responsible for the flavor of vanilla.
  • Cabernet sauvignon and green peppers have the same chemical responsible for their smell. In cabernet, it’s strongest when the grapes aren’t ripe, so smelling green pepper would suggest a low quality wine. Aside: I definitely did not know that. I actually thought it wasn’t bad to have the green pepper scent. I also almost never drink cabernet, so maybe nothing should surprise me.
  • Diacetyl, a chemical commonly used in artificial butter flavorings (but also present in actual butter, potential chemophobes), develops in wines that have undergone a further fermentation process that converts the more sour malic acid (found in green apples) to lactic acid (found in milk).

NPR talks about sniffing all the foods with the same chemicals so you can “follow your nose”, if you will.

We went there.

They even suggest putting the good things in a cheap wine and comparing it’s smell to a more expensive one so you can find the similarities. But maybe I’m just taking the wrong lesson from this article, because I want to spray Pam into a wine glass and add some vanilla flavoring after pouring some Two Buck Chuck in and seeing if that tastes good.

*Just a quick thought on the “wine science wars”. I don’t think wine critics view themselves as scientific arbiters of wine, but I do think they present themselves as having far more precision than the studies suggest they do. Wine blogger Heimoff asks why we never see a headline saying that restaurant reviews are all junk science. Because they don’t claim to be picking up 12 distinct flavors from a single component, unlike a wine reviewer who honestly said a single wine had flavors of “red roses, lavender, geranium, dried hibiscus flowers, cranberry raisins, currant jelly, mango with skins, red plums, cobbler, cinnamon, star anise, blackberry bramble, whole black peppercorn” (perhaps take that review with a grain of salt, since the story sounds like it is coming from an ad almost).

I also think they do have a harder job than the restaurant critics. At a restaurant, you get to examine multiple things: the food, the service, the atmosphere, etc. Heck, even if you only focus on the food, that still leads to several different things to examine, whether that’s multiple courses at a Michelin-rated restaurant or just the multiple ingredients in a sandwich. A wine critic has one thing to look at, and they try to go into intense detail. But humans aren’t meant for analytical chemistry. I think things like this Salt article are perfect. It does show what people can appreciate in a wine and what the industry tries to create.

Maybe They Could Bottle It

The Atlantic, once again, proves to be a source of weird and wonderful science stories.  And I am learning I love Rebecca Rosen’s reporting/blogging significantly more than Alexis Madrigal. The LA Times interview goes into a bit more detail. Dr. Barbara Lollar and her group from the University of Toronto found water trapped underground in a copper mine in Ontario that has basically been isolated from the rest of the Earth for at least a billion years. And it’s gotten kind of… ripe after being stuck in dissolvable minerals after all this time. Lollar describes it as having “the consistency of a very light maple syrup”. And it has so many minerals dissolved in it that contact with air starts to turn the water orange.

And yet that still seems less weird than this new water at Harris Teeter

And yet that still seems less weird than this new water at Harris Teeter

Evidently it is also very salty. There’s no numbers listed for that. Lollar just mentioned that she tasted it and said it was the saltiest water she ever tried. Yeah, so evidently she not only drank a sample of this, but she semi-regularly drinks other ancient water samples to get a feel for the mineral content. But she won’t let her students sample the most vintage H2O ever. What amuses me most is that Lollar and others say the water could support life and yet she still drinks it. This just sounds like the set-up of a terrible sci-fi B movie about an ancient microbe infecting a person in the present to take over Earth in the present.*

*Yes, I know, the odds of a 1 billion year old microbe being able to infect a modern human after their environments are  separated and they evolve separately are slim. But we do still have instances of invasive species being able to thrive in environments they weren’t native to. And it seems slightly more likely that a billion year old microbe will find something it could attack in a eukaryotic cell, since eukaryotes (the giant group of organisms with cells that have nuclei and organelles that includes plants, animals, and fungi) have been around for an estimated 1.6 billion years, than the few hundred million year old mammalian immune system having any idea how to respond to that.