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dont forget the crystals

Magnesium sulfate crystals, clingin’ to a petri dish. Chillin’.

Another quick lab snap. These are some nice crystals I grew. I was washing an earlier, less photogenic crystal garden with alcohol, and catching the runoff in a petri dish. I let it evaporate and was greeted with this happy little accident! The crystals are magnesium sulfate, available as Epsom salt at most pharmacies.

I had thought that once I graduated college, annoying student publications would quit being so… annoying. Alas, this isn’t the case. A previous article examined the quality of analysis at the Carolina Review, UNC’s ‘journal of conservative thought and opinion’; let’s see if things have approved any in the handful of years that I’ve been away.

Okay, checking their blog… mhmm… skim the headlines, clickety clicky….

… oh sweet cthulu, rise from your watery slumber and please make it stop.

The linked article describes environmentalism as factually challenged and lacking a vision of “the overall big picture”; let us categorically examine the main evidence presented in support of this thesis:

  1. “global warming, or climate change, or whatever they feel like calling it now” has been grossly exaggerated.
  2. Lighter cars are inherently more dangerous than gas-guzzlers.
  3. Recycling is bad.
  4. Fossil fuels can be greenwashed.

Ready? Let’s go.

Why is [head of NASA's GISS program and accomplished geophysicist Dr. James] Hanson [sic] so important?” – Carolina Review columnist Alex Thomas

I was disappointed by the coverage of climate change. I expected it to be lousy, and it was, but I didn’t expect it to be so… unsatisfying. The only evidence presented is the claim that Dr. Hansen’s 1988 congressional testimony was critically flawed, greatly overestimating the amount of temperature change to come. This is a PRATT, a Point Refuted A Thousand Times, so my treatment will be a bit superficial.  (For more detail, read this)

Some of Hansen’s scenarios gave realistic predictions, and some didn’t. The real question is why.

A climate simulation isn’t a magickal box that spits out numbers. In order to run it, you have to input certain parameters, like how bright the sun is, the greenhouse gas concentrations, and so on. For the past you might have direct measurements or proxy records; the future is not only unwritten, but contingent upon human agency. So you have to come up with plausible scenarios for what’s coming. Maybe we cut down on fossil fuel usage; maybe we ramp it up; maybe we relax clean air standards; maybe we have a nuclear war. You run the scenarios you’re interested in on climate models, and you compare, contrast, and interpret the output. One of the scenarios that Dr. Hansen used (“Scenario A”) overestimated greenhouse gas emissions – but not carbon dioxide. Scenario A assumed that we continued to emit CFCs, which are potent greenhouse gasses. Because they threatened the ozone layer, CFCs were phased out under the Montreal Protocols, which went into effect in 1989 – the year after Hansen’s testimony. Nowhere in the Carolina Review article do we hear about such confounding factors, nor the general success of government regulation in cutting down on ozone depletors. Nor is there mention that Scenarios B and C match observations well (see above), nor that Hansen’s 1981 predictions were freakinshly accurate. * Also, why is Dr. Hansen important? Because he was an adviser to Al Gore, of course!

Usually investigators only present and discuss the risk to occupants of the car or truck in question—as if society at large has no stake in the mayhem caused by some vehicles as long as those riding in them aren’t themselves killed.” – Wenzel and Ross 2008

View full article »

haxor hijinx: a DIY hotplate

I have, once again, found myself at the helm of a DIY lab, this one with a chemical wetlab focus. I’m sure this will provide lots of material in the future; right now, I want to share a protip I came up with the other night. I have been using soda can alcohol stoves for heat, but this isn’t always appropriate. You can’t heat flammable mixtures, and they leave soot on my glassware. But I don’t have a hotplate yet! What’s a gutterpunk labnerd to do?

Don’t forget the boiling chips!

It’s won’t spin a stir bar, but a clothes iron will do fine as a hotplate! You can see that I’ve secured this one to the lab bench with wood and a clamp for extra stability.



I’ve been working through Michael Barnsley’s book, “Fractals Everywhere”; it’s a relatively advanced textbook on fractal geometry. The first chapter is a survey of analysis and topology, which has been a nice opportunity to refresh my math skills, as well as a more thorough exploration of metric spaces than I’d gotten before. I was double checking one of the problems and wrote it out all organized, and then I decided to tell you about it. So I scanned it in, started cleaning it up in GIMP, one thing led to another…

Learnin me some GIMP skillz

I later realized that I could actually generalize the bulk of the proof into a lemma: Any subset of a totally bounded set is itself totally bounded.

Images used:




I sit at the Carrboro Really Free Market, on the first caturday in July. I sit in the shade and the banners are blowing lazily in the breeze; still it’s nearly 100 degrees; the humidity jacks it up to 103, and the breeze is welcome but ineffectual. Air quality is ‘Orange’: ozone levels ‘may approach or exceed unhealthy standards.’ A parade is planned but only a handful want to move; I’m definitely not going back out. I keep a cold pack in my bag to refridgerate my computer, but I worry that the condensation from the humid air will offset the benefits of a cool processor. Whatever; I need chill tunes if I’m going to bike around in this weather.

A constant source of frustration for me is communicating the local importance of global problems. Climate change is real, and it’s serious – but at the same time it can be intangible and diffuse. I live in the North Carolina piedmont, hours away from the beach. I can explain to my neighbors that ocean acidification is a serious problem, that the demise of coral reefs would mean the loss of food and resources for the third world. But even if they believe me, even if they agree that it’s bad news, it can still be hard to see how global warming effects them personally, as a homeowner, a farmer, a pet owner or the parent of a young child, a worker with a daily commute. How does carbon dioxide pollution impact North Carolina and beyond?

rock me momma like the wind and the rain//rock me momma like a hurricane

Let’s start at the beach. An obvious problem here is rising sea levels. As the ocean heats up, it expands; as ice heats up, it melts and drains into the sea (or, it calves, falls into the sea, and then melts). This causes a slow but steady rise in sea level. Sea level is predicted to rise by a meter (maybe more) over the 21st century, and 4-6 m over the next few centuries. This is bad news bears – in many coastal counties, more than 10% of the population lives within a meter of high tide. The threat to homes and businesses is worsened by storm surges, which will also be higher as the seas rise [Strauss 2012]. North Carolina has a unique relationship with sea level rise. The coastal salt marshes have recorded 2,100 years of sea level history in their smelly mucky sediments; the ocean stayed relatively stable up until about 1880, when it began to creep upwards. The average rate of sea level rise for the NC coast over the 20th century was ‘greater than any other persistent, century-scale trend’ in the marsh’s memory. During this time period, the seas rose 3.5 times faster than they did even during the Medieval Warm Period, and regional sea level rose faster than model predictions over the 20th century (though the uncertainties involved overlap.) [Kemp et al. 2011]

Sea level rise at the North Carolina coast over the past two millenia. Things are pretty stable, even during climatic episodes like the MWP – until we get to the late 19th century. Then the hockey stick gets hockey stuck. GIA is glacial isostatic adustment, an additional factor which must be considered. It deals with the fact that the North American landmass is still rebounding from the weight of Ice Age glaciers. Image from Figure 2 of Kemp et al. 2011

But what’s really special is the state legislature’s reaction to the rising tide. This June, the NC Senate infamously outlawed the use of accelerating sea level scenarios in planning urban development. The usual astroturfing seems to be at play: the money trail for this legislation leads back to the Locke Foundation; spokespeople and nonprofits proliferate to establish a consent factory. These hijinks are as cynical as they are asinine: not only is global sea level rise accelerating [Church & White 2006], but North Carolina is at the southern end of a ‘hotspot’ where the sea is rising 3-4 times as fast as the global average, [Sallenger et al. 2012] putting its coastline at exceptional risk. The legislation is also a lovely inversion on a popular skuptik trope, that of an authoritarian scientific Orthodoxy dictating Truth and squelching dissidents. In this case, it’s the state government which has declared which climatic scenarios are kosher and which are thought crimes, favoring the least alarming. The proposed law would not merely declare what course sea level rise will take in the years to come, but also prohibit state planning agencies from considering alternatives. Not content to legislate straight marriage as the only valid relationship, the Old North State is considering straight lines as the only acceptable graph.

“You need to move indoors right now.”

Meteorologist Dr. Forbes, on Philadelphian extreme weather.

It’s Friday night, 29 June, and forecasts of a sweltering weekend have already started to come true. I am sifting through hardware at work when the power goes out. View full article »

“this kitteh it are mine”



Koko the gorilla and All Ball the cat



Editor’s note: I am very busy and/or have major writer’s block. I am thus recycling my greater hits. Here we see a review of a review (a metareview if you will) of Ben Stein’s dawkumentary “Expelled”. The original review appeared in the Carolina Review. For those unfamiliar with CR (you blessed souls!), it is UNC-CH’s ” journal of conservative thought and opinion”. It is a perennial lulz-bucket, attributing climate change to solar forcings and/or Milankovich cycles, mangling ocean acidification, and wondering out loud, in public, why a 2008 paper was not included in the IPCC AR4 (published in 2007). They consider community reclamation of a long-standing eyesore to be a ‘hostile act‘ worthy of paramilitary response, citing the presence of ‘posters’. Here’s my response to one of their more abysmal publications. The article it responds to can be found here; my critique originally ran in CackalakConspiracy, back in a time when I still cared about typos.

Walker’s review, like Stein’s movie, is full of florid talk about “freedom”: freedom of speech, religion, science (the last ironic, for the creationist/intelligent design movement has done everything it can to prevent science from being taught in public schools). America has “an amazing record for upholding freedoms.” Stein rolls footage of Soviets and Nazis; Walker calls the dismantling of science and science education “a struggle against a great tyranny.”

But this talk of freedom is merely an emotional appeal. The speech of creationist “scientists” and ID advocates is not being squelched; it is just not taken seriously. For whatever successes creationism may have in philosophy or religion, it has failed as a science. This is why the mainstream rejects creationism for funding, publishing and inclusion in school curricula, not because of atheistic preconceptions. Film critic Roger Ebert drew this analogy: The final question on “Who Wants To Be A Millionaire” asks you for a scientific explanation for the patterning of life on Earth. You phone not just a friend, but the scientists of the world, who overwhelmingly advise you to choose (A) evolutionary biology. Yet you choose (B), intelligent design, and claim censorship upon being denied your millions. This is not an expulsion; it is a flunking.

Walker characterizes evolution and ID as rival “theories” in the “scientific community”. However, in science the word ‘theory’ does not mean a guess or an opinion the way it does in popular speech; it refers to an explanatory construct which is used to interpret data and to make predictions. By this standard, evolution wins hands down and ID falls flat on its face. Because any piece of data can be interpreted as evidence for a Designer (for example, by sufficiently muddying the proposed design goals), ID makes no predictions and no explanations (a “theory” that accommodates anything explains nothing). On the other hand, evolution makes several strong predictions about the world (the existence of a nested hierarchy of physical traits, for example.) ID is not a rival scientific theory; it is an attempt to inject religious propaganda into public education.

We don’t accept non-explanations elsewhere in science. Why should the origins and evolution of life on earth be different? Image from the internets….

Nor is evolution “all a question of faith,” a rival religion. It is purely descriptive, not perscriptive. It has no infalliable holy text; it has no ritual structure; it has no ineffable mystery. Though some may use it to bolster their religious beliefs like “renowned evolutionary biology [sic] and atheist Richard Dawkins,” the theory of evolution is no more a religion than the theory of gravity or relativity. Walker claims that “by definition and practice creationists and ID scientists are quite different”. This is incorrect, both because ID is not science and because it is accurately classified as a subset of creationism. Classical creationism and ID are both are antiscientific programs with thinly veiled religious agendas. They both negate accepted evolutionary biology, often along with other aspects of mainstream science such as molecular biology, genetics, and paleontology. Both reject “naturalism” in the scientific study of life, as though science was not based upon methodological naturalism to begin with. Both tend to blame various social ills on the theory of evolution, and erroneously infer from this that it is incorrect. Perhaps most tellingly, Expelled’s own publicity team advertised the movie as “Evolution vs creationism”.  View full article »

A while back, we started looking at a poorly thought-out article from the website C3Headlines. C3 is starting to make a name for itself as a goldmine of climate comedy- their claims have recently been addressed at Tamino and SkepticalScience.

We’re going to keep digging into C3‘s claim that carbon dioxide concentrations have been increasing linearly over the 20th century. They seemed to draw this claim by eyeballing the graph of CO2 concentrations and qualitatively describing them as linear, apparently using the inset in their first figure to compare linear, quadratic, and exponential trends. This is a faulty method: it’s an elementary fact of calculus that ANY smooth curve, when viewed appropriately, will appear linear. The point has already been made but it’s worthwhile to keep looking because there are some interesting graphical follies at play; examining them further might help us understand how and why graphs are misunderstood.

Figure 1: From C3Headlines’ article on “The Left/Liberal Bizarro Anti-Science Hyperbole”, which claims that CO2 concentrations are increasing linearly. Click to read it, if you dare…

C3‘s second graph in this article measures the change in atmospheric CO2 by calculating a month-to-month percentage change. It’s not entirely clear why they are using a percent change, rather than the standard practice of expressing rate of change as concentration change per year (like the source of their data uses). Whereas ppm/year is an absolute measure, each datum generated by the percentage-change method depends strongly upon the value of the previous month. As a measure of long-term rate of change, it is a bit questionable.

My primary concern, though, is with their use of monthly data in the first place. In my last article, we noted that, without explanation, C3 confined their focus to January CO2 concentrations. Were they consistent, they’d also look at January rates of change – of course, doing so might lead to unacceptable conclusions.

 Figure 2. Rates of CO2 accumulation have been calculated for the month of January, consistent with earlier investigation of January CO2 concentration. Over the period of observation, rates have increased at a significant (P~0.0005) acceleration of 0.11 ppm/year^2. Monthly rates throughout this article have been calculated by considering the change in CO2 between adjacent months, and assuming that a month is 1/12 of a year. Interpolated values of CO2 were used to avoid annoying data holes early in the record.

Instead, they look at the rate of change for every single month on record. Why do I find that problematic? Well, let’s look at the full record, with monthly resolution: View full article »

It is a lovely spring day and I am absorbing some sunlight, hanging out in the tail end of the Carrboro Really Free Market while I type up my notes on the Duke Mycology Symposium. [CLICK HERE FOR DAYS ONE AND TWO]

There were a couple of posters which really caught my eye. One thing that I think is very interesting about fungi is their symbiotic relationships with plants. So I was excited when I saw two posters, both put together by Ryoko Oono and colleauges: “Populations structure in Lophodermium spp., a common fungal endophyte of loblolly pine” and “Effcts of foliar fungal endophyte diversity on plant protection against pathogens”. The first presents some preliminary information about the distribution of Lophodermium amongst pine trees in North Carolina. They found that there are three distinct subgroups of the of the fungus, despite not being geographically isolated. This suggests that there is limited gene flow between the subgroups. The second poster discusses the ecological role of fungal symbiotes: both single and multiple fungal colonizations can increase pathogen resistance, and since individual fungi types antagonize specific pathogens, you might expect a diverse group of colonizers to repel the most pathogens. However, there may also be a sort of tragedy of the commons effect, in which the individual members of diverse group of symbiotes have no particular dedication to protecting the host plant. Clarifying these issues will require more research, and the poster outlines a plan for further study.

The biochemistry of metals was a recurring theme in this symposium. We’ve already looked at iron, nickel, and cobalt; so let’s wrap up our tour of the transition metals with “Copper homeostasis as a virulence factor in systemic infection by the human fungal pathogen Cryptococcus neoformans,” by Chen Ding and colleauges at Duke. They describe the susceptibility of Cryptococcus to copper toxicity in the host, and the role of a class of biomolecules called metallothionens in protecting Cryptococcus from the metal. Interestingly, they also present data showing that copper levels are elevated in the serum of Cryptococcus patients – evidence, perhaps, for the immune system incorporating copper into its chemical weaponry! This would be the exact opposite reaction that it has when it comes to iron, which it withholds in an attempt to starve pathogens of nutrients (Nesse and Williams 1994; p. 29-30)

Yeast colony macrostructure - photo from the Magwene Lab - click to visit them

Finally, there was “Genetics, genomics, and variation in yeast colony morphology”, presented by Josh Granek and colleagues at Duke. They studied the yeast saccharomyces cerevisiae under a variety of different growing conditions. They found that, under conditions of abundant nitrogen but scarce fermentable carbon, the yeast colonies developed complex, organized structures large enough to see with the naked eye. This sort of emergent behavior is very interesting; it shows the bottom-up organization of biology by which relatively simple units can have complex system-level behavior … and understanding how cells communicate and cooperate in a colony can provide insights to the transition from unicellularity to multicelluarity.

That’s all there is to say about the symposium. One thing that I have been thinking about is the involvement of mycology communities in doing environmental monitoring. Simple citizen science monitoring programs already exist for animals and plants (Cohn 2008). Why not monitor the third domain of eukaryotes? Mycological enthusiasts already have local clubs, and the data gathered could provide insights into fungal biogreography and ecological change.

Further Reading
Cohn, J. (2008). Citizen Science: Can Volunteers Do Real Research? BioScience, 58 (3) DOI: 10.1641/B580303

Randolph Nesse, & George Williams (1994). Why We Get Sick: The New Science of Darwinian Medicine. Vintage Books: New York

Mycology Symposium, Day 2

Day 2 of the Duke Mycology Symposium has wound to a close, [DAY 1 HERE] and I am sitting on my porch contemplating the afternoon’s lectures:

“Pathogen recombination during the amphibian Chytridiomycosis pandemic: Why change what’s working?”

A genetics perspective on Bd, a fungus responsible for widespread amphibian mortality. Apparently one of the factors in its spread is the abundance and transport of bullfrogs (raised for food) and xenopus frogs (used in medical research), which can carry the disease without being killed by it. The recent spread is caused by a single Bd strain which reproduces by cloning itself – it should therefor be genetically uniform. Yet, in practice Bd has a ‘dynamic genome’. This led to discussion led to mechanisms for genetic change without sex, such as mitotic crossover and gene conversion.

“Pathogenicity factors in the chytrid fungus and amphibian pathogen B. dendrobatidis”

Further discussion of Bd, this time from a molecular / genomic perspective. Perhaps the most interesting part was evidence that chytrids contain rhodopsin, a light-sensitive pigment. [] I was also alerted to the existence of the 1000 fungal genomes project.

“Pleiotropic roles of the UPR pathway in Cryptococcus”

UPR is the unfolded protein response – when there are bits of proteins floating around inside a cell, it’s a bad sign. Maybe those proteins were torn apart by heat, or a toxin. This talk looked at the responses of Cryptococcus to the presence of the UPRs. In some cases, they release ‘chaperones’, proteins which help other molecules assemble correctly. Or, they might release dedegredation enzymes to clean up the mess. In extreme cases, they may even trigger apoptosis, a sort of cellular suicide.

“The adaptive value of Flo11‐dependent flocculation and adhesion in yeast”

Epigenetics: Not just for woo-meisters! Click for sauce.

Proteins on the surface of certain yeast cells act  to let the cells stick together and form clusters, which then fall out of their liquid medium. The gene for this surface protein is under considerable epigenetic control – there was a really beautiful picture the speaker presented, in which genetically identical yeast cells nonetheless have different levels of gene expression. Additionally, this phenomenon is an example of the green beard effect.

“Fear the Titans: When bad yeast get worse”

Titan cells are variants of cryptococcus. as much as 20 times as large as typical cells. View full article »


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