What’s Up with the Bad Chemistry?

Watts Up With That is a very, very silly website.

Here’s what I mean: In a recent article at WUWT, chemical engineering graduate Steve Burnette tries to dismiss concerns about ocean acidification, but his claims are outright wrong when they are coherent. The centerpiece of the article is a calculation meant to estimate the change in ocean pH over the 20th century. Unfortunately, it’s been badly bungled.

First, let’s go over a few preliminaries.

Figure 1: The carbonic acid equilibrium system. Atmospheric CO2 is in equilibrium with dissolved CO2, which in turn is in equilibrium with carbonic acid. The acid has a tendency to lose its hydrogen ions, forming bicarbonate ion, which it is also in equilibrium with. The bicarbonate can also lose a hydrogen ion, forming carbonate. Keep in mind that these steps work in reverse; in particular, carbonate ions can react with hydrogen ions to form bicarbonate.

When fossil fuels are burned, about a third of the resulting carbon dioxide ends up dissolved in the oceans. There, it undergoes a series of reactions, first combining with water to form carbonic acid, then losing protons one at a time. The result is a mixture of dissolved CO2, bicarbonate, and carbonate ions, as well as an increase in hydrogen ions, which increase the acidity of the seawater.

Burnette mentions a few principles which are useful for analyzing this scenario. The equilibration between gaseous CO2 and dissolved CO2 is expressed by Henry’s law, which states that the concentration of dissolved CO2 is proportional to the partial pressure of atmospheric CO2. This means that, as CO2 concentrations increase in the air, they will increase in the oceans too. Mathematically:

Light and Noise in the Anthropocene

There is a companion article exploring the issue from the perspective of environmental monitoring over at ArkFab.

Human influence on the environment has increased dramatically over the last 10,000 years, to the point that some geologists have argued that human reworking of the earth defines a new geologic age, The Anthropocene. (Zalasiewicz et al, 2008) Much of the focus has been on relatively robust, tangible changes in biogeochemistry. Examples include:

• the climate change and ocean acidification resulting from the addition of fossil fuel emissions to the carbon cycle.

• megafaunal extinction, accelerated erosion (Zalasiewicz et al, 2008) and nitrogen fixation resulting from the spread of intensive subsistence patterns
• the loss of stratospheric ozone resulting from the release of novel chlorofluorocarbons

However, fleeting and less tangible effects are also important. Two examples are:

• the light pollution resulting from urbanization and transportation infrastructure
• changes in the acoustic environment resulting from direct addition of sonic energy and memes, as well as indirect sources.

A year-long composite view of the earth at night, showing human light generation. White lights are cities; blue lights are fishing boats; green lights are natural gas flares, and red lights are ‘ephemeral light sources’, interpreted as fires. Image from  NOAA National Geophysical Data Center – click for source + discussion.

Light pollution, the scourge of urban astronomers, is a well-accepted phenomenon with serious consequences. A 2004 review begins:

In the past century, the extent and intensity of artificial night lighting has increased such that it has substantial effects on the biology and ecology of species in the wild. We distinguish “astronomical light pollution”, which obscures the view of the night sky, from “ecological light pollution”, which alters natural light regimes in terrestrial and aquatic ecosystems. Some of the catastrophic consequences of light for certain taxonomic groups are well known, such as the deaths of migratory birds around tall lighted structures, and those of hatchling sea turtles disoriented by lights on their natal beaches. The more subtle influences of artificial night lighting on the behavior and community ecology of species are less well recognized, and constitute a new focus for research in ecology and a pressing conservation challenge. (Longcore & Rich 2004)

The amount of sonic energy released by human activity is recognized as an urban nuisance as well as an occupational safety concern. It also has recognized ecological effects: urban European robins have begun singing at night, when they have less acoustic competition. (Fuller et al 2007) Frogs have begun changing the pitch of their croaks in order to talk over traffic noise (Paris et al 2009)  In addition to sonic energy, human activity has released sonic memes into the environment. A meme is a self-replicating information pattern; jokes and computer viruses are two examples of memes. A person or computer acquires a meme and then spreads it, through retelling or infected emails. Sonic memes, such as ambulance sirens and cellphone ringtones, have been picked and repeated by songbirds. (Stover 2009) This is very interesting: human memes, the basis of Richard Dawkins’ ‘extended phenotype’ concept, have organically extended into other animals’ extended phenotype. (Recent reports of dolphins mimicking human speech are also very interesting in this context. The reverse flow also occurs, as animal communications are repackaged as ringtones or ambient music.)

Airbag Saved My Life: the Carolina Review’s Clinical Derpitude Continues

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

Graphing Out Loud: ups and downs

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:

Mycology Symposium, Day 1

When I’m not too busy raging at skuptaloids online, I enjoy molecular biology and mycology, the study of fungi. Towards those ends, I’m visiting the Duke Symposium in Celebration of Mycology and Mycologists. I was only able to attend a few afternoon lectures on the first day of this conference, but am enjoying it greatly! Some of the lectures I attended:

“Glycoengineered yeast: from platform to product”

A completely qualitative assesment of the information storage in various biochemical media. You can see why I have a huge crush on glycans. Souce is "Emerging Glycomics Technologies" by Turnbull and Feild 2007; click for lynkz

Discussed the engineering considerations is convincing yeasts to produce biochemicals – for example, drugs. A major challenge is in glycosylation, the addition of complex sugars to proteins. Glycochemistry is very interesting to me; it is still very much a biochemical frontier.

“Membrane lipids and fungal virulence”

Glucosylceramides in fungi and humans are different, with fungal compounds featuring an unsaturated site and a methyl side group. Humans and fungi also have slightly different enzyme active sites to deal with these differences, suggesting that drugs can be developed to target the active sites in fungal pathogens without disrupting human biochemistry. The drug candidates discussed actually have analogs in commercial fungicides.

Graphing Out Loud: curves and lines

I love graphs – my eyes quickly glaze over at a table of numeric data, but a graph, used correctly, can quickly and easily tell the whole story.

‘Used correctly’ is the key phrase – for all their power, graphs are infamously easy to bungle, and when used incorrectly they can misinform – or lie outright.

I’m going to look at an example that touches on a few graphical and statistical concepts near and dear to my heart, as well as carbon geochemistry.

Fig. 1: An image from C3Headlines; the 3 C's are "Climate, Conservative, Consumer". Oh, and the article is titled "The Left/Liberal Bizarro, Anti-Science Hyperbole Continues". It sure would be tragic if they made obvious n00b mistakes after using such language. Click for link!

Coming from an article on the website C3Headlines, this image claims that carbon dioxide concentrations have ‘Linear, Not Exponential Growth’. thereby ‘expos[ing] the lunacy of typical left/liberal/progressive/Democrat anti-science’, The author has reached this conclusion by graphing January CO2 levels* and fitting a linear trendline to them.

Already this is a warning sign – the comparisons the author makes are entirely qualitative, apparently  based up on eyeballing the graph. However, trend lines are created by a statistical process called a linear regression, which comes with a caveat: it will fit a trend line to ANY data given to it, linear or nonlinear. Fortunately, there are also ways of evaluating how good a trend line is.

CO2 Trouble: Ocean Acidification, Dr. Everett, and Congressional Science Standards

A companion article at ArkFab shares my thoughts on peer review in regards to this project and DIY/community/citizen science in general. 

At long last, the much-anticipated booklet, “CO2 Trouble: Ocean Acidification, Dr. Everett, and Congressional Science Standards” is available and approved for human consumption! Download and share HERE (or at Scribd HERE).

In this document, I have bundled, updated, and expanded my series of essays debunking the congressional testimony of Dr. John Everett regarding the environmental chemistry of carbon dioxide.

It has been designed to be a fairly short (less than 30 pages, including images, appendicies, etc.) and accessible read. It has been challenging but fun to write; I have had to learn a lot about GIMP, Python, Scribus, social networking, and of course ocean acidification to get to this point.

It was also very useful for me as an opportunity to go back through my earlier remarks and double-check my work. For example, I later realized that the documentation which Dr. Everett provides for his CO2 data in part two is ambiguous: Although the citation for the rate data is referred to as “Recent Global CO2”, the URL provided links to the longer record as measured at Mauna Loa Observatory. This confusion had led me in the past to make incorrect claims about some of the figures he presents. Ultimately it was inconsequential to my argument, but it was frustrating to have to deal with such ambiguities. On the other hand, this led me into comparing the Mauna Loa record with the global record (Appendix B) which was an interesting exercise.

In researching this project, I also came across new phenomena I wasn’t previously aware of. For example, while I was calculating historical rates of CO2 change, I ran though the 1000-year Law Dome record and saw this:

unknowns, uncertainties, and obsolesence

Antiscience campaigns often share the characteristic that they

A schematic of a climate model - By NOAA via WikiMedia Commons; click for sauce.

complain about the open questions, anomalies, and experimental limitations inscience. Scientists, on the other hand, work

hard to resolve these issues. Creationists complain about uncertainties on the chemical origins of life; biochemists generate and test hypotheses, developing useful technology and techniques in the process. (Bullard et al. 2006) A paper, championed by climate change skuptix, (eg, here) complains about the use of large flux corrections in climate models. (Soon et al. 2001) It was published a decade ago.

What was the state of computation back in 2001? There were no iPhones; cellphones still had hinges and were just starting to become controversial in schools. I didn’t see an iPod until late 2002, and for a long time it was just one person who had one*. We had just started trading AIM screen names instead of phone numbers. There was no Facebook, there was no Twitter, there was no YouTube. Xanga didn’t even appear on my radar until 2003. The Flash Revolution was in its infancy: StrongBad answered his first email in August 2001. It was, simply put, Peanut Butter Jelly Time.

Since then, while skuptix have done little more than whine, climatologists have been hard at work  improving climate models. It’s 2011 and climate models no longer use flux corrections. They still confirm the obvious: blankets are warm. More blankets are warmer.

* ❤ 😛

~~~—~~~

Bullard, T., Freudenthal, J., Avagyan, S., & Kahr, B. (2007). Test of Cairns-Smith’s ‘crystals-as-genes’ hypothesis Faraday Discussions, 136 DOI: 10.1039/b616612c

Soon, W., Baliunas, S., Idso, S., Kondratyev, K., & Posmentier, E. (2001). Modeling climatic effects of anthropogenic carbon dioxide emissions: unknowns and uncertainties Climate Research, 18, 259-275 DOI: 10.3354/cr018259

John Everett, Part IV.8: Deep Time is Deep.

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.

John Everett, part 4.4: Has this happened before?

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.