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.
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.
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.
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)
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.
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
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”
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 »
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”
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. View full article »
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.
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.
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. View full article »
you might be asking yourselves,
have they been doing all these recent months instead of writing high-octane science friction and science fact here on the intarwubs?
Answer: All sorts of zany things! During a recent Really Free Market hosted by Occupy Durham, I had the opportunity to do another chemistry show. Like the demonstration in my CO2 Problems video, I used soapy water and phenol red pH indicator to help illustrate the properties of frozen carbon dioxide. The color change is particularly dramatic, and is a good tie-in to the environmental effects of CO2. The greenhouse effect seems harder to demonstrate effectively – if anyone has a good way of demonstrating the idea, let me know!
One thing I showed in this demo which wasn’t in CO2 Problems is the strange noises that dry ice makes in response to metal. If you try to cut a piece of dry ice with a knife, or press a paperclip into it, the ice will make a horrible screeching shriek. It’s most dramatic if you put a larger chunk of dry ice into a metal pot – it will scream and skitter around! My explanation? The warm, thermally conductive metal speeds up the sublimation of CO2 near its edge; the expanding gas pushes the metal away briefly and then the pressure buildup dissipates, bringing the metal back in contact with the ice. This oscillation makes the screeching noise. Try it out yourself and see if you think I’m right!
If you are new to climate science, you might be wondering what, exactly, this ‘temperature anomaly’ thing is that you keep hearing about. I know I was a bit confused at first! This post explains the concept, using a real-world example.
Cities tend to be warmer than their surrounding countrysides, a fact known as the urban heat island effect (UHI). This occasionally is offered as an alternative explanation for greenhouse warming, but it fails on closer inspection. We can use data from Jones et al. (2008) [PDF] to see one reason UHI can’t explain observed warming. One time series is from St. James Park, in the city of London; the other is from nearby Rothamsted, a rural site some tens of miles away. As you can see, the urban location is consistently about 2 C warmer; however, the warming is nearly identical at both sites (a strongly significant 0.03 deg C/year). Jones et al. note:
“… the evolution of the time series is almost identical. As for trends since 1961 all sites give similar values … in terms of anomalies from a common base period, all sites would give similar values.”
This gives us a hint about what a temperature anomaly is: View full article »
In solidarity with countless other sites (most of them with higher traffic and cultural relevance >_< ) TopOc is temporarily going offline for the 18th of January 2012 in protest of the Stop Online Piracy Act (SOPA) and the Protect IP Act (PIPA).
If you are unfamiliar with these lovely bits of legislation, they would effectively mean the end of the internet as we know it. If someone posts a link on my site which supposedly violates copyright law, TopOc can disappear – for good. Given the notoriously itchy trigger finger on certain copyright holders, that should scare the pants off you.
Tor, an piece of anonymity software developed by the US Navy for use in repressive countries, would effectively be outlawed. Indeed, the proponents of SOPA and PIPA believe that it would be effective because it is based on censorship techniques which have been used effectively in Syria, China, and Uzbekistan.
Additionally, this legislation would seriously compromise internet security.
Perhaps most disturbingly, members of the US Congress have rejected expert testimony critical of SOPA and PIPA, deriding the critics as ‘nerds’. Considering the poor quality of testimony that they are willing to entertain, this is a real slap in the face.
What can you do? Call your Senators and Representatives! Tell them to keep the IntarTubes free!
Regularly scheduled programming will resume shortly, I swear. The next post will be about the concept of a temperature anomaly – stay tuned! Additionally, I apologize for the relative lack of citations; it is not in my nature to make unsupported assertions. But I got a late start and, well, most of my sources are also participating in the blackout so it would sort of be a moot point.
UPDATE: …aaaaand we’re back. Thanks to everyone who participated; we’re making a difference!
Some people think that the existence of workarounds for the blackout is somehow a problem for it. On the contrary, that people are finding and using them is a further success of the action. When people use these hacks, it puts them in direct contact with the inner workings of the technology they depend on, and this understanding is as critical for maintaining internet freedom (and freedom in general) as our legal system. Every n00b who is introduced to caches or proxies by the blackout is a success for the world’s first cyber-strike, a success in addition to its influence on policymakers.
Back to writing…