I’m not very good at singing songs, but here’s a try

Posted by Matt

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I’mma let you finish…

Posted by Matt

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Sorry for the nonexistent posting recently. Life has gotten real in the past few weeks and so I imagine I will write less frequently until I graduate next May. One of the reasons I asked Nick to write too was so that there would be less dead space, but of course he goes to school too and so life is just as busy for him.

But anyway, I just wanted to share this internet gem with the world. Alfred Russel Wallace was an British naturalist and contemporary of Charles Darwin. He is famous for his work in the Amazon River basin and the Malay archipelago, and developed a theory of natural selection independently of Darwin. In fact, he sent Darwin an article outlining his theory while in Malaysia, which prompted Darwin to publish both Wallace’s article and his own findings. Too often, Darwin receives sole credit (or blame, depending) for the theories of natural selection and evolution, when in reality they represent the work of countless great scientists, Wallace and Darwin included.

The frog in the header is actually an illustration from Wallace’s book The Malay Archipelago. It is Wallace’s flying frog, Rhacophorus nigropalmatus.

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Nanoink!

Posted by Nick

In general, I hate that “nano-” has turned into such a buzzword in the sciences.   Vendors try to sell nanoprep kits and charge more for them.  Unfortunately, these kits are not 9 orders of magnitude smaller than ordinary kits – they tend to be exactly the same with snazzier packaging.  I honestly believe that if you went to a biochemistry conference selling “nanocookies” that the scientists would pay twice as much for them than if you merely labeled them cookies.

In spite of the regrettable buzzword, a lot of nanotechnology is incredibly cool stuff and has tons of very important potential applications.  Nanoparticles have some particularly cool electronic properties related to them being a sort of in between atomic substance and bulk substance, leading to unique behaviors.  These properties make some types of nanoparticles good candidates for use in photovoltatic cells.  The main obstacle of solar energy currently is that solar cells are expensive and hard to produce.  Chemical engineers at UT-Austin, however, are working on a way to synthesize photovoltaic cells in “nanoparticle inks” cheaply and easily.  These inks would not only present production advantages, they would also make deployment a good deal easier.  Unfortunately these “inks” are about 10 times less efficient than is feasible for a commercial solar cell.

In any case, the idea of a painted-on solar cell is incredibly cool, regardless of how realistic it is.

_______________________________

Lower Cost Solar Cells To Be Printed Like Newspaper, Painted On Rooftops [ScienceDaily]

Abstract at JACS [Journal of the American Chemical Society]

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The good doctor’s bad questions, cont’d.

Posted by Matt

PEPPERED MOTHS. Why do textbooks use pictures of peppered moths camouflaged on tree trunks as evidence for natural selection — when biologists have known since the 1980s that the moths don’t normally rest on tree trunks, and all the pictures have been staged?

This was something I didn’t know much about, but before I even did any research it struck me as dishonest to cite “staged textbook photos” as evidence to invalidate scientific studies. It turns out I was right: photoillustrations of the difference between peppered moth types are often staged with dead specimens to provide the clearest illustration of the point, but they don’t pretend to be from the original studies and experiments they are meant to illustrate.

Wells is referring to the English peppered moth Biston betularia. Until 1848, only light-colored individuals had been documented, but that year the first dark-colored carbonaria variant was recorded. By 1895, the percentage of the carbonaria variant was reported at 98%. The hypothesis for this was that the industrial revolution had coated previously light-barked trees with soot, giving dark moths better camouflage protection against predators. Evidence throughout the 20th century has supported this claim, but in the past two decades Bernard Kettlewell’s classic study has come under legitimate criticism for aspects of its design which may not have fully accounted for the diversity of moths’ daytime resting places.

However, between 2001 and 2007 Michael Majerus carried out a study that included moths found all over the tree (including the trunk, despite Wells’ claim) which nevertheless supported the differential camouflage theory. Much of creationists’ ammunition against the peppered moth as an example of natural selection comes from a review by Jerry Coyne of Majerus’ 1998 book Melanism: Evolution in Action. However, Majerus and others have stated that Coyne’s review misrepresents the book’s content, and Coyne himself has even expressed dismay that people have tried to use the article to argue against natural selection.

DARWIN’S FINCHES. Why do textbooks claim that beak changes in Galapagos finches during a severe drought can explain the origin of species by natural selection — even though the changes were reversed after the drought ended, and no net evolution occurred?

I should hope that the changes were reversed when conditions were reversed. Otherwise, that wouldn’t speak very highly of natural selection, would it? The thing is that evolution never stops. Whenever conditions change, new pressures cause different traits to be selected for. This “net evolution” business is misleading, and no one is citing this study as an example of new species creation. It is, however, a vivid example of natural selection at work.

MUTANT FRUIT FLIES. Why do textbooks use fruit flies with an extra pair of wings as evidence that DNA mutations can supply raw materials for evolution — even though the extra wings have no muscles and these disabled mutants cannot survive outside the laboratory?

Whether the flies in question are viable or not is not the point. These mutant flies are a simple and striking way to show that genetic mutations can produce radical changes in body plan and structure. Wells is missing the forest for the trees. The random nature of mutation suggests that most will be nonviable or at least nonadvantageous, as is the case here. Nevertheless, these dramatic mutations are evidence against the notion that mutation cannot produce enough change to generate new species.

HUMAN ORIGINS. Why are artists’ drawings of ape-like humans used to justify materialistic claims that we are just animals and our existence is a mere accident — when fossil experts cannot even agree on who our supposed ancestors were or what they looked like?

Phrases like “just animals” and “mere accident” seem intended to make people feel insulted by the theory of evolution, but that’s just one narrow-minded way to look at things. Drawings that appear in respected literature are scientific recreations based on fossils believed from the genus Homo and current knowledge about body plans and how vertebrate animals function. While there will continue to be debate over the details, there is little debate that these fossils represent our closest genetic relatives.

EVOLUTION A FACT? Why are we told that Darwin’s theory of evolution is a scientific fact — even though many of its claims are based on misrepresentations of the facts?

Damn scientific terminology to hell. For the last time, evolution is a scientific theory. The only things that are called facts in biology are observable data points. Theories are comprehensive and mechanistic explanations for how a process works. Gravity is the current accepted theory for why objects in the atmosphere fall to earth. Evolution is the current accepted theory for how species change in response to their environment and for how new species form. Both are based on a massive amount of evidence and are the best scientific explanations available for the facts at hand. I have yet to see any compelling scientific evidence that evolution misrepresents the facts.

While I was looking around online today i found this site, a point-by-point refutation of Wells’ book Icons of Evolution that covers a lot of the same ground I have here. I’m sure there’s tons of these things all over the internet, but like I said, I wanted to address these questions for my own satisfaction and to show that, to anyone with a working knowledge of the science, these questions are nowhere near the probing criticism of evolution that Wells wants them to be.

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Talk to your biology teacher about evolution

Posted by Matt

So there’s this list of questions that’s been circulating the internet for a few years now entitled “Ten questions to ask your biology teacher about evolution”. It’s abundantly clear at this point that American adults are bitterly divided over the subject of evolution and neither side will budge. You’re tired of hearing about it. I’m tired of hearing about it. We’re all tired of hearing about it.

But this list from Jonathan Wells is targeted at teenagers still trying to make up their minds. It feeds into teens’ natural desire to stick it to the man by providing them with “Gotcha!” questions that seem like they would catch any stooge of Big Evolution off guard. The problem is that they are filled with misconceptions and false premises. Wells holds PhDs in Molecular and Cell Biology from Berkeley and Religious Studies from Yale, so he’s obviously no slouch and I do not believe he is deliberately trying to deceive people. The questions are nevertheless misleading, so, mostly for my own satisfaction, I’ll answer them here.

ORIGIN OF LIFE. Why do textbooks claim that the 1953 Miller-Urey experiment shows how life’s building blocks may have formed on the early Earth — when conditions on the early Earth were probably nothing like those used in the experiment, and the origin of life remains a mystery?

It’s true that many scientists now believe that earth’s early atmosphere was mostly nitrogen and carbon dioxide rather than the ammonia and methane used in the Miller-Urey experiment. Nitrites form under these conditions, which would prevent the stable formation of amino acids. However, Jeffrey Bada at the Scripps Institute of Oceanography has shown that when iron and carbonates, also likely abundant on primitive earth, are added to the mix, the nitrites are neutralized and amino acids do indeed form. Check out this article at Scientific American. Still, the prevailing view now is that at least some of the organic molecules essential to life arrived here on comets or meteors. All of this is pretty much educated guesswork – we’ll never definitively know until those slackers at MIT finally get a time machine up and running and —

Wait, I thought these questions were about evolution. While speculating about abiogenesis is fun, the theory of evolution works perfectly fine without it. You’re a tricky one, Wells.

DARWIN’S TREE OF LIFE. Why don’t textbooks discuss the “Cambrian explosion,” in which all major animal groups appear together in the fossil record fully formed instead of branching from a common ancestor — thus contradicting the evolutionary tree of life?

Well, I thought the book I used in freshman biology could be considered a “textbook”, but there’s the Cambrian explosion, right there in Chapter 32, so I guess it’s not a textbook after all.

When he says “all major animal groups” he can only be speaking in the broadest sense. I’m talking Porifera vs. Bilateria and protostomes vs. deuterostomes. Technically, these are the groups into which all extant animals can be classified, and they first appeared over a relatively short (“short” in this case meaning millions of years) timeframe during the Cambrian period, about 530 mil. years ago. But to say that they were “fully formed” is nonsense, unless all your friends look like this. Mammals, for one, don’t appear in the fossil record until about 190 mil. years ago, and only in most primitive form.

So I suppose his argument is that the major animal classifications arose separately and simultaneously during the Cambrian, rather than from a common ancestor. Well, we may never discover a fossil of the single organism from which all animals are descended. But current exidence suggests that these groups appeared far more gradually than was previously believed, and while we have, at best, an incomplete picture of the development of animals during these times, the rest of the fossil record overwhelmingly suggests that species develop by gradually branching off from existing evolutionary lines. I see no reason why the Cambrian should be any exception.

HOMOLOGY. Why do textbooks define homology as similarity due to common ancestry, then claim that it is evidence for common ancestry — a circular argument masquerading as scientific evidence?

This isn’t actually a circular argument. Homology was developed by studying similarities between the structures of different organisms. The textbook example is often that mammal limbs such as bat wings, whale fins, cat legs and human arms are actually composed of the same number and types of bones, shaped differently. Similarities like these suggest a greater degree of relation than analogous structures, which bear little resemblance but perform similar functions (bat wings vs. fly wings). It’s not hard to surmise that the first example suggests that the species adapted the same structure for different functions, while in the second species adapted different structures for the same function.

Today, structural homology is used mostly as anecdotal evidence to support evolutionary similarity defined by genetic homology. The genomes of many organisms have now been fully or partially sequenced, and are logged in databases accessible by nearly anyone with an internet connection. These genomes can be compared for similar sequences by powerful programs based on all current knowledge of genetic structure, transcription, and mutation. In many cases, you can trace a large number of genes among related species back to a parent gene and say with a high degree of confidence how each daughter gene mutated or changed. Through genetic knockout or amplification experiments, you can then determine the functions of these genes, and in many cases they perform a very similar role. Comparative genetics has revolutionized the study of evolution and has provided heaps of evidence that homology does indeed reflect common descent.

VERTEBRATE EMBRYOS. Why do textbooks use drawings of similarities in vertebrate embryos as evidence for their common ancestry — even though biologists have known for over a century that vertebrate embryos are not most similar in their early stages, and the drawings are faked?

Wells is referring to the embryo drawings of Ernst Haeckel (1834-1919), who infamously fudged the drawings so that vertebrates were most similar at the earliest stages of development and gradually grew apart. He did this to fabricate support for his own peculiar theory of Biogenetic Law, which holds that embryonic development sort of “replays” the evolution of that species in fast-forward. Wikipedia has a good article for background. I have seen these drawings in textbooks, but always in the context of the history of embryology and they make clear that both his drawings and theories are discredited. They also include accurate drawings or photographs showing real similarities between vertebrate embryos in order to show that embryology really does provide evidence for evolution, just not in the way Haeckel thought. I agree that books that take these drawings at face value are incorrect, but that doesn’t discredit current evolutionary theory.

ARCHAEOPTERYX. Why do textbooks portray this fossil as the missing link between dinosaurs and modern birds — even though modern birds are probably not descended from it, and its supposed ancestors do not appear until millions of years after it?

No one is suggesting that the tree should be drawn Dinosaurs -> Archaeopteryx -> Birds. It is nevertheless significant that Archaeopteryx fossils, along with fossils of many many dinosaur species, clearly show evidence of feathers remarkably similar to those of modern birds. This is one of several compelling pieces of evidence that theropod dinosaurs and birds shared a significant common ancestor. Check this article for more information.

This is getting pretty long, so I’ll post the second half of the questions tomorrow.

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Fighting fire with smog

Posted by Matt

Graeme Wood, one of the best Iraq/Afghanistan on-location correspondents I’ve read, has a review in the July/August Ideas Issue of The Atlantic of some of the more radical and potentially apocalyptic proposals to reverse the effects of global climate change. The most emblematic of these is probably the proposal that calls for tons and tons of sulfur dioxide to be pumped into the atmosphere, effectively blotting out the sun and shielding the earth’s surface from its warming effects. Other plans propose to accomplish this by different means, like a fleet of cloud-seeding ships or a giant visor in space. Still others would attempt to sequester atmospheric carbon dioxide in chemical compounds, underground, or in the oceans.

It’s not hard to imagine that these plans would have potentially disastrous consequences for local climates, flora, and fauna the world over. The question is whether these consequences are preferable to the consequences of inaction. It sounds like a question that should only be pondered by multinational coalitions. Actions with worldwide consequences should have worldwide consensus. But the danger, Wood points out, is that these “solutions” are cheap enough for a poor state or even a single (very wealthy) individual to implement should they see the need. A lone, well-intentioned crusader fed up with timidity and inaction from the state could take matters into his own hands, inflicting lasting damage on the globe in the process.

The saddest part of such a scenario would be that, despite their radical and far-reaching effects, none of these engineering projects gets to the root of the problem: irresponsible emissions levels and unsustainable lifestyles. Are we willing to accept the environmental costs of these programs simply to cover up a problem that would return if the program broke down?

I hope that these extreme scenarios will be seen as warnings to make healthy changes now rather than blueprints for a bleak future.

I will return to the idea of seeding blooms of phytoplankton to consume carbon dioxide at some point in the future. At first, the proposal seems promising, but it remains unproven and algal blooms can be devastating to oceanic ecosystems.

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More than one writer?

Posted by Nick

Science is a way of thinking much more than it is a body of knowledge.

– Carl Sagan

Smart guy, Carl Sagan.  The cosmos isn’t necessarily my thing, but it doesn’t make him any less insightful.  Science in general boils down to a pretty simple question: how does ______ work?  Masses of socially awkward people we call scientists lock themselves away in little labs to ask, sometimes even answer, that question and its derivatives.  It is a simple question that’s grown into something quite broad and rather vague – ask 10 people what they define as “science” and you’ll get varying responses, especially if you ask 10 scientists.

And that, in a roundabout way, brings me here.  As an undergrad in a relatively small chemistry department, I’m just scratching the surface of how cool most of science can be, so when Matt asked me to to be a chemistry contributor here it made a lot of sense to hop on board.   I’m primarily interested in inorganic chemistry, so most of what I throw up on here would presumably be about that, as well as whatever else I find worth writing about, science related or no. So thanks for stopping by, and we hope you like what you read.

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