A Little More Land

Gordy Slack’s unwieldily named The Battle Over the Meaning of Everything: Evolution, Intelligent Design, and a School Board in Dover, PA is an account of the people, ideas, and events surrounding the 2005 Kitzmiller v. Dover Area School District trial. Occasionally beleaguering with details and descriptions, often jocular, and informative throughout, it provides a thorough look at what went on before, during, and after this groundbreaking trial.

Beyond a simple narrative of the facts of the trial, Slack often focuses on the perceived motivations of the participants as well as the history and backstory of the ideas that clashed during the momentous trial. Also present and quite engaging, to me at least, was the theme throughout of Slack attempting to better understand the views of his father, who wholeheartedly accepted Christianity and creationism years before the trial. While Slack himself accepted the evolutionary account, he attempted to come to terms with the views of his father, which at times expanded into a comparison between materialistic and non-materialistic worldviews. My own father being a creationist, I can appreciate this line of consideration, and the heartfelt effort he put into its resolution. In the end, this was in no way a major focus of the book, but he ended with the observation: “My father is a theist. I am a materialist. It is painful to acknowledge that we live in different worlds.” This is the same battle that America and, to a lesser, or at least quite different, extent the rest of the world is still faced with. Is the meaning and origins of life within the purview of science? Or does religion have the right to comment on such topics not merely in the pulpit, but also in the classroom?

I myself, as well as, thankfully, Judge Jones, feel that intelligent design (and its forebear creationism) is not a scientific topic, and is not one that should be presented to young minds within the context of a biology classroom. Perhaps it is worth some consideration in classes regarding culture or religion, but it is in no way a scientific discipline. Beyond that, it is a topic that foments a lack of curiosity and scientific progress. As such, its advance into the teachings of science among less informed and less developed minds needs to be halted, and guarded against with a keen eye.

As I did not follow the proceedings of the Dover trial closely when they were occurring, I found this book an eminently readable review of them, with all the necessary subtexts and details an informed reader should need to appreciate what occurred and its import. I highly recommend it to anyone interested in the evolution/creationism debate and the related culture war currently underway of which it is a symptom.

Tags: Evolutionary Biology

Here are two beautiful caterpillars I photographed in my backyard recently. I believe they were attracted to the large amount of Virginia Creeper growing on one side of the yard.

Eight-spotted Forester Caterpillar (Alypia octomaculata)

Common Buckeye Caterpillar (Junonia coenia)

Tags: Entomology

A recent ScienceDaily article summarized a July 18 paper in the journal Science that described the mechanism by which a type of RNA is able to regulate gene expression in some bacteria. It was already known that this RNA, cyclic di-guanosine monophosphate (di-GMP), was a so-called second messenger molecule in bacteria. Basically, di-GMP is generated and diffused in a bacterium, signalling the activation of various proteins which lead to a wide range of changes in activity such as motility, changes in virulence, and biofilm formation. What wasn’t known was just how di-GMP was able to regulate gene expression. The authors of the paper found that this was accomplished via an interesting and relatively recently discovered set of molcules called riboswitches.

The lab of the lead author, Ronald Breaker, discovered riboswitches just a few years ago. They are essentially a small part of an mRNA molecule that has the ability to bind to various metabolites. The part of the riboswitch that is able to bind is known as the apatamer. The apatamer binding is very selective, only applying to particular molecules for the various riboswitch types. More and more types are being discovered, but most of the current ones are listed here. Once the apatamer has undergone binding, the other part of the riboswitch, the expression platform, is changed in response. This expression platform is what then affects gene expression. (I am not very clear on how that step works, nor have I been able to find much information on it as of yet).

This discovery is especially interesting because basically all such fundamental genetic activations in cells were thought to be brought about by proteins, not RNA. It helps illuminate our understanding of some of the earliest ancient lifeforms on Earth, for in providing an alternative for proteins it provides and escape from the circular issue of how either DNA or proteins evolved without the other being present. RNA may very well have filled some of the critical roles before proteins came on the scene. This idea is central to the validity of the RNA World hypothesis.

Tags: Genetics, Molecular Biology

A beautiful specimen of a female Common Whitetail dragonfly (Plathemis lydia), taken yesterday at Sandy Point State Park:

More detailed, original image here. The females can be distinguished by having three black patches on their wings, while the males only have one, larger patch. This page shows many examples of the different sexes.

The mature males of this species have a brilliant bluish-white abdomen, an example of pruinescence¹, which they use to threaten other males who enter their territory.

1. A waxy secretion onto the insect’s cuticle which covers up the cuticle’s color. This is often bluish white. [↩]

Tags: Entomology

Phylogenetic trees are tree-like diagrams showing the relationships among a group of creatures, often with their most recent common ancestor serving as the base of the trunk (rooted versus unrooted). They illustrate how groups of organisms originated, divided, and endured or died off over time. An example of a very low resolution (i.e. only showing a very high level grouping of the organisms represented) tree of the entirety of life may be found here.

Phylogenetic trees are formed using a number of genetic analyses, in combination with various heuristic methods. While they have a number of limitations and their formulation isn’t a trivial matter, they serve an important role in phylogenetics and evolutionary biology in general. Ever since Darwin’s tree-like diagrams in the Origin of Species, they have been used to illustrate the history and branching of groups of organisms, as well as particular genes and traits.

Phylogenetic supertrees are, intuitively enough, large phylogenetic trees. More importantly, they are formed of multiple, smaller, phylogenetic trees that share some nodes (i.e. leaves of the tree, taxons) in common. This seems simple to imagine, but they are difficult to construct, and often require significant computing power. The end result can appear quite stunning. Here is an example (this is a relatively large PDF; but it is worth it) of such a supertree, in this case of the entire 5000-member class Mammalia, created in a study last year concerning the relationship of the dinosaurs to the rise of mammals. The study found that the extinction of the dinosaurs did not cause an explosion in mammal diversity. The standard view had held that once dinosaurs died out as a result of an asteroid or comet striking the earth some 65 Myr ago, mammals were free to diversify, without the fierce and entrenched competition that dinosaurs provided. The conclusion of the study becomes apparent when viewing the tree diagram, which is marked with a dotted ring at the K-T Boundary time (the time corresponding to when it is hypothesized that a large asteroid or comet struck the earth). One can see that well before this time, the major groups of mammals had already formed. Nearly 28 Myr before, in fact. It is only 10 Myr after the dinosaurs were off the scene that mammal diversity greatly increased, due to various climatic changes. What made such a large and convincing tree possible was the combination by the authors of hundreds of other studies and trees. “If we had done this from scratch, we would have had to get molecular and morphological data for 4,000 different species”, said Dr. Kate Jones, co-author of the study in Nature.

And this is what gives phylogenetic supertrees their power. As diagrams, they appear simply as larger phylogenetic trees, which they are. But forming them through analysing and re-coding pre-existing studies and phylogenetic trees means that researchers can formulate a wide-ranging and potentially revolutionary tree that simply would not have been possible with only the smaller trees alone.

Another example of an powerful supertree is found in a study published just last month regarding dinosaur diversity and how it was affected by the KTR (”Cretaceous Terrestrial Revolution”; see bottom of this page). The diagram (again, large file, but worth it) was computed using over 155 previous phylogenetic trees, and shows the relationships among some 440 out of the 600 known dinosaur species. The paper’s lead author Graeme Lloyd describes it thus: “Our supertree summarises the efforts of two decades of research by hundreds of dinosaur workers from across the globe and allows [one] to look for unusual patterns across the whole of dinosaurs for the first time.” It reveals that the period of perceived increased dinosaurian diversity at the end of the Cretaceous was a resulting of various sampling biases. Dinosaurs experienced the greatest diversity during the first one-third of their existence. They diversified at a constant rate through the end of the Cretaceous, neither in a state of decline nor increasing along with the KTR.

Through clever techniques and modern computing power, the results of many disparate research projects can be synthesized into profoundly impacting illustrations that get us even closer to what life’s true family tree might resemble.

Tags: Evolutionary Biology, Genetics