Evolution vs. creationism in the classroom: evolving student attitudes.

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The August 2008 issue of Integrative and Comparative Biology has the following papers in a special section entitled Evolution vs. creationism in the classroom: evolving student attitudes.

Teaching evolution: challenging religious preconceptions
by Eric C. Lovely and Linda C. Kondrick

Trickle-down evolution: an approach to getting major evolutionary adaptive changes into textbooks and curricula
by Kevin Padian

Still creationism after all these years: understanding and counteracting intelligent design
by Barbara Forrest

Thomism and science education: history informs a modern debate
by Linda C. Kondrick

Teaching evolution (and all of biology) more effectively: strategies for engagement, critical reasoning, and confronting misconceptions
by Craig E. Nelson

Curricular reform and inquiry teaching in biology: where are our efforts most fruitfully invested?
by Brianna E. Timmerman, Denise C. Strickland, and Susan M. Cartsensen

Misc media.

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Busy preparing for the start of the semester, so to tide you over here are some links of things to check out.

1) In our genes, old fossils take on new roles
by David Brown, Washington Post

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

2) Gaming evolves
by Carl Zimmer, New York Times

Evolutionary biologists like Dr. Near and Dr. Prum, who have had a chance to try the game, like it a great deal. But they also have some serious reservations. The step-by-step process by which Spore’s creatures change does not have much to do with real evolution. “The mechanism is severely messed up,” Dr. Prum said.

Nevertheless, Dr. Prum admires the way Spore touches on some of the big questions that evolutionary biologists ask. What is the origin of complexity? How contingent is evolution on flukes and quirks? “If it compels people to ask these questions, that would be great,” he said.

I may have to check out this game.

3) Research raises questions about DNA barcoding methodology
by Andrea Anderson, GenomeWeb Daily News

This one is about the PNAS article by Song et al. that at first seemed like it was going to get a lot of hype (it did from NSF, but other venues decided it wasn’t worth a story). A lot of silliness going on with this one that I can’t really talk about, but suffice it to say I am not impressed with this paper or the conduct of the authors. I’ll just quote from the linked story.

“Sadly, the authors of this paper do not understand barcoding protocols,” Paul Hebert, director of the Biodiversity Institute of Ontario at the University of Guelph, told GenomeWeb Daily News. Calling the title of the paper misleading, he said barcoders have been aware of nuclear pseudogenes for years and have already designed some strategies for dealing with the problems described in the paper.

…

“Given that pseudogenes were reported 25 years ago, it’s not new news to us,” Hebert said. He said the team focused on species in which numts are particularly common and drew conclusions based on these eight species. Barcoding projects such as iBOL, he said, include data from thousands of species and are carried out using methods that differ from those described in the paper.
Hebert emphasized that the Barcoding of Life Data Systems, or BOLD, database scours sequences for indels, stop codons, and other tell-tale pseudogene signs. Barcoding sequences are also screened against a pool of sequences representing known contaminants, he said. Sequences that raise red flags are then set aside for further assessment, including longer sequence analysis or RT-PCR.
And, he noted, large barcoding studies typically amalgamate DNA barcode data with information provided by taxonomy, morphology, ecology, and other biological measures. “We’ve never advocated that sequence information alone is declarative for species boundaries,” he said.

…

For his part, Crandall conceded that large barcoding projects such as iBOL “have excellent strategies for quality control of data” and are already applying many of the steps he and his colleagues recommended. Still, he said, even though some people are already worrying about numts does not mean everyone in the field is addressing the problems appropriately.

Kudos on the placozoan genome!

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Trichoplax adhaerens is a bizarre little animal with a decidedly simple morphology. (You can see some here). There has been some question as to the relationship between this critter and other animal groups, but mitochondrial sequences (Dellaporta et al. 2006) and, as of this week, a complete nuclear genome sequence (Srivastava et al. 2008), suggest that it is a modern representative of the earliest branch to split from the rest of the animal lineages (for more detail, check out John Timmer’s discussion). The term “basal” is usually applied to lineages like this, often with the assumption that basal means primitive. Sometimes genome sequencing articles exhibit misunderstanding of what “early branching” actually means, but I must give kudos to Srivastava et al. (2008) for their refreshingly apt conclusions:

Trichoplax‘s apparent genomic primitiveness, however, is separate from the question of whether placozoan morphology or life history is a relict of the eumetazoan ancestor. For example, the flat form and gutless feeding could be a ‘primitive’ ancestral feature, with the cnidarian–bilaterian gut arising secondarily by the invention of a developmental process for producing an internal body cavity (as in Bütschli’s ‘plakula’ theory), or it could be a ‘derived’, uniquely placozoan feature that resulted from the loss of an ancestral eumetazoan gut. Unfortunately, the genome sequence alone cannot answer these questions, but it does provide a platform for further studies.

And the junk DNA train rolls on…

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This appeared in my weekly automated journal search. I have ordered the paper as I can’t find an online copy, but the abstract pretty much covers what the argument will be. Same old pre-1980s adaptationist idea presented as radically novel.

Mallik, M. and Lakhotia, S.C. 2008. Noncoding DNA is not “junk” but a necessity for origin and evolution of biological complexity. Proceedings of the Indian National Science Academy Section B – Biological Sciences 77 (Sp. Iss.): 43-50.

All eukaryotic genomes contain, besides the coding information for amino acids in different proteins, a significant amount of noncoding sequences, which may or may not be transcribed. In general, the more evolved or biologically complex the organisms are, greater is the proportion of the noncoding component in their genomes. The popularity and success of “central dogma of molecular biology” during the last quarter of the 20(th) century relegated the noncoding DNA sequences to a mortifying status of “junk” or “selfish”, even though during the pre-“molecular biology” days there were good indications that such regions of the genome may function in as yet unknown ways. A resurgence of studies on the noncoding sequences in various genomes during the past several years makes it clear that the complex biological organization demands much more than a rich proteome. Although the more popularly known noncoding RNAs are the small microRNAs and other similar species, other types of larger noncoding RNAs with critical functions in regulating gene activity at various levels are being increasingly,identified and characterized. Many noncoding RNAs are involved in epigenctic modifications, including imprinting of genes. A comprehensive understanding of the significance of noncoding DNA sequences in eukaryotic genomes is essential for understanding the origin and sustenance of complex biological organization of multicellular organisms.

See also: Junk DNA and the Onion Test.

"Intelligent design is not a theory" says DI fellow.

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The Panda’s Thumb (PT) has a short post giving a quote from Michael Medved, a new fellow at the Discovery Institute (DI) (which promotes intelligent design, or ID). In it, Medved notes that intelligent design is not a theory itself, but merely a challenge to evolution. We already knew that, of course, and well known ID advocates have made similar statements before1. What interested me was my reaction to seeing the PT post. My first thought was, “Ok, but what’s the context?”. Not that I expected PT to be disengenuously quote-mining (this is, instead, a major creationist maneuver), but I wanted to know why he would say such a thing and what the full quote might have been. PT links to the source, which is an interview in the Jerusalem Post in which Medved is asked about a variety of issues, most of them political, with just a short exchange on ID. Here is the relevant portion, in full.

Speaking of your desire for this kind of particularity, you are a senior fellow at the Discovery Institute that studies and believes in Intelligent Design. How do you, as an Orthodox Jew, reconcile with this kind of generality – with the view of their being a hierarchy with a chief “designer” – while believing in and praying to a very specific God?

The important thing about Intelligent Design is that it is not a theory – which is something I think they need to make more clear. Nor is Intelligent Design an explanation. Intelligent Design is a challenge. It’s a challenge to evolution. It does not replace evolution with something else.

The question is not whether it replaces evolution, but whether it replaces God.

No, you see, Intelligent Design doesn’t tell you what is true; it tells you what is not true. It tells you that it cannot be that this whole process was random.

This is actually quite interesting. What is happening is that a religious interviewer is expressing concern that ID is a challenge to God as the designer. This puts ID creationists in a tough position. In order to sound “sciency”, they pretend that ID is not about God and say that the designer could be anything intelligent (God, gods, aliens). This is not science, and it is also not very good theology, as the interviewer indicates. As a result, ID creationists usually say one thing in debates (we can’t know who the designer is) and another in speeches to religious groups (obviously, the designer is God).

The thing is, there already are qualified people who constantly challenge evolutionary explanations. They are known as evolutionary biologists. We argue, we trash each other’s papers as peer reviewers, and we force one another to present more convincing data on even the smallest issues. The outside commentary by ID creationists — if indeed they are offering no testable alternatives (which they aren’t) — is not useful. Evolutionary biology will continue to study how complex features arise without creationists’ challenges because it is the job of science to explain such things. And they will do it in the field, in the lab, and in the peer-reviewed literature.

____________

1 Note that these are second-hand quotes so interpret them accordingly.

“‘I’m not pushing to have [ID] taught as an ‘alternative’ to Darwin, and neither are they,” he says in response to one question about Discovery’s agenda. ”What’s being pushed is to have Darwinism critiqued, to teach there’s a controversy. Intelligent design itself does not have any content.” George Gilder, interviewed in the Boston Globe, July 27, 2005.

“Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a real problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as “irreducible complexity” and “specified complexity”—but, as yet, no general theory of biological design.” Paul Nelson, interviewed in Touchstone vol 17, July/August, 2004.

“I also don’t think that there is really a theory of intelligent design at the present time to propose as a comparable alternative to the Darwinian theory, which is, whatever errors it might contain, a fully worked out scheme. There is no intelligent design theory that’s comparable. Working out a positive theory is the job of the scientific people that we have affiliated with the movement. Some of them are quite convinced that it’s doable, but that’s for them to prove…No product is ready for competition in the educational world.” Phillip Johnson, quoted in Berkeley Science Review, Spring 2006.

TravelBlogue, or How to live vicariously through one’s student.

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The very first post here was called “My grad student made me do it“, and explained that a then-newly-arrived PhD student in my lab was a blogger and got me interested in blogging. He is still a blog author, and most recently has posted a very enjoyable series about his travels from more or less the bottom to the top of the USA/Canada parts of North America looking for aquatic creatures. I personally did not get to go anyplace exciting this summer, but it has been great having the option to live vicariously, especially as he was most recently at one of the coolest (literally?) places on Earth: Devon Island in the high Arctic. Follow his adventures:


Florida to Guelph:


Guelph to Thompson:

Churchill:


Resolute and True Love:

  • Coming soon

Blogs by scientists.

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In case you aren’t reading them yet, take a minute to check out these relatively new blogs by scientists:

BdellaNea
A blog about leeches — Mark Siddall (American Museum of Natural History)

Evolutionary Novelties
A blog about evolution, with a soft spot for ostracod(e)s and eyes — Todd Oakley (University of California Santa Barbara)

The Rough Guide to Evolution
A blog loosely accompanying a soon to be released book of the same name — Mark Pallen (University of Birmingham)

Chance and Necessity
A blog about evo with a twist of devo — Anonymous “Faculty member in the South”.

At least three of these bloggers are high end researchers, so do have a look.

A pronounced affection for parasites.

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According to Peter Olson of the Natural History Museum in London, “All free-living organisms host one or more parasites”. This can be taken two ways, both of them generally true: a) that each individual multicellular organism hosts at least one individual parasite within its body, and b) that each free-living species plays host to at least one species of parasite that attacks it exclusively. Consider this second point for a moment. For each free living species there is one or more (usually several more) parasite species — that is, as a category (polyphyletic, obviously), parasites may very well be the most diverse types of organisms on the planet.

On the other hand, most parasites are much smaller than their hosts, and so it has typically been assumed that they contribute a negligible fraction to any particular ecosystem’s total biomass. Nuh-uh. In a report published in Nature this week, Kuris and colleagues presented five years’ worth of analyses of estuaries in California and Baja California in which they measured the amount of biomass made up of parasites and free-living organisms.

In sum, Kuris et al. (2008) examined 138 species of infectious agents, 199 species of free-living animals (including invertebrates as well as fishes and birds), and 15 species of free-living plants in their study. They found that plants contributed the most biomass to all three of the estuaries they studied, followed by groups such as snails, bivalves, and crabs. Parasites made up only about 0.2% to 1.2% of the animal biomass of each environment, and on average parasite groups had biomasses 1000 times lower than the average free-living group. However, as Kuris et al. (2008) report,

Certain parasitic groups dominated the parasite biomass, reaching levels similar to those of common free-living groups. For instance, the biomass of trematode worms was comparable to that of the fishes, burrowing shrimps, polychaetes or small arthropods. In all estuaries, trematode biomass exceeded bird biomass by threefold to ninefold.

In other words, parasites make up a larger fraction of the living matter in these environments than do the top predators. In particular, parasites that castrate their hosts (i.e., prevent them from diverting resources into reproductive effort) were the most abundant. The world is not fishy or feathery, it is fluky.

So, whereas the famous quote attributed to J.B.S. Haldane that if there is a creator he must have “an inordinate fondness for beetles” still applies, it may be that he has an even more pronounced affection for parasites. Especially the castrating sort.

_____

Kuris, A.M., R.F. Hechinger, J.C. Shaw, K.L. Whitney, L. Aguirre-Macedo, C.A. Boch, A.P. Dobson, E.J. Dunham, B.L. Fredensborg, T.C. Huspeni, J. Lorda, L. Mababa, F.T. Mancini, A.B. Mora, M. Pickering, N.L. Talhouk, M.E. Torchin, and K.D. Lafferty. 2008. Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nature 454: 515-518.

Update: For more detailed discussions, see Not Exactly Rocket Science and keep your eyes open for a post at The Loom.

Species-Scape: very cool, but…

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Larry Moran directs us to have a look at Species-Scape at the Cornell website. It’s great.

But…

1. It has one group of “prokaryotes”, Kingdom Monera, which is pretty old school. (Same goes for “Protists“). You don’t like dividing the Archaea and Bacteria? Ok, but how about a note that many people now consider this one of the deepest divisions of life? If they can mention something as esoteric to most readers as the phylogenetic species concept, surely they could include a brief line about, you know, phylogenetic groupings at the highest level.

2. And I quote:

This is a taxonomic view of life on earth — based on systematic classifications — which challenges our typical “mammal-centric” understanding of the world around us. Today there is increasing awareness of the enormous diversity of life on earth, but few people probably appreciate the fact that the Species-Scape is completely dominated by multilegged (more than 4 legs) and legless animals, fungi and microbes. Mammals, with a mere 4,000 species, are dwarfed by “lower” animals.

Do we really have to use a misconception to correct a misconception?