Dispelled

Primer on GFP

noreply@blogger.com (NP) — Sat, 21 Feb 2009 03:48:00 +0000

This week's issue of Nature Chemical Biology has a short, free primer on GFP.

Nobel Prize for Green Fluorescent Protein

noreply@blogger.com (NP) — Sun, 12 Oct 2008 00:01:00 +0000

This year's Nobel Prize for Chemistry has gone to Drs. Roger Tsien, Martin Chalfie and Osamu Shimomura for their role in turning green fluorescent protein into one of the most widely used tools in biological research. GFP is a wonderful protein with a wide array of applications - you can read more about it in one of my older posts.

Support the Environment

noreply@blogger.com (NP) — Sun, 05 Oct 2008 22:30:00 +0000

Petition America's next leader to take initiative in protecting the environment and investing in greener energy at the following link:

http://action.edf.org/campaign/first_hundred_days

In George W. Bush's first 100 days in office, he refused to sign the Kyoto Protocol and put forth a policy favoring increased exploration for fossil fuels and rapid construction of new power plants, rather than exploring conservation and sustainable power generation. Actions like these, put out so early in his administration, set the tone for eight environmentally destructive years.

As you may be the next President, I am writing to ask you to differentiate yourself from Bush's policies of the past, and accomplish the following during your first 100 days in office:

1. Introduce legislation to cap global warming pollution.
2. Commit to creating new incentives to unleash energy innovation and build the green jobs sector.
3. Invest in public transportation alternatives to help Americans drive less.
4. Support alliances of industry, environmentalists, and landowners to protect endangered wildlife.
5. Take on the overfishing crisis through new economic incentives for fisherfolk.

By accomplishing these 5 tasks, you will be setting the stage for an environmentally protective administration, and taking the first steps toward undoing the damage the past 8 years have caused. I urge you to implement this To-Do List within your first 100 days in office.

The EDF is also giving freebies to those who sign the petition.

Neanderthal Mitochondrial Genome Sequenced

noreply@blogger.com (NP) — Sat, 09 Aug 2008 02:59:00 +0000

A team of researchers led by Dr. Richard Green and Dr. Svante Pääbo of the Max-Planck Institute for Evolutionary Anthropology have unveiled the first complete sequence of a Neanderthal mitochondrial genome. The researchers derived the DNA from a bone of a 38,000 year old individual, and they have published their findings in the latest issue of Cell [abstract]. The editor of Cell had a short conversation about the paper with Dr. Pääbo, which you can listen to here. Basically, they touch upon the key findings, which include the different amino acid sequence for the COX2 gene and the overall difference between the Neanderthal mitochondrial genome and that of humans. The mitochondrial genome is much easier to sequence as each cell has multiple copies and it tends to be much smaller than the nuclear genome. Nonetheless, the team hopes to have over half of the nuclear genome sequenced by the end of the year, which would help to shed further light on questions about Neanderthals. For instance, did neanderthals and humans interbreed, and what were the genetic differences between the two hominid species? You can read more about this latest research in Nature online.

PZ Myers Reviews Only a Theory

noreply@blogger.com (NP) — Wed, 30 Jul 2008 22:12:00 +0000

In this week's Nature issue, PZ Myers reviews Kenneth Miller's Only a Theory, a book about the recent socio-political controversy of intelligent design creationism:

The United States has a big problem: although we maintain a strong scientific establishment, competitive with the rest of the world in many fields, we also have some of the most backwards proponents of superstitious nonsense in both our electorate and at the highest levels of politics. It is an embarrassment to host laboratories that are at the forefront of scientific research in the same country where presidential candidates are discussing whether Earth is really 6,000 years old as some Bible scholars say, or whether they believe in evolution.

Science and evolution have an advocate in Kenneth Miller, one of North America's eminent knights-errant, a scientist who is active in defending evolutionary theory in the conflict between evolution and creationism. He has been at the centre of many recent debates about science education, most prominently testifying against intelligent design creationism in Pennsylvania's Dover trial, which decided that intelligent design was a religious concept that should not be taught in public schools. He is also a popular speaker, offering the public a grass-roots defence of good science education. Miller's new book Only a Theory is a tour of creationist misconceptions about evolution, such as the one referred to in the book's subtitle — a creationist predicted an inevitable victory in the Dover trial because evolution is "only a theory". The book is also a celebration of the power of evolutionary theory to explain our existence.

Miller is a fine writer who sharply addresses the details of the arguments about intelligent design creationism. When tackling old chestnuts such as the "only a theory" complaint, or Michael Behe's argument for a maximum limit for the number of genetic mutations, or William Dembski's rehash of William Paley's watchmaker argument for complexity, Miller discusses the contemporary biological explanations while refuting the errors.

Miller is sympathetic to the creationists' perspective but opposes them uncompromisingly. The book does not try to place the blame for creationism on ignorance, stupidity or malice, but suggests that the ideas are rooted in traditions and values that biologists share. He admires the clever rhetorical trick of appropriating the term 'design' for creationism, thereby implying that scientists favour the opposite and believe that human life is meaningless and without purpose. He recognizes that the concept of intelligent design creationism taps effectively into human desires and prejudices. Miller does not confuse sympathy for the intent of creationists with sympathy for its effects. The conflict has wider consequences than the teaching of one discipline in US public schools — the creationists aim to revise what science means, discarding rationalism, naturalism, materialism and other Enlightenment values to incorporate the supernatural and loosen the rigour of all sciences.

Only a Theory deals poorly with one central aspect of this battle: why this problem is so much greater in the United States than elsewhere. Miller's rationalizations are sometimes painful to read. Europe's relative freedom from the scourge of creationism is explained with a condescending anecdote: a British colleague offers that any outbreak of such nonsense is rapidly quashed by "dispatch[ing] a couple of dons from Oxford or Cambridge" to overawe the locals with their prestigious degrees, to which the populace will defer. The popularity of creationism in the United States is ascribed to independence and rebelliousness rather than religiosity, which, as someone who has dealt with many creationists, I find disingenuous. The hallmark of almost any creationist argument is the tireless bleating of the same points we have rebutted since the trial of teacher John Scopes in Tennessee in 1925, which tested the law on teaching Darwinian evolutionary theory; the only twists come from new creationist authorities that enter the fray. An equivalent US variant of Miller's British anecdote is that the enemies of science need only dispatch Dembski or Behe from the Discovery Institute in Seattle, Washington, to stir up more doctrinaire creationism among school boards and in elections and churches. To call US citizens more independent-minded than European citizens flatters the creationists too much and demeans Europeans.

If Miller is on shaky ground in his explanations of the origins of creationism, he is rock-solid on where the creationists want to take us: "To the intelligent design movement, the rationalism of the Age of Enlightenment, which gave rise to science as we know it, is the true enemy ... science will be first redefined, and then the 'bankrupt ideologies' of scientific rationalism can be overthrown once and for all." Although his own religious leanings blind him to conflict between faith and science, they also give him insight into both sides of the struggle. Only a Theory is a useful overview of a perilous political attack on the nature of science.

Feminizer and The Evolution of Sex Determination in Honeybees

noreply@blogger.com (NP) — Sun, 27 Jul 2008 00:04:00 +0000

In humans and most mammals, sex is governed by a chromosome determination system, specifically an XX/XY sex determination system whereby individuals with two X chromosomes are female and those with X and Y chromosomes are male. In honeybees (Apis mellifera), a single gene has been shown to be responsible for sex determination. The gene is known as csd (complementary sex determiner), and if an individual has two heterozygous copies it will be a female, whereas if it is homozygous or hemizygous (i.e. it has only one copy of the gene instead of two) it will be male. The csd gene is located in a region known as the sex determination locus (SDL). In last week's issue of Nature, Martin Hasselmann and his colleagues report a new component of the honeybee sex determination system that acts downstream of csd. They found that the SDL contains four other genes, and in order to test whether these genes play a role in sex determination, they used a technique known as RNA interference (RNAi). RNAi is commonly used in certain model organisms to knockdown the expression of a gene of interest using small interfering RNAs (siRNAs). Basically, with the help of certain enzymes found in the cell, the siRNAs form a complex that can bind to messenger RNAs with a complementary sequence and prevent them from being translated. For a more in-depth look at how RNAi works, you can check out this animation.

As expected, when the researchers used this technique to knock down csd expression in female embryos, this resulted in the individuals developing male characteristics. They also discovered that when another gene in the SDL known as fem (feminizer) was knocked down in females during development, this would have the same effect. When fem was knocked down in males, there was no discernible effect on sex differentiation. The researchers were also able to determine that fem is alternatively spliced. Messenger RNA is typically made up of introns and exons - introns get spliced out when the mRNA matures whereas exons are the regions that can be retained and translated into peptide sequences. Sometimes, certain exons can also be spliced out, resulting in peptides with different primary sequences. This is how our cells are able to produce several more kinds of proteins than the number of genes we have. In honeybees, males have a fem variant with three exons that are spliced out in female variants. When csd expression is knocked down using RNAi, this results in females having predominantly male fem splice variants, thereby suggesting that csd exerts its effect on sex determination by controlling how the fem mRNA gets spliced. Knocking down csd in males has no effect, indicating that two different alleles of csd are necessary for it to affect splicing of fem.

When the sequences of csd and fem were compared, the researchers noted that they show a strong similarity. Furthermore, some regions of fem also show sequence similarity with tra (transformer), a gene that is known to play a similar role in sex determination in the fruit fly, Drosophila melanogaster (unlike in Apis mellifera, sex determination in Drosophila is determined by the ratio of sex chromosomes to autosomes rather than a single gene locus - you can read about sex determination in Drosophila here). The researchers also compared fem and csd to the tra gene in the Mediterranean fruit fly (Ceratitis capitata) and noticed that they shared a 30-amino acid motif (the yellow box in the diagram). Given the similar function and sequence identity between fem and tra, it is highly likely that the two genes share a common evolutionary origin. Likewise, the sequence similarities also suggest that csd arose from a duplication of fem. The arrangement of domains is quite similar for both genes, except that csd contains a hypervariable region (the green box), in which the differences between various csd alleles can usually be found, and fem has an extra Arginine/Serine domain (the red box).

Although D. melanogaster and C. capitata lack the csd gene, they are in a different order (Diptera) than honeybees, which belong to the order Hymenoptera. Therefore, the researchers then looked at these genes in related species in order to determine when csd evolved. They discovered that while bumblebees (Bombus terrestris) and stingless bees (Melipona compressipes) share the fem gene with honeybees, they lack the csd gene. In contrast, asiatic honeybee species like A. dorsata and A. cerana have the csd gene, suggesting that it evolved fairly recently i.e. before the divergence of honeybees but after the honeybee lineage split from the bumblebee and stingless bee lineages. In analyzing the sequences, the researchers also determined that csd has undergone a higher rate of substitutions with a higher proportion of non-synonymous substitutions (i.e. resulting in a different amino acid sequence) than fem in these species. This is consistent with positive selection acting on csd, and stabilizing selection operating on fem. A copy of a gene can provide a good substrate for evolution as it can tolerate a higher rate of mutations that can impart novel functions on the gene and enable it to become fixed within the lineage. In the case of honeybees, homozygous male larvae are usually eaten by the female worker bees, which results in selection pressure. Since heterozygous csd alleles are needed to produce female honeybees, non-synonymous substitutions or indels that contribute towards the formation of new alleles would be strongly favoured by selection. Thus, there are at least 12 known alleles of the csd gene, which reduces the odds of a fertilized egg producing a male that would inevitably be eaten.

Overall, these findings demonstrate how gene duplication can result in evolutionary novelty, in this case a novel sex determination pathway in honeybees. While fem has retained its ancestral function of determining the organism's sex depending on how it is spliced, its paralogous "descendant" csd evolved to become the "master switch". More studies will be needed to identify the sex determination pathways in the other bee species, specifically the pathways influencing the alternative splicing of fem. It would also be interesting to know the specific mechanism by which csd heterozygosity results in a particular splice variant of fem. Nonetheless, the work of Hasselmann et al. provides a fascinating example of the important role of gene duplication in evolution and sheds more light on one of the many sex determination systems in nature.

All images are copyright of the Nature Publishing Group.

Hasselmann, M., Gempe, T., SchiÃ¸tt, M., Nunes-Silva, C.G., Otte, M., Beye, M. (2008). Evidence for the evolutionary nascence of a novel sex determination pathway in honeybees. Nature, 454(7203), 519-522. DOI: 10.1038/nature07052

Caught in the Middle: Transitional Flatfishes

noreply@blogger.com (NP) — Thu, 10 Jul 2008 01:41:00 +0000

One of the quirkiest products of evolution is the flatfish, of which there are several different species in the Pleuronectiformes order. They inhabit the sea-floor, and display some rather clumsly-looking adaptations. The ancestors of the flatfish, like other species of bony fish, were not flattened horizontally. But over time, they evolved into flat creatures that glide over the sea floor. The evolutionary history of these creatures isthought to be recapitulated in their development, which can be seen in the following videos:

As you can see, one of key developments is the migration of one eye from the bottom-facing side to the top. You can view the result of this curious adaptation in the picture below of the witch flounder (Glyptocephalus cynoglossus), which I snapped at an aquarium in Quebec City. The flatfish presents a textbook example of an evolutionary adaptation, although for a long time fossils that captured a transitional state between a symmetrical and asymmetrical skull were lacking. But this has changed with a new paper in this week's Nature, which describes Eocene fossils that support a gradual evolution of the flatfish.

Matt Friedman, the author of the paper, made his discovery while searching through neglected specimens in the basements of museums. One of the specimens is of a new species, which Friedman named Heteronectes chaneti, and it displays asymmetrical skull bones. The frontal bone on one side is smaller than on the other, and the orbit is displaced. However, unlike in most modern flatfish species, the orbit does not cross the dorsal midline to the other side. It represents an intermediate condition. Friedman also studied specimens of the Amphistium genus, which were once thought to have symmetrical skulls. However, Friedman used a computed tomography (CT) scan to study these skulls with greater detail, and was able to determine that they too exhibit an asymmetrical cranial morphology. He was also able to determine that these specimens are of adults by noting that they had completely mineralized skulls, which would not be the case if these were juveniles. Furthermore, all the Amphistium specimens are within a consistent size range, making it unlikely that they belong to a juvenile stage. The anatomical characteristics were also compared with the living Psettodes, a primitive flatfish, in order to confirm that the fossil specimens correspond to the adult stage. Friedman was also able to place Amphistium in the same lineage as modern flatfish species, by noting other shared characteristics in addition to the displaced orbits. Heteronectes and Amphistium also retain certain features of the ancestral perciformes. Some flatfish species tend to flatten towards one side, whereas the more primitive ones like Psettodes are observed to flatten in either direction. The Amphistium specimens display a similar pattern, with some flattening to the left and others to the right.

Friedman's findings provide strong evidence for a gradual evolution of Pleuronectiformes by bringing key fossil evidence to the table. They also highlight the fact that many exciting discoveries are made not only out in the field, but also in dusty basements of museums, where forgotten specimens are waiting to be examined with modern techniques and a fresh perspective. You can read more about this paper at The Loom, Not Exactly Rocket Science, and GrrlScientist's blog.

(Heteronectes chaneti)

Friedman, M. (2008). The evolutionary origin of flatfish asymmetry. Nature, 454(7201), 209-212. DOI: 10.1038/nature07108

Joggins Fossil Cliffs Named UNESCO World Heritage Site

noreply@blogger.com (NP) — Tue, 08 Jul 2008 22:19:00 +0000

The famous Joggins fossil cliffs in Joggins, Nova Scotia have been designated as a World Heritage Site by UNESCO. The area features several well preserved fossils from the Carboniferous Period, dating back to around 360 million years ago. At the time, Nova Scotia was close to the equator, and Joggins was covered in a rainforest ecosystem that featured amphibians and early reptiles. The site is also popular with creationists because of its several polystrate tree fossils.

Full story from the CBC:

Nova Scotia's Joggins fossil cliffs, regarded as the best record of life in the Coal Age 300 million years ago, have been added to the exclusive ranks of World Heritage Sites designated by UNESCO.

For nearly 200 years, scientists have been fascinated with the 10-kilometre stretch of cliffs at the head of the Bay of Fundy, where tides continually erode stone to expose fossils dating back hundreds of millions of years. The site has even garnered a mention in Charles Darwin's landmark work, On the Origin of Species.

Late Monday, members of a committee meeting in Quebec City to review applications for UNESCO designation voted unanimously in favour of inducting the fossil cliffs into the exclusive list.

About 100 people gathered in the newly built Joggins tourism centre erupted into cheers when they heard the announcement via video link.

The fossil cliffs are home to enormous fossilized trees and what's believed to be the remains of the world's oldest reptile.The Joggins cliffs were submitted last February for consideration by UNESCO's World Heritage Committee. (Joggins Fossil Institute)
"There really isn't anywhere in the world that's as good as Joggins as far as we know," said Martin Gibling, a professor of earth sciences at Dalhousie University in Halifax.

"It's truly a marvelous place — you can see the entire ancient landscapes of the Earth laid out before you, so to speak."

The community of Joggins is hoping fossil tourism will breathe new life into their economy, lagging since the local coal mine closed in the early 1960s.

Sandi Cooper, one of the dozens gathered to hear the announcement, compared the good news to Christmas morning. "Fantastic, excited, happy!" is how she described her reaction.

Joggins residents have been working toward a UNESCO designation for more than 10 years in hopes of cashing in on a new wave of wealth by attracting tourists.

A key part of the attempt to have it designated a World Heritage Site was building the new $9-million interpretive centre, which opened in April. The centre houses displays, lab space for researchers, a cafe and store.

Nova Scotia's premier also heralded UNESCO's designation of the site. "The Joggins fossil cliffs are one of Nova Scotia's, and the world's, great natural treasures," Rodney MacDonald said in a news release.

The Joggins cliffs were submitted last February for consideration by the World Heritage Committee, an educational, scientific and cultural arm of the United Nations founded in 1972 and charged with protecting heritage worldwide.

The cliffs are the second site in Nova Scotia to gain the designation, with the old town of Lunenburg named in 1995.

Twelve other sites were named to the heritage list Monday, including a series of wooden churches dating back to the 16th century and two 500-year-old cities on the Straits of Malacca in Malaysia.

Before Monday's additions, there were only 14 World Heritage Sites in Canada and 855 sites worldwide.

Pringles are not potato crisps

noreply@blogger.com (NP) — Mon, 07 Jul 2008 05:44:00 +0000

As per this BBC report:

Pringles, the popular snack food in a tube, are not potato crisps, a High Court judge has ruled.

Their packaging, "unnatural shape" and the fact that the potato content is less than 50% helped Mr Justice Warren make his crunch decision.

As a result, Pringles, in all flavours are free from Value Added Tax (VAT).

Manufacturer Procter & Gamble (P&G) is likely to save millions of pounds as a result of the decision - with customers also likely to pay less.

Spud impact

P&G had gone to court to challenge a VAT and Duties Tribunal decision that the Pringle was subject to the standard 17.5% rate of VAT because it was "a potato crisp product", which are, unlike most food, subject to the tax.

But the manufacturer had insisted that their best-selling product was not similar to potato crisps, because of their "mouth melt" taste, "uniform colour" and "regular shape" which "is not found in nature".

It also argued that potato crisps - unlike Pringles - did not contain non-potato flours, and were not packaged in tubes.

Pringles are more like a cake or a biscuit, it claimed, because they are manufactured from dough.

Mr Justice Warren ruled that Pringles were not "made from the potato" - as set out in the definition laid down by the 1994 VAT Act.

To be subject to VAT, a product "must be wholly, or substantially wholly, made from the potato".

But he said that Pringles did not meet these criteria - being made from potato flour, corn flour, wheat starch and rice flour together with fat and emulsifier, salt and seasoning, with a potato content of about 42%.

Taking the biscuit

Separately, the Food and Agricultural Organisation and the World Health Organisation have decided - after seven years of debate - what qualifies as a proper tomato.

The ruling means tomatoes may be round, ribbed, oblong or elongated, or can be cherry tomatoes or cocktail tomatoes. Other characteristics include being clean, whole, fresh in appearance, and free from foreign smells and pests.

Earlier this year the European Court of Justice (ECJ) ruled that the UK Treasury had wrongly imposed VAT on a Marks and Spencer teacake. Customers paid VAT for 20 years before the authorities accepted the product was a cake, which does not command VAT.

Under UK tax rules, most traditional bakery products such as bread, cakes, flapjacks and Jaffa Cakes are free of VAT, but the tax is payable on cereal bars, shortbread and partly-coated or wholly-coated biscuits.

Bones and Molecules #3

noreply@blogger.com (NP) — Wed, 02 Jul 2008 00:56:00 +0000

Just another periodic round-up of interesting posts from around the sciblogosphere:

Ventastega: A tetrapod perched on a different branch
In last week's issue of Nature, there was a paper on Ventastega, a fishapod like Tiktaalik and Acanthostega. Brian Switek provides a short summary of the findings.

Evolving proteins in snakes
PZ writes about a fascinating case of evolution in action - populations of garter snakes that have evolved resistance to tetradotoxin.

Morning Sickness is an Adaptation, not a Sickness
Greg Laden writes about the hypothesis that morning sickness has an adaptive purpose.

Life's Modest Majesty
From his new webdigs, Carl Zimmer writes about a paper from this week's Science. A consortium of scientists catalogued all the marine invertebrates in the fossil record, and plotted the number of genera against time to suggest that the number has not increased exponentially.

Lenski Eviscerates Schlafly

noreply@blogger.com (NP) — Wed, 25 Jun 2008 02:59:00 +0000

Richard Lenski has replied to Conservapedia's absurd demands and insinuations of fraud, and whilst still exhibiting some constraint, he isn't as nice as in his first letter. The entire reply can be found on RationalWiki's page dedicated to this exchange.

...Finally, let me now turn to our data. As I said before, the relevant methods and data about the evolution of the citrate-using bacteria are in our paper. In three places in our paper, we did say “data not shown”, which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website.

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [ http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. [ http://en.wikipedia.org/wiki/Allusion] ...

So what is Conservapedia's response to this? The talk page is rather interesting. At the time of this posting, Schlafly (posting under the handle "Aschlafly") has not yet responded to a question asking whether he is satisfied with the response. As Lenski notes in his response, the additional data will be available on his website, and anybody who is competent and has the adequate resources to handle bacteria may ask for the samples. After all, there are strict regulations when it comes to biological materials, so somebody off the street can't just walk into Lenski's lab and demand that he provide him or her with bacterial samples for no specified reason.

Although Schlafly has not as yet issued a response, a blurb on the Conservapedia main page says, "Lenski's latest response to a request for his data is revealing ... about Lenski's attitude. Take a good look at the attitude our tax dollars are paying for." Indeed, it does say something about Lenski's attitude. Given that some nutjobs have essentially accused him, his collaborators, and his students of perpretrating fraud, that Schlafly has also implicated the journal, editors and reviewers of the paper of wrongdoing, and the utter arrogance, rudeness, and overall dimwittedness of Schlafly's two letters, Lenski's response shows some admirable constraint. He might have accused Schlafly of being "not very bright", but that hardly compares to Schlafly's impudent attacks on the integrity of Lenski and his colleagues. This shows something about Lenski's attitude - that he is willing to devoted to protecting the integrity of his collaborators and students, that is he willing to take the time to address misrepresentations of his work in a manner that is understandable to the public, and his compliance to provide the data as well as bacterial samples to anybody who anybody who meets the basic qualifications required by university and federal policies. However, this also says a lot about Schlafly's character and the ignorance of some of his followers. The next time Schlafly is on his moral high horse, will he remember the time he broke the ninth commandment? Given what has been revealed about his attitude through the Lenski affair, I would think not.

Vancouver Sun Trashes Expelled

noreply@blogger.com (NP) — Sun, 22 Jun 2008 16:45:00 +0000

With Expelled: No Intelligence Allowed set to open in Canada later this week, columnist Peter McKnight of the Vancouver Sun has weighed in with critical review of the film. Although McKnight has not said anything that hasn't been said before, his comments about the premises of the film seem to be spot on. There's a reason why intelligent design is not considered to be science. The following video has an interesting take on the purported issue of "academic freedom" (HT to Pharyngula):

Creationists Take On Lenski

noreply@blogger.com (NP) — Sat, 21 Jun 2008 22:55:00 +0000

The recent publication of a paper describing the ability of a population of E. coli bacteria to absorb citrate has created quite a buzz on the blogosphere and in the popular press. The importance of the findings published by Dr. Richard Lenski and members of his lab is that the experiment not only documents the emergence of a major evolutionary novelty, but the design of the experiment also allowed the researchers to "replay the tape" of the population's evolutionary trajectory. In doing so, they were able to bring empirical evidence to the long-standing debate between the late Stephen Jay Gould and Simon Conway Morris about historical contingency. Carl Zimmer and PZ Myers have provided excellent summaries of the paper, which is also available for download here.

The paper has also caused a stir in the creationist community. Some like Michael Behe and Don Batten have responded with what appear to be a futile exercises in handwaving and obfuscation. Others, like Andy Schlafly of Conservapedia have responded with incredulity. Andy Schlafly sent the following letter to Dr. Lenski:

June 13, 2008

Dear Professor Lenski,

Skepticism has been expressed on Conservapedia about your claims, and the significance of your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study. Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations. In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000. A recent article about your claims appears in New Scientist here: http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

Submission guidelines for the Proceedings of the National Academy of Science state that "(viii) Materials and Data Availability. To allow others to replicate and build on work published in PNAS, authors must make materials, data, and associated protocols available to readers. Authors must disclose upon submission of the manuscript any restrictions on the availability of materials or information." Also, your work was apparently funded by taxpayers, providing further reason for making the data publicly available.

Please post the data supporting your remarkable claims so that we can review it, and note where in the data you find justification for your conclusions.

I will post your reply, or lack of reply, on www.conservapedia.com . Thank you.

Andy Schlafly, B.S.E., J.D. Conservapedia

To Lenski's credit, he did not simply send Schlafly's email to the recycling bin, but took the time to respond to Schlafly's misunderstandings of the study. He also pointed out that all the relevant data can be found in the paper itself:

Dear Mr. Schlafly:

I suggest you might want to read our paper itself, which is available for download at most university libraries and is also posted as publication #180 on my website. Here's a brief summary that addresses your three points.

1) "... your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study." We (my group and scientific collaborators) have already published several papers that document beneficial mutations in our long-term experiment. These papers provide exact details on the identity of the mutations, as well as genetic constructions where we have produced genotypes that differ by single mutations, then compete them, demonstrating that the mutations confer an advantage under the environmental conditions of the experiment. See papers # 122, 140, 155, 166, and 178 referenced on my website. In the latest paper, you will see that we make no claim to having identified the genetic basis of the mutations observed in this study. However, we have found a number of mutant clones that have heritable differences in behavior (growth on citrate), and which confer a clear advantage in the environment where they evolved, which contains citrate. Our future work will seek to identify the responsible mutations.

2. "Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations." You will find all the relevant methods and data supporting this claim in our paper. We also establish in our paper, through various phenotypic and genetic markers, that the Cit+ mutant was indeed a descendant of the original strain used in our experiments.

3. "In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000." We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not "appear out of the blue", in any case. We do show that what we call a "potentiated" genotype had evolved by generation 20,000 that had a greater propensity to produce Cit+ mutants. We also show that the dynamics of appearance of Cit+ mutants in the potentiated genotypes are highly suggestive of the requirement for two additional mutations to yield the resulting Cit+ trait. Moreover, we found that Cit+ mutants, when they first appeared, were often rather weak at using citrate. At least the main Cit+ line that we studied underwent an additional mutation (or mutations) that refined that ability and led to a large improvement in growth on citrate. All these issues and the supporting methods and data are covered in our paper.

Sincerely,

Richard Lenski

Yet, Schlafly was not satisfied. He seemingly wants Lenski to release any raw data pertinent to the experiments for "public scrutiny". He sent yet another letter to Lenski:

Dear Prof. Lenski,

This is my second request for your data underlying your recent paper, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli," published in PNAS (June 10, 2008) and reported in New Scientist ("Bacteria make major evolutionary shift in lab," June 9, 2008).
http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf
http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

Your work was taxpayer-funded, and PNAS represents that its authors will make underlying data available. I'd like to review the data myself and ensure availability for others, including experts and my students. Others have expressed interest in access to the data in addition to myself, and your website seems well-suited for public release of these data.

If the data are voluminous, then I particularly request access to the data that was made available to the peer reviewers of your paper, and to the data relating to the period during which the bacterial colony supposedly developed Cit+. As before, I'm requesting the organized data themselves, not the graphs and summaries set forth in the paper and referenced in your first reply to me. Note that several times your paper expressly states, "data not shown."

Given that this is my second request for the data, a clear answer is requested as to whether you will make the key underlying data available for independent review. Your response, or lack thereof, will be posted due to the public interest in this issue. Thank you.

Andy Schlafly, B.S.E., J.D.
www.conservapedia.com
cc: PNAS, New Scientist publications

The accusatory tone is more palpable, and so is the lunacy. The relevant data is included in the Blount et al. paper, so this is a bizarre request to begin with. Furthermore, it's so general that it betrays the fact that even Schlafly probably doesn't know what he's looking for. Does he expect Lenski to ship him all his lab notebooks from the past twenty years? Or does he want him to Fedex the frozen bacterial colonies from each experimental checkpoint? It is an absurd request - nay, a demand (taxpayers' rights and all) - that is not normally asked of a professional scientist. If a colleague has any concerns about a specific method used or specific conclusions, he or she might request the pertinent raw or derived data. This level of scrutiny is not even reached during the normal peer review prior to publication. Schlafly's request is much like a subpoena on Lenski's data, which is not surprising considering Schlafly is a lawyer, not a scientist.

This also raises the important question as to what Schlafly plans to do with all the data, assuming Lenski is gracious enough to comply. He is not qualified to evaluate it. The question has been raised by some more level-headed contributors on Conservapedia's talk page on this issue. It seems to be a common ploy to appeal to lofty ideals in the absence of something concrete, and in true fashion, Schlafly proclaims that this is about "public scrutiny". In fact, on the talk page Schlafly is bullying other contributors to sign on to his cause. If they question his motives, they are added to a list of detractors who are "opposed to public scrutiny". Of course, this is a frivolous exercise that renders "public scrutiny" meaningless. After all, any professional scientist or otherwise qualified person who requests specific data would not be shunned by Lenski. On the other hand, to expect just about any Tom, Dick or Harry off the street (and that is what Schlafly essentially is in this context, despite what he may think) to be entitled to see a lab's intellectual property is a ridiculous notion. Of course, it may be Schlafly's plan to forward the data to creationist wackaloons like Ken Ham and his ilk, so that they can manufacture an alternative "interpretation" of the data and once again bring the integrity of science into question. Mike the Mad Biologist thinks Lenski should just ignore Schlafly's demands because of this.

The most disturbing aspect of this saga is that Schlafly and a few other contributors have gone as far as to suggest that Lenski is guilty of fraud. Not only is this insinuated in the two letters to Lenski, but the Conservapedia talk page on this issue even invokes Piltdown Man! Ignoring the fact that Piltdown Man was met with a lot of skepticism from many scientists even before it was determined to be a hoax, Conservapedia's insinuations are not only insulting to Lenski and his collaborators, but to the scientific process itself. Sure, fraud does happen in science. But scientific fraud is taken very seriously, and can even jeopardize a scientist's career. So accusations of fraud should not be made for the simple reason that the results do not agree with a layman's mythology. I guess the silver lining here is the hilarity of the whole exchange.

It's a Long Way to Amphioxus

noreply@blogger.com (NP) — Thu, 19 Jun 2008 08:47:00 +0000

A short while ago, a draft sequence of the Platypus genome was announced in Nature. In this week's issue of Nature, another consortium of researchers reports the draft sequence of the Amphioxus (also known as lancelets) genome. Amphioxus is a group of worm-like organisms that live in the sea floor. Like us, they are chordates, which means that they possess a notochord - a rod of tissue in the dorsal part of the organism - amongst other common features. Chordates are comprised of three lineages: Urochordates (also known as tunicates, or sea squirts), Cephalochordates (Amphioxus), and Vertebrates. In Amphioxus, the notochord persists throughout its entire life and provides structural support. In vertebrates, the notochord goes on to become the vertebral column. The last common ancestor of vertebrates is thought to have been closely related to members of the Amphioxus lineage, which makes the latter useful model organisms for understanding the evolution of vertebrates.

The Amphioxus species used for the genome sequencing was the Florida lancet, Branchiostoma floridae. The reason this species was chosen is because it resembles the fossils of primitive chordates from the early and middle Cambrian, and thus scientists believe that it provides a good approximation of what the last common ancestor of chordates was like.

In this paper, the researchers also compare the newly sequenced Amphioxus genome with those of other organisms. Some scientists have argued that Hemichordates, another group of worm-like marine organisms, should be considered as a fourth sub-phylum of chordates. However, they are generally given their own phylum and considered to be more closely related to echinoderms, which include starfishes and sea cucumbers. This classification was validated in this paper through phylogenetic analyses of 1,090 orthologous sequences taken from members of representative echinoderms, hemichordates, and various chordates. The phylogenetic analyses suggest that Amphioxus branched off the chordate lineage earlier than the tunicates and vertebrates, confirming previous hypotheses based on morphological evidence and more limited genetic evidence.

When comparing the Amphioxus genome to the human genome, they found that we share 17 linkage groups. A linkage group, simply put, is comprised of genes that tend to be inherited together, providing a key exception to Mendel's Law of Independent Assortment. Genes on the same chromosome are usually linked, although they can be separated by a process known as crossing over, where two chromosomes swap segments of their DNA. With any given lineage, one would expect that genes that were once linked will become separated due to events like crossing-over. However, assuming that enough time has not passed for the entire set of originally linked genes to become unlinked, one should expect to find some shared linked genes in organisms that share a common ancestor. Indeed, for B. floridae and Homo sapiens, it appears that we share 17 linkage groups left over from the genome of our last common ancestor. The figure shows some of these conserved linkages on Human chromosome 17. The "scaffolds" refer to segments of DNA cloned from the Amphioxus genome. The Amphioxus genome was sequenced using a method known as whole genome shotgun sequencing, which basically entails breaking up the genome into smaller fragments in order to make it easier to sequence. These sequences are then put together and ordered into scaffolds using computer algorithms. The figure represents four of these scaffolds from the Amphioxus genome sequencing, and shows how these linkages are conserved in the human chromosome 17 as well.

Another interesting finding that emerged from comparing the Amphioxus genome to that of vertebrates is that our vertebrate lineage has undergone two rounds of whole genome duplications since Amphioxus branched off from the rest of the chordate lineage. These two duplications mean that the human genome contains more than two copies (many of them have undergone subsequent deletions) of some conserved genes present in the Amphioxus genome. This corroborates previous evidence from studies of specific regions, which also indicated the occurence of two duplications in the chordate lineage. The researchers were also able to infer when these duplications had occured. Since the teleost fish genome also shows evidence of the two duplications, we can safely say that they occured prior to the split between the teleost and tetrapod lineage. Furthermore, since the sea squirt genome shows no evidence of these duplications, they presumably occured after the divergence of the urochordate lineage. By comparing these conserved linkages in our genome with gene families from the sea lamprey (Petromyzon marinus), the researchers were able to conclude that lamprey lineage split from the jawed vertebrates either before the second duplication, or at around the same time. However, until a more complete sequence of the lamprey genome is available, we will not be able to better resolve the timing of the second duplication.

While some of the conserved linkages exhibit macro-synteny, i.e. on the same chromosome but not necessarily in the same region, there are also instances of micro-synteny, where linked genes neighbour one another. We know from studies in the fruitfly, that the homeobox genes that are important in development have undergone tandem duplications - which basically means that the copies of the gene are adjacent to one another on the chromosome - long before chordates split from other phyla in the Deuterostome lineage. In fact, these duplications occured even earlier than the divergence of Bilaterians. In humans and other vertebrates, many of these tandem duplicates have become separated through genome rearrangements over time, although the Nkx2-1/Nkx2-2 gene pair remains linked. Therefore, if humans descended from the same common ancestor as Amphioxus and if the Amphioxus lineage has undergone fewer genome rearrangements, we might expect to find this pair linked in the Amphioxus genome as well. This is indeed the case, and the researchers also determined that many of the paired duplicates observed in the fruit fly genome are also conserved in Amphioxus, since Deuterostomes share common ancestry with the fruit fly.

The researchers also did some preliminary comparisons of non-coding sequences. By comparing the teleost and mammalian genomes, they were able to come up with 3,100 non-coding regions that are conserved in both lineages. They then aligned these regions from the human genome with the Amphioxus genome, and determined that 77 of the putative non-coding elements of a length greather than 50 base pairs showed more than a 60% identity. Further investigation into these conserved regions and their possible roles in development might be fruitful for evolutionary developmental biologists.

Overall, this paper represents a significant milestone in our understanding of chordate evolution. The authors also have an upcoming publication in the journal Genome Research (doi: 10.1101/gr.073676.107), in which they will look deeper into the implications that their findings have on the evolution of vertebrates. This paper also highlights the importance of sequencing the genomes of exotic organisms that can provide valuable insights into the epic history of life. Also be sure to check out this song about Amphioxus (lyrics here)!

Image of Amphioxus from Wikipedia. All other images from Putnam et. al (2008), and copyright of the Nature Publishing Group.

Putnam, N.H., Butts, T., Ferrier, D.E., Furlong, R.F., Hellsten, U., Kawashima, T., Robinson-Rechavi, M., Shoguchi, E., Terry, A., Yu, J., Benito-GutiÃ©rrez, E., Dubchak, I., Garcia-FernÃ ndez, J., Gibson-Brown, J.J., Grigoriev, I.V., Horton, A.C., de Jong, P.J., Jurka, J., Kapitonov, V.V., Kohara, Y., Kuroki, Y., Lindquist, E., Lucas, S., Osoegawa, K., Pennacchio, L.A., Salamov, A.A., Satou, Y., Sauka-Spengler, T., Schmutz, J., Shin-I, T., Toyoda, A., Bronner-Fraser, M., Fujiyama, A., Holland, L.Z., Holland, P.W., Satoh, N., Rokhsar, D.S. (2008). The amphioxus genome and the evolution of the chordate karyotype. Nature, 453(7198), 1064-1071. DOI: 10.1038/nature06967

Green Fluorescent Protein

noreply@blogger.com (NP) — Fri, 13 Jun 2008 05:21:00 +0000

If you've heard of Alba the glowing bunny, you've probably heard of Green Fluorescent Protein, or GFP. The protein was isolated from the Aequorea jellyfish in the 1960s, and scientists discovered that a solution containing the protein would appear bright green when exposed to ultraviolet light. After the gene was identified and cloned, scientists were able to express the gene in E. coli and the nematode C. elegans. Ever since, GFP has become widely used and versatile tool in biological research.

GFP is a barrel-shaped molecule, and the chromophore - the part of the molecule responsible for the emission of the green colour - is located at the centre. When light of a particular wavelength is absorbed by a chromophore, this induces a chemical change which results in the emission of light of a different wavelength. In the case of wild-type GFP, the chromophore absorbs light at wavelengths in the ultraviolet region and in the blue region . The Aqueorea jellyfish also contains another fluorescent protein known as aequorin, which emits blue light of a 469 nm wavelength when bound to calcium. For this reason, aqueorin is useful in biological research as a calcium indicator. Interestingly, the blue light emitted by aequorin molecules activated by calcium is absorbed by the green fluorescent protein, which in turn emits green light at a wavelength of 509 nm.

After the gene for the wild-type GFP was cloned, researchers have been able to create several different mutants of GFP to tailor it for different applications. As mentioned above, wild-type GFP can be excited by light at two different absorption peaks, of which the one in the visible range is only a minor one. This means that in order to get optimal excitation of the chromophore, one would have to irradiate the molecules with UV light. This is problematic if one wants to use GFP in live cells, since UV radiation can damage them. Hence, using techniques such as site-directed mutagenesis, mutants have been created with strong absorption peaks corresponding to blue light. Another drawback with wild-type GFP is that is folds poorly at 37°C, which is not a problem in the Aequorea jellyfish that lives in colder waters, but it limits its usefulness for in vivo experiments in the lab. Fortunately, mutants of GFP such as Enhanced Green Fluorescent Protein (EGFP) get around this problem. Another drawback of GFP is that it can take upto four hours to fold correctly, but an engineered version known as Superfolder GFP partly solves this problem. Furthermore, a smorgasbord of mutants have been derived from GFP to emit different wavelengths of light; these include cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and blue fluorescent protein (BFP). The palette of fluorescent proteins available to researchers is supplemented by DsRed, a red fluorescent protein derived from the Discosoma coral, and its derivatives.

These fluorescent proteins, or fluorophores, have a variety of different applications if they can be expressed in live cells. The first step involves transfecting the target cell(s) with a DNA vector containing the GFP gene or construct. Once these cells are successful transfected, they can be visualized using fluorescence microscopy. One of the straightforward uses of GFP is to help visualize a cell in vivo. There are fluorescent dyes that can be used for this purpose, but these can usually be toxic for the cell or require them to be fixed before staining. GFP is thus useful for observing motility as well morphological change of a living cell over time. For example, the following video shows the radial migration of a cortical neuron transfected with GFP in utero:

Another simple but useful application of GFP is as a reporter. By cloning the GFP sequence downstream of a gene of interest, it is possible to create a fusion, or chimeric, protein. GFP can then serve as a useful marker to verify the successful transfection of the gene of interest into target cells. GFP may also be useful as a marker for identifying specific cell types. For instance, astroglial cells exclusively express a protein known as glial fibrillary acidic protein (GFAP). The promoter for this gene can be cloned upstream of the GFP gene, and the construct can then be transfected into cells in the central nervous system in order to identify the lineage of a cell. Alternatively, transgenic animals containing these constructs can be made. This approach can also be useful in cancer research, in order to identify and track certain cells that may be expressing markers for a particular type of cancer.

Chimeric proteins can also be powerful tools for studying the localization of a protein of interest, i.e. whether the fusion protein localizes to the nucleus, cytoplasm, plasma membrane, et cetera. They can also provide a more informative way to study the morphology of a cell and the localization of specific organelles. For instance, proteins known to associate with specific organelles can be fused to a fluorescent protein of one colour, whereas others that localize in the cytoplasm can be fused to a fluorescent protein of a different colour. Förster resonance energy transfer (FRET) is a principle behind a technique that is especially useful for studying protein:protein interactions. The basic principle of FRET is that one fluorescent protein is the donor, while another is the acceptor, which will receive energy from the former. When the donor is activated by light of a specific wavelength, it will transfer energy to the acceptor if it is within a range of a few nanometers. This will cause the acceptor to emit light of a specific wavelength. CFP is commonly used as the donor, while YFP is the acceptor. CFP may be fused with protein A, and YFP with protein B. Both chimeric proteins can be transfected into a cell, and if both proteins come into close proximity of another, FRET will occur, and the YFP will have an emission of 535 nm. This principle is also useful in the engineering of molecular indicators. A well-known example is Chameleon, a calcium sensor with a calcium-binding motif that has YFP fused on one end and CFP on the other. When calcium binds to Chameleon, this induces a conformational change in the molecule that will bring the YFP into close proximity of the CFP, resulting in emission of 535 nm.

Two techniques that are useful for studying protein dynamics are fluorescence loss in photobleaching (FLIP) and fluorescence recovery after photobleaching (FRAP). They both take advantage of the photobleaching that occurs when the fluorophores are exposed to light over a period of time. In FLIP, a section of the cell expressing the fusion protein is bleached using a laser, and the loss of fluorescence can be tracked in order to study the dynamics of the protein. FRAP is similar, except it measures how normal emission returns to the bleached area due to trafficking of unbleached proteins into the region.
Over the last two decades, the popularity of GFP and related proteins has increased dramatically and led to several innovative techniques for the study of cell biology. Visit this website to see more cool uses of these proteins. One of my favourite applications is Brainbow, a process in which transgenic mice have neurons expressing genes of fluorescent proteins that have undergone Cre-lox recombination in order to exhibit several different shades. This technique ensures that individual neurons can easily be identified and traced, something that is difficult if just one fluorescent protein is used. Apart from being a very useful method for studying the connectivity of the brain, the results also make for some dazzling photography!

Image Credits:
1. Picture of Aequorea jellyfish courtesy of CorruptKitten.
2. Picture of GFP model courtesy of Vik Nanda.
3. Picture of eppendorf wreath containing fluorescent proteins taken from Dr. Roger Tsien's website.
4. Picture of labelled cells from Nikon MicroscopyU website.
5. Brainbow picture from Livet et al. (2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. Nov 1. doi:10.1038/nature06293

References:
1. "Green Fluorescent Protein". Wikipedia. <http://en.wikipedia.org/wiki/Green_fluorescent_protein> (Accessed June 15th, 2008)
2. Piston, David et al. "Introduction to Fluorescent Proteins". Nikon MicroscopyU. <http://www.microscopyu.com/articles/livecellimaging/fpintro.html> (Accessed June 15th, 2008)
3. Tsien R (1998). "The green fluorescent protein". Annu Rev Biochem 67: 509-44. doi:10.1146/annurev.biochem.67.1.509.
4. Zimmer, Marc. Green Fluorescent Protein - The GFP Site. <http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP-1.htm> (Accessed June 15th, 2008)

Expelled Making In-Roads in Canada

noreply@blogger.com (NP) — Thu, 12 Jun 2008 05:40:00 +0000

Kevin Miller, screenwriter of Expelled: No Intelligence Allowed has announced on his blog that the film will be opening across Canada on the 27th of June. As far as I know, there's no word yet on which theatres will be showing the film, although a blogger for Maclean's reports that Premise Media invited members of parliament to a private screening in Ottawa. The invite read as follows:

From: Vellacott, Maurice - Assistant 1
Sent: June 10, 2008 4:49 PM
To: - BQ DÉPUTÉS/MEMBERS; - BQ: ADJOINTS; - CONSERVATIVE ASSISTANTS CONSERVATEURS; - CONSERVATIVE MEMBERS/DÉPUTÉS CONSERVATEURS; - INDEPENDENT MEMBERS/DÉPUTÉS INDÉPENDANTS; - LIBERAL MEMBERS/DÉPUTÉS; - LIBERAL ASSISTANTS; - NDP MEMBERS/DÉPUTÉS NPD; - NDP/NPD ASSISTANTS
Subject: Private Screening of “Expelled, No Intelligence Allowed”

From: Charles McVety
Sent: June 10, 2008 4:32 PM

Change of Venue

Fairmont Chateau Laurier

Canadian Room, 1 Rideau Street
Ottawa, Ontario

At 7:30pm

The writer and Executive Producer of Expelled, No Intelligence Allowed, Walt Ruloff, wants to personally meet you and invite you to privately screen his new film Wednesday evening, June 11th at 7:30 pm at the Fairmont Chateau Laurier, Canadian Room, 1 Rideau Street, Ottawa, Ontario.

In a time when an African-American can win the nomination of the Democratic Party to be the President of the United States of America, you would think that our educational system would be free from racism, and open to freedom of thought, expression, and inquiry. Nothing could be further from the truth. North America’s Universities do not allow academic freedom–if you question the orthodoxy of “Darwinism”. The last vestiges of the horrible scourge of racism remain firmly entrenched in the science classrooms of our society. This new film cuts to the heart of racism. In the United States of America, this film opened in 1,100 theatres, and was number 10 at the box-office. Over 1.3 million people have paid to see the film, and now it is coming to Canada opening on June 27th.

How could a film, created by a Canadian, Walt Ruloff, cause so much controversy? Walt Ruloff, is a very successful entrepreneur. By thinking outside of the box, he developed complex computer systems to optimize logistics for large organizations. A majority of Fortune 2000 companies use his logistics systems to control the movements of millions of products and goods around the world. Walt wanted to apply his ingenuity to the biological world to help find cures and treatments for troubling diseases. He quickly found that the scientific community would not allow you to think outside of the box of Darwinism, thereby restricting the advancement of knowledge. Instead of bowing to the high priests of Darwinism, Walt made a movie to challenge their “supremacy”.

Many people do not realize how overt racism is in Darwin’s writings. The full of the textbook found in every science classroom is The Origin of Species Through the Process of Natural Selection of the Preservation of the Favoured Races in the Struggle for Life. On page 178 of Darwin’s book The Descent of Man, he states, “At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate, and replace, the savage races throughout the world…The break between man and his nearest allies will then be wider, instead of as now between the negro or Australian (Aboriginals) and the gorilla.”

Racism must be countered and I believe this film will mobilize millions of Canadians to blot out this terrible scourge in our society.

Please clear a couple of hours this Wednesday to meet Walt and view his film. www.expelledthemovie.com

Please call 416.391.5000 RSVP.

Dr. Charles McVety

President, Canada Christian College

P.S. An anti-Racism Rally will follow at the Darwin exhibit at the Royal Ontario Museum, Toronto, Thursday, June 12th at 12:30. Please invite your friends.

On the one hand, I see this as an attempt to garner some publicity for the film. From my experience, the controversy over creationism does not feature as heavily in the public discourse in Canada as it does down south. A film on the topic would be a hard sell, especially since it would be competing with the summer blockbusters. So Expelled probably needs this kind of publicity.

On the other hand, it appears the film is being utilized according to its...um... design, i.e. a propaganda film for creationism. If you are familiar with the evolution of creationism, you would know that creationism in its latest form has adopted scientific pretensions and a sham secularism in order to adapt to the legal environment in the United States, which forbids the proselytizing of religious views in public classrooms. This latest form known as Intelligent Design has fine-tuned its approach over the last decade or so in response to legal setbacks, of which the most notable is that of Kitzmiller vs the Dover Area School District. Whereas there was once a sustained attempt to push intelligent design in the classroom, the judge in the Dover trial ruled that the teaching of intelligent design is unconstitutional and it has thus forced the Discovery Institute, the hub of the Intelligent Design movement, to backtrack. But like cockroaches, they are a hardy bunch, and they were able to adapt by ditching the "teach the [manufactured] controversy" approach with one under the guise of "academic freedom". Expelled embodies this latest approach, and while it purportedly attempts to manufacture a controversy amongst scientists about the factuality of evolution, one of it's major premises is that scientists who question evolution are stripped of their academic freedom. At first glance, championing the cause of the underdog may seem like a noble endeavour, but when one digs deeper into the cases of Expelled's "martyrs", it becomes clear that other factors are at play. The National Center for Science Education has launched a website to counter many of the false claims made by the film, especially with respect to the supposed martyrdom of certain Intelligent Design proponents.

The second major premise of the film is that the theory of evolution is dangerous by virtue of the fact that it was misappropriated under the Nazi regime. This angle has been criticized by many reviewers as being gratuitous, since it abuses the tragedy of the Holocaust. The implication seems to be that the teaching of evolution leads to societal ills and could set the stage for another Holocaust. This line of argument is flawed on multiple levels. Most importantly, it fails to recognize the is/ought fallacy. This is to say that science describes who we are, rather than prescribing how we ought to behave. Furthermore, it is an insult to the millions who accept evolutionary theory without subscribing to certain philosophies.

While the "academic freedom" angle was pushed heavily during the film's promotion in the United States, it appears that it's first foray into Canada will be built upon a version of the second. That is, it will aim to build a strawman of evolution based on guilt by association. The promoters of this film are disingenuously playing the race card by absurdly equivocating evolutionary theory with racism. The ample disingenuity in the invitation presented above is palpable. Firstly, it neglects to mention that the "races" Darwin refers to in the title of the Origin of Species was applicable to all organisms, not just human races specifically. Secondly, the Origin of Species is not a textbook found in every science classroom to begin with. Furthermore, Darwin lived in an overtly racist society during a time in which colonization of the "less civilized" parts of the world was ongoing. Darwin's vocabulary was not a novelty during the time. Moreover, whether or not he was a racist is immaterial as far as the science presented in his works is concerned. It would also be foolish to assume that evolutionary biology has remained static for 150 years. As future research has borne out, Darwin was right about a some things and he was clearly wrong about others. Scientists don't assume his words are gospel truth, and the majority of practising scientists certainly don't cling to any racial notions that Darwin may have shared with his peers.

As noted in the postscript of the invitation letter, there are plans for an "anti-Racism Rally" in front of the Royal Ontario Museum, which is currently hosting an exhibit to commemorate Darwin's monumental contributions to the study of biology. Creationists have their beef with evolution for theological reasons, and will go to several lengths to try and discredit it. It's important to recognize that, ultimately, such attempts must be construed as an attack on science as a whole. They may be attacking strawmen, but their actions still denigrate the integrity of science in the public eye. The Darwin Exhibit at the Royal Ontario Museum does not showcase human skulls from different races arranged to give the impression of increasing brain size, or feature a list of commandments derived from the principle of natural selection. Yet, to someone who has not seen the exhibit, seeing people on the street making unwarranted accusations of racism might suggest that something rather sinister is going on behind the walls of the museum. The tragedy is that such exercises detract from what is really being showcased, i.e. the beauty of natural processes such as evolution, and the elegance with which the theory can explain the origin of biological diversity on our planet.

UPDATE (12/06): Larry Moran has taken some pics of the huge turnout at the "Anti-Racism Rally".

The Truth(s) about Dinosaur Extinction

noreply@blogger.com (NP) — Mon, 09 Jun 2008 07:31:00 +0000

Emile of The World We Don't Live In has provided a list of alternative theories about dinosaur extinction that various parties including Big Science don't want you to know about. Somebody needs to pass on this list to Ben Stein for Expelled 2. Students need to know that there are alternative hypotheses out there!

Brains and Hairpins: What RNA structure could tell us about brain evolution

noreply@blogger.com (NP) — Sat, 07 Jun 2008 06:25:00 +0000

Protein-coding DNA makes up only a small part of our genome. The rest of it is either not transcribed, or codes for RNA that does not become translated into proteins. Some of these non-coding RNAs include transfer RNA and ribosomal RNA, both key components of the translation machinery. Recently, scientists have discovered that many of the other non-coding RNAs are small RNAs, some of which may regulate gene expression and some which may turn out to be functionless i.e. transcriptional noise.

In 2006, Pollard et al. discovered an intriguing RNA gene when screening the human genome for human accelerated regions (HARs), sequences that show accelerated evolution since the split from the chimpanzee lineage. One of these, the 118-base pair human HAR1 sequence exhibits 18 substitutions, even though this gene is highly conserved in another amniotes, with the chimpanzee and chicken sequences differing by only 2 nucleotides. The HAR1 sequence consists of two overlapping genes that transcribe in opposite directions. The forward one, HAR1F, was found to be highly expressed in the developing human and macaque neocortices, which suggest that this many be an important player in brain evolution. HAR1F is also present in the testes and ovaries, although at lower levels. One crucial step towards determining whether or not HAR1F played a role in human brain evolution would be to determine the function of the RNA transcript.

A recent paper by Artemy Beniaminov, Eric Westhof, and Alain Krol published online in the journal RNA reports findings that could be important in reaching this goal. The researchers discovered that human and chimpanzee HAR1 transcipts differ in their secondary structure, i.e. the way the molecule folds to form stems and loops (as shown in the diagram). They were able to do this by treating the RNA with molecular probes and running it on a gel to infer whether each nucleotide is part of a stem or a loop. The results provide a structural basis for variation in the function of this RNA gene - whatever it may be. Since Pollard et al. have shown that HAR1F co-expresses with reelin, a protein known to regulate cortical development, one possibility is that HAR1F regulates the expression of reelin. If future experiments can determine whether this is indeed the case, and if the different structure of HAR1F alters reelin signalling in the developing human brain, they would provide a valuable contribution to the puzzle of how our brains evolved.

Beniaminov, A., Westhof, E., Krol, A. (2008). Distinctive structures between chimpanzee and human in a brain noncoding RNA. RNA DOI: 10.1261/rna.1054608

Pollard, K.S., Salama, S.R., Lambert, N., Lambot, M., Coppens, S., Pedersen, J.S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A.D., Dehay, C., Igel, H., Ares, M., Vanderhaeghen, P., Haussler, D. (2006). An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443(7108), 167-172. DOI: 10.1038/nature05113

Bones and Molecules #2

noreply@blogger.com (NP) — Thu, 05 Jun 2008 22:04:00 +0000

I have another round-up of interesting blogposts on the various biological topics, and I've decided to make it a part of a blog-series (the first one can be found here).

Can you pick up a drop of water with tweezers?
Herman Mays writes about a recent paper in Science that describes the mechanical action by which the beaks of shorebirds known as phalaropes are able to take up their prey. MIT scientists created mechanical models based on the properties of these beaks that are able to pick up small amounts of liquids (see the video here). Phalaropes are interesting birds; you can watch a video of how they feed here.

Parasitic wasp turns caterpillars into head-banging bodyguards
The first of two well written summaries by Ed Yong that piqued my interest this week is about parasitic wasps that lay their eggs in unsuspecting caterpillars. These caterpillars then act as incubators till the wasp eggs hatch. But that's not all - when the eggs hatch, some larvae remain in the body of the debilitated caterpillar and alter its behaviour so that it acts like a sentinel for the other larvae.

The wasp that walks cockroaches
Another kind of parasitic wasp injects the brains of roaches with a venom that makes them groggy, and wasps are then able to lead them to their lair by their antennae. Researchers found that this venom does not paralyze the roach's muscles as their motor responses seem to be normal. Instead, the venom appears to affect the motivation of the roaches.

Terrestrial stalking azhdarchids, the paper
Darren Naish writes about his paper that was published last week in PLoS ONE, in which he re-evaluates the hypothesis that azhdarchids, a family of pterosaurs, were skim-feeders. He and co-author Mark Witton argue that the evidence suggests that they were terrestrial stalkers.

Nobody's Perfect - but It's a Good Thing for a Sexual Mimic

noreply@blogger.com (NP) — Wed, 04 Jun 2008 06:17:00 +0000

Last week I wrote about orchid species which attract wasps by mimicking the scent given off when caterpillars feed on leaves. It is one of the many fascinating ways in which orchids use mimicry in order to attract pollinators. In last Tuesday's Proceedings of the National Academy of Sciences, there was a paper on a different kind of mimicry. Some orchids use sexual mimicry to attract insects by tricking them into thinking that the flowers are their female counterparts. This is partly based on visual cues, whereby the flowers of the plant (the mimic) have evolved a morphology that resembles the insects (the model). More importantly though, these flowers also emit scents that mimic the sex pheromones of the pollinating insects. So the flowers release their scent, and this triggers an innate response in male insects who attempt to copulate with the flower whilst getting covered in pollen in the process. When the insect comes into the vicinity of another flower of the same species, he once again attempts to copulate and in doing so, deposits the pollen from the other flower.

One might predict that the floral scent would be refined by natural selection to optimally mimic the pheromones of the pollinators in their habitat. Researchers Nicolas Vereecken and Florian Schiestl tested this hypothesis using the bee model Colletes cunicularius and its orchid mimic Ophrys exaltata. They collected samples of the female bees and orchids from various locations across Western Europe, and they extracted and analyzed the wax from the bees and the floral scent from unpollinated orchids. The samples were analyzed for three biologically active compounds known to be detected by male bees: (Z)-7-heneicosene, (Z)-7-tricosene, and (Z)-7-pentacosene. The researchers found that while the absolute amounts of each of these three compounds was similar in both the female bees and the orchids, they differed in the relative proportions of each compound. (Z)-7-tricosene and (Z)-7-pentacosene are found in relatively higher proportions in the floral scents. Thus, there is imperfect mimicry even when the orchid scent is compared to sympatric bees, i.e. those found in the same habitat.

Vereecken and Schiestl went to a location in Cadillon, France, where O. exaltata and C. cunicularius are sympatric, in order to perform behavioural experiments. They applied scents collected from the bee or orchid samples to cylindrical plastic beads and placed them in this natural environment as dummies to see if they could attract male bees. As a metric for the attractiveness of each scent, they recorded the number of times an inspecting flight was made without contact, and the number of times contact was made for each dummy with a different scent. They applied the scents from locally collected bees and orchids, as well as those collected from foreign locations. What they found was that the local males remarkably preferred the scents of foreign female bees.

They also observed that bees prefer the floral scent to female pheromones, suggesting that it is the different proportions of the biologically active compounds that conveys a higher attractiveness. To verify this, they concocted a mixture of the female sex pheromone and added (Z)-7-tricosene and (Z)-7-pentacosene. When this concoction was applied to dummies, they found that this manipulated concoction attracted more males.

Overall, the scientists were able to determine that contrary to the hypothesis that the orchids would evolve towards perfect mimicry, imperfect mimicry is actually favoured. This is probably because males are more attracted to the pheromone cocktails of foreign females in order to promote more outbreeding. Thus the yearning for novel pheromone scents by the male bees drives the divergence of the floral scent of the orchid, resulting in imperfect mimicry. Others have hypothesized that imperfect mimicry may exist in order to attract a variety of pollinators, but this can be ruled out as C. cunicularius is the only known pollinator of O. exaltata; the alternative hypothesis presented by Vereecken and Schiestl is more plausible in this case and may also be useful in understanding the basis of imperfect mimicry in other instances.

Vereecken, N.J., Schiestl, F.P. (2008). The evolution of imperfect floral mimicry. Proceedings of the National Academy of Sciences, 105(21), 7484-7488. DOI: 10.1073/pnas.0800194105

Citrate-Eating Bugs

noreply@blogger.com (NP) — Tue, 03 Jun 2008 06:42:00 +0000

Carl Zimmer has written an excellent summary of an upcoming paper in PNAS that reports an exciting innovation in E. coli lines that have been studied in the lab for 20 years by Richard Lenski of Michigan State University. Lenski and his lab members have observed that a line of E. coli has evolved the ability to ingest citrate, something normal E. coli are not able to do. I am looking forward to reading this paper, as it presents evidence of natural selection that has been documented almost in real-time. The design of Lenski's longitudinal study ensures that he and his students will be able to thaw out the ancestors of these bacteria and perform any further experiments to identify the genetic changes behind this microbial innovation.

Fair Use Upheld

noreply@blogger.com (NP) — Tue, 03 Jun 2008 06:13:00 +0000

Yoko Ono has lost the court case against Premise Media over their alleged copyright infringement of "Imagine". The judge ruled that the use of a short clip of the song in Expelled is covered by the fair use doctrine. This means that the producers and distributors will not have any restrictions on the distribution of the film, and it is good news for those looking to save a few bucks and watch the film on DVD instead.

For Canadians who are interested in watching the film, screenwriter Kevin Miller reports on his blog that it will be released later this month.

Underwater Colonies

noreply@blogger.com (NP) — Thu, 29 May 2008 06:26:00 +0000

Greg Laden has written a brief summary of a recently published Nature paper looking at microbes inhabiting basalt rocks on the sea floor. The study found that microbes are far more abundant and diverse in this environment than previously thought, which highlights the fact that there is still a lot of biodiversity that is yet to be discovered on our own planet. You can watch a video of a lead investigator, Dr. Katrina J. Edwards talking about the group's findings here. This comes a week after the publication of a Science paper that reports the presence of prokaryotic cells over 1626 meters below the sea floor at a temperature of between 54 and 100 degrees Celsius.

The findings of the Nature paper may have implications for the early evolution of life on Earth. The abundance of life on the sea floor may suggest that life could have evolved here rather than closer to the surface.

Meanwhile, the Phoenix Mars Lander has landed on Mars' north pole, which has sent back images and will collect soil samples for analysis later this week. Scientists believe that ice lies beneath the surface of Mars, which if found would raise the possibility of the planet being suitable for life.

On a related note, oceanographer Robert Ballard gave a recent TED Talk on the exploration of our oceans. He mentions that while millions of dollars are spent every year on space exploration programs, there is still a lot of our own planet that remains undiscovered. The discovery of life teeming in unexpected places under the sea should be a justification to invest into more research on the oceanic depths. There really are two frontiers for human exploration; the space above and the space below.

To Bee Or Not To Bee: Using Mimicry to Attract Wasps

noreply@blogger.com (NP) — Mon, 26 May 2008 08:25:00 +0000

Different orchid species have evolved intriguing ways of attracting pollinators. The most common method is one where the flower has morphological structures that mimic those of other species that provide food for the pollinators. In a recent paper in Current Biology, Brodmann et al. report the use of chemical mimicry in Epipactis helleborine. The E. helleborine orchid is a wasp-flower that inhabits dark forest understories where pollinators like honey bees and butterflies are rare. Instead, wasp-flowers like E. helleborine, E. latifolia, and E. purpurata have adaptations that attract social wasps of the Vesipidae family. In The Various Contrivances by which Orchids Are Fertilised by Insects, Charles Darwin noted how wasp-flowers would only seem to attract wasps:

Although hive-bees and humble-bees of many kinds were constantly flying over the plants, I never saw a bee or any Dipterous insect visit the flowers; but in Germany Sprengel caught a fly with the pollinia of this plant attached to its back. On the other hand I have repeatedly observed the common wasp (Vespa sylvestris) sucking the nectar out of the open cup-shaped labellum. I thus saw the act of fertilisation effected by the pollen-masses being removed by the wasps, and afterwards carried attached to their foreheads to other flowers. Mr. Oxenden also informs me that a large bed of E. purpurata (which is considered by some botanists to be a distinct species, and by others a variety) was frequented by "swarms of wasps." It is very remarkable that the sweet nectar of this Epipactis should not be attractive to any kind of bee. (p.101)

The authors of this paper set out to determine how wasp-flowers are able to attract wasps. Social wasps are known to prey on caterpillars such as those of Pieris rapae. When herbivores feed on plants, the leaves often release volatile compounds known as Green-leaf volatiles (GLVs)that attract predators like wasps. Thus, the researchers hypothesized that these GLVs may be mimicked by wasp-flowers in order to attract wasps for pollination.

They were able to identify hexyl acetate, Z-3-hexenyl acetate, and Z-3-hexen-1-ol in the the scent of E. helleborine flowers using gas chromatography coupled with an electroantennographic detector (GC-EAD). The EAD is basically an apparatus which helps to detect those compounds which would be perceived by the wasps. When receptors in the antennae of insects bind to olfactory compounds, a nerve impulse is generated. Hence, the tip of an insect's antenna can be cut off and hooked to the EAD, which amplifies the electrical signal generated in response to specific odors.

The researchers determined that the same GLVs isolated in the wasp flower are released by cabbage (Brassica oleracea gemifera) infested by P. rapae caterpillars. They also discovered that these GLVs are found at a lower concentration in the scent of another species in the Epipactis genus, E. atrorubens, which relies on bees for pollination.

To confirm that the wasps were attracted to GLVs, the researchers performed a series of behavioural experiments using a Y-tube olfactometer to test the preference of the wasps for different olfactory stimuli. The researchers found that the wasps showed a preference for cabbage infested with P. rapae caterpillars as opposed to uninfested cabbage and an empty control. They also showed a preference for E. helleborine flowers, as well as a synthetic mixture of the volatile compounds and GLVs detected in the E. helleborine scent as opposed to the control. Furthermore, the behavioural tests showed that the wasps had a preference for E. helleborine flowers rather than E. atrorubens flowers. The researchers did similar experiments with honeybees (Apis mellifera) and found that the bees are not attracted to the scent of E. helleborine or GLVs.

Brodmann et al. thus show how wasp-flowers are able to attract wasps by producing GLVs, although it is still unclear why bees are not attracted to these flowers. The authors suggest that differences in the nectar of wasp-flowers may render it unsuitable for bees. Nonetheless, this is a fascinating case study of mimicry whereby a flower produces a scent that resembles the odors released by leaves infested by the prey of the pollinators.

(Picture of E. helleborine is taken by Jennifer Brodmann)

BRODMANN, J., TWELE, R., FRANCKE, W., HOLZLER, G., ZHANG, Q., AYASSE, M. (2008). Orchids Mimic Green-Leaf Volatiles to Attract Prey-Hunting Wasps for Pollination. Current Biology, 18(10), 740-744. DOI: 10.1016/j.cub.2008.04.040

Bones and molecules

noreply@blogger.com (NP) — Mon, 26 May 2008 05:36:00 +0000

Just a round-up of a few interesting articles from the blogosphere:

What’s a cell-adhesion protein like you doing in a unicellular organism like me?
Professor Olsen takes a look at cadherins, a family of proteins that are vital for cell adhesion and intercellular signalling in multicellular organisms. But recently researchers also identified cadherins in choanoflagellates, unicellular organisms that are thought to share a common ancestor with metazoans. So what do they do in these organisms? It turns out that cadherin molecules in choanoflagellates may be useful for latching on to bacteria in order to consume them. This is probably an excellent example of co-option, whereby a trait may evolve a different function.

Hatena - when two cells are better than one
Ed Yong writes about the intriguing symbiotic relationship between Hatena and Nephroselmis, as reported in a 2005 Science paper. Hatena is a unicellular organism that engulfs a specific strain of the algae Nephroselmis, which becomes an endosymbiont. Mitochondria and chloroplasts arose through endosymbiosis millions of years ago. Could Hatena provide an insight into the early stages of the evolution of these organelles?

Gerobatrachus hottoni
Nimvarid blogs about an exciting discovery of a fossil that shares both frog and salamander traits. There has been considerable debate about the phylogeny of amphibians, but Gerobatrachus hottoni should add another piece to the puzzle.

A Camptosaurus infested with dermisted beetles
The fossilized remains of an organism can tell us not only when and where it died, but also how it died or lived. Brian Switek takes a look at a recent paper which suggests that the rotting bones of a Camptosaurus may have been feasted upon by dermisted beetles, or similar organisms. Such clues may tell us something about the environment in which the dinosaurs lived; for instance, we know that today dermisted beetles live in relatively hot and humid environments and so this may indicate the sort of environment the Camptosaurus inhabited.