Primer on GFP

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

Nobel Prize for Green Fluorescent Protein

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

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

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

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

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., Schiøtt, 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

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