From DNA enzymes to cone snail venom: the work of Baldomero M. Olivera

Processivity of DNA Exonucleases (Thomas, K. R., and Olivera, B. M. (1978) J. Biol. Chem. 253, 424–429)Neuronal Calcium Channel Inhibitors. Synthesis of ω-Conotoxin GVIA and Effects on ⁴⁵Ca Uptake by Synaptosomes (Rivier, J., Galyean, R., Gray, W. R., Azimi-Zonooz, A., McIntosh, J. M., Cruz, L. J., and Olivera, B. M. (1987) J. Biol. Chem. 262, 1194–1198)The two papers being recognized here as JBC Classics speak to the journeys Baldomero “Toto” Olivera at the University of Utah has made in his life. A director of a program project funded by the National Institute of General Medical Sciences and a professor at the Howard Hughes Medical Institute, Olivera''s papers highlight how doing research in two different countries ultimately influenced his focus and contributions to molecular biology and biochemistry.Open in a separate windowBaldomero “Toto” Olivera. Photo courtesy of Olivera.Olivera began his career as a DNA biophysical chemist and enzymologist. He arrived in the United States in the 1960s to do his graduate work at the California Institute of Technology after completing a bachelor''s degree in chemistry in the Philippines. He joined the laboratory of Norman Davidson to study the biophysical chemistry of DNA. When Olivera was ready to graduate with his Ph.D. degree, Davidson suggested that Olivera go to I. Robert Lehman''s laboratory at Stanford University for his postdoctoral training. “He knew it was my intention to return to the Philippines,” recalls Olivera. Davidson felt it would be easier for Olivera to study DNA enzymology, rather than biophysical chemistry, in a Philippine academic setting because the field did not necessarily demand expensive and sophisticated instrumentation.Olivera followed his thesis advisor''s suggestion and, as a result, became an expert in DNA enzymology, including exonucleases, a large class of DNA-degrading enzymes. The first JBC paper recognized here as a Classic was published in 1978 as Olivera was starting out as an independent researcher. In it, Olivera and his first graduate student, Kirk Thomas, investigated whether or not exonuclease I, first discovered in Escherichia coli by Lehman, and other exonucleases of E. coli were processive. This was at a time when little was known about nucleic acid enzymes: restriction enzymes were just starting to gain traction, and genome sequencing was far from reality. Olivera explains that no one had given much thought to how exonucleases functioned. “The significance of this paper was that it showed that the enzymes that we examined were very different using a new parameter processivity that had never been assessed for exonucleases,” he says.Olivera and Thomas designed an assay that was based on a synthetic nucleic acid chain that contained ³H on one end and ³²P on the other. Researchers knew that exonucleases selected either the 5′- or 3′-end of the DNA to start chewing. The rationale of the Thomas and Olivera assay was that if the enzyme dissociated after every single catalytic event, one label, either the ³H or ³²P, would come off the polymer. However, if the enzyme clung to the polymer and kept chewing until the whole polymer was degraded, both radioactive labels would appear simultaneously in solution.Open in a separate windowOlivera with his first graduate student, Kirk Thomas. Photo courtesy of Olivera.Thomas and Olivera demonstrated that of the eight exonucleases they tested, only the E. coli exonuclease I and λ-exonuclease were processive, meaning that once they got started, they kept on cutting the same piece of DNA before dissociating. The others, such as the spleen and T7 exonucleases, were not processive and frequently came off the DNA.Lehman explains that at the time of this JBC paper, “methods had not yet been developed to measure quantitatively the processivity of either a DNA polymerase or a DNA exonuclease. Their paper made an important contribution to the field of DNA enzymology by describing for the first time a quantitative method for doing so and applied it to eight different DNA exonucleases, an enzymological tour de force.”The second paper highlighted as a JBC Classic was published ten years later and shows a shift in Olivera''s career. The article concerns the synthesis of a peptide found in the venom of the cone snail Conus geographus, which is indigenous to the Indo-Pacific region. All 700 types of cone snails have a special tooth that they use like a harpoon. A venom gland attached to the tooth releases the poisonous peptides to paralyze or even kill prey. These snails have to be handled with great care or not handled at all. Some can sting and cause pain like bees, but C. geographus can kill humans when it stings.There is no scientific connection between DNA enzymes and snail venom. Olivera explains that when he had returned to the Philippines as an assistant professor in the College of Medicine at the University of the Philippines, his laboratory “had absolutely no equipment. It was clear I wasn''t going to be very competitive in DNA replication [research], so we decided we''d find a project that we could start without any equipment. I collected shells as a kid, so I knew about this particular snail that killed people. I had purified enzymes as a post-doc and figured I could purify toxins by injecting them into mice, which didn''t require any equipment at all.”Olivera''s group was soon isolating and characterizing peptides from the cone snail venom. The peptides are known as conotoxins. In doing so, Olivera established the field of conotoxin research, which had a significant impact on fundamental research and medicine. For example, a peptide isolated by Olivera''s group has been approved as a drug for severe pain that cannot be relieved by morphine.Olivera had part-time appointments in the United States while maintaining his full-time position in the Philippines. He first began as a visiting associate professor at Kansas State University and later at the University at Utah. “I would spend seven or eight months in the Philippines and five or four months in the U.S,” he says. Olivera became a full-time member of the faculty at the University of Utah in the 1970s after political and economic upheaval in the Philippines over Ferdinand Marcos'' rule made Olivera decide to return full-time to the United States.Open in a separate windowConus snails. Photo courtesy of Olivera.Open in a separate windowConus snail attacks a fish. Photo courtesy of Olivera.The toxins made by the Conus snails are highly specific for particular targets in the nervous system, such as ion channels. For example, the μ-conotoxins hit sodium receptor ion channels, and ω-conotoxins (one of which, ω-GVIA, is described in this JBC Classic) bind to neuronal calcium channels to inhibit calcium uptake at the presynaptic junction and shut down biochemical signaling at certain synapses.ω-Conotoxin GVIA is a 27-amino acid peptide originally called the “shaker” peptide because it made mice shake. “A number of physiological experiments were done to suggest that it acted at synapses, potentially on calcium channels,” says Olivera. “The importance of this paper is that for the first time the peptide was chemically synthesized and became available to the whole neuroscience community.”The neuroscience community desperately needed this peptide. Up to this point, neuroscientists relied on dihydropyridines to study voltage-gated calcium channels. However, these dihydropyridines had confusing effects on neuronal voltage-gated calcium channels, which made data interpretation difficult. With ω-conotoxin GVIA as a synthetic peptide, neuroscientists now had a molecular tool that clearly targeted a very specific type of neuronal voltage-gated calcium channel.The peptide was short enough to be amenable to synthesis, and Olivera is grateful to his collaborator, Jean Rivier, who was an expert in synthesizing neuropeptides, for the successful synthesis of this peptide. The peptide had only 27 amino acids but contained three disulfide bonds, “so there were fifteen possible isomers,” recalls Olivera. “You had to get the cross-linking right to end up with the biologically active isomer.”The advantage was that Olivera and colleagues had purified the native peptide, so they could compare their synthesis attempts with the native molecule. “At the beginning, we didn''t even know what the true disulfide bonding was, so we did the work qualitatively to just show the synthetic material and native material co-eluted in a column.” The investigators later established how the disulfide bonds were arranged. Rivier, Olivera, and the rest of the team went on to show that their synthetic peptide behaved just like the natural one in inhibiting calcium entry at chicken synaptosomes and was biologically active.John Exton at Vanderbilt University says “The conotoxins have proved to be extremely important molecular probes in neuroscience in defining functional roles for many receptors and ion channels.”When the paper was published, Olivera was deluged with requests for the peptide. Rivier had been able to synthesize a sizeable amount, and because it was active at subpicomolar concentrations, a little bit of it went a long way. Olivera was able to distribute the peptide, and eventually, several commercial enterprises got into the business of producing and supplying it.“I believe there is something on the order of two thousand studies in the literature using this particular peptide,” says Olivera. “It''s interesting that there are hundreds of thousands of peptides in Conus venom that we call conotoxins. But among physiologists, if you say conotoxin, this is the peptide they think of because this is the one that''s most widely used.” In fact, points out Olivera, when the neuronal calcium channel was purified eight years later, it was actually called the conotoxin receptor.     

The puzzle of sympatry. Recent evidence supports the notion of sympatric speciation--the rise of new species in the same location--but the reasons for this phenomenon remain elusive

Sympatric speciation—the rise of new species in the absence of geographical barriers—remains a puzzle for evolutionary biologists. Though the evidence for sympatric speciation itself is mounting, an underlying genetic explanation remains elusive.For centuries, the greatest puzzle in biology was how to account for the sheer variety of life. In his 1859 landmark book, On the Origin of Species, Charles Darwin (1809–1882) finally supplied an answer: his grand theory of evolution explained how the process of natural selection, acting on the substrate of genetic mutations, could gradually produce new organisms that are better adapted to their environment. It is easy to see how adaptation to a given environment can differentiate organisms that are geographically separated; different environmental conditions exert different selective pressures on organisms and, over time, the selection of mutations creates different species—a process that is known as allopatric speciation.It is more difficult to explain how new and different species can arise within the same environment. Although Darwin never used the term sympatric speciation for this process, he did describe the formation of new species in the absence of geographical separation. “I can bring a considerable catalogue of facts,” he argued, “showing that within the same area, varieties of the same animal can long remain distinct, from haunting different stations, from breeding at slightly different seasons, or from varieties of the same kind preferring to pair together” (Darwin, 1859).It is more difficult to explain how new and different species can arise within the same environmentIn the 1920s and 1930s, however, allopatric speciation and the role of geographical isolation became the focus of speciation research. Among those leading the charge was Ernst Mayr (1904–2005), a young evolutionary biologist, who would go on to influence generations of biologists with his later work in the field. William Baker, head of palm research at the Royal Botanic Gardens, Kew in Richmond, UK, described Mayr as “one of the key figures to crush sympatric speciation.” Frank Sulloway, a Darwin Scholar at the Institute of Personality and Social Research at the University of California, Berkeley, USA, similarly asserted that Mayr''s scepticism about sympatry was central to his career.The debate about sympatric and allopatric speciation has livened up since Mayr''s death…Since Mayr''s death in 2005, however, several publications have challenged the notion that sympatric speciation is a rare exception to the rule of allopatry. These papers describe examples of both plants and animals that have undergone speciation in the same location, with no apparent geographical barriers to explain their separation. In these instances, a single ancestral population has diverged to the extent that the two new species cannot produce viable offspring, despite the fact that their ranges overlap. The debate about sympatric and allopatric speciation has livened up since Mayr''s death, as Mayr''s influence over the field has waned and as new tools and technologies in molecular biology have become available.Sulloway, who studied with Mayr at Harvard University, in the late 1960s and early 1970s, notes that Mayr''s background in natural history and years of fieldwork in New Guinea and the Solomon Islands contributed to his perception that the bulk of the data supported allopatry. “Ernst''s early career was in many ways built around that argument. It wasn''t the only important idea he had, but he was one of the strong proponents of it. When an intellectual stance exists where most people seem to have gotten it wrong, there is a tendency to sort of lay down the law,” Sulloway said.Sulloway also explained that Mayr “felt that botanists had basically led Darwin astray because there is so much evidence of polyploidy in plants and Darwin turned in large part to the study of botany and geographical distribution in drawing evidence in The Origin.” Indeed, polyploidization is common in plants and can lead to ‘instantaneous'' speciation without geographical barriers.In February 2006, the journal Nature simultaneously published two papers that described sympatric speciation in animals and plants, reopening the debate. Axel Meyer, a zoologist and evolutionary biologist at the University of Konstanz, Germany, demonstrated with his colleagues that sympatric speciation has occurred in cichlid fish in Lake Apoyo, Nicaragua (Barluenga et al, 2006). The researchers claimed that the ancestral fish only seeded the crater lake once; from this, new species have evolved that are distinct and reproductively isolated. Meyer''s paper was broadly supported, even by critics of sympatric speciation, perhaps because Mayr himself endorsed sympatric speciation among the cichlids in his 2001 book What Evolution Is. “[Mayr] told me that in the case of our crater lake cichlids, the onus of showing that it''s not sympatric speciation lies with the people who strongly believe in only allopatric speciation,” Meyer said.…several scientists involved in the debate think that molecular biology could help to eventually resolve the issueThe other paper in Nature—by Vincent Savolainen, a molecular systematist at Imperial College, London, UK, and colleagues—described the sympatric speciation of Howea palms on Lord Howe Island (Fig 1), a minute Pacific island paradise (Savolainen et al, 2006a). Savolainen''s research had originally focused on plant diversity in the gesneriad family—the best known example of which is the African violet—while he was in Brazil for the Geneva Botanical Garden, Switzerland. However, he realized that he would never be able prove the occurrence of sympatry within a continent. “It might happen on a continent,” he explained, “but people will always argue that maybe they were separated and got together after. […] I had to go to an isolated piece of the world and that''s why I started to look at islands.”Open in a separate windowFigure 1Lord Howe Island. Photo: Ian Hutton.He eventually heard about Lord Howe Island, which is situated just off the east coast of Australia, has an area of 56 km² and is known for its abundance of endemic palms (Sidebar A). The palms, Savolainen said, were an ideal focus for sympatric research: “Palms are not the most diverse group of plants in the world, so we could make a phylogeny of all the related species of palms in the Indian Ocean, southeast Asia and so on.”…the next challenges will be to determine which genes are responsible for speciation, and whether sympatric speciation is common

Sidebar A | Research in paradise

Alexander Papadopulos is no Tarzan of the Apes, but he has spent a couple months over the past two years aloft in palm trees hugging rugged mountainsides on Lord Howe Island, a Pacific island paradise and UNESCO World Heritage site.Papadopulos—who is finishing his doctorate at Imperial College London, UK—said the views are breathtaking, but the work is hard and a bit treacherous as he moves from branch to branch. “At times, it can be quite hairy. Often you''re looking over a 600-, 700-metre drop without a huge amount to hold onto,” he said. “There''s such dense vegetation on most of the steep parts of the island. You''re actually climbing between trees. There are times when you''re completely unsupported.”Papadopulos typically spends around 10 hours a day in the field, carrying a backpack and utility belt with a digital camera, a trowel to collect soil samples, a first-aid kit, a field notebook, food and water, specimen bags, tags to label specimens, a GPS device and more. After several days in the field, he spends a day working in a well-equipped field lab and sleeping in the quarters that were built by the Lord Howe governing board to accommodate the scientists who visit the island on various projects. Papadopulos is studying Lord Howe''s flora, which includes more than 200 plant species, about half of which are indigenous.Vincent Savolainen said it takes a lot of planning to get materials to Lord Howe: the two-hour flight from Sydney is on a small plane, with only about a dozen passengers on board and limited space for equipment. Extra gear—from gardening equipment to silica gel and wood for boxes in which to dry wet specimens—arrives via other flights or by boat, to serve the needs of the various scientists on the team, including botanists, evolutionary biologists and ecologists.Savolainen praised the well-stocked researcher station for visiting scientists. It is run by the island board and situated near the palm nursery. It includes one room for the lab and another with bunks. “There is electricity and even email,” he said. Papadoupulos said only in the past year has the internet service been adequate to accommodate video calls back home.Ian Hutton, a Lord Howe-based naturalist and author, who has lived on the island since 1980, said the island authorities set limits on not only the number of residents—350—but also the number of visitors at one time—400—as well as banning cats, to protect birds such as the flightless wood hen. He praised the Imperial/Kew group: “They''re world leaders in their field. And they''re what I call ‘Gentlemen Botanists''. They''re very nice people, they engage the locals here. Sometimes researchers might come here, and they''re just interested in what they''re doing and they don''t want to share what they''re doing. Not so with these people. Savolainen said his research helps the locals: “The genetics that we do on the island are not only useful to understand big questions about evolution, but we also always provide feedback to help in its conservation efforts.”Yet, in Savolainen''s opinion, Mayr''s influential views made it difficult to obtain research funding. “Mayr was a powerful figure and he dismissed sympatric speciation in textbooks. People were not too keen to put money on this,” Savolainen explained. Eventually, the Leverhulme Trust (London, UK) gave Savolainen and Baker £70,000 between 2003–2005 to get the research moving. “It was enough to do the basic genetics and to send a research assistant for six months to the island to do a lot of natural history work,” Savolainen said. Once the initial results had been processed, the project received a further £337,000 from the British Natural Environment Research Council in 2008, and €2.5 million from the European Research Council in 2009.From the data collected on Lord Howe Island, Savolainen and his team constructed a dated phylogenetic tree showing that the two endemic species of the palm Howea (Arecaceae; Fig 2) are sister taxa. From their tree, the researchers were able to establish that the two species—one with a thatch of leaves and one with curly leaves—diverged long after the island was formed 6.9 million years ago. Even where they are found in close proximity, the two species cannot interbreed as they flower at different times.Open in a separate windowFigure 2The two species of Howea palm. (A) Howea fosteriana (Kentia palm). (B) Howea belmoreana. Photos: William Baker, Royal Botanical Gardens, Kew, Richmond, UK.According to the researchers, the palm speciation probably occurred owing to the different soil types in which the plants grow. Baker explained that there are two soil types on Lord Howe—the older volcanic soil and the younger calcareous soils. The Kentia palm grows in both, whereas the curly variety is restricted to the volcanic soil. These soil types are closely intercalated—fingers and lenses of calcareous soils intrude into the volcanic soils in lowland Lord Howe Island. “You can step over a geological boundary and the palms in the forest can change completely, but they remain extremely close to each other,” Baker said. “What''s more, the palms are wind-pollinated, producing vast amounts of pollen that blows all over the place during the flowering season—people even get pollen allergies there because there is so much of the stuff.” According to Savolainen, that the two species have different flowering times is a “way of having isolation so that they don''t reproduce with each other […] this is a mechanism that evolved to allow other species to diverge in situ on a few square kilometres.”According to Baker, the absence of a causative link has not been demonstrated between the different soils and the altered flowering times, “but we have suggested that at the time of speciation, perhaps when calcareous soils first appeared, an environmental effect may have altered the flowering time of palms colonising the new soil, potentially causing non-random mating and kicking off speciation. This is just a hypothesis—we need to do a lot more fieldwork to get to the bottom of this,” he said. What is clear is that this is not allopatric speciation, as “the micro-scale differentiation in geology and soil type cannot create geographical isolation”, said Baker.…although molecular data will add to the debate, it will not settle it aloneThe results of the palm research caused something of a splash in evolutionary biology, although the study was not without its critics. Tod Stuessy, Chair of the Department of Systematic and Evolutionary Botany at the University of Vienna, Austria, has dealt with similar issues of divergence on Chile''s Juan Fernández Islands—also known as the Robinson Crusoe Islands—in the South Pacific. From his research, he points out that on old islands, large ecological areas that once separated species—and caused allopatric speciation—could have since disappeared, diluting the argument for sympatry. “There are a lot of cases [in the Juan Fernández Islands] where you have closely related species occurring in the same place on an island, even in the same valley. We never considered that they had sympatric origins because we were always impressed by how much the island had been modified through time,” Stuessy said. “What [the Lord Howe researchers] really didn''t consider was that Lord Howe Island could have changed a lot over time since the origins of the species in question.” It has also been argued that one of the palm species on Lord Howe Island might have evolved allopatrically on a now-sunken island in the same oceanic region.In their response to a letter from Stuessy, Savolainen and colleagues argued that erosion on the island has been mainly coastal and equal from all sides. “Consequently, Quaternary calcarenite deposits, which created divergent ecological selection pressures conducive to Howea species divergence, have formed evenly around the island; these are so closely intercalated with volcanic rocks that allopatric speciation due to ecogeographic isolation, as Stuessy proposes, is unrealistic” (Savolainen et al, 2006b). Their rebuttal has found support in the field. Evolutionary biologist Loren Rieseberg at the University of British Columbia in Vancouver, Canada, said: “Basically, you have two sister species found on a very small island in the middle of the ocean. It''s hard to see how one could argue anything other than they evolved there. To me, it would be hard to come up with a better case.”Whatever the reality, several scientists involved in the debate think that molecular biology could help to eventually resolve the issue. Savolainen said that the next challenges will be to determine which genes are responsible for speciation, and whether sympatric speciation is common. New sequencing techniques should enable the team to obtain a complete genomic sequence for the palms. Savolainen said that next-generation sequencing is “a total revolution.” By using sequencing, he explained that the team, “want to basically dissect exactly what genes are involved and what has happened […] Is it very special on Lord Howe and for this palm, or is [sympatric speciation] a more general phenomenon? This is a big question now. I think now we''ve found places like Lord Howe and [have] tools like the next-gen sequencing, we can actually get the answer.”Determining whether sympatric speciation occurs in animal species will prove equally challenging, according to Meyer. His own lab, among others, is already looking for ‘speciation genes'', but this remains a tricky challenge. “Genetic models […] argue that two traits (one for ecological specialisation and another for mate choice, based on those ecological differences) need to become tightly linked on one chromosome (so that they don''t get separated, often by segregation or crossing over). The problem is that the genetic basis for most ecologically relevant traits are not known, so it would be very hard to look for them,” Meyer explained. “But, that is about to change […] because of next-generation sequencing and genomics more generally.”Many researchers who knew Mayr personally think he would have enjoyed the challenge to his viewsOthers are more cautious. “In some situations, such as on isolated oceanic islands, or in crater lakes, molecular phylogenetic information can provide strong evidence of sympatric speciation. It also is possible, in theory, to use molecular data to estimate the timing of gene flow, which could help settle the debate,” Rieseberg said. However, he cautioned that although molecular data will add to the debate, it will not settle it alone. “We will still need information from historical biogeography, natural history, phylogeny, and theory, etc. to move things forward.”Many researchers who knew Mayr personally think he would have enjoyed the challenge to his views. “I can only imagine that it would''ve been great fun to engage directly with him [on sympatry on Lord Howe],” Baker said. “It''s a shame that he wasn''t alive to comment on [our paper].” In fact, Mayr was not really as opposed to sympatric speciation as some think. “If one is of the opinion that Mayr opposed all forms of sympatric speciation, well then this looks like a big swing back the other way,” Sulloway commented. “But if one reads Mayr carefully, one sees that he was actually interested in potential exceptions and, as best he could, chronicled which ones he thought were the best candidates.”Mayr''s opinions aside, many biologists today have stronger feelings against sympatric speciation than he did himself in his later years, Meyer added. “I think that Ernst was more open to the idea of sympatric speciation later in his life. He got ‘softer'' on this during the last two of his ten decades of life that I knew him. I was close to him personally and I think that he was much less dogmatic than he is often made out to be […] So, I don''t think that he is spinning in his grave.” Mayr once told Sulloway that he liked to take strong stances, precisely so that other researchers would be motivated to try to prove him wrong. “If they eventually succeeded in doing so, Mayr felt that science was all the better for it.”? Open in a separate windowAlex Papadopulos and Ian Hutton doing fieldwork on a very precarious ridge on top of Mt. Gower. Photo: William Baker, Royal Botanical Gardens, Kew, Richmond, UK.     

How the Glycine and GABA Receptors Were Purified

Purification by Affinity Chromatography of the Glycine Receptor of Rat Spinal Cord (Pfeiffer, F., Graham, D., and Betz, H. (1982) J. Biol. Chem. 257, 9389–9393)A γ-Aminobutyric Acid/Benzodiazepine Receptor Complex of Bovine Cerebral Cortex (Sigel, E., Stephenson, F. A., Mamalaki, C., and Barnard, E. A. (1983) J. Biol. Chem. 258, 6965–6971)In 1982, two papers appeared in the Journal of Biological Chemistry that laid the foundation for our current understanding of certain molecular aspects of neurotransmission. Eric A. Barnard of the Imperial College of Science and Technology in the United Kingdom led a team to purify the first receptor for γ-aminobutyric acid (GABA; which later became known as the GABA_A receptor) from bovine brain samples (1). In Germany, Heinrich Betz at the Max Planck Institute of Psychiatry and his team purified the glycine receptor from rat spinal cord (2). The biochemical purification of these proteins eventually led to the cloning of their genes; the analysis of the genes revealed the existence of the Cys loop ligand-gated ion channel superfamily of neurotransmitters.By the early 1980s, the nicotinic acetylcholine receptor was the only neuronal ion channel that was understood in some detail, simply because it was plentiful in the organs of electric eels and fish and easy to purify. “There was very little other information and molecular detail about other neurotransmitter receptors,” explains F. Anne Stephenson at University College London, who was a member of the Barnard team. For this reason, researchers were hotly pursuing the purification of other neurotransmitter receptors.Both the glycine and GABA receptors are ligand-gated ion channels that conduct chloride ions. When glycine and GABA bind to their respective receptors, the channels open up to allow chloride ions into the neuron. The ions cause the neuron to hyperpolarize and be less willing to undergo an action potential, so the glycine and GABA receptors are also known as inhibitory receptors.The introduction of radioligand binding activity assays in the 1970s allowed researchers to measure the activity of neurotransmitter receptors in biochemical preparations. Researchers radiolabeled a molecule that bound to a receptor and tracked the radioactive signal to detect the receptor. The investigators on the two JBC papers here coupled the radioligand binding assay with affinity chromatography. Because a receptor naturally bound to its ligand, “you could use that property to purify the protein and study it in the test tube,” explains Richard Olsen, a molecular neuroscientist at the University of California at Los Angeles who was not affiliated with the two papers.The Barnard and Betz teams knew it was going to be impossible to get the tiny molecules of radiolabeled GABA and glycine molecules on appropriate purification columns without affecting their structure and abilities to bind to the receptors, so they took another tack and used other molecules that bound to the receptors. For example, the poison strychnine binds to the glycine receptor with nanomolar affinity. The Betz team attached radiolabeled strychnine to beads (Fig. 1). They poured rat spinal cord preparations solubilized in detergent over the beads so that only the glycine receptor bound. After washing away all of the unbound material, the researchers eluted the purified receptor from the beads with glycine and cleaned up the preparation to get the pure protein. A similar approach was taken with the purification of the GABA receptor from bovine brain, for which the Barnard team used a benzodiazepine, a class of neuroactive molecules that include the famous Valium, on their purification column (Fig. 2). They used a radiolabeled benzodiazepine for detecting the GABA receptors after the purification process.Open in a separate windowFIGURE 1.The Barnard team used a radiolabeled benzodiazepine for detecting the GABA receptors after the purification process.Open in a separate windowFIGURE 2.The Betz team attached radiolabeled strychnine to beads to pull out the glycine receptor from rat spinal cord preparations.The purified proteins revealed that the receptors were composed of multiple subunits, but as time and further research showed, all of the details in the two papers were not accurate. For the GABA receptor, Barnard''s group reported two bands on SDS-polyacrylamide gels. These two polypeptides were used to obtain protein sequence, which then led to the cloning of the GABA receptor. However, molecular neuroscientists soon learned that the GABA receptor family actually consists of 19 different polypeptides classified into groups such as α, β, and γ. These polypeptides combine in different ways to form heteropentamers that result in various GABA receptor subtypes.For the glycine receptor, Betz''s group observed three polypeptides on a SDS-polyacrylamide gel at 48, 58, and 93 kDa, but research later showed that the 93-kDa band was a different protein called gephyrin. The protein is important because it “forms a matrix in the synaptic region to cluster receptor proteins together,” Olsen says. “Gephyrin was another breakthrough step in understanding neurotransmitter receptors that just happened to co-purify with the receptor [in the Betz study] because it binds the receptor tightly.”The purification of the two receptors led to the cloning of their genes in 1987 (3, 4). Peter Seeburg, now at the Max Planck Institute for Medical Research in Germany, was enlisted by Barnard for the GABA_A receptor gene cloning project. Seeburg explains that the cloning approach for the two receptors was similar. The proteins were broken into fragments by peptidases and cyanogen bromide. The small peptide fragments were sequenced. From the amino acid sequence, the researchers created complementary oligonucleotide probes. They then used the probes to screen cDNA libraries to find the gene that encoded the protein fragment.Stephenson points out that the two JBC papers “had no functional data to show that they were actually ion channels,” but with the cloning of the genes, two avenues of research were now possible. First, the individual genes for the GABA and glycine receptors were coexpressed in Xenopus oocytes and analyzed by electrophysiology to prove the receptors were bona fide ion channels that conducted chloride ions. Second, the clones revealed the relationship between the ion channels.Both glycine and GABA receptors are inhibitory chloride channels, so it was logical to expect them to be similar. However, when the researchers extended the sequence alignment to the nicotinic acetylcholine receptor, which conducts sodium ions, all three receptors had similar predictions in the number of membrane-spanning regions. Olsen says, “The amazing outcome was that the GABA and glycine receptors are related to each other in a family, and they are also in the same superfamily of genes as the nicotinic acetylcholine receptor.”The three receptors bore similarities in their transmembrane domains but also had a conserved N-terminal motif called a Cys loop. For this reason, the receptor class is sometimes referred to as the Cys loop ligand-gated ion channel superfamily.Both Olsen and Seeburg point out that these two papers and the subsequent cloning papers were the last of their kind. The two JBC papers represent “a superhuman effort to purify these proteins that took years,” says Olsen. “It''s fair to say, after these were done and the protein sequences were used to identify the clones, almost nobody ever did that [approach] again. The technology had advanced so much that we didn''t need to do protein purifications in order to clone.” Molecular biologists could now use homologies to pull out related sequences and exploit functional expression of cDNA and mRNA libraries.Seeburg says that the GABA and glycine receptor purification and cloning stories reveal how resourceful nature is. “The interesting lesson, especially for the GABA_A receptor, holds true for most of these ligand-gated ion channels. The lesson is that you have a single neurotransmitter like GABA but then you have a whole plethora of receptors that respond to the same neurotransmitter in different ways.”     

Ligand Binding in Hemoglobin: the Work of Quentin H. Gibson

Oxygen Binding and Subunit Interaction of Hemoglobin in Relation to the Two-state Model(Gibson, Q. H., and Edelstein, S. J. (1987) J. Biol. Chem. 262, 516–519)Ligand Recombination to the α and β Subunits of Human Hemoglobin(Olson, J. S., Rohlfs, R. J., and Gibson, Q. H. (1987) J. Biol. Chem. 262, 12930–12938)Quentin Howieson Gibson was born in Aberdeen, Scotland in 1918. He attended Queen''s University Belfast and received his M.B., Ch.B. degree in 1941, his M.D. in 1944, and his Ph.D. in 1946. After graduating, he became a lecturer in the Department of Physiology at the University of Sheffield and worked his way up to become Professor and Head of the Department of Biochemistry by 1955.Open in a separate windowQuentin H. GibsonIn 1963, Gibson came to the U.S. and joined the faculty of the Graduate School of Medicine at the University of Pennsylvania as a Professor of Physiology. He remained at Penn until 1965 when he became the Greater Philadelphia Professor of Biochemistry, Molecular and Cell Biology at Cornell University. In 1996, Gibson joined the Department of Biochemistry and Cell Biology at Rice University.Gibson is probably best known for his research on the structure and function of hemoglobin. The hemoglobin molecule consists of four globular protein subunits, each of which contains a heme group that can bind to one molecule of oxygen. The binding of oxygen to hemoglobin is cooperative, the first bound oxygen alters the shape of the molecule to increase the binding affinity of the additional subunits. Conversely, hemoglobin''s oxygen binding capacity is decreased in the presence of carbon monoxide because both gases compete for the same binding sites on hemoglobin, carbon monoxide binding preferentially in place of oxygen.Gibson started his hemoglobin studies in graduate school, submitting a thesis titled “Methaemoglobin,” in which he studied the form of hemoglobin where the iron in the heme group is in the Fe³⁺ state rather than the Fe²⁺ state and is thus unable to carry oxygen. He followed this up with research on familial idiopathic methemoglobinemia, a hereditary hematological disease in which hemoglobin is unable to bind to oxygen, causing dyspnea and fatigue after physical exertion. He was able to identify the pathway involved in the reduction of methemoglobin (1), thereby describing the first hereditary disorder involving an enzyme deficiency. As a result, the disease was named “Gibson''s syndrome.” Since then, Gibson has made numerous additional contributions to the study of hemoglobin, some of which are detailed in the two Journal of Biological Chemistry (JBC) Classics reprinted here.In the first Classic, Gibson and Stuart J. Edelstein look at the oxygen binding and subunit interaction in hemoglobin. In 1965, Jacques Monod, Jeffries Wyman, and Jean-Pierre Changeux proposed a model which stated that proteins that exhibit cooperativity can exist in only two conformational states, and the equilibrium between these two states is modified by binding of a ligand, oxygen in the case of hemoglobin (2). This became known as the “concerted” or the “MWC” model, for Monod, Wyman, and Changeux. (More information on Wyman''s research on protein chemistry and allosterism can be found in his JBC Classic (3).)By the mid-1980s, several groups had found evidence that challenged this model as it related to the mechanistic basis of ligand binding by hemoglobin. For example, Frederick C. Mills and Gary K. Ackers reported that the subunit interactions of hemoglobin decreased on binding of the fourth molecule of oxygen to hemoglobin (4). The effect, which they called “quaternary enhancement,” was incompatible with the two-state MWC allosteric model. In the first Classic, Gibson and Edelstein measured the free energy of binding of the fourth oxygen molecule and compared their result of −8.6 kcal/mol with Mills and Acker''s result of −9.3 kcal/mol. Gibson''s smaller value was consistent with other values found in the literature, and it also allowed reasonable representation of the equilibrium curve using the two-state model without invoking quaternary enhancement.In the second JBC Classic, Gibson looks at ligand binding in human hemoglobin. This paper was an extension of an analysis Gibson had done the previous year on ligand rebinding to sperm whale myoglobin (5). In the paper reprinted here, Gibson and his colleagues explored the rebinding of CO, O₂, NO, methyl, ethyl, n-propyl, and n-butyl isocyanide to the isolated α- and β-chains of hemoglobin as well as the intact molecule. From these experiments the researchers were able to determine the differences between the overall rate constants of the two hemoglobin subunits as well as the differences in binding of the various ligands.In recognition of his contributions to science, Gibson has earned many honors including memberships in the Royal Society of London, the National Academy of Sciences, and the American Association for the Advancement of Science. He served as an Associate Editor for the JBC from 1975 to 1994.     

Bit by bit: the Darwinian basis of life

All known examples of life belong to the same biology, but there is increasing enthusiasm among astronomers, astrobiologists, and synthetic biologists that other forms of life may soon be discovered or synthesized. This enthusiasm should be tempered by the fact that the probability for life to originate is not known. As a guiding principle in parsing potential examples of alternative life, one should ask: How many heritable “bits” of information are involved, and where did they come from? A genetic system that contains more bits than the number that were required to initiate its operation might reasonably be considered a new form of life.Thanks to a combination of ground- and space-based astronomical observations, the number of confirmed extrasolar planets will soon exceed 1,000. An increasing number of these will be said to lie within the “habitable zone” and even be pronounced as “Earth-like.” Within a decade there will be observational data regarding the atmospheric composition of some of those planets, and just maybe those data will indicate something funny going on—something well outside the state of chemical equilibrium—on a potentially hospitable planet. Perhaps our astronomy colleagues should be forgiven for their enthusiasm in declaring that humanity is on the brink of discovering alien life.But haven''t we heard this before? Didn''t President Clinton announce in 1996 that a Martian meteorite recovered in Antarctica [1] “speaks of the possibility of life” on Mars? (No, it turned out to be mineralic artifacts.) Wasn''t some “alien” arsenic-based life discovered recently in Mono Lake, California [2]? (No, it''s a familiar proteobacterium struggling to survive in a toxic environment.) Didn''t Craig Venter and his colleagues recently create a synthetic bacterial cell [3], “the first self-replicating species we''ve had on the planet whose parent is a computer”? (No, its parent is Mycoplasma mycoides and its genome was dutifully reconstructed through DNA synthesis and PCR amplification.)Why are we so confused (or so lonely) that we have such trouble distinguishing life from non-life and distinguishing our biology from another? A key limitation is that we know of only one life form, causing us to regard life from that singular perspective (Figure 1). We see life as cellular, with a nucleic acid genome that is translated to a protein machinery. Life self-reproduces, transmits heritable information to its progeny, and undergoes Darwinian evolution based on natural selection. Life captures high-energy starting materials and converts them to lower-energy products to drive metabolic processes. Life exists on at least one temperate, rocky planet, where it has persisted for about four billion years. There are likely to be tens of thousands of “habitable” planets within a thousand light years of Earth, and more than a billion such planets in our galaxy, so surely (say the astronomers) we are not alone.Open in a separate windowFigure 1Phylogenetic tree of life based on small-subunit ribosomal RNA sequences, showing representative species from each of the three kingdoms (compiled by Pace [11]).The root of the tree is indicated by a horizontal line. The locations on the tree of Halomonas sp. (GFAJ-1) [2] and Mycoplasma mycoides (JCVI-syn1.0) [3] are indicated by black circles adjacent to Escherichia and Bacillus, respectively.     

It's life, but just as we know it

A consensus definition of life remains elusiveIn July this year, the Phoenix Lander robot—launched by NASA in 2007 as part of the Phoenix mission to Mars—provided the first irrefutable proof that water exists on the Red Planet. “We''ve seen evidence for this water ice before in observations by the Mars Odyssey orbiter and in disappearing chunks observed by Phoenix […], but this is the first time Martian water has been touched and tasted,” commented lead scientist William Boynton from the University of Arizona, USA (NASA, 2008). The robot''s discovery of water in a scooped-up soil sample increases the probability that there is, or was, life on Mars.Meanwhile, the Darwin project, under development by the European Space Agency (ESA; Paris, France; www.esa.int/science/darwin), envisages a flotilla of four or five free-flying spacecraft to search for the chemical signatures of life in 25 to 50 planetary systems. Yet, in the vastness of space, to paraphrase the British astrophysicist Arthur Eddington (1822–1944), life might be not only stranger than we imagine, but also stranger than we can imagine. The limits of our current definitions of life raise the possibility that we would not be able to recognize an extra-terrestrial organism.Back on Earth, molecular biologists—whether deliberately or not—are empirically tackling the question of what is life. Researchers at the J Craig Venter Institute (Rockville, MD, USA), for example, have synthesized an artificial bacterial genome (Gibson et al, 2008). Others have worked on ‘minimal cells'' with the aim of synthesizing a ‘bioreactor'' that contains the minimum of components necessary to be self-sustaining, reproduce and evolve. Some biologists regard these features as the hallmarks of life (Luisi, 2007). However, to decide who is first in the ‘race to create life'' requires a consensus definition of life itself. “A definition of the precise boundary between complex chemistry and life will be critical in deciding which group has succeeded in what might be regarded by the public as the world''s first theology practical,” commented Jamie Davies, Professor of Experimental Anatomy at the University of Edinburgh, UK.For most biologists, defining life is a fascinating, fundamental, but largely academic question. It is, however, crucial for exobiologists looking for extra-terrestrial life on Mars, Jupiter''s moon Europa, Saturn''s moon Titan and on planets outside our solar system.In their search for life, exobiologists base their working hypothesis on the only example to hand: life on Earth. “At the moment, we can only assume that life elsewhere is based on the same principles as on Earth,” said Malcolm Fridlund, Secretary for the Exo-Planet Roadmap Advisory Team at the ESA''s European Space Research and Technology Centre (Noordwijk, The Netherlands). “We should, however, always remember that the universe is a peculiar place and try to interpret unexpected results in terms of new physics and chemistry.”The ESA''s Darwin mission will, therefore, search for life-related gases such as carbon dioxide, water, methane and ozone in the atmospheres of other planets. On Earth, the emergence of life altered the balance of atmospheric gases: living organisms produced all of the Earth'' oxygen, which now accounts for one-fifth of the atmosphere. “If all life on Earth was extinguished, the oxygen in our atmosphere would disappear in less than 4 million years, which is a very short time as planets go—the Earth is 4.5 billion years old,” Fridlund said. He added that organisms present in the early phases of life on Earth produced methane, which alters atmospheric composition compared with a planet devoid of life.Although the Darwin project will use a pragmatic and specific definition of life, biologists, philosophers and science-fiction authors have devised numerous other definitions—none of which are entirely satisfactory. Some are based on basic physiological characteristics: a living organism must feed, grow, metabolize, respond to stimuli and reproduce. Others invoke metabolic definitions that define a living organism as having a distinct boundary—such as a membrane—which facilitates interaction with the environment and transfers the raw materials needed to maintain its structure (Wharton, 2002). The minimal cell project, for example, defines cellular life as “the capability to display a concert of three main properties: self-maintenance (metabolism), reproduction and evolution. When these three properties are simultaneously present, we will have a full fledged cellular life” (Luisi, 2007). These concepts regard life as an emergent phenomenon arising from the interaction of non-living chemical components.Cryptobiosis—hidden life, also known as anabiosis—and bacterial endospores challenge the physiological and metabolic elements of these definitions (Wharton, 2002). When the environment changes, certain organisms are able to undergo cryptobiosis—a state in which their metabolic activity either ceases reversibly or is barely discernible. Cryptobiosis allows the larvae of the African fly Polypedilum vanderplanki to survive desiccation for up to 17 years and temperatures ranging from −270 °C (liquid helium) to 106 °C (Watanabe et al, 2002). It also allows the cysts of the brine shrimp Artemia to survive desiccation, ultraviolet radiation, extremes of temperature (Wharton, 2002) and even toyshops, which sell the cysts as ‘sea monkeys''. Organisms in a cryptobiotic state show characteristics that vary markedly from what we normally consider to be life, although they are certainly not dead. “[C]ryptobiosis is a unique state of biological organization”, commented James Clegg, from the Bodega Marine Laboratory at the University of California (Davies, CA, USA), in an article in 2001 (Clegg, 2001). Bacterial endospores, which are the “hardiest known form of life on Earth” (Nicholson et al, 2000), are able to withstand almost any environment—perhaps even interplanetary space. Microbiologists isolated endospores of strict thermophiles from cold lake sediments and revived spores from samples some 100,000 years old (Nicholson et al, 2000).…life might be not only stranger than we imagine, but also stranger than we can imagineAnother problem with the definitions of life is that these can expand beyond biology. The minimal cell project, for example, in common with most modern definitions of life, encompass the ability to undergo Darwinian evolution (Wharton, 2002). “To be considered alive, the organism needs to be able to undergo extensive genetic modification through natural selection,” said Professor Paul Freemont from Imperial College London, UK, whose research interests encompass synthetic biology. But the virtual ‘organisms'' in computer simulations such as the Game of Life (www.bitstorm.org/gameoflife) and Tierra (http://life.ou.edu/tierra) also exhibit life-like characteristics, including growth, death and evolution—similar to robots and other artifical systems that attempt to mimic life (Guruprasad & Sekar, 2006). “At the moment, we have some problems differentiating these approaches from something biologists consider [to be] alive,” Fridlund commented.…to decide who is first in the ‘race to create life'' requires a consensus definition of lifeBoth the genetic code and all computer-programming languages are means of communicating large quantities of codified information, which adds another element to a comprehensive definition of life. Guenther Witzany, an Austrian philosopher, has developed a “theory of communicative nature” that, he claims, differentiates biotic and abiotic life. “Life is distinguished from non-living matter by language and communication,” Witzany said. According to his theory, RNA and DNA use a ‘molecular syntax'' to make sense of the genetic code in a manner similar to language. This paragraph, for example, could contain the same words in a random order; it would be meaningless without syntactic and semantic rules. “The RNA/DNA language follows syntactic, semantic and pragmatic rules which are absent in [a] random-like mixture of nucleic acids,” Witzany explained.Yet, successful communication requires both a speaker using the rules and a listener who is aware of and can understand the syntax and semantics. For example, cells, tissues, organs and organisms communicate with each other to coordinate and organize their activities; in other words, they exchange signals that contain meaning. Noradrenaline binding to a β-adrenergic receptor in the bronchi communicates a signal that says ‘dilate''. “If communication processes are deformed, destroyed or otherwise incorrectly mediated, both coordination and organisation of cellular life is damaged or disturbed, which can lead to disease,” Witzany added. “Cellular life also interprets abiotic environmental circumstances—such as the availability of nutrients, temperature and so on—to generate appropriate behaviour.”Nonetheless, even definitions of life that include all the elements mentioned so far might still be incomplete. “One can make a very complex definition that covers life on the Earth, but what if we find life elsewhere and it is different? My opinion, shared by many, is that we don''t have a clue of how life arose on Earth, even if there are some hypotheses,” Fridlund said. “This underlies many of our problems defining life. Since we do not have a good minimum definition of life, it is hard or impossible to find out how life arose without observing the process. Nevertheless, I''m an optimist who believes the universe is understandable with some hard work and I think we will understand these issues one day.”Both synthetic biology and research on organisms that live in extreme conditions allow biologists to explore biological boundaries, which might help them to reach a consensual minimum definition of life, and understand how it arose and evolved. Life is certainly able to flourish in some remarkably hostile environments. Thermus aquaticus, for example, is metabolically optimal in the springs of Yellowstone National Park at temperatures between 75 °C and 80 °C. Another extremophile, Deinococcus radiodurans, has evolved a highly efficient biphasic system to repair radiation-induced DNA breaks (Misra et al, 2006) and, as Fridlund noted, “is remarkably resistant to gamma radiation and even lives in the cooling ponds of nuclear reactors.”In turn, synthetic biology allows for a detailed examination of the elements that define life, including the minimum set of genes required to create a living organism. Researchers at the J Craig Venter Institute, for example, have synthesized a 582,970-base-pair Mycoplasma genitalium genome containing all the genes of the wild-type bacteria, except one that they disrupted to block pathogenicity and allow for selection. ‘Watermarks'' at intergenic sites that tolerate transposon insertions identify the synthetic genome, which would otherwise be indistinguishable from the wild type (Gibson et al, 2008).Yet, as Pier Luigi Luisi from the University of Roma in Italy remarked, even M. genitalium is relatively complex. “The question is whether such complexity is necessary for cellular life, or whether, instead, cellular life could, in principle, also be possible with a much lower number of molecular components”, he said. After all, life probably did not start with cells that already contained thousands of genes (Luisi, 2007).…researchers will continue their attempts to create life in the test tube—it is, after all, one of the greatest scientific challengesTo investigate further the minimum number of genes required for life, researchers are using minimal cell models: synthetic genomes that can be included in liposomes, which themselves show some life-like characteristics. Certain lipid vesicles are able to grow, divide and grow again, and can include polymerase enzymes to synthesize RNA from external substrates as well as functional translation apparatuses, including ribosomes (Deamer, 2005).However, the requirement that an organism be subject to natural selection to be considered alive could prove to be a major hurdle for current attempts to create life. As Freemont commented: “Synthetic biologists could include the components that go into a cell and create an organism [that is] indistinguishable from one that evolved naturally and that can replicate […] We are beginning to get to grips with what makes the cell work. Including an element that undergoes natural selection is proving more intractable.”John Dupré, Professor of Philosophy of Science and Director of the Economic and Social Research Council (ESRC) Centre for Genomics in Society at the University of Exeter, UK, commented that synthetic biologists still approach the construction of a minimal organism with certain preconceptions. “All synthetic biology research assumes certain things about life and what it is, and any claims to have ‘confirmed'' certain intuitions—such as life is not a vital principle—aren''t really adding empirical evidence for those intuitions. Anyone with the opposite intuition may simply refuse to admit that the objects in question are living,” he said. “To the extent that synthetic biology is able to draw a clear line between life and non-life, this is only possible in relation to defining concepts brought to the research. For example, synthetic biologists may be able to determine the number of genes required for minimal function. Nevertheless, ‘what counts as life'' is unaffected by minimal genomics.”Partly because of these preconceptions, Dan Nicholson, a former molecular biologist now working at the ESRC Centre, commented that synthetic biology adds little to the understanding of life already gained from molecular biology and biochemistry. Nevertheless, he said, synthetic biology might allow us to go boldly into the realms of biological possibility where evolution has not gone before.An engineered synthetic organism could, for example, express novel amino acids, proteins, nucleic acids or vesicular forms. A synthetic organism could use pyranosyl-RNA, which produces a stronger and more selective pairing system than the natural existent furanosyl-RNA (Bolli et al, 1997). Furthermore, the synthesis of proteins that do not exist in nature—so-called never-born proteins—could help scientists to understand why evolutionary pressures only selected certain structures.As Luisi remarked, the ratio between the number of theoretically possible proteins containing 100 amino acids and the real number present in nature is close to the ratio between the space of the universe and the space of a single hydrogen atom, or the ratio between all the sand in the Sahara Desert and a single grain. Exploring never-born proteins could, therefore, allow synthetic biologists to determine whether particular physical, structural, catalytic, thermodynamic and other properties maximized the evolutionary fitness of natural proteins, or whether the current protein repertoire is predominately the result of chance (Luisi, 2007).In the final analysis, as with all science, deep understanding is more important than labelling with words.“Synthetic biology also could conceivably help overcome the ‘n = 1 problem''—namely, that we base biological theorising on terrestrial life only,” Nicholson said. “In this way, synthetic biology could contribute to the development of a more general, broader understanding of what life is and how it might be defined.”No matter the uncertainties, researchers will continue their attempts to create life in the test tube—it is, after all, one of the greatest scientific challenges. Whether or not they succeed will depend partly on the definition of life that they use, though in any case, the research should yield numerous insights that are beneficial to biologists generally. “The process of creating a living system from chemical components will undoubtedly offer many rich insights into biology,” Davies concluded. “However, the definition will, I fear, reflect politics more than biology. Any definition will, therefore, be subject to a lot of inter-lab political pressure. Definitions are also important for bioethical legislation and, as a result, reflect larger politics more than biology. In the final analysis, as with all science, deep understanding is more important than labelling with words.”     

Nothing but the truth

Many scientists blame the media for sensationalising scientific findings, but new research suggests that things can go awry at all levels, from the scientific report to the press officer to the journalist.Everything gives you cancer, at least if you believe what you read in the news or see on TV. Fortunately, everything also cures cancer, from red wine to silver nanoparticles. Of course the truth lies somewhere in between, and scientists might point out that these claims are at worst dangerous sensationalism and at best misjudged journalism. These kinds of media story, which inflate the risks and benefits of research, have led to a mistrust of the press among some scientists. But are journalists solely at fault when science reporting goes wrong, as many scientists believe [1]? New research suggests it is time to lay to rest the myth that the press alone is to blame. The truth is far more nuanced and science reporting can go wrong at many stages, from the researchers to the press officers to the diverse producers of news.Many science communication researchers suggest that science in the media is not as distorted as scientists believe, although they do admit that science reporting tends to under-represent risks and over-emphasize benefits [2]. “I think there is a lot less of this [misreported science] than some scientists presume. I actually think that there is a bit of laziness in the narrative around science and the media,” said Fiona Fox, Director of the UK Science Media Centre (London, UK), an independent press office that serves as a liaison between scientists and journalists. “My bottom line is that, certainly in the UK, a vast majority of journalists report science accurately in a measured way, and it''s certainly not a terrible story. Having said that, lots of things do go wrong for a number of reasons.”Fox said that the centre sees everything from fantastic press releases to those that completely misrepresent and sensationalize scientific findings. They have applauded news stories that beautifully reported the caveats and limitations of a particular scientific study, but they have also cringed as a radio talk show pitted a massive and influential body of research against a single non-scientist sceptic.“You ask, is it the press releases, is it the universities, is it the journalists? The truth is that it''s all three,” Fox said. “But even admitting that is admitting more complexity. So anyone who says that scientists and university press officers deliver perfectly accurate science and the media misrepresent it […] that really is not the whole story.”Scientists and scientific institutions today invest more time and effort into communicating with the media than they did a decade ago, especially given the modern emphasis on communicating scientific results to the public [3]. Today, there are considerable pressures on scientists to reach out and even ‘sell their work'' to public relations officers and journalists. “For every story that a journalist has hyped and sensationalized, there will be another example of that coming directly from a press release that we [scientists] hyped and sensationalized,” Fox said. “And for every time that that was a science press officer, there will also be a science press officer who will tell you, ‘I did a much more nuanced press release, but the academic wanted me to over claim for it''.”Although science public relations has helped to put scientific issues on the public agenda, there are also dangers inherent in the process of translation from original research to press release to media story. Previous research in the area of science communication has focused on conflicting scientific and media values, and the effects of science media on audiences. However, studies have raised awareness of the role of press releases in distorting information from the lab bench to published news [4].In a 2011 study of genetic research claims made in press releases and mainstream print media, science communication researcher Jean Brechman, who works at the US advertising and marketing research firm Gallup & Robinson, found evidence that scientific knowledge gets distorted as it is “filtered and translated for mass communication” with “slippages and inconsistencies” occurring along the way, such that the end message does not accurately represent the original science [4]. Although Brechman and colleagues found a concerning point of distortion in the transition between press release and news article, they also observed a misrepresentation of the original science in a significant portion of the press releases themselves.In a previous study, Brechman and his colleagues had also concluded that “errors commonly attributed to science journalists, such as lack of qualifying details and use of oversimplified language, originate in press releases.” Even more worrisome, as Fox told a Nature commentary author in 2009, public relations departments are increasingly filling the need of the media for quick content [5].Fox believes that a common characteristic of misrepresented science in press releases and the media is the over-claiming of preliminary studies. As such, the growing prevalence of rapid, short-format publications that publicize early results might be exacerbating the problem. Research has also revealed that over-emphasis on the beneficial effects of experimental medical treatments seen in press releases and news coverage, often called ‘spin'', can stem from bias in the abstract of the original scientific article itself [6]. Such findings warrant a closer examination of the language used in scientific articles and abstracts, as the wording and ‘spin'' of conclusions drawn by researchers in their peer-reviewed publications might have significant impacts on subsequent media coverage.Of course, some stories about scientific discoveries are just not easy to tell owing to their complexity. They are “messy, complicated, open to interpretation and ripe for misreporting,” as Fox wrote in a post on her blog On Science and the Media (fionafox.blogspot.com). They do not fit the single-page blog post or the short press release. Some scientific experiments and the peer-reviewed articles and media stories that flow from them are inherently full of caveats, contexts and conflicting results and cannot be communicated in a short format [7].In a 2012 issue of Perspectives on Psychological Science, Marco Bertamini at the University of Liverpool (UK) and Marcus R. Munafo at the University of Bristol (UK) suggested that a shift toward “bite-size” publications in areas of science such as psychology might be promoting more single-study models of research, fewer efforts to replicate initial findings, curtailed detailing of previous relevant work and bias toward “false alarm” or false-positive results [7]. The authors pointed out that larger, multi-experiment studies are typically published in longer papers with larger sample sizes and tend to be more accurate. They also suggested that this culture of brief, single-study reports based on small data sets will lead to the contamination of the scientific literature with false-positive findings. Unfortunately, false science far more easily enters the literature than leaves it [8].One famous example is that of Andrew Wakefield, whose 1998 publication in The Lancet claimed to link autism with the combined measles, mumps and rubella (MMR) vaccination. It took years of work by many scientists, and the aid of an exposé by British investigative reporter Brian Deer, to finally force retraction of the paper. However, significant damage had already been done and many parents continue to avoid immunizing their children out of fear. Deer claims that scientific journals were a large part of the problem: “[D]uring the many years in which I investigated the MMR vaccine controversy, the worst and most inexcusable reporting on the subject, apart from the original Wakefield claims in the Lancet, was published in Nature and republished in Scientific American,” he said. “There is an enormous amount of hypocrisy among those who accuse the media of misreporting science.”What factors are promoting this shift to bite-size science? One is certainly the increasing pressure and competition to publish many papers in high-impact journals, which prefer short articles with new, ground-breaking findings.“Bibliometrics is playing a larger role in academia in deciding who gets a job and who gets promoted,” Bertamini said. “In general, if things are measured by citations, there is pressure to publish as much and as often as possible, and also to focus on what is surprising; thus, we can see how this may lead to an inflation in the number of papers but also an increase in publication bias.”Bertamini points to the real possibility that measured effects emerging from a group of small samples can be much larger than the real effect in the total population. “This variability is bad enough, but it is even worse when you consider that what is more likely to be written up and accepted for publication are exactly the larger differences,” he explained.Alongside the endless pressure to publish, the nature of the peer-reviewed publication process itself prioritizes exciting and statistically impressive results. Fluke scientific discoveries and surprising results are often considered newsworthy, even if they end up being false-positives. The bite-size article aggravates this problem in what Bertamini fears is a growing similarity between academic writing and media reporting: “The general media, including blogs and newspapers, will of course focus on what is curious, funny, controversial, and so on. Academic papers must not do the same, and the quality control system is there to prevent that.”The real danger is that, with more than one million scientific papers published every year, journalists can tend to rely on only a few influential journals such as Science and Nature for science news [3]. Although the influence and reliability of these prestigious journals is well established, the risk that journalists and other media producers might be propagating the exciting yet preliminary results published in their pages is undeniable.Fox has personal experience of the consequences of hype surrounding surprising but preliminary science. Her sister has chronic fatigue syndrome (CFS), a debilitating medical condition with no known test or cure. When Science published an article in 2009 linking CFS with a viral agent, Fox was naturally both curious and sceptical [9]. “I thought even if I knew that this was an incredibly significant finding, the fact that nobody had ever found a biological link before also meant that it would have to be replicated before patients could get excited,” Fox explained. “And of course what happened was all the UK journalists were desperate to splash it on the front page because it was so surprising and so significant and could completely revolutionize the approach to CFS, the treatment and potential cure.”Fox observed that while some journalists placed the caveats of the study deep within their stories, others left them out completely. “I gather in the USA it was massive, it was front page news and patients were going online to try and find a test for this particular virus. But in the end, nobody could replicate it, literally nobody. A Dutch group tried, Imperial College London, lots of groups, but nobody could replicate it. And in the end, the paper has been withdrawn from Science.”For Fox, the fact that the paper was withdrawn, incidentally due to a finding of contamination in the samples, was less interesting than the way that the paper was reported by journalists. “We would want any journal press officer to literally in the first paragraph be highlighting the fact that this was such a surprising result that it shouldn''t be splashed on the front page,” she said. Of course to the journalist, waiting for the study to be replicated is anathema in a culture that values exciting and new findings. “To the scientific community, the fact that it is surprising and new means that we should calm down and wait until it is proved,” Fox warned.So, the media must also take its share of the blame when it comes to distorting science news. Indeed, research analysing science coverage in the media has shown that stories tend to exaggerate preliminary findings, use sensationalist terms, avoid complex issues, fail to mention financial conflicts of interest, ignore statistical limitations and transform inherent uncertainties into controversy [3,10].One concerning development within journalism is the ‘balanced treatment'' of controversial science, also called ‘false balance'' by many science communicators. This balanced treatment has helped supporters of pseudoscientific notions gain equal ground with scientific experts in media stories on issues such as climate change and biotechnology [11].“Almost every time the issue of creationism or intelligent design comes up, many newspapers and other media feel that they need to present ‘both sides'', even though one is clearly nonsensical, and indeed harmful to public education,” commented Massimo Pigliucci, author of Nonsense on Stilts: How to Tell Science from Bunk [12].Fox also criticizes false balance on issues such as global climate change. “On that one you can''t blame the scientific community, you can''t blame science press officers,” she said. “That is a real clashing of values. One of the values that most journalists have bred into them is about balance and impartiality, balancing the views of one person with an opponent when it''s controversial. So on issues like climate change, where there is a big controversy, their instinct as a journalist will be to make sure that if they have a climate scientist on the radio or on TV or quoted in the newspaper, they pick up the phone and make sure that they have a climate skeptic.” However, balanced viewpoints should not threaten years of rigorous scientific research embodied in a peer-reviewed publication. “We are not saying generally that we [scientists] want special treatment from journalists,” Fox said, “but we are saying that this whole principle of balance, which applies quite well in politics, doesn''t cross over to science…”Bertamini believes the situation could be made worse if publication standards are relaxed in favour of promoting a more public and open review process. “If today you were to research the issue of human contribution to global warming you would find a consensus in the scientific literature. Yet you would find no such consensus in the general media. In part this is due to the existence of powerful and well-funded lobbies that fill the media with unfounded skepticism. Now imagine if these lobbies had more access to publish their views in the scientific literature, maybe in the form of post publication feedback. This would be a dangerous consequence of blurring the line that separates scientific writing and the broader media.”In an age in which the way science is presented in the news can have significant impacts for audiences, especially when it comes to health news, what can science communicators and journalists do to keep audiences reading without having to distort, hype, trivialize, dramatize or otherwise misrepresent science?Pigliucci believes that many different sources—press releases, blogs, newspapers and investigative science journalism pieces—can cross-check reported science and challenge its accuracy, if necessary. “There are examples of bloggers pointing out technical problems with published scientific papers,” Pigliucci said. “Unfortunately, as we all know, the game can be played the other way around too, with plenty of bloggers, ‘twitterers'' and others actually obfuscating and muddling things even more.” Pigliucci hopes to see a cultural change take place in science reporting, one that emphasizes “more reflective shouting, less shouting of talking points,” he said.Fox believes that journalists still need to cover scientific developments more responsibly, especially given that scientists are increasingly reaching out to press officers and the public. Journalists can inform, intrigue and entertain whilst maintaining accurate representations of the original science, but need to understand that preliminary results must be replicated and validated before being splashed on the front page. They should also strive to interview experts who do not have financial ties or competing interests in the research, and they should put scientific stories in the context of a broader process of nonlinear discovery. According to Pigliucci, journalists can and should be educating themselves on the research process and the science of logical conclusion-making, giving themselves the tools to provide critical and investigative coverage when needed. At the same time, scientists should undertake proper media training so that they are comfortable communicating their work to journalists or press officers.“I don''t think there is any fundamental flaw in how we communicate science, but there is a systemic flaw in the sense that we simply do not educate people about logical fallacies and cognitive biases,” Pigliucci said, advising that scientists and communicators alike should be intimately familiar with the subjects of philosophy and psychology. “As for bunk science, it has always been with us, and it probably always will be, because human beings are naturally prone to all sorts of biases and fallacious reasoning. As Carl Sagan once put it, science (and reason) is like a candle in the dark. It needs constant protection and a lot of thankless work to keep it alive.”     

Women and telomeres

Last year''s Nobel Prizes for Carol Greider and Elizabeth Blackburn should be encouraging for all female scientists with childrenCarol Greider, a molecular biologist at Johns Hopkins University (Baltimore, MD, USA), recalled that when she received a phone call from the Nobel Foundation early in October last year, she was staring down a large pile of laundry. The caller informed her that she had won the 2009 Nobel Prize in Physiology or Medicine along with Elizabeth Blackburn, her mentor and co-discoverer of the enzyme telomerase, and Jack Szostak. The Prize was not only the ultimate reward for her own achievements, but it also highlighted a research field in biology that, unlike most others, is renowned for attracting a significant number of women.Indeed, the 2009 awards stood out in particular, as five women received Nobel prizes. In addition to the Prize for Greider and Blackburn, Ada E. Yonath received one in chemistry, Elinor Ostrom became the first female Prize-winner in economics, and Herta Müller won for literature (Fig 1).Open in a separate windowFigure 1The 2009 Nobel Laureates assembled for a photo during their visit to the Nobel Foundation on 12 December 2009. Back row, left to right: Nobel Laureates in Chemistry Ada E. Yonath and Venkatraman Ramakrishnan, Nobel Laureates in Physiology or Medicine Jack W. Szostak and Carol W. Greider, Nobel Laureate in Chemistry Thomas A. Steitz, Nobel Laureate in Physiology or Medicine Elizabeth H. Blackburn, and Nobel Laureate in Physics George E. Smith. Front row, left to right: Nobel Laureate in Physics Willard S. Boyle, Nobel Laureate in Economic Sciences Elinor Ostrom, Nobel Laureate in Literature Herta Müller, and Nobel Laureate in Economic Sciences Oliver E. Williamson. © The Nobel Foundation 2009. Photo: Orasis.Greider, the daughter of scientists, has overcome many obstacles during her career. She had dyslexia that placed her in remedial classes; “I thought I was stupid,” she told The New York Times (Dreifus, 2009). Yet, by far the biggest challenge she has tackled is being a woman with children in a man''s world. When she attended a press conference at Johns Hopkins to announce the Prize, she brought her children Gwendolyn and Charles with her (Fig 2). “How many men have won the Nobel in the last few years, and they have kids the same age as mine, and their kids aren''t in the picture? That''s a big difference, right? And that makes a statement,” she said.The Prize […] highlighted a research field in biology that, unlike most others, is renowned for attracting a significant number of womenOpen in a separate windowFigure 2Mother, scientist and Nobel Prize-winner: Carol Greider is greeted by her lab and her children. © Johns Hopkins Medicine 2009. Photo: Keith Weller.Marie Curie (1867–1934), the Polish–French physicist and chemist, was the first woman to win the Prize in 1903 for physics, together with her husband Pierre, and again for chemistry in 1911—the only woman to twice achieve such recognition. Curie''s daughter Irène Joliot-Curie (1897–1956), a French chemist, also won the Prize with her husband Frédéric in 1935. Since Curie''s 1911 prize, 347 Nobel Prizes in Physiology or Medicine and Chemistry (the fields in which biologists are recognized) have been awarded, but only 14—just 4%—have gone to women, with 9 of these awarded since 1979. That is a far cry from women holding up half the sky.Yet, despite the dominance of men in biology and the other natural sciences, telomere research has a reputation as a field dominated by women. Daniela Rhodes, a structural biologist and senior scientist at the MRC Laboratory of Molecular Biology (Cambridge, UK) recalls joining the field in 1993. “When I went to my first meeting, my world changed because I was used to being one of the few female speakers,” she said. “Most of the speakers there were female.” She estimated that 80% of the speakers at meetings at Cold Spring Harbour Laboratory in those early days were women, while the ratio in the audience was more balanced.Since Curie''s 1911 prize, 347 Nobel Prizes in Physiology or Medicine and Chemistry […] have been awarded, but only 14—just 4%—have gone to women…“There''s nothing particularly interesting about telomeres to women,” Rhodes explained. “[The] field covers some people like me who do structural biology, to cell biology, to people interested in cancers […] It could be any other field in biology. I think it''s [a result of] having women start it and [including] other women.” Greider comes to a similar conclusion: “I really see it as a founder effect. It started with Joe Gall [who originally recruited Blackburn to work in his lab].”Gall, a cell biologist, […] welcomed women to his lab at a time when the overall situation for women in science was “reasonably glum”…Gall, a cell biologist, earned a reputation for being gender neutral while working at Yale University in the 1950s and 1960s; he welcomed women to his lab at a time when the overall situation for women in science was “reasonably glum,” as he put it. “It wasn''t that women were not accepted into PhD programs. It''s just that the opportunities for them afterwards were pretty slim,” he explained.“Very early on he was very supportive to a number of women who went on and then had their own labs and […] many of those women [went] out in the world [to] train other women,” Greider commented. “A whole tree that then grows up that in the end there are many more women in that particular field simply because of that historical event.Thomas Cech, who won the Nobel Prize for Chemistry in 1989 and who worked in Gall''s lab with Blackburn, agreed: “In biochemistry and metabolism, we talk about positive feedback loops. This was a positive feedback loop. Joe Gall''s lab at Yale was an environment that was free of bias against women, and it was scientifically supportive.”Gall, now 81 and working at the Carnegie Institution of Washington (Baltimore, MD, USA), is somewhat dismissive about his positive role. “It never occurred to me that I was doing anything unusual. It literally, really did not. And it''s only been in the last 10 or 20 years that anyone made much of it,” he said. “If you look back, […] my laboratory [was] very close to [half] men and [half] women.”During the 1970s and 1980s; “[w]hen I entered graduate school,” Greider recalled, “it was a time when the number of graduate students [who] were women was about 50%. And it wasn''t unusual at all.” What has changed, though, is the number of women choosing to pursue a scientific career further. According to the US National Science Foundation (Arlington, VA, USA), women received 51.8% of doctorates in the life sciences in 2006, compared with 43.8% in 1996, 34.6% in 1986, 20.7% in 1976 and 11.9% in 1966 (www.nsf.gov/statistics).In fact, Gall suspects that biology tends to attract more women than the other sciences. “I think if you look in biology departments that you would find a higher percentage [of women] than you would in physics and chemistry,” he said. “I think […] it''s hard to dissociate societal effects from specific effects, but probably fewer women are inclined to go into chemistry [or] physics. Certainly, there is no lack of women going into biology.” However, the representation of women falls off at each level, from postdoc to assistant professor and tenured professor. Cech estimated that only about 20% of the biology faculty in the USA are women.“[It] is a leaky pipeline,” Greider explained. “People exit the system. Women exit at a much higher proportion than do men. I don''t see it as a [supply] pipeline issue at all, getting the trainees in, because for 25 years there have been a great number of women trainees.“We all thought that with civil rights and affirmative action you''d open the doors and women would come in and everything would just follow. And it turned out that was not true.”Nancy Hopkins, a molecular biologist and long-time advocate on issues affecting women faculty members at the Massachusetts Institute of Technology (Cambridge, MA, USA), said that the situation in the USA has improved because of civil rights laws and affirmative action. “I was hired—almost every woman of my generation was hired—as a result of affirmative action. Without it, there wouldn''t have been any women on the faculty,” she said, but added that: “We all thought that with civil rights and affirmative action you''d open the doors and women would come in and everything would just follow. And it turned out that was not true.”Indeed, in a speech at an academic conference in 2005, Harvard President Lawrence Summers said that innate differences between males and females might be one reason why fewer women than men succeeded in science and mathematics. The economist, who served as Secretary of Treasury under President William Clinton, told The Boston Globe that “[r]esearch in behavioural genetics is showing that things people previously attributed to socialization weren''t [due to socialization after all]” (Bombardieri, 2005).Some attendees of the meeting were angered by Summers''s remarks that women do not have the same ‘innate ability'' as men in some fields. Hopkins said she left the meeting as a protest and in “a state of shock and rage”. “It isn''t a question of political correctness, it''s about making unscientific, unfounded and damaging comments. It''s what discrimination is,” she said, adding that Summers''s views reflect the problems women face in moving up the ladder in academia. “To have the president of Harvard say that the second most important reason for their not being equal was really their intrinsic genetic inferiority is so shocking that no matter how many times I think back to his comments, I''m still shocked. These women were not asking to be considered better or special. They were just asking to have their gender be invisible.”Nonetheless, women are making inroads into academia, despite lingering prejudice and discrimination. One field of biology that counts a relatively high number of successful women among its upper ranks is developmental biology. Christiane Nüsslein-Volhard, for example, is Director of the Max Planck Institute for Developmental Biology in Tübingen, Germany, and won the Nobel Prize for Physiology or Medicine in 1995 for her work on the development of Drosophila embryos. She estimated that about 30% of speakers at conferences in her field are women.…for many women, the recent Nobel Prize for Greider […] and Blackburn […] therefore comes as much needed reassurance that it is possible to combine family life and a career in scienceHowever, she also noted that women have never been the majority in her own lab owing to the social constraints of German society. She explained that in Germany, Switzerland and Austria, family issues pose barriers for many women who want to have children and advance professionally because the pressure for women to not use day care is extremely strong. As such, “[w]omen want to stay home because they want to be an ideal mother, and then at the same time they want to go to work and do an ideal job and somehow this is really very difficult,” she said. “I don''t know a single case where the husband stays at home and takes care of the kids and the household. This doesn''t happen. So women are now in an unequal situation because if they want to do the job, they cannot; they don''t have a chance to find someone to do the work for them. […] The wives need wives.” In response to this situation, Nüsslein-Volhard has established the CNV Foundation to financially support young women scientists with children in Germany, to help pay for assistance with household chores and child care.Rhodes, an Italian native who grew up in Sweden, agreed with Nüsslein-Volhard''s assessment of the situation for many European female scientists with children. “Some European countries are very old-fashioned. If you look at the Protestant countries like Holland, women still do not really go out and have a career. It tends to be the man,” she said. “What I find depressing is [that in] a country like Sweden where I grew up, which is a very liberated country, there has been equality between men and women for a couple of generations, and if you look at the percentage of female professors at the universities, it''s still only 10%.” In fact, studies both from Europe and the USA show that academic science is not a welcoming environment for women with children; less so than for childless women and fathers, who are more likely to succeed in academic research (Ledin et al, 2007; Martinez et al, 2007).For Hopkins, her divorce at the age of 30 made a choice between children or a career unavoidable. Offered a position at MIT, she recalled that she very deliberately chose science. She said that she thought to herself: “Okay, I''m going to take the job, not have children and not even get married again because I couldn''t imagine combining that career with any kind of decent family life.” As such, for many women, the recent Nobel Prize for Greider, who raised two children, and Blackburn (Fig 3), who raised one, therefore comes as much needed reassurance that it is possible to combine family life and a career in science. Hopkins said the appearance of Greider and her children at the press conference sent “the message to young women that they can do it, even though very few women in my generation could do it. The ways in which some women are managing to do it are going to become the role models for the women who follow them.”Open in a separate windowFigure 3Elizabeth Blackburn greets colleagues and the media at a reception held in Genentech Hall at UCSF Mission Bay to celebrate her award of the Nobel Prize in Physiology or Medicine. © University of California, San Francisco 2009. Photo: Susan Merrell.     

To hype, or not to(o) hype. Communication of science is often tarnished by sensationalization, for which both scientists and the media are responsible

Scientists and journalists try to engage the public with exciting stories, but who is guilty of overselling research and what are the consequences?Scientists love to hate the media for distorting science or getting the facts wrong. Even as they do so, they court publicity for their latest findings, which can bring a slew of media attention and public interest. Getting your research into the national press can result in great boons in terms of political and financial support. Conversely, when scientific discoveries turn out to be wrong, or to have been hyped, the negative press can have a damaging effect on careers and, perhaps more importantly, the image of science itself. Walking the line between ‘selling'' a story and ‘hyping'' it far beyond the evidence is no easy task. Professional science communicators work carefully with scientists and journalists to ensure that the messages from research are translated for the public accurately and appropriately. But when things do go wrong, is it always the fault of journalists, or are scientists and those they employ to communicate sometimes equally to blame?Walking the line between ‘selling'' a story and ‘hyping'' it far beyond the evidence is no easy taskHyping in science has existed since the dawn of research itself. When scientists relied on the money of wealthy benefactors with little expertise to fund their research, the temptation to claim that they could turn lead into gold, or that they could discover the secret of eternal life, must have been huge. In the modern era, hyping of research tends to make less exuberant claims, but it is no less damaging and no less deceitful, even if sometimes unintentionally so. A few recent cases have brought this problem to the surface again.The most frenzied of these was the report in Science last year that a newly isolated bacterial strain could replace phosphate with arsenate in cellular constituents such as nucleic acids and proteins [1]. The study, led by NASA astrobiologist Felisa Wolfe-Simon, showed that a new strain of the Halomonadaceae family of halofilic proteobacteria, isolated from the alkaline and hypersaline Mono Lake in California (Fig 1), could not only survive in arsenic-rich conditions, such as those found in its original environment, but even thrive by using arsenic entirely in place of phosphorus. “The definition of life has just expanded. As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it,” commented Ed Weiler, NASA''s associate administrator for the Science Mission Directorate at the agency''s Headquarters in Washington, in the original press release [2].Open in a separate windowFigure 1Sunrise at Mono Lake. Mono Lake, located in eastern California, is bounded to the west by the Sierra Nevada mountains. This ancient alkaline lake is known for unusual tufa (limestone) formations rising from the water''s surface (shown here), as well as for its hypersalinity and high concentrations of arsenic. See Wolfe-Simon et al [1]. Credit: Henry Bortman.The accompanying “search for life beyond Earth” and “alternative biochemistry makeup” hints contained in the same release were lapped up by the media, which covered the breakthrough with headlines such as “Arsenic-loving bacteria may help in hunt for alien life” (BBC News), “Arsenic-based bacteria point to new life forms” (New Scientist), “Arsenic-feeding bacteria find expands traditional notions of life” (CNN). However, it did not take long for criticism to manifest, with many scientists openly questioning whether background levels of phosphorus could have fuelled the bacteria''s growth in the cultures, whether arsenate compounds are even stable in aqueous solution, and whether the tests the authors used to prove that arsenic atoms were replacing phosphorus ones in key biomolecules were accurate. The backlash was so bitter that Science published the concerns of several research groups commenting on the technical shortcomings of the study and went so far as to change its original press release for reporters, adding a warning note that reads “Clarification: this paper describes a bacterium that substitutes arsenic for a small percentage of its phosphorus, rather than living entirely off arsenic.”Microbiologists Simon Silver and Le T. Phung, from the University of Illinois, Chicago, USA, were heavily critical of the study, voicing their concern in one of the journals of the Federation of European Microbiological Societies, FEMS Microbiology Letters. “The recent online report in Science […] either (1) wonderfully expands our imaginations as to how living cells might function […] or (2) is just the newest example of how scientist-authors can walk off the plank in their imaginations when interpreting their results, how peer reviewers (if there were any) simply missed their responsibilities and how a press release from the publisher of Science can result in irresponsible publicity in the New York Times and on television. We suggest the latter alternative is the case, and that this report should have been stopped at each of several stages” [3]. Meanwhile, Wolfe-Simon is looking for another chance to prove she was right about the arsenic-loving bug, and Silver and colleagues have completed the bacterium''s genome shotgun sequencing and found 3,400 genes in its 3.5 million bases (www.ncbi.nlm.nih.gov/Traces/wgs/?val=AHBC01).“I can only comment that it would probably be best if one had avoided a flurry of press conferences and speculative extrapolations. The discovery, if true, would be similarly impressive without any hype in the press releases,” commented John Ioannidis, Professor of Medicine at Stanford University School of Medicine in the USA. “I also think that this is the kind of discovery that can definitely wait for a validation by several independent teams before stirring the world. It is not the type of research finding that one cannot wait to trumpet as if thousands and millions of people were to die if they did not know about it,” he explained. “If validated, it may be material for a Nobel prize, but if not, then the claims would backfire on the credibility of science in the public view.”Another instructive example of science hyping was sparked by a recent report of fossil teeth, dating to between 200,000 and 400,000 years ago, which were unearthed in the Qesem Cave near Tel Aviv by Israeli and Spanish scientists [4]. Although the teeth cannot yet be conclusively ascribed to Homo sapiens, Homo neanderthalensis, or any other species of hominid, the media coverage and the original press release from Tel Aviv University stretched the relevance of the story—and the evidence—proclaiming that the finding demonstrates humans lived in Israel 400,000 years ago, which should force scientists to rewrite human history. Were such evidence of modern humans in the Middle East so long ago confirmed, it would indeed clash with the prevailing view of human origin in Africa some 200,000 years ago and the dispersal from the cradle continent that began about 70,000 years ago. But, as freelance science writer Brian Switek has pointed out, “The identity of the Qesem Cave humans cannot be conclusively determined. All the grandiose statements about their relevance to the origin of our species reach beyond what the actual fossil material will allow” [5].An example of sensationalist coverage? “It has long been believed that modern man emerged from the continent of Africa 200,000 years ago. Now Tel Aviv University archaeologists have uncovered evidence that Homo sapiens roamed the land now called Israel as early as 400,000 years ago—the earliest evidence for the existence of modern man anywhere in the world,” reads a press release from the New York-based organization, American Friends of Tel Aviv University [6].“The extent of hype depends on how people interpret facts and evidence, and their intent in the claims they are making. Hype in science can range from ‘no hype'', where predictions of scientific futures are 100% fact based, to complete exaggeration based on no facts or evidence,” commented Zubin Master, a researcher in science ethics at the University of Alberta in Edmonton, Canada. “Intention also plays a role in hype and the prediction of scientific futures, as making extravagant claims, for example in an attempt to secure funds, could be tantamount to lying.”Are scientists more and more often indulging in creative speculation when interpreting their results, just to get extraordinary media coverage of their discoveries? Is science journalism progressively shifting towards hyping stories to attract readers?“The vast majority of scientific work can wait for some independent validation before its importance is trumpeted to the wider public. Over-interpretation of results is common and as scientists we are continuously under pressure to show that we make big discoveries,” commented Ioannidis. “However, probably our role [as scientists] is more important in making sure that we provide balanced views of evidence and in identifying how we can question more rigorously the validity of our own discoveries.”“The vast majority of scientific work can wait for some independent validation before its importance is trumpeted to the wider public”Stephanie Suhr, who is involved in the management of the European XFEL—a facility being built in Germany to generate intense X-ray flashes for use in many disciplines—notes in her introduction to a series of essays on the ethics of science journalism that, “Arguably, there may also be an increasing temptation for scientists to hype their research and ‘hit the headlines''” [7]. In her analysis, Suhr quotes at least one instance—the discovery in 2009 of the Darwinius masillae fossil, presented as the missing link in human evolution [8]—in which the release of a ‘breakthrough'' scientific publication seems to have been coordinated with simultaneous documentaries and press releases, resulting in what can be considered a study case for science hyping [7].Although there is nothing wrong in principle with a broad communication strategy aimed at the rapid dissemination of a scientific discovery, some caveats exist. “[This] strategy […] might be better applied to a scientific subject or body of research. When applied to a single study, there [is] a far greater likelihood of engaging in unmerited hype with the risk of diminishing public trust or at least numbing the audience to claims of ‘startling new discoveries'',” wrote science communication expert Matthew Nisbet in his Age of Engagement blog (bigthink.com/blogs/age-of-engagement) about how media communication was managed in the Darwinius affair. “[A]ctivating the various channels and audiences was the right strategy but the language and metaphor used strayed into the realm of hype,” Nisbet, who is an Associate Professor in the School of Communication at American University, Washington DC, USA, commented in his post [9]. “We are ethically bound to think carefully about how to go beyond the very small audience that follows traditional science coverage and think systematically about how to reach a wider, more diverse audience via multiple media platforms. But in engaging with these new media platforms and audiences, we are also ethically bound to avoid hype and maintain accuracy and context” [9].But the blame for science hype cannot be laid solely at the feet of scientists and press officers. Journalists must take their fair share of reproach. “As news online comes faster and faster, there is an enormous temptation for media outlets and journalists to quickly publish topics that will grab the readers'' attention, sometimes at the cost of accuracy,” Suhr wrote [7]. Of course, the media landscape is extremely varied, as science blogger and writer Bora Zivkovic pointed out. “There is no unified thing called ‘Media''. There are wonderful specialized science writers out there, and there are beat reporters who occasionally get assigned a science story as one of several they have to file every day,” he explained. “There are careful reporters, and there are those who tend to hype. There are media outlets that value accuracy above everything else; others that put beauty of language above all else; and there are outlets that value speed, sexy headlines and ad revenue above all.”…the blame for science hype cannot be laid solely at the feet of scientists and press officers. Journalists must take their fair share of reproachOne notable example of media-sourced hype comes from J. Craig Venter''s announcement in the spring of 2010 of the first self-replicating bacterial cell controlled by a synthetic genome (Fig 2). A major media buzz ensued, over-emphasizing and somewhat distorting an anyway remarkable scientific achievement. Press coverage ranged from the extremes of announcing ‘artificial life'' to saying that Venter was playing God, adding to cultural and bioethical tension the warning that synthetic organisms could be turned into biological weapons or cause environmental disasters.Open in a separate windowFigure 2Schematic depicting the assembly of a synthetic Mycoplasma mycoides genome in yeast. For details of the construction of the genome, please see the original article. From Gibson et al [13] Science 329, 52–56. Reprinted with permission from AAAS.“The notion that scientists might some day create life is a fraught meme in Western culture. One mustn''t mess with such things, we are told, because the creation of life is the province of gods, monsters, and practitioners of the dark arts. Thus, any hint that science may be on the verge of putting the power of creation into the hands of mere mortals elicits a certain discomfort, even if the hint amounts to no more than distorted gossip,” remarked Rob Carlson, who writes on the future role of biology as a human technology, about the public reaction and the media frenzy that arose from the news [10].Yet the media can also behave responsibly when faced with extravagant claims in press releases. Fiona Fox, Chief Executive of the Science Media Centre in the UK, details such an example in her blog, On Science and the Media (fionafox.blogspot.com). The Science Media Centre''s role is to facilitate communication between scientists and the press, so they often receive calls from journalists asking to be put in touch with an expert. In this case, the journalist asked for an expert to comment on a story about silver being more effective against cancer than chemotherapy. A wild claim; yet, as Fox points out in her blog, the hype came directly from the institution''s press office: “Under the heading ‘A silver bullet to beat cancer?'' the top line of the press release stated that ‘Lab tests have shown that it (silver) is as effective as the leading chemotherapy drug—and may have far fewer side effects.'' Far from including any caveats or cautionary notes up front, the press office even included an introductory note claiming that the study ‘has confirmed the quack claim that silver has cancer-killing properties''” [11]. Fox praises the majority of the UK national press that concluded that this was not a big story to cover, pointing out that, “We''ve now got to the stage where not only do the best science journalists have to fight the perverse news values of their news editors but also to try to read between the lines of overhyped press releases to get to the truth of what a scientific study is really claiming.”…the concern is that hype inflates public expectations, resulting in a loss of trust in a given technology or research avenue if promises are not kept; however, the premise is not fully provenYet, is hype detrimental to science? In many instances, the concern is that hype inflates public expectations, resulting in a loss of trust in a given technology or research avenue if promises are not kept; however, the premise is not fully proven (Sidebar A). “There is no empirical evidence to suggest that unmet promises due to hype in biotechnology, and possibly other scientific fields, will lead to a loss of public trust and, potentially, a loss of public support for science. Thus, arguments made on hype and public trust must be nuanced to reflect this understanding,” Master pointed out.

Sidebar A | Up and down the hype cycle

​AlthoughAlthough hype is usually considered a negative and largely unwanted aspect of scientific and technological communication, it cannot be denied that emphasizing, at least initially, the benefits of a given technology can further its development and use. From this point of view, hype can be seen as a normal stage of technological development, within certain limits. The maturity, adoption and application of specific technologies apparently follow a common trend pattern, described by the information technology company, Gartner, Inc., as the ‘hype cycle''. The idea is based on the observation that, after an initial trigger phase, novel technologies pass through a peak of over-excitement (or hype), often followed by a subsequent general disenchantment, before eventually coming under the spotlight again and reaching a stable plateau of productivity. Thus, hype cycles “[h]ighlight overhyped areas against those that are high impact, estimate how long technologies and trends will take to reach maturity, and help organizations decide when to adopt” (www.gartner.com).“Science is a human endeavour and as such it is inevitably shaped by our subjective responses. Scientists are not immune to these same reactions and it might be valuable to evaluate the visibility of different scientific concepts or technologies using the hype cycle,” commented Pedro Beltrao, a cellular biologist at the University of California San Francisco, USA, who runs the Public Rambling blog (pbeltrao.blogspot.com) about bioinformatics science and technology. The exercise of placing technologies in the context of the hype cycle can help us to distinguish between their real productive value and our subjective level of excitement, Beltrao explained. “As an example, I have tried to place a few concepts and technologies related to systems biology along the cycle''s axis of visibility and maturity [see illustration]. Using this, one could suggest that technologies like gene-expression arrays or mass-spectrometry have reached a stable productivity level, while the potential of concepts like personalized medicine or genome-wide association studies (GWAS) might be currently over-valued.”Together with bioethicist colleague David Resnik, Master has recently highlighted the need for empirical research that examines the relationships between hype, public trust, and public enthusiasm and/or support [12]. Their argument proposes that studies on the effect of hype on public trust can be undertaken by using both quantitative and qualitative methods: “Research can be designed to measure hype through a variety of sources including websites, blogs, movies, billboards, magazines, scientific publications, and press releases,” the authors write. “Semi-structured interviews with several specific stakeholders including genetics researchers, media representatives, patient advocates, other academic researchers (that is, ethicists, lawyers, and social scientists), physicians, ethics review board members, patients with genetic diseases, government spokespersons, and politicians could be performed. Also, members of the general public would be interviewed” [12]. They also point out that such an approach to estimate hype and its effect on public enthusiasm and support should carefully define the public under study, as different publics might have different expectations of scientific research, and will therefore have different baseline levels of trust.Increased awareness of the underlying risks of over-hyping research should help to balance the scientific facts with speculation on the enticing truths and possibilities they revealUltimately, exaggerating, hyping or outright lying is rarely a good thing. Hyping science is detrimental to various degrees to all science communication stakeholders—scientists, institutions, journalists, writers, newspapers and the public. It is important that scientists take responsibility for their share of the hyping done and do not automatically blame the media for making things up or getting things wrong. Such discipline in science communication is increasingly important as science searches for answers to the challenges of this century. Increased awareness of the underlying risks of over-hyping research should help to balance the scientific facts with speculation on the enticing truths and possibilities they reveal. The real challenge lies in favouring such an evolved approach to science communication in the face of a rolling 24-hour news cycle, tight science budgets and the uncontrolled and uncontrollable world of the Internet.? Open in a separate windowThe hype cycle for the life sciences. Pedro Beltrao''s view of the excitement–disappointment–maturation cycle of bioscience-related technologies and/or ideas. GWAS: genome-wide association studies. Credit: Pedro Beltrao.     

In the womb's shadow. The theory of prenatal programming as the fetal origin of various adult diseases is increasingly supported by a wealth of evidence

How does the womb determine the future? Scientists have begun to uncover how environmental and maternal factors influence our long-term health prospects.About two decades ago, David Barker, Professor of Clinical Epidemiology at the University of Southampton, UK, proposed a hypothesis that malnutrition during pregnancy and resultant low birth weight increase the risk of developing cardiovascular disease in adulthood. “The womb may be more important than the home,” remarked Barker in a note about his theory (Barker, 1990). “The old model of adult degenerative disease was based on the interaction between genes and an adverse environment in adult life. The new model that is developing will include programming by the environment in fetal and infant life.”This new idea about the influence of the environment during prenatal development on adult disease risk comes with a better understanding of epigenetic processes…The ‘Barker theory'' has been increasingly accepted and been expanded to other diseases, prominently diabetes and obesity, but also osteoporosis and allergies. “In the last few years, the evidence [of an extended] range of potential disease phenotypes with a prenatal developmental component to risk […] has become much stronger,” said Peter Gluckman at the University of Auckland, New Zealand. “We also need to give greater attention to the growing evidence of prenatal and early postnatal effects on cognitive and non-cognitive functional development and to variation in life history patterns.” Similarly, Michael Symonds and colleagues from the University Hospital at Nottingham, UK, wrote: “These critical periods occur at times when fetal development is plastic; in other words, when the fetus is experiencing rapid cell proliferation making it sensitive to environmental challenges” (Symonds et al, 2009).This new idea about the influence of the environment during prenatal development on adult disease risk comes with a better understanding of epigenetic processes—the biological mechanisms that explain how in utero experiences could translate into phenotypic variation and disease susceptibility within, or over several, generations (Gluckman et al, 2009; Fig 1). “I think it has been the combination of good empirical data (experimental and clinical), the appearance of epigenetic data to provide molecular mechanisms and a sound theoretical framework (based on evolutionary biology) that has allowed this field to mature,” said Gluckman. “Having said that, I think it is only as more human molecular data (epigenetic) emerges that this will happen.”Open in a separate windowFigure 1Environmental sensitivity of the epigenome throughout life. Adapted from Gluckman et al (2009), with permission.Epidemiological data in support of the Barker theory have come from investigations of the effects of the ‘Dutch famine''. Between November 1944 and May 1945, the western part of The Netherlands suffered a severe food shortage, owing to the ravages of the Second World War. In large cities such as Utrecht, Amsterdam, Rotterdam and The Hague, the average individual daily rations were as low as 400–800 kcal. In 1994, a large study involving hundreds of people born between November 1943 and February 1947 in a major hospital in Amsterdam was initiated to assess whether and to what extent the famine had prenatally affected the health of the subjects in later life. The Dutch Famine Birth Cohort Study (www.hongerwinter.nl) found a strong link between malnutrition and under-nutrition in utero and cardiovascular disease and diabetes in later life, as well as increased susceptibility to pulmonary diseases, altered coagulation, higher incidence of breast cancer and other diseases, although some of these links were only found in a few cases.More recently, a group led by Bastiaan Heijmans at the Leiden University Medical Centre in The Netherlands and Columbia University (New York, USA) conducted epigenetic studies of individuals who had been exposed to the Dutch famine during gestation. They analysed the level of DNA methylation at several candidate loci in the cohort and found decreased methylation of the imprinted insulin-like growth factor 2 (IGF2) gene—a key factor in human growth and development—compared with the unexposed, same-sex siblings of the cohort (Heijmans et al, 2008). Further studies have identified another six genes implicated in growth, metabolic and cardiovascular phenotypes that show altered methylation statuses associated with prenatal exposure to famine (Heijmans et al, 2009). The overall conclusion from this work is that exposure to certain conditions in the womb can lead to epigenetic marks that can persist throughout life. “It is remarkable to realize that history can leave an imprint on our DNA that is visible up to six decades later. The current challenge is to scale up such studies to the genome,” said Heijmans. His team is now using high-throughput sequencing to see whether there are genomic regions that are more susceptible to prenatal environmental influences. “Genome-scale data may also allow us to observe the hypothesized accumulation of epigenetic changes in specific biological processes, perhaps as a sign of adaptive responses,” he said.Epigenetic modification of genes involved in key regulatory pathways is central to the mechanisms of nutritional programming of disease, but other factors also seem to have a role including altered cell number or cell type, precocious activation of the hypothalamic–pituitary–adrenal axis, increased local glucocorticoid and endocrine sensitivity, impaired mitochondrial function and reduced oxidative capacity. “The particular type of mechanism invoked seems to vary between tissues according to the duration and timing of the nutritional intervention through pregnancy and/or lactation,” commented Symonds et al (2009).“If we just focus on metabolic, cardiovascular and body compositional outcome, I think the data is now overwhelming that there is an important life-long early developmental contribution. The emergent data would suggest that the underpinning epigenetic processes are likely to be at least as important as genetic variation in contributing to disease risk,” commented Gluckman. His research in animal models has shown that epigenetic changes are potentially reversible in mammals through intervention during development, when the growing organism still has sufficient plasticity (Gluckman et al, 2007). For instance, the neonatal administration of leptin has a bidirectional effect on gene expression and the epigenetic status of key genes involved in metabolic regulation in adult rats; an effect that is dependent on prenatal nutrition and unaffected by post-weaning nutrition (normal compared with high-fat diet). In rats that were manipulated in utero by maternal under-nutrition and fed a hypercaloric diet after weaning, leptin treatment normalized adiposity and hepatic gene expression of proteins that are central to lipid metabolism and glucose homeostasis. “The experimental data showing that programming is reversible is a critical proof of concept. I think there is still confusion as to the role of catch-up growth—its effect may be dependent on its timing and this may have implications for infant nutrition,” Gluckman said.The Dutch Famine Birth Cohort Study […] found a strong link between malnutrition and under-nutrition in utero and cardiovascular disease and diabetes in later life…Central to this view of the link between the developing fetus and its later risk of metabolic disease is the idea of ‘developmental mismatch''. The fetus is programmed, largely through epigenetic changes, to match its environment. However, if the environment in childhood and adult life differs sharply from that during prenatal and early postnatal development, ill adaptation can occur and bring disease in its wake (Gluckman & Hanson, 2006). Poor nutrition during fetal development, for example, would lead the organism to expect a hostile future environment, adversely affecting its ability to cope with a richer environment. “Developmental factors do not cause disease in this context, rather they create a situation where the individual becomes more (or less) sensitive in an obesogenic postnatal environment,” said Gluckman. “The experimental and early clinical data point to both central and peripheral effects and this may explain why lifestyle intervention is so hard in some individuals.”Yet there is another nutrition-related pathway that goes beyond mismatch. According to a recent, large population-based study published in The Lancet, maternal weight gain during pregnancy increases birth weight independently of genetic factors, which increases the long-term risk of obesity-related disease in offspring (Ludwig & Currie, 2010). To reduce or eliminate potential confounds such as genetics, sociodemographic factors or other individual characteristics, the researchers examined the association between maternal weight gain—as a measure of over-nutrition during pregnancy—and birth weight using State-based birth registry data in Michigan and New Jersey, allowing them to compare outcomes from several pregnancies in the same mother. “During pregnancy, insulin resistance develops in the mother to shunt vital nutrients to the growing fetus. Excessive weight or weight gain during pregnancy exaggerates this normal process by further increasing insulin resistance and possibly also by affecting other maternal hormones that regulate placental nutrient transporters. The resulting high rate of nutrient transfer stimulates fetal insulin secretion, overgrowth, and increased adiposity,” the authors speculated (Ludwig & Currie, 2010).It could be that epigenetic malprogramming is also involved in these cases. The group of Andreas Plagemann at the Charitè–University Medicine in Berlin, Germany, analysed acquired alterations of DNA methylation patterns of the hypothalamic insulin receptor promoter (IRP) in neonatally overfed rats. They found that altered nutrition during the critical developmental period of perinatal life induced IRP hypermethylation in a seemingly glucose-dependent manner. This revealed an epigenetic mechanism that could affect the function of a promoter that codes for a receptor involved in the life-long regulation of food intake, body weight and metabolism (Plagemann et al, 2010). “In parallel with the general ‘diabesity'' epidemics, diabetes during pregnancy and overweight in pregnant women meanwhile reach dramatic prevalences. Consequently, mean birth weight and frequencies of ‘fat babies'' rise,” said Plagemann. “Taking together epidemiological, clinical and experimental observations, it seems obvious that fetal hyperinsulinism induced by maternal hyperglycaemia/overweight has ‘functionally teratogenic'' significance for a permanently increased disposition to obesity, diabetes, the metabolic syndrome, and subsequent cardiovascular diseases in the offspring” (Fig 2).Open in a separate windowFigure 2Pathogenetic framework, mechanisms and consequences of perinatal malprogramming, showing the etiological significance of perinatal overfeeding and hyperinsulinism for excess weight gain, obesity, diabetes mellitus and cardiovascular diseases in later life. Credit: Andreas Plagemann.Added to the mix is the ‘endocrine-disruptor hypothesis'', one nuance of which proposes that prenatal—as well as postnatal—exposure to environmental chemicals contributes to adipogenesis and the development of obesity by interfering with homeostatic mechanisms that control weight. Several environmental pollutants, nutritional components and pharmaceuticals have been suggested to have ‘obesogenic'' properties—the best known are tributyltin, bisphenol and phthalates (Grün & Blumberg, 2009). “While one cannot presently estimate the degree to which obesogen exposure contributes to the observed increases in obesity, the main conclusion to be drawn from research in our laboratory is that obesogens exist and that prenatal obesogen exposure can predispose an exposed individual to become fatter, later in life,” said Bruce Blumberg at the University of California at Irvine, USA, who is also credited with coining the term ‘obesogen''. “The existence of such chemicals was not even suspected as recently as seven years ago when we began this research.”Several environmental pollutants, nutritional components and pharmaceuticals have been suggested to have ‘obesogenic'' properties…It is clear that diet and exercise are important contributors to the body weight of an individual. However, weight maintenance is not as simple as balancing a ‘caloric checkbook'', or fewer people would be obese, Blumberg commented. Early nutrition and chemical exposure could alter the metabolic set-point of an individual, making their subsequent fight against weight gain more difficult. “We do not currently know how many chemicals are obesogenic or the entire spectrum of mechanisms through which obesogens act,” Blumberg said. “Our data suggest that prenatal obesogen exposure alters the fate of a type of stem cells in the body to favour the development of fat cells at the expense of other cell types (such as bone). In turn, this is likely to increase one''s weight with time.”Obesogen exposure in utero and/or during the first stages of postnatal growth could therefore predispose a child to obesity by influencing all aspects of adipose tissue growth, starting from multipotent stem cells and ending with mature adipocytes (Janesick & Blumberg, 2011). “Epigenetics may also allow us to have a clearer view of the role of xenobiotics, such as bisphenol A, where traditional teratogenetic approaches to analysis seem inappropriate,” Gluckman said. “I expect the potential for either direct or indirect epigenetic inheritance will get much focus in human studies over the next few years.”The impact of the mother''s emotional state during pregnancy on the child''s behaviour and cognitive development of the child is also fertile ground for research. “It has been known from over 50 years of research in animals that stress during pregnancy can have long-term effects on the behavioural and cognitive outcome for the offspring. Over the last ten years many studies, including our own, have shown that the same is true in humans,” said Vivette Glover, a leading expert in the field from Imperial College (London, UK). “If the mother is stressed or anxious while she is pregnant, her child is more likely to have a range of problems such as symptoms of anxiety or depression, [attention deficit hyperactivity disorder] ADHD or conduct disorder, and to be slower at learning, even after allowing for postnatal influences.” Most children are not affected, but if the anxiety level of the mother is in the top 15% of the general population, the risk of her child having these problems increases from about 5% to 10%, Glover explained.Early nutrition and chemical exposure could alter the metabolic set-point of an individual, making their subsequent fight against weight gain more difficultFocusing on the mechanisms that underlie this, Glover''s team has shown that the cognitive development of the child is slower if the fetus is exposed to higher levels of the stress hormone cortisol in the womb (Bergman et al, 2010). Cortisol in fetal circulation is a combination of that produced endogenously by the fetus and that derived from the mother, through the placenta. Glover''s hypothesis is that the placenta might have a key role as a programming vector: if the mother is stressed and more anxious, the placenta becomes a less effective barrier and allows more cortisol to pass from the mother to the fetus (O''Donnell et al, 2009). “Our most recent research has studied how these prenatal effects can be altered by the later quality of the mothering, and we have found that the effects can be exacerbated if the child is insecure and buffered if the child is securely attached to the mother. So the effects are not all over at birth. There are both prenatal and postnatal effects,” Glover said. “There are large public health implications of all this. If we, as a society, cared better for the emotional wellbeing of our pregnant women we would also improve the behavioural, emotional and cognitive outcome for the next generation,” she concluded (Sidebar A).A more integrated view of the developmental ontogeny of a human from embryo to adult is needed…

Sidebar A | Focus on fetal life to help the next generation

“The global burden of death, disability, and loss of human capital as a result of impaired fetal development is huge and affects both developed and developing countries,” concludes a recent World Health Organization technical consultation (WHO, 2006). It advocates moving away from a focus on birth weight to embrace more factors to ensure an optimal environment for the fetus, to maximize its potential for a healthy life. As our knowledge of developmental biology expands, there is progressively greater awareness that events early in human development can have effects in later stages of life, and even inter-generational consequences in terms of non-communicable diseases, such as cardiovascular disease and diabetes.Calling for a radical change in medical attitudes—which they say are responsible for not giving enough credit to “the concept that environmental factors acting early in life (usually in fetal life) have profound effects on vulnerability to disease later in life”—Peter Gluckman, Mark Hanson and Murray Mitchell have recently proposed several prevention and intervention initiatives that could reduce the burden of chronic disease in the next generation (Gluckman et al., 2010). These include limitation of adolescent pregnancy, possibly delaying the age of first pregnancy until four years after menarche; promotion of a healthy diet and lifestyle among women becoming pregnant to avoid the long-term effects of both excessive and deficient maternal nutrition, smoking, or drug and alcohol abuse; and encouraging breastfeeding for optimal growth, resistance to infection, cardiovascular health and neurocognitive development. Clearly, such actions would face a mix of educational, political and social issues, depending on the geographical or cultural area.“None of these solutions seems sophisticated, although it may have taken the recent insights into underlying developmental epigenetic mechanisms to emphasize them. But, when viewed in terms of their potential impact, especially in developing societies and in lower socioeconomic groups in developed countries, it is clear that their importance has been underestimated” (Gluckman et al., 2010).A more integrated view of the developmental ontogeny of a human from embryo to adult is needed, grounded by appreciation of the fact that the developmental trajectory of the fetus is influenced by factors such as maternal nutrition, body composition and maternal age (Fig 3). This must not be limited to the offspring of gestational diabetics and obese mothers. “While these are more extreme influences on the fetus and will lead to immediate consequences (blurring the boundary between what is physiological and pathophysiological), I think the most important observations and conceptual advances will emerge from understanding the long-term implications and underpinning mechanisms of relatively normal early development still having plastic consequences,” Gluckman said. “Thus, what seem to be unremarkable pregnancies still have important influences on the destiny of the offspring.” Though this might be easy to say, the regulatory mechanisms that underlie the complex journey of development await further clarification.Open in a separate windowFigure 3Leonardo Da Vinci: Studies of the fetus in the womb, circa 1510–1513. In Da Vinci''s words, referring to his treatise on anatomy, for which these drawings were made: “This work must begin with the conception of man, and describe the nature of the womb and how the fetus lives in it, up to what stage it resides there, and in what way it quickens into life and feeds. Also its growth and what interval there is between one stage of growth and another. What it is that forces it out from the body of the mother, and for what reasons it sometimes comes out of the mother''s womb before the due time” (Dunn, 1997).     

DNA Repair Mechanisms: the Work of Aziz Sancar

Action Mechanism of Escherichia coli DNA Photolyase. III. Photolysis of the Enzyme-Substrate Complex and the Absolute Action Spectrum(Sancar, G. B., Jorns, M. S., Payne, G., Fluke, D. J., Rupert, C. S., and Sancar, A. (1987) J. Biol. Chem. 262, 492–498)Reconstitution of the Human DNA Repair Excision Nuclease in the Highly Defined System(Mu, D., Park, C.-H., Matsunaga, T., Hsu, D. S., Reardon, J. T., and Sancar, A. (1995) J. Biol. Chem. 270, 2415–2418)Aziz Sancar was born in Savur, Turkey in 1946. Although both his parents were illiterate, they valued the importance of education and did their best to see that Sancar received a good one. They succeeded, and he excelled in many scientific subjects in high school. However, he also dreamed of playing on Turkey''s national soccer team, and this dream almost came true when, as a senior in high school, he was invited to attend tryouts to be a goalie on the national under-18 team. Ultimately he decided not to accept the invitation, later explaining, “upon serious consideration, I decided I wasn''t tall enough to be an outstanding goalie, and instead I concentrated on my studies” (1).Open in a separate windowAziz SancarAfter graduating in 1963, Sancar enrolled at Istanbul Medical School with the idea of becoming a doctor. However, after taking a biochemistry class during his 2nd year, he decided to become a research biochemist. Surprisingly, when he discussed his desire to pursue a Ph.D. with his biochemistry professor, he advised Sancar to practice medicine briefly before plunging into research, reasoning that anyone who spends the time getting a medical degree should at least practice for a couple years. So, Sancar spent 2 years as a rural physician near his hometown of Savur.In 1973, Sancar came to the United States to study with Claud Rupert in the molecular biology department of the University of Texas at Dallas. While in Turkey, Sancar had developed an interest in photoreactivation, the process by which DNA damaged by UV light is repaired by longer wavelength blue light. Rupert had identified photolyase, the enzyme that mediated the process by catalyzing the opening of the cyclobutane ring in pyrimidine dimers, and Sancar was eager to work him. The main topic of study in the Rupert laboratory in the early 1970s was the nature of photolyase''s chromophore. To that end, Sancar spent several years cloning and characterizing the gene for photolyase (2). After finally succeeding, he set out to purify the protein, but Rupert told him he had done enough research for his thesis and advised him to write his dissertation and graduate.After earning his Ph.D. in 1977, Sancar applied to three different laboratories hoping to continue studying DNA repair. All three laboratories rejected him. However, he learned that Dean Rupp at Yale University was interested in cloning repair genes, and although he didn''t have a postdoctoral position available, he was looking for a technician. Sancar accepted the job and joined the lab. Working with Rupp, Sancar identified and cloned several Escherichia coli repair genes, including the uvrA, uvrB, and uvrC genes involved in excision repair (3–5). He then purified the three uvr proteins and reconstituted the UVRABC nuclease, which he termed “excision nuclease” or “excinuclease” (6).In 1982, Sancar left Yale to become an associate professor of biochemistry at the University of North Carolina, Chapel Hill. There he resumed his work on photolyase and discovered that the enzyme contains two chromophores: FADH⁻ and a pterin (7–9). He also proposed a model for the reaction mechanism of photolyase repair, which is the subject of the first Journal of Biological Chemistry (JBC) Classic reprinted here.At the time the Classic was published, there were two possible mechanisms for the repair reaction: the first involved energy transfer from a sensitizer to pyrimidine dimers, and the second involved electron transfer between the pyrimidine dimer and the photosensitizer. By determining the absolute action spectrum of the enzyme, Sancar and his colleagues were able to determine that the flavin cofactor of the enzyme is fully reduced in vivo and that, upon absorption of a single photon in the 300–500 nm range, the photolyase chromophore donates an electron to the pyrimidine dimer causing its reversal to two pyrimidines. Eighteen years after publishing this Classic paper, Sancar was able to capture the excited flavin intermediate and observe the photolyase electron transfer, definitively proving his model (10).Sancar also continued studying other DNA repair pathways and soon turned his attention to excision repair in humans. The second JBC Classic is a result of Sancar''s studies on xeroderma pigmentosum, a hereditary disease caused by a defect in nucleotide excision repair as a result of mutations in one of several genes: XPA through XPG. In the paper, Sancar and his colleagues purified the components known to be required for the incision reaction and reconstituted the excision nuclease activity with these proteins. Using this system, they determined that the excised fragment remains associated with the post-incision DNA-protein complex, suggesting that accessory proteins are needed to release the excised oligomer.Sancar is currently the Sarah Graham Kenan Professor of Biochemistry and Biophysics at the UNC School of Medicine. He has received many honors and awards in recognition of his contributions to science, including the Presidential Young Investigator Award from the National Science Foundation (1984) and the highest awards from the American Society for Photobiology (1990) and the Turkish Scientific Research Council (1995). Sancar was also the first Turkish-American member of the National Academy of Sciences (2005).     

When life gets physical

Does the spin of an electron allow birds to see the Earth''s magnetic field? Andrea Rinaldi investigates the influence of quantum events in the biological world.The subatomic world is nothing like the world that biologists study. Physicists have struggled for almost a century to understand the wave–particle duality of matter and energy, but many questions remain unanswered. That biological systems ultimately obey the rules of quantum mechanics might be self-evident, but the idea that those rules are the very basis of certain biological functions has needed 80 years of thought, research and development for evidence to begin to emerge (Sidebar A).

Sidebar A | Putting things in their place

Although Erwin Schrödinger (1887–1961) is often credited as the ‘father'' of quantum biology, owing to the publication of his famous 1944 book, What is Life?, the full picture is more complex. While other researchers were already moving towards these concepts in the 1920s, the German theoretical physicist Pascual Jordan (1902–1980) was actually one of the first to attempt to reconcile biological phenomena with the quantum revolution that Jordan himself, working with Max Born and Werner Heisenberg, largely ignited. “Pascual Jordan was one of many scientists at the time who were exploring biophysics in innovative ways. In some cases, his ideas have proven to be speculative or even fantastical. In others, however, his ideas have proven to be really ahead of their time,” explained Richard Beyler, a science historian at Portland State University, USA, who analysed Jordan''s contribution to the rise of quantum biology (Beyler, 1996). “I think this applies to Jordan''s work in quantum biology as well.”Beyler also remarked that some of the well-known figures of molecular biology''s past—Max Delbrück is a notable example—entered into their studies at least in part as a response or rejoinder to Jordan''s work. “Schrödinger''s book can also be read, on some level, as an indirect response to Jordan,” Beyler said.Jordan was certainly a complex personality and his case is rendered more complicated by the fact that he explicitly hitched his already speculative scientific theories to various right-wing political philosophies. “During the Nazi regime, for example, he promoted the notion that quantum biology served as evidence for the naturalness of dictatorship and the prospective death of liberal democracy,” Beyler commented. “After 1945, Jordan became a staunch Cold Warrior and saw in quantum biology a challenge to philosophical and political materialism. Needless to say, not all of his scientific colleagues appreciated these propagandistic endeavors.”Pascual Jordan [pictured above] and the dawn of quantum biology. From 1932, Jordan started to outline the new field''s background in a series of essays that were published in journals such as Naturwissenschaften. An exposition of quantum biology is also encountered in his book Die Physik und das Geheimnis des organischen Lebens, published in 1941. Photo courtesy of Luca Turin.Until very recently, it was not even possible to investigate whether quantum phenomena such as coherence and entanglement could play a significant role in the function of living organisms. As such, researchers were largely limited to computer simulations and theoretical experiments to explain their observations (see A quantum leap in biology, www.emboreports.org). Recently, however, quantum biologists have been making inroads into developing methodology to measure the degree of quantum entanglement in light-harvesting systems. Their breakthrough has turned once ephemeral theories into solid evidence, and has sparked the beginning of an entirely new discipline.How widespread is the direct relevance of quantum effects in nature is hard to say and many scientists suspect that there are only a few cases in which quantum mechanics have a crucial role. However, interest in the field is growing and researchers are looking for more examples of quantum-dependent biological systems. In a way, quantum biology can be viewed as a natural evolution of biophysics, moving from the classical to the quantum, from the atomic to the subatomic. Yet the discipline might prove to be an even more intimate and further-reaching marriage that could provide a deeper understanding of things such as protein energetics and dynamics, and all biological processes where electrons flow.Recently […] quantum biologists have been making inroads into developing methodology to measure the degree of quantum entanglement in light-harvesting systemsAmong the biological systems in which quantum effects are believed to have a crucial role is magnetoreception, although the nature of the receptors and the underlying biophysical mechanisms remain unknown. The possibility that organisms use a ferromagnetic material (magnetite) in some cases has received some confirmation, but support is growing for the explanation lying in a chemical detection mechanism with quantum mechanical properties. This explanation posits a chemical compass based on the light-triggered production of a radical pair—a pair of molecules each with an unpaired electron—the spins of which are entangled. If the products of the radical pair system are spin-dependent, then a magnetic field—like the geomagnetic one—that affects the direction of spin will alter the reaction products. The idea is that these reaction products affect the sensitivity of light sensors in the eye, thus allowing organisms to ‘see'' magnetic fields.The research comes from a team led by Thorsten Ritz at the University of California Irvine, USA, and other groups, who have suggested that the radical pair reaction takes place in the molecule cryptochrome. Cryptochromes are flavoprotein photoreceptors first identified in the model plant Arabidopsis thaliana, in which they play key roles in growth and development. More recently, cryptochromes have been found to have a role in the circadian clock of fruit flies (Ritz et al, 2010) and are known to be present in migratory birds. Intriguingly, magnetic fields have been shown to have an effect on both Arabidopsis seedlings, which respond as though they have been exposed to higher levels of blue light, and Drosophila, in which the period length of the clock is lengthened, mimicking the effect of increased blue light signal intensity on cryptochromes (Ahmad et al, 2007; Yoshii et al, 2009).“The study of quantum effects in biological systems is a rapidly broadening field of research in which intriguing phenomena are yet to be uncovered and understood”Direct evidence that cryptochrome is the avian magnetic compass is currently lacking, but the molecule does have some features that make its candidacy possible. In a recent review (Ritz et al, 2010), Ritz and colleagues discussed the mechanism by which cryptochrome might form radical pairs. They argued that “Cryptochromes are bound to a light-absorbing flavin cofactor (FAD) which can exist in three interconvertable [sic] redox forms: (FAD, FADH^•, FADH⁻),” and that the redox state of FAD is light-dependent. As such, both the oxidation and reduction of the flavin have radical species as intermediates. “Therefore both forward and reverse reactions may involve the formation of radical pairs” (Ritz et al, 2010). Although speculative, the idea is that a magnetic field could alter the spin of the free electrons in the radical pairs resulting in altered photoreceptor responses that could be perceived by the organism. “Given the relatively short time from the first suggestion of cryptochrome as a magnetoreceptor in 2000, the amount of studies from different fields supporting the photo-magnetoreceptor and cryptochrome hypotheses […] is promising,” the authors concluded. “It suggests that we may be only one step away from a true smoking gun revealing the long-sought after molecular nature of receptors underlying the 6^th sense and thus the solution of a great outstanding riddle of sensory biology.”Research into quantum effects in biology took off in 2007 with groundbreaking experiments from Graham Fleming''s group at the University of California, Berkeley, USA. Fleming''s team were able to develop tools that allowed them to excite the photosynthetic apparatus of the green sulphur bacterium Chlorobium tepidum with short laser pulses to demonstrate that wave-like energy transfer takes place through quantum coherence (Engel et al, 2007). Shortly after, Martin Plenio''s group at Ulm University in Germany and Alán Aspuru-Guzik''s team at Harvard University in the USA simultaneously provided evidence that it is a subtle interplay between quantum coherence and environmental noise that optimizes the performance of biological systems such as the photosynthetic machinery, adding further interest to the field (Plenio & Huelga, 2008; Rebentrost et al, 2009). “The recent Quantum Effects in Biological Systems (QuEBS) 2011 meeting in Ulm saw an increasing number of biological systems added to the group of biological processes in which quantum effects are suspected to play a crucial role,” commented Plenio, one of the workshop organizers; he mentioned the examples of avian magnetoreception and the role of phonon-assisted tunnelling to explain the function of the sense of smell (see below). “The study of quantum effects in biological systems is a rapidly broadening field of research in which intriguing phenomena are yet to be uncovered and understood,” he concluded.“The area of quantum effects in biology is very exciting because it is pushing the limits of quantum physics to a new scale,” Yasser Omar from the Technical University of Lisbon, Portugal commented. ”[W]e are finding that quantum coherence plays a significant role in the function of systems that we previously thought would be too large, too hot—working at physiological temperatures—and too complex to depend on quantum effects.”Another growing focus of quantum biologists is the sense of smell and odorant recognition. Mainstream researchers have always favoured a ‘lock-and-key'' mechanism to explain how organisms detect and distinguish different smells. In this case, the identification of odorant molecules relies on their specific shape to activate receptors on the surface of sensory neurons in the nasal epithelium. However, a small group of ‘heretics'' think that the smell of a molecule is actually determined by intramolecular vibrations, rather than by its shape. This, they say, explains why the shape theory has so far failed to explain why different molecules can have similar odours, while similar molecules can have dissimilar odours. It also goes some way to explaining how humans can manage with fewer than 400 smell receptors.…determining whether quantum effects have a role in odorant recognition has involved assessing the physical violations of such a mechanism […] and finding that, given certain biological parameters, there are noneA recent study in Proceedings of the National Academy of Sciences USA has now provided new grist for the mill for ‘vibrationists''. Researchers from the Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece—where the experiments were performed—and the Massachusetts Institute of Technology (MIT), USA, collaborated to replace hydrogen with deuterium in odorants such as acetophenone and 1-octanol, and asked whether Drosophila flies could distinguish the two isotopes, which are identically shaped but vibrate differently (Franco et al, 2011). Not only were the flies able to discriminate between the isotopic odorants, but when trained to discriminate against the normal or deuterated isotopes of a compound, they could also selectively avoid the corresponding isotope of a different odorant. The findings are inconsistent with a shape-only model for smell, the authors concluded, and suggest that flies can ‘smell molecular vibrations''.“The ability to detect heavy isotopes in a molecule by smell is a good test of shape and vibration theories: shape says it should be impossible, vibration says it should be doable,” explained Luca Turin from MIT, one of the study''s authors. Turin is a major proponent of the vibration theory and suggests that the transduction of molecular vibrations into receptor activation could be mediated by inelastic electron tunnelling (Fig 1; see also The scent of life, www.emboreports.org). “The results so far had been inconclusive and complicated by possible contamination of the test odorants with impurities,” Turin said. “Our work deals with impurities in a novel way, by asking flies whether the presence of deuterium isotope confers a common smell character to odorants, much in the way that the presence of -SH in a molecule makes it smell ‘sulphuraceous'', regardless of impurities. The flies'' answer seems to be ‘yes''.”Open in a separate windowFigure 1Diagram of a vibration-sensing receptor using an inelastic electron tunnelling mechanism. An odorant—here benzaldehyde—is depicted bound to a protein receptor that includes an electron donor site at the top left to which an electron—blue sphere—is bound. The electron can tunnel to an acceptor site at the bottom right while losing energy (vertical arrow) by exciting one or more vibrational modes of the benzaldehyde. When the electron reaches the acceptor, the signal is transduced via a G-protein mechanism, and the olfactory stimulus is triggered. Credit: Luca Turin.One of the study''s Greek co-authors, Efthimios Skoulakis, suggested that flies are better suited than humans at doing this experiment for a couple of reasons. “[The flies] seem to have better acuity than humans and they cannot anticipate the task they will be required to complete (as humans would), thus reducing bias in the outcome,” he said. “Drosophila does not need to detect deuterium per se to survive and be reproductively successful, so it is likely that detection of the vibrational difference between such a compound and its normal counterpart reflects a general property of olfactory systems.”The question of whether quantum mechanics really plays a non-trivial role in biology is still hotly debated by physicists and biologists alikeJennifer Brookes, a physicist at University College London, UK, explained that recent advances in determining whether quantum effects have a role in odorant recognition has involved assessing the physical violations of such a mechanism in the first instance, and finding that, given certain biological parameters, there are none. “The point being that if nature uses something like the quantized vibrations of molecules to ‘measure'' a smell then the idea is not—mathematically, physically and biologically—as eccentric as it at first seems,” she said. Moreover, there is the possibility that quantum mechanics could play a much broader role in biology than simply underpinning the sense of smell. “Odorants are not the only small molecules that interact unpredictably with large proteins; steroid hormones, anaesthetics and neurotransmitters, to name a few, are examples of ligands that interact specifically with special receptors to produce important biological processes,” Brookes wrote in a recent essay (Brookes, 2010).The question of whether quantum mechanics really plays a non-trivial role in biology is still hotly debated by physicists and biologists alike. “[A] non-trivial quantum effect in biology is one that would convince a biologist that they needed to take an advanced quantum mechanics course and learn about Hilbert space and operators etc., so that they could understand the effect,” argued theoretical quantum physicists Howard Wiseman and Jens Eisert in their contribution to the book Quantum Aspects of Life (Wiseman & Eisert, 2008). In their rational challenge to the general enthusiasm for a quantum revolution in biology, Wiseman and Eisert point out that a number of “exotic” and “implausible” quantum effects—including a quantum life principle, quantum computing in the brain, quantum computing in genetics, and quantum consciousness—have been suggested and warn researchers to be cautious of “ideas that are more appealing at first sight than they are realistic” (Wiseman & Eisert, 2008).“One could easily expect many more new exciting ideas and discoveries to emerge from the intersection of two major areas such as quantum physics and biology”Keeping this warning in mind, the view of life from a quantum perspective can still provide a deeper insight into the mechanisms that allow living organisms to thrive without succumbing to the increasing entropy of their environment. But does quantum biology have practical applications? “The investigation of the role of quantum physics in biology is fascinating because it could help explain why evolution has favoured some biological designs, as well as inspire us to develop more efficient artificial devices,” Omar said. The most often quoted examples of such devices are solar collectors that would use efficient energy transport mechanisms inspired by the quantum proficiency of natural light-harvesting systems, and quantum computing. But there is much more ahead. In 2010, the Pentagon''s cutting-edge research branch, DARPA (Defense Advanced Research Projects Agency, USA), launched a solicitation for innovative proposals in the area of quantum effects in a biological environment. “Proposed research should establish beyond any doubt that manifestly quantum effects occur in biology, and demonstrate through simulation proof-of-concept experiments that devices that exploit these effects could be developed into biomimetic sensors,” states the synopsis (DARPA, 2010). This programme will thus look explicitly at photosynthesis, magnetic field sensing and odour detection to lay the foundations for novel sensor technologies for military applications.Clearly a number of civil needs could also be fulfilled by quantum-based biosensors. Take, for example, the much sought-after ‘electronic nose'' that could replace the use of dogs to find drugs or explosives, or could assess food quality and safety. Such a device could even be used to detect cancer, as suggested by a recent publication from a Swedish team of researchers who reported that ovarian carcinomas emit a different array of volatile signals to normal tissue (Horvath et al, 2010). “Our goal is to be able to screen blood samples from apparently healthy women and so detect ovarian cancer at an early stage when it can still be cured,” said the study''s leading author György Horvath in a press release (University of Gothenburg, 2010).Despite its already long incubation time, quantum biology is still in its infancy but with an intriguing adolescence ahead. “A new wave of scientists are finding that quantum physics has the appropriate language and methods to solve many problems in biology, observing phenomena from a different point of view and developing new concepts. The next important steps are experimental verification/falsification,” Brookes said. “One could easily expect many more new exciting ideas and discoveries to emerge from the intersection of two major areas such as quantum physics and biology,” Omar concluded.     

The process of reversible phosphorylation: the work of Edmond H. Fischer

Edmond H. Fischer was awarded the 1992 Nobel Prize in Physiology or Medicine for his joint research with Edwin G. Krebs on reversible protein phosphorylation. The two Classics reprinted here relate some of Fischer and Krebs'' early discoveries in their phosphorylase researchPhosphorylase Activity of Skeletal Muscle Extracts (Krebs, E. G., and Fischer, E. H. (1955) J. Biol. Chem. 216, 113–120)Conversion of Phosphorylase b to Phosphorylase a in Muscle Extracts (Fischer, E. H., and Krebs, E. G. (1955) J. Biol. Chem. 216, 121–132)Edmond H. Fischer was born in Shanghai, China in 1920. He was sent to boarding school in Switzerland at age 7, and in 1935, he entered Geneva''s Collège de Calvin. There, he became friends with his classmate Wilfried Haudenschild, and together, they decided that one of them should go into the sciences and the other into medicine so they could cure the world of all ills. Fischer chose science.Open in a separate windowEdmond H. FischerJust before the start of World War II, Fischer completed high school and entered the School of Chemistry at the University of Geneva. He earned two Licences ès Sciences, one in biology, the other in chemistry, and 2 years later, he was awarded a Diploma of “Ingénieur Chimiste.” For his thesis, he worked with Kurt H. Meyer on the purification of amylase from hog and human pancreas, as well as saliva and several strains of bacteria.In 1950, Fischer went to the United States to do a postdoctoral fellowship with Paul Karrer at CalTech. However, when he arrived in Pasadena he received a letter from Journal of Biological Chemistry (JBC) Classic author Hans Neurath (1), chairman of the department of biochemistry at the University of Washington, offering him an assistant professorship in his department. Fischer visited Seattle and accepted the offer, in part because the surrounding mountains, forests, and lakes reminded him of his native Switzerland.Within 6 months of his arrival, Fischer started working on glycogen phosphorylase with Edwin G. Krebs, who was featured in a previous JBC Classic (2). Krebs had trained with JBC Classic authors Carl and Gerty Cori who had discovered that muscle phosphorylase exists in two forms, phosphorylase a, which was easily crystallized and was active without the addition of AMP, and phosphorylase b, a more soluble protein, which was inactive without AMP (3). They believed that AMP served some kind of co-factor function for the enzyme, facilitating its transition between the two forms.However, in Geneva, Fischer had purified potato phosphorylase, which had no AMP requirement. Because it seemed unlikely that muscle phosphorylase but not potato phosphorylase would require AMP as a co-factor, Fischer and Krebs decided to try to elucidate the role of AMP in the phosphorylase reaction. They never discovered what the nucleotide was doing (this problem was solved several years later when Jacques Monod proposed his allosteric model for the regulation of enzymes), but they did discover that muscle phosphorylase was regulated by an enzyme-catalyzed phosphorylation-dephosphorylation reaction.The two JBC Classics reprinted here relate some of Fischer and Krebs'' early discoveries in their phosphorylase research. In the first Classic, the pair performed experiments to determine whether environmental temperature affects the phosphorylase content of skeletal muscle. They were unable to detect any temperature effects, but they did make the surprising discovery that the muscle extracts contained mainly phosphorylase b rather than phosphorylase a. The pair concluded that “If resting muscle contains mainly phosphorylase b… then pronounced activation of the phosphorylase reaction under various conditions is possible.”The second JBC Classic was printed back-to-back with the first. In it, Krebs and Fischer examine the requirements for the phosphorylase conversion and present evidence that the conversion of phosphorylase b to a in cell-free muscle extracts requires a nucleotide containing high energy phosphate and a divalent metal ion. However, they state that “whether this implies that during conversion there is a direct phosphorylation of the enzyme or the formation of an ‘active’ intermediate cannot be stated at this time. It is also possible that the function of ATP is concerned with the synthesis of a prosthetic group.”Similar work was being carried out on liver phosphorylase at approximately the same time by Earl Sutherland. As discussed in a previous JBC Classic (4), Sutherland discovered the second messenger cyclic AMP (cAMP), which he showed promoted the phosphorylation and activation of phosphorylase. The way in which cAMP promoted phosphorylase activation was eventually elucidated when Krebs and Fischer discovered phosphorylase kinase, which was responsible for phosphorylating phosphorylase. Phosphorylase kinase itself existed in a highly activated phosphorylated form and a less active nonphosphorylated form.As a result of the significance of their studies, Krebs and Fischer were awarded the 1992 Nobel Prize in Physiology or Medicine “for their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism.”In addition to the Nobel Prize, Fischer has received many awards and honors in recognition of his contributions to science. These include the Werner Medal from the Swiss Chemical Society, the Lederle Medical Faculty Award, the Prix Jaubert from the University of Geneva, and jointly with Krebs, the Senior Passano Award and the Steven C. Beering Award from Indiana University. Fischer was elected to the American Academy of Arts and Sciences in 1972 and to the National Academy of Sciences in 1973.¹     

Darwin and Dostoyevsky: twins

The Russian poet Fyodor Dostoyevsky published an insightful treatise on human nature in his novel ‘The Brothers Karamazov'' in 1880. His account of humanity may offer as much insight into human nature for scientists as Darwin''s The Descent of Man.Late in the nineteenth century, Charles Darwin (1809–1882) and Fyodor Dostoyevsky (1821–1881) published accounts of their investigation of humankind. Darwin did so in 1871 in his book The Descent of Man, Dostoyevsky in 1880 in the parable of The Grand Inquisitor in his book The Brothers Karamazov. Last year we celebrated Darwin''s anniversary; for biologists, 2010—the 130th anniversary of Dostoyevsky''s book—might have been the year of Dostoyevsky.Dostoyevsky was familiar with Darwin''s doctrine and he was willing to admit “man''s descent from the ape”. An orthodox Christian, he put this sentiment in religious terms: “It does not really matter what man''s origins are, the Bible does not explain how God moulded him out of clay or carved him out of stone. Yet, he saw a difference between humans and animals: humans have a soul.The philosopher Nikolay Berdyayev noticed: “[Dostoyevsky] concealed nothing, and that''s why he could make astonishing discoveries. In the fate of his heroes he relates his own destiny, in their doubts he reveals his vacillations, in their ambiguity his self-splitting, in their criminal experience the secret crimes of his spirit.”The Grand Inquisitor can be read as Dostoyevsky''s treatise on human nature. In the tale, Jesus Christ revisits Earth during the period of the Inquisition and is arrested by the Church and sentenced to death. The Grand Inquisitor comes to visit Jesus in his prison cell to argue with him about their conceptions of human nature. He explains that humankind needs to be ruled to be happy and that the true freedom Jesus offered doomed humanity to suffering and unhappiness. Dostoyevsky''s superposition of these two points of view on humankind reminds us of the principle of complementarity, by which the physicist Niels Bohr attempted to account for the particle-wave duality of quantum physics.Dostoyevsky conceives of humans as complex, contradictory and inconsistent creatures. Humans perceive personal liberty as a burden and are willing to barter for it, as the Grand Inquisitor explained to Christ, for “miracle, mystery, and authority”. In addition, “the mystery of human being does not only rest in the desire to live, but in the problem: for what should one live at all?” We might say that these faculties make Homo sapiens a religious species. Not in the sense of believing in gods or a god, but in the sense of the Latin word religare, which means to bind, connect or enfold. Humans are mythophilic animals, driven by a need to find a complete explanation for events in terms of intentions and purposes.Research into the neurological bases of imagination, transcendence, metaphorability, art and religion, as well as moral behaviour and judgement (Trimble, 2007) is consistent with Dostoyevsky''s views. It has identified areas of the brain that have been labelled as the ‘god module'' or ‘god spot'' (Alper, 2001). These areas represent a new stratum of evolutionary complexity, an emergence specific to the human species. Their mental translations might be tentatively designated as the Darwinian soul, anchored in the material substrate and neither immortal nor cosmic. As consciousness and volition have become legitimate subjects of neuroscience (Baars, 2003), the Darwinian soul, and with it spirituality, seems to be ripe for scientific inquiry: the quest for meaning, creation and perception of metaphors, the experience of the trinity of Truth, Good and Beauty, the capacity for complex feelings that Immanuel Kant called sublimity, the thrill of humour and play, the power of empathy and the follies of boundless love or hate. Secularization does not erase the superstructure of spirituality: it is reflected, however queer it might seem, in the hypertrophy of the entertainment industry and also, more gloomily, in spiritual conflicts on a global scale.Dostoyevsky''s views on the human soul might be closer to those of Alfred Russel Wallace, who believed that an unknown force directed evolution towards an advanced organization. We can identify this ‘force'' as the second law of thermodynamics (Sharma & Annila, 2007). By moving evolving systems ever farther away from equilibrium, the second law eventually became the Creator of the ‘Neuronal God''.Christ, in the parable of the Grand Inquisitor, might be conceived of as a symbol of the truth outside the human world. Christ was listening to the assertions and questions of his interlocutor, but did not say a single word. His silence is essential to the parable.Similarly, the cosmos, to which humanity has been addressing its questions and predications, remains silent. By science, we increase knowledge only by tiny increments. The ‘god modules'' of our brains, unsatisfied and impatient, have hastily provided the full truth, deposited in the Holy Scripture. There are at least three books claiming to contain the revealed and hence unquestionable truth: the Judaic Torah, Christian Bible and Muslim Qur''an. A dogma of genocentrism in biology might offer an additional Scripture: the sequence of DNA in the genomes.Dostoyevsky''s legacy may suggest an amendment to the UN Charter. We, united humankind, solemnly declare: No truth has ever been revealed to us; we respect and tolerate each other in our independent searching and erring.