We learned about the double helix over 50 years ago with publication of the Watson Crick formulation (Watson and Crick 1953) and the fiber X-ray diffraction patterns of groups led by Maurice Wilkins (Wilkins and Randall 1953) and Rosalind Franklin (Franklin and Gosling 1953). Analysis of the diffraction pattern, especially the fibers of the hydrated B form, could be immediately interpreted as consistent with a double helix. The weakness of the first-layer line relative to the second and the virtual absence of the fourth-layer line clearly suggested two chains wrapping around each other with the phosphate groups on the outside. More complex and not answered at the time was the question of why there were two forms. What was the nature of the less-hydrated fibers that produced the better oriented and crystalline A form that could convert to the B form? In those days a half-century ago, fiber diffraction was the only way such large, elongated molecules could be studied. Generally, the patterns had rotational disorder around the fiber axis, which could be at the molecular level in the case of the B form and often involved crystalline segments in the A form. The diffraction patterns were limited in resolution, but it could be said that they were consistent with the formulation. Over the next several years, work by Maurice Wilkins and his colleagues gradually refined the nature of the double-helical model that could give rise to the increasingly detailed diffraction patterns. However, the diffraction pattern could not “prove” the structure of the molecule, as there were too little data.
The ribose sugar ring contains five atoms, but they cannot all lie in one plane, and at least one atom must be out-of-plane (Fig. 1).With the continued analysis of the fiber patterns, it became clear that the B form contained a ribose ring pucker in which the C2' atom was out-of-plane on the same side as the base (C2' endo). Because of that pucker, the phosphate groups were nearly 7 Å apart, yielding an extended polynucleotide chain. Study of the more complex A form led to the conclusion that the C3' atom was out-of-plane (C3' endo). In that conformation, the phosphate groups were about 5.8–6 Å apart. Thus, the sugar phosphate backbone was shortened, leading to a double helix in which the base pairs were slightly displaced from the center of the helix to produce a flatter helix and a somewhat thicker molecule. A relative scarcity of water molecules stabilized that conformation. It became clear that the normal conformation in the hydrated in vivo environment involved the C2' endo sugar pucker of B form DNA.
Source: RNA Towards Medicine 2009
The increase in disorder is evident in our everyday lives. Each day, food is consumed and largely converted into heat, which is a more disordered state than the original food items. In general, it could be argued that all life forms have devised methods of taking ordered resources, such as molecules or food, and converting them into disordered states in order to generate energy. If all processes are moving to a disordered state, how can highly organized states such as crystals or biological cells be created? The answer lies in considering the overall state and not just one part. For example, your bedroom may tend to become very disordered with daily use until you decide to clean it up. While the clothes and other objects in the room may be more ordered, the process of cleaning the room involves the expenditure of energy in the form of heat. Thermodynamics would say that the disorder associated with the heat is greater than the order associated with the folding and stacking of the clothes.
In a sense, the change in order of an object provides a direction for chemical reactions. When a process results in a change from one state to another that occurs in an irreversible way, the process is called spontaneous. Only irreversible changes are spontaneous; truly reversible processes are not. Truly reversible processes do not occur in nature, as it would require all forces to be perfectly balanced with no driving force for the system to move. However, by moving objects very slowly while keeping forces in nearly perfect balance, processes that are very close to reversible can be created. As an example, gas inside a piston expanding under constant pressure inside and outside does not have any net force to drive the expansion, and the piston does not move. By making the imbalance very small, the piston moves, although at a very slow rate. Such a motion would take a considerable amount of time to be completed, but the rate is not under consideration here, only the direction.
Source: Biophysical Chemistry 2008
It’s not just what a DNA sequence says, but how it looks. NHGRI’s Elliott Margulies and Boston University’s Thomas Tullius found that certain topographical features of a stretch of DNA — particularly when conserved across species — are correlated to its function. “When we think of primary sequences being conserved throughout evolution, we think that those sequences are maintained because they do some important function. And now we are extending that onto the structural topography of DNA,” Margulies says.
Margulies had been trying to think up new ways to look at DNA and study its function when he came across Steve Parker, who was investigating how DNA topography related to functional elements within a species. “This made me think, gosh, if we can convert this DNA topography across a bunch of species, it’ll give us a different way of looking at similarities in DNA,” Margulies says. Parker is the first author on the new Science paper.
Source: Genome Technology May 2009
The conservation movement in North America emerged in part due to the shock of the extinction of the passenger pigeon and the near extinction of the American bison, species that had once been considered too numerous to be depleted. By the 1960s, a broad consensus emerged in the United States that species should not be driven to extinction by human activity. Since then, however, the Endangered Species Act and major programs to restore endangered and threatened species have become controversial.
Private property rights advocates claim that endangered species protection hampers economic activity and land development to an unreasonable extent. At the same time some conservationists are concerned that too much money and effort are devoted to endangered species, diverting efforts from protection of entire ecosystems that support numerous species. They argue that given the limited resources available, preventing common species from becoming rare is the most effective long-term strategy. Defenders of endangered species programs claim that protecting endangered species usually entails protecting entire ecosystems, and endangered species can serve as effective symbols to rally support for ecosystem protection.
Source: Glenn D. Dreyer in Saving Biological Diversity
ISBN: 978-0-387-09566-0
The carbon cycle has a central role in climate change. For example, during glacial–interglacial cycles, atmospheric carbon dioxide has altered radiative forcing and amplified temperature changes. However, it is unclear how sensitive the climate system has been to changes in carbon cycling in previous geological periods, or how this sensitivity may evolve in the future,
following massive anthropogenic emissions. Here we develop an analytical relationship that links the variation of radiative forcing from changes in carbon dioxide concentrations with changes in air–sea carbon cycling on a millennial timescale.We find that this relationship is affected by the ocean storage of carbon and its chemical partitioning in sea water. Our analysis reveals that the radiative forcing of climate is more sensitive to carbon perturbations now than it has been over much of the preceding 400 million years. This high sensitivity is likely to persist into the future as the oceans become more acidic and the bulk of the fossil-fuels inventory is transferred to the ocean and atmosphere.
Source:Nature Geoscience February 2009
Science, particularly my field of biology—has changed dramatically over the past 50 years and continues to evolve. A field once dominated by small research groups working largely in isolation is transforming, in part, into enterprises increasingly reminiscent of the efforts in physics that have led to the Large Hadron Collider (LHC) and other expensive, personnel- and data-intensive projects.
The organizations and projects I have led during the course of my 37-year career illustrate some of the changes that biology has undergone. But there are significant differences between biology and physics; no single large government program dominates biological science like the LHC dominates physics. Rather, the techniques responsible for the industrialization and digitization of biology, and new approaches for funding science, are enabling scientists to achieve unprecedented independence and scale in their work. These changes have had the effect of moving all of us to an age in which more data can be gathered—and, more importantly, grander questions asked and hypotheses discarded or validated—than has ever been possible before.
When I obtained my doctorate degree in 1975, science wasn't much different from the way it had been in the 1950s. There were about 150,000 scientists in the US, and I, like some 70 percent of my fellow PhDs, went into academia. But things have changed. For one thing, there are more than 2.6 million scientists working in America today. But the essentially binary decision I had to make when I left graduate school has largely evaporated. Where for me and my peers it was a decision between academia or industry, today, only about 20 to 30 percent of the more than 7,000 new PhDs in the life sciences will stay in academia. Furthermore, a significant percentage of "academic" biologists at major institutions have at least one foot in at least one biotech company. One reason for this could be that funding from the US government in constant dollars has changed little over the past 40 years, whereas industry funding has increased more than tenfold; as a result, federal money for biological research, once more than twice as great as that coming from industry, is now less than half as much.
Source Seed magazine
In this State of Science, we examine the changes within science and investigate the role of scientists in society. The change has been so profound in the last years that a closer look is warranted. Six aspects of the current scientific landscape have got our interest:money, intellectual property,public perception, informatics, publishing and innovation. We will exam each of these and try to get some insight in how science is made today, who are our scientists, and who are they working for.
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