University of California, San Francisco, USA

To an epigeneticist, cancer is encrypted in genes and their packaging.

Early in my career I had the good fortune to study epigenetics in a lab focused on the molecular genetics of cancer. At the time, geneticists typically thought that in cancer, epigenetic changes — which affect regulation of the genome but not the genome's sequence — were epiphenomena less worthy of study.

This might have made the experience akin to being a Republican mayoral candidate in left-leaning San Francisco; instead it was positively transforming.

As my own research group took shape, I began to integrate genetic and epigenetic theories of malignant transformation. Now, hereditary human cancers and genetically engineered mice once held up as evidence for genetic models also provide evidence for epigenetic models, and we study the interactions of the two mechanisms.

In this light, a recent paper (G. G. Wang et al. Nature Cell Biol. 9, 804–812; 2007) captured my attention because it dissects how one genetic change leads to epigenetic changes that ultimately cause leukaemia.

The work focuses on an abnormal fusion protein — produced after part of one gene fused, or translocated, with part of another — and narrows down its cancer-causing properties to a particular region of the protein. This region mediates an epigenetic change: it adds a methyl group to one amino acid of a histone, part of a gene's packaging in the nucleus.

The team found that the fusion protein misdirects its methylation to the histones that package HoxA genes, triggering further miscoding of the histones. This activates the genes, which promote self-renewal of blood-cell precursors, contributing to leukaemia.

I wonder if the interactions could be traced back even further. Given the role of epigenetics in stabilizing chromosomes; might it have been epigenetic miscoding that made the gene susceptible to translocation in the first place?

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California Institute of Technology, USA

A planetary scientist foresees a shift in the debate about Earth's heat flow.

Measurements of the heat coming out of Earth's interior have long posed a puzzle for understanding the planet's history.

Earth's heat output is estimated to be around 44 terawatts, about twice that expected from radioactive decay. The difference can be attributed to cooling of the deep Earth, implying a present-day cooling rate of 100 kelvin per billion years. But simple models with this much cooling 'blow up' when they are run back in time, predicting ridiculous temperatures for the early Earth. Acceptable models rely on unconventional deviations from the usual simple scaling laws for mantle convection. This is an attractive but untested idea.

I and many others have wondered whether an alternative explanation is that today's heat flow is higher than the average for the past half a billion years. Such fluctuations could arise as a result of the dispersal and accumulation of continental land masses.

A recent paper (J. Korenaga Earth Planet. Sci. Lett. 257, 350–358; 2007) assessed this possibility by taking advantage of a long-known connection between sea level and the heat flow from sea-floor spreading. It finds little room for more than a few percent fluctuation in heat flow around its long–term decline.

I think this pushes the problem back into the realm of models, focusing attention on plate tectonics, the deep water cycle (because water affects how rocks flow), and perhaps even the long-standing question of whether Earth's mantle is well mixed from top to bottom.

On a decadal timescale, we can hope that better measurements of heat generation and flow will be combined with more realistic theory. Like many central Earth science questions, the heat-flow problem resists quick resolution.

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University of Nottingham, UK

A champion of environmentally friendly chemistry encourages attempts to identify reactions ripe to be turned 'green'.

The aim of 'green chemistry' is to make the design, production and use of chemicals more sustainable. This means that, unusually for an academic discipline, industrial implementation is an inherent goal.

Research groups in this field, including mine, strive to reduce waste by identifying selective catalysts, alternative solvents or renewable feedstocks that could lead to new industrial processes.

But how do we choose which reactions to try to green? Some targets are obvious; the reactions are notoriously inefficient. However, many chemical manufacturers are understandably reticent about the shortcomings of their processes.

It was therefore particularly refreshing to find a paper that results from the collaboration of seven pharmaceutical companies and highlights key research areas for green chemists (D. J. C. Constable et al. Green Chem. 9, 411–420; 2007). The paper describes several classes of reaction that, if 'greened', would significantly lessen the pharmaceutical industry's effect on the environment.

For example, the paper asks that researchers develop methods to carry out oxidations safely in non-chlorinated solvents (chlorinated solvents are non-flammable but toxic); or to find ways to tame the fearsome reactivity of fluorine so that fluorination occurs selectively.

Another clear message is that new strategies for using solvents could lead to substantial reductions in waste. Could reaction vessels be cleaned out at the end of a process without using organic solvents?

This paper is a great start, but I think the authors have been too conservative. They could have asked for more, such as catalysts that can trigger two or more reactions in sequence. We need really tough challenges to intrigue academic chemists and bring new blood to the task of greening chemistry.

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New York University, USA

An evolutionary geneticist wonders why certain crops were 'invented' not once but multiple times.

Crop species have always captured my imagination — perhaps because Darwin saw domestication as a model for the evolutionary process, or maybe because I am an inveterate foodie. Whatever the reason, I work on the evolution of crop species as diverse as rice, barley and cauliflower, using genomic methods to trace their origins.

I was struck by two recent molecular studies that indicate that key crops may have evolved more than once in association with different cultures, after Neolithic farmers began to cultivate various wild plants and select desirable traits 12,000 years ago.

Rice seems to have originated from the wild rice Oryza rufipogon separately in China and in India and southeast Asia (J. P. Londo et al. Proc. Natl Acad. Sci. USA 103, 9578–9583; 2006). Meanwhile, barley, which originated once in the Fertile Crescent — a region defined by an arc through Lebanon, Syria, Turkey and Iraq, and home to the oldest archaeological evidence for agriculture — may also have had a second origin in present-day eastern Iran (P. L. Morrell and M. T. Clegg Proc. Natl Acad. Sci. USA 104, 3289–3294; 2007).

Previous genetic mapping studies of the loss of seed shattering in rice and barley suggests that the trait is controlled by different genes in different lineages of these crops. This makes sense in the light of a multiple-origins scenario.

The pattern is not unique — cattle, sheep and goats were also domesticated multiple times. So did different cultures learn how to go about domesticating wild plants and animals from each other, or did they arrive at the same evolutionary solutions independently when faced with similar challenges? Hopefully the genetic data will motivate archaeologists to dig for evidence of how groups of people went about developing these crops.

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The Natural History Museum, London, UK

A palaeobotanist finds answers to the origin of roots in the genes of a living moss.

Roots have been called the hidden half of plant diversity. Confined mainly to the subterranean, their unseen influence extends well beyond the plant that they sustain to form an integral component of soil ecosystems and a significant link in the carbon cycle.

In my research, I use fossils to piece together how the fundamental organs and basic lifecycles of plants evolved, and roots are one of the key systems. The fossil record shows that roots were an early innovation in the colonization of the land, and that they evolved remarkably rapidly, developing a diversity of forms comparable to those of the aerial shoots, stems and leaves. Comparative morphology is good for documenting how roots evolved, but are there any underlying molecular developmental similarities among the rooting structures of early plants?

An elegant piece of recent research shows that a similar transcription factor encoded by the gene ROOT HAIR DEFECTIVE 6 regulates root-hair development in the flowering plant Arabidopsis thaliana and rhizoid development in the moss Physcomitrella patens (B. Menand et al. Science 316, 1477–1480; 2007). Because flowering plants and mosses diverged more than 400 million years ago, this surprising result implies that the cells with a key role in nutrient acquisition and anchorage in most land plants share a molecular developmental pathway that is very ancient indeed.

More surprising still is the notion that these genes are expressed in both haploid and diploid plants — that is, those whose cells have one or two sets of chromosomes, respectively. Many plants cycle between haploid and diploid forms during their lifecycles. Menand et al. propose that genes expressed in early haploid plants were turned on in many tissues during the evolution of plants with diploid phases. Pending further testing, this interesting model is plausible for components of the vascular system, cortex, epidermis, shoot and root.

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