University of Oxford, UK

A palaeontologist ponders how biodiversity is spread across the vertebrate tree of life.

Why do some biological groups burst at the seams with many different species, whereas others, despite their deep evolutionary heritage, contain only a handful of members? Many of my old vertebrate-biology textbooks are rife with qualitative scenarios, peddled with surprising degrees of confidence, that explain how species-rich branches can chalk up their success to key evolutionary 'innovations' and how less-diverse ones haven't kept up with changing conditions. What you won't find are details of how these exceptional groups might be identified in the first place.

Michael Alfaro of the University of California, Los Angeles, and his colleagues have now quantified this black art (Proc. Natl Acad. Sci. USA 106, 13410–13414; 2009). They marry statistically explicit models with fossil-calibrated evolutionary trees and counts of living species to ask a basic, but surprisingly unanswered question: precisely which branches of the vertebrate family tree are more or less species-rich than expected given their age?

The authors identify nine groups that show substantial changes from the background tempo of vertebrate evolution: 'living fossils' such as lungfishes are characterized by lower-than-predicted diversity, whereas other branches, such as the perch-like fishes and a subset of mammals, contain vastly more species than expected.

As a palaeontologist, I am intrigued that three of the exceptionally diverse radiations are thought (although not without controversy) to have proliferated following the mass extinction that killed off the dinosaurs, hinting at the far-reaching consequences of this event in structuring the modern vertebrate fauna. Most importantly, these authors establish a clear quantitative framework that can be used to test all those textbook stories. I'm confident that in a few years, my students will learn a much more nuanced picture of vertebrate diversification than I ever did, one that will trace its own roots back to studies such as this.

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University of California, San Francisco

A computational biologist looks at how mRNA length changes during development.

I am always amazed by how we start as a fertilized egg and develop into a complex, multicellular organism. This feat occurs despite the fact that the DNA in every cell — even the most specialized ones — remains, for the most part, unchanged.

One method of regulating gene activity in differentiated, or specialized, cells is through the messenger RNA (mRNA), the code of which is translated to make proteins. For example, proteins and other RNAs can bind to the untranslated regions (UTRs) at the 5' and 3' ends of mRNAs to regulate mRNA stability and translation.

The constitution of the 3' UTR itself can be regulated through alternative polyadenylation, whereby one of several possible UTR sites is cleaved, followed by the addition of adenosine-based molecules to its end. A broad shift in cleavage site choice — and thus 3' UTR length — during mammalian development was recently described by Bin Tian and his team at the University of Medicine and Dentistry of New Jersey in Newark (Z. Ji et al. Proc. Natl Acad. Sci. USA 106, 7028–7033; 2009).

By analysing genomic data, they show that 3' UTRs generally get longer during development and cell differentiation. The authors further show that most of the genes in which 3' UTRs are lengthened are also those that are increasingly suppressed during differentiation, such as the genes for DNA replication and cell division.

These findings bring to the forefront an underappreciated mechanism of genetic regulation that is likely to be important for normal cell differentiation. It is fascinating how many steps of the central dogma (DNA to RNA to protein) are controlled. This seems to be how evolution has managed to take a relatively simple cell and multiply it to form the complex body plan of the human.

Posted by Corie Lok at 07:38 PM | Permalink | Comments (0) | TrackBacks (0)

Leiden University, the Netherlands

A theoretical physicist journeys to a hairy black hole's horizon.

Rumour has it that Steven Spielberg is producing the ultimate science fiction movie, using state-of-the-art general-relativity simulations to create a realistic image of the warped space-time near a black hole. But wouldn't it be great to see such worlds in real life? In fact, you can: by extending your eyesight with 'AdS/CFT', a mathematical result of string theory that describes a 'through the looking-glass' experience that would embarrass the imagination of Lewis Carroll.

AdS/CFT states that information about the strange world of the black hole is, in a very indirect way, encoded in or 'imaged' by the properties of certain quantum-weird forms of matter. Scientists realized recently that these 'quantum critical' states of matter are routinely produced in condensed-matter laboratories. But a particular prediction of AdS/CFT made the string theorists nervous: the event horizon of the special black hole that is imaged by the quantum critical electrons seems to imply that the latter should show a macroscopic entropy at zero temperature. It has further been predicted that the black hole would be unstable and would eventually suck up 'stuff' from its surroundings, covering its horizon with 'hair' (S. A. Hartnoll et al. J. High Energy Phys. 2008, 015; 2008). In the electron system, out of the blue and at a quite low temperature, some unexpected order will set in that removes the ground-state entropy, giving it a unique ground state.

Intriguingly, I learned the other day that condensed-matter experimentalists, unaware of the string theorists' nervousness, are now in the grip of the same idea. The latest thermodynamic experiments on quantum-critical electrons are suggestive (albeit inconclusive) of a developing zero temperature entropy — for the experimentalists, a catastrophe — interrupted at a very low temperature by the onset of an exotic quantum liquid crystalline order (Z. Fisk Science 325, 1348–1349; 2009). It may be that we don't need spacecraft or Spielberg to visit black holes, just a little patience with the condensed-matter experimentalists.

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