A natural polypeptide chain can fold into a native protein in microseconds, but predicting such stable three-dimensional structure from any given amino-acid sequence and first physical principles remains a formidable computational challenge. Aiming to recruit human visual and strategic powers to the task, Seth Cooper, David Baker and colleagues turned their 'Rosetta' structure-prediction algorithm into an online multiplayer game called Foldit, in which thousands of non-scientists competed and collaborated to produce a rich set of new algorithms and search strategies for protein structure refinement. The work shows that even computationally complex scientific problems can be effectively crowd-sourced using interactive multiplayer games. Predicting the structure of a folded protein from first principles for any given amino-acid sequence remains a formidable computational challenge. To recruit human abilities to the task, these authors turned their Rosetta structure prediction algorithm into an online multiplayer game in which thousands of non-scientists competed and collaborated to produce new algorithms and search strategies for protein structure refinement. This shows that computationally complex problems can be effectively 'crowd-sourced' through interactive multiplayer games. People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully ‘crowd-sourced’ through games1,2,3, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology4, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.

/pdf/predicting-protein-structures-with-a-multiplayer-online-game-3md0x4a9x0.pdf

Predicting protein structures with a multiplayer online game

Foldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.

https://www.pnas.org/content/pnas/108/47/18949.full.pdf

Algorithm discovery by protein folding game players

Progressive aqueous alteration of CM carbonaceous chondrites

Our Sun and planetary system were born about 4.5 billion years ago. How did this happen, and what is the nature of our heritage from these early times? This review tries to address these questions from an astrochemical point of view. On the one hand, we have some crucial information from meteorites, comets and other small bodies of the Solar System. On the other hand, we have the results of studies on the formation process of Sun-like stars in our Galaxy. These results tell us that Sun-like stars form in dense regions of molecular clouds and that three major steps are involved before the planet-formation period. They are represented by the prestellar core, protostellar envelope and protoplanetary disk phases. Simultaneously with the evolution from one phase to the other, the chemical composition gains increasing complexity.

Our astrochemical heritage

The development of manipulation tools that are not too ‘fat’ or too ‘sticky’ for atomic scale assembly is an important challenge facing nanotechnology1. Impressive nanofabrication capabilities have been demonstrated with scanning probe manipulation of atoms2,3,4,5 and molecules4,6 on clean surfaces. However, as fabrication tools, both scanning tunnelling and atomic force microscopes suffer from a loading deficiency: although they can manipulate atoms already present, they cannot efficiently deliver atoms to the work area. Carbon nanotubes, with their hollow cores and large aspect ratios, have been suggested7,8 as possible conduits for nanoscale amounts of material. Already much effort has been devoted to the filling of nanotubes8,9,10,11 and the application of such techniques12,13. Furthermore, carbon nanotubes have been used as probes in scanning probe microscopy14,15,16. If the atomic placement and manipulation capability already demonstrated by scanning probe microscopy could be combined with a nanotube delivery system, a formidable nanoassembly tool would result. Here we report the achievement of controllable, reversible atomic scale mass transport along carbon nanotubes, using indium metal as the prototype transport species. This transport process has similarities to conventional electromigration, a phenomenon of critical importance to the semiconductor industry17,18.

Carbon nanotubes as nanoscale mass conveyors

Petrography of Very Primitive CO3 Chondrites: Dominion Range 08006, Miller Range 07687, and Four Others

Automatic Identification of Presolar Al- and Ti-rich Oxide Grains from Ordinary Chondrites

High Abundance of Presolar Materials in CO3 Chondrite Dominion Range 08006

Here we present results obtained with NanoSIMS raster ion imaging to determine the abundance of presolar SiC in the insoluble organic matter (IOM) extracted from a number of different classes of chondrites (both carbonaceous and ordinary). This builds on previous work [1] aimed at obtaining SiC abundances in primitive meteorites by
SIMS and comparing them with noble gas analyses.

Both IOM and presolar grains are found in similar
CI-like relative abundances in the matrices of the most
primitive chondrites [2, 3], indicating that a homogeneous
mixture of grains was incorporated in the various parent bodies [3]. Both are then subjected to thermal and hydrothermal processing after parent body formation [4]. However, there are significant variations in the matrix-normalized abundances of SiC grains estimated from noble gases carried by presolar grains, which suggest that the primitive chondrites did not form from a well-mixed reservoir of presolar grains. Variations in the source material were attributed to the destruction of presolar grains by heating in the solar nebula (temperatures that may have exceeded 700°C) and were linked to the volatile element fractionations in chondrites [5].

The CR chondrites have amongst the lowest matrix-normalized SiC abundances, and largest volatile element ractionations, reported in the carbonaceous chondrites [5]. However, they contain the most primitive IOM of any chondrite class [6-7], which has experienced peak temperatures of <300°C [8]. These lowtemperatures could not have affected the SiC grains or their noble gas concentrations, indicating that either the IOM escaped heating (implying that it is not presolar)or SiC was degassed/destroyed at low temperatures,
perhaps during parent body processing [3]. Thus, in order to resolve this contradiction, it is necessary to determine SiC abundances independently of noble gases. Ion imaging of SiC grains is a direct technique that has been shown to successfully identify presolar SiC grains amongst others.

Presolar SiC Abundances in Primitive Meteorites by NanoSIMS Raster Ion Imaging of Insoluble Organic Matter

Isotopic studies of IDPs collected from the comet Grigg-Skjellerup dust stream reveal extremely high abundances of presolar grains in two of four IDPs. These abundances exceed those of any other extraterrestrial material analyzed and support a cometary origin for these IDPs.

https://www.lpi.usra.edu/meetings/lpsc2007/pdf/2332.pdf

L. R. Nittler

Papers

Petrography of Very Primitive CO3 Chondrites: Dominion Range 08006, Miller Range 07687, and Four Others

Automatic Identification of Presolar Al- and Ti-rich Oxide Grains from Ordinary Chondrites

High Abundance of Presolar Materials in CO3 Chondrite Dominion Range 08006

Presolar SiC Abundances in Primitive Meteorites by NanoSIMS Raster Ion Imaging of Insoluble Organic Matter

Remarkably high abundance of presolar grains in interplanetary dust particles collected from the comet Grigg-Skjellerup dust stream