•  1
    A reference genome for common bean and genome-wide analysis of dual domestications
    with J. Schmutz, P. E. McClean, S. Mamidi, G. A. Wu, S. B. Cannon, J. Grimwood, J. Jenkins, S. Shu, Q. Song, C. Chavarro, M. Torres-Torres, V. Geffroy, S. M. Moghaddam, D. Gao, B. Abernathy, K. Barry, M. Blair, M. A. Brick, M. Chovatia, P. Gepts, D. M. Goodstein, M. Gonzales, U. Hellsten, D. L. Hyten, G. Jia, J. D. Kelly, D. Kudrna, R. Lee, Richard M. M. S., P. N. Miklas, J. M. Osorno, J. Rodrigues, V. Thareau, C. A. Urrea, M. Wang, Y. Yu, R. A. Wing, P. B. Cregan, D. S. Rokhsar, and S. A. Jackson
    Common bean is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differe…Read more
  •  2
    Copyright © 2016 by the American Society for Biochemistry and Molecular Biology, Inc.Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution.…Read more
  •  2
    Knowledge of three-dimensional structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins' functions; but their structures are difficult to determine. Electron tomography provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional reconstruction due to the imperfect mechanical control capability of the specimen goniometer under …Read more
  •  144
    Empirical adaptationism is often said to be an empirical claim about nature, which concerns the overall relative causal importance of natural selection in evolution compared with other evolutionary factors. Philosophers and biologists who have tried to clarify the meaning of empirical adaptationism usually share, explicitly or implicitly, two assumptions: (1) Empirical adaptationism is an empirical claim that is scientifically testable; (2) testing empirical adaptationism is scientifically valua…Read more
  •  7
    Prior work has found that Americans’ views on evolution are significantly and positively related to their understanding of this theory. However, whether this relationship is cross-culturally robust is unknown. This article extends earlier work by measuring and comparing the acceptance and understanding of evolution among highly educated individuals in China and the United States. We find a significantly higher evolution acceptance level in the Chinese sample than in the US sample, but no signifi…Read more
  •  94
    The use and limitations of null-model-based hypothesis testing
    Biology and Philosophy 35 (2): 1-22. 2020.
    In this article I give a critical evaluation of the use and limitations of null-model-based hypothesis testing as a research strategy in the biological sciences. According to this strategy, the null model based on a randomization procedure provides an appropriate null hypothesis stating that the existence of a pattern is the result of random processes or can be expected by chance alone, and proponents of other hypotheses should first try to reject this null hypothesis in order to demonstrate the…Read more
  •  12
    Why does the Chinese public accept evolution?
    Studies in History and Philosophy of Science Part A 81 116-124. 2020.
    A substantial proportion of Chinese nationals seem to accept evolution, and the country is sometimes held up to show that the sorry state of evolution acceptance in the United States is not inevitable. Attempts to improve evolution acceptance generally focus on improving communication, curricular reform, and even identifying cognitive mechanisms that bias people against evolution. What is it that the Chinese scientific community did so well, and can it be generalized? This paper argues that evol…Read more