News

November 2014 PLoS Biology published “Thermodynamic System Drift in Protein Evolution,” a collaboration by Mike Harms and Joe with Katie Hart and Susan Marqusee at Berkeley. The collaboration was great fun, because Katie and Susan are superb scientists and excellent people to work with. Richard Robinson wrote a very nice accompanying news story in PLoS Biology, which you can read by clicking on the icon at right.

July 2014 Nature published “Evolutionary Contingency and its Biophysical Basis in Glucocorticoid Receptor Evolution,” by Mike Harms and Joe. The paper is the culmination of a huge amount of work by Mike at the bench and at the computer. It directly addresses Gould’s classic tape-of-life question — “What would happen if we could replay history from ancestral starting points” — by experimentally characterizing a huge library of alternative “might-have-been” evolutionary trajectories starting from the reconstructed ancestral glucocorticoid receptor. It’s also the first paper in which we have discussed the Persian cavalry.
July 2013 Scientific American published a very nice article, “Evolution is an opportunist,” on the role of exaptation in the evolution of biological systems.  It discusses our work on molecular exploitation in hormone-receptor evolution, along with Andreas Wagner’s recent paper on exaptation in the evolution of metabolic networks. Click on the icon at right to read it. Science News
July 2013 Scientific American published a very interesting article, “The Surprising Origins of Evolutionary Complexity,” on the evolution of complex biological systems by neutral processes.  It discusses at length our Nature paper on the evolution of the vATPase molecular machine and features the quotation, ““Everybody in their right mind would totally agree with it,” from biochemist David Speijer. Science News
June 2013 Our paper was published in PNAS on the mechanisms by which two ancient mutations caused a huge shift in hormone sensitivity during the evolution of steroid hormone receptors. Press coverage focused on the effect-size distribution of mutations in evolution: whether new phenotypes and functions evolve suddenly by a few revolutionary mutations or gradually by many changes of tiny effect. You can read the press releases here and here or listen to a podcast about it. For coverage in popular press/blogs, see the highly original stories in Wired and ScienceDaily.  
February 2012 Nature published a feature story, “Prehistoric Proteins: Raising the Dead,” about the Thornton lab’s work and Joe’s unusual path into science.   Click at right to read the story.  
January 2012 Discover and Nature both posted stories discussing our recent paper on the evolution of increased complexity in a molecular machine. Click at right to read the stories.  
October 2010 The Guardian published a news story (here) on our paper, Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor, published in PLOS Biology. The research traces the evolution of the entire nuclear receptor superfamily from a single ancestral receptor deep in the animal lineage. We show how subtle tinkering with the ancestral structure produced the remarkable functional diversity of extant members of this important family of transcription factors. The press release is here. Click at right for the paper.
September 2009 In his blog at Discover magazine, Carl Zimmer posted my response to “Intelligent Design” advocate Michael Behe’s claim that our recent paper in Nature actually supports his anti-evolution argument. Click on the logo to read it. It was picked up by a number of other blogs, with some amusing comment threads here and there.
September 2009 The New York Times editorial page featured our paper on the irreversibility of evolution. Who would have predicted that? You can read the editorial here or by clicking on the logo at right.
September 2009 The New York Times published news story on our Nature paper on the reversibility of evolution. The story is by Carl Zimmer, the superb science journalist. Click at right to read it.
September 2009 Science magazine published a news story on our Nature paper on the reversibility of evolution. Gunter Wagner and Bob Dylan are quoted. Click at right to read it.
September 2009 Nature published a news story and an “Authors/Abstractions” feature on our paper, also in Nature, on the reversibility of evolution.
September 2009 Nature published our paper (with our collaborator Eric Ortlund at Emory) on the reversibility of evolution. Click here or on the logo at right to read it. You can also read HHMI’s news story on the paper here.
March 2009 Joe was appointed as an Early Career Scientist of the Howard Hughes Medical Institute. You can read the UO news story here or click at right to go to the HHMI page. HHMI’s list of the 50 awardees is here.
February 2009 NIH’s general audience magazine Findings published a very nice profile of the lab’s research. Click at right to go to the story. This special issue has several great stories on interesting research in evolution and a great profile of Sarah Tishkoff’s lab at Penn, as well.
January 2009 Endocrine News published a news article on June Keay’s paper, “Estrogen receptors in annelid invertebrates: implications for evolution and endocrine disruption. Click at right to read it.
April 2008 Paul Cziko was awarded an NSF Graduate Research Fellowship. Congratulations to Paul! You can read the UO story about it here.
October 2007 Joe was awarded the U.S. Presidential Early Career Award for Scientists and Engineers at the White House. Click at right for the NSF press release and watch the video of several of the awardees (including Joe) discussing their work and background. You can also click here to see the awardees in the very presence of George W. Bush at the White House.
August 2007 The New York Times published a news story on our paper in Science on the first atomic structure of an ancient protein and its implications for contingency vs. determinism in evolution. Click at right for the link or here for the pdf.
August 2007 Newsweek‘s Sharon Begley published a news story on the implications for Intelligent Design of our paper in Science on the first atomic structure of an ancient protein. Click at right for the link.
August 2007 The National Science Foundation released this story about our paper on the first structure of an ancient protein. Click at right for the link.
August 2007 Science magazine published a news feature on our paper about the first crystal structure of an ancient protein. Click at right for the article.
August 2007 Nature Reviews Molecular Cell Biology published a feature on our paper about the first crystal structure of an ancient protein. Click at right for the article.
August 2007 Published in Science: Our paper — by Jamie Bridgam, our collaborator Eric Ortlund at Emory, and Joe — on the first crystal structure of an ancient protein. This work revealed the atomic mechanisms for the evolution of a new function in the glucocorticoid receptor more than 400 milliion years ago. Click at right for the paper.
September 2006 Endocrine News published a news feature on our paper — by graduate student June keay, postdoc Jamie Bridgham, and Joe — on the presence and function of estrogen receptors in mollusks. Click at right for the issue.
April 2006 Published in Science: Our paper — by postdoc Jamie Bridgam, graduate student Sean Carroll, and Joe — on the evolution of hormone-receptor complexity. By resurrecting an ancient hormone receptor, we show that the mineralocorticoid receptor/aldosteorne partnership evolved by Molecular Exploitation, and identify the two crucial amino acid changes that led to the evolution of present-day corticoid receptor specificity. Click at right for the paper.
April 2006 Chris Adami wrote a very elegant commentary in Science on our paper about the evolution of complexity. Click at right for the website or here for a pdf.
April 2006 The New York Times published a news story on our paper in Science and its implications for Intelligent Design. Click at right for the link or here for the pdf.
April 2006 The Wall Street Journal published a news story on our paper in Science and its implications for Intelligent Design. Click at right for the link or here for the pdf.
April 2006 The Christian Science Monitor published a nice column about our paper in Science on the evolution of complexity. Click at right for the link.
April 2006 Nature Reviews Genetics published a brief summary of our paper in Science on the evolution of complexity. The review is a nice treatment of three recent studies examining the trajectories by which new molecular functions evolve. Click at right for the link.
April 2006 Carl Zimmer wrote several incisive entries about our Science paper on his brilliant blog about evolution, The Loom. Read the story here.
April 2006 The Eugene Register-Guard published a nice news story on our paper in Science and its implications for Intelligent Design. Click at right for the link or here for the pdf.
April 2006 The National Science Foundation, which funded the work in our Science paper, wrote this summary of the work, along with some very nice images illustrating it. Click on the icon to read it.
April 2006 The Eugene Register-Guard has a very nice editorial, “Keeping it Real,” on the implications of our paper and recent paleontological discoveries for the “controversy” about evolution. Click at right for the link or here for the pdf.
March 2006 Joe was named a fellow of the Alfred P. Sloan Foundation. Click here for the UO news story.
January 2005 Joe received an NSF CAREER award. Click here to read the UO news story.
June 2005 View the photos and video from Hagfishpalooza ’05. Click the photo at right.
April 2005 New Scientist article on resurrecting ancestral genes. This is a terrific popular story about how the Benner, Chang, and Thornton labs are using ancestral gene resurrection to test hypotheses about the evolution of ancient proteins.
March 2005 Listen to a CBC radio interview with Joe and Belinda Chang (U. Toronto) on resurrecting ancestral genes. Click on the icon at right to listen. (Belinda’s interview lasts until about minute 9, then Joe comes on.)
March 2005 Published in Cell: Our evolutionary analysis of SF-1 and LRH-1 structures and sequences, in collaboration with Holly Ingraham and Robert Fletterick’s groups at UCSF. We show that the rodent LRH-1 transcription factors evolved constitutive activity from a ligand-regulated ancestor, and identify a small number of amino acid changes that caused this shift. Along with our similar findings on mollusk estrogen receptors, this result adds to the evidence against the “ancestral orphan” theory of nuclear receptor evolution. Click at right to read the paper.
October 2004 Published in Nature : Our paper, “Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous.” We show that heterogeneity in the evolutionary process can make current methods for phylogenetic inference strongly biased. Click at right to go to the paper.
May 2004 Wall Street Journal story on resurrecting ancient genes, based on ourNature Reviews Genetics article. Click at right to read.
May 2004 Published in Nature Reviews GeneticsOur paper, “Resurrecting ancient genes: Experimental Analysis of Extinct Molecules,” in which we discuss the history, technology, advantages, and pitfalls of this new approach to experimentally testing evolutionary hypotheses. Click at right to read.
September 2003 Published in Science Our paper, “Resurrection of the ancestral steroid receptor: ancient origin of estrogen signaling.” By identifying the first steroid receptor in an invertebrate — the estrogen receptor of the sea slugAplysia californica – we show that the steroid receptor gene family is far more ancient than previously thought. We then resurrect the gene for the ancestor of all present-day steroid receptor genes and show that it had the specific functions of an estrogen receptor. Click at right to read the paper.
September 2003 Portland Oregonian story about our paper in Science. Click on the sea slug at right to read the article.
September 2003 Nature Reviews Genetics feature by Tanita Casci about our paper inScience. Click on the sea slug at right to read the article.
A long, long
time ago
Review of Pandora’s Poison in Nature by Prof. Terry Collins. This isn’t exactly “news”, but why not post it? Click at right to read.