Adaptive evolution and non-coding regions

This morning I attended an excellent talk: Adaptive Evolution of Gene Expression (see paper and video below), by Hunter Fraser of Stanford. His results support the hypothesis that non-coding regions of the genome play at least as large a role in evolution and heritable variation as protein coding genes. From an information-theoretic perspective, it seems …

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Big Chickens

More evidence that common genetic variants can produce many standard deviations of change in average phenotype. Also, while wild chickens lay ~1 egg per month, modern agricultural types lay ~1 per day. The study is described in more detail here. Thanks to Carl Shulman for the link. See also Plenty of room at the top and sections 3.1 …

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Sufficient biological replication is essential for differential expression analysis of RNA-seq

I just took part in a twitter discussion about the trade-offs between sequencing depth and number of independent biological replicate (per treatment group) for differential gene expression analysis. While there are applications of RNA-seq where  sequencing deeply (more than say 50 million reads for a given sample) can be important for discovery. However, most researchers …

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Another Cup

Passing through an indiscernible hiatus our cruise vessel steams quietly into the safe harbor of routine activity. Yes, folks, it’s September. If you didn’t notice any major change of key it’s probably because the start of any month is kind of arbitrary. It’s the job of bloggers everywhere to chronicle these passages, holding them out …

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Metabolic costs of human brain development

This paper quantifies the unusually high energetic cost of brain development in humans. Brain energy requirements and body-weight growth rate are anti-correlated in childhood. Given these results it would be surprising if nutritional limitations that prevented individuals from achieving their genetic potential in height didn’t also lead to sub-optimal cognitive development. Nutritional deprivation likely stunts …

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2014 MSU Weed Tour Review

Yesterday’s 2014 MSU Weed Tour was yet another successful event, with over 230 people in attendance. Thank you to all of you whom attended and to the many people in front and behind the scenes who made it all possible. Please enjoy a few photos of the event below. The plot signs will probably remain …

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Vertebrate sexual systems

Awesome figure of the sexual systems used by 2,145 vertebrates species (705 fish, 173 amphibian, 593 non-avian reptilian, 195 avian, 479 mammalian).Similar figures for plants and invertebrates. Tree structure is derived from taxonomy, where each tip represents all species in a single genus. Diploid chromosome number is indicated by the height of the innermost ring. …

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The Monarchs are in Michigan!

Yesterday I was very excited to see my first monarch caterpillars of the year on Michigan State University’s campus, in the 4-H Children’s Garden.  The first monarch butterflies were only sighted in Michigan in mid-May, but the vast majority were sighted the past two weeks, as seen on the Journey North maps created by reports …

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Pragmatic definitions in biology

Biology is littered with concepts that biologists cannot always agree on how to define or where there are special cases where the common definition have to be amended. Species. Complexity. Modularity. Evolvability. Evolution. Genes. Community. Robustness. Open-ended evolution. Fitness. Life. Take species. The current state of affairs is that there are many different definitions, and …

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So… how’d your interview go?

March 5th-7th, 2014, I had the pleasure to participate in the CIRTL (Center for the Integration of Research, Teaching, and Learning) Network Exchange program as a former Future Academic Scholars in Teaching (FAST) Fellow at Michigan State University. I traveled down to The University of Georgia (UGA) to give presentations on both my Teaching-As-Research (TAR) …

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Organic options page has added materials

-E. Hill We have put all of our extension and research findings related to organic weed management now in one place at MSUweeds.com called “Organic options“. In this section you will find: Extension materials (that have resulted from our research and work with area farmers) Peer reviewed publications relating to organic weed management Presented research …

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Darwin, Mendel and statistical fluctuations

Freeman Dyson discusses Darwin’s failure to discover Mendelian inheritance. Had Darwin a stronger grasp of statistics (then under development by his cousin Francis Galton), he might have discovered the properties of the basic units of inheritance, so central to his theory of natural selection. See also Bounded cognition. NYBooks: … Seven years after Darwin published …

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Cancer genomics

A great article in Esquire on the frontier of cancer genomics. It’s only a matter of time before many wealthy individuals diagnosed with cancer seek out this standard of care. (I’m told that sequencing alone can lead to actionable conclusions in more than a few percent of all cases, even now.) The resulting advances will …

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The dawn of genetic engineering?

Some CRISPR links. This technology is for real. See earlier post CRISPR. Watch realtime action here. GeCKO knockout in human cells. Zhang and Church raise $43M for new venture Editas. Application to Cystic Fibrosis in human stem cells , Cataracts in mouse. The Scientist: It was less than a year ago that scientists first applied CRISPR, a …

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Reddit AMA FAQ

I did a Reddit/r/IAmA AMA yesterday and got a huge amount of questions. Some of them were repeats, so I post them here with answers. I’m planning to do another AMA perhaps next month, so this can serve as a reference. Update 11/12/13: Randy’s interview about this AMA is featured on BEACON’s blog. Q. What …

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pictures in my head: What is that on the wing of the fly? What does it tell us about adaptation?

Over the past week or so, there has been an absolutely amazing image that has made the rounds on the internet of a fly (Goniurellia tridens)with markings on its wings reminiscent to many viewers of ants. Goniurellia tridens is a 3-in-1 insect [photo: Peter Roosenschoon] pic.twitter.com/i8ThAOkrvN — Ziya Tong (@ziyatong) November 4, 2013 As described …

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