Coming home

The second part of my project involves DNA extraction from my soil samples. For that, I travel to Nanjing and work in the lab of Dr. Fang Wang in the Chinese Academy of Sciences, Soil Science Institute.  Nanjing is only about an hour from Shanghai, which makes my presence much less of a novelty, as …

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The tipping point

This is only the beginning. To serious people who read this blog, but may have been confused over the past 5+ years about things like missing heritability, genomic prediction, complex genetic architecture, gloomy prospects: isn’t it about time to consider updating your priors? Read all about it here. FT.com: Genetic scoring predicts how children do …

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Genetic Testing

This week we are considering a case from the back end of the food ethics continuum: the “devious defecator.” It concerns a legal finding against Atlas Logistics Group Retail Services, an Atlanta-based grocery distributor. It seems that Atlas was having a problem policing their warehouse. They could not positively identify the culprit named above, who …

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Improved CRISPR–Cas9: Safe and Effective?

Two groups (Zhang lab at MIT and Joung lab at Harvard) announce improved “engineered” Cas9 variants with reduced off-target editing rates while maintaining on-target effectiveness. I had heard rumors about this but now the papers are out. See CRISPR: Safe and Effective? Nature commentary Genome Editing: The domestication of Cas9. High-fidelity CRISPR–Cas9 nucleases with no …

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DNA Dreams at Harvard

This is a panel discussion of the documentary film DNA Dreams (see below), about BGI and its Cognitive Genomics Lab. DNA DREAMS Moderator: Dr. Evelynn Hammonds, Director of the Project on Race & Gender in Science & Medicine, Hutchins Center for African & African American Research/Barbara Gutmann Rosenkrantz Professor of the History of Science Panelists include: (L …

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Après nous le déluge

You can always blame the Chinese. See also A prudent path forward for genomic engineering and germline gene modification (Baltimore et al.) and Germ line editing and human evolution. Science: Embryo engineering alarm … In 1975, the Asilomar conference center hosted a meeting where molecular biologists, physicians, and lawyers crafted guidelines for research that altered …

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The Fourth Law of Behavior Genetics?

I believe the law stated below almost follows from the observation that humans brains are complex machines: hence the DNA blueprint has many components, and variance is spread over these components  :^) However, note the evidence for discrete genetic modules of large effect in other species: Discrete genetic modules can control complex behavior (burrowing behavior in …

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Garbage, Junk, and non-coding DNA

About 1% of the genome codes for actual proteins: these regions are the ~20k or so “genes” that receive most of the attention. (Usage of the term “gene” seems to be somewhat inconsistent, sometimes meaning “unit of heredity” or “coding region” or “functional region” …) There’s certainly much more biologically important information in the genome …

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Multiallelic copy number variation

These new results probe surprisingly large variation in copy number (duplicated genomic segments) and its impact on gene expression. Earlier posts involving CNVs. Large multiallelic copy number variations in humans Nature Genetics (2015) doi:10.1038/ng.3200 Thousands of genomic segments appear to be present in widely varying copy numbers in different human genomes. We developed ways to …

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Designer babies: selection vs editing

The discussion in this video is sophisticated enough to make the distinction between embryo selection — the parents get a baby whose DNA originates from them, but the “best baby possible” — and active genetic editing, which can give the child genes that neither parent had.The movie GATTACA focuses on selection — the director made a …

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Announcing khmer 1.0

The khmer team is pleased to announce the release of khmer version 1.0. khmer is our software for working efficiently with fixed length DNA words, or k-mers, for research and work in computational biology. Links: khmer documentation PyPI link Announcement ChangeLog Citation handle khmer v1.0 is the culmination of about 9 months of development work …

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Neanderthals leave their mark on us

Neanderthals shared a common ancestor with humans about 600,000 years ago, and didn’t go extinct until 30,000 years ago.  Scientists have been able to reconstruct most of the Neanderthal genome using fossil fragments, and found that humans must have interbred with them in the past, since some DNA is similar between Neanderthals and modern-day Europeans …

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