How the brain does face recognition

  This is a beautiful result. IIUC, these neuroscientists use the terminology “face axis” instead of (machine learning terminology) variation along an eigenface vector or feature vector. Scientific American: …using a combination of brain imaging and single-neuron recording in macaques, biologist Doris Tsao and her colleagues at Caltech have finally cracked the neural code for …

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Meat Camp!

Summer field season is upon us, and our first stop: Meat Camp! As strange as it sounds, this isn’t a summer camp of sorts, but rather the small North Carolina town where some adorable young bluebirds, and their tiny parasites, can be found. Above and to the left, you can see a nest box with …

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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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GCTA, Missing Heritability, and All That

Bioinformaticist E. Stovner asked about a recent PNAS paper which is critical of GCTA. My comments are below. It’s a shame that we don’t have a better online platform (e.g., like Quora or StackOverflow) for discussing scientific papers. This would allow the authors of a paper to communicate directly with interested readers, immediately after the paper …

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Largest repositories of genomic data

This list of the largest repositories of genetic data appeared in the 25 September 2015 issue of Science. Note that the quality and extent of phenotyping varies significantly. 23andME SIZE: >1 million GENETIC DATA: SNPs This popular personal genomics company now hopes to apply its data to drug discovery (see main story, p. 1472). ANCESTRY.COM …

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Endings and beginnings

I returned from my first trip to China. Happily I was able to recover enough to get back into the field, but alas only once. We hiked to the border of Wolong Nature Reserve and the reserve to the north, Caopo. This area had excellent panda habitat and we found four different fecal samples. From …

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No genomic dark matter

Let me put it very simply: there is NO genomic “dark matter” or “missing heritability” — it’s merely a matter of sample size (statistical power) to identify the specific variants that account for the total expected heritability. The paper below (see also HaploSNPs and missing heritability) suggests that essentially all of the expected heritability can …

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Go see Ant-Man. Right now.

Photo courtesy of imdb.com Another Marvel blockbuster, Ant-Man, has come out this summer. With polite nods to previous Avengers and Shield storylines, this is the tale of a good guy, a super-cool shrinking suit, and a pretty amazing scientist with an affinity for ants. Not to give too much away about the plot, I’ll just leave …

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What is medicine’s 5 sigma?

Editorial in the Lancet, reflecting on the Symposium on the Reproducibility and Reliability of Biomedical Research held April 2015 by the Wellcome Trust. Offline: What is medicine’s 5 sigma? … much of the [BIOMEDICAL] scientific literature, perhaps half, may simply be untrue. Afflicted by studies with small sample sizes, tiny effects, invalid exploratory analyses, and …

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Hopfield on physics and biology

Theoretical physicist John Hopfield, inventor of the Hopfield neural network, on the differences between physics and biology. Hopfield migrated into biology after making important contributions in condensed matter theory. At Caltech, Hopfield co-taught a famous course with Carver Mead and Richard Feynman on the physics of computation. Two cultures? Experiences at the physics-biology interface (Phys. …

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One Hundred Years of Statistical Developments in Animal Breeding

This nice review gives a history of the last 100 years in statistical genetics as applied to animal breeding (via Andrew Gelman). One Hundred Years of Statistical Developments in Animal Breeding (Annu. Rev. Anim. Biosci. 2015. 3:19–56 DOI:10.1146/annurev-animal-022114-110733) Statistical methodology has played a key role in scientific animal breeding. Approximately one hundred years of statistical …

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Fifty years of twin studies

The most interesting aspect of these results is that for many traits there is no detectable non-additivity. That is, gene-gene interactions seem to be insignificant, and a simple linear genetic architecture is consistent with the results. Meta-analysis of the heritability of human traits based on fifty years of twin studies Nature Genetics (2015) doi:10.1038/ng.3285 Despite …

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Gene drive

IIUC, there is a self-referential (“auto-catalyzing”) aspect to this method which is very interesting. The Cas9 gene (payload) also encodes the guide RNA (target) information, which determines the location of the DNA cut. Needless to say, this is a very powerful and potentially dangerous technology. Enrico Fermi (speaking about atomic weapons): Once basic knowledge is …

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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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Analogies between Analogies

As reported by Stan Ulam in Adventures of a Mathematician: “A mathematician is a person who can find analogies between theorems; a better mathematician is one who can see analogies between proofs and the best mathematician can notice analogies between theories. One can imagine that the ultimate mathematician is one who can see analogies between …

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Mapping Michigan’s lake habitats

Our main hypotheses are that habitats affect the the distribution, abundance, diets, and growth rates of Largemouth Bass. How do we get this habitat data? In previous posts I’ve discussed how we catch fish and collect their gut contents, so this article will focus on our vegetation mapping. Vegetation mapping techniques have advanced rapidly in …

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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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