Ask and ye shall receive :-) In an earlier post I recommended a talk by Ilya Sutskever of OpenAI (part of an MIT AGI lecture series). In the Q&A someone asks about the status of backpropagation (used for training of artificial deep neural nets) in real neural nets, and Ilya answers that it’s currently not …
The figures below are from the recent paper Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations (Nature Genetics), discussed previously here. As you can see, genomic prediction of risk allows to identify outliers for conditions like heart disease and diabetes. Individuals who are top 1% in polygenic risk score are …
It seems to me we are just at the tipping point — soon it will be widely understood that with large enough data sets we can predict complex traits and complex disease risk from genotype, capturing most of the estimated heritable variance. People will forget that many “experts” doubted this was possible — the term …
Years ago I predicted that: 1. Cognitive ability would turn out to be influenced by many thousands of genetic variants, each of small effect. 2. With large enough sample size we would detect these variants and eventually construct genomic predictors. The Nature Genetics paper (below) from the SSGAC collaboration takes a significant step in that …
Will knowledge from neuroscience inform the design of better AIs (neural nets)? These results from startup Vicarious AI suggest that the answer is yes! (See also this company blog post describing the research.) It has often been remarked that evolved biological systems (e.g., a baby) can learn much faster and using much less data than existing artificial neural nets. …
This is video of an excellent talk on the human connectome by neuroscientist Bobby Kasthuri of Argonne National Lab and the University of Chicago. (You can see me sitting on the floor in the corner :-) The story below is for entertainment purposes only. No triggering of biologists is intended. The Physicist and the Neuroscientist: A …
The Spring 2017 issue of the Stanford Medical School magazine has a special theme: Sex, Gender, and Medicine. I recommend the article excerpted below to journalists covering the Google Manifesto / James Damore firing. After reading it, they can decide for themselves whether his memo is based on established neuroscience or bro-pseudoscience. Perhaps top Google …
James Damore, Harvard PhD* in Systems Biology, and (until last week) an engineer at Google, was fired for writing this memo: Google’s Ideological Echo Chamber, which dares to display the figure above. Here is Damore’s brief summary of his memo (which contains many citations to original scientific research), and the conclusion: Google’s political bias has …
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 …
Humans are going to have to learn to “trust the AI” without understanding why it is right. I often make an analogous point to my kids — “At your age, if you and Dad disagree, chances are that Dad is right” :-) Of course, I always try to explain the logic behind my thinking, but …
I was honored and humbled to speak at the Doctoral Hooding Ceremony last weekend at the University of North Carolina at Chapel Hill. I received my Ph.D. there in 1982. It was great to be back in Chapel Hill, seeing some old friends and making many new ones. There was also one of those interesting …
To quote James Lee, the first author listed below: “Shock and Awe” for those who doubt that cognitive ability is influenced by genetic variants. See work from a year ago: ~100 hits from 300k individuals. Now ~600 hits from 750k. (SNPs associated with EA are likely to also be associated with cognitive ability — see …
Male brains exhibit larger variance across all morphological measures. (Don’t tell Larry Summers! ;-) Note, as far as I can tell the authors don’t normalize the SD by mean value for each gender to obtain the typical percentage fluctuation (a dimensionless quantity). The male brain is about 10% larger and each of the subregions is …
James Miller interviews Greg Cochran on a variety of topics. Some comments on the early part of the interview (you might need to listen to it to make sense of what I write below): 1. The prediction I’ve made about the consequences of additive genetic variance in intelligence is not that we’ll be able to …
This summer’s research adventures took us from Atlanta north. Most recently, we completed an 18-hour road trip (one-way!) to collect various bluebird and tree swallow nests. We survey and collect from hundreds of nests to find just a few parasites on which to do our work. It’s lots of effort, sure, but we’ve had great …
My interview with Thomas O’Reilly of Trinity College Dublin, covering topics such as genomics, CRISPR, genetic engineering, computational genomics, technology startups. Tweet
This is a recent MSU seminar on genomic prediction. Vimeo won’t let me embed the video, so click here to watch the talk. Results are presented for models ranging from simple linear and linear + dominance to reproducing Hilbert space kernels and neural nets. Results are consistent with sub-dominant nonlinear (non-additive) effects, but interesting GxE …
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 …
GCTA is a statistical method for estimating the heritability of a complex trait using (phenotype | genotype) data from unrelated individuals. It has been applied to many human phenotypes, including disease conditions and behavioral traits. GCTA results tend to be consistent with earlier twin and family studies of heritability, and suggest that significant heritability is …
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 …
This paper describes a method for estimating heritability of a complex trait due to a single locus (DNA region), which the authors refer to as local heritability. It does not make the GCTA assumption of random effects. Instead, it uses GWAS estimates of individual effect sizes and the population LD matrix (covariance matrix of loci). …
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 …
“I have no idea what this thing is, some sort of a spiny-headed worm or something,” called out Michelle, a technician in the lab. Transfixed by the insidious creature, she zoomed in with the microscope to take a closer look as she described what she saw. “It looks something like a small leech, but instead …
A new paper from the Kruglyak lab at UCLA shows yet again (this time in yeast) that population variation in quantitative traits tends to be dominated by additive effects. There are deep evolutionary reasons for this to be the case — see excerpt below (at bottom of this post). For other examples, including humans, mice, …
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 …
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 …
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 …
So, below is the press release for this work that has been in the making since spring 2011. I cannot convey enough how amazing it is to *finally* see it out! Background: For the BEACON course which pairs computer scientists and biologists, I pitched the idea of looking at signals, and lucky me, my co-authors …
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 …
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 …
Interesting results in this recent Nature article. The dominance effect is quite strong: the equivalent of first cousin inbreeding (homozygosity ~ 1/8) results in a decrease in height or cognitive ability of about 1/6 or 1/3 of an SD. That means the effect from alleles which depress the trait increases by significantly more than 2x …
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. …
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 …
As an experiment I recorded this video using slides from a talk I gave last week at NIH. I will be giving similar talks later this spring/summer at Human Longevity Inc. and BGI. The commonality between these institutions is that all three are on the road to accumulating a million human genomes. Who will get …
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 …
Another good talk from the Genomics, Big Data, and Medicine Seminar Series at the Icahn School of Medicine (Mt. Sinai). Peter starts his talk by discussing height as a classical model trait, giving credit to Galton for first investigating heritability and related ideas, and noting the approximate additivity of genetic effects. @16min, state of the art …
We’ve been trying to breed Pollimyrus isidori in the lab for the last couple of months, which are well reputed good parents . Withstanding some pH problems that we have been having over the past months, we’ve finally witnessed the fruits of our labor. As of another big clutch of eggs this morning, we have more …
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 …
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 …
This is the 3rd installment in my responses to Jeremy Fox’s questions about the LTEE (my lab’s long-term evolution experiment with E. coli), which he asked at the Dynamic Ecology blog. This response addresses his 2nd and 7th questions, which I’ve copied below. I like all of Jeremy’s questions, but I especially like his 2nd one …
Answer is Genesis (i.e., Ken Ham and the Creation Museum) has published a really nice description of the bedbug paper that came out earlier this year. The story is in short that bedbugs used to be one species feeding on bat blood, but now they are in the process of splitting into two species, with …
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 …
I have gotten busy enough with the start of a new semester that I haven’t posted all the science news I have saved in over a week. For now, I will do some briefer entries just so I can get through some of them. The California Condor used to be so close to extinction that …
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 …
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 …
Lakes made of asphalt (commonly known as tar or pitch) are found around the world in areas where oil deposits seep up through sedimentary rock. (See my previous post on tar lilies for descriptions and technical details on different components of oil and how they come to the Earth’s surface.) AtlasObscura’s article provides some fascinating …
It is quite amazing to consider that scientists may have only discovered 10% of the Earth’s species. Of course, many of the unknown species are small (insects, microbes) or in remote or extreme environments (deserts, the deep sea), which provides some explanation for why we have not found or identified them yet. Luckily, certain research …
You know those bedbug epidemics from apartments and hotels in big cities you have heard about, or perhaps unfortunately experienced? Soon bedbug outbreaks can be treated quickly, easily and affordably. Biologists have developed a new, effective bedbug trap through a painful process – by allowing bedbugs to feed on their own skin! The researchers started …
Scientists, beekeepers and farmers have been very worried recently about the sharp declines in bee populations. Native bees and bumblebees are being affected, and not just non-native honeybees. Researchers recently examined pinned bees from insect collections in the Northeastern U.S. Naturalists and entomologists have been collecting bees in the region (that are now kept in …
Some lakes in Ontario have experienced greatly-altered water chemistry in the past decades due to acid rain and human impacts. This acid reacts with calcium in soils surrounding the lakes, reducing the amount of calcium that makes it from the watershed into the lakes. This is impacting Daphnia, a kind of zooplankton that incorporates calcium …