linkstream2 microblog

https://www.nature.com/news/2010/100715/full/news.2010.356.html

QT:[[”

It should be possible to scan the genome for sequences encoding peptides shorter than 100 amino acids, says Mark Gerstein, a computational biologist at Yale University in New Haven, Connecticut, but sorting through the many ‘hits’ to determine which are functional is likely to be much more difficult.

Meanwhile, Gerstein notes that the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. “Maybe this would provide a new way for pseudogenes to have some sort of function,” he says.
“]]

http://www.duhaime.org/LegalDictionary/B/ButFor.aspx

http://causality.cs.ucla.edu/blog/index.php/2016/06/28/on-the-classification-and-subsumption-of-causal-models/

QT:[[”
The taxonomy that has helped me immensely is the three-level hierarchy described in chapter 1 of my book Causality: 1. association, 2. intervention, and 3 counterfactuals. It is a useful hierarchy because it has an objective criterion for the classification: You cannot answer questions at level i unless you have assumptions from level i or higher.
“]]

https://www.washingtonpost.com/world/2019/02/23/kalashnikov-assault-rifle-changed-world-now-theres-kalashnikov-kamikaze-drone/?noredirect=on&utm_term=.a8418c6bef8e

https://www.nytimes.com/2019/01/17/magazine/ancient-dna-paleogenomics.html

has an interesting discussion of review process at Nature

QT:[[”
It has not gone unnoticed that the stunning, magisterial sweep of genetic revisionism, on the one hand, and a genetic emphasis on radical prehistoric migrations, on the other, bear more than a little in common. Some anthropologists
and archaeologists accept this analogy with gallows humor. One told me that I should
model this article after the format of the standard Nature paper: “Ancient DNA Reveals Massive Population Turnovers in the Humanities,” she suggested as a title,
and proposed this as an abstract: “The aristocratic lab scientists arrived with their
superior technology and displaced the pre-existing researchers and their primitive
truth-implements and overcomplicated belief systems.
…
Serious challenges to its soundness were laid out during
Nature’s peer-review process. And yet, in a highly unusual move, the paper was accepted over the steadfast objections of two of the three peer reviewers on its anonymous panel. Confidential documents made available to me reveal deep concerns with the paper’s methods and its conclusions.
“]]

https://www.amazon.com/gp/product/B07H7B1L41/

https://www.nature.com/articles/s41586-019-0933-9

Using single-cell combinatorial indexing, we profiled the
transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment.

https://www.nature.com/articles/s41586-019-0969-x.epdf

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Product Review: Melissa & Doug’s Suspend Is Addictive! | WIRED https://www.wired.com/2012/07/melissa-doug-suspend-review/