jm + genetics   12

A Controversial Virus Study Shows Flaws in How Science Is Done - The Atlantic
Absent clearer guidelines, the burden falls on the scientific enterprise to self-regulate—and it isn’t set up to do that well. Academia is intensely competitive, and “the drivers are about getting grants and publications, and not necessarily about being responsible citizens,” says Filippa Lentzos from King’s College London, who studies biological threats. This means that scientists often keep their work to themselves for fear of getting scooped by their peers. Their plans only become widely known once they’ve already been enacted, and the results are ready to be presented or published. This lack of transparency creates an environment where people can almost unilaterally make decisions that could affect the entire world.

Take the horsepox study [the main topic of this article]. Evans was a member of a World Health Organization committee that oversees smallpox research, but he only told his colleagues about the experiment after it was completed. He sought approval from biosafety officers at his university, and had discussions with Canadian federal agencies, but it’s unclear if they had enough ethical expertise to fully appreciate the significance of the experiment. “It’s hard not to feel like he opted for agencies that would follow the letter of the law without necessarily understanding what they were approving,” says Kelly Hills, a bioethicist at Rogue Bioethics.

She also sees a sense of impulsive recklessness in the interviews that Evans gave earlier this year. Science reported that he did the experiment “in part to end the debate about whether recreating a poxvirus was feasible.” And he told NPR that “someone had to bite the bullet and do this.” To Hills, that sounds like I did it because I could do it. “We don’t accept those arguments from anyone above age 6,” she says.
the-atlantic  science  news  smallpox  horsepox  diseases  danger  risk  academia  papers  publish-or-perish  bioethics  ethics  biology  genetics 
13 days ago by jm
One in five genetics papers contains errors thanks to Microsoft Excel | Science | AAAS
'Autoformatting in Microsoft Excel has caused many a headache — but now, a new study shows that one in five genetics papers in top scientific journals contains errors from the program, The Washington Post reports. The errors often arose when gene names in a spreadsheet were automatically changed to calendar dates or numerical values.'
science  microsoft  excel  spreadsheets  autoformatting  clippy  fail  papers  genetics 
8 weeks ago by jm
Antonio Regalado Twitter thread on genetic genealogy, DNA privacy, and total DNA de-anonymity
I used to know some technicians in the NYC Medical Examiner's lab. They had all been DNA typed (to detect accidental contamination). So, their little society was a picture of what is to come, of total DNA transparency.

They would do stuff like find out who stuck gum under the table. Also, who was peeing on the toilet seat in the bathroom.

So There’s a second technology at play: environmental DNA sampling. Once police get a name they tail the suspect and try to get some DNA he leaves behind. To make the match to crime scene sample. Police have gotten DNA from:
- a car door handle
- a straw
- a paper napkin

Imagine storm troopers of a repressive regime descending on a meeting place of the resistance. Just swab the whole place and find out who was there from DNA left behind.
Technically, total DNA de-anonymity is possible. Far as I know there’s no law, no protection, against identifying you from your DNA.

In crime cases, [this is] being done by “amateur” using a database (GEDmatch) that itself is highly informal.
privacy  dna  genetics  genetic-genealogy  gedmatch  law  transparency 
june 2018 by jm
why Cheddar Man was dark skinned
'But why should that be surprising? He's over 10,000 years old, while mutations that led to white skin [the depigmentation gene SLC24A5] only began to spread widely [across Europe] 5,800 years old!'
europe  history  prehistory  skin-colour  cheddar-man  race  skin  slc24a5  genetics  david-grimes 
february 2018 by jm
Modern Irish genome closely matches pre-Celt DNA, not Celtic
Radiocarbon dating shows that the bones discovered at McCuaig's go back to about 2000 B.C. That makes them hundreds of years older than the oldest artifacts generally considered to be Celtic — relics unearthed from Celt homelands of continental Europe, most notably around Switzerland, Austria and Germany.

For a group of scholars who in recent years have alleged that the Celts, beginning from the middle of Europe, may never have reached Ireland, the arrival of the DNA evidence provides the biological certitude that the science has sometimes brought to criminal trials.

“With the genetic evidence, the old model [of Celtic colonisation of Ireland] is completely shot,” John Koch, a linguist at the Center for Advanced Welsh and Celtic Studies at the University of Wales.
celts  ireland  history  dna  genetics  genome  carbon-dating  bronze-age  europe  colonisation 
march 2016 by jm
Health of purebred vs mixed breed dogs: the actual data - The Institute of Canine Biology

This study found that purebred dogs have a significantly greater risk of developing many of the hereditary disorders examined in this study. No, mixed breed dogs are not ALWAYS healthier than purebreds; and also, purebreds are not "as healthy" as mixed breed dogs. The results of this study will surprise nobody who understands the basics of Mendelian inheritance. Breeding related animals increases the expression of genetic disorders caused by recessive mutations, and it also increases the probability of producing offspring that will inherit the assortment of genes responsible for a polygenic disorder. 


In conclusion, go mutts.
dogs  breeding  genetics  hereditary-disorders  science  inheritance  recessive-mutation  data 
march 2016 by jm
Gene patents probably dead worldwide following Australian court decision
The court based its reasoning on the fact that, although an isolated gene such as BRCA1 was "a product of human action, it was the existence of the information stored in the relevant sequences that was an essential element of the invention as claimed." Since the information stored in the DNA as a sequence of nucleotides was a product of nature, it did not require human action to bring it into existence, and therefore could not be patented.


Via Tony Finch.
via:fanf  australia  genetics  law  ipr  medicine  ip  patents 
october 2015 by jm
100 Years of Breed “Improvement” | Science of Dogs
The English bulldog has come to symbolize all that is wrong with the dog fancy and not without good reason; they suffer from almost every possible disease. A 2004 survey by the Kennel Club found that they die at the median age of 6.25 years (n=180). There really is no such thing as a healthy bulldog. The bulldog’s monstrous proportions makes them virtually incapable of mating or birthing without medical intervention.


(via Bryan)
dogs  eugenics  breeding  horror  science  genetics  traits  animals  pets  bulldog  pedigree 
december 2013 by jm
_Intellectual property rights and innovation: Evidence from the human genome_ (PDF)
'Do intellectual property (IP) rights on existing technologies hinder subsequent
innovation? Using newly-collected data on the sequencing of the human genome by
the public Human Genome Project and the private rm Celera, this paper estimates
the impact of Celera's gene-level IP on subsequent scienti c research and product
development. Genes initially sequenced by Celera were held with IP for up to two
years, but moved into the public domain once re-sequenced by the public e ort.
Across a range of empirical speci cations, I nd evidence that Celera's IP led to
reductions in subsequent scienti c research and product development on the order of
20 to 30 percent. Taken together, these results suggest that Celera's short-term IP
had persistent negative e ects on subsequent innovation relative to a counterfactual
of Celera genes having always been in the public domain.' (via Tony Finch)
via:fanf  genetics  ip  copyright  open-source  celera  patents  papers  pdf 
february 2012 by jm
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks — PNAS
'we present a comparison between the transcriptional regulatory network of a well-studied bacterium (E. coli) and the call graph of a canonical OS (Linux) in terms of topology and evolution. ... both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. ... These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.' (via adulau)
via:adulau  papers  toread  genetics  genome  call-graph  linux  kernel  e-coli  operating-systems  transcriptional-regulatory-network  from delicious
may 2010 by jm
TCD researchers first to find genes unique to humans
go Aoife! “This is the first ever discovery of novel human-specific protein coding genes,” said Dr McLysaght. “They are found in humans and nowhere else.”
science  genetics  research  biology  evolution  tcd  sfi  genome  junk-dna  from delicious
september 2009 by jm

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