jm + dna   13

The Impenetrable Program Transforming How Courts Treat DNA Evidence | WIRED
'So the lab turned to TrueAllele, a program sold by Cybergenetics, a small company dedicated to helping law enforcement analyze DNA where regular lab tests fail. They do it with something called probabilistic genotyping, which uses complex mathematical formulas to examine the statistical likelihood that a certain genotype comes from one individual over another. It’s a type of DNA testing that’s becoming increasingly popular in courtrooms. '

[...] 'But now legal experts, along with Johnson’s advocates, are joining forces to argue to a California court that TrueAllele—the seemingly magic software that helped law enforcement analyze the evidence that tied Johnson to the crimes—should be forced to reveal the code that sent Johnson to prison. This code, they say, is necessary in order to properly evaluate the technology. In fact, they say, justice from an unknown algorithm is no justice at all.'
law  justice  trueallele  software  dna  evidence  statistics  probability  code-review  auditing 
12 days ago by jm
Building a Regex Search Engine for DNA | Hacker News
The original post is pretty mediocre -- a search engine which handles a corpus of "thousands" of plasmids from "a scientist's personal library", and which doesn't handle fuzzy matches? I think that's called grep -- but the HN comments are good
grep  regular-expressions  hacker-news  strings  dna  genomics  search  elasticsearch 
april 2016 by jm
A programming language for E. coli
Mind = blown.
MIT biological engineers have created a programming language that allows them to rapidly design complex, DNA-encoded circuits that give new functions to living cells. Using this language, anyone can write a program for the function they want, such as detecting and responding to certain environmental conditions. They can then generate a DNA sequence that will achieve it.
"It is literally a programming language for bacteria," says Christopher Voigt, an MIT professor of biological engineering. "You use a text-based language, just like you're programming a computer. Then you take that text and you compile it and it turns it into a DNA sequence that you put into the cell, and the circuit runs inside the cell."
dna  mit  e-coli  bacteria  verilog  programming  coding  biohacking  science 
april 2016 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
Your Relative's DNA Could Turn You Into A Suspect
Familial DNA searching has massive false positives, but is being used to tag suspects:
The bewildered Usry soon learned that he was a suspect in the 1996 murder of an Idaho Falls teenager named Angie Dodge. Though a man had been convicted of that crime after giving an iffy confession, his DNA didn’t match what was found at the crime scene. Detectives had focused on Usry after running a familial DNA search, a technique that allows investigators to identify suspects who don’t have DNA in a law enforcement database but whose close relatives have had their genetic profiles cataloged. In Usry’s case the crime scene DNA bore numerous similarities to that of Usry’s father, who years earlier had donated a DNA sample to a genealogy project through his Mormon church in Mississippi. That project’s database was later purchased by Ancestry, which made it publicly searchable—a decision that didn’t take into account the possibility that cops might someday use it to hunt for genetic leads.

Usry, whose story was first reported in The New Orleans Advocate, was finally cleared after a nerve-racking 33-day wait — the DNA extracted from his cheek cells didn’t match that of Dodge’s killer, whom detectives still seek. But the fact that he fell under suspicion in the first place is the latest sign that it’s time to set ground rules for familial DNA searching, before misuse of the imperfect technology starts ruining lives.
dna  familial-dna  false-positives  law  crime  idaho  murder  mormon  genealogy  ancestry.com  databases  biometrics  privacy  genes 
october 2015 by jm
FBI admits flaws in hair analysis over decades
Wow, this is staggering.
The Justice Department and FBI have formally acknowledged that nearly every examiner in an elite FBI forensic unit gave flawed testimony in almost all trials in which they offered evidence against criminal defendants over more than a two-decade period before 2000. [....]

The review confirmed that FBI experts systematically testified to the near-certainty of “matches” of crime-scene hairs to defendants, backing their claims by citing incomplete or misleading statistics drawn from their case work. In reality, there is no accepted research on how often hair from different people may appear the same. Since 2000, the lab has used visual hair comparison to rule out someone as a possible source of hair or in combination with more accurate DNA testing. Warnings about the problem have been mounting. In 2002, the FBI reported that its own DNA testing found that examiners reported false hair matches more than 11 percent of the time.
fbi  false-positives  hair  dna  biometrics  trials  justice  experts  crime  forensics  inaccuracy  csi 
april 2015 by jm
Of Course 23andMe's Plan Has Been to Sell Your Genetic Data All Along
Today, 23andMe announced what Forbes reports is only the first of ten deals with big biotech companies: Genentech will pay up to $60 million for access to 23andMe's data to study Parkinson's. You think 23andMe was about selling fun DNA spit tests for $99 a pop? Nope, it's been about selling your data all along.

testing  ethics  dna  genentech  23andme  parkinsons  diseases  health  privacy 
january 2015 by jm
Herbal supplements are often 'rice and weeds'
DNA tests show that many pills labeled as healing herbs are little more than powdered rice and weeds. [...] Among their findings were bottles of echinacea supplements, used by millions of Americans to prevent and treat colds, that contained ground up bitter weed, Parthenium hysterophorus, an invasive plant found in India and Australia that has been linked to rashes, nausea and flatulence.
herbal-remedies  scams  quality  medicine  dna  testing  fillers  allergies  st-johns-wort  echinacea 
november 2013 by jm
How I decoded the human genome - Salon.com
classic long-read article from John Sundman: 'We are becoming the masters of our own DNA. But does that give us the right to decide that my children should never have been born?' part two at http://www.salon.com/2003/10/22/genome_two/
human  genome  genomics  eugenics  politics  life  john-sundman  disability  health  dna  medicine  salon  long-reads  children 
may 2013 by jm
All polar bears descended from one Irish grizzly
'THE ARCTIC'S DWINDLING POPULATION of polar bears all descend from a single mamma brown bear which lived 20,000 to 50,000 years ago in present-day Ireland, new research suggests. DNA samples from the great white carnivores - taken from across their entire range in Russia, Canada, Greenland, Norway and Alaska - revealed that every individual's lineage could be traced back to this Irish forebear.' More than the average bear, I guess
animals  biology  science  dna  history  ireland  bears  polar-bears  grizzly-bears  via:ben 
january 2013 by jm
CloudBurst
'Highly Sensitive Short Read Mapping with MapReduce'. current state of the art in DNA sequence read-mapping algorithms.
CloudBurst uses well-known seed-and-extend algorithms to map reads to a reference genome. It can map reads with any number of differences or mismatches. [..] Given an exact seed, CloudBurst attempts to extend the alignment into an end-to-end alignment with at most k mismatches or differences by either counting mismatches of the two sequences, or with a dynamic programming algorithm to allow for gaps. CloudBurst uses [Hadoop] to catalog and extend the seeds. In the map phase, the map function emits all length-s k-mers from the reference sequences, and all non-overlapping length-s kmers from the reads. In the shuffle phase, read and reference kmers are brought together. In the reduce phase, the seeds are extended into end-to-end alignments. The power of MapReduce and CloudBurst is the map and reduce functions run in parallel over dozens or hundreds of processors.

JM_SOUGHT -- the next generation ;)
bioinformatics  mapreduce  hadoop  read-alignment  dna  sequencing  sought  antispam  algorithms 
july 2012 by jm
This Bacteria is Violating Copyright | tor.com | Science fiction and fantasy | Blog posts
the Joyce estate playing their usual role. 'are we now nearing a point where copyright law can result in the retraction of a life form?' (via John Looney)
copyright  dna  bacteria  james-joyce  joyce-estate  frivolous  lawsuits  copyfight  craig-venter  from delicious
april 2011 by jm

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