Tag: Genetics


Finally, a court has ruled that in order for a DNA test to be admitted as evidence, the source code must be made available to the defense.

To my mind, any software used for prosecutions should be publicly available for review:

A New Jersey appeals court has ruled that a man accused of murder is entitled to review proprietary genetic testing software to challenge evidence presented against him.

Attorneys defending Corey Pickett, on trial for a fatal Jersey City shooting that occurred in 2017, have been trying to examine the source code of a software program called TrueAllele to assess its reliability. The software helped analyze a genetic sample from a weapon that was used to tie the defendant to the crime.

The maker of the software, Cybergenetics, has insisted in lower court proceedings that the program’s source code is a trade secret. The co-founder of the company, Mark Perlin, is said to have argued against source code analysis by claiming that the program, consisting of 170,000 lines of MATLAB code, is so dense it would take eight and a half years to review at a rate of ten lines an hour.

MATLAB is a pretty high level language, so if you have 170,000 lines of code in it, you are writing bloated code. 

Also, if you have 170,000 lines of code in it, I guarantee that there are bugs, and likely substantial ones, because most of those lines of code are there to handle edge (unlikely) cases, where the programmer has to make broad assumptions about the data.


On Wednesday, the appellate court sided with the defense [PDF] and sent the case back to a lower court directing the judge to compel Cybergenetics to make the TrueAllele code available to the defense team.

“Without scrutinizing its software’s source code – a human-made set of instructions that may contain bugs, glitches, and defects – in the context of an adversarial system, no finding that it properly implements the underlying science could realistically be made,” the ruling says.

Kit Walsh, senior staff attorney for the Electronic Frontier Foundation, hailed the appellate ruling. “No one should be imprisoned or executed based on secret evidence that cannot be fairly evaluated for its reliability, and the ruling in this case will help prevent that injustice,” she said in a blog post. If TrueAllele is found wanting, presumably that will not affect the dozen individuals said to have been exonerated by the software.

It should be noted that the studies “validating” TrueAllele have been conducted by Mark Perlin, and as such are suspect.

Also, though these are slightly different application, we already know that algorithms used for health care software, Zoom face detection, educational evaluations, and criminal sentencing are all explicitly racist.

It is no stretch to assume that an algorithm explicitly developed for police and prosecutors would be biased in their favor.

That is how you make sales.

Rule 1 of Monsanto, Monsanto is Evil

Rule 2 of Monsanto is SEE RULE 1.

After creating a plague of Roundup resistant weeds, Monsanto decided to double down on Dicamba, which had the effect of KNOWINGLY poisoning neighboring farmers’ crops, if they did not pay for Monsanto’s own genetically modified crops:

The US agriculture giant Monsanto and the German chemical giant BASF were aware for years that their plan to introduce a new agricultural seed and chemical system would probably lead to damage on many US farms, internal documents seen by the Guardian show.

Risks were downplayed even while they planned how to profit off farmers who would buy Monsanto’s new seeds just to avoid damage, according to documents unearthed during a recent successful $265m lawsuit brought against both firms by a Missouri farmer.

The documents, some of which date back more than a decade, also reveal how Monsanto opposed some third-party product testing in order to curtail the generation of data that might have worried regulators.


The new crop system developed by Monsanto and BASF was designed to address the fact that millions of acres of US farmland have become overrun with weeds resistant to Monsanto’s glyphosate-based weedkillers, best known as Roundup. The collaboration between the two companies was built around a different herbicide called dicamba.


The companies said they would make new dicamba formulations that would stay where they were sprayed and would not volatilize as older versions of dicamba were believed to do. With good training, special nozzles, buffer zones and other “stewardship” practices, the companies assured regulators and farmers that the new system would bring “really good farmer-friendly formulations to the marketplace”.

But in private meetings dating back to 2009, records show agricultural experts warned that the plan to develop a dicamba-tolerant system could have catastrophic consequences. The experts told Monsanto that farmers were likely to spray old volatile versions of dicamba on the new dicamba-tolerant crops and even new versions were still likely to be volatile enough to move away from the special cotton and soybean fields on to crops growing on other farms.

Why did Monsanto do something so evil, beyond the fact that they are one step away from having a white Persian cat?

Because we allow companies to patent crops, and prevent farmers from replanting crops, and so we create an incentive to sabotage people into buying their (very) pricey seed.

This sh%$ is criminogenic, and for the life of me I do not understand how this does not constitute a criminal conspiracy under the RICO statutes.

The Bedbug at “All the News That’s Fit to Print” Endorses Eugenics

I am referring, of course, to Brett Stephens, who is now claiming that Ashkenazi Jews are genetically more intelligent, at least a bit:

Ashkenazi Jews might have a marginal advantage over their gentile peers when it comes to thinking better. Where their advantage more often lies is in thinking different.

Seriously, between Brett Stephens and Bari Weiss, I’m beginning to wonder if the Times Editorial Page Editor James Bennet is literally trying to find the most contemptible Jews possible to become regular columnists.

Seriously, as a human being and an American, I find Stephens an embarrassment, and as a Jew, I find him a Shanda fur die Goyim.*

*Yiddish for a, “Shame before the nations,” meaning that this person is an embarrassment to the whole Jewish people.

Live in Obedient Fear, Citizen!

Family Tree DNA, one of the largest private genetic testing companies whose home-testing kits enable people to trace their ancestry and locate relatives, is working with the FBI and allowing agents to search its vast genealogy database in an effort to solve violent crime cases, BuzzFeed News has learned.

Federal and local law enforcement have used public genealogy databases for more than two years to solve cold cases, including the landmark capture of the suspected Golden State Killer, but the cooperation with Family Tree DNA and the FBI marks the first time a private firm has agreed to voluntarily allow law enforcement access to its database.

While the FBI does not have the ability to freely browse genetic profiles in the library, the move is sure to raise privacy concerns about law enforcement gaining the ability to look for DNA matches, or more likely, relatives linked by uploaded user data.

For law enforcement officials, the access could be the key to unlocking murders and rapes that have gone cold for years, opening up what many argue is the greatest investigative tactic since the advent of DNA identification. For privacy advocates, the FBI’s new ability to match the genetic profiles from a private company could set a dangerous precedent in a world where DNA test kits have become as common as a Christmas stocking stuffer.


Until now, investigators have limited their searches to public and free databases, where genealogy enthusiasts had willingly uploaded the data knowing it could be accessible to anyone.

Now, under the previously undisclosed cooperation with Family Tree, the FBI has gained access to more than a million DNA profiles from the company, most of which were uploaded before the company’s customers had any knowledge of its relationship with the FBI.


“We are nearing a de-facto national DNA database,” Natalie Ram, an assistant law professor at the University of Baltimore who specializes in bioethics and criminal justice, told BuzzFeed News. “We don’t choose our genetic relatives, and I cannot sever my genetic relation to them. There’s nothing voluntary about that.” 

Aldous Huxley’s Brave New World is looking increasingly prophetic.

Given the FBI’s anti-abortion biases, this is particularly chilling in the area of reproductive freedom.

You Are Not 23andMe’s Customer, You Are Their Product

The online genetic testing service 23andMe is looking to sell your genetic data to big pharma, and you ain’t gonna get nothin for it:

Since the launch of its DNA testing service in 2007, genomics giant 23andMe has convinced more than 5 million people to fill a plastic tube with half a teaspoon of saliva. In return for all that spit (and some cash too), customers get insights into their biological inheritance, from the superficial—do you have dry earwax or wet?—to mutations associated with disease. What 23andMe gets is an ever-expanding supply of valuable behavioral, health, and genetic information from the 80 percent of its customers who consent to having their data used for research.

So last week’s announcement that one of the world’s biggest drugmakers, GlaxoSmithKline, is gaining exclusive rights to mine 23andMe’s customer data for drug targets should come as no surprise. (Neither should GSK’s $300 million investment in the company). 23andMe has been sharing insights gleaned from consented customer data with GSK and at least six other pharmaceutical and biotechnology firms for the past three and a half years. And offering access to customer information in the service of science has been 23andMe’s business plan all along, as WIRED noted when it first began covering the company more than a decade ago.


“I think we’re just operating now in a much more untrusting environment,” says Megan Allyse, a health policy researcher at the Mayo Clinic who studies emerging genetic technologies. “It’s no longer enough for companies to promise to make people healthy through the power of big data.” Between the fall of blood-testing unicorn Theranos and Facebook’s role in the 2016 election attacks, “I think everything from here on out will be subject to much higher levels of public scrutiny,” Allyse says.

23andMe maintains that transparency is a core tenet of the company. “I think a really important distinction to make is that 23andMe operates under an independent ethical review board that oversees all of our research,” says Emily Drabant Conley, 23andMe’s vice president of business development, who oversaw the announcement of the GSK deal. “The guidelines we follow are essentially the same as what other research institutions follow.” So they should apply to any of the analyses GSK might want to run on 23andMe data, like a PheWAS, which connects constellations of symptoms and conditions across many people with a single genetic mutation they all share.

Yeah, sure.

It’s there in a very small print at the end of a long and confusing document.

Here is the money quote:

It’s also worth pointing out that 23andMe can, in theory, unilaterally change those terms and conditions and privacy policies at any time, says Katherine Drabiak, a legal expert in health law and research ethics at the University of South Florida. As a commercial enterprise, it’s not bound by the same obligations as medical professionals. 23andMe doesn’t have to take an oath to act in the interest of consumers or to promote their well being.

They say not to worry, because they will obey the voluntary guidelines of the Future of Privacy Forum, whose supporters include, “AT&T, Comcast, Facebook, Google, Intelius and Microsoft,” which is kind of like the, “Knife Safety Forum,” founded by noted barber Sweeney Todd.

I will leave you to this: Self-regulation is to regulation as self-importance is to importance.

Seriously Neat Tech

Spider silk has some remarkable mechanical properties. Its low weight, high strength, an low modulus make it a potential break through in body armor.

The problem is spiders, which produce the material in very limited quantities, and their cannibalistic proclivities mitigate against high intensity farming.

Well, it looks like the DoD is trying to get silk genetically engineered worms to produce spider silk an alternative:

The U.S. Army is upping its investment in genetically engineered spider silk for body armor. Last year, the service paid almost $100,000 to Kraig Biocraft Laboratories, which makes spider silk that can be produced at scale — with silkworms. On Wednesday, the company announced that the Army will move to the second phase of the contract and will look to Kraig to produce a customized strain of the silk for “high-performance fibers for protective apparel applications.” That is: flexible body armor made from genetically engineered spider silk. The total contract amount would reach $900,000 if parameters are met. Army representatives said that interested in the material purely from a research perspective, for now.

Kraig Biocraft injects spider DNA into silkworm eggs, enabling the worms to produce its custom silk. The researchers describe the process in this 2011 PNAS paper.

Spider silk is much tougher than regular worm silk, and about half as tough as Kevlar. But it’s far more flexible, (3 percent elasticity for kevlar versus nearly 40 percent for spider silk.) The Army believes that the energy absorption of the material could be much higher than kevlar (as determined by multiplying the strength of the fiber by the elongation.)

It’s also much more elastic and flexible than kevlar. But getting enough spider silk to clothe an Army is a tall order. The crawly arachnids don’t produce silk in high volume and when you crowd spiders too close together, they eat each other. The quest to produce spider silk in hosts other than spiders has led researchers to use a variety of other methods such as yeast, e. coli bacteria and mammalian cells. 

There is also the fact that the techniques for handling silkworms, and harvesting the silk, have been known for thousands of years.

It is also far less alarming than the prospect of an escape of motherf%$#ing mutant spiders.

Evil Megalomaniac Seeks to Revive Monster from Primeval Times

There are certain people who I will assume that anything they do is in furtherance of evil.

One of them is Peter Thiel, who literally has aspirations to be a vampire.

Now, he’s dropping big bucks on an attempt to revive the species of the Woolly Mammoth.

I do not know how reviving the Woolly Mammoth will make life more miserable for the rest of us, but given that Thiel is funding it, I guarantee that it will make life more miserable for the rest of us.

At least he’s not a one of the megalomaniacs planning on mounting a private operation to mine asteroids, which could easily be turned into a devastating weapon.

We are F%$#ed

Up in the arctic, there is a vault holding the seeds of thousands of species of crops.

Its purpose is to protect the biodiversity of agriculture in an increasingly commercial and monoculture system.

An unexpected thaw in permafrost just flooded portions of the complex:

It was designed as an impregnable deep-freeze to protect the world’s most precious seeds from any global disaster and ensure humanity’s food supply forever. But the Global Seed Vault, buried in a mountain deep inside the Arctic circle, has been breached after global warming produced extraordinary temperatures over the winter, sending meltwater gushing into the entrance tunnel.

The vault is on the Norwegian island of Spitsbergen and contains almost a million packets of seeds, each a variety of an important food crop. When it was opened in 2008, the deep permafrost through which the vault was sunk was expected to provide “failsafe” protection against “the challenge of natural or man-made disasters”.

But soaring temperatures in the Arctic at the end of the world’s hottest ever recorded year led to melting and heavy rain, when light snow should have been falling. “It was not in our plans to think that the permafrost would not be there and that it would experience extreme weather like that,” said Hege Njaa Aschim, from the Norwegian government, which owns the vault.

“A lot of water went into the start of the tunnel and then it froze to ice, so it was like a glacier when you went in,” she told the Guardian. Fortunately, the meltwater did not reach the vault itself, the ice has been hacked out, and the precious seeds remain safe for now at the required storage temperature of -18C.

But the breach has questioned the ability of the vault to survive as a lifeline for humanity if catastrophe strikes. “It was supposed to [operate] without the help of humans, but now we are watching the seed vault 24 hours a day,” Aschim said. “We must see what we can do to minimise all the risks and make sure the seed bank can take care of itself.”


“The Arctic and especially Svalbard warms up faster than the rest of the world. The climate is changing dramatically and we are all amazed at how quickly it is going,” Isaksen told Norwegian newspaper Dagbladet

Anthropogenic climate change is real, and we are only beginning to see the consequences.

Muck Fonsanto

The New York Times has looked into the potential benefits of transgenic crops, and found no evidence that these benefits exist:

The controversy over genetically modified crops has long focused on largely unsubstantiated fears that they are unsafe to eat.

But an extensive examination by The New York Times indicates that the debate has missed a more basic problem — genetic modification in the United States and Canada has not accelerated increases in crop yields or led to an overall reduction in the use of chemical pesticides.

The promise of genetic modification was twofold: By making crops immune to the effects of weedkillers and inherently resistant to many pests, they would grow so robustly that they would become indispensable to feeding the world’s growing population, while also requiring fewer applications of sprayed pesticides.

Twenty years ago, Europe largely rejected genetic modification at the same time the United States and Canada were embracing it. Comparing results on the two continents, using independent data as well as academic and industry research, shows how the technology has fallen short of the promise.

An analysis by The Times using United Nations data showed that the United States and Canada have gained no discernible advantage in yields — food per acre — when measured against Western Europe, a region with comparably modernized agricultural producers like France and Germany. Also, a recent National Academy of Sciences report found that “there was little evidence” that the introduction of genetically modified crops in the United States had led to yield gains beyond those seen in conventional crops. Continue reading the main story

At the same time, herbicide use has increased in the United States, even as major crops like corn, soybeans and cotton have been converted to modified varieties. And the United States has fallen behind Europe’s biggest producer, France, in reducing the overall use of pesticides, which includes both herbicides and insecticides.

Here’s a suggestion, how about invalidating patents on plant species and granting farmers the unconditional right to replant their seeds. 
This was the state of affairs for about 15,000 years of human history, and we did just fine.

The 3rd Worst Job on Earth

Tasmanian Devil Milker:

Milk from Tasmanian devils could offer up a useful weapon against antibiotic-resistant superbugs, according to Australian researchers.

The marsupial’s milk contains important peptides that appear to be able to kill hard-to-treat infections, including MRSA, say the Sydney University team.

Experts believe devils evolved this cocktail to help their young grow stronger.

The scientists are looking to make new treatments that mimic the peptides.

They have scanned the devil’s genetic code to find and recreate the infection-fighting compounds, called cathelicidins.

Milking a Tasmanian Devil is not high on my list of career options.