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Posts Tagged ‘genetics

“All of today’s DNA, strung through all the cells of the earth, is simply an extension and elaboration of [the] first molecule”*…

 

The first biological teleporter sits in a lab on the lower level of the San Diego building that houses Synthetic Genomics Inc. (SGI), looking something like a super-sized equipment cart.

The device is actually conglomeration of small machines and lab robots, linked to each other to form one big machine. But this one can do something unprecedented: it can use transmitted digital code to print viruses.

In a series of experiments culminating last year, SGI scientists used genetic instructions sent to the device from elsewhere in the building to automatically manufacture the DNA of the common flu virus. They also produced a functional bacteriophage, a virus that infects bacterial cells.

Although that wasn’t the first time anyone had made a virus from DNA parts, it was the first time it was done automatically, without human hands.

The device, called a “digital-to-biological converter” was unveiled in May. Though still a prototype, instruments like it could one day broadcast biological information from sites of a disease outbreak to vaccine manufacturers, or print out on-demand personalized medicines at patients’ bedsides…

… or project life-as-we-know it into outer space. More at “Biological Teleporter Could Seed Life Through Galaxy.”

* Lewis Thomas, The Medusa and the Snail

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As we beam up, we might spare a thought for Sidney Walter Fox; he died on this date in 1998.  A biochemist, he was responsible for a series of discoveries about the origin of life.  Fox believed in the process of abiogenesis, by which life spontaneously organized itself from the colloquially known “primordial soup,” poolings of various simple organic molecules that existed during the time before life on Earth.  In his experiments (which possessed, he believed, conditions like those of primordial Earth), he demonstrated that it is possible to create protein-like structures from inorganic molecules and thermal energy.  Dr. Fox went on to create microspheres that he said closely resembled bacterial cells and concluded that they could be similar to the earliest forms of life or protocells.

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Written by LW

August 10, 2017 at 1:01 am

“Race does not stand up scientifically, period”*…

 

The genetic distance between some groups in Africa, such as the Fulani of West Africa (above) and the Hazda of Tanzania, is greater than supposedly racially divergent groups such as East Asians and Europeans.

If race categories were meant primarily to capture differences in genetics, they are doing an abysmal job. The genetic distance between some groups within Africa is as great as the genetic distance between many “racially divergent” groups in the rest of the world. The genetic distance between East Asians and Europeans is shorter than the divergence between Hazda in north-central Tanzania to the Fulani shepherds of West Africa (who live in present-day Mali, Niger, Burkina Faso, and Guinea). So much for Black, White, Asian, and Other.

Armed with this knowledge, many investigators in the biological sciences have replaced the term “race” with the term “continental ancestry.” This in part reflects a rejection of “race” as a biological classification. Every so-called race has the same protein-coding genes, and there is no clear genetic dividing line that subdivides the human species. Another reason for using the term “continental ancestry” in lieu of “race” is improved precision for locating historical and geographic origins when we look at the genome. Thus, continental ancestry allows for more genetically accurate descriptors. For example, President Barack Obama was not just the first socially “black” president. He was also the first (as far as we know) who has European and African ancestry.

In sum, racial categories now in use are based on a convoluted and often pernicious history, including much purposefully created misinformation.

It is a good time, then, to dispel some myths about genetic variation that have been promulgated by both the left and the right alike…

Setting the scientific record straight on race, IQ, and success: “What Both the Left and Right Get Wrong About Race.”

* Dalton Conley and Jason Fletcher

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As we hear Bob Marley sing “One love, one heart, let’s get together and feel all right,” we might recall that it was on this date in 1795 that the first (but still provisional) official standard “metre bar” was forged in Paris.  Made of brass, its length was one ten-millioneth of the northern quadrant of the Paris meridian.

In the aftermath of the French Revolution (1789), the traditional units of measure used in the Ancien Régime had replaced; the livre monetary unit was replaced by the decimal franc, and a new unit of length was introduced– the metre.

This first prototype was short by 0.2 millimeters because researchers miscalculated the flattening of the earth due to its rotation.  Still this length became the standard– replicated in platinum– until 1889, when new, more accurate measurements were used to create a new standard metre, that gained acceptance across the world.

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Written by LW

June 9, 2017 at 1:01 am

“When you have mastered numbers, you will in fact no longer be reading numbers, any more than you read words when reading books. You will be reading meanings.”*…

Errors of judgment about large numbers can have a big impact on the way you view policies and government decisions. The rationale goes like this: The National Science Foundation received $7.463 billion for fiscal year 2016 through the Consolidated Appropriations Act. The total United States budget outlay for 2016 was $3.54 trillion. If you’re someone who perceives the difference between a billion and a trillion as relatively small, you’d think the US is spending a lot of money on the National Science Foundation—in fact, depending on your politics, you might applaud the federal government’s investment or even think it wasteful. But, if you understand that a billion is a thousand times less than a trillion, you can calculate that the Foundation got a paltry 0.2 percent of the budget outlay last year. (It may be more straightforward to think of the budget as roughly one-half to one-third of reported costs for the proposed US-Mexico border wall, and let your values guide you from there.)…

On the significance of scale: “How to Understand Extreme Numbers.

[The image above is, of course, from the ever-wonderful xkcd.]

* W.E.B. Du Bois

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As we nudge ourselves toward numeracy, we might spare a thought for Sewall Wright; he died on this date in 1988.  A geneticist, he was known for his influential work on evolutionary theory and also for his work on path analysis. He was a founder (with Ronald Fisher and J.B.S. Haldane) of population genetics– a major step in the development of the modern evolutionary synthesis combining genetics with evolution.   He is perhaps best remembered for his concept of genetic drift (called the Sewall Wright effect): when small populations of a species are isolated, the few individuals who carry certain relatively rare genes may fail, out of pure chance, to transmit them. The genes may therefore disappear and their loss may lead to the emergence of new species– although natural selection has played no part in the process.

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Written by LW

March 3, 2017 at 1:01 am

“Why should things be easy to understand?”*…

 

Dunning-Kruger Effect

The less competent an individual is at a specific task, the more likely they are to over-estimate their ability at that task.

Sure, ignorance is bliss. But being convinced you’re an expert at something, even though actually you’re ignorant — DAYUM — that’s the the best thing ever. People with poor abilities at some task can sometimes mistakenly believe that they are much more skilled at the task then they actually are. Examples of this are everywhere, from people who have never played a sport before, but just know they’ll be great at it, to people who’ve had one semester of french back in high school, but have no doubt that when the plane lands in Paris they’ll be able to talk like a native…

More on this all-too-timely phenomenon here— one the regular entries in Chris Spurgeon‘s marvelous newsletter, The Laws of the Universe, a regular series of postings…

Every once in a while — very rarely in the grand scheme of things — someone figures out how a tiny, tiny bit of the universe works. Through this newsletter I celebrate these discoveries, and the people they’re named after.

These tiny discoveries are known by many terms — laws, rules, constants, principles, theorems, effects. And they pop up in all areas of human endeavors — science of course, but also law and politics, arts and entertainment, popular culture and everyday life. Hubble’s Law, Dunbar’s Number, the Barbara Streisand Effect, Murphy’s Law — they’re all fair game. The only rules are:

1) the law must be named for someone, and
2) the law must shine a tiny bit of light onto one tiny bit of how the universe operates.

Browse the archive (and sign up) here.

* Thomas Pynchon

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As we revel in rules, we might spare a thought for Gregor Johann Mendel; he died on this date in 1884.  After a profoundly-unpromising start, Mendel became a scientist, Augustinian friar, and abbot of St. Thomas’ Abbey in Brno, Moravia (today’s Czech Republic).  A botanist and plant experimenter, he was the first to lay the mathematical foundation of the science of genetics (of which he is now consider the “Father”).  Over the period 1856-63, Mendel grew and analyzed over 28,000 pea plants.  He carefully studied for each their height, pod shape, pod color, flower position, seed color, seed shape and flower color– and from those observations derived two very important generalizations, known today as the Laws of Heredity.

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Written by LW

January 6, 2017 at 1:01 am

“Pseudoscience often relies on a witches’ brew of scientific terms… half-baked into simplistic metaphors that do not correspond with testable reality”*…

 

A new wine delivery service called Vinome is promising to deliver “the ultimate personalized wine experience” — customized to your DNA.

There isn’t much (or, really, any) science to back it up. But it’s got a very big name in its corner. Vinome just inked a deal with a startup called Helix, which in turn is backed by the world’s biggest DNA sequencing company, the powerhouse known as Illumina. For the past 15 years, Illumina has been selling machines that can quickly decode the human genome. Medical researchers around the world use them. But the company wants to conquer the consumer market, too. That’s why it spent $100 million to launch Helix, which teams up with app developers who can find creative ways to use a customer’s genetic data. Such as selling them wine.

For about $65 per bottle, Vinome promises to pick out “great wines that are perfectly paired to you” based on an analysis of 10 genetic variants in your DNA, collected via saliva samples. The company — which is based, of course, in Northern California’s wine country — even incorporated the distinctive double helix of DNA into its logo of a corkscrew.

Medical geneticist Dr. Jim Evans isn’t impressed.  “It’s just completely silly. Their motto of ‘A little science and a lot of fun’ would be more accurately put as ‘No science and a lot of fun,’” said Evans, who’s a professor and researcher at the University of North Carolina. “I’d put this in the same category as DNA matching to find your soulmate,” he said. “We just simply don’t know enough about the genetics of taste to do this on any accurate basis.”…

For more, pop the cork at: “Fruity with a hint of double helix: A startup claims to tailor wine to your DNA.”

And for more on the larger phenomenon of which Vinome is a part, see “‘Personalized nutrition’ isn’t going to solve our diet problems.”

[Image above sourced here]

K. Lee Lerner

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As we ponder personalization, we might recall that today is International Merlot Day.  As Wine Cellar Insider observes

When asked for the most widely planted grape in Bordeaux , many wine lovers would say Cabernet Sauvignon. That is not the case. There are more hectares devoted to Merlot than any other grape in Bordeaux. To give you an idea on how much Merlot is planted in Bordeaux, close to 62% of all vines in Bordeaux are Merlot taking up about 69,138 hectares. Cabernet Sauvignon is a distant second with about 25% of the region’s planting’s totaling close to 28,347 hectares.

Merlot is not only popular in Bordeaux. In fact, it’s the most widely planted grape in France! Merlot is also successfully planted in Switzerland, Australia, Argentina and numerous other countries, as well as in America…

 

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Written by LW

November 7, 2016 at 1:01 am

“The greatest enemy of knowledge is not ignorance, it is the illusion of knowledge”*…

 

We’ve looked before at the methodological problems that beset (too) much science, and at the work of John Ioannidis, who’s done more than anyone else to uncover them (see here and here).  Ioannidis is back…  and the news is troubling:

Over the past decade, scientists have increasingly become ashamed at the failings of their own profession: due to a lack of self-policing and quality control, a large proportion of studies have not been replicable, scientific frauds have flourished for years without being caught, and the pressure to publish novel findings—instead of simply good science—has become the commanding mantra. In what might be one of the worst such failings, a new study suggests that even systematic reviews and meta-analyses—typically considered the highest form of scientific evidence—are now in doubt.

The study comes from a single author: John Ioannidis, a highly respected researcher at Stanford University, who has built his reputation showing other scientists what they get wrong. In his latest work, Ioannidis contends that “the large majority of produced systematic reviews and meta-analyses are unnecessary, misleading, or conflicted.”

 Systematic reviews and meta-analyses are statistically rigorous studies that synthesize the scientific literature on a given topic. If you aren’t a scientist or a policymaker, you may have never heard of them. But you have almost certainly been affected by them.

If you’ve ever taken a medicine for any ailment, you’ve likely been given the prescription based on systematic reviews of evidence for that medication. If you’ve ever been advised to use a standing desk to improve your health, it’s because experts used meta-analyses of past studies to make that recommendation. And government policies increasingly rely on conclusions stemming from evidence found in such reviews. “We put a lot of weight and trust on them to understand what we know and how to make decisions,” Ioannidis says…

More at “The man who made scientists question themselves has just exposed huge flaws in evidence used to give drug prescriptions.” See also “The Inevitable Evolution of Bad Science” and “Trouble at the Lab.”

And lest we think “hard scientists” alone in their misery, consider the plight of economists: “The Emperor’s New Paunch.”

*Daniel J. Boorstin

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As we check, check, and check again, we might send disingenuous birthday greetings to Trofim Denisovich Lysenko; he was born on this date in 1898.  A Soviet biologist and agronomist, he believed the Mendelian theory of heredity to be wrong, and developed his own, allowing for “soft inheritance”– the heretability of learned behavior. (He believed that in one generation of a hybridized crop, the desired individual could be selected and mated again and continue to produce the same desired product, without worrying about separation/segregation in future breeds.–he assumed that after a lifetime of developing (acquiring) the best set of traits to survive, those must be passed down to the next generation.)

In many way Lysenko’s theories recall Lamarck’s “organic evolution” and its concept of “soft evolution” (the passage of learned traits), though Lysenko denied any connection. He followed I. V. Michurin’s fanciful idea that plants could be forced to adapt to any environmental conditions, for example converting summer wheat to winter wheat by storing the seeds in ice.  With Stalin’s support for two decades, he actively obstructed the course of Soviet biology and caused the imprisonment and death of many of the country’s eminent biologists who disagreed with him.

Interestingly, some current research suggests that heretable learning– or a semblance of it– may in fact be happening, by virtue of epigenetics… though nothing vaguely resembling Lysenko’s theory.

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Written by LW

September 29, 2016 at 1:01 am

“The mind is a machine that is constantly asking: What would I prefer?”*…

 

As an increasing number of folks “modify” their bodies, hacking them to add (often electronic) enhancements, the Age of Radical Evolution is upon us…

Dallas is at the center of two movements that are each trying to bring implants to the mainstream. Tattoo artists and technophiles head one, and well-heeled university neurologists and medical device engineers form the vanguard of the other.

The fringe commercial types, who design and inject mail-order devices into their bodies, call themselves “grinders.” The high-end researchers, with advanced degrees and government contracts, call themselves “bioengineers.” They have radically different approaches, but they’re actually pulling humanity in the same direction — toward a fusion of hardware and wetware by incorporating technology into the body.

The prime driver of both of these movements is the shrinking size of wireless electronics. Implanted electronic devices are not new; surgeons in Sweden installed the first heart pacemakers in 1958 and researchers first implanted cochlear implants to mitigate hearing loss in the 1970s. But this is the iPhone generation, and electronics have grown small and powerful enough to appear in some unlikely places…

More at “Body hackers and bioengineers are trying to make DFW a hub of implantable electronics.

* George Saunders, “Buddha Boy,” The Braindead Megaphone

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As we conspire in our futures, we might send bio-identifiable birthday greetings to Sir Alec John Jeffreys; he was born on this date in 1950.  A geneticist, Sir Alec discovered and developed the techniques of DNA fingerprinting and profiling, used for unique identification of humans, animals and other organisms from their DNA material.

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Written by LW

January 9, 2016 at 1:01 am

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