How I could use a DNA social networks to move around during a lockdown.
Since May 4th, Italians are allowed to travel again within their Regions to visit their “next-of-kin”, according to a new government rule seeking to relax a strict, nationwide Covid-19 lockdown in place since early March.
After a deluge of wild interpretations (it turns out that the wording “next-of-kin” has no legal meaning) the government clarified that people will be allowed to visit relatives up the sixth degree.
I don’t like uber-paternalistic governments telling people who they should meet in the first place, instead of instructing them more effectively about the safest behaviours to keep.
However, the news immediately triggered my DNA-obsessed mind to ask a few nerdy questions.
What if we had a system to look at our DNA and tell where are our relatives, whether we know them or not?
And how many sixth-degree relatives do I have around?
The question is not theoretical. In this very moment, you can almost picture millions of Italians desperately scavenging their family trees and calling their grandmums for a hint to locate a far, forgotten cousin living close to the sea, or in a nice mountain place far from the city. Just to have a legal excuse for a daily escape.
The ideal genetic tool would not only identify my relatives but also allow me to contact them so that we could arrange mutual visits. Everything would be perfectly legal since we could scientifically prove to be relative.
It didn’t take much before I realized that such a tool is already there. Actually, I have been using it for eight years.
In my book DNA NATION: How the Internet of Genes is Changing Your Life I investigated the world of home DNA testing firsthand. Millions of people are spitting into a tube to turn their DNAs into a file and use it to establish a link with others.
Some of these applications find your relatives around the World by comparing their DNA with yours and create a social network out of it. The Relative Finder from 23andme.com is the one I used. Other companies like Ancestry.com have similar offerings.
I have currently over 1,300 “DNA relatives” in my network, mostly cousins up to the fifth degree.
We all have thousands of far cousins and a part of this extended tribe just pops out from my Relative Finder.
There is even a map showing where they are, provided that they shared the information. As a user I can filter the results to locate my “next-of-kins” up to the sixth degree in my region (Tuscany).
Which I did.
Unfortunately (or not, depending on how far you want to keep your relatives from you) the bulk of my DNA-extended tribe lives in the US and only a few are in Italy. This is just a technical artefact due to the fact that most 23andMe spitters are Americans.
Besides, only a fraction of spitters has actually added a location to their profile (I didn’t, for example).
Nevertheless (Bingo!) I found a couple of “DNA relatives”, apparently living in Tuscany. One is even not too far from the coast, where I would like to go.
Should I contact them now? It’s legally OK, but is it the right thing to do?
I had my answer before I even started the search: it’s not necessarily the right thing to do, and I am not really looking for new relatives to escape the lockdown.
And even if I already have close “next-of-kins” on the coast of Tuscany that I could call, I’m not thinking of visiting them now. I see no reason to put me and other people unnecessarily at risk when we should limit our contacts responsibly instead.
However, the very fact that I could do it is new and interesting.
It is also a demonstration of how pre-genomic rules are often unable to work now that DNA data become pervasive. I collected many other examples of this in my book.
DNA social networks are a reality, and their scope is far bigger than just escaping lockdowns. These tools have revolutionized fields as diverse as the study of genetics, genealogy, and drug research and are reshaping our view of family, race, ancestry and law.
We need to adapt to a world where DNA data are ubiquitous and will even define our real or perceived identity.
Scientific American, Feb 6 2020
Remember that when you buy one of those genome testing kits—and eventually, you will
When I was a young student in Paris, the City of Love, girls at parties would ask what I did for a living. I still recall their unsettled looks when I answered “molecular biologist,” which would send them running to powder their noses. They never came back. Back in the early 2000s, the only people who could get stuck in a dreary conversation about DNA, Mendel’s peas and alleles were four-eyed genetic nerds who wasted their lives in laboratories. We were undateable, and the level of endogamy amongst us was startling.
Today, the tables have turned. Millions of people are spitting into a tube to get their genes analyzed and share the results on social networks. Genealogy websites, the second-most visited category in the U.S. after porn, are full of enthusiasts discussing chromosome markers like they were at a laboratory meeting. Celebrities get their genes tested during talk shows, and YouTubers upload videos on their spit-into-the-tube experience. Everyone is hungry to learn about their DNA. DNA has become trendy, my social life has significantly improved, and it’s a wonderful time to be a genetic nerd.
Much of the credit goes to direct-to-consumer genomics for shifting the public perception of DNA from “boring stuff” to fascinating, personal journey. Reading our DNA and using it online is incredibly informative and fun, and these tools have engaged the public into genetics to a level that science writers could have only dreamed of. To write my book DNA Nation I tried out at least two dozen applications where I could use my DNA file.
With the pervasive success of this technology, however, also comes a reality distortion field. In the enthusiasm surrounding the progress of genomics, we end up overstating the real nature of our DNA and believing that it is more important than it is. The Oscar for Genetic Ravings goes to Advanced Technologies, an Indian DNA company whose website claims that genetic code is a “Divine Writing,” but genetic determinism—the idea that DNA will determine our fate and identity—is deeply ingrained in our culture. Make a Google search, and you’ll find hundreds of sources (including textbooks and leading scientists) describing DNA as the blueprint of life. It would be a great, easy-to-understand analogy, if it wasn’t wrong and outdated.
DNA is not a blueprint: it’s a recipe coding for thousands of different proteins that interact with each other and with the environment, just like the ingredients of a cake in an oven. Whereas a blueprint is an exact, drawn-to-scale copy of the final product, a recipe is just a loose plot that leaves much more room to uncertainty. Open a packet of cookies: each one was made from the same recipe and baked in the same conditions, but there are no two that are identical. Look closely, and you’ll spot hundreds of little differences: a burn here, a chocolate chip there, bumps and lumps appearing in distinct places, all because of chaotic interactions between the ingredients and the environment.
Take two identical twins: they share the same DNA, and their embryos developed side-by-side in the same uterus. Yet, they have different tastes, characters and attitudes, and make different choices in life. When you read the DNA of twins, you find a duplicate copy of the same recipe, but two distinct personalities. Not what you would call a fixed plan.
We do not inherit specific instructions on how to build a cell or an organ. Our DNA contains a list of biochemical ingredients (the proteins coded in the genes) and the basic rules for their assembly (some proteins are labeled as “master” and can control the activity of others, while others can start a dominolike cascade of events) but the pieces self-organize into biochemical pathways, cells and tissues without reading a manual. The genetic recipe for a cat will not give an elephant, but you can’t read the DNA of an individual and see a Mini-Me of his features.
The long-standing blueprint analogy, with its attached determinism, is a toxic meme we have to fight in the era of genetic consumerism. As long as people will believe that our identity and fate is programmed into their DNA, there will be a market for questionable genetic tests aimed at predicting intelligence, music, reading and math abilities, and even sexual preferences.
DNA testing for talents is especially thriving in China, where the one-child policy in place for decades and a rampant economy have put an enormous pressure on parents to give their offspring a competitive edge. Local clinics offering these tests proliferate, and thousands of Chinese parents are taking into account the results of DNA analyses before selecting a school for their child. Blinded by the blueprint rhetoric, these people believe themselves to be in the vanguard of a new approach in parenting, while they are being bamboozled into costly and inaccurate tests that their children will probably throw in their teeth one day.
Make no mistake: some traits are indeed genetically programmed, and some diseases are deterministic: people with a pathogenic mutation in the CFTR gene will develop cystic fibrosis regardless of their lifestyle. Even abilities once considered only a matter of upbringing like language, abstract thinking and many behavioral traits have a significant genetic component. But it doesn’t mean that DNA always has the upper hand. The opposite is true: an overwhelming majority of our traits depend on the blending of many genetic and nongenetic factors and therefore are hard to predict from DNA.
If we are a slow-baking cake, the world surrounding us is a capricious oven changing every minute. Science can peek through the glass and check if something looks funny inside the oven, but it cannot predict what our life, experiences and luck will bring tomorrow and the day after tomorrow.
Powered by petabytes of data and intelligent algorithms, the genetic profiles of the future will be mighty, and their breadth will be frightening. Yet, no test will ever be able to predict our personalities accurately, not to mention our fates, because a significant part of what we are is not written into DNA.
When the postman knocks at your door with the DNA kit you bought online (because you will definitely buy one eventually), promise to relax for a minute and repeat to yourself: “DNA is not a blueprint. And my genes are not destiny.”
Sergio Pistoi is a science writer with a PhD in molecular biology. His latest book, DNA Nation: How the Internet of Genes is Changing your Life (Crux Publishing, 2019), is an account of the emerging world of consumer genomics and DNA social networks.
This article originally appeared on the Scientific American website.
Genetic investigations are the latest tool for busting unsafe microorganisms and improving air quality in buildings
By Sergio Pistoi
Youris.com, April 10, 2017
Usually associated with humid and sordid slums, mould is a frequent finding in wealthy homes too. Even the fanciest buildings may harbour hot spots where fungi and other microorganisms subtly proliferate, triggering problems that range from unpleasant smells to severe sickness.
Miia Pitkäranta, a Finnish molecular microbiologist, pioneered the use of DNA investigations to identify and study indoor microorganisms during her Ph.D. at the University of Helsinki. She later became a practitioner in the building industry, specialising in indoor air quality.
Pitkäranta is a member of the International Society of Indoor Air Quality and Climate (ISIAQ) and has contributed to updating the national guidelines on air quality in Finland. youris.com asked her about the fascinating world of microbes in buildings, their impact on our health and how DNA technologies are becoming a tool to improve the air quality of buildings.
Which communities of microorganisms live in our homes and offices? Which of them need more attention?
Of course, it’s okay to find microorganisms in any building. Some come from outdoors, and many are yeasts or bacteria that are symbiotic with the users themselves or their pets. Nobody expects to live in a sterile environment. Problems arise when some microorganisms grow excessively. One of the first signs we look for when we investigate a building is the presence of mould and moisture because they are usually associated with microbial hot spots.
In a dry environment, microbes tend to lay dormant in the dust or on the surfaces. Dust is dirt, but it will go away when you ventilate or clean. Mould and moisture hot spots are entirely different ecosystems. Whereas dust is basically a collection of microorganisms that are already found in our bodies and in the outdoor dust, hot spots contain a few types of filamentous fungi, yeasts and bacteria that proliferate in moisture.
What problems are associated with indoor hotspots?
We have over 100 years of research showing that moisture and mould in buildings correlate with sickness. Many studies have associated them with asthma. I would say that asthma is the most studied symptom because it’s easier to identify. Other warning signs, such as eye irritation or dripping nose are even more widespread, but they are harder to quantify and record. There may be several mechanisms involved: direct toxicity, irritation, allergies.
However, it’s difficult to establish a clear cause and effect relationship, because the symptoms are also common to many other pathologies. Some research has linked moisture and mould to a series of non-specific symptoms: headaches, fatigue, dizziness, neurological or autoimmune disorders. We definitively need more research on the topic.
The term sick building syndrome (or SBS) was once used to include many health conditions linked to living indoors, but SBS is not considered an existing entity anymore. Today we believe there is not one syndrome associated with buildings as such, but rather a wide variety of agents and individual sensitivities that create an array of possible symptoms.
How can DNA be used to identify indoor microbes and what are the advantages?
The standard way to analyse a microbial hot spot is to take samples from it, cultivate the organisms in the laboratory and identify them with a microscope. One problem with cultivation is that you select only those species that can grow in the laboratory, and you lose the majority of the original biodiversity. By looking at the DNA instead, we identify directly which genomes, and therefore which species, are present.
DNA methods are faster than cultivation – they take days instead of weeks – and are non-selective. Another advantage of DNA methods is that they discriminate between single species, whereas with cultivation we usually identify microbes at the genus level, and each genus may include dozens of species. Today we know, for example, there are a lot of interesting species in indoor moulds that were underestimated with cultivation studies. As for any ecosystem, it’s important to know as much as possible about the diversity of species to understand how the community functions.
[…. ] Read the full interview here: http://www.youris.com/Health/Interviews/Is-Your-Home-Healthy-Ask-The-DNA
Research on gut bacteria may change the way we look at anxiety, depression, and behavioural disorders
by Sergio Pistoi, Youris, 17 October 2016
If aliens were to examine a human, they would think we were just slavish organisms designed to feed microbes and carry them around. Our bodies contain ten times more bacteria than cells, and there are an estimated 3.3 million genes in the total bacteria DNA, which is 160 times the number of human genes. Our intestine hosts about one kilogram of bacteria which help to digest and metabolise food, produce vitamins and protect us from infections.
The above is textbook knowledge, but loads of recent studies are uncovering new and unsuspected roles for these little companions. There is evidence that gut bacteria can protect or predispose us to pathologies ranging from inflammation to diabetes and obesity. And, as far-fetching as it sounds, a remarkable amount data shows that they can even modify our mood and behaviour.
Microbes are hot on the scientific agenda. In May, the US government launched a National Microbiome Initiative with an overall budget of half a billion dollars, while the EU is funding more than 300 projects related to the microbiome.
Yolanda Sanz, a researcher at the Institute of Agrochemistry and Food Technology (IATA) of the Spanish National Research Council in Valencia, Spain, coordinates MyNewGut, the largest EU consortium in the field with 30 partners in 15 Countries. We asked Sanz about the perspectives of research and the intriguing connections between the microbiome and the brain.
What makes our gut flora, and how does it change over time?
Our intestine hosts a complex ecosystem of bacteria; we call it the gut microbiota, which includes at least 1000 difference species. We get most of our gut microbes soon after birth, although there is evidence of colonisation even during prenatal life.
Over the first 2-3 years of life, the microbiota is very unstable in its composition. This condition overlaps with a period in which the immune system is still immature. At this stage, the microbiota is greatly influenced by diet, for example whether you are breastfed or not.
When an adult diet takes over, the composition of the gut microbiota becomes more stable and a microbiotic profile emerges. This usually prevails until old age when the diet goes back to being less diverse and more unstable, such as in babies. In some way, the evolution of microbiota reflects our growth and senescence.
Do we therefore have a sort of microbial identity, a bacterial fingerprint that is unique to an individual?
—-> Continue reading
Choosing between wild and farmed fish is often a dilemma for consumers. Science gives us a heads-up for choosing at the counter and helps in the struggle to save the global fish stocks
Sergio Pistoi, Youris.com
Wild-captured fish cost twice as much as their farmed counterparts; a difference that many believe is justified by their better taste and nutritional properties.
However, with wild stocks declining, fish farming – also called aquaculture – provides not only cheaper, but also a seemingly more sustainable alternative to open sea fisheries.
Personal preferences rule at the fish counter. However, experts have used objective methods to judge the taste and nutritional qualities of farmed fish, and their results may put a few noses out of joint among those people who spend more to go for the wild-caught version.
“Fish coming from aquaculture can have more fat, but that’s because they move less and eat more regularly than what they would do in the wild. Apart from that, the nutritional profiles can be indistinguishable,” says Sadasivam Kaushik, founder-director of Fish Nutrition Laboratory at the National Institute of Agronomical Research (INRA) in Bordeaux, France.
When it comes to taste, wild fish usually have more diverse and distinct flavours, depending on the compounds they absorb from the environment, such as bromophenols, which give a distinct “sea” aroma. Many people swear to be able to distinguish wild fish once they are on the plate, but it’s not always the case.
Emilio Tibaldi, a professor of aquaculture at the University of Udine who co-authored a report for the Italian Ministry of Agriculture, says that a panel of tasters he put together for the study could not distinguish between wild and farmed sea bass [article continues here]
Read more: http://www.youris.com/Bioeconomy/Food/Which-Is-More-Wholesome-Wild-Or-Farmed-Fish.kl
Does technology expose cities more to terrorist attacks?
Sergio Pistoi, Youris.com
Link to the original article: http://www.youris.com/Energy/Ecocities/Cyber-Attacks–Are-Smart-Cities-Safer-Or-More-Vulnerable.kl#ixzz4AEuSWq4n
In the wake of the Brussels bombings, the French blogger Francis Pisani addressed the quandaries of modern, connected European cities facing terrorist threats. There is no simple answer to attacks, he noted, but most measures have an impact on our mobility.
More controls mean that we need to wait for our luggage to be X-rayed, or to line up for double checks at a gate. And many train stations are slowly turning to airport-like security measures. Mobility, a feature of modern, connected economies, is the first victim of security.
A freelance journalist with credits in various French newspapers and an enduring interest in information technology (IT), Pisani embarked on a world tour in 2012 and 2014 to look for examples of urban innovation. He then gave a clued-up account of this in an ebook published by the UNESCO (available in English and French).
Most of his recent work is devoted to studying and reporting examples of participatory technologies that can improve city life.
Let’s start with the basics. You have often criticized the term “smart cities”. Why?
The sociologist and politician Jean-Louis Missika once said the term smart city is a pleonasm because humanity has not done anything more intelligent than cities. I agree with him: all cities are smart. So I think the question becomes: what is the process to make a city smarter?
In this process, I see a tension between what I call the datapolis, a city based on data, and participolis, which thrives on participation and where citizens use IT while also contributing with their minds.
During my tour I was amazed to see how many applications people create independently of any municipality. And that’s where you find most smartness. After all, the internet has evolved in a similar way: with the web 2.0, we moved from an architecture of data to one of participation.
Can cities use technologies to improve security without sacrificing our freedom to travel?
I think they can, but always at the expense of our privacy. For example, airports or stations can create a fast lane for those who accept background checks, biometric controls or smart cards connected to databases which expose their privacy to the authorities. Or they can facilitate security with pervasive cameras and sensors that also have an impact on privacy.
Someone who promises more security, mobility and privacy at the same just isn’t credible. It’s just an illusion: there is always a trade-off in one of these variables.
Negotiating between these needs should be a central topic in the political debate. I would like to see politicians who are technology-savvy and to put the question high on their agenda, but it’s not happening.
City officials often have a poor understanding of technology. Many just want their cities to be “smart”, and give the keys to IT companies that say: we are going to make it happen! That’s not the best way to proceed.
Cities should have an autonomous and participative strategy and then look around for the best technological solution. In Lyon, for example, the city decided what they wanted, they control the data, and the IT company only provides the technology they need.
Are smart cities safer, or are they more vulnerable, because their infrastructure can be a target for cyber criminals?
Photo credit: Laetitia Attali, courtesy of F. Pisani
A celebrity in the materials world, Mark Miodownik dreams of colour-changing walls and looks at the future of renewable buildings
Sergio Pistoi, Youris.com 20 April 2016
Link to the original article: http://www.youris.com/Energy/Interviews/The-Social-Life-Of-Bricks.kl
Mark Miodownik will never forget the day he became obsessed with materials. He was a schoolboy in 1985 when he was stabbed in the London Underground. “When I saw that weapon in the police station later, I was mesmerized. I had seen razors before of course, but now I realized that I didn’t know them at all. (…) its steel edge was still perfect, unaffected by its afternoon’s work,” he writes in his bestselling book Stuff Matters.
Growing up, Miodownik turned his fixation into a successful career. He became a materials scientist at the University College London, the director of the UCL’s Institute of Making and a widely known speaker and BBC presenter. His research interests include biomaterials, innovative manufacturing, and sensoaesthetics, a science that investigates the intricate relationship between people and the materials they use.
We asked Miodownik to share his views about the rediscovery of traditional materials in modern architecture, and how tomorrow’s buildings will cross the border between new and old technologies.
Do you think there is still value in using wood, straw, wool, or other traditional materials for buildings?
I don’t see being “traditional” as a value per se. The choice of materials has to be assessed with modern criteria, which include sustainability and energy consumption. If you ask me whether traditional materials are appropriate for modern buildings, I think the answer is yes. Partly because traditional materials have a portfolio of properties that are sometimes better than anything we have created recently: wool, for example, is a fantastic insulator.
Partly because it’s the whole ecosystem that matters. In the old days, the building materials we used were part of the landscape, and they were easier to recycle. New materials are not usually like that. When it comes to sustainability, traditional materials are often more efficient.
Construction experts point to limits in the public perception. Some described the three little pigs syndrome, a misconception by which buildings made with traditional materials, such as wood, would not be not as stable or durable as concrete. Is this vision widespread? And does our cultural background influence how we perceive materials?
There is no simple answer. Anthropological studies show that different cultures favour different materials, but the ways people relate to materials is extremely complex. The texture, the feel, the colour or even the imperceptible smell of an object can affect our emotional state. The materials we choose for our house, or the clothes we wear, not only represent us are but they also change how we are. Therefore, the materials we choose for a building can have subtle social consequences.
However, I don’t think that the “three little pigs syndrome” you describe is so widespread. People generally trust the engineers and rarely think about buildings collapsing, unless they live in an earthquake zone.
Rather, I believe that the influence of the global culture is predominant. People worldwide associate concrete, glass, and steel with modernity – think of the iconic image of a skyscraper – and this cuts across many cultures, especially in countries that are switching from rural to urban.
In the industrialised countries, I see much more of the opposite syndrome: many people don’t like concrete and are looking for alternative materials to build their homes.
My sports shoes have a new waterproof layer and a classic leather upper. Will buildings go the same way, layering technologies and crossing the border between old and new materials?
THE INTERVIEW continues here. Please read on!
In a world hungry for energy, top scientist Michael Grätzel hopes to make solar cells more affordable by copying photosynthesis
By Sergio Pistoi
Youris.com, 14 March 2016
In the late 1980s, the German-born chemist Michael Grätzel literally tied his name to an invention that is hailed as a revolution in renewable energy.
Dye-sensitized solar cells (DSSC) – officially dubbed Grätzel cells to honour their creator – are transparent photovoltaic cells inspired by the way plants generate energy.
Artificial photosynthesis is a term often used to describe this technology. A professor at the Ecole Polytechnique fédérale de Lausanne (EPFL), Grätzel has an impressive catalogue of honours that include a Millennium Prize, the top global award in technology. Thomson Reuters listed him among the most influential scientific minds of 2015.
What is the difference between a conventional solar cell and a Grätzel cell?
Traditional photovoltaic cells are made of silicon crystals. It’s a solid-state system based on a semiconductor, very much like the transistors we see on a computer or radio. When light hits the silicon, it produces electrons and also works as a conductor for them. The movement of electrons creates an electric current.
Instead, DSSCs mimic the natural process of photosynthesis by using dyes to capture light and produce a current in a semiliquid gel, just like a leaf does.
A green leaf is like a miniature solar field. We know from school that the first step of photosynthesis is a photoelectric event in which pigments, such as chlorophyll, react with light and produce the electrons. These are transported to other molecules that ultimately reduce CO2 and water to sugar and oxygen.
DSSCs follow the same idea: they contain a dye that reacts with light and produces electrons that flow to other molecules in the gel. Instead of doing photosynthesis, they end up at an electrode, generating an electric current that we can use. The whole system takes place inside a transparent glass or plastic.
What are the pros and cons with DSSC?
In standard conditions, they are still less efficient than silicon cells. However, in cloudy conditions and diffuse light DSSCs are three times more effective, which makes them ideal for indoor use, even with artificial lighting.
DSSCs are also transparent and can be made in different colours, so you can replace windows with stained glass that produce electricity. They are creating a market for many new applications.
Where have they been used?
The first product to be commercialised was a backpack powered by DSSC cells. Our Convention Center in Lausanne has a façade made with DSSC panels produced by the Swiss company Solaronix. An Australian company, Dyesol, is working with the Turkish government to scale up the production of renewable energy with DSSC.
Another Swiss company, G2E, set up a huge DSSC installation for the Austrian pavilion at the 2015 World’s Fair in Milan. My wife and I went there this summer. It was our birthday, we were born the same day, and she’s also a scientist in my group. We saw “our” solar panels capturing the Italian sun and transforming it into electricity to charge a car. It was a very moving moment for us both.
Who owns the patents on this technology?
There are hundreds of patents on DSSC technology today. The EPFL, where I work, owns about 60. In 1988, we registered the first patent on DSSC and in 1993 the EFPL signed the first licence agreement.
The patents are licenced to companies on a non-exclusive basis. This decision was difficult at the beginning. Licencing was widespread in the US but there were few or no examples in Europe, where people just sold their patents.
The French government has recently announced a project to cover 1,000 kilometers of roads with solar panels . What do you think about it?
It strikes me as a crazy idea. The panels will need protecting if cars and lorries are to pass over them. I suspect that the maintenance costs alone will be prohibitive. Isn’t it just simpler to make many solar fields?
I think policy-makers should be more mindful about the feasibility of their projects, otherwise they could jeopardise the entire sector.
Five years ago, the Spanish government suddenly stopped subsidising solar energy which had been an ambitious programme that was meant to last longer. But the money ran out. Because of this failure, many companies went broke. It brought about a crisis that threatened the whole solar industry.
The interview continues! Read on here.