Authoriteh's Restive About What You Peasants Get Up To With Synthetic Biology

FT  |  Paul Dabrowa does not know if it is illegal to genetically modify beer at home in a way that makes it glow. The process involves taking DNA information from jellyfish and applying it to yeast cells, then using traditional fermenting methods to turn it into alcohol. But he is worried that it could be against the law given that it involves manipulating genetic material. “This stuff can be dangerous in the wrong hands, so I did that in an accredited lab,” he says, adding that he himself has only got as far as making yeast cells glow in a Petri dish. For the most part Dabrowa, a 41-year old Melbourne-based Australian who styles himself as a bit of an expert on most things, prefers to conduct his biohacking experiments in his kitchen. He does this mostly to find cures for his own health issues. Other times just for fun.

In recent years the community of hobbyists and amateurs Dabrowa considers his kin has been energised by the falling cost and growing accessibility to gene-editing tools such as Crispr. This has led to an explosion of unchecked experimentation in self-constructed labs or community facilities focused on biological self-improvement.

Despite a lack of formal microbiological training, Dabrowa has successfully used faecal transplants and machine learning to genetically modify his own gut bacteria to lose weight without having to change his daily regime. The positive results he’s seen on himself have encouraged him to try to commercialise the process with the help of an angel investor. He hopes one day to collect as many as 3,000 faecal samples from donors and share the findings publicly.

Much of his knowledge — including the complex bits related to gene-editing — was gleaned straight from the internet or through sheer strength of will by directly lobbying those who have the answers he seeks. “Whenever I was bored, I went on YouTube and watched physics and biology lectures from MIT [Massachusetts Institute of Technology],” he explains. “I tried the experiments at home, then realised I needed help and reached out to professors at MIT and Harvard. They were more than happy to do so.”

At the more radical end of the community are experimentalists such as Josiah Zayner, a former Nasa bioscientist, who became infamous online after performing gene therapy on himself in front of a live audience. Zayner’s start-up, The Odin — to which Crispr pioneer and professor of genetics at Harvard Medical School George Church is an adviser — has stubbornly resisted attempts to regulate its capacity to sell gene-editing kits online in the idealistic belief that everyone should be able to manage their own DNA.

These garage scientists might seem like a quirky new subculture but their rogue mindset is starting to generate consternation among those who specialise in managing biological threats in governments and international bodies.

In 2018 the states that are signatories to the 1972 Biological Weapons Convention (BWC) identified gene editing, gene synthesis, gene drives and metabolic pathway engineering as research that qualifies as “dual use”, meaning it is as easy to deploy for harmful purposes as it is for good.
 

The Fungus Among Us...,

scientificamerican |  We are likely to think of fungi, if we think of them at all, as minor nuisances: mold on cheese, mildew on shoes shoved to the back of the closet, mushrooms springing up in the garden after hard rains. We notice them, and then we scrape them off or dust them away, never perceiving that we are engaging with the fragile fringes of a web that knits the planet together. Fungi constitute their own biological kingdom of about six million diverse species, ranging from common companions such as baking yeast to wild exotics. They differ from the other kingdoms in complex ways. Unlike animals, they have cell walls, not membranes; unlike plants, they cannot make their own food; unlike bacteria, they hold their DNA within a nucleus and pack cells with organelles—features that make them, at the cellular level, weirdly similar to us. Fungi break rocks, nourish plants, seed clouds, cloak our skin and pack our guts, a mostly hidden and unrecorded world living alongside us and within us.

That mutual coexistence is now tipping out of balance. Fungi are surging beyond the climate zones they long lived in, adapting to environments that would once have been inimical, learning new behaviors that let them leap between species in novel ways. While executing those maneuvers, they are becoming more successful pathogens, threatening human health in ways—and numbers—they could not achieve before.

Surveillance that identifies serious fungal infections is patchy, and so any number is probably an undercount. But one widely shared estimate proposes that there are possibly 300 million people infected with fungal diseases worldwide and 1.6 million deaths every year—more than malaria, as many as tuberculosis. Just in the U.S., the CDC estimates that more than 75,000 people are hospitalized annually for a fungal infection, and another 8.9 million people seek an outpatient visit, costing about $7.2 billion a year.

For physicians and epidemiologists, this is surprising and unnerving. Long-standing medical doctrine holds that we are protected from fungi not just by layered immune defenses but because we are mammals, with core temperatures higher than fungi prefer. The cooler outer surfaces of our bodies are at risk of minor assaults—think of athlete's foot, yeast infections, ringworm—but in people with healthy immune systems, invasive infections have been rare.

That may have left us overconfident. “We have an enormous blind spot,” says Arturo Casadevall, a physician and molecular microbiologist at the Johns Hopkins Bloomberg School of Public Health. “Walk into the street and ask people what are they afraid of, and they'll tell you they're afraid of bacteria, they're afraid of viruses, but they don't fear dying of fungi.”

Ironically, it is our successes that made us vulnerable. Fungi exploit damaged immune systems, but before the mid-20th century people with impaired immunity didn't live very long. Since then, medicine has gotten very good at keeping such people alive, even though their immune systems are compromised by illness or cancer treatment or age. It has also developed an array of therapies that deliberately suppress immunity, to keep transplant recipients healthy and treat autoimmune disorders such as lupus and rheumatoid arthritis. So vast numbers of people are living now who are especially vulnerable to fungi. (It was a fungal infection, Pneumocystis carinii pneumonia, that alerted doctors to the first known cases of HIV 40 years ago this June.)

Not all of our vulnerability is the fault of medicine preserving life so successfully. Other human actions have opened more doors between the fungal world and our own. We clear land for crops and settlement and perturb what were stable balances between fungi and their hosts. We carry goods and animals across the world, and fungi hitchhike on them. We drench crops in fungicides and enhance the resistance of organisms residing nearby. We take actions that warm the climate, and fungi adapt, narrowing the gap between their preferred temperature and ours that protected us for so long.

But fungi did not rampage onto our turf from some foreign place. They were always with us, woven through our lives and our environments and even our bodies: every day, every person on the planet inhales at least 1,000 fungal spores. It is not possible to close ourselves off from the fungal kingdom. But scientists are urgently trying to understand the myriad ways in which we dismantled our defenses against the microbes, to figure out better approaches to rebuild them.

 

 

 

No Super Soldiers, Just Drug-Moderated Virally-Delivered Epigenetic Cellular Regeneration...,

nature |   In Sinclair’s lab, geneticist Yuancheng Lu looked for a safer way to rejuvenate cells. He dropped one of the four genes used by Belmonte’s team — one that is associated with cancer — and crammed the remaining three genes into a virus that could shuttle them into cells. He also included a switch that would allow him to turn the genes on by giving mice water spiked with a drug. Withholding the drug would switch the genes back off again.

Because mammals lose the ability to regenerate components of the central nervous system early in development, Lu and his colleagues decided to test their approach there. They picked the eye’s retinal nerves. They first injected the virus into the eye to see if expression of the three genes would allow mice to regenerate injured nerves — something that no treatment had yet been shown to do.

Lu remembers the first time that he saw a nerve regenerating from injured eye cells. “It was like a jellyfish growing out through the injury site,” he says. “It was breathtaking.”

The team went on to show that its system improved visual acuity in mice with age-related vision loss, or with increased pressure inside the eye — a hallmark of the disease glaucoma. The approach also reset epigenetic patterns to a more youthful state in mice and in human cells grown in the laboratory.

It is still unclear how cells preserve a memory of a more youthful epigenetic state, says Sinclair, but he and his colleagues are trying to find out.

In the meantime, Harvard has licensed the technology to Boston company Life Biosciences, which, Sinclair says, is carrying out preclinical safety assessments with a view to developing it for use in people. It would be an innovative approach to treating vision loss, says Botond Roska, director of the Institute of Molecular and Clinical Ophthalmology in Basel, Switzerland, but will probably need considerable refinement before it can be deployed safely in humans, he adds.

The history of ageing research is littered with unfulfilled promises of potential fountains of youth that failed to make the leap to humans. More than a decade ago, Sinclair caused a stir by suggesting that compounds — including one found in red wine — that activate proteins called sirtuins could boost longevity. Although he and others continue to study the links between sirtuins and ageing that were originally observed in yeast, the notion that such compounds can be used to lengthen human lifespan has not yet been borne out, and has become controversial.

Ultimately, the test will be when other labs try to reproduce the reprogramming work, and try the approach in other organs affected by ageing, such as the heart, lungs and kidneys, says Judith Campisi, a cell biologist at the Buck Institute for Research on Aging in Novato, California.

Those data should emerge swiftly, she predicts. “There are many labs now who are working on this whole concept of reprogramming,” says Campisi. “We should be hopeful but, like everything else, it needs to be repeated and it needs to be extended.”

 

Curiously Satisfying...,

To return to Hebrews, the writer goes on to say: ' ... it is impossible to please God without faith' (xi.6). That is, it is impossible without the basis or foundation of faith, which makes it possible for a man to think beyond the evidence of his senses and realise the existence of invisible scale and understand psychological meaning. To realise scale means to realise that there are different levels of meaning. Literal meaning is one thing, psychological or spiritual meaning is another thing - although the words used are the same. For example, we saw that the word yeast used in the incident quoted indicated two levels of meaning. The disciples took it on the lower level and were told it was because their faith was little. Their thinking was sensual.

They had difficulty in thinking in a new way on another level. And their psychological thinking was so weak just because they were based on sense and not on faith. Thus sense and faith describe two ways of thinking, not opposites, not antagonistic, but on different levels. For without the perception of scale and levels, things are made to be opposite when they are not so, and Man's mind is split into 'either - or', which leads to endless confusions and mental wrangles and miseries. The writer goes on to say: 'Nobody reaches God's presence until he has learned to believe that God exists and that He rewards those that try to find Him' (xi.6). It is apparent that if scale is behind all things, if order is scale, and if to set in order is to set in scale then what is higher and what is lower must exist. To everything there must be an above and a below. A man who cannot perceive scale, visible and invisible, as did that centurion by means of his psychological understanding due to his great faith, will be shut to the intuitions that only faith opens out to every mind that hitherto has been asleep in the senses and the limited world revealed by them.

The chief preliminary voluntary act - and it needs to be lifelong in its voluntaryness - towards the inner spirit, the source and conveyor of meaning, is that of affirmation. Only by this act does all that is outward, external and dead become connected with what is internal and alive. This is the chief of all psychological acts. It is the preliminary and at the same time the continually renewable act whereby psychology, in the deepest sense - (that is, the science of personal evolution) begins. The final goal of it, far ahead, is the unity of oneself. Man becomes gradually united through himself with himself and not merely with what he accidentally has become and believes himself to be. Affirmation is not by argument but by understanding. Negation leads always to an inner deprivation and so to an increasing superficiality, impatience, loss of meaning, and violence. One can always deny. What is easier? One can always follow the path of negation, if one evades all acts of understand-
ing as sentimental or as scientifically and commercially valueless.

For St. Augustine and many more before and after him, the sick, the deaf, and the dead in the Gospels are the sick and deaf,  and the dead within. And in speaking of the two blind men who, sitting by the way side as Jesus was passing, cried out and asked that their eyes might be opened, he asks if we can really suppose that this is merely an account of a miraculous event concerning two physically blind men? Why does it say that the crowd try to restrain them, and that they fight against it and insist on attracting the attention of Jesus? 'They overcame the crowd, who kept them back, by the great perseverance of their cry, that their voice might reach the Lord's ears. . . . The Lord was passing by and they cried out. The Lord stood still and they were healed. For the Lord Jesus stood still and said, What will ye that I shall do unto you? They said unto him, That our eyes may be opened.' (Matthew xx.30-34) The blind here are those who cannot see but wish to see. Augustine says they are those who are blind in their hearts and realise it. Like the deaf, like the sick and the dead, the blind are a certain kind of people. They are, in this case, people in a certain inner state, knowing they are blind, and wishing to see clearly. 'Cry out among the very crowds', he says, 'and do not despair.' Who are these two blind men who know they cannot see but who recognise the spiritual meaning typified in the person of Jesus - what individual functions of the soul are shewn here that struggle with the crowd of commonplace meanings and thoughts and finally, by their own determination, receive their power of vision? 'If two or three are gathered together in my name . . . ' said Christ (Matthew xviii.20). What two sides of ourselves must first take part that our eyes may be opened - that is, our understanding? Why two, to make it effective?  Nicoll The Mark

Future Genomics: Don't Edit A Rough Copy When You Can Print A Fresh New One

technologyreview  |  It took Boeke and his team eight years before they were able to publish their first fully artificial yeast chromosome. The project has since accelerated. Last March, the next five synthetic yeast chromosomes were described in a suite of papers in Science, and Boeke says that all 16 chromosomes are now at least 80 percent done. These efforts represent the largest amount of genetic material ever synthesized and then joined together.

It helps that the yeast genome has proved remarkably resilient to the team’s visions and revisions. “Probably the biggest headline here is that you can torture the genome in a multitude of different ways, and the yeast just laughs,” says Boeke.

Boeke and his colleagues aren’t simply replacing the natural yeast genome with a synthetic one (“Just making a copy of it would be a stunt,” says Church). Throughout the organism’s DNA they have also placed molecular openings, like the invisible breaks in a magician’s steel rings. These let them reshuffle the yeast chromosomes “like a deck of cards,” as Cai puts it. The system is known as SCRaMbLE, for “synthetic chromosome recombination and modification by LoxP-mediated evolution.”

The result is high-speed, human-driven evolution: millions of new yeast strains with different properties can be tested in the lab for fitness and function in applications like, eventually, medicine and industry. Mitchell predicts that in time, Sc2.0 will displace all the ordinary yeast in scientific labs.

The ultimate legacy of Boeke’s project could be decided by what genome gets synthesized next. The GP-write group originally imagined that making a synthetic human genome would have the appeal of a “grand challenge.” Some bioethicists disagreed and sharply criticized the plan. Boeke emphasizes that the group will “not do a project aimed at making a human with a synthetic genome.” That means no designer people.

Ethical considerations aside, synthesizing a full human genome—which is over 250 times larger than the yeast genome—is impractical with current methods. The effort to advance the technology also lacks funding. Boeke’s yeast work has been funded by the National Science Foundation and by academic institutions, including partners in China, but the larger GP-write initiative has not attracted major support, other than a $250,000 initial donation from the computer design company Autodesk. Compare that with the Human Genome Project, which enjoyed more than $3 billion in US funding.

Neuroeconomics: Dopaminergy In The Individual Brain (REDUX Originally Posted 01/26/08)

A couple months ago, I introduced the concept of neuroeconomics in the context of collective psychology. It's time to take that a step further - a la the philosopher Daniel Dennett, channeling the late ATL Gurdjieffian prankster Jan Cox.

Several people have sent me notes about their problems and apparent failures, and have attempted to attribute a psychological basis to them. This is one of the great cutoff points. It is an immediate slap in the intellectual face: to a Revolutionist there is no such thing as "psychological." It is a flawed piece of data. It is as outmoded to a Revolutionist alive today as is the idea of a "capital-g" god. What is called "psychological" is serving, and has served, a purpose with some people. But you must see that any apparent psychological pressures arising from influences apparently "out there" -- your boss, your mother, your mate -- have to enter in through the five senses. Always stop and remind yourself of that even if you can't do anything else. If one or all of your senses were knocked out, you would not be suffering this "psychological pressure." You have to face up to that. Whatever is going on in you is chemical. There are really no such things as drunks; it is people with an alcohol deficiency. Absolutely religious people have a chemical deficiency. The same with people who have phobias, as they are called. It is a chemical imbalance outside the normal bell curve of the populace at their time and place. Jan Cox

From that earlier article I stated that "For decades it has been known that these neurons and the dopamine they release play a critical role in brain mechanisms of reinforcement. Many of the drugs currently abused in our society mimic the actions of dopamine in the brain. This led many researchers to believe that dopamine neurons directly encoded the rewarding value of events in the outside world."

Today's post is one of those hidden in plain sight elaborations on that theme, this time addressing the rewarding value of events in the INSIDE WORLD, the world comprised of the neurons making up your brain. Think about it. That's all I ever ask you to do, and in the process, you will inevitably be led to draw your own validating conclusions. Here's Dennett;

brain cells — I now think — must compete vigorously in a marketplace. For what?

What could a neuron "want"? The energy and raw materials it needs to thrive–just like its unicellular eukaryote ancestors and more distant cousins, the bacteria and archaea. Neurons are robots; they are certainly not conscious in any rich sense–remember, they are eukaryotic cells, akin to yeast cells or fungi. If individual neurons are conscious then so is athlete’s foot. But neurons are, like these mindless but intentional cousins, highly competent agents in a life-or-death struggle, not in the environment between your toes, but in the demanding environment of the brain, where the victories go to those cells that can network more effectively, contribute to more influential trends at the virtual machine levels where large-scale human purposes and urges are discernible.

I now think, then, that the opponent-process dynamics of emotions, and the roles they play in controlling our minds, is underpinned by an "economy" of neurochemistry that harnesses the competitive talents of individual neurons. (Note that the idea is that neurons are still good team players within the larger economy, unlike the more radically selfish cancer cells. Recalling Francois Jacob’s dictum that the dream of every cell is to become two cells, neurons vie to stay active and to be influential, but do not dream of multiplying.)

Intelligent control of an animal’s behavior is still a computational process, but the neurons are "selfish neurons," as Sebastian Seung has said, striving to maximize their intake of the different currencies of reward we have found in the brain. And what do neurons "buy" with their dopamine, their serotonin or oxytocin, etc.? Greater influence in the networks in which they participate.

So simple, elegant, and obvious. Selective governance via the natural tendency of the brain's neuronal circuits to Do What They Do..., what could be easier, more powerful, and more durable than that. The lengths to which some folks will go to furnish elaborate post hoc rationalizations of What It Do - and how that basic fact is exploited by those with the wherewithal to "engineer" values in the outside world - just crack me up.

A Programming Language For Living Cells?

MIT |  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.”

Voigt and colleagues at Boston University and the National Institute of Standards and Technology have used this language, which they describe in the April 1 issue of Science, to build circuits that can detect up to three inputs and respond in different ways. Future applications for this kind of programming include designing bacterial cells that can produce a cancer drug when they detect a tumor, or creating yeast cells that can halt their own fermentation process if too many toxic byproducts build up.

The researchers plan to make the user design interface available on the Web.

The Genome Project - Write

NYTimes |  “By focusing on building the 3Gb of human DNA, HGP-write would push current conceptual and technical limits by orders of magnitude and deliver important scientific advances,” they write, referring to three gigabases, the three billion letters in the human genome.

Scientists already can change DNA in organisms or add foreign genes, as is done to make medicines like insulin or genetically modified crops. New “genome editing” tools, like one called Crispr, are making it far easier to re-engineer an organism’s DNA blueprint.

But George Church, a professor of genetics at Harvard Medical School and one of the organizers of the new project, said that if the changes desired are extensive, at some point it becomes easier to synthesize the needed DNA from scratch.

“Editing doesn’t scale very well,” he said. “When you have to make changes to every gene in the genome it may be more efficient to do it in large chunks.”

Besides Dr. Church, the other organizers of the project are Jef Boeke, director of the Institute for Systems Genetics at NYU Langone Medical Center; Andrew Hessel, a futurist at the software company Autodesk; and Nancy J. Kelley, who works raising money for projects. The paper in Science lists a total of 25 authors, many of them involved in DNA engineering.

Autodesk, which has given $250,000 to the project, is interested in selling software to help biologists design DNA sequences to make organisms perform particular functions. Dr. Church is a founder of Gen9, a company that sells made-to-order strands of DNA.

Dr. Boeke of N.Y.U. is leading an international project to synthesize the complete genome of yeast, which has 12 million base pairs. It would be the largest genome synthesized to date, though still much smaller than the human genome.

open thread - do my "smart" frog friends feel the west coast pot getting hot yet?

As population increases, while resources (and the associated wealth) decreases, and more people struggle to simply survive, social "niceties" are bound to diminish. In northern California and southern Oregon, there are more and more "transients"/ homeless people... with no investment in what is clearly falling apart, yet interestingly, with an inflated Californian sense of entitlement.

Overseers in every municipality are being put to the test to maintain civility. City councils are passing severe ordinances which prohibit camping, sitting on sidewalks, curbs or the ground, no loitering, no panhandling etc. The Mount Shasta situation has been exasperated given two years with no snow, so what was once a very inhospitable winter climate just a few years ago, now affords year round camping and hanging outdoors.

The mass shootings are a symptom of "overshoot". You humans have gone over the plateau and are on the down edge of collapse.  Meanwhile, down in So-Cal

At Myra Marquez’s house, she checks the gauge on her 2500 gallon water tank before she touches a faucet. The tank gets filled every Monday.

Rationing 2000 gallons over five or six days is tough.

"It’s hard,” she said.
 
It takes $38 million dollars from the state’s Emergency Drought Relief Program to pay for the town’s drinking water and fill residents’ water tanks. (1700 residents)

Isn't anyone else surprised or annoyed that a household in Central California can't make it on 2500 gallons of H2O each week?

Isn't anyone else incredulous that California is paying $38,000,000 to truck water to just 1700 folks?

That's over $22,000 for each person!
 

Who's organizing that water drive, the Pentagon? That's $88,000 for a family of four. California could drill a $30,000 well for each family and save a bundle.

I hear there are plenty of idle drilling rigs in Texas... But, is there any water left?

Who was it that said, "Are humans smarter than yeast?"

Collapse is taking a whole lot longer than I thought it would - which is good - because in the intervening decade, my children have achieved young adulthood and waxed very strong - while I've been afforded an opportunity to carefully observe and study what you do under such self-inflicted, mass, stress conditions.

illinois politricians dumber than yeast...,

illinoispolicy |  Illinois is the only state in the Midwest to have added more people to food-stamp rolls than to employment rolls during the recovery from the Great Recession. Job losses from the Great Recession occurred from January 2008 to January 2010, and since then, states have had five-and-a-half years of recovery.

During the recovery from the Great Recession, the Land of Lincoln, alone in the Midwest, had more people enter the food-stamps program than start jobs. Food-stamps growth in Illinois has outpaced jobs creation by a 5-4 margin.

In every other Midwestern state, jobs growth has dramatically outpaced food-stamps growth during the recovery. In fact, in every other state in the region, jobs growth dwarfs food-stamps growth. But during the recovery, Illinois put more people on food stamps than every other Midwestern state combined.

Manufacturing has borne the brunt of Illinois’ policy failures. From the state’s broken workers’ compensation system, to the highest property taxes in the region, to the lack of a Right-to-Work law while surrounding states enact Right to Work, Illinois has the worst policy environment in the Midwest for manufacturers.

The result for Illinois factory workers? The Land of Lincoln has put 25 people on food stamps for every manufacturing job created during the recession recovery.

synthetic genomics and genome engineering rewriting the blueprint of life

genomebiology |  Biology is now undergoing a rapid transition from the age of deciphering DNA sequence information of the genomes of biological species to the age of synthetic genomes. Scientists hope to gain a thorough mastery of and deeper insights into biological systems by rewriting the genome, the blueprint of life. This transition demands a whole new level of biological understanding, which we currently lack. This knowledge, however, could be obtained through synthetic genomics and genome engineering, albeit on a trial and error basis, by redesigning and building naturally occurring bacterial and eukaryotic genomes whose sequences are known. 

Synthetic genomics arguably began with the report from Khorana’s laboratory in 1970 of the total synthesis of the first gene, encoding an artificial yeast alanine tRNA, from deoxyribonucleotides. Since then, rapid advances in DNA synthesis techniques, especially over the past decade, have made it possible to engineer biochemical pathways, assemble bacterial genomes and even to construct a synthetic organism [1]–[11]. Genome editing approaches for genome-wide scale alteration that are not based on total synthesis of the genome are also being pursued and have proved powerful; for example, in the production of a reduced-size genome version of Escherichia coli[4] and engineering of bacterial genomes to include many different changes simultaneously [8]. 

Progress has also been made in synthetic genomics for eukaryotes. Our group has embarked on the design and total synthesis of a novel eukaryotic genome structure - using the well-known model eukaryote Saccharomyces cerevisiae as the basis for a designer genome, known as ‘Sc2.0’. The availability of a fully synthetic genome will allow direct testing of evolutionary questions that are not otherwise approachable. Sc2.0 could also play an important practical role, since yeasts are the pre-eminent organisms for industrial fermentations, with a wide variety of practical uses, including production of therapeutic proteins, vaccines and small molecules through classical and well-developed industrial fermentation technologies. 

This article reviews the current status of synthetic genomics, starting with a historical perspective that highlights the key milestones in the field (Fig. 1) and then continuing with a particular emphasis on the total synthesis of the first functional designer eukaryotic (yeast) chromosome, synIII, and the Sc2.0 Project. Genome engineering using nuclease-based genome editing tools such as zinc finger nucleases, transcription activator-like effector nucleases and RNA-guided CRISPR-Cas9 is not within the scope of this minireview (Box 1). Recent advances in gene synthesis and assembly methods that have accelerated the genome synthesis efforts are discussed elsewhere [12].

darpa, synthetic biology, terraforming mars...,

motherboard |  It’s no secret that the Defense Advanced Research Projects Agency is investing heavily in genetic engineering and synthetic biology. Whether that excites or terrifies you depends on how you feel about the military engineering totally new life forms. If you’re in the excitement camp, however, here’s a nugget for you: DARPA believes that it's on the way to creating organisms capable of terraforming Mars into a planet that looks more like Earth.

The goal of terraforming Mars would be to warm up and potentially thicken its atmosphere by growing green, photosynthesizing plants, bacteria, and algae on the barren Martian surface. It’s a goal that even perpetual techno-optimists like Elon Musk think isn’t going to happen anytime soon, but it’s a goal that DARPA apparently already has its eyes on.

“For the first time, we have the technological toolkit to transform not just hostile places here on Earth, but to go into space not just to visit, but to stay,” Alicia Jackson, deputy director of DARPA’s new Biological Technologies Office said Monday at a DARPA-hosted biotech conference. As she said this, Jackson was pointing at an artist's rendering of a terraformed Mars.

So what’s this technological toolkit she’s talking about? For the last year, Jackson’s lab has been working on learning how to more easily genetically engineer organisms of all types, not just e. coli and yeast, which are most commonly used in synthetic biology projects.

“There are anywhere from 30 million to 30 billion organisms on this Earth. We use two right now for engineering biology,” she said. “I want to use any organism that has properties I want—I want to quickly map it and quickly engineer it. If you look at genome annotation software today, it’s not built to quickly find engineer able systems [and genes]. It’s built to look for an esoteric and interesting thing I can publish an academic paper on.”

DARPA and some of its research partners have created software called DTA GView, which Jackson calls the “Google Maps of genomes.” At the conference, she pulled up the genomes of several organisms on the program, which immediately showed a list of known genes and where they were located in the genome. 

“This torrent of genomic data we’re now collecting is awesome, except they sit in databases, where they remain data, not knowledge. Very little genetic information we have is actionable,” she said. “With this, the goal is to, within a day, sequence and find where I can best engineer an organism.”

The goal is to essentially pick and choose the best genes from whatever form of life we want and to edit them into other forms of life to create something entirely new. This will probably first happen in bacteria and other microorganisms, but it sounds as though the goal may to do this with more complex, multicellular organisms in the future.

increasing human grasp of GOD...,

wired | At the most basic level, scientists create phylogenetic trees by grouping species according to their degree of relatedness. Lining up the DNA of humans, chimpanzees and fish, for example, makes it readily apparent that humans and chimps are more closely related to each other than they are to fish.

Researchers once used just one gene or a handful to compare organisms. But the last decade has seen an explosion in phylogenetic data, rapidly inflating the data pool for generating these trees. These analyses filled in some of the sparse spots on the tree of life, but considerable disagreement still remains.

For example, it’s not clear whether snails are most closely related to clams and other bivalves or to another mollusk group known as tusk shells, said Rokas. And we have no idea how some of the earliest animals to branch off the tree, such as jellyfish and sponges, are related to each other. Scientists can rattle off examples of conflicting trees published in the same scientific journal within weeks, or even in the same issue.

“That poses a question: Why do you have this lack of agreement?” said Rokas.

Rokas and his graduate student Leonidas Salichos explored that question by evaluating each gene independently and using only the most useful genes — those that carry the greatest amount of information with respect to evolutionary history — to construct their tree.

They started with 23 species of yeast, focusing on 1,070 genes. They first created a phylogenetic tree using the standard method, called concatenation. This involves stringing together all the sequence data from individual species into one mega-gene and then comparing that long sequence among the different species and creating a tree that best explains the differences.

The resulting tree was accurate according to standard statistical analysis. But given that similar methods have produced trees of life that are rife with contradiction, Rokas and Salichos decided to delve deeper. They built a series of phylogenetic trees using data from individual yeast genes and employed an algorithm derived from information theory to find the areas of greatest agreement among the trees. The result, published in Nature in May, was unexpected. Every gene they studied appeared to tell a slightly different story of evolution.

“Just about all the trees from individual genes were in conflict with the tree based on a concatenated data set,” says Hilu. “It’s a bit shocking.”

They concluded that if a number of genes support a specific architecture, it is probably accurate. But if different sets of genes support two different architectures equally, it is much less likely that either structure is accurate. Rokas and Salichos used a statistical method called bootstrap analysis to select the most informative genes.

In essence, “if you take just the strongly supported genes, then you recover the correct tree,” said Donoghue. Fist tap Dale.

are the shambling yeast monkeys REALLY inching up the kardashev scale?

arvix | An experimental investigation of possible anomalous heat production in a special type of reactor tube named E-Cat HT is carried out. The reactor tube is charged with a small amount of hydrogen loaded nickel powder plus some additives. The reaction is primarily initiated by heat from resistor coils inside the reactor tube. Measurement of the produced heat was performed with high-resolution thermal imaging cameras, recording data every second from the hot reactor tube. The measurements of electrical power input were performed with a large bandwidth three-phase power analyzer. Data were collected in two experimental runs lasting 96 and 116 hours, respectively. An anomalous heat production was indicated in both experiments. The 116-hour experiment also included a calibration of the experimental set-up without the active charge present in the E-Cat HT. In this case, no extra heat was generated beyond the expected heat from the electric input. Computed volumetric and gravimetric energy densities were found to be far above those of any known chemical source. Even by the most conservative assumptions as to the errors in the measurements, the result is still one order of magnitude greater than conventional energy sources. Fist tap Dale.

"junk" be busy...,

cshlp | At least since the publication of Susumu Ohno's Evolution by Gene Duplication (Ohno 1970), the conventional wisdom has been that, in the emergence of novel genes, “natural selection merely modified, while redundancy created.” In other words, new genes generally arise by the duplication of existing genes. While the notion that duplication plays a prominent role in the emergence of novel genes is perhaps most famously associated with Ohno, it actually traces back to the early days of the modern evolutionary synthesis (Bridges 1935; Muller 1936). Decades of modern sequence-based research have largely supported this general view (Graur and Li 2000). In recent years, the classic model of whole gene duplication and subsequent divergence has been enlarged to include phenomena such as exon shuffling, gene fusion and fission, retrotransposition, and lateral gene transfer (for review, see Long et al. 2003). Nevertheless, despite their additional complexity, these mechanisms remain essentially duplicative, in the sense that sequences encoding one or more protein-coding genes are copied, by one mechanism or another, and used as the starting point for a new gene sequence. (An exception is the exonization of noncoding transposable elements, such as Alus, but this process tends to generate individual exons rather than entire genes;Makalowski et al. 1994; Nekrutenko and Li 2001.) By contrast, the origination of protein-coding genes de novo from nonrepetitive, noncoding DNA has been thought to occur only as an exceptionally rare event during evolution. Indeed, the emergence of complete, functional genes—with promoters, open reading frames (ORFs), and functional proteins—from “junk” DNA would seem highly improbable, almost like the elusive transmutation of lead into gold that was sought by medieval alchemists. 

Over the past few years, this view has begun to change, with several reports of de novo gene origins in Drosophila and yeast (Levine et al. 2006; Begun et al. 2007; Chen et al. 2007; Cai et al. 2008). Zhou et al. (2008) have estimated that as many as ∼12% of newly emerged genes in the Drosophila melanogaster subgroup may have arisen de novo from noncoding DNA, independently of transposable elements. Recently, Toll-Riera et al. (2009) identified 15 such genes in primates. Now, in this issue, Knowles and McLysaght (2009) demonstrate for the first time that human genes have arisen de novo from noncoding DNA since the divergence of the human and chimpanzee genomes. They identify and analyze three human genes that have no known homologs, in the human genome or any other, and do not appear to derive from transposable elements. Rather, these are cases in which mutation, natural selection, and/or neutral drift have evidently forged ORFs and functional promoters out of raw genomic DNA, like a blacksmith shaping a new tool from raw iron.

evolving multicellularity

Multicellular Yeast from thescientistllc on Vimeo.

The Scientist | In as little as 100 generations, yeast selected to settle more quickly through a test tube evolved into multicellular, snowflake-like clusters, according to a paper published today (January 16) in Proceedings of the National Academy of Sciences. Over the course of the experiment, the clusters evolved to be larger, produce multicellular progeny, and even show differentiation of the cells within the cluster—all key characteristics of multicellular organisms.

“It’s very cool to demonstrate that [multicellularity] can happen so quickly,” said evolutionary biologist Mansi Srivastava of the Whitehead Institute for Biomedical Research in Massachusetts, who was not involved in the research. “Looking at the fossil record, we learned it took a very long time whenever these different transitions to multicellularity happened. Here they show it can happen very quickly.”

“[The study] was provocative,” agreed biochemist Todd Miller of Stony Brook University in New York, who did not participate in the work. “It’s a different way of attacking the problem [of how multicellularity evolved]—coming from a simple system that doesn’t normally do this and seeing what it takes to make it do it.”

The evolution of multicellular life has long intrigued evolutionary biologists. Cells coming together and cooperating for the good of the group goes against basic Darwinian principles. Yet multicellularity has evolved some two dozen times independently in nature, and has shaped the world as we know it.

But because most transitions to multicellularity happened more than 200 million years ago, many questions remain about how it happened. What were the ecological conditions that drove the transitions? And how did organisms overcome the conflicts of interest that accompany any sort of cooperative effort?

the siege of leningrad

DailyMail | The German siege of Leningrad lasted 900 days from September, 1941 to January, 1944. During that time 800,000 people, nearly a third of the population at the siege’s beginning, starved to death. Roughly one in three. Many of them in the streets.
Terrible times: Citizens of Leningrad after the German bombing in the winter of 1941

Terrible times: Citizens of Leningrad after the German bombing in the winter of 1941

Twenty years later I visited Leningrad. They took me to see the front line - a canyon gashed out of the landscape lined with shattered ruins of houses - as if a giant excavator had taken a mouthful of the city. Because we were still in the city, that was the shock. The Germans got that close.

The Leningraders still bore the signs. Here were so many old and shrivelled faces. Often you saw the flash of steel teeth. Dentists’ amalgam had run out early. The city’s stunning architecture (after all, it was, and now again is, St Petersburg) looked sadly worn except for certain restored cathedrals and palaces.

Few people outside realised what the siege was like. For years afterwards Stalin kept it dark. Deaths were underestimated. Its party leaders were purged. There were to be no other heroes of the war besides himself.

After the Khrushchev thaw, a new legend was propagated of a Leningrad whose heroic citizens unflinchingly disregarded the bombs and shells and starved quietly as willing sacrifices to defend the cradle of the Revolution.

Then, with the collapse of communism, archives began to open with their police records and siege diaries. This book seeks to tell objectively what really happened. It is a stark shocking tale.

The toll of that first winter is staggering. Leningrad was totally unprepared for siege - as Russia was for the German attack. It took only 12 weeks for the German and Finnish armies to cut off the city. In that time the evacuation of civilians and obtaining of food supplies were hugely bungled.

Andrei Zhdanov, the city’s Communist Party chief, actually telephoned Stalin to tell him that their warehouses were full - in order that he should look prepared. So several relief food trains were diverted elsewhere.

Over a million children and dependants were still in the city when the ring closed. In all there were 3.3 million mouths to feed.

Quite soon the bread ration had to be halved. By mid-November manual workers received 250 grams a day, the rest only half of that. But the bread had been adulterated with pine shavings. So people were existing (or failing to) on 400, even 300 calories.

Pet owners swapped cats in order to avoid eating their own. There wasn’t a dog to be seen. Only the zoo preserved its star attractions, like ‘Beauty’ the hippopotamus, with special rations of hay.

People searched desperately for substitute food. Cottonseed cake (usually burned in ships’ boilers), ‘macaroni’ made from flax seed for cattle, ‘meat jelly’ produced from boiling bones and calf skins, ‘yeast soup’ from fermented sawdust, joiners’ glue boiled and jellified, toothpaste, cough mixture and cold cream - anything that contained calories. They even licked the dried paste off the wallpaper.

The Black Market flourished openly on street stalls with ever rising prices. A fur coat fetched fewer and fewer kilograms of flour. Meanwhile the Party chiefs and their friends and connections, continued to look well fed to general resentment.

The first news that people had died from starvation met with incredulity: ‘Not the one I know? In broad daylight? With a Masters Degree?’

But before long people were concealing deaths in the family, hiding the bodies so that the deceased’s ration card could be used until it expired. Husbands and fathers helped to feed their families posthumously.

It was a very severe winter - temperatures of minus 35 degrees. Trams froze in their tracks. Buildings burned for days - fire services ceased to function. Factories closed, hospitals were overwhelmed, cemeteries could not keep pace. Bodies, shrouded but uncoffined, were dragged through the streets on sleds. At one cemetery gate a corpse propped upright with a cigarette in its mouth extended a frozen arm and finger as a sign post to the newest mass graves.
Commemoration: A Russian guard of honour marches at a ceremony for the 61st anniversary of the end of the siege

Commemoration: A Russian guard of honour marches at a ceremony for the 61st anniversary of the end of the siege

Of course there was a crime wave, mainly of adolescent muggers thieving food and ration cards. One 18-year-old killed his two younger brothers for their cards. Another murdered his granny with an axe and boiled her liver. A 17-year-old stole a corpse from a cemetery and put it through a mincer.

Rumours of cannibalism abounded. Amputated limbs disappeared from hospital theatres. Police records released years later showed that 2,000 people were arrested for cannibalism; 586 of them were executed for murdering their victims. Most people arrested however were women. Mothers smothered very young children to feed their older ones.

The spring of 1942 brought a thaw and with it edible dandelions and nettles. The population, now much reduced, set about raising vegetables.

yeast nasty...,

LiveScience | It doesn't take much to get the fungus that causes thrush and other infections in the mood. New research suggests that in addition to chemical signals from its own species, the yeast, called Candida albicans, also gets turned on by the so-called pheromones sent out by other species.

And when turned on, this yeast isn't selective. If cells of the opposite sex aren't around, then it mates with same-sex partners, according to Richard Bennett, one of the study researchers and an assistant professor at Brown University in Rhode Island.

This type of fungus is a natural inhabitant of our bodies, particularly our guts, but, given the opportunity, the yeast can also cause harmful infections, ranging from a superficial thrush infection in the mouth to potentially lethal blood infections among those with weakened immune systems.

C. albicans cells come in two forms: white and opaque, names derived from the appearance of their colonies. Opaque cells are the reproductive ones. They produce a pheromone that prompts other opaque cells to turn on genes associated with mating. In the presence of this pheromone, the opaque cells also put out long projections that search for another cell with which to fuse (the yeast equivalent of sex), according to Bennett.

The white cells do not reproduce, but they also respond to the pheromone, which activates an entirely different set of genes. They become sticky, and start to glom together and to surfaces, such as a catheter, forming what is known as a biofilm. This is a common route to harmful infections.

The researchers synthesized a variety of pheromones produced by this species and a variety of other fungal species, and found that the white and opaque cells were not picky about a trigger for their responses. The normal opaque cell pheromone is a string of 13 amino acids, which are organic compounds.

“In some of the pheromones eight of 13 residues were different,” Bennett said. “That’s why we were so surprised with these pheromones. We didn’t expect them to work because they look so different.”

It is not unusual for one species to respond to pheromones from another, however, it is unusual for that response to lead to productive mating, he said.

C. albicans' lax standards may mean that it could respond to other signals from its environment, including signals directly from the host. The next step, Bennett said, is to figure out how these findings fit in with disease.

The research was published online today (Jan. 24) by the journal Proceedings of the National Academy of Sciences. Fist tap Nana.

the gates of immortality?

The Scientist | I had to wonder, what is aging after all? Is it something positively tangible, something that we could define otherwise than a loss: loss of fitness, loss of potential, loss of viability? There is at least one type of molecular marker that correlates well with aging, at least in yeast: extrachromosomal ribosomal DNA circles (ERCs). These circles, or plasmids, of DNA are excised from the ribosomal DNA (rDNA) locus on the chromosome and replicate at each division cycle. The ERCs, however, are redundant to the chromosomal ribosome genes—unnecessary elements that accumulate in the nucleus of the mother cell as it ages. Although ERCs do not represent the only mechanism of aging in yeast, their accumulation is related to aging: cells in which ERC formation is delayed live longer, whereas cells with increased ERC formation die sooner. It would follow then, that their retention by the mother cell contributes largely to the age asymmetry between mother and bud.

Mortal and immortal lineages
Most buds produced by a mother cell will also become bud-producing mothers themselves. A new mother has the capacity to produce 30 buds before she dies with a large number of extrachromosomal rDNA circles (ERCs) accumulated in her nucleus. When the barrier separating the mother from the bud was experimentally disrupted, it allowed ERCs to enter the bud in large number. As a result, the mother lived longer, while the reproductive life of her daughters was shortened proportionate to the amount of ERCs she received.

ERC retention, then, must rely on some intrinsic asymmetry of the nucleus. For example, the yeast nucleus, which does not disassemble during mitosis, as in mammalian cells, always sends its oldest spindle pole body (SPB) to the bud. The SPB, which organizes the duplicate genomes during mitosis, is embedded in the nuclear envelope, and duplicates at each cycle to form a single new SPB. If we forced the nucleus to send the old SPB to the bud only half of the time, would the ERCs then segregate to the bud the other half of the time? To our surprise, this did not happen; the ERCs remained in the mother cell. The exclusive retention of the ERC plasmids within the nucleus of the mother cell only diminished when we disturbed the septin diffusion barrier that divided the nuclear envelope.8

As a consequence, yeast cells lacking the septin diffusion barrier can pass these molecular markers of aging to their daughters. Without the diffusion barrier the mothers were longer lived, but their daughters behaved as if they were older at birth: in other words, they had the capacity to replicate fewer times. The fact that ERCs remained in the mother’s part of the nucleus indicated that the plasmids had to be linked to something embedded in the nuclear membrane. Since septins only blocked diffusion of molecules in the membrane (they did not, for example, create a webbing across the cytoplasm), none of the molecules freely floating in the nucleoplasm would be affected. We observed that these plasmids were associated with the nuclear envelope, more precisely with the basket of nuclear pores on the inside of the nuclear membrane, and that this association was required for their retention in the mother cell. Taken together, our data suggest the intriguing idea that aging, whatever it is, respects diffusion barriers, and that these boundaries prevent the propagation of aging-related molecules into newborn buds.

It may be that the cell’s solution to its unsolvable problems is simply to age, to compartmentalize the components that bear too much resemblance to self and slough them off.

It is still unclear at this point whether these findings have any parallel in other eukaryotes, but we think they might. Indeed, the process of sperm generation shows intriguing similarities with the budding process in yeast, at least in terms of the maturation of the future sperm’s nuclear envelope. The emergence of the sperm head involves the migration of the nucleus through a perinuclear ring. During this process, the nuclear envelope is combed, leaving behind its nuclear pores, which, in many cases, are then excluded from the sperm nucleus. Thus, it is tempting to speculate that we, too—like yeast—keep our sperm as young as possible each time we prepare to form a newborn.

Over the years, these observations and findings have led me back to Gödel and his ideas of unsolvable problems. Aging seemed the perfect example of a process in which the cell could not detect ambiguous molecules (either overtly damaging, or beneficial) and repair itself.

To my mind, ERCs are emblematic of objects that are ambiguous to the cell. They have the same chemical nature, the same repeating composition as the chromosome, and therefore cannot be targeted for destruction without risking damaging the chromosomes as well. They take on the characteristics of entities that are both self and nonself. Gödel was able to mathematically characterize the unsolvable problems he encountered and describe them with a universal rule. Might ERCs help define the universal properties of the unfixable errors that accumulate with age? What prevented biological systems from being complete?

At its core, the generation and accumulation of ERCs is a problem of symmetry—ERCs are generated by errors in DNA repair. When the DNA repair (or recombination) machinery resolves the Holliday Junction, it has one of two options, excision or repair. But because of the local symmetry at the Holliday Junction, the recombination machinery cannot detect a difference between the incoming strands of DNA, and therefore cannot favor one solution over the other. In order to handle such an unsolvable problem, the cell simply produces both outcomes with equal probability, with the production of ERCs and DNA repair occurring exactly 50 percent of the time.

What if structural asymmetries, such as cell polarity, might have actually emerged to counteract the logical problems that symmetric events such as DNA repair generate for the cell? If true, it implies that studying symmetric processes in biology could reveal new insights about aging.

It may be that the cell’s solution to its unsolvable problems is simply to age, to compartmentalize the components that bear too much resemblance to self and slough them off, producing a life that lacks these deformities. Although the yeast cell might not be able to distinguish ERCs from the chromosomes, it found ways to sort them out and confine them to the mother cells. Diffusion barriers could play a central role in this process. It is interesting because they are likely to simply retain in the mother cell anything that is not actively being chosen and pulled into the bud, such as chromosomes or vesicles. Thus, they offer a remarkable solution to the retention of ambiguous objects, that is, objects that the cell cannot distinguish as being right or wrong, objects that therefore remain invisible to cellular machineries.

Last, if aging is a consequence of Gödel’s theorem in biology and of the cell’s incompleteness, then aging is not a program but an inescapable fact. The quest for a cure to the aging “disease” will inevitably fail. But there is a bright side to the fact that the cell is logically incomplete. Would any complete system—one able to detect any damage and repair itself perfectly—have the ability to evolve?

yeast banksters....,

The Scientist | Yeast colonies with mooches, thieves and cheats actually grow faster and larger than colonies without these freeloading individuals, according to a study published 15th September in PLoS Biology, challenging the widely held belief that cheaters bring only bad news to cooperating populations.

Researchers found that when some yeast cheat their neighbors out of glucose, the entire population grows faster. "This is a most surprising result," said Laurence Hurst of the University of Bath in the UK, who coauthored the study. "The theory of cooperation was one of the best worked theories in all of evolution. Everyone assumed that it had to be the case that the world is better off when everyone cooperates."

The results may explain why yeast populations tolerate the presence of cheaters, added Michael Travisano, a biologist at the University of Minnesota, who was not involved in the research -- "because a mixed strategy is to everyone's benefit."

Most yeast secrete invertase, which hydrolyzes sucrose into fructose and glucose, their preferred food. However, some yeast are known to cheat the system. Cheater yeast don't secrete invertase and therefore don't contribute to the glucose production, yet they still eat the glucose that is generated by the rest of the population.

According to the theory of cooperation, which states that organisms are better off when everyone cooperates, yeast populations should be best off when all the yeast produce invertase. This would maximize the availability of glucose, which should enable more yeast growth. But when Hurst and his colleagues grew yeast populations with both producers and non-producers of invertase, this is not what they saw. Instead, the yeast grew the fastest and saw the highest population numbers when a proportion of the population was cheating.