Over The Counter Culture » New science

Stewart Brand, on viruses and the scale of things

bradley — Thu, 09 Jun 2011 02:29:06 +0000

“Everything about viruses is extreme,” Zimmer began. The number of viruses
on Earth is estimated to be 1 followed by 31 zeroes. Small as they are, if
you stacked them all up, the stack would reach 100 million light years. They
are the planet’s most abundant organism by far.

They’re fast. We take decades to reproduce. A flu virus can generate
billions of itself in us within hours. And they evolve
10,000 times faster than us, because they’re creatively sloppy about making
copies of their genomes, and they readily combine genes among varieties when
jointly infecting a cell. Each of us has four trillion viruses on board, in
1,500 all-too-fungible varieties.

Yet they can also be “time stealthy.” You may have a bout of childhood
chickenpox that is over in days, but the viruses may hide in your nervous
system and emerge decades later as shingles. HIV spreads inexorably because
of the lag of months or years between infection and visible symptoms.

The earliest record of a virus in human history is the smallpox marks you
can see on the mummified face of Ramses V, who died in 1145 BCE.
Viruses leave no fossils, but in a sense they ARE fossils, with the ancient
gene sequences of retroviruses buried in the genomes of every creature
they’ve infected over the ages. About 8 percent of our genome—some
100,000 elements—comes from viruses, and some of those genes now work for
us (enabling the mammalian placenta, for instance). One French scientist
revived from our genome a functioning 2-million-year-extinct virus just by
deducing the original code from the current variety in that stretch of DNA.

For billions of years the planet’s life consisted solely of bacteria and
their viruses, the bacteriophages. They became a planet force, and remain
so today, determining the makeup of the atmosphere, among other things. Every
day half of all the bacteria in the oceans are killed by phages. Some of
the carbon from the bodies sinks to the bottom, some is freed up to
fertilize other life. Ocean viruses cart around and transmit genes for
photosynthesis to previously incapable
microbes—10 percent of oceanic photosynthesis happens that way. If some
day we have to geoengineer the atmosphere to manage climate change, we may
want to employ the viruses that are already doing it.

Virology will be revolutionizing science for decades to come. One body of
investigation suggests that the so-called giant viruses may be a whole
fourth domain of life (added to bacteria, archaea, and eukaryotes). As the
ultimate parasite, viruses were assumed to come along after life evolved,
but they might an instrument of that evolution. One hypothesis is that
viruses took primordial RNA and generated DNA to better protect the
genes. They might have created life as we know it, a long time ago.

–Stewart Brand

Using viruses to deliver upgrades to your brain

bradley — Tue, 22 Mar 2011 13:06:09 +0000

The use of viruses to deliver beneficial genes to upgrade your brain is very much a reality: check out this article from Nature this week:

read here: http://www.nature.com/news/2011/110317/full/news.2011.167.html

Last week saw the news that it is now possible to create superblood by taking it out of the body and using very clever, targeted gene therapy to upgrade the DNA. It’s currently being trialled in AIDS patients, making a subtle mutation to their white blood cells so that they’re more like the HIV-immune cells of so-called HIV controllers – people that can resist HIV attacks because of different ‘flags’ on their cells. Once upgraded, you infuse the blood cells back into the patients where they can start taking on HIV with newfound immunity.

read here: http://www.nature.com/news/2011/110301/full/471016a.html

The usage is therapeutic so far, but each year sees new approaches to blood doping in the Tour de France. How long until this becomes one? How long until someone creates a safe virus capable of boosting your brain functions, and sells it on the Internet? What happens when not just your organs are modified, but also the DNA capable of being passed on to your children (“germ line” modification) – would you leave them with a trust fund, or spend the money permanently making your progeny handsome geniuses?

So humans can now be patched and bugfixed. How long until we have open-source humans? Jokingly, the time is apparently already upon us – a user of popular software source code sharing, review and editing site GitHub uploaded his genome for ‘patching’. We don’t yet have widespread technology to implement the patches that are being written and suggested, but as gene therapy progresses and gets commercialised (and maybe even amateurised), we one day doubtless will.

What a bizarre feeling it must be, knowing that the open-source crowd can pore over the very blueprints to you and start imagining and coding “You, version 2.0“…

Genetically engineering human tissues enters clinical age

bradley — Mon, 07 Mar 2011 00:30:59 +0000

http://www.nature.com/news/2011/110301/full/471016a.html?WT.ec_id=NATURE-20110303

Here we go, people: medicine based on targeted genetic engineering human tissues is henceforth a reality.

In Phase I (early stage) medical trials, the blood of HIV sufferers was taken out, genetically engineered to make it more resistant to the virus, before pumping the super-blood back into the sufferers’ body.

Thanks to genome sequencing of those lucky few humans that are naturally resistant to HIV, we know that the virus relies on the sufferer having white blood cells that have the CCR5 ‘handle’ on their cell surface to pull itself in, copy itself, and kill the white blood cell (and repeat, ad mortem). So the blood, once extracted, had its CD4+ T cells isolated and their DNA modified by a special “zinc finger” protein capable of targeted gene editing.

We’re not talking about directly engineering adult humans (like Peter Parker’s genetic transformation into Spiderman after the mythical bite) – yet – because such a challenge is ethically very difficult, makes cancer more likely, and is technologically very hard to achieve.

Still – it presumably won’t be too long until this sort of blood engineering becomes the latest Tour De France blood doping scandal.

Things you probably never knew toxoplasmosis could do to you

bradley — Mon, 22 Mar 2010 13:12:37 +0000

Mice and rats infected with toxoplasmosis are less scared of cats and can even start ‘deliberately’ hanging around areas where they can smell cats. Inevitably, that means they’ll get eaten, the cat will get the disease, and will help spread it around.

In humans, there is some evidence that toxoplasmosis is linked to schizophrenia.

Most amazingly, in women who get toxoplasmosis, the likelihood of a boy being born goes from slightly over 50% potentially all the way up to 72% – so for every 10 girls, 26 boys would be born.

If you have a specific blood type (Rh-), you’re 2.5 times more likely to have a car accident than uninfected people.

There’s controversial evidence that men become more anti-social, grumpy, risky/rebellious, but less curious – and that women become friendlier, keener to have sex, more outgoing, and might be considered more attractive by men.

In most healthy human beings, toxoplasmosis merely presents with flu-like symptoms, then sits dormant.

source

On the Happiness of the Fat and the Bereaved

bradley — Thu, 04 Feb 2010 06:04:22 +0000

Snippets from some astounding happiness, obesity and widowhood research. via Chris Dillow on Stumbling & Mumbling (with more findings, details on what was controlled for, and his thoughts as to whether this is true, and what it shows)

Marina-Selini Katsaiti finds that “obesity has a negative and statistically significant effect on individual well being”. She estimates that, in Germany, a three-point rise in BMI (from, say 24 to 27 – equivalent to gaining around 20 pounds for someone who’s 5’8”) reduces happiness on average by so much that it would require a 67% pay rise to compensate. In Australia it would require a doubling of income to offset the adverse effect of such a weight gain.
Now, contrast this to a new paper (pdf) by Andrew Clark and Yannis Georgellis. They show that, in the UK, men and women who have been widowed are happier in the 3-4 years after their loss than they were the year before it. Yes, their well-being slumps in the 12 months after bereavement, but it recovers thereafter.

Now, remember of course that winning the lottery will statistically do very little, if anything, to make you a happier person in the long run

How very peculiar!

Evil capitalists are out to get you – salad edition

bradley — Sun, 03 May 2009 07:12:00 +0000

The mere presence of salads on a McDonalds menu makes people more likely to consume the unhealthier food, according to a new paper published last month. Here’s the abstract:

This research examines how consumers’ food choices differ when healthy items are included in a choice set compared with when they are not available. Results demonstrate that individuals are, ironically, more likely to make indulgent food choices when a healthy item is available compared to when it is not available. The influence of the healthy item on indulgent choice is stronger for those with higher levels of self?control. Support is found for a goal?activation?based explanation for these findings, whereby the mere presence of the healthy food option vicariously fulfills nutrition?related goals and provides consumers with a license to indulge

One thing to consider, though – true or not, there’s a rumour floating around that the salads are unhealthier due to the oily dressing. Shouldn’t this have been controlled for in the study?

Original paper; Initial coverage (Matt Yglesias); More

TED assembly

bradley — Thu, 23 Apr 2009 04:55:00 +0000

How I wish that instead of dull sermons from the chaplain or stern slobbers from the headmaster, assembly at school had been a TED video (or better yet, a live speaker of that caliber).

What a way to start the day.

Here’s a particularly interesting one I just watched, prompting further reading and me seeking to reconnect with an entrepreneur in the electric car industry:

Shai Agassi discusses the economics of mass electric car adoption in a scheme involving removable electric batteries and universal charge points that completely rethinks the economics of running a car. You get paid if you have to change your battery more than x times a year.

How feasibly can we actually drop our global CO2 production?

bradley — Thu, 07 Aug 2008 10:07:15 +0000

I hate talking about global warming – its boring, cliche, and largely depressing, because any careful thinking about it invariably leads to the conclusion that the only true solution, if climate change models based on CO2 are correct, is a mass human extinction event, or exodus (to other planets); your child is a much greater environmental nightmare than your Hummer H2 is.

If our primary objective as a species is a global reduction in happiness and development inequalities, allowing global population growth to continue apace is totally counterproductive. And that’s a sad thought, and one that may motivate a global terrorism movement far worse than Al Qaeda.

But take a look at this graph (source: McKinsey). It estimates the cost and effectiveness of the various proposed things society can do to bring emissions down. On the left, the negative y axis values show that we save a lot of money and abate CO2 emissions, with certain strategies like insulating our houses and offices. To the right, expensive strategies. It’s clear from the graph that the real gains to be made (measured as progress along the x axis) are in this economically costly zone.

The worst part: even with all known strategies pursued, we still hit the dangerously (*according to current climate models) high levels of 450ppm by 2030.

I’d like to be able to play with the graph and generate data based on different population and oil price forecasts. Their assumptions aren’t clearly stated, disappointingly. This link offers a modest amount of skepticism regarding this graph, and highlights some further insights it gives us, alongside some auxiliary information about the bang-for-buck of different climate change prevention schemes.

Paradoxical lifestyles

bradley — Fri, 18 Jul 2008 14:43:28 +0000

Just came across an interesting behavioural economics paper by Stutzer & Frey. Behavioural science is an extremely ‘hot’ field of academia at the moment, hitting the mainstream with books such as Freakonomics (Dubner & Levitt), Predictably Irrational (Ariely), Blink (Gladwell), Nudge (Thaler), etc), and with increasing influence in politics, notably within the Conservative Party here in the UK.

The key finding is this:

Our main result indicates [...] that people with long journeys to and from work are systematically worse off and report significantly lower subjective well-being

So you make yourself systematically worse off, and much unhappier, by buying a large suburban house (with long commute) with an extra bedroom for the rare occasions when your parents come to visit, instead of a short-haul townhouse – even though at the time of purchase, going for the larger suburban house seemed like a totally rational decision.

Same deal with getting a highly paid city job in Canary Wharf or on Wall Street or Madison Avenue even though it dramatically extends commute time – when we would lead a happier job working a ‘worse’ job locally.

The conclusion is not totally unexpected, but it’s an interesting example that makes you think about how irrational human existence can be – pretty depressing really. It highlights the importance of behavioural economics: we may be able to achieve a much happier society if it can succeed in revealing these paradoxical lifestyle choices and thus helping us to avoid them.

We don’t understand, long term, the relative contributions to our happiness and well-being of different factors in our lifestyle. Behavioural science in the 21st century could have a similar ‘enlightenment’ effect to nutritional/dietary science in the 20th.

I’d be interested to know what other examples there are, from your life, where you now think/suspect a decision you took at some point in life *thinking* it was totally rational has led to you being worse off overall?

(hat tip)

Backyard boffins beating Europe’s biggest

bradley — Wed, 16 Jul 2008 11:19:50 +0000

Spectre’s put together a great set of articles about Surrey Satellite Technology ltd. (SSTL). Get this, from a 2005 article: “A company formed by a small team of boffins in Guildford yesterday launched the first Galileo satellite, beating a rival consortium of three of Europe’s technology giants [Alcatel, EADS and Thales].

“SSTL expects to have a turnover of £30m this year, with pre-tax profits of around £1.5m. The company has grown by 25pc a year since it was spun out of Surrey University in 1985. The consortium, Galileo Industries, originally tendered at five times the price quoted by SSTL, but their satellite is still in testing and not expected to launch until mid-2006.”

“We specifically make low-cost and quick satellites,” he said. Giove-A, which weighs 600kg, has gone
from drawing board to launch in 30 months. “We take these components out of iPods and so on, and work out whether we can fly them in our spacecraft.” Sir Martin said conventional components can take up to 15 years to test, by which time they may be obsolete. “Imagine if you bought a PC that was 15 years old.”

The best thing about this: Surrey University owns 80% of the company (the rest is owned by the employees, and by Elon Musk, a name that should be familiar to anyone in the dotcom scene). So they held 80% of a very profitable company growing 20-25% y/y that makes its living stripping bits out of your gadgets to make ultra cheap, ultralight satellites – in a country with no real culture or history of space exploitation/exploration – in fact, SSTL was formed just when Maggie Thatcher nabbed the entire UK space budget! Surrey University really cashed recently when it sold SSTL to EADS earlier this year.

I don’t think we in the UK realise just how much potential we have locked up in our universities, waiting to be exploited and to take on commercial giants from way out leftfield.

Stanford owns the patent to Google’s search engine technology. Would tuition fees faced by students be so onerous if UK universities were doing the same with their bright stars?

WTF-of-the-day: Friday 30th May ’08

bradley — Sat, 31 May 2008 00:13:42 +0000

A US cleantech company called Blacklight Power has raised $60m for a new, very clean form of electricity production. Nothing astounding there, really – cleantech is very much du jour. What’s “WTFotd”-worthy about this story is that the technology they claim to have developed runs against a key part of quantum physics: they claim that they have discovered a lower energy level for electrons than the 1s shell resting state: the hydrino.

To the layman: hydrogen has been extensively studied because it’s the simplest periodic element, and when you’re talking quantum physics, studying basic, simple systems helps… a lot. So physisicts think they understand it pretty damn well. A fundamental tenet is that the lowest energy ‘shell’ (think of it as an orbiting satellite around a planet) that electrons can take around a hydrogen nucleus is called 1s. This is the ‘resting state’, and most physicists don’t believe it could be pushed any lower. *If* it could, then you could take out the difference in energy, use it to power a plant. But physicists believe that hydrogen electrons can’t go any lower: try to squish it in any closer, and it will just press back; so the only energy you would get out of it is energy you put in. Not the way to run a power plant. This is something that the general scientific body holds to be true (or so I understand – but IANAQP).

The hydrino controversy last churned up in 2005 – even hitting mainstream media. Apparently Blacklight is now moving on to scaling up to a 50kW reactor. It would be earth-quaking enough for this key tenet of physics to be proven false in a physics lab somewhere in a university. But for it to have been discovered by a startup in the industry by a non-physicist, and to be on its way to becoming a commercially viable power source? And for it to be roughly 10x cheaper than the cheapest solar power we have available (and even cheaper than the cheapest coal power?), at just 1cent a kWh? This scenario isn’t impossible, but seriously, come on!!

There’s a lot to be skeptical about here. The fact that none of his papers have been coauthored, or that a discovery as revolutionary as this can’t get into Nature or Science, or even any attention in New Scientist. Some scientists claim Randell Mills’ papers are ‘riddled with mathematical errors’, and with Mills’ background in medicine, not theoretical physics or even chemistry, that would be understandable. Various scientists have taken turns ripping his research to shreds. And yet Blacklight’s got great backers, NASA has taken an interest, and $60m has been stumped up. Wtf indeed.

[cf Venturebeat]

Energy

bradley — Sun, 25 May 2008 22:04:38 +0000

(just did some reading on means for capturing sunlight and how efficient they are; it challenged some of my preconceptions of where the solution might lie, so I though I’d share it with you guys too. I omit energy sources that are many thermodynamic steps removed from incident solar radiation, like hydroelectric, wind and waves – I *assume* these are extremely inefficient converters).

Chlorophyll (in plants, converts sunrays into ‘redox potential’ – useful chemical energy that can smash carbon dioxide and water together to form hydrocarbons – like sugar or biodiesel): ~100%

Conversion of chlorophyll-derived energy to useful molecules, like sugars: 50%

Factor in the energy spent by the plant so that it can live, and the sunlight reflected off the leaves, and your big green plant could theoretically convert just 11% (other sources quote 34%). Sugar cane is at the top end of the ones that have been measured: 4%; corn is 0.5% (corn is a major crop being used for bioethanol); wheat is 0.3%

Solar panels: 20%

Algae: 13%

I’d also like to know what the energy efficiency of a snickers bar or a sausage is (in terms of energy used by plants to make the individual components, energy to make the bar, energy to transport it to me, versus the energy it refuels my body with); my (largely baseless) guess is that it must be anywhere in the 0.000x – 0.0000000x% range. What a waste of sunrays!

UPDATE: http://venturebeat.com/2008/05/29/sapphire-energy-gets-open-checkbook-from-investors-for-algae-based-gasoline/ “Green crude” project putting bacteria in dirty water or seawater and extracting petroleum gets ‘blank cheque’ to make it happen, and quick. The Wellcome Trust is getting in on this, which is interesting – and probably a good sign for the viability of the technology