'We took apart a rat and rebuilt it as a jellyfish'

We took a jellyfish, and did a bunch of studies to understand how it activates its muscles. We studied its propulsion and we made a map of where every single cell was. We used a software programme that we had developed a few years ago, borrowed from law enforcement agencies for doing quantitative analysis of fingerprints, and we used it to analyse the protein networks inside the cells.

We found something very interesting right away: the electrical signals that the jellyfish uses to coordinate its pumping are exactly like that of the heart. In the heart, the action potential [electrical signal that travels along nerves – Ed] propagates as a wave through cardiac muscle. That’s how you get this nice, smooth contraction. The activation has to spread like when you drop a pebble in water. The same thing happens in the jellyfish, and I don’t think that’s by accident. My bet is that to get a muscular pump, the electrical activity has got to spread as a wavefront.

After we had the map of where every cell was, we took a rat apart and rebuilt it as a jellyfish.

-- Kit Parker in an interview with Ed Yong.  His team also hope to reverse-engineer other marine life forms. “We’ve got a whole tank of stuff in there, and an octopus on order.”

The Matrix and the Rambunctious Garden

Matt Ridley has a vision of the future:

With much of the world’s meat grown, brain-free and legless, in factories, and much of its fruit and vegetables in multi-storey urban farms lit with cheap fusion power, there will again be vast steppes, savannahs, prairies and rain forests, teeming with herds of wild game. Perhaps even a few woolly mammoths among them.

To some, parts of this scenario may look more like a nightmare.  Even on the most optimistic reasonable view there are grounds for doubt. How do we know future 're-wilded' ecosystems will take the form we want them to if system interactions and changes are more complex than we can model and predict? The uncertainties are even greater if,  as the evidence indicates,  large scale  changes to the Earth system as a whole are also already underway?

Perhaps, in the event of relatively benign outcomes in which humans are still a major presence, the future will see not so much 'the revival of wild ecosystems' as the creation of new ones -- hard to predict combinations of old and new by human hand and accident.

See Emma Marris on the Rambunctious Garden and Garry Hamilton on Welcome Weeds: How alien invasion could save the Earth.

And on this blog Sperm to worm, womb to tomb and erection to resurrection.

Future fish

The construct also contains a stretch of DNA from the promoter region of an ocean pout, an eel-like creature that lives in extremely cold environments (the promoter is a switch that controls the expression of a downstream gene). Normally, the eel uses this promoter to keep an antifreeze gene turned on constantly so it does not freeze. The promoter is therefore “constitutive,” meaning it is always active, and coupling it with a growth factor gene in an Atlantic salmon results in the salmon experiencing a continual growth spurt—since the growth factor is continually produced. Studies have shown that the genetically-altered Atlantic salmon’s appetite would make it constantly ravenous, meaning that it would eat everything around in sight.

-- FDA Decision Will Lead To First Ever Genetically-Modified Animal For Consumption

A new world

Freeman Dyson asks if the world is entering a new 'Age of Wonders', with a shift backward in the culture of science from organizations to individuals, [1] from professionals to amateurs, and from programs of research to works of art:

If this dream comes true, and the new art form emerges triumphant, then a new generation of artists, writing genomes as fluently as Blake and Byron wrote verses, might create an abundance of new flowers and fruit and trees and birds to enrich the ecology of our planet. Most of these artists would be in close touch science, like the poets of the earlier Age of Wonder. The new Age of Wonder might bring together wealthy entrepreneurs...and a worldwide community of gardeners and farmers and breeders, working together to make the planet beautiful as well as fertile, hospitable to humming birds as well as to humans.

Dyson's optimism is a welcome challenge in a world where pessimism can sometimes come a little too easily. [2] How lovely, some may say, if his vision were to come true. [3]

But for all his strengths, Dyson has clearly been wrong-headed about some things (nuclear explosions to send rockets into space, anthropogenic climate change). Creating living entities is not the same as creating poems, and 'the bad guys' are unlikely ever to be far away. [4]


Footnotes

[1] Dyson's heroic individuals include Craig Venter, Kary Mullis and Dean Kamen.

[2] For a sober view see The seven terrors of the world. For pessimism that is perhaps a little too much see, for example, Cold Comfort. In the delightful book which is the occasion for Dyson's essay, Richard Holmes notes three themes introduced into scientific biography during the Romantic age:

1) 'Newton syndrome', the notion of 'scientific genius' in which science is largely advanced by a small number of preternaturally gifted (and usually isolated) individuals;

2) the 'Eureka moment', in which discoveries are made without warning (or much preparation) in a sudden blazing instant or revelation and synthesis; and

3) the 'Frankenstein nightmare', in which all scientific progress is really a disguised form of destruction.

All three, surely, are simplifications that can make for 'good stories'. Dyson is, perhaps, overly partial to the first two. 'Environmentalists' etc. (and I include myself in that category) may sometimes get a little stuck on the third. P.S. 7 Aug: Braden Allenby criticizes environmentalists like this:

sustainability discourse generally has a really, really hard time engaging with emerging technologies and their implications, not to mention the inherent complexity of these systems, which means that, in some very important ways, it’s obsolete.

[3] Could we have the humming fish from The Lorax, please?

[4] See, for example, Birdsong of the Eremozoic.

P.S. 6 Aug: George Dyson writes:

On July 24, 2009, a small group of scientists, entrepreneurs, cultural impresarios and journalists [met to be] offered a glimpse, guided by George Church and Craig Venter, of a future far stranger than Aldous Huxley had been able to imagine [in his 1948 work Ape and Essence].

In this future — whose underpinnings...are here already— life as we know it is transformed not by the error catastrophe of radiation damage to our genetic processes, but by the far greater upheaval caused by discovering how to read genetic sequences directly into computers, where the code can be replicated exactly, manipulated freely, and translated back into living organisms by writing the other way. "We can program these cells as if they were an extension of the computer," George Church announced, and proceeded to explain just how much progress has already been made.

Back in 1997, Lee Smolin expressed three doubts about the similarity between DNA and a computer programme:

1) what is inherited in real biology is more than just a naked sequence of DNA;
2) DNA is part hardware and part software; and
3) genetic code is not able to run on arbitrary hardware.

How far, if at all, are these doubts still valid?

P.S. 20 Aug: a useful account by Ed Regis of the meeting mentioned by George Dyson.

ID in the bone

Ever inclined to make an inscription, human beings have figured out how to write their own messages in the heart of the [otolith]. By sequentially altering the temperature of the water in which salmon fry are hatched and raised, researchers can lay a distinctive “batch label” into the chemical layers of the otolith—a kind of barcode, inscribed in stone, and indelibly preserved within the maturing adult fish (a puckish early student of this technique used it to write “hi mom” in binary inside his experimental animal). Later, when these free-swimming creatures are captured at sea, each can be traced unfailingly to its hatchery of origin. Some five billion Pacific salmon have now been marked in this way, their inner qibla reconfigured to refer to their point of origin, and thus the point to which they seek return.

from The Orienting Stone

A gift

What [the] drive to mastery misses is an appreciation of the gifted character of human powers and achievements.

-- Michael Sandel in his third Reith Lecture, expressing caution about genetic manipulation and other biotechnology. Matt Ridley seemed unconvinced:

My main issue is how we take the decision as to whether something is an enhancement or a cure.

Can there be common ground?

Perhaps the idea of 'gift' can be accommodated both by those who believe a (supernatural) giver is at work and those (including me) who do not. [1] The latter can apply it figuratively (a little like the term 'natural selection', in which 'selection' does not imply the literal existence of a selector). A naturalistic outlook need not be incompatible with a sense of "openness to the unbidden" [2] which requires (among other things) a strong sense that existence is astonishing, that knowledge, while powerful, has limits, and that wisdom is elusive.

"Nature is more various than observation though observers be innumerable."

Footnotes

[1] Examine how people construct the idea of 'gift'. See, for example, Lewis Hyde.

[2] Sandel quotes this phrase from William F. May, a theologian. But surely, like "negative capability", it can be grounded in non-theological, lived experience.

Image: Hyalinobatrachium pellucidum, an endangered 'glass' frog (Luis Coloma). The quote underneath it is from Christopher Smart

Run slowly, night-horses

Half of vertebrate species may be gone by the end of this century. Elizabeth Kolbert's The Sixth Extinction? is good on, among other things, the frogs, the bats and some of the people who care for them. [1] At least one take-home point is familiar:

In the end, the most deadly aspect of human activity may simply be the pace of it.[2]

One of the consequences of frenetic human activity as currently organised is, of course, rapid climate change. [3] In Heatstroke: Nature in Age of Global Warming, Anthony Barnosky writes that, before Man, the typical species life span of a mammal was 1.7 to 2.5 million years [4]. For plants, reptiles or amphibians the likely span was somewhat longer. For birds and fish perhaps a little shorter. And, he says,

In order to have that long a life span a species must be able to withstand (or, in an evolutionary sense, adapt to) the broad, slow shifts in climate that are natural as tracked over many millions of years, and also the more rapid fluctuations in climate that are nested within individual million-year time slices.

On 'the lowest reasonable estimate', Barnosky continues, the global average temperature will rise will be 1.1 Centigrade by 2050, and the earth will be hotter than modern humans have ever seen it -- hotter than in at least 160,000 years. On a 'worst case scenario' the heating by 2100 will be 4 to 6 C; the Earth will be hotter than at any time in the last three million years, and:

Three million years ago, not one species of mammal or bird that lives on Earth was alive, as far as we know.

But Barnosky's worst case scenario may be actually be over-optimistic. A recent analysis at MIT calculates the odds as worse than previously thought: without effective policies a temperature rise of more than 7 C becomes a distinct possibility.

In all events, efforts at ecosystem protection are likely to continue, along with the kind of hedging Kolbert describes at EVACC, an amphibian conservation centre in Panama:

It might be thought of as a preserve, except that, instead of protecting the amphibians from their natural habitat, the center's aim is to isolate them from it.

...their former habitat being 'natural' no more. [5]

Another option -- one that may be more widely discussed before too long -- is whether and how some animals and other living entities can be engineered not for medical research but to withstand rapid change. [6]


Footnotes

[1] It also contains, among other things, a fairly good working sketch of the Anthropocene:

Most of the world's waterways have been diverted or dammed or otherwise manipulated -- in the United States, only two per cent of rivers run unimpeded -- and people now use half the world's readily accessible freshwater runoff. Chemical plants fix more atmospheric nitrogen than all natural processes combined, and fisheries remove more than a third of the primary production of the temperate coastl waters of the oceans. Through global trade and international travel, humans have transported countless species into ecosystems that are not prepared for them. We have pumped enough carbon dioxide into the air to alter the climate and to change the chemistry of the oceans.

[2] Kolbert asks Andrew Knoll to compare the current situation with past extinction events. He says he doesn't want to exaggerate recent losses, or to suggest that an extinction on the order of the end-Cretaceous or end-Permian is imminent. At the same time he notes, when an asteroid hit the Yucatan 65 million years ago,

it was one bad afternoon, but it was a short-term event, and then things started to get better. Today, it's not like you have a stress and the stress is relieved and recovery starts. [Instead,] it gets bad and then it keeps being bad, because the stress doesn't go away. Because the stress is us.

[3] One, but by no means the only one. Over-consumption is another. See, for example, 'turbo-evolution' of cod.

[4] Incidentally, the species life span of Erectus may lie within this range, or at least approach it. Perhaps Floresiensis lived longer.

[5] The world ocean itself ceases to be natural as its chemistry changes faster than at any time in more than fifty million years.

[6] A major extinction is a field day for fungi, pathogens, micro-organisms etc. In the long run (the next few millions to tens of millions of years), the current extinction event may, other things being equal, open up space for a new flowering of beings. Some of them could be as strange and marvelous as those of the cetacean radiation. Peter Ward argues that, looking to the even longer run (hundreds of millions of years), there is "only one chance for survival": planetary, not (just) genetic engineering. Humans [post-humans?] must, he says, "seize the controls of the various elemental cycles that determine the future of life on earth."

--

The title of this post is based on a line in Act 5, Scene 2 of The Tragical History Faustus, where Marlowe quotes Ovid

O lente, lente currite noctis equi!

but continues

The stars move still, time runs, the clock will strike.

Red dog

Ruppy the transgenic puppy at 10 days old under ultraviolet light, showing the red fluorescent protein produced by sea anemones.

Let's build a creature

The competition began in 2004 with five entrants. This year, more than 100 teams from all over the world have signed up.

--from Scientists compete to build best living machine.

Birdsong of the Eremezoic

It seems feasible that over the coming century human nature will be scientifically remodelled. If so, it will be done haphazardly, as an upshot of struggles in the murky realm where big business, organised crime, and the hidden parts of government vie for control. If the human species is re-engineered it will not be as a result of humanity assuming a godlike control of its destiny. It will be another twist in man's fate.

Thus John Gray (2002) in pessimism of the grand style, which sweeps along so boldly that you may sometimes question if it sweeps away too much. [1]

For Gray, the prospect of conscious human evolution evoked by E O Wilson is a mirage.

Further extensions for Freud's prosthetic (brutal infant) god(s) are likely. Whatever is coming down the track may not be godlike in the sense Gray means, but it may be as arbitrary and unpredictable, as kind and as cruel as the gods in Ovid's Metamorphosis.


Footnote

[1] So, for example, Man may well be "a highly inventive species that is also one of the most predatory and destructive"; but it may be more than that. Man, and especially women, may also be "naturally" cooperative and compassionate. Pity, like a naked new-born babe, striding the blast...shall blow the horrid deed in every eye, that tears shall drown the wind.

Sperm to worm, womb to tomb, erection to resurrection

In New Scientist, Henry Nicholls suggests Ten extinct beasts that could walk the Earth again. The list includes the mammoth, Tasmanian tiger, glyptodon (pictured) and -- surprisingly -- the gorilla (because "the first species to be brought back from extinction will most likely be one that is alive today").


An accompanying editorial observes:

Neither [geo-engineering nor a technological fix for species extinction] is an adequate substitute for efforts to cut emissions, preserve habitats and conserve endangered species. They are, all the same, welcome reminders of what human ingenuity can achieve, and of the fact that there is only a fine line between schemes that are wild-eyed and those that are far-sighted.

P.S. 2 Feb: Extinct animal cloned for the first time.

Bioterror

The greatest potential danger of do-it-yourself biotechnology, says Richard Ebright of Rutgers University, is that someone might intentionally synthesise or recreate deadly pathogens like the 1918 flu strain, which killed an estimated 40 million people worldwide. "That is on the edge of being within the technical capabilities of someone working outside the laboratory environment."

-- Rise of the garage genome hackers.

Cooking up trouble

One of the fastest-growing technologies is DNA synthesis, which offers new capabilities to alter the genes of existing pathogens or synthesize them artificially. While governments, trade groups and professional organizations are experimenting with various voluntary controls over such new capabilities, the United States should lead a global effort to strengthen oversight and clamp down on the unregulated export of deadly microbes...

-- Report Sounds Alarm Over Bioterror


Image: Ebola virus

Humans, chimeras, humility

Many bioconservatives are addicted to a notion of humanness that is very specific to Judeo-Christianity. [But] when you look at India and Thailand, Japan, Korea and China, and you ask should parents be able to use biotechnology to make their children more virtuous or more intelligent?, the vast majority in those countries say yes. But in Europe and North America people are very pessimistic. And that’s largely because of the Judeo-Christian hangover that there's a certain humanness was created by God at the beginning of time, and by playing around with this you’re playing God. There are natural boundaries beyond which it’s hubris to go. And those are western problems, for the most part. In eastern cultures you don’t have that problem. You have chimeric gods in Hinduism which are half-human, half-animal. In Buddhism you have the implicitly notion that humans can become more than the gods, achieve greater states of mind and physical abilities than the gods.

--James Hughes in conversation [1] on existential threats at Buddhist Geeks.

Yes, but hubris (ὕβρις) predates Judeo-Christianity. The word comes from a culture that had no problem imagining chimeric beings and gods that could take animal forms but still thought Man could over reach with terrible consequences. [2]

Who are most humble? Those who most skillfully prepare for the deepest and most catastrophic errors in their own beliefs and plans.

-- from the Twelve Virtues of Rationality by Eliezer Yudkowsky.

Notes

1. this is a rough transcript, not verbatim.

2. In Shame and Necessity, Bernard Williams argues that the basic ethical ideas possessed by the ancient Greeks were "in better condition" than modern ones

Meat 2.0?

Frankly, if the end product is to be the white meat of a month-old broiler chicken or the minced meat of a hamburger, prepared without care and eaten absent-mindedly, why make the detour through a sentient vertebrate which needs kilos of grain just to keep upright and has a brain that may feel fear and frustration?

-- Anna Olsson.