Magna ludentis naturae varietas

Eighteenth in a series of notes and comments on The Book of Barely Imagined Beings

Chapter 9: Iridogorgia

page 139: spirals [ubiquitous]... in living things -- even, it seems, in the human uterus. See also this on the golden ratio.

page 142: Nuvvuaqittuq. Looking for the most off-putting and obscure possible title for my book, I thought of combining this rock and this device for Nuvvuaqittuq Eidouranion. See here and this essay.

page 143: inserting sequences that code for text into non-coding DNA. Things have moved on a long way since I wrote this chapter! See, for example, this:

Scientists have for the first time used DNA to encode the contents of a book. At 53,000 words, and including 11 images and a computer program, it is the largest amount of data yet stored artificially using the genetic material.

An early analogy between the material (and living) world and language is found in De Rerum Natura by Lucretius, which argues that:

just as the elementa (letters of the alphabet), limited in number, are common to many different words and combine in many different orders to produce the different words included in the verses of the poem, so likewise the different kinds of atom, though limited in number, combine in different ways to produce humans, animals, plants, and all that exists.

page 143: The 10^1834097  books in the Library of Babel. This figure is from The Unimaginable Mathematics of Borges' Library of Babel by William Goldbloom Bloch which was reviewed by Alberto Manguel here.

page 144: central dogma of molecular biology.  It turns out that things are not so simple. See, for example, The ever deepening mystery of the human genome and, especially, The Epigenetic Revolution by Nessa Carey.

page 146: the single biggest threat to Man...is the virus.  See Spillover by David Quammen and The Viral Storm by Nathan Wolfe. But see also A Planet of Viruses by Carl Zimmer.

page 147: dependent arising. David Barash draws parallels between ecology and Buddhism:

The interconnected and interdependent nature of things is the heart of ecology. It is also remarkably similar to the fundamental insight of Buddhism: ‘dependent co-arising’ or pratītyasamutpāda in Sanskrit

page 149: Beauty [can help us] see that things exist independently of our own attachments.  So, most famously, "there is grandeur in this view of life..."

page 149: deep places that are out of sight. See this on the case for deep sea conservation.

The ocean of the air

femur of an elephant bird, skeleton of a hummingbird

The November/December edition of New Humanist includes an article by me about some of the largest and smallest animals ever to have flown, and how life has shaped the atmosphere.

Here is something to think about:

• In every cubic meter of [normal] air there are between 1.6 million and 40 million viruses.
• In every cubic meter of [normal] air there are between 860,000 and 11 million bacteria.

Half of the viruses trapped by the scientists who made these observations didn’t match any known virus species. But most belong to groups that infect plants or mammals. Given that we breathe roughly 0.01 cubic meters of air each minute, a simple calculation based on these results suggests we breathe in a few hundred thousand viruses every minute.

Hummingbirds, by the way, fly forwards and backwards with equal ease.

P.S. 13 Nov: The piece is now online here.

Outbreak

David Quammen cranks up his argument:

We're unique in the history of mammals. No other primate has ever weighed upon the planet to anything like the degree we do. In ecological terms, we are almost paradoxical: large-bodied and long-lived but grotesquely abundant. We are an outbreak.

Viruses like bees

Viruses, instead of being single-minded agents of disease and death, now begin to look more like mobile genes. Evolution is still an infinitely long and tedious biologic game, with only the winners staying at the table, but the rules are beginning to look more flexible. We live in a dancing matrix of viruses; they dart, rather like bees, from organism to organism, from plant to insect to mammal to me and back again, and into the sea, tugging along pieces of this genome, strings of genes from that, transplanting grafts of DNA, passing around heredity as though at a great party. They may be a mechanism for keeping new, mutant kinds of DNA in the widest circulation among us. If this is true, the odd virus disease, on which we must focus so much of our attention in medicine, may be looked on as an accident, something dropped.

-- from Lives of a Cell by Lewis Thomas (1971)

Cellular origins in a viral world

The discovery of an unusual hybrid virus living in one of the harshest environments on the planet suggests a solution to the conundrum of how RNA-based life 'updgraded' to DNA-based life. More

P.S. A good phrase: "It's a mythological beast of a virus, but it actually exists.”

Megavirus

Its genome is 1.259 million base pairs long, which is 6.5 percent longer than the previous record holder among giant viruses. In that abundance of DNA are 1120 genes. That’s hundreds more genes than found in a lot of bacteria.

-- Carl Zimmer on a the world's most ginormous virus.

Some have even argued that they represent a new domain of life, although others aren’t so sure, Zimmer notes.

Jean-Michel Claverie, who discovered it, says the fact that it shares cell-like genes with the mimivirus is 'definitive proof' of a cellular ancestor.

A virus bestiary

There are more viruses on Earth than there are stars in the universe.

If you stacked every virus end to end they would stretch 100,000 light years.

10 percent of all the photosynthesis on the Earth is carried out with virus genes.

Life as we know it may owe its existence to viruses.

Astonishing facts such as these pepper Carl Zimmer's A Planet of Viruses, a book whose ten short and clear chapters offer as good an introduction to these extraordinary entities -- microbiology's polymorphous Trimurti -- as you could wish for. [1]

Research into the nature of viruses and their significance to life as a whole has exploded in the last couple of decades. There is, surely, much more to discover. For now at least three fundamental points seem clear: viruses are ubiquitous, diverse, and have played a central role in the evolution of (virtually) all life forms.

chart from Pennisi, Science, 25 March 2011

Nowhere is this more apparent than in the world ocean, which holds about 1,000,000,000,000,000,000,000,000,000,000 of the blighters. [2]  As Zimmer notes, ocean viruses are stunning not just for their sheer numbers but also for their genetic diversity:

The genes in a human and the genes in a shark are quite similar -- so similar that scientists can find a related counterpart in the shark genome to most genes in the human genome. The genetic makeup of viruses, on the other hand, matches almost nothing. In a survey of viruses in the Arctic Ocean, the Gulf of Mexico, Bermuda and the northern Pacific, scientists identified 1.8 million viral genes. Only 10 percent of them showed any match to any gene from any microbe, animal, plant or other organism -- even [to] any other known virus. The 90 percent were entirely new to science. In 200 litres of seawater, scientists typically find 5,000 genetically distinct kinds of viruses. In a kilogram of marine sediment, there may be a million kinds.

One speculation: if -- as has been suggested [3] -- the ancestors of viruses predate cells, could they have played a role in the emergence of life itself from what Martin Nowak has called 'pre-life'? [4], [5]

A virus within this eukaryote, Cafeteria roenbergensis,  has the largest genome of any known marine virus, with ~730,000 base pairs of double-stranded DNA. It may be a member a fourth domain of life.

Notes

[1] Like other reviewers such as Maggie Koerth-Baker at Boing Boing I received a free review copy.

[2] If I count correctly that's 10^{30 --} a nonillion.

[3] Eugene Koonin, Tatiana Senkevich and Valerian Dolja: The ancient Virus World and evolution of cells.

[4] 'Life', suggests Nowak, can be seen as 'an infection of pre-life.' See Super-Cooperators by Martin Nowak and Roger Highfield, and Prevolutionary dynamics and the origin of evolution by Martin Nowak and Hisashi Ohtsuki.

[5] As Zimmer reports, Patrick Forterre has proposed that in an RNA world, viruses invented double stranded DNA as a way to protect their genes from attack. 'Eventually their hosts took over their DNA, which then took over the world. Life as we know it...may have needed viruses to get its start.'

P.S. In the second section of this essay drawing on his book The Mathematics of Life, Iain Stewart explores how the structure of viruses can be explained by maths.

Meat your maker

A genetic chimera probably conceived in the faecal mire of an industrial pigsty, suddenly threatens to give the whole world a fever

writes Mike Davis. This "lays bear the meat industry's monstrous power".

See also Tom Philpott (added 29 April: but don't jump to conclusions, says Merritt Clifton).

Last year in his letter to the president Michael Pollan highlighted feedlot meat as a major flaw in the U.S. agricultural system:

As Wendell Berry has tartly observed, to take animals off farms and put them on feedlots is to take an elegant solution -- animals replenishing the fertility that crops deplete -- and neatly divide it into two problems: a fertility problem on the farm and a pollution problem on the feedlot. The former problem is remedied with fossil-fuel fertilizer; the latter is remedied not at all.

The tree

A crude sketch......with interesting antecedents inspires a tatoo, a sculpted vault, and maybe even (via a universal phylogenetic tree) this:
origin of the Mimivirus

Virus world

[The] diversity in the virosphere is also coming as a surprise. There are now thought to be around 100 million types of virus. They boast a more varied biochemistry than cellular life, storing their genetic information as both single and double-stranded DNA and RNA. Recent virus-hunting expeditions have uncovered one with a unique hybrid genome structure, part single-stranded and part double-stranded DNA, plus a menagerie of novel forms - bottle-shaped viruses, viruses with tails at both ends, viruses shaped like droplets and viruses that resemble stalk-like filaments. Most astonishing of all is the giant mimivirus, which is bigger than some bacteria. And we have only scratched the surface. "In terms of diversity, I don't think we even have an inkling yet what's out there," says [one] microbiologist.

...All in all, biologists are confronting what may be the biggest advance in evolutionary thinking since the discovery of the gene. Our emerging knowledge of viruses challenges many tenets of evolution, not least that it is driven by competition between selfish genes. Viruses provide a strong argument for the idea that evolution is also driven by fitness boosts gained through give and take.

-- from Viruses: The unsung heroes of evolution by Garry Hamilton. See also:

Viruses have an important role in global biogeochemical cycles, in deep-sea metabolism and the overall functioning of the largest ecosystem of our biosphere.

-- from Major viral impact on the functioning of benthic deep-sea ecosystems (doi:10.1038/nature07268).