Saturday, September 1, 2012

Thank god for rots!

Fungal brown and white rot species evolved in time to prevent terminal carbon burial.

Take your mind back- way back- to the carboniferous epoch. A luxurious 60 million years of high temperatures, high CO2, and high growth and burial of trees and other plant life to form the coal deposits for which it is named. Amphibians were the dominant animal, and trees the dominant plant life, having evolved bark and woody cores with the critical component lignin, a heavily crosslinked carbohydrate polymer that is incredibly tough. We certainly can't eat it, and nor can other animals.

Life was great for the trees. They had come up with a great solution to competing with their fellow plants for height and light. But it was a little too good. The carbon they sequestered into their dead hulks was impervious to decay, to the point that it was left to get buried with the ongoing geological processes, as coal. The carboniferous thus experienced a dramatic drop of atmospheric CO2, from the high levels inherited from the foregoing eras of lower plant productivity / higher recycling, never to be seen again, to some of the lowest on record towards its end, until the recent ice ages.

Geological time scale, with very rough graphs of inferred CO2 (purple) and temperature (blue). Note the dramatic drop of CO2 through the carboniferous, and its subsequent return to higher levels. Then eventually  its descends to very low levels through the recent ice ages, followed by the anthropogenic blip at the end.

Then came the rots- brown rots, which partially degrade lignin, and white rots, which chew it up completely. A recent paper describes how the earliest fossils of white rot are from ~260 million years ago, well after the close of the carboniferous (363 to 290 MYA). The researchers decided to sequence genes from a bunch of fungal rot species to determine from their molecular relationships when the true origin of this group took place. Their results indicate an origin of lignin-digesting enzymes in these fungi about 295 million years ago, consistent with a slowdown of carbon burial and the geologic resumption of net CO2 emission into the atmosphere.

How did they do that? Lignin is a heterogeneously crosslinked polymer of several short aromatic alcohols. This means that it is structurally very tough, and chemically a mess. There is no single point of attack by the usual clever catalytic enzymes that bacteria have been so successful in developing. Rather, a more blunderbuss approach is used, in the form of custom, secreted peroxidases, which harness the oxidizing power of H2O2 to blow away the lignin chemical bonds. The problem is that, if the fungus takes a too-aggressive approach to degrading the lignin, there may not be anything left to eat. Its food will have turned to ashes, (i.e. CO2), rather than a nicely slow-cooked meal of carbohydrates. Unfortunately, the details of how this is all managed are not yet known, though it is of some interest to the biofuels industry.

What is known now, through this paper, is when these key lignin peroxidases evolved, and how they diversified (to a maximum of 26 copies in one existing species of white rot. The rather complex  tree of descent is shown below, with a rough time scale at the bottom, and the key development and diversification of these lignin peroxidases (dark blue line shades). They point to node "A" as the common origin of all the current white and brown rot species, and show the copy numbers of the relevant enzymes in red throughout the tree.

Phylogenetic tree of many fungal species, focussing (top) on brown and white rot species that digest wood. 

Now, if only we could globally shut off these enzymes for a few hundred years to help us clean up the atmosphere!


  • Taibi on Mitt: pluto-hypocrite, financial mobster. Purveyor of a truly destructive form of debt. "But what most voters don't know is the way Mitt Romney actually made his fortune: by borrowing vast sums of money that other people were forced to pay back."
  • Republican unworthiness, continued. How would Romney like it if Obama started making magic underwear jokes?
  • Unworthiness, continued: A ticket of lies. I guess, if your plan is to reduce your own tax rate to 0.8%, you have to say something other than that.
  • Speaking of which, what the heck is up with Dinesh D’Souza?
  • Mitt's solution to a lack of jobs: "Or when you lost that job that paid $22.50 an hour, with benefits, you took two jobs at $9 an hour." This is a little hard to fathom, if a) Mitt was the one that screwed you out of that first job, and b) there are five applicants for every job opening.
  • Death of privacy, facebook-style.
  • Religion and spirituality keeps yielding dividends in violence.
  • Hell is not just other people, it is for other people.
  • Ideology and the creation of suffering.
  • 12-step cults.
  • Interesting proposal for stock market quantization.
  • Yes, the civil war was all about slavery.
  • Economics quote of the week, from Mark Thoma:
"When all of the misleading arguments are set aside, Romney’s economic proposal comes down to a simple tradeoff, less social insurance and other government programs for the working class, perhaps higher taxes as well, and more tax cuts for the wealthy. Perhaps that’s a tradeoff America wants to make, perhaps not – I suspect not."
  • Economics image of the week: Corporate profits (and income of the rich) are higher than ever. If they saw demand, they could invest plenty in growth & hiring. But they are saving instead.


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