27 May 2007

Super mushrooms and fishy fingers

Oh, to be a mycologist in this day and age! A paper was just published in PLoS ONE by Dadachova et. al. describing the effects of ionizing radiation on the growth of melanin-containing fungi. Many fungi produce the pigment melanin; it's what makes your average dark mushroom dark, and is chemically the same as the pigment your skin produces to give you that summer tan. As it turns out, melanin-containing fungi have a significant growth advantage over non-melanin fungi in the presence of ionizing radiation, such as at the site of the 1986 Chernobyl disaster. The paper demonstrates that the electron properties of melanin are changed in the presence of radiation, and that growth increases according to a number of different assays. Based on this and previous evidence, they "cautiously suggest that the ability of melanin to capture electromagnetic radiation combined with its remarkable oxidation-reduction properties may confer upon melanotic organisms the ability to harness radiation for metabolic energy."

I remain skeptical for now, but it's certainly exciting enough to be worth further investigation. The paper already addressed two concerns that I had: the effect of temperature, and the effect of shielding. The paper did a fair job demonstrating that the increased growth of melanized fungi was due neither to increased temperature (melanin normally is thought to disperse absorbed radiation as heat) nor shielding against radiation damage. The next major step, as they say in the paper, will be finding a mechanism by which melanin might contribute to metabolic energy. Furthermore, I'd personally like to see what ranges of radiation (frequencies and intensities) can impact growth, and to what degree. The better we can characterize the effect, the better we may be able to understand when and how such a mechanism evolved, and where we might find it elsewhere in nature. And, of course, since so many other organisms produce melanin, can they harvest radiation for metabolic energy in the same way?

The implications are exciting, both in terms of understanding biology and finding possible applications. Space travel immediately comes to mind; space is rife with ionizing radiation, and a radiation-eating crop of mushrooms would be a great asset.

Of course, leave it to the folks at Uncommon Descent to sour a perfectly good find. "Dacook" writes:

The question naturally arises; whence came this unusual ability? Where in the evolutionary past of fungi are the Chernobyls or other high radiation environments? How will Darwinism explain the development of this surprising trait? Why ON EARTH would fungi need this ability?

Certainly for panspermia to work, there must exist organisms that can survive the rigors of space travel, including radiation. We already know about bacteria that can do this. Now we have another possibility.
And another difficulty for Darwinism.

Yes, of course, because radiation is completely man-made and never comes from natural sources ever. Dacook is basically saying that, for fungi to have evolved a mechanism for harnessing high levels of radiation, they must have been exposed to high levels of radiation. Since no nuclear reactors existed when the fungi first evolved, they must have been designed in advance. This line of reasoning completely ignores the fact that these fungi encounter radiation all the time, just not to the degree of that at Chernobyl. Our planet does orbit a giant nuclear fusion reactor, after all. If melanin has a role in metabolism, it isn't likely to be exclusive to Chernobyl-level radiation. The mechanism would have evolved under less extreme circumstances, and is only now going into overdrive in the presence of intense electromagnetic radiation. I consider it to be analogous to mankind's current obesity problem. Our bodies evolved on a low-fat diet, and as a result became quite adept at storing energy. Now that we have McDonald's (the Chernobyl of dining options), our bodies have access to more fat than it knows what to do with, but we keep on storing it, because that's what we evolved to do. It's not that we were designed to get fat and happy off cheeseburgers. We're just using an old mechanism to tp into a new energy source. The same goes for the fungi; they weren't designed to munch solely on Chernobyl glow, they're just making extra use of a mechanism they already had lying around.

As for further evolutionary evidence and the "Chernobyls" of the past, consider this paragraph from the Dadachova et. al. paper:

The role of melanin in microorganisms living in high electromagnetic radiation fluxes is even more intriguing when the pigment is considered from a paleobiological perspective. 1Many fungal fossils appear to be melanized [10], [11]. Melanized fungal spores are common in the sediment layers of the early Cretaceous period when many species of animals and plants died out which coincides with the Earth's crossing the “magnetic zero” resulting in the loss of its : “shield” against cosmic radiation [12]. Additionally, radiation from a putative passing star called Nemesis has been suggested as a cause of extinction events [13]. The proliferation of melanotic fungi may even have contributed to the mass extinctions at the end of Cretaceous period [14]. A symbiotic association of plants and a melanotic fungus that allows for extreme thermotolerance has been attributed to heat dissipating properties of melanin [15]. Melanotic fungi inhabit the extraordinarly harsh climate of Antarctica [5]. Hence, melanins are ancient pigments that have probably been selected because they enhance the survival of melanized fungi in diverse environments and, perhaps incidentally, in various hosts. The emergence of melanin as a non-specific bioprotective material may be a result of the relative ease with which these complicated aromatic structures can be synthesized from a great variety of precursors [2], [4], [5], [16]–[23].

It's truly fascinating what can be found in the fossil record.

On the subject of faulty reasoning coming out of UncDesc: PaV warps the interpretation of a new finding in fish genetics.

First, a little background in this study (please excuse any inaccuracies, I'm trying to sum up based on what little I know of Hox genes). Development in vertebrates is largely driven by a family of genes called the Hox genes. In tetrapods (four-limbed critters, like lizards and people), there are two stages of Hox expression, with the latter stage resulting in hand development. Zebrafish, the model organism for studying fish genetics and a favorite of developmental geneticists, only have one stage of Hox expression during development, resulting in fins. Therefore, it has been hypothesized that the transition from fins to hands involved adding a stage of Hox expression.

A recent study looked at gene expression in the paddlefish, which is thought to be evolutionarily very old (paddlefish today are genetically very similar to their ancient ancestors). The paddlefish, it turns out, has two stages of Hox expression (like tetrapods) instead of one (like zebrafish). This suggests that, instead of starting with one Hox stage and adding a second in the transition from fins to hands, fish started with two Hox stages and zebrafish just lost a stage over time. That is to say, some of the genetic setup for hand development might be a lot older than we thought.

That's all well and good. Then PaV makes this gaff:

"This is the first molecular support for the theory that the genes to help make fingers and toes have been around for a long time—well before the 375-million-year-old Tiktaalik roseae, the newly found species discovered in 2004 by Shubin and colleagues. Tiktaalik provided a missing evolutionary link between fish and tetrapods and was among the first creatures that walked out of water onto land." (Taken from PhysOrg.com. Here’s the link.)
Poor old Tiktaalik roseae! It’s [sic] fifteen minutes of fame is [sic] over. So much for “a missing evolutionary link”.

Correct me if I'm wrong, but fish don't have hands, yes? Even if the Hox genes themselves and certain aspects of their expression were around before Tiktaalik, there had to have been some evolutionary change that gradually turned fins into hands.

PaV continues more seriously in the comments of his post, talking about genetic "front-loading," the idea that information was lying dormant in the DNA, just waiting for a chance to make a name for itself. I don't know nearly enough about the present study or Hox expression to tackle this specific case. I'll just say that the front-loading concept seems really fishy (so to speak) to me. The Hox genes obviously had some purpose before hand development. What are your criteria for saying something was front-loaded, as opposed to just co-opted or adapted? For one thing, that presumes you know the final ideal state of the information, as well as the method for getting to that state.

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