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.

25 May 2007

Happy LOL Day!

I never thought I'd ever contribute to a meme like this, but give me the right theme, and boy howdy...

24 May 2007

Good company

You scored as Scientific Atheist, These guys rule. I'm not one of them myself, although I play one online. They know the rules of debate, the Laws of Thermodynamics, and can explain evolution in fifty words or less. More concerned with how things ARE than how they should be, these are the people who will bring us into the future.

Scientific Atheist


Militant Atheist


Spiritual Atheist




Apathetic Atheist


Angry Atheist




What kind of atheist are you?
created with QuizFarm.com

(via Pharyngula)

22 May 2007

Poe's Law in action

Poe's Law: "Without a winking smiley or other blatant display of humor, it is impossible to create a parody of Fundamentalism that SOMEONE won't mistake for the real thing... having seen similar REAL ideas from real religious/political Fundamentalists."

The blagosphere is in a tizzy over this post in a blog supporting Senator Sam Brownback for President. It says heliocentrism is atheist doctrine, even worse than "Darwinism." Not everyone is convinced that this guy is serious. I'll let you decide for yourself. Personally, I'm not seeing a whole lot of reason to think it's a joke. He cites Answers in Genesis at length, for one thing... crazy as it is to insist the universe pivots upon the Earth based on some old fairy tales, it's a real fundamentalist belief, so we can't dismiss it as a joke based solely on the absurdity of it. Furthermore, the rest of the blog seems too much in earnest. If this is a joke, it has one hell of a setup.

So I say it's real. The ideas are, anyway, even if this particular collection of them turn out to be a farce. But if it IS a joke, then it's an elegant example of Poe's Law in action. (Well, either that, or an example of a really poorly executed joke.)

21 May 2007

Quick Observation

Every religious tradition is based on certain false claims about the way the universe operates. Inherent to every religious system, therefore, are bound also to be certain logical inconsistencies. Eventually, someone will notice these inconsistencies and set about to solve them.

The person who finds a solution that successfully (if provisionally) resolves this logical conflict in a way that preserves the integrity of the system for a while is called a Theologian.

But the person who, rather than attempt to patch a broken system with yet another layer of baroque, convoluted, ad hoc logic, decides instead to suggest that the system is flawed beyond repair and is based on impossibilities -- that person is labeled a sinner, a liar, and a fool.

Ultimately, the Skeptic and the Theologian are engaged in the same enterprise, but with different priorities. Both of them wrestle with inconsistencies in the received wisdom of their weltanschauung: but whereas the Theologian is willing to sacrifice logic on the altar of his belief, the Skeptic is willing to sacrifice belief in his adherence to logic.

Which would you choose?

15 May 2007

Jerry Falwell: he will be missed (by someone, I'm sure)

Jerry Falwell passed away today at the age of 73. According to his physicians, Falwell had a history of heart problems. You'll find no argument from me.

The DI cries discriminification and conspiracity!

The Discovery Institute's treatment of ISU's denial of tenure to Guillermo Gonzales is embarrassing. Their cries of discrimination and conspiracy remind me somewhat of this recent comic from Saturday Morning Breakfast Cereal:

13 May 2007

My first foray into Discworld

On highly punitive religion and society:

Borvorius produced a flask from somewhere.

"Will you go to hell if you have a drop of spirit?" he said.

"So it seems," said Simony, absently. Then he noticed the flask. "Oh, you mean alcohol? Probably. But who cares? I won't be able to get near the fire for priests. Thanks."

"Small Gods" is a fun read. There's a metaphor involving sheep and goats that by itself makes the book worthwhile. I'd recommend it to you, but you've probably already read it. (Ben has; he's the one who convinced me to read it.) I'm sadly behind the times when it comes to Terry Pratchett.

10 May 2007

Natural selection and stable equilibrium of alleles

Science Daily reports on an interesting new study of fruit fly population genetics. Fruit fly larvae have two different behavioral phenotypes, depending on which allele they have for a single foraging gene. Rovers will wander about for food, whereas sitters will stay put and nosh on whatever is in front of them. As it turns out, the two alleles are subject to negative frequency-dependent selection; that is, for certain characteristics, in a competing population, the minority has the advantage:

"If you're a rover surrounded by many sitters, then the sitters are going to use up that patch and you're going to do better by moving out into a new patch," says Sokolowski. "So you'll have an advantage because you're not competing with the sitters who stay close to the initial resource. On the other hand, if you're a sitter and you're mostly with rovers, the rovers are going to move out and you'll be left on the patch to feed without competition."

This particular case is interesting because the difference in behavior relies on a single gene, one that also happens to be homologous to genes in other species (including honeybees, mice, and humans).

It's a beautiful example of how natural selection can maintain diversity. It will be interesting to see whether they find a similar effect in the wild, where so many more environmental factors come to play in selection.

PaV at Uncommon Descent has problems understanding how this sort of system could arise via natural selection. The ignorance is hardly worth addressing, but since his post directed me to the study in the first place, it's only fair I address his concerns. He writes:

[H]ow would you explain NS being able to virtually decide that it is “best” to conserve both forms, rather than to single out one of the two forms?

And later, in the comments:

Isn’t it true that over time one trait is more advantageous than another? So, then, how does one define the “fittest”? And if there isn’t just one definition for the “fittest”, then how can evolution—the “survival of the fittest”, supposedly—make a choice? And, if it is then protested that in only certain situations this proves to be the case, then this only further obscures the equivocation that is Darwinism: Who survives? The “fittest”. Who are the “fittest”? Those who survive. Now we can add: Who survives? The “rarest”. Who are the “rarest”? Well, that all depends…..

As I initially stated, NS is virtually making a choice to “balance” these two forms. And we can see the reason why this is “good”, but we have foresight, and NS, as someone already posted, has none—it’s non-teleological, it can’t see purpose. So why does NS balance forms here, but not in the case of rhinoceroses?

Or, to put it another way, if only the “rovers” existed, would anybody be saying, “Oh, there ought to be a “sitter” population to balance them off”? I seriously don’t think so. Then how does NS ‘blindly’ come up with this ‘choice’?

First of all, natural selection doesn't "virtually decide" anything. Natural selection is not conscious, it's just a label for a process that nature undergoes.

As for how this process could result at this natural equilibrium without planning it out in advance, that should be obvious. Let's say we started with only rovers. The rovers are surviving just fine; there's no need to introduce any variation. But then variation happens, and you get a sitter. Given the current population, the sitter has the advantage being the rarer, and proliferates. It's not a choice anyone made. The sitter allele cropped up randomly, and was favored in the given environment.

So why doesn't natural selection get rid of all the rovers in favor of the new sitters? Because natural selection is a process determined by the environment. And as the sitter population changes, that changes the environment. If a sitter and a rover are surrounded by mostly rovers, the sitter will face less competition and be favored. If the same sitter and rover are instead surrounded by mostly sitters, then the rover will be favored, because the environment is different. Note that natural selection doesn't always have this effect; the increase in frequency of a certain allele doesn't always negatively impact that allele's propagation.

This particular case is a beautiful example of stable equilibrium in a biological population, and it's really interesting to think about what kind of other environmental factors (selective predation upon rovers or sitters, for example) could affect that equilibrium in the wild. It's a shame that some people have such a narrow and warped conception of natural selection that they can't appreciate how much we're learning about the workings of nature.

Taxonomy is Bunk

Plenty of people so far have commented on how the recent Nightline debate was inexcusably abominable, and they've said it better than I, so I won't bother to give my own rehashing of the catastrophe.

Instead, I wanted to comment on one point that the atheist side would have done well to have had in its pocket - and which we all would do well to keep in mind when debating the ignorant on the subject of evolution.

Cameron and pal seemed to have a difficult time understanding the concept of an "intermediate form" of an organism - citing the absurdity of freakish chimeratic hybrids (argumentum ad lapidem) as proof that one species couldn't turn into another. Given the source, I can understand and almost excuse his ignorance for reasons I will explain below. But what bothered me most of all was that he was not alone in this shortcoming: the moderator didn't understand the concept either (and I hope beyond hope he was simply playing devil's advocate), and our valiant defender (Brian Sapient) did a rather terrible job of setting things right by not attacking the misconception on its most fundamental level.

The reason the theists (and, to be fair, people in general) have difficulty with this concept is due in part to humanity's excessive faith in its systems of categorization. Any linguist or anthropologist (since Saussure, anyway) will tell you that all human systems of symbolic organization and classification are completely arbitrary. That is: there is no intrinsic link between an object or group of objects and the words or symbols used to describe them. Amazing studies have been done on cross-cultural variation in color words (the classic crayola set of seven colors is far from universal: many cultures combining blue and green, for example, or having only words for black, white, and red), emotions, and so forth. We talk about and perceive the world according to arbitrary systems of classification that work through common consensus.

The same is true for Biology, in which discipline this system is called taxonomy - the organizational structure by which we classify all living beings, the finest resolution being the level of species. Although rigorous science now has a less-arbitrary way of determining speciation (I believe that to be of different species, two animals must not be able to successfully breed, or to produce potent offspring by their union), this logic is a relatively recent innovation. Far more representative of human thinking as a whole, I think, was Cameron's revealing comment that Horses, Mules, Donkeys, and Zebras were all "horses" - meaning that they were of the same species. But by what criteria does he make this assertion? I doubt a horse breeder would agree. I wonder whether he would include Camels as well, being similar in at least some respects? But because the distinctions among these species are not relevant to Cameron, his brain feels perfectly justified in lumping them all together as a category.

The point here is that, for the sake of clarity and brevity, we only have a functioning vocabulary of words large enough to get by - and again, that vocabulary is entirely arbitrary.

So where does this leave us? If we can explain that our classification system is not black and white, then we can begin to tackle the mistaken image that the intermediary species between a crocodile and a duck would be a crocoduck. Sapient hit on it when he said that every organism that has ever lived is an intermediate form: we can only make the distinction between species by looking synchronically at every living being and drawing meaningful and useful distinctions between them as they presently appear. But the creationists seem to believe that this kind of rigid, functional taxonomy should also be visible diachronically as well - when in fact the process of change is so arduously slow and incremental that changes visible to the human eye only happen on an order of thousands of generations.

Take the breeding of dogs as a smaller-scale example. You would say that a Wolf and a Poodle are not the same species (I assume this is so - if merely for the fact that trying to get a wolf and poodle to mate would be ugly). Let's assume, now, that we have a complete genealogy for every wolf and every dog that has ever lived. Now, take the wolf from which all dogs supposedly derive (a tautology in itself) in the one hand, and an actual, living poodle in the other (any one will do). We can now draw an unbroken line of succession (patriarchal or matriarchal - doesn't matter) from primordial wolf to modern poodle. Now, compare the bookends to the organism directly in the middle: chances are you can tell the difference easily, and if you had occasion to you would come up with a name for this critter. But now disregard one half of the line and do the same to the other, examining the center point against its bookends. Now do it again, and again, and again. The more often you split and compare, the less drastic will be the degree of difference among the three examples. If you carried this process on indefinitely, you would ultimately end up with a group comprising only three generations: great-grandparent, grandparent, and parent. Clearly each of these is also different (we humans might not be able to tell, but the canines in question certainly could - another distinction between useful and non-useful information), but we would not call them different species.

At what point, then, do we draw the line? The point is that we can't. Our taxonomy is purely qualitative, and we only have so many levels of qualitative resolution. We can distinguish between individuals of our species (usually), and we can distinguish between individuals of different species. But when we try to resolve an order of magnitude between these two, we do not have the conceptual or linguistic equipment to draw a distinction without beforehand agreeing on a rigid set of objective standards based on homology or chemistry rather than the "squishy bit" logic of our brains.

What, then, would the name be for the missing link between species X and species Y? If we haven't found one yet, we don't have a name for it precisely because we've never yet had cause to refer to it. When we do find it, though, we will probably know it by a Latin version of its discoverer's name - because those are our arbitrary cultural rules for naming unnamed species.

Taxonomy, and language more generally, is merely a convention that allows us to create meaningful symbolic representations for both subdivisions of an unbroken spectrum on the one hand, and agglomerations of discrete instances on the other.

08 May 2007

The republic of heaven

If you could put one book in the hands of every atheist on the planet, what would it be?

I recently finished re-reading one of my absolute favourite books of all time: the "His Dark Materials" trilogy by Philip Pullman. This was actually my first time reading the book since coming out as an atheist, and it's so much clearer now what Pullman was trying to accomplish. For that, I love it all the more.

You may recognize Pullman's name from the back cover of "The God Delusion," where he writes, "Dawkins gives human sympathies and emotions their proper value, which is one of the things that lends his criticisms of religion such force." If anyone is qualified to comment on human sympathies and emotions, it's Pullman. I'm generally not a weepy sort of guy (I am a soulless atheist, after all), but "His Dark Materials" moves me to tears every time.

I won't bother with a thorough synopsis or review... you can find that elsewhere if you're interested. I encourage you to just read it for yourself. It may be marketed as a children's book, but that's a false characterization. All in all, it's a fantastic piece of writing. Perhaps not perfect, but it rings true to me, anyway. This book is a solid indication that humanists have something to contribute to the culture.

Apart from telling a fantastic tale, Pullman accomplishes a brilliant bit of humanist writing. People tend to focus on the war against God with respect to this, and it's true, Pullman set up an interesting conflict between freethought and religious authority. But just as striking is his treatment of death. Pullman creates a rich, elaborate mythology complete with an afterlife and multiple universes, then breaks it down to enhance by contrast the merits of living a full life followed by oblivion in death. Pullman invokes a supernatural incarnation of a naturalistic worldview. It's an appeal to the imagination; not a literal representation of our beliefs, but one more familiar perhaps to those entrenched in a supernatural worldview.

The response to the trilogy from the religious is fairly interesting. Some embrace the first book, then abandon the latter two when our universe comes into play and the war against God starts heating up. The other sort of reaction I find more interesting, since I fell into that camp when I first read the books. They assert that the god and Church of the books are not their God and church. "A god like Pullman describes should be destroyed," I used to think, "it's a good thing my God isn't like that." I was such a good little apologist. I feel that the error of that reasoning is something that people have to discover for themselves. It worked for me, anyway.

A movie version of the first book in the trilogy, "The Golden Compass," is scheduled for release on Dec 7, 2007. I'll withhold judgment until I see it... they're working with fantastic source material and a couple great actors (Nicole Kidman and Daniel Craig), but Hollywood has screwed this sort of thing up in the past, and there were apparently issues with the director. I implore you to read the books beforehand... you owe it to your imagination.

07 May 2007

You can trust him, he's a doctor

Today's episode of The Adventures of Dr McNinja inadvertently offers a great retort to the inductive reasoning argument so often employed by intelligent design proponents:

"If it looks like a zombie... and smells like a zombie... it could still be a crazy homeless man."

You hear that, IDists? Even if something "looks designed," there can still be a natural explanation for its appearance.