Wonderous Stories

Science is sometimes criticized as draining the meaning and beauty out of existence, when in reality it has the opposite problem.

Because it allows one to acquire knowledge otherwise inaccessible to common perception, science gives us access to a whole other landscape, with terrifying and beautiful scenery. It is hard to discuss the history of earth through deep time without falling into epic geopoetry: an oxygen catastrophe so intense the oceans rusted; the sudden diversification of life at the beginning of the Cambrian; the collapse of a habitable Antarctica with the opening of the Drake passage and the start of the circumpolar currents.

I’m going to share a few of the stranger creatures that live in this landscape, or the glimpses that we’ve gotten of them through the haze. They are horrifying, but beautiful, and I think that they make us look at everyday things in new, challenging ways.

“He spoke of lands not far
nor lands they were in his mind.
Of fusion captured high
where reason captured his time.”

Life on land is hard. It’s dry, for one thing; a lot of evolutionary engineering goes into maintaining moisture, and it’s irradiated by ultraviolet light. It’s a really interesting story how complex life spread to the land, but one of the creepier chapters is the evolution of land plants. Did early algae just throw themselves on the beach, slowly evolving in intermediate environments? Some scientists have theorized that something more interesting was happening on those primordial shores.

More than 90% of plants are mycorhizal. That is to say, they have fungal symbiotes in their root systems. These associations are ancient; fossils in the Rhynie cherts show that they were around 400 million years ago. And they’re weird. For one thing, the fungi can siphon off nutrients from the host plant, then feed them to other plants which get their nutrition solely through this exchange.  They also probably play a role in gathering mineral nutrition from the soil for their host plant. Some associations are obligate and very specific; this is why orchids can be difficult to grow.

Indian pipes (monotropa) are shown here poking out of the forest floor. They feed exclusively off of a mycorrhizal network which exchanges nutrients with surrounding trees.

What if land plants, what we think of as single organisms, are actually so closely associated with fungi as to be considered partly compose of fungus? That’s the basic idea of the fungal fusion hypothesis. Working together, the fungus and the alga would have been better able to move onto land than either individually. For example, the fungus could have extracted mineral nutrition to the benefit of the alga, while the photosynthetic alga provided food, or compounds to screen the two of them from UV light. Mycorhizal interactions create oily substances in modern plants which protect them from drying out; such an interaction could have protected an early land plant from desiccation as well.

It may have been that land plants were merely an association of fungi and algae, essentially overgrown, vascularized lichens. “Mycotrophism made terrestrial plant life possible,” writes (Pirozynski and Malloch 1975). But it may have been more intimate. Living together, the fungi may well have become an endosymbiont, living inside of the algal cells. Over time, this relationship could have been restructured, fusing fungal genes into a single consolidated genome. Land plants could well be a remix of preexisting creatures. Its not the first such endosymbiosis; chloroplasts and mitochondria arrived on the scene the same way.

 
Pirozynski KA, & Malloch DW (1975). The origin of land plants: a matter of mycotrophism. Bio Systems, 6 (3), 153-64 PMID: 1120179
 
Jorgensen R (1993). The origin of land plants: a union of alga and fungus advanced by flavonoids? Bio Systems, 31 (2-3), 193-207 PMID: 8155852
 

“…It is no lie I can see deeply into the future.
Imagine everything
You’re close
And were you there to stand
So cautiously at first and then so high….“

What is cancer?

Usually, the answer is that it’s cells which have gone on a solo career. They consume the body’s resource and produce nothing useful to the organism, only more of themselves. They are selfishness personified. But there are anomalies which this simplistic account doesn’t explain. For example, why would selfish cancer cells cooperate with one another in tumor formation?

A cancer cell. Click for source.

“A longstanding criticism of cancer biology and oncology research is that it has so far taken little account of evolutionary biology,” write (Davies & Lineweaver 2011). They’ve taken a new look through an evolutionary lens and come to the conclusion that cancer is an atavism.

Atavisms are regressions to a more primitive evolutionary states. For example, birds are evolutionarily derived from reptiles with teeth, but do not have teeth themselves. Usually. In rare cases, those ancestral reptilian genes are reactivated, and a bird with teeth will result. That’s an atavism. The notion which these researchers propose is that cancer is an evolutionarily primitive state which emerges when cells are damaged by chemicals, radiation, or time.

The evolution of multicellular life, they propose, required a robust toolkit of cellular communication pathways in order for individuals to cooperate first as a loosely knit colonies with basic division of labor. These tumor-like growths, the first steps toward multicellular life, are what the authors call “Metazoa 1.0“. On top of this basic genetic framework for the self-organization of cells there evolved a further regulatory network responsible for the complex organization of Metazoa 2.0 like us. It’s this delicate regulatory network which goes awry in cancer. At that point, the ancient toolkit is activated and the atavistic mode kicks in.

If true, this framework is a hopeful one. Conventionally, the impressive arsenal of skills available to cancer has been explained as evolutionary adaptations, fed by the cells’ high rate of growth and mutation. This would mean that its arsenal is open-ended, able to evolve dynamically in response to therapy. But if it’s an atavism, though, its toolkit is a finite set limited by what was available to metazoa 1.0.

 
Davies, P. C. W.,, & Lineweaver, C. H (2011). Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors Physical Biology, 8 (1) DOI: 10.1088/1478-3975/8/1/015001
 

 

“Sound did silence me
leaving no trace.
I beg to leave,
to hear your wonderous stories.”

It’s one thing to find unsettling fossils in the genomes of plants, or in pathologies. It would be something else entirely if there was something strange and beautiful lurking deep inside ourselves.

The human genome is littered with dead viruses. It starts with a retrovirus, something like HIV maybe. It reproduces by inserting its genes into its host’s DNA, where they get expressed by the cell’s transcription/translation machinery. Most of these cells die with the host, but every now and then a germ line cell gets infected, a sperm or egg. This viral hitchhiker then gets passed on to the organism’s progeny. Over time, they’re usually inactivated by mutations, or actively silenced, but they pile up. 8% of the human genome is composed of dead viruses.

The structure of syncytin, a retrovirus protein which has been recycled in the human genome. Image source from Renard et a 2005; click for link.

It gets weirder. Meet syncytin; it’s a protein which is involved in placental formation in humans. It’s also part of an ancient, repurposed viral gene. Not only was this virus integrated into our genomes, it was rebuilt into an essential part of the mammalian life cycle. It’s happened several times, too: mouse syncytin is derived from a different viral infection than primate syncytin. Experiments on mice show that without this gene, the placenta misforms. Another retrovirus is involved in placenta formation in sheep.

Apparently, mammals across the evolutionary tree have been independently infected by retroviruses, incorporated those viruses into their genomes, and specifically put them to work building placentas. Did these particular viruses just happen to carry genes preadapted for placental formation? Or did mammals evolve and diversify as a result of viral genes flowing into their genomes? What other key biological pathways used to be free-floating viruses?

 
Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, & McCoy JM (2000). Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature, 403 (6771), 785-9 PMID: 10693809
 

 Dupressoir, A.,, Vernochet, C.,, Bawa, O.,, Harper, F.,, Pierron, G.,, Opolon, P.,, & Heidmann, T. (2009). Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene. Proceedings of the National Academy of Sciences of the United States of America, 106 (9) DOI: 10.1073/pnas.0902925106

Intelligent Design apologetics from the Carolina Review

Editor’s note: I am very busy and/or have major writer’s block. I am thus recycling my greater hits. Here we see a review of a review (a metareview if you will) of Ben Stein’s dawkumentary “Expelled”. The original review appeared in the Carolina Review. For those unfamiliar with CR (you blessed souls!), it is UNC-CH’s ” journal of conservative thought and opinion”. It is a perennial lulz-bucket, attributing climate change to solar forcings and/or Milankovich cycles, mangling ocean acidification, and wondering out loud, in public, why a 2008 paper was not included in the IPCC AR4 (published in 2007). They consider community reclamation of a long-standing eyesore to be a ‘hostile act‘ worthy of paramilitary response, citing the presence of ‘posters’. Here’s my response to one of their more abysmal publications. The article it responds to can be found here; my critique originally ran in CackalakConspiracy, back in a time when I still cared about typos.

Walker’s review, like Stein’s movie, is full of florid talk about “freedom”: freedom of speech, religion, science (the last ironic, for the creationist/intelligent design movement has done everything it can to prevent science from being taught in public schools). America has “an amazing record for upholding freedoms.” Stein rolls footage of Soviets and Nazis; Walker calls the dismantling of science and science education “a struggle against a great tyranny.”

But this talk of freedom is merely an emotional appeal. The speech of creationist “scientists” and ID advocates is not being squelched; it is just not taken seriously. For whatever successes creationism may have in philosophy or religion, it has failed as a science. This is why the mainstream rejects creationism for funding, publishing and inclusion in school curricula, not because of atheistic preconceptions. Film critic Roger Ebert drew this analogy: The final question on “Who Wants To Be A Millionaire” asks you for a scientific explanation for the patterning of life on Earth. You phone not just a friend, but the scientists of the world, who overwhelmingly advise you to choose (A) evolutionary biology. Yet you choose (B), intelligent design, and claim censorship upon being denied your millions. This is not an expulsion; it is a flunking.

Walker characterizes evolution and ID as rival “theories” in the “scientific community”. However, in science the word ‘theory’ does not mean a guess or an opinion the way it does in popular speech; it refers to an explanatory construct which is used to interpret data and to make predictions. By this standard, evolution wins hands down and ID falls flat on its face. Because any piece of data can be interpreted as evidence for a Designer (for example, by sufficiently muddying the proposed design goals), ID makes no predictions and no explanations (a “theory” that accommodates anything explains nothing). On the other hand, evolution makes several strong predictions about the world (the existence of a nested hierarchy of physical traits, for example.) ID is not a rival scientific theory; it is an attempt to inject religious propaganda into public education.

We don’t accept non-explanations elsewhere in science. Why should the origins and evolution of life on earth be different? Image from the internets….

Nor is evolution “all a question of faith,” a rival religion. It is purely descriptive, not perscriptive. It has no infalliable holy text; it has no ritual structure; it has no ineffable mystery. Though some may use it to bolster their religious beliefs like “renowned evolutionary biology [sic] and atheist Richard Dawkins,” the theory of evolution is no more a religion than the theory of gravity or relativity. Walker claims that “by definition and practice creationists and ID scientists are quite different”. This is incorrect, both because ID is not science and because it is accurately classified as a subset of creationism. Classical creationism and ID are both are antiscientific programs with thinly veiled religious agendas. They both negate accepted evolutionary biology, often along with other aspects of mainstream science such as molecular biology, genetics, and paleontology. Both reject “naturalism” in the scientific study of life, as though science was not based upon methodological naturalism to begin with. Both tend to blame various social ills on the theory of evolution, and erroneously infer from this that it is incorrect. Perhaps most tellingly, Expelled’s own publicity team advertised the movie as “Evolution vs creationism”. 

arthropod an’ an anthrope. chillin.

TopOc is occupying Durham, for great win and/or lulz! One highlight on the horizon is a leet haxor skillshare – I want to show off the sweet alcohol stove I built! (via this video)

In the meantime, enjoy this pleasing image 🙂

Praying mantis.... or preying mantis??? Clearly the tyrannosaur of the insect world. Photo via Ildar Sagdejev; clix four phool.

Yay!

unknowns, uncertainties, and obsolesence

Antiscience campaigns often share the characteristic that they

A schematic of a climate model - By NOAA via WikiMedia Commons; click for sauce.

complain about the open questions, anomalies, and experimental limitations inscience. Scientists, on the other hand, work

hard to resolve these issues. Creationists complain about uncertainties on the chemical origins of life; biochemists generate and test hypotheses, developing useful technology and techniques in the process. (Bullard et al. 2006) A paper, championed by climate change skuptix, (eg, here) complains about the use of large flux corrections in climate models. (Soon et al. 2001) It was published a decade ago.

What was the state of computation back in 2001? There were no iPhones; cellphones still had hinges and were just starting to become controversial in schools. I didn’t see an iPod until late 2002, and for a long time it was just one person who had one*. We had just started trading AIM screen names instead of phone numbers. There was no Facebook, there was no Twitter, there was no YouTube. Xanga didn’t even appear on my radar until 2003. The Flash Revolution was in its infancy: StrongBad answered his first email in August 2001. It was, simply put, Peanut Butter Jelly Time.

Since then, while skuptix have done little more than whine, climatologists have been hard at work  improving climate models. It’s 2011 and climate models no longer use flux corrections. They still confirm the obvious: blankets are warm. More blankets are warmer.

* ❤ 😛

~~~—~~~

Bullard, T., Freudenthal, J., Avagyan, S., & Kahr, B. (2007). Test of Cairns-Smith’s ‘crystals-as-genes’ hypothesis Faraday Discussions, 136 DOI: 10.1039/b616612c

Soon, W., Baliunas, S., Idso, S., Kondratyev, K., & Posmentier, E. (2001). Modeling climatic effects of anthropogenic carbon dioxide emissions: unknowns and uncertainties Climate Research, 18, 259-275 DOI: 10.3354/cr018259

John Everett, part VII: Help, help, I’m being repressed!

Supposedly posts with images get all the clix. So here is an image. Via PictureIsUnrelated; clix for sauces.

Part VI of John Everett’s testimony is a criticism of a geoengineering approach to ocean acidification. I agree with his conclusion (that adding alkaline calcium carbonate to the oceans is not a useful approach to ocean acidification) but nevertheless find this section to be problematic. I’ll return to it once I’ve finished with the rest of his testimony.

Part VII is a collection of research suggestions “that would go a long way toward establishing the likely effects of an increased CO2 world.” On the surface, it’s hard to take issue with his suggestions, but in the context of the rest of his testimony, they ring rather hollow.

For example, his first research suggestion is the development of

“a CO2/temperature timeline based on extant research on past climates, at least back to about 600 million years before the present. This effort would provide a critical review of candidate papers and unpublished work that goes well beyond a typical peer-reviewed journal publication, or prior summary reports of the IPCC.”

I think that it would be great to have a comprehensive review of the state of paleoclimatology and paleogeochemistry. But Dr. Everett ignores what we already know about those topics– so what good would such an effort be?

Suggestion #2:

John Everett, part IV.0: Things and Things’ Changing, dva

A part of my John Everett series – read more: 0/I – II.0 – II.5 – II.75 –  III.0 – III.3 – IV.0 – IV.4 – IV.8 – V – VII – VIII – Full Report 

People who minimize or deny the threat of climate change (or ocean acidification, as in part IV of Dr. Everett’s testimony) will often demand that the change be “unprecedented” – that nothing like it has ever happened before in Earth history. (eg, here) The reasoning seems to be that if there have been ecological events like anthropogenic climate change in the past, then current events must not be alarming, since life on earth has each time survived and recovered:

“We know that the Earth has seen these conditions before, and that all the same types of animals and plants of the oceans successfully made it through far more extreme conditions. ” – Everertt (part V)

 

This has always seemed to me like it’s setting the bar a bit low: Do we only become alarmed when faced with the possibility of sterilizing the planet? And considering the amount of violence which earth life has withstood over the ages, it doesn’t seem a very strong statement that human impact is unlikely to wipe it out.

Why do people catch swine flu, but not tobacco mosaic virus?

I’m going to take a break from our regularly scheduled debunking of John Everett’s Senate testimony, to pose a question for creationists and cDesign Proponentsists: Why do people catch swine flu but not tobacco mosaic virus?

I’m not asking why people get sick. I’m not interested in a rehashing of the tired old arguments about the coexistence of god and human suffering. I want an explanation of the fact that, despite the myriad pathogens which infect other branches of the tree of life, it’s only pathogens from other animals (usually other vertebrates) which make humans sick. Poxes, tuberculosis, and anthrax infect cattle. HIV is a mutant variant of Simian Immunodeficiency Virus, which infects other primates. Why don’t we fall ill from Partitivirus, pathogen of fungi? Or T4 phage, parasite of bacteria?