A bicycle without a wheel.

I won’t get into this in detail, in part because I wrote about it in my paper The evolution of complex organs in the special issue of Evolution: Education and Outreach about eyes.

It seems the most recent analogy drawn by anti-evolutionists to support the idea of irreducible complexity is a bicycle — yeah, a unicycle works but a bicycle missing a wheel doesn’t, therefore it’s irreducibly complex. You can find out more at The Loom, where Carl shows people riding single-wheel bikes.

I am only weighing in because the discussion seems to be overlooking an important point about exaptation/co-option: the function need not be the same in both instances. So, although riding a bike with one wheel the way you would ride a two-wheeled bike a la wheelie is fine to show that it wouldn’t be totally non-functional, an even more relevant counter-example would involve a bicycle with one wheel that worked well for some other role.

Voila.

This is just the first single-wheeled, functional-for-something-different, co-option example I found. This actually involves one shift and one addition of function. Loss of wheel to make it useful for exercise indoors, then addition of other parts to run a laundry machine. Of course, modern stationary bicycles used for exercise are more specialized, but you can still find gear to convert a normal bicycle into a stationary one, sometimes by taking off the front wheel.

So, basically, bicycles with one wheel provide a very nice illustration of how co-option with shift in function can and does work.

The peppered moth.

The peppered moth, Biston betularia, has been used as a classic example of natural selection in action. This moth (like many others) includes both light and dark forms that change in frequency under conditions of higher or lower pollution. Anti-evolutionists have challenged this, and unfortunately they gained ammunition in this regard from a book review by Jerry Coyne.


As part of their Top 10 evolution articles, New Scientist provides a story entitled Reclaiming the peppered moth for science.

Bad news, the New Scientist story is subscription only.

Good news, Evolution: Education and Outreach will include a paper about the peppered moth by leading expert Michael Majerus in the next issue, and it’s a) already available in pre-print, and b) free.

While you’re visiting the journal, check out the last issue which is a special volume all about eyes.

Look at it this way…

Todd Oakley reports on a dust-up over at Panda’s Thumb in which a commentator is not convinced that eyes evolved, in large part because the specific details of the early origin of the phototransduction pathway have yet to be worked out. Not surprisingly, responses have pointed out that the gaps are getting smaller and smaller and that a lot is known about how phototransduction may have arisen from precursors in other systems through duplication, co-option, and the various processes discussed in this paper.

I think this debate misses a much larger and more significant point. Darwin suggested that eyes evolved in the Origin, published 150 years ago. This was before even the basics of heredity were generally understood. It was before the discovery of DNA. Before the elucidation of the structure of DNA. Before the rise of molecular biology. Before the advent of phylogenetics. Before evolutionary developmental biology. Before genome sequencing.

And yet, through the emergence of all these major new sources of data, not a single reliable observation in any of these fields has contradicted the general hypothesis that eyes are the product of evolutionary mechanisms. Quite the opposite, as the picture of how this probably occurred in different lineages is become increasingly clear thanks in large part to this rapidly expanding body of knowledge. Gaps remain, of course, which is why it’s an intriguing field of inquiry. But the notion of waiting until every last detail is known before accepting the basic historical reality badly misinterprets the nature of science and scientific evidence.

Calling fellow bloggers!

Calling fellow bio bloggers — help get the word out for the special issue of Evolution: Education and Outreach all about eye evolution. The content is free to access online and the authors include many of the world’s top eye evolution researchers. A handy table of contents with links is provided below for easy copy and paste maneuvers.

Evolution: Education and Outreach
Volume 1 Issue 4

Editorial

351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)

352-354. Introduction by T. Ryan Gregory (PDF)

355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)

Original science / evolution reviews

358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)

390-402. Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)

403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)

415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)

427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)

439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)

448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)

463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)

476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)

487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)

493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)

Curriculum articles

498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)

505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)

509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)

Book reviews

548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)

All about eye evolution.

The most recent issue of Evolution: Education and Outreach is now available free online. This is a special issue devoted to the evolution of eyes. Enjoy.

Evolution: Education and Outreach
Volume 1 Issue 4
The evolution of eyes
Edited by T. Ryan Gregory

Editorial

351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)

352-354. Introduction by T. Ryan Gregory (PDF)

355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)

Original science / evolution reviews

358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)

390-402. Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)

403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)

415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)

427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)

439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)

448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)

463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)

476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)

487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)

493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)

Curriculum articles

498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)

505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)

509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)

Book reviews

548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)

Science and Spore.

Tomorrow’s issue of Science features a new installment of “The Gonzo Scientist” by writer John Bohannon. This edition is all about Spore, the game that is based on “evolution” from primordial ooze to interstellar society [Flunking Spore]. I had heard about the game on blogs, but I had not really planned to play it until John asked a few of us to give our perspective on the science behind it.

I can’t say I didn’t have fun with this, although it is a shame that the game bears little relation to actual evolution (see here for apparent claims otherwise).

Here’s the creature Niles Eldredge and I came up with, dubbed Punky Quillibra:

You can read our review at the wiki that John made.

________

Updates:

Small genome sizes in pterosaurs, too.

My colleagues Chris Organ and Andrew Shedlock, who provided evidence that theropod dinosaurs already had (somewhat) reduced genome sizes prior to the evolution of birds (Organ et al. 2007) have followed up their study by estimating the genome sizes of several species of pterosaurs.

Pterosaurs were the first vertebrates to evolve powered flight, having taken to the air 70 million years before birds and 150 million years prior to bats. Interestingly (though perhaps not surprisingly at this point), they seem to have possessed reduced genome sizes, and these downsizings of DNA amount began before flight arose.

On the other hand, it is clear that the estimates for non-avian dinosaurs are not as small as modern birds and that the estimated ancestral genome size for birds was larger than the genome seen in various groups. Patterns can be observed in terms of flight ability across living avian species. Notably, my student Chandler Andrews showed that genome size is correlated with wing loading (and indication of flight capacity) within perching birds, and we are currently writing up major projects on bird groups with different flight ability as well as a study of hummingbirds; Jill Smith, another student, also has a large bat study to write up.

The story thus seems to be that genome reduction occurred in the dinosaur lineage of which birds are descendants before flight (so did feathers, bipedalism, and other characteristics), but were later further adjusted when flight arose (as were feathers, etc.). The same reductions before flight probably occurred in the pterosaur and bat ancestors. So it’s not flight per se that matters, but a feature linked with flight.

As Organ and Shedlock put it, “we hypothesize that a metabolic intensity required for flight, not flight itself, explains the correlated evolution between genome size and flight in amniotes.” — this seems very plausible given the growing amount of data on this topic.

References

Andrews, C.B., S.A. Mackenzie, and T.R. Gregory. Genome size and wing parameters in passerine birds. Proceedings of the Royal Society of London B, in press.

Organ, C.L., A.M. Shedlock, A. Meade, M. Pagel, and S.V. Edwards. 2007. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446: 180-184.

Organ, C.L. and A.M. Shedlock. 2008. Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates. Biology Letters, in press.

Zimmer, C. 2007. Jurassic genome. Science 315: 1358-1359.

No such thing as natural selection?

In reading an interesting article in the New York Times (in part because it quotes my colleague Andrew MacDougall), I came upon this statement that caused a bit of a cough.

“There’s no such thing as natural selection,” Ziska confides. He is not, he hastens to explain, a creationist. He is merely pointing out that the original 19th-century view of evolution, the one presented by Charles Darwin and Alfred Wallace, is obsolete. Their model presented evolution as a process taking place in a nature independent of human interference. That is almost never the situation today — even at sea, where less than 4 percent of the oceans remain unaffected by human activity, according to a recent article in the journal Science. This interference with nature has set the stage for the success of a growing category of weeds, one exemplified by cheatgrass: invasive plant species.

Yes, humans have some impact on a great portion of the globe, but this is nonsense for at least three reasons. One, just because humans are involved does not make something "artificial selection" and therefore disqualify it as natural selection, even within the formulation of Darwin and Wallace which drew a distinction . Artificial selection is the intentional breeding of organisms on the basis of some characteristic (e.g., sleek body shape in dogs or high yield in crops). If we dump waste in the ocean and this creates new selective pressures on marine animals, this hardly counts as artificial selection. From the point of view of the organisms involved, it is simply a change in the environment, and natural selection will then operate as usual. (As a matter of fact, I don't consider "artificial" and "natural" selection to be fundamentally distinct processes anyhow — feel free to discuss in the comment section). Two, we may influence environments generally, but there are, as we speak, gazillions of organisms out there struggling for survival and hunting, parasitising, avoiding, mating with, and otherwise interacting with one another independent of human action. Three, natural selection is still occurring both in human populations and indeed within human bodies (among pathogenic agents, for example).

(Hat tip: John Hawks blog)

 

Abiogenesis vs. evolution.

At The Panda's Thumb, Nick Matzke has a post about abiogenesis (the origin of life from non-life) and evolution. He, PZ, and others argue that abiogenesis is part of evolutionary biology and that it is a cop-out to deflect challenges about it from anti-evolutionists. Allow me a brief summary of my interpretation.

—-

Question: Do we need evolutionary biology to understand the origin of life?

Answer: Very probably. Early replicators, once they arise, would undergo evolution. Mutation, natural selection, etc., would have been important before cellular life as we understand it appeared. However, there are components to the issue that predate the occurrence of natural selection, which are more properly understood in terms of organic chemistry than biology. The line is not sharp, though, so keeping evolution out of abiogenesis research is unwise.

Evidence: Whether "cells" (membranes with stuff inside) or replicator molecules (e.g., RNA) appeared first, if there was heritable variation and reproduction and survival that differed among them, then selection would have happened.

—-

Question: Do we need to understand how life arose to understand the subsequent evolution of cellular life?

Answer: No.

Evidence: We have been studying evolution seriously for 150 years and understand quite a bit about how it happens, yet we don't know how life arose.

So, Nick and others are correct that we should not say that abiogenesis is independent of evolution. However, if they are implying that abiogenesis is part of — more importantly, a crucial part of — evolutionary theory, then I do not agree. The influence is one-way, and this is the opposite of the way anti-evolutionists perceive it. They argue that if we do not know how life started, then evolution is false. In actuality, knowing how life started has nothing to do with studying how life has evolved since the first complex cells appeared. However, understanding how complex cellular life evolves probably tells us something about how life arose because the same processes are relevant whenever there are variable replicating entities.

In my opinion, it remains a valid and useful argument to point out that uncertainty regarding the origin of life is irrelevant to the factual standing of evolution over the past 3.8 billion years.