Wednesday, December 23, 2009

Ostra-blog 9. Postasterope barnesi

It's unfortunately been too long since I've posted an 'ostra-blog', a post about my main study group, the Ostracoda. If you haven't seen these, I encourage you to read some of them. Most contain little anecdotes, personal vignettes about interesting experiences I've had with ostracods.

Try this link, if you interested.

This installment is a quick post inspired by a colleague who is trying to collect bioluminescent Vargula (subject of previous posts). He did some plankton tows out by Catalina Island, and came up with some ostracods, but these are a different family. See our exchange below, and a picture sent by his student:

The query:
Hi Todd,

I apologize for the out of focus, low magnification photo attached -- but is it likely that these ostracods are Vargula tsuji? These are not from a trap, but instead from night surface plankton tows from the dock at Wrigley. These are quite large for ostracods (up to 1.5 mm or so in length, I'd guess), fairly bright orange, and very abundant in the plankton soon after dusk.

Thanks for any simple confirmation/rejection of our tentative id. I appreciate it. Sorry again for the low quality image; I'm not at Catalina or I'd take a better one. This was sent to me by a student.

The Picture:

The reply:

No, those are not Vargula, which is in the family cypridindiae. These that you found are in the family cylindroleberididae. I think the common sp out at Catalina is Postasterope barnesi, and this looks like it could be that species. Both are myodocopids, which are larger than the somewhat more common podocopids...

I've found males of this family to be attracted to lights at night. Most myodocopids mate in the water column after sunset, and the males of some sp are attracted to lights. Probably just about all the individuals they found are males, I'd guess. The one pictured looks like a male, based on the tapered carapace (hard for someone to see who hasn't looked at a million ostracods). But an easy way to tell a male in these is that the males have a REALLY long sensory bristle. It's a "hair" (2 actually, one on each side) that emerges from the front of the carapace along with the swimming appendages. But this sensory "hair" is really long, longer than the body in many cases. I actually can't tell from this picture if there are the long sensory bristles because of the focus, but I'll bet they are there... I do see a white line across the carapace in the right spot, but I can't tell if that is part of the swimming appendage, or the sensory bristle....

Friday, November 27, 2009

Why is the "black box" so complicated??

I received an e-mail question about a recent article I wrote with a graduate student. The question shows a common misunderstanding of evolution, and I thought it would be interesting, or at least potentially useful to more that one person, to post my response here.
Hi Dr. Oakley,

I am writing a research paper and came across your paper entitled, Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution. I was hoping you could give me your perspective on a question that is part of my research interest.

Since a simpler mechanisms for phototransduction would theoretically work, why would evolution favor a more complicated phototransduction cascade with intermediates such as transducin and PDE? I would greatly appreciate any insight you could provide me.

The implication in the e-mail is that evolution is a force that produces sleek perfection. Expensive solutions to problems should not arise by evolution (or at least they should not be maintained), especially if the complexity is unnecessary. This is a modernist view of biology, a view that can be found in 20th Century biological research, and a view that is also common today among students, and the general public outside the field of evolutionary biology. It is a view that results from an often unstated assumption natural selection is a supremely powerful force that leads to perfection.

From this Modernist, Bauhaus perspective, it is indeed perplexing to learn that opsin initiates a complex, baroque, Rube Golddberg-like cascade to turn light energy into a nervous impulse. This cascade includes reactions from opsin->transducin->PDE->CNG; each protein signaling in one way or another to another protein down the line - and this description is even VERY simplified compared to the actual complexity!

So the question is, why would evolution "favor this complicated phototransduction cascade", when all that seems to matter is that opsin signal directly to the CNG ion channel protein to cause the nervous impulse.

The most direct answer is that evolution is not an Intelligent Designer, rather it is a bricoleur, a tinkerer. Evolution acts upon what is available, and things that are useful are kept. In the case of the phototransduction cascade, evolution co-opted existing components: an existing GPCR cascade gained light sensitivity. We know this because the components of phototransduction pre-date opsin (e.g. here). Phototransduction was not invented from scratch, in the most efficient way possible. Instead, it was cobbled together using available parts.

This can be conceived as an example of a phylogenetic or historical constraint. In other words, history matters. All living things and all components of living things share a common history. Because of this, and because of the interdependence of components of living things, it is usually not easy to completely re-invent something. The number of shared genes in all animals (for example) clearly illustrates that history matters. Components are used and re-used, not invented anew.

This answers the proximate question, of why phototransduction is so complex. But doesn't address the question of why all GPCR cascades are so complex. I don't know the answer to this, but perhaps the complexity allows for flexibility. In fact, GPCR cascades are supremely flexible, and underlie signaling from outside to inside cells for many processes in animals, including vision and other senses, hormone signaling, metabolism, development, reproduction, etc, etc.

Interestingly, this question showed me yet another new perspective on the flawed argument for Intelligent Design. ID proponents suggest that when we see something outlandishly complex, then it must have been designed by an intelligent agent. However, as this question points out, extravagant complexity is not a sign of intelligence. Why use 50 components when 2 will suffice? Elegant simplicity is far more intelligent than excessive complexity. Again, evolutionary biology provides a logical and plausible explanation for the biological processes that we are coming to understand.

Saturday, November 21, 2009

Dispatch from the front lines of Ray Comfort's Krazee crusade

The "special" 150th anniversary edition of Origin of Species - the one with 59 pages of anti-scientific banana mush as an introduction - was handed out at UC-Santa Barbara on Thursday. Word on the street was that a number of campuses were hit on Wednesday, and by ~10:30am on Thursday, we at UCSB were starting to feel somehow let down, like we wouldn't get our chance to see the circus, and maybe just a little like a wallflower at the junior high dance.

Then the news hit. Graduate student Sabrina poked her head into my office around 11 and asked if I was ready. I was. Mostly I wanted my souvenir. Graduate student Chris Evelyn was already on the scene. Chris is an evolutionist with a strong competitive streak, and he was not about to let Ray Comfort's propaganda be distributed freely. Chris had found two people handing out the books near our library, and he contacted Sabrina, who let me know. I rattled off an e-mail to our Biology email list, and headed off to battle.

Aside from people paying to throw pies in the face of frat boys (fund raiser), demonstrations to save ESS (UCSB's exercise department is getting cut), flyers from "Jews for Jesus" (sounded interesting, but I didn't get one), and some other activity and demonstrations around the library (Free Palestine!), I saw no copies of the Origin, and no sign of Chris or Sabrina.

"We're over at the UCEN", Sabrina sent me a text. I walked 5 minutes over to the University Center. It was another fine Santa Barbara day, crystal clear blue skies, 70 degrees, and crisp shadows from the intense sunlight. The Comfort-ites, two of them, had run out of books. They had each carried a backpack-full to near the library, where Chris had found them. Now they were making plans to get more books. They had to park in Isla Vista, a 15-20 minute walk from the library. Chris followed them to their van - he didn't want a single book to be handed out without an NCSE flyer. Sabrina and I went back by the library to wait for the return.

By that time, my email had hit the biology department. About 10-15 other biologist found us and together we waited for the return of the banana editions. Independent of us, an Undergraduate Skeptics group called SURE was on the scene. They were prepared with flyers from Don't Diss Darwin and had written a counter argument to Comfort's banana-mush preface. Chris, still following the distributors, kept us updated by text messages. "They have hundreds of books in a van!"

Finally, they arrived, and I got my copy. I talked a bit to one of the distributors. "Jason" had a full red beard and wore a baseball cap. I learned he lives in Ojai, and he's 35 and unemployed. He had a calm demeanor, and he didn't know what he was getting into. He had recently joined a bible study group, and his friend "Mike" asked him to help pass out some books. He did not expect any sort of confrontation at all, and went out of his way to make clear that he didn't really know about what was in the book. He'd hand out a book and say things like "make sure you get a flyer and see the other side of the argument".

The other distributor, "Mike" was a older than Jason, maybe 60. He was a bit more evasive, and for a while seemed to want to get away from the skeptics and the biologists. I didn't get a chance to talk to Mike myself, but I learned that he was a veteran of military service. After a while, he too was telling people to get our flyers, to be fair. Poor Mike - most everyone I saw was a biologist just trying to get one of these laughable souvenirs. Poor Jason - he was just helping out a new friend, handing out some books.

We invited Jason and Mike to come to our screening of "Judgment Day: Intelligent Design on Trial". They declined. Their goal was to hand out all the books. Chris made sure flyers were present, and the Skeptics were troopers, too, sticking with the distributors through the evening; although several came to the screening.

After the screening, I got another text from Sabrina "Debating going on near the library". I already had plans to take my kids to the UCSB soccer game, first round of the NCAA tourney (we won, 1-0). Chris and Sabrina, and probably Nathan, were fighting the good fight though, and I think almost no books were handed out without a flyer or NCSE banana-bookmark, or both, as accompaniments.

A little activism was fun, and I was proud that evolutionism and rationalism had a much stronger presence than anti-science banana-mush. Although this sort of thing can be energizing, in the end, I mostly feel bad for Mike and Jason. This feeling was echoed by an email I got just now from Chris.

Chris thinks that, in the end, all this was just a cheap scam perpetrated by Ray Comfort. We found out that Mike put up money to buy these books. Comfort wrote a bunch of crap, tagged it to the beginning of Darwin's classic, published cheap copies, and then used his propaganda machine to get gullible buyers to spend their money.

I shouldn't be surprised. This to me is the lowest point of religion: the fact that (somehow) charismatic, yet underhanded people seem always to be able to lighten people's wallets in the name of religion. It's happened for centuries. Still, seeing it in action, and meeting the victims, makes me feel completely empty. I'm reminded of a time when I visited New York City and street con artists pulled cash right out of the hand of my friend. The rest of the trip was not the same. It seems to me that Ray Comfort is no better than one of these street con-artists. Perhaps it would've been more fun to be at UCLA, where Ray himself was, instead of witnessing his victims gradually realize they were caught in a scam.

Wednesday, November 4, 2009

10 Great advances in evolution-Nova Beta has a new format for their web-based information on Evolution. There is a lot of great information there. Here is an article by Carl Zimmer entitled "Ten Great Advances in Evolution", which draws upon similar material to his new textbook.

Thursday, October 1, 2009

Conference and Blog contest

Dear Colleagues,

Apologies if you have already received notice of this opportunity.

It is my great pleasure to announce that the National Evolutionary Synthesis Center (NESCENT) in Durham will be funding 2 travel awards for Science Online 2010 in Research Triangle Park, NC. This annual (un)conference ( to "explore science on the web" takes place January 15-17 and is free to attend. Two awards for $750 each are meant to offset the costs of participating in the conference and are open to anyone from any country. To qualify, you need to write a blog post about evolutionary research that was published in 2009!

"To apply for an award, writers should submit a blog post that highlights current or emerging evolutionary research. In order to be valid, posts must deal with scientific results appearing in 2009. Posts should be 750‐1500 words, and must mention the NESCent contest."

For more details:

Please spread the word on your own blogs, tweets, webpages, news blurbs ,etc. It is great for such a prestigious organization to support online science communication in this way!

Monday, September 21, 2009

Refuting Comfort's Eye evolution claims

As I mentioned in my last post, Comfort and Cameron will be distributing co-opted copies of Darwin's ...Origin... I've looked at the introduction Comfort wrote. Of course it contains the same old tired anti-evolutionist arguments that have not changed in hundreds of years, despite the fact the field of evolutionary biology has matured into a rich, detailed, predictive science that forms the core of modern understanding of all biology.

[If you don't read the entire rather long post, please read the last 2 paragraphs]

A prime reason evolutionists don't often debate these simplistic claims is that it's been done before, for hundreds of years, and anti-evolutionists keep re-using the same tired arguments, ignoring advances in science. Scientists really like to argue, but not about things that have been resolved for hundreds of years, over and over again, in increasing detail.

Comfort's simplistic, tired arguments are no exception. I'll focus on his section on eye evolution. The arguments boil down to:

  1. It looks soooo complex. It had to be designed.
  2. Comfort can't imagine how "random" processes could drive evolution.
  3. There are a bunch of parts working together, and each couldn't originate without the other.
Of course there is nothing new here. For #1, Hume famously critiqued the design argument in the 1700's. It part, this is a false analogy: Watch is to human designer as Complex biological feature is to God.

#2 Natural selection is not a random process, e.g. Blind Watchmaker.
#3 There is no evidence that "separate" parts of the visual system cannot work separately, and in fact it is known that parts DO function separately. As one of many possible examples, the cnidarian polyp Hydra magnipappillata uses photosensitivity without eyes or brain (ref).

Below, I will paste Comfort's text, and a few comments on his text.
Or, consider the human eye. Man has never developed a
camera lens anywhere near the inconceivable intricacy of the
human eye. The human eye is an amazing interrelated system of
about forty individual subsystems, including the retina, pupil,
iris, cornea, lens, and optic nerve. It has more to it than just
the 137 million light-sensitive special cells that send messages
to the unbelievably complex brain. About 130 million of these
cells look like tiny rods, and they handle the black and white
vision. The other seven million are cone shaped and allow us
to see in color. The retina cells receive light impressions, which
are then translated into electric pulses and sent directly to the
brain through the optic nerve.

A special section of the brain called the visual cortex
interprets the pulses as color, contrast, depth, etc., which then
allows us to see “pictures” of our world. Incredibly, the eye,
optic nerve, and visual cortex are totally separate and distinct
subsystems. Yet together they capture, deliver, and interpret
up to 1.5 million pulse messages per millisecond! Think
about that for a moment. It would take dozens of computers
programmed perfectly and operating together flawlessly to
even get close to performing this task.
Yes, eyes are pretty complicated - that is one reason they are fun to study and understand from a scientific perspective.

The eye is an example of what is referred to as “irreducible

There is no evidence that eyes or any other biological structure are 'irreducibly complex'. Here is a paper describing processes that have led to the evolutionary origins of "phototransduction", the cascade of protein signaling events that results in animals' ability to detect light.

It would be absolutely impossible for random

It would indeed be difficult for purely random processes to evolve complex systems, but natural selection is not a random process.

...operating through gradual mechanisms of genetic
mutation and natural selection, to be able to create forty
separate subsystems when they provide no advantage to the
whole until the very last state of development.
This is factually wrong. For example, one of these eye "subsystems" provides an advantage to Hydra even though the animal does not possess other of the "subsystems". As mentioned above, Hydra utilizes phototransduction without lens, retina, brain, or even pigment cells. One response to light is for the animal to scrunch into a ball, hypothesized to purge its one-way gut at first morning light. [If there is a designer, at least She had a sense of humor when She made one-way guts - what a great design that is!]. So as evidenced by mouse trap tie clips in the Dover trial; claims of irreducible complexity usually represent a lack of imagination about what sub-systems can do.

Ask yourself
how the lens, the retina, the optic nerve, and all the other parts
in vertebrates that play a role in seeing not only appeared
from nothing, but evolved into interrelated and working parts.

This sounds like an argument against divine design, which claims that eye parts came from dust. In fact evolutionary biology teaches us that proteins of the lens came from other proteins.

Evolutionist Robert Jastrow acknowledges that highly trained
scientists could not have improved upon “blind chance”:

To paraphrase Orgel - evolution is cleverer than you are; that doesn't mean that goddidit.
Again, natural selection is not "blind chance".

The eye appears to have been designed; no designer
of telescopes could have done better. How could
this marvelous instrument have evolved by chance,
through a succession of random events? Many people
in Darwin’s day agreed with theologian William
Pauley, who commented, “There cannot be a design
without a designer.”

William Paley, not Pauley. Yes it is truely amazing that evolution produced eyes, and other complex things like livers or brains. Nevertheless, it is a well established scientific fact that evolution did produce these traits.

And this marvelous design occurs not just in humans, but
in all the different creatures: horses, ants, dogs, whales, lions,
flies, ducks, fish, etc. Think about what the theory of evolution
claims: the eyes, in working pairs, of all these creatures slowly
developed over millions of years. Each of them was blind until
all the parts miraculously came together and interrelated with
the others, because all parts are needed for the eye to function.
Then each creature had its two eyes work in harmony with
the brain to interpret those images. Fortunately, each of these
creatures simultaneously evolved whatever matching parts
each would need: sockets, skin, eyelids, eyelashes, tear ducts,
muscles to blink, etc.

Again, Comfort is arguing more against his own claims that against evolution. Eyes appearing separately in every tetrapod is VERY unlikely, but this is what the creationist fable of eye origins would entail. In fact, evolutionary biology teaches us that all living things share a common ancestry, and that shared features usually evolved once, prior to the common ancestor of creatures sharing a trait. This is backed up by mounds of genetic evidence showing shared use of many genes in most animal eyes, including opsin, Pax-6, and many more.

You’ve probably been led to believe that the first simple
creatures had rudimentary eyes, and that as creatures slowly
evolved their eyes evolved along with them. However, that’s
not what scientists have found. Not only is there no evidence

Robert Jastrow, “Evolution: Selection for perfection,” Science
Digest, December 1981, p. 86.
It is simply false that scientists have found the first simple creatures to have had complex eyes. "The first simple creatures" Comfort seems to be referring to are trilobites. There are highly complex arthropods, far far far removed from the first simple creatures. Trilobites are not even the first animals, not even the first arthropods.

of this occurring, but some of the most complex eyes have
been discovered in the “simplest” creatures.
Riccardo Levi-Setti, professor emeritus of Physics at the
University of Chicago, writes of the trilobite’s eye:

"This optical doublet is a device so typically
associated with human invention that its discovery in
trilobites comes as something of a shock. The realization
that trilobites developed and used such devices half a
billion years ago makes the shock even greater. And a
final discovery—that the refracting interface between
the two lens elements in a trilobite’s eye was designed
in accordance with optical constructions worked out
by Descartes and Huygens in the mid-seventeenth
century—borders on sheer science fiction...The design
of the trilobite’s eye lens could well qualify for a patent
disclosure. "

--Riccardo Levi-Setti, Trilobites (Chicago: University of Chicago
Press, 1993), pp. 57–58.

How could the amazing, seeing eye have come about
purely by blind chance? Based on the evidence, wouldn’t a
reasonable person conclude that the eye is astonishingly
complex and could not have evolved gradually, and that each
creature’s eyes are uniquely designed?

Even Charles Darwin admitted the incredible complexity
of the eye in The Origin of Species:

To suppose that the eye, with all its inimitable
contrivances for adjusting the focus to different
distances, for admitting different amounts of light,
and for the correction of spherical and chromatic

aberration, could have formed by natural selection,
seems, I freely confess, absurd in the highest degree."

Even more incredible, though, is that Darwin went on
to say that he believed the eye could nonetheless have been
formed by natural selection. He was right on one point. If a
Designer is left out of the equation, such a thought is absurd
in the highest degree.

Yes, it is still amazing - and still true - that eyes evolved. No natural selection still cannot be equated with blind chance.

At least he included the end of this famous quote, where Darwin writes that anyone with any bit of logical reasoning ability can see that evolution can produce even complicated things.

I didn't spend a lot of time on this because these arguments of Comfort are not worth a lot of my time. They are tired, recycled, un-creative jabs at evolution that have been known to be false for hundreds of years.

In the end, I'll use Comfort's own words to describe what he is doing to evolution. He was writing about Buddhism, but his words apply nicely to his ignorance of evolutionary biology:

Amazingly, the religion of Buddhism [substitute 'Ray Comfort' for 'Buddhism'] denies that God [substitute 'Evolution' for 'God'] even exists. It teaches that life and death are sort of an illusion. That’s like standing at the door of the plane and saying, “I’m not really here, and there’s no such thing as the law of gravity, and no ground that I’m going to hit.” That may temporarily help you deal with your fears, but it doesn’t square with reality.
A few word changes lead to:

Amazingly, the religion of Cameron and Comfort denies that evolution even exists. It teaches that two hundred years of hard work by countless scientists across the globe to elucidate the details of evolution are sort of an illusion. That’s like standing at the door of the plane and saying, “I’m not really here, and there’s no such thing as the law of gravity, and no ground that I’m going to hit.” That may temporarily help Comfort and Cameron deal with their fears, but it doesn’t square with reality.

Saturday, September 19, 2009

Cameron Comfort Co-Opt Darwin's Origin

I've had my head in the sand writing revisions of papers before the quarter starts, so I'm sure there is information all over the net about this that I am not integrating here, sorry. But apparently, Kirk Cameron and Ray Comfort have co-opted Darwin's ..Origin of Species... and inserted creationist propaganda into in introduction that is mixed with some facts (i.e. biographical facts on Darwin). It also includes propaganda linking Nazi-ism and evolution, etc.

They plan to had out published copies at the 'Top 50' research institutions in the US. Cameron in a video mentions he will come to a local university personally (here at UCSB? UCLA? I'm not sure what "local" is to Mr. Cameron).

Apparently, Richard Dawkins has been involved in getting the word out to evolutionists to expect this, kudos to him and his crew for doing that.

I personally disagree with the plan of action I'm told Dawkins' camp is promoting (I haven't confirmed that he is actually promoting this). That plan entails obtaining as many copies of the book as possible and removing the Comfort introductory propaganda.

In my opinion, this is not a good strategy. It seems that this could look desperate, as if scientists actually have something to worry about (when it comes to the facts of evolution, we do not have to worry), and it looks like book burning or censoring.

Instead, I think a concise pamphlet refuting the bogus claims of the introdution would be outstanding. It could have references and web links, and could also expose what I see as the breathtaking inanity of Comfort and Cameron's crusade against critical, rational thinking.

It would be great if someone like the NCSE were involved. Time is short and an organized response would nice.

Below, I attach an email that was sent around here at UCSB, which includes web links to some of this stuff:


We all loved Kirk Cameron on Growing Pains:

Years later we were amused and perhaps a bit alarmed at his
'Origin of the Banana' video:
(That's Ray Comfort there with him)

But in November of 2009 he and Ray Comfort are taking it to the
next level:

The Important thing for us: *THIS GIVE AWAY WILL HAPPEN AT
UCSB! On November 19th!
Richard Dawkins has proposed a strategy: Collect as many of these
books as possible, remove the 50 page intro and donate the copies
to schools, libraries, or the whoever

We can stick with this strategy or come up with something else but
we should do *SOMETHING*

Basically we need to get organized if they are coming here. Ready
with information &/or to get these books. Ready with pamphlets
answering his questions or just trying to keep them off campus?

*Who would be into meeting within the next couple of weeks to
start to get ourselves organized?*

If you are not ready for action now here are some highlights from
Comfort's 50 page Intro:

1) So, even though we share 96 percent of our genetic make-up with
chimps, that does not mean we are 96 percent chimp. Be careful you
don’t fall for the illogic of this “evolutionary proof,”
2) here are some interesting questions for the thinking
evolutionist: Can you explain which came first—the blood or the heart—and why?
3) You’ve probably been led to believe that the first simple
creatures had rudimentary eyes, and that as creatures slowly
evolved their eyes evolved along with them. however, that’s not
what scientists have found.

Wednesday, September 9, 2009

Phylogenetics Conference - Seattle

Actually, the meeting is more general than "phylogenetics", but I'd like more phylogeneticsts to attend (and this was my "campaign" platform when running for secretary of the division of systematic biology. "Campaign" is quoted since I'm less than 100% positive I wanted to win). The title of this blog post is an attempt to get people from dechronization interested in the conference- this blog is on their roll, so the title appears.

The meeting is the Society of Integrative and Comparative Biology (formerly American Zoologist), which will run from Jan 3-7, 2010 in Seattle.

Note the abstract deadline of Sept 11 2009. This is often a hard deadline without extensions!! So we'd better get crackin'!

Strengths of the meeting are student funding and in general its being student friendly. Topical strengths include physiology (comparative), evo-devo, and invertebrate biology. Given my interest in eye evolution in inverts, it's become my main meeting. There is often a strong showing of phylogeneticists, usually those using phylogenetic tools to address comparative biological questions, with fewer people presenting on phylogenetic methods for methods' sake, the strength of the summer evolution meetings.

Thursday, August 27, 2009

Mermaid's Tale Blog

I haven't been too active with reading or writing blogs lately - I've been traveling and trying to get some (publishable) analyses and writing done. But I just stumbled upon a blog I hadn't seen before by Ken Weiss and Anne Buchanan. Ken Weiss is an anthropologist at Penn State. He writes a lot about evolutionary concepts (some call it theory, but the math theorists don't like that). He had a published column for a while that I was a fan of - I even assign a few of them for my evolution class.

I am a fan because Professor Weiss is an ardent pluralist, comfortable with some ambiguity, and the fact that "dichotomies" are spectra, etc. This is a general philosophy I share, and use to make sense of the world and others' arguments.

So, I look forward to reading their blog, called the Mermaid's Tale (I'm not sure I'm fond of pun-ambiguity, but I guess it works in this case). It looks prolific, I don't think I'll be able to keep up.

Monday, August 24, 2009

The art of naming and recognizing species

There is an article in the New York Times about the decline in number of taxonomists. More generally, the article is about people's increasing disconnect from nature, and especially from recognizing different living things around them. I've seen this first hand and have been surprised, for example, that many of the students in my invert zoology class grew up in CA, but never visited a tidepool before the class. These are people with passion enough for biology to declare it as a major.

As for alpha taxonomy, I've also witnessed the decline in professional prestige for writing species descriptions (see post here). Just last month, two undergraduate students and I discovered a new species of Euphilomedes (ostracod crustacean) on our collecting trip to Panama (the trip is a reason why no posts here for a while). We are thinking of describing it officially. But is this good training for me to teach them how to do this? Will the skills be at all useful in their future?

We were also joking about auctioning naming rights on e-bay. Some taxonomists are against this, but I am all for it.

Yet naming new species CAN actually lead to significant scientific cache. Witness several new species of annelid worms, described in Science. They shoot out green bioluminescent bombs, presumably to distract predators (not unlike the function of bioluminescence in Vargula hilgendorfii).

Friday, June 19, 2009

Eyes abound

Unraveling and disentangling homology and convergence is one of the most fascinating endeavors in biology. Homology indicates common origin and maintenance, and is often taken as evidence for importance: ancient features are thought to be maintained because they are too useful to dispose of during evolution. In contrast, convergence, is the separate invention of similar features or functions during evolution. Convergence is taken as evidence for an element of predictability in evolution. For a simple example, fish and dolphins are highly convergent, and we can use this knowledge to predict that when vertebrates evolve to live in the ocean, that evolution will produce particular features like flippers/fins.

I recently came across a fascinating paper, arguing that structures that interact with light - either by altering or receiving it - are highly convergent, and may even be homologous at some level. Namely, bird feathers that reflect UV light have some striking similarities with eyes! Furthermore, a paper I am a co-author on just came out in PNAS that further supports this general claim. We found that the light producing structure of a bioluminescent squid shares many features with eyes, including the ability to detect ('see') the light it produces!

First, the feathers. Bleiweiss studied the uv/blue feathers of Tanagers and Bluebirds. In nature, short wavelength colors are often produced by structures, as opposed to pigments which produce longer wave colors like orange and red. Structural colors work by differentially interfering/reflecting different wavelengths of light. A familiar example of structural color is a CD/DVD. These disks contain grooves that are spaced very closely together. Because the spacing is similar to the wavelengths of visible light, interference of certain wavelengths occurs, leaving other specific wavelengths that we see as color. These spaced grooves are called diffraction gratings, and they are known in nature, for example on the antennae of some ostracod crustaceans which reflect blue light. Bluebird and tanager feathers do not use diffraction gratings, but instead a different structural mechanism. In the course of studying these feathers, Bleiweiss found some striking similarities with eyes. Perhaps similar to fins/flippers that push water for locomotion, the physical similarities of feathers and eyes may reflect convergence due to shared physical necessities of interactions with light.

An attractive tanager.  Image from

What are these similarities between eyes and structurally colored feathers? First is a wide, domed surface to receive the light. Second is tissue that is transparent to some light but reflective of other wavelengths. In eyes, this is the cornea and lens, which are transparent to much light, but often reflect UV (human retinas are actually sensitive to UV, except the light never gets there because the cornea and lens reflect it.). Tanager feathers have physically similar tissues with similar properties to reflect UV/blue light and allow other light to pass through. Third, there is a large central space in both eyes and ocular feathers: eyes contain humors and feathers a space filled with gas (air). Finally, at the bottom is a reflective layer. In eyes, this is the tapetum lucidum, which produces eye shine in cats, coons and other night-active animals. Again, optical feathers share a similar pigmented structure also designed to reflect light.

These similarities seem to be a perfect case of convergent evolution: two structures that perform physically similar functions (light gathering, or light reflecting) have converged on similar solutions. However, Bleiweiss also raises the intriguing possibility that eyes and feathers actually share some (partial) homology. Complex traits like eyes and feathers are made of many components, each with a potentially different evolutionary history. Amazingly, some of the genetic components, developmental features, and signal transduction cascades of eyes and feathers are also shared, in addition to their functional similarities. These similarities might be evidence of a deep shared ancestry between multiple organs, including eyes, feathers, and even teeth.

I was particularly struck by Bleiweiss' paper because I've been thinking about similar things in the context of a collaboration studying the light-producing organ of a squid that yielded a PNAS paper this week. Not unlike tanager feathers and eyes, the convergence of squid light-producing organs and eyes has long been noted. Many squid, including Euprymna scolopes, the object of our study, are bioluminescent. Euprymna seems to use its bioluminescence for camouflage. In the ocean, most light comes from straight above, so animals would cast a distinct and conspicuous shadow below them. Instead of eliciting the shadow response of a predator or prey, Euprynma matches downwelling light to make itself more cryptic. The light is produced in a light organ that houses symbiotic bacteria. It is the bacteria that actually generate the light. Consistent with Bleiweiss' general hypotheis, this light organ has many similarities with eyes.

Light organs and eyes both have lenses. Eyes focus incoming light for better visual acuity, and light organs focus outgoing light, similar to a flashlight. Eyes and light organ have an open space below the lens, and a pigmented layer opposite to the lens. In addition to these similarities, we found that the light organ responds physiologically to light using the same genes (opsin and its signaling components) that are used in eyes. Just as with optical feathers, squid light organs are functionally convergent, yet also share structural components in common, indicating some elements of homology.

Euprymna scolopes Hawaiian Bobtail Squid.  Picture by Chris Frazee, image from

These findings indicate an interesting new research program using the tools of phylogenetics. By reconstructing the evolutionary history of multiple components of convergent/partially homologous traits, we can see how and when these components came together, illustrating the pathways by which evolution has produced new features. This will allow a richer, more fundamental understanding of the origins of biodiversity and complexity, topics that intrigue everyone.

Bleiweiss, R. (2009). Feathers with Ocular Architecture: Implications for Functional and Evolutionary Similarities of Visual Signals and Receptors Evolutionary Biology, 36 (2), 171-189 DOI: 10.1007/s11692-009-9059-6

Tong, D., Rozas, N., Oakley, T., Mitchell, J., Colley, N., & McFall-Ngai, M. (2009). From the Cover: Evidence for light perception in a bioluminescent organ Proceedings of the National Academy of Sciences, 106 (24), 9836-9841 DOI: 10.1073/pnas.0904571106

Tuesday, June 16, 2009

Taxi-cab creationism: Idaho style

I have witnessed a thousand evolutionists descend upon Moscow, Idaho. At this conference, I've heard biologists discuss in exquisite detail new research connecting specific genes to specific evolved phenotypes, I've been regaled with stories tracing the pathways of evolution, I've seen tests of explicit historical hypotheses, and I've seen yet more data supporting predictions made by evolutionary science.

I have also been driven to my hotel by a friendly local taxi-cab creationist, something that is not at all unusual. In fact taxi drivers are my main interaction with creationism, in Rhode Island, in Georgia, and now in Idaho. When I teach Macroevolution to biology majors in California, I have come to realize that many of the students are unaware of the evolution denialism that is common in this country. I show them the DVD of the PBS documentary of the Dover trial (Judgment Day), and that is enlightening for many. I also teach them about anti-evolution arguments, and about the evidence against those arguments, and this is quite popular. But I also tell try to begin to relay some of my own experiences with anti-evolutionism, which has usually involved taxi drivers.

"So, what are you in town for", I lecture in my best southern drawl, mimicking some typological taxi driver.

"Well, I'm giving a lecture at the university".

"Aw, so whadya do".

"I'm an evolutionary biologist".

Moment of stunned silence. "Mmmm. I've heard evolution's pretty debatable".

Well, tonight I again entered a taxi, and the conversation started something like the lecture snippet above. But today, since my hotel is out of town I had some time in the cab, and since I was curious, I asked my driver a few questions, and I mostly listened. He was quite friendly, seemed determined to avoid a debate, but also shared many of his beliefs with me. I think he had given this pretty much thought, and he'd argued before about this. He'd always have his caveat, however non-factual.

I didn't ask his name, but he wore a red had, a T-shirt and had several days worth of stubble. He started making small talk about the conference, and said that he had driven someone from the conference recently. I asked him point blank what he thought about evolution - consider it field research for teaching my class, I suppose.

"Well, I'm a creationist, to be quite honest", he said. "But I don't push my beliefs on anyone".

He seemed to value greatly the fact that he wouldn't push his beliefs on anyone. Maybe he just wanted to maintain a chance at a tip.

"I used to be on the opposite side of God", he said. For a brief moment, I thought he meant he was once an evolutionist, but I came to realize he was saying he was once a "sinner". I suppose this means he was once an addict. I've known many people to convert drug or alcohol addiction into an obsession with religion.

"I used to live in New Zealand for 10 years". This seemed important to him, I'm not sure why. "We can debate, but I believe in my faith and my science, and other people believe in their faith and their science, so in the end no one will change their mind. It's fun to debate, but I guess we'll know when we die."

I said it sounds like he is really agnostic, since he says we won't know until we die. He reiterated his faith in God.

At one point I asked him how old he thought the earth is. He said 50,000 years old. "Of course that's debatable, my number comes from scripture. I know there's this carbon dating stuff, and yeah maybe the earth is billions of years old. But carbon dating has been proven to be wrong. Sure, some people argue it's right, but some people argue it's wrong. I'm actually really into collecting fossils", he said, "when I was in New Zealand, I found a turtle egg, a really rare thing, and this had the embryo in it. It was carbon dated, not the whole thing, just a little piece, and the date came back 70,000 years, even though science says these turtles are only 15,000 years old. You can do this carbon dating stuff, but you can't prove it."

I asked him why he required proof of Carbon dating, but didn't require proof in God.

"I just have faith, and I guess we'll see when we die."

At some points it sounded like he accepted some parts of evolution. I said at one point, that an important thing for me is that we share common ancestry with every single other living thing, and that I found that continuity of life beautiful.

"Well, yeah sure, but if we're connected to some green slime and apes and everything, then there is nothing that makes us special", he said. "I believe in the literal word of genesis, and - yeah sure it was translated by man, and humans make mistakes - but genesis and evolution are incompatible".

I asked him if it were possible that God said "let there be evolution". Sometimes he did sound like a deist.

In the end, he said his faith gets him through another day. "Nothing wrong with that", I said, as I got out of the cab, and paid the fare. I did give him a good tip.

Tomorrow I'll go back to the conference. I'm sure I'll see yet more amazing, detailed science, fueled by the predictions of decent with modification. That is what will get me through another day.

Monday, June 15, 2009

Everybody's doin' it

I'm happy to be here at the evolution conference in Idaho. One thing I've noticed is that most everyone I talk to is working to collect data using "next generation" sequencing technology. In my field of macroevolution/phylogenetics, this means 454 sequencing usually, since longer individual reads are possible, good for organisms without genome projects. Most people are working out the protocols, as we are, but one talk I saw yesterday had some great data from 454, which the authors are using to investigate the ancestral land plant genome.

The talk was delivered by Ruth Timme with Chuck Delwiche as a co-author. They sequenced transcriptomes of multiple green algae species, using Sanger and 454. They have a huge data set and will be able to address questions about the ancestral land plant genome. Given the vast amount of data they have, it's early days for the analyses, but already they found some interesting results. For example they found that components of ethylene receptor pathways predate the colonization of land. How aquatic organisms, like green algae, use a gas receptor is pathway is not yet known. I felt this talk was a great glimpse into a rapidly emerging trend in evolutionary biology.... The genomic, or at least transcriptomic age is upon us, even in evolutionarily interesting, non-model organisms.

Friday, June 5, 2009

Who's Afraid of the Big Black Wolf?

Morphological variation within and across species is a subject of great scientific interest. The molecular basis of such variation, including the differences in size, shape, and oftentimes color within a species can be due to numerous factors. Often, random mutations in the melanin biochemical pathway or in the promotor regions of these genes lead to variations in the common agouti phenotype. Occasionally, however, phenotypic variations enter a population as a result of hybridization rather than spontaneous mutation. In wolves, coat color variation probably arose from a surprising pairing…

Fig. 1 - Black wolves may have inheirited their coat color through hybridization with domestic dogs. Photo taken from here

In a recent Science article, Anderson and colleagues attempted to determine the molecular history of the Melanocortin 1 receptor (Mc1r) in North American gray wolves. They studied the melanistic K locus in dogs, coyotes, Italian wolves and North American gray wolves (specifically a small population derived from reintroduced wolves in Yellowstone National Park where genealogy could be easily traced). They noted that the mutation was more frequent in forested areas than on the tundra/taiga, which alone wasn’t exactly earth-shattering news considering a white wolf would stick out like a sore thumb in a dark forest. What was most interesting was that they suspected that the K locus mutation present in the gray wolves in both Italy and from North America as well as coyotes originated from a mutation in domestic dogs. Melanism is very widely distributed in domestic dogs, from Chihuahuas to Great Danes, but is not found in wolves outside of North America who have not been recently hybridized with dogs. It was hybridization between wolves and dogs brought across on the Bering Strait land bridge that allowed wolves the potentially adaptive advantage of having darker coats (or, if it was a trait that was present in ancient Eurasian wolves, it was lost in wolves on that continent after they crossed the bridge).

Interestingly enough, it’s the dog, that animal which has been artificially selected over time to be more suited to life on couches and in cars than one in the wild, which has provided the wolf with a trait so critical to survival. A trait, the paper proposes, that may become even more vital as global warming reduces available tundra territory and prey.

NOTE: This post was written by Lea Mehrkens, an undergraduate in my evolution class. I gave the class the opportunity for extra credit to write a blog-style post on a scientific paper. I think Lea did a nice job on this one... THO

Anderson, T., vonHoldt, B., Candille, S., Musiani, M., Greco, C., Stahler, D., Smith, D., Padhukasahasram, B., Randi, E., Leonard, J., Bustamante, C., Ostrander, E., Tang, H., Wayne, R., & Barsh, G. (2009). Molecular and Evolutionary History of Melanism in North American Gray Wolves Science, 323 (5919), 1339-1343 DOI: 10.1126/science.1165448

Sunday, May 31, 2009

A critique of experimental phylogenetics

A new book entitled Experimental Evolution and edited by Ted Garland and Michael Rose, will be published soon. Since I once made a minor foray into Experimental Phylogenetics (Oakley and Cunningham, 2000) and since I decided I would not do that type of research any more, I contributed a chapter to the Garland and Rose book explaining why I think experimental phylogenetics may be a waste of time. Below, I paste a draft.

Abstract – The primary goal of the field of experimental phylogenetics is to generate branching histories of biological entities in the laboratory for use in testing methods of phylogenetic reconstruction. Here, I explore possible reasons why this field has remained small, despite hints of a bright future 15 years ago. Specifically, I examine three primary arguments that researchers have used to motivate the field of experimental evolution. The first involves claims that hypotheses in phylogenetics and molecular evolution are difficult to unambiguously falsify, and therefore an experimental approach is required. I argue that these claims do not specifically motivate experimental phylogenetics because they are based on an incorrect interpretation of the philosophy of historical science, and they do not differentiate between experimental evolution and its competitor, computer simulation. A related argument is that experimental phylogenetics can be used to understand the strengths and limitations of various methods of historical inference. This is a valid argument, but again does not distinguish between experimental evolution and computer simulation. In fact, I argue that high replication under different conditions is most important for testing methods, putting a premium on speed and leading to a disadvantage of experimental phylogenetics compared to computer simulation. A third argument does compare experimental phylogenetics to computer simulation, claiming that experimental evolution has increased realism compared to computer simulation. For example, experimental phylogenies may present modes of evolution not often implemented by computer simulations, such as common parallel or generally convergent evolution. These arguments do not decrease the value of completed experimental phylogenetic studies, but call for caution when weighing the costs of future studies that generate phylogenies in the lab.

Already as an undergraduate, I had an inordinate fondness for phylogenetic trees, and few papers sparked my imagination more than one announcing the birth of experimental phylogenetics (Hillis et al. 1992). In that paper, Hillis and colleagues generated experimentally a phylogeny of viruses and used it to compare various phylogenetic methods. For the first time, researchers had at their disposal a phylogeny of “living” organisms generated in the lab for the express purpose of studying phylogenetic methods. This known phylogeny came at a time when the enterprise of testing phylogenetic methods was in its heyday. Even popular culture was enamored with the ability to simulate life, as the Maxis software company released their enormously popular video game SimLife in the same year. In 1992, I expected experimental studies to be a wave of the future in phylogenetics.

Sometimes crystal balls can be foggy. Despite the enthusiasm of a decade and a half ago, the field of experimental phylogenetics remains very small (see also Forde and Jessup this volume). Was my enthusiasm misplaced? Here, I will discuss what I believe to be the reasons why the field has barely grown since its inception 15 years ago. Specifically, I will critique three primary arguments used to justify experimental phylogenetics. Most importantly, I conclude that experimental phylogenetics is an overly expensive simulation procedure. Even if experimental phylogenies have more biological realism than computer simulations, this realism comes at the considerable expense of decreased speed and potential for replication. This inherent trade-off between speed and biological realism is a recurring theme in experimental phylogenetics studies. Although an explicit understanding of the trade-off does not diminish the value of several previous studies, it may provide a guiding principle for those contemplating future contributions to experimental phylogenetics.

Motivation 1 – The perceived inferiority of historical science
One motivation in the literature for experimental phylogenetics has been a perceived inferiority of historical science, compared to experimental science. Here, I argue that there is no philosophical support for the claim that historical science is inferior to experimental science, thus negating one possible motivation for experimental evolution. Even though negating one motivation does not alone negate the entire rationale for experimental evolution, it is nevertheless important to promote a clearer understanding of historical science.
To some authors, experimental phylogenetics is a motivated by the self-consciousness of historical scientists in the face of experimental science. We learn from an early age that “real” science relies on the possibility of unambiguously falsifying hypotheses. Yet specific events that happened in the past – like the phylogenetic branching of mammals – can never be recreated. Like the legal system of the United States, historical science relies on demonstrating “beyond a reasonable doubt” that particular events did or did not occur. In science, reconstructing past events often takes the form of statistical/probability statements. Additionally, verifying specific historical occurrences may rely on various signatures left by historical events, such as the presence of a crater, high levels of iridium, and absence of previously prevalent fossils all dating to 65 million years ago, which congruently support the historical hypothesis of mass extinction by extraterrestrial impact. Although philosophers of science argue for the efficacy of such historical inference (Cleland 2001), there is still widespread perception of its inferiority.
This inferiority complex that burdens historical scientists is evident in the writing of Bull et al. (1993), illustrating it as a motivator for the field of experimental phylogenetics:

From a cold and cruel perspective of the scientific method, the major weakness of this field is its difficulty in unambiguously falsifying hypotheses of phylogenetic relationships, and hence, of molecular evolution.

Here, the authors are stating that “the scientific method” – which I take to mean Popperian falsificationism – is the preferred way to perform science. A difficulty in falsifying historical hypotheses is seen by the authors as a major liability for phylogenetics and molecular evolution studies. If only we could actually test historical hypotheses through experimentation – the logic goes – this liability would be lessened. This attitude seems pervasive. For example, Nature editor Henry Gee (Gee 1999) wrote that historical hypotheses “can never be tested by experiment, and so they are unscientific… No science can ever be historical.” Yet another author, Skell (2005) wrote “much of the evidence that might have established the theory [referring to “Darwin’s theory of evolution”] on an unshakable empirical foundation, however, remains lost in the distant past.” That article makes many errors, especially the conflation of and unvalidated value judgments on historical and experimental scientific studies. Skell’s article also naively equates all of evolution with a few “Just so Stories” about natural selection, and ignores many practical applications of evolutionary theory; including gene function prediction and measures of biodiversity, to name just two of many. Unfortunately, that article was written by a member of the National Academy of Sciences, thereby suggesting scientific credibility on the issue, and has been highlighted by the anti-evolution religious organization, the Discovery Institute.

Despite common perception, this inferiority complex for historical science is unwarranted for at least two reasons (Cleland 2001). First – despite what we learn in introductory science classes – there are problems with strict falsificationism. For example, probability statements are not falsifiable, yet they are still scientific because they are testable, indicating that a better theory of testability than falsificationism is required (Sober 2007). Furthermore, strict falsificationism is rarely followed, even by practicing experimental scientists. The reason is that, in any experiment, numerous variables are not controlled by the investigator. Even the seemingly simplest experiments do not control many potential variables, such as sun flares, humidity, season, etc, because it is usually safe to assume that many variables do not affect the experiment at hand. As a result, the possibility always remains that an unsupported hypothesis is not supported because of one of these ancillary assumptions, even if the original hypothesis is true. Therefore, experimental scientists often examine these ancillary assumptions to show that they are responsible for the failure of the hypothesis at hand. For example, I remember many hypotheses about physical laws that were not supported by my experiments in Introductory Physics Lab. Rather than falsifying established laws of physics, I invoked the failure of ancillary assumptions, such as “this ancient and abused student balance produces reliable data.”
A second reason to reject claims of inferiority for historical science, regardless of the status of falsificationism, is that historical hypotheses that explain observable phenomena provide predictions to be tested, and are therefore scientific. In practice, these predictions often act as confirmatory hypotheses; historical scientists seek to demonstrate a “smoking gun” – strong evidence for a specific event (Cleland 2001). As an example, Darwin’s historical hypothesis that all living organisms derive from a common ancestor has left numerous traces consistent with that hypothesis, including the use of RNA and DNA by all organisms, shared use of the same subset of all possible amino acids, and a nearly universal genetic code (for more detailed discussion of the hypothesis and difficulties in testing it see Sober and Steel 2002). This “smoking gun” perspective is not necessarily falsificationist, yet it is clearly scientific by presenting testable hypotheses.

Another way that historical scientists work is to test ancillary assumptions of historical models. For example, Darwin hypothesized that natural selection gradually built complex eyes from simple precursors. This model assumes that functional intermediates exist at all stages between simple and complex eyes. Darwin (1859), and later Salvini-Plawen and Mayr (1977), provided support for this model by describing the functioning eyes of living animals at numerous stages of complexity. In addition, Nilsson and Pelger (1994) found strong support for another ancillary assumption of the natural selection hypothesis – that there has been sufficient time for gradual selection to build eyes of observed complexity. It is true that we cannot recreate the evolution of the human eye. Nevertheless, we can make models of how eye evolution proceeded and test the ancillary assumptions of that model. Clearly, historical inference is scientific and – while philosophically different than experimental science – should not be construed as inferior. Therefore, a perceived inferiority should not be used as a motivation for experimental phylogenetics.

Thus far, I have only negated one argument (the perceived inferiority of historical science) for experimental phylogenetics, and as such have not yet provided any arguments against it, or for any alternative approach. The next two sections make explicit comparisons between experimental phylogenetics and the alternative approach of computer simulation. Before considering whether experimental phylogenetics allows for increased biological realism over computer simulation, I will consider the value of experimental phylogenetics for testing methods of phylogenetic inference.

Motivation 2- Testing phylogenetic methods

Although claims for the inferiority of historical science do not have a sound philosophical basis, another motivation for experimental phylogenetics appears philosophically sound. Specifically, understanding the relative strengths and weaknesses of methods of inference is an important scientific endeavor, and experimental phylogenies can be used to attain these goals. However, simply realizing that experimental phylogenetics can be of use is not sufficient, because other approaches can be used to the same end. Therefore, a convincing argument for conducting experimental phylogenetics must provide justification over and above other possible approaches.
Computer simulation, statistical analysis, and congruence all can be used to assess the performance of phylogenetic methods (Hillis 1995). While a full review of methods and philosophies for testing phylogenetic methods is beyond the scope of this chapter, and they have been reviewed elsewhere (e.g. Grant 2002; Hillis 1995), I conclude here that generating biological phylogenies is an overly expensive enterprise, costing a prohibitively large amount of investigator time compared to computer simulation. Speed can be increased in specific situations, but perhaps at the expense of biological realism. The question then becomes whether increased biological realism overcomes the increased cost over computer simulation. I will argue that it does not, concurring with others who have pointed out that experimental phylogenetics is subject to the same constraints as simulations: in either situation, it is necessary to assume the evolutionary processes present in the tests apply universally (Grant 2002; Sober 1993). This assumption is especially true when trying to establish the efficacy of methods, as opposed to the shortcomings. Any one replicate history can call into question the reliability of a method, but because any single replicate could be non-general, establishing reliability of methods requires generating replicates under many different assumptions or parameter values.

The need for speed: Costs and creative solutions

The goal of experimental phylogenetics is to generate clades of organisms (or genes or historical documents) with a known history and to examine the performance of methods for reconstructing that known history. Perhaps the most compelling advantage (discussed in detail below as motivation 3) of experimental phylogenetics over computer simulations comes down to the possibility for increased biological realism. As Hillis et al. (1993) wrote:

“The point of the experimental approach is to avoid approximating biological evolution by examining actual cases of biological evolution.”

To be practical, experimental phylogenetics requires the ability to generate clades on a timescale of months or less, which in turn requires using systems with brief generation times and rapid rates of evolution. Obtaining such rapid rates of evolution restricts the set of organisms that can be utilized. This is the first cost of the need for speed: a reliance on assumption that rapidly replicating biological systems faithfully model other systems, including those that evolve on long time scales. Even some of the most rapidly evolving systems have been further modified to increase their rate of evolution, leading to additional departures from natural biological systems. For example, the mutagen N-methyl-N’-nitrosoguanidine (NG) was added to increase the mutation rate of viruses in experimental phylogenetics (Hillis et al. 1992). The mutagen increases mutation rate, but also changes the mutational profile, causing G->A or C->T changes to be most common (Bull et al. 1993). Here again, the altered mutational profile may be considered a deviation from biological realism that is a necessary byproduct of increasing the speed of evolution.

As necessity is often the mother of invention, the demonstrated need for speed in experimental phylogenetics inspired some creative solutions. For example, Cunningham et al. (1997) and Cunningham et al. (1998) produced a modular experimental phylogeny, which could be analyzed in multiple ways. Starting from a wild-type T7 bacteriophage, they evolved six separate lineages, each of which was bifurcated once. As a result, they were able to assemble multiple different four-taxon phylogenies with varying relative branch lengths, from a single original experiment (Cunningham et al. 1998). This highlights one major difference between testing methods of phylogenetic tree inference and methods of ancestral state reconstruction. Any phylogeny has multiple nodes, such that ancestral state reconstruction methods can be examined on each of them. For ancestral states, there is an automatic replication. For testing phylogenetic trees, and for testing correlations between characters (correlative comparative methods: review in Garland et al. 2005), it may always be wise for the experiment to be modular, to allow for increased replication from the expensive experiment.

Another ingenious compromise between the need for speed in simulation studies and “biological realism” is hypermutagenic polymerase chain reaction (PCR). Instead of using living organisms or viruses, researchers have generated experimental phylogenies by utilizing the mutagenic properties inherent in copying DNA. By winnowing the evolving biological system to DNA and polymerase, the researchers have greatly increased the speed at which replicates can be generated. For example, Vartanian et al. (2001) copied a dihydrofolate reductase gene of Escherichia coli into a phylogeny of 124 “pseudogenes.” Sanson et al. (2002) used similar methodology to generate sequence data (over 2200 bp each) for an experimental phylogeny with 15 ancestor and 16 terminal sequences. However, just as in viral phylogenies, the increased speed in PCR-generated phylogenies comes at the expense of biological realism. In the PCR experiments, the biological system is reduced to an enzyme and DNA. The complexities of mutation and selection in the face of changing environments are greatly simplified in a PCR system compared to nature.

A third creative solution to the trade-off between speed and biological reality was parametric bootstrapping. Parametric bootstrapping involves estimating parameters of a model from real data, and using those parameter estimates and model to simulate multiple datasets (Efron 1985; Felsenstein 1988). Bull et al. (1993) estimated parameters for restriction site evolution from a bacteriophage experimental phylogeny. Using these parameters, they simulated by computer the evolution of multiple datasets to test methods of phylogeny reconstruction and molecular evolutionary inferences. Some may argue that this parametric bootstrap procedure provides a balance between biological realism and speed. Parameters are estimated from a biological system and speed is gained by simulating multiple replicates by computer. However, the parameters of molecular evolution do not have to be estimated using experimental phylogenetic data; any comparative data set could be used to infer model parameters. Furthermore, if experiments on model selection are any guide, then model parameters might be well estimated even if the true phylogeny is not known precisely. That is, in simulation experiments, the specific starting tree had little effect on the models of molecular evolution chosen as statistically best-fit (Posada and Buckley 2004; Posada and Crandall 2001), suggesting that the same might hold for parameter estimates of those models. In summary, parametric bootstrapping is a valuable tool that can extend the results gained from experimental phylogenetics (Bull et al. 1993). However, I remain unconvinced that experimental phylogenetic data are more valuable for parameter estimation than are comparative data from any naturally evolving system.

Motivation 3- Increased Biological Realism

Perhaps the most plausible justification for the use of experimental phylogenetics relates to arguments that it provides increased biological realism. Unlike the previous arguments I discussed, this one is based on an explicit comparison between experimental phylogenetics and computer simulation. If experimental phylogenetics really does add increased biological realism over computer simulation, then this would be a powerful argument for the approach.

What is biological realism?
Experimental evolutionists take biological realism to mean elements that contribute to an evolving system that are not decided a priori by the investigator (see also Huey and Rosenzweig this volume). I will refer to this as the degree of specification. In a computer simulation, usually the only factor that is not specified by the investigator is one or more sequences of random numbers. Of course, these random numbers can be used to specify many elements of a simulation, such as timing of branching events, or rates of evolution. In experimental evolution, many elements are also specified, for example the branching pattern of the phylogeny (Hillis et al. 1992). However, some aspects of experimental are not specified by the investigator, such as the mutational process and the relationship between mutations and a phenotype like virus replication rate (Oakley and Cunningham 2000). The claim of proponents of the field is that these non-specified elements increase biological realism over computer simulation.

My own biological reality
The above claims for increased realism may be difficult to assess with generality because they involve comparing a real-world system to a mathematical statistical model. We must decide, then, how well the models used in computer simulation account for real-world evolution. The models used in simulation, and the real-world trajectory of evolutionary history are so varied, it is difficult to know where to begin when attempting such a comparison. Nevertheless, this perspective suggests that the value of experimental phylogenies might be increased over computer simulations if experimental approaches are more likely to present the researcher with situations that are not explicitly modeled, but are produced by the non-specified aspects evolutionary process itself.

Such a situation occurred in my only foray into experimental phylogenetics. I was using the bacteriophage phylogeny generated by Hillis et al (1992) to study methods of ancestral state reconstruction for phenotypic traits (Oakley and Cunningham 2000). I found that virulence evolved in a way I didn’t expect a priori – there were large amounts of homoplasy. Systematists often assume that characters should usually evolve phylogenetically, such that close relatives share traits that are more similar than distant relatives. This is the inherent assumption behind methods like independent contrasts (Felsenstein 1985; Garland et al. 2005), and it is an assumption that is often tested now (e.g.Abouheif 1999; Blomberg et al. 2003). However, simulated data are often neutral. In real-world systems, homoplasy may be very common, driven by structural and functional demands on organisms (reviewed in Conway Morris 2003).
In the case of the bacteriophage phylogeny, instead of close relatives being more similar in virulence characteristics than distant relatives, the character was highly convergent. I observed parallel decreases in virulence in all the experimental lineages, which was rapid enough to erase all phylogenetic signal of the character. For example, a non-phylogenetic model of character evolution (Lee and Yin 1996; Mooers and Schluter 1998; Mooers et al. 1999; Oakley et al. 2005) is the best-fit among nine Brownian-motion based models. Had I used neutral computer simulations exclusively in testing ancestral state reconstruction methods, I might not have modeled the evolutionary trajectory actually taken by the viruses. Here, the viruses might have provided more biological realism than computer simulation in that the biological system is arguably less specified than a computer simulation.

One counter argument to this discussion of the enhanced biological realism of experimental studies is that a wholly empirical system arrived at very similar conclusions to my study of ancestral virulence in bacteriophage: Webster and Purvis (2002) investigated extinct and living foraminifera and found that strong directional change in body size erased phylogenetic signal for this character. If an empirical system showed the same results, then perhaps an experimental system was not needed to find the results. Yet, appropriate fully empirical systems may be rare, and may have higher costs than even experimental evolution in investigator time spent understanding the system.

Despite enthusiasm in the early 1990’s for a future of experimental phylogenetics, the field has stalled and produced very few papers and few novel insights. Part of this explanation is that phylogenetic methodologies have become rather standardized tools for evolutionary inference. However, as I argued above, two other considerations point to fundamental flaws in the foundations of the field. First, historical science is not inferior to experimental science. Historical and experimental sciences are philosophically different, and historical science is not inferior or less scientific. Therefore, the perceived inferiority of historical science cannot be used to justify any experimental approach in science, including experimental phylogenetics. Second, I argued that experimental phylogenies are probably not inherently more valuable than any other "simulation," and they are vastly more expensive in terms of investigator time and resources. As such, experimental phylogenetic studies that are already conducted are no less valuable than any simulation study, but researchers contemplating new experimental phylogenetics should carefully weigh the costs. One possible saving grace for experimental phylogenetics is the possibility that computer simulations are highly specified, such that experimental approaches might be more likely to produce unanticipated but biologically realistic results (see also Swallow et al. this volume on one important value of replication in selection experiments -- the possibility of finding "multiple solutions"). This is a difficult proposition to argue for or against quantitatively, but certainly highlights the requirement that simulations must be based on as much biological knowledge as possible, which might limit generality and/or increase the cost of performing them. I hasten to point out that the critique presented here does not apply to experimental evolution in general, which can still serve as a valid demonstration of evolutionary processes. However, my own foray into experimental phylogenetics left me unsatisfied, and this paper presents the reasons why.

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Monday, May 11, 2009

Evolver Zone

This is just a quick post to help spread the word about Ryan Gregory's new site EvolverZone. It is a website for evolution resources, like educational materials, announcements, books, journals, etc etc.

I found the design and visuals to be very slick, and I found a lot of useful new things on this website.

Sunday, May 3, 2009

Evolutionary Novelty: Get Milk?

The "Got Milk?" slogan has to be one of the most often mimicked ads of all time.  I did a quick search, and found the figure above, apparently compiled by the milk folks themselves.

So, how did animals "Get Milk" in the first place?  In other words, how did this novelty originate during evolution?

A new paper published by Lemay et al in Genome Biology has taken advantage of the recently completed genome sequence of the bovine, Bos taurus, and has begun to address this very question.

Although I am not a mammalian biologist (meaning I don't study mammals, despite being one myself), this is the third mammalian novelty I have highlighted here (see also placenta and hair).  Mammalian genome biology is ahead of other animal groups, for obvious reasons.  All my mammalian novelty posts tell a common story: the building blocks of complex biological features pre-date the origin of the integrated traits themselves.  What I wrote for hair, can also apply to milk and mammary glands:

"Just ten years ago, results ... clarifying the molecular components of trait evolution were rare, but they have become common now that genome sequences are available for many species. Before we had some idea of gene function, and before genome sequencing, scientists could only examine one level of biological organization – the trait (hair [milk] in this case). And that could only get science so far. In the case of hair [milk], it mainly got science as far as Figure 1, which leads to the inference that hair [milk] evolved a bit before the common ancestor of living mammals. But “hair [milk]” is not one thing. It is a complex of building blocks, including structural genes (like [casein]) and developmental processes. Today, scientists can decompose a trait, like hair [milk], into its components and study the evolutionary history of each part separately, tracing the parts through various genomes."
Figure 1 is here, again, replace hair with "milk".

I learned many amazing things about the genomics of milk and mammary glands from the Lamay et al paper.

  • Some 6000 genes are considered "mammary related" and are found on all the bovine chromosomes.  There are 197 unique milk protein genes!
  • Compared to non-mammary genes, mammary genes are more commonly present in all mammal genomes studied.  This indicates that mammary genes are evolving more slowly and may be lost less often than other genes.  This could indicate purifying selection owing to the importance of lactation for mammalian life history.
  • Milk does vary a lot among species - some babies need more fat or a bigger immunity boost, depending on the lifestyle of the species.  Variation tends to be caused by variation in number of gene duplicates, but not in the sequence of the milk proteins themselves.  One explanation for milk variation could be the levels of expression of different genes (regulatory variation).
  • Mammary genes are found together in the genome.  Also milk proteins are found along with mammary genes in the genome.  This could indicate that these clusters are expressed/regulated together as groups.
  • The genes expressed in milk fat globule secretion have similarity with other secretory organs.

This final result suggests that mammary glands might be considered "duplicates" (paralogs in molecular evolution parlance) of other secretory organs.  It reminds us that traits do not come from nothing.  Some designer did not shoot a lightening bolt into the first mammal, imparting it with mammary glands and milk. Furthermore, natural selection did not modify lactation genes to perfection, thereby erasing their history.  These traits, like all other traits, evolved from existing building blocks, duplicating and recombining them to form something new.  The evidence for common descent is strong and it is deep.  

As the authors wrote about lactation:

"the ontogeny of the mammary gland [may have] occurred by co-opting existing structures and developmental pathways.  Lactation may be less than 200 million years old, but its biological roots are far more ancient."

Lemay, D., Lynn, D., Martin, W., Neville, M., Casey, T., Rincon, G., Kriventseva, E., Barris, W., Hinrichs, A., Molenaar, A., Pollard, K., Maqbool, N., Singh, K., Murney, R., Zdobnov, E., Tellam, R., Medrano, J., German, J., & Rijnkels, M. (2009). The bovine lactation genome: insights into the evolution of mammalian milk Genome Biology, 10 (4) DOI: 10.1186/gb-2009-10-4-r43