Evolutionary Novelties

Mnemonic 2010

2010-05-27T01:13:00.001-07:00

Another year another mnemonic contest! Each year, in my Macroevolution class I ask for mnemonics for geological ages. The top vote-getter receives extra credit.

Vote now:

Click here to take survey

Check out previous years entries, too!!

Other Years' Mnemonics

Ostra-blog 9. Postasterope barnesi

2009-12-23T00:08:00.000-08:00

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....

Why is the "black box" so complicated??

2009-11-27T16:34:00.000-08:00

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.

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

2009-11-21T13:54:00.000-08:00

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.

10 Great advances in evolution-Nova Beta

2009-11-04T10:49:00.000-08:00

pbs.org 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.

Conference and Blog contest

2009-10-01T09:08:00.000-07:00

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 (http://www.scienceonline2010.com/index.php/wiki/) 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: http://deepseanews.com/2009/09/travel-awards-for-scienceonline-2010/

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!

Refuting Comfort's Eye evolution claims

2009-09-21T08:54:00.000-07:00

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:

It looks soooo complex. It had to be designed.
Comfort can't imagine how "random" processes could drive evolution.
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
complexity.”

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
processes,

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.

Cameron Comfort Co-Opt Darwin's Origin

2009-09-19T10:25:00.001-07:00

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:

Colleagues,

We all loved Kirk Cameron on Growing Pains:
http://www.youtube.com/watch?v=6Vo2i3NFq78&feature=related

Years later we were amused and perhaps a bit alarmed at his
'Origin of the Banana' video:
http://www.youtube.com/watch?v=2z-OLG0KyR4
(That's Ray Comfort there with him)

But in November of 2009 he and Ray Comfort are taking it to the
next level: http://www.youtube.com/watch?v=GN9zpf5cT0M

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
(http://www.facebook.com/group.php?gid=155609217391)

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.

Phylogenetics Conference - Seattle

2009-09-09T14:48:00.001-07:00

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.

Mermaid's Tale Blog

2009-08-27T12:55:00.000-07:00

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.

The art of naming and recognizing species

2009-08-24T23:27:00.000-07:00

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).

Eyes abound

2009-06-19T03:15:00.000-07:00

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 britannica.com

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 pnas.org

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.

References
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

Taxi-cab creationism: Idaho style

2009-06-16T02:52:00.000-07:00

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.

Everybody's doin' it

2009-06-15T09:53:00.000-07:00

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.

Who's Afraid of the Big Black Wolf?

2009-06-05T11:49:00.000-07:00

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

Reference
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

A critique of experimental phylogenetics

2009-05-31T22:22:00.000-07:00

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.

Summary
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.

References

Abouheif, E. 1999. A method for testing the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1:895-909.
Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution Int J Org Evolution 57:717-745.

Bull, J. J., C. W. Cunningham, I. J. Molineux, M. R. Badgett, and D. M. Hillis. 1993. Experimental molecular evolution of bacteriophage T7. Systematic Biology 47:993-1007.

Cleland, C. 2001. Historical science, experimental science, and the scientific method. Geology 29:987-990.

Conway Morris, S. 2003, Life's Solution: Inevitable humans in a lonely universe. Cambridge University Press, Cambridge.

Cunningham, C. W., K. Jeng, J. Husti, M. Badgett, I. J. Molineux, D. M. Hillis, and J. J. Bull. 1997. Parallel molecular evolution of deletions and nonsense mutations in bateriophage T7. Molecular Biology and Evolution 14:113-116.

Cunningham, C. W., H. Zhu, and D. M. Hillis. 1998. Best-fit maximum likelihood models for phylogenetic inference: Empirical tests with known phylogenies. Evolution 52:978-987.

Darwin, C. 1859, On the origin of the species by means of natural selection, or, The preservation of favoured races in the struggle for life. London, John Murray ...

Efron, B. 1985. Bootstrap confidence intervals for a class of parametric problems. Biometrika 72:45-58.

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1-15.
—. 1988. Phylogenies from molecular sequences: inferences and reliability. Annual Review of Genetics 22:521-565.

Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035.

Gee, H. 1999, In search of deep time: Beyond the fossil record to a new history of life. New York, The Free Press.

Grant, T. 2002. Testing methods: The evaluation of discovery operations in evolutionary biology 18:94-111.

Hillis, D. M. 1995. Approaches for assessing phylogenetic accuracy. Syst. Biol. 44:3-16.

Hillis, D. M., J. J. Bull, W. M.E., M. R. Badgett, and I. J. Molineux. 1993. Experimental approaches to phylogenetic analysis. Evolution 42:90-92.

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592.

Lee, Y., and J. Yin. 1996. Detection of evolving viruses. Nature Biotechnology 14:491-493.

Mooers, A. Ø., and D. Schluter. 1998. Fitting macroevolutionary models to phylogenies: an example using vertebrate body sizes. Contributions to Zoology 68:3-18.

Mooers, A. Ø., S. M. Vamosi, and D. Schluter. 1999. Using phylogenies to test macroevolutionary hypotheses of trait evolution in Cranes (Gruinae). American Naturalist 154:249-259.

Nilsson, D. E., and S. Pelger. 1994. A pessimistic estimate of the time required for an eye to evolve. Philisophical Transactions of the Royal Society of London B 256:53-58.

Oakley, T. H., and C. W. Cunningham. 2000. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54:397-405.

Oakley, T. H., Z. Gu, E. Abouheif, N. H. Patel, and W. H. Li. 2005. Comparative Methods for the Analysis of Gene-Expression Evolution: An Example Using Yeast Functional Genomic Data. Mol Biol Evol 22:40-50.

Posada, D., and T. Buckley. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53:793-808.

Posada, D., and K. A. Crandall. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology 50:580-601.

Salvini-Plawen, L. V., and E. Mayr. 1977, On the evolution of photoreceptors and eyes: Evolutionary Biology, v. 10. New York, Plenum Press.

Sanson, G. F., S. Y. Kawashita, A. Brunstein, and M. R. Briones. 2002. Experimental phylogeny of neutrally evolving DNA sequences generated by a bifurcate series of nested polymerase chain reactions. Mol Biol Evol 19:170-178.

Skell, P. S. 2005. Evolutionary theory contributes little to experimental biology. The Scientist 19:10.

Sober, E. 1993. Experimental Tests of Phylogenetic Inference Methods 42:85-89.
—. 2007. What is wrong with intelligent design? The Quarterly Review of Biology 82:3-8.

Sober, E., and M. Steel. 2002. Testing the hypothesis of common ancestry. J Theor Biol 218:395-408.

Vartanian, J. P., M. Henry, and S. Wain-Hobson. 2001. Simulating pseudogene evolution in vitro: determining the true number of mutations in a lineage. Proc Natl Acad Sci U S A 98:13172-13176.

Webster, A. J., and A. Purvis. 2002. Testing the accuracy of methods for reconstructing ancestral states of continuous characters. Proc R Soc Lond B Biol Sci 269:143-149.

Evolver Zone

2009-05-11T09:13:00.000-07:00

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.

Evolutionary Novelty: Get Milk?

2009-05-03T01:46:00.000-07:00

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."

Reference
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

We have a winner

2009-04-29T09:00:00.000-07:00

It was a close race for the geological eras mnemonic contest, but Fox edged out NBC in the end. The Family Guy inspired mnemonic garnered 28% of the vote, with the runner up inspired by The Office, getting 26% of the 249 total votes.

WINNER: Inspired by The Family Guy:
Cartoonist, MacFarlane, presents plot:
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quagmire takes Chinese, Japanese, Thai
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
prostitutes plus Meg.
[Permian, Pennsylvanian, Missisippian]
Devious Stewie organizes crime.
[Devonian, Silurian, Ordovician, Cambrian]

RUNNER UP: The Office
Clever Mockumentary Paper People.
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Question... That's Classy Jim, Talented Pennsylvanian Paper Merchant?
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian, Missisippian]
Dwight Schrute Openly Counters.
[Devonian, Silurian, Ordovician, Cambrian]

I did notice some funny business, with many voters coming from Facebook. I didn't say that was not allowed though. So, the winner gets extra credit. I'll give the runner up some, too, since it was so close...

Ostra-blog - Euphilomedes morini

2009-04-27T22:29:00.000-07:00

Male eyes Apollo, Nyx the female eyes

Stearn’s Wharf, the landmark wooden pier that effectively extends Santa Barbara’s main drag of State Street 1900 feet into the Pacific, is usually crowded with sightseers, diners, and fishermen; locals and tourists alike. Yet, unless they enter the Sea Center, probably very few of the visitors to the wharf stop and consider what is living just meters below the wooden pier where they walk. The ostracod crustacean species Euphilomedes morini is one of these denizens of the not-so-deep, and because of its distinctive eyes, it is an object of scientific study within the Cheadle Center for Biodiversity and Ecological Restoration at the University of California-Santa Barbara. Euphilomedes morini males have compound eyes that would make proud Apollo, the Greek God of light. But females lack these eyes, nixed not by the Goddess of night (Nyx), but by evolution and development.

Fig. 1 - Stearn's Wharf, Santa Barbara, CA

Class Ostracoda

Before discussing E. morini and its eyes, I will first introduce the class of animals to which the species belongs, Ostracoda, the ostracod crustaceans. Ostracods are small and ancient crustaceans, usually the size of sesame seeds or smaller. Sometimes known as “seed shrimp”, they make their debut in the fossil record in deposits of Ordovician Age, rocks that are some 450 million years old. Following this ancient appearance, ostracods are notoriously abundant in the fossil record. In some places, ostracod density can reach up to several thousand individuals per 100 g (3.5 oz) rock mass!

In addition to the estimated 30,000 different fossil ostracod species, some 15,000 species are alive today. But only roughly half of these living ostracods are known to science (have official scientific names). On one research expedition to a marine lab in Puerto Rico, I dipped a bucket in the ocean and chanced to find an unknown species, which we later named Euphilomedes chupacabra. This was on the pier of the marine lab, where hundreds of marine biologists have walked, and where their boats are docked. If unknown species live here, imagine what remains to be discovered in the farthest depths of the oceans, or the remotest ponds and pools. Even the subject of this piece, E. morini was first named as recently as 1997, after Jim Morin, an ostracodologist who has contributed much to our knowledge of the “fireflies of the sea”, a family of ostracods whose males produce brilliant blue light flashes to attract females (those females have eyes).

Ostracods are not confined to oceans. They live almost anywhere there is water. The small temporary ponds (vernal pools) that fill with California’s winter rains are home to hundreds of ostracod species. Life stages are resistant to drying over California’s long and often rainless summers. On a hike in the foothills above Montecito one winter, I once found a crevice in a boulder that had filled with rain water. To my surprise, that tiny bit of water teemed with ostracods. These animals also live in the water filled cups of bromeliad flowers, and some species even live without standing water, for example in the damp leaf litter of Australian rainforests, and just above the tides in the United Kingdom.

Not surprisingly, given the diversity of habitats occupied by ostracods, different species make a living in a wide variety of different ways. Some ostracods are scavengers. Others are predators, like the “giant” deep sea ostracod, Gigantocypris. Almost the size of a ping pong ball, Gigantocypris uses large silvery reflectors to focus light on its tiny retina and track down prey like plankton and even small fishes. Many ostracods are “deposit feeders”, feeding indiscriminately on organic matter found on the bottom of oceans or lakes.

Like the common housefly, ostracods are arthropods. Both houseflies and some ostracods see the world using compound eyes. Unlike our own eyes, which focus light through a single lens like a camera, compound eyes sample light through many lenses each a part of a separate facet called an ommatidium. Housefly compound eyes have hundreds of facets, while ostracod eyes have at most about 60, but usually fewer. Interestingly most living ostracods lack compound eyes, but some have them.

Euphilomedes morini

Although many ostracod species live locally, one in particular has been the subject of research in our lab for two reasons. First, E. morini is quite common and easily collected from Stearn’s Wharf or Goleta Pier. We simply drop a grab-sampler into the the water and bring up a bit of sand from the bottom of the Pacific. E. morini is one of the commonest animals of its size (~1 mm) in the shallow waters of the California coast. Second, E. morini has an interesting feature: Males have large compound eyes, but females do not.

Figure 2 (A, B) Lateral view of adult animals with half of carapace removed. Anterior is to the left. One lateral eye is visible (arrows). The female eye (A) is small and rudimentary without ommatidia and is only faintly pigmented. The male eye (B) is much larger, dominating the head of the animal with clearly visible ommatidia and a small rudiment (arrowhead) (C, D, E). Lateral view of instar IV male eyes from Euphilomedes longiseta (C) and Euphilomedes morini (D) and instar V Euphilomedes carcharodonta. Arrowheads denote rudiments. Stage matched lateral eyes from these three species are indistinguishable. Panel (E) depicts the development of a male compound eye. Pigment was photobleached under UV to allow a better view of the morphology. All rudiment pigmentation was removed in the photobleaching. The largest lenses and darkest pigmentation are at the distal end of the ommatidial field. Growth appears to occur in the direction of the curved arrow, as suggested by the presence of smaller lenses and fainter pigmentation. A putative morphogenic front is marked with a red arrowhead. (F, G) Eyes of late stage embryos (carapace fully formed) of the cylidroleberid Postasterope barnesi (F) and E. carcharodonta (G). Ommatidia are forming in the cylindroleberid embryo (arrows) but are absent in E. carcharodonta. (H, I) Ommatidial structure of E. morini. The schematic is based on panel (H), DAPI nuclear staining, and previous data on ostracod eyes (Land and Nilsson 1990). The distal portion of the ommatidia is the two lenses, which are clear and highly autofluorescent. These overlie two pigment cells (P) and the crystalline cone cells (C). Three retinular cells (R) were clearly visible, but six to eight have been reported in previous literature (Huvard 1990; Land and Nilsson 1990). A singe cone cell nucleus (C) was visible; the other may have been lost during preparation. Scale bar: (A, B) 500 μm, (C, D, F) 40 μm, (F) 55 μm (G, H, I) 15 μm. DAPI, 4',6-diamidino-2-phenylindole.

The surprising presence of eyes in male, but not female E. morini raises a number of questions. The first is, “Why?” In natural history, “why” questions are evolutionary questions. Why has a particular feature evolved to its present form? Evolutionary hypotheses are often inspired by adaptive explanations – what benefit does a particular trait bestow upon the individuals that posses it? Based on adaptive reasoning, and our knowledge of the natural history, we are currently testing two hypotheses to explain why E. morini males have eyes, but females do not.

The first idea is that males might be using their eyes to find mates. In nature, when females and males differ significantly, the reason often boils down to mating, to the process called sexual selection. Sexual selection occurs when sex-specific traits, like peacock feathers or larger body size, increase the chance of mating. If the trait is heritable, increased mating success will cause the trait to become more common. Peacocks with longer tail features are more attractive and may mate more often, having sons with longer tail feathers. In E. morini, males having eyes might allow them to find more mates.

A second explanation for differences between male and female E. morini is that differing life histories impose different demands on their visual systems. Specifically, we hypothesize that males encounter higher exposure to predators than females. In the E. morini and its closest ostracod relatives (the myodocopids), mating occurs in the water column. Even though most ostracods spend most of their lives in the sediment at the bottom, many swim toward the surface in search of romantic encounters, not unlike the nuptial flights of social insects like ants and bees, where virgin queens take flight to mate. It is at this time, during mating, that E. morini might be especially susceptible to predation, for example by fishes seeking a tasty crustacean morsel. Since females seem to mate only once, and males seem to enter the water column night after night to look for a mate, the males have a higher chance of becoming a meal. Perhaps their eyes allow them to avoid this fate. This predation risk hypothesis is based on piecing together information about myodocopid life history – how then do we know when these tiny animals mate, and how often they mate?

Although we currently know very little about the life history of Euphilomedes morini, we are making informed guesses based on related ostracod species. We perhaps know the most about a different family, the Cypridinidae, studied by James Morin (the namesake of E. morini) and Anne Cohen. Most cypridinid ostracods live in the warm waters of the Caribbean Sea. Since the animals produce a bright blue light (bioluminescence) that is visible by humans, and since the ostracods use this light as a pre-mating display, humans can study aspects of behaviors that could not be studied in E. morini, which does not produce light. Not unlike fireflies that are conspicuous on midsummer’s nights in the eastern and central US, the Caribbean cypridinids (‘sea fireflies’) produce coded messages by flashing. Male sea fireflies swim into the water column shortly after sunset and begin flashing their bioluminescent signal in hopes of attracting a female. Some males, called ‘sneakers’, follow the more industrious males without producing any light codes themselves. These sneakers hope to mate with an attracted female, without expending the energy to produce the signal. Mating presumably takes place in the water, after which females brood their young inside their shells. In captivity, females stored sperm from one mating event, which was used to fertilize multiple broods, and the females might not mate again after their first nuptial swim.

Fig 3. Small blue circles represent discrete flashes of light produced by male bioluminescent cypridinid ostracods. Patterns of different species are illustrated, with white arrows showing the direction of swimming of an individual animal producing the pattern over time. Each pattern is characteristic of a different species and are performed above different microhabitats. Original figure in black and white line drawing by Jim Morin and Anne Cohen. Color and photos added by T. Oakley.

There is also indirect evidence that Euphilomedes females only mate once and that males seek mates more often. In museum-preserved animals, females with broods are missing their swimming appendages. In many of these females, swimming appendages have been found in their guts. This suggests that after mating, female Euphilomedes consume their own swimming appendages, committing them to a celibate life in the sediment. Such behavior may seem strange by human standards, but it is not without analog in other animals. For example, ants hydrolyze their flight muscles after their nuptial flight, gaining energy from a structure that will no longer be needed. In contrast to females, we think that Euphilomedes males swim in search of females more commonly. In Puerto Rico, we found by sweeping nets through the water that swimming males outnumbered swimming females some 1000:1 at the peak activity time after sunset. Taken together, these data suggest a life history whereby eager males swim very often in search of mates. But females spend much less time swimming, instead mating once or few times before returning to the sediment to brood their young. All these small swimming male ostracods could provide a feast for predators such as small fishes, which are known to consume Euphilomedes.

To test the hypotheses that male E. morini eyes help them find mates and/or help them evade predators, we will make calculations of their optics, and perform behavioral experiments. Estimates of the visual abilities of males can be made by measuring aspects of their eyes, such as the number of facets, and the size of the lenses. If male eyes have enough resolution to see larger predators at a distance, but not enough resolution to see females until they are very, very close; this would support the predator-evasion hypothesis. We will also experimentally inhibit the vision of males. If the experimental animals are poorer at finding mates or evading predators, either hypothesis could be supported. Nature often shows us that there are multiple answers for “why” questions, perhaps even some answers we have not considered here.

For many, the beauty and allure of biology lies in the rich diversity of life. This diversity is apparent when we gaze at a tangled bank, or hike through a rainforest. But this amazing diversity is everywhere. The next time you walk on Stearn’s Wharf or Goleta Pier realize that many amazing creatures are living just meters below your feet. Even the cryptic have lessons to teach us about biodiversity.

Mnemonic 2009 - Please Vote

2009-04-16T12:34:00.000-07:00

We've completed the 2nd annual mnemonic contest for the eras or periods of the geological time line. I run this contest in my course EEMB 102 (Macroevolution), which has about 160 students. Both years I've been amazed at the diversity and creativity of mnemonics. I also pick some of my favorites and post them here, for people to vote on, the top vote-getter receives extra credit. Last year's blog entry I named "Sex, drugs, and macroevolution" because sex and drugs were the most common themes of the mnemonics. This year is similar, but more variable, and there are still a few other themes that are common. I. My favoirtes tended to be about life as a UCSB undergraduate, I'll list those first. II. Second, perhaps because last year's winner was inspired by Lord of the Rings, I got quite a few inspired by movies, TV shows, and books. III. Just like last year, quite a few about sex and drugs. I suppose that could be put into the category of life as a UCSB student, too.

By the way, last year's winner was:

Cruel Mordor, perilous place
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quest too crucial, jeopardous task,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Persistently pursuing Mount
[Permian, Pennsylvanian, Missisippian]
Doom, Sauron’s orcs challenge.
[Devonian, Silurian, Ordovician, Cambrian]

AND THIS YEARS NOMINEES ARE (Please vote by number at right):
1) Floatopia (Floatopia is an ad hoc spring break 'event' where thousands flooded the beach near UCSB, without bathrooms or trashcans, but with lots of alchohol and makeshift water craft)

Chugging quickly, towing my craft, juggling thirtypacks
(Cenozoic - quaternary, tertiary. Mesozoic - cretaceous, jurassic, triassic)
Professionally partying patrons made drunken sexual outbursts constantly
(Paleozoic - permian, pennsylvanian, mississipian, devonian, silurian, ordovician, cambrian)

2) Here is what I meant about no bathrooms at floatopia
Can men pee publically?
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quiet tinkling can justify tickets
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Prompt police measure
[Permian, Pennsylvanian, Missisippian]
Defined strictly: obscene conduct
[Devonian, Silurian, Ordovician, Cambrian

3) And c'mon, everyone Poops, even UCSB undergraduates
Center My Pale Posterior
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quickly, Towards Commode, Joyous Tenement,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Porcelain Palace: Marred.
[Permian, Pennsylvanian, Missisippian]
Done. Sigh Of Contentment.
[Devonian, Silurian, Ordovician, Cambrian]

4) And what if you got hold of some back poultry before Floatopia?
Contamination Makes People Puke
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Question Tasting Chicken Just Tainted
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Purple Poultry Makes
[Permian, Pennsylvanian, Missisippian]
Doctors Stay On Call
[Devonian, Silurian, Ordovician, Cambrian]

5) Surfing inspired
Continually maintaining powerful paddles
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quick through currents, just timing
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Positioned positively my
[Permian, Pennsylvanian, Missisippian]
Dank surfboard owns crests
[Devonian, Silurian, Ordovician, Cambrian]

6) At UCSB, students work hard
Cramming, memorizing, pondering plentiful,
Quizzes, tests: curriculum's just terrible.
Preferably pursuing merriment,
Disaronno shots obliterate conscience.

7) And party hard:
College manufactures plentiful parties,
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quenching the countless juveniles' thirsts,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Producing prolific merriment,
[Permian, Pennsylvanian, Missisippian]
Discouraging studying or coursework.
[Devonian, Silurian, Ordovician, Cambrian]

8) Usually looking for love:
Chasing Mind-blowing Pretty Person
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quickly to Create Joyous Time
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Pursuing Phenomenal Match
[Permian, Pennsylvanian, Mississippian]
Dumbfounded, Stupefied, obtained call!
[Devonian, silurian, ordovician, cambrian]

9). Despite the distractions, some still notice nature's beauty:
California mountain peaks plenty quiet,
(Cenozoic, Mesozoic, Paleozoic, Proterozoic, Quarternary)
The clouds jacket the pristine peaks,
(Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian)
Morning drizzle sweeps over crests.
(Mississippian, Devonian, Silurian, Ordovician, Cambrian)

II. Some of the best movie, music or TV-inspired mnemonics are also nominees.

10) Inspired by The Family Guy:
Cartoonist, MacFarlane, presents plot:
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quagmire takes Chinese, Japanese, Thai
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
prostitutes plus Meg.
[Permian, Pennsylvanian, Missisippian]
Devious Stewie organizes crime.
[Devonian, Silurian, Ordovician, Cambrian]

11) The Office
Clever Mockumentary Paper People.
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Question... That's Classy Jim, Talented Pennsylvanian Paper Merchant?
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian, Missisippian]
Dwight Schrute Openly Counters.
[Devonian, Silurian, Ordovician, Cambrian]

12) Monty Python
Crazy Monty Python pack,
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Questions to cross junction through,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Pardon pompous Malapert,
[Permian, Pennsylvanian, Missisippian]
Deliver Shrubbery on Crusade,
[Devonian, Silurian, Ordovician, Cambrian]

13) A TV show starring Brett Michaels of Poison “Rock of Love with Bret Michaels”
Crude Michaels promotes Poison.
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
“Quality” television created just to
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Pick promiscuous moms
[Permian, Pennsylvanian, Mississippian]
During several obscene competitions.
[Devonian, Silurian, Ordovician, Cambrian]

14) Pokemon (I assume Quagsire and Jigglypuff are actual Pokemon characters)
Come My Pokemon Pets
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quagsire, Togepi, Clefairy, Jigglypuff, Tentacool
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Play Pocket Monsters!
[Permian, Pennsylvanian, Missisipian]
Do Something Or Cease.
[Devonian, Silurian, Ordovician, Cambrian]

15). Harry Potter
Creepy Magicians Practice Playing Quidditch To Curse, Jinx, Terrorize, Plunder, Pilage Mr Draco's Secret Organized Club.
[Cenozoic, Mesozoic, Paleozoic, Proterozoic, Quaternary, Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian, Missisippian, Devonian, Silurian, Ordovician, Cambrian]

16). Cold Play
Chris Martin Plays Piano
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quickly Turning Coldplay's Joint's Triumphant
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Paramore Plays Misery
[Permian, Pennsylvanian, Missisipian]
Discussing Sorrows Of Children
[Devonian, Silurian, Ordovician, Cambrian]

17). Star Wars
C-3PO's mini pal's Princess quest takes courageous Jedi trainee past perils, making Dark Side order collapse.
[Cenozoic, Mesozoic, Paleozoic, Proterozoic, Quaternary, Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian, Missisippian, Devonian, Silurian, Ordovician, Cambrian]

III. And of course sex and drugs. (If you are not over 18, if you are offended by explicit sexual material, or if sex is illegal in your state, read no further!!)

18). Overnight Company
Carry Me, Proud Philanderer,
[Cenozoic Mesozoic Paleozoic Proterozoic]
Questing To Conquer Juicy Twat.
[Quaternary Tertiary Cretaceous Jurassic Triassic]
Promised Pleasure? Maybe.
[Permian Pennsylvanian Missisippian]
Don't Speak, Overnight Company.
[Devonian Silucian Ordovician Cambrian ]

19). Curious Men
Curious Men, Past Plastered
Queer Trannys Come Jovially To
Play, Probably Married,
Double-Sided, and Outta the Closet

20). Serious XXX
Charlie munches pink pussy
quickly till Carey Jane's
tight pink pussy makes
Dean skeet on Carey.

21). The scene: people smoking a joint... near them, a poster for an anti-drug campaign.
Cannabis Makes People Paranoid.
"Quite The Contrary," John Thought,
Peacefully Passing Marijuana,
Doubting Some Outsider's Confusion.

Citizen Scientist

2009-04-16T09:40:00.001-07:00

Last night, I became a trained Grunion Greeter. I want to take the kids on a few grunion runs this spring/summer - a late night run to the beach to watch perhaps thousands of fish party on the beach.

Grunions are fish endemic to Southern California and Baja. Each spring, they spawn on beaches by the thousands, a few days after the new and full moons. Females dig their tails into the sand, and the males spawn on the back of the females. The eggs develop in the damp sand, a few inches below the surface. At the next high tide after fertilization, the little fish pop out of their eggs and swim out into the ocean with the tide.

Grunion Greeters are volunteers who check a particular beach at a particular time, and report data to a website. This group of citizen scientists collects data in a fun way that is used for analyses that teach us about grunions, and have impacted coastal policy, such as protocols for cleaning beaches. Some beaches have been raked to clean up kelp and debris, but raking the beach disrupts grunion eggs.

Here is a youtube grunion video:

Other citizen scientist projects that I've heard about are the

Christmas Bird Count
Firefly Watch
Project Budburst

Let There Be Light!

2009-04-02T23:59:00.000-07:00

I'm looking forward to attending a Darwin Day event next week in Iowa City. I will be delivering a lecture entitled,

Let There Be Light!

Evolution and the Genesis of Light Sensitivity in Animals

I'll discuss our lab's work to try to learn about how light sensitivity, which today allows vision, first originated in animals. Some of our work is published, and I've discussed some of it before on the blog here.

Namely, we have been studying the genetic basis of photosensitivity in the cnidarian Hydra magnipapillata. Cnidarians are the most distant relatives of humans that possess (type-II) opsin-based photosensitivity. As such, components of the mechanisms of light sensitivity shared in humans and cnidarians may have been present at the very origin of this type of photosensitivity, and can inform us about how this amazing sense originated during evolution.

To test whether particular genes are used in sensing light in hydra, we are taking advantage of a behavioral response to light. Hydra have no eyes - they do not have pigmented spots. But they do respond to light. I've today been working on a video to illustrate a contraction response that hydra undergoes when light is shined on them. We can knock out candidate photo genes, and if the animal doesn't contract, this supports the hypothesis that the knocked out gene could be used in sensing light.

The video is time-lapse, shot through a dissecting microscope. The animal is small, less than half an inch long. Its base, to the right, is attached to a petri dish, and its tentacles are out to the left. The hydra does a little stretch, and then the contraction. This happens over about a minute or two, but is condensed to a few seconds here.

This type of behavior was noted in a different species way back in 1744 by Abraham Trembly. At that time, people thought polyps were plants. Trembly saw a hydra polyp move, and decided it was probably an animal. To test this hypothesis, he cut one in half: animals should die, and plants could regenerate. But hydra can regenerate even though they are animals. So Trembly discovered animal regeneration, and (sort of) stem cells.

Evolutionary Novelty: Mammalian Placenta

2009-02-28T14:03:00.000-08:00

For me one of the most visceral confirmations of the common descent of humans and other mammals came while witnessing the birth of my children. Having grown up on a small farm, I have vivid memories of the birth of kittens, lambs, and goats; and after the births of my children, I was struck by the similarity of human placenta and umbilical cord to those of other mammals. Given common descent, how did something as complex as the mammalian placenta originate in the first place? The answer, according to research published last summer in Genome Research, involves the evolutionary mechanisms of co-option and gene duplication.

Fig 1. For me, witnessing the birth of goats, humans, kittens, and sheep - and especially umbilical cords and placentas, was a visceral re-enforcement of the scientific fact of the common ancestry of eutherian mammals.

Mammalian placentas can be considered an evolutionary novelty, like light sensitivity, hair and animal photosynthesis. Like these other traits, a placenta is not one thing, but a collection of many structural and functional components. We know that placentas are present in "Eutherian" mammals, but absent in marsupials, monotremes, and most non-mammals. Therefore, based on simple parsimony, placentas originated prior to the common ancestor of eutherians. This presents us with a null hypothesis, that components of placentas also originated at the same time.

Figure 2 - Mammal phylogeny. Only Eutherians have placentas. Monotremes lay eggs, and marsupials carry babies in a pouch. Did all the components of placentas also originate with eutherians?

Research published last summer by Knox and Baker investigated the timing of the evolutionary origins of genes expressed in mouse placentas. Since scientists have determined the sequence of all genes of the mouse genome, placental expression of all those genes could be investigated simultaneously using microarray technology. The genes expressed in early development of mouse placentas have ancient origins. In contrast, the genes expressed later during the development of mouse placentas have much more recent evolutionary origins. Here, the authors define the origins of genes to be related to when the last time was they were duplicated.

When the genes expressed in a structure originated before the structure itself, we can consider this a co-option event: Genes used for other purposes are incorporated (co-opted) into the new structure. Given common ancestry of all genes and organisms, it should not be surprising when we demonstrate co-option. Nevertheless, there are not many cases where comprehensive gene expression within a structure has been studied in the context of evolution. In the case of placentas, early development involves rapid growth of tissue, and deploys many genes involved in cell proliferation. Cell proliferation and the genetic machinery for accomplishing this is conserved in evolution. In the case of placentas, instead of re-inventing a new way of proliferating cells, or instead of duplicating cell proliferation genes especially for use in the placenta, existing genes were deployed in a new context. This can be thought of as co-option. An observation further consistent with co-option is that egg-laying relatives of eutherians use a membrane in eggs for oxygenation that may be similar to placentas.

Unlike the genes in early development of placentas, genes expressed later in placental development tend to be recently duplicated. To test whether or not recent duplication of late expressed placental genes was unique to mice, the authors also examined genes expressed in human placentas. Here again, many human placental genes were recently duplicated. The authors suggest that the diversity of placental forms may in part be due the expression of recently duplicated genes.

The visceral re-enforcement of common ancestry I felt when seeing a human placenta and umbilical cord extends to the genes used in developing placentas, which themselves have ancient origins, and are shared across many organisms.

Reference
K. Knox, J. C. Baker (2008). Genomic evolution of the placenta using co-option and duplication and divergence Genome Research, 18 (5), 695-705 DOI: 10.1101/gr.071407.107

I was a teenaged nerd boy

2009-02-21T01:53:00.000-08:00

I guess I've always made nerdy hypotheses about the world. Over at Observations of a Nerd, there is an interesting post that is in line with an hypothesis I remember making long ago, when I was a teenager or so.

Here is the gist of the post:

An ingenious study published in Personality and Social Psychology Bulletin (PDF) looked at how well people knew their own face. They took neutral photos of people and morphed their images to different degrees to either be more "attractive" (like a composite face) or "less attractive" (people with craniofacial syndrome). They then asked the participants to choose their actual, unmorphed photo from the variety of choices.
But instead, more than half the participants picked the morphs that were more attractive (even by their own opinions) than their real photos. In other words, they thought they were hotter than they really were....
Participants in the study were also asked to do the same lineup-picking for close friends, and their bias towards attractiveness also extended to them.

I actually remember making this hypothesis long ago, and wanting to test it in a similar way. My "data" were that when I saw people I knew well in a mirror, like family, I was surprised at how asymmetrical they looked to me. Of course symmetry is linked with attractiveness, thus the link with the work above. Back then, I hypothesized that I was somehow correcting in my mind for people's asymmetries. Similarly, when I saw a double-reflection of myself, I was struck by how asymmetrical (=ugly) I actually am, compared to what I "see" when I view my single reflection. Again, I was somehow correcting for my own asymmetries when viewing my reflection, and that correction didn't work the same when seeing a double-reflected image.

I haven't had a chance to read the original paper, but here is an extension based on my nerdy observations of the world: I think this symmetry-enhancement extends to pets. I remember seeing my cat PeeWee in the mirror, and being struck in the same way at how asymmetrical her reflection appeared to me.

I remember trying to explain this to some friends once. They thought I was crazy. So I thought maybe I am the only one who experiences this reflection asymmetry shock. The work described at OoaN makes me feel like I might not be the only one!

Losing meme virginity

2009-02-10T00:46:00.000-08:00

I vowed I don't actually have time for memes, but since I got tagged twice, once by Pleion, and once by Observations of a Nerd, I suppose I should oblige. I normally don't like to do things without thinking a lot about them. I mean a lot. So, I think it would take me a long time to feel satisfied I could really do this meme right. I mean a long time. Like more than 1 life time. But, since I can't now indulge in thinking of great science books for a few life times, I will name some off the top of my head:

The meme:
Imagine: YOU are asked to assign a half-dozen-or-so books as required reading for ALL science majors at a college as part of their 4-year degree; NOT technical or text books, but other works, old or new, touching upon the nature of science, philosophy, thought, or methodology in a way that a practicing scientist might gain from.

1. Darwin, C. R. 1881. The formation of vegetable mould, through the action of worms, with observations on their habits.

2. Thompson, D. 1917. On growth and form.

3. Capra, F. 1975. The Tao of Physics: An Exploration of the Parallels Between Modern Physics and Eastern Mysticism

4. Gould S.J. 1989. Wonderful Life. paired with Conway-Morris. Life's Solution: Ineviteble Humans in a lonely universe.

5. Kuhn. T. The Structure of Scientific Revolutions

6. Tufte. E. The visual display of scientific information

I won't tag other blogs though. I don't like to promote pyramid schemes, in general.

Two Animal Nervous Systems?

2009-01-27T22:34:00.000-08:00

Why would anyone ever care about a phylogeny? Why on Earth should we care which species are each others' closest relatives?

The reason boils down to traits. If two species share a very similar trait, but they are distantly related phylogenetically, then something interesting has happened in evolution. Perhaps that trait has evolved twice separately, and if that is true, perhaps we could predict that under similar conditions, another species would also evolve that trait. Alternatively, maybe the trait in question was lost multiple times in intervening groups - were the genes also lost? Now this is the interesting stuff, trait evolution!

Unfortunatley, I think that phylogeneticists sometimes short change traits. Phylophiles' papers can tend to get wrapped up in the relationships of a particular group, to the point of forgetting why anyone would ever care, forgetting what those relationships might mean (anyone else attend an Evolution meeting during the heyday of molecular phylogenetics, circa 1995? You know what I mean).

Symptomatic of this focus on the tree and not on the traits are cases where a paper spends an enormous amount of energy (mental and computational) on inferring the best tree; but then makes claims about the evolution of traits without a single statistic.

A paper this week by Shierwater et al, published in Plos-Biology precisely illustrates this point. The authors do an admirable job of resolving the major branches of the animal tree of life. They present a large dataset and compare many approaches and models with a statistical rigor that would make Willi Hennig, RA Fisher and Reverand Bayes proud. The authors end up with a well-supported, and fascinating result: Animals are divided into two epic clades - the bilaterians (e.g. flies, clams, and humans) on one hand and all other animals (sponges, jellies, and the enigmatic Trichoplax) on the other. But why might we care where Trichoplax falls on the tree? It's because of the traits.

It's in the traits that the paper disappoints me. After putting the computational pedal to the metal to estimate the tree and check its sensitivity to different statistical approaches, the paper simply asserts the paradigm-shifting claim that organ, nervous, and sensory systems must have evolved in parallel in the two epic clades. Here is how they stated it:

"We conclude that the higher animals (Bilateria) and lower animals (diploblasts), probably separated very early, at the very beginning of metazoan animal evolution and independently evolved their complex body plans, including body axes, nervous system, sensory organs, and other characteristics."

in the press:

"Nervous systems are found in both groups (among the lower animals, jellyfish have nervous systems), so the new arrangement means that these systems must have evolved twice in the history of animal evolution..."

and also in the paper:

"Most notable of these aspects is the evolution of the nervous system, which in the hypothesis in [the figure showing their tree], can only be explained by convergent evolution of Cnidaria and Bilateria nervous system organization."

So, what about the possibility of loss? Let's examine this possibility with the most rudimentary, and intuitive of phylogenetic methods, parsimony. Let's also assume that the phylogeny presented in the paper is the correct tree.

panel a and b show the phylogenetic tree supported by the recent paper. Panel a shows two separate gains of nervous systems (black vertical bars). Panel b shows an alternative hypothesis, not mentioned in the paper (unless it's in the supplement, which I haven't read yet). In the alternative, nervous systems originated with animals, and were lost (white vertical bars) in the lineages leading to Trichoplax and sponges.

Yes, two changes is fewer than three, and this is the story the paper and the press went with. But is it really more parsimonious (OED definition "the simplest state, process, evolutionary pathway, etc")? Can we really argue that it is simpler to evolve a nervous system twice than it is to gain it once and lose it twice? Maybe we can? This is what we are left with when using parsimony. (Likelihood and Bayesian methods often get us only slightly farther when dealing with characters).

That said, perhaps we can use these two alternative evolutionary pathways - two gains versus one gain and two losses - as alternative hypotheses (of course there are other possible pathways, but I'll ignore those for now). Do these hypotheses make alternative predictions? (Self promotion: please cite Oakley and Cunningham, 2000 if you buy this alternative hypothesis bit. You only have to read the last paragraph).

If the bilaterian and jelly nervous systems are independently evolved, we might expect them to be quite different, and use mostly different genes. This is not the case. We know of many similarities of the nervous systems of jellies and bilaterians.

Alternatively, if nervous systems were lost, we might expect to find remnants of nervous systems littering the genomes of sponges and Trichoplax. In fact, this is exactly what is found. Sponges and Trichoplax have many genes homologous to genes used in bilaterian nervous systems. (Shameless self promotion: please cite Sakarya et al 2007 which shows many synaptic genes are present in the sponge Amphimedon. We mostly assumed sponges as sister to other animals for that paper. But we still mentioned the possibility that the sponge lineage could've lost synapses).

Of course, in the end a "nervous system" is not one thing. Therefore, the question of homology becomes a bit of a red herring. Everything, except protein domain homology is partial homology! Instead, it becomes much more interesting and instructive to break down multi-part systems like nervous systems into components and to trace the evolutionary history of those components. Do these components evolve in a concerted way? Do components come and go? What processes drive divergences of these genes?

I know Shierwater et al are aware of these issues, but I'd have appreciated a more balanced discussion of alternative possibilities (what if Trichoplax is reduced, and not the ancestral animal? See Ryan, Chuck, and Bart on this one.) In the end, the traits are the interesting bit, so we should analyze them with the same statistical rigor as the tree, and treat interpretaions with the same caution and balance!!

Refer

Bernd Schierwater, Michael Eitel, Wolfgang Jakob, Hans-Jürgen Osigus, Heike Hadrys, Stephen L. Dellaporta, Sergios-Orestis Kolokotronis, Rob DeSalle (2009). Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis PLoS Biology, 7 (1) DOI: 10.1371/journal.pbio.1000020

Ostra-blog 7 - Trapping ostracods

2009-01-25T01:08:00.000-08:00

Some ostracods are attracted to traps, namely bait traps and light traps. My first experience with ostracod trapping came in 1998, during my trip to Japan (see ostrablog-5) as a graduate student intern.

My Japanese host, Katsumi Abe took me, along with members of his lab to his "mountain home", near Tateyama. Abe's mountain home was a geodesic dome, mostly without walls on the inside, except for the bathroom (complete with remote-controlled toilet), which thankfully had walls. This mountain home seemed to be designed as a well spring for creativity: puzzles, games, and books littered the structure. I remember signing the guest book, and writing a Haiku, inspired by the well spring, and by the beautifully wooded and mountainous surroundings. My lab mates and Abe's son constructed flutes from bamboo growing outside.

In nearby Tateyama, there is a pier, and this is a very famous place to catch "umihotaru", which translates to "sea fireflies" - the scientific name is Vargula hilgendorfii, an ostracod. This animal is a scavenger. At sunset and later, they rise from the bottom, where they rest all day, and follow the scent of dead flesh to find and feast on fresh carcasses. We can take advantage of this behavior and design traps to attract umihotaru. In Tateyama at this pier, the animals come to the traps by the thousands.

We arrived at the pier just before sunset. Professor Abe was a celebrity there. Meeting us were a class of high school students and several members of a biochemistry lab, who study the light producing chemistry of umihotaru. Abe walked the pier proudly. Many people came up to him asking him questions, bowing deeply. The show was about to begin.

We placed traps in the water; glass jars with holes drilled through the lids. Inside, we placed pig liver, which attracted the umihotaru nicely. After leaving the traps in the water for 20 or so minutes, we pulled up the ropes, and dumped the contents into an aquarium net to separate ostracod from liver and from water. When the ostracods hit the net, they were disturbed, and when they are disturbed, the produce their intense blue light. The light producing chemicals mixed with the sea water, and cascaded down on to the pier, through the planks, and back into the ocean. The biochemistry lab was thinking big. They came from far away in Japan, and needed a large haul of umihotaru to support their studies for a while. They had many traps, and one after the other, they emptied animals into a square container, perhaps 2feet wide by 3 feet long by 2 feet deep. By the end of the night, this container was half full with ostracods; thousands upon thousands of them.

The night felt festive. Enthusiastic students were asking questions, and marveling at the light show. I felt a part of this community. Despite my knowing very little Japanese, I felt I understood a lot from context, from body language. By that time I had also built a language with my lab mates - I'd learned which English words they knew, and which phrases and verb tenses to avoid because they caused confusion. I remember naturally answering someone excitedly in the affirmative with "so so so so", as I'd often heard the Japanese do, and this came naturally to me. Caught up in the festiveness, I decided it would be fun to eat some umihotaru. The ostracods tasted like .... seawater. My mouth glowed with the bright blue light we'd watched cascading down the pier all night. I'm quite certain the students thought me a crazy "gaijin", and they were happy to laugh and talk excitedly among themselves, and my mouth continued to glow.

I have some video of trapping umihotaru, taken at this very pier. This video is from a Japanese science documentary that featured Abe's lab. I copied the VHS tape while there, and I moved some parts to computer a while back (I also sped up the video a little, so I could show it in seminars and not take too much time):

Since my first introduction to trapping ostracods, I've designed my own traps. These are cheaper, lighter, and safer to transport than glass jars. Since I'm working on an invited book chapter on how to collect ostracods, I've made a figure describing my design. Perhaps you want to try to trap ostracods where you live:

Figure 1 - a. Inexpensive 50 ml conical tubes are available from many vendors, and are nearly ubiquitous in labs conducting molecular biology. b. The first step is to saw the end off of the tube, above the conical portion c. a hole is drilled in the bottom of the cone. The size of the hole can be varied; only animals that fit through this hole will be trapped. d. The cap is removed, and the cone-end is placed in the opening. Friction holds the cone tightly in place. e. Bait (such as imitation crab meat made of pollack) is placed in the tube, and the open, sawed end is covered with material (such as that cut from an old t-shirt), and secured with a rubber band. Numerous traps can be secured to nylon rope with plastic zip ties.

Creationism and Evolution in our society

2009-01-24T23:55:00.000-08:00

I was asked in an email to complete a survey about "creationism and evolution in our society". I came up with some answers, spur of the moment, and I thought I would paste them here. If it really is a student, I would like to help him out, and pasting it here gives me a little more incentive to complete it. (Anyone know what is a "Facharbeit"?)

Dear Reader.
I'm a german student who works on a "Facharbeit". We had to choose a subject and I think that the controversy between Evolutionists and Creationists is very interesting. Therefore I decided to learn more about it. I've created a survey and now I'm sending it around, hoping that many people are going to write something in the gaps. It would be very helpful if you answer me because here in my town I'm not able to talk to someone about this subject. If you are able to open the word file you can fill in the gaps there and send it back. This would make it very easy for me to evaluate the documents. Well, if this doesn't work, I've just copied the survey and you can fill in the gaps in this E-mail and send it back.
Hope hearing from you soon. Thank you.

Survey
Creationism and Evolution in our society

1) Do you support the evolution or the creationist theory?

I fully accept the enormous weight of scientific evidence that has accumulated for the theory of evolution. By "the theory of evolution", I mean the common ancestry of all living things, and descent of living things with modification.

I am not sure what "creationist theory" means. There are many stories of creation, many of which are not consistent with known facts and observations. I have not heard a creation myth that I support, and I know of no creation story that could be called a "theory" in the sense of a scientific theory.

2) Do you think that the other theory is non-sense? (Can you explain why you think that the other theory is non-sense?)

I would need more information about what is meant by "the other theory"; but many of the creation myths I've heard are non-sense in my opinion. For example, the Iriquois creationist story states that people once lived in the sky until a woman, pregnant with twins, was forced down to the Earth. At that time, the Earth was covered with water, there was no land. A giant turtle wanted to help the woman who had fallen to earth, so the turtle swam to the bottom of the sea and placed mud on its back to generate North America.

Yes, I think this creation theory is non-sense. There is no evidence of any turtle the size of North America, nor any evidence of any animal that could reach such a size. There is no evidence that this turtle is under North America today.

3) Are you sure that the theory you believe in is the right one? Why, why not?

Science should not be a matter of "belief". Given the enormous weight of evidence for common descent of all living things, and for descent with modification, I might say that I "believe" that this explanation will remain "the right" explanation for a very long period of time.

4) Do you think that there could be a danger if the world believed in the opposite theory?

Again, I am not certain what is meant by "the opposite theory". But, yes, I imagine that if belief in creation stories is a symptom of a potentially dangerous pattern of thought: When people believe what they are told without thinking critically about it for themselves, they are prone to dangerous manipulations.

5) Do you think that there’s a possibility that there’s an answer in between those two theories?

Again, I'd have to know which 2 theories. I don't think there is a true answer between the theory of evolution and the Iriquois creation story.

6) Maybe you’ve got an idea how that theory would look like?

7) If someone would find out that the theory you believe in is surly not the right one, would there be an effect on your life? Would you be frightened? Would you think that there’s something missing in our world?

Yes, if common descent and descent with modification were proven false, it would have an impact on my career. I would change the scientific questions I am studying. I do not think this would lead to something missing in the world, because the current scientific view of the history of life would simply be replaced with another scientific view of the history of life.

Was Darwin Wrong?

2009-01-22T12:03:00.001-08:00

[Update: I understand that the cover of New Scientist says "Darwin was wrong" and as Bjorn has just told me, this is the original article. I'll read that one as soon as I can.]

A new article in the Guardian (hat tip Bjorn at Pleion) has the headline :

Evolution: Charles Darwin was wrong about the tree of life

I think this headline, and the spin of the article in general is a rather extreme over-simplification, and more importantly, it is subject to misinterpretation by anti-evolutionists.

The main points I want to make are:

1. It is an oversimplification to say that Darwin was "wrong" on this point. It is not a clear cut case of right or wrong. Instead, the facts as we understand them today are more complex than what Darwin envisioned, or could have envisioned (given he didn't know about DNA).

2. The primary, most general implication for the history of life is not changed. Darwin's tree of life posits common ancestry of all life. This is the central scientific fact that anti-evolutionists rebel most against (because they don't want to admit we are all related to slime-molds, etc). In fact, the new observations about biology continue to reinforce Darwin's history-changing insight that all life shares a common ancestry. Yes, we share a common ancestor with a chimp and a fungus, get over it.

Below is what I wrote about our changed view of the Tree of Life in a paper with Michael Rose, published here in the Open Access journal Biology Direct.

Complications for "The Tree of Life"

Nineteenth and 20^thCentury biologists generally conceived of a "Tree of Life" – a mostly bifurcating graph connecting species in an order that reflects their common ancestry. At least three processes complicate such a view of a tree of life, horizontal transfer, symbiogenesis, and differential lineage sorting of genes. Each of these processes are at odds with fundamental assumptions of the Modern Synthesis [7,8] and a Tree of Life for the new biology is necessarily more complex than a graph joining species.

In the middle part of the 20^thCentury, it was often supposed that organisms and their cells are sleekly functional (Fig. 2A). Given such assumptions, passing genes from one species to another would not be favorable if those genes were finely tuned for the necessary functions of the species from which they originate. Even the movement of genes within a single genome was not accepted by the biological mainstream at that time, despite McClintock's early discovery of accessory elements in maize [9]. Nevertheless, molecular characterization of transposable elements in the late 1970s finally undermined the view of the genome as a static, well-organized library of genetic information [reviewed in [10]]. With the advent of genome sequence data, researchers studying the molecular phylogenetics of bacteria realized how common prokaryotic horizontal transfer is [11,12].

Similarly, modernist preconceptions led some to discount the importance of endosymbioses in the origins of new life forms, like eukaryotes. Broad theories of endosymbiotic origins for species had been suggested in the late 19^thand early 20^thCenturies [7], but were ignored save for a few well-established cases like lichens. By the 1980s, the evidence for symbiogenesis in major cell biological events was voluminous [13,14].

Even systematics has had to abandon many strictures that were part of the Modern Synthesis. If species are the durable unit of biology, and if natural selection quickly molds genes to current utility, then most genes should diverge at the time of speciation events, given views like Mayr's. Here again, analyses of newly abundant sequence data in the late 20^thCentury showed that rather than a highly congruent coalescence of genes at the times of speciation events, the coalescence times of alleles among species are highly variable. As such, species trees and gene trees often cannot be equated [15,16].

These phenomena complicate the tree of life. Rather than a graph connecting species, the tree of life itself is hierarchical: A universal tree of species is largely a human-imposed ideal because the components of any particular species have evolutionary histories that are not congruent with each other. This incongruence has a clear and well documented mechanistic basis in horizontal transfer, symbiogenesis and differential lineage sorting (not to mention gene duplication explained above). These processes together undermine the existence of a tree of life defined only at the level of species, pointing instead to branching histories that often differ among levels of organization and scales of analysis.

Figure 2. Old and new views of the evolution of prokaryote genomes. (A) 20^thCentury biologists sometimes assumed a close congruence between gene history and species history. Horizontal gene transfer was assumed to be uncommon, as the process of genes entering a new genome is counter to the idea of a sleek and well adapted genome. (B) After analyzing the genomes of many prokaryotes, biologists recognized that horizontal gene transfer may be a common event. Furthermore, prokaryote species trees may be viewed as a patchwork of gene trees with varying levels of congruence. A similarly hierarchical view of eukaryote evolution has been articulated by Maddison [15], except that differential coalescent times – usually not horizontal transfer – is the primary mechanism used to explain incongruence of gene and species trees.

And in the response to reviews:

2. Rose and Oakley bring up the newly apparent prevalence of horizontal gene transfer as one of the major blows to the 20^thcentury perspective in biology. This is, certainly, true, but I think the discussion in the paper stops short of really driving the nail down. The real issue is that, when fully conceptualized, extensive HGT undermines the very notion of the Tree of Life (the TOL paradigm) which, certainly, is a big part of the Modern Synthesis (as well as the classical, Darwinian foundation of biology). Simply put, although trees are crucial in depicting certain phases and aspects of life's history, there is no TOL as such, i.e, evolution of life cannot be presented as a tree, so Darwin's famous simile fails as an overarching generalization. The demise of the TOL paradigm is covered in several recent papers [91,92]. Again, this is related to the problem of "eukaryotic chauvinism": the tree pattern might hold for the evolution of the major divisions of eukaryotes (although not necessarily for all eukaryotes taken together) but, certainly, not for prokaryotes, let alone the entire history of life.

Authors response – Here we disagree with Dr. Koonin. HGT does not necessarily undermine Darwin's "Tree of Life" completely, even though in post-Modernist biology this Tree of Life is much more complex. Today's Tree of Life, as Dr. Koonin points out, is different from what Darwin envisaged, in that it is multi-dimensional – branching histories characterize in a complex way multiple levels of organization, not just the species level. Further, as discussed in the article, HGT is not the only blow to a two-dimensional tree; paralogy, endosymbiosis and lineage sorting also contribute to a new, highly multi-dimensional view of evolutionary history.

This emerging understanding of the trees of life is pluralistic, encompassing the branching history of biological units at all different levels of organization [81]. The evolutionary histories of units at different levels (gene domains, genes, species, etc) are not always congruent with each other, yet there are still branching histories that characterize each of these levels. Branching history is a pattern that results from well known mechanisms including exon shuffling, gene duplication, genome duplication (polyploidy), co-option, speciation, and vicariance of multiple species. HGT is one example of a mechanism that causes branching histories at different levels of organization to be incongruent. It clearly points out the failed assumption that the history of components is congruent with the history of the higher level unit to which it belongs. Nevertheless, this assumption can be used as a valuable null model to understand macroevolutionary patterns and processes [93]. As we discussed in this article, the species was usually seen as the durable unit driving branching at all levels, but the existence of multiple evolutionary levels and mechanisms violates this assumption.

Processes to split biological units pervade all levels of the biological hierarchy. Protein domains duplicate within genomes and may be "horizontally transferred" from one gene to another. Genes may form units of synteny or operons, but individual genes may also be copied from one part of the genome to another or from one genome to another, independently of the rest of a synteny unit or operon. Whole chromosomes and whole genomes may also duplicate by various mechanisms. All these processes create the new tree of life. But that tree is a postmodern tree, rich in complexity. Components coalesce to form units with a congruent path for a time, only to be broken up. There is no reason to provide anti-intellectual, anti-evolutionists with quotes like "The Darwinian paradigm is dead", because this complexity only enhances Darwin's most profound insight – the universal common ancestry of life.

Please Vote!

2009-01-20T21:08:00.000-08:00

About three years ago, my brother broke his 5th cervical vertebra in a skiing accident. He had just switched jobs to work in public schools as a special education teacher, and since he was only in that job for 6 months or so, he lost his insurance a few months after his accident. After a long time in the hospital, he gained back some of his mobility, especially on his left side. Today, he has has learned to walk again (he's not running quite yet), and is even living on his own in an apartment in Milwaukee. Despite the significant physical progress he has worked for, he has been in financial debt since his accident, due to his lack of insurance, and to the lack of a public health care in the US.

He has now used his creative and computational skills and entered an advertising contest where he could win $5000. He created an ad for a company called innocentive.com. Five finalist ads are posted on YouTube, and the finalist with the most views and the highest rating will win the $5000 prize.

I'm quite positive that he would not want people to vote for his ad unless they think it is the best. But, if you do think it is the best of the finalists, please rate his ad highly, and visit it often - he could really benefit from this prize.

Here is the ad (Please click on the YouTube logo in the embedded video to visit YouTube and rate the ad highly, if you like it):

Wildlife Photography

2009-01-16T09:50:00.000-08:00

I indulged in a little wildlife photography during the holidays. From my parents' kitchen table. There is a bird feeder just outside the window. These are my favorite 2 pix:

A festive chickadee.

and a chillin' squirrel.

The glamour of marine biology

2009-01-05T22:57:00.000-08:00

When people ask what I do, I sometimes tell them I am a "marine biologist". There is a certain glamour to it, at least in the public eye. Sadly, sometimes, I am just too tired to answer the more truthful "evolutionary biologist" and risk incurring the wrath, judgement, and "breathtaking inanity" of a brainwashed anti-evolutionist.

Once, I was collecting sludge in Half Moon Bay, California, in an attempt to find Euphilomedes ostracods. A group of 10 or so girls, about aged 11 or so, were having a picnic nearby on the beach with 3 or 4 or their moms. The gaggle of young girls soon came running over toward me, yelling girlishly, and separately..... "Are you a marine biologist????". I paused. I looked down at my sludge, and my wet suit, and then threw out my chest slightly, and lowered my voice, "Why, yes, I am a marine biologist". I had just gotten a shrimp in my sieve, flopping around, and I showed it to them. For that one shining moment, I felt like a rock star.

But my type of marine biology usually has far less fanfare, and far more sludge. Case in point is my most recent collecting expedition. I am curretly in Boston at the SICB conference, having a great time. Given the proximity to the famous marine lab Wood's Hole Oceanographic Inst., I thought I would make a quick trek there to collect a mystacocarid crustacean. These are tiny animals that live on beaches in between sand grains, below the surface of the beach. They are close to my main study group, ostracods, and mystacocarids lack any eyes, given their lifestyle of living several cm under the beach. Do they have genes for vision? I'd like to answer this question, but I need live animals to answer it. My quest to find them fully lacked glamour.

It started with a tragedy of errors. There was a problem with my hi-tech amphibious vehicle. Oh wait, I mean my rented Nissan Sentra from Dollar Rent-a-car. Who knew that there was a 209 Cambridge St. and a 209 E. Cambridge street within a few miles of each other in Boston? Who knew I would trek to the wrong one and find not a Dollar Rent a Car, but an abandoned flower shop? Who knew that I'd go all the way back to my hotel to find out the problem before going back to find the amphibous vehicular remotely operated submarine.... I mean Sentra?

Given my very late start, I'd be lucky to get to the beach in Wood's Hole before dark. It's an hour and a half drive from Boston. Given that I scribbled down driving directions on paper, luck would not help me. Hwy 28 is where I needed to be - but I crossed it earlier than my scribbled directions suggested. I made the choice to get on 28 right away, but it was slow, painfully slow. Had I followed my directions, I'd have found Interstate 495 and taken that in a much faster way, before finally hitting 28 again. Then there was the bridge that was under repair. But mostly, I was ill prepared.

I finally found the beach in question. A place that was sampled for mystacocarids, near the place that these enigmatic crustaceans were first discovered. I parked my amphibious marine vessel - I mean Sentra. It's January. The wind was howling and the sun had already set. Collecting these animals involves pounding PVC pipes into the beach to obtain cores of sand. But the cold made the pipes brittle, and they broke on the small rocks. I persevered, fighting the howling wind, and my frozen hands. It's times like these I take solace in the fact that I feel like a dedidated biologist. Glamour be damned.

I brought the buckets of sand back to the car and back to my hotel. Cheap bucket, $4. Rented Sentra $38. Hauling buckets of beach into the Boston Waterfront Westin - priceless.

I haven't yet found the mystacocarids in the sample. There is still more sand to look through under the scope set up in my room. But I am not optimistic.

Marine Biology. Frolicking with dolphins in azure Carribean seas? No. Marine Biology: Fighting howling winds and frozen hands, only to come up empty.

Until next time!

Evolutionary Novelties: Faves of 08

2008-12-31T12:21:00.000-08:00

As 2008 winds down, I thought I would look back at Evolutionary Novelties and pick some of my favorite posts of the year.

The major theme of this blog is to explore how it's possible that all life has a common origin and still has diversified into the riotous diversity/complexity/disparity that we see today. New features evolve through duplication and recombination (at all levels of biological organization).

1. Box Jellies and the Red Herring of Eye Evolution is one of my favorite posts. The main thesis is that people always ask an inappropriate question "how many times did eyes evolve?". I'd thought about this idea for quite a while, and when a paper came out in PNAS that re-inforced my thesis, I incorporated the new research into the idea.

2. Coming to grips with common descent discusses the idea that during the history of evolution, people have tended to forget that everything evolves from something else. This was not conceived as a blog post, but as a chapter of a book I've toyed around with writing. In some ways, blogging satisfies my urge to write a book, so the book probably won't happen for a long time.

3. Gould: Pluralism by Monism My thesis that Gould was practicing pluralism by taking an opposing stance to the whole field of evolutionary biology. This is perhaps my favorite post of 2008 because I've never seen anyone else with this idea, and the more I think about it the more I think it explains a lot, a general theory of Gould, if you will.

The above are posts that present an idea I've had. I've also recently been writing a few posts on others' research. I find that writing about the work helps me internalize and understand the work. I'm not a rocket-science journalist, but some of the posts have been okay, I think:

4. Evolutionary Novelty: Photosynthetic Slug

5. Evolutionary Novelty: Hair

I also have a series of posts about ostracods, my ostrablogs. I haven't had time to do these for a while, but I do have one half written, so more are coming. My favorites are probably:

6. Ostrablog 5 - Three shows and a funeral retells a story that I've told many, many times in person.

7. Ostrablog 3 - How we discovered chupacabra tells about our discovery of a new ostracod species.

8. Ostra-blog 2 - to e or not to e Ostracod or ostracode?

But much of what I do is promotion of my research and papers, or posting drafts of things I'm writing:

9. Phylogeny, evolution, biodiversity and ecology discusses some research recently published in PNAS. I also noticed this was featured at NESCENT.

10. Opsins: An amazing evolutionary convergence. Slightly expanded from part of an encyclopedia article I was asked to write.

Those are 10 of my favorites from this year. Happy New Year!!

Two New Blogs

2008-12-30T22:15:00.000-08:00

Greetings from the frozen tundra. I've been in Milwaukee catching up with family and friends during the holidays. Visiting has been a full time job, and I've been online very little, but 2 new blogs have come to my attention, both by colleagues of mine:

First is "A Fish Eye View"

Next is "The EEB and Flow":

Opsins: An amazing evolutionary convergence

2008-12-19T14:39:00.000-08:00

How predictable is evolution? If we could travel back in time 4 billion years and make a few changes, what would remain the same upon our return? This is an enduring topic of evolutionary inquiry (and movies and sci-fi shorts for that matter).

In his book Life's Solution, Conway-Morris made the case for a semblance of predictability in evolution. He argued that convergence - the independent origin of similar traits - represents an element of predictability in evolution. Octopus and humans have outwardly similar eye designs, so if we reply animal history over and over, these camera-type eyes would likely evolve in most replays.

Here I'll describe a truly amazing molecular convergence that was not discussed by Conway-Morris: the independent evolution of opsin proteins (a protein responsible for light perception) in two different groups of organisms. It turns out that a 7-transmembrane protein (opsin), bound to a light reactive chemical on the 7th transmembrane domain, has evolved twice to sense light!

If we could go back a few billion years and replay the evolution of life on earth a few times, chances are, opsins would evolve in many of our replicates.

[Disclaimer - the following is text from an encyclopedia article I've been asked to write on opsin evolution, so the writing style is a bit terse from here on out. I will add a little bit though, specially for the blog. But since many people I know think opsin originated only once, I feel it's my duty to spread the word of opsin convergence, starting here, at Evolutionary Novelties].

What is opsin and rhodopsin?
Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis. Opsins are sometimes called retinylidene proteins because they bind to a light-activated, non-protein chromophore called retinal (retinaldehyde). Opsins are also in some cases called “rhodopsins”, a name originally given to isolated visual pigments that contained both opsin protein and non-protein chromophore in a time before the two separate components were known. Today, the term “Rhodopsin” is used commonly to describe the opsin expressed in vertebrate rod (dim-light) photoreceptors, and the opsins of certain organismal groups, like bacteria. All opsin proteins are embedded in cell membranes, crossing the membrane seven times.

Type I and Type II opsins
Two major classes of opsins are defined and differentiated based on primary protein sequence, chromophore chemistry, and signal transduction mechanisms. Several lines of evidence indicate that the two opsin classes evolved separately, illustrating an amazing case of convergent evolution.

Type I opsins are present in bacteria and algae and are referred to by various names, including bacteriorhodopsin, bacterial sensory rhodopsins, channelrhodopsin, halorhodopsin, and proteorhodopsin. Type I opsins have varied function, including bacterial photosynthesis (bacteriorhodopsin), which is mediated by pumping protons into the cell, and phototaxis (channelrhodopsin), which is mediated by depolarizing the cell membrane. Type II opsins are present in eumetazoans (animals not including sponges), but are unknown from sponges or any non-animals. Because opsins are known from cnidarians and bilaterian animals (animals with bilateral symmetry, including humans, flies, and earthworms), Type II opsins are inferred to have been present in their common ancestor, which lived about 600 million years ago. Type II opsins have varied function, including phototransduction and vision, circadian rhythm entrainment, mediating papillary light reflex (pupil constriction), and photoisomerization (recycling the chromophore).

Despite their functional similarity and despite both being 7-transmembrane proteins, multiple lines of evidence indicate that Type I and Type II opsins evolved independently. First, the primary amino acid sequences of Type I and Type II opsins are no more similar than expected by chance. For example, try to align a Type I (say bacteriorhodopsin) and Type II opsin together. I just tried this with blastalign, with the following result:

Exhibit A. Blast search find "no significant similarity" of the amino acid sequences.

Sequence 1: gi|163443|rhodopsin
Length = 348

Sequence 2: gi|208055|bacteriorhodopsin >gi|208057|gb|AAA72603.1| bacteriorhodopsin
Length = 249

No significant similarity was found

CPU time:     0.04 user secs.     0.02 sys. secs     0.06 total secs.

Second, the orientation of the transmembrane domains differs between the major groups. We now have crystal structure data for both Type I and Type II opsins, and the arrangements of the parts of the protein that are stuck in the cell membrane are quite different, inconsistent with a single origin of opsins (unless this changed a lot during evolution, which is not impossible).

Exhibit B. Type I on the left, Type 2 on the right. Denser lines are positions of transmembrane domains. Figure is from Spudich et al (2000)

Third, the major opsin groups differ in chromophore chemistry. Prior to light activation, the chromophore of Type I opsins is an all-trans isomer. Light activation then involves isomerization of the chromophore to 13-cis retinal. In contrast, prior to light activation, the chromophore of type II opsins is 11-cis retinal. Light activation of Type II opsins involves isomerization to all-trans retinal.

Exhibit C. Type I on the left, Type 2 on the right. Chromophore chemistry differs. Figure is from Spudich et al (2000)

Fourth, Type II opsins belong to the larger protein family called G-protein coupled receptors (GPCRs), which transmit varied signals from outside to inside cells by activating GTPase proteins, which in turn signal to second messengers that affect the state of the cell in various ways. Type I opsins do not activate G-proteins. Furthermore, Type II opsins are more closely related to non-opsin, light insenstive GPCR’s than they are to Type I opsins. So even if there is some very, very distant and *undetectable* common origin of Type I and Type II opsins, chromophore binding likely evolved twice. Since chromophore binding is what allows photosensitivity, it is the crux of being an opsin (but see), and the realization that Type II opsins are closer to non-opsin GPCR's than Type I opsins is strong support for two separate origins.

Exhibit D. (Dashed lines mean no sequence similarity beyond random. Light bulbs mean origin of chromophore binding=light sensitivity=opsin.)

Finally, with two CS students, I tested the single origin hypothesis in a different way and found no support. Type I opsins show similarity of membrane domains 1-2-3 and 5-6-7, consistent with an origin by duplicating a 3-domain protein (and adding one). However, Type II opsins show no such similarity. If they Type I and Type II share a single origin, the duplication pattern of the domains should be shared too (unless there were drastically different rates of evolution in the 2 lineages, which is not impossible). This work is described here: Larusso et al (2008) J Mol Ev.

John L. Spudich, Chii-Shen Yang, Kwang-Hwan Jung, Elena N. Spudich (2000). RETINYLIDENE PROTEINS: Structures and Functions from Archaea to Humans Annual Review of Cell and Developmental Biology, 16 (1), 365-392 DOI: 10.1146/annurev.cellbio.16.1.365

Exaptation! PT flare up #2

2008-12-10T15:09:00.000-08:00

Continuing on with my thoughts about the flare up at Panda's Thumb (part 1 here):

Basically, I think "Green" the anonymous undergrad from a University in the UK, raised a few valid issues that are worth thinking about. A lot of the evolutionists, while I agree with their points on general terms, are not addressing the concern of "Green" directly.

Her main point is (from the comments at Panda's Thumb):

“Co-option may not be the de novo formation of genes, but it still requires mutations (such as, for example, the gain of a cis regulatory region). My whole point was that simultaneous mutations are required for the evolution of the phototransduction cascade. Correct me if I’m wrong, …”

This is in part true, and raises the point that we should be discussing EXAPTATION and not co-option, to most clearly convey the point.

Green is stating that even if all the components of phototransduction are present an ancestral genome that lacks phototransduction, multiple mutations would be required to assemble all those components into a phototransduction cascade. So, multiple co-option events would be required, and this is what she is having a problem with.

HOWEVER, what is false is the requirement for all these mutations to occur simultaneously. Instead, the components could be assembled one by one in a graduated, step-wise (Darwinian) fashion.

Instead of focusing on co-option, Green should focus on "exaptation". Exaptation is the idea (roughly) that features can arise for one function, and then change function later on. In the case of phototransduction, much of the phototransduction cascade originated for another purpose - sensing some signal from outside the cell to elicit changes inside the cell. (And just because a yeast pheromone cascade isn't THE phototransduction precursor, doesn't mean there wasn't one). One response to a signal evolves, changing the signal that is detected (to light) seems pretty surmountable. In fact, this has happened independently in the lineage leading to C. elegans (see my post here).

For another example of exaptation, we've found that many components used in synapses predate synapses themselves. See these posts in pharyngula, Newsweek. The open access paper and other news sites (including radio interview) are here.

PT eye evolution flare up

2008-12-09T19:01:00.000-08:00

I was notified that there was a little flare up at Panda's Thumb about our recent article on eye evolution, entitled:

Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF) published in Evolution: Education and Outreach.

Warning: Long Post. If you only read one thing, read this:

One might argue that we are just pushing back the origins, changing the question of "phototransduction" origin to the question of "transduction" origins. In a way this is true, but it is also a fundamental insight about how evolution works. New features are not breathed into organisms by some unknown force, they evolve by duplication/divergence or recombination of existing features. Trace a feature like phototransduction back far enough in evolutionary time, component by component, and it grades into something else altogether.

Here is the story:
A week or two ago, I was contacted by an undergraduate from a university in the UK (I see no reason to reveal her name). She had questions about the article, writing:

I've just been reading your 2008 paper 'Opening the Black Box: the genetic and biochemical basis of eye evolution' and found it really interesting! I'm just writing an essay on eye evolution atm and am trying to get to the crux of the issue, and find out how the phototransduction cascade itself evolved. After explaining that opsin probably arose by a mutation in a serpentine gene/protein, you mention in your paper that:

"In yeast...these receptors [GPCR's - the serpentine proteins] are sensitive to pheremones, and they even direct a signal through proteins homologous to non-opsin phototransduction proteins."

What I'm wondering is, is it this whole yeast pathway that has been modified for the metazoan phototransduction cascade? Or is it only the opsin which has been derived from it? (With the subsequent molecules involved in the phototransduction cascade being co-opted from other proteins not involved in the yeast signalling pathway).

Based on this email, it seemed the student had a pretty good grasp of the issues, and I replied:

Thanks for you questions.  I found out after writing the paper that the yeast pheromone proteins are not the "rhodopsin type" GPCR, so they are distantly related at best to opsins.  So they should not be considered anything like direct ancestors of opsin.

As for other components of the yeast pheromone cascade, these are different than phototransduction.  Yeast pheromones activate a MAP kinase cascade. So, I think all that is similar is the GPCR and G-protein.

So, it really is an open question as to what the ancestral function was of some of the genes of phototransduction, although some of these genes do function in other sensory transduction pathways...

Unfortunately, she misinterpreted this email, understanding it to mean (written over at PT, using the pseudonym "Green"):

"Yeah I knew that co-option thing would be coming. Turns out there was a mistake in that Oakley and Pankey paper.

The yeast intracellular signalling cascade turns out not to be homologous in any way to the metazoan signalling cascade. It just got published before the authors realised."

First of all, this is an incorrect interpretation of what I wrote. In fact, I wrote "So, I think all that is similar is the GPCR and G-protein." This is far from "not homologous in any way", as claimed by the student. The G-protein is undeniably homologous, and the yeast pheromone receptor is a 7-transmembrane protein, at least conformationally like opsin (whether or not the opsin and pheromone receptor sequences are homologous is a trickier issue).

But the larger issue is I think an issue of "linear thinking", which I address quite often on this blog. The student seems to think that if we cannot identify in yeast (taken as a linear ancestor of animals) a cascade identical to phototransduction except for opsin, then the origin of phototransduction requires numerous simultaneous mutations. This is not the case. First of all, yeast is a more distant relative of animals with phototransduction than is sponges. I just mentioned the yeast pheromone photoreceptor in the paper as a well studied example of a pathway outside of animals with partial homology (some components homologous, some not) to photoreception. There are closer "relatives" of phototransduction in sponges (poorly studied functionally, but the genes are known) and in other animals (better studied).

Another issue is a difficulty that people have with thinking about partial homology - that some components can be homologous and some not, depending on the time scale of the comparison (see my post The Red Herring of Eye Evolution).

Partial homology is a pattern that indicates a mechanism of co-option in the evolution of features. Co-option is the combination of existing things in a new way (analogy: dijonaisse = dijon mustard plus mayonaisse). All of the components of phototransduction pre-date animals, except opsin. And if we consider opsin to be a GPCR, which it is, then all of the components of phototransduction pre-date animals. This may be considered a pattern of co-option, or exaptation. Signaling pathways were already present before phototransduction. Some of the phototransduction components function together as far back as the yeast + human common ancestor (GPCR + G-protein). Other components of phototransdcution function together in non-phototransduction cascades of other animals. This indicates that phototransduction did not assemble all at once, but built incrementally upon an existing scaffold.

One might argue that we are just pushing back the origins, changing the question of "phototransduction" origin to the question "transduction" origins. In a way this is true, but it is also a fundamental insight about how evolution works. New features are not breathed into organisms by some unknown force, they evolve by duplication/divergence or recombination of existing features. Trace a feature like phototransduction back far enough in evolutionary time, and it grades into something else, component by component.

There were other comments, too. Again at PT, she also commented:

Yeah I read Oakley and Gregory’s articles on eye evolution a couple of weeks ago. Unfortuantely neither address the crux of the issue: namely the origin of the biochemical phototransduction cascade.

To be fair, Oakley’s article (the ‘Black Box’ one) at least tries to give some biochemical details. But it only scratches the surface by suggesting a potential origin of the opsin protein. Unfortunately the origin of a new opsin protein is not equivalent to the origin of an entire phototransduction cascade.
So it seems the Darwinian account still falls quite far short of any satisfactory biochemical explanation. Descriptions of morphological change, comparisons of genes, crystallins, etc. all skirt the issue if it cannot be shown how the phototransduction cascade itself arose

The difficulty with this comment is that the origin of opsin defines the origin of phototransduction. The other components of the cascade were already there, they all predate opsin, as described above.

This is also a "God in the Gaps" argument, or maybe, a "God under the surface" argument, stating that describing the origin of the keystone molecule of phototransduction (opsin) "only scratches the surface".

Also, I don't understand what the difference is between "comparisons of genes" and "biochemical explanation". What would a biochemical explanation be for the evolutionary origins of things that doesn't involve "comparisons of genes". The genes of the phototransduction pathway have biochemical interactions with each other, many mediated by interactions between specific amino acids.

Eye evolution issue printed

2008-12-08T14:48:00.000-08:00

The new issue of Evolution education and outreach has been printed, and the issue is all about eye evolution. The links to all the articles are below, they are available free of charge.

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)

Online Lecture

2008-11-28T01:38:00.001-08:00

I've been shopping around trying to find a fairly easy way to combine audio with PowerPoint slides to post lectures online. I tried some movie-editing software, but that had some problems. Then I saw that Carl Zimmer over at The Loom used a piece of software called Soundslides. I thought I'd try Soundslides with a lecture I delivered recently.

(The lecture was to help inaugurate a new organization at UCSB called SUB - Society for Undergraduate Biologists. I was asked to speak about undergraduate research. I chose to talk about "paths to undergraduate research"; my own path, the path of one undergraduate from my lab, and the path that others might take to undergraduate research.)

I concur with Carl's comments that Soundslides is mostly nice, but determining the timing for when the slides change is a bit of a hassle. The quality of the slides ends up to be very high, because it uses jpeg graphics within Macromedia Flash, I gather. Other methods make a movie, and the graphics don't come across as well, or they take much more memory. Anyway, I post the result from soundslides below, which took me a few hours to complete. There is one more program I want to try that was recommended to me, I will try to post comparisons here, in case anyone is interested. After that, I want to buy the program I like best and then get many of my lectures from my Macroevolution course online, including lectures on the basics of phylogeny reconstruction. Then I just point students to the online lectures, retire from teaching, and focus on research (wink)...

How Complexity Evolves

2008-11-24T15:54:00.000-08:00

[Slightly altered excerpt from an invited review on the evolution of (nervous system) complexity]

The evolution of complexity is an enduring and fundamental topic in biology. Recent research is allowing new insights into the origins of complexity. Namely, scientists now have access to the components of complex structures, and their evolutionary histories. "The eye" is no longer an anonymous collection of components - Darwin may have known an eye is composed of lens retina and nerve - but he did not know what lenses or retinas were composed of, nor did he know in much detail how they functioned. We now know many of the protein components of structures like eyes and how they function, and we know that these components have evolutionary histories. Since biological entities from genes to ecosystems arise from existing entities, general patterns emerge as to where those entities came from. They either duplicate/diverge; split/diverge; or fuse in new combinations.

What is biological complexity?
Numerous definitions have been suggested for biological complexity, from mathematical and information theoretic formulas [2,3] to intuitive definitions, such as the numbers of parts or components that can be counted in a system [4,5]. In practice, a researcher’s choice of definition for complexity often boils down to his ability to measure it. In investigator-defined computer simulations [2] or circumscribed biological systems [3], information theoretic definitions using explicit mathematical formulas are tractable. However, in extensive biological systems, especially those that encompass multiple levels of biological organization with varied properties, the relationship between structure and function (e.g. genotype and phenotype) is often largely unknown, and may itself be complicated and variable. These unknowns complicate the formulation of explicit, yet general, mathematical definitions of complexity for extensive biological systems. Instead, some have argued that counting the numbers of parts of a system is an appropriate measure of complexity [4]. Although often focused on structural units, such as cell types, genes, or species, and not on the functions of those units, McShea [5] has also argued that counting structural parts should often be a good estimate of functional complexity.
Herein, we follow previous authors [4,5] and define more complex systems as those that have more parts. “Part” is used as a term that spans levels of biological organization [4]. Species are parts of ecological communities. Organs (like brains or ganglia) are parts of species. Cell types (like neuronal types) are parts of organs and of species. Proteins are parts of cells and of networks, and domains and amino acids are parts of proteins. Many other biological units are also parts [6]. For the current discussion, we are concerned less with defining or counting parts, and concerned more with how new parts originate during evolution. According to the definition of complexity that we employ, new parts (that do not come at the expense of existing parts) increase biological complexity. Therefore, those mechanisms that cause the evolution of new parts are of particular interest because those are the mechanisms that cause increases in biology complexity.

"those mechanisms that cause the evolution of new parts are of particular interest because those are the mechanisms that cause increases in biology complexity."

General patterns of increased complexity
By definition, complex systems have many parts, and the histories of those parts are varied. As such, we cannot expect a simple, one dimensional answer to the question of how complexity evolved. Nevertheless, at all levels of biological organization, conceptually similar patterns (Figure 1) have resulted from a varied array of mechanisms that historically increased complexity.

Figure 1 - Generalized patterns of increased biological complexity. The top of the figure represents an ancestral state, the bottom a descendant state. Shapes represent “parts”, a generic term for a biological feature at any level of organization. Parts can be species, genes, protein domains, pathways, brain regions, and many other biological units [see 6]. A. Copying and divergence B. Fission and divergence C. Copying and fusion. Without copying or fission, complexity does not increase because divergence (or fusion) maintains the same number of parts. Without differential divergence or fusion of parts, complexity only increases marginally.

First, parts may exhibit a pattern consistent with differential divergence of copied elements (Fig. 1a). A prime example of a specific mechanism leading to this pattern is gene duplication plus divergence. Duplicated genes are initially identical, and they gradually diverge over time, increasing genomic complexity. Second, parts may exhibit a pattern consistent with differential divergence of split elements (Fig. 1b). Here, a prime example is speciation, where populations of individual organisms, originally all of the same species, split into multiple populations that diverge to the point of becoming separate species. Splitting (fission) can also occur in an asymmetric fashion (Fig 1c), generating two uncoupled parts that together would sum to one ancestral part. Third, parts may exhibit a pattern consistent with fusion of copied parts (Fig. 1d). For example, copied protein domains often join together to generate a new gene. Another example of fusion is expression of genes in new combinations, a process termed co-option [reviewed in 7]. A primary goal of this paper is to review cases in nervous system evolution that provide specific and more detailed mechanisms that account for these patterns at different levels of biological organization.

The patterns in figure 1 are produce by a number of different mechanisms, including gene duplication, alternative splicing, retrotransposition, co-option, etc.

[The specific mechanisms leading to the general patterns is the topic of the rest of the paper from which this excerpt is taken].

References Cited
1. Striedter GF: Principles of Brain Evolution. Sunderland, MA: Sinauer; 2005.

2. Adami C, Ofria C, Collier TC: Evolution of biological complexity. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:4463-4468.
3. Adamowicz SJ, Purvis A, Wills MA: Increasing morphological complexity in multiple parallel lineages of the Crustacea. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:4786-4791.
4. Bonner JT: The Evolution of Complexity. Princeton: Princeton University Press; 1988.
5. McShea DW: Functional complexity in organisms: Parts as proxies. Biology & Philosophy 2000, 15:641-668.
6. McShea DW, Venit EP: What is a part? In The Character Concept in Evolutionary Biology. Edited by Wagner GP: Academic Press; 2001:259-284.
7. True JR, Carroll SB: Gene co-option in physiological and morphological evolution. Annual Review of Cell and Developmental Biology 2002, 18:53-80.

Evolutionary novelty: Photosynthetic slug

2008-11-20T13:13:00.000-08:00

All of biology, from genes to species, is united by common descent. Therefore new biological entities – novelties – must come from the modification of existing entities. Lightening does not strike and impart new features into organisms; new features evolve from existing ones. New research in PNAS provides fascinating new insights into the evolutionary origin of a 'photosynthetic slug'.

Given new features evolve from existing ones, one way novelties originate is through duplication and divergence. Another way is through new combinations of existing biological entities. In fact, biological entities can be recombined at many levels. Protein domains fuse to form new genes, genes become expressed together in new combinations in developmental time or space, even species can merge together to form new species, as occurred at the origin of eukaryotic cells when one species merged with a bacteria that became our cells’ energy factories, the mitochondria.

Imagine if evolution happened to produce a photosynthetic animal, and ask, what are some of the ways it might happen? One likely way is to utilize existing organisms (or their genes) that already have the ability to convert light energy into chemical energy. This is exactly what has happened during the evolution of the gastropod mollusk Elysia chlorotica, a green “sea slug”. Like other types of animal including reef-building corals, E. chlorotica harbors the photosynthetic machinery of other organisms. In the case of reef corals, a symbiotic relationship with dinoflagellates provides photosynthetic ability. But in the green sea slug, only the photosynthetic machinery itself is sequestered, by ingesting an algae, and using the algae’s plastids, the photosynthetic sub-cellular structure of the algae (interestingly, the plastid joined the algal cell in an ancient novel merger of species).

This presents a puzzle. The algae’s plastid, which is being used by the green sea slug for photosynthesis, does not itself contain all of the machinery required for photosynthesis. Instead, many of the photosynthesis genes reside in the algae, only some reside in the plastid. Yet the green sea slug can photosynthesize for months using only the plastid, even in the absence of algae, and therefore in the absence of the algae’s photosynthesis machinery. How is this possible?

The authors found that at least one gene (psbO) is integrated into the genome of the green sea slug. This gene is identical in sequence to an algal gene, yet the sequence adjacent to the gene in the slug analyses make clear that the gene is in the slug’s genome and not an experimental artifact, like contamination.

As the authors indicate, this work raises many interesting questions. How does the slug’s gene target the plastids? What about all the other genes absent from the plastid that are required for photosynthesis – are those transferred to the slug, too? Or could some of the slug’s genes replace the function of the missing genes? What is the specific mechanism for horizontal transfer of genes from one species to another? Clearly, the authors are thinking about these interesting questions, and likely future research will provide us with answers.

I noticed that Carl Zimmer already posted on this article in his fine blog, The Loom

Self-promotion*

As I wrote in an article with Michael Rose called “The New Biology: Beyond the Modern Synthesis”, acceptance of biological mergers was slow, perhaps because the modern synthesis viewed genomes as sleekly functional, finely tuned to current utility. As such, moving genes from one genome to another seems like it should be suboptimal, and therefore rare. No one doubts the importance of biological mergers any more, but they are still fascinating and under-documented, in part because they were neglected for so long.

*One reason I write blog entries is to present my research interests and ideas to a potentially broader audience. As such, I like to like papers of mine when possible.

M. E. Rumpho, J. M. Worful, J. Lee, K. Kannan, M. S. Tyler, D. Bhattacharya, A. Moustafa, J. R. Manhart (2008). From the Cover: Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica Proceedings of the National Academy of Sciences, 105 (46), 17867-17871 DOI: 10.1073/pnas.0804968105

There once was a man named Chuck

2008-11-18T22:09:00.001-08:00

I decided to write a quick Darwin Limerick, inspired by the contest over at Dispersal of Darwin, and by the concepts of pluralistic Darwinism and common descent:

There once was a man from Down House
Who convinced me I'm cousin to a brown mouse
I'm glad as can be
That all life is a tree
Toe fungus to red grouse to crown louse

I'm still working on "There once was a man named Chuck"

Evolutionary Novelty: Hair

2008-11-11T22:13:00.000-08:00

Mammals have hair but no other animals do. As such, hair is a clear evolutionary novelty, present in one group but absent in all others. In my macroevolution course (EEMB 102), I use hair as a clear character that can be used in phylogenetics. Hair groups all mammals to the exclusion of other organisms. In systematics jargon, hair is therefore a “synapomorphy”, grouping mammals together.

We can map the trait of hair on a family tree of animals. From this perspective, we can infer that the ancestor of all mammals very likely had hair, but that the ancestor of sauropods (birds, reptiles, and mammals) lacked hair. Therefore, hair originated prior to the common ancestor of all mammals.

Figure 1 – Hair originated before mammals, but after the common ancestor of birds, reptiles and mammals. Grey ellipse (hard to see except as a broken branch, I'd fix it but I'm too lazy) is the origin of hair keratin protein.

So where did hair come from - how did this evolutionary novelty evolve? A new paper by Eckhart et al in PNAS [link] provides evidence that the building blocks of hair pre-date the origin of hair itself. Namely, they found alpha-keratin (“hair keratin”) proteins are encoded in the genomes of chickens and the green anole lizard. In the green anole they studied, ‘hair keratin’ proteins were used in claws.

Just ten years ago, results like this 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 in this case). And that could only get science so far. In the case of hair, it mainly got science as far as Figure 1, which leads to the inference that hair evolved a bit before the common ancestor of living mammals. But “hair” is not one thing. It is a complex of building blocks, including structural genes (like keratin) and developmental processes. Today, scientists can decompose a trait, like hair, into its components and study the evolutionary history of each part separately, tracing the parts through various genomes.

What do we expect for the evolution of hair’s components? Figure 1 suggests that “hair” and all its components arise at the same time, near the origin of mammals. The origin of “hair” on figure 1 can be considered a first-pass hypothesis for the origins of ALL the components of hair. If hair itself originated near the origin of mammals, a logical idea is that the components originated then too.

Today, we can test this first-pass hypothesis because we know some of the molecular components of hair. A particularly important part is “hair keratin”. Mutate this protein and the hair built from that mutant protein is fragile and brittle. The expectation based on figure 1 is that hair keratin proteins originated with hair itself. But the discovery of these genes in an anole indicates an earlier origin for this component. In other words, components of hair originated before hair itself. In this case the protein “hardened” by mutations to cysteine amino acids that may have functioned to molecularly harden the proteins. Since these changes were later useful in the structure of hair, they may be considered exaptations, features that originated for functions other than current utility: keratins may have hardened before that feature became useful for hair formation. [Note for scientific accuracy – the biochemistry of the anole protein has not been studied, so while it is cysteine rich, we don’t know yet if the anole protein is ‘hardened’].

This work also illustrates that in evolution, new things do not appear from nowhere [see my post Coming to Grips]. In evolution, new things come from the duplication/differential modification and recombination of existing parts. Morphologists know this, as one dominant idea about the origin of hair is that hair evolved by modification of scales. Hair keratin is not expressed in anole scales, so the scale hypothesis is not supported by the new PNAS paper. Also unfortunate for the scale hypothesis is the fact that the fossil record retains no transitional forms between scale and hair. Even though morphological relatives of hair are ambiguous, the molecular relatives in this case are clear. Hardened keratin comes as two types, which share an evolutionary relationship, and hardened keratins may share an evolutionary relationship with soft keratins, proteins that are present in numerous tetrapods, and therefore have a more ancient origin than the hard variety. In sum, keratin has an ancient heritage, and through gene duplications and differential modification, two related groups of these proteins have specialized as hair keratins. Fascinatingly, some of the hair keratin modifications pre-dated hair itself.

If you are interested phylogenetic analyses of trait evolution, and the evolutionary history of trait components, this is a common theme of research in my lab.

We’ve found:

Synaptic components are present in sponges and therefore may predate synapses. [paper] [blog]

Phototransduction components were first assembled for vision in the eumetazoan ancestor (cnidaria + bilateria), yet some components pre-date animals [blog] [blog] [paper] [paper]

See also: Red Herring Blog

Probing Darwin's Black Box

2008-11-10T17:01:00.000-08:00

The 'God of the Gaps' strategy is to assert that anything we do not yet understand is attributable to a god or gods. Two thousand years ago there were a lot of gaps in our understanding, and plenty of room for inventing ad hoc explanations for things. There were a lot of gaps where gods might reside.

Even recently, the god of the gaps argument is sometimes used. One example is the idea of 'Darwin's black box', the false assertion that the exquisite details of molecular biology cannot be understood in an evolutionary context.

There are two facets of 'god of the gaps' that are particularly bankrupt, one scientific and one theological. Scientifically, god of the gaps is equivalent to suicide, an admission that one simply cannot imagine how to go on any farther. God of the gaps is giving up on science, with no reason to do so. Theologically, god of the gaps means that the realm of god gets smaller each time a gap in our knowledge is filled.

Here, I give two recent examples from my life where the molecular details of evolution have been explicated in greater detail. In neither case are the gaps fully filled - this can never be the case - split a gap in half and we have two smaller gaps. But the gaps are getting sooo small - is it really worth trying to stuff gods in those tiny little gaps?

First, I saw a seminar by Joe Thornton on his work on the evolution of steriod receptors. Joe uses statistical inference to reconstruct the sequence of ancestral proteins. Then he brings them to life in the lab and conducts experiments on the proteins. He is able to reconstruct the order of specific mutations that occurred and that change the function of the proteins he studies.

I found particularly interesting that one particular receptor could identify 3 different steroids at the origin of the protein. Later on, specializations occurred through particular mutations that Joe and his group could identify. When thinking about the evolution of novelty, we often assume that multiple functions are added over evolutionary time. However, Joe's results show how functional complexity can be the original state, and that structural complexity can follow by parsing an ancestral function across subsequently duplicated genes.

To view Joe's presentation, go here.

The second recent example is that a paper from my lab was recently published that reviews our progress on understanding the evolution of the molecular basis of vision (phototransduction). This paper is available for free from the Springer web site.

Todd Oakley and M. Sabrina Pankey (2008) Opening the "Black Box": The genetic and biochemical basis of eye evolution. Evolution Education and Outreach. [Link]

Linear Evolution: McCain and Obama

2008-11-03T11:55:00.000-08:00

A common theme of this blog is to share cases of "linear evolutionary thinking". These are instances, usually graphics, that illustrate the common conception of evolution as a line of progress, from worst to best. Evolution actually occurs by branching processes. We could pull out a line of evolution from the tree, but that line by necessity has an arbitrary endpoint, often humans or a human-like feature. And living species or their traits cannot necessarily be equated with ancestral forms.

Ostracod eye evolution has been depicted as a straight line from simple to compound eye, illustrated here. Textbooks use such diagrams (see also this), and these diagrams can impact the way people think about evolution.

Here is another variation on the human march of progress, which shows Barack Obama as the more advanced political candidate, compared to John McCain.

Thanks to my brother for sending this to me.

New Blog

2008-10-29T14:18:00.000-07:00

I've noticed that a former student who worked in our lab has started a blog called Pleion. Bjørn enjoys discussing evolution and politics, cannibalism, and teasing Americans for not being able to pronounce "Bjørn Østman". He was made for blogging because he likes to be provocative. If you do go over there, ignore the post on predictions for Obama's first term, or else you'll get the wrong idea about him. If you do read that post, make sure to click on the links [English] to help clarify the sarcasm.

You can pick your friends - etc

2008-10-27T08:46:00.000-07:00

When I give presentations, I always try to have a joke prepared in case of technical difficulties. This came in handy when I gave a symposium talk a few years back at Chico State, at the Botany meetings (long story, I'm no botanist... not that there's anything WRONG with being a botanist). The talks were delivered on a large stage, so my joke was that if the slides went out ... which they did temporarily... I'd offer to use the stage to do an interpretive dance of my research presentation. I got a pretty good laugh, pretending like it was completely spontaneous.

Little did I know that interpretive dance is such a powerful medium for scientific communication. Check gonzo scientist for the contest here.

And a plug for my colleague Wendy Grus. I first met Wendy at the evolution meetings in Alaska a few years back, and I took notice of her research on receptors expressed in the vomeronasal organs of vertebrates. She didn't dance in Alaska - at least not that I know of. But she does have an interpretive dance of her PhD work up on YouTube for the contest. She uses sparkly gene phylogenies to reel in odorants. Pay her video a visit - she could win a trip to Chicago, and professional choreography service:

Wendy is quite multi-talented. Check out the music video to her smash hit new single, Seminarcolepsy:

Optical Allusions Book Review

2008-10-23T08:53:00.000-07:00

As mentioned at The Loom, and Genomicron, there is a new issue of Evolution, Education and Outreach available, devoted to my favorite topic, the evolution of eyes. I've contributed two pieces, one is available now, and is a book review of Optical Allusions, by Jay Hosler.

Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley

The other paper I contributed is inspired in part by Behe's claim of irreducible complexity of phototransduction in Darwin's Black Box. That paper is not available yet, but should be soon. For a small taste of the paper, I will quote from the it:

"Unfortunately, instead of pointing to the molecular evolution of multi-component systems as a rich area for new scientific research and synthesis, Behe chose to commit scientific suicide by incorrectly claiming that the only way for multi-step biochemistry to arise is by intelligent design."

Phylogeny, evolution, biodiversity and ecology

2008-10-20T18:08:00.000-07:00

We are in the midst of massive upheaval in the world’s ecosystems, driven by species invasions and the sixth mass extinction in Earth’s history. How will these changes in biodiversity affect the functions of ecological communities? Will the functions of ecological systems that humans rely on for survival, such as production of oxygen, be impacted by all this upheaval?

Answering these questions requires that biologists have a good metric for biodiversity. New research by Marc Cadotte, Brad Cardinale and I, and published this week in Proceedings of the National Academy of Sciences, indicates that one particular metric of biodiversity - evolutionary diversity - is a particularly strong predictor of the biomass produced in plant communities: The more biodiversity present (measured as evolutionary diversity), the more productive the community. In fact, for the datasets we examined, evolutionary diversity was a better predictor of productivity than raw species number or number of functional groups in the community. This suggests that the most evolutionarily diverse communities may function best, and that the most evolutionarily distinct species might be the best targets of conservation efforts aimed at maximizing ecosystem productivity.

Measuring Biodiversity
One common theme in current ecological research is to ask questions about how changes in biodiversity impact or influence ecological systems or communities. This has obvious importance when we know that many species are going extinct, and that many species are being shipped around the world by human transportation. Often in ecological research, a measure of biodiversity is placed on the X-axis, and some predicted response is placed on the Y-axis, to test if there is a strong relationship. For example, one might predict that less diverse and simpler communities are more susceptible to invasive species compared to more diverse and complex communities. One might also predict that more ecological diversity leads to a healthier ecosystem, as measured by higher production. Namely, a higher diversity of organisms could make more efficient or more complete use of available resources, ultimately leading to a healthier, better functioning ecosystem.

These types of ecological studies usually use a measure of biodiversity referred to as “species richness” as the X-axis variable. “Species richness” is simply a count of the number of species. However, simply counting species makes the assumption that, say, two very closely related grass species contribute the same amount to the diversity measure as two much more distantly related species, such as a grass and a magnolia. In contrast to this implicit assumption of “species richness”, phylogeneticists often think of biodiversity in terms of evolutionary relationships, assuming that differences between species (one way to conceive of diversity) accumulate over the time since they last shared a common ancestor. To a phylogeneticist then, species that share a very recent common ancestor – like the two similar grasses mentioned above – should be nearly identical and therefore represent less total diversity compared to the much more distantly related grass and magnolia species.

We wondered if evolutionary diversity really does matter for predicting how much biomass a community produces, one measure of the health of ecological communities. Decades of experiments have already established that species number (“species richness”) is in fact correlated with productivity – the more species of plants growing together, the more biomass is produced. We extended these studies, weighing different species by how closely related they are evolutionarily. Could we better predict biomass production by also accounting for evolutionary (phylogenetic) diversity? Based on our analyses, the answer was a clear “yes”. Incorporating evolutionary distances into our biodiversity metric resulted in better predictive power of the productiveness of experimental plant communities. The metric including evolutionary history was better than “species richness” and better than the number of functional plant groups, two commonly used metrics of biodiversity.

Our data set was a collection of 40 different previously published experimental studies, conducted around the world using a total of 177 different species of flowering plants. Researchers planted experimental ecological communities, using many different combinations of plant species, and using different numbers of species. Then they let the communities grow, and measured the biomass produced by the different combinations. We added an analysis of the phylogenetic relationships of the plants using publicly available genetic data from four different genes commonly used in other studies of plant phylogeny.

Phylogenetics and Nihilism

Do all ecologists now need to become phylogeneticists? This question is similar to one asked of comparative biologists in the mid 1980’s.

In 1985, Joe Felsenstein wrote a landmark paper introducing the method of phylogenetic independent contrasts, which is now standard in comparative biology. The core message is that we cannot treat species as independent entities because they share a nested set of common ancestors. In other words, species are similar because of descent, not only because of adaptations, and traits might be correlated across species because of shared evolutionary history. At that time, comparative biologists were told they must consider phylogeny when testing for correlations among traits. Felsenstein addressed the question, “What if we do not take phylogeny into consideration [in comparative biology]?” His answer:

“Some reviewers of this paper felt that the message was “rather nihilistic,” and suggested that it would be much improved if I could present a simple and robust method that obviated the need to have an accurate knowledge of the phylogeny. I entirely sympathize, but do not have a method that solves the problem…. Comparative biologists may understandably feel frustrated upon being told that they need to know the phylogenies of their groups in detail, when this is not something that they had much interest in knowing. Nevertheless, efforts to cope with the effects of the phylogeny will have to be made. Phylogenies are fundamental to comparative biology; there is no doing it without taking them into account.”
-Felsenstein (1985)

Although other systems and other questions might differ from our study in how diversity relates to ecological processes, it seems to me that counting species is far too simplistic of a metric of biodiversity. If adding phylogenetic information was valuable in one case, it seems worthy of strong consideration any time a metric of diversity is below the X-axis in a graph. To paraphrase Joe, ecologists may understandably feel frustrated upon being told that they need to know the phylogenies of their groups in detail, when this is not something that they had much interest in knowing. Nevertheless, the evolutionary history of their focal communities or systems will often have a lot to tell them. Species are not independent entities, and biodiversity cannot be measured as if they were.

M. W. Cadotte, B. J. Cardinale, T. H. Oakley (2008). Evolutionary history and the effect of biodiversity on plant productivity Proceedings of the National Academy of Sciences, 105 (44), 17012-17017 DOI: 10.1073/pnas.0805962105

Tawk Amongst Yah-selves

2008-10-15T08:35:00.000-07:00

Anyone seen an old SNL skit called Cawfee Tawk, where Mike Myers, dressed as a women, hosted a talk show? Every once in a while s/he became vaclempt, and would throw out a topic to discuss. Tawk amongst yah-selves s/he would say, before collecting him/herself.

I keep a few topics for discussion in mind, for different situations (not directly from SNL, those were much funnier than my bio-geek stuff). Still, they are quite useful for breaking out of one of those awkward silences that can occur when a group of semi-strangers is talking together. I'll throw one out at a conference or at a bar, and think "Tawk amongst yah-selves". I usually like to sit back and listen, whether vaclempt or not.

If I am with a group of physiologists or evolutionists, I throw out this one:

Why has bioluminescence evolved SO many times in the marine environment, but almost never in freshwater environments?

Or, if you're more interested in one for a bar that includes someone other than a biologist -

Why are all the best rock bands British, but all the best individuals of rock n roll American?

A joke creationists don't get

2008-10-10T16:44:00.000-07:00

My daughter told me a joke just the other day with two alternative punchlines, neither of which any young-earth creationist would understand:

1. Why did T. rex cross the road?

Answers in the comments

Ostra-blog 6 - Ostracodology and the Nobel Prize

2008-10-08T13:40:00.000-07:00

Dagummit! I've been scooped again by the guys at the other 95% by this post: The Other 95%: The Nobel Jelly - Aequorea victoria . They point out that one of the winners of this year's Nobel Prize for chemistry is marine biologist, chemist, and one time ostracodologist, Osamu Shimomura. [By the way, I didn't invent the word ostracodologist - we actually use that to describe ourselves].

Early in his career, Shimomura studied bioluminescence in Vargula hilgendorfii (he called it Cypridina hilgendorfii, which is a synonym for Vargula hilgendorfii. Vargula is usually used today, the taxonomy is a bit complicated, and I won't go into it here). After that, Shimomura went to work on the jellyfish Aequorea and its bioluminescence. It turns out that Aequorea produces light with a protein called aequorin, which sends light to another protein (Green Flourescent Protein=GFP) that emits green fluorescence. GFP is today used in all sorts of applications, as Eric at TO95% nicely explained.

There also is one more connection between GFP and ostracodology. An ostracodologist actually named GFP (Morin and Hastings, 1971)! Jim Morin is a prominent ostracodologist, who, with Anne Cohen has described, in often exquisite detail, the biology of bioluminescent ostracods from the Caribbean. In my talks on ostracods, I often use a slide based on their work:

Fig 1. Small blue circles represent discrete flashes of light produced by male bioluminescent cypridinid ostracods. Patterns of different species are illustrated, with white arrows showing the direction of swimming of an individual animal producing the pattern over time. Each pattern is characteristic of a different species and are performed above different microhabitats. Original figure in black and white line drawing by Jim Morin and Anne Cohen. Color and photos added by T. Oakley.

Male ostracods of this family signal to females using flashes of light in rather complex species-specific patterns, often over sterotyped microhabitats. These Caribbean species are related to Vargula hilgendorfii (ostrablog 5), which does not signal. In the Caribbean species, there are even "sneaker males", males that follow a signalling male, without using the energy to signal themselves, in an attempt to mate with females attracted to those signals. I guess in bars, humans call this something like a "wing man".

I think this is a great example of how solid basic research will often lead to great advances. Shimomura was interested in bioluminescence because of pure scientific curiosity. I doubt he was aiming for a Nobel. The general public often does not understand this. In the 1970's, I'm sure some people wondered why anyone would want to spend enormous time and energy studying a glowing protein of a jellyfish. But that scientific curiosity has now paid big dividends!

Fallen Giants

2008-10-07T01:42:00.000-07:00

In the 1880's loggers felled many ancient and giant sequoia trees in an area that is now in King's Canyon National Park. The wood from these majestic trees is brittle, and mostly wasted when the trees would shatter upon impacting the ground. The 50% or so of the timber that did make it to the mills was probably used for shingles, fence posts, or matchsticks. High tannin levels make sequoia wood resistant to decay, so remnants of the fallen giants remain to this day. I visited Big Stump Grove on Saturday while clouds shrouded the tops of the living trees and drips of rain fell from the skies. Giant blackened stumps were like ghosts and piles of sawdust like blood stains.

(These pictures were snapped from my little Mino Flip Video camera because I forgot to take my still camera. I like this little video camera more and more, the more I use it.)

UCSB Job

2008-09-29T15:40:00.000-07:00

Assistant Professor - UCSB - Evolutionary Genomics

The Department of Ecology, Evolution, and Marine Biology at the University of California, Santa Barbara invites applications for a tenure-track faculty position starting at the rank of Assistant Professor. We are searching broadly for an interactive scientist who addresses fundamental questions in evolutionary biology via analysis of large-scale gene sequence and/or expression data sets. Applications from those who can take advantage of UCSB’s world class marine facilities and international standing in marine biology are especially encouraged. The successful candidate is expected to develop an internationally recognized research program and to teach graduate and undergraduate students in his or her area of expertise. The successful applicant will have a PhD and clear evidence of research productivity.

Applicants should submit 1) an application letter 2) a curriculum vitae 3) a statement of research accomplishments and future plans 4) a statement of teaching experience and interests, 5) up to three selected publications and 6) names and contact information of three persons willing to provide letters of reference (the committee will solicit letters for a short-list of candidates). Submit applications to:

Evolution Search Committee
Department of Ecology, Evolution, and Marine Biology
University of California
Santa Barbara, CA 93106-9610 U.S.A

Alternatively, applications can be sent electronically, and questions addressed to:
evolutionsearch@lifesci.ucsb.edu

Review of applicants will begin November 1 and will continue until the position has been filled

The department is especially interested in candidates who can contribute to the diversity and excellence of the academic community through research, teaching and service

UCSB is an Equal Opportunity Affirmative Action Employer

Chance and Necessity: The fate of graduate students

2008-09-23T21:44:00.000-07:00

There have been a few posts relating to a story in Science about the fate of 30 students who began graduate school at Yale in 1991.

Chance and Necessity: The fate of graduate students

Sandwalk: What Happened....?

The upshot is that most of those students in the story are not currently in tenure track academic jobs. This has inspired me to complete a little exercise that I've been meaning to do for a while - to list some of my graduate colleagues from Duke and where we are now. It is truly amazing how such a large number of us have landed really good academic jobs. I'm not sure if the late 1990's was a special time at Duke, or whether the early 2000's were a ripe time for academic jobs in general (or both). Perhaps Duke grads always do well in the academic job market. This is not a scientific study. I am only conveying the awe I have for my own graduate experience, and the gratitude I have for being able to be surrounded by a tremendous group of students. I think we all raised the bar for each other, and of course this was all possible because of the collaborative and empowering environment fostered by Duke Biology faculty. Here are some of the folks who started or ended graduate school about the same time I did at Duke. I was there 1996-2001. This list is straight off the top of my head, in no particular order (except my lab and office mates are first), and I am certain that I am forgetting people. I apologize to them. Yet the point still stands, we did okay.

Todd Oakley (me) Professor Univ. CA Santa Barbara
John Wares, Professor University of Georgia
Mike Hickerson, Professor Queens College NY
Mike Gilchrist, Professor University of Tennessee
Laura Miller, Professor University of North Carolina
Rebecca Zufall, Professor University of Houston
John Stinchcomb, Professor University of Toronto
Sheila Patek, Professor U-Mass-Amhurst
Kirk Zigler, Professor Sewanee University
Armin Moczek, Professor Indiana University
Matt Hahn, Professor Indiana University
Leonie Moyle, Professor Indiana University
Matt Rockman, Professor NYU
Ehab Abouheif, Professor, McGill University
Peter Tiffin, Professor, University of Minnesota
Tami Mendelson, Professor, U Maryland-BC
Janneke Hille Ris Lambers, Professor, University of Washington
Anne Pringle, Professor Harvard University

Even now, this is a great academic network (some call it the Duke Mafia, especially after they witness the secret handshake).

It's all been done

2008-09-15T14:01:00.000-07:00

A few people have liked the idea of bioluminescent beverages, after I posted a picture of glowing ostracods in a wine glass. Sounds like fun, but we'd have to pay royalties. An existing patent seems pretty comprehensive, even including "slimy play material".

This patent represents the origin of novel novelty items by combining entities: manufactured articles and bioluminescence.

Title:

Bioluminescent novelty items

Document Type and Number:

United States Patent 6152358

Abstract:

Novelty items that are combinations of articles of manufacture with bioluminescence generating systems and/or fluorescent proteins are provided. These novelty items, which are articles of manufacture, are designed for entertainment, recreation and amusement, and include toys, paints, slimy play material, textiles, particularly clothing, bubbles in bubble making toys and other toys that produce bubbles, balloons, personal items, such as cosmetics, bath powders, body lotions, gels, powders and creams, toothpastes and other dentifrices, soaps, body paints, and bubble bath, foods, such as gelatins, icings and frostings, beverages such as beer, wine, champagne, soft drinks, and glowing ice, fountains, including liquid "fireworks" and other such jets or sprays or aerosols of compositions that are solutions, mixtures, suspensions, powders, pastes, particles or other suitable formulation.

Ostrablog 5 - Three shows and a funeral

2008-09-09T21:57:00.000-07:00

In 1998, I spent nine weeks in Japan in an international graduate student program co-sponsored by the National Science Foundation of the United States and the Japanese ministry of Science, Monbusho. The trip was for me a memorable and life-changing experience I many ways. Besides a high school trip to Mexico, Japan was my first trip abroad, and the magnitude of cultural differences between the US and Japan was a big part of the memories. For me, immersion in a different culture is mind-stretching. If you haven’t been to Japan and want to get a sense of what I mean, I found the film Lost In Translation to be quite a good [although decidedly amplified and somewhat stereotyped] facsimile of total immersion in the culture. Besides culture shock, another vivid memory of my Japan trip involves the subject of today’s ostra-blog, the ostracod Vargula hilgendorfii.

Vargula hilgendorfii. Male on top female on bottom. Image from umiho.net

Vargula hilgendorfii is known to the Japanese as ‘umihotaru’. “Umi” means “sea” and “hotaru” means "firefly". Umihotaru are vividly, potently, bioluminescent. When threatened, they spit out a liquid cloud of light that is the blue of a sun-drenched Caribbean bay. The animal is only about 2 mm in length, roughly the size and shape of a sesame seed. Yet the “light bomb” (as one of my Japanese friends called it) can be seen from meters away. To detonate this bomb, umihotaru spits out an enzyme and its substrate from glands on its “upper lip”, an organ just above its mouth that also spits out digestive enzymes. My Japanese advisor and host, Katsumi Abe, had the idea that the light producing enzyme is actually derived from a digestive enzyme, and evolutionary novelty that arose by duplication and divergence. It was hundreds of light-vomiting umihotaru that provided one of my most potent, and decidedly surreal memories of my Japanese adventure.

Light from the ostracods of the species Vargula hilgendorfii. Image from http://www.kanko-otakara.jp

Imagine a nearly full sheet of plywood (4 x 8 feet) standing in the back of the room. Attached to the plywood are rows and rows of vials filled with seawater. The vials are capped and through each cap runs two thin wires, dipping into the water. The wires all bundle together behind the plywood and snake back to a console. The console looks like a mixing board at a rock concert, with a row of sliders. The consoled is plugged into an electrical outlet in the wall so that the wires can deliver a potentiated jolt of electricity to the vials of sea water. I would soon find out that swimming in the numerous vials of seawater, were hundreds of ostracods, umihotaru.

While I examined this strange contraption, trying to imagine the purpose, the room lights when dark, and cheesy, achingly theatrical, synthesized new age music filled the room. An operator took his position behind the electric console, leaning forward with his hands on the sliders like a rock star keyboard player. He dexterously began moving the sliders in time with the music, sending pulses of electricity into the bodies of the umihotaru. They felt threatened, and they were vomiting their luciferase enzymes into the vials of brine, producing effervescent azure explosions of light, pulsing in time with the music.

The vials were not the only part of the show. Hidden behind curtains, the electric console-wielding front man had assistants. Poised precariously on top of a step ladders, their instruments were funnels aquarium nets and buckets of water. Inside the nets? Hundreds more umihotaru! Precisely choreographed with the music, the assistants vigorously poured water into the nets of umihotaru. Too large to pass through the nets, the water coursing over them threatens them until they spit out their light, illuminating the coursing water. The water cascaded into the funnels, which were directly attached to clear aquarium tubing. The tubing ran the length of the room, 30 feet at least, descending and arcing gracefully like garland at Christmas time. The water stayed lit on its journey through the tubes, the entire length of the room. The same electric blue that pulsed in the vials punctuated cymbal crashes by coursing through the tubing.

As if that weren’t enough, umihotaru was on display in one more way. Larger clear tubing hung in “U” shapes in a few places in the room. One each side of the U, wires ran, connecting back to the electric console. These larger tubes stayed filled with seawater, and again, umihotaru swam in the water. Dedicated sliders jolted the U with electricity, and umihotaru swam, leaving behind illuminated contrails, like tiny psychedelic fighter jets – and again choreographed to the blaring music.

I’ve told this story many times, and depending on my mood, and how well I know the listeners, I will sometimes stop here. People laugh incredulously, ask a question or two, and we move on to other stories. Because the story takes a more somber turn here, I often leave out the most unbelievable part of the story. The kitchy, surreal display I just described actually began the funeral of my Japanese advisor Katsumi Abe. People even took pictures and video. Of a funeral.

A week earlier, Abe was tragically killed when his car struck an oncoming truck head on. He was young, in his mid-40s I suppose, full of energy, full of life. He had five children. I was one of the last people to see him alive. He left a conference that we were at late at night. He probably fell asleep at the wheel and never woke up. I felt so alone in that foreign land without my host and I felt guilty for feeling alone. What right did I have to feel bad, compared to five children who lost their dad, or to a wife who lost her husband? The night after the funeral, I had to go to Tokyo. My plane was scheduled to leave the next day. Fitting my mood, a torrential storm from a typhoon drenched me while I waited for trains with a Japanese friend who kindly escorted me. He also was at the funeral and knew Abe well. A few days later, I would be a world away in sunny Bermuda to collect other ostracods. But no matter the distance I travel, I will never forget Japan. Abe wrote a book in Japanese which translates to "The Light of the Marine Firefly". Whenever I see that electric blue light, I think of him.

Ostra-blog 4 - Colymbosathon ecplecticos

2008-09-02T03:27:00.000-07:00

Last week, somewhere near the top of my mental list of candidate species for ostra-blogs was Colymbosathon ecplecticos. A couple years ago, this species burst on to the ostracod scene, causing a global media event. Ostracodologists are not used to seeing their favorite animals in the headlines, so Colymbosathon caused quite a sensation. On Friday, Eric at The Other 95% generated a post, Who's Got the Oldest?, with Colymbosathon playing the prominent role. Eric described some of the species' vitals. Yes, it's the oldest fossil with identifiable male parts. Yes, its species name means "amazing swimmer with a large penis". Eric's post prompted me to make Colymbosathon the star of this, ostra-blog #4.

Colymbosathon first exposed itself to me at a scientific conference. I was immediately drawn to its rather prominent.... eyes. We were in Seattle in November of 2003, about a month before the Science paper was to be published, and cause the aforementioned media blitz. So it came as a complete surprise to me when the first picture of this 425 year-old fossil flashed on the screen. I remember a seeing on the screen a photo similar to Figure 1 below.

Figure 1. Colymbosathon ecplecticos, a 425 million year old fossil ostracod. Image copyright Science Magazine.

I study ostracod eyes, and I've dissected many of them. My attention went directly to the compound eyes. One is marked "le" in the figure above for "lateral eye". That's the left eye, the right eye is higher on this figure, just below the "H" in the figure.

This fossil was preserved about 425 million years ago in three dimensions inside a volcanic nodule. The scientists break open such nodules in search of interesting fossils. When they find one, they make an image of the fossil at the point it broke, and then grind away a tiny bit of rock (10 microns or so, if memory serves) and take another picture. Doing this procedure over and over again gives them a stack of images, which they can put together computationally to yield full 3-dimensional reconstructions of the fossils. For ostracods and other small animals, this is completely amazing. For most ostracod fossils, only their carapace is preserved, it's made of calcium carbonate. On a few fairly rare occasions the "soft parts" of ostracods are also preserved. (Soft parts refers to the non-carapace parts, even though they are not all that soft, having a chitinous exoskeleton). But even when soft parts are preserved, there were no cases where the full 3-dimensional structure was visible. With digital reconstructions, movies can be made, and specific parts of the animal can be highlighted or removed in order to view other structures.

Figure 2 - Computer generated image of Colymbosathon (side view). Different parts of the animal are colorized differently to make them easier to see. Faint parallel lines are visible, which is where the original was ground, 10 microns at a time, to yield an image stack of the 3-dimensionally preserved fossil. Image copyright Science Magazine.

It was obvious right away that this was something very special. It clearly impacted my own work on ostracod eye evolution. This marked the oldest ostracod compound eye in the fossil record, pushing back the date some 200 million years. In 2002, I published a molecular phylogeny of ostracods that shows that ostracods with lateral compound eyes are nested phylogenetically within multiple groups that lack lateral eyes. One possible interpretation of this is that lateral eyes evolved within Ostracoda (of course eyes don't evolve from nothing, so if this idea is true, many of the genes used in all animal eyes should still be present in the ostracod lateral eyes). Colymbosathon doesn't itself change these conclusions because it is a member of the same group (myodocopids) that today have lateral eyes. Nevertheless, the Colymbosathon fossil pushes back the origin of ostracod compound eyes quite a bit.

Of course not many other people cared about the eyes. They had other things on their mind. In particular, many journalists really rose to the occasion, devising many very entertaining headlines. Some of my favorites are below, and I've taken the liberty to put them into a few categories.

1. The "size matters" category

Scientists Discover Ancient Gargantuan Penis
Sea creature impressive in its maleness
Well-endowed sea creature is nearly half a billion years old
He's 425 million years old and clearly virile
Male fossil makes a big impression

2. The "age before beauty" category

Ancient penis brings fame to lowly fossil
Oldest male fossil bares all
World's oldest genitals found in Scotland

3. Wonderful alliteration category

Phallic fossil found

4. And last but not least, the winkle category, a clipping of which hangs in the lab

Fossilised shrimp has the oldest winkle in the world

Evolutionary Novelty: Optical Allusions

2008-08-29T14:42:00.000-07:00

Below is a draft of a book review I am writing on Optical Allusions by Jay Hosler. Thanks to T. Ryan Gregory of Genomicron for asking me to do this, and thereby pointing this book out to me.

Optical Allusions, by Jay Hosler. Columbus, OH: Active Synapse, 2008. Pp 127. S/b $20.00.

The stereotypical scientist is focused: Intensely focused. Imagine an aging white man with wild, graying hair, and wide eyes behind thick, dark-rimmed glasses. He is so focused that nothing matters but science. A social life? Superfluous. Hobbies? Unnecessary. Fashion? “My neon pocket protector fits squarely in my lab coat”. Stereotypes often have some basis in reality, but they over-simplify, ignoring the complexities of life. True, scientists are usually focused and driven. But they are also people; usually well-rounded, intelligent people. My scientist-colleagues are musicians, athletes, artists, and naturalists. They travel, play video games, and care for children. Yet (probably owing at least in part to my own unconscious predilection to stereotype) I am often surprised and awed when I find examples of scientists who excel in an arena decidedly different from scientific pursuits. Surprise and awe was exactly my reaction when Optical Allusions by Jay Hosler showed up in my mailbox because the book displays not only Hosler’s talent for teaching science, but also for producing art.

My favorite thing about Optical Allusions is its originality. New things often come from the combination of established entities or traditions. Examples of this abound in eye evolution, a common topic on this blog. Even inventors have fused existing things into something new, such as the lottery ticket-scratcher that is a combination of coin and key chain (another hat tip for that example to Ryan Gregory). Even the word blog is provides a etymological version of fusion. The combination of comic book and educational scientific text, which Hosler has also used in two previous books, is the fantastically novel idea explored in Optical Allusions to convey information about evolution, eyes, and vision in the context of a fun and creative comic story. Having a comic story that introduces science concepts is a great advantage for visual learners (like me). Hosler has used his comic illustrations to great effect, producing several highly memorable images that convey scientific concepts.

Combining comics and science is not the only original feature. The comic story itself is wildly inventive. The story follows the main character, Wrinkles the Wonder Brain, who is a brain without a person – no stranger than all the people walking around without a brain, as Wrinkles points out. Oh, and by the way, that is not his bottom. It is his cerebellum, thank you very much. In Chapter 1, Wrinkles quickly encounters trouble when he accidentally drops a magic eye into a vat of distilled human imagination. Armed with a bagful of newt eyes that allow him to go where and when he wants, Wrinkles plunges (ploops) into the vat to try to retrieve the lost magic eye. This is no easy task. Human imagination is vast, as Hosler demonstrates with this book.

In Chapter 2, Wrinkles meets Charles Darwin on an island, sitting behind a stand that Charles obviously acquired from Lucy van Pelt of Peanuts fame (“the doctor is IN”). Darwin teaches Wrinkles how to make an eye using evolution. This takes 364,000 years (but only one comic page), with Wrinkles and Charles acting as predators on little brains that gradually evolve complex eyes to help evade predation. Charles Darwin yelling “tuck in kid”, before playing dominant predator on a gaggle of scurrying brains is one of the unforgettable images I mentioned. This is all fine and good for Wrinkles, but after all those millennia, he gets impatient. “When do the eyes become magical?” Wrinkles asks, anxious to find his lost magic eye. Darwin replies that magic only exists in books, and suggests that Wrinkles find the mythical Cyclops of Homer’s Odyssey. With a bite on one of the magic newt eyes, Wrinkles wishes to go to the Cyclops.

Charles Darwin and Wrinkles the Wonderbrain play a friendly game of "Dominant Predator" to illustrate how natural selection can gradually produce something even as complex as an eye. Image copyright Jay Hosler. It may not be copied without permission, except for a review. (I assume this means a book review, like I'm doing here, so I haven't asked for permission).

In Chapter 3 we discover there is one problem with Wrinkles’ wish: Cyclops is not only a mythical creature, but also a giant, killer eye-bot (spelled “C.Y.K.L.O.P.S.”) built by an evil villain named “The Perfectionist” as an exact robotic replica of a human eye. The superhero Cow-boy recruits Wrinkles and together they seek to destroy the killer eye-bot who is wreaking havoc on the town of Pasteurville. The Perfectionist has created a perfect replica of a human eye that even includes perfectly replicated imperfections. This leads to one of my favorite images of the book. Wrinkles and Cow-boy make their way to the retina, and Cow-boy teaches Wrinkles about the eye-bot’s perfectly copied blind spot. Cow-boy reaches down and yanks on a “cable” (a ganglion cell axon), uprooting a rod cell as if harvesting a carrot. “Why are rods buried beneath all those cables, shouldn’t they face the light?” asks Wrinkles. Cow-boy shows Wrinkles the blind spot, where all axons are bundled together to make the optic nerve, which plunges down through the retina, leaving no place for any rods or cones in that place. These images provide an immediate understanding of why we have a blind spot.

Wrinkles the Wonderbrain ponders the imperfections of the human eye with super hero Cow-Boy. Image copyright Jay Hosler. It may not be copied without permission, except for a review. (I assume this means a book review, like I'm doing here, so I haven't asked for permission).

Another of these replicated imperfections of real human eyes becomes the eye-bot’s Achilles heel. Cow-boy and Wrinkles find and block the Canal of Schlemm (which is labeled “Do Not Block”), producing a glaucoma that explodes the eye-bot. As Cow-boy hauls him away, The Perfectionist gets the last laugh by tricking Wrinkles into wishing he were tied up on a pirate ship. This wish comes true, and Wrinkles goes on to meet some pirates. But these are no ordinary pirates.

In Chapter 4, Wrinkles finds himself tied up on the deck of a pirate ship crewed by misfit stalk-eyed flies. After teaching the human captain and his wife that acquired traits (like lost limbs) are not passed to offspring, Wrinkles learns about the plight of the crew. Where they are from, there is strong discrimination – only the males with the longest eye stalks can mate. Long stalked flies are better at fighting, and the females also prefer longer stalks, which might be an indicator of better genes. The flies’ tale of heartache is a lesson for Wrinkles on sexual selection. But Wrinkles does not win any friends by bluntly distilling the flies’ story as a description of “a bunch of wimpy, unattractive guys with bad genes”. Those wimps also own a big cannon, which they use to shoot Wrinkles off the ship. A short time later, Wrinkles finds himself on another island.

This time, Wrinkles washes up on an island inhabited by Clio, the muse of history in Greek mythology. After another brief, but still striking visual, where Wrinkles demonstrates the function of his wrinkles by inflating, showing how they allow folding more brain into a small skull, Clio introduces Wrinkles to the Cyclops. This time, it is the Cyclops that Darwin suggested, Polyphemus. He goes by “Polly”. Although Polly lost his eye in a battle with Odysseus, he has the support of a bunch of cave animals that lost their eyes naturally, over evolutionary time. Wrinkles meets a blind cave fish, and after donning a pair of X-ray specs, he learns how cavefish lens cells die during development. In other vertebrates, the lens signals to the optic cup, and without those signals, cavefish eyes do not develop properly. Wrinkles learns that mutations occurred during the evolution of cavefish favored more taste receptors at the expense of eyes and this is probably the reason why cavefish lost their eyes during evolution. Clio asks Polly to take Wrinkles to the “cerebro-expand-o-matic” (the library), so Wrinkles can devise a plan to find the lost magic eye. During his five-year sabbatical, Wrinkles the brain creates a robotic body for himself. The mildly flirtatious Clio pinches Wrinkles’ back side (the rear of his new robo-bod, not his cerebellum), revealing a fatal flaw: the butt-activated ejector seat. Wrinkles is abruptly sent into orbit.

In Chapter 6, Wrinkles meets the sun while in orbit. We learn about different kinds of radiation that the sun produces. Wrinkles apparently learned something on his five-year sabbatical in Clio’s library, because he eloquently explains how three different kinds of cone cells work together to produce color vision in humans. Wrinkles begins to feel the effects of the thin air at the edge of the atmosphere, so he bites another wish-granting newt eye, asking to be back down on Earth. When he lands, he finds that one of the Men In Black is convinced Wrinkles is an alien.

In Chapter 7, we learn that the man in black (Igor) actually works for Dr. Kleeshay, who plans to use a protein named Larry to take over the world. Larry is a self-described “ginormous rhodopsin molecule engineered by Dr. Kleeshay”. Some people call Larry the - here I can almost hear a dissonant organ chord to heighten the suspense, just before the squiggly text that reads - “Were-protein”. Larry, like any rhodopsin, can change shape. Larry’s shape changes when the retinal that is part of him is struck by light and changes itself. Next is another of my favorite set of images, simple but effective. Hosler draws a pretty standard line-representation of the chemical chromophore retinal, and Wrinkles shines a flashlight on it. In the next panel, the retinal straightens out, with motion lines and a sound effect, “ding”. Later, when light shines on Larry (the rhodopsin were-protein), the retinal makes a “clink” sound, and Larry changes shape, howling at the moon.

Larry the Were-protein is a giant rhodopsin molecule, complete with light reactive chemical, retinal. When light hits retinal, "ding", it changes shape. Below, Larry in his trans state after being exposed to light. Dr. Kleeshay wants to exploit Larry's Jeckyll and Hyde tendency to control the minds of millions. Image copyright Jay Hosler. It may not be copied without permission, except for a review. (I assume this means a book review, like I'm doing here, so I haven't asked for permission).

It turns out that Dr. Kleeshay is raising mutant zombie G-proteins, to be activated by Larry. Since a single opsin activates many G-proteins, which eventually lead to a photoreceptor sending a signal to the brain, Kleeshay plans to use Larry to turn millions into mindless zombie slaves. Luckily, Wrinkles knows that phosphates will quench rhodopsin signaling. Wrinkles adds phosphates to Larry, which happen to look like breasts in Hosler’s drawings, leading Larry to change his name to Lariette. After saving Larry(ette), Wrinkles pops another newt eye and hastily wishes to be as far away from Dr. Kleeshay and Igor as possible.

In Chapter 8, Wrinkles finds himself frustrated and sitting beneath a large shady tree. Actually, he finds out it is the tree, an idealized construct of the imagination, a Platonic type. The tree has been Yggdrasil, has dropped an apple on Newton, has eaten Charlie Brown’s kites, and has shaded the Buddha. The tree is also phylogenetic trees, and it teaches Wrinkles how phylogenies are constructed, that they are no “lower animals” living today, only evolutionary survivors, and that lineages can converge separately on similar forms during evolution. The tree also teaches Wrinkles that there is a unity to all life. For example, Pax-6 genes are involved in the development of all animal eyes. Wrinkles sees this similarity for himself when various animals spit out a ticker tape with their Pax-6 gene printed on it. All this information frustrates Wrinkles even more. He just wants to find the magic eye. But the tree inspires Wrinkles to simplify. Wrinkles has the wish-granting newt eyes, he just has to wish to go where the magic eye is. This works, but Wrinkles is alarmed to find out where the magic eye actually is. I won’t reveal here the story of the last chapter, where Wrinkles finally finds the magic eye. I will only say that there is a (somewhat) happy ending. Wrinkles again encounters the flirtatious student of history from Chapter 5. She calls his “bottom” (cerebellum) adorable. Wrinkles is ecstatic, as anyone who is proud of their intelligence would be. After all, she likes Wrinkles for his brain.

The comic story is interleaved with text and figures describing in more detail the actual science behind Wrinkles’ adventures. These cover a lot of scientific ground in a short time, using an unconventional, somewhat snarky and irreverent writing style, that I think many will find entertaining, yet informative.

I have essentially no criticisms of Optical Allusions. There were a few very minor errors of interpretation. For example, in cavefish, we do not know what is the precise mutation that causes a change in gene expression level, or if multiple mutations are involved. Also, Pax is not “the gene” that co-ordinates all eye developmental genes. But these slight oversimplifications are inconsequential for the goals of this book. Optical Allusions seeks to present the wonders of science in a new way. In some ways, it is difficult to say who exactly the target audience is. But I expect any focused person, probably high school aged or older, with thick glasses, and a neon pocket protector in their lab coat, will have a great time reading Optical Allusions. Even though my area of specialty is eye evolution, I learned some new things from this book. I was especially inspired with new teaching ideas using the drawings. I highly recommend this book for its entertainment and educational value.

Evolutionary origin of a light sensitive nerve

2008-08-25T18:38:00.000-07:00

The origin of a light sensitive nerve was almost certainly an early step in the evolution of animal eyes, and this was thought to have happened only once, some 600 million years ago. But new open access research on the nematode C. elegans indicates a heretofore unknown instance where a nerve evolved light sensitivity.

One of the common, but incorrect, claims of anti-evolutionists is that the origin of complex features like eyes cannot be explained by evolutionary biology. As an example (although perhaps not written by an anti-evolutionist) see the comment on this post. For some history and a response to the incorrect anti-evolutionists claim, see this post.

It turns out that, as is often the case, the difficulty in understanding comes from trying to make a continuum into a dichotomy. An eye or even the genetic machinery for light sensitivity doesn't have to be all there or all not there. Instead, these features can build up gradually, by classical Darwinian evolution.

An early step in the evolution of complex eyes was almost certainly the origin of a light sensitive nerve. Darwin imagined that nerves might easily become light sensitive, but because of a lack of understanding of the molecular basis of photoreception, not to mention the molecular mechanisms of heredity, he could not even fathom a guess as to how nerves came to see the light. But just because Darwin didn't know how the machinery of light sensitivity could be built gradually by evolution doesn't mean it couldn't occur gradually.

Light sensitivity is a multi-step genetic process, where one protein signals to another. But all those proteins were not "turned on" all at once to suddenly allow for light sensitivity. Instead, light sensitivity evolved from existing "senses". Many signals are detected outside of a cell and they trigger proteins to send a signal inside a cell. Even yeast use proteins to sense pheromones outside their single cell and direct growth toward a potential mating partner. Many of these signaling genes are shared across all of our senses, and we can pinpoint by comparative study when a signaling gene became a light sensitive protein called opsin (again see this).

This brings us to the worm research. C. elegans has no visible eyes and its genome lacks light sensitive opsin genes. Yet it does display sensitivity to UV light!

Here is a link to a video showing light sensitivity.

How does it do this without opsin? It turns out that a different protein has become light sensitive. In this case, homologous proteins are known to be taste receptors (Gustatory receptors) in insects. Therefore, at some point in evolutionary history, the worm protein
gained light sensitivity, independently of the opsin "light switch"!

This is really fantastic work that suggests many new lines of research. For example, the mechanism of photoreception is unknown for the worm gustatory/light receptor. If this could be understood, we could get a specific idea about how a protein gained light sensitivity during evolution. Second, it is not known when light sensitivity was gained, which would require comparative study. These genes are present in insects - are the insect genes light sensitive? It would be great fun to put an insect gene in a worm to see if it could rescue the loss of light sensitivity due to a mutation.

Finally, I'll point out that this work is similar to another study published just last month . That workfocused not on the receptor, but on genes later in the cascade; especially on the gene responsible for "firing" (ie changing the concentration of the ions in) the light sensitive nerve. It turns out that that the "firing" gene is homologous to the "firing" gene used in vertebrate rod and cone cells - another example of how evolution often uses similar tools to produce parallel results.

Pluralism- Optimal versus non-optimal

2008-08-15T22:02:00.000-07:00

Once people get passed the tired, unimaginative, recycled, anti-evolution claims that creationists often make (snore), there are still some common obstacles to a deeper understanding of how evolution has produced the wondrous diversity of life that we see around us every day. Primary among these misunderstandings are the monistic view that evolution produces perfectly optimal phenotypes, and the related idea that natural selection is the only process that shapes evolution.

Of course this point is also a bit tired and unimaginative of me to point out, since Gould and Lewontin famously wrote on this subject almost 30 years ago. And even then, they were not even considered original by everyone, as they were accused by some of strawmandering, of erecting a simplistic caricature of peoples' views on evolution to be argued against. But never fear, I think I do have an original contribution to offer - I think I've stumbled upon a really nifty example to help understand a pluralistic view of optimal versus non-optimal evolution. Like Gould and Lewontin's famous spandrels (architectural objects that originate because of constraint instead of optimal functionality) I provide a non-biological example. I hope to try out this example on my students in next year's Macroevolution course.

The Panglossian barriers of Joshua Tree

Somehow these examples of the struggle between optimal and non-optimal come to me while traveling. My previous best personal example illustrates how people by nature tend to think adaptively. We tend to ask what something was made for - even though many things could simply arise as by-products, not as optimal "for" anything. I found myself falling into this Panglossian trap myself while driving in Joshua Tree National Monument. This is a place I've been to often, as it marks the half way point between my home in Santa Barbara, and relatives' home in Tucson. We usually arrive late in Joshua Tree, leaving SB after 6:00pm to avoid the traffic of the Inland Empire. When we arrive, Joshua Tree is dark, and the star gazing is amazing. Driving in, our mini-van headlights are no match for the vast darkness of the desert, and so the road becomes a singular focus. Some times of the year kangaroo rats dart just out of our path, but others the monotony of the dirt road induces a hypnotic trance. It was in one of these trances that I began to wonder the function of the ridges of dirt that edged the road. Along the edges of the dirt roads in Joshua Tree, sand lays in a neat pile, sloping from a maximum of foot or two in height gradually to the surface of the road. Except for the tan color, it was as if I had just followed a plow through a fresh coat of fallen snow.

[I'll paste a picture here when I find one].

Perhaps these ridges are an attempt to keep animals off the road, serving as a barrier between the raw wilderness and these capillaries of civilization that penetrate the desert. "Wait a minute, what am I thinking??", I thought, jarred from my trance (or was I?). Why to the road ridges have to be "for" anything? It makes so much more sense if these are simply by-products of making a road in the desert. My snow analogy is probably right on. Probably to make and up-keep the roads, plows simply carve a path through the desert, resulting in a pile of desert sand on either side as a by-product. These are not adaptive barriers, these are simply by-products of a need for efficient auto travel. Yet it was so natural for me to assume there is some function, and I so easily came up with an explanation, just so. I can see how one could see the natural world in a similar and Panglossian fashion.

What's even more wondrous is that similar by-products can be later elaborated, to give an even more distinct, yet ultimately false, impression of optimality. Growing up in Wisconsin, we had one glorious winter when the long driveway of our farm house was plowed by a neighbor (as opposed to shoveled, or cleared with a snow-blower). Just like the sand in Joshua Tree, the plow of my childhood left a by-product of a flat clear path, in the form of piles of snow flanking our driveway. Through the winter, these banks piled high, and they packed tight. My brother and I soon found an outstanding use for these by-products. We created the most fantastical snow fort Germantown Wisconsin has ever seen. We spent hours tunneling through the banks, building rooms where the snow piled wide. The plow packed the snow tight enough that we could build shelves and windows in the walls and sunroofs in the ceilings. So spectacular was our fortress, it was hard for our friends not to wonder whether the banks were plowed for the express purpose of creating our winter wonderland. But similar to Gould and Lewontin's elegantly painted spandrels in the chapel of San Marco, and just like the sand banks of the Joshua Tree desert, my childhood snow bank was simply a by-product of a need for efficient car travel, no matter how optimal our resulting snow fort turned out.

The Pluralistic spires and arches Utah

It's true that some structures sometimes arise as by-products. But what I find even more appealing is a pluralistic interplay between optimality and non-optimality. Natural selection may be an optimizing force, but it is not all powerful. There are constraints on the system. Driving through Utah this week, I saw a perfect illustration of this in the inspirationally beautiful wild lands of Utah.

Water, when pulled by gravity, will find an optimal path to the lowest point. And water, when it courses over rock, gradually wears that rock away, leaving a trace of its path. If all rock were created equal, canyons would be arrow straight, as water would continually trace a single optimal path to the oceans. But canyons are complex because all rock is not created equal. As a result, water faces constraints to optimality. When softer rock lies adjacent to harder rock, the softer breaks away more quickly, producing a circuitous path to the lowest point. The harder rock constrains and controls the outcome, in combination with the optimizing pull of gravity on water. The spires, arches and canyons are stunning examples of the intricate interplay between optimization and constraint. With constraints imposed by heterogeneous rock alone, the structures do not appear. Similarly with water acting optimally on homogeneous rock, the structures do not appear. It is only through the interaction that this beauty arises.

Bryce canyon photo by James Gordon, posted on flickr.

The geology is amazing in its own right, and I am sure I have not done it justice by my oversimplification (e.g. I've ignored wind and ice erosion). But my point here is to focus one how these pluralistic ways of thinking can inform us of how evolution proceeds. Nothing in nature works without constraint, without trade-off. Only by seeing natural selection as one player in a complex (though undeniably natural) interplay of various processes, do we gain a more nuanced and pluralistic understanding of how evolution has shaped our world.

[Caveat: These are purely non-biological examples, meant as analogies to prime one's pluralistic thinking. However, where the rubber hits the road for evolution is with biological examples, but that is beyond the scope of the current post.]

Ostra-blog 3 – How we discovered chupacabra

2008-08-13T18:33:00.000-07:00

I’m having a lot of fun with these ostra-blogs, which I started on a whim to increase awareness of my study taxon, Ostracoda (here are links to the first two posts: 1, 2). There are so many ostracods and related stories I want to share, that I hardly know where to begin. I’ve also decided to restrict myself to one ostra-blog per week, so as not to interfere with my ever-so-important other activities, like reviewing papers and sitting in on meetings. Therefore, if there are roughly 30000 ostracod species (fossil plus living), I will finish telling you about all of them by about my 600^th birthday, unless of course new species are described by then. In any event, I have reached a decision on this week’s ostra-blog. Since new species have been the subject of some recent blogs, and since I just saw chupacabra on the internet news, today, I will tell you the story of how my lab discovered and described the ostracod species Euphilomedes chupacabra. (Here is a link to the paper).

On new species

First of all, a word or two about new species: As relayed by The Other 95%, there is little academic reward for describing a species this day in age. Today, scientists are judged by their citation rate, and to a lesser but often still significant extent, by the number of grant dollars they pull in. True, in some cases describing a new species - for example by naming it after, say, Neil Young or Steven Colbert - can bring media attention. But media attention does not translate to grant dollars, and probably doesn’t usually increase citation rate.

Still, there are a few intangible perks to describing a new species. One is a certain understandability that the general public has about new species. If I tell a new acquaintance at a cocktail party (which I attend at least 8 days a week… anyway you know the figure of speech) that “we discovered a new species”, he or she seems to think it is significant. In contrast, if I say, we found a new class of vision genes in jellyfish, their eyes glaze over. Or in response, they might ask something like, “oh wow, so will that help us cure blindness, or better yet vision cancer?”). Another perk is a certain “geek cred” among those who value natural history. After all, you must be a real expert to be able to find a new species right? As I’ll discuss later, a final perk is that you get to name it!

Despite these few advantages, finding new species of ostracods for us is a bit of a hassle, honestly. It means that we really should describe the species before analyzing it (but see above regarding citation rate and grant funds – also I don’t think geek cred increases linearly with the number of species described, I think it asymptotes at about 1.1). This “hassle” of finding new ostracods is a common occurrence. In many places, roughly half of the ostracods I’ve collected are unknown to science. These are not inaccessible places. These places are beaches in the Florida Keys, where tens of tourists snorkel every day, or piers in Japan where people fish, all the time. The coral patch reefs of Australia and Belize sound exotic, and they are fantastically beautiful, but I can get there from here in a day or so in air conditioned comfort while listening to science podcasts. My best case in point for how understudied ostracods are brings me (finally!) to the story of E. chupacabra. I found this species by dipping a bucket in the water on the pier of a marine lab!

The initial discovery

A few years ago, I was visiting the University of Puerto Rico-Mayaguez marine lab, which is in Magueyes, near the famous bioluminescence bay. I was visiting my friend, who is a professor there, and we were using their ship to collect some deep sea ostracods. Before that cruise, I decided to do a bit of collecting near the pier. The marine lab is on a tiny little island. It used to be a zoo, and there are large lizards all over the island, which I’m told are descended from those that escaped from the zoo. To get to the island, one must take a boat across a small channel; they have attendants there 24 hours a day!

I’d collected in the Caribbean before, and I expected to be able to collect Skogsbergia lerneri, a species I’ve collected in Florida and Belize (and a species sure to be on a future ostra-blog). Skogsbergia come to baited traps, so I deployed a trap off the pier of the marine lab. While waiting for the animals to come to the trap, I dipped my bucket in the water. To my great surprise, I saw an ostracod buzzing around in the water like Michael Phelps on steroids. Ostracods are quite small, but they have a pretty distinctive swimming behavior (myodocopids at least). Unlike other things of their size, like copepods, ostracods swim very smoothly. I sucked it up into a pipette, and brought it back into the lab. I couldn’t believe my eyes, I suspected immediately I had a Euphilomedes!!

I was so surprised for two reasons. First, Euphilomedes is one of my favorite genera (another certain ostra-blog candidate), because the males have large compound eyes and the females do not. My lab is interested in how this strange eye dimorphism occurs developmentally and genetically. Second, Euphilomedes had never been described from the Caribbean before, so I knew I almost certainly had a new species on my hands. It turns out that it was a species unknown to science, and I had discovered it literally by dipping my bucket in the water in a place where hundreds of marine biologists, and even ostracodologists had passed; a marine lab of a major university. Still, it would be a few years before we mounted the expedition to find more individuals of this new animal, and before we’d decide on its name.

Study and description

Fast forward a couple of years. I decided it would be a good idea to describe this species I had found back at Isla Magueyes. First, we had started studying eye development of Euphilomedes from California. California water is cold, and the animals do not develop very quickly. I suspect that the new species from the warm waters of Puerto Rico might develop faster, and therefore be better suited as a lab animal. Second, I thought it would be fun to go back to Puerto Rico, and to take a couple students along to help me find out more about this species. The National Science Foundation kindly provided money for an REU (research experience for undergraduates) supplement, which would cover travel expenses for two students go to PR for a month. In addition, they would spend some time in the lab back in Santa Barbara beginning to describe the species. I think it is great to get students out doing field work, where they can gain a real appreciation for the wonder of the natural world. Our first order of business was to find more of this animal.

Why was this Euphilomedes in my bucket when I had just dipped it into the ocean? Well, ostracods usually live down in the sediment, making a living between the sand grains. But some swim, often just after sunset, usually to mate. Some ostracods are bioluminescent, the males signal with flashing lights to attract females (yet another future ostra-blog). I’ve collected some animals (mostly males) in light traps. So, I hypothesized that this Euphilomedes was being attracted to the lights at the pier. The undergrads’ first experiment was to test this hypothesis. To do this, they passed a small net through the water, the length of the pier. They put the resulting critters into a dish and counted what they had, repeating this every 15 minutes. They found that this Eupilomedes had a strong peak of activity about 2 hours after sunset. Essentially all of the Eupilomedes they collected were males, consistent with the idea that males swam around trying to find females to mate with. Females probably only mate once, and then do not swim up any more, thus the strong bias in males versus females.

The students also made many SCUBA dives to find where else this Eupilomedes lives. Another way to collect ostracods is by dragging a net across the bottom of the ocean, where the animals usually spend most of their time. We then sort the sand to keep the size class that will have ostracods, and laboriously sort sand grain from ostracod. This is another reason why it was so great to find this Eupilomedes – it is fairly rare to be able to get so many animals just by dragging a net through the water – we could get hundreds of males at a time this way, without having to sort them from sand. In the end, the students found that this Eupilomedes was living all over around the nearby patch reefs, some times very abundantly, especially in fine grained sand. Hundreds of boats, fishermen, wind surfers and SCUBA divers pass through these waters, all the time; while this unknown and fascinating species lurked inconspicuously between the sand grains below them.

Deciding on a name

A really fun part about describing a species is naming it. I took this pretty seriously, especially given some of the great names that people have come up with. Some of my favorite ostracods (again future ostra-blog candidates) are Harleya davidsoni, coined by my colleagues and motorcycle aficionados Kerry Swanson and Thomas Jellinick, and Kornickeria marleyi, named after Bob by Anne Cohen and Jim Morin. Some scientific names are pretty hard to top, like the clam formerly known as Abra cadabra or the wasp named Pison eyvae. (If you like these, you'll have fun if you check curioustaxonomy.net ). I won't go into some of the other candidate names, just suffice to say that in the end, we decided to name our new species after a mythical creature, "el chupacabra". On our first trip, I had fun joking around about the chupacabra with one of my friends who came along. Also, since the myth started in Puerto Rico, it seemed fitting to name this species after it. We simply dubbed it Euphilomedes chupacabra.

If you don’t know chupacabra already, the myth surfaced in the mid-90’s or so, when livestock, especially goats, began being found dead and ensanguinated, with puncture marks on their necks. The legend of el chupacabra (the goatsucker) has since migrated to other, especially Latin American countries. I just saw a headline today, suggesting people have captured video footage of the elusive chupacabra. Looks like a dog with a big nose to me.

So that is the story of Euphilomedes chupacabra. Perhaps one day, you too can discover a new species by dipping a bucket in the water. They are everywhere, and just think of the fun you can have at your next cocktail party. Oh, and by the way, Euphilomedes chupacabra does not suck the blood of goats, unlike the beetle Agra sasquatch, which really does have big feet. I’m not sure about its sister species, Agra yeti.

Evolve: Guts

2008-08-06T15:47:00.000-07:00

Many evolution buffs, like myself, have been watching the History Channel Series called Evolve, which are airing here in CA at 10pm on Tuesdays. These are well produced pieces that focus each week on a particular trait (eyes last week, guts this week). Both shows have been collections of ~5 narratives, mostly showing how the focal trait works in different animals. The narratives are tied together by asserting that evolution occurred (which I am quite certain it did). As such, these are not really about the historical science of evolution, but rather they are using evolution as an organizing principle to tie together experimental science on how particular traits work in different animal groups, with a preference for charismatic vertebrates. In the end, it all works quite well, and I would recommend the series.

In honor of Guts, I thought I would post a link to some of my favorite gut science. Work by Dirk Haller and (separately) Ruth Ley lies at the interface of ecology, evolution, and medicine. They wonder, how does the composition of bacteria in the gut of humans and mice affect the host - and how does that composition of bacteria get established?

You can think of the bacteria as a community, like a forest or grassland ecosystem, living inside each of us. Communities can have different levels of diversity - they can be comprised of many of just a few species. Those species could be closely or distantly related evolutionarily. And those communities could be established from environmental sources, or established by inheritance.

I saw Dirk and Ruth talk about some of this work at last years GAFOS conference, which is a conference of about 20 Americans and 20 Germans, under the age of 40, who were invited because someone took notice of his or her work. GAFOS is funded by the National Academy of Sciences and the von Humboldt Foundation. I described it in a bit more detail in a previous post, where I linked a symposium this year on the evolution of complex adaptations.

Some of the conclusions that Ruth and her colleagues have made are that certain groups of bacteria are associated with obesity of the host. There exists an experimentally generated line of sterile mice - mice that are born and live in sterile conditions, ie with no bacteria anywhere (amazing!). Some of these sterile and genetically identical mice were seeded with different bacteria, and some combinations were more likely to result in obesity of the mice, given the same amount of food.

Another interesting result is that gut bacteria tend to be passed from mother to offspring, as opposed to being obtained from the environment. This result is based on phylogenetic trees of gut bacteria from different populations. It is heritage, not locality that determines the bulk of gut bacteria.

Dirk's presentation was a really great example of pluralism, which I like to promote. He contrasted the germ theory of disease with the genetic/inherited theory of disease. He hints at a possible link between our currently germ-o-phobic society and the increase of genetic, especially auto-immune diseases like Crohn's disease and asthma. It may be that without the insult of germs, our bodies find it more difficult to distinguish self from non-self. By just having a germ theory of disease, we lose the full picture.

(These are my memories from over a year ago, so I may have some details wrong. Check out Ruth's and Dirk's presentations on this site, to see for yourselves!)

Next week Evolve, Jaws!