Tuesday, January 27, 2009

Two Animal Nervous Systems?

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!!


Bernd Schierwater, Michael Eitel, Wolfgang Jakob, Hans-J├╝rgen 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

Sunday, January 25, 2009

Ostra-blog 7 - Trapping ostracods

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.

Saturday, January 24, 2009

Creationism and Evolution in our society

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.

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.

Thursday, January 22, 2009

Was Darwin Wrong?

[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 20th Century 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 20th Century, 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 19th and early 20th Centuries [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 20th Century 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) 20th Century 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 20th century 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.

Tuesday, January 20, 2009

Please Vote!

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):

Friday, January 16, 2009

Wildlife Photography

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.

Monday, January 5, 2009

The glamour of marine biology

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!