Wednesday, October 13, 2010

BARP Goes the Weasel!

By Kristopher Hite

Looking back at discoveries of the past year the one that sticks out above all others to me was the identification of a single protein; a bacterial actin homologue dubbed BARP - Bacterial Actin Related Protein. The brilliance of this discovery comes from its directly contributing to our understanding of evolution, overturning decades of dogma, and providing a shiny new teaching tool.  The discovery was published in late 2009 as part of a massive sequencing project to fill in gaps of knowledge among bacterial and archael genomes.

With all the other sexy and more controversial stories about evolution - Ardi, Ida and so on, why do I pick this one? Aside from my biochemical inclination I thought this little piece of biological hardware deserved more exposure.  Though the paper was covered and lead author Jonathan Eisen interviewed for the nature podcast, it received relatively little coverage on the science blogs. Yes, the prolific science writer Carl Zimmer wrote a nice summary for the New York Times but the BARP bit is mentioned only briefly. I don't know if anyone realized what a great tool this discovery is to hammer even more nails in the coffin of the "irreducible complexity" argument for intelligent design. 

In January 2010 I had the pleasure to sit down and interview Eugenie Scott - executive director of the National Center for Science Education (NSCE).  As she explained the history of science education in the United States we came to an agreement on what one "take home" message should be for the average high school student - that all living things on earth share common ancestors, that all species have a common descent. This point may not seem earth-shattering to comprehend but I think many in America fail to realize the significance of this fact. The procession of science has uncovered an armory of teaching tools - fossilized trilobites, floating whale hip bones, and common DNA sequences. The more is known about the inner workings of the natural world the easier it should be for students to see and accept the facts. What then is the barrier to getting students to accept take-home messages like common descent? I would posit that fundamentalist opposition to evolution and the idea of the rapture have more than a little to do with it. Proponents of intelligent design often use a phrase coined by Lehigh University professor Michael Behe - irreducible complexity - in their defense of a necessary designer. This was a large part of Behe's arguments against teaching evolution as fact in the Kitzmiller vs. Dover, PA landmark court case.

Behe defines an irreducibly complex system as one "composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." Brown University Biology Professor Ken Miller uses the analogy of a mouse trap to explain away irreducible complexity. Yes, all components of a mouse trap are necessary for overall function but each component can be have alternate uses.

In the logical chronology of evolution complexity emerges incrementally by the acquisition of functional structures that appear by chance and remain due to conferred advantage. Behe has tried over and over to use the molecular structure of the bacterial flagellum as an example of an irreducibly complex system.  In response Ken Miller did an excellent job explaining how the components of bacterial flagella could emerge incrementally.

So what IS actin and how does its showing up in a bacterial specimen add to the arsenal of teaching tools against irreducible complexity?

actin filament

As you move your cursor around this page your muscles are contracting and relaxing, your brain is sending signals along tiny electrified strands called axons guiding these contractions. Among the myriad things that make this possible is the little protein called actin.  Deriving its name from the word "activating" actin enables muscular motion, provides train tracks inside each cell for directional transportation of other tools, and gives shape to most cells in your body.  Like oddly shaped legos these tiny building blocks bind to each other and form long filaments that grow and shrink.  A mesh-work of actin filaments push on the perimeter of each cell establishing shape.  Those long axons I mentioned before are extensions of brain cells (neurons). During development neurons send out these long extensions and it is the mesh-work of actin that leads the charge enabling all those millions of electronic connections between brain and body to form. 

The gene that codes for this little protein exists without much variation in all eukaryotic organisms. Eukaryote means simply "true nucleus." The distinction is made because the more ancient but still surviving bacteria do not have "true nuclei" they are therefore dubbed prokaryotes. The moment at which the first eukaryote appeared on earth marked the beginning of an explosion of diversity, and a fundamental branch point in the phylogenetic tree of life.

(Haliangium ochraceum)
 Unlike the carefully crafted nuts and bolts you can pick up at the hardware store cellular machinery is not designed for a purpose, it just appears by duplication, mutation, or other spontaneous variations of genetic material.  If it works it is retained, if its merely eating up metabolic resources it usually goes extinct.  This represents an important variation on pure chance that the process of evolution carries with it.  Richard Dawkins has illustrated the power of evolving systems to accumulate positive variation in his classic "Weseal" thought experiment. Self-replicating systems have the ability to retain random variation in their code by copying themselves. When a variation carries a positive effect for the code carrier (organism) then that carrier is more likely to make more copies of that advantageous variation.  New variation is possible because there are usually redundant bits of cellular machinery.  This is exactly what we see in the case of BARP.

If you asked any professor of cell biology any time prior to a year ago "Do bacteria contain a gene for actin?" they would, without hesitation, say "of course not." It was understood that the gene for actin was one that separated eukaryote from prokaryote. Bacteria have an unrelated gene  - MreB - that has a scaffolding function. They don't need actin.   Now it is shown that the gene for actin may have shown up in  marine bacteria (specifically the one named Haliangium ochraceum) prior to the evolutionary branch-point. If this is the case it means that actin was later recruited to its now prolific function giving shape and motion to eukaryote cells. Actin was not designed then implemented like machined parts in human created contraptions. According to this research it probably appeared by chance in marine bacteria, served some other unknown function, then just happened to work later on in evolution.  This, I think, is why many mechanical engineers have an aversion to studying the slimy, oozing, organic structures in nature. They are inherently messy and imperfect.  This is because they are not designed! They are the result of chance events captured inside self-replicating systems - us included.

This post has been submitted to the NESCent competition for a travel award for the ScienceOnline 2011 un-conference January 13-15 in North Carolina’s Research Triangle Park.


Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656


Anonymous said...

It's not necessarily true that this gene appeared in the bacteria before the eukaryote/prokaryote split occurred... it could have been 'stolen' by the bacteria from some eukaryote later on (horizontal gene transfer).

tompainesghost said...

Excellent point. I had thought of that scenario and should have mentioned it. Regardless if BARP represents a genetic vestige that has remained in Haliangium ochraceum since before the eukaryote - prokaryote branch point or is a new in the natural history of this particular bacteria, this finding forces us to ask these question which we did not have to think about before. How would we best approach the question? It is nearly impossible to sequence genetic information from ancient bacteria. Would we survey the genomes of similar species for this BARP gene? If we saw many homologues and they were nearly identical would this indicate more recent horizontal gene transfer? If we saw a tapering in sequence matching of the gene as we got further away form this species would that indicate the gene as an ancient vestige? I have given a couple suggestions on my hypothesis. Any thoughts or suggestions on how to approach the excellent question brought up by this first commenter?