Culturing Science – biology as relevant to us earthly beings

Archive for September 2010

The evolution of the eukaryotes and our human story

“Taxonomy and classification are funny,” my father joked recently, “because the organisms being classified really don’t care what they are. We’re the only ones who care!”

Well, at least I thought it was a good joke.  And it speaks to a certain truth: humans generally are obsessed with organizing and putting things into categories.  It is evident in the way we divide our music into genres (“Is this chillwave or witch house?”) or put our pants in a different drawer than our shirts. This may seem silly, but, with our consciousness and perception, we need to categorize in order to make sense of our world, to generalize, and, well, to help us find things.

We no longer have unicorns in our taxonomical literature. From the Ashmole Bestiary, 1504. Via BibliOdyssey.

Long before any ideas of natural selection and evolution as we know them now, people were trying to organize the natural world around them.  In 350 BCE, Aristotle published his History of Animals, which attempted to categorize the various “natures” of animals based on their characteristics.  For example, he identified what we now know as arthropods as animals that do not have blood and, “if they have feet, have many” (French 1994).  Some of his categorizations were not so on-par; for example, he placed foxes and snakes in the same category because they both burrow underground and thus have “sympathetic natures.”  Accurate or not, the effort is there: making sense of the world through categorization.

Although we’ve been at it for a long time, we are not close to being finished identifying all extant species, much less cataloging them.  Just this week it was announced that, due to double-counts, the estimate of the number of flowering plant species will be cut by 600,000.  600,000!  And those are just the plants that are living today, excluding all the known and unknown species that have gone extinct.

It would be easy to say, “whatever, who cares about the extinct ones?  If I’m categorizing to make sense of the world, I want to pay attention to the world I’m living in.  Leave the past in the past, man!”  But if people view the world as stories as I believe we do, we need this history of organisms to construct our narrative1.

A basic illustration of the 3 domain system of taxonomy. The yellowish circles indicate the 3 nodes and the 3 domains of the Bacteria, Eukarya and Archaea. The Eukarya and Archaea share a common ancestor but evolved separately from there. Not to scale in terms of time or breadth. Drawn by Hannah Waters.

And, in particular, we need to know the history of our own species: where do we fit into the puzzle?  How far back can we trace our own ancestors?  When I was 14, I was taught that we are part of the Animal Kingdom, one of the five kingdoms of life.  When I was 17, I was instead taught the three domain system: the Bacteria, the Archaea, and the Eukarya, a classification developed by the microbiologist Carl Woese in the late 1970s.  This new system organized the world based on cell type, in particular dividing the Monera, which previously described all single-celled life, into the Bacteria and the Archaea, which are each single-celled but have many differences in structure.  (See this great post by Labrat for more information on their distinction.)  No longer were we humans described as “animals” as in ancient times, but rather based on an ancient ancestor, the first to embody the type of cell that makes up our bodies.

In the three-domain system, we eukaryotes are more closely related to the archaea, but evolved separately from a common ancestor (sister lineages).  We evolved a unique nucleus composed of specific proteins, and later acquired mitochondria or plastids from bacteria through endosymbiosis.  However, a different hypothesis has arisen in the past couple of decades: the 2-domain system.  In this system, the Eukarya are even more closely related to the Archaea.  In fact, we are a subgroup, having evolved from a singular lineage within the Archaea.  A mere secondary domain, replacing Eukarya as a “primary domain” or sister lineage as put forth in the 3-domain system.

A basic illustration of the 2 domain system of taxonomy. The yellowish circles indicate the 2 nodes and the 2 domains of the Bacteria and Archaea. Of note is that the Eukarya evolved from the Archaean domain. Not to scale in terms of time or breadth. Drawn by Hannah Waters.

Why is the 2-domain system being considered at all?  The Archaea and Eukarya share many of the same components of their genetic information systems, such as over 30 ribosomal proteins, RNA polymerases, transciption factors, promoters to initiate transcription of the genome, and replication enzymes (Gribaldo et al. 2010).  A general tenet of constructing phylogenies, evolutionary trees through time, is that the simpler answer is usually better.  Proponents of the 2-domain system argue that it is simpler for these genetic pathways to have evolved once in the older domain, the Archaea, and been retained in the newer subdomain, the Eukarya.  Proponents of the 3-domain system hold that these systems evolved earlier before the lineages split and were preserved in both the groups over time.

Eukaryotes also share many genes with the Bacteria, even more than with the Archaea.  Do these genes “even out the score” and support the 3-domain system, or were they acquired as a remnant of bacterial endosymbiosis?  An early edition PNAS paper (2010) by James Cotton and James McInerney of the National University of Ireland argues its title: “Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.”

The authors compared every gene in the yeast genome to bacterial and archaeal genomes, finding that 952 genes have bacterial homologues, while 216 show homology to archaeal genes.  Using these genes, they performed two main tests.  First, they examined how frequently each of these genes killed the cell when deleted from the genome – a test to see just how imperative each is to the cell’s survival.  They found that lethal genes are twice as likely to be of archaeal origin than bacterial origin, giving the Archaea one “important point” in their book.  Second, they looked at how frequently these genes were actually transcribed, or copied into a form from which they can be made into proteins.  Using RNAseq, they found that there was significantly more expression of genes with archaeal homologues than bacterial.  Another “important point” for Archaea.

This study seems to support the 2-domain hypothesis: the genes that come from Archaea are used more frequently and are more necessary for cell survival, despite being fewer in number than Bacterial genes.  But remember: both systems of taxonomy support the idea that Eukarya are more closely related to Archaea.  Importance is merely a factor of correlation, not evolutionary causation.  It provides evidence that the two domains are related, but not the direct evolution of Eukarya from the line of Archaea.

These lineages have been diverging from one another for at least 2.5 billion years – it seems like a bit of a stretch to be doing genomic studies at all!  Think of all the mutations and changes that have been made in the DNA over those 2.5 billion years, obscuring the true relationships and further separating these domains morphologically.  A review coming out next month in Nature Reviews Microbiology goes through a number of studies that attempted to analyze eukaryotic evolution and found that none drew a strong conclusion, or even found conflicting results, “despite analyzing largely overlapping data sets of universal genes.”  They conclude that “it is premature to label any one of these analyses as definitive” and that these large-scale genomic studies have “not yet yielded a resolution to this debate and ha[ve], if anything, intensified it.”

Even if we did know the truth, what would this mean for the “story of human evolution” I was babbling on about earlier?  Well, it means that we’re Archaea deep down!  Those badasses who live in hot springs and sulfur!  We had the potential to be hardy, tough organisms, but instead we’re frail and get cold really easily and get hunger pangs after just a few hours…

More than anything, the fact that this debate exists in the first place gives us a great perspective on our story.  Under 2500 years ago, Aristotle categorized foxes and snakes together.  Now, we’re splitting hairs over the type of ancient cell that foxes, snakes, and ourselves evolved from over 2.5 billion years ago.  It provides the history of our progress.  And look how far we’ve come!

1 Of course there are many applications for studying evolution beyond a desire to learn about our own history.  This 2005 interview with Massimo Pigliucci, an evolutionary biologist at SUNY Stony Brook, and the 1998 collective paper “Evolution, Science and Society: Evolutionary Biology and the National Research Agenda” are good places to start.

NOTE: Molecular evolution is incredibly hard to explain (in my opinion), and I did my best to do so in English.  If you have any questions or think some parts need clarification, please let me know in the comments or write me at hannah.waters [at]  I’d really appreciate it! Thanks!

Cotton, J., & McInerney, J. (2010). Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1000265107

French, Roger.  Ancient Natural History.  New York: Routledge, 1994.

Gribaldo S, Poole AM, Daubin V, Forterre P, & Brochier-Armanet C (2010). The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature reviews. Microbiology, 8 (10), 743-52 PMID: 20844558

Written by Hanner

September 29, 2010 at 7:52 am

Introducing… Sleeping with the Fishes!

Hello dear readers,

I’m excited to announce a new Hannah Waters production: a marine ecology blog on the Southern Fried Science Network called Sleeping with the Fishes!


It seems a bit excessive, I know.  But give me a second to explain myself, OK?

You may know that the science blogosphere is changing, and that the people at the top are working to create and manage a number of networks, and then to network those networks.  While independent bloggers are still perfectly acceptable and welcome (Culturing Science will remain independent unless something totally irresistible pops up.), I do like the idea of these networks.  It promotes community between us bloggers and scientists, and could help to increase visibility to science blogs generally and thus promote science education and the sharing of knowledge.

Despite offers, I’ve put a lot of thought into decisions to join (or not join) various networks.  I want to join one(s) that feel right to me, communities that fit my goals and my style.  I would never join a network solely for the increased exposure; that doesn’t feel right to me.

The Southern Fried Science Network is a group of bloggers focusing mainly on marine science (with a few exceptions).  When I got the offer from them, I was ecstatic.  The idea of writing in a community of shared interest and thus trying to create a marine science stronghold on the web is an exciting prospect, and I want to be a part of it.

As you know, I don’t only write about marine science on Culturing Science.  Thus I created a new blog, to keep my writing on the SFSN focused, but also to retain an outlet for writing on other topics.  It doesn’t mean I’m going to abandon this space; not by any means.  That is just about all I can tell you because it’s all that I know.  The rest will unfold with time.

So come along and join me at Sleeping with the Fishes!  I’m excited about this addition to the Hannah Waters brand (haha) and hope you are too.

You should probably subscribe to the Sleeping with the Fishes RSS feed to stay up to date.

Thanks for reading,


Written by Hanner

September 26, 2010 at 11:00 am

Can seabirds overfish a resource? The case of cormorants in Estonia

This post was chosen as an Editor's Selection for

Published in Open Lab 2010, a print compilation of the best science blog posts of the year.

“Overfishing” is a term associated with resource depletion, extinction, and human greed.  While the definition of overfishing is technically a subjective measure (How much fishing is too much?), it has been widely accepted to mean catching more of an aquatic resource than can be replenished naturally by the system.  The idea of depleting a marine resource is ubiquitous and familiar these days, with the bluefin tuna even featured as the cover article of the New York Times Magazine this past June.

That’s a lot of mackerel for one net! Image: NOAA

The idea may be commonplace now, but this was not always so.  A 2003 paper by Nicholas Dulvy and others enumerates the reasons why it was long believed that marine populations were more resilient than terrestrial species, and less likely to go extinct due to overfishing, habitat loss, invasive species, disease, and other causes.  Jean Baptiste de Lamark himself was a proponent of the “paradigm of ocean inexhaustibility” due to the high fecundity of fish.  He (and others) argued that because fish lay so many eggs and have excessive offspring (with little care put into each), we could never actually catch enough of a population to cause any damage.  One problem with this argument is that fecundity often increases with size of an individual.  Since we selectively catch larger fish, we’re catching the most reproductively able of a population and causing a large impact per fish caught.  Other arguments about the impossibility of aquatic extinction include broad geographic range and dispersal, and that economic extinction of a fishery would precede biological extinction of a species (all of which have counter-arguments).

In all the discussion of overfishing, it is always humans that are doing the fishing to the detriment of non-human species, either through depletion of a fished species itself, or by reducing resources for other species that rely on it for prey.  It is we humans who must reduce our impacts and allot resources for other species on our fair planet.

Last month (August 2010), an article from ICES Journal of Marine Science asks whether humans are the only species capable of overfishing.  More interesting than the research itself is the questions it raises about our own relationship with “nature.”

The story of cormorants in the Baltic Sea


The Great Cormorant (Phalacrocorax carbo) is a seabird that lives in the Baltic Sea, along with many other locales.  According to the Helsinki Commission, in the 1950s and 1960s the bird was overhunted to near-extinction locally, at which point they were put under government protection.  Over the rest of the 20th century, the bird population improved dramatically, recolonizing old haunts with great success.  They were so successful that they began expanding their original range, initially colonizing Estonia in 1983.  In 2005, there were 20 great cormorant colonies in Estonia with an estimated 10,000 nesting pairs.

Over the course of this period, fishing decreased in Estonia waters, in part to conserve the estuarine wetlands that are important for bird migration and fish spawning.  Despite this, many commercially valuable fish stocks plummeted.  Though working with a limited data set (fish were sampled only in 1995 and 2005), in the ICES paper, the scientists satisfactorily concluded that this loss of fish species was due to overexploitation, not by humans, but by these great cormorant colonies.  The cormorants were fishing 10-20 times more than the commercial catch of fish species such as perch Perca fluviatilis and roach Rutilus rutilus, decreasing the fishes’ ability to recover year after year.

Population development of the Cormorant in the eastern and northern Baltic (Estonia and Finland). Data from SYKE (2008, 2009), Lilleleht (2008), and Evironmental Board of Estonia (2009, pers. com). From the Helsinki Commission

How this questions our typical relationship with “nature”

This is an interesting story for several reasons.  The birds were able to spread their range as far as they did and, in the end, compete with humans for food resources because we were trying to protect them.  Their near-extinction in the 1950s probably led the government to be hesitant to lift protection because the birds were no longer birds, but a symbol of species recovery.  After such a great success, how could we take their resources away and potentially lead them to extinction once more?

The fact alone that they are seabirds also makes their presence hard to define.  Some cases of “invasive species” are very clear cut.  For example, brown tree snakes are not from Guam, but were brought there and are now wreaking havoc on native animal populations.  But seabirds toe the line.  They are able to fly anywhere, and simply live on colonies at sea.  Who are we to determine where geographically those colonies exist?  The authors of the paper do not even use the word “invasive” to describe the expansion of great cormorants into Estonia until the end of the paper.

Are these birds invasive?  It depends on your definition of the term.  Some would argue that, yes, they did not live there before but do now, and are affecting the ecosystem to the detriment of other species.  But it’s all relative: invasive species are defined by an anthropocentric view of the world, in which what is “natural” is the distribution of organisms we initially encountered and recorded.  But who are we to decide that a species belongs or does not belong in a certain place?  Who are we to tell the cormorants that they cannot live on that rock near an ample food supply?  We’re the only species that sets these sorts of boundaries; all the other species are just trying to utilize resources and survive.

The idea that humans are the only species able to overexploit a resource is also anthropocentric.  It makes Homo sapiens the center of the world, the ones who determine the fate of all other organisms, who can harvest them for ourselves or choose to spare them.  This case of the cormorants places us back in our role as a competitive species: we have to decide whether or not we are willing to take back our resource, even if it means losing some of these big, aesthetically-valuable cormorants.  We are no longer the masters of nature, but rather are inserted back into it.

I hope I manage to keep up with this case and find out what happens in Estonia.  At this point, “taking back our resource” would not mean going in and competing by fishing; there are too many cormorants, so we would simply deplete the resources further.  Instead, the Estonian government would have to enter the colonies and manage the population through oiling or pricking eggs to kill the developing birds (the Helsinki Commission estimates that this is done to 18% of nests in Denmark).  Already 10,000-20,000 birds are shot in the Baltic Sea area each year, but public protests limit the amount of population control that is performed.

We may have simply lost control of the situation at this point.  There may just be too many cormorants to keep them from overfishing, for our own sake or to preserve the fish as an ecosystem resource.

Dulvy, N., Sadovy, Y., & Reynolds, J. (2003). Extinction vulnerability in marine populations Fish and Fisheries, 4 (1), 25-64 DOI: 10.1046/j.1467-2979.2003.00105.x

Vetemaa, M., Eschbaum, R., Albert, A., Saks, L., Verliin, A., Jurgens, K., Kesler, M., Hubel, K., Hannesson, R., & Saat, T. (2010). Changes in fish stocks in an Estonian estuary: overfishing by cormorants? ICES Journal of Marine Science DOI: 10.1093/icesjms/fsq113

Written by Hanner

September 17, 2010 at 9:33 am