Monday, January 28, 2008

On the replacement of inaccurate and misleading scientific terms or: how I learned to stop worrying and love the ‘periphyton’.

Paul Frost is a good friend and long-time collaborator of mine at Trent University in Canada. He's spent most of his career working on ecological stoichiometry and animal physiology. Today's post is an essay Paul wrote about the use of the word periphyton in stream ecology. I've often referred to this article when arguing with people about the use of terms in ecology in general, so I asked Paul if I could publish it here. Enjoy!


The sciences of limnology and oceanography require the use of specialized terminology. Also known as jargon, this terminology can save us the time and effort used to describe explicitly every article and action involved in doing aquatic science. Articles as diverse as seston (suspended particulate organic matter) and thermocline (a depth in lakes and oceans showing some prescribed temperature change) would be awkward to define in every instance of their use. While obviously useful, many scientific terms are a potential source of confusion. This confusion comes about when one term has several alternative meanings or when alternative and competing terms have the same meaning. In addition, a few terms while used to refer to one thing can literally mean something else. The desire to avoid terminological confusion can stimulate calls for change, which, if successful, result in the addition and deletion of words or expressions from the working lexicon of aquatic scientists. While such change might offhand appear desirable, we should all pause to consider the potential effects of eliminating well-established scientific terms that happen to be inaccurate, vague, or ill-defined. For example, the retirement of an offending misnomer could potentially create confusion for future readers of the literature due to a temporal disjunction in terms referring to the same item or action. Ironically, the desire to reduce confusion may ultimately lead to further and potentially more confusion (at least over the short-term).

Fig. 1. Yearly occurrences of terms referring to the attached organic matter in the benthos (aufwuchs, biofilm, and periphyton) found in Limnology and Oceanography between 1957 and 2002. Numbers of occurrences were counted by searching JSTOR and the ASLO website for each year. (click to enlarge)

So we are left with seemingly contradictory concerns when making decisions regarding whether to retain an established term or seek a better alternative. Isn’t it better if we find the most accurate term for an article or action and use it instead of other incorrect but more established terms? Or maybe we should keep well established terms because changing terms, in and of itself, produces confusion. Does it really matter if we go one way or the other as long as each term is accurately defined at the first use in each manuscript? In this paper, I examine an example of this uncertainty by presenting the current confusing situation regarding the terms used to characterize the particulate organic matter (POM) attached to rocks, plants, and the sediments of aquatic ecosystems. This particular example illustrates the problems of having multiple terms referring to the same item and how terminological change may not be helpful especially if the new terms are equally misleading or vague. With this problem in mind, I consider several solutions to resolving the general issue of multiple terms referring to one article and provide suggestions for the future use of benthic POM terminology.

There are a bevy of terms that refer to the particulate organic matter attached to rocks and other submerged surfaces: “aufwuchs”, “biofilm”, “benthic algae”, the epi-s (epilithon, epipssamon, epixylon, and epiphyton), and “periphyton”. These terms can be found in the limnological literature referring to the POM or distinct parts of it, are sometimes used concurrently in the same article, and have widely varying levels of scientist support (based on comments I have received in more than one review provided by more than one reviewer). Given that these terms often refer to essentially the same thing and most of them are found fairly often in the literature, there appears to be no current consensus on what to call the attached particulate organic matter in benthic ecosystems or any strong rationale with which to decide the term to use.

Each of these terms if examined closely and/or literally are somehow deficient in their ability to precisely define the attached POM. For example, periphyton, if taken literally, simply means “around the plant” and thus fails to provide any information about what it is that is around the plant. In addition, periphyton is commonly used to refer to materials attached to non-plant substrates (i.e., rocks). A different take on periphyton is that it means “plants around”, which is as uninformative as the first definition. Clearly, ‘periphyton’ fails to convey an exact meaning of the attached benthic POM. Biofilm is another commonly used term for the POM, which is also vague and somewhat inaccurate. This term literally means a living film or perhaps a film derived from living organisms. Biofilm is deficient in its lack of acknowledgment of the non-living components of the attached particulate organic matter. Benthic algae only refers to the attached algae of benthic ecosystems and fails to capture the complex nature of the attached POM. There are also the terms consisting of ‘epi-’ and a Greek-derived root. These terms simply mean ‘on the’ and your substrate of choice. For example, epilithon means ‘on the rock’. This term includes all organic types (including living and non-living material) and specify the type of substrate under investigation. Such terms avoid confusion over whether we are talking about rocks, sand, mud, or plants as substrates. A literal dissection of the ‘epi-’ terms shows the terms could be regarded as overly inclusive. For example, epilithon could mean, as it is commonly intended to, particulate organic matter attached to rocks. But it could also mean, if taken literally, a bed of zebra mussels. It doesn’t say what is actually attached to the rocks. One final alternative, sometimes seen in the literature, is the use of a combination of these terms as in ‘epilithic biofilm’. This solves some of the problems noted above except that all of the above terms (e.g., periphyton, biofilm, benthic algae, epilithon) which would be used in some combination are, one way or another, problematic and therefore ultimately fail refer to the entire complex mixture of organic matter.

There are several solutions to this terminological problem. We could simply choose the most established or well-known term and then stand united behind it. Alternatively, we could look for the most correct alternative and use it. Or we might instead look for an innovative and relatively unencumbered term. In this case, the most established term is periphyton (see below), the most correct alternative would probably be found in using a mix of the terms, and a new term might be something like ‘organofilm’.

Fig. 2. Total yearly usage of terms (periphyton, benthic algae, biofilm, and the epi’s) found in the titles and abstracts of six widely read limnological journals (Limnology and Oceanography, Freshwater Biology, Journal of the North American Benthological Society, Canadian Journal of Fisheries and Aquatic Sciences, Archiv für Hydrobiologie, and Hydrobiologia) during the years 1985-2005. Term usage was assessed using root (i.e., periphyt*) searches in the Web of Knowledge. (click to enlarge)

Barring the widespread adoption of a new term (i.e., organofilm), the already discussed terms, periphyton and its alternatives, will continue to battle for usage in the aquatic literature. It might be that one term will ultimately win out and eliminate the usage of all of the competing terms. One indication of whether that is happening is provided by examining the patterns of term usage over the relatively recent past. During the past twenty years, the annual occurrence of all terms (i.e., periphyton, benthic algae, biofilm, and the “epi’s”) in the titles and abstracts of papers published in 6 aquatic journals has steadily increased from 31 times per year in 1986 to 83 times per year in 2005 (Fig. 2). The use of periphyton, on the other hand, has remained relatively steady, being found 30 times per year both in 1987 and 2005 (Fig. 2). It thus appears that the relative use of periphyton (compared to the other terms) has decreased somewhat over the last twenty years (64% of occurrences in 1988 to 33% in 2001; Fig. 3). Despite this, periphyton was the most common term over the entire period being found a total of 539 times at an average annual rate of 26.9 times per year. This total exceeded the number of occurrences (425) of the second most common group of terms (the “epi’s”) by about 26%. Similar to periphyton, the “epi’s” and benthic algae have seen relatively steady use in the literature (Fig. 3). Biofilm, on the other hand, has increased in the total number of occurrences per year (from 0 in 1987 to 15 in 2004) and, consequently, has increased its percentage share of total references (0% in 1983 to 19% in 2002; Fig. 3).

Fig. 3. The percentage of total occurrences for terms (periphyton, benthic algae, biofilms, and the epi’s) found in the titles and abstracts of six widely read limnological journals (Limnology and Oceanography, Freshwater Biology, Journal of the North American Benthological Society, Canadian Journal of Fisheries and Aquatic Sciences, Archiv für Hydrobiologie, and Hydrobiologia) during the years 1985-2005. Term usage was assessed using root (i.e., periphyt*) searches in the Web of Knowledge. (click to enlarge)

These results indicate that the term, biofilm, has taken hold and we should perhaps expect increased usage of this term in the future at the expense of periphyton and the ‘epi-‘ terms. This increased usage of biofilm may eventually create a positive feedback mechanism, where its prevalence leads to its greater use and increased disuse of the alternative terms. I recognize that predicting future patterns of term usage is difficult given that authorial preferences, editorial advice and direction, and perceived proper usage are all likely to influence these patterns. Nonetheless, I suspect that biofilm will ultimately replace periphyton in the common parlance of the limnological vocabulary. That is unless we choose not to follow this route of replacing one ill-conceived term with another. Why not keep and promote periphyton along with a clear and distinct definition of what the term means?

I remain perplexed by some of spirited arguments against the continued use of periphyton that I have received in both oral and written form. Would I have fewer readers of my scientific paper or would it have less impact if I were to choose to use the term, ‘periphyton’? As I generally define the term, ‘periphyton’, when I first use it in a paper, how much confusion could possibly arise? Why would adopt an alternative term (i.e., biofilm) that is also misliteral and borrowed from another biological discipline (i.e., microbiology) over our own troubled term? If we were to start replacing all vague, confusing, or multidefinitional terms, we would have a considerable task ahead of us. For example, we might consider changing ‘limnology’ which means the study of lakes to a term that includes the study of rivers, streams, and other freshwater ecosystems (e.g., limnopotamology). Or perhaps we should phase out ‘oceanography’ for an alternative term (e.g., oceanothalassology) that means more than the charting of the ocean. Once started, we would find terms in need of replacement throughout our scientific vocabulary (Box 1). The problem with this is that we would generate a lot of confusion by doing so; more so than that caused by the original misliteral or multiple terms. In the end, maybe we shouldn’t overly worry about the arbitrary nature of language and learn to live (or love) the unique and interesting patterns of word usage that science and history has provided us.


Frost, P.C., H. Hillebrand, and M. Kahlert. 2005. Low algal carbon content and its effect

on the C:P stoichiometry of periphyton. Freshwater Biology 50: 1800-1808.

Monday, January 14, 2008

Ionic liquids: Model for future chemical design

Blogging on Peer-Reviewed Research

Just had to point out that a paper which I'm a co-author on came out today:

Aquatic toxicity and biodegradation of ionic liquids: A synthesis.

The first author is Konrad Kulacki, and he's certain the guy who put in the most work on this actual paper, but the paper is a review/synthesis of an entire group's research on the effects of ionic liquids on aquatic ecosystems.

So what are ionic liquids?

Ionic liquids (ILs) are essentially organic salts that happen to be liquid at room temperature. There's been a lot of research into ILs, because they seem to be able to perform all kinds of industrial functions that are currently performed by volatile organic compounds (VOCs). VOCs work great, but they are also a huge health risk to workers and the environment because they evaporate. Most ILs do not evaporate at all and therefore switching from VOCs to ILs will reduce air pollution.

And that is fantastic. The downside is that many of the ILs being developed for industry are extremely water-soluble. That means they are going to end up in water-ways. So a group of ecologists at the University of Notre Dame (lead by Gary Lamberti and Charles Kulpa) teamed
up with some chemical engineers and civil engineers (also from Notre Dame and lead by Joan Brennecke) to see if ILs could be developed that had minimal impacts on the aquatic environment. As it turns out, there are literally billions of different possible ILs, and so designing ones that aren't harmful to the environment should be possible.

While the research on environmental effects has failed to keep pace with the research on the usefulness of ILs, a significant amount of data has now been gathered. From studying a small number of ILs spanning a wide range of possible IL properties, we've been able to isolate some traits that seem important in terms of toxicity and biodegradation (i.e., alkyl chain length). We've also been able to get a feel for how different taxa will respond to ILs. For instance, duckweed seem to be more sensitive than algae. Fish and snails seem to be less sensitive than Daphnia. All of this information can help us figure out why ILs cause toxic effects, what ecosystems and biota are most at-risk, and what can be done to mitigate any harm.

The Notre Dame IL research group (which put me through grad school) isn't the only research group working on the environmental impacts of ILs. A group out of Germany (I think) is also hard at work on the same subject. They've actually published a series of papers exploring the idea of incorporating environmental effects into the design phase of chemical development (you can see their list of pubs here, the ones in Green Chemistry are particular interesting). What both groups (and numerous others) are really interested in is finding ways to design more environmentally benign chemicals that are also able to perform in industrial applications. This same approach is being somewhat adopted for nano-materials.

I could go on and on about the IL story, and maybe I will at some point in the future. Today I just wanted to celebrate a new publication.

Monday, January 7, 2008

Wind Farms

I'm a big proponent of alternative energy solutions. On a broad scale, I think producing energy that doesn't rely on simply burning fossil fuels, combined with a reduced consumption, is the only long-term solution to global climate change issues.

However, global climate change is only one step of the environmental issues we're facing as a society. We're also threatening the healthy functioning of ecosystems by eliminating species through habitat destruction, introducing new species, etc.

Wind power is one of the most cost-effective alternatives to coal available today. The physics are simple, the mechanics are well-understood, and the supply of wind is abundant in many locations. Indeed, wind power is growing so fast the suppliers of turbines are having a hard time keeping up. The overall picture is that wind power is going to become an increasingly important part of our energy budget.

The downside? Like just about everything else we push up into the sky, wind turbines may take a pretty heavy toll on the bird populations. This paper suggests that most of the birds killed by a Minnesota wind farm were migrants, and in case anyone forgot, we have a treaty that covers migrants. Overall though, I haven't been able to find a lot of hard data on the magnitude of effects on birds, but as I've mentioned before, I have terrible journal access here. I'll be at the library later this week and I'll have to see if I can find out more then.

There seems to be some inherent reason to believe that this might be similar to what happens with bird-kills around cell and radio towers. The basic idea with the towers is that lights on the towers reflect off clouds, creating a "false dawn" that the birds respond to en-masse. The response? Flying around in circles while waiting for the sun to come up. Unfortunately, flying around a 400 foot tower supported by guyed wires isn't a great idea, even for birds with as much dexterity as a sparrow. Of course, the wind turbines don't have wires supporting them (at least, not as many), but the swinging blades might pose a similar hazard.

I mention this because a battle over the environmental impacts of wind is raging down in Texas. Essentially, the use of wind is going to lead to whole new areas of land being given over to energy production that were previously being used for something else. I think the large-scale, long-term benefits of increasing wind production and subsequently decreasing coal/petroleum use probably outweigh the impacts on migratory birds, but I'm not sure. I'm not sure enough information about the effect of wind turbines on bird populations is even known to answer that question.

Any thoughts?

Thursday, January 3, 2008

Kansans = Awesome

Not only did the Kansas Department of Health and the Environment make Kansas the first state to deny the construction of a new power plant based solely on greenhouse emissions, it turns out Kansans are totally on-board. From a poll paid for by the Land Institute out of Salina:

By a 2:1 margin (62% agree, 31% disagree), Kansas voters agree with the Kansas Department of Health and Environment's decision to block constrcution of the two new coal burning plants near Holcomb, Kansas. [cite]

Predictably, the Kansas State legislators from the Western district are unwilling to believe the results.

"I just can’t imagine that would be an accurate poll,” [Senate President Steve Morris, a Hugoton Republican] said. “Virtually everyone I’ve talked to has been concerned about the decision.” [cite]
Yes, well when you're only talking to Sunflower Electric and other entities with a financial stake in the issue, I suppose you might get that impression. Note the key here, Mr. Morris is solely saying that by virtue of the result the poll must be inaccurate. I know the Bush Administration has always taken the position that facts which contradict them are inherently suspect. I am disappointed to learn that philosophy is trickling down to local politicians.

For the record, the people of Kansas are seeing right through the non-sense that has been thrown at them from the various agencies who have a political or financial stake in building an unnecessary coal power plant.