Archive for: July, 2012

Ambiguity in phylogenies

Jul 31 2012 Published by under Uncategorized

As I noted in an earlier post, thinking about branching phylogenies (which represent variational evolution) is very much an acquired skill that needs training. Without it, people are prone to mis-reading phylogenies. Understanding and perception are highly inter-twined, so that the way one "reads" a phylogeny influences understanding, but prior understanding also influences the way one "reads" a phylogeny in the first place.

This problem has been studied by many researchers; and I have listed some of them in the Further Reading below. In this post I will cover just a few of their more important findings about the most common mis-interpretations made by non-experts.

The basic theme will be familiar to you from my previous blog posts — people look for transformational evolution not variational evolution when they view a phylogeny. It is easier to grasp a simple linear sequence than it is to comprehend an inter-linked set of lineages. However, there are a number of ways in which a single lineage can be "extracted" from a phylogeny, either intentionally or unintentionally, and I will briefly introduce these to you in this post.

There have been a number of studies of students taking introductory biology courses at tertiary institutions (mostly in the U.S.A.), aimed at identifying the "major misconceptions" entertained by these students. Certain basic problems are discussed by almost all of the authors listed below, and I assume that these are therefore the ones that we need to be most aware of and guard against.

As I noted in the previous post, I think that the ultimate source of these problems is evolutionists themselves, as they sometimes present ambiguous evolutionary diagrams, ones that are left open to an unintended transformational interpretation in addition to the intended variational one. This problem can be corrected only by the evolutionists themselves.

The first issue is the one I identified above, that people incorrectly emphasize a single lineage in the phylogeny, which they see as the "main branch" of the tree, with the other lineages as side branches. People have a preference for simplified stories with unambiguous beginnings and ends, and a single lineage provides this.

As an example, consider the first phylogeny. It shows six (unlabeled) taxa at the top, which represents the present, and a single ancestor at the bottom, which is the past. The lineages branch progressively from the ancestor to the current taxa. The order of the branching indicates the relationships among the taxa, without any intended emphasis on any one lineage.

A phylogeny of six (unlabeled) taxa.

However, many people do apparently interpret this type of diagram as having a main lineage, with the other lineages as side branches, as shown by the bold line in the next figure. That is, the taxon on the right is seen (incorrectly) as the "goal" of an evolutionary series, rather than merely being one of six equal taxa linked by branches. Technically, this is an example of "good continuation", where a straight line can be seen as continuing though the diagram and is therefore treated as a single entity.

The same phylogeny, with one lineage emphasized.

The research shows that this potential mis-interpretation can often be avoided by using an angled or circular diagram, rather than one with sloping lines. A comparison of a sloped and angled phylogeny is shown in the next picture. The sloped diagram potentially has a main lineage leading to E, but this is not as obvious in the angled diagram, because there is no continuous straight line running through the diagram.

A phylogeny of five taxa, drawn in two different way.

Interestingly, circular trees are apparently the representation most disliked by students, but this type also gets interpreted correctly most often. It seems that the ambiguity is reduced, thus leading to correct interpretation, but the observer has to work harder because their (incorrect) preconceptions can't come into play.

The same phylogeny drawn in a circular manner.

Another concern is that phylogenies are sometimes drawn in what is called a "ladderized" manner that unnecessarily emphasizes a "main branch with side-branches", as shown on the left of the next picture. The non-ladderized version on the right shows exactly the same branching sequence but re-arranges the order of the taxa to reduce the ladder effect.

A ladderized version of a phylogeny, on the left, compared to a non-ladderized one.

Another potential problem is having the observer locate a well-known organism in the phylogeny and then treating the lineage to that organism as the "main branch" of the tree. This is shown in the next picture, where the non-humans have been visually relegated to side-branches. There may be little we can do to stop this, at least in cases where Homo sapiens is in the phylogeny.

A phylogeny of some vertebrates, with a well-known lineage highlighted.

The next potential problem is that people often pay more attention to the order of the taxa at the tips of the phylogeny than they do to the branching order of the lineages. Most commonly, they interpret a transformation series from left-to-right across the diagram or from top-to-bottom. That is, the organism in the top-left corner is treated as being the ancestor, with an evolutionary series starting there. Each taxon is then interpreted as being most closely related to the taxon next to it, rather than using the branching order to interpret the genealogical relationships. That is, there appears to be a natural progression in the order of the taxa, and this pattern dominates over the branching pattern.

Two ways of drawing the same phylogeny of six taxa are shown in the next picture. In the first diagram the taxa are arranged in an order that represents the most common preconception about evolutionary change of vertebrates, so that mis-interpretation is quite likely. In the second diagram there is likely to be much less incentive to see an evolutionary series from left-to-right, so that the branching order can take precedence in displaying the relationships.

Two phylogenies of the same set of six organisms. The top one is often mis-interpreted as showing an evolutionary series from left-to-right.

The top-left corner is a key location in any visual interpretation, particularly for anyone whose native language is read left-to-right and top-to-bottom. However, the ancestor is not one of the tips, and the order of the tips has no special meaning.

This potential problem particularly occurs when there is no direct reminder about the direction of time in the phylogeny, since it is then left to the observer to deduce it. If this is combined with an anthropocentric ordering of the taxa (eg. humans at the top-right corner), then clearly there is enormous potential for mis-understanding. This will also be true if the observer has the idea that "simpler" (or "primitive") organisms have evolved into more "complex" (or "advanced") ones, and the supposedly simpler ones are presented at the left.

One of the most blatant examples of this problem occurred in 2008, when the highly ranked journal Nature put out a press release concerning a paper they had published, which concerned the completion of the sequencing of the platypus genome. The press release contained a picture of a phylogeny, supposedly illustrating the evolutionary relationships of various animal species in various stages of having their complete genomes sequenced, as shown here.

Phylogeny from the Nature press release.

Given what I have said above, you can see that almost everything about the way this phylogeny is drawn is blatantly inappropriate. First, this is the sloped version of a phylogeny; second it has a sequence of organisms from top-to-bottom leading to humans; and third, just in case you missed the sequence, it is emphasized by a set of arrows down the left side. The branching sequence appears to be the least important thing for whoever drew this diagram. Worst of all, the branching sequence is wrong, as well!

And just to add salt to the wound, when the equally highly ranked journal Science covered the same topic they published a picture with the same wrong phylogeny! At least this one is drawn in the square manner, and does not have the inappropriate arrows. (I am grateful to the evolgen blog for drawing my attention to these two pictures.)

Phylogeny from Science magazine.

My basic theme in these posts has been that evolutionists are, in some ways, their own worst enemy, because they often use potentially ambiguous language and ambiguous pictures when communicating. However, most of the research studies listed below offer practical advice for overcoming ambiguity and mis-interpretation, and I have indicated some of the suggestions above. The point is that merely instructing someone in how to interpret a diagram is insufficient for understanding — the design of the diagram also needs to take into account the perceptual viewpoint of the viewer, and be adjusted to ensure that it is unambiguous.

Unfortunately, the problems listed above commonly manifest themselves both in textbooks and in museums, as well as in books specifically written for the general public. I have listed below some of the formal studies that have demonstrated that this is a widespread problem. Not unexpectedly, it is diagrams of hominoid relationships that suffer the worst treatment at the hands of the educators.

The example shown below is taken from Novick, Shade & Catley (2011). Part (A) of the figure is taken from a textbook (published in 2002), and it incorrectly emphasizes a transformational evolutionary series through time, leading from extinct horses (at the bottom) to the modern ones (at the top). Part (B) is a sloped version of the phylogeny, which inadvertently emphasizes the lineage to the modern horse Equus, both by having a straight line leading to Equus and by having a temporal sequence lead from left to right. It is reported that sloped diagrams are the most common form found in textbooks! Part (C) is the same phylogeny drawn in the angled style, which is an improvement over the other versions, but it still has the inappropriate left-right temporal sequence (especially with the horses running left-to-right!). So, even this last version leaves itself open to ambiguous interpretation.

Three ways of drawing the phylogeny of horses. The figure is adapted from Novick, Shade & Catley (2011).

Clearly, people bring certain pre-conceptions into any educational setting, which may not be appropriate for that setting. These natural pre-conceptions come from their prior training and from their own personal experiences. What is being learned will be fitted into the pre-existing thought processes, and what is said and shown will be interpreted in the light of the pre-conceptions. Ambiguity of words and icons is fatal under these circumstances, as it allows multiple interpretations, most of which are not intended by the presenter. Sadly, the studies done to date make it clear that ambiguity on the part of evolutionists simply re-inforces pre-conceptions rather than providing new knowledge about evolutionary biology.

Interestingly, this problem of ambiguity is not confined to evolutionary biology. In his first book of anecdotes about his life (Surely You're Joking, Mr Feynman! 1985), the Nobel-prize-winning physicist Richard P. Feynman criticized almost all of the physics schoolbooks available in the state of California at the time he was on the State Curriculum Commission. His comment was:

"Everything was written by by somebody who didn't know what the hell he was talking about, so it was a little bit wrong, always! ... [The books] were false. They were hurried. They would try to be rigorous, but they would use examples which were almost OK, but in which there were always some subtleties. The definitions weren't accurate. Everything was a little bit ambiguous — they weren't smart enough to understand what was meant by 'rigor'. They were faking it. They were teaching something they didn't understand ... And how we are going to teach well by using books written by people who don't quite understand what they're talking about, I cannot understand. I don't know why, but the books were lousy; UNIVERSALLY LOUSY!"

This is a comment that all textbook authors should heed. Understanding phylogenies as representations of evolutionary relatedness is a cognitively complex task that requires instruction, and ambiguity can play no part in that process. Moreover, diagrams of all sorts are important in science, not just as tools for communicating ideas but as tools for learning and reasoning. If one is to be a biologist, reasoning and communicating about evolution is essential, and this can only be done if one can interpret a phylogeny correctly.

To me, the most surprising result of the research listed below is that students who had previously completed a course in evolution were not necessarily any better at interpreting phylogenies than were other students. Apparently, evolution students are not taught phylogenetics, at least in a way that allows the students to connect their knowledge of evolutionary biology (usually micro-evolutionary processes) to the study of phylogeny (a macro-evolutionary process). So, phylogenetics ends up being taught as a subject independent of evolutionary biology, which is a ridiculous situation.

Further Reading

Distorted pictures occur in several ways in modern evolutionary biology. This topic has received considerable attention in the literature, and there are a number of very readable expositions of various parts of it.

Gregory T.R. (2008) Understanding evolutionary trees. Evolution: Education and Outreach 1: 121-137.

O'Hara R.J. (1992) Telling the tree: narrative representation and the study of evolutionary history. Biology and Philosophy 7: 135-160.

Crisp M.D., Cook L.G. (2005) Do early branching lineages signify ancestral traits? Trends in Ecology and Evolution 20: 122-128.

Krell F.-T., Cranston P.S. (2004) Which side of a tree is more basal? Systematic Entomology 29: 279-281.

Omland K.E., Cook L.G., Crisp M.D. (2008) Tree thinking for all biology: the problem with reading phylogenies as ladders of progress. BioEssays 30: 854-867.

Sandvik H. (2009) Anthropocentrisms in cladograms. Biology and Philosophy 24: 425-440.

Communication with non-experts has been a fundamental theme in these blog posts. A number of people have investigated how well evolutionists communicate in various educational settings, such as in the classroom, in textbooks, and in museums.

Catley K.M., Novick L.R. (2008) Seeing the wood for the trees: an analysis of evolutionary diagrams in biology textbooks. BioScience 58: 976-987.

Clark C.A. (2001) Evolution for John Doe: pictures, the public, and the Scopes Trial debate. Journal of American History 87: 1275-1303.

Hellström N.P. (2011) The tree as evolutionary icon: TREE in the Natural History Museum, London. Archives of Natural History 38: 1-17.

Ladouceur R. (2010) 20th century high school biology textbooks reviewed and ranked.

MacDonald T., Wiley E.O. (2012) Communicating phylogeny: evolutionary tree diagrams in museums. Evolution: Education and Outreach 5: 14-28.

Torrens E., Barahona A. (2012) Why are some evolutionary trees in natural history museums prone to being misinterpreted? Evolution: Education and Outreach 5: 76–100.

Other researchers have carefully investigated how students respond when confronted with a phylogeny, and what things can be done to improve their understanding and interpretational skills.

Baum D.A., Smith S.D., Donovan S.S. (2005) The tree-thinking challenge. Science 310: 979-980.

Catley K.M., Novick L.R., Shade C.K. (2010) Interpreting evolutionary diagrams: when topology and process conflict. Journal of Research in Science Teaching 47: 861-882.

Gendron R.P. (2000) The classification & evolution of caminalcules. American Biology Teacher 62: 570-576.

Goldsmith D.W. (2003) Presenting cladistic thinking to biology majors & general science students. American Biology Teacher 65: 679-682.

Halverson K.L., Pires C.J., Abell S.K. (2011) Exploring the complexity of tree thinking expertise in an undergraduate systematics course. Science Education 95: 794-823.

Meir E., Perry J., Herron J.C., Kingsolver J. (2007) College students’ misconceptions about evolutionary trees. American Biology Teacher 69: e71-e76

Miesel R.P. (2010) Teaching tree-thinking to undergraduate biology students. Evolution: Education and Outreach 3: 621-628.

Morabito N.P., Catley K.M., Novick L.R. (2010) Reasoning about evolutionary history: post-secondary students' knowledge of most recent common ancestry and homoplasy. Journal of Biological Education 44: 166-174.

Novick L.R., Catley K.M. (2012) Reasoning about evolution’s grand patterns: college students’ understanding of the Tree of Life. American Educational Research Journal 49: in press.

Novick L.R., Catley K.M., Funk D.J. (2010) Characters are key: the effect of synapomorphies on cladogram comprehension. Evolution: Education and Outreach 3: 539-547.

Novick L.R., Shade C.K., Catley K.M. (2011) Linear versus branching depictions of evolutionary history: implications for diagram design. Topics in Cognitive Science 3: 536-559.

Sandvik H. (2008) Tree thinking cannot taken for granted: challenges for teaching phylogenetics. Theory in the Biosciences 127: 45–51.

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Contradictory messages in phylogenies

Jul 30 2012 Published by under Uncategorized

We are often told that a picture is worth a thousand words, and so I guess that mis-communication will be several-fold greater with a diagram than with a sentence. This certainly seems to be true in evolutionary biology, which is a pity because the visual representation of a phylogeny is such a powerful tool for communication.

I have emphasized in previous posts that the principal problem interpreting a phylogeny is seeing a single linear sequence of evolution rather than seeing an inter-connected set of lineages. I am sorry to say that many phylogenies are drawn so that it is very easy to discern a single lineage from within the set of lineages, which is thus almost guaranteed to be a source of mis-communication.

This issue seems to have started with Ernst Haeckel in the late 1800s. Haeckel was an important scientist as well as a popularizer of science (and also a brilliant artist). He coined many words that are common today in evolutionary biology (including "phylogeny"), because he was the first to study several new fields. He is often credited as the first person to publish phylogenetic trees following the publication of Charles Darwin's Origin of Species, but he was actually beaten by several people (including Franz Martin Hilgendorf, St George Jackson Mivart and Albert Gaudry). However, it is definitely true that "more people by the turn of the century had learned of evolutionary theory through Haeckel's depictions than even from Darwin's own writings" (Richards 2011).

Haeckel's first phylogenies (published in 1866) were drawn as multi-branched bushes, rather similar to the diagram that Darwin himself had published. These diagrams were intended to represent ideas about continuity of descent through time, and the role of speciation in increasing biodiversity and extinction in counter-balancing this. They thus emphasized the branching nature of variational evolution.

From Haeckel (1866). Note that Homo is on a side-branch in the top right-hand corner.

However, Haeckel then veered away from this approach when explicitly discussing the evolution of humans. Here, he drew trees with a distinct central trunk and much smaller side-branches (presumably modeled on an oak tree, rather than a bush). This image emphasizes one particular lineage at the expense of the others, because there is one taxon obviously sitting at the crown of the tree while the others are relegated to side-branches. As Richards (2011) has noted: "Haeckel regarded these two types of diagrams as having different purposes. The first represented ... a proper stem-tree, one highly branched. The latter diagram simply looked back from a given organism — in this case man — to its lineal progenitors. It's as if one began with the first kind of tree and traced back the series of man's direct ancestors — and this would result in that second kind of tree."

From Haeckel (1874). Note that Homo is at the top of the central trunk.

It should be obvious that the second diagram is much more prone to be incorrectly interpreted as transformational evolution than is the first diagram. Indeed, it is very close to a "tree" version of Huxley's human evolution diagram as discussed in my earlier blog post. And like Huxley's picture, Haeckel's tree has made it into the 20th century, as shown in the next picture.

From Smallwood et al. (1948). Note that Homo is at the top of the central trunk.

This approach to drawing a phylogeny can be used to put any chosen organism at the crown of the tree, not just human beings, as illustrated by the following diagram from James Scott (which looks like it is modeled on a pine tree). This is a fundamental characteristic of a phylogeny — it can be drawn so that any part of the diagram is at the crown. However, to be accurate it should always be drawn so that no one lineage is emphasized over any other one — there should be no taxa sitting at the crown.

From Scott (1986). Note that butterflies are at the top of the central trunk.

The issue here is that emphasizing one lineage at the expense of the others is inappropriate. The phylogeny shows the relationships of all of the taxa, and those relationships are reciprocal (brothers and sisters are equal). Emphasizing a single lineage seems to add information to the phylogeny (one taxon is more important than the others), but that extra information is false. The phylogeny is thus mis-interpreted.

If you are interested to see a modern version of human evolution that does not emphasize any one lineage, then one of the best examples is the phylogeny of ~3,000 species, based on ribosomal-RNA gene sequences, produced by the people in the Hillis/Bull laboratory at the University of Texas. You can see (and download, since it is not small!) the diagram here. Note that the diagram says "You are here", to indicate the location of the Homo lineage.

Finally, trees with a central trunk also occur outside biology. Most parts of human culture have a history of some sort that is analogous to variational evolution, with many descendant lineages arising from a single ancestor. This next diagram shows the history of jazz music in the U.S.A. Note that it is drawn as a tree with a central trunk, thus implying that each form of jazz was derived from a single previous form. This is incorrect, as any jazz afficionado will tell you, because the evolutionary history of jazz is more complex than this. Furthermore, all that the side branches are doing in this example is listing some of the practitioners of each type of jazz. This is not what the branches should mean in an evolutionary diagram.

The Story of Jazz in the U.S.A.

My basic point in this post is that evolutionists often present ambiguous evolutionary diagrams, ones that leave themselves open to an unintended transformational interpretation in addition to the intended variational one. It is the branching sequence that matters in a phylogeny, but it is incorrect to "see" the diagram as a tree with side-branches — all lineages are equally important in a phylogenetic bush because they are all equally part of the genealogical history.

In the next post I will look at more subtle ways that a single lineage can be "extracted" from a phylogeny, thus resulting in evolutionists mis-communicating with their audience.


E. Haeckel (1866) Generelle Morphologie der Organismen. Reimer, Berlin.

E. Haeckel (1874) Anthropogenie oder Entwickelungsgeschichte des Menschen. Engelmann, Leipzig.

R.J. Richards (2011) Images of evolution. American Scientist 99: 165-167.

J.A. Scott (1986) The Butterflies of North America: a Natural History and Field Guide. Stanford University Press, Stanford.

W.M. Smallwood, I.L. Reveley, G.A. Bailey, R.A. Dodge (1948) Elements of Biology. Allyn & Bacon, Boston.


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Evolutionists are poor communicators

Jul 27 2012 Published by under Uncategorized

In the last post I pointed out that the biggest problem trying to communicate about evolutionary history is that transformational evolution is much easier to grasp than is variational evolution. A linear sequence can be understood almost instantly but a branching sequence cannot, because it is an inter-linked set of linear sequences. People have a preference for simplified stories with unambiguous beginnings and ends. Unfortunately, variational evolution is a process of continual branching and extinction, apparently without end, whereas transformational evolution is a simple linear process, usually leading to a predictable end.

This has important consequences for communication among evolutionists, and between evolutionists and the general public. For example, while I have no intention of entering the debate between evolutionists and creationists, it seems to me that there is a lot of talking but not a lot of communicating between these two groups. In this post I will argue that a lot of the problem is sloppy communicating on the part of the evolutionists.

This can have two aspects: (a) sloppy language (ambiguous use of words), and (b) sloppy diagrams (poor choice of iconography). I think that evolutionists have been guilty of both of these things. In this post I will discuss words, and in subsequent posts I will cover pictures.

In order to make contact with an audience you have to communicate on their terms. Using language that can have two meanings, no matter how subtle that difference may seem to you, will result in failure, at least some of the time. You have to see the other person's point of view clearly, and then express yourself in words that will address that point of view, rather than assuming that your own point of view will be obvious.

For example, the simple claim that "humans evolve" will always be ambiguous, because "humans" can refer to both the species and the individuals within that species, and "evolution" can be applied to both of them, but with very different meanings. For individuals, evolution is transformational, while for species evolution is variational. So, exactly what does the statement "humans evolve" mean? The speaker/author may mean one thing, but we would all be perfectly justified in interpreting it very differently from that intention.

I was inspired to write this blog post by reading the introduction to Daniel Fairbanks' recent book Evolving: the Human Effect and Why it Matters (Prometheus Books, 2012), in which he says: "Along with the rest of life, we evolved and we are evolving." One can interpret this sentence as "You and I evolve through time", or as "The human species evolves through time". I assume (hope?) that the author means the latter, but everyone (including creationists) could be excused for reading the former, and thus possibly dismissing the author's idea.

Any statement made by an evolutionist that leaves itself open to this sort of dual interpretation is simply perpetuating the problem caused by the two meanings of the word "evolution".

I do not intend "to pillory the few for errors which many commit with impunity" (to quote Björn Andersen, Methodological Errors in Medical Research: an Incomplete Catalogue, 1990), and so singling out Daniel Fairbanks is perhaps unfair. However, if a professional geneticist can leave himself open to this sort of simple (but profound) misinterpretation when trying to communicate with the general public, then we can easily see that there is a fundamental problem: the evolutionists are assuming a lot about the meaning of their words that is not necessarily assumed by the general public.

In Darwinian biology, species evolve not individuals. Transformational change in individuals is called "development" or "ontogeny" rather than "evolution". Thus, I do not evolve, and I am not descended from a monkey; and yet my species has evolved over a long period of time, and I share rather a lot of ancestors with the monkeys. These distinctions seem quite clear to an evolutionist, and yet the language used by evolutionists frequently fails to clearly distinguish between them, to the great detriment of communication.

In a similar vein, in a 2011 press release from the highly respected journal PLoS Biology, Peter Currie, a developmental biologist at the Australian Regenerative Medicine Institute, is quoted as saying: "Humans are just modified fish. The genome of fish is not vastly different from our own." Clearly, the first statement is nonsense, although the second one is quite correct. The only fish whose genomes we know about are extant not extinct. We share an ancestor with these fish, and our genomes are similar because we both inherited our genomes from that ancestor. However, the ancestor was not a fish, and thus we are not modified fish, any more than fish are modified humans. We are both modified from our common ancestor — both fish and humans share characteristics with that ancestor, but they differ from that ancestor (and from each other).

Sadly, professionals also engage in mis-communication when trying to communicate with each other. I won't indulge in a detailed discussion here, but there are at least two misleading expressions that one very commonly encounters in the professional literature: "basal branch of the tree", and "derived species". The first expression is used to refer to an unbranched lineage arising near the common ancestor, when compared to a more-branched lineage. For example, in the diagram below we might say that taxon A is on a "basal branch", whereas taxon B is not. But, how can one lineage be more basal than another? After all, both lineages connect to the "base" at the same point. To claim that one is basal and the other not is like saying that one brother is more basal than another in a family tree just because he has fewer children! The second expression refers to a species that has more "derived" characters than another. For example, in the diagram we might say that taxon B is more derived than taxon A. Characters change from ancestral to derived through time (eg. scaly skin covering is ancestral while fur is derived, because the latter arose later in time). However, this does not make any species more derived. It is the characters that are derived not the species — each species has a combination of ancestral characters and derived ones (including humans) .

A simple phylogeny. Only two of the six taxa are labeled.

Hanno Sandvik (Tree thinking cannot taken for granted: challenges for teaching phylogenetics. 2008, Theory in the Biosciences 127: 45–51) has noted another aspect of potential mis-communication among professionals in phylogenetics — the semantics of language differences. He points out that some languages (eg. German, Swedish, Norwegian) have a specific word for referring to genealogical relationship whereas English does not:

"The German word for 'relationship' is 'Verwandtschaft', but while the English word has all kinds of abstract and symbolic connotations, including overall similarity, the German term is reserved for true, genealogical bonds."

This simplifies communication in the one language by being unambiguous, whereas ambiguity is a potential problem in the other language. Sandvik comments that historically this semantic difference has created all sorts of mis-communication among English speakers, each of whom has had their own idea about what "relationship" means.

I suppose that I would be remiss not to point out that mis-communication works both ways between evolutionists and the general public, although that is not my main thesis here. Constance Clark (Evolution for John Doe: pictures, the public, and the Scopes Trial debate. 2001, The Journal of American History 87: 1275-1303) noted that:

"the most dramatic event at the Scopes trial of 1925 occurred when William Jennings Bryan announced, incredibly, that he was not a mammal ... The trial transcript shows that Bryan did not precisely deny his place within the zoological class Mammalia. He did, however, emphatically object to a diagram that located humans among the mammals ... For scientists this was a version of a familiar branching diagram depicting natural relationships. From Bryan’s point of view it seemed to mock traditional verities about human significance."

Bryan's point of view was not well expressed by denying being a mammal, and would be better expressed as a claim that humans have extra characteristics not shared with other mammals (such as what he referred to as "an immortal soul"). After all, this is apparently what he meant by his statement — humans may have mammalian bodies, but there is more to them than that.

Henshaw Ward (Evolution for John Doe, 1925) expressed what seems to me to be the typical attitude of evolutionists:

"the average man ... thinks evolution is 'the doctrine that man is descended from monkeys', and he is so amused or offended at this theory that his whole mind is occupied with it. His conception is ridiculously false. Until John Doe discards that notion and takes a fresh start, he will never understand the subject."

As I have suggested here, asking the readers to change their attitude is a futile request unless the writers first undertake to change their own attitude, and to write unambiguously.


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Linear versus branching evolution

Jul 26 2012 Published by under Uncategorized

In the last post I pointed out that probably the most important problem with the word "evolution" is that it has two distinct meanings in biology. Transformational evolution refers to a linear set of changes in a single object, whereas variational evolution refers to a branching sequence created by unequal survival among a group of objects. Variational evolution is a process of continual branching and extinction, apparently without end, whereas transformational evolution is a simple linear process, usually leading to a predictable end. A phylogeny is principally designed to communicate variational evolution, since that is the important one in evolutionary biology.

The main point that I wish to make about this is that people seem to  easily grasp transformational evolution but not variational evolution. As David Baum & Stacey Smith have noted in their recent book (2012):
"We do not know why it should be so, but we have learned from working with thousands of students that, without contrary training, people tend to have a one-dimensional and progressive view of evolution. We tend to tell evolution as a story with a beginning, a middle, and an end. Against that backdrop, phylogenetic trees are challenging; they are not linear but branching and fractal, with one beginning and many equally valid ends. Tree thinking is, in short, counter-intuitive."

A phylogeny displays a set of lineages proceeding through time. We can trace an ancestor down to any one of many different descendants, and it is a single line from that ancestor to each descendant. This looks superficially like transformational evolution. However, the phylogeny is a whole series of these lines, inter-linked by their connections through different ancestors and descendants, and so a phylogeny actually represents variational evolution.

This is illustrated in the next figure, which is modified from one in an earlier post, showing the family tree of the current Swedish Royal Family. In this case I have emphasized a single line leading through those people who became monarch. So, even though the family tree is a branching one, with many children in each generation, we can still "see" a single lineage if we choose to. In this case that is exactly what history does, of course, since history books tend to be about monarchs rather than their their non-monarchial relatives.

The family tree of the current Swedish Royal Family, with the lineage of the monarchs emphasized.

However, even in this case the lineage of monarchy is not really linear. There is one branch (the dashed line) that leads to a dead end (an "extinction"), where the line of monarchial descent terminated because none of the offspring were alive to inherit the crown. So, even in this simple case, seeing a single transformational lineage is inappropriate.

The issue is that people fundamentally have more trouble with inter-linked and over-lapping structures, such as a branching phylogeny, compared to a single linear sequence. A linear sequence can be grasped almost instantly, whereas inter-linked structures take time. A family tree is like a telegraph pole if you trace only one lineage, but it's not really a family tree if you do that.

Probably the single most famous image in evolutionary biology is the one showing a series of primate species, each walking from left to right. This first appeared in a 1965 book by the anthropologist Francis Howell, but it has now become an integral part of modern life in many modified forms, as illustrated by this Google search. (The full-size picture, with labels, can be viewed here.)

Zallinger’s linear depiction of human evolution for the book by Howell.

In this context, human evolution seems to be presented as a transformation series. What we are apparently being told is that each species evolved into the next species in the sequence, leading ultimately to humans. That is, human evolution has been transformational, rather than variational. Equally importantly, since transformational evolution often leads to a single predictable end, we are apparently being told that humans are the "goal" of this evolutionary sequence. This has a certain psychological charm. As Sean Nee (2005) has noted: "Our persistence in placing ourselves at the top of the Great Chain of Being suggests we have some deep psychological need to see ourselves as the culmination of creation."

Biologists reject this anthropocentric view, of course. However, the image is such a powerful one, and the message is so clear and so easily grasped, that this one single image seems to dominate most people's view of biological evolution.

That many members of the general public see this image as representing "evolutionary theory" is clearly attested by scores of web pages (e.g. this one, and this one). Indeed, Laurence Smart has gone so far as the claim that: "It is found in many science and evolution textbooks, and is exhibited at museum displays about human evolution", which has unfortunately been all too true.

The diagram is apparently based on a much earlier one, which was published as the frontispiece to Thomas Henry Huxley’s book about primate anatomy (1863), which itself was a collection of Huxley's oral and written work from 1860-1862. The important thing to note is that this appeared several years after Darwin and Wallace published their works emphasizing that biological evolution is variational rather than transformational, and yet it still communicates the idea that evolution is transformational. I sometimes wonder just how much Huxley really understood Darwin's idea, even though history credits him with being one of Darwin's staunchest supporters.

Huxley's infamous frontispiece.

Huxley's image is apparently the one that took hold of both the public and the scientific imagination, rather than Darwin's variational idea. Even educational institutions such as museums used the same idea for their public displays, as claimed by Smart and as illustrated here.

A display of a series of skeletons showing the evolution of humans, at the Peabody Museum circa 1935.

Once again, these earlier illustrations apparently show a linear series, and so that is naturally how they are interpreted by the viewer. However, the same image could also be presented without the apparent linear series. The next picture shows a version as modified for Wikipedia. Note that there are three main changes: (i) The gibbon has been re-sized to match the other species (it is shown at twice its size in the Huxley original); (ii) the species have been re-ordered, notably without humans as the apparent culmination of the series; and (iii) two species have been re-orientated, so that there is no obvious sense of transformation.

Huxley's diagram as modified for Wikipedia.

It is worth noting that Huxley was a persistent menace at confusing transformational and variational evolution. In the 1870s he did it again, this time with horse evolution. The paleontologist Othniel Charles Marsh published a description of newly discovered horse fossils from North America, describing them as a sequence, with the fossil species "Eohippus" being transformed into a totally different modern descendent "Equus" through a series of clear intermediates. Huxley was very active at popularizing this inappropriate transformational series. Sadly, some years later the American Museum of Natural History assembled a famous exhibit of these fossil horses; and this story of the horse family was soon included in most biology textbooks.

What we are dealing with here is mis-communication. Both Huxley and Howell probably did understand the concept of variational evolution, but they each presented images that completely subverted that idea by showing transformational evolution, instead. This mis-interpreted image has come to dominate people's understanding of biological evolution, because a linear series is much more easily grasped than is a branching sequence. Ancestors lead to descendants both in transformational evolution and in variational evolution, but the relationships between the ancestors and descendants are quite different. In transformational evolution we can potentially see all stages of the transformation at the same time, because different objects will be at different stages of their transformation — we can, for example, see infants, children, adolescents and adults all around us, at any time. But in variational evolution, the ancestors are gone and all we can see are the descendants — gibbons are not human ancestors but instead are descendants of a (now extinct) ancestor that they share with humans.

Much of the problem with mis-communication is due to: (a) sloppy language (ambiguous use of words), and (b) sloppy diagrams (poor choice of iconography). In the absence of body language, such as when talking face to face, all we have for communication are words and pictures, and so we need to get both of them right if we are to communicate effectively. Some modern-day examples of this problem will be discussed in the next few posts.


David A. Baum, Stacey D. Smith (2012) Tree Thinking: An Introduction to Phylogenetic Biology. Roberts & Company Publishers, Greenwood Village, CO.

Francis C. Howell (1965) Early Man. Time-Life International, New York.

Thomas H. Huxley (1863) Evidence as to Man’s Place in Nature. Williams & Norgate, London.

Sean Nee (2005) The great chain of being. Nature 435: 429.


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What does a phylogeny communicate?

Jul 25 2012 Published by under Uncategorized

In the last post I pointed out that when studying evolutionary history we take the same approach as do all scientists: we try to explain observable natural phenomena in terms of other natural phenomena. In this case, we extrapolate what we observe in human genealogies back over hundreds of millions of years, to explain the history of species, which we cannot observe directly.

One large problem with this approach  is that using human genealogies (family trees) as a model for species phylogenies is not necessarily a good thing. We need to think carefully about what phylogenies might look like, and thus how to describe and display phylogenetic history.

Perhaps the most important aspect of this problem is confusion about the words "evolution" and "phylogeny". Rather unfortunately, in biology the word evolution has two quite distinct meanings, whereas it usually has only one of those two meanings outside of biology. I am not sure that non-biologists realize the importance of this fact. Both of the meanings are involved in a phylogeny.

Outside of biology (e.g. in physics), "evolution" refers to a change in an object through time. That is, there is a (possibly predictable) transformation of the object through two or more distinctly different states.

For example, we might talk about the evolution of a star, which changes from a main sequence star through the stages of sub-giant, red giant and finally white dwarf. Alternatively, we might refer to the evolution of a website's homepage, as discussed by Ann Smarty at this link. We might even read about the evolution of the Haggunenons, those beings who, in the work of Douglas Adams, could change into armchairs, escape capsules and even other species.

In biology, the most obvious transformational changes occur during our own lifetimes, where we start out as infants and then progress through childhood, adolescence, adulthood and old age. However, biologists rarely call this "evolution", even though that is exactly what it would be called by non-biologists. (Biologists call it "ontogeny".)

In biology, "evolution" usually refers to variational change rather than transformational change. Here, a group of objects appear to change because some of the objects survive and some do not. Each object differs from the other objects in some way but each also remains unchanged. The group as a whole changes because through time the proportion of the different types of object changes. There is a change in the group without a change in any one object within the group.

A cat and a rose

In biology, the most obvious variational changes occur in domesticated organisms. Over the millennia, we have selected specific variants of dogs and cats and roses, for example, and those variants are now more common than they were. So, modern dogs, cats and roses look very different from what we know dogs, cats and roses looked like several hundred years ago, even though each individual dog, cat and rose remained the same for its whole life. What has changed is the group rather than any member of the group.

What is equally important is the obvious increase in the biodiversity of domesticated organisms. There are now more types of dogs, cats and roses (and cows, horses and apples) than there were in the past. That is, a single type of ancestor has "evolved" into many types of descendants. This is a branching process, just as in a family tree.

So, variational evolution is a branching process whereas transformational evolution is a linear (non-branching) process. This needs to be represented in a phylogeny.

A horse and some apples

In addition, some variants do not survive. Genealogical lineages come to an end when there are no descendants left. This happens repeatedly in human pedigrees; and the fossil record is usually interpreted as showing that the same thing happens for species, too. Indeed, geological time-periods are actually defined by dramatic changes in the fossil record, indicating what are referred to as "mass extinctions".

So, variational evolution is a process of continual branching and extinction, apparently without end, whereas transformational evolution is a simple linear process, usually leading to a predictable end. This is what a phylogeny must represent.

The idea that evolution in biology is a more complex process than that in non-biology is usually credited to Charles Darwin, although Alfred Russel Wallace independently developed the same idea at the same time. Darwin did not use the word "evolution" in the first edition of The Origin of Species (it made its appearance only in the 6th and final edition, in 1876), which suggests that he could see the potential confusion between the ideas of transformational evolution and variational evolution. The subsequent history of biology shows that we would all have been wise to follow this lead, as the confusion has been widespread and irksome.

Nevertheless, in a phylogeny we might also like to represent transformational evolution as well as variational evolution. For instance, if we treat each species as a separate object (instead of a collection of individuals) then if a single species changes through time, without any branching or extinction, then this would look like transformational evolution. This was the idea of Jean-Baptiste Lamarck, who didn't believe in extinction of species but instead thought that each biological form transformed into another form through time. Thus, Lamarck's version of evolution was essentially a transformation series among species, with occasional branching into new forms.

Where does this leave us? Well, there is a lot of potential confusion here, with two different types of evolution, and the differences between family trees and species phylogenies. One possible solution is to drop all of these terms, and to create a model of a phylogeny using new words with explicit meanings. This is basically what phylogeneticists have done, as shown in the next figure.

A phylogenetic tree of three types of organism

Cladogenesis refers to the branching process of evolution, represented by the diverging lines in the diagram.
Phylesis (or sometimes also called anagenesis) refers to unbranched evolutionary change through time, represented by the length of the lines (longer lines = more change).
Taxon (the plural is taxa) refers to each observed object in the phylogeny, which may be a species or a genus or even an individual.
The phylogeny is the unobserved history connecting the taxa, which consists of a series of inferred ancestors, linked to their descendants, leading backwards from the observed taxa to their inferred common ancestor.
Note that the diagram does go from the past to the present (or vice versa), but the branch lengths do not represent time. Thus, the fact that the branches end at different places does not indicate that some of the taxa became extinct — they are all observed taxa that exist in the modern world.

Hopefully, it is clear from the phylogeny that the closest relative of Taxon 2 is Taxon 3. We might think of them as "sisters" (or siblings, if you want a neutral term), because they share the same "parent". Taxon 1 is a "cousin" to the other two taxa, because it shares their "grandparent" (but not their parent), in the same way that we interpret a family tree. This is the information that a phylogeny contains — it shows who is the closest relative to whom, by indicating the branching order of their genealogical history.

Here is an example of a real phylogeny for eight animal species, which makes it more concrete. This history was constructed from the DNA sequence of a single gene, which explains why the fruitfly (Drosophila) branch is longer than the others (it would be shorter than some of the others if all of the genes were included). Do not be confused by the fact that the phylogeny proceeds from bottom to top, whereas the previous one proceeds from left to right. The information is in the branching pattern and the line lengths, not in which way round it is drawn.

A phylogeny of 8 species of animal

Note that the branching order shows that Rat and Mouse are the closest relatives. Rat is not historically derived from Mouse, and nor is Mouse historically derived from Rat — instead, they are derived from a common parental species (or ancestor). Human is shown as the next closest relative, sharing an ancestor with both Rat and Mouse. Obviously, there are a lot of other mammals that are not included in the diagram (such as the dog, cat, cow and horse referred to above), but we would expect them to also appear in this part of the diagram. This interpretation of the diagram proceeds until we get to the ancestor that all eight animals share, called their most recent common ancestor.

The phylogeny does not end there, of course. All organisms have a history, and so all of them fit into the phylogeny somewhere (including the rose and apple referred to above). The phylogeny simply extends further and further back in time, including more and more species as it goes. Any one diagram only includes a subset of the organisms, for convenience' sake if nothing else.

This is what a phylogeny communicates, and nothing more — the historical information is in the branching pattern (which tells you about the relationships) and the line lengths (which tell you about the amount of evolutionary change).

The problem is what happens when people try to add more to the phylogeny, or to read more into it than is really there. This is covered in the next post, which will be about what happens if we confuse transformational and variational evolution.


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If biology is a science, then ...

Jul 24 2012 Published by under Uncategorized

Since the time of Isaac Newton (the 1600s), scientists have tried to explain the natural phenomena around themselves in terms of other observable natural phenomena. They observe something happen, and then play a "what if?" game to see whether they can explain something else in terms of the first one. That is, they try to extrapolate from something they can study to something they cannot study, by the simple expedient of assuming that the "same thing" is occurring in both cases.

Newton, the apple and the moon

For example, Newton (famously) observed an apple fall from a tree, and concluded that there must be some natural explanation for this behaviour. He had previously observed the behaviour of the moon (assumed to orbit around the earth) and the sun (where the earth orbits around the sun). It then occurred to him that these three observations might all be manifestations of the same "thing", which we now call gravity. All he had to do was assume that gravity acts in the same way on the apple that is right next to him as well as on the stars and planets that are millions of miles away. Thus, by studying the behaviour of objects as they fall on earth, where we can freely perform experiments, we can learn something about the behaviour of stars. From this simple approach Newton derived a whole scheme of celestial mechanics, which made him one of the most famous scientists in history. Not bad for a young man.

Charles Lyell did the same thing for geology. We can observe flowing water washing away soil to form ditches next to roads and paths. This natural phenomenon takes relatively little time to happen. But what happens if we have a lot of time, perhaps millions of years? Well, Lyell suggested that we'd end up with the Grand Canyon. So, once again, an observable phenomenon is used to explain another observable phenomenon — all we have to do is assume that the same "thing" happens over very large distances and/or times.

Aerial view of the Grand Canyon

We can't observe those large distances and times, of course, so the "what if?" exercise cannot be tested experimentally. Nevertheless, this is the basis of modern science — observe and experimentally study whatever phenomena you can, and then use this as a basis for explaining those phenomena that can't be subjected to experiment. If the explanations form a coherent set of ideas, and those ideas are capable of predicting as-yet-unobserved phenomena, or they tie together a lot of observable phenomena, then the "what if?" exercise will be considered to be a success.

Some people reject this approach, of course. These people are not scientists, and there is no reason why they should be. They have their own explanations for observable phenomena, and their own opinions about what needs explaining and what does not. We often refer to these explanations as "super natural", because they postulate the existence of things beyond the observable world. If super-natural phenomena exist, of course, then scientists can say nothing more about them than can anyone else, because science is restricted to a study of natural phenomena only.

The point for this blog post is that in biology we take the scientific approach. For example, we accept that we and the plants and animals around us have a genealogical history. I have a father and a grandfather and a great-grandfather. I have personally met the first one (I talked to him on the phone just the other day) but I never met his father. However, I am sure that his father existed, as did his father in turn, because other people did observe these "phenomena". (What a way to talk about your own relatives!) Furthermore, this observable genealogical history involves relatives that all look different and yet somehow also look the same. Indeed, the closer they are as relatives then the more similar they usually look. You cannot put my father and his two brothers together, along with their several sons (see one of them here), and not suspect that they are all closely related. It's almost embarrassing!

Modern biology is based on the idea that this history of relationships proceeds for millions of years into the past and involves all living things. That is, through time the differences and similarities among all individuals and species have arisen through genealogical descent. In one sense, this is no different from geology and the Grand Canyon — small patterns accumulate through time to create big effects.

There is, however, one difference from geology and physics, and it has created enormous difficulties for the study of biology, not just in the modern world but for centuries. The phenomena being observed seem to be much more complex in biology. As Craig Bohren has pointed out: "The prestige of physics originates partly from its success in achieving its aims. This success, however, has been obtained by applying extremely complicated methods to extremely simple systems ... The electrons in copper may describe complicated trajectories but this complexity pales in comparison with that of an earthworm."

Thus, those scientists studying the non-biological world have often failed to grasp the difficulty of the task being undertaken by biologists, and they have frequently looked on biological experimentation with disdain. What is worse, however, is that it is much harder to explain biology to non-biologists. One only has to look at the plethora of books trying to explain biology to the general public to realize that physicists apparently have it much easier — there are far fewer books because the concepts only need to be explained once.

We now refer to biological complexity as "biodiversity", to distinguish it from the much simpler diversity observed in the non-biological world. I do not know why it took until the 1980s to create a word that we had clearly needed for 3000 years!

The concept of biodiversity leads us to the inevitable question: what does genealogical history look like if we extrapolate it over hundreds of millions of years? It is unlikely to be a simple linear sequence, as in geology, or a mathematical extrapolation from falling apples to orbiting planets, as in physics.

The study of long-term genealogy is called phylogenetics, and the genealogy is called a phylogeny. The latter is a term created by Ernst Haeckel in the late 1800s to describe the reconstructions of species histories that occurred in response to Charles Darwin's ideas on biological evolution. But what does a phylogeny look like?

If we take the observed phenomenon of a genealogy, it is often called a "family tree". Historically, these trees show the male lineage descending from some specified ancestral male, as shown in the picture below, which refers to the current Swedish Royal Family. This shows a branching arrangement, rather than a linear sequence, with (usually) several children in each generation. Nevertheless, a linear sequence does exist in the diagram, since the tree follows only the lineage of those people who became monarch.

The family tree of the House of Bernadotte, the current Swedish Royal Family

(It is worth noting here that recently Sweden change the laws of inheritance, so that it is now the oldest child of either sex who becomes monarch, rather than the oldest male. We thus currently have a "crown princess", Victoria, rather than a "crown prince", as would be usual in other monarchies. This did not happen in the previous generation, for example, where Carl Gustaf became monarch, rather than any of his four older sisters.)

However, a family genealogy isn't a tree either, is it? The different lineages inter-connect through reproduction. My own ancestry, for example, can be traced through either my father's family or my mother's; and their ancestry can be traced through either their own mothers or their fathers.

So, a genealogy is a complex thing. Does this make a family tree a good model for a phylogeny? That is, we are extrapolating from something we can observe, a family genealogy covering several generations, to something we cannot observe, a phylogeny of species covering millions of years. We are also jumping from individual organisms (people) to groups of organisms (species). This has turned out to be more complex than extrapolating from an apple to a planet. This issue is something that phylogeneticists have struggled with for a long time, both in communicating with each other and with non-experts.

I shall look at the possible solutions in the next post.


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Welcome to the thoughts of a new Scientopian

Jul 23 2012 Published by under Uncategorized

G'day. My name is David Morrison, and I will be responsible for the posts here at Scientopia's Guest Blogge for the next couple of weeks. I am happy to be here; and I hope that you will find the discussions enjoyable as well as informative.

My professional blog is called The Genealogical World of Phylogenetic Networks, which is a mouthful, but basically it is an ongoing discussion about scientists' attempts to reconstruct the "Tree of Life" while actually believing that evolutionary history is much more complex than a tree (ie. a network). Indeed, the very first published diagrams that explicitly depict evolutionary history (= phylogeny) were networks showing the hybridization history of domestic dogs and strawberries, in 1755 and 1766 respectively. This apparently long history (briefly summarized here) was subverted somewhere along the line, notably by Charles Darwin, who popularized the Tree of Life metaphor; and biologists are only now trying to get back on track again.

Along the way, the GWPN blog also looks at the lighter side of things. For example, it has presented network analyses of, among other popular subjects:

  • voting in the Eurovision Song Contest (2006 and 2012)
  • characteristics of Scotch whiskies
  • the opinions of Bordeaux wine critics (part I and part II)
  • characteristics of Bordeaux wines
  • winners of  the FIFA World Cup

For the cognoscenti, we have also had a selection of evolutionary trees used as tattoos, which appears to be quite popular among younger phylogeneticists:

Personally (see my home page), I am an elderly Australian now living in Sweden (mainly because my wife is Swedish). I have spent my whole adult life either studying or working in universities. I spent my early career as a botanist, mainly in ecology but also in systematics. (Yes, I have named several new species of plants, and I have one species named after me!) Somewhere along the line I started working with some parasitologists on using molecular data (mostly DNA sequences) to study the evolutionary history of parasites, including the apicomplexans (which cause malaria and coccidiosis, among many other nasty diseases) and the nematodes (parasitic roundworms). This work has been aimed at developing control strategies for these organisms. From there I branched into bioinformatics, studying the various computer techniques used to analyze the molecular data, which is what I mostly do these days. I have written one introductory book on this work.

However, I am also interested in the way in which evolutionary biologists communicate with each other, and with the rest of the world. Evolutionary history is a basic concept in biology, and yet it is not a simple one. New students take time to grasp the complexity involved; and the general public sometimes seem not to grasp it at all, unfortunately. Evolutionary biologists need to take responsibility for rectifying this situation; and in the forthcoming posts here at Scientopia I intend to explore some of the issues involving verbal and visual (mis)communication.


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So Long, and Thanks for all the Fish.

Jul 22 2012 Published by under Uncategorized

I've packed up my dormitory room in the Scientopia catacombs. I've secured Fonzie the Genetically Engineered Flying Helper-Lemur in an attachment-parenting baby sling, much to his vociferous consternation. I'm loaded up and heading home, back to Infactorium, where I'll continue blogging about health care engineering, sobriety, and other matters of academic and industrial interest (I hope). I've enjoyed my time here. I hope you've gotten something out of it too.

I hope you've gotten a little bit of appreciation for the kind of interdisciplinary work that needs to be done to improve health systems, from understanding how medical research is done to describing how systems theory applies to the delivery of health care. I didn't get to do quite as much of the latter as I wished, given my strange travel schedule during the time. But I hope the basic introduction I did give was a tiny bit enlightening in terms of how engineers see the problem of delivery of care.

I hope that I've left you with a little bit of perspective on people in recovery, people with extant mental illnesses, which must be managed through regular diligence. If you have an alcoholic in your life, an addict, there's help, for you and for them. When we addicts reach for help, we are generally capable of recovery. But it has to come from within; recovery cannot be imposed from without. I hope, if nothing else, I've shown that addicts in recovery are capable of being ordinary people, of doing science and participating in society.

Fonzie is scratching. There's a door, and a bright light. I think the sun is shining. Thank you to all the denizens here that let me stomp around in your labs and muck up your glassware. Thanks for letting me see the future of science, long before the world at large gets to! It's like having been let into the archives of the Closed Access Journal. The people here at Scientopia are doing amazing things. And only 60-70% of them are aimed at global dominion. Don't worry. I've sabotaged the Genomic Repairman's ophidian perfidy, and GertyZ's (Not her real name! Her real name is GertyX!) and Scicurious's new mind control powder, while potent, no longer has a reliable delivery system.

Good luck to the next inhabitant of this space. Please ignore the rubbery substance on the window ledge. By most definitions, it's not even really alive.

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Thoughts on another Shooting.

Jul 20 2012 Published by under Uncategorized

Over at my personal blog, I've reposted my thoughts on mental illness, responsibility, political rhetoric, and mass killings.

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Applications of Systems Theory.

Jul 19 2012 Published by under Uncategorized

OK, this post will involve a bit of what I like to call "the conceit of the engineer", which is that many of us tend to think of our skill set as a hammer and when we look around, we see a lot of nails, most of which need a good pounding. So, I tend to see anything that has a bunch of pieces, or can be modeled with a differential equation, as an application of systems theory. So, today I'm going to simply write a bit about two basic examples in straightforward terms: Climate Science, and Health Care Delivery. Finally, I'm going to describe a tiny bit about how I see systems theory applying to one of science's current Big Debates: Open Access.

Climate Science: I'm no expert. This will be essentially at the third grade level. But this is an area where the applicability of systems theory should be apparent upon a moment's reflection to anyone. The water cycle, for example, is a subsystem of climate science. And a deeply troubling one. As the earth warms, enormous quantities of fresh water currently trapped in ice are at risk to melt. At the same time, warming air will hold more water vapor. Having huge amounts of water in these more volatile forms (ice is pretty sedentary) allows for it to move and change form more readily, meaning additional rainfall, heavy snows when the temperature does drop below 0 degrees Celsius, and rising coastlines.

Of course, there are also a lot of hollywood-style doomsday scenarios to which you probably shouldn't give a lot of credence. It is incredibly difficult to make specific predictions regarding local effects of climate change in any area smaller than say, Western Canada. Localized effects of these very complex systems are (a) highly sensitive to initial conditions, (b) not fully understood even in the realm of theoretical abstraction. As a result, even if we had an incredibly faithful climate model of the whole world, that modeled down to the level of the briefest zephyr, it's going to get the specifics wrong most of the time.

So why bother? Because it will probably get the global behavior correct in ways that are critically important and vital to planning for the consequences of climate change. It doesn't matter if you successfully predict the weather in Astoria, Oregon on Sept 3rd, 2012 (probably kind of grey and rainy). It matters a lot if you want to know things like "within 10%, what will the mean high tide on the western seaboard be over the course of the next 20 years". Climate science is doing an excellent job of generating useful predictions of those sorts. So local weather effects, like hot or cold waves, like tornadoes, hurricanes etc., are not going to be predictable in any useful way by climate models (though, they will likely be good at predicting that they will increase, or change basic locations, like moving north). Systems theory is good at predicting global (system-wide) effects, rather than local (small "features") effects.

So in summary, pay attention to the global predictions. Small-seeming effects over large areas and long time periods. These are the things that climate science is really good at predicting. Weather? That's always going to be random. But the media gets it wrong a lot. Go to the source, if you can, and you'll see that the actual papers explain their confidence intervals, limitations, assumptions, etc. Those things are rarely reported.

Health care delivery has similar strengths and weaknesses. The models are, as yet, not nearly as sophisticated as those in climate science. This is due to a few simple things: the discipline is younger, and so hasn't had as much time to develop, and  health care delivery deals with units which are not as easily divisible as those in climate (i.e., it's more natural to deal with non-integer quantities of water then with people).

However, many key concepts are similar. People and material flow from place to place over time. Stocks and flows and relationships between objects and subsystems all contribute to the global behavior of the system. I work at the middle level of systems analysis when it comes to healthcare delivery. Large scale healthcare systems modeling looks like climate science or economic modeling. Determining how huge numbers of people and processes move with very little specificity. Small scale systems work in healthcare delivery is at the level of the individual: feedback control systems for artificial limbs, mannequin simulators, anaesthesia pumps.

Mid-level systems work in healthcare delivery is what I do: optimizing clinical systems. Determining how clinical policy and capacity is likely in influence the health and outcomes of the patients who visit that clinic. When the policy or infrastructure of a hospital, or a clinical system, changes, this influences how the subsystem of providers interacts with the subsystem of consumers. Ensuing increased or decreased efficiency will result in increased or decreased capacity. Those who do receive care may have better or worse outcomes. It will be non-obvious how these things interact. To do this, we need to model how patients receive care, how they arrive, what care and processes they will need, etc.. Then, but tuning the system, changing policies, capacities, resources, we can simulate how best to serve the population that depends on the system for care.

Finally, I'm going to wade into dangerous waters. Open Access. There's a big movement in the scientific community to require that all research be published in open access journals, meaning that authors pay to publish their research, presumably using grant or institution money, and then the papers are free to libraries and individuals. It's an interesting model. Currently, most science is published by journals which (usually) publish without charge to the author, and then charge for access by libraries an individuals. Journal subscriptions are very expensive, and often bundled in ways which are not beneficial to the consumer. It's a serious expense for libraries and researchers.

I'm not here to take a position on the debate as to which one is better. I would merely like to point out that the systems which produce and publish scientific knowledge are vastly complex and interrelated, and form a complex system. It involves universities, governments, libraries, private research facilities, for-profit corporations and non-profit foundations. Many are intertwined in ways that are difficult to understand (and I don't claim understanding).

Many foundations publish their own journals, under the closed access model, and take the proceeds from that to further their foundation's agendas, and reinvest in granting or other research activity. Some closed access journals are run from universities, and support professor's lines. The flow of science and knowledge and money and education is enormously complicated. Changes to this system will have unpredictable consequences.

People who argue on both sides of this debate seem to me to take very reductionistic views of how changes will influence the industry. If systems theory tells us anything about these very complicated interactions with many different agendas and agents, it's that we cannot predict the outcomes simply by thinking about them. I suspect that a large model (presumably using systems dynamics) which captured the flow of money, time, resources, and publications in the various types of publishing models would be very enlightening. We could see, what are the global effects on publishing if we augment the open access sector, or if we institute policies requiring greater levels of open access? What happens when non-profit models (and open access does not necessarily mean non-profit) are given favor over for-profit models?

Making predictions about how large systems will change based on the adoption of new policy is extraordinarily difficult. It requires a lot of math, and a lot of computing power. People who tell you how their policy will improve or change an entrenched system, without doing some kind of reasonably sophisticated systems analysis, will almost certainly be wrong. Remember 50 years ago (I don't, but I've read about it) when people were worried about a coming ice age? They weren't stupid. They just hadn't done the systems theory.

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