Recently in Phylogenetics Category

A big story in the press today. Scientists – mechanical engineers and physicists, one working for Boeing with his office only a few miles from my home – show that the evolution of airplanes works the same way as the evolution of organisms:

The evolution of airplanes

A. Bejan, J. D. Charles and S. Lorente

J. Appl. Phys. 116, 044901 (2014);

http://dx.doi.org/10.1063/1.4886855

(fortunately this paper can be downloaded for free).

They make allometric plots of features of new airplane models, log-log plots over many orders of magnitude. The airplanes show allometry: did you know that a 20-foot-long airplane won’t have 100-foot-long wings? That you need more fuel to carry a bigger load?

But permit me a curmudgeonly point: This paper would have been rejected in any evolutionary biology journal. Most of its central citations to biological allometry are to 1980s papers on allometry that failed to take the the phylogeny of the organisms into account. The points plotted in those old papers are thus not independently sampled, a requirement of the statistics used. (More precisely, their error residuals are correlated). Furthermore, cultural artifacts such as airplanes do not necessarily have a phylogeny, as they can borrow features from each other in massive “horizontal meme transfer”. In either case, phylogeny or genealogical network, statistical analysis requires us to understand whether the points plotted are independent.

The paper has impressive graphs that seem to show trends. But looking more closely we notice that neither axis is actually time. If I interpreted the graphs as trends, I would conclude that birds are getting bigger and bigger, and that nobody is introducing new models of small airplanes.

At least we may rejoice that the authors are not overly shy. They make dramatic statements on the implications for biology:

The engine mass is proportional to the body size: this scaling is analogous to animal design, where the mass of the motive organs (muscle, heart, lung) is proportional to the body size. Large or small, airplanes exhibit a proportionality between wing span and fuselage length, and between fuel load and body size. The animal-design counterparts of these features are evident. The view that emerges is that the evolution phenomenon is broader than biological evolution. The evolution of technology, river basins, and animal design is one phenomenon, and it belongs in physics.

and

Evolution means a flow organization (design) that changes over time.

Thanks, now I finally know what evolution is. And that biologists should go home and leave its study to the physicists and engineers.

[Note: I will pa-troll the comments as aggressively as I can and send trolling and troll-chasing to the Bathroom Wall.]

Musings from the mind of a mouse

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Casey Luskin is such a great gift to the scientific community. The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn't the slightest smattering of background, and he keeps falling flat on his face. It's hilarious! The Discovery Institute is so hard up for competent talent, though, that they keep letting him make a spectacle of his ignorance.

I really, really hope Luskin lives a long time and keeps his job as a frontman for Intelligent Design creationism. He just makes me so happy.

His latest tirade is inspired by the New York Times, which ran an article on highlights from the coelacanth genome. Luskin doesn't think very deeply, so he keeps making these arguments that he thinks are terribly damaging to evolution because he doesn't comprehend the significance of what he's saying. For instance, he sneers at the fact that we keep finding conserved elements in the genome, because as we all know, there are lots of conserved elements.

The coelacanth genome has been sequenced, which is good news all around…except that I found a few of the comments in the article announcing it disconcerting. They keep calling it a "living fossil" — and you know what I think of that term — and they keep referring to it as evolving slowly

The slowly evolving coelacanth

The morphological resemblance of the modern coelacanth to its fossil ancestors has resulted in it being nicknamed 'the living fossil'. This invites the question of whether the genome of the coelacanth is as slowly evolving as its outward appearance suggests. Earlier work showed that a few gene families, such as Hox and protocadherins, have comparatively slower protein-coding evolution in coelacanth than in other vertebrate lineages.

Honestly, that's just weird. How can you say its outward appearance suggests it is slowly evolving? The two modern species are remnants of a diverse group — it looks different than forms found in the fossil record.

Phylogenetics and population genetics, that is. Larry Moran calls attention to the confusion of Ann Gauger, ID-pushing BioLogic Institute “researcher.” My favorite comment in the thread is from (PT crew member) Joe Felsenstein:

I must be totally confused. I wrote a book on reconstructing evolutionary trees – and it’s the standard textbook in that area. But it does not mention many basic population genetics concepts. I have another book (a free downloadable e-book) that is a textbook of theoretical population genetics. And it does not mention homoplasy at all.

So I must misunderstand what “population genetics” is. And here I’ve been giving courses on it for the last 44 years. At the university where Ann Gauger got her Ph.D. degree, for that matter.

Silly me.

My second favorite is from Piotr Gasiorowski:

Cargo cult science

Precisely. The cult members gather in mock laboratories full of imitation equipment, where they mimic the way scientists speak and behave.

It’s time for the annual birthday greeting to Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, born 1 August 1744. Born into the impoverished nobility, he distinguished himself in the army, then had to leave military life because of a peacetime injury. In Paris, he started writing books on plants and ended up as Professor in the Natural History Museum. He was the great pioneer of invertebrate biology (he coined the terms “invertebrate” and “biology”). But of course he is best known as the first major evolutionary biologist, who propounded a theory of evolution which had an explanation for adaptation. (A wrong explanation, but nevertheless an explanation).

This time let’s use an image of the tree of animals, from his Philosophie Zoologique (1809):

LamarckTree.jpg

This is not entirely a tree of history: it is also paths up which evolution proceeds (actually, on this diagram, down which evolution proceeds). So it is not quite the same as the trees we use now. Note that not all animals are connected on this tree.

Of course, it goes without saying that Lamarck was not responsible for inventing or popularizing “Lamarckian inheritance”. He invoked it but everyone already believed it. And to add one last jibe: epigenetics is not in any way an example of the use-and-disuse mechanisms that Lamarck invoked.

It has been announced that Robert Sokal died on April 9. I wrote a brief obituary here last autumn for his co-worker Peter Sneath. Together they pioneered the use of clustering algorithms in taxonomy, and argued for the adoption of phenetic methods based on clustering there. While they were ultimately unsuccessful in this, they became founding fathers of work on mathematical clustering, and their book Principles of Numerical Taxonomy was widely-noticed and greatly stimulated the development of phylogeny algorithms. A paper by Michener and Sokal (1957) is, as far as I can tell, the first one publishing a numerical phylogeny. His publication of the 1965 paper by Camin and Sokal in Evolution, and a visit he made to the University of Chicago that year, inspired me to start working on phylogeny algorithms.

sokal1964.jpg Sokal2-n.jpg
Robert Sokal in 1964 at the International
Entomological Congress in London
Bob Sokal, more recently

Bob’s Stony Brook colleague Michael Bell has written a fine obituary, which I reprint below with his permission.

Good news! The gorilla genome sequence was published in Nature last week, and adds to our body of knowledge about primate evolution. Here's the abstract:

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

I've highlighted one phrase in that abstract because, surprise surprise, creationists read the paper and that was the only thing they saw, and in either dumb incomprehension or malicious distortion, took an article titled "Insights into hominid evolution from the gorilla genome sequence" and twisted it into a bumbling mess of lies titled "Gorilla Genome Is Bad News for Evolution". They treat a phenomenon called Incomplete Lineage Sorting (ILS) as an obstacle to evolution rather than an expected outcome.

Peter H. A. Sneath (1923 - 2011)

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Word has reached me that Peter Sneath died last Friday at his home in Leicestershire. He was 87 years old. For a more complete and entertaining autobiographical account see page 77 of this Bulletin of Bergeys International Society for Microbial Systematics.

Peter was a medical microbiologist, who, in the late 1950s, began to work on numerical methods for classifying bacteria. He developed numerical clustering methods. He soon came into contact with Robert Sokal, who was doing the same. Together they wrote Principles of Numerical Taxonomy, a widely-noticed textbook advocating taking a phenetic approach to classification, basing it on measures of overall similarity rather than any inference of phylogeny. The smartest thing Sokal and Sneath did was to not fight over who invented numerical taxonomy, but to join together to promote it (Sneath was first author on the 1973 revision Numerical Taxonomy).

sneath.jpg

                 Peter Sneath with his children, about 1960. Photo by Joan Sneath, courtesy of the late Peter Sneath

Numerical taxonomy rattled the systematic establishment, then dominated by followers of Ernst Mayr and George Gaylord Simpson’s school of “evolutionary systematics”. It encouraged and stimulated many younger people to look into numerical approaches. By about 1980 phenetic approaches had been pushed aside by phylogenetic systematics, but Sneath and Sokal’s work is still regarded by mathematical clusterers as the most important founding work in their field. The most widely-used of Sneath’s methods is the UPGMA clustering method (independently also invented by F. J. Rohlf). [See comment of September 30 below for correction of this statement].

I always enjoyed meeting Peter and Joan Sneath. Peter was intrigued by any and all uses of numerical and computer methods in science, and was even willing on occasion to violate his own precepts and come up with methods for analyzing phylogenies.

He wrote a pioneering 1975 paper (with Sackin and Ambler) on detecting recombination between lineages, for example. I remember Peter telling me that as he traveled around he collected soil samples to study their bacteria. He carried no sterile vials for that – he simply went out and bought a ream of typing paper, as it was sterile, then used some to scoop up the sample and fold it into an envelope. It was a brilliant common-sense improvisation typical of the best of his generation of English scientists.

One of the goals of the intelligent design (ID) movement is to show that evolution cannot be random and/or unguided, and one way to demonstrate this is to show that an evolutionary transition is impossibly unlikely without guidance or intervention. Michael Behe has attempted to do this, without success. And Doug Axe, the director of Biologic Institute, is working on a similar problem. Axe’s work (most recently with a colleague, Ann Gauger) aims (in part, at least) to show that evolutionary transitions at the level of protein structure and function are so fantastically improbable that they could not have occurred "randomly."

Recently, Axe has been writing on this issue. First, he and Gauger just published some experimental results in the ID journal BIO-Complexity. Second, Axe wrote a blog post at the Biologic site in which he defends his approach against critics like Art Hunt and me. Here are some comments on both.

Read the rest at Quintessence of Dust.

Blogging on Peer-Reviewed Research

I've been giving talks at scientific meetings on educational outreach — I've been telling the attendees that they ought to start blogs or in other ways make more of an effort to educate the public. I mentioned one successful result the other day, but we need more.

I give multiple reasons for scientists to do this. One is just general goodness: we need to educate a scientifically illiterate public. Of course, like all altruism, this isn't really recommended out of simple kindness, but because the public ultimately holds the pursestrings, and science needs their understanding and support. Another reason, though, is personal. Scientific results get mangled in press releases and news accounts, so having the ability to directly correct misconceptions about your work ought to be powerfully attractive. Even worse, though, I tell them that creationists are actively distorting their work. This goes beyond simple ignorance and incomprehension into the malign world of actively lying about the science, and it happens more often than most people realize.

I have another painful example of deviousness of creationists. There's a paper I've been meaning to write up for a little while, a Nature paper by David and Alm that reveals an ancient period of rapid gene expansion in the Archaean, approximately 3 billion years ago. Last night I thought I'd just take a quick look to see if anybody had already written it up, so I googled "Archaean genetic expansion," and there it was: a couple of references to the paper itself, a news summary, one nice science summary, and…two creationist distortions of the paper, right there on the first page of google results. I told you! This happens all the time: if there's a paper in one of the big journals that discusses more evidence for evolution, there is a creationist hack somewhere who'll quickly write it up and lie about it. It's a heck of a lot easier to summarize a paper if you don't understand it, you see, so they've got an edge on us.

Over the past few years there have been increasing numbers of calls for governments to properly fund systematics and taxonomy (and a number of largely molecular-focused biologists insisting they can do the requisite tasks with magic molecule detectors, so don't fund old-school, fund new-fangled-tech). But I think that there is considerable confusion about what systematics and taxonomy are.

Now the usual way a philosopher resolves such questions, apart from interrogating their intuitions relying upon what they learned in grade school, is to go find a textbook or some other authoritative source and quote that. If it is someone they already know, all the better, like Mayr or Dawkins. This is problematic, so I thought I'd do a slightly better job at reviewing what people think. And then I will of course give my own view.

Teaching Tree-Thinking to Undergraduate Biology Students

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Phylogenetic trees are essential tools for representing evolutionary relationships. Unfortunately, they are also a major conceptual stumbling block for budding biologists. Anyone who has taught basic evolutionary concepts to college undergrads (and probably high school students as well) has most likely dealt with students struggling to properly read and draw phylogenies.

Lucky for us, there is also a growing body of literature on the most effective ways to teach what has been dubbed “tree-thinking”. I have summarized this literature in a review due to be published in the journal Evolution: Education and Outreach (doi:10.1007/s12052-010-0254-9). The full text of the article is available at that link, and I have reproduced the abstract below.

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.

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This page is an archive of recent entries in the Phylogenetics category.

Junk DNA is the previous category.

Transitional Fossils is the next category.

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