Carl Woese, Discoverer of the Archaea, RIP

One of the first things that students learn today about the diversity of life is the concept of the Three Domains of Bacteria, Archaea, and Eukarya. In the past, they would have learned about the Five Kingdoms — Prokaryotes, Animals, Plants, Fungi, and Protists —a concept popularized by the late Lynn Margulis, but we now know that the animals, plants, and fungi are relative newcomers on the evolutionary scene, and that the "prokaryotes" actually contain two ancient lineages, the Bacteria and Archaea, which split long before the eukaryotic kingdoms.

Carl Woese in 2006, via U Illinois

For this insight, we can thank Carl Woese, who passed away just before the New Year at the age of 84 (U Illinois press release, NY Times obituary). Woese made his discovery in the 1970s, when sequencing DNA and RNA was anything but routine. At that time, the prokaryotes were classified primarily by physiological characteristics and morphological appearance. There was little attention paid to microbial evolution, except in a speculative way, simply because there was no easy way to go about studying it.

Lynn Margulis - an appreciation

Lynn Margulis passed away recently at the age of 73 (NY Times obituary). She was responsible for one of the great ideas of modern biology -- the endosymbiotic theory for the origin of organelles. This is the idea that chloroplasts and mitochondria of eukaryotic cells originated as independent prokaryotes that became associated symbiotically with host cells, and eventually became indispensable organelles. The whole process she called "symbiogenesis". Siva blogged about this here two days ago, and suggested that I share something to.

The story of the theory itself is also quite well known. Margulis put forward the hypothesis in a paper titled "On the origin of mitosing cells" (Journal of Theoretical Biology 14: 225, under her married name L. Sagan - PubMed, ScienceDirect) in 1967, but before it was accepted for publication there, it had been rejected 15 times by other journals. It was initially controversial--to think that an essential part of our own cells are actually bacteria in disguise!--but today it is textbook knowledge. Much like the theory of plate tectonics, this is one of the great Cinderella stories of modern science.

I was fortunate enough to hear Margulis speak a few years ago when I was in college. I don't remember the details now, but I do remember a few things she said. She recalled that the last time she was at Harvard, it was at a seminar where Ernst Mayr (one of the pioneers of the Neo-Darwinian Synthesis) was in the audience, sitting right there; she pointed at the seat in front of my friend Noor and me and we got a little thrill from it. "Although he was almost a hundred years old, he was still the sharpest mind in the room!"

(She wrote a reminiscence of Mayr when he passed away in 2005, which gives some flavor of their personalities. Mayr: "You don't have to tell me what 'symbiosis' is! I studied symbiosis with Paul Buchner in Griefswald [in the 1920s]." Buchner later wrote one of the classic books on symbiosis, Endosymbiose der Tier mit pflanzlichen Mikroorganismen.)

She also showed a video of protists from termite guts, some of which have symbiotic bacteria living on their surface, which act more or less as surrogate flagella. One could tell that she was really captivated by the beauty of these organisms, and I heard later from someone that she often showed this video at her talks.

Margulis's 1967 paper is best known for its hypotheses about chloroplasts and mitochondria, which have been validated by lines of evidence, such as DNA sequencing, that were not available to her at the time. Her remaining hypothesis was that eukaryotic flagella evolved from symbiotic spirochaetes, which are corkscrew-shaped bacteria that swim helically. This idea hasn't done so well, and hasn't been supported by evidence in the way which the chloroplast and mitochondrial hypotheses have, but as her fascination with the video shows, she was still thinking about it. One of her last papers, published in 2010, was on the microscopical structure of one kind of these bacteria on a termite-gut protozoan.

On rereading her 1967 paper, a few things stood out to me. She managed to synthesize a tremendous amount of information (the paper is 49 pages long) from very different fields, including microbiology, palaeontology, geology, cytology, and evolution.

This was where she first put forward many of the concepts and themes which she would continue to think about and work on for long afterwards. For example, the scenario for eukaryote evolution that appears as a figure is re-presented in modified form in her popular book, Five Kingdoms.

The book, which she coauthored with Karlene Schwartz, was one of my favorite books as a student. The latest edition is from 1998, but it's still a good read, giving a brief overview of all the major phyla of living organisms in the classical five kingdoms: Prokaryotes, Protoctists (i.e. protists), Plants, Fungi, and Animals. It was my first introduction to the weird and wonderful world of protist and microbe diversity, which otherwise get such short shrift in introductory biology. It also shows how effective she was as an encyclopedic collator and system-builder.

In her thoroughness she also delved into the older literature. She had an interest in the history of biology, and what might be called her intellectual predecessors. She was involved in a recent project to translate a 1924 Russian book titled Symbiogenesis: A New Principle of Evolution by Boris Kozo-Polyansky. She did not shy from acknowledging these "forbears" and other early insights and ideas that were "before their time".

I think that she represented a very "classical" sort of biology, informed by visual thinking and reasoning by analogy. Looking at older books of zoology, botany, or cytology, one finds a similar frame of mind and emphasis on pattern-recognition. Modern biology is definitely still about pattern-recognition, but much of it is now impossible to "eyeball", such as searching for gene homology.

Unfortunately, reasoning by analogy can sometimes lead us down the wrong track, and an over-enthusiasm for it seems to have been responsible for a controversy that involved her in 2009. As a member of the National Academy of Science in the USA, she sponsored a paper for publication in its Proceedings, which hypothesized that "caterpillars evolved from onychophorans [velvet worms] by hybridogenesis" with insects. The paper never made it into print, but attracted a storm of protest and the imputation that she misused the submission process to push through a paper which would never have been published elsewhere.

That episode didn't help her reputation for "eccentricity", which is a word which seems to crop up in describing her, alongside "maverick" or "rebel". Nonetheless, her place in biology is secured, and I think it's important to acknowledge why. She gave us a whole new way of thinking about evolution, spurred scientific interest in endosymbiosis and early evolution, brought protists and other formerly obscure organisms to the attention of scientists and public, and defended the importance of symbiosis to the evolutionary process.

In doing so, Lynn Margulis gave us a glimpse into the biological world as it could have been at its origin, and also into the present, where we still make regular use of the concepts that she pioneered. RIP.

Lynn Margulis, RIP

In my first year at university, my cell biology text book stopped me right in my tracks. It was my first encounter with endosymbiosis.

See UCMP's Understanding Evolution

More than twenty years later, advances in several fields have seen the protists finally break out of their artificial confinement and endosymbiosis is now firmly at the cornerstone of the relationships between major eukaryotic groups. A work in progress (which heightens attention), it's providing a fascinating insight into the evolutionary process.

That endosymbiosis was in my textbook in the first place, was due to the efforts of Lynn Margulis. While we associate her with the "Five Kingdoms", it was endosymbiosis which stunned me, a most enjoyable and lasting phenomenon.

Last night I heard (via the Twitterverse reporting her son's facebook post) that Lynn Margulis had passed on peacefully - and by this morning, UMass Amherst had issued a news release: "Lynn Margulis, Renowned Evolutionary Biologist and Author at UMass Amherst, Dead at 73."

Photo courtesy of U Mass Amherst

Quite beautifully, grad student Leila Battison pens this heartfelt note on "Life in pen and ink" - "Lynn Margulis: An Unforgettable Woman.

End of a botanical tradition

Botanical Latin is a curious creature, with a grammar and vocabulary very different from classical or medieval Latin. It dates back to the traditional use of Latin in scientific and scholarly works as the common language of learning in multi-lingual Europe. In modern times, it has been restricted to the formal description, called a 'diagnosis', of a newly-published plant species.

As Latin grew less important to general education, however, botanists have had to seek help from other quarters in writing these diagnoses, but because of the independent evolution of botanical Latin for its special purposes:

... when a botanical author thanks a professor of classics for providing a Latin description, this is usually in bad or at any rate unconventional botanical Latin... (W.T. Stearn, Botanical Latin, viii.)

The use of Latin was codified in the International Code of Botanical Nomenclature - a set of rules for keeping the profusion of scientific names in order. It was preserved for both tradition's sake and also because taxonomists have usually argued that a common language is needed to keep communication possible amidst a profusion of vernacular languages. The parallel Zoological Code, however, did away with Latin descriptions a long time ago.

New editions of the Code are voted upon at meetings of the International Botanical Congress, and at the latest meeting in Melbourne, Australia, this tradition of botanical Latin may have met its demise (Nature news and editorial). Attendees have voted for several amendments to the code (full list of proposals here), including dropping the requirement for botanical Latin in new descriptions, and allowing the publication of new species names in electronic journals. The full congress will have to ratify these amendments before they become permanent.

The demise of botanical Latin might have been just a matter of time, but the issue of electronic publication is a relatively new one. Electronic-only journals have been proliferating, but for taxonomy, which is concerned with permanence and record-keeping rather than rapid communication of information, they have distinct disadvantages. There is no guarantee that a server crash or corrupted computer file may not wipe out a species description forever, resulting in a book-keeping nightmare when species names have to be revised or updated. The zoological Code, for example, still requires that a number of hard paper copies be sent to libraries around the world as an insurance against that possibility. This is what the Raffles Bulletin of Zoology, which is published in Singapore as an online journal, does to fulfill the requirements of the code.

So does this mean that William T Stearn's classic reference book, Botanical Latin, will become obsolete immediately? Not necessarily. A big fraction of the historical botanical literature, especially the earliest works from the time of Linnaeus onwards, are written exclusively in Latin and no translations exist for them. We also owe much of our technical nomenclature to Latin and Greek. Botanical Latin may be newly dead, but it still lives on.

RIP, G.C. Williams

The American biologist George C. Williams has died at the age of 84. Williams worked and taught for a long time at SUNY Stony Brook, and is best known for his book Adaptation and Natural Selection, published in 1966, where he criticized the idea of 'group selection', which can be caricatured as the idea that traits evolve 'for the good of the species'. He emphasized how natural selection can only act on individuals; his book was one of a clutch in the 1960s that led to the formulation of the gene's-eye view of natural selection. This change of perspective would bring evolutionary thinking back to the basics of selectionism and population-thinking, as first proposed by Darwin.

These are topics that are standard fare in any biology or evolution course today, so it is with some difficulty that I first appreciated its importance when reading his book. It's a problem that my roommate, a big movie buff, complained about in a different setting: when he watched a classic Western for the very first time, he thought that it was cliched and boring, using all the tropes and tricks found in every Western outlaw film. Why did people say that it was such a great movie, then? Because it was the first to do these things, and all the other films in the genre since then have been imitating it. A similar situation awaits the modern reader of Adaptation - we've been steeped so thoroughly in the gene's-eye view by popular science writers such as Richard Dawkins, so much so that we might think that Williams's book is just stating the obvious. In the early 1960s, though, biologists could still seriously speak of groups or whole populations as having adaptive traits, i.e. that natural selection could work at the level of the group. The demolition of this so-called 'group selection' was so complete that even today the term still has a whiff of taboo. The anthology Group Selection published in 1971, and edited by Williams, gives a good overview of the transformations in biological thinking during this period, through selections from the original literature.

Williams is also known for his theory of aging, or senescence. Growing old is a problem, not just for people, but for science. Why should an organism age? Why not be immortal? Wouldn't a gene for immortality be selected for? He explained it in evolutionary terms as a trade off - suppose a given trait allowed the individual to be more fecund earlier in life, but at a cost to it when it grew older. That trait would be selectively favored, because in a natural setting, the probability of reaching old age is low given the pressures of predation and the harsh environment. If you knew that you were going to die young, wouldn't you empty out your bank balance, too? This observation is borne out in humans, as modern medicine has allowed us to increase our lifespans way beyond what we would expect to live in the wild. As a result, so-called 'diseases of aging' are becoming ever more prevalent. In the mid-1990s, Williams and a medical doctor, Randolph Nesse, collaborated on a book that explored just this topic for a general audience, Why we get sick: The new science of Darwinian medicine. It was indeed a new science, which even today is still experiencing growth, but it traced its beginnings to Williams's theory of aging which he first proposed in the 1950s.

Aside from his original writings, Williams also served editorially at the Quarterly Review of Biology - the main book review for the biological sciences - for over forty years. He was not a flashy popularizer in the mold of Dawkins or Stephen Jay Gould, but his books remain readable and very relevant today. They are still among the best introductions for general audiences or biology students to gene-centered thinking, which has become populated by modelers and theoreticians to the extent that the basic biology can be obscured. In science, primary sources and original writings often become obsolete - because important ideas are repackaged and worked over and sometimes even overturned. It then becomes unnecessary to go back to the original publication because it doesn't necessarily improve your understanding. To understand newtonian mechanics, for example, one doesn't read the Principia but instead the latest version of some college textbook which (hopefully) incorporates refinements in our understanding and pedagogy that have been accumulated in the centuries since Newton. For biology, though, and with Williams in particular, the philosophical nature of these changes in theoretical framework, and their frequent subtlety, make the original texts worthwhile to read, and certainly even today can still stimulate renewed debate and appreciation.

Obituaries:
Chronicle of Higher Education
Edge Magazine
Wikipeida article

John Maddox Dies

Longtime editor of the journal Nature, John Maddox, has passed away at the age of 83. Aside from ushering in major changes to the journal's format, he famously was a member of the team that investigated a claim made by a French laboratory to have demonstrated efficacy of antibodies in aqueous 'high dilution', widely thought to be evidence in support of homeopathic medicine. Together with magician James Randi and expert in scientific misconduct Walter Stewart, he wrote a comprehensive contradiction (Nature 334: 287-290, 28 Jul 1988) of the original claims.

The journal itself has also put out a special feature in commemoration of him. Although his background was in physics, he made substantial contributions to science journalism in general. Let's hope those standards will be maintained as we enter the age of science blogging.

Knut Schmidt-Nielsen, R. I. P.

First posted in Otterman speaks, 11 Mar 2007

The study of animal physiology demonstrates a diversity of strategies that have evolved to handle the environment. Those of us in the department of Zoology and later Biological Sciences at the National University of Singapore (in the 80's and early 90's at least) were fortunate to to learn about this diversity and escaped the insularity of the mouse-rabbit-hamster models. Amidst all this was Schmidt-Nielsen, father of the field and author of our very expensive text book!

His 5th edition was first available in Borders Singapore and later in the National University of Singapore's Science Co-op.

Just now, my Google News Alerts for Duke University picked this up: "Knut Schmidt-Nielsen dies." By Kirsten Weir. The Scientist, 08 Mar 2007. International Prize for Biology winner was a pioneer in the field of comparative physiology.

Knut Schmidt-Nielsen, who helped create the modern field of comparative animal physiology, died of natural causes January 25 at his home in Durham, North Carolina. He was 91.

"He was driven by an intense curiosity about how animals work," said his former graduate student Barbara Block, now a professor of marine sciences at Stanford University. "He was the father of the field of animal physiology."

...

In the first part of the 20th century, most physiology research revolved around dogs -- but Schmidt-Nielsen changed all that ... [he] championed a comparative approach to physiology ... which helped to integrate the field with evolutionary biology and ecology.

For instance, Schmidt-Nielsen and his students applied their questions to a broad range of species -- camels and sand rats, ostriches and alligators, fish and snails. He'd study any creature that he thought might help him answer the big questions about how animals were constructed, Vogel said. "He wanted to know how kidneys worked, so he looked at the animal that places the most severe demands on the kidneys."

Schmidt-Nielsen "was one of the very first people to look at how different animals solve the same problems," agreed Sonke Johnsen, a Duke University biologist who considered Schmidt-Nielsen an "intellectual grandfather."

...

Schmidt-Nielsen was also an accomplished writer, penning five books in addition to some 270 papers. He published a memoir in 1998, and his Animal Physiology textbook, now in its fifth edition, is still widely used, Johnsen and Fedak said.

[Vogel]: "He had a great deal of fun doing science," he said, "but it was fun in the sense of working hard at it."

Schmidt-Nielsen is survived by his wife Margareta, a son and a daughter.

Read the complete article at The Scientist.

John Maynard Smith, biologist

B. January 6 1920; died April 19 2004

Read the Obituary by David Harper in The Guardian, 22 Apr 2004. And see his homepage at Univ. Sussex.

"...JMS helped to illuminate so many areas in biology that it is hard to know where to begin." "By introducing mathematical models from game theory into the study of behaviour, he showed that the success of an individual's behaviour often depends on what other individuals do. He introduced the idea of an "evolutionarily stable strategy": a strategy that, once common, cannot be bettered by alternatives. This work has completely revolutionised the way biologists think about behavioural evolution, and game theory is now one of the most commonly used tools in evolutionary thinking."

"JMS also tackled one of the most vexed - but superficially least obvious - conundrums of evolutionary biology: why has sex evolved? His book The Evolution Of Sex (1978) pointed out "the twofold cost of sex". One way to understand this cost is to notice that sexually reproducing organisms must produce both female and male offspring, whereas asexual, or clonal, organisms need only produce females. Since in most sexual populations around half the offspring produced are male, an asexual population with the same fecundity will produce twice as many daughters. This advantage applies generation after generation, seemingly providing a huge evolutionary advantage to clonal reproduction. Thus the problem is: why do we see so much sex in the world?

Like his mentor, Haldane, JMS was deeply committed to making evolutionary ideas accessible to a wide audience. His "little Penguin", The Theory Of Evolution (1958, 1966, 1975, 1993), inspired many leading researchers to become biologists.

Despite his fame, he would nevertheless take time to discuss ideas with undergraduate students and eminent professors alike. He displayed almost limitless intellectual energy, even in his 80s. On one recent occasion, a junior researcher from another university sent him a paper and included a question with it. Within a day, JMS had written three pages of detailed notes and calculations, to the questioner's surprise and appreciation."