Carl Woese: from Biophysics to Evolutionary Microbiology

This article is a tribute to Carl R. Woese, a biophysicist turned evolutionary microbiologist who passed away on December 30, 2012. We focus on his life, achievements, the discovery of Archaea and contributions to the development of molecular phylogeny. Further, the authors share their views and the lessons learnt from Woese’s life with the microbiologists in India. We also emphasize the need for interdisciplinary collaboration and interaction for the progress and betterment of science.     

Hunters and Horticulturalists: A Preliminary Report of the 1972–4 Excavations in the Manim Valley,Papua New Guinea

Ole Christensen, a PhD scholar in the Department of Prehistory in the Research School of Pacific Studies at the Australian National University, was killed in a car accident on his way to work on 16 December last year. Ole was a Canadian citizen of Danish birth, whose parents settled in rural Alberta. He took his BA(Hons) in 1970 and his MA in 1972, both in the Department of Archaeology at the University of Calgary. His MA thesis, ‘Banff Prehistory: prehistoric subsistence and settlement in Banff National Park, Alberta’, is evidence of an early interest in economically and ecologically oriented archaeology, which he furthered by taking courses and laboratory work in pollen analysis. A visit to South America in 1970 with an archaeological team investigating early farming settlements in the Cauca Valley, Colombia, combined with a long standing interest in Polynesian anthropology to encourage him to seek to do graduate work on tropical agricultural systems somewhere in the Pacific. When he subsequently applied for the ANU scholarship which he took up in early 1972, he seemed a highly suitable person to work in association with the Department of Prehistory's project into New Guinea Highlands' agricultural history then about to start at Kuk in the upper Wahgi valley (see Mankind, 3:177–83). The proposition put to Ole was that he should undertake a study of the hydraulic technology and agrarian organization of one of the large scale agricultural systems operating in drained swamp that still flourish in Irian Jaya at the Paniai (Wissel) Lakes and in the Baliem valley, to supplement the archaeological work in the Wahgi where such systems had once but no longer existed. He felt, however, that his ethnographic background was too slim and he chose instead to do work for which he was better trained, the study of resource utilization over time in a side valley off the Wahgi close to the site of the Department's swamp excavations. The beautifully designed project that he carried out is described in the following article by him. It is based on a seminar he gave at ANU shortly before his death. I should like to make two points about this project that the article does not stress. One is the wealth of plant materials recovered from the excavations by wet sieving every ounce of excavated soil, when the nearest water source was sometimes some hundreds of precipitous yards away. The abundant pandanus seeds found in all levels of the excavated sites and their change over time from thick-walled, allegedly wild, to thin-walled, allegedly cultivated, varieties may hold important evidence for the chronology of horticulture in New Guinea and the question of whether an independent development of plant domestication took place there. The second point I want to make is that against his expectations he found himself to be a born and insatiable ethnographic fieldworker. With his Wurup friends he surveyed and recorded all the resource zones in terms of which his selection of sites for excavation was made and took part in all the activities of food procurement and processing that were responsible for the archaeological evidence that he set out to recover and interpret. A practical man of quiet and simple tastes, he was as settled in his bush house at Wurup as in his rural retreat near Canberra. He was unassertive, tolerant and deeply sympathetic and made undemanding and unobtrusive friendships with people in both homes. He is a loss to them and to his profession. His colleagues at the University of Calgary are establishing an academic prize in his memory. To his colleagues at ANU falls the responsibility of ensuring that the important work of this promising young scholar is brought to completion.     

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the ‘active'' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population''s growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.     

Riccardo (Rico) Wittek (1944-2008)

Riccardo (Rico) Wittek died 26 September 2008 in Switzerland. Rico was well known for his work on the molecular biology of poxviruses and for his work with the World Health Organization on biosafety that led to international guidelines for work with dangerous infectious agents. His colleagues Erwin G. Van Meir, Daniel Lavanchy, and Bernard Moss have written Rico''s memorial.Lynn W. EnquistEditor in Chief, Journal of Virology     

Remembering Malcolm J. Casadaban

Malcolm J. Casadaban died on 13 September 2009 from an infection and was found to have a weakened strain of the bacterium Yersinia pestis in his blood. This tragic event took the life of one of the most creative and influential geneticists of our time. In the late 1970s and ''80s, Malcolm invented novel approaches which changed the way many of us did science. Jon Beckwith, Tom Silhavy, and Olaf Schneewind have chronicled his scientific life from graduate school to his death and give us insight into Malcolm''s genius.Philip Matsumura Editor in Chief, Journal of Bacteriology     

The 2009 Lindau Nobel Laureate Meeting: Peter Agre, Chemistry 2003

Peter Agre, born in 1949 in Northfield Minnesota, shared the 2003 Nobel Prize in Chemistry with Roderick MacKinnon for his discovery of aquaporins, the channel proteins that allow water to cross the cell membrane.Agre''s interest medicine was inspired by the humanitarian efforts of the Medical Missionary program run by the Norwegians of his home community in Minnesota. Hoping to provide new treatments for diseases affecting the poor, he joined a cholera laboratory during medical school at Johns Hopkins. He found that he enjoyed biomedical research, and continued his laboratory studies for an additional year after medical school.Agre completed his clinical training at Case Western Hospitals of Cleveland and the University of North Carolina, and returned to Johns Hopkins in 1981. There, his serendipitous discovery of aquaporins was made while pursuing the identity of the Rhesus (Rh) antigen.For a century, physiologists and biophysicists had been trying to understand the mechanism by which fluid passed across the cell''s plasma membrane. Biophysical evidence indicated a limit to passive diffusion of water, suggesting the existence of another mechanism for water transport across the membrane. The putative "water channel," however, could not be identified.In 1988, while attempting to purify the 30kDa Rh protein, Agre and colleagues began investigating a 28 kDa contaminant that they believed to be a proteolytic fragment of the Rh protein. Subsequent studies over the next 3-4 years revealed that the contaminant was a membrane-spanning oligomeric protein, unrelated to the Rh antigen, and that it was highly abundant in renal tubules and red blood cells. Still, they could not assign a function to it.The breakthrough came following a visit with his friend and former mentor John Parker. After Agre described the properties of the mysterious 28 kDa protein, Parker suggested that it might be the long-sought-after water channel. Agre and colleagues tested this idea by expressing the protein in Xenopus oocytes, which typically have low water permeability. When the test oocytes were placed in a hypotonic solution, they swelled and exploded, thus revealing the function of the unknown protein as a water channel, which they named aquaporin.The Nobel Prize enabled Agre to take his research and scientific interests in new directions. He felt that over the years his work had continually taken him further from his original interests in third-world diseases, so he shifted his focus back in that direction. He now serves as the director of the Malaria institute at Johns Hopkins where he has applied his knowledge to the study of the malarial parasite and the Anopheles mosquito, which both express aquaporins. In addition, since winning the Nobel Prize, he has enjoyed increased opportunities for bringing science to the public and for "encouraging young people to go into science."Download video file.^{(110M, mp4)}     

Prasanna K. Mohanty (1934–2013): a great photosynthetiker and a wonderful human being who touched the hearts of many

Prasanna K. Mohanty, a great scientist, a great teacher and above all a great human being, left us more than a year ago (on March 9, 2013). He was a pioneer in the field of photosynthesis research; his contributions are many and wide-ranging. In the words of Jack Myers, he would be a “photosynthetiker” par excellence. He remained deeply engaged with research almost to the end of his life; we believe that generations of researchers still to come will benefit from his thorough and enormous work. We present here his life and some of his contributions to the field of Photosynthesis Research. The response to this tribute was overwhelming and we have included most of the tributes, which we received from all over the world. Prasanna Mohanty was a pioneer in the field of “Light Regulation of Photosynthesis”, a loving and dedicated teacher—unpretentious, idealistic, and an honest human being.     

How Charles Darwin received Wallace's Ternate paper 15 days earlier than he claimed: a comment on van Wyhe and Rookmaaker (2012)

Van Wyhe and Rookmaaker (2012) postulate a set of events to support their claim that Wallace's ‘evolution’ letter, posted at Ternate in the Moluccas in the spring of 1858, arrived at Darwin's home on 18 June 1858. If their claim were to be proven, then evidence that Darwin probably received Wallace's letter 2 weeks earlier than he ever admitted would clearly be erroneous, and any charges that he plagiarized the ideas of Wallace from that letter would be shown to be wrong. Here, evidence against this interpretation is presented and it is argued that the letter did indeed arrive in the port of Southampton on 2 June 1858 and would have been at Darwin's home near London the following day. If this were true, then the 66 new pages of material on aspects of Divergence that Darwin entered into his ‘big’ species book in the weeks before admitting he had received the letter could be interpreted as an attempt to present Wallace's ideas as his own. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 472–477.     

Warwick Hillier: a tribute

Warwick Hillier (October 18, 1967–January 10, 2014) made seminal contributions to our understanding of photosynthetic water oxidation employing membrane inlet mass spectrometry and FTIR spectroscopy. This article offers a collection of historical perspectives on the scientific impact of Warwick Hillier’s work and tributes to the personal impact his life and ideas had on his collaborators and colleagues.     

Q & A. Carl R. Woese. [interview

Carl R. Woese was born and raised in Syracuse, New York. His undergraduate training was at Amherst College (AB 1950) and graduate work at Yale University (PhD 1953). He is currently the Stanley O. Ikenberry University Professor and Center for Advanced Study Professor of Microbiology at the University of Illinois (Champaign-Urbana), where he has been for the past forty years. He was trained as a biophysicist and molecular biologist. He views himself as a molecular biologist in search of Biology. Consequently, his career has been devoted to using molecular methods to approach evolutionary problems. His most notable accomplishments have been determining the universal phylogenetic tree, through molecular sequence analysis, and the discovery of the Archaea, the so-called ‘third form’ of life. For these he has received numerous awards, including a John D. and Catherine T. MacArthur Award, the Leeuwenhoek Medal 1990 (Netherlands Royal Academy), the Waksman Award (National Academy of Science USA), and the Crafoord Prize (Swedish Royal Academy). At present he works on the evolution of cellular organization.     

The sacredness of human life

Christian De Duve''s decision to voluntarily pass away gives us a pause to consider the value and meaning of death. Biologists have much to contribute to the discussion of dying with dignity.Christian de Duve''s voluntary passing away on 4 May 2013 could be seen as the momentous contribution of an eminent biologist and Nobel laureate to the discussion about ‘last things''. In contrast to his fellow scientists Ludwig Boltzmann and Allan Turing, who had made a deliberate choice to end their life in a state of depression and despair, de Duve “left with a smile and a good-bye”, as his daughter told a newspaper.What is the value and meaning of life? Is death inevitable? Should dying with dignity become an inalienable human right? Theologians, philosophers, doctors, politicians, sociologists and jurists have all offered their answers to these fundamental questions. The participation of biologists in the discussion is long overdue and should, in fact, dominate the discourse.We can start from de Duve''s premise—expressed as a subtitle of his book Cosmic Dust—that life is a cosmic imperative; a phenomenon that inevitably takes place anywhere in the universe as permitted by appropriate physicochemical conditions. Under such conditions, the second law of thermodynamics rules—prebiotic organic syntheses proceed, matter self-organizes into more complex structures and darwinian evolution begins, with its subsequent quasi-random walks towards increasing complexity. The actors of this cosmic drama are darwinian individuals—cells, bodies, groups and species—who strive to maintain their structural integrity and to survive as entities. By virtue of the same law, their components undergo successive losses of correlation, so that structures sustain irreparable damage and eventually break down. Because of this ‘double-edge'' of the second law, life progresses in cycles of birth, maturation, ageing and rejuvenation.Death is the inevitable link in this chain of events. ‘The struggle for existence'' is very much the struggle for individual survival, yet it is the number of offspring—the expression of darwinian fitness—that ultimately counts. Darwinian evolution is creative, but its master sculptor is death.Humans are apparently the only species endowed with self-consciousness and thereby a strongly amplified urge to survive. However, self-consciousness has also made humans aware of the existence of death. The clash between the urge for survival and the awareness of death must have inevitably engendered religion, with its delusion of an existence after death, and it might have been one of the main causes of the emergence of culture. Culture divides human experience into two parts: the sacred and the profane. The sacred constitutes personal transcendence: the quest for meaning, the awe of mystery, creativity and aesthetic feelings, the capacity for boundless love and hate, the joy of playing, and peaks of ecstasy. The psychologist Jonathan Haidt observed in his book The Righteous Mind: Why Good People Are Divided by Politics and Religion that “The great trick that humans developed at some point in the last few hundred thousand years is the ability to circle around a tree, rock, ancestor, flag, book or god, and then treat that thing as sacred. People who worship the same idol can trust one another, work as a team and prevail over less cohesive groups.” He considers sacredness as crucial for understanding morality. At present, biology knows almost nothing about human transcendence. Our ignorance of the complexity of human life bestows on it both mystery and sacredness.The religious sources of Western culture, late Judaism and Christianity, adopted Plato''s idea of the immortality of the human soul into their doctrines. The concept of immortality and eternity has continued to thrive in many secular versions and serves as a powerful force to motivate human creativity. Yet, immortality is ruled out by thermodynamics, and the religious version of eternal life in continuous bliss constitutes a logical paradox—eternal pleasure would mean eternal recurrence of everything across infinite time, with no escape; Heaven turned Hell. It is not immortality but temporariness that gives human life its value and meaning.There is no ‘existence of death''. Dying exists, but death does not. Death equals nothingness—no object, no action, no thing. Death is out of reach to human imagination, the intentionality of consciousness—its directedness towards objects—does not allow humans to grasp it. Death is no mystery, no issue at all—it does not concern us, as the philosopher Epicurus put it. The real human issue is dying and the terror of it. We might paraphrase Michel Montaigne''s claim that a mission of philosophy is to learn to die, and say that a mission of biology is to teach to die. Biology might complement its research into apoptosis—programmed cell death—by efforts to discover or to invent a ‘mental apoptosis''. A hundred years ago, the micro-biologist Ilya Mechnikov envisaged, in his book Essais Optimistes, that a long and gratifying personal life might eventually reach a natural state of satiation and evoke a specific instinct to withdraw, similar to the urge to sleep. Biochemistry could assist the process of dying by nullifying fear, pain and distress.In these days of advanced healthcare and technologies that can artificially extend the human lifespan, dying with dignity should become the principal concern of all humanists, not only that of scientists. It would therefore be commendable if Western culture could abandon the fallacy of immortality and eternity, whilst Oriental and African cultures ought to be welcomed to the discussion about the ‘last things''. Dying with dignity will become the ultimate achievement of a dignified life.     

How many scientists does it take to change a paradigm?: New ideas to explain scientific observations are everywhere—we just need to learn how to see them

The scientific process requires a critical attitude towards existing hypotheses and obvious explanations. Teaching this mindset to students is both important and challenging.People who read about scientific discoveries might get the misleading impression that scientific research produces a few rare breakthroughs—once or twice per century—and a large body of ‘merely incremental'' studies. In reality, however, breakthrough discoveries are reported on a weekly basis, and one can cite many fields just in biology—brain imaging, non-coding RNAs and stem cell biology, to name a few—that have undergone paradigm shifts within the past decade.The truly surprising thing about discovery is not just that it happens at a regular pace, but that most significant discoveries occurred only after the scientific community had already accepted another explanation. It is not merely the accrual of new data that leads to a breakthrough, but a willingness to acknowledge that a problem that is already ‘solved'' might require an entirely different explanation. In the case of breakthroughs or paradigm shifts, this new explanation might seem far-fetched or nonsensical and not even worthy of serious consideration. It is as if new ideas are sitting right in front of everyone, but in their blind spots so that only those who use their peripheral vision can see them.Scientists do not all share any single method or way of working. Yet they tend to share certain prevalent attitudes: they accept ‘facts'' and ‘obvious'' explanations only provisionally, at arm''s length, as it were; they not only imagine alternatives, but—almost as a reflex—ask themselves what alternative explanations are possible.When teaching students, it is a challenge to convey this critical attitude towards seemingly obvious explanations. In the spring semester of 2009, I offered a seminar entitled The Process of Scientific Discovery to Honours undergraduate students at the University of Illinois-Chicago in the USA. I originally planned to cover aspects of discovery such as the impact of funding agencies, the importance of mentoring and hypothesis-driven as opposed to data-driven research. As the semester progressed, however, my sessions moved towards ‘teaching moments'' drawn from everyday life, which forced the students to look at familiar things in unfamiliar ways. These served as metaphors for certain aspects of the process by which scientists discover new paradigms.For the first seven weeks of the spring semester, the class read Everyday Practice of Science by Frederick Grinnell [1]. During the discussion of the first chapter, one of the students noted that Grinnell referred to a scientist generically as ‘she'' rather than ‘he'' or the neutral ‘he or she''. This use is unusual and made her vaguely uneasy: she wondered whether the author was making a sexist point. Before considering her hypothesis, I asked the class to make a list of assumptions that they took for granted when reading the chapter, together with the possible explanations for the use of ‘she'' in the first chapter, no matter how far-fetched or unlikely they might seem.For example, one might assume that Frederick Grinnell or ‘Fred'' is from a culture similar to our own. How would we interpret his behaviour and outlook if we knew that Fred came from an exotic foreign land? Another assumption is that Fred is male; how would we view the remark if we discover that Frederick is short for Fredericka? We have equally assumed that Fred, as with most humans, wants us to like him. Instead, perhaps he is being intentionally provocative in order to get our attention or move us out of our comfort zone. Perhaps he planted ‘she'' as a deliberate example for us to discuss, as he does later in the second chapter, in which he deliberately hides a strange item in plain sight within one of the illustrations in order to make a point about observing anomalies. Perhaps the book was written not by Fred but by a ghost writer? Perhaps the ‘she'' was a typo?The truly surprising thing about discovery is […] that most significant discoveries occurred only after the scientific community had already accepted another explanationLooking for patterns throughout the book, and in Fred''s other writing, might persuade us to discard some of the possible explanations: does ‘she'' appear just once? Does Fred use other unusual or provocative turns of phrase? Does Fred discuss gender bias or sexism explicitly? Has anyone written or complained about him? Of course, one could ask Fred directly what he meant, although without knowing him personally, it would be difficult to know how to interpret his answer or whether to take his remarks at face value. Notwithstanding the answer, the exercise is an important lesson about considering and weighing all possible explanations.Arguably, the most prominent term used in science studies is the notion of a ‘paradigm''. I use this term with reluctance, as it is extraordinarily ambiguous. For example, it could simply refer to a specific type of experimental design: a randomized, placebo-controlled clinical trial could be considered a paradigm. In the context of science studies, however, it most often refers to the idea of large-scale leaps in scientific world views, as promoted by Thomas Kuhn in The Structure of Scientific Revolutions [2]. Kuhn''s notion of a paradigm can lead one to believe—erroneously in my opinion—that paradigm shifts are the opposite of practical, everyday scientific problem-solving.A paradigm is recognized by the set of assumptions that an observer might not realize he or she is making…Instead, I propose here a definition of ‘paradigm'' that emphasizes not the nature of the problem, the type of discovery or the scope of its implications, but rather the psychology of the scientist. A scientist viewing a problem or phenomenon resides within a paradigm when he or she does not notice, and cannot imagine, that an alternative way of looking at things needs to be considered seriously. Importantly, a paradigm is not a viewpoint, model, interpretation, hypothesis or conclusion. A paradigm is not the object that is viewed but the lenses through which it is viewed. A paradigm is recognized by the set of assumptions that an observer might not realize he or she is making, but which imply many automatic expectations and simultaneously prevent the observer from seeing the issue in any other fashion.For example, the teacher–student paradigm feels natural and obvious, yet it is merely set up by habit and tradition. It implies lectures, assignments, grades, ways of addressing the professor and so on, all of which could be done differently, if we had merely thought to consider alternatives. What feels most natural in a paradigm is often the most arbitrary. When we have a birthday, we expect to have a cake with candles, yet there is no natural relationship at all between birthdays, cakes and candles. In fact, when something is arbitrary or conventional yet feels entirely natural, that is an important clue that a paradigm is present.It is certainly natural for people to colour their observations according to their expectations: “To a man with a hammer, everything looks like a nail,” as Mark Twain put it. However, this is a pitfall that scientists (and doctors) must try hard to avoid. When I was a first-year medical student at Albert Einstein College of Medicine in New York City, we took a class on how to approach patients. As part of this course, we attended a session in which a psychiatrist interviewed a ‘normal, healthy old person'' in order to understand better the lives and perspectives of the elderly.A man came in, and the psychiatrist began to ask him some benign questions. After about 10 minutes, however, the man began to pause before answering; then his answers became terse; then he said he did not feel well, excused himself and abruptly left the room. The psychiatrist continued to lecture to the students for another half-hour, analysing and interpreting the halting responses in terms of the emotional conflicts that the man was experiencing. ‘Repression'', ‘emotional blocks'', and ‘reaction formation'' were some of the terms bandied about.However, unbeknown to the class, the man had collapsed just on the other side of the classroom door. Two cardiologists happened to be walking by and instantly realized the man was having an acute heart attack. They instituted CPR on the spot, but the man died within a few minutes.The psychiatrist had been told that the man was healthy, and thus interpreted everything that he saw in psychological terms. It never entered his mind that the man might have been dying in front of his eyes. The cardiologists saw a man having a heart attack, and it never entered their minds that the man might have had psychological issues.The movie The Sixth Sense [3] resonated particularly well with my students and served as a platform for discussing attitudes that are helpful for scientific investigation, such as “keep an open mind”, “reality is much stranger than you can imagine” and “our conclusions are always provisional at best”. Best of all, The Sixth Sense demonstrates the tension that exists between different scientific paradigms in a clear and beautiful way. When Haley Joel Osment says, “I see dead people,” does he actually see ghosts? Or is he hallucinating?…when scientists reach a conclusion, it is merely a place to pause and rest for a moment, not a final destinationIt is important to emphasize that these are not merely different viewpoints, or different ways of defining terms. If we argued about which mountain is higher, Everest or K2, we might disagree about which kind of evidence is more reliable, but we would fundamentally agree on the notion of measurement. By contrast, in The Sixth Sense, the same evidence used by one paradigm to support its assertion is used with equal strength by the other paradigm as evidence in its favour. In the movie, Bruce Willis plays a psychologist who assumes that Osment must be a troubled youth. However, the fact that he says he sees ghosts is also evidence in favour of the existence of ghosts, if you do not reject out of hand the possibility of their existence. These two explanations are incommensurate. One cannot simply weigh all of the evidence because each side rejects the type of evidence that the other side accepts, and regards the alternative explanation not merely as wrong but as ridiculous or nonsensical. It is in this sense that a paradigm represents a failure of imagination—each side cannot imagine that the other explanation could possibly be true, or at least, plausible enough to warrant serious consideration.The failure of imagination means that each side fails to notice or to seek ‘objective'' evidence that would favour one explanation over the other. For example, during the episodes when Osment saw ghosts, the thermostat in the room fell precipitously and he could see his own breath. This certainly would seem to constitute objective evidence to favour the ghost explanation, and the fact that his mother had noticed that the heating in her apartment was erratic suggests that the temperature change was not simply another imagined symptom. But the mother assumed that the problem was in the heating system and did not even conceive that this might be linked to ghosts—so the ‘objective'' evidence certainly was not compelling or even suggestive on its own.Osment did succeed eventually in convincing his mother that he saw ghosts, and he did it in the same way that any scientist would convince his colleagues: namely, he produced evidence that made perfect sense in the context of one, and only one, explanation. First, he told his mother a secret that he said her dead mother had told him. This secret was about an incident that had occurred before he was born, and presumably she had never spoken of it, so there was no obvious way that he could have learned about it. Next, he told her that the grandmother had heard her say “every day” when standing near her grave. Again, the mother had presumably visited the grave alone and had not told anyone about the visit or about what was said. So, the mother was eventually convinced that Osment must have spoken with the dead grandmother after all. No other explanation seemed to fit all the facts.Is this the end of the story? We, the audience, realize that it is possible that Osment had merely guessed about the incidents, heard them second-hand from another relative or (as with professional psychics) might have retold his anecdotes whilst looking for validation from his mother. The evidence seems compelling only because these alternatives seem even less likely. It is in this same sense that when scientists reach a conclusion, it is merely a place to pause and rest for a moment, not a final destination.Near the end of the course, I gave a pop-quiz asking each student to give a ‘yes'' or ‘no'' answer, plus a short one-sentence explanation, to the following question: Donald Trump seems to be a wealthy businessman. He dresses like one, he has a TV show in which he acts like one, he gives seminars on wealth building and so on. Everything we know about him says that he is wealthy as a direct result of his business activities. On the basis of this evidence, are we justified in concluding that he is, in fact, a wealthy businessman?About half the class said that yes, if all the evidence points in one direction, that suffices. About half the class said ‘no'', the stated evidence is circumstantial and we do not know, for example, what his bank balance is or whether he has more debt than equity. All the evidence we know about points in one direction, but we might not know all the facts.Even when looked at carefully, not every anomaly is attractive enough or ‘ripe'' enough to be pursued when first noticedHow do we know whether or not we know all the facts? Again, it is a matter of imagination. Let us review a few possible alternatives. Maybe his wealth comes from inheritance rather than business acumen; or from silent partners; or from drug running. Maybe he is dangerously over-extended and living on borrowed money; maybe his wealth is more apparent than real. Maybe Trump Casinos made up the role of Donald Trump as its symbol, the way McDonald''s made up the role of Ronald McDonald?Several students complained that this was a ridiculous question. Yet I had posed this just after Bernard Madoff''s arrest was blanketing the news. Madoff was known as a billionaire investor genius for decades and had even served as the head of the Securities and Exchange Commission. As it turned out, his money was obtained by a massive Ponzi scheme. Why was Madoff able to succeed for so long? Because it was inconceivable that such a famous public figure could be a common con man and the people around him could not imagine the possibility that his livelihood needed to be scrutinized.To this point, I have emphasized the benefits of paying attention to anomalous, strange or unwelcome observations. Yet paradoxically, scientists often make progress by (provisionally) putting aside anomalous or apparently negative findings that seem to invalidate or distract from their hypothesis. When Rita Levi-Montalcini was assaying the neurite-promoting effects of tumour tissue, she had predicted that this was a property of tumours and was devastated to find that normal tissue had the same effects. Only by ‘ignoring'' this apparent failure could she move forward to characterize nerve growth factor and eventually understand its biology [4].Another classic example is Huntington disease—a genetic disorder in which an inherited alteration in the gene that encodes a protein, huntingtin, leads to toxicity within certain types of neuron and causes a progressive movement disorder associated with cognitive decline and psychiatric symptoms. Clinicians observed that the offspring of Huntington disease patients sometimes showed symptoms at an earlier age than their parents, and this phenomenon, called ‘genetic anticipation'', could affect successive generations at earlier and earlier ages of onset. This observation was met with scepticism and sometimes ridicule, as everything that was known about genetics at the time indicated that genes do not change across generations. Ascertainment bias was suggested as a much more probable explanation; in other words, once a patient is diagnosed with Huntington disease, their doctors will look at their offspring much more closely and will thus tend to identify the onset of symptoms at an earlier age. Eventually, once the detailed genetics of the disease were understood at the molecular level, it was shown that the structure of the altered huntingtin gene does change. Genetic anticipation is now an accepted phenomenon.…in fact, schools teach a lot about how to test hypotheses but little about how to find good hypotheses in the first placeWhat does this teach us about discovery? Even when looked at carefully, not every anomaly is attractive enough or ‘ripe'' enough to be pursued when first noticed. The biologists who identified the structure of the abnormal huntingtin gene did eventually explain genetic anticipation, although they set aside the puzzling clinical observations and proceeded pragmatically according to their (wrong) initial best-guess as to the genetics. The important thing is to move forward.Finally, let us consider the case of Grigori Perelman, an outstanding mathematician who solved the Poincaré Conjecture a few years ago. He did not tell anyone he was working on the problem, lest their ‘helpful advice'' discourage him; he posted his historic proof online, bypassing peer-reviewed journals altogether; he turned down both the Fields Medal and a million dollar prize; and he has refused professorial posts at prestigious universities. Having made a deliberate decision to eschew the external incentives associated with science as a career, his choices have been written off as examples of eccentric anti-social behaviour. I suggest, however, that he might have simply recognized that the usual rules for success and the usual reward structure of the scientific community can create roadblocks, which had to be avoided if he was to solve a supposedly unsolvable problem.If we cannot imagine new paradigms, then how can they ever be perceived, much less tested? It should be clear by now that the ‘process of scientific discovery'' can proceed by many different paths. However, here is one cognitive exercise that can be applied to almost any situation. (i) Notice a phenomenon, even if (especially if) it is familiar and regarded as a solved problem; regard it as if it is new and strange. In particular, look hard for anomalous and strange aspects of the phenomenon that are ignored by scientists in the field. (ii) Look for the hidden assumptions that guide scientists'' thinking about the phenomenon, and ask what kinds of explanation would be possible if the assumptions were false (or reversed). (iii) Make a list of possible alternative explanations, no matter how unlikely they seem to be. (iv) Ask if one of these explanations has particular appeal (for example, if it is the most elegant theoretically; if it can generalize to new domains; and if it would have great practical impact). (v) Ask what kind of evidence would allow one to favour that hypothesis over the others, and carry out experiments to test the hypothesis.The process just outlined is not something that is taught in graduate school; in fact, schools teach a lot about how to test hypotheses but little about how to find good hypotheses in the first place. Consequently, this cognitive exercise is not often carried out within the brain of an individual scientist. Yet this creative tension happens naturally when investigators from two different fields, who have different assumptions, methods and ways of working, meet to discuss a particular problem. This is one reason why new paradigms so often emerge in the cross-fertilization of different disciplines.There are of course other, more systematic ways of searching for hypotheses by bringing together seemingly unrelated evidence. The Arrowsmith two-node search strategy [5], for instance, is based on distinct searches of the biomedical literature to retrieve articles on two different areas of science that have not been studied in relation to each other, but that the investigator suspects might be related in some fashion. The software identifies common words or phrases, which might point to meaningful links between them. This is but one example of ‘literature-based discovery'' as a heuristic technique [6], and in turn, is part of the larger data-driven approach of ‘text mining'' or ‘data mining'', which looks for unusual, new or unexpected patterns within large amounts of observational data. Regardless of whether one follows hypothesis-driven or data-driven models of investigation, let us teach our students to repeat the mantra: ‘odd is good''!? Open in a separate windowNeil R Smalheiser     

The 2009 Lindau Nobel Laureate Meeting: Martin Chalfie,Chemistry 2008

American Biologist Martin Chalfie shared the 2008 Nobel Prize in Chemistry with Roger Tsien and Osamu Shimomura for their discovery and development of the Green Fluorescent Protein (GFP).Martin Chalfie was born in Chicago in 1947 and grew up in Skokie Illinois. Although he had an interest in science from a young age-- learning the names of the planets and reading books about dinosaurs-- his journey to a career in biological science was circuitous. In high school, Chalfie enjoyed his AP Chemistry course, but his other science courses did not make much of an impression on him, and he began his undergraduate studies at Harvard uncertain of what he wanted to study. Eventually he did choose to major in Biochemistry, and during the summer between his sophomore and junior years, he joined Klaus Weber''s lab and began his first real research project, studying the active site of the enzyme aspartate transcarbamylase. Unfortunately, none of the experiments he performed in Weber''s lab worked, and Chalfie came to the conclusion that research was not for him.Following graduation in 1969, he was hired as a teacher Hamden Hall Country Day School in Connecticut where he taught high school chemistry, algebra, and social sciences for 2 years. After his first year of teaching, he decided to give research another try. He took a summer job in Jose Zadunaisky''s lab at Yale, studying chloride transport in the frog retina. Chalfie enjoyed this experience a great deal, and having gained confidence in his own scientific abilities, he applied to graduate school at Harvard, where he joined the Physiology department in 1972 and studied norepinephrine synthesis and secretion under Bob Pearlman. His interest in working on C. elegans led him to post doc with Sydney Brenner, at the Medical Research Council Laboratory of Molecular Biology in Cambridge, England. In 1982 he was offered position at Columbia University.When Chalfie first heard about GFP at a research seminar given by Paul Brehm in 1989, his lab was studying genes involved in the development and function of touch-sensitive cells in C. elegans. He immediately became very excited about the idea of expressing the fluorescent protein in the nematode, hoping to figure out where the genes were expressed in the live organism. At the time, all methods of examining localization, such as antibody staining or in situ hybridization, required fixation of the tissue or cells, revealing the location of proteins only at fixed points in time.In September 1992, after obtaining GFP DNA from Douglas Prasher, Chalfie asked his rotation student, Ghia Euskirchen to express GFP in E. coli, unaware that several other labs were also trying to express the protein, without success. Chalfie and Euskirchen used PCR to amplify only the coding sequence of GFP, which they placed in an expression vector and expressed in E.coli. Because of her engineering background, Euskirchen knew that the microscope in the Chalfie lab was not good enough to use for this type of experiment, so she captured images of green bacteria using the microscope from her former engineering lab. This work demonstrated that GFP fluorescence requires no component other than GFP itself. In fact, the difficulty that other labs had encountered stemmed from their use of restriction enzyme digestions for subcloning, which brought along an extra sequence that prevented GFP''s fluorescent expression. Following Euskirchen''s successful expression in E. coli, Chalfie''s technician Yuan Tu went on to express GFP in C. elegans, and Chalfie published the findings in Science in 1994.Through the study of C. elegans and GFP, Chalfie feels there is an important lesson to be learned about the importance basic research. Though there has been a recent push for clinically-relevant or patent-producing (translational) research, Chalfie warns that taking this approach alone is a mistake, given how "woefully little" we know about biology. He points out the vast expanse of the unknowns in biology, noting that important discoveries such as GFP are very frequently made through basic research using a diverse set of model organisms. Indeed, the study of GFP bioluminescence did not originally have a direct application to human health. Our understanding of it, however, has led to a wide array of clinically-relevant discoveries and developments. Chalfie believes we should not limit ourselves: "We should be a little freer and investigate things in different directions, and be a little bit awed by what we''re going to find."Download video file.^{(152M, mp4)}     

PARENT DEVELOPMENT

Today''s parents tend to be overwhelmed with advice from many sources. In his role as family counselor, the pediatrician must understand and consider the emotional development of parents in relation to their child''s development; otherwise, his advice and counsel do not “take” and he becomes tired and frustrated and angry.Parents progress through definite stages of development: Stage 1: Learning the cues—the struggle of the parents to interpret the infant''s needs. Stage 2: Learning to accept growth and development—the parent learning to accept some loss of control of the toddler. Stage 3: Learning to separate—the parent learning to allow the child to develop independently. Stage 4: Learning to accept rejection, without deserting—the struggle of the parents not to intrude and yet to be there when needed. Stage 5: Learning to build a new life having been thoroughly discredited by one''s teenager—the parent learning to live independently while the teenager struggles to develop his own identity.The pediatrician who is accepting, sensitive and a good listener and who keeps in mind that parents as well as children have capacities for growth and development, will be a potent factor in promoting good parent-child relationships and many times more effective in dealing with the child in health and disease.     

The evolutionary pattern of aromatic amino acid biosynthesis and the emerging phylogeny of pseudomonad bacteria

Pseudomonad bacterial are a phylogenetically diverse assemblage of species named within contemporary genera that includePseudomonas, Xanthomonas andAlcaligenes. Thus far, five distinct rRNA homology groups (Groups I through V) have been established by oligonucleotide cataloging and by rRNA/DNA hybridization. A pattern of enzymic features of aromatic amino acid biosynthesis (enzymological patterning) is conserved at the level of rRNA homology, five distinct and unambiguous patterns therefore existing in correspondence with the rRNA homology groups. We sorted 87 pseudomonad strains into Groups (and Subgroups) by aromatic pathway patterning. The reliability of this methodology was tested in a blind study using coded cultures of diverse pseudomonad organisms provided by American Type Culture Collection. Fourteen of 14 correct assignments were made at the Group level (the level of rRNA homology), and 12 of 14 correct assignments were made at the finer-tuned Subgroup levels. Many strains of unknown rRNA-homology affiliation had been placed into tentative rRNA groupings based upon enzymological patterning. Positive confirmation of such strains as members of the predicted rRNA homology groups was demonstrated by DNA/rRNA hybridization in nearly every case. It seems clear that the combination of these molecular approaches will make it feasible to deduce the evolution of biochemical-pathway construction and regulation in parallel with the emerging phylogenies of microbes housing these pathways.     

Darwin and Dostoyevsky: twins

The Russian poet Fyodor Dostoyevsky published an insightful treatise on human nature in his novel ‘The Brothers Karamazov'' in 1880. His account of humanity may offer as much insight into human nature for scientists as Darwin''s The Descent of Man.Late in the nineteenth century, Charles Darwin (1809–1882) and Fyodor Dostoyevsky (1821–1881) published accounts of their investigation of humankind. Darwin did so in 1871 in his book The Descent of Man, Dostoyevsky in 1880 in the parable of The Grand Inquisitor in his book The Brothers Karamazov. Last year we celebrated Darwin''s anniversary; for biologists, 2010—the 130th anniversary of Dostoyevsky''s book—might have been the year of Dostoyevsky.Dostoyevsky was familiar with Darwin''s doctrine and he was willing to admit “man''s descent from the ape”. An orthodox Christian, he put this sentiment in religious terms: “It does not really matter what man''s origins are, the Bible does not explain how God moulded him out of clay or carved him out of stone. Yet, he saw a difference between humans and animals: humans have a soul.The philosopher Nikolay Berdyayev noticed: “[Dostoyevsky] concealed nothing, and that''s why he could make astonishing discoveries. In the fate of his heroes he relates his own destiny, in their doubts he reveals his vacillations, in their ambiguity his self-splitting, in their criminal experience the secret crimes of his spirit.”The Grand Inquisitor can be read as Dostoyevsky''s treatise on human nature. In the tale, Jesus Christ revisits Earth during the period of the Inquisition and is arrested by the Church and sentenced to death. The Grand Inquisitor comes to visit Jesus in his prison cell to argue with him about their conceptions of human nature. He explains that humankind needs to be ruled to be happy and that the true freedom Jesus offered doomed humanity to suffering and unhappiness. Dostoyevsky''s superposition of these two points of view on humankind reminds us of the principle of complementarity, by which the physicist Niels Bohr attempted to account for the particle-wave duality of quantum physics.Dostoyevsky conceives of humans as complex, contradictory and inconsistent creatures. Humans perceive personal liberty as a burden and are willing to barter for it, as the Grand Inquisitor explained to Christ, for “miracle, mystery, and authority”. In addition, “the mystery of human being does not only rest in the desire to live, but in the problem: for what should one live at all?” We might say that these faculties make Homo sapiens a religious species. Not in the sense of believing in gods or a god, but in the sense of the Latin word religare, which means to bind, connect or enfold. Humans are mythophilic animals, driven by a need to find a complete explanation for events in terms of intentions and purposes.Research into the neurological bases of imagination, transcendence, metaphorability, art and religion, as well as moral behaviour and judgement (Trimble, 2007) is consistent with Dostoyevsky''s views. It has identified areas of the brain that have been labelled as the ‘god module'' or ‘god spot'' (Alper, 2001). These areas represent a new stratum of evolutionary complexity, an emergence specific to the human species. Their mental translations might be tentatively designated as the Darwinian soul, anchored in the material substrate and neither immortal nor cosmic. As consciousness and volition have become legitimate subjects of neuroscience (Baars, 2003), the Darwinian soul, and with it spirituality, seems to be ripe for scientific inquiry: the quest for meaning, creation and perception of metaphors, the experience of the trinity of Truth, Good and Beauty, the capacity for complex feelings that Immanuel Kant called sublimity, the thrill of humour and play, the power of empathy and the follies of boundless love or hate. Secularization does not erase the superstructure of spirituality: it is reflected, however queer it might seem, in the hypertrophy of the entertainment industry and also, more gloomily, in spiritual conflicts on a global scale.Dostoyevsky''s views on the human soul might be closer to those of Alfred Russel Wallace, who believed that an unknown force directed evolution towards an advanced organization. We can identify this ‘force'' as the second law of thermodynamics (Sharma & Annila, 2007). By moving evolving systems ever farther away from equilibrium, the second law eventually became the Creator of the ‘Neuronal God''.Christ, in the parable of the Grand Inquisitor, might be conceived of as a symbol of the truth outside the human world. Christ was listening to the assertions and questions of his interlocutor, but did not say a single word. His silence is essential to the parable.Similarly, the cosmos, to which humanity has been addressing its questions and predications, remains silent. By science, we increase knowledge only by tiny increments. The ‘god modules'' of our brains, unsatisfied and impatient, have hastily provided the full truth, deposited in the Holy Scripture. There are at least three books claiming to contain the revealed and hence unquestionable truth: the Judaic Torah, Christian Bible and Muslim Qur''an. A dogma of genocentrism in biology might offer an additional Scripture: the sequence of DNA in the genomes.Dostoyevsky''s legacy may suggest an amendment to the UN Charter. We, united humankind, solemnly declare: No truth has ever been revealed to us; we respect and tolerate each other in our independent searching and erring.     

In Memorium: Herman P. Schwan [1915–2005]

Herman P. Schwan [1915–2005] was a distinguished scientist and engineer, and a founding father of the field of biomedical engineering. A man of integrity, Schwan influenced the lives of many, including his wife and children, and his many students and colleagues. Active in science until nearly the end of his life, he will be very much missed by his family and many colleagues.     

Doctors accept a challenge: self-assessment exercises in continuing medical education.

A new approach to continuing medical education by distance learning has been implemented. A series of six patient-management problems or challenges were posted to 20 000 doctors throughout Britain. Each doctor had to decide on the diagnosis, investigations, and treatment of the patients described. The challenges covered problems that were important in the doctor''s day-to-day work and were designed so that he could obtain immediate feedback about his decisions and compare his own responses with those of a specialist and those of his colleagues. Additional information was available by telephone and by post on request. The series has been well received and is being widely used.     

The 2009 Lindau Nobel Laureate Meeting: Roger Y. Tsien,Chemistry 2008

American biochemist Roger Tsien shared the 2008 Nobel Prize in Chemistry with Martin Chalfie and Osamu Shimomura for their discovery and development of the Green Fluorescent Protein (GFP). Tsien, who was born in New York in 1952 and grew up in Livingston New Jersey, began to experiment in the basement of the family home at a young age. From growing silica gardens of colorful crystallized metal salts to attempting to synthesize aspirin, these early experiments fueled what would become Tsien''s lifelong interest in chemistry and colors.Tsien''s first official laboratory experience was an NSF-supported summer research program in which he used infrared spectroscopy to examine how metals bind to thiocyanate, for which he was awarded a $10,000 scholarship in the Westinghouse Science Talent Search. Following graduation from Harvard in 1972, Tsien attended Cambridge University in England under a Marshall Scholarship. There he learned organic chemistry --a subject he''d hated as an undergraduate-- and looked for a way to synthesize dyes for imaging neuronal activity, generating BAPTA based optical calcium indicator dyes.Following the completion of his postdoctoral training at Cambridge in 1982, Tsien accepted a faculty position at the University of California, Berkeley. There he and colleagues developed and improved numerous small molecule indicators, including indicators fura-2 and indo-1.In 1989, Tsien moved his laboratory to the University of California at San Diego, where he and his colleagues developed the enhanced mutant of GFP as a way to devise a cyclic AMP (cAMP) sensor for use in live cells. They initially engineered molecules to take advantage of the conformational change that occurs when cAMP binds to protein kinase A (PKA). By labeling one part of PKA with fluoroscein and another with a rhodamine, they hoped to detect Fluorescence Resonance Energy Transfer (FRET), which would occur when the two molecules were in close proximity. The initial experiments presented numerous difficulties due to the challenges of expressing PKA subunits in E. coli, labeling the protein without destroying its function, and delivering the protein to cells via microinjection.Eventually, Tsien sought a more elegant approach, hoping to use and modify a naturally fluorescent protein that could be expressed in the cell. GFP originally described by Davenport in 1955, extracted and purified by Shimomura in 1965, and cloned by Prasher in 1992 was an appealing candidate. To make the protein more useful for their FRET studies, Tsien and colleagues modified the amino acid structure of the protein (S65T). The improved protein had an excitation peak near that of fluoroscein, and was photostable. Tsien and colleagues also solved the protein''s crystal structure, enabling them to generate additional colors with spectral properties suitable for FRET. However, when they attempted to use the GFP proteins in the detection of cAMP, they experienced further difficulties with PKA. Instead, their first successful use of GFP derivatives for FRET was in the detection of intracellular calcium using their engineered calmodulin-based calcium indicator, Cameleon.In a short time, Tsien''s work has led to further technological developments and important scientific findings. GFP and its derivatives have been used in a wide range of biological applications, from the study of protein localization to understanding how HIV spreads from cell to cell. The need for such probes is highlighted by the abundance of research conducted using these fluorescent proteins, as well as the continued development of similar fluorescent proteins, such as the coral-derived dsRED.Tsien is currently developing genetically encoded Infrared Fluorescent Proteins (IFPs), which with their long emission wavelengths of >700 nm, have the ability to pass through living tissue and improve imaging in living organisms. He is also building synthetic molecules for use in humans. He cites team effort and the contributions of students and post-docs as key components of progress and success: "Even if I had the time, I couldn''t have done the experiments, because I don''t know how. It''s very much a team effort."Download video file.^{(144M, mp4)}