About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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I doubt that anyone reading Bitesize Bio has never heard of Richard Dawkins. He’s always been controversial in one way or another, ever since the release of arguably his most popular book, The Selfish Gene (Amazon US/UK). But despite Dawkins’ notoriety, maybe there are some readers here who haven’t read The Selfish Gene – I didn’t until two years ago, actually. So, what specifically is The Selfish Gene about?

Dawkins coined the term selfish gene as a way of expressing the gene-centred view of evolution, which holds that evolution is best viewed as acting on genes and that selection at the level of organisms or populations almost never overrides selection based on genes. In chapter three, he explains:

“Genes are competing directly with their alleles for survival, since their alleles in the gene pool are rivals for their slot on the chromosomes of future generations. Any gene that behaves in such a way as to increase its own survival chances in the gene pool at the expense of its alleles will, by definition, tautologously, tend to survive. The gene is the basic unit of selfishness.”

This way of looking at selection, from the perspective of the gene, gets extended to such emergent behaviors as kin selection, eusociality, and altruism, by way of the fact that an allele not only gets propogated through the gene pool by helping the immediate organism survive, it also helps other copies of itself survive in other members of its species. Meaning, altruistic behavior is a natural outcome of selection, even if it is bad for the individual organism, because the genes themselves are acting selfishly by protecting other copies of themselves. Of course most genes don’t directly influence behavior, meaning that most genes are, at best, indirectly selfish – but in the case of parochial altruism (within a family or other inbreeding group), most organisms benefiting from altruism likely carry copies of the same non-behavioral genes anyway.

At a time when the idea of group selection was being shown not to be a stable evolutionary strategy, this model provided one way of explaining why kin selection was a much better description of sociality in animals.

For these reasons, The Selfish Gene has rightfully received wide acclaim. But, it is just a metaphor, and no gene is an island. Each gene must act in concert with the rest of an organisms’ genome, which in turn must act to cooperate and compete with other members of its species and within a given ecosystem. As a result, tradeoffs get made. Many times, it is not the allele that is most effective at performing its usual task that is propogated in the gene pool, but the allele that works best with the rest of its genome to generate a successful phenotype that survives.

As a result, one of the primary scientific criticisms of The Selfish Gene has been on the idea that the gene is the unit of selection. Most even criticize the idea that the genome is the unit of selection, instead arguing that the phenotype is what is being selected. Instead, the gene is the unit of evolution, some argue, viewing evolution as the long-term trend of shifting allele frequencies.

Being a molecular biologist and not having studied evolutionary biology formally, my first reaction was to take these two perspectives at face value. After a thrashing from Larry Moran (see the comments), my conclusion that macroevolution is just a “very long-term trend of shifting allele frequencies” was blown apart. As a result, I’ve since come around to be very critical of the view that the gene is the unit of evolution.

Instead, the population appears to be the best candidate as the unit of evolution, with phyletic change (shifting allele frequencies) of a single population over time being “microevolution”, and isolation/divergence of two or more populations representing “macroevolution”.

All of this means that the impact of The Selfish Gene is very restricted as a metaphor of how evolution occurs, being successful at solving a very specific set of problems relating to social animal behavior, and is limited to discussions of phyletic change.

The implications for social behavior coming out of The Selfish Gene has also directed much of Richard Dawkins’ career since its publication. His follow-up book, The Extended Phenotype, subtitled “The Gene as the Unit of Selection”, and later, “The Long Reach of the Gene”, argued that a gene may effect an organism’s environment through that organism’s behaviour, citing as examples caddis houses and beaver dams.

He also coined the term “meme” (the cultural equivalent of a gene) to describe how Darwinian principles might be extended to explain the spread of ideas and cultural phenomena, an idea that has been developed into a new area of study principally by Susan Blackmore. Dawkins used the word meme to refer to any cultural entity which an observer might consider a replicator. He hypothesised that people could view many cultural entities as capable of such replication, generally through exposure to humans, who have evolved as efficient (although not perfect) copiers of information and behaviour. Most notably in his more recent book, The God Delusion, he argues that religions are basically memes (among other things).

I don’t know if his arguments about religions as memes are all that great, but he sparks discussion either way about how it is useful to view the origins of social behaviors. But that’s a story for another post, some other time.

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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With it almost being Darwin Day, it seems only right to review a book on perhaps the best popularizer of evolutionary biology in the 20th Century, Stephen Jay Gould. As a paleontologist and historian of science, he taught at Harvard, and contributed regularly with over 300 monthly essays to the magazine Natural History, between 1974 and 2001.

Some of his articles have been boons for high school teachers trying to relate to their students, such as an article on the evolution of Mickey Mouse, which was republished in The Panda’s Thumb. Other essays had different impacts, including things on punctuated equilibria, spandrels, and the false appearance of progress in evolution. Still other times, he took direct issue with Richard Dawkins and The Selfish Gene, and to a lesser degree, E.O. Wilson and Sociobiology.

The Richness of Life: The Essential Stephen Jay Gould (Amazon US/UK) is sort of a posthumous “highlight reel”.

I’ve never been quite sure if this style of book, a “greatest hits” if you will, is the way to go, as it cuts so much out. On the other hand, the number of essays and books that Gould authored are probably intimidating to most potential readers. Maybe only the most dedicated fans would be willing to go that far. Heck, I know that I had only read Full House, The Mismeasure of Man, and The Lying Stones of Marrekeck, although I’ve heard many of his essays described to me by teachers and professors in high school and college.

So I think that The Richness of Life: The Essential Stephen Jay Gould was a great book for me.

The review from Publisher’s Weekly:

Harvard professor and National Book Award winner Gould was one of science’s best ambassadors to the general public until his death at 60 in 2002. These 44 essays represent his best-known pieces from his books and from essays for Natural History magazine, as well as never before published speeches. The editors have selected pieces on a wide range of subjects—from the ever-shrinking Hershey Bar, to his and Niles Eldredge’s theory of punctuated evolution and Freud’s adaptation of the (now abandoned) biological notion of recapitulation—which showcase Gould’s immense curiosity as well as his skill at explaining even the most obscure topics with clear and vivid language. Autobiographical essays are followed by scientific ruminations on evolutionary theory and how it has been understood, misunderstood and misused, ever since Darwin put pen to paper. This collection demonstrates Gould’s passion for life as well as his enthusiasm for, and awe at, the “majesty” of “the continuity of the tree of life for 3.5 billion years.” Gould’s many fans, as well as new readers, should find this collection intriguing as well as entertaining, an eminently suitable last hurrah for an amazing thinker.

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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We all know that surviving in the publish-or-perish world of academia requires that we write a lot. For myself, I view blog-writing as a form of writing practice — I used to really suck at it. Okay, actually I still get stuck sometimes when trying to write, especially for grants.

So, psyching myself up for a new postdoc position, I went out and got a copy of Paul J. Silvia’s book How to Write a Lot: A Practical Guide to Productive Academic Writing, wondering if writing experts had any helpful suggestions.

Reading through Silvia’s book, it occurred to me that while building a set of habits is much needed for academic writing (which the book does rather well), writing for science-related reasons really shouldn’t be as frightening as some might make it out to be. One passage from the book echoed this impression of mine:

When people tell me they have writer’s block, I ask, “What on earth are you trying to write?” Academic writers cannot get writers block. Don’t confuse yourself with your friends teaching creative writing in the fine arts department. You’re not crafting a deep narrative or composing metaphors that expose mysteries of the human heart. The subtlety of your analysis of variance will not move readers to tears, although the tediousness of it might.

What’s more, this tedious analysis is tied to just the thing that makes you a good scientist or not: your ability to choose and plan good experiments. That’s an important thing that you have to write about — the experiments you have done and those that you want to do. And sure enough, Silvia spends a lot of time in the book talking about writing for journals and for books.

But that’s only half the story of course. You have to sell your research, especially when writing grant proposals. Grantsmanship is a skill, no doubt about it, and it’s perhaps the most difficult and stressful aspect of academic writing. You need to be shrewd in selecting a title, a popular subject, and a solid body of data to draw from. And even then, not having the most sympathetic refereeing group can really hurt.

The worst part of it is that these issues of grantsmanship aren’t so much a skill that you can teach, or learn from a book.

Some scientists have it, and others don’t.

About the author

Greg Caramenico

After undergraduate work in molecular and cell biology, Greg received his MA in history from Vanderbilt University. He has worked on various topics in intellectual history and the history of biology, especially on theories of memory in premodern and modern science.

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If you’ve ever wondered how molecular biology came to prominence in biomedical research, why so many famous molecular biologists of the past century were trained as physicists, or when bacteriophages were first used as cloning vectors, you may be looking for a good read on the history of molecular biology.

Unlike in evolutionary biology, where there are many current issues informed by historical research and which has a fair amount of engagement between practicing scientists and historians, much of the story of molecular biology has been told sporadically and unevenly, often in the memoirs of scientists or by science journalists.

Navigating through these numerous popular histories of molecular and cell biology can be challenging.

Some suffer from a  bias toward the achievements of the English-speaking research community, or often the tell only the story of a single research group; others are so popular as to sound condescending to the scientifically literate.  (Many fun books are autobiographical rather than historical, from Watson’s The Double Helix to Francois Jacob’s meditative and literary The Statue Within, as much war memoir as a scientific tale).

I recently reread Michel Morange’s A History of Molecular Biology, and think it avoids these pitfalls well, and makes a great first read for those who are curious about the history their field.

Morange, a molecular biologist at the Ecole Normale Superieure, is at his best chronicling the early days of molecular biology.

Almost everyone agrees that Post-War molecular biology was shaped – to some extent – by the contributions of physicists who joined many labs in biochemistry and genetics.

But there is a fair amount of debate regarding how influential they were.

Morange argues that the reductionism of, and sometimes bewilderment at biochemical complexity which many physicists brought to their newly adopted field led them toward a “unifying vision,” simplifying things as much as possible, and this greatly accelerated the pace of research.

Salvador Luria, for instance, was influenced by the reasoning of physicists to break with the experimental models of classical genetics and develop new calculation methods for phenomena such as mutation rates. He drew from statistical physics in demonstrating Darwinian inheritance among bacteria.

Morange makes a good case that the technical and procedural emphasis in molecular biology has been enhanced, if not created, by the influence of twentieth-century physics.  He writes:

“The development of the techniques of genetic engineering shows that the molecular understanding of biology, acquired between 1940 and 1965, was an operational understanding. Today both molecular biologists and physicists share a scientific world view in which knowledge and action are intimately linked.

Physicists played an important role in this change in the form of biological knowledge, by the way they conceived and carried out their     experiments.  In following Delbruck and asking simple questions of biological objects, they     obliged these objects to reply in the same language.” (p101)

For readers who’ve not encountered the classic works of Fran?§ois Jacob and others, Morange introduces  “The “French School,” recounting how what initially were enzymology  research groups engendered some intrinsic priorities of molecular biology.

On the question of  how France, whose post-war institutions lagged behind in classical genetics and even biochemistry, managed to accomplish so much in molecular biology, the institutional history is instructive.  Morange points to the scientists at The Pasteur Institute, which was the autonomous center of the most crucial French research in the 1960s, including the development of the allosteric model.

It’s  impressive to see how far they made their resources stretch and how vast their collaboration was.

After a more than a decade, this book holds up well. Some readers may disagree with the definition that starts the book:  molecular biology “consists of all those techniques and discoveries that make it possible to carry out a molecular analysis of the most fundamental biological processes – those involved in the stability, survival, and reproduction of genes.”

Much more dated and tendentious (early 1990s) is Morange’s claim that molecular biology has yet to make a significant impact on evolutionary biology.  Evo-devo’s meteoric rise complicates this considerably.

One chapter, “Molecular Biology in the Life Sciences,” makes the claim that nothing of value has come from strictly molecular approaches to evolutionary biology or population genetics (p249), and speculates if Ernst Mayr’s distinction between “individual” and “population” biologies will disappear, to the detriment of one or both fields.

As our understanding of regulatory genes and developmental biology increases, it seems less likely that this is less likely to be the case.

Finally, Morange contrasts the difference between our current gene-centered molecular biology, and it’s precursor, which focused on proteins via enzymology.

This distinction is crucial, because before the working out of the genetic code, and the development of molecular genetics, separating molecular biology from its precursor disciplines (such as genetics and biochemistry) was difficult: so was figuring out when the newer discipline emerged.

The contemporary molecular biology began when it became less defined by study of structures and more concerned with information:

“The new molecular biology has become a way of “reading” life. “Classical” molecular biology had shown the importance of genetic code, of information linked to nucleotide sequences. Sanger, followed by many others, sequenced proteins and substituted the linear sequence of their amino acids for their structural complexity.

But this classical molecular biology was centered on proteins. In experimental terms, studies of the structure, function, and specificity of proteins came before studies of their amino acid sequence, anticipating the study of the nucleotide sequence in the genes that coded for these proteins.”  (215)

If the development of molecular biology was directed historically by physics, its current boundaries have been shaped by technology more than any field of “pure” science.

Morange writes that the technological discoveries like gene cloning, DNA polymerase, and PCR made the “new molecular biology,” which is a field defined by its techniques of  “reading” biological information.

Putting aside the metaphor of “reading”life – which has a fascinating but very off-topic history, I’m not certain I find the science/technology distinction useful in this context.

But I think readers will find these latter chapters raise interesting questions about whether to view molecular biology as a foremost as a scientific field or collection of experimental approaches which are useful in other biological and biomedical disciplines.

Check it out in our bookstore, and if you read it, let us know what you think.

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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Since last year’s discovery of a way to “reprogram” skin cells into induced pluripotent stem cells (iPS cells), there may or may not be a political way out of this controversy. But there are legal reasons why a quick end to the controversy may not be so easy to come by. (No, that’s not the point of the book, as author Russell Korobkin did not anticipate iPS cells – that’s just a personal observation.)

Russell Korobkin’s book Stem Cell Century: Law and Policy for a Breakthrough Technology is the first book to address not just embryo destruction but the full range of important policy questions raised by stem cell research and regenerative medicine.

The book description available on the book’s website is as follows:

“The explosion of interest in stem cell research raises a raft of controversial policy questions. When should human embryos be used to create stem cells? Should cloning be outlawed? Should egg and tissue donors be paid? Should we allow scientists to patent stem cells? Is the government entitled to a portion of the revenue from stem cell technology created with public funds? How should the regulators and courts balance the competing goals of access to revolutionary treatments and protection of the public from unknown risks?

“Russell Korobkin, with contributions from Stephen R. Munzer, provides the first thorough discussion and analysis of these and other unsettled questions of law, policy, and ethics that surround stem cell science. His clear and concise description of complex problems coupled with logical and well-balanced conclusions makes this volume essential reading for all Americans, general readers and experts alike, interested in the promise of stem cell research and the future of regenerative medicine.”

The chapter descriptions are pretty helpful as well.

I’m no expert of law, but it appeared like a very comprehensive and well-researched book. To someone looking for a book that delves into the science of stem cell research, this isn’t the book for you though. Oh, it provides several-page descriptions of the relevant science that are accurate, for non-scientists, but this is a book about law and legislation.

If that’s what you’re looking for, then by all means, check this book out.

About the author

Paul Hengen

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For our “fresh new” version of the website, I’ll kick off with a series of articles on describing the contents of my professional “toolbox”. So, let’s open ‘er up and see what we get. In this installment, I’ll skim the top tray and produce my list of basic gizmos that, just like beer and pizza, I just can’t live without.

I’ve identified these key gizmos – books, lectures and software tools – along the path of my career transition from lab rat molecular geneticist to computational biologist slash programmer slash software engineer,  – I think, once you’ve tried them, you won’t be able to live without them either.

Presentation Fever. This one is so essential it belongs on the top of the list.

If you’re like me, you spend a large amount of time either in seminars, preparing to give a seminar, or
running from seminar to seminar. So my first essential gizmo in the toolbox is a book… about
how to prepare the most awesome Powerpoint presentation ever. This book, “Why Most PowerPoint Presentations Suck” by Rick Altman, has become my bible.

If you read it you will be able to identify the deadliest of sins committed in every seminar you attend, or give.

It is the BEST book for telling you what to do AND what NOT to do while presenting yourself. For example,
have you ever been in a seminar while the presenter was nervously making circles upon circles on the screen with a laser pointer until the audience is heaving in synchrony?

Rick Altman exposes the most annoying habits of distraction, and how to avoid them. Do us all a favor and give a copy of this book to every science grad student you know.

Time management. Speaking of grad school, another essential for every grad student is an academic lecture on time management by Randy Pausch. Okay, this is not really a gizmo any more than a book is, but this lecture should be required learning material for every incoming graduate student. Take Randy’s wonderful free advice and run with it. You can view the lecture online by clicking here.

Now, onto the software gizmos…

Convert doc2pdf. Ever need to convert just one or two Word documents to pdf format?  What can I say but WOW! Go online and convert your resume or other Word document to PDF in an instant… and your Done!

Snagit. I use this little tool almost every day of my life. I never thought I’d do this, but I snap bitmap images of everything from web results pages to gnuplot graphs (see below) while documenting my research electronically. It is even faster to do this than to write a description of what I did today. I can’t live
without it.

ThumbsPlus. Hands-down the most useful picture editor and organizer there is.

PhotoGadget. I shudder to think you bought one of those high-end, high-price, space-hogging photo editors. Check out my avatar built using this exceptional right-click gadget.

BioVenn. This is a very cool way to create and display overlapping sets of data. John would be proud.

eTBlast Website. PubMed on steroids. Nuff said.

Norton Ghost. I can’t count the number of times this program has saved my ARtichokeS. Not free, but it sometimes will be bundled free with a new external hard drive. Scout out the HD specials online.

SpySweeper. If you don’t get in the habit of cleaning house, you will just end up eventually re-installing your system with Norton Ghost. Just be careful out there.

Gnuplot for windows (wgnuplot). I am sooo sick of those Excel-generated blue diamonds and pink squares! Those of you who churn out these plots know who you are. You should be ashamed of yourself. Learn some new tricks and buy that book I was talking about up top.

So those are the gizmos I would consider to be my essential basics I have in my toolbox. Stay tuned and I will delve deeper to bring you more gems that I use in my work, and that you will hopefully find useful too.

What gizmos could you not live without?

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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Following up on my recent post about The Nature of Scientific Observation, I left two-thirds of Chalmers’ book What is This Thing Called Science untouched, including discussions on Bayes’ theorem and the New Experimentalism.

I left off right before Popper’s falsificationism and Kuhn’s paradigms came into view. Each of them has their own problems. Popper, for instance, introduced the falsificationist concept with simplistic examples that the actual scientist rarely encouters. Nevertheless, Popper’s Logic of Scientific Discovery does seem to reflect some of the approach that the typical scientist has been taught to apply in formulating testable hypotheses. As a result, sophisticated falsificationism takes a somewhat defendable position by reiterating falsificationism in strongly qualified statements.

Thomas Kuhn then introduced scientific revolutions as “paradigm shifts”, exposing the hard truth that science is normative. No argument there. But the problem lies in the logical conclusion that many people draw from the realization that science is normative: science is therefore more subjective and more falliable than we originally may have supposed, and pseudoscience might find comfort in the doubt sowed in science therein. Kuhn simply could not reconcile his normative description of science with what is obvious to any empirical scientist, which is that many scientific theories can explain wide ranges of natural phenomena with a high degree of precision. In other words, though science may be normative in practice, it is also grounded in high-level approximations of reality, and basic facts exist which can be said to be objective.

As a result, I characterize Kuhnsian paradigms as not a philosophy of science, but a sociology of science. That view has gotten me in some strongly-worded discussions with other scientists, but it’s a position that I stick to. It is very clear that some theories are better than other, and that science does indeed represent progress. One needs only to look to the offspring of science, technology. Advancements in biomedical, mechanical, electrical, and chemical technology are not mere paradigms.

Enter the Bayesian theorem of science and the New Experimentalism.

Thomas Bayes, an 18th-century mathematician, established a theorem that has a great deal of bearing for philosophy of science. Bayes’ theorem is about conditional probabilities, which prescribes how probabilities of truth statements are to be changed in the light of new evidence. Chalmers describes, on page 175:

In the context of science the issue is how to ascribe probabilities to theories or hypotheses in the light of evidence. Let P(h/e) denote the probability of a hypothesis h in the light of evidence e, P(e/h) denote the probability to be ascribed to the evidence e on the assumption that the hypothesis h is correct, P(h) the probability ascribed to h in the absense of knowledge of e, and P(e) the probability ascribed to e in the absense of any assumption about the truth of h. Then Bayes’ theorem can be written:

P(h/e) = P(h) x P(e/h)/P(e)

P(h) is referred to as the prior probability, since it is the probability ascribed to the hypothesis prior to consideration of the evidence, e, and P(h/e) is referred to as the posterior probability, the probability after the evidence, e, is taken into account.

So the formula tells us how to change the probability of a hypothesis to some new, revised probability in the light of some specified evidence.

This symbolic calculus serves to illustrate that any disagreements in science between proponents of rival research paradigms or programs must have their source in the prior probabilities held by those scientists, since the evidence is taken as given and the inference considered to be objective. But the prior probabilities are themselves totally subjective and not subject to a critical analysis.

Consequently, those who raise questions about the relative merits of competing theories and about the sense in which science can be said to progress will not have their questions answered by the Bayesian. Bayes’ theorem of science does, however, reflect the importance of the relevance of new data. That is, empirical evidence is not all considered equal – some evidence is strongly weighted as far as importance goes, whilst other evidence is considered irrelevant.

The New Experimentalism is an intriguing contrast. Chalmers starts off with an example (an experiment by Michael Faraday on electromagnetism) and then asks (page 195), “Is it useful or appropriate to regard this accomplishment of Faraday’s as theory-dependent and falliable?” Without question we can say that, at best, one can only refute the extreme empiricist position that facts must be established directly by the entry of sensory data into a mind that otherwise knows nothing, and that the recognition of a new experimental effect cannot be said to be falliable in any sense.

Thus, the production of controlled experimental effects can be accomplished and appreciated independently of high-level theory. Molecular biology is replete with examples of experimental observations that are tightly controlled, and the results derived therein can be considered objective. Extrapolating from those observations to theoretical implications is not always straightforward, to be sure, but possible if the experiment itself has relevance to aspects of those theories which are in contention among scientists.

Deborah Mayo offers the best articulation of the New Experimentalism in her 1996 book, Error and the Growth of Experimental Knowledge. She sides with Kuhn’s notion of normal science, reformulating it in such a way that reflects the ability for scientists to make factual statements independent of theory, even though they remain subjective and fallible to a degree.

So I found myself nodding very much through reading about Deborah Mayo and the New Experimentalism. I am surprised that I hadn’t read much about this area of the philosophy of science before.

Overall though, I think it also helpful to note that each of the major philosophers of science tackle a separate aspect of science – how hypotheses are made; how science is normative; the role of inductive and deductive logic; how experiments are formulated; how facts and theories are inter-dependent; etc. Each of them has a point, but none of them can be extrapolated to science as a whole.

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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Currently I’m reading Alan Chalmers’ What is this thing called science?, with specific interest in the questions of expertise and the uniqueness of science as a foundation for knowledge. (Coturnix’s recent post on Information, Knowledge, and Experience helped crystallize my thoughts – check that out as well.)

Philosophy of Science has come a long way since the days of Popper and Kuhn, and I was suggested to read Chalmers about six months ago. This is a very good book, clear and well written, and provides an excellent overview of philosophy of science (including all the major players: Popper, Kuhn, Lakatos, Laudan…) and the problem of demarcation between science and non-science.

I haven’t yet reached the chapters on Bayesianism and New Experimentalism. Most philosophers of science share concerns about falsificationism versus verificationism (or deduction versus induction) – and Bayesianism and Experimentalism provide some sort of response to these concerns, or so I’ve been told.

The opening chapters however nicely clear away some popular misconceptions about science, by contrasting what science is with what it is not.

Expertise

The experienced and skilled observer does not have perceptual experiences identical to those of the untrained novice when the two confront the same situation. This clashes with a literal understanding of the claim that perceptions are given in a straightforward way via the senses.

…observers viewing the same scene from the same place see the same thing but interpret what they see differently. I wish to dispute this… These experiences are not uniquely given and unchanging but vary with the knowledge and expectations possessed by the observer. (page 8 )

Chalmers is tearing down the notion that the acquisition of facts precedes the formulation of laws and theories. While many scientists may not care much about philosophy of science, and assume that facts come before theory, all scientists at least implicitly understand this situation.

Pre-supposed knowledge

According to our modified stand, we freely acknowledge that the formulation of observation statements presupposes significant knowledge, and that the search for relevant observable facts in science is guided by that knowledge. Neither acknowledgement necessarily undermines the claim that knowledge has a factual basis established by observation. (page 13)

While science is in part a method, it is also an ediface of knowledge that acts as a starting point for discovery.

In the specific case of the molecular biologist, every hypothesis and experiment is founded on volumes of information which must be assumed. It is, in fact, falliable to some degree. How than can science be made more reliable?

Open discourse

The point that action can be taken to explore the adequacy of claims put forward as observable facts has the consequence that subjective aspects of perception need not be an intractable problem for science. Ways in which perceptions of the same scene can vary from observer to observer depending on the background, culture and expectations were discussed in the previous chapter. Problems that eventuate from this undoubted fact can be countered to a large extent by taking appropriate action. (page 21)
[...]
According to the view put forward here, observations suitable for constituting a basis for scientific knowledge are both objective and fallible. They are objective insofar as they can be publicly tested by straightforward procedures, and they are fallible insofar as they may be undermined by new kinds of tests made possible by advances in science and technology. (page 25)

I read this as a strong rationale for not just standard modes of knowledge dissemination such as the published literature and attending symposia, but for the extreme case of Open Science. That is, the greater the transparency and openness of the discussion over relevant data, the more objective we can claim the current state of scientific knowledge.

Deriving knowledge

According to the unqualified inductivist, observation statements that form the factual basis for science can be securely established directly by careful use of the senses. [...]

Attractive as it may have appeared, we have seen that the inductivist position is, at best, in need of severe qualification and, at worst, thoroughly inadequate. We have seen that facts adequate for science are by no means straightforwardly given but have to be practically constructed, and in some important senses dependent on the knowledge that they presuppose… (page 57)

This is the pragmatic empiricist position, that science is not exclusively inductive or deductive. It is, in fact, quite a bit of both. And again, neither can operate in a vacuum free from pre-supposed knowledge.

Which brings me to a passing note on creationism, which seems to misrepresent or ignore the existing body of literature. And those few creationists who do attempt to insert their inductions into the scientific literature (e.g., Stephen Meyers and Jonathan wells) have completely refused to do anything deductive to back up their fundamental inductive observations. That is, the falliability of their observations cannot be seen independently and corroborated practically.

Thus far, the What is This Thing Called Science has been more about what science is not however. I can’t wait to get to some more intruiging sections about what science is – and New Experimentalism and Bayesianism in particular. Be sure to check back.

For more: Biology and the Scientific Method.

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

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I just came across a very interesting book relating to biotechnology, but sadly it’s not due out until next year. By Janine Benyus and Gunter Pauli, Nature’s 100 Best: World-Changing Innovations Inspired By Nature, this book promises to tell of stories of past innovations coming from biology.

A collaborative effort of Janine Benyus’ Biomimicry Guild and Gunter Pauli’s ZERI Foundation, Nature’s 100 Best brings to light fascinating secrets of nature capable of revolutionizing nearly every aspect of our economy, and changing our destructive relationship with the environment to one of mutual benefit. The team behind Nature’s 100 Best recognizes that the best way to solve the world’s most intractable problems is to look where we haven’t looked before: in the extremely successful R&D lab that’s been operating on this planet for 3.8 billion years. In that time, 10-30 million species have learned to do everything we want to do, without guzzling fossil fuels, polluting the planet, or mortgaging our common future. They’ve learned what works, what is appropriate, and what lasts here on earth.

(more…)

About the author

Dan Rhoads

Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.

To enable tagging you will need to register on Bitesize Bio. We're sorry for the inconvenience, but it's free, only takes a few seconds, and it will enable you to view our seminars for free, ask questions from the professional community, and take part in the lively community of Bitesize Bio

After some of the blog posts that I’ve written on animal rights’ extremists and violence against animal researchers, there’s now a review of a most appropriate book on the topic available in Science – Scientists Under Siege.

Suppose you are a scientist and a finalist for the position of vice president for research at the University of South Florida (USF). Before leaving for your interview trip, you receive copies of letters sent to the university’s administration informing them of your “ignominy” and stating that you are unwelcome in the university’s town. Animal rights activists meet your plane and (because of an open meetings law) are present at most of your interviews. Activists outside the meeting room doors lobby attendees and distribute fliers that make false and preposterous claims about your research. Demonstrators wear T-shirts demanding that you not be hired. When you deny the accusations being hurled at you, a faculty member calls you a “son of a bitch” and a liar. At your hotel room, you receive threatening calls and knocks on your door in the middle of the night. Fortunately, the campus police provide you with protection. Arriving at the airport for your return trip, you are surrounded and harassed by demonstrators until airport security rescues you. At home, you find protesters standing not far from your house, shouting at you. And USF’s president now refuses to speak to you. You don’t get the job.

Now suppose that really happened.

This and more is the situation that animal rights’ extremists have placed many biomedical researchers into. I say “and more,” because P. Michael Conn didn’t actually have his house firebombed, his car blown up, or been physically assaulted.

As a result, Conn has his new book out – The Animal Research War. While I haven’t gotten the chance to read it, it purportedly aims to educate and inform the general public as to what actually happens with animal research.

As to what position to take on bioethical questions surrounding research, of course one should read available materials such as this book, guidelines addressing animal welfare concerns written by the National Academies of Science, and other resources. And then come to your own conclusions. If you disagree with the status quo, address them through appropriate channels, like bioethics committees.

But above all, arm yourself with the knowledge of the tactics of extremism and terrorism, so that you can work against such destructive elements and forge towards a better world.