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.

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

First, a handy little reminder on group meetings from Biocurious. The suggestions are so simple, and yet so many people in group meetings do not think about what they want to say ahead of time, or they drag on and on. And those that respond to questions with “I don’t know”, as a full answer, just get me. Not knowing is fine, but not coming up with a plan for finding out, or a defense of why it doesn’t matter, is poor group meeting conduct.

Now, only a themed group of some links around the blogs. I don’t follow personal genomics closely, but four posts caught my attention discussing the Coriell Personalized Medicine Collaborative study and Navigenics.

Coriell Goes Live!!!
at Gene Sherpas,
Free Personal Genomics… Sort Of
at Genetic Future,
Will Coriell PMC Kill Navigenics?
at Think Gene, and
Navigenics Interview: Annual Insight
at ScienceRoll.

Coriell is offering a free service – a full genome scan, plus a genetic health report and genetic counselling – that would cost you at least $500 from Navigenics. The pay-off to them is a massive database to mine for new gene-disease associations and information about patient responses to genetic testing; the pay-off for you is free genetic disease risk predictions. The deal may attract customers to Coriell over Navigenics, changing who is leading the field of personal genomics for consumers. Or not.

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

Three selected articles for your blog-reading pleasure:

The Stimulus – How much is marked for science funding?

Let’s not mess things up this time! The last major increase to the NIH caused major problems years later. Money was simply pumped into new and existing grants, PIs hired many new grad students and postdocs, and the pyramid scheme got a major influx bloating the bottom of the academic edifice. As the bottom rose, many chunks fell of and as one Nobel Lauriate stated, we sacrificed a generation of scientists.

And two useful new tools for the molecular and cellular biologist:

Move over GFP, it’s FlAsH and ReAsH
A brief news item (news to me anyway) on the smallest fluorescent tag available. We all know that GFP is a rather bulky protein tag, but using biarsenical labelling of tetracysteine motifs, you can get a fluorescent tag that’s only 6aa long.

Hot off the Press: Fluorescent timers
By directed evolution of a protein that normally fluoresces in the red, it was possible to generate variants of the protein that had differing maturation rates for the chromophore, as well as a temporal shift in the fluorescence spectrum from blue to red. Different mutants resulted in fast-, medium-, and slow-fluorescent timer molecules.

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

I’m a frequent lurker on a wide variety of life science blogs, and one of those blogs that I’ve recently started to really appreciate is What’s New in Life Science Research at Scienceblogs. As a blog it has promise, although I’m hoping that some of the posts go into greater depth with their analyses of up-and-coming biotechnologies. One great post was by Hsein-Hsein:

It’s All About Money [GMO and Profits]
A quote from the article: “But add the profit motive and the ability to patent lifeforms and you get attempts by individual corporations to corner the worldwide market in one species after another, which is bad for farmers and consumers, and you also get thuggish attempts to subvert independent research, which is bad for science.”

How the Texas Board of Ed. misrepresented a Nobel Prize winner
The title says it all really and isn’t that surprising perhaps — but for those following the evolution-creation wars for American classrooms, it’s the latest hot news.

And to round out this brief survey of the blogosphere…
Peering into the Genetic Future: trends in human genomics in 2009

Okay, that’s it. There just weren’t any recent posts with strong analysis outside of Scienceblogs that I could find lately. Come on you independents. Get to it! (Bitesize Bio however has been great this past week — check out some of our posts!)

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

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

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

Welcome back from the Winter Holidays, it’s time to start the regular ‘Around the Blogs’ segment again. I’ve taken notice of a handful of interesting articles around the blogs on human genetics, so I’ll focus on that this week.

Genetic differences between human populations: more drift than selection?
Dan MacArthur points to a paper claiming that large allele frequency differences between populations are due to demographic effects, rather than selection. That is, most of the differences between different races are due to drift rather than selection.

p-ter also contributes with:
Selection or demography in differences between human populations?

As does John Hawks with:
Surfing and recent selection

And the study was also blogged on a couple months ago by Dienekes:
Allele-surfing versus positive selection

Lastly, and related but on a slightly different topic:
A genetic test to tell you what “population” you are?

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

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

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

Books About DNA: DNA: Promise and Peril
In one of a series of posts on books on DNA, Hsien-Hsien discusses a book about the genetic revolution and its implications for our lives.

The Problem with Publication-Driven Science
Mike laments the consequences of publication-driven research, and how it can inspire problems associated with secrecy and withholding data.

The Genetic Architecture of Metabolic Traits: A Data Explosion
Daniel discusses six papers on one topic appearing in Nature Genetics, with an extra helping of data – “These papers use genome-wide association data from very large numbers of individuals to analyse the genetic architecture of disease-associated traits like blood lipid and glucose levels.”

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

Three story highlights from related blogs:

All Graduate Student Supervisors Take Note
“This lovely piece has been circulating of late, but Sonke has been kind enough to allow the SCQ to present his “Advice for Potential Graduate Students” as a handy dandy pin-up, suitable for pinning up in some visible area of your lab.”

FDA Interested in Collaborating with Personal Genomics Companies
“[Genetic Future] describes an intriguing twist in the ongoing struggle between the nascent personal genomics industry and regulatory bodies: apparently the FDA is exploring the possibility of collaborating with consumer genomics providers to track adverse drug reactions”…

Increased Secretion in Senescent Cells, and Chris Patil on the Campisi Lab’s New PLoS Biology Paper: Cellular Senescence, Protein Secretion, and the Aging/Cancer Paradox
Chris Patil (Ouroboros) co-authors an interesting new paper in PLoS Biology, and bloggers discuss.

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

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.