Category Archives: Philosophy

BIO101 – Biology and the Scientific Method

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.

Today, we start with the very beginning – the introductory lecture on Biology and the Scientific Method. Follow me under the fold:

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UC Berkeley Genetic Testing Affair: Science vs Science Education – guest post by Dr.Marie-Claire Shanahan

Marie-Claire Shanahan is an Assistant Professor of Science Education at the University of Alberta, in Edmonton, Alberta, Canada. As a former science teacher, she was always surprised by the ways that students talked themselves out of liking science – and she decided to do something about it. She now researches the social and cultural aspects of science and science education, especially those related to language and identity.

Marie-Claire and I first met online, then also in Real World when she attended ScienceOnline 2010, after which I interviewed her for my blog. You can check out her website and follow her on Twitter. Very interested in her scholarly work, I asked her if she would write a guest-post on one of her topics, and she very graciously agreed. Here is the post about the Berkeley genetic testing affair.

Outside of issues related to teaching evolution in schools, the words controversy and science education don’t often come into close contact with one another. It would be even rarer to be reporting on legislative intervention aimed at halting science education activities. So what’s going on with the UC Berkeley genetic testing affair?

News started to surface in May that Berkeley was going to be asking incoming first year and transfer students to send in a DNA swab. The idea was to stimulate discussion between students as part of the yearly On the Same Page program. A heated debate ensued that has ultimately lead to proposed state legislation that would bar California’s post secondary institutions from making unsolicited requests for DNA samples from students. Both the controversy and the legislation are excellently reported by Ferris Jabr at Scientific American here and here.

It would be reasonable to assume that this seems controversial because it involves genetic testing and therefore personal information. But is there more to it than that?

I chatted informally with some friends about the issue. One expressed her divided feelings about it saying (roughly quoted) “It seems like they [university admin] have addressed the ethical concerns well by being clear about the use of the swabs and the confidentiality but something still just doesn’t feel right. There’s still a part of me that shivers just a little bit.”

What is the shiver factor? Genetic testing and the idea that institutions might have access to our DNA do conjure some imaginative science fiction possibilities. So that could be causing the shivers. But from my perspective as a science education researcher, I think there’s also an underlying issue that makes this particular situation feel controversial: despite having science education goals, this looks and feels a lot more like science. That look and feel leads to confusion about how this initiative should be judged both from an ethical perspective and an educational one.

Science and science education are not the same thing (nor should they be). One way to think of them is through activity analysis, paying attention to who is involved, what are their objectives and what are the artefacts (e.g., tools, language, symbols), actions, and rules that those involved generally agree are used to accomplish the goals of the activity. Studies in activity theory emphasize the importance of shared understanding for accomplishing and progressing in any activity. I would argue that science and science education are different (though obviously related) activities. They have, in particular, different objectives and different artefacts, rules and actions that guide and shape them. As participants in one or the other (or both), teachers, parents, students, researchers, administrators have both tacit and explicit understandings of what each activity entails – what are the rules, the acceptable tools and practices and the appropriate language.

This is where the Berkeley project places itself in a fuzzy area. The objectives of the project are clearly stated to be educational. From the On the Same Page website: “we decided that involving students directly and personally in an assessment of genetic characteristics of personal relevance would capture their imaginations and lead to a deeper learning experience.” Okay, that sounds like the same reasons teachers and professors choose to do many activities. Sounds like science education.

But what about the tools? Testing students’ blood type or blood pressure uses tools commonly available in high school labs (or even at the drug store). The tools used here though are not commonly available – these samples are being sent to a laboratory for analysis. Participants don’t therefore have a shared perspective that these are the tools of education. They seem like the tools of science.

What about the language? One of the main publically accessible sources of information is the On the Same Page website, in particular an FAQ section for students. It starts with the questions: What new things are going on in the scientific community that make this a good time for an educational effort focused on personalized medicine? and Why did Berkeley decide to tackle the topic of Personalized Medicine? These are answered with appeals to educational discourse – to academic strengths, student opportunities, and the stature of Berkeley as an educational center. The agent or actor in the answers to these questions is the university as an educational institutional: “This type of broad, scholarly discussion of an important societal issue is what makes Berkeley special. From a learning perspective, our goal is to deliver a program that will enrich our students’ education and help contribute to an informed California citizenry.”

Beside these educational questions, however, are questions that are part of the usual language and processes of science: Will students be asked to provide “informed consent” for this test of their DNA? What about students who are minors? How can you assure the confidentiality and privacy of a student’s genetic information? What will happen to the data from this experiment? Has this project been approved by Berkeley’s Human Subjects Institutional Review Board? These questions are the questions that appear in human subjects information letters. They make this sound like this is science. The answers to these questions take a different perspective to the ones above. The technical terms are not educational ones but scientific ones. The actor in these responses is neither the educational institution nor the student as an educational participant but the student as a research object: “All students whether they are minors or not will be asked to provide informed consent. They will read and sign a detailed form describing exactly what will be done with their DNA sample, how the information will be used and secured for confidentiality, how this information might benefit them, and what the alternatives are to submitting a sample.”

Anyone who has done human subjects research will recognize this language is almost word for word from typical guidelines for informed consent documents. My consent forms usually don’t deal with DNA samples (usually something much less exotic, such as student writing or oral contributions during class) but the intent is the same. This language sets out the individuals under consideration as the objects of scientific research.

The overall effect is one of a mixed metaphor – is this research or is it teaching? Are the students actually acting in the role of students or are they the objects of research? What standards should we be using to judge if this is an appropriate action. The materials posted by UC Berkeley suggest that they believe this should be judged as an educational project. But the reaction of bioethicists and advocacy groups (such as the Council for Responsible Genetics) suggests that it be judged by research standards.

Why does it matter? Because the ethical considerations are different. As I said above, I don’t usually deal with any materials that would be considered very controversial. I research the way people (including students) write, read, speak and listen in situations related to science. When dealing with students, many of the activities that I use for research could also be used for educational purposes. For example, in a project this year I distributed different versions of scientific reading materials. I asked students to read these in pairs. I tape recorded their conversations and collected their written responses to the text. As a classroom teacher, these are strategies that I have used for educational purposes. Tape recording students allows me to listen to the struggles they might have had while reading a text. Collecting their written responses allows me to assess their understanding. Parents would not object to their child’s teacher using these tools for these purposes. When I visit a classroom as a researcher though, I am judged differently. Parents often do not consent to me collecting their children’s writing. They object, especially frequently, to my requests to videotape or photograph their children. This is because they rightfully understand educational research as a different activity from education. They use different judgments and expect different standards.

From the sequence of events, it sounds as if Berkeley admin started this project with their own perspective that this was clearly educational without adequate consideration that, from an outside position, it would be judged from a research perspective. I don’t want to suggest that this whole thing is a simple miscommunication because there are serious ethical implications related to asking for DNA samples. As people try to figure out how an educational idea ended up in the state legislature, though, I just wanted to add my perspective that some of the controversy might come from that shiver factor – something just doesn’t feel right. One aspect of that feel might be that this challenges the boundaries of our understanding of the activities of science and science education. The language and the tools and the objectives are mixed, leading to confusion about exactly what standards this should be judged against. As tools that have traditionally been associated with laboratory science become more accessible (as genetic testing is becoming) this boundary is likely to be challenged more and more. Those making the decisions to use these tools for educational, rather than research, purposes need to understand that challenging peoples conceptions of the boundaries between science and science education can and will lead to conflict and that conflict should be addressed head on and from the beginning.

Immanuel Kant Song (video)

Science Saturday: Doctors’ Obligations – ethics by SciBlings

Listen to my SciBlings Janet and Pal,MD discuss scientific and medical ethics:

Participate in an experiment – how do you compare to philosophers on solving moral dilemmas?

Eric Schwitzgebel, Associate Professor in the Department of Philosophy at the University of California, Riverside, and Fiery Cushman, a psychology post-doc at Harvard, are conducting an online experiment which involves comparing philosophers’ and non-philosophers’ responses to questions about moral dilemmas.
They got plenty of philosophers to do the experiments, but they need more non-philosophers for the comparison group. Their “Moral Sense Test” asks respondents for their takes on various moral dilemmas. They say that people who have taken other versions of this test have found it interesting to ponder the moral dilemmas they ask about. The test should take about 15-20 minutes and can be found at
Please help them out by doing the experiment and telling others as well.

The Human & The Humanities

From The National Humanities Center:

The National Humanities Center will host the third and final conference on “The Human & The Humanities,” November 13 – 15, 2008, once again attracting scientists and humanities scholars to discuss how developments in science are challenging traditional notions of “the human.” Events will begin on the evening of November 13 with a lecture from noted neurologist and author Oliver Sacks at the William and Ida Friday Center in Chapel Hill, NC.
This event is free, but guests must register in advance to guarantee seating.
Other speakers and special guests confirmed for Friday and Saturday’s sessions at the National Humanities Center include:
Anthony Appiah, Princeton University
Patricia Churchland, University of California, San Diego
Michael Gazzaniga, University of California, Santa Barbara
Michael Gillespie, Duke University
Katherine Hayles, Duke University
David Krakauer, Santa Fe Institute
Jesse Prinz, University of North Carolina, Chapel Hill
Peter Railton, University of Michigan
Robert Sapolsky, Stanford University
Raymond Tallis, University of Manchester
Holden Thorp, University of North Carolina, Chapel Hill
Mark Turner, Case Western Reserve University
The entire conference is open to the public. A registration fee of $30 provides admission to all sessions along with meals during Friday and Saturday’s events.
To register for either the Oliver Sacks lecture or the ASC conference, please click here or visit to learn more about the ASC initiative.

Systems Biology – Obligatory Readings of the Day

Alex, Dan and John Wilkins have wise things to say about metaphors in biology, Big Biology and a recent article by Sir Paul Nurse.

Some light weekend reading for you – philosophy of biology :-)

John Wilkins is in Arizona attending a Philosophy of Biology conference (another one of those “I wish I could be there” things) and liveblogging the whole thing:
When philosophers really embarrass themselves
Liveblogging the conference: Mishler
Liveblogging the conference: Piotrowski
Liveblogging the conference: Jim Griesemer
Liveblogging the conference: Bill Wimsatt
Liveblogging the conference: Stephen Peck
Liveblogging the conference: Jay Odenbaugh
Liveblogging the conference: Julia Clarke and Todd Grantham
Liveblogging the conference: Jon Seger
Liveblogging the conference: Roberta Millstein
Postblogging the conference
Lots of interesting stuff on ecology, populations, barcoding…

The Hopeless Monster? Not so fast!

Olivia Judson wrote a blog post on her NYTimes blog that has many people rattled. Why? Because she used the term “Hopeful Monster” and this term makes many biologists go berserk, foaming at the mouth. And they will not, with their eye-sight fogged by rage, notice her disclaimer:

Note, however, that few modern biologists use the term. Instead, most people speak of large morphological changes due to mutations acting on single genes that influence embryonic development.

So, was Olivia Judson right or wrong in her article? Both. Essentially she is correct, but she picked some bad examples, overgeneralized a bit, over-reached a little and she used the dreaded term that was bound to shut down all rational processes occurring in some biologists’ brains. Remember that she wrote to general audience. If she took time and space to explain all the nuances and details she would have lost her audience somewhere in the middle of the second paragraph. I think that her post explains the topic just fine for the intended audience, pointing out that not all evolutionary changes take millions of years of imperceptible change – some do, indeed, happen relatively abruptly (yet it can be explained completely mechanistically, not giving Cdesign Proponentsists any hope). Not every day, but they do.
So, who jumps first into the fray with an angry rebuttal – one of the Usual Suspects: Jerry Coyne in a guest-post on The Loom:

Unfortunately, her piece is inaccurate and irresponsible, especially for a journalist with a strong science background (Judson has a doctorate from Oxford). I’ve admired Judson’s columns and her whimsical and informative book Dr. Tatiana’s Sex Advice to All Creation. But this latest posting is simply silly. As an evolutionary biologist, I’m used to seeing our field twisted out of shape to satisfy the demands of journalists who love sensational new findings–especially if they go against long-held Darwinian beliefs like the primacy of gradual, stepwise evolution. But I’m not used to seeing one of my own colleagues whip up excitement about evolutionary biology by distorting its findings.

Unfortunately, in bashing Judson along with making legitimate points (how many people will ignore this caveat in their responses?), Coyne ends up being more wrong than she is. And his intended audience is, arguably, better scientifically educated than hers – it’s the readers, not NYTimes. While bashing her head into a rock, Jerry makes visible his emotional enmity towards everybody who has a bigger picture of evolution than he has and has at their disposal both a methodological and a conceptual toolkit that Jerry lacks.
Before you jump on me, read the historical reviews of the concept of the Hopeful Monster by Brian and John. Then, read Greg and Razib who are far too lenient on Coyne but add good points of their own. Finally, read PZ Myers and especially Larry Moran for a clear explanation of the entire set of issues – the history, sources of current emotional disputes, and the current science. Reading all of these is essential to understanding the claims in this post as I do not have space/time to repeat all of their claims at length – so click on the links and read first before commenting.
In a back-and-forth with a commenter, Coyne defends himself that he is talking about the changes in genes, not evolution. This just shows his bias – he truly believes that evolution – all of it – can be explained entirely by genetics, particularly population genetics. His preferred definition of evolution is probably the genocentric nonsense like “evolution is a change of gene frequencies in a population over time”. I prefer to think of it as “evolution is change in development due to ecology” (a softening of Van Valen’s overly-strong definition “evolution is control of development by ecology”). Population genetics is based on the Hardy-Weinberg equilibrium – pretty much all of it is a build-on and embellishment of it. Population geneticists tend to forget, once they get into complex derivations of HW, that HW has about a dozen completely unrealistic assumptions underlying it. Now, in a case-to-case basis, some of those assumptions can be safely ignored, some can be mathematically taken care of, but some are outside of the scope of mathematics (or at least the kind of math that can be integrated into the development of HW). Those are ignored or dismissed and, if this is pointed out by those working on evolution from a Bigger Picture perspective, met with anger.
When Goldshmidt’s book The Material Basis of Evolution was reissued, Stephen Jay Gould wrote a lengthy Introduction. About a dozen years ago I checked the book out of the library and skimmed the book itself. I read Gould’s intro very carefully (I wonder if it is available somewhere online for free? Update: Gould’s introduction is available online here, hat-tip to Michael Barton.). It is also worthwhile to read Gould’s 1980 essay The Return of Hopeful Monsters keeping in mind that evo-devo was barely beginning at the time (yes, it is 28 years old, so do not judge it by current knowledge – put a historian’s cap on when reading it).
In his Big Book, Gould wrote:

“By proposing a comprehensive formalist theory in the heyday of developing Darwinian orthodoxy, Richard Goldschmidt became the whipping boy of the Modern Synthesis–and for entirely understandable reasons. Goldschmidt showed his grasp, and his keen ability to utilize, microevolutionary theory by supporting this approach and philosophy in his work on variation and intraspecific evolution within the gypsy moth, Lymantria dispar. But he then expressed his apostasy by advocating discontinuity of causality, and proposing a largely nonselectionist and formalist account for macroevolution from the origin of species to higher levels of phyletic pattern. Goldschmidt integrated both themes of saltation (in his concept of “systemic mutation” based on his increasingly lonely, and ultimately indefensible, battle to deny the corpuscular gene) and channeling (in his more famous, if ridiculed, idea of “hopeful monsters,” or macromutants channeled along viable lines set by internal pathways of ontogeny, sexual differences, etc.). The developmental theme of the “hopeful monster” (despite its inappropriate name, virtually guaranteed to inspire ridicule and opposition), based on the important concept of “rate genes,” came first in Goldschmidt’s thought, and always occupied more of his attention and research. Unfortunately, he bound this interesting challenge from development, a partially valid concept that could have been incorporated into a Darwinian framework as an auxiliary hypothesis (and now has been accepted, to a large extent, if under different names), to his truly oppositional and ultimately incorrect theory of systemic mutation, therefore winning anathema for his entire system. Goldschmidt may have acted as the architect of his own undoing, but much of his work should evoke sympathetic attention today.”

So, Coyne’s Gould-bashing, as Larry Moran demonstrated, is just petty and baseless sniping by one scientist of limited scope at another who actually “got it”.
I thought the discussion so far has been far too tame. So, here is the red meat! I want to see a real fight – a blogospheric war that brings in some serious traffic, OK?

Cool new Open Access Journal

From Sage Ross, via John Lynch come exciting news about a new Open Access Journal – Spontaneous Generations: A Journal for the History and Philosophy of Science

Spontaneous Generations is a new online academic journal published by graduate students at the Institute for the History and Philosophy of Science and Technology, University of Toronto. The journal aims to establish a platform for interdisciplinary discussion and debate about issues that concern the community of scholars in HPS and related fields.
Apart from selecting peer reviewed articles, the journal encourages a direct dialogue among academics by means of short editorials and focused discussion papers which highlight central questions, new developments, and controversial matters affecting HPS.

Check out the first issue – there is some very cool stuff in there.

Animal Cognition

Thanks to John Wilkins, I want to point you to an excellent review on the current state of research (both scientific and philosophical) in Animal Cognition.

Theory and Practice

First: the difference between theory and practice.
Second: the theory.
Third: still to come, I hope, a YouTube video of Steinn demonstrating the practice of parallel parking.

Has the word “gene” outlived its usefulness?

Blogging on Peer-Reviewed Research

When Wilhelm Johannsen coined the word “gene” back in 1909 (hmmm, less than two years until the Centennial), the word was quite unambiguous – it meant “a unit of heredity”. Its material basis, while widely speculated on, was immaterial for its usefulness as a concept. It could have been tiny little Martians inside the cells, it would have been OK, as they could have been plugged into the growing body of mathematics describing the changes and properties of genes in populations. In other words, gene referred to a concept that can be mathematically and experimentally studied without a reference to any molecules or intracellular processes.
Fast-forward half a century to the discovery of DNA and subsequent discoveries of the genetic code, transcription, translation, various types of gene regulation, etc. Everyone was happy – finally, we had a material gene. We had a molecule of inheritance that we could study. And an army of thousands started studying it, announcing breakthroughs at a breath-taking pace.
The confusion about the use of the term ‘gene’, as everyone used it differently, grew over the years. The use of terminology from information theory (e.g., program, transcription, translation, algorithm) affected the way researchers thought and designed experiments, limiting for a long time all discourse on inheritance to just DNA and worse, just to the DNA sequence.
But research went on, hit the walls, and smart people found the ways around the conundrum. What the research uncovered undermined the “gene” as a unit of inheritance, and for that matter undermined DNA as the molecule of inheritance. What we have learned is that:
– there is a difference between what an organism gets from parents (a static concept of the gene) and what it does with it to properly develop, function and behave in a species-specific way (a dynamic concept of the gene)
– the DNA sequence is just one of many properties of DNA that is important for proper development, function and behavior of an organism – there are other properties of DNA, as well as other non-DNA factors that are equally important.
– a sequence of nucleotides that gets transcribed is a very poor definition of a gene, as so much happens between transcription and the generation of the final protein shape, not to mention the complexity of the question how a single protein contributes to the appearance of a phenotypic trait.
– DNA is not the only “thing” that an organism gets from the parents. There is also a DNA methylation pattern, the transcription/translation machinery of the egg cell, various molecules (RNA, proteins, steroid hormones, etc.) present in the egg cell or introduced by the sperm cell, the environment inside the egg or womb, and the external environment into which the parents deposit the progeny (including the special case of teaching/learning).
I have thought about this quite a lot over the years (see, for instance this, this, this, this and this) and more I thought about it, more I liked the ideas that Developmental Systems Theory had to offer. Last ten years of published research changed the way we think about this and changed my mind in many ways. In a way, I was right all along – it’s not just DNA that confers heredity (static concept of the gene). In other cases, I was wrong: it turned out that it is, in fact, DNA, just not its sequence, that does this or that job in running the organism (the dynamic concept of the gene).
Two of the books I have read over the years that tackled the problem in a very good way (though sometimes not going far enough for my own tastes) are Refiguring Life and The Century of the Gene by Evelyn Fox Keller, one of the most prominent thinkers about the problem right now.
Thus, I got really excited when I heard that Chris Surridge, editor of PLoS ONE, after mulling over it for a long time (philosophy of science is not supposed to be one of the topics ONE publishes papers on, at least officially and at least until now), decided to go with the reviewers’ recommendations and publish a paper by Evelyn Fox Keller and David Harel – Beyond the Gene – in which the concept of the gene is discussed. What the paper does, on top of coming up with concepts that clearly differentiate between the static and the dynamic meanings and incorporate the current understanding of the complexity of both, is propose new names for those concepts. Read it carefully – it is quite thought-provoking.
Proposing new terminology is easy. Having it accepted and used by others is far more difficult. Especially when the terms are picked very cleverly to pick up on particular mental associations, while at the same time being (probably intentionally) catchy and funny (if you read them out loud they sound like deans, beans and janitors). The straight-laced researchers will probably balk at the new words. The folks that give funny names to Drosophila genes (e.g., Sonic hedgehog or fruity…er, fruitless) will probably grok why these new proposed terms are potentially useful.
Just like their conception of gene in everyday work differs, I expect that the response to this article’s proposal will differ between a biochemist, a bioinformatics scientist, a biological anthropologist, a medical researcher and a developmental biologist, between someone who works on microbial genomes, or mammalian genetics, or compares all genomes or looks at the way viral and mammalian genomes interract, or someone who looks at evolution of genes, or population genetics, history of biology or philosophy of biology. I hope they and others chime in.

On Being Human

Three good talks at Duke this Fall:

This year’s series explores how advances in neuroscience, genomics, robotics, and artificial intelligence are not only changing our conception of what it is to be human but also creating possibilities for changing ‘human nature’ in fundamental ways.

Monday, October 29, 2007 – 5:00 pm
Love Auditorium, Levine Science Research Center
How are we to think about Human Nature?
Simon Blackburn, Professor of Philosophy
University of Cambridge
Thursday, November 8, 2007 – 4:00 pm
Biological Sciences Building, Room 111
Our Inner Ape: A Leading Primatologist Explains Why we Are Who We Are
Frans B.M. de Waal
C.H. Candler, Professor of Psychology, Emory University Director, Living Links Center, Yerkes National Center
Tuesday, November 13, 2007 – 5:00 pm
Love Auditorium, Levine Science Research Center
Human Nature: Bad Biology and Bad Social Theory
Richard Lewontin, Professor of Biology and Zoology
Harvard University

There is no Soul. Deal with it.

Galilei kicked us out of the Center of the Universe.
Darwin kicked us off the Pinnacle of Creation
Freud kicked the Soul out of our Brains.
Few remain adherents of Geocentrism.
The opponents of evolution are legion and very vocal (in this country, and a couple of Middle Eastern ones), but they have been defeated so soundly so many times, they had to concede more and more ground, and though they are getting sneakier with time, their efforts are becoming more and more laughable and pitiful.
So, the last Big Fight will be about the Soul. The next area of science to experience a big frontal attack will be Neuroscience.
There is no Soul. Your mind is the subjective experience of what the molecules in your brain cells are doing. Period. But for many, that is the last straw. And the attack will, unlike Creationism, be coming from all sides of the political spectrum, as there are as many adherents of Spirituality crap on the Left as there are believers in the Soul on the Right. They just cannot bear the idea that there isn’t “something more to it” than “just materialism”!
Witness the new book “Spritiual Brain” which is so bad that it cannot even be fisked argument by argument as no arguments are actually presented (at least Creationists have their usual list of idiotic statements that can be effectively demonstrated to be wrong). Shelley Batts and PZ Myers tried hard, but there is just no ‘there’ there.
And even serious neurofolks, like Alvaro and colleagues who are organizing a meeting in Aspen on some of the coolest aspects of neuroplasticity – a hot area of neuroscience that studies how events in the internal and external environment modify the functioning of the brain, which affects the subjective experience, something that is potentially useful in treating people with mental or emotional problems, get slammed for being too materialistic.
If it is non-materialistic, then, by definition, it does not exist. Not just that it is not amenable to scientific study. It.Does.Not.Exist.

Ethics Code for Scientists?

BBC reports that scientists working in the UK government have adopted a Scientific Ethics Code, written by Professor Sir David King. Here is the Code:

Act with skill and care, keep skills up to date
Prevent corrupt practice and declare conflicts of interest
Respect and acknowledge the work of other scientists
Ensure that research is justified and lawful
Minimise impacts on people, animals and the environment
Discuss issues science raises for society
Do not mislead; present evidence honestly

Several bloggers have responded to this. Here is Janet’s take:

They seem like quite sensible principles — so sensible, in fact, that you might ask why they need to be formalized in a code of ethics. Don’t scientists already know that they should be honest, be fair to their fellow scientists, avoid conflicts of interest, keep up with the literature in their field, and all that good stuff?
Surely they do, but we’ve noted before that knowing what you ought to do and actually doing it are two different things. The question then becomes, how exactly does having a code of ethics help?

Oldcola has several suggestions to edit or add to the Code – I like them all but of course I especially like this one:

In general, I would like to make it mandatory to spend a week per year discussing issues science raises for society for every single scientist. And maybe mandatory to read and rate papers on PLoS ONE. Now, come on, I’m not joking. And yes, I do started doing so myself, with a minimal objective of 3/week.
And maybe the scientists should be trained to blog, also.

Perhaps they will discuss the Code at the ESF-ORI First World Conference on

What do you think?

A kick-ass Conference: Autonomy, Singularity, Creativity

Unfortunately, due to the Murphy’s Law of conference dates, I will have to miss this fantastic meeting, because I will at the time be at another fantastic meeting, but if you can come, please do – registration will be open online in a few days.

Autonomy, Singularity, Creativity

The conference theme is about bringing scientists and humanities scholars to talk about ways that science is changing human life.

November 8th, 9th, and 10th, the National Humanities Center will host the second ASC conference.

And the program features a Who’s Who list:

Thursday, November 8th
Frans de Waal
Martha Nussbaum
Friday, November 9th
Dan Batson
Margaret Boden
Joseph Carroll
Frans de Waal
Evelyn Fox Keller
David Krakauer
William Lycan
Martha Nussbaum
Steven Pinker
Paul Rabinow
Margery Safir
Robert Sapolsky
Saturday, November 10th
Terrence Deacon
Daniel Dennett
Alex Rosenberg
Mark Turner

Of those, I have seen Sapolsky, Fox Keller and Deacon speak before, and I know Alex Rosenberg, and for each one of them alone, it is worth showing up!

Bravo, Bravissimo!

John Wilkins just published a paper (…”a review of the centenary festschrift for Mayr…”) and got a book accepted for publication (the book grew out of series of excellent blog posts about species definitions – who says that blogging is bad for your health?)

Obligatory Reading of the Day

All you need to know about Philosophy of Science (but were too afraid to ask) you can read in John Wilkins’ triptych:
Philosophy is to science, as ornithologists are to birds: 1. Introduction
Philosophy is to science, as ornithologists are to birds: 2. Two topics of philosophy of science
Philosophy is to science, as ornithologists are to birds: 3. Science is a Dynamic Process

And now the scientists will do whatever they damned please (start shouting, most likely)

Google was really no help in finding the exact quote, but everyone in the animal behavior field has heard some version of the Harvard Rule of Animal Behaviour:

“You can have the most beautifully designed experiment with the most carefully controlled variables, and the animal will do what it damn well pleases.”

Anyone here knows who actually said that and what were the exact words?
Anyway, one way to re-word the “whatever they damned please” is to call it “free will”. Björn Brembs says so but apparently not everyone agrees. The discussion in the media and on blogs is just about to start because Bjorn’s paper about spontaneous behavior in Drosophila just came out today (after quite a long wait). You can read the summary by Bjorn, but I also suggest you try to read the actual paper. If seemingly spontaneous behavior can be described by mathematical formulas, even if it is chaotic dynamics, is it then, really, quite deterministic? If so (or if not) can it be called “free will”? If not, is there a better term for it?
Keep an eye on the discussion on Bjorn’s blog as well as the discussion attached to the PLoS-ONE paper itself and, if you have read and understood the paper, please contribute to the discussion. This is bound to get very interesting over the next several days.

Darwinian Method

Darwinian MethodOK, this is really ancient. It started as my written prelims (various answers to various questions by different committeee members) back in November 1999, and even included some graphs I drew. Then I put some of that stuff together (mix and match, copy and paste) and posted (sans graphs) as a four-part post here, here, here and here on December 2004. Then I re-posted it in January 2005 (here, here, here and here). Finally, I reposted two of the four parts here on this blog (Part 2 and Part 3) in July 2006.
This all means that all this is quite out of date. The world has moved on, more research has been done, and I have learned a lot since then. But still, today being Darwin Day, this may be a good opportunity to move the Part I here as well and you decide if it is out of date or not….
Part 2 will be reposted here again in a just a few minutes…..

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If only people read the Bible the way they read their contracts…

If only people read the Bible the way they read their contracts...So, why do Creationists and other quacks try so hard to sound all ‘scienc-y’? (June 15, 2005)

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Jumping on the “omics” Bandwagon

Sandra Porter is having fun collecting all the new-fangled biological subdisciplines that end with “-omics”. The final product of each such project also has a name, ending with “-ome”.
You have all heard of the Genome (complete sequence of all the DNA of an organism) and the Genomics (the effort to obtain such a sequence), but there are many more, just look at this exhaustive list! In my written prelims back in 1999, I suggested that sooner or later there will be an organismome…until someone whispers that the term “physiology” already exists.
There are a couple of things that strike me when looking at such a long list of omes and omics’.
First, the fact it does not end with “-ology” suggests that the endeavor is not a study in order to understand, but an endeavor to complete a collection and tabulate all the items. I am not saying this is not science – not everything in science is “hypothesis testing” as your Intro textbooks erroneously tell you. It is just a different kind of scientific method. The idea is that collecting and tabulating all the elements in the system will allow for hypothesis-testing later in the future. It is providing important tools for future understanding. In other words, a system needs to be described before one can start trying to explain it.
Second, with a couple of exceptions, all the omes are collections of molecules, be it DNA, RNA, proteins, or the particular configurations of those molecules, or patterns of gene expression, etc. Behaviorome is one of such exceptions. Biome is another, though its inclusion on the list is probably incidental – its “ome” ending, when it was initially introduced back in 1916, had a different philosophical connotation in the spirit of the science of the times. Economics is on the list only because the person compiling the list had a sense of humor, of course (or is it?!).
In any case, each -ome is a collection of something physical. Perhaps a ‘skeletome’ could be the name for the collection of all the bones in a body…oh, wait! It is also a collection of parts that make up the system. This last sentence leads to the question posed by RPM: is a person doing some kind of “-omics” inevitably a reductionist?
Well, what is a reductionist? Many have written about this problem and giving it different names, usually not in a binary form but a triad, e.g., philosophical (or “vulgar”) reductionism, methodological reductionism and holism. Of all the treatments of scientific methodologies, I most like Robert Brandon’s analysis, in the last chapter of his 1995 book Concepts and Methods in Evolutionary Biology. It is not available online, but here is an article (PDF) that discusses it pretty fairly. I have also written about this issue before. Briefly:
– a holist refuses to “dissect” the system, choosing to study it as a whole only, arguing that breaking it apart is misleading and does not explain how the whole works.
– a philosophical reductionist supposes that phenomena observed at one hierarchical level can be explained by the identification of parts at the next lower level (you can see how easily this can slide into genetic determinism, as it denies or ignores emergent properties of the system).
– a methodological reductionist understands that “upward causation” is erroneous and pays more attention to the “downward causation”. A complex problem (not neccessarily a complex system) is broken down into manageable sub-problems (not neccessarily parts) that can be studied easily and can provide clear-cut data. Emphasis is more on the nature of interactions between elements of the system than the identity of the elements. However, knowing the identity of the elements allows one to recognize, tag and follow the elements as they interact with each other, thus revealing the rules of such interactions. Thus, having a Genome handy is a great tool for the study of interactions between molecules inside the cells, but the Genome in itself is un-informative.
So, two genomics researchers working side by side may differ – one being a philosophical, the other a methodological reductionist – depending on the understanding of the work they are doing: is sequencing a genome an end in itself, supposed to miraculously reveal the Mysteries Of Life (The Holy Grail, the Blueprint of Life), or is it building a tool for some exciting research to be done in the future.
Third thought that struck me as I glanced over the long list of omes and omics is that each ome, i.e., each collection of the parts, can be obtained by killing or freezing an organism (or organ, or cell, or ecosystem) and using various techniques to count and identify chemicals (or other parts) found in it. Even embryogenomics is concerned with gene expression at a particular time in development, primarily in order to “catch” the elusive genes – those that are not expressed in the adult.
The only ‘ome’ that cannot be studied this way but HAS to be studied in a living, breathing organism over time is Chronome:

Chronome n. The full complex of rhythms and temporal trends in an organism. The chronome consists of a multi-frequency spectrum of rhythms, trends, and residual structures, including intermodulations within and among physiological variables as well as changes with maturation and aging. // adj. = chronomic.

You can do a Google or Google Scholar search to see how much it is actually used in the (human/medical) chronobiological literature and in what context. I was surprised myself!

Google =
chronome = about 380 July 11, 2002, about 920 Aug. 10, 2005, about 18,400 Oct. 25, 2006
chronomics = about 42 July 11, 2002, about 423 Aug. 10, 2005, about 737 Oct. 25, 2006

Here is a bit longer description:

chronome: Derived from chronos (time), nomos (rule, law) and in the case of biological chronomes, chromosome, describes features in time, just as cells characterize the spatial organization of life. The chronome complements the genome (derived from gene and chromosome). The chronome consists of 1) a partly genetic, partly developmental, partly environmentally influenced or synchronized spectrum of rhythms; 2) stochastic or deterministic chaos; 3) trends with growth, development, maturation and aging in health and/ or trends with an elevation of disease risk, illness and treatment in disease; and 4) unresolved variability. The chronome is genetically coded: it is environmentally synchronized by cycles of the socio- ecologic habitat niche and it is influenced by the dynamics of the interplanetary magnetic field. The chronome constituents, the chrones, algorithmically formulated endpoints, are inferentially statistically validated and resolved by the computer. Chronomes and their chrones 1) quantify normalcy, allowing an individualized positive health quantification; 2) assess, by their alterations, the earliest abnormality, including the quantification of an elevated risk of developing one (or several) disease(s), chronorisk, by the alteration of one or several chrones; and 3) provide, by the study of underlying mechanisms, a rational basis in the search for measures aimed at the prevention of any deterioration in properly timed, mutually beneficial environmental- organismic interactions. [Franz Halberg et. al “The Story Behind: Chronome/ chrone” Neuroendocrinology Letters 20: 101 1999]
Gubin D, Halberg F. et. al, “The human blood pressure chronome: a biological gauge of aging” In Vivo 11 (6): 485- 494, Nov- Dec. 1997
Google = about 494 May 8 2003; about 16,800 Nov 10, 2006
chronomics: Technology allows the monitoring of ever denser and longer serial biological and physical environmental data. This in turn allows the recognition of time structures, chronomes, including, with an ever broader spectrum of rhythms, also deterministic and other chaos and trends. Chronomics thus resolves the otherwise impenetrable “normal range” of physiological variation and leads to new, dynamic maps of normalcy and health in all fields of human endeavor, including, with health care, physics, chemistry, biology, and even sociology and economics. [F. Halberg et. al. “Essays on chronomics spawned by transdisciplinary chronobiology. Witness in time: Earl Elmer Bakken” Neuroendocrinology Letters 22 (5): 359- 384 Oct. 2001]
Google = about 184 May 8, 2003, about 412 Aug. 17, 2005; about 768 Nov 10, 2006
Narrower terms: bacterial chronomics, cardio-chronomics

The term ‘chronome’ was coined by Franz Halberg, the same guy who coined the word “circadian”. This paper is freely available so you can see what it is all about. Frankly, the idea of collecting all temporal/rhythmic phenomena in the human body in health and disease sounds like a good idea for medical purposes. On the other hand, making such collections for other organisms does not make too much sense – we want to know the hows and whys of biological timing and using a couple of well-defined rhythms as markers is sufficient for such an endeavor as well as much more economical. Also, if you pore over that paper, you will see that Halberg is, in some places, pushing too hard and too far. To be perfectly honest, I do not believe all of the data presented in that paper and do not see the utility of much of his philosophizing either.
For an evolutionary/ecological/comparative chronobiologist, chronomics has little or no utility. On the other hand, I’d love to have a genome, transcriptome and proteome available for the critters I study – those would be super-useful tools.

Atlantis, lost and found, again

John bemoans the state of science journalism, with some added history of the Atlantis hypothesis.

Nice essay by Simon A. Levin in the latest PLoS – Biology

Fundamental Questions in Biology. Here is a quote from the end:

The questions that biologists from diverse subdisciplines are asking have commonalities that make clear the continued existence of fundamental challenges that unify biology and that should form the core of much research in the decades to come. Some of these questions are as follows: What features convey robustness to systems? How different should we expect the robustness of different systems to be, depending on whether selection is operating primarily on the whole system or on its parts? How does robustness trade off against adaptability? How does natural selection deal with environmental noise and the consequent uncertainty at diverse scales? When does synchrony emerge, and what are its implications for robustness? When and how does cooperative behavior emerge, and can we derive lessons from evolutionary history to foster cooperation in a global commons?

Now go and read it from the beginning.

Mananimals in the news again

Not just in the USA. Visceral queeziness coupled with religious sentiment coupled with scientific ignorance appears in other parts of the world as well, as in the UK

The Scottish Council on Human Bioethics, a professional group based in Edinburgh, has published a report on the ethical implications of the practice in the journal Human Reproduction and Genetic Ethics. The report is online at

The article lists some examples of research:

Later research has spawned human-animal creations, the report said. These usually die at the embryonic stage, but often survive if the mixtures involve only a few cells or genes transferred from one species to another.
The council cited the following examples:
* In 2003, scientists at Cambridge University, U.K. conducted experiments involving fusing the nucleus of a human cell into frog eggs. The stated aim was to produce rejuvenated master cells that could be grown into replacement tissues for treating disease. It was not clear whether fertilization took place, but some kind of development was initiated, the report said.
* In 2005, U.K. scientists transplanted a human chromosome into mouse embryos. The newly born mice carried copies of the chromosome and were able to pass it on to their own young.
* The company Advanced Cell Technologies was reported, in 1999, to have created the first human embryo clone by inserting a human cell nucleus into a cow s egg stripped of chromosomes. The result was an embryo that developed and divided for 12 days before being destroyed.
* Panayiotis Zavos, the operator of a U.S. fertility laboratory, reported in 2003 that he had created around 200 cow-human hybrid embryos that lived for about two weeks and grew to several hundred cells in size, beyond the stage at which cells showed the first signs of developing into tissues and organs.
* In 2003, Hui Zhen Sheng of Shanghai Second Medical University, China, announced that rabbit-human embryos had been created by fusing human cells with rabbit eggs stripped of their chromosomes. The embryos developed to the approximately 100-cell stage that forms after about four days of development.

All of this sounds like useful basic science to me.

Such procedures mix human and animal biological elements to such an extent that it questions the very concept of being entirely human, the report said. This raises grave and complex ethical difficulties.

So? Learn to deal with it. It won’t apply for a passport any time soon.

Some ethicists worry that the experiments might force society to make confounding decisions on whether, say, a human-chimp mix would have human rights. Other concerns are that such a creature could suffer from being outcast as a monster, from having a chimp as its biological father or mother, or from unusual health problems.

That was a quick leap from clumps of cells with mixed genes or cells to walking, talking human-chimp chimeras which, as far as I can tell, no scientists are considering of ever making, except mad scientists in cartoons.

Some inter-species mixtures are powerful research tools, the report said.
This became clear about a decade ago in a series of dramatic experiments in which small sections of brains from developing quails were taken and transplanted into the developing brains of chickens. The resulting chickens exhibited vocal trills and head bobs unique to quails, proving that the transplanted parts of the brain contained the neural circuitry for quail calls. It also offered astonishing proof that complex behaviours could be transferred across species.

Those were realy cool experiments by Evan Balaban, but have nothing to do with mananimals. Those are not genetic chimaeras. Those are surgically transplanted tissues, like you and I getting a pig heart if needed.

While there is revulsion in some quarters that such creations appear to blur the distinction between animals and humans, it could be argued that they are less human than, and therefore pose fewer ethical problems for research than fully human embryos, the committee wrote.

What? What anthropocentric essentialism! And of course, the image accompanying the article is supposed to make you all squeamish:
Why didn’t they put this picture instead?

Teaching Biology Lab – Week 2

Teaching Biology Lab - Week 2This is by far the most popular of the four installments in this series because it contains the nifty puzzle exercise. Click on the spider-web-clock icon to see the comments on the original post.
Just like last week, I have scheduled this post to appear at the time when I am actually teaching this very lab again. If there are any notable difference, I’ll let you know in the afternoon.

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If you are bored, read this. Know thyself!