Showing posts with label philosophy of science. Show all posts
Showing posts with label philosophy of science. Show all posts

How many species concepts are there?

Thursday, October 21, 2010 at 11:00 AM Bookmark and Share
Do you remember the definition of species from your high school or college biology class?  Me neither -- but worry not!  Even if you remembered it word for word, there's a good chance it's not the same definition your friends and co-workers learned and it's certainly not the only definition floating around out there.  So how many species concepts are there?

According to John S. Wilkins in his recent guest post over at Punctuated Equilibrium (also here on John's blog) there are either 26-27, 7, 2, 1 or 0.  The article is well worth the read as John gives a nice, brief overview of the many different definitions of a biological species, their similarities and differences, and the key concepts behind those definitions. 


If you don't mind my giving away the punchline, here's what it all boils down to:

Final score: 26-27, 7, 2, 1 or 0.

What to think? My solution is this:

There is one species concept (and it refers to real species).

There are two explanations of why real species are species (see my microbial paper, 2007): ecological adaptation and reproductive reach.

There are seven distinct definitions of "species", and 27 variations and mixtures.

And there are n+1 definitions of "species" in a room of n biologists.
For a more detailed treatment of the idea of biological species, see John's book 'Species: A History of the Idea'.

[Hat tip to John Hawks and GrrlScientist]

Philosophy of Science

Tuesday, August 17, 2010 at 11:01 PM Bookmark and Share
Massimo Pigliucci has a few videos up on his YouTube channel on the philosophy of science.  If you're unfamiliar with with the philosophy of science, you might enjoy them.

Part I

More on what Fodor and Piattelli-Palmarini Got Wrong

Friday, July 30, 2010 at 12:12 AM Bookmark and Share
Jerry Fodor and Massimo Piattelli-Palmarini have received quite a bit of criticism since the publication of their book What Darwin Got Wrong, which attempts to argue that evolution by natural selection is basically nonsense.  The consensus seems to be that Fodor and Piattelli-Palmarini don't understand modern evolutionary theory, and that they're plainly wrong. However, in case you think they might be onto something you should check out this July 2010 critique of their book, which also takes them to task for getting it wrong.  The review is written by Harvard philosopher Peter Godfrey-Smith. You should of course click over to the review and give it a good read, but I thought I'd comment here on a few highlights.

Peter begins by recalling a young Noam Chomsky's scathing book review of B. F. Skinner's 1957 book Verbal Behavior, which seems to have rightfully blown those ideas right off the map.  He suggests there is a parallel here, to what Fodor and Piattelli-Palmarini seem to have attempted with their book... except this time it's they who have it wrong.
... A young linguist, Noam Chomsky, published a review of Verbal Behaviour... It was perhaps the most devastating book review ever written.

Chomsky argued that Skinner’s theoretical vocabulary could be applied to human linguistic behaviour only in an empty, post hoc way. He also thought that Skinner’s behaviourism had a simple architectural flaw: it held that external factors – especially experiences of reinforcement – were of ‘overwhelming importance’ in the explanation of behaviour. Hardly any role was given to what Chomsky referred to simply as ‘the internal structure of the organism’. It is unusual to do serious damage to a scientific research programme with a set of general arguments – not by citing experimental or mathematical results, but by looking at the basic ideas and revealing a crack in the foundations. Though the impact of the review itself is sometimes exaggerated, this is the effect Chomsky had on the behaviourist study of humans.

Jerry Fodor now hopes to do something similar to Darwinism in biology. Fodor has been making sceptical remarks about Darwinian ideas for decades. Three years ago he wrote a direct attack on Darwinian evolutionary theory in the LRB, and he has now published What Darwin Got Wrong, along with Massimo Piattelli-Palmarini. Fodor and Piattelli-Palmarini believe that they can replicate Chomsky’s demolition job on Skinner because ‘Skinner’s account of learning and Darwin’s account of evolution are identical in all but name.’ As we shall see, ‘identical’ is quite a stretch, but there is a real analogy.
Peter then recounts the criticism others have made of Fodor and Piattelli-Palmarini, specifically the argument that natural selection needs to be an 'intensional process' that can distinguish between 'co-extensive' properties of organisms (translation: natural selection allows correlated traits to piggy back advantageous traits, and this somehow implies natural selection doesn't work...)  Now, while there's a more to the book than that (again, see the review for details) this argument sounds so blatantly wrong that I wonder if I'm even understanding it correctly!  I mean really?  Correlated neutral traits are the big showstopper for natural selection? Sadly, I don't think I'm wrong. This really appears to be part of their argument!  If that's true, then the book What Darwin Got Wrong should be given the more appropriate title, What Fodor and Piattelli-Palmarini Got Wrong.

Now, I'm not just making this interpretation up... and neither is Peter Godfrey-Smith.  Here's what F&P-P had to say in their response to an earlier criticism by Block and Kitcher (links below, emphasis mine):
For example, suppose random variation produces a trait that tends to make its bearers invisible to their predators. Then, all else equal, the predators gobble up the creatures that don’t have it, and the relative frequency of the trait in the population increases from generation to generation. To repeat, we haven’t the slightest doubt that this is the process that Darwin called natural selection and that Darwinists have always believed in some or other version. In fact, it sounds pretty good. It sounds like it ought to work.

But it doesn’t. A way to see that it doesn’t (not by any means the only way) is to consider confounded (linked) phenotypic traits, one but not the other of which is fitness-enhancing. Both traits are then correlated with fitness, so both should count as adaptations according to the formulation of natural selection given above. But only one of them is a cause of selection, so only one of them is an adaptation, and, though both are selected, only one is selected-for. Thus the free-rider problem. Prima facie, free riding is a counterexample to natural selection.
Massive sadness... They botched it.  Prima facie, Fodor and Piattelli-Palmarini are simply confused about modern evolutionary biology (which is forgivable) and publicly wielding some philosophical sledge hammers at it, creating some confusion in their wake (this fact is way less forgivable, in my opinion).

Peter I think sums it up nicely when he writes...
Fodor and Piattelli-Palmarini criticise the tendency to talk of selection as if it were an agent. They are right that this is often misleading, but they seem to be making a similar mistake when they treat it as something over and above the ordinary facts of life, death and reproduction.
After all, recalling how natural selection works in a population, there really isn't much more to it that "life, death and reproduction." Just combine (1) some variation that is (2) heritable with (3) those variants achieving differential reproductive success.  Let that process run for a few generations, and blammo - evolution happens. The distribution of variation in the population changes and the rest is (natural) history. Darwin nailed it, over a century worth of scientific progress has confirmed it, yet unfortunately it appears Fodor and Piattelli-Palmarini simply got it wrong.

But... perhaps one day they'll recognize their mistake, do the right thing, and admit they were wrong?  After all, they themselves say in their reply to Block and Kitcher (again, emphasis mine)...
Everybody makes mistakes. Even biologists do; even lots of biologists assembled together do; even great biologists like Darwin do...
Yes, gentlemen, so do very respectable cognitive scientists and philosophers, even those not unlike yourselves.

Related Links

  1. Misunderstanding Darwin: Darwin's Secular Critics Get It Wrong | Great critique by Block and Kitcher.
  2. "Misunderstanding Darwin" An Exchange. | Dialogue where Fodor and Piattelli-Palmarini Respond

Coyening a New Term: "New Creationism"

Sunday, April 18, 2010 at 1:46 PM Bookmark and Share
Recently, Jerry Coyne proposed a new term -- "New Creationism" -- to describe a set of commonly held natural and metaphysical beliefs: basically an acceptance of "Darwinian evolution" and simultaneous acceptance of certain beliefs about God being the creator of it all.  The term is reminiscent of Stephen Jay Gould's idea of Non-overlapping Magisteria (NOMA), although New Creationism is more specific than NOMA, having been "coyned" to...
...describe the body of thought that accepts Darwinian evolution but with the additional caveats that 1) it was all started by God, 2) had God-worshipping humans as its goal, and 3) that the evidence for all this is that life is complex, humans evolved, and the the “fine tuning” of physical constants of the universe testify to the great improbability of our being here—ergo God.
I'm not sure (yet) if I'll use the phrase, as I do like having such a nifty term to describe these or similar beliefs. Unfortunately, the part of me that likes terminology that is both broadly applicable and precise has some objections...
  1. It seems too narrow in it's list of religious beliefs, which others have already mentioned, and too particular to catch on without evolving another (related) meaning. 
  2. The root term "Creationism" brings to mind the kind of dogmatic science-denial found in young earth creationism, which is contrary to Jerry's new category of religious and scientific belief.
  3. It isn't all that "new" (which has also been a criticism of the term "New Atheism") and  
  4. just like "New Atheism" it will probably get used more as a derogatory term then as a useful characterization of human belief as plenty of "New Creationists" would probably consider it an insult to be labeled any kind of creationist.
If you're wondering why we need a new term when we've already got "intelligent design creationism" and we can make reference to Gould's NOMA, Jerry has at least a partial answer for you...
New Creationism differs from intelligent design because it rejects God’s constant intervention in the process of evolution in favor of a Big, One-Time Intervention, and because these ideas are espoused by real scientists like Kenneth Miller and Simon Conway Morris.
So what do you think? Like it? Hate it? Do we need it? Can we improve the definition? Will it catch on? Share your thoughts in the comments below.

Sam Harris on Morality, Science and Religion

Sunday, March 28, 2010 at 3:31 PM Bookmark and Share
Update: I've appended to this post some commentary from philosopher and (ex?)scientist Massimo Pigliucci on Harris' assertions about science and morality. Follow the link below for more from Pigliucci and a link to a response from Harris. 

It's uncommon to see overt criticisms of religion (at least Christianity) in the mainstream media, so I did a bit of a double-take when I saw this CNN video piece entitled "Philosopher: Why we should ditch religion."

That philosopher is Sam Harris and if you have a few minutes to spare, you should check out the CNN video and his recent TED talk on science and morality (both embedded below).


Here's the video of his recent TED talk, entitled "Sam Harris: Science can answer moral questions."


Update:

What Fodor and Piattelli-Palmarini Got Wrong

Saturday, February 27, 2010 at 12:39 PM Bookmark and Share
There's been a bit of a stir the past few weeks over a book that recently came out titled What Darwin Got Wrong (which I haven't read... and probably won't).  In short, the book is written by a philosopher and cognitive scientist with apparently no expertise in evolutionary biology.  From what others have written, the book appears to assert that the theory of evolution is deeply flawed because the concept of natural selection is philosophically bogus.  Not surprisingly, a lot of biologists (and philosophers) take issue with that conclusion, and some are calling them out on their errors.

If you haven't heard of the book and how much the intelligent design (creationism) crowd is loving it, I'd encourage you to read up on the fracas here and here.  After that, there's a nice critique I'd urge you to read through titled "Misunderstanding Darwin: Natural selection’s secular critics get it wrong" by Ned Block and Philip Kitcher.

 - - - - Updated (2 March)

I neglected to mention that you can read more from Fodor and Piattelli-Palmarini here at The New Scientist. I'm not sure they really understand the theory of evolution by natural selection, especially when I read things like...

... it is not self-evident why species that have a recent common ancestor - as opposed, say, to species that share an ecology - are generally phenotypically similar. Darwin's theory of natural selection is intended to answer this question. Darwinists often say that natural selection provides the mechanism of evolution by offering an account of the transmission of phenotypic traits from generation to generation which, if correct, explains the connection between phenotypic similarity and common ancestry.


Moreover, it is perfectly general: it applies to any species, independent of what its phenotype may happen to be. And it is remarkably simple. In effect, the mechanism of trait transmission it postulates consists of a random generator of genotypic variants that produce the corresponding random phenotypic variations, and an environmental filter that selects among the latter according to their relative fitness. And that's all. Remarkable if true.

- - - -

After providing a biological perspective of the book's core argument, Block and Kitcher get into the philosophical argument -- and why it's irrelevant.  This requires some background (which they provide) on key concepts: intensional and extensional properties of a statement or claim.

You should really read their explanation, but as I (mis?)understand it, the gist of what F&PP got wrong was in asserting that natural-selection-in-action can't distinguish between a trait with fitness advantages and a tightly linked/correlated neutral trait that's just along for the ride. Who survives and reproduces is the same no matter which trait is advantageous.  Therefore, they seem to claim, natural selection is inadequate to provide an explanation for observed patterns of the diversity of life. Block and Kitcher rephrase F&PP's main contention as follows:
Here, then, is the problem restated: the causal processes at work in evolution cannot distinguish between coextensive properties, but selection-for requires that they be distinguished.
This (in my mind) points out their confusion about how natural selection works.  It isn't some sort of external force acting on populations of organisms, as they seem to present it. Instead it's merely a consequence of heritable traits resulting in differential reproduction and survival of individuals.  The causal mechanisms, as we understand them, work whether or not additional neutral traits are carried along for the ride.

After describing the problem with F&PP's argument against natural selection (which apparently has been criticized before) Block and Kitcher end their critique quite nicely...
Fodor and Piattelli-Palmarini take the role of philosophy to consist in part in minding other people’s business. We agree with the spirit behind this self-conception. Philosophy can sometimes help other areas of inquiry. Yet those who wish to help their neighbors are well advised to spend a little time discovering just what it is that those neighbors do, and those who wish to illuminate should be sensitive to charges that they are kicking up dust and spreading confusion. What Darwin Got Wrong shows no detailed engagement with the practice of evolutionary biology, nor does it respond to the many criticisms that have been leveled against earlier versions of its central ideas. In this latter respect, the authors resemble the creationist debaters who assert that evolution is incompatible with the second law of thermodynamics, hear detailed refutations of their charge, and repeat their patter in the next forum.

We admire the work that both Jerry Fodor and Massimo Piattelli-Palmarini have produced over many decades. We regret that two such distinguished authors have decided to publish a book so cavalier in its treatment of a serious science, so full of apparently scholarly discussions that rest on mistakes and confusions—and so predictably ripe for making mischief.
So what do you think?  Do Kitcher and Block have it right?

The Symphony of Science

 at 7:00 AM Bookmark and Share
Recently, I came across a website called "The Symphony of Science" by way of their youtube page. It's a pretty interesting endeavor by producer John Boswell towards an honorable goal: to "deliver scientific knowledge and philosophy in musical form."

Their latest video, The Poetry of Reality (An Anthem for Science), features a nice mix of popular skeptics and scientists - some of whom you are sure to recognize.  Check it out!


So far, they've produced a few videos and audio tracks which are available on their website (and youtube). It's not exactly the sort of music I'd expect to hit the top of the pop charts, but it's a pretty catchy way to present some (hopefully) thought provoking ideas to a wider audience.

Feel free to browse the videos and songs then share your thoughts in the comments below.

Free Harvard course anyone? (or "Justice" on YouTube)

Sunday, September 27, 2009 at 6:18 PM Bookmark and Share
Ever since taking our only class on the topic in high school, philosophy has always been my most neglected of interests. During my teenage years, the internet was a relatively new and rapidly growing wealth of information. Even then it seemed to provide access to more ideas and data and history than one could digest in a single lifetime. I read a few random essays here and there, and recall finding  some of John Stuart Mill's works quite agreeable.  Of them all, I remember having relished reading through his essays on Liberty and Utilitarianism.

Busy with science and math classes as an undergraduate, I managed to squeezed in a class or two. Sadly, however I still lack much experience soaking my brain in the major philosophical works of the past and present, including those most applicable to my more scientific interests.

Once again, the internet provides an opportunity just too good to refuse! 

Over on Jerry Coyne's blog, he posted a link to the Harvard course Justice.   A fantastic opportunity to hear a top notch lecturer and learn about some really practical and interesting topics all for just one hour of your time each week. 

The lectures for each week are available free online via Harvard's YouTube page and I fully intend on devoting an hour each week for the next few months to watch them all.

If you'd like to follow along as well, you can get caught up with what's below (just two episodes as of September 27, 2009):

So what's the course about?? Lecturer Michael Sandel explains in the first video above, but here's the gist of it. In the course, the students will be reading the classic works by folks you've likely heard of (Lock, Kant, Mill, etc..).  The video we'll see looks like it will be a lot of debate and reflection back to the big ideas coming out of that reading.  In addition to those classics, they'll also
...take up contemporary political and legal controversies that raise philosophical questions. [The class] will debate equality and inequality, affirmative action, free speech versus hate speech, same sex marriage, military conscription - a range of practical questions. Why? Not just to enliven these abstract and distant books, but to make clear - to bring out - what's at stake in our every day lives including our political lives, for philosophy.
The first lecture begins with a couple hypotheticals - the first of which I had heard before and I clearly remember being quite frustrated with as I found myself caught justifying my hypothetical "moral actions" with logic and moral presuppositions that just didn't seem work as well as I had thought.

The examples basically work as follows [spoiler alert!].  You're faced with a life or death decision: your holding a steering wheel of an unstoppable trolly car facing one of two options: whether to take the tracks to the left and kill 5 people or take a right and kill 1 person.  The decision is easy - right. Right? Right... or is it. After all, we should clearly aim to prevent as much death as possible! Right?

Next, consider a similar but slightly different scenario.  There's a single rail with 5 people down the track (say, in a tunnel) each facing certain death by an approaching runaway, unmanned trolley car. You and one rather large stranger are on a bridge above the tracks when you notice the gravity of the situation.  You know for certain that (don't worry about how, just assume you do) that pushing the bulky stranger towards the edge, down onto the tracks ahead of the car, will derail it saving the lives of the 5 people that would otherwise certainly perish.  So now - fighting that urge to make excuses here - what do you do?  Still just as simple as 1 life versus 5 lives?? Do you push, or let the 5 workers die?  Seems like the same question, right, so why isn't the decision so easy this time?

In the first episode Sandel presents these and a couple other hypotheticals to highlight and compare two of many kinds of moral reasoning - that is, ways of basing our decisions on some moral foundation, some basis for establishing what is right or wrong, good or bad, etc. - that we each use to make decisions on a daily basis.  In this case, these are
  1. Consequentialist moral reasoning, which "Locates morality in the consequences of an act."
  2. Categorical moral reasoning which "Locates morality in certain duties and rights."
The classic question of whether we look to the "ends" or the "means" (or both? or something else?) in establishing the moral value of our potential decisions.

While I'm looking forward to the rest of the lectures (and hope some of you are too), I should mention Michael Sandel's warning to students about the risks of taking his course:
To read these books, in this way, as an exercise in self knowledge. To read them in this way can carry certain risks. Risks that are both personal and political. Risks that every student of political philosophy has known. These risks spring from the fact that philosophy teaches us - and unsettles us - by confronting us with what we already know.

There's an irony - the difficulty of this course consists in the fact that it teaches what you already know it. It works by taking what we know from familiar unquestioned settings and making it strange. That's how those examples worked. Those hypotheticals with which we began, with their mix of playfulness and sobriety. It's also how these philosophical books work. Philosophy estranges us from the familiar - not by supplying new information, but by inviting and provoking a new way of seeing.

But, and here's the risk, once the familiar turns strange it's never quite the same again. Self knowledge is like lost innocence - however unsettling you find it, it can never be un-thought or un-known.

What makes this enterprise difficult - but also riveting - is that moral and political philosophy is a story, and you don't know where the story will lead. But what you do know is that the story is about you.

Those are the personal risks. Now what of the political risks? One way to introduce a course like this would be to promise you that by reading these books and by debating these issues you will become a better more responsible citizen. You will examine the presuppositions of public policy, you will hone your political judgment, you will become a more effective participant in public affairs. This would be a partial and misleading promise.

Political philosophy for the most part hasn't worked that way. You have to allow for the possibility that political philosophy may make you a worse citizen rather than a better one. Or at least a worse citizen before it makes you a better one. And that's because philosophy is a distancing (even debilitating) activity.

...philosophy distances us from conventions, from established assumptions, and from settled beliefs.
In short, one could justify not taking such risks by something like the following: If the greatest philosophers of the past centuries couldn't resolve these issues - who are we to think we can do it?! As Sandel puts it, "Maybe it's just a matter of each person having his or her own principles, and there's nothing more to be said about it?"

This might seems like a reasonable objection, but to this he offers the following reply:
... the very fact [these questions] have recurred and persisted may suggest that though they are impossible in one sense, they're unavoidable in another. And the reason they're unavoidable, the reason they're inescapable, is that we live some answer to these questions every day... just throwing up your hands and giving up on moral reflection is no solution.
Hope to see you in class ;)

Experiments, Mathematics and Theory in Ecology (part II)

Wednesday, April 15, 2009 at 2:00 PM Bookmark and Share
I thought it was time that I made good on my promise to follow up my previous post regarding experiments, theory and science in ecology (and related disciplines). We left off asking the question "Why has it taken so long for some of the sciences [e.g. ecology] to progress to their current state?" For what it's worth, here are my two cents on the matter:

To avoid unnecessary suspense, here is the quick version of at least some of the major factors contributing to the (relatively) recent advancement of ecology (and other areas of science):
1. The proper application of the scientific method.
2. Technological advances and advances in other natural and physical sciences.
3. Various other factors (some helpful, some not) arising from our growing population. Foremost among this last category are some of the big questions regarding things like climate change, responsible (sustainable) use of natural resources, public health issues, and so on. On to the not-so-quick version!
So how have these factors shaped ecology? Lets have a look...

Ecology is a relatively new science - born of numerous biological disciplines, only arriving as its own field in the late 1800s to early 1900s. It is broad and overarching in scope, and is rooted in many of the other sciences - after all, that bit about the environment in the given definition of ecology frequently requires ecologists to dabble in other areas of the physical and natural sciences in order to answer ecological questions. Because of this, progress in other scientific fields affect progress in ecology (e.g. imagine doing ecological research without chemistry or genetics!).

So what about that "using the scientific method" bit? Just to give things some context (and yes, this is a bit of a tangent), consider the question "How long have people been using critical thought and (even crude implementations of) the scientific method as a way to understand the physical and natural world?" If you need a refresher on the history of life and the geologic timescale, you might check out my previous post on the subject, or the geologic time scale page on Wikipedia.

The punchline here is that modern humans are thought to have appeared around 200,000+ years ago with the first known attempts to try and learn about the world through reason and careful observation of natural phenomena occurring a little over 3,000 years ago. So as far as human existence goes, we're pretty new to the game of doing science!

Why this little diversion back to the pleistocene and the formation of the earth? First, because a lot went on before we humans showed up to the party, and that immense history has shaped the world we live in. It took us a while to get even a crude understanding of the big picture (e.g. we recently thought the earth was flat!) and the more that history of life on earth is pieced together (thanks to the efforts of scientists in areas like physics, chemistry, geology, biology, and paleontology), the better we understand today's world and how it works.

Secondly, the human population size and ability to create and share knowledge has changed dramatically in recent centuries, and this has had a resounding impact on the world of science. As you may know, the human population has experienced near exponential population growth over the past few thousand years. It has more than doubled in the past 50 years, and has increased more than 20 fold in the last 1000 years. The increase has raised new problems and questions to address (although, human population growth isn't just a 20th century concern), and it has also lead to increased means of communication, transportation, the accumulation and availability of knowledge (e.g. the internet), and of course the simple increase in worker-hours available for doing scientific research. In short - demographic changes have had (and will likely continue to have) a bit impact on the progression and direction of scientific advancement.

With that, let's finish with a more focused look at ecology (and its ancestors like natural history, biogeography, botany, zoology, etc.), by comparing it to what are commonly considered "hard sciences" like physics and chemistry.

Reaching to my nearest chemistry text (Physical Chemistry, by P. Atkins) and opening it to page 1, the book begins with an introductory chapter laying out what physical chemistry is: "the branch of chemistry that establishes and develops the principles of the subject. Its concepts are used to explain and interpret observations on the physical and chemical properties of matter." The first section of this chapter isn't about chemistry, or physics for that matter - but instead something more basic and fundamental to the topic of physical chemistry: the section is titled "The structure of science," and gives an overview of terms like law, hypothesis, and theory as applied to the subject at hand. This is how (again, in my opinion) every science text book should begin: lay out the foundations of using the scientific method for the subject at hand, then build up from there.

This is in large part what makes a "hard science" - emphasizing how to do good science, and properly applying it to understand natural phenomena. Admittedly, it also helps that atoms and molecules are more predictable in their behavior when it comes to chemistry and physics (versus the behavior of organisms), and in many ways easier to measure for purposes of data collection.

Field ecology, for example has its roots in natural history - which I'll (perhaps unfairly) use here as an example of a field that was slow to move from making observations to making testable hypotheses and conducting experiments to see which ideas about how things work would hold up to empirical evidence. In addition to the significant practical difficulties of studying living organisms, this relatively slow acceptance to use the scientific method to understand ecological phenomena seems attributable to: (1) the fact that life is amazingly diverse, and broad generalizations about that diversity are hard to make. Plus, for some those generalizations can spoil the beauty and mystique of nature, leading to less focus on general and easy to understand phenomena, and more focus on things that are unique, complex and harder to understand; and (2) insightful observations of natural (undisturbed) phenomena were long deemed valuable enough - which can elevate the process of observation above the importance of doing experiments (that is, testing hypotheses) - distracting from the development of general theories by the scientific method, while perhaps over-focusing on describing observed phenomena.

As technology and our understanding from other areas in science have progressed, so to have our observational capabilities (and thus what sorts of things we can test experimentally). In ecology and other areas of biology, these advancements have opened up entire new worlds to observe and questions to be answered.

Early on, physics and chemistry had had a few things going in their favor in this regard. First, they are by their very nature easier to think about and study in a quantitative and general sense (perhaps early physics more so than early chemistry). This imparts to them three important qualities as disciplines in science. First, theories apply broadly to natural phenomena (e.g. nearly all objects fall just the same when dropped from a moderate distance - contrast with understanding the basic aspects of respiration, which pose greater practical challenges to study and don't generalize as easily to broad categories of organisms). Second, the quantitative nature of important phenomena allows the use of powerful mathematical and statistical tools, leading to well defined predictions about measurable quantities and a greater ease in testing and ruling out bad hypotheses. Science is all about ruling out bad hypotheses, and doing this efficiently means efficient progress towards well supported theories. Finally, there are fewer ethical conflicts in studying things that aren't alive - people don't respond to seeing someone smash a rock, drop a marble, or melt down metals in the same way they respond to seeing someone dissect a live dog. All biologists know about animal rights but to a geologist, mineral rights are rarely a problem in the lab!

Finally, thanks to the suggestion by Nick Sly, I took a look at the 1964 Science article "Strong Inference: Certain systematic methods of scientific thinking may produce much more rapid progress than others". I highly recommend reading it over, as well as T.C. Chamberlin's 1890 paper "The Method of Multiple Working Hypotheses" which can be found here (from the Wikipedia entry on Chamberlin), plus the text here (ed. 1999) with typographical errors corrected, and subheadings added, and lastly this modern version re-written by L. Bruce Railsback in case you find "Chamberlin's paper is too long, too high-blown, and too sexist for modern students."

In Platt 1964, he describes how some areas of science fail to progress by leaving behind the method of testing multiple hypotheses and "strong inferences" - complete with a rather entertaining list of pseudoscientific approaches I'll leave you to consider:
I think, there are other areas of science today that are sick by comparison, because they have forgotten the necessity for alternative hypotheses and disproof. Each man has only one branch-or none-on the logical tree, and it twists at random without ever coming to the need for a crucial decision at any point. We can see from the external symptoms that there is something scientifically wrong. The Frozen Method. The Eternal Surveyor. The Never Finished. The Great Man With a Single Hypothesis. The Little Club of Dependents. The Vendetta. The All-Encompassing Theory Which Can Never Be Falsified.
If you've made it this far, I hope you enjoyed the read and found it at least somewhat thought provoking. Feel free to share any comments or questions by posting below :)

Is Science Agnostic??

Thursday, April 9, 2009 at 9:29 PM Bookmark and Share
Here's Eugenie Scott, director of the National Center for Science Education giving a pretty darn good answer to that question back in January of 2006.

I first came across this footage as the first clip below, but found it was really part 5 of 10 of a 2006 talk on Intelligent Design Creationism (also provided below, or go here for part 1 of 10). Originals available from the Research Channel.



Experiments, Mathematics and Theory in Ecology

Friday, March 13, 2009 at 9:50 PM Bookmark and Share
If you check wikipedia or dust off your favorite dictionary and look up the definition of "ecology" you will find something like the following:
Ecology: The branch of biology concerned with the relations between organisms and their environment.
As a branch of biology, and thus a science, you might think that ecologists have centuries old traditions (much like physicists and chemists) - doing controlled experiments in their laboratories or gardens and using the scientific method to test hypotheses and formulate scientific theories. Right?

Well, not quite. History tells us almost the opposite has been the case up until recently... very recently, come to think of it!

I had originally set out to write a single piece, but it got a bit long so I've split it into two parts: the first basically revisits the recent conversation (from the course I TA) that prompted all this, and the second is a bit of a followup heavily seasoned with a few tangents that are likely of interest.

Earlier this week in class, a friend of mine raised a question in class that caught me a little off guard. It made me realized something I had taken overlooked or granted during the past decade or two of my science education: only very, VERY recently did we begin to develop a real understanding of how organisms interact with (and respond to) the world around them. The same could probably be said of knowledge about the natural world!

But on to our example. In lecture this week (for the course "Theoretical Ecology"), we discussed some really nice work that included research done by Dr. Jef Huismann and others, currently at the Institute for Biodiversity and Ecosystem Dynamics at the University of Amsterdam.

During the hot summer months, a lake used for recreation near Amsterdam turns into a smelly, stagnant health hazard due to blooms of toxic cyanobacteria. Understandably, local parks officials wanted to find a way to continue recreational use of this increasingly smelly and toxic body of water without the drastic measures require to stop the actual problem of nutrient pollution (e.g. fertalizers) in the lake.

His group used very controlled laboratory experiments in conjunction with mathematical models of those experimental systems to understand how mixing patterns in water (e.g. due to temperature gradients) influence competition for light among different types of algae under controlled laboratory conditions (think little green beakers). These factors are known to shape the types and numbers of algae you see in small ponds and lakes, and presumably play a role in our lake. (For the philosophically inclined reader, this is using good ol' scientific reductionism being used to lay a conceptual foundation.)

Results from those small scale experiments were then combined with more complicated computer models of the hydrodynamics of an actual lake in order to understand how mixing could be used to control the algal community residing there. With that, they were able to use the models to see how different ways of artificially changing the hydrodynamics in the lake might provide a solution to the problem.

So what was the solution? Based on all the modeling and experimental work, it turned out that a little extra mixing in the right places would cause the good algae to replace the bad. With a few properly placed pumps to bubble the lake, it was returned to its more recreation-friendly state. (More details can be found in Jef's scientific papers, and also in Chapter 7 of the book Harmful Cyanobacteria - if you're interested.)

Along with the many other scientific details uncovered along the way, this is a really cool example of using experimental findings in conjunction with mathematical and/or computer models in order to do exemplary scientific work. The models extend our reasoning and deductive abilities and combined with nice experimental results, lead to a deeper understanding of how algal communities form in these sorts of ponds and lakes.

Much as mathematical models helped Newton understand and describe the laws of motion, Huismann and many other modern day ecologists use similar mathematical models to describe and make predictions about biological systems. But if the math is so similar, why weren't Newton's biologist friends (or at least their grandchildren) doing the same sorts of thing back in the 1700s?? What's so different now that we had to wait 200 years for in order to apply these techniques to biological systems the way Newton and his colleagues applied them to planetary motion?

After the instructor finished talking about Huismann's work (and some of its more technical details), a friend of mine raised his and asked essentially this question: Why didn't someone do this 50 years ago?? It seems so... rudimentary!

Naturally, we looked to the instructor anticipating his response, which was essentially this: Physicists have been using experiments and models to understand and describe natural processes since Galileo (around 1600) - Ecologists (and their biologist and other predecessors) have only been doing it since the early 1900s or later. It just took that long for folks to embrace the idea of doing experiments and using mathematics understand and describe the natural phenomena being observed.

This, admittedly, caught me a little off-guard. I'm sure my thoughts were something like "Wait, what? But, why!?" But in truth, it is an interesting question: why has it taken so long for some of the sciences to gain prominence in recent centuries and (more generally) throughout human history? What walls were broken down recently that unleashed the flood of scientific inquiry we see today?

Well, there are of course a number of ways to answer these questions - certainly many more than I am aware of. Still, I can point to a few of them. Check back for part II of this post in the next couple of days, where I'll try to address some of them.

Darwin Days @ Cornell: Dr. Massimo Pigliucci

Tuesday, February 10, 2009 at 9:40 PM Bookmark and Share
This week, many people across the globe are celebrating Charles Darwin's 200th birthday (this Thursday the 12th), and the 150th anniversary of the publication of the Origin of Species. Cornell University and the Museum of the Earth have put together a fantastic lineup of lectures and events and a website with all the details which can be found here.

This evening, and yesterday afternoon during the Ecology and Evolutionary Biology weekly seminar, I had the great pleasure of listening to Dr. Massimo Pigliucci. I won't go into great detail, but the bulk of his second talk "What's science got to do with it? When scientists talk nonsense about religion" was a gem to listen to, and touched on a many interesting issues central to the conflict between religion and science.

I would strongly encourage you to check out his website and blog, where you can find some of his writing, publications, lecture slides, and mention of some of his books on science, evolution, and philosophy.

Here is a short list of points that caught my attention during his talk, here written in my words and not his. These mostly related to evolution and creationism/intelligent design, but touch on aspects of general science as well:
  • When talking with someone (in his case, usually students) who is conflicted between their religious beliefs and learning about evolution, he gives these following words of advice: I won't ask you to believe it, I simply ask that you understand it.
  • Quoting Richard Feynman (the physicist) from The Meaning Of It All: Thoughts Of A Citizen-scientist, he reiterated that the root of much conflict between religion and science comes from the notion that (to use another Feynman quote) "Religion is a culture of faith; science is a culture of doubt. "
  • The conflict between evolutionary theory and creationism/intelligent design is not a scientific conflict, but a sociological and philosophical one. Science can only prove or disprove assertions about the natural world and is limited (if not unable) to prove or disprove assertions of a supernatural nature.
  • That said, when religions make claims about the natural world (e.g. the earth 10,000 years old) a scientific approach can be used to evaluate them.
  • Scientists would do well to learn about and apply the philosophy of science in their pursuits! Understanding the strengths and limitations of science can (of course) make for better science. I particularly enjoyed his commentary on statistics, which can be found on his website.
  • Waiting until high school or college to teach basic science and critical reasoning is a no-no! This should be taught from early on, just like we teach reading, writing and mathematics.
My time is up for now, but I hope you get a chance to check out some of Massimo's work as well as any of the "Darwin Day" events that might be going on in your neck of the woods. That's all for now! :)