Philosophy of Science
scientificactivist | September 12, 2007Earlier this year, Malcolm Gladwell wrote an article for The New Yorker called "Open Secrets" in which he discussed the distinction between two types of problems: what he called "puzzles", which are simpler, and "mysteries", which are more complex. Building on the work of national security expert Gregory Treverton, he wrote:
"Osama bin Laden's whereabouts are a puzzle. We can't find him because we don't have enough information. The key to the puzzle will probably come from someone close to bin Laden, and until we can find that source bin Laden will remain at large."
"The problem of what…
evolvingthoughts | September 7, 2007
Now we turn to the modern accounts of life.
In 1828, Friedrich Wöhler produced uric acid without using “kidney of man or dog”. Prior to that time, there was considered to be something different between organic chemistry and inorganic chemistry. Living things had some “vital fluid” that other things lacked. Most often this was expressed in Aristotelian terms even if, like Buffon, they were very anti-Aristotelian. But still life was not fully explicable in chemical terms.
Vitalism, as this idea was termed, did not die with Wöhler, though. In fact, we can find instances of it until the…
evolvingthoughts | September 5, 2007
Carl Zimmer has one of his usually clear and precise articles on recent work on the nature of life, focussing on the work of Carol Cleland, who is at the National Astrobiology Institute, despite reduced funding for actual science by the present administration. I met Carol last year when we both spoke at the Egenis conference on the philosophy of microbiology.
Carol argues that we do not have a theory of what life is. She may be right. One of her arguments is that if there were multiple "origins of life" events that used different chemistry, we may not even be able to "see" the others…
evolvingthoughts | September 1, 2007
Continuing on from my last post, let's consider the modes of speciation that are called into account for the existence of species.
Here is a list taken from Sergey Gavrilets, which I put in my most recent paper in Biology and Philosophy (2007).
Vicariant – divergent selection and stochastic factors like drift after division of a population by extrinsic factors such as geographical changes;
Peripatric – a small subpopulation, mostly isolated, at the extreme of the parent range. The idea is that it will have both a non-standard sampling of alleles, and also be subjected to divergent…
evolvingthoughts | August 31, 2007
A lot of people have said something like "species are the units of evolution". What does this even mean? So far as I can tell, nobody has really fleshed this out.
What, to begin, are the units of evolution? It depends a lot on what theory is being employed. If you are talking about population genetics, then the basic unit is, of course, the allele and the locus. That is, alternative genes (a concept that is itself rather problematic) at a given point or position on the genome. If you are talking about development, then the unit is the organism, as it also is when you are talking about…
evolvingthoughts | August 23, 2007
The "angry atheist" debate has broken out again, like a fire that smolders on until it finds new fuel. I am moved to make a few points, which are worth all you paid for them.
1. There is an assumption that reasonable people can only come to one conclusion. To theists this is theism of some kind. To atheists this is atheism. It presumes that people who are reasonable in one domain (say, science) are reasonable in all. But I know atheists who are libertarians, and a more irrational faith in rights I haven't found, and I know theists who are absolutely in line with all the social, scientific…
evolvingthoughts | August 23, 2007
You'll remember, because you have all memorised my blog going back two years, that I blogged on what microbial species are before, and have a paper on that subject coming out in History and Philosophy of the Life Sciences. In it I argue that microbial species, particularly bacterial species, are maintained as phenomenal clusters by two mechanisms. One is the exchangeability of genetic material, which is akin to interfertility in sexual organisms, a hypothesis proposed by Dykhuizen and Green called the "core genome" hypothesis. The other is adaptive niche tracking.
Now a paper has come out…
evolvingthoughts | August 22, 2007
The National Geographic and the news services are touting a new ape fossil found in Ethiopia as "forcing a rethink on human evolution". As usual, the headlines are hyperbolic. This ape is fragmentary, and so far only teeth and a jaw bone have been found, and the teeth are similar to gorilla teeth. Gorillas are thought on molecular grounds to have split off from the chimp-human clade about 7 million years ago, but this specimen is 10 million years old. What gives?
I can think of a couple of options. One is that, as I have reported previously, teeth are not great diagnostic material for…
evolvingthoughts | August 22, 2007
Historian Mary P. Winsor published recently (2006b, in the December 2006 edition, but it just came out) a paper discussing how the Essentialism Story was constructed by Arthur Cain, Ernst Mayr, and David Hull.
The Essentialism Story is the claim that before Darwin systematists and biologists in general treated natural kinds such as species as being defined by necessary and sufficient conditions. That is, to be a member of a species, an organism has to have all the right properties. After Darwin, goes the story, "population thinking", which denies that there are such necessary properties…
evolvingthoughts | August 21, 2007
... I'm teaching. First years. Cognitive science.
It turns out that a lot of what I thought was common knowledge isn't common at all. And what I count as a simple introduction leaves a lot of folk behind.
Now I know I'm not that ordinary in many senses - the obsession with complex concepts may give it away if the lack of social skills don't - but it is a big shock to me how under-educated these kids are. I find myself having to explain simple argument skills, and many of them have already done the critical reasoning course! This is no excuse, of course - it's my job to see they…
evolvingthoughts | August 14, 2007
I have a book forthcoming, Species definitions: a sourcebook from antiquity to today, which gives and commentates definitions of "species" in logic and biology for 2,500 years, from Plato to Templeton and beyond. It's designed as a reader for scholars to see how the notion[s] have evolved separately in the logical definitional sense - for Aristotle, eidos, which we translate as "form", "species", and "kind", was a logical term, not a biological one, which had to wait until the 16th century, and even then they were distinct notions.
I argue in the commentaries that there was nothing…
evolvingthoughts | August 14, 2007
I normally don't respond the to IDiocy of Uncommon Dissent, but John Lynch, may he rot in purgatory for a thousand years, has made me. As usual, I won't dignify it with links. If you are that interested you can find it.
There are two items: one is by DaveScot, who argues (!) that because Popper's falsification hypothesis means that until we find non-white swans, a hypothesis that swans are white stands, we should somehow assume that Intelligent Design stands as a scientific view. This is silly for a couple of reasons. One is that we have got counterinstances to the need for ID to explain…
evolvingthoughts | August 12, 2007
I have a review of the centenary festschrift for Mayr, published by the National Academies of Science, in the latest Biology and Philosophy here. I worked pretty hard on this one, so it's more than your average dashed off review article...
Hey, Jody; Fitch, Walter M.; Ayala, Francisco J., eds. 2005. Systematics and the origin of species: On Ernst Mayr’s 100th Anniversary. Washington, DC: National Academies Press. Pages: 367 + xiii. ISBN: 0-309-09536-0
evolvingthoughts | August 10, 2007
Rob Wilson has a new entry up at the Stanford Encyclopedia of Philosophy, entitled "The Biological notion of an individual". It discusses an interesting problem, one that goes back to discussions by Julian Huxley in 1911. What is an individual in biology?
The term "individual" means, etymologically, that which is not divisible. Of course we can divide up organisms, but if we do this physically, they immediately thereafter cease to be the organism. Except... there are colonial organisms that can be so divided - sponges, hydras, slime molds, and so on. To make matters worse (much worse, as…
evolvingthoughts | August 7, 2007
Kate Devitt, a PhD student at Rutgers, as a rather wonderful blog, Mnemosynosis, on matters relating to memory. She's got at present a very interesting post on bacterial cognition worth reading.
evolvingthoughts | August 7, 2007
I have a soft spot for Herbert Spencer [see also here]. Supposedly the founder of social Darwinism and the precursor to American libertarianism and justifier of the robber barons of the Gilded Age, he has been the whipping boy of progressives and anti-evolutionists alike. Ever since Richard Hofstadter fingered him as the source of rough individualism and eugenics in his Social Darwinism in American Thought in 1943, Spencer has been the evil demon of philosophy, political thought, and evolution. But a recent article in The New Yorker occasioned by a new book Herbert Spencer and the Invention…
evolvingthoughts | August 7, 2007
I've been pretty quiet of late. In part this is because I've been travelling with little internet access, but also it's because I'm teaching a subject I haven't studied in years, and because I was asked to write a popular essay for a magazine.
It's COSMOS Magazine, an Australian popular science magazine, and what the editor wanted was something like my posts on philosophy of science as the ornithology of science. It takes effort to write clearly to a word limit (which is why I blog - I'm fundamentally lazy), but with the help of the editor, Tim Dean, I managed to say one thing rather than…
evolvingthoughts | August 3, 2007
So I'm home from Ish, and the front part of my brain is giddy and tired while the rest has just shut down. I don't travel well, I'm afraid.
One thing that I came back fired up over are the unfinished projects I have running. So I intend to finish them. They are, in no particular order:
1. Denying that genes have information [heresy #1] Status: Written and needing to be submitted.
2. Denying that functions in biology exist outside models [heresy #2] Status: Written but badly in need of a rewrite.
3. Denying that essentialism ever existed in biology [#3. Four more and I get a free auto…
omnibrain | July 28, 2007Here begins another new series at Omni Brain. This one is called, Review copies of books Steve gets in the mail from publication companies, like Prometheus Books, that love bloggers, Long enough title for you?
I actually don't have time to read anywhere near all of these books so I'm going to give you the Amazon shtick ;) These books really do look interesting and are definitely worth checking out! If you've read them please let us know what you think in the comments section.
Our first book is... Science and Ethics: Can Science Help Us Make Wise Moral Judgments?
Book Description:
In a…
tfk | July 21, 2007Denyse O'Leary uses Bill Dembski's blog (and a dozen other ID blogs) to report a comment from a friend about the mission statement for Nature. The mission statement reads:
First, to serve scientists through prompt publication of significant advances in any branch of science, and to provide a forum for the reporting and discussion of news and issues concerning science. Second, to ensure that the results of science are rapidly disseminated to the public throughout the world, in a fashion that conveys their significance for knowledge, culture and daily life.
Her friend replies:
To report…