Species and systematics
evolvingthoughts | November 20, 2007
The African apes don't get much good news these days. But the Congo has just announced they are setting up a preserve to protect the bonobo. The size of the Sankuru Nature Reserve is 11,803 square miles (in real money, 30 569.629 square kilometers), which makes it nearly half the size of Tasmania, or bigger than Massachusetts or Hawai'i.
This is a cooperative venture between a partnership involving American and Congolese conservation groups and government agencies, and they are addressing the local practices of hunting bonobos as well. All bonobos in the wild live in the Congo.
Hat tip…
evolvingthoughts | November 17, 2007
I have always enjoyed reading the work of Frans de Waal, a primatologist who focuses on the social structure and psychology of apes, particularly the two chimp species, and monkeys. His previous books, Good Natured: The Origins of Right and Wrong in Humans and Other Animals, The Ape and the Sushi Master: Cultural Reflections of a Primatologist, and Peacemaking among Primates have all entranced me and inspired my reflections on such diverse topics as evolutionary psychology, the origins of political and social structures, and, of course, the evolution of religion.
His recent book, Our Inner…
evolvingthoughts | November 11, 2007
Following on from my previous post "Are species theoretical objects", I want now to discuss what the status of species as phenomenal objects is.
Some recent papers by Ingo Brigandt and Paul Griffiths (see refs), a view has been developed for some core concepts of biology - gene and homology - in which the theoretical status of these ideas is challenged. This view treats the concepts as referring to either obervational or operational objects or properties, just as I have suggested that species does. Brigandt has suggested that these objects or concepts are "units of explanation", and he and…
evolvingthoughts | November 10, 2007
I've been so busy reading and assimilating the latest issue of Biology and Philosophy I forgot to let you all know about it. It's a special issue on Homology, edited by Paul Griffiths and Ingo Brigandt. A discussion group has now been set up at Matt Haber's blog The Philosophy of Biology Café.
The papers are:
The importance of homology for biology and philosophy by Brigandt and Griffiths, which gives a clear and interesting summary of the issues;
The phenomena of homology by Griffiths, which argues that homology is a phenomenal, rather than a theoretical concept (as I have argued that…
evolvingthoughts | November 8, 2007
Some things that piqued my interest without triggering a full post:
The readability of this blog is high school level, which is good. That's pretty much how I pitch it:
There's a new species of killer whale in the Antarctic. [HT: Jason]
Toads will mate across species if things get tough. This has also been documented in other species such as ducks.
evolvingthoughts | November 6, 2007
I can't believe Laelaps beat me to this (shows how on the ball he is) but he's just noted a paper that I watched getting written, and discussed in detail with Chris Glen, a very smart and talented young paleontologist, before I got to. So I will now, before he goes and does a better job.
Chris and his advisor Michael Bennett have come up with a possible way to test the "trees down or ground up" controversy about the origins of flight. That is, they have some independent evidence that early birds were basically ground dwellers, but that there was, as there is now, a mix of lifestyles…
evolvingthoughts | November 5, 2007
What with Hollywood archetypes of "animal rights activists" coming out of the woodwork lately, Ryan Gregory and Larry Moran pose the following question:
And so I ask, on what basis do you draw the sharp moral line between "humans" and "animals", "human rights" and "animal rights", "us" versus "them"? What rational argument do you bring in defense of speciesism? Perhaps you argue that only humans are capable of suffering, or that our intellectual capabilities are of a different kind from those of other animals. As Dawkins has noted, neither is compatible with what we understand about…
evolvingthoughts | November 3, 2007
[This started as a discussion of the debate mentioned below. It got lost somewhere, and became me riffing on my favourite topics. Sorry.]
I love it when people I know have a barny* in public, but it presents some delicate choices and sensibilities to be honoured. The case in point today is between Malte Ebach and David Williams in the red corner, and Joseph Felsenstein in the blue. I'm not the referee - I'm just the seasoned journalist in the front row...
The issue is what counts when we classify in biology, and why. Malte and David argue that there are some notions of classification…
evolvingthoughts | October 30, 2007
Here is an article in Harvard Magazine on bacteria and other wee beasties that make up the bulk of the living world, that is worth reading. It's called "The Undiscovered Planet". Hat tip to Jason Grossman.
evolvingthoughts | October 28, 2007
UPDATED:
To give some of my colleagues at the University of Queensland some link love, it is being reported that they have sequenced the Queensland lungfish (currently under threat by a proposed dam) opsin genes, showing that they see in ultraviolet and visible light, as well as having the ability to see in dim and bright light. The paper is now accessible at BMC Evolutionary Biology.
The conclusion drawn from this is that early land dwelling vertebrates saw in colour, which is probably true, but not, I think, because the lungfish is a "living fossil that dates back 400 million years…
evolvingthoughts | October 23, 2007
The estimable Drs David Williams and Malte Ebach have started a blog on Systematics and Biogeography, which supports a recent book they haven't sent me a free copy of yet. Expect much puncturing of pretensions and orthodoxies.
evolvingthoughts | September 24, 2007
This is a nice post by Christopher Taylor at Catalogue of Organisms, a kiwi studying spider systematics (and what's not to love about that; cephalopods be buggered!) on the species of moas that used to live in New Zealand. I didn't realise they'd be forest dwellers. It's a worthwhile blog to get the feed for.
evolvingthoughts | September 22, 2007
One of the things I have previously discussed (see the "Best of ET" tab) is microbial species concepts. Two new papers have come out on this, and it seems to be a hot research topic right now.
Eppley, et al., in the journal Genetics, argue that the claim that I happened to make in my as-yet unpublished paper in History and Philosophy of the Life Sciences, that microbial species are clusters of genomes maintained by, among other things, homologous recombination of genes, is supported by experimental evidence based on genomic data of two microbial species of Archae bacteria, of the genus…
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 6, 2007
So, you thought that Colony Collapse Disorder, which is causing billions of dollars in losses in American agriculture, was an act of nature? You poor fools! It's a plot, I tell yez. We Australians have hardier bees than you do, so they can carry an infectious disease that your weakly pathetic American bees just can't deal with. And it's no accident that we sent them to you. Now you have to buy our produce! BWAHAHAHAHA!!!!!
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 24, 2007
I'm very late to this, but one of the significant figures in the synthesis, Verne Grant, died in May. Grant's book The Origin of Adaptations (1963) was one that influenced a lot of theorising about evolution. His essay on species concepts in 1957 pointed out that botanical notions of species had to be very different to the reigning Mayrian biospecies concept.
Grant, Verne. 1957. The Plant Species in Theory and Practice. In The Species Problem, edited by E. Mayr. Washington DC: American Association for the Advancement of Science.———. 1963. The origin of adaptations. New York: Columbia…
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…