"Climategate, global warming, and the tree rings divergence problem"
"A 2,000-page epic of science and skepticism" Part I of a series that continues on Monday, apparently.
Enjoy.
Interesting a reasoned takes on "Climate gate"
Just a couple of articles worth reading:
"Climategate, global warming, and the tree rings divergence problem"
"A 2,000-page epic of science and skepticism" Part I of a series that continues on Monday, apparently.
"Climategate, global warming, and the tree rings divergence problem"
"A 2,000-page epic of science and skepticism" Part I of a series that continues on Monday, apparently.
I never thought of science as a sausage before...
...but maybe that's because I'm a scientist who happens to be a vegetarian.*
Anyway, John Wilkins has a nice little comment on the CRU emails fiasco. This will definitely be useful for those civilized discussions you're planning on having with that global warming denier in your family over the holidays.
Enjoy!
* and thus, by default, my socialist overlords have decided that I must also believe that global warming is human-caused. Easy enough, because I do.
Anyway, John Wilkins has a nice little comment on the CRU emails fiasco. This will definitely be useful for those civilized discussions you're planning on having with that global warming denier in your family over the holidays.
Enjoy!
* and thus, by default, my socialist overlords have decided that I must also believe that global warming is human-caused. Easy enough, because I do.
Stop the closure of the MSU geology department!
I received the following message recently, via the Society of Vertebrate Paleontology. Please sign the petition.
The Department of Geological Sciences at Michigan State University is home to a nationally and internationally prominent, vibrant group of students, faculty and staff. As a response to current budget distress, the Board of Trustees and Provost Kim A. Wilcox are considering a proposal to close the Department, along with all of the graduate and undergraduate programs offered by the Department. The immediate effect will be the loss of three tenure-track untenured faculty positions and one technical and three office staff support positions. Longer term effects of such a closure would include the loss of formal geosciences as a fundamental part of undergraduate and graduate training, and would impair Michigan State University’s service to students, the local community, and the global scientific community.
To offer your support to geosciences at MSU and oppose closing the department, please add your signature to the petition located at:
http://new.ipetitions.com/petition/savegeosciencesatmsu/
Please also consider passing the petition along to others who would offer their support.
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Dawkins on O'Reilly
Bill O'Reilly is a dunce, but Dawkins could've done a lot better.
Sometimes, it takes comedians to communicate science more effectively than scientists themselves:
O'Brien has every answer that Dawkins needed for this debate against O'Reilly.
Sometimes, it takes comedians to communicate science more effectively than scientists themselves:
O'Brien has every answer that Dawkins needed for this debate against O'Reilly.
The return from SVP
I returned from the UK on Tuesday after attending the SVP meeting and then visiting a friend in Oxford. Sorry I've not been posting. My talk went well, and I hope to be able to post a summary with some slides here. The meeting was quite productive, at least in terms of making some contacts and plotting some plots, etc.
"We have a village idiot in this country; it's called Fundamentalist Christianity"
Wise words from Frank Schaeffer.
The video is well worth a watch, if you like to see a former Christian fundamentalist use some damning rhetoric against the batshit crazy group he used to be part of.
(Via Evolving Thoughts)
Visit msnbc.com for Breaking News, World News, and News about the Economy
The video is well worth a watch, if you like to see a former Christian fundamentalist use some damning rhetoric against the batshit crazy group he used to be part of.
(Via Evolving Thoughts)
Rampant paraphyly on Wikipedia
I've just been having a look at some of the Wikipedia pages about certain bony fish groups, particularly Sarcopterygii and Rhipidistia. These need some serious fixing. There's a lot of stuff out there about 'ancestral groups'. That is to say, describing a group as the ancestor of another group.
"Tetrapods — four legged[sic] vertebrates were the terapodomorphs'[sic] descendants."
"Rhipidistia is now understood to be an ancestr for the whole of Tetrapoda."
The notion that a group is 'ancestral' is a bit misleading, especially if we accept that groups (i.e. clades) are actually the descendents of a single common ancestor. That's not really the problem, though.
Let's look at each of the quotations below the fold.
The first one claims that tetrapods descended from tetrapodomorphs. The actual meaning of 'Tetrapodomorpha' is the tetrapod total group (Ahlberg, 1991). By definition, this group includes all tetrapods, and any and all fossil taxa that are more closely related to tetrapods than to any other extant group (in this case, probably lungfishes: the Dipnomorpha). Tetrapods are a subset of Tetrapodomorpha, not descendents of them.
The second quotation is similar. Ahlberg (1991) also re-defined 'Rhipidistia' cladistically as the Dipnomorpha + Tetrapodomorpha. In this sense, Rhipidistia is monophyletic. However, the Rhipidistia was a pre-cladistic grouping meant to encompass porolepiforms and 'osteolepiforms'. Porolepiforms (probably a real clade) and the 'osteolepiforms' (not a real clade) represent an assemblage of lobe-finned fishes that would look quite similar to an 'untrained observer'. This similarity is mostly just shared primitiveness. That is, it does not unite them to the exclusion of other taxa (namely lungfishes in the case of porolepiforms; and tetrapods in teh case of 'osteolepiforms').
What is significant about 'rhipidistians' in the classical sense (i.e. before Ahlberg's 1991 paper) is that they lack synapomorphies or homologies. They have to be defined on the basis of a set of characters and character absences, implicit and explicit, that is hand picked to exclude other groups. They are 'fishes', meaning they have fins (not digits) with lepidotricia, bony dermal rays. But these are also found in the early tetrapods Ichthyostega and Acanthostega. However, these latter taxa lack an intracranial joint, a division of the front part of the braincase from the back part that contains the ear capsules. Coelacanths also have this division, but they are not rhipidistians. However, coelacanths lack the dermal skull bone characters, such as a maxilla, that are found in 'rhipdidistians' such as Eustheonopteron and Holoptychius showing in Figure 1., above.
As you can see, it quickly becomes obvious how the defining characters are arbitrary, in some sense. They are picked to justify a group of taxa that share some overall similarity. It does not reflect an attempt to discover the hierarchical relationships among characters. This latter process is the discovery of homology: the characters that unite monophyletic groups. It is in this way that real evolutionary relationships are discovered; not through the nomination of "ancestral groups".
Ahlberg, P.E. 1991. A re-examination of sarcopterygian interrelationships, with special reference to the Porolepiformes. Zoological Journal of the Linnean Society 103: 241-287.
"Tetrapods — four legged[sic] vertebrates were the terapodomorphs'[sic] descendants."
"Rhipidistia is now understood to be an ancestr for the whole of Tetrapoda."
The notion that a group is 'ancestral' is a bit misleading, especially if we accept that groups (i.e. clades) are actually the descendents of a single common ancestor. That's not really the problem, though.
Let's look at each of the quotations below the fold.
The first one claims that tetrapods descended from tetrapodomorphs. The actual meaning of 'Tetrapodomorpha' is the tetrapod total group (Ahlberg, 1991). By definition, this group includes all tetrapods, and any and all fossil taxa that are more closely related to tetrapods than to any other extant group (in this case, probably lungfishes: the Dipnomorpha). Tetrapods are a subset of Tetrapodomorpha, not descendents of them.
The second quotation is similar. Ahlberg (1991) also re-defined 'Rhipidistia' cladistically as the Dipnomorpha + Tetrapodomorpha. In this sense, Rhipidistia is monophyletic. However, the Rhipidistia was a pre-cladistic grouping meant to encompass porolepiforms and 'osteolepiforms'. Porolepiforms (probably a real clade) and the 'osteolepiforms' (not a real clade) represent an assemblage of lobe-finned fishes that would look quite similar to an 'untrained observer'. This similarity is mostly just shared primitiveness. That is, it does not unite them to the exclusion of other taxa (namely lungfishes in the case of porolepiforms; and tetrapods in teh case of 'osteolepiforms').
Figure 1. Some 'rhipidistian fishes'. Top: Holoptychius. Bottom: Eusthenopteron along with an illustration of its pelvic and pectoral fin endoskeletons.
What is significant about 'rhipidistians' in the classical sense (i.e. before Ahlberg's 1991 paper) is that they lack synapomorphies or homologies. They have to be defined on the basis of a set of characters and character absences, implicit and explicit, that is hand picked to exclude other groups. They are 'fishes', meaning they have fins (not digits) with lepidotricia, bony dermal rays. But these are also found in the early tetrapods Ichthyostega and Acanthostega. However, these latter taxa lack an intracranial joint, a division of the front part of the braincase from the back part that contains the ear capsules. Coelacanths also have this division, but they are not rhipidistians. However, coelacanths lack the dermal skull bone characters, such as a maxilla, that are found in 'rhipdidistians' such as Eustheonopteron and Holoptychius showing in Figure 1., above.
As you can see, it quickly becomes obvious how the defining characters are arbitrary, in some sense. They are picked to justify a group of taxa that share some overall similarity. It does not reflect an attempt to discover the hierarchical relationships among characters. This latter process is the discovery of homology: the characters that unite monophyletic groups. It is in this way that real evolutionary relationships are discovered; not through the nomination of "ancestral groups".
Ahlberg, P.E. 1991. A re-examination of sarcopterygian interrelationships, with special reference to the Porolepiformes. Zoological Journal of the Linnean Society 103: 241-287.
Brief update
This week, I've been working on my presentation for this year's Society of Vertebrate Paleontology meeting in Bristol. The conference is next week and I've got my own talk, plus contributions to another talk and a poster. Unfortunately, I can't post details of my talk until after the meeting, because the abstract is embargoed. This year looks somewhat promising. There was a record number of abstract submissions, so a lot of the papers that focused on strict descriptive alpha taxonomy did not make the cut. I'm quite happy with that, to be honest. I don't really need to travel a long way to see talks on descriptions of new animals when, in a few months, I can read and use the paper. I'm a bit more interested in seeing progress on sorting out the relationships of problematic taxa, and maybe learning about novel uses for fossils. There's some promising stuff this year.
Spent part of last week on holiday in Prague. One of the great things about living in Europe is the short distance to all these great places.
Spent part of last week on holiday in Prague. One of the great things about living in Europe is the short distance to all these great places.
First reactions to The Greatest Show On Earth
The Guardian has run a review by Richard Fortey of Richard Dawkins' upcoming book The Greatest Show On Earth. I won't get a free review copy, I'm sure... so I'm probably not going to spend time reviewing it myself. However, it looks like it's a feed of standard fare. I'm a bit comforted by this video, as it sounds like Dawkins doesn't waste much time with fossil apologetics. However, I'm wondering to what extent concepts such as homology, palaeontology, biogeography, and embryology are disjoined in their presentation. I wonder when someone is going to write a book about that for general consumption.
Anyway, here's the video plug:
Anyway, I'm off to Prague until Friday. Probably won't have much of a chance to blog again before that. Consider this an open thread.
Anyway, here's the video plug:
Anyway, I'm off to Prague until Friday. Probably won't have much of a chance to blog again before that. Consider this an open thread.
What's been going on? Some academic musings.
So, what's been happening in the past few days (weeks?) since I last posted? Well, autumn is setting in here, so it's not like I'm spending a lot of time outside right now. I've been focused pretty much on a few things: writing a manuscript, updating a dataset, writing a job application, and learning some programming skills.
One of the nice things about being a postdoc is the flexibility of your time. It is an important period in the life of a researcher where you not only apply those skills you already learned towards being productive, but you have the opportunity to learn new ones. I'm picking up where I left off early in my postgraduate education, learning new tools and tricks for the software environment R. This really is an indispensable tool for biologists, or anyone who applies statistics. I would hope that in the near future, R will become an integral part of undergraduate biology curricula. It combines the ability to analyze data with a programming environment.
As much fun as being a postdoc is, I really want a permanent job—a good one, with lots of interaction with enthusiastic and creative students. Being a postdoc can be limiting, too. There are lots of small cash funds for Ph.D. research projects from various scientific societies, institutions, or funding agencies. I've had a lot of success with these as a Ph.D. student, and I really think they are important in helping students b. On the other hand, faculty tend to operating grants: a fund that supports their research throughout the year or several years. Somewhere in the middle is the postdoc, who has to rely either on his host's grant (allusions to parasitism here may or may not be intended), or the very few small (and therefore competitive) external sources. Thankfully, my current project can make use of a lot of published data, as well as data existing within our collections at this museum. However, I certainly feel the need to grow and develop something much larger and sustained.
One of the nice things about being a postdoc is the flexibility of your time. It is an important period in the life of a researcher where you not only apply those skills you already learned towards being productive, but you have the opportunity to learn new ones. I'm picking up where I left off early in my postgraduate education, learning new tools and tricks for the software environment R. This really is an indispensable tool for biologists, or anyone who applies statistics. I would hope that in the near future, R will become an integral part of undergraduate biology curricula. It combines the ability to analyze data with a programming environment.
As much fun as being a postdoc is, I really want a permanent job—a good one, with lots of interaction with enthusiastic and creative students. Being a postdoc can be limiting, too. There are lots of small cash funds for Ph.D. research projects from various scientific societies, institutions, or funding agencies. I've had a lot of success with these as a Ph.D. student, and I really think they are important in helping students b. On the other hand, faculty tend to operating grants: a fund that supports their research throughout the year or several years. Somewhere in the middle is the postdoc, who has to rely either on his host's grant (allusions to parasitism here may or may not be intended), or the very few small (and therefore competitive) external sources. Thankfully, my current project can make use of a lot of published data, as well as data existing within our collections at this museum. However, I certainly feel the need to grow and develop something much larger and sustained.
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