Rank-free classification

We didn't have time to cover this topic on Thursday so I'm going to permit myself a repeat here and introduce it in case any of you want to investigate it further. Good search terms would be Phylogenetic taxonomy or Rank free classification.
 
You may have heard the saying 'Science progresses by the death of scientists.' Several people have said something like this, perhaps the most famous being Max Planck the German theoretical physicist and generally accepted as the founder of the quantum theory in physics.

“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

Creating a taxonomy that reflects evolutionary history is now firmly established in biology and the the techniques of cladistics are used to classify organisms into hierarchical taxonomic groups. None of this is very controversial, at least not any more.

However the question of whether we should continue with the Linnean taxonomic code for the naming of the taxa or adopt something different is a very hot topic. I suspect that this is one of those changes that is going to take the death of a generation of biologists to change. There was a good article about the issue in American Scientist in 2006: Attacks on Taxonomy.

Unlike the PhyloCode, Linnean taxonomy does not formally incorporate phylogeny. However, its ranks (species within genus, genus within family, family within class and so on) imply evolutionary relationships. The main drawback of the Linnean system is that groups must be named with suffixes that denote their rank in this hierarchy. For instance, all animal families end in -ae, as in Hominidae. Reclassification of an existing species or discovery of new one can lead to changes in rank and therefore require renaming whole suites of taxonomic groups—a cascade of renaming—even without any new information on those groups. The Phylo-Code solves this problem.

Discover magazine also had a nice article that focused a little more on the people and the controversy: Pushing Phylocode.

“This would be very similar to a set of politicians who decided to bypass the Constitution to create a whole new set of laws.”

New techniques for sequencing

I mentioned that genetic sequencing is now one of the important tools used in systematics. However up until now this has been problematic when working with early human specimens, or close relatives. This is because the technique involved multiplying up small fragments of DNA and so even a tiny amount of contamination from a modern human (eg an archaeologist who handled the bones) could become a huge problem if this contaminant were multiplied.

'Using the remains of humans that lived in Russia about 30,000 years ago, Svante Pääbo and his colleagues now make use of the latest DNA sequencing (i.e., reading the sequence of bases that make up the DNA strands) techniques to overcome this problem. These techniques, known as "second-generation sequencing," enable the researchers to "read" directly from ancient DNA molecules, without having to use probes to multiply the DNA. Moreover, they can read from very short sequence fragments that are typical of DNA ancient remains because over time the DNA strands tend to break up. By contrast, DNA that is younger and only recently came in contact with the sample would consist of much longer fragments. This and other features, such as the chemical damage incurred by ancient as opposed to modern DNA, effectively enabled the researchers to distinguish between genuine ancient DNA molecules and modern contamination. "We can now do what I thought was impossible just a year ago -- determine reliable DNA sequences from modern humans -- but this is still possible only from very well-preserved specimens," says Pääbo.'

The paper is in the Jan 12 edition of Current Biology and there's a more popular write up on the ScienceDaily website.

Alternative titles

It's a little fast and hard to keep up with in places, especially in the latter stages but the fast moving style, pop culture references and connections to Thursday's class make this video well worth a look. Eddie Izzard suggests some of the rejected titles for Darwin's big book....

Bypassing the constitution

You may have heard the saying 'Science progresses by the death of scientists.' Several people have said something like this, perhaps the most famous being Max Planck the German theoretical physicist and generally accepted as the founder of the quantum theory in physics.

“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

Creating a taxonomy that reflects evolutionary history is now firmly established in biology and the the techniques of cladistics are used to classify organisms into hierarchical taxonomic groups. None of this is very controversial, at least not any more.

However the question of whether we should continue with the Linnean taxonomic code or adopt something different is a very hot topic. I suspect that this is one of those changes that is going to take the death of a generation of biologists to change. There was a good article about the issue in American Scientist in 2006: Attacks on Taxonomy.

Unlike the PhyloCode, Linnean taxonomy does not formally incorporate phylogeny. However, its ranks (species within genus, genus within family, family within class and so on) imply evolutionary relationships. The main drawback of the Linnean system is that groups must be named with suffixes that denote their rank in this hierarchy. For instance, all animal families end in -ae, as in Hominidae. Reclassification of an existing species or discovery of new one can lead to changes in rank and therefore require renaming whole suites of taxonomic groups—a cascade of renaming—even without any new information on those groups. The Phylo-Code solves this problem.

Discover magazine also had a nice article that focused a little more on the people and the controversy: Pushing Phylocode.

“This would be very similar to a set of politicians who decided to bypass the Constitution to create a whole new set of laws.”

Writing, Reading, and Reviewing Scientific Articles

This coming week in the bio colloquium we're reading an article from the primary literature. To provide general background on the elements of a scientific paper we also handed out "guidelines for writing a scientific paper". To help you think about it from the other end (reviewer vs. writer) you may want to see what guidelines the scientific journals provide their reviewers, that is, what helps us decide whether a paper is "publishable" by a given journal. This is useful in writing (and reading) a paper to see what the "critics" are looking for.

Here is the link for reviewers for the journal, Ecology:
http://esapubs.org/esapubs/reviewers.htm

Also informative is the "Reviewers Information Pack" (http://www.nxtbook.com/nxteu/elsevier/reviewersinfopack/) for everything you might want to know about the review process for journal articles. This is provided by Elsevier, which publishes Developmental Biology, and hundreds of other journals (http://www.elsevier.com/wps/find/journal_browse.cws_home)

Here's their reviewers' home page:
http://www.elsevier.com/wps/find/reviewershome.reviewers

The best stats you've ever seen

I used this video in a different class but I think everyone should see it, and it is relevant to our discussion about human population growth.

You've never seen data presented like this. With the drama and urgency of a sportscaster, statistics guru Hans Rosling debunks myths about the so-called "developing world."

And the best part about it is that the software is now available at the Gapminder website so you can play with it yourself and look at changes through time of all sorts of environmental, social and geographical parameters.

Wolfram Alpha

Kathy sent me some information about a new tool from Wolfram (the people that make Mathematica). It is called Wolfram Alpha and promises to change the way we use the internet for research. At the moment there is more hype than actual information but Kathy saw a demo and was impressed. Basically it looks like a search engine but instead of just searching for websites with keywords it will take questions in natural language and return answers, provided the data is available, even if no-one has addressed that question before.

There is clearly a huge market for such a tool. Currently there is a ton of data out there on the internet - but unless someone has already asked your question you are out of luck in getting a quick easy answer. Say I want to know the relationship between seed size and mature plant size, or how stomatal density varied over the Cenozoic, or how VO2 max varies with animal body size. Unless someone has already asked these questions I would be left to combine data sets on my own. If this product lives up to its promise it will present the data to me - and in graphical form. Cool. I'm sold. I like the last line in the blog posting:

I think it’s going to be pretty exciting. A new paradigm for using computers and the web.
That almost gets us to what people thought computers would be able to do 50 years ago!

Carbon dating and global warming

The prodigious mobilization of science that produced nuclear weapons was so far-reaching that it revolutionized even the study of ancient climates. Nuclear laboratories, awash with funds and prestige, spun off the discovery of an amazing new technique — radiocarbon dating.

The discovery of carbon dating is an interesting story in its own right and is described in several places, for example here. It is also described here, at the American Institute of Physics, part of a rather nice collection of essays on the discovery of global warming. The ratio of C-14 to C-12 on earth has varied significantly during the Earth's history. This variation is due to changes in the intensity of the cosmic radiation bombardment of the Earth, and changes in the effectiveness of the atmosphere in deflecting that bombardment. To compensate for this variation, dates obtained from radiocarbon laboratories are now corrected using standard calibration tables.

It was particularly interesting that, as Stuiver had suspected, the carbon-14 wiggles correlated with long-term changes in the number of sunspots. Turning it around, Suess remarked that "the variations open up a fascinating opportunity to perceive changes in the solar activity during the past several thousand years." The anomalies were evidence for something that many scientists found difficult to believe — the surface activity of the Sun had varied substantially in past millennia. Carbon-14 might not only provide dates for long-term climate changes, but point to one of their causes.

Toucan time

I put all the toucans on one page for convenience. If you click the image you should get a larger version - or if you click here you can get them as a pdf file that you can enlarge. Seeing all 16 toucans will actually help in picking characters but make it harder to construct the phylogeny. If you want to go hardcore you could construct the table of character states and then use a computer program to work out the most parsimonious tree.

There are numerous programs that can do this. The problem is that many of them do a great many things so can be difficult to get started with. I tried to find one that can do what we require here and SimpleClade looks like it will be up to the task.