by Matthew Cobb
The Howard Hughes Medical Institute has created a fantastic little set of slides to help everyone – students, the lay-person – understand how we make what are called ‘phylogenetic’ trees from DNA data. These trees show the patterns of relatedness between organisms, and have changed the way we understand the tree of life. We have regularly referred to them here, including the notorious discovery that insects are crustaceans!
This exercise takes about 20 minutes to complete and can be found by clicking on the picture above. Click on the “Start Click and Learn” symbol to get going. There is also a worksheet you can go through – or use with students if you are an educator. I think this would be suitable for any age from 16 upwards.
Read it all and be enlightened!
This is great! Thanks Matthew.
very interesting.
Just a reminder: the 30 min. conversation on the site – religionforlife.podomatic.com has Jerry’s interview for anyone who missed it.
I should pass on a comment regarding the interview just in case some might not hear it. A very friendly interview, which is good because that means Prof. Coyne gets to talk more. One important note about a comment the interviewer made that I had not heard before:
Galileo put g*d out of the home and Darwin put him out of a job. Not sure if Jerry had heard this one either but he had a good reply – something like, He may be out of a job but there are many keeping him on welfare.
Pretty good, though one might wish they had concentrated less on “more similar, more closely related”, which, though easy to explain, is also one of the more common misconceptions about how phylogenetic methods work.
For anyone with expertise on systematics:
Could you discuss if it is true that Popperian philosophy is used in systematics to validate cladistics?
Is this something that is relevant to most taxonomists or is it a vocal philosophy-bothered few?
It has been used by some; in fact Popper is quite popular with the Willi Hennig Society and its journal Cladistics.
But it’s the second of your two options. What most systematists care about isn’t philosophical validation but whether a particular model of evolution approximates the truth closely enough to provide a valid analysis of data. And that’s an empirical question, not a philosophical one.
Popperian philosophy is invoked by systematists but is not actually used to reconstruct phylogenies. If you take seriously the idea that, in a DNA alignment, a site falsifies a tree when it does not perfectly fit it, you are in trouble, because all trees will be falsified by one site or another.
But some schools of systematists like to believe that they are being Popperian, so they describe what they are doing that way.
Doesn’t seem different than any other scientific field or research. It does sound full of pomp to call oneself “popperian”!
It depends on whether you can do an experiment that absolutely rules out one hypothesis. Then you can be Popperian.
But in systematics, and in molecular evolution, outcomes have a lot of randomness in them, or at least a lot of uncertainty of interpretation. So using Popper’s terminology is not appropriate.
But even in the case of the conclusive experiment, we generally want *confirmation* and connection to background knowlege too. But in Popper’s PoS *there is no such thing*, so Popper’s philosophy of science is too simple. However, he was right to suggest that low-level hypotheses should be falsifiable and to indict certain aspects of (e.g.) psychoanalysis for that reason.
Great comment! I don’t think it’s really worthwhile trying to assess the relative merits of each aspects of inquiry. Scientific ideas and facts should be shown to be true by whatever way works.
I produced my first tree on a 286. Had to run it overnight, with PHYLIP. Thanks Joe.
You’re welcome. But probably the readers here don’t recall what “a 286” was.
FYI, I produce my first tree on a mainframe using PHYSYS. Apparently some universities actually paid for it.
This is fascinating. Thanks for sharing.
You’re welcome. But probably the readers here don’t recall what “a 286” was.
Oops, this reply was meant to go upthread, where I reposted it.
Waaaaay cooool! Thanks, Matthew!
This is fantastic, thanks so much. Phylogenetic inference is one of major areas of interest, and I’ve been looking for a resource like this to pass around to folks who want to learn the basics of what it’s about.
I am picking my way through. It is a pretty basic activity, but still well made (of course!)
That was so well done that even a dummy with a Communications degree could follow it.
It even made perfect sense to me, so don’t be scared off if you’re not a scientist and are pretty ignorant on the topic!
Thanks Matthew. 🙂
This looks great, Matt. I must confess myself a little hazy on how this is done. Thanks!
sub
That was a great little slide sequence!
One serious suggestion though:
While the embedded short videos were perfect for the bits like Prof. Olivera explaining cone snail trees, they should really get one of their 14-year-old friends to teach them the wonders of how to embed .gifs for the shorter bits.
There’s no sense in 2015 in clicking on a 20-second .wmv to watch a “G” replace a “T”.
A nice little review after having taken Mohamed Noor’s wonderful on-line intro course on genetics and evolution.
Is there a known difference between SNP and Indel rates? I would imagine that SNP is more common but I’m no biologist. I also assume that this would be important information for determining how long ago two species have diverged.