Tuesday, September 30, 2014

My Year of Darwin 9/30/2014: Death and destruction everywhere: but it isn't so bad!

 Charles Darwin

"It is good thus to try in imagination to give to any one species an advantage over another. Probably in no single instance should we know that to do. This ought to convince us of our ignorance on the mutual relations of all organic beings; a conviction as necessary as it is difficult to acquire. All that we can do, is to keep steadily in mind that each organic being is striving to increase in a geometrical ratio; that each at some period of its life, during some season of the year, during each generation or at intervals, has to struggle for life and to suffer great destruction. When we reflect on this struggle, we may console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, that death is generally prompt, and that the vigorous, the healthy, and the happy survive and multiply." Charles Darwin, Origin of Species 2nd edition


This passage closes the change Struggle for Existence & he was just discussing that competition is strongly within species and then varieties within species and then between closely related species. So the advantages he alludes to would be within a species or closely related species and I suppose he's is suggesting something like disease resistance, climate adaptations, better escape from predators. These are things we can think of but are these the actual causes of success and failure - that is what, at the time, we weren't sure about. And I would suggest we still are largely ignorant of genotypic differences between individuals and their consequences on fitness. 

Monday, September 29, 2014

My Year of Darwin 9/29/2014: Owen the Jerkasaurus

 Charles Darwin

"I added that I would endeavor to modify the 'believes' & 'convinced.' He took me up short, -'You will then spoil your book, the charm of it is that it is Darwin himself.' Charles Darwin, Letter to Charles Lyell, December 1859

Owen's beef with Darwin was that Darwin was too inductive - extrapolating conclusions without properly testing those ideas. We often get caught up in hypothesis testing. The National Science Foundation, seeks applications with "tight" hypotheses but we should never forget that the greatest advances in science were inductive leaps: the double helix of DNA, the big bang, and anything Einstein put forward. It isn't that all inductions are equal but those that are tested and whose metal proves toughest should be commended. 

Sunday, September 28, 2014

My Year of Darwin 9/28/2014: Lyell, if I convert you, I'm done

 Charles Darwin

"I cannot too strongly express my conviction of the general truth of my doctrines, & God knows I have never shirked a difficulty. - I am foolishly anxious for your verdict. Not that I shall be disappointed if your are not converted; for I remember the long years it took me to come round; but I shall be deeply delighted if you do come around, especially if I have a fair share in the conversion. I shall then feel that my career is run, & care little whether I ever am good for anything again in this life...Charles Darwin, Letter to Charles Lyell, September 1859

There's one thing I have noticed about scientists of a certain age - they want to leave a legacy. Early in life it is about feeding the ego: getting the papers out, producing lectures, getting the grants. My sample size is small and only men - but this is what they're saying. For Darwin, it is convincing the geologist Charles Lyell that organisms can, and have been, evolving. 

For me, I'd like to convince my community (1) that tropical bird populations respond to human disturbance as a result of altered abiotic changes and (2) presenting the probability of your hypothesis instead of p-values.  

Saturday, September 27, 2014

Lacawac This!

Spent the afternoon at the Lacawac Ecology Conference at the Lacawac Sanctuary

Best thing was catching up with John Steffen - we did our Ph.D.'s together at Auburn and he ended up at Penn State - Erie and is working on coloration in turtles. Gave a great talk about it. The plenary was particularly interesting - mosquitoes and urbanization. Something I've been interested in for some time (though I would like to know how that affects birds). 

There were a number of talks about lakes. Interesting stuff and there's a network of limnologists studying lakes in the context of changing climate. Quite clear that North American lakes are seeing the effects of warming. East Stoudsburg University had three talks: an intro to the wildlife genetics lab, a talk about ticks in Warren County, NJ (where I used to hike), and a talk on plant genetics (to do forest forensics!). 

The site was gorgeous. Fall colors were just coming in around the lake. A bear walked by twice and I caught a glimpse the second time. Looked like a teenager wearing over sized black pajamas.  Food was great (wraps and sandwiches). And the cookies... perfect. The lodge was super-swanky for a field site. Must return. 

I'll be back next year! 

My Year of Darwin 9/27/2014: To hell with Owen

 Charles Darwin

"Owen, I do not doubt, will bitterly oppose us; but I regard this very little; as he is a poor reasoner & deeply considers the good opinion of the world, especially the aristocratic world.Charles Darwin, Letter to A.R. Wallace, April 1859

Sir Richard Owen is not remembered well. Though he gave dinosaurs their name (and it was a good one - "terrible lizard"), he opposed evolution and, in particular, the idea that man and ape shared common ancestry. He lost (though many cling to the same ridiculous notion).
Portrait of Owen from Wikipedia

Friday, September 26, 2014

My Year of Darwin 9/26/2014: Darwin the Evangelist

 Charles Darwin

"I forget whether I told you that Hooker, who is our best British Botanist & perhaps best in the World, is a full convert, & is now going immediately to publish his confession of FaithCharles Darwin, Letter to A.R. Wallace, April 1859

Wallace independently (we think) came up with natural selection so he a co-conspirator with Darwin. Origins, the manuscript, is about to be in the hands of the publisher. Darwin's health is crap but he must be excited at this point to see his book - his very own ideas - go to the press. 

Interesting use of terms and probably appropriate. I've seen arguments (mostly on Facebook, of course) by creationists that evolution is a religion - and the evolutionists deny. But I'm totally OK if you consider evolution a religion if you define religion as a world-view. Then evolution naturally follows a naturalistic world view - though this would change if evidence, yes evidence, were provided that evolution wasn't true. If you consider religion to be something based solely on argument from authority - then no, evolution isn't true. As for the word faith - that comes down to how you're using it. 

And I'm totally cool with saying I believe in evolution. Much as I believe gravity pulls me to the earth and the sun will rise tomorrow. 

Thursday, September 25, 2014

And today on Youtube: Ellen and Machine Learning

There was funny and statty (and still kinda funny).

First, the funny:

Then there was the statty. I haven't watched the whole thing but I watched the first half twice. These guys are well known statisticians and I'm looking forward to listening to the whole series on machine learning. They have some interesting commentary on the state of statistics. 

My Year of Darwin 9/25/2014: Origin: read it all or read nothing!

 Charles Darwin

"P.S. I would add that it is impossible for you or anyone to judge of real merit my Book, without reading the whole, as the whole is one long argumentCharles Darwin, Letter to Origins publisher John Murray, April 1859

One Long Argument is the name of a 1993 book by Ernst Mayr on the history of evolutionary thinking.  At the time at would entirely agree. Now I like going through and reading bits and pieces. I find it amazing and I learn something every time I read it and I'm now on my fifth or sixth iteration.  

And I need to come up with a lab on natural selection in two days. Eek! 

Wednesday, September 24, 2014

My Year of Darwin 9/24/2014: "Natural Selection" almost wasn't

 Charles Darwin

"I am, also, sorry about term "Natural Selection", but I hope to retain it with Explanation, somewhat as thus, - "Through Natural Selection or the preservation of favoured races"
  Why I like the term is that it is constantly used in all works on breeding, & I am surprised that it is not familiar to Murray; but I have so long studied such works, that I have ceased to be a competent judge." Charles Darwin, Letter to Charles Lyell, January 1859

Murray is the publisher of Origin but apparently objected to the use of "natural selection."  I wonder what alternative was suggested: I'm not sure if survival of the fittest was suggested to Darwin yet (by his cousin Herbert Spencer). I need a first edition to look over.