My Year of Darwin 8/31/2014: Darwin's science for science's sake

"For myself I would, however, take higher ground, for I believe there exists, & I feel within me, an instinct for truth, or knowledge or discovery, of something same nature as the instinct of virtue, & that our having such an instinct is reason enough for scientific researchers without any practical results ever ensuing from them."  Charles Darwin,letter to J. S. Henslow, September 1848

Henslow is one of Darwin's mentors from his undergraduate days (see, we matter). And I get this. Science for curiosity's sake. Twice in our convocation the administration practical knowledge gained by our faculty as is science for science's sake was disdainful. That wasn't uplifting.  More internal grants available - that was. 

My Year of Darwin 8/30/2014: Highs and lows in taxonomy: end it!

"With respect to "highness" & "lowness", my ideas are only eclectic & not very clear. It appears to me that an unavoidable wish to compare all animals with men, as supreme, causes some confusion; & I think that nothing besides some vague comparison is intended or even possible, when the question is whether two kingdoms such as the articulata or mollusca are the highest. Within the same kingdom, I am inclined to think that the "highest" usually means that form, which has undergone most "morphological differentiation" from the common embryo or archetype of the class" Charles Darwin,letter to J. D. Hooker, September 1853

One of the issues I go over in our sophomore-level evolution and ecology course is that we should no longer use "higher" and "lower" when describing species when we should be using "ancestral" (changed less) and "derived" (changed more). Higher and lower imply attributes that are what? Organisms can be more derived and be morphologically simpler. Think of parasites. So I completely agree with Darwin and lets stop using it. 

My Year of Darwin 8/29/2014: more on species to Hooker

"Farewell, good luck to your work, - whether you make the species hold their heads or hang them down, as long as you don't quite annihilate them or make them quite permanent; it will be all nuts to me" Charles Darwin,letter to J. D. Hooker, September 1853

This is the same letter as yesterday. I imagine that if populations are just starting to split and you are only dealing with phenotypes then the differences between the populations are probably minimal. 

Happy Friday peeps. Lecturing on hypotheses and hypothesis testing today and maybe getting to some tests. 

My Year of Darwin 8/28/2014: The frustration of describing species and favorite

"After describing a set of forms, as distinct species, tearing up my M.S. & making them one species; tearing that up & making them separate, & then making them one again (which has happened to me) I have gnashed my teeth, cursed species, & asked what sin I had committed to be so punished." Charles Darwin,letter to J. D. Hooker and quoting Snagsby, September 1853

Darwin has been working on his barnacle book; having specimens sent to him from all over the world as he worked from home. He is working on the taxonomy of the group and I sense a small bit of frustration. 

My Year of Darwin 8/27/2014: Darwin hates homeopathy and other woo

"You speak to me of Homoeopathy, which is a subject which makes me more wrath, even than does Clair-voyance; clairvoyance so transcends belief, that one's ordinary faculties are put out of question, but in Homoeopathy common sense & common observation come into play, & both these must go to the Dogs, if the infinitesimal does have any effect whatsoever." Charles Darwin,letter to cousin W.D. Fox, September 1850

Homeopathy dilutes and agent to the point where the agent is unlikely to be in the sample. Water memory is invoked - that water remembers the property of the agent and applies it to the person. It's bullshit of course and we knew it was bullshit over 150 years ago yet I can go to Wegman's and pick up a bottle.

Sigh. 

My Year of Darwin 8/26/2014: Darwin, a skeptic of homeopathy

"I grieve to say that Dr. Gully gives me homoeopathic medicines three times a day, which I take obediently  without an atom of faith." Charles Darwin,letter to sister Susan Darwin, 19 March 1849

Awesome! 

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I big frustration, and I probably have remarked on this before, is the limits of my intelligence. 

I know, for instance, that I need to use a beta distribution to model the percent data I have for canopy cover. However, I struggle to turn that idea into BUGS/JAGS code. 

My Year of Darwin 8/25/2014:

"My dear Susan, As you say you want my hydropathical diary, I will give it to you - though tomorrow it is to change to a certain extent. - 1/4 before 7, get up, & am scrubbed with rough towel in cold water for 2 or 3 minutes, which after the first few days, made & makes me very like a lobster - I have a washerman, a very nice person, & he scrubs behind, whilst I scrub in front." Charles Darwin,letter to sister Susan Darwin, 19 March 1849

I was going to go through the Origin then another book but I realized that i would miss some letters and, consequently, some insights into Darwin's thinking. So back to some letters. 

Darwin was ill. Perhaps from Chagas disease - though not diagnosed. And Darwin was a man of his time and took the "water cure."  Though not treating the disease it did make him feel better at least temporarily. 

My Year of Darwin 8/24/2014: climate and populations

"Climate plays an important part in determining the average number of a species, and periodical seasons of extreme cold or drought seem to be the most effective of all checks." Charles Darwin, Origin of Species 2nd edition

Funny that he goes from saying that we don't know anything about checks to identifying the primary check.

My understanding of the role of climate is this: it is important for ectotherms  throughout their range and for endotherms on the fringes of their range. 

Climate is a big deal, which makes climate change a big deal. Duh! 

School starts tomorrow and a little distracted. 

My Year of Darwin 8/23/2014: Quantitative Darwin strikes again

"on a piece of ground three feet and two wide, dug and cleared, and where there could be no choking from other plants, I marked all the seedlings of our native weeds as they come up, and out of 357 no less than 295 were destroyed, chiefly by slugs and insects." Charles Darwin, Origin of Species 2nd edition

The Origin of Species is a book of awesome ideas and not so good experimentation - at least from a statistical point of view. 

Missed yesterday. Went down towards Allentown to a huge used furniture place, then to get some native plants at Edge of Woods Nursery, then some Cherry Divine wine at Wyncrest Vineyards, then the ALS ice bucket challenge, then some wine.   

My Year of Darwin 8/22/2014: What keeps organisms from increasing exponentially?

"The causes which check the natural tendency of each species to increase are most obscure." Charles Darwin, Origin of Species 2nd edition

I would say that this question went largely unanswered until recently. What was it that shed the most light on this question? Was it a technology? 

I would argue that the question of population regulation is best addressed analytically. Getting the data to answer the question is easy: counting babies, individuals, marking, capturing, etc. But the data by themselves tell us nothing. 

Leslie or Lefcovitch population models address this question directly and, though these tools have been a around for a few decades, the raw data, the computing power, and the stastical methods (e.g., Bayesian and maximum likelihood) were not able to come together until recently. 

I am disgusted when I hear Spanish in the States...

I am disgusted because I have trouble understanding. Being multilingual is a mark of an intelligent human with a liberal arts education - which I have. The more languages you know, the smarter you are considered (and probably are). I had two years of Spanish in high school, I've spent time in Mexico and Costa Rica, I have Mexican and Hispanic neighbors and I can barely read a menu at a Mexican restaurant. There is great literature in Spanish, I want to do research in Latin American, and there are some great TV shows. And all lost to me. 

I don't feel more patriotic because I don't know Spanish, I just feel dumber. 

This reminds me of a good test to see if you're racist:

If you think an old woman speaking Italian or Welsh is cute but an old woman speaking Spanish is annoying - you might be racist. 

My Year of Darwin: 8/21/2014 Represent, yo! That's what natural selection is

"A struggle for existence inevitably follows from the high rate at which all organic beings tend to increase." Charles Darwin, Origin of Species 2nd edition

Without any check, organisms increase exponentially. I've taken advantage of this with homebrewing and the population of yeast added to the wort. Biologists take advantage of this in microbiology. In the wild organisms do have checks - even if they initially increase exponentially. The struggle for existence is not species against species but individual against individual of the same species to leave more representatives in future generations.

But that's nature, and what lesson is there for human morality? None. Because it is too easy to cherry pick the case.