Evolution is, in fact, a theory, not a fact.

I made my first post on Daily Kos this morning.

It was well received. Six and half hours after I posted, it, there are almost 500 comments, and more than 1400 people have voted in my poll.

Close to 1000 of those agreed with the statement, " Evolution is the only non-idiotic way to explain the data."

The text of the post was as follows:

I've decided to start my diarying with a couple of entries about evolution. I'm working on my PhD in evolutionary biology, and while I can tell most people here understand that there is no logical way to reject evolution, I thought it might be helpful to clarify a few important points about evolution. Those who reject evolution often use the inconsistencies in the understanding of those they argue with to "prove" that evolution does not make sense. So I'd like to see us all on the same page.

For those of you who reject evolution as a matter of faith, it is not my goal to convince you of anything. If you were open to being swayed by facts, reasons or logic, it would, by definition not be faith. If you like, imagine this was written in a fantasy realm in which evolution is real and your genetic code is 95% identical to that of a chimp. I don't want the comments section to turn into an argument about whether evolution is real or people on the other side are questionable. No one is going to change his mind on the topic.

With no further ado, I list insights about evolution after the jump.
Intro

I've decided to start my diarying with a couple of entries about evolution. I'm working on my PhD in evolutionary biology, and while I can tell most people here understand that there is no logical way to reject evolution, I thought it might be helpful to clarify a few important points about evolution. Those who reject evolution often use the inconsistencies in the understanding of those they argue with to "prove" that evolution does not make sense. So I'd like to see us all on the same page. For those of you who reject evolution as a matter of faith, it is not my goal to convince you of anything. If you were open to being swayed by facts, reasons or logic, it would, by definition not be faith. If you like, imagine this was written in a fantasy realm in which evolution is real and your genetic code is 95% identical to that of a chimp. I don't want the comments section to turn into an argument about whether evolution is real or people on the other side are questionable. No one is going to change his mind on the topic. With no further ado, I list insights about evolution after the jump.


1. A fact is the most trivial piece of science. A theory is the most complete.

"The average density of granite is 2.75 g·cm^-3," is a fact. Facts are important, but are the starting point, not the goal. To a scientist, theory is the entire body of understanding about a particular phenomenon, the best unifying description of all the relevant facts. Theory is the whole structure of knowledge. To say that "evolution is a fact" is like saying "the Himalayas are a stone."

2.

Nothing in Biology Makes Sense Except in the Light of Evolution

Theodosius Dobzhansky (1900-1975)
(see http://www.2think.org/... for a truly classic essay.)

Evolution is the central organizing principle behind biology. Without it, biology is a list of facts and equations, a series of observations. You can study the various types and formations of igneous rock, learn that pumice is useful for this and basalt for that, but without knowing that there was molten rock involved, your understanding would be pretty limited. This is very equivalent to trying to understand biology without evolution.

3. We are all highly evolved.

Because all organisms have evolved from a common ancestor, we all have as many years of evolution behind us. Bacteria, often seen as the least evolved, actually evolve a lot faster than we do. We see the traits that are human like as being "highly evolved." Yeah us! But when we do this, it is just chauvinism.
Evolution does not push towards any kind of subjective perfection.
In order to pass on its genes, an organism needs to be as good or better than the competition. It does not need to be morally or intellectually appealing. It does not need to be perfectly efficient or maximally beautiful. It just needs to be good enough to get past the competition.
The popular view of evolution is a progression from bacteria to squiggly guys to fish to lungfish to amphibians to reptiles to mammals to primates to great apes to Neanderthals to cavemen to us us US, the pinnacle of God's design! But wait, we are talking about science here, no supernatural explanations need apply. If we overcome our religious biases and our anthropocentrism, it becomes clear that the world's organisms are not striving to be us. Some populations evolve to be bigger, others to be smaller. Brains get bigger and smaller. Number of limbs increases and decreases. There is no direction to it. Every population just drifts towards whatever happens to encourage survival and reproduction in their peculiar environment at that moment. There is no force driving things towards being human like.
Because there is no direct to evolution, the term "devolve" is not one that has a biological meaning. See
http://en.wikipedia.org/... for a discussion of misunderstanding and misuses of "devolution."
A trait can be highly evolved, in that it has changed a great deal from the ancestral state (e.g. frogs have a highly evolved pelvis) but after billions of years, all organisms are highly evolved.

4. Biologist don't, and will likely never, agree how to define "species."

In a creationist world view, it is easy to define a species. The decedents of each pair of organisms that lived on Noah's ark form a species. Simple process leads to easy defining.

The problem is, looking at the diversity of life, we find much more complexity, much more messiness than can be explained through static, preordained species. A single "species" can have tremendous geographic variation. Oaks hybridize like mad. Salamanders that look like the same species won't interbreed, except in particularly wet years. Salamanders that can't interbreed with each other will both interbreed with an intermediate population. Some populations, through spontaneous mutation, spawn clonal populations that don't breed with anybody. There is a tremendous diversity of process.

Pity the poor taxonomist. Everyone expects a list of species, the laws are written around endangered species and migratory species, which means we have to decide what is a species, and what is not. If two populations interbreed only once every thousand years, are they one species or two? If two groups swap nuclear DNA but not mitochondrial, can they be considered separate? Can species be delineated based on ecological traits? On behaviors? What does the word species mean when applied to organisms that reproduce asexually?

There are literally hundreds of definitions of species supported by different biologists. And there is no one right definition; the underlying process that we are trying to shoehorn is so complex that every conceivable definition simply won't work in some cases. In order to applicable in all cases a definition would have to be so broad that it was applicable in none. No matter how much data we have, there is no final answer to how many species are out there, because no single definition can be applied. Nature is messy, and doesn't read our rule books.

5. Not all evolution is because of natural selection.

Biological evolution is the heritable change in populations over time. Natural selection is one extremely important factor in driving heritable change. But it is not the only one. In small populations, there is genetic drift. A trait that is in no way advantageous can increase in frequency simply because the two guys who happen to have that trait also happen to impregnate a whole bunch of females. Mutations in and of themselves constitute evolution. Basically, in order to avoid evolving, a population would have to be infinitely large, completely homogeneous, in a completely stable environment, under no selective pressures and without either a dearth or a glut of disadvantageous mutations.

6. Evolution is an ongoing process.

I often hear people say things along the lines of, "back in evolutionary times" or "when evolution was happening." Evolution is happening now. Humanity is currently evolving. Certain populations are increasing while other with different genetic backgrounds are decreasing. Change in genetic make up of the population over time is evolution. That is how geneticists define evolution. Humans are also undergoing selective evolution, and specific genes have been identified that are currently being selected for or against. Our genes for disease resistance are under particularly strong selection.

7. Evolution can act incredibly rapidly.

Spray a field with an insecticide. There are a million crickets in the field. 9,999,998 of them keel over. The remaining two survive because they happened to have a mutation that made them resistant to the insecticide. The male calls, the female comes, candles, moonlight. 100 resistant baby crickets. The farmer comes back and sprays again. Maybe half the crickets die. The remainder all carry the resistance gene. Repeat the process and the gene that causes resistance becomes more common with each generation. Pretty soon most of the crickets have not one but two copies of the resistance gene, having gotten one from each parent. The population has evolved to be resistant. This is also why we have antibiotic resistant bacteria. And why the Cane Toad, introduced into Australia, can now survive in habitats much drier than they could have a few decades ago.

9. Almost everything you have ever read about evolution in the popular press gets it wrong.

Populations do not evolve in order to achieve a certain goal. Biologists do not disagree about evolution any more than geologists disagree about tectonics. Individuals do not act for the good of the species (present company excepted, of course). Darwin did not coin, or like, the term "survival of the fittest." Our ancestors did not look like modern day chimps. We are not descended from the lungfish. There is no such thing as "adaption." Darwin did not base his theory of evolution primarily on Darwin's Finches. Darwin did not set out to form a theory of evolution. His main interest was barnacles.

Evolution is that heritable change in populations over time. There is no way for an individual to evolve. An individual can reproduce, or die, and contribute to the evolution of her species. But there is no biological evolution of individuals.

10. Darwin got some details wrong.

Darwin had no clear concept of genetics. Mendel sent Darwin a copy of his book. Darwin never opened it. Darwin made lots of wild guesses as to the mechanisms behind heredity, and some of those guesses lead him down dead ends. Modern biologists are awed by Darwin's genius, but we are not under the delusion that he had all the answers, nor are we simply accepting him at his word. Many of Darwin's guesses have been shown to be sound. Others have been shown to be flawed.

Tell me what you think. Let me know if you disagree with something, or want a source or more information. There will be some slightly more provocative evolutionary musing tomorrow.

Professional science is hard

Late at night, with a weary brain, I attempted to document some of the process of data analysis, typesetting, and the general level of complexity involved in the production of a moderately novel physics journal article. Using direct-screen-capture video software, I just flipped through the content that I have been staring at for weeks, giving a 4 minute silent film of my work. The production of this low-res video was a greatly refreshing 6 am escape from my writing, and stands as a slightly surreal and fuzzy look at the reality of being a physicist. Do not attempt to understand any technical content, that is not the point, this is just art therapy for the sleep-deprived.

If I had to choose a sound track to this, the first thing that comes to mind is the scene at the end of 2001 where Dave has to float into the airlock, and then slowly, manually deactivate the optic circuits of Hal.

Here it is:

From Data to a Paper

- Let me know any reactions that this may incite,

Stephen

20,000,000 years of evolution, killed as bycatch

" First human-caused extinction of a cetacean species?"

Abstract from Biology Letters:
"The Yangtze River dolphin or baiji (Lipotes vexillifer), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November–December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis)." (emphasis mine)

BBC coverage

A Deluge of Data

The International Species Information System is an organization charged with coordinating data gathering, storage and usage among zoos and aquaria around the world. They started out keeping track of things like which zoos had which animals, how individuals were related to each other and so on. Over time they have come to have enormous demographic and physiological databases and they hold individual data on millions of captive animals.

These data were originally collected for the use of ISIS member organizations in the management of their captive populations, but as the amount and quality of data has improved, these data sets have becomeof interest to a wide range of other researchers.

In my work, I am interested to know for as many species of primates as possible, whether the males live longer, the females live longer, or the longevity of the two species is approximately the same. I am specifically interested in the capacity for longevity of each sex of each species, rather than how long they live when exposed to disease, predators and famine. And so when I heard that ISIS had longevity data on hundreds of thousands of captive primates, I was very interested.

But of course, there are problems. The data were collected by, and are owned by, ISIS's member organizations. The fact that they were collected in a decentralized way means that a chimp can be recorded as having been born in 1692 when it was probably born in 1962. Some individuals have birth dates recorded, but no death dates, and so on.
Also, the zoos consider this type of data to be potentially sensitive. No zoo wants to be known as the zoo where Gorillas have the shortest life expectancy. So the data needed to have all possible identifying information removed before ISIS could get permission from the zoos to share the data with researchers. And only someone who is really familiar with zoo data could prune the bad data, process the data into sex*species specific life tables and get approval to let me use these.

Enter Laurie Bingaman Lackey of ISIS. She agreed to get me as much of the data as she could. But she is a busy woman, and this was for her basically a side project, undertaken to help me and get her name on a paper or two. And she had to go through each species individually, look for bad data, compile a life table from what remained. So it took a little over three years to get the data to me. Sex specific life tables for all 120 species of primates that ISIS has enough data on for my purposes. A Herculean effort. Now that I have the data, I have to remember what exactly I was going to do with them.