Tuesday, November 22, 2011

Darwin's Pilgrims: The Video

In February 2009, I hosted 'Darwin's Pilgrims": a visit to England by two Americans with links to the Dover Pennsylvania trial, Cynthia Sneath and Lauri Lebo, and Canadian Lit Hop artist Baba Brinkman to celebrate Darwin's 200th birthday. The trip involved a "pilgrimage" to Darwin-related sites and a series of performances in English cities, including the premiere of the Rap Guide to Evolution. Previous blog posts captured the spirit of the event
But this is the first time I have presented the complete video, covering trips to Malvern, Cambridge and London, even though I finished it a couple of years ago. I hope you enjoy the footage and the great music! For a bunch of non-believers, we spent a lot of time in churches!

Monday, November 21, 2011

Don’t want to believe in evolution?

Is it possible to be a rationalist (a believer in the laws of logic) but not believe in evolution? Just about! But only just!

There are several philosophical show stoppers that bring rational argument to a halt.

Perhaps requiring the least mental gymnastics is the "Omphalos hypothesis", so-named after an 1857 book by English naturalist (and local Worcester man) Philip Gosse. Gosse argued that even if creation occurred from nothing, the creator would necessarily leave traces of previous existence that had never actually occurred. Although Adam was never hooked up to a placenta, he required a navel ("omphalos" in Greek) because it made him a complete human being. Similarly, God must have created trees with rings that they never grew and rocks with a fossil record of life that never actually existed.

This kind of thinking has drawn adverse responses from Catholic scientist Ken Miller and the "Zoo Rabbi" Natan Slifkin, who both reject it as depicting God as a dishonest charlatan. A secular response, Last Thursdayism, proposes, that by this logic, the world might just as easily have been created last Thursday, but with the appearance of age such as false memories and fictitious history books. There is even a parody religion, The Church of Last Thursday.

The first real philosophical show stopper is metaphysical solipsism: the belief that you, the reader, is all there is and that this blog and this author, this world and the evolution of life in it, are all just figments of your imagination. However, it is scarcely possible to hold this belief in your mind for even a minute and, as English philosopher Bertrand Russell once pointed out, solipsism
“is rejected in fact even by those who mean to accept it. I once received a letter from an eminent logician… saying that she was a solipsist, and was surprised that there were no others. Coming from a logician and a solipsist, her surprise surprised me.”
One modern variant on solipsism is the brain-in-a-vat idea, taken seriously by, among others, Berkeley philosopher Barry Stroud. In this scenario, your brain has been removed from your body, placed in a vat of life-sustaining liquid and your neurons hooked up to a supercomputer that provides you with a virtual reality indistinguishable from any “real” reality. So, the argument goes, if you are in a vat, all your conclusions about evolution in the real world are false. And, as you have no way of knowing whether you are in a vat or not, this leaves you free to doubt the reality of evolution.

But why suppose you ever had a body in the first place, why not suppose you are a disembodied brain created yesterday with false memories of a biological world built by evolution? Some cosmologists are seriously discussing the idea of Boltzmann brains, self-conscious entities that arise from random fluctuations in vacuum energy (named after Austrian physicist Ludwig Boltzmann, who suggested that the whole universe resulted from such a fluctuation). If the universe lasts long enough, such entities are inevitable, say the cosmologists. But why stop at a brain—viewing yourself as a Boltzmann-brain-in-a-vat breaks none of the laws of physics and also gets you off the hook of having to believe in evolution.

A more general case of the brain-in-a-vat idea is the simulation hypothesis. According to this viewpoint, popularized by the Matrix films, we are all living in a simulated reality, run on a computer powerful enough to create a internally consistent simulation, so detailed that it could not be distinguished from “real” reality. Swedish philosopher Nick Bostrom argues that it is more likely than not that we are living in such a simulation. His argument rests on the assumption that any sufficiently advanced civilization capable of creating simulations that contained intelligent individuals would be unlikely to restrict itself to a single simulation, instead, it would run billions of them. Thus, he asks, why suppose that we are the one civilization that develops the simulations rather than one of the billions run in simulation? Richard Dawkins points out that this merely pushes the need for evolution back stage as the only plausible source of the intelligences running the simulation.

Mathematical physicist Frank Tipler has controversially attempted to interweave cosmology, simulation and religion. He posits that as the universe comes to an end in a singularity, the computational capacity of the universe will outrun time, so that an intelligent civilization could run an infinite simulation within a finite time. Tipler borrows a term from Pierre Teilhard de Chardin to describe this final state of infinite information the Omega point. Recently, Tipler has come to identify his Omega point with God and to equate the associated infinite simulation with the resurrection of the dead. But why not assume we are already dead in Tipler’s sense, i.e. already living in his Omega point simulation and thus free to dispense with any direct evolutionary explanation for our own origins?

How is an evolutionary biologist to respond to all this? The obvious response is to adapt a line from George Orwell and say that you have to be a real philosopher to believe all that, no scientist could be so foolish! In fact, insofar as none of these scenarios is verifiable, they fall outside the realm of science and bring no additional explanatory power. So, you don't really have any excuses for dismissing evolution! Wise up and smell the cladogenesis!

Sunday, November 20, 2011

Bio380 Human Evolution Genes and Genomes Bioinformatics Practical

I have a bioinformatics practical class tomorrow and rather than hide it away, I thought I might as well share it with the world via this blog. Happy to receive comments on any mistakes or suggestions for improvements or additional reading.

Bio380 Human Evolution Bioinformatics Practical 2011

Follow this link to the entry for the FOXP2 chimpanzee protein:
Take a minute to explore the information on the page.
  • Q. What is the evidence that this gene is functional in the chimpanzee?
  • Q. Why is this entry called FOXP2_PANTR
  • Q. What does the Forkhead domain do?
Scroll down to the sequence at the bottom of the page
  • Q. What is unusual about the first third of the protein sequence?
Click on the pop-up Fasta view button
  • Q. What is a FASTA sequence?
Select the sequence that pops up and copy it to the clipboard. Then return to the previous window.

Open in a new tab and go to http://www.ncbi.nlm.nih.gov/BLAST/
Select “protein blast”
  • Q. What is BLAST?
Paste the FoxP2 FASTA sequence into the search box. Click on the algorithm parameters link, then tick the box indicating Filter low complexity regions
  • Q. What does this do?
Start the Blast search. The Blast search may take some time, so open a fresh tab and go to http://www.uniprot.org/
Search for “foxp2_human”
Spend some time exploring the information therein, while you wait for the Blast search to finish.

Return to the Blast search result. Scroll through the results. In the segment of the query spanning residues 241-698, how many differences does the chimp protein show from the following:
Orang utan (Pongo pygmaeus) Gorilla (Gorilla gorilla)
Lar gibbon (Hylobytes lar) Macaque (Macaca mulatta)
Horse (Equus cabellus) Mouse (Mus musculus)
Humans (Homo sapiens)
PS: use the sequence with header "FoxP2_Human"
  • Q. What differences do you find?
  • Q. How conservative or radical are the changes in amino-acid properties?
Go to http://www.nature.com/nature/journal/v418/n6900/full/nature01025.html
This paper suggests that the human sequence undergoes an additional post-translational modification compare to the chimp sequence
  • Q. What is this difference and how significant is likely to be?
Go to http://www.ncbi.nlm.nih.gov/omim
Search for FoxP2, then click on the first entry and explore the information therein, particularly that under the Evolution heading.
  • Q. Does this confirm or deny any of your previous conclusions?
Follow the link to this recent paper:
Speed-read the abstract and introduction
  • Q. On the basis of this, would you expect Neandertals to be able to speak?
  • Q. What would you expect their FoxP2 gene to look like?
Follow this link to another recent paper
  • Q. What do you conclude?
Now read these blog entries
  • Q. Do your conclusions change?
  • Q. Are blogs are useful source of scientific information?

The genome of James Watson, Nobel laureate and co-discoverer of the structure of DNA can be found here: http://jimwatsonsequence.cshl.edu/

  • Q. Is Jim Watson a black man?
And, finally, is Watson’s recent gaffe on race more likely to be due to:
  1. A single gene disorder (the “butt-head racist gene”?)
  2. A polygenic disoder (the “butt-head racist gene complex”?)
  3. The racist culture in which he grew up?

Sunday, November 6, 2011

Darwin and Mendel: The Great What If?

Charles Darwin and Gregor Mendel were contemporaries. One of the great “what ifs” in the history of science is “what if Darwin and Mendel had met to discuss each other’s work, or, at least, had exchanged notes?”

The closest they came to meeting was in the summer of 1862, when Mendel visited England to attend the International Exhibition, a world fair held in South Kensington. Charles Darwin was less than twenty miles away, but their paths never crossed as the Darwins were stuck at home, nursing their son Leonard through scarlet fever.

Mendel read a German translation of Darwin’s Origin before publishing his seminal paper in 1865, but he did not see any connection between his work and Darwin’s. It has been claimed that Mendel’s paper sat on a shelf at Down House, unread, but this is just a myth. Although Darwin possessed two books that briefly referred to Mendel’s work, there is no evidence that he read the relevant sections; in one of the books, the pages are clearly uncut. Darwin leant one of these two books to his friend George Romanes, who used it to write an encyclopedia entry, priming another myth: that Darwin wrote about Mendel in the Encyclopaedia Britannica.

How close was Darwin to discovering Mendel’s laws of inheritance? As early as 1838, Darwin scribbled in his notes a question that, in retrospect, seems pregnant with potential: “Do races of peas become intermixed & gardener have hybrid seedlings?” In a letter written to Wallace in February 1866, Darwin recognizes that inheritance can be non-blending:

“My dear Wallace… I do not think you understand what I mean by the non-blending of certain varieties… I crossed the Painted Lady and Purple sweetpeas, which are very differently coloured varieties, and got, even out of the same pod, both varieties perfect but not intermediate.”

Furthermore, as Chinese plant scientist Yongsheng Liu has pointed out, Darwin describes experiments that are uncannily similar to Mendel’s, in his 1868 work Variation Under Domestication:

Now I crossed the peloric snapdragon… with pollen of the common form; and the later, reciprocally, with peloric pollen. I thus raised two great beds of seedlings, and not one was peloric. The crossed plants, which perfectly resembled the common snapdragon, were allowed to sow themselves, and out of a hundred and twenty-seven seedlings, eighty-eight proved to be common snapdragons, two were in an intermediate condition between the peloric and normal state, and thirty-seven were perfectly peloric, having reverted to the structure of their one grandparent…”

The ratio, at 2.4 to 1, is close enough statistically to conform to an expectation of 3 to 1, so this might count as a glimpse by Darwin of Mendel’s first law.

But given that Mendel himself did not recognize the universality of his own work, it is unfair to expect Darwin or anyone else to do so, particularly in the face of less easily interpreted results from crosses in other species of plants and animals. Instead, the modern synthesis of Darwin's and Mendel's work had to wait until the mid-Twentieth Century.


The extent of Charles Darwin’s knowledge of Mendel by Andrew Sclater

The Monk in the Garden: The Lost and Found Genius of Gregor Mendel, the Father of Genetics by Robin Marantz Henig