Saturday, February 06, 2016

A DNA quiz

Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.

I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.

Try the quiz yourself before reading any further. There are spoilers below!

Tuesday, February 02, 2016

What is "structuralism"?

The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.

You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.

Saturday, January 30, 2016

The most intellectual creationists explain why there are still Darwinists when Darwinism has been falsified

You are probably wondering why "Darwinism" persists after the creationists have thoroughly demonstrated that it is a failed theory. Lucky for you, the most intelligent and intellectual of all Intelligent Design Creationists, David Berlinski and Michael Denton, have gotten together to explain it in a short (15 mins) podcast.

It's moderated by David Klinghoffer who introduces it like this ... [Michael Denton and David Berlinski Discuss: How Does Darwinism Hang On?]
If the most brilliant Darwin critics, like David Berlinski and Michael Denton, are right, how then does Darwinism hang on? How does a failed theory maintain its grip on our science and on our culture? Why is there a sense of stalemate? On ID the Future, we posed these questions to Dr. Berlinski and Dr. Denton.

If you are interested in the conflict between Intelligent Design and science you owe it to yourself to see/hear the best they've got on their side.

ID the Future: More Berlinski and Denton.

Friday, January 29, 2016

Berlinski and Denton challenge Darwinism

It's fun to listen to the "ID the Future" podcasts. It shows us the very best of Intelligent Design Creationists. This time we get a twofer— David Berlinski and Michael Denton posing their most challenging questions to Darwinists. Here's how David Klinghoffer introduces the pair ... [Berlinski and Denton: If You Could Pose One Challenge to a Thoughtful Darwinist, What Would It Be?].
You can always dream. While the evolutionist side in the Darwin debate is long on rhetoric and insults, serious debate or dialogue is woefully rare. But imagine you had the opportunity to sit down with a thoughtful, honest, well-informed Darwinist and pose one question or challenge. What would it be?

I had the opportunity to pose that question to two of the most brilliant minds in the intelligent design community -- Michael Denton and David Berlinski. Take a well-spent 15 minutes and listen to their answers -- focusing respectively on the insect body plan and the enigma of whale evolution -- recorded as an episode of ID the Future.
Berlinski wants a detailed mathematical estimate of the number of mutations required to go from a land animal to a whale. Denton wants details on the formation of insect body plans.

It's important to note that these are questions about the history of life. You could easily answer "I don't know" to both questions and it would not affect our understanding of evolution and common descent one iota. The answers have nothing to do with "Darwinism" per se and nothing to do with evolutionary theory (which is not Darwinism).

Listen to the very best minds in the Intelligent Design Creationist community ... and weep for them. This is all they've got.

Id the Future: Berlinski and Denton

Thursday, January 28, 2016

"The Selfish Gene" turns 40

Richard Dawkins published The Selfish Gene 40 years ago and Matt Ridley notes the anniversary in a Nature article published today (Jan. 28, 2016): In retrospect: The selfish gene.

I don't remember when I first read it—probably the following year when the paperback version came out. I found it quite interesting but I was a bit put off by the emphasis on adaptation (taken from George Williams) and the idea of inclusive fitness (from W.D. Hamilton). I also didn't much like the distinction between vehicles and replicators and the idea that it was the gene, not the individual, that was the unit of selection ("selection" not "evolution").
It is finally time to return to the problem with which we started, to the tension between individual organism and gene as rival candidates for the central role in natural selection...One way of sorting this whole matter out is to use the terms ‘replicator’ and ‘vehicle’. The fundamental units of natural selection, the basic things that survive or fail to survive, that form lineages of identical copies with occasional random mutations, are called replicators. DNA molecules are replicators. They generally, for reasons that we shall come to, gang together into large communal survival machines or ‘vehicles’.

Richard Dawkins

Is there a conflict between science and religion?

Some of you may not be able to come to our little "dialogue" tomorrow night. Don't worry, you can watch it on YouTube: Is There a Conflict Between Science and Religion?.

Where did the glucose come from?

Currently there are two distinct views on the origin of life. The majority of scientists think that life arose in a prebiotic soup of complex organic molecules. Most of them think this "warm little pond" was the ocean (!) and most of them have bought into the stories about asteroids and comets delivering complex organic molecules to create a soup of amino acids and sugars. Presumably, all the earliest forms of life had to do was to join together the amino acids to make proteins and hook up the nucleotides to make RNA. The energy for these reactions was derived from breaking down all the glucose in the sweet ocean.

Monday, January 25, 2016

Are the humanities a different way of knowing?

The answer is "no" according to Jerry Coyne and I agree with him [“Other ways of knowing”: Out of Africa].

What about music, art, and literature? I agree with him on that as well. Read Faith vs Fact.

James McGrath disproves atheism

James McGrath is a professor of religion at Butler University in Indianapolis, Indiana, USA.

He is one of those "sophisticated theologians" who dismiss modern atheists because we haven't spent years studying theology and because we haven't experienced the true existential angst of Jean-Paul Sartre. As a group, they hold to the position that the "New Atheists" are amateurs in the study of religion and their arguments can be easily dismissed.

Saturday, January 23, 2016

Richard Dawkins makes a mistake when describing why gene trees are evidence of evolution

Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."

There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.

Friday, January 22, 2016

Confirmation bias

Confirmation bias is one of the major logical fallacies. When philosopher Chris DiCarlo and I were teaching a course on critical thinking we used to spend quite a bit of time on it because it's a very common trap. We are all guilty, from time to time, of focusing on just the evidence that confirms our belief and ignoring all the evidence that refutes it.

Some examples of confirmation bias are a bit more complicated than others and people typically mix together several different fallacious forms of argument. Here's an example from Denis Alexander's book Creation or Evolution (p. 213) that combines begging the question and confirmation bias.

An undergraduate biochemistry lecture converts an atheist to Christianity

I'm reading Creation or Evolution: Do we have to choose? by Denis Alexander in preparation for our discussion next Friday at Wycliffe College on the University of Toronto downtown campus [Discussing the conflict between science and religion with Denis Alexander].

Denis Alexander is a biochemist at the University of Cambridge (UK). I thought I'd share one of the stories in his book.
At the church I attend in Cambridge we baptised an undergraduate in the natural sciences who had come to a personal, saving faith in Christ from a completely atheistic background. As is usual in our church, just before being baptised she explained publicly to the whole congregation how she had become a Christian, telling us she had become convinced there must be a God while sitting through a standard biochemistry lecture, hearing the amazing story of how two meters (about six feet) of DNA are packaged into a single cell. Of course the lecturer was not talking in religious terms at all, but she described to us how the beauty of that engineering feat overwhelmed her as she listened, giving her the deep intuition there must be a God, so leading her onward in he personal pilgrimage to put her trust in this creator God through Christ. Truly natural theology at work!
That got me thinking. I've been describing chromatin and packing in my textbooks since the first version in 1987. There must have been several hundred thousand students who have read my descriptions since then.

I wonder how many I've converted?

Wednesday, January 20, 2016

Bryony Graham: another scientist who writes about the junk DNA controversy without doing her homework

I was searching for information about Craig Venter and his position on junk DNA when I stumbled upon this post by Bryony Graham: Why we still don’t have personalised medicine, 15 years after sequencing the human genome. She is a postdoc in Molecular Genetics at the University of Oxford so the subject is within her area of expertise.1

The post is from Dec. 1, 2015—that's only one month ago so she should be aware of all the facts concerning junk DNA.

If you are going to write about a subject in your area of expertise then it's reasonable to make yourself informed, especially if you know that the subject is controversial. For some strange reason, this common sense approach seems to be ignored when discussing genomes, evolution, and junk DNA. I don't know why some researchers think they know enough about a subject when all they've done (apparently) is read a few popular press reports.

Let's look at what Bryony Graham (@byrony_g) writes to see whether she is behaving like a proper scientist should behave when writing for the general public. It's worth noting that she was on the shortlist for the 2011 Max Perutz Science Writing Award so somebody must think she's a good science writer.
Not all junk DNA is rubbish

Tuesday, January 19, 2016

All about Craig

The sequence of the human genome was announced on June 26, 2000 although the actual sequence wasn't published until a year later. There were two sequences. One was the product of the International Human Genome Project led by Francis Collins who said,
"It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."
The sequence was a composite of a number of individuals.

The second sequence was from Celera Genomics, led by Craig Venter. It was mostly his genome, making him the second being to know his own instruction book ... right after God.

It took another seven years to finish and publish the complete sequence of all of Craig Venter's chromosomes. The paper was published in PLoS Biology (Levy et al., 2007) and highlighted in a Nature News article: All about Craig: the first 'full' genome sequence.

What's unique about this genome sequence—other than the fact that it's God's Craig Venter's—is that all 46 chromosomes were sequenced. In other words, enough data was generated to put together separate sequences of each pair of chromosomes. That produces some interesting data.

There were 4.1 million differences between homologous chromosomes (22 autosomes). 78% of these events were single nucleotide polymorphisms (SNPs). The rest were indels (insertions and deletions) and these accounted for 0.9 million nucleotides. Thus, indels made up 74% of the total number of variant nucleotide sequence.

In addition, there were 62 copy number variants (duplication) accounting for an additional 10Mb of variation between haploid sets of chromosomes. The total number of nucleotide differences is 13.9Mb when you add up all the indels, SNPs, and duplications. The two haploid genomes differ by about 0.5% by this calculation (total amount sequenced was 2,895Mb).

When the two copies of all annotated genes were compared, it turned out that 44% were heterozygous—the two copies were not identical.

Craig Venter's genome sequence differs from the composite human reference genome at 4,118,889 positions. Most of these were already known as variants in the human population but 31% were new variants (in 2007).

Venter has written about his genome sequence in A Life Decoded. He has variants in his APOE gene sequence that are associated with Alzheimer's and cardiovascular diseases. He has variants in his SORL1 that also make him at risk for Alzheimer's according to 2007 data. Just about everyone who gets their genomes sequenced will find variants that put them at greater risk for some genetic disease.

Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., Denisov, G., Lin, Y., MacDonald, J.R., Pang, A.W.C., Shago, M., Stockwell, T.B., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S.A., Busam, D.A., Beeson, K.Y., McIntosh, T.C., Remington, K.A., Abril, J.F., Gill, J., Borman, J., Rogers, Y.-H., Frazier, M.E., Scherer, S.W., Strausberg, R.L., and Venter, J.C. (2007) The diploid genome sequence of an individual human. PLoS Biol, 5(10), e254. [doi: 10.1371/journal.pbio.0050254]