What Is Darwinism?

Allen MacNeill at The evolution list asks What is "Darwinism" and am I a "Darwinist"?.

Read his posting to see what real modern scientists actually think about evolution and Darwinism. For more information you can read my own thoughts on the matter at: What Is Evolution, The Modern Synthesis of Genetics and Evolution, and Why I'm Not a Darwinist.

Now, here comes the fun part. Over on Uncommon Descent Barry Arrington asked the Intelligent Design Creationists to define "Darwinism". The contrast between what they're saying in the comments and what the modern textbooks say about evolution is truly astonishing.

And amusing.

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Bad Faith Awards

 
From the New Humanist

After a nomination period that saw you put forward those you feel have made the most egregious contributions to irrationalism and superstition during the course of this year, we've whittled them down to a shortlist of eight. Now all that's left for you to do is vote for the person you think should take the Bad Faith crown from last year's winner, Pope Benedict XVI.

Here's the list. I'm not going to tell you who I voted for.

Lauren Booth
Prince Charles
Baroness Warsi
Sheikh Maulana Abu Sayeed
Ann Widdecombe
Hojatoleslam Kazem Sedighi
Cardinal Walter Kasper
Pastor Terry Jones

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Human Mutation Rates

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.

Motoo Kimura (1968)We know a great deal about the error rate of DNA replication. The replisome makes a mistake about once in every 100 million bases incorporated. This is an error rate of 10^-8. The repair mechanism fixes 99% of these errors for an overall mutation rate of 10^-10. Given the size of the human genome and the number of replications between zygote and germ cells, this translates to approximately 130 mutations per individual per generation [Mutation Rates].

Recently there have been two attempts to verify this calculation. In one, the Y chromosomes of two men separated by 13 generations in a paternal lineage from a common male ancestor were sequenced. The differences correspond to a mutation rate of 0.75 × 10^-10 per generation, or almost the same as theory predicts [Human Y Chromosome Mutation Rates]. This is based on the fact that if most mutations are nearly neutral (they are) then the rate of fixation by random genetic drift should be the same as the mutation rate [Random Genetic Drift and Population Size].

The other study, by Roach et al. (2010), compared the genome sequences of two offspring and their parents. By adding up all the differences in the offspring they arrived at an estimate of 70 mutations in the offspring instead of the expected 130 [Direct Measurement of Human Mutation Rate]. This is half the expected value but the study is fraught with potential artifacts and it's best not to make a big deal of this discrepancy.

John Hawks was worried about this last March [A low human mutation rate may throw everything out of whack ] and he's still worried about it today [What is the human mutation rate?].

What John is really interested in isn't the mutation rate per se since we have pretty good handle on that number. What interests him is Calibrating the Molecular Clock and that's not the same thing. What it boils down to is the number of years per generation—or the number of fixed mutations per million years.

John thinks that if the actual mutation rate is only half of the value we though it was then the dating of many evolutionary events will need to be recalculated. For example, the human-chimp divergence would have to be re-set to eight or nine million years ago. But that's not strictly correct. We don't calibrate the molecular clock by taking the known mutation rate and multiplying by the number of generations then throw in a known value for the number of years per generation.¹

None of those values are known for even the most recent events in the primate lineages. What we usually do is work from a fixed point in the fossil record, count the number of differences between species, and estimate a mutation rate per million years. That value is then used to calibrate other divergences.

Sometimes these rates of change can be related to the mutation rate by estimating the generation times and they often seem reasonable when we come up with generation times of,say, 25 years. Even if the known mutation rate were half of the current consensus value, the most reasonable adjustment would not to be recalibrate the time of divergence but to reconsider our assumption abut generation time. Maybe there were twice as many generations per million years.

But this is actually a non-problem right now since the Roach et al. (2010) estimate is not very reliable. I don't think John Hawks should be worried.

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1. Plus estimates of the effective population size, N_e.

Roach, J.C., Gustavo Glusman, G., Smit, A.F.A., Huff, C.D., Hubley, R., Shannon, P.T., Rowen, L., Pant, K.P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L.B., Hood, L., and Galas, D.J. (2010) Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science (Published Online March 10, 2010) [doi: 10.1126/science.1186802]

Happy Blogiversary Sandwalk!

 
Today is the 4th anniversary of Sandwalk. My first posting. Welcome to my Sandwalk, went up at 9:07 pm on Nov. 4, 2006. I didn't think I was going public when I created that posting but it contained a link to Pharyngula and PZ noticed. He mentioned it on his blog and that was the end of my attempt to experiment in private. Things have never been the same since then.

That first posting was followed by 3506 others and 28,465 comments from readers—most of whom disagreed with me!

Sandwalk pages have been viewed 3,255,306 times. There are about 3,500 visits per day from Monday to Friday and 2,500 on Saturdays and Sundays.

None of my top five most popular postings are science postings. That's kinda sad.

1. Dear Royal Ontario Museum ...


2. A Challenge to Theists and their Accommodationist Supporters


3. Who's the Grownup in the Science vs Religion Debate?


4. Arguing Against God


5. Sophisticated Religion

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Illinois Federation of Teachers: Resolution #11

The Illinois Federation of Teachers has passed Resolution #11: KEEP SUPERNATURALISM OUT OF THE SCIENCE CURRICULUM. It represents a certain point of view that I don't agree with so I'll make a few comments in order to provoke discussion.

WHEREAS, science is a systematic method for investigating natural phenomena through experimentation, observation and measurement leading to falsifiable explanations that are open to continuous testing; and ...

I think of science as a way of knowing ... everything. It is not limited to "natural phenomena" in the sense that's normally attributed to that phrase. The scientific way of knowing applies rational thinking, evidence, and skepticism to any problem we encounter and this includes history and English literature. Thus, by my definition, "experimentation" isn't a requirement and "measurement" is far too restrictive. I also don't accept "falsifiability" as an important criterion for science.

What the Illinois Federation of Teachers should have said was "There are many different definitions of science. We adopt the following definition, recognizing that many scientists and philosophers disagree."

Right from the start, the teachers have created a situation where they can keep religion out of the science class but not out of art, history, and geography classes.

WHEREAS, science proceeds on the basis of methodological naturalism and assumes observed phenomena of the universe are real, nature is consistent and understandable, and nature is explainable in terms of laws and theories; and ...

The teachers should have said the following, "Whereas many philosophers and scientists restrict science to the practice of methodological naturalism while others disagree, we adopt the methodological naturalism position for the purposes of this resolution."

Then they should have gone on to say, "We believe that nature can eventually be fully explained by laws and theories because so far there's no evidence to suggest otherwise."

WHEREAS, a scientific theory is consistent with evidence from multiple and independent sources of evidence, explains many different facts and allows predictions of subsequent discoveries; and

WHEREAS, the theory of evolution satisfies these criteria fully, is the foundation of biological science, is supported by a coherent body of integrated evidence from other disciplines in science and is consistent with theories from other scientific disciplines including anthropology, geology, physics, astronomy and chemistry; and ...

Evolution is much more than a theory [Evolution Is a Fact, Evolution Is a Fact and a Theory]. Most of what's taught in public school is not evolutionary theory but evolution fact and the history of life. It's a fact that humans and chimpanzees share a recent common ancestor, for example. It's a fact that natural selection leads to antibiotic resistance in bacteria.

We should not be referring to these fact as "the theory of evolution."

WHEREAS, there have been attempts in some states to include supernaturalism in the science curriculum as an alternative to scientific explanations of nature, particularly as an alternative to evolutionary theory; and

WHEREAS, arguments that invoke supernaturalism are grounded in religious or philosophical considerations outside the realm of science; and ...

I do not agree that supernaturalism is outside the realm of science. Supernatural explanations have been investigated by scientists and have been shown to be false or unnecessary. They are excluded from the classroom because they are bad science, not because they are "not science."

Statements like this imply that supernaturalism is a separate way of knowing. A supernatural explanation may even be correct but you can't teach it in science class because we say so. This is a very puzzling situation. What if there really is a God and He guides evolution? How would we be justified in keeping that from our children?

We need to teach critical thinking and this means addressing all claims—including the supernatural—to see if they are right or wrong.

WHEREAS, attempts to subvert the validity or teaching of evolutionary theory are also attacks on all scientific inquiry and, therefore, also attacks on the validity of using reason and experimentation to understand the universe; and ...

This is correct. Attacks on evolution are attacks on science. That's why we need to teach children why those attacks are unjustified and wrong. Ignoring them or banning them from the classroom won't demonstrate why they subvert the validity of science.

WHEREAS, legislation that conflates supernaturalism, or limits, or prohibits the teaching of any scientific theory negatively impacts our ability to make informed decisions; and

WHEREAS, it is the responsibility of the Illinois Federation of Teachers to preserve the integrity of science in the classroom; therefore be it

resolved, that the Illinois Federation of Teachers affirm, through a positional statement on its website, the validity of science as a methodology for understanding the nature of the universe, and affirm the validity and foundational importance of organic evolution to science as a whole and biology, specifically; and be it further

RESOLVED, that the IFT affirm, through a positional statement on its website, that supernaturalism is not a scientific endeavor and, therefore, is inappropriate for inclusion in the science curriculum; and be it further

RESOLVED, that this resolution does not make it the official position of the IFT that there is no God and should not be interpreted as a statement either for or against religion or belief in God; and be it further

RESOLVED, that the IFT call upon its members to assist those engaged in overseeing science education policy to understand the nature of science, the content of contemporary evolutionary theory and the inappropriateness of including non-science subjects (e.g., intelligent design and creationism) in our science curriculum; and be it further

RESOLVED, that the IFT communicate to the local, regional and national public media, to educational authorities and to appropriate legislators its opposition to the inclusion of non-science approaches and subjects (e.g., creationism and intelligent design) into the science education curricula of our public school system; and be it finally

RESOLVED, that the IFT members also promote these concerns and help resolve these issues in their home communities among educators, parents, school boards and students in appropriate public forums.

I hope that Illinois teachers are going to make a strong effort to teach evolution and critical thinking in their classrooms in spite of any opposition they may encounter from local schools boards and parents.

This is one of 27 resolutions that they passed.

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[Hat Tip: Panda's Thumb]

Atheist Don't Have No Songs

 

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[Hat Tip: Canadian Atheist]

Guns and the Moral Law

 
From MSNBC and Associated Press: Police: Teen shot dead after Halloween prank.

ATLANTA — Authorities say a driver enraged after his Mercedes was splattered with eggs on Halloween fatally shot a 17-year-old in the neck and leg as the teen tried to run away.

Atlanta police spokeswoman Kim Jones says the driver confronted the teen and fired 10 shots at him around 8 p.m. Sunday. The Fulton County Medical Examiner's office says the teen, Tivarus King, died as he was being taken to Grady Memorial Hospital.

Just keep repeating to yourself, "Guns aren't the problem, criminals are the problem."

The real problem is that if you give a gun to a Mercedes owner in Atlanta he can soon become a criminal. (Ten Shots!)

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[Hat Tip: Greg Laden]

Carnival of Evolution #29

 
The latest Carnival of Evolution is up on Byte Size Biology [Carnival of Evolution #29].

Check it out ... there's lots of good stuff from all the best biology bloggers.

Sandwalk readers might be interested in the post by Hannah Waters. She not only defends the "Three Domain Hypothesis" but goes one step further by merging eukaryotes and archaebacteria into a single domain making the "Two Domain Hypothesis"!

Of course we all know that she's wrong but her posting is still worth reading.

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Penn Jillette Defines Respect

 
Here's an excerpt from an article in Saturday's Toronto Star [Penn Jillette and the gospel of disbelief ]. I agree with Penn Jillette about the meaning of "respect." This point about respect and confrontation comes up in a discussion on John Wilkins' blog [Tone Wars]. Penn may be impressed by how many people get it but I'm more impressed by how many people don't.

If you know Penn & Teller — the famed magicians, humourists and debunkers, stars of the cable series Bullshit! — you know, broadly speaking, what to expect from their long-running show in Las Vegas and their appearance Wednesday at Massey Hall. If not, you might be surprised by Penn Jillette: first of all by how positively evangelical a man can be about atheism, and secondly by how happy he is to clash with genuinely who fervently disagree.

“We get a lot of people coming up to us after shows and saying ‘I’m a Christian but I really enjoy your passion,’ ” Jillette, 55, says on the phone from Sin City, where Penn & Teller’s show has been running at the Rio Hotel for nine years.

“There’s a big difference between tolerance and respect. Tolerance is you saying something crazy and me smiling and saying ‘that’s nice.’ Respect is when you say something crazy and I say ‘you’re out of your f---ing mind.’ Direct confrontation, direct conversation is real respect. And it’s amazing how many people get that.”

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[Hat Tip: Canadian Atheist]

Saturday Morning Cartoons

 
This one is from Pharyngula. PZ Myers thinks this guy is nuts. I think he's just trying to be funny.

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God Plays Bridge

 
The creationists tell us that anything in biology with a probability of 10^-39 or less is impossible [see God Designed My Great-Grandparents].

That's a very tiny number. Let's see just what kind of probabilities we're dealing with.

Imagine four people sitting down to play a hand of bridge. They shuffle the deck and deal out 13 cards to each player. The probability that the particular hand would be dealt is very low because the total number of possible hands is 51!/13! = 53,644,737,765,488,792,839,237,440,000. Let's round this off to a probability of 0.2 × 10^-28.

Assuming that there have been at least 100,000,000 bridge players and that they've played at least 2000 hands of bridge, that represents a total of 5 × 10¹⁰ separate hands of bridge. The probability that all of these particular hands would have been dealt in a particular time and place is 10^-39. That's equivalent to the total number of bacteria and it's the kind of probability that makes creationists think of God.

I wonder if God plays bridge? If he does, I wonder if he ever loses since he can control the deal?¹

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1. Sounds like a good plot for a Mr. Deity video.

God Designed My Great-Grandparents

On the thread Impossible Molecular Machines we are being treated to a lesson in probabilities from several creationists. Here's an example of a comment from Livingstone Morford.

By Darwinism I mean the notion that everything we observe in the biological world are purely the result of stochastic processes, and I am critical of that notion.

On a different topic, I might add that intelligent design proponents need only demonstrate that the odds of a particular biochemical system evolving are 10^-40 or less in order for intelligent design to be a more adequate explanation for the origin of such a biochemical system. This is because there have been no more than 10^39 bacterial cells in the history of life on earth.

Speaking of stochastic processes, the average number of sperm contributed by a man in a mating process is 100,000,000 (10⁸). That means that every single human is the product of a single sperm cell uniting with a single egg cell and the probability that one particular sperm was successful is 10^-8.

This probability of existence applies to each of my great-grandparents.

Johann Betker was born in 1859 in Volhynia in the western part of Ukraine. The probability that he was produced from a particular sperm cell is 10^-8. His future wife, Amalie Schmuland, was born in 1868, also in Volynia. This was also an improbable event from the point of view of sperm selection. The probability that BOTH of my grandparents were born is (at least): 10^-8 × 10^-8 = 10^-16.

The same probabilities apply to Thomas Keys Foster born 1852 in country Tyrone, Ireland and his wife Eliza Ann Job born 1852 in country Tyrone. Their two births were very lucky with a total probability of only 10^-16. Now, if you combine all four of these great-grandparents you end up with a probability of 10^-32. Add in the other four great-grandparents and you end up with the total probability that all eight of these individuals would be born = 10^-64. (The real probabilities are much, much lower when you take the eggs into account.)

Since this total probability is a lot less than the total number of bacteria that have ever existed, it follows that God must have intervened somewhere. Two of my great-grandparents must have been designed by God. I wonder which two it was? My bet is that it wasn't any of the four mentioned above because they were all born outside of Canada. It was probably the two grand-parents who were born in Canada 'cause God likes Canadians.

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Michael Egnor Answers the Questions

 
I treid to answer Michael Egnor's questions as best I could [A Quiz for Atheists from a Creationist]. Now Egnor has answered his own questions at: What I Really Believe.¹

Some Sandwalk readers will be delighted to discover that Egnor refers to Aristotle in support of his beliefs, proving that Aristotle is good for something!

Most Sandwalk readers will be interested in this ...

That's what I believe. Note that these beliefs are entirely compatible with modern science; in fact, classical philosophy and classical theism is the source for modern science, which only originated in civilizations that embraced this classical view of the world. Some enlightenment philosophers moved away from some aspects of classical philosophy (e.g. final causes), but classical philosopohy and classical theism remain the foundation of Western Civilization and of modern science.

Many of you are modern scientists. How many think that classical theism is important in your work? How about classical philosophy?

Really? No one thinks that? Where do the IDiots come up with these ideas?

More and more scientists, philosophers, and theists are recognizing that science and theism are incompatible. That sort of makes it hard to claim that classical theism remains the foundation of modern science, doesn't it?

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1. Comments aren't allowed on Evolution News & Views so you can leave comments for Michael here.

Jesus and Mo Read Sandwalk

 
Jesus and Mo

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HuffPost Heatlh?

 
I don't read the Huffington Post but Orac over at Respectful Insolence does. He notes that it is about to start a new section called HuffPost Health. Here's how it's going to work.

HuffPost Health will be a clear and balanced resource to provide a comprehensive view of the state of health and health news in a given day. It will provide a forum for intelligent discourse and divergent but respectful points of view. HuffPost Health will empower you with state of the art information you can use to make informed and intelligent decisions that affect your life in meaningful ways.

In this spirit, HuffPost Health's articles and videos will include the best of evidence-based allopathic Western medicine (including drugs and surgery), lifestyle and functional medicine (including nutrition, fitness, stress management, supplements, and love and support), mind/body medicine (including mental and emotional health), women's and men's health issues, and integrative medicine (including complementary and alternative medicine).

I bet you can hardly wait! Neither can Orac 'cause "there'll be a lot of new blogging material." More importantly, Orac notes that HuffPost Health might soon become a handy source of all quackery: HuffPost Health: A soon-to-be one-stop shop for quackery. We're going to need something like this once the Oprah Show and Larry King Live go off the air.

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