Waterloo

 
Yesterday we took Zoë on her first major outing. We visited the site of the battle of Waterloo. Here's a photo of Jane, Michael, and Zoë in front of the entrance to the visitor center located on the ridge overlooking the farms of La Haye Sainte and Hougoumont. This was the location of some of the bloodiest fighting of the entire battle (Ney's cavalry charge and the attack of the Imperial Guard).

Today there's a huge artificial hill on the site. You can climb the stairs to the top and see the entire battlefield.


The last time I visited Waterloo was 35 years ago with our niece and nephew. Ever since I've wanted to take my own kids to see this famous site and yesterday was the day for Jane and my new granddaughter. My son Gordon will be so sad that he missed this battlefield () but since he'll be here in a few months I'm sure his sister will take him to Waterloo.

For more pictures, see Family Outing.

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The Difference between Truth and Framing

 
Chris Mooney is at it again. This time he address the question What Should Science Organizations Say About Religion? Answer: A Lot.

It's the accommodationist debate all over again although this time it's more focused. What should scientific organizations say about the compatibility of science and religion? It seems like an question with an obvious answer. Since there is considerable debate about whether science and religion are compatible then there can't be a definitive answer. Why would any scientific organization claim that science and religion are compatible? It's not a scientific question and it's not a true statement. The correct statement is that philosophers are debating the issue. It may be true that science and religion are compatible or it may be true that science and religion are not compatible. That's all that scientific organizations should say.

Chris Mooney thinks that scientific organizations should not tell the truth. He says that in the interest of American politics these organizations should lie about the compatibility issue. They should say that science and religion are compatible. It's called "framing."

I call it lying.

Aware of this context, groups like the National Center for Science Education (NCSE) take a stance likely to help some religious believers reject what they’ve been told from the pulpit, and move toward a more moderate stance on science and religion–in essence, from anti-science fundamentalism to middle-ground reconciliationism. To this end, NCSE states something factually true and indeed, undeniable: that not every religious person thinks science and religion are incompatible.

The veracity of this statement is not really open to debate. The issue here is simply whether such people exist, and of that there’s no doubt whatsoever. In this blunt factual sense, at least, science and religion are compatible–they are reconciled all the time by actual living, breathing human beings. You might take issue with the logical basis for such reconciliation in a particular mind, but you can’t deny that it happens regularly.

Wow! According to this kind of "framing," science is compatible with Young Earth Creationism because it's undeniable that there are YEC's who are scientists. There are actual living breathing human beings who have no problem reconciling science and Genesis. I wonder if Chris Mooney would be comfortable if NCSE and NAS declared that science is compatible with the Bible?

Of course he wouldn't. Chris Mooney only wants scientific organizations to lie according to his version of reality.

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A Philosopher's View of "Darwinism"

 
Most people think of "Darwinism" as equivalent to "evolution" but that can't be right. There are some mechanisms of evolutionary change—like random genetic drift—that clearly don't fall under the general beliefs of Darwin and his modern followers.

In today's terminology, Darwinism refers to a worldview that emphasizes natural selection as the most important mechanism of evolutionary change. Some extreme Darwinists even deny that change by random genetic drift counts as evolution.

Those of us who adhere to a broader view of evolution are called "pluralists" because we we consider several different mechanisms of evolution and several different levels of evolutionary change.

Jim Lennox is a philosopher. He has written a revised version of the "Darwinism" entry in Stanford Encyclopedia of Philosophy [Darwinism]. Now we all know that philosophers can be wordy, if it can be said by a normal person in two paragraphs then a philosopher can't possible write anything less than a small book. However, at the very least you expect to see a conclusion that makes sense. Is "Darwinism" a viable position in the 21st century? What does "pluralism" mean?

And wouldn't you expect a serious discussion of adaptationism and how it relates to Darwinism? I would.

Read the entry and see if you can decide whether "Darwinism" is a good synonym for "evolution."

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[Hat Tip: John Wilkins]

Epigenetics and the Calico Cat

This is our friendly calico cat. She lives on the farm where we are staying. Almost all calico cats are female—do you know why? It has something to do with epigenetics.

See: Calico Cats—it's one of my most popular postings.

Can anyone explain how some very rare calico cats might be male?

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[Photo by Ms. Sandwalk]

Name This Tree

 
Seriously, what kind of tree is this? It grows in Belgium.

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[Photo by Ms. Sandwalk]

Who Does This Remind You Of?

 

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[Photo by Ms. Sandwalk]

Herent Belgium

 
We're staying in a town called Herent, in Belgium. Our apartment is in a renovated manor house on a working farm (goats, chickens, ponies, cat).

Herent is a few kilometers north of Leuvan and only 20 minutes from Jane, Michael and our new granddaughter Zoë.

It's an easy drive back and forth except for the snow and Belgium drivers. Today we're off to our first babysitting job!!!!

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Critical Thinking

 
Phil Plait of Bad Astronomy posted this video from QualiaSoup. It's one of the best descriptions of critical thinking I've ever seen. Critical thinking is what we're supposed to be teaching our students in school and university.

We're not doing a very good job.

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Homeopathy and Avogadro's Number

 
Avogadro's Number, or it's more modern equivalent, Avogadro's Constant, is 6.022 × 10²³ mol^-1.

There's a new website called "Homeopathy: There's nothing in it" that explains why Avogadro's Number is important in understanding why homeopathy is a fraud.

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[Hat Tip: Phil Plait]

Zoë Jane

This is my new granddaughter, Zoë Jane. Congratulations to my daughter Jane and her husband Michael. In a few hours we'll be flying to Paris then taking a train to Brussels to visit them. Meanwhile, there are more pictures at The First Picture's on Ms. Sandwalk's blog and a video of her first bath on Jane and Michael's blog [Zoë's First Bath].

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The Key Darwin and Design Science News Stories of the Year

 
The people at Access Research Network have compiled a list of the best stories of 2009. These are stories that lend support to the idea that God exists and that he plays an important role in creation of the universe.

The stories are supposed to fall into two categories; anti-science stories that cast doubt on modern scientific explanations, and stories about evidence supporting intelligent design creationism.

Here's the list from: “The Key Darwin and Design Science News Stories of the Year”. Judge for yourselves how many fall into each of the two categories.

1. The Modern Synthesis is Gone
2. Cell Motors Work in Concert
3. Early Large Galaxies Stun Cosmologists
4. The Ida Hype and Bust
5. Walking White Blood Cells
6. Signature in the Cell
7. Cells Use Cloud Computing
8. Peppered Moths Oscillates Back to Gray
9. Reverse Engineering Biological Designs
10. Cambrian Explosion Continues to Challenge Materialistic Theories
11. The Collectivist Revolution in Biology
12. Failed Assault on Irreducible Complexity
13. Intelligent Input Required for Life
14. The Edge of Evolution Confirmed
15. The Ardi Hype and Bust

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Communicating Science

 
The primary goal of science writers and science journalists is to be effective communicators of science. However, they have had little impact on the general public over the past few decades since the level of science literacy has barely budged.

Most citizens have little idea of how science works and many reject outright the basic fundamentals of science.

Having failed to achieve their goal, and finding themselves irrelevant when it comes to making a profit (largely because of their own failure), they are now looking for someone to blame. Chris Mooney has decided to blame scientists for not being science journalists. See his latest contribution at On issues like global warming and evolution, scientists need to speak up. He doesn't really mean "speak up" as scientists, of course. What he means is that scientists should learn how to "frame" and fudge their position in order to please the general public. Making friends with theists and promoting religious scientists is supposed to help.

What's interesting about this debate is that science writers like Chris Mooney are convinced they know how to teach the general public in spite of the fact that science writers—as a profession—have not been successful in the past.

Why should scientist listen to them?

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How Long Does It Take to Recognize an IDiot?

Ken Ham is the man behind Answers in Genesis and the Creation Museum. He's upset with Lawrence Krauss because Krauss has been critical of anti-science creationists in general and the Creation Museum in particular. Ken Ham is particularly upset because Krauss was critical of th Creation Museum before he had actually visited it.

Krauss himself got criticism from some in the secular press because he had not even visited the museum to see it for himself. Presumably because of this criticism, he did come some time later and walked through the Creation Museum exhibits with AiG’s CCO, Mark Looy. Mark actually timed Krauss’s visit. He took a whole 22 minutes to walk through the museum, most of the time asking Mark Looy questions and only occasionally glancing at some of the exhibits. Considering it would take a person nearly one and a half hours to watch the programs in the various theatres, including the Planetarium and SFX theatre, plus take 2 hours to watch all the 50-plus videos in the various exhibits, and a further two hours to read all the signage—it was obvious Krauss wasn’t the least bit interested in researching the content of the museum (as one would expect from a real scientist and well-known anti-creationist commentator), but only visited presumably to tell people he has seen the Creation Museum and thus could comment on it—what a farce!

Now, let's be fair to Lawrence Krauss. He's a very smart guy and I'm certain that it didn't take him 22 minutes to recognize that the museum was a farce. I'm sure he stayed an extra 21 minutes just to be polite to his host.

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Time Magazine's Top 10 Scientific Discoveries

Here's the list of Time Magazine's Top 10 Scientific Discoveries. Given all the hype about The Darwinius Affair last May it's amazing that the discovery of this fossil didn't make the list.

There were several other huge scientific breakthroughs that failed to make the list: proof that Darwin was wrong, the overthrow of evolutionary theory, exposing the fraud of climate change, and the publication of Unscientific America.

There are some real scientific stories that were ignored by Time magazine: the creation of artificial stem cells (continuing), the 150th anniversary of the publication of Origin of Species, Nobel Prizes for telomeres and ribosome structure, and rapid human genome sequencing.

1. Our Oldest Ancestor, "Ardi"
2. The Human Epigenome, Decoded
3. Gene Therapy Cures Color Blindness
4. A Robot Performs Science
5. Breeding Tuna on Land
6. Water on the Moon
7. The Fundamental Lemma, Solved
8. Teleportation!
9. The Large Hadron Collider, Revived
10. A New Planet (or Brown Dwarf?) Discovered

It looks like a bad year for science if this is the best of the best.

In case you've forgotten, here's the top 10 list from last year [2008].

1. Large Hadron Collider
2. The North Pole — of Mars
3. Creating Life
4. China Soars into Space
5. More Gorillas in the Mist
6. Brave New Worlds
7. The Power of Invisibility
8. Cenozoic Park?
9. Can You Spell Science?
10. First Family

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Does Excess Genomic DNA Protect Against Mutation?

Many eukaryotic genomes have a large amount of "excess" DNA that doesn't have any of the functions we normally assign to DNA (protein-coding, regulatory, origins of replication, centromeres, RNA genes etc.). Many of us think this is junk DNA. It has no function and could easily be dispensed with.

One of the adaptive explanations for this excess DNA is that it protects the functional DNA from mutations. Ryan Gregory thinks this is a serious scientific hypothesis even though he's skeptical. He has a wonderful post that reviews the history of the idea and how the hypothesis should be tested [Does junk DNA protect against mutation?].

The bottom line is that this hypothesis is not taken very seriously by the scientific community for some very good reasons.

First, most spontaneous mutations in the germ line seem to be due to errors in DNA replication. The overall rate of evolutionary change is consistent with the mutation rate of DNA replication + repair, suggesting that it is the dominant form of mutation. This mutation rate is based on the number of nucleotides replicated. What this means is that the rate of mutation in functional DNA is independent of how much other DNA is being replicated. Excess DNA offers no protection from the spontaneous error rate of DNA replication.

THEME

Genomes & Junk DNA
However, the protection hypothesis may be applicable to other kinds of mutation such as those caused by chemicals or ionizing radiation. In multicellular organisms such as animals, fungi, and plants, this possible protection may prolong the lifetime of somatic cells or prevent them from becoming deregulated (e.g., cancer).

The idea is that excess DNA may shield the functional DNA from the effects of these mutagens but this would only work if the excess DNA was specifically organized so that it surrounded the functional DNA and provided physical shielding. There's no evidence that this is the case and, furthermore, it doesn't make much sense. The functional DNA in a nucleus is already shielded by lots of proteins, lipids and membranes so it's unlikely that a bit more DNA is going to make a difference.

Not only that, but some kinds of DNA damage caused by these mutagens will cause strand breakage. What does that mean? It means that the larger the genome the greater the chance that damage will occur. In other words, excess DNA leads to greater rates of mutation, not lower rates of mutation, for those types of mutagens. Ryan Gregory shows results from several studies during the 1970s that establish that fact.

I sympathize with Ryan's call for experimental support of the hypothesis but I'd also like to point out that not only does it not have direct evidence to back it up but it's not even theoretically feasible. It's just a bad hypothesis based largely on a misunderstanding of mutations and how they arise.

Also, the protection hypothesis doesn't pass The Onion Test which is one of the first requirements for an adaptive explanation of junk DNA.

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