Monday, October 31, 2011

Introducing the Scientific Theory of Redemptive Suffering

 
Before introducing you to this new scientific theory we need to remind ourselves of the difference between intelligent design and creationism. This is from the Evolution News & Views website [Is intelligent design the same as creationism?]
Is intelligent design the same as creationism?

No. The theory of intelligent design is simply an effort to empirically detect whether the "apparent design" in nature acknowledged by virtually all biologists is genuine design (the product of an intelligent cause) or is simply the product of an undirected process such as natural selection acting on random variations. Creationism typically starts with a religious text and tries to see how the findings of science can be reconciled to it. Intelligent design starts with the empirical evidence of nature and seeks to ascertain what inferences can be drawn from that evidence. Unlike creationism, the scientific theory of intelligent design does not claim that modern biology can identify whether the intelligent cause detected through science is supernatural.

Honest critics of intelligent design acknowledge the difference between intelligent design and creationism. University of Wisconsin historian of science Ronald Numbers is critical of intelligent design, yet according to the Associated Press, he "agrees the creationist label is inaccurate when it comes to the ID [intelligent design] movement." Why, then, do some Darwinists keep trying to conflate intelligent design with creationism? According to Dr. Numbers, it is because they think such claims are "the easiest way to discredit intelligent design." In other words, the charge that intelligent design is "creationism" is a rhetorical strategy on the part of Darwinists who wish to delegitimize design theory without actually addressing the merits of its case.
John Blumenthal wrote a piece at Huffington Post where he tried to apply this approach [Intelligent Design? Not If You're Over 50]. He noted that, "If you're over 50 and your body is starting to fall apart, it's pretty obvious that the design is anything but intelligent." I'm told that Blumenthal used to be an editor at Playboy magazine.

An anonymous correspondent at the Discovery Institute's blog, Evolution News & Views, decided to set Blumenthal straight by giving us the scientific, non-creationist, intelligent design, explanation [My Back Hurts Therefore It Wasn't Designed].
For some reason, the former Playboy magazine editor has never heard of redemptive suffering and assumes that any Designer worth his salt would have created a universe where everyone has a rollicking orgy in his own Playboy Mansion until one day, he has a painless death. How cruel of the Designer not to have taken Hugh Hefner's plan for a fulfilling life as a model.
Redemptive Suffering? I try to keep up with the scientific literature but that's a new one on me. It can't have anything to do with trying to deduce the motives of the Christian God of the Bible, can it?


Beavers vs Polar Bears

 
Here's the complete press release from Canadian Senator Nicole Eaton issued just a few days ago [Statment about the Polar Bear]. Her proposal has been widely publicized. Most people think it's a serious suggestion from the Conservative Government. I'll treat it in the spirit that it was intended.

Sunday, October 30, 2011

The Case for Socialized Medicine

 
From MNT: Medical New Today.

Religious, Spiritual Support Benefits Men And Women Facing Chronic Illness, MU Study Finds


Individuals who practice religion and spirituality report better physical and mental health than those who do not. To better understand this relationship and how spirituality/religion can be used for coping with significant health issues, University of Missouri researchers are examining what aspects of religion are most beneficial and for what populations. Now, MU health psychology researchers have found that religious and spiritual support improves health outcomes for both men and women who face chronic health conditions.

"Our findings reinforce the idea that religion/spirituality may help buffer the negative consequences of chronic health conditions," said Stephanie Reid-Arndt, associate professor of health psychology in the School of Health Professions. "We know that there are many ways of coping with stressful life situations, such as a chronic illness; involvement in religious/spiritual activities can be an effective coping strategy."

Religious and spiritual support includes care from congregations, spiritual interventions, such as religious counseling and forgiveness practices, and assistance from pastors and hospital chaplains. The recent publication from the MU Center for Religion and the Professions research group, authored by Reid-Arndt, found that religious support is associated with better mental health outcomes for women and with better physical and mental health for men.
In a society that believes in individualism, it's good to find a group that will help you and your family in your time of need. It doesn't matter whether that group is your local Lion's Club, your Jehovah's Witness Kingdom Hall, or your Harvard Alumni buddies.

If you live in such a society and you're too poor to afford decent health care, then the group could save your life.


[Hat Tip: Uncommon Descent, although Denyse reaches a different conclusion.]

Wise Beyond Her Years

 
The Dallas News published an interview with 9-year-old Mason Crumpacker. You might remember her as the girl who asked Christopher Hitchens about his favorite books. Since most of us don't read the Dallas News1, Jerry Coyne posted the entire interview on his blog website: Interview with a 9-year-old skeptic.

I'm stealing the entire interview from Jerry's website and reproducing it here just in case there are some Sandwalk readers who might not look at Why Evolution Is True and might not read the Dallas News2.

Why can't we create a society where every child can give answers like this?



Saturday, October 29, 2011

Creationism and Climate Change Denial: What's the Connection?

 
You probably know already that creationists are more likely to fall for other kooky ideas like denying that humans cause global climate change. Do they just have a fondness for stupid ideas or is there some kind of connection between creationism and disbelief in anthropomorphic climate change?

GilDodgen explains the "logic" at: Junk Science as Ersatz Religion.
Why are ID theorists skeptical of “man-caused carbon dioxide emissions leading to the destruction of the planet” theory? The reason is that we follow the evidence, and have a nose that smells out junk science in the name of an ideological (indeed, a religious) agenda.

At a recent men’s church retreat I chatted with our pastor about how it seemed obvious to me that the global-warming thing exhibited all the attributes of a religion.

Mother earth is a goddess. We have sinned against her with technology. If we do not repent and return to primitive living she will call down her wrath and fry us all with vengeance.

Little did I know that Michael Barone, in his essay Collapse of the global-warming cult came to the same conclusion.

The same thing applies to the cult of Darwinism, which is promoted in the name of science. Darwinian theory (in particular, the presumed creative power of random mutations, and attempts to explain away the fact that the fossil evidence consistently contradicts gradualism) exhibits all the attributes of an ersatz religion.

It is the creation story of the religion of materialism.
Turns out I was right the first time. They're just kooks.


Friday, October 28, 2011

The Core Genome

Hundreds of genomes have been sequenced. It should be relatively easy to search all these genomes to identify those genes that are found in every single species. This small class of genes should represent the core genome—the genes that were probably present in the first living cell.

Turns out it's not that easy. For one thing, you have to remove parasitic bacteria from your set of genomes because these species could easily be getting by without some essential genes that are supplied by their hosts. Next you have to make sure you have a huge variety of different species that cover all possible forms of life. In practice, this means that you need about 300 different genomes, mostly bacteria.

I'm reading The Logic of Chance: The Nature and Origin of Biological Evolution, by Eugene Koonin. This is just one of many books that are critical of the most popular views of evolution. Most of these books are written by kooks or religious nutters but some of them are valid scientific critiques of modern evolutionary theory. Koonin's book is one of those and I agree with most of what he has to say. One of his topics is genome evolution.

As Koonin describes it, the first genome comparisons looked at Haemophilus influenzae and Mycoplasma genitalium, two species of bacteria that aren't distantly related. There were about 240 orthologous genes found in both species.1 The first surprise was that this core set was missing some very important members that should have been there.

Some essential metabolic reactions must have been catalyzed by enzymes in the very first cells but the Haemophilus enzyme isn't present in Mycoplasma and vice versa. It took a bit of digging but eventually the problem was solved with the discovery of different enzymes that carried out the same reaction. The genes for these enzymes are completely unrelated.

As more and and more genomes were sequenced, the size of the core genome set shrunk until today it comprises fewer than 100 genes. Most of these genes are genes for the three ribosomal RNAs, about 30 tRNAs, and a few other essential RNA molecules. There are only about 33 protein-encoding genes in the universal core set. They include genes for the three large RNA polymerase subunits and 30 proteins required for translation (mostly ribosomal proteins).

DNA polymerase isn't in the core set because some species of bacteria have unusual DNA polymerases that replicate DNA just fine but are unrelated to the enzymes found in most cells. There are multiple, unrelated, versions of the aminoacyl tRNA synthetases—the enzyme that attaches an amino acid to its cognate tRNA. Some species have one version and other species have the second version. Some species have both. In any case, no single synthetase gene is found in every species so it's not part of the core set.

Koonin refers to this observation as non-orthologous gene displacement (NOGD). He envisages a scenario where a cell with gene X takes up a copy of a non-orthologous gene (gene Y) that catalzyes the same reaction. Over time the newly acquired gene displaces the original version. In this way a non-orthologous version (e.g. gene Y) could have arisen after the formation of the first cell and spread to a variety of different species by horizontal gene transfer. The scenario doesn't rule out the possibility that the two non-orthologous versions could have arisen independently in two separate origins of life but this seems less likely.

Let's look at a couple of examples. Biochemistry textbook writers have known for decades that there are different versions of some common metabolic genes 2 The aldolase enzyme in gluconeogenesis & glucolysis is a classic. Some species have the class I enzyme/gene while others have the class II enzyme/gene. Some species have both.

This is an example of convergent evolution. The enzymes have different mechanisms and, as you can see from the figure, completely different structures. It doesn't seem to matter if a species has a class I enzyme or a class II enzyme since both enzymes are very good at catalyzing the fusion of two three-carbon molecules into a six-carbon fructose molecule or cleaving the six-carbon molecule in the reverse reaction.

The pyruvate dehydrogenase complex (PDC) is a huge enzyme that catalyzes an important metabolic reaction making acetyl-CoA—the substrate for the citric acid cycle. It seemed likely that every single species would have the genes for all of the PDC subunits but many species of bacteria were missing the entire complex. They have a different enzyme, pyruvate:ferredoxin oxidoreducatase that catalyzes a similar reaction. The enzymes have completely different mechanisms and are unrelated.

In this case, we have reason to believe that the enzyme requiring ferredoxin is more primitive and the more common pyruvate dehydrogenase complex evolved later. The PDC genes displaced the gene for pyruvate:ferredoxin oxidoreductase in many, but not all, species. That's why the genes for neither enzyme are part of the core set.

We don't know whether the existing core set of 100 genes truly represents genes that were present in the first living cell or whether they completely displaced the original versions. The fact that many of these genes are part of large operons might have made it easier for them to be transferred by horizontal gene transfer. (The selfish operon model.)

The bottom line is that attempts to reconstruct the genome of the first cell have failed because of NOGD and we now have to incorporate that concept into our way of thinking about early evolution. The good news is that the evolution of completely new genes seems to be much easier than we first imagined. We even have examples of three or four completely different enzymes carrying out the same reaction.3


1. Koonin refers to conserved genes as Clusters of Orthologous Genes or COGs. It actually counts conserved domains rather than entire genes but the differences aren't great so I'll just refer to them as genes.

2. That is, those textbook writers that emphasize comparative biochemistry or an evolutionary approach to biochemistry. Some textbooks just cover human (mammalian) biochemistry so they won't even mention whether bacteria do biochemistry.

3. I'm not sure how the Intelligent Design Creationists explain these observations. Maybe there were several different designers who each came up with their ideal solution to the problem? Maybe there was only one designer who just got a kick out of making different versions of the same enzyme activity but got bored at only two or three?

Atheist Calls Religious People 'Idiots' On British Debate Show

 
Good for her. Kate Smurthwaite tells it like it is! It's fun to watch the theists try to defend themselves. Note that none of them tries to offer a rational explanation for their belief in heaven.

Kate's statement is undoubtedly something that the accommodationists would complain about. They probably thing it's counter-productive to point out that believing in heaven makes about as much sense as believing in the tooth fairy.

They probably think it's perfectly respectable to say that all aborted babies are in heaven. In most other contexts, people making statements like that would be candidates for the loony bin and nobody would be criticized for saying so. But if you say stupid things in the name of religion you need to be protected from criticism. According to theists, it has to be "rude" to criticize faith because otherwise it might be subjected to the same scrutiny that we reserve for belief in homeopathy, UFO abductions, and 9/11 conspiracy theories.

Society will undoubtedly fall apart if we criticize religious faith, right? I think we're about to find out.




[Hat Tip: Friendly Atheist]

Read Kate Smurthwaite's blog: CRUELLA_BLOG

The "Intelligent Design" Version of Creationism

The IDiots are at it again. Over the past few months there's been an noticeable increase in the number of whining complaints about the way Intelligent Design Creationism is being treated in the popular press and on science blogs.

Here's the latest from David Klinghoffer on the Discovery Institute website: Here There Be Dragons: The Journalists' War on Science. Kinghoffer thinks that his movement is being treated unfairly by journalists. Let's see why.
If there's one thing we've learned from repeated uniform experience it is that on one scientific issue, the most contentious there is -- evolution -- it's treated as taboo for writers to inform themselves properly, to know the facts and evidence behind the scientific challenge to Darwinian theory.
Hmmm ... here's an Intelligent Design Creationist complaining that his critics haven't taken the time to "inform themselves properly" about a 100-year old version of evolutionary theory that's been modified and extended so that modern evolutionary theory no longer qualifies as "Darwinian theory." I don't know a single IDiot who has the gumption to refer to modern evolutionary theory by its proper description. I'm not even sure there's a single IDiot who understands modern evolutionary theory. That includes David Klinghoffer [see, The IDiots Respond].

Can you say "hypocrisy"?

Wednesday, October 26, 2011

Detecting God's Signature

Stephen Meyer has two main objectives. He wants to prove that Intelligent Design Creationism is the best explanation for the origin of information in the cell and he wants to prove that Intelligent Design Creationism is genuine science.

Let's look at the form of argument he uses in Signature in the Cell: DNA and the Evidence for Intelligent Design. This is from Chapter 17 where he's trying to refute the accusation that Intelligent Design Creationism is nothing more than an argument from ignorance.
... the argument made in this book ... takes the following form:
Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for information in the cell.
Or, to put it more formally, the case for intelligent design made here has the form:
Premise One: Causes A through X do not produce evidence E.
Premise Two: Cause Y can produce E.
Conclusion: Y explains E better that A through X.
In addition to a premise about how material causes lack demonstrated causal adequacy, the argument for intelligent design as the best explanation also affirms the demonstrated causal adequacy of an alternative cause, namely, intelligence. This argument does not omit a premise providing positive evidence or reasons for preferring an alternative cause or proposition. Instead, it specifically includes such a premise. Therefore, it does not commit the informal fallacy or arguing from ignorance. It's really as simple as that.
Scientist are often accused of picking on the most idiotic of the IDiots and avoiding the really big guns who have all the best arguments for Intelligent Design Creationism.1 See A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates, where David Klinghoffer asks,
How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?
So, here's my response to the very best that the IDiots can offer.

Premise One
Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
On the surface this looks like a purely scientific statement. I'm sure that most creationists accept it at face value since the leaders of the movement have been saying for years that evolution can't account for specified complexity or irreducible complexity.

Stephen Meyer is a philosopher but he's confident that his knowledge of biology is sufficient to establish the truth of this claim. He says on page 341 ...
Undirected materialistic causes have not demonstrated the capacity to generate significant amounts of specified information.
This is an important point since the logic of his argument depends on establishing that specified complexity can never arise from natural (materialistic) causes. You might think that a large part of this book would be devoted to backing up his premise. You would be wrong. Turns out, the real premise isn't exactly how it appears above.

Dennis Venema has written a critical review of Signature in the Cell and one of his criticisms is that there are many excellent examples of new information evolving by entirely materialistic mechansims that not violate the laws of physics and chemistry [Seeking a Signature]. We're all familiar with the examples of gene duplication and divergence but he might just as well have used dozens of other examples where specified complexity evolved. The wings of birds are for flying but they evolved from legs and fins. The irreducibly complex citric acid cycle evolved from simpler pathways.

These examples establish beyond a shadow of a doubt that there are perfectly reasonable, materialistic explanations for the evolution of specified complexity. That seems to negate Premise One.

Hang on. Meyer responds to the Venema criticism by pointing out that he was not referring to the origin just any specified information. He was only referring to the kind of specified information that appeared when life first formed. It's an origin of life problem.
The balance of [Venema's] review is spent refuting an argument that Signature in the Cell does not make and, thus, the evidence he cites is irrelevant to the main argument of the book; in short, Venema "refutes" a straw man. ... I happen to think -- but do not argue in Signature in the Cell -- that there are significant grounds for doubting that mutation and selection can add enough new information to account for various macroevolutionary innovations. Nevertheless, the book that Venema was reviewing, Signature in the Cell, does not address the issue of biological evolution, nor does it challenge whether mutation and selection can add new information to DNA. That is simply not what the book is about. Instead, it argues that no undirected chemical process has demonstrated the capacity to produce the information necessary to generate life in the first place. The book addresses the subject of chemical evolution and the origin of life, not biological evolution and its subsequent diversification. To imply otherwise, as Venema does, is simply to critique a straw man. [Stephen Meyer Resonds]
Meyer is correct. The book is about the origin of life and the problem of getting information into DNA 3.5 billion years ago, before there were cells, and before evolution. Meyer isn't always clear about this distinction but the argument that he frames above is about the origin of life.

Here's how he should have expressed Premise One ...
After decades of research, biologists have good explanations of how specified information can arise by evolution but they do not have a good explanation of how life began 3.5 billion years ago.

Premise Two
Intelligent causes have demonstrated the power to produce large amounts of specified information.
He's referring, of course, to the fact that bees make beehives and beavers make dams. There are hundreds of examples where animals produce complex structures full of specified information. That's what he means by "intelligent causes." All of this creation obeys the laws of physics and chemistry, therefore the explanation is entirely materialistic.

Don't forget that the argument is not about the creation of specified information throughout the history of life. It's about the ultimate origin of the information. Animals can create complex structures just as living cells can create new genes. What Meyer really wants to know is where do animals get this ability? Where did the information to create more information come from?

Animals evolved from more primitive ancestors. It's quite reasonable to postulate that all animals evolved from a common ancestor that had very rudimentary intelligence and that intelligence evolved from primitive neurons. Thus, the ability of intelligent animals to create complex structures—like pocket watches—ultimately traces back to the origin of life.

We can re-word Premise Two ...
Intelligent animals can produce large amounts of specified information by purely materialistic means. The ability to do this depends on the evolution of animals from the first living cells that arose 3.5 billion years ago.

Conclusion
Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.
This conclusion does not follow from either of the corrected premises.

Here's a better conclusion.
All of the information we see in biology, including the ability of beavers to make dams, can be traced back to the information present in the first cells. We don't currently have a good explanation for how DNA and cells arose.
It's difficult to see how you can squeeze a supernatural intelligent designer into this conclusion. Whenever we have good explanations for the origin of specified complexity, those explanations involve materialistic actions and not actions that require violation of the known laws of physics and chemistry. Beavers do not wave a wand to poof their dams into existance and bees don't get their beehives by praying for them

Therefore, it seems quite reasonable to assume that all examples of biological information arise by natural means, including the very earliest examples of DNA in the first cell.

(I don't address information theory, which takes up a significant part of the book for some unknown reason. See Jeffrey Shallit's take-down on Stephen Meyer in: More on Signature in the Cell.)


1. Atheists have the same problem. We're always going after the most stupid theists and avoiding the really sophisticated arguments for the existence of God. You'll find a list of those arguments at: A Challenge to Theists and their Accommodationist Supporters.

Tuesday, October 25, 2011

Is Creationism Anti-Science?

 
It's very hard to define science—it's the demarcation problem and, in spite of what you've been told, philosophers don't agree on how to define science.

A lot of the activities of Intelligent Design Creationists qualify as science, as far as I'm concerned. That's why I spend so much time arguing against their attacks on evolution. Many of the IDiots accept common descent. Their attacks on other aspects of evolution aren't much different than similar attacks from legitimate, non-theistic scientists (e.g. objecting to junk DNA, questioning the Cambrian explosion, challenging strict Darwinism). It counts as "science" but it's very bad science and it's wrong.

All IDiots are anti-evolution but some go farther than others. If you are a Young Earth Creationist who believes that the universe was created less than 10,000 years ago, then you are not just anti-evolution, you are anti-physics, anti-chemistry, anti-geology, anti-astronomy, and anti-biology. I think it's fair to say that Young Earth Creationists are anti-science. This includes most (all?) of the Republican Presidential candidates in the United States and more than half the citizens of that country.

The only way YECs can possibly justify their strange beliefs is to assume that all the experts in all those fields are completely wrong about the fundamental concepts in their discipline. How could they possibly trust anything else those scientists have to say about their areas of expertise?

Let me introduce you to a "new voice" in the Intelligent Design Creationist world. Here's what Evolution News & Views says about him [A New Voice in the Debate Over Evolution and Intelligent Design].
There is literally a new voice in the debate over evolution and intelligent design. If you're a regular listener to the Center for Science & Culture's very popular and thrice weekly podcast, ID The Future, you have probably come to recognize familiar personalities, like ENV's Casey Luskin. (If you're not yet a listener, then you should be.) Now you will be hearing more often from radio broadcaster David Boze of Seattle's KTTH.
I assume David Boze is a heavy-weight and it's okay to criticize him.

Listen to the Discovery Institute podcast where Boze defends Young Earth Creationism against the charge that it's anti-science ["Anti-Science": Unpacking a Vague & Distorted Label]. (You can click on the embedded copy below.) Note the sleight of hand where he lumps together the Young Earth Creationists with all other IDiots. His point is that just because you're opposed to "atheistic Darwinian evolution" does not mean you're anti-science.

Perhaps not. But if you believe in the literal truth of the Bible then you are definitely anti-science. You are a genuine idiot. Does David Boze do a good job of defending Republican Presidential candidates against the charge of being anti-science? Will a YEC President harm the reputation of the United States? You be the judge.

Personally, I don't think the new kid on the block is much of a threat. Is this the best they can do?




Monday, October 24, 2011

Ravel's Bolero at the Copenhagen Central Train Station

 
I love these things!




An Interview with Maarten Boudry

 
As most of you know already, I've been a big fan of Maarten Boudry ever since I first met him in Toronto a few years ago. Last year I visited him in Gent and he bought me a beer (or three). Maarten's thesis (Here be dragons) has been published on the internet. If you haven't read it by now, you're in for a treat.

Now you can hear him in person in an interview on Think Atheist: Episode 31 Dr. Maarten Boudry OCT 23, 2011.

It almost makes you want to be a philosopher.


Stephen Meyer Talks About Junk DNA

Stephen C. Meyer has a Ph.D. degree (1991) in the History and Philosophy of Science from Cambridge University in the UK. He is currently Program Director of the Center for Science and Culture at the Discovery Institute in Seattle, Washington, USA.

Meyer's book, Signature in the Cell: DNA and the Evidence for Intelligent Design, is an attempt to present Intelligent Design Creationism as genuine science. I'll have more to say about this later but for now I want to concentrate on one particular aspect of his case.

Mayer claims that one requirement of a genuine scientific theory is the ability to make falsifiable predictions. Does Intelligent Design Creationism make such predictions? Yes, one of the predictions is that genomes will not contain very much junk DNA. It will be instructive to see how Intelligent Design Creationists handle this issue, especialy since I've just finished a thorough review of The Myth of Junk DNA by Jonathan Wells.

Here's what Meyer says about junk DNA.

The Myth of Junk DNA by Jonathan Wells

This is the final installment of my review of The Myth of Junk DNA by Jonathan Wells (Discovery Institute Press, 2011). The other posts are listed at the bottom of this summary and in the theme posting "Genomes & Junk DNA."

Most of the IDiots at the Discovery Institute feel threatened by the existence of large amounts of junk DNA in some eukaryotic genomes, including our own. That's why they are determined to refute this idea by showing that most putative junk DNA actually has a function. Jonathan Wells feels confident enough about his reading of the scientific literature to announce that junk DNA is a "myth" and he's written a book to promote this idea.

Wells never defines "junk DNA" correctly. The correct definition of "junk" is DNA that has no known function. Wells pretends that the original definition of junk DNA was "noncoding" DNA. Thus, all those bits of noncoding DNA that have a function are evidence that refutes the notion of junk DNA.

The truth is that no knowledgeable scientist ever suggested that regulatory regions, origins of replication, centromeres, telomeres, genes that produce functional RNA molecules, and chromatin organizing regions were ever classified as junk DNA. They all knew that there was lots of noncoding DNA that had a well-defined function. Right from the beginning of his book, Wells is attacking a strawman and misleading his readers.

Monday's Molecule #146

 
Give me the complete, unambiguous, name of the molecule to win a free lunch with me.1 Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but usually there are traditional names that will do.

UPDAYE: The winner is DK.


1. Or with Johnny Depp or Angelina Jolie, depending on who's available on a given day.

Sunday, October 23, 2011

Pray for Peterborough

 
Tomorrow the city council of Peterborough, Ontario will open their meeting with The Lord's Prayer [Agenda].

Saying Christian prayers at public meetings was declared illegal following an Ontario Court of Appeals ruling in 1999. The city council of Peterborough is announcing in advance that it will be performing an illegal act tomorrow at 6:30 PM. I assume the police will be there to arrest the mayor and council members (not).

Veronica will be there.

What's the point of having council members recite a Christian prayer before their meeting? Probably half the council members are not practicing Christians. What's the point of making the audience sit through the Lord's prayer? Many of them are at the meeting to make a presentation. What message does it send if they are not Christian?


[Photo Credit: Saying prayers at a Durham council meeting [Praying before City Council Meetings]]

Saturday, October 22, 2011

Daniel Belden and the Deerfield Massacre

 
William Beldon (1609-1655) was born in Heptonstall Parish, Yorkshire, England. He settled in Wethersfield in the Colony of Connecticut in 1641. (Wethersfield is just south of Hartford.)

William Beldon married Thomasine Sherwood (1615-1655) and they had the following children.
  1. Samuel Beldon (1647-1737)
  2. Daniel Belden (Belding) (1648-1732)
  3. John Belden (1650-1713)
  4. Susannah Beldon (1651-1706)
  5. Mary Beldon (1653-1724)
  6. Nathaniel Beldon (1654- )
I descend from John Beldon (1659-1713) and his wife Ruth Hale Hayes (1646-1700). But this is story about his brother, Daniel Beldon (sometimes known as Daniel Belding).

Friday, October 21, 2011

More than a Blog?

Mainstream scientists and mainstream journals are still trying to figure out what blogging is all about. They aren't alone. Science journalists are also puzzled. Even the bloggers are confused.

The latest contribution from the mainstream has just been published in the journal EMBO Reports: More than a blog. It discusses, among other things, the effect blogging had on the Wolfe-Simon et al. (2010) paper claiming that a strain of bacteria could incorporate arsenic into its DNA in place of phosphorus.

The author of the EMBO Reports article is Howard Wolinsky, an American journalist. I want to address one part of his article. Wolinsky writes,
This incident, like a handful before it and probably more to come, has raised the profile of science blogging and the freedom that the Internet offers to express an opinion and reach a broad audience. Yet it also raises questions about the validity of unfettered opinion and personal bias, and the ability to publish online with little editorial oversight and few checks and balances.
It's true that there's no editorial oversight on science blogs. It's not quite true that there are no checks and balances since most science bloggers read and comment on each other's posts and bad science bloggers are easily exposed (e.g. creationist sites).

But that's not what I want to comment about. Wolinsky's implies that the world of traditional science communication is free of personal bias and regulated by checks and balances. That's not true. The incident he's referring to is the "arsenic affair" and it a good idea to keep in mind what happened last December.

First, most of the fuss arose over the press release where the lead author made claims that were not in the Science paper and were not supported by evidence. Up until the advent of science blogging there were no serious checks and balances on press releases save for the occasional journalist who sometimes expressed a bit of skepticism. Science blogs are actually serving as checks and balances on press releases and irresponsible science journalism. That needs to be stated more often.

Second, it's simply not true that papers published in the scientific literature undergo rigorous editorial/peer review that is subject to checks and balances. It's simply not true that papers in the scientific literature are free of "unfettered opinion and personal bias." We've all known about this for decades. Science bloggers are now bringing that knowledge to the general public and (among other things) exposing bad papers to the critical analysis they should have received before being accepted for publication. There's general agreement that the Wolfe-Simon et al. (2010) paper was not subjected to rigorous peer review before it was published online. Thanks to the bloggers, publication of the print version of the paper was delayed for months and when it appeared it was accompanied by several letters of criticism. That never would have happened without science bloggers.

Science bloggers are providing the checks and balances that have gone missing in the so-called "peer-reviewed" scientific literature. The bloggers are becoming the "peers" that review the papers when the system breaks down.

While it is true that science bloggers may have an agenda and aren't subjected to rigorous peer review before publication, this should not be treated as a new phenomenon that's peculiar to blogs. If you're going to raise these issues in an article about blogging then you should also raise them with respect to the traditional scientific literature.

Third, science journalists are partly responsible for the increased role that science bloggers are playing in exposing bad science. Traditionally it was supposed to be science journalists who acted as a check on bad science and bad press releases. Recent incidents have shown us that we can no longer count on science journalists to act as skeptical reviewers. The "arsenic affair" is a good example (Carl Zimmer is a notable exception).

Today it's more likely that science journalists will follow the lead of science bloggers rather than do the required homework on their own. Many science journalists just publish paraphrased versions of press releases leaving it up to the science bloggers to expose the flaws in the press releases, and in the published paper.


[HatTip: Jarry Coyne: An EMBO report on science blogging]

Tuesday, October 18, 2011

Junk & Jonathan: Part 13—Chapter 10

This is part 13 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."


The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.
In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).
Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)

Monday, October 17, 2011

Better Biochemistry: Near-Equilibrium Reactions

This is part of a series on important concepts in biochemistry. I'm concentrating on those concepts that may be widely understood and/or not well described in most textbooks. Naturally, I think we do a pretty good job in our book!

Biochemical reactions are characterized by a Gibbs free energy change that describes the amount of energy produced or consumed in the reaction. In order to compare different reactions, chemists have developed a standard Gibbs free energy change that can be used to describe all reactions. The standard Gibbs free energy change in biochemical reactions is the energy produced or consumed when all the reactions and products are at a concentration of 1M, the temperature is 25°C (298 K), the pressure is 1 atm, the pH is 7.0, and the concentration of water is 55M.

Here's an example from the gluconeogenesis/glycolysis pathway (see below). It's the reaction catalyzed by aldolase where a six-carbon molecule (fructose) is cleaved to produce two three-carbon molecules. The reaction shown here is the one in the glycolysis pathway that breaks down glucose.

The standard Gibbs free energy change for this reaction is ...

ΔG'°reaction = +28 kJ mol-1

In a chemistry course you might learn that this reaction is NOT spontaneous because the standard Gibbs free energy change is positive. In other words, you need to supply energy—as indicated by the plus sign in the standard Gibbs free energy change—in order to make the reaction go from left to right. The reaction will be "spontaneous" in the opposite direction where ΔG'°reaction = -28 kJ mol-1.


The concept of "spontaneous" and "not spontaneous" based on the standard Gibbs free energy change make no sense in a biochemical context. The aldolase reaction, for example is part of the gluconeogenesis pathway where the two three-carbon molecles are joined to produce fructose-1,6-bisphosphate. This eventually leads to the production of glucose.

The adolase reaction is also part of the glycolysis pathway that runs in the opposite direction (as shown above). Cells can easily switch from making glucose to degrading it. How can this happen if the free energy change is +28 kJ mol-1.1

It isn't. The actual Gibbs free energy change inside the cell is very different than the standard Gibbs free energy change. This reaction rapidly reaches equilibrium inside the cell. Under those conditions the rates of the forward and reverse reactions are equal and ΔG = 0.

In the case of the aldolase reaction, the concentrations of the reactants and products at equilibrium will not be equal as the standard Gibbs free energy change requires. Instead, the concentration of fructose-1,6-bisphosphate will be much higher than the concentrations of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

In biochemical terms we say that this is a "near-equilibrium" reaction. Most metabolic reactions are near-equilibrium reaction with ΔG = 0 (or close to it).

This is an important concept in biochemistry. You can't understand pathways and flux if you don't know that most of the reactions are near-equilibrium reactions where ΔG = 0.Sup>1 You also can't understand regulated reactions, where ΔG is not zero, unless you've grasped the fundamentals. (Regulated reactions are called "metabolically irreversible reactions.")

Many textbooks do a poor job of explaining near-equilibrium reactions and their importance in metabolic pathways. Some still use standard Gibbs free energy changes as a measure of direction. Fortunately, the teaching of this concept has improved enormously over the past 15 years.3 The bad news is that if you took your last biochemistry course before 1995 you may be hopelessly out-of-date!

Here's an example of bad teaching from a 2003 textbook!
Although the cleavage of fructose-1,6-bisphosphate is frequently unfavorable (ΔG'° = +23.8 kJ/mol), the reaction proceeds because the products are rapidly removed.


1. You also have to understand the concept of steady-state—the concentrations of intermediates in a pathway don't change very much.
2. Some textbooks use +24 kJ mol-1.
3. The best textbooks had it right long before that.

Monday's Molecule #145

 
I'm restarting Monday's Molecule. The last one was almost two years ago [Monday's Molecule #144].

The rules have changed a bit. Monday's Molecule will no longer be linked to a Noble Prize because I'm running out of Nobel Prizes that lend themselves to such a linkage. All you have to do is supply the complete, unambiguous, name of the molecule to win a free lunch. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. Many of them have kindly donated their free lunch to the next contest.

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but there are several traditional names that will do.




Sunday, October 16, 2011

Kevin O'Leary Is a Jerk

 

Kevin O'Leary is one of those people who think that the world revolves around entrepreneurs and making money. He's well known in Canada because he's one of the "dragons" on Dragon's Den.

O'Leary recently got in trouble by saying that if he were Prime Minister he would "make unions illegal" and throw union members in jail. He also said; ""Unions are sheer evil." … "Unions themselves are born out of evil. They must be destroyed with evil." … "Look, no one could contain unions in hell. They were so evil they came out of hell and they came upon earth." [NUPGE / OPSEU file complaint with CBC Ombudsman over offensive anti-union comments by Kevin O'Leary].

As you might imagine, Kevin O'Leary is against the "Occupy Wall Street" movement even if he doesn't understand it. To him it must sound like a bunch of "left-wing nutbars" trying to muscle in on his God-given right to exploit the gullible.

Unfortunately he used that expression ("left-wing nutbar") on national television (CBC) and applied it to the guest they were interviewing (Chris Hedges). You can see it for yourself in the video. It's very embarrassing. I'm normally a supporter of the CBC but this makes it look like FOX News.

O'Leary has already been reprimanded by CBC's Ombudsman [CBC ombudsman says O'Leary's 'nutbar' remark violated journalistic standards]. I think it's time he was removed from the "The Lang & O'Leary Exchange."1




1. Not because he has a different opinion than I do. Because he's stupid.

Friday, October 14, 2011

Is Intelligent Design Creationism a Scientific Theory?

 
You should recall that Casey Luskin is one of those "serious science bloggers" who strikes fear into the hearts of evolutionary biologists. In fact, we are so afraid of people like Casey Luskin and Jonathan M that we go out of our way to avoid responding to their posts [see: A Reason to Doubt the IDiots].

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...
ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

The scientific method is commonly described as a four-step process involving observations, hypothesis, experiments, and conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesize that if a natural object was designed, it will contain high levels of CSI. Scientists then perform experimental tests upon natural objects to determine if they contain complex and specified information. One easily testable form of CSI is irreducible complexity, which can be tested for by reverse-engineering biological structures through genetic knockout experiments to determine if they require all of their parts to function. When scientists experimentally uncover irreducible complexity in a biological structure, they conclude that it was designed.

Wednesday, October 12, 2011

A Twofer

A few weeks ago David Klinghoffer criticized science bloggers for only going after "extremely marginal and daffy creationists." He challenged us to take on the "real scientists" like Jonathan M. [A Reason to Doubt the IDiots]

Today you're in for a treat, dear readers, 'cause I'm going to respond to a daffy creationist who happens to be Jonathan M. It's a twofer!

Tuesday, October 11, 2011

A Reason to Doubt the IDiots

 

David Klinghoffer is one of the most entertaining bloggers at Evolution News & Views. His version of logic never fails to bring a smile to my face.

Klinghoffer's latest posting is: A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates.
Much of the debate about Darwinian evolution is conducted in public online forums. If interpreted with some care, these give a convenient way of measuring the real confidence of leading spokesmen on the Darwin side. I don't mean the level of bluster -- they're all full of bluster -- but rather what they really must feel at some level deep down.

If you follow the top Darwin blogs you'll notice how eagerly and often they go in for mocking extremely marginal and daffy creationists. PZ Myers specializes in this. So too, in his books, does Richard Dawkins. How about answering the arguments of a real scientist who advocates intelligent design on scientific rather than Bible-thumping grounds -- a Douglas Axe or Ann Gauger, for example? How about a thoughtful critique of The Myth of Junk DNA or Signature in the Cell? A response to serious science bloggers like ENV's Casey Luskin or Jonathan M.?

Uh, no, thank you!

It's quite a contrast with intelligent-design advocates who, like them or not, wrestle with the top scientists and thinkers on the other side, while ignoring the small timers.
I really don't think this merits further comment by me.1 I'll let the words stand for themselves. I hope you were as amused as I am.


1. I assume those "serious scientists" don't read Sandwalk, Why Evolution Is True, Panda;s Thumb, Thoughts from Kansas, or dozens of other blogs and books that refute the nonsense spouted by those "serious scientists."

Image Credit: conservababes

Junk & Jonathan: Part 12—Chapter 9

 
This is part 12 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."


The title of Chapter 9 is "Summary of the Case for Functionality in Junk DNA." It is Wells' attempt to summarize the "evidence" he has presented so far.

Wells tells us that the "evidence" falls into two broad categories: (1) evidence that putative junk is probably functional, and (2) evidence that small specific bits of the genome are functional.

Within the first category there are two subdivisions: (1a) evidence that most of the genome is transcribed, and (1b) genome comparisons. Let's look at these two subcategories.

Who Owns the Information in Your Genome?

 
More and more people are having their genome sequenced or having it scanned for the presence of various traits. Should the information that comes out of those studies be made public without your permission?

The answer is, no. I think we can all agree on that. Nobody should have access to your personal genetic information without your permission.

Is your permission sufficient or do other people have a say in whether your genome information makes it into the public realm? Let's say you want to publish your own genomic sequence, do you have the right to do this on your own without seeking approval from anyone else?

Razib Khan of Gene Expression is passionately interested in this question. A few weeks ago he published an article about the sequencing of the genome of an Australian aboriginal using cells from a hair follicle deposited in a museum in the 19th century. Scientists sought permission from a local tribal council before publishing the genome sequence [All your genes belong to the tribal council!].

Clearly this is a case where scientists felt that ethnically-related individuals should have have a say in whether the genome of a long-dead member of the tribe was published.

Razib focuses the issue by asking whether an identical twin has the right to publish their genome over the objections of the other twin. Do you have the right to publish your genome sequence over the objections of your non-identical siblings and your parents? Razib says yes.
For that matter, people who put their genotypes in the public domain are partially exposing their whole families. Do they have to go ask for permission? Obviously I don’t think so. I didn’t ask my siblings or my parents.
This is one of those cases where "rights" and the "law" might conflict with social responsibility. I think Razib is dead wrong. I think he had to ask his sibling and his parents for permission and, if they refused, he should not have published his genome sequence. That's the ethical way to behave.

A few days later, Rasmus Nielsen posted a response to Razib Khan on his (Nielson's) blog: Evolutionary Genomics Blog. Nielson defended the decision to get permission from the tribal council and he also criticized Razib for not consulting his siblings before publicizing his genome information. Here's what Rasmus Nielson said .... [Do the genes belong to the tribal council?]
I cannot help but worry about the issues regarding disclosure of genetic information. As long as the public has faith in the geneticists ability to predict phenotypes, the implications of disclosing genetic information are enormous. When my brother in a few years are being considered for a position as CEO for a major company, I am sure he wouldn’t appreciate if I disclose that I carry a mutation that disposes me to early onset of Alzheimer’s disease. He might after all then also carry the mutation with 50% chance. Even if we wouldn’t want to ban me from disclosing information about myself, the nice thing for me to do would nonetheless be to talk with my brother before making the disclosure.
Again, it's the "nice thing to do," that should determine your behavior and not whether you have the legal "right" to do something. Nielson attributes the difference between him and Razib to an American preference for individualism.

Razib Khan responded to the criticism [Decency not by law alone].
Going back to Nielsen’s post he contends that it would be the “nice thing” for him to do to consult his sibling if he was going to disclose genetic information which might have broader impact upon him (in this case, the potential presence of a gene predisposing someone to Alzheimer’s). I think that’s key: I don’t have much of an issue with scientists who follow their conscience, and try to be decent human beings. Scientists are people too; not just analytic computation machines. The problem is when a legal framework emerges which regulates what science is, and isn’t, done. Obviously at the boundary I totally agree with the idea that science has some ethical constraints. We wouldn’t want a thousand Mengele’s to bloom. But I think the legal threshold should be set rather high. If governmental bodies begin to regulate the bounds of scientific inquiry at a fine-grained level that’s a pretty strong incentive for aspiring Leon Kass’ to take over such agencies.
I'm not sure what to make of that response. Rasmus Nielson was not proposing a law that says you can't publish your genome information without the permission of your family members. He was merely saying, as am I, that Razib behaved badly by not consulting his family. I don't have much respect for people who behave like that even if the law allows it.

What do the rest of you think? Are you the only one who has a stake in the information in your own genome? Should you be allowed to make it public even if your siblings and/or parents refuse permission?

There's a long list of prescriptions and warnings for those who want to participate in the Personal Genomes Project run by George Church. Here's what it says about consulting your family ...
Your publicly available DNA sequence data, trait data and other information will include certain information that applies to your family members. Some people may draw conclusions from your publicly available information, including speculating about what such information might reveal about you and your family members. As a result, the PGP cannot predict all of the risks, or the severity of the risks, that the public availability of this information may pose to you and your relatives. You are strongly encouraged to discuss this study and its potential risks, including the fact that not all of the risks are known, with your immediate family members.
Is this strong enough or should participants actually have to obtain written permission from their immediate family members? (They do have to get written permission from an identical twin.)


Image Credit: The Spittoon.

Saturday, October 08, 2011

Ancient Plants

 
The Botany Photo of the Day site is currently covering fossil plants. One of them is Cooksonia pertoni. There's a nice picture of the fossil and a photo of a reconstruction from the Evolution House at the Royal Botanic Gardens, Kew (shown here).

This species dates from about 400 million years ago and it shows what a primitive vascular plant looked like. It has no leaves, only a branching stalk with sporangia at the tips.

I often wonder what the Intelligent Design Creationists think when they see fossils like Cooksonia. Do they imagine that the intelligent designer built them over 400 million years ago then gradually modified them over the next 400 million years or so to produce modern flowers and trees? Do they think that the sporangia are examples of specified complexity that he/she/it simply abandoned for a better design later on?


Friday, October 07, 2011

Carnival of Evolution #40

 
This month's Carnival of Evolution (40th version) is hosted by Kevin Zelnio, a marine biologist/science writer living in North Carolina. He blogs at EvoEcoLab: The Carnival of Evolution.

There are 25 articles. Read them all!

The next Carnival f Evolution will be hosted by the mermaid's tale. You can submit your articles for next month's carnival at Carnival of Evolution. Here's the website: Carnival of Evolution.


Canada's Office of Religious Freedom

 
John Baird is the Minister for Foreign Affairs in Canada's federal government under our Conservative Prime Minister, Stephen Harper. A few days ago he announced the establishment of an Office for Religious Freedom [Rights and freedoms and religion].
Societies that protect religious freedom are more likely to protect all other fundamental freedoms. They are typically more stable and more prosperous societies. This view has been reinforced in consultations I’ve had around the world so far.

I honestly believe it is critically important that Canada is uniquely placed to protect and promote religious freedom around the world.

We are a country of many ethnicities and religions, but we all share one humanity—one of tolerance, one of acceptance, one of peace and security.

Canada has spoken out against violations of freedom around the world.

....

It was former Prime Minister John Diefenbaker who, during his time in office, championed human rights both in Canada and around the world. On the day he introduced the Canadian Bill of Rights in Parliament, he spoke these words:

“I am a Canadian, …, free to speak without fear, free to worship God in my own way, free to stand for what I think right, free to oppose what I believe wrong, free to choose those who shall govern my country. This heritage of freedom I pledge to uphold for myself and mankind.”

I pledge to continue this tradition. But I of course can’t do this alone.

And we as a country are compelled to get this right.

That’s why I’m glad each of you is here to share your expertise, insights and experiences.

I’m extremely pleased at the calibre of people gathered here.

I know this is a challenging task, but, then again, Canadians stand for what is right, not what is easy, so I have no doubt we here today are up to that challenge.

It is our common duty to defend the rights of the afflicted, and to give voice to the voiceless.

Our positions will not soften, our determination will not lessen, and our voices will not be diminished until all citizens can enjoy the freedoms and rights we hold to be universal and true.

Through our combined efforts, I am confident that the Office of Religious Freedom can help do just that.
This is so exciting. It means that Canada will soon delete "God keep our land glorious and free!" from the national anthem. It means that all provinces will have to stop funding religious schools—especially when they give preference to one religion over another. It means that there will be federal laws enforcing a ban on saying prayers at public meetings (e.g. Praying before City Council Meetings). It means an end to tax-exempt status for religious institutions.

And, best of all, it means that "Whereas Canada is founded upon principles that recognize the supremacy of God and the rule of law: " will be removed from our constitution.

That is what John Baird meant, right?


An Ugly Little Fact

 
The great tragedy of science—the slaying of a beautiful hypothesis by an ugly fact.

attributed to Thomas Henry Huxley (1825 - 1895)
A group of scientists from Italy and Switzerland have reported that neutrinos can travel a bit faster than the speed of light [Measurement of the neutrino velocity with the OPERA detector in the CNGS beam]. If true, it will change our understanding of general relativity.

So how do the knowledgeable scientists deal with this ugly little fact"? Are they ready to abandon general relativity? No, they aren't. The typical response is skepticism combined with a "wait and see" attitude while the result is confirmed. Chad Orzel of Uncertain Principles has a nice analysis of the experiment: Faster Than a Speeding Photon: "Measurement of the neutrino velocity with the OPERA detector in the CNGS beam". Chad concludes with,
So, if you had money to bet on it, bet that this result is wrong. But these guys aren't complete chumps, and if something is wrong with their experiment, it's something pretty subtle, because they've checked all the obvious problem areas carefully.
Victor Stenger expresses similar skepticism in an article published on Huff Post [No Cause to Dispute Einstein].
As someone who worked in neutrino physics for thirty years before retiring from research in 2000, I should be more excited than most by the report from CERN that neutrinos have been observed moving faster than light. And I am. The experiment looks very well done and the scientists involved are saying all the right things -- that their result is very preliminary and must be independently replicated before accepting it as scientific fact. If the observation is confirmed, it may be the most important discovery in science in the last 100 years.

However, a big fly in the ointment is the supernova in the Large Magellanic Cloud, which sits just outside our galaxy 168,000 light-years from Earth. It was first seen by the naked eye on February 24, 1987. Three hours before the visible light reached Earth, a handful of neutrinos were detected in three independent underground detectors. If the CERN result is correct, they should have arrived in 1982. So, if I were a wagering man, I would bet the effect will go away because of some systematic error no one has yet been able to think of.
These responses are typical. Instead of immediately rewriting the textbooks in light of a new discovery, scientists initially express skepticism of results that conflict with well-established models. They do this because history has convinced them that most of those discoveries will never be confirmed and the standard model remains intact. [See alos Sean Carroll: Can Neutrinos Kill Their Own Grandfathers?]

Thomas Huxley was wrong. That's not how science works.

Scientists and Poets

 
Scientists and poets are very different. Yes, it's true that some scientists are poets but when it comes to real scientific debates poetry is a poor excuse for science.

Unless, of course, you're an evolutionary psychologist. Evolutionary psychologists seem to be quite incapable of recognizing real scientific problems with their just-so stories. Instead, they fall back on a tactic that's much more common in modern humanities departments. They attack presumed motives and misconceptions.1

Jesse Marczyk of Pop Psychology is a defender of evolutionary psychology. He posted a poem on the thread: Boobies, Blue-footed And Otherwise. Instead of actually dealing with the science behind the study he assumes that all criticism of evolutionary psychology comes from people who don't understand the difference between "is" and "ought" and who don't understand that genes can influence behavior.

Unfortunately, this sort of response is all too typical of the mindset of evolutionary psychologists. Isn't there a single evolutionary psychologist who can behave like a scientist instead of like Rudyard Kipling?
When silly critics of evolutionary psych
Tell the world these studies are like
Excuses for misogyny
And evil behavior apology
Threatening to bring back Third Reich,

Those critics will proclaim,
“Those who rape and maim
Will turn to our field
For a convenient shield
In order to avoid any blame”

When the topic under discussion gets heated
The misunderstandings are always repeated
“Genes don’t determine behavior”
Is always their savior
Despite this point long being defeated

Their sense of self-satisfaction
Persists without any retraction,
Admission of fallibility,
Lack of civility,
Or awareness of any infraction

It would seem their moral outrage
Has left them biased and unable to gauge
Accurately the research they hope to dismiss
Leaving them only to curse and to hiss
In a manner unbefitting a sage.

These critiques are quite the bore,
and we’ve all heard this shit before.
We’re left only to shake our fist,
As they seem persist
Not unlike an academic cold sore.


1. The term "post-modernism" is much abused but that's what I'm thinking

Thursday, October 06, 2011

The Internal Brand of the Scarlet W

The Internal Brand of the Scarlet W by Stephen Jay Gould was first published as an essay in Natural History. It's reprinted in the anthology, The Lying Stones of the Marrakech. You can find it online here.

This is one of my all-time favorite Gould essays. The theme is genetic determinism and evolutionary psychology. The hook is a discussion of Charles Davenport's claim that some people have a wanderlust gene (W) that makes them undesirable as immigrants to the United States.
Of course, no one would now defend Davenport's extreme view of single genes determining nearly every complex human behavior. Most colleagues eventually rejected Davenport's theory; he lived into the 1940s, long past the early flush of Mendelian enthusiasm and well into the modern era of understanding that complex traits usually record the operation of many genes, each with a small and cumulative effect (not to mention a strong, and often predominant, influence from nongenetic environmental contexts of growth and expression). A single gene for anger, conviviality, contemplation, or wanderlust now seems as absurd as a claim that one assassin's bullet, and nothing else, caused World War I, or that Darwin discovered evolution all by himself, and we would still be creationists if he had never been born.

Nonetheless, in our modern age of renewed propensity for genetic explanations (a valid and genuine enthusiasm when properly pursued), Davenport's general style of error resurfaces on an almost daily basis, albeit in much more subtle form, but with all the vigor of his putative old gene - yes, he did propose one - for stubbornly persistent behavior.

We are not questioning whether genes influence behavior; of course they do. We are not arguing that genetic explanations should be resisted because they have negative political, social, or ethical connotations - a charge that must be rejected for two primary reasons. First, nature's facts stand neutral before our ethical usages. We have, to be sure, often made dubious, even tragic, decisions based on false genetic claims. But, in other contexts, valid arguments about the innate and hereditary basis of human attributes can be profoundly liberating.

Consider only the burden lifted from loving parents who raise beautiful and promising children for twenty years and then "lose" them to the growing ravages of schizophrenia - almost surely a genetically based disease of the mind, just as many congenital diseases of bodily organs also appear in the third decade of life, or even later. Generations of psychologists had subtly blamed parents for unintentionally inducing such a condition, then viewed as entirely environmental in origin. What could be more cruel than a false weight of blame added to such an ultimate tragedy? Second, we will never get very far, either in our moral deliberations or our scientific inquiries, if we disregard genuine facts because we dislike their implications. In the most obvious case, I cannot think of a more unpleasant fact than the inevitable physical death of each human body, but a society built on the premise that King Prospero will reign in his personal flesh forever will not flourish for long.
Take this lesson to heart. You should never oppose a valid evolutionary argument just because you don't like the ethical implications.

On the other hand, you should rigorously oppose silly evolutionary arguments no matter what the ethical implications.


Boobies and Evolutionary Psychologists

 
Robert Kurzban is a researcher at the University of Pennsylvania. He writes for a blog called Evolutionary Psychology. It is associated with an "open-access peer-reviewed journal" of the same name. Kurzban's article is about me: Boobies, Blue-footed And Otherwise.

As you might imagine, Robert Kurzban is heavily into evolutionary psychology. Here's what he says on his website.
Research, Philosophy, and Motto. Evolution gave rise to mechanisms designed to solve the bewildering array of problems that humans faced, from problems of survival to navigating the intricate strategic dynamics of the social world. Was there an adaptive problem faced by our ancestors for a substantial period of human history? If so, then, yeah, there's an adaptation for that.

Research in the lab is currently being conducted on morality, cooperation, friendship, mate choice, supernatural beliefs, modularity, self-control, and other topics.
Robert Kurzban was upset by my critique of science journalism and evolutionary psychology [Evolutionary Psychology Crap in New Scientist]. You might recall that my criticism is based on many common features of evolutionary psychology but the most important are the unwarranted assumptions that: (1) a particular specific behavior has a strong genetic component. (2) that the behavior is adaptive, and (3) that we know how our ancestors behaved.

The particular example I discussed is domestic violence and whether there has been selection in the past for alleles promoting violent behavior of men toward their wives. I discussed this in terms of the possible genetics of violence-toward-women in order to make the point that even if there was such an allele, it's adaptive value is highly questionable.

Robert Kurzban got a real bee in his bonnet over this comparison. He claims that the violence-toward-women that was adaptive was restricted to special circumstances. According to him, it's not just general violence toward women that was being selected it was violence only under special circumstances. In other words, the specific allele that Kurzban is proposing is one that cause males to only attack their mates some of the time—like when they suspect infidelity. That's correct, that's what the paper discusses even though the distinction isn't clear in the article in New Scientist.

Like it makes a difference. All that Kurzban is doing is making the genetics and the evolution more difficult by restricting the behavior to special circumstances. What he is saying is that there is an allele (or a combination of alleles) that makes men respect women most of the time but, under special circumstances, they attack their mates violently. Since these special circumstances are, presumably, rare, it becomes even more difficult to imagine what kinds of genes/alleles might be involved and how such alleles could become fixed in the population. (Especially if most males never encountered those special circumstances.)1

This is supposed to make evolutionary psychology much more acceptable?

Here's what Kurzban says,
Now suppose our hypothetical author said that because this trait, predicted to occur only in certain circumstances was not, in fact, seen all the time, then,well, there is something “seriously wrong” with the field from which the paper is drawn.
Let me try and be clear about what I said using Kurzban's terminology. What he is saying is that violent behavior toward women under certain circumstances was adaptive in our ancient ancestors. Therefore the alleles (or combination of alleles) for this behavior became fixed in the population. Therefore all modern men have this genetic tendency to act violently toward women under particular circumstances.

Most modern men do not act violently toward women under those particular circumstances even though they presumably carry the adaptive allele (or combination of alleles). It's reasonable to ask how such a behavior could be possibly adaptive enough to have been fixed in the population. It hard enough to believe this just-so story but it becomes even harder if the penetrance of the genotype is low.

Robert Kurzban seems to think that my simplified version was a serious mistake that calls into question the critique of evolutionary psychology. I think that his scenario does not rescue the field—in fact it makes it look even more ridiculous.

Kurzan also tries another defense of evolutionary psychology.
Now, finally, because the topic at hand is something with moral overtones, let’s say the author punctuated the critique with a pious remark about how siblicide is bad, bad, bad, and that the boobies who engage in it are “assholes,” and added that, hey, we can all overcome our bad, bad traits.

What kind of person would thoroughly botch an argument about a paper, condemn an entire discipline on the basis of the incorrect analysis, and then brandish their moralistic piety by condemning the behavior in question? I don’t know…some kind of Moran?
I know damn well that there's a difference between genetics/evolution and ethical behavior and anyone who reads my blog knows this. We've discussed the naturalistic fallacy and the is-ought problem many times on this blog and I've said repeatedly that I'm a big fan of Gould's position on those issues. [See The Internal Brand of the Scarlet W.]

What pisses me off is the way evolutionary psychologists turn those arguments upside down. They postulate—often without any scientific evidence—that bad behavior has a strong genetic component and that such behavior was beneficial in our ancestors. According to them, we are stuck with these alleles today even though we don't like the consequences. We all understand that possibility.

Just because it's a possibility doesn't mean it's correct. According to many evolutionary psychologists, anyone who criticizes the science must be doing so because they don't like the behavior and not because the science is bad.

It's a convenient way to avoid dealing with the real problems in evolutionary psychology.


1. Wouldn't it be nice if evolutionary psychologists could actually do some research to establish the existence of these amazing alleles and show where they map in the human genome? Heck, I'd settle for just a decent speculation on what kinds of alleles could possibly be involved.

Take this particular case as an example. There must have been a combination of alleles in our ancestors that caused men to be nice to their wives all the time. Then, 50,000 years ago, a mutation (or several mutations) arose that caused men to start beating their wives under special circumstances but to be nice to them most of the time. We have 20,000 genes. Which ones control that kind of behavior?

And if all those subtle behaviors were so strongly adaptive then how come evolution didn't fix some more serious problems like impacted wisdom teeth, hernias, susceptibility to breast cancer, and stupidity?