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.

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.

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[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?

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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.

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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

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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.

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[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"?

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.)

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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.

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?

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Ravel's Bolero at the Copenhagen Central Train Station

 
I love these things!

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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.

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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.

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

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?

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