Emma Hale Is My (Distant) Cousin

 
You're probably wondering who the heck is Emma Hale? Up until a few days ago I couldn't have helped you, but now I know a great deal more. She was born in Harmony Township, Susquehanna County, Pennsylvania. This is in the northern part of the state not too far from Binghampton, New York. She died in Nauvoo, Illinois in 1879.

Emma was the wife of Prophet Joseph Smith, founder of the Mormon religion (The Church of Jesus Christ of Latter-Day Saints). The religion is based on the Book of Mormon, which is a translation of the inscriptions on some gold plates that Joseph discovered. The inscriptions tell of a visit by Jesus to the natives of North America.

The following description of Emma Hale's marriage is from the Wikipedia article on Emma Smith.

Emma was born July 10, 1804, in Harmony Township, Susquehanna County, Pennsylvania, as the seventh child of Isaac Hale and Elizabeth Lewis Hale. Emma first met her future husband, Joseph Smith, Jr. in 1825. Smith lived near Palmyra, New York, but boarded with the Hales in Harmony while he was employed in a company of men hoping to unearth buried treasure (specifically a silver mine for Josiah Stowell, a farmer whose farm home still stands on the north side of the Susquehanna River on New York State Route 7 in Ninevah, New York, Just West of Afton). Although the company found no treasure, Smith returned to Harmony several times seeking the hand of Emma. Isaac Hale refused to allow the marriage because he considered Smith's occupation disreputable. Finally, on January 17, 1827, Smith and Emma eloped across the state line to South Bainbridge (Afton), New York, where they were married the following day. The site of the marriage is on the site of the present day Afton Fairgrounds located on New York State Route 41 within the Village of Afton, in the Town of Afton. The Afton Fairgrounds is located on the East side of the Susquehanna River and a New York State Historical Marker commemorates the location. The couple moved to the home of Smith's parents on the edge of Manchester Township near Palmyra.

While there, on September 22, 1827, Joseph and Emma took a horse and carriage belonging to Joseph Knight, Sr. and went to a hill now known as the Hill Cumorah where Joseph claimed to receive a set of Golden Plates. This created a great deal of excitement in the area. In December 1827, the couple decided to move to be with Emma's parents' in Harmony where they reconciled to an extent with Isaac and Elizabeth Hale, who helped Emma and Joseph obtain a house and a small farm. While living there, Joseph began work on the Book of Mormon, and for a time, Emma acted as a scribe. She became a physical witness of the plates, reporting that she felt them through a cloth, traced the pages through the cloth with her fingers, heard the metallic sound they made as she moved them, and felt their weight. She later wrote in an interview with her son, Joseph Smith III: "In writing for your father I frequently wrote day after day, often sitting at the table close by him, he sitting with his face buried in his hat, with the stone in it, and dictating hour after hour with nothing between us."[3]

While in Harmony on June 15, 1828, Emma gave birth to her first child—a son named Alvin—who lived only a few hours.

In May 1829, Emma and Joseph left Harmony and went to live with David Whitmer in Fayette, New York. While there, Joseph finished work on the Book of Mormon, which was published by March 1830.

Emma's father was Issac Hale (1763-1839) and his mother (Emma's grandmother) was Diantha Ward (1741-1771). She is the daughter of Arah Ward (1718-1780) and Arah's father is William Ward (1678-1768). William is the son of Andrew Ward Jr. (1645-1691) who is the son of Andrew Ward Sr. (1597-1660) [Ancestors of Joseph Smith and Emma Hale].

Andrew Ward Sr. is Emma Hale's great⁴-grandfather and my great⁹-grandfather. So Emma Hale and I are distant cousins (very distant). The Ward family is from the New Haven area of Connecticut. It was Emma's father, Issac, who first moved to northern Pennsylvania near the New York state border.

Think about it. I am a Mormon in some alternate universe that isn't very different than this one. Only a few minor changes are required.

Contingency is scary.

UPDATE: Turns out I am not related to Andrew Ward so I'm not related to Emma Hale.

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Why People Believe Weird Things

 

WHY PEOPLE BELIEVE WEIRD THINGS

FEATURING DR. MICHAEL SHERMER

Friday, October 2, 7pm
J.J.R. MacLeod Auditorium
Medical Sciences Building
University of Toronto (1 King's College Circle)

Ever wonder why people believe in UFO abductions, mind-reading, reincarnation, urban legends, not to mention "scientific creationism" and the pernicious myth that the Holocaust never happened?

Dr. Michael Shermer, the Founding Publisher of Skeptic magazine, is a genuine ghost-buster, a relentless crusader against superstition and pseudoscience. Based on his bestselling book, Why People Believe Weird Things, Dr Shermer^Òs lecture will debunk junk science, bad science, voodoo science, pathological science, pseudoscience, and plain old nonsense. The event will be filled with humour,insight, and personal anecdotes - a highly entertaining wake-up call that has proved a hit on college campuses.

Dr. Michael Shermer is the Founding Publisher of Skeptic magazine, the Executive Director of the Skeptics Society, a monthly columnist for Scientific American, the host of the Skeptics Distinguished Science Lecture Series at Caltech, and Adjunct Professor of Economics at Claremont Graduate University.

ADMISSION
$8 regular
$5 students and Centre for Inquiry Members.
This event is FREE to New and Renewing Centre for Inquiry members and one guest.

CONTACT
Visit the event webpage at http://tinyurl.com/ntssw7 or contact
416-971-5676 or jtrottier@centerforinquiry.net

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IDiots, Epigenetics, and Jean-Baptiste Lamarck

 
What do IDiots, epigenetics, and Jean-Baptiste Lamarck have in common? Nothing much, actually, but that never stopped the Intelligent Design Creationists before.

For the latest attempt by IDiots to connect epigenetics and Lamarck see: A Bogey Moment with PZ Myers by Cornelius Hunter.

It is interesting to see how evolutionists respond to failures of their theory. For all their talk of following the evidence and adjusting to new data, evolutionists find all kinds of ways to resist learning from their failures. Consider one of the major failures of evolution, its view of the very nature of biological change. Twentieth century evolutionary theory held that biological change is a rather simple process that is blind to the needs of the organism. As Julian Huxley, grandson of Darwin confidant T. H. Huxley, put it, mutations "occur without reference to their possible consequences or biological uses."

Observations have long since been made to the contrary, but evolutionists cast it as the Lamarckian heresy. Researchers knew they should not suggest a correlation between environmental pressure and biological response, as the careers of those who did were ruined.

Now, you might be asking yourself what this has to do with supporting creationism.

Good question. It means you're starting to think critically.

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Nobel Prize Predictions

 
My colleague, Alex Palazzo, has just posted his annual list of potential Nobel Prize winners in the biological sciences [Gaze into the crystal ball - Nobel Prize Predictions].

I'm hoping for Ernest McCulloch and James Till for their discovery of stem cells. My second choice would be Harry Noller and some combination of others for their work on ribosome structure and function.

Post your prediction on Alex's new blog Transcription and Translation.

If you have time, you might want to correct his misguided views about scientific facts [Science - Building Models, Not Facts].

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Questions for Bill Maher and Richard Dawkins

 

Sometime tomorrow Richard Dawkins will be presenting the Richard Dawkins Award to Bill Maher at the Atheist Alliance International convention in Los Angeles.

Why is this a problem? It's a problem because Bill Maher is a kook. He believes in all kinds of strange things about alternative medicine, cancer, and immunizations.

Orac has the documentation at Respectful Insolence: Some "inconvenient questions" for Bill Maher and Richard Dawkins tomorrow. He also has a list of question for Bill Maher and Richard Dawkins.

PZ Myers will be at the convention. His attempt to defend Maher and Dawkins isn't working, in my opinion. Orac takes him on and exposes the hyprocrisy of the whole sorry episode. Maybe there will be fireworks at the convention tomorrow? I sure hope so. Giving the Richard Dawkins Award to Bill Maher is a travesty.

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What's on American Television?

 
One of the things I see on American television is Glenn Beck. PZ Myers says that Glenn Beck is completely insane.

It certainly seems that way to me but one can't help but wonder why he's given a show on a major cable news network. Surely he represents a substantial number of Americans?

Watch the video. Keep in mind that the song "Battle Hymn of the Republic" was originally "Canaan's Happy Shore" then transformed into "John Brown's Body." The significance of the changing lyrics to this memorable tune will become important near the end of the video.

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Ardipithecus ramidus

 
A (relatively) new hominid named Ardipithecus ramidus is described in several papers that appear in the Oct 2 issue of Science.

Carl Zimmer is ahead of the curve on his one¹ and I urge you to read his blog and learn about this important new ancestor of ours [Ardipithecus: We Meet At Last]. The main point is that this represents the earliest well-described species in our lineage. Ardipithecus ramidus lived in what is now Ethiopia about 4.4 million years ago.

The publicity surrounding these papers gives me an opportunity to raise a related issue. Here at the University of Toronto we are about to reorganize our first year biology courses. One of the required half courses will be BIO130H: Molecular and Cell Biology and the other will be BIO120H: Adaptation and Biodiversity.

The stated goal in the second course is to teach evolution, recognizing that "All science students require an understanding of evolutionary and ecological principles so they can make informed decisions on pressing societal issues ...."

I know what you're thinking ... you're thinking that Moran will be upset about the adaptationist slant in that course. You're right, I'm angry about that, but that's not what I want to talk about today.

The course will not mention fossils and it will not describe the history of life as determined by the fossil record. I think this is a mistake. I think that in order to understand evolution you need to examine all of the evidence that supports it and learn to appreciate that many different disciplines converge on the same conclusion; namely, that living things evolved over hundreds of millions of years.

Not only that, there are many fascinating parts of the fossil record that provide good opportunities for learning about evolution and for critical thinking. Hominid evolution and our relationship to the other apes is only one of them. There's also the Cambrian explosion, mass extinctions, the relationship between birds and dinosaurs, and punctuated equilibria.

It's true that you can't cover everything in a first year half course but the fossil record is too important to leave out, in my opinion. We also have a proposed new required second year course that's supposed to teach evolution. It's called BIO220H: From Genomes to Ecosystems in a Changing World. The fossil record isn't going to be taught in that course either.

What do Sandwalk readers think? Should we be graduating students with a life sciences degree when they've never heard of the fossil record in class?

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1. Where does he find the time to write so many excellent articles and books? Has he been cloned?

[Reconstructions: Copyright 2009, J.H. Matternes.]

The College Student’s Back to School Guide to Intelligent Design Creationism

 
The Evolution News website is run by the Discovery Institute in Seattle, Washington USA. In spite of the title, their goal is not to inform you about evolution. Instead, their goal is to promote anti-evolution thinking and Intelligent Design Creationism.

I'm in the middle of teaching a course about evolution and creationism so the latest posting on their website caught my eye. I urge my students to read the latest posting: Introducing The College Student’s Back to School Guide to Intelligent Design. They have lots of helpful hints about how to deal with evil Professors who oppose intelligent design. Not only that, they have a book for sale called "The College Student’s Back to School Guide to Intelligent Design." It's sort of like "Evolution for Dummies."

The main part of the book is about dealing with your Professor's "misinformed" opinions about Intelligent Design Creationism. Here's a list of nine such opinions. I better read up on how students are going to refute these arguments—at least the ones that aren't farcical or obvious strawmen.

1. Intelligent Design Is Not Science
2. Intelligent Design Rejects All of Evolutionary Biology
3. Intelligent Design Has Been Banned From Public Schools by the Federal Courts
4. Intelligent Design Is Just Politics
5. Intelligent Design Is a Science Stopper
6. Intelligent Design Is “Creationism” and Based on Religion
7. Intelligent Design Is Religiously Motivated
8. Intelligent Design Proponents Don’t Conduct or Publish Scientific
   Research
9. Intelligent Design Has Been Refuted by the Overwhelming Evidence for Neo-Darwinian Evolution

Hmmm ... on second thought, I hope my students don't see this. It looks like a pretty devastating attack on everything I've been saying in class. I'm shaking in my boots.

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Monday's Molecule #138: Winner

 
The purple molecule is cyclin bound to phospho-cyclin-dependent kinase 2 (CDK2) (yellow) and kinase-associated phosphatase (KAP) (blue). The Nobel Laureate is Tim Hunt.

There were lots of correct answers from Asia and Europe this time around but also a few from North America.

This week's winner is Joshua Johnson of Victoria University in Australia. The posting time was convenient for Australians since his email message was sent at 2 o'clock in the afternoon. There wasn't an undergraduate winner this week so I'll carry over the undergraduate prize for next week's molecule.

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This is the earliest posting of a Monday's Molecule. It should make the contest open to a whole new category of Sandwalk readers, especially those in Europe who will see it long before the readers in North America are awake.

It will also work for Asian readers and a few North and South Americans who are up very late at night. (Note to the latter group: get a life! )

The molecule is a compex of three different proteins. One of them—the yellow one—has already been featured as a Monday's Molecule last April. This time I want you to identify the purple molecule. It was first identified and characterized in the organism shown below then subsequently found in lots of other species.

The Nobel Laureate from last April shared the prize with the person who discovered today's molecule. Name that Nobel Laureate.

The first person to identify the molecule and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Philip Johnson of the University of Toronto, Ben Morgan of the University of North Carolina at Chapel Hill and Frank Schmidt of the University of Missouri.

Frank has agreed to donate his free lunch to a deserving undergraduate. Consequently, I have an extra free lunch for a deserving undergraduate so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

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You Can't Go Home Again

This is a resurrected version of a steroid hormone receptor. It was derived from the modern glucocorticoid receptor (GR) gene by mutating various codons to make them like the predicted ancestral gene. When all of the mutations were introduced, the protein was expressed and its structure was determined.

Glucocorticoid receptor specifically binds cortisol but the ancient protein binds other steroids as well as cortisol. This is pretty much what you might expect. Various gene duplication events lead to a family of proteins and each family member evolved to recognize a single ligand. The fact that you can reconstruct the presumed ancestral protein and show that it bound to multiple ligands is pretty amazing. The work comes out of Joseph Thornton's lab (Ortlund et al. 2007).

Altogether there were about 60 amino acid substitutions along the lineage leading from the ancestral broad-specificity receptor to the cortisol-specific receptor but only two of these turned out to be ones that shifted the specificity. Most of the rest probably had little effect of the function or specificity of the protein. This is the expected result. Most amino acid substitutions during evolution are neutral.

If there are really only two key amino acid substitutions that change specificity then it should be possible to convert a modern glucocorticoid receptor into one that recognizes a broad range of hormones by merely changing two amino acids. In other words, you could revert to the ancient form by reversing evolution and only a few mutations should do it.

Can you go back in time this easily? Apparently not, according to a recent paper from the same lab (Bridgham et al. 2009). Carl Zimmer is on top of this story in a article he published in yesterday's issue of the New York Times "Can Evolution Run in Reverse? A Study Says It’s a One-Way Street."

There's no conceptual advances in this paper, at least for those scientists who have a proper understanding of evolution. Some of the neutral changes along the pathway prepared the way for additional changes that were not possible in the ancestor protein. In other words, strictly neutral changes can add up to significant differences in structural stability making it possible for some adaptive change to occur that could not have otherwise occurred.

This isn't a breakthrough, it's an excellent study that confirms what was predicted on the basis of what we know about evolution. Here's how the authors describe their result in the abstract ...

Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent ‘restrictive’ mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key functionswitching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

Because of "historical contingency" you can't reverse evolution. The path that lineages follow as they evolve is determined, in part, by chance and accident and not by natural selection alone.

You can't go home again.

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Bridgham, J.T., Ortlund, E.A., and Thornton, J.W. (2009) An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519. [PDF]

Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., and Thornton, J.W. (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548. [PDF]

Naked Adaptationism

 
Most other mammals think that humans are excessively ugly. They probably see us in the same way we see naked mole rats. We (mostly) have no hair.

What happened to our hair? There are many explanations for human hairlessness but they all share one common characteristic—they are adaptationist just-so stories.¹

If you're looking for the best example of an adaptationist then you need look no further than Elaine Morgan, author of the Aquatic Ape speculation [see Elaine Morgan and Aquatic Apes]. She has written an article for last week's issue of New Scientist: Why are we the naked ape?. It won't come as a big surprise to learn that she dismisses all of the speculations about the evolution of hairlessness, except one: we lost our hair because our ancestors lived in the water.

That's not the point I want to make. Here's what Elaine Morgan says in the first few sentences.

RIGHT from the start of modern evolutionary science, why humans are hairless has been controversial. "No one supposes," wrote Charles Darwin in The Descent of Man, "that the nakedness of the skin is any direct advantage to man: his body, therefore, cannot have been divested of hair through natural selection."

If not natural selection, then what?

The idea that our lack of hair might just be an accident is completely foreign to someone like Elaine Morgan. She's probably being deadly serious when she asks the question, "If not natural selection, then what?" For adaptationists, natural selection is the only game in town and no other sorts of explanation are possible.

If it's genetic and visible, then it must be an adaptation. If one just-so story is refuted then make up another one to take it's place. That's what the article is all about. One by one, she dismisses sexual selection, overheating on the savannah, neoteny, avoiding parasites, evaporating sweat, leaving only aquatic ape speculation that hasn't been refuted, or so she claims.

One of the problems with the adaptationist program was described by Gould and Lewontin (1979), "If one adaptationist argument fails, assume that another must exist ...." Why not start thinking about other, non-adaptationist explanations?

Why is that so hard?

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1. The one exception is the idea that our nakedness is an epiphenomenon resulting from neotony.

Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205:581-598.

Science Education by Press Release

 
Futurity was officially launched on September 15th.

As an online research magazine, Futurity highlights the latest discoveries from leading universities in the United States and Canada.

Who is Futurity?

Duke University, Stanford University, and the University of Rochester lead a consortium of participating universities (see list below) that manages and funds the project. All partners are members of the Association of American Universities (AAU), a nonprofit organization of leading public and private research universities.

Futurity aggregates the very best research news. The content is produced by the partner universities, and submitted to Futurity’s editor, Jenny Leonard, (editor@futurity.org) for consideration. The site, which is hosted at the University of Rochester, covers news in the environment, health, science, society, and other areas.

We're talking about press releases. Most of the information comes from press releases written by the "leading" universities. Does anyone see a problem with that?

Carl Zimmer does. He rightly points out that universities and reasearch hospitals have a vested interest in promoting the work done at their institutions [Apocalypse Via Press Release].

What Futurity does do, however, is allow universities and research institutions to go straight to the reader. Originally, press information officers at these places wrote press releases, which, as the name implies, were things intended to get the attention of the press in the hopes that they’d cover something you’re doing. Futurity calls what it publishes “news,” but it’s still being written by employees of the organizations that are the subject of that news.

I have great respect for some public information officers; the stuff they write is, in some cases, wonderfully clear and informative. There’s good information to be had on Futurity. But I always treat press releases as a starting point. I do not, for example, assume that a piece of research is actually important just because a press release says it is. Imagine a press release with the headline, “Minor study published that is really not all it claims to be.” Such things just don’t exist.

This makes a lot of sense. I really like the fact that Carl is speaking out against the excesses of bad journalism and the gross misunderstandings of science education. He's exactly right about university press releases. They are entirely one-sided—don't look for balance from a PR department.

Not only that, most press releases are horrible. I think it's fair to say that many of the worst examples of science journalism come from university press offices. That's not to say that they're all bad. I've seen some pretty good examples from my own university and from some others, but they are the exceptions, not the rule.

How soon we forget. Remember The Darwinius Affair?

You can't blame science journalists for getting their science wrong if they get it straight from the horse's mouth, right? Wrong! Read Carl Zimmer and learn how real science journalist should behave. They should investigate a story to see if the hype is justified.

Investigative science journalism is the subject of yesterday's posting by Bora Zivkovic over on A Blog Around the Clock. He points out that most science journalists do not investigate in spite of the fact that this is often what they claim to be doing. This is what distinguishes the average science journalist from the good ones, like Carl Zimmer.

That much we know. Where Bora and I part company is when it comes to press releases. Here's what Bora says ...

While we have all screamed every now and then at some blatantly bad press releases (especially the titles imposed by the editors), there has been generally a steady, gradual improvement in their quality over the years. One of the possible explanations for this is that scientists that fall out of the pipeline as there are now so many PhDs and so few academic jobs, have started replacing English majors and j-school majors in these positions. More and more institutions now have science-trained press officers who actually understand what they are writing about. Thus, there is less hype yet more and better explanation of the results of scientific investigation. Of course, they tend to be excellent writers as well, a talent that comes with love and practice and does not necessitate a degree in English or Communications.

That's not been my experience. Just look at the main page on the Futurity website for examples of bad science journalism. As I write this, the top story is ....

Wonder drug may treat cancer, addiction

UC IRVINE—A drug in development to treat cancer could have the added benefit of helping prevent relapse in people trying to overcome cocaine addiction.

In mice conditioned to cocaine, drug-seeking activity was inhibited faster and to a greater extent with sodium butyrate than without it, neuroscientists at the University of California-Irvine say.

"Our results are exciting because sodium butyrate taps into fundamental molecular mechanisms, providing a novel approach to understanding and treating drug addiction," says the study’s lead author Marcelo Wood, assistant professor of neurobiology and behavior....

That's sounds just like the kind of story that could come from the PR office of a political party or the head office of a major pharmaceutical company.

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Yom Kippur

 
My lunch buddy isn't here today. At first I was worried, maybe he's sick or been in a car accident? Then I realized that it's Yom Kippur, the most sacred of the Jewish holidays.

This is the Day of Atonement, for Jews. It's a day characterized by fasting, prayer, and seeking forgiveness. This is the one day of the year when attending synagogue is practically mandatory—even for secular Jews.

Who are "secular" Jews, you might ask? They're people who belong to the culture of Judaism but who don't believe in God. That can be a substantial percentage of Jews in some countries. Even in Israel, about 30% of the citizens are atheists (adherents.com).

I'm pretty sure this phenomenon (secular "religion") is quite common. I know lots of secular Roman Catholics and secular Anglicans.

Happy Yom Kippur¹ to all Jews, secular and otherwise.

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1. It seems a bit strange to be wishing happy Yom Kippur on a day devoted to atonement but I'm told this is appropriate for an atheist or other goya.

A Young Scientist in Italy

 
Like John Wilkins, I too have visited Italy.

Whereas John is interested in spandrels, I was more interested in the native wildlife.

John is there now [An Adaptationist in Piazza San Marco], I was there in prehistoric times.

John is old and wise, I was young and naive. (I didn't even know about spandrels back then.)

I had a Michelin guide, I bet John doesn't have a Michelin guide!

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An Adaptationist in Piazza San Marco

John Wilkins of Evolving Thoughts is currently in Venice, Italy. He has just visited the Basilica San Marco (St. Mark's Basilica) according to What I am doing on my holidays….

This visit is significant since the Spandrels of San Marco are famous in evolutionary biology. They are part of the attack on adaptationism launched in 1979 by Gould and Lewontin. This is a paper that every student of evolution should read. Here's an online version: The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.

John has been struggling with adaptationism for almost fifteen years. When he first began studying evolutionary biology he, like many others, was unaware of the importance of random genetic drift and other anti-adaptationist perspectives. He certainly didn't know that random genetic drift is by far the dominant mechanism of evolution in terms of frequency of allele fixation. Over time John has developed an unusual perspective on adaptionism—one that I don't really understand.

Here's how he explains it in his latest posting ...

This is interesting, I think, in the context of Gould’s and Lewontin’s paper. It shows that claims of things being adaptive or not depend crucially on what one counts as the “task” of a structure. Since I think that everything is subjected to selection pressure at all times (sometimes not enough to overcome the noise of statistical properties), counting what is, and what isn’t, adaptive is a bit of a personal call, in the absence of access to the historical processes of particular traits. I am becoming more of an adaptationist these days.

The idea that many alleles might be slightly beneficial or slightly detrimental isn't very controversial. But that's not what John is saying. As I understand him, he's saying there can be no such thing as a truly neutral allele. He seems to be saying that anyone who believes otherwise is making a "personal call." A personal call that he believes is wrong since he thinks (i.e. his personal call) that everything is subject to natural selection.

He's also making a somewhat trivial point that doesn't contribute to the debate, as far as I'm concerned. Many alleles that are slightly beneficial are lost due to random genetic drift and many alleles that are slightly deleterious are fixed by random genetic drift. To me, that says that adaptationism can't explain all of evolutionary biology. To call yourself an adaptationist while knowing that slightly deleterious alleles can be fixed by random genetic drift seems somewhat unsatisfying.

John has a paper in the latest issue of Biology and Philosophy, an issue devoted to Adaptationism. It's not a very enlightening issue, from my perspective. The main problem with adaptationism isn't that it can't explain adaptation and it isn't that some just-so stories are wrong. The main problem is that adaptationists don't even consider any other alternatives to fixation by natural selection. Everything, especially everything with a visible phenotype, is automatically assumed to be adaptive and the arguments proceed from there.

One of the papers I liked was Seven Types of Adaptationism by Tim Lewens (Lewens, 2009). The seven types are:

A Empirical adaptationisms

1. Pan-selectionism–natural selection is the most significant of the evolutionary forces that act on populations.
2. Good-designism–evolutionary processes tend to result in organisms with suites of well-designed traits. Most lineages are highly evolvable.
3. Gradualism–adaptation is always the result of selection acting on gradual
variation.

B Methodological Adaptationisms

4. Weak heuristic adaptationism–those traits that are adaptations are likely to be correctly recognised as such only if we begin by assuming that all traits are adaptations.
5. Strong heuristic adaptationism–only by beginning to think of traits as adaptations can we uncover their true status, whether they are adaptations or not.

C Disciplinary Adaptationism

6. Explanatory adaptationism–an evolutionary biologist’s proper business is the study of adaptations.

D Epistemological Adaptationism

7. Epistemological optimism–investigators have access to the data that reliably discriminate between conflicting evolutionary hypotheses.

There are problems with all seven forms of adaptationism but the nice thing about Lewens' paper is that he effectively refutes #4, #5, and #7. In the case of methodological adaptationism it's just not true that the default assumption has to be adaptation. Evolutionary biology will be just as productive in the long run if drift is the default assumption and adaptation has to be proven.

In explanatory adaptationism, the assumption is that all of the interesting parts of evolution are adaptations and fixation of alleles by random genetic drift is so boring that it might as well not even be evolution. This is the stance taken by many adaptationists, like Richard Dawkins. As you might imagine, it doesn't take much effort to refute that kind of argument. One's personal opinion about what's interesting and what's not interesting should not play a role in determining how everyone else should go about studying evolution.

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Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205:581-598.

Lewens, T. (2009) Seven types of adaptionism. Biol. Philos. 24:161–182. [doi: 10.1007/s10539-008-9145-7]