Horse Thieves, Skeletons and Black Sheep in the Family

My mother does genealogy. She has dozens of binders full of notes about our ancestors—some date back to 450 AD but most lineages can't be traced back much before 1500. It's fun to find out about your ancestors and about the history that they lived.

Sometimes there are surprises. Some of our ancestors were United Empire Loyalists who left New Jersey for Prince Edward Island after the American Revolution. We are descended from Isabella Robins, daughter of Richard Robins of Monmouth Co. in New Jersey (b. 1746). Richard's father was Benjamin Robins (b. 1686) and Benjamin's father (Richard's grandfather) was Daniel Robins who was born in Scotland in 1627 and sent to Connecticut in 1652 as an indentured servant after being captured by Cromwell's army following the battles of Dunbar and Wocester. (Our relatives were frequently on the losing side!)

After serving his eight years as an indentured servant, Daniel Robins married Hope Potter in New Haven Conn. in 1641. Now here's the interesting part. Hope Potter's father was William Potter (b. 1608) who first came to New England in 1635. When searching for information about William Potter, my mother came across this opening paragraph on a listserve.

Every amateur genealogist has in the back of his or her mind that someday an ancestral skeleton will appear, perhaps the legendary "horse thief". For those who are descendants of William Potter, the skeleton has appeared, but he did not steal the horses.

Hmmm ....

Turns out that William Potter, my great- great- great- great- great- great- great- great- grandfather, is pretty well known to genealogists. He had lots of descendants but that's not the only reason he's so famous. He was an animal lover.

William Potter was hung in 1662 for bestiality. By his own admission he had a fondness for horses, dogs, cows, sheep and pigs. His wife and children, having caught him in the act, laid charges before the Court of Magistrates in Newhaven (New Haven) [William Potter's Crime].

The Court haveing considered the case p'ceeded to sentence, & first read the law to him, & then the Governor asked him if he had anything to say why the court should not p'ceede to judge him according to the law.

He answered noe, but his great matter was betweene God & his soule, to desire him to give him repentance.

The Governor then declared, that seeing it is soe, they could doe noe otherwise, and he therefore in the name of the court did declare to William Potter that the law read was the sentence of the court, to be executed upon him, viz: that he be hanged on the gallowes till he be dead, & then cut downe & buried, & the creatures with whome he hath thus sinfully acted to be put to death before his eyes.

Twelve generations ago, I have about 4000 direct ancestors. William Potter was only one of them. All the others, I'm sure, were fine god-fearing, outstanding, citizens and a credit to their communities. Especially the ones that weren't Americans.

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Monday's Molecule #83

 

In honor of the Olympics, today's molecule is one that every athlete is afraid of. None of them want to allow this molecule to accumulate in their tissues during the competition.

Your task if to identify the molecule and its precursor and the enzyme responsible for the reaction. Be as specific as possible, especially when identifying the dangerous molecule on the right.

There's a indirect connection between today's molecule and a Nobel Prize. The Noble Laureate was among the first to identify the relationship between production of the molecule and the activity associated with the athletes. He won the prize for explaining, in part, why athletes get hot.

The first person to correctly identify the reaction and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are only two ineligible candidates for this week's reward. You know who you are.

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 and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) 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. I reserve the right to pick multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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Nisbet Attacks PZ Myers (again)

 
Mathew Nisbet has unleashed another attack on vocal atheists in general and PZ Myers¹ in particular [Two Images of Atheism: Hate versus Community].

Atheists have a major image problem. There's a reason that when people ask me what I believe I have to say with a smile: "I'm an atheist...but a friendly atheist." For sure, atheists for a long time have been unfairly stereotyped in the mainstream media and in popular culture. But we also have a lot of lousy self-proclaimed spokespeople who do damage to our public image. They're usually angry, grumpy, uncharismatic male loners with a passion for attacking and ridiculing religious believers. Any fellow atheist who disagrees with their Don Imus rhetoric, they label as appeasers.

These "new atheists" are the dark under belly of atheism. In books, blogs, and public statements, they sell us ideological porn, sophomoric rants that feed our dark sides and reinforce our own unfair stereotypes about the "other," i.e. the religious.

Yet all of this does far more harm than good. The addictive nature of their rhetoric radicalizes us and leads us to an ever more closed off conversation about how we are superior and everyone else is delusional.

Nisbet thinks he's an expert on how to deal with the problems of religion. He just doesn't get it. Several decades of being "nice" and "friendly" toward those who believe in superstitious nonsense got us nowhere. We atheists were ignored at best, and denigrated at worst.

Now, just a few years after publication of The God Delusion (and other books), atheism is on the radar and the believers have to deal with the fact that non-believers exist. Not only that, the non-believers are fighting back against the religious bigots. People like PZ Myers have done more to advance the case for rationalism over superstition than all the Nisbets have done in decades of accommodation. That makes Matt really, really mad. He just can't cope with the fact that his version of framing didn't work.

The guest blogger on Pharyngula took note of the attack (PZ is in the Galapagos) [Oh, the Drama]. Needless to say, the comments on that blog are not kind to Nisbet, but, then again, neither are the comments on his own blog. Not too many people like Matt Nisbet these days. I can't imagine why. Could it have something to do with bad framing?

Afarensis recognizes the injustice of Nisbet's attack: Framing Science Embraces the Willie Horton Strategy

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1. The picture that Nisbet posted of PZ Myers is beyond the pale. Whatever remaining credibility Nisbet had (not much) is gone.

What Is the "t-complex" and Why Should You Know About It?

 
I used to know all about it and even taught the underlying concept to undergraduates. That was 25 years ago and I'd forgotten what the t-complex was all about. Anonymous Coward¹ wanted to find out and (s)he posted a description on bayblab [WTF is transmission ratio distortion]. Normally I don't like linking to anonymous blogs but I'll make an exception here because this is cool.

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1. What a good pseudonym!

40 Years Ago Today

 
Today is our 40th wedding anniversary.

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The Genius of Charles Darwin

 
This is a really excellent TV series narrated by Richard Dawkins. I'm very impressed with Dawkins as a TV personality and I agree completely with his view of Darwin as an extraordinary genius. The one thing that bothers me is the adaptationist bias of Dawkins—the same thing I've been complaining about in several other postings.

At the beginning of Part 1, Dawkins says ...

This series is about perhaps the most powerful idea ever to occur to a human mind. The idea is evolution by natural selection and the genius who thought of it was Charles Darwin.... What Darwin achieved was nothing less than the complete explanation of the complexity and diversity of all life. And yet it's one of the simplest ideas that anyone ever had.

This is not correct. The complete explanation requires knowledge of genes, genetics, population genetics, random genetic drift, speciation, horizontal gene transfer, biochemistry, physiology, embryology, developmental biology, molecular drive, mutation, recombination, punctuated equilibria, species selection (possibly), cladistics, mass extinctions, plate tectonics, and much more. Even with all that there are still some things we're unsure about, like how to explain the Cambrian explosion

Part 1


Part 2


Part 3


Part 4


Part 5

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How Do Ligands Bind to Proteins?

When glutamine is bound to glutamine-binding protein, the protein is wrapped around the ligand to form a closed binding site that brings more amino acid side chains into contact with the ligand. The unbound protein has a much more open confromation.

The traditional explanations of binding is that the ligand binds to to open form of the protein and causes it to undergo a conformational change creating a closed pocket. The mechanism is called "induced fit." Now, there is evidence that the protein may transiently adopt the closed conformation in the absence of ligand and the ligand binds directly to the closed conformation.

Discount Thoughts reviews a recent paper [Do conformational changes precede or follow binding?]

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[Figure credit: Okazaki, K., Takada, S. (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms. Proc. Nat. Acad. Sci. (USA) 105:11182-11187. [DOI: 10.1073/pnas.0802524105]

The End Is Nigh

 

The Large Hadron Collider is due to be activated on September 10th. Estimates on how long it will take to create a black hole vary from microseconds to about 24 hours. Let's be optimistic and assume that it will take until Thursday morning (September 11th).

I figure the airport (Cointrin) will be sucked in before noon and Geneva should be swallowed up by at least 2pm. France will be gone by 4pm and we in Toronto will encounter the event horizon at midnight.

The good news is that I won't have to buy Ms. Sandwalk a birthday present on Friday. The bad news is that we may be spending an infinite amount of time together as we cross the event horizon so I might wish I had.

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nigh: Common Teutonic: OE. néah, néh = OFris. nei, nî, MDutch na, nae (Dutch na), OS. nâh (MLG. nâge, nâ), OHG. nâh adv., nâher adj. (MHG. nâ, nâh-, nâch, G. nah), ONor. ná- (in combs. like ná-búi neighbour; Sw. and Da. na-), Goth. nêhwa (nêhw): the stem appears to be unrepresented outside Teutonic. OHG. is the only one of the older languages in which a fully developed adjectival use of the word exists along with the adverbial. In OE. there are very scanty traces of adjectival inflexion, néah being commonly employed either as a simple adv. or with a dependent dative: in predicative use it may sometimes be taken as an adjective, but it is more probable that in such cases also it is an adverb. It is not till the 14th or 15th cent. that the attributive use becomes common.

The original comparative of néah as an adv. is néar, néor, near adv.1, while the adj. form néarra finally became ner, nar a. The OE. superlative níe(hook)hst(a is latterly represented by next a. and adv. After phonetic changes had obscured the relationship of these forms to the positive, a new compar. and superl., nigher and nighest, were formed, and have been in common use since the 16th cent.

= near adv.2 and a. (which in all senses has taken the place of nigh except in archaic or dialect use). [Oxford English Dictionary]

The Hype About Darwin Continues

 
Let me be clear about one thing. I've said it many times but it bears repeating. In my opinion Charles Darwin is the greatest scientist who ever lived and natural selection is one of the greatest ideas in science.

That should never be an excuse for exaggerating Darwin's contribution to modern evolutionary theory yet that's what we're seeing in the run-up to the 150th anniversary of the publication of On the Origin of Species. I was tremendously disappointed in the Royal Ontario Museum symposium a few weeks ago [Darwinism at the ROM] and in several articles that have been published since then.

I'm going to keep harping on this point until it sinks in. Here's the latest example from TimesOnline in the UK [Darwin's Bulldogs].

Next year marks the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of his On The Origin of Species. The Natural History Museum and the BBC plan extensive education programmes. Anticipating the anniversaries, Professor Richard Dawkins is presenting a series on Channel 4. These are welcome ventures. On the evidence of its first episode, Professor Dawkins's exposition of Darwinism will be an important public resource.

Darwin founded a branch of learning that has remarkable explanatory power and also grandeur. That the mechanism of evolution is natural selection is one of the great discoveries of science, with implications far beyond evolutionary biology. As Ernst Mayr, the biologist, wrote: “No educated person any longer questions the validity of the so-called theory of evolution, which we now know to be a simple fact.”

It is an unfortunate wonder of the modern age that people who are highly educated in some areas may still be resistant to scientific inquiry. We customarily think of objectors to Darwinism as Protestant fundamentalists. There is in fact a worrying trend for Muslim children to be taught the myths of creation, and the pseudoscience of “intelligent design”, as an explanation of the origins of life.

There are three things wrong with this short article.

First, the statement, "That the mechanism of evolution is natural selection is one of the great discoveries of science ..." is just plain wrong. Natural selection is one of the mechanisms of evolution but it is not the only one. Why can't people grasp this simple concept? It does not denigrate Charles Darwin's contribution to point out that we discovered other mechanisms in the 20th century.

Second, Mayr's statement, taken out of context, is misleading. Evolution is a fact but evolutionary theory is not a fact [Evolution Is a Fact and a Theory].

Third, I object to the term "Darwinism" and I am not a Protestant fundamentalist, a Muslim, or an IDiot. I wish journalists would make the effort to realize that modern evolutionary theory is no longer called "Darwinism." [Why I'm Not a Darwinist]. This does not mean that Charles Darwin was wrong. It simply means that the science of evolutionary biology has advanced a smidgen since 1859.

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[Hat Tip: RichardDawkins.net]

Amazing Catch by Ball Girl

 
Friday's Urban Legend: FALSE

This video is making the rounds. It shows a ball girl making an amazing catch of a fly ball then casually tossing it to the left fielder. Too bad it's a fake [Ballgirl].

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Are You Disappointed in Barack Obama?

 
I've always been a bit skeptical of Obama. It seemed to me that he wasn't as sincere about his "progressive" stance as, say, Dennis Kucinich. I wondered whether he wasn't playing to a particular audience in order to win the nomination.

Apparently I'm not the only one. There are a group of Americans who have become very nervous about Obama's move to the center. They've written an open letter to Barack Obama that's been published in The Nation [Change We Can Believe In].

The authors of the letter make the important point that the progressives who were attracted to the Obama campaign are the very ones who will ensure a victory in November. They are worried that these progressives will not make the effort to work for Obama if he continues to abandon the core principles that attracted them to the primary campaign.

We urge you, then, to listen to the voices of the people who can lift you to the presidency and beyond.

Since your historic victory in the primary, there have been troubling signs that you are moving away from the core commitments shared by many who have supported your campaign, toward a more cautious and centrist stance--including, most notably, your vote for the FISA legislation granting telecom companies immunity from prosecution for illegal wiretapping, which angered and dismayed so many of your supporters.

We recognize that compromise is necessary in any democracy. We understand that the pressures brought to bear on those seeking the highest office are intense. But retreating from the stands that have been the signature of your campaign will weaken the movement whose vigorous backing you need in order to win and then deliver the change you have promised.

I think they have a point but the more interesting question, from my perspective, is which one is the real Obama? Does he really believe in universal health care but is willing to make compromises for the sake of political expediency, or is he lukewarm on socialized medicine? Does he really believe that the USA needs to get out of Iraq because it never should have been there in the first place, or is he willing to compromise on that stance? What does he really think about the death penalty? Is he opposed on principle, in which case there's no compromise, or are his "principles" negotiable? Does he really expect to change the way things are done in Washington, or is that just something he says in order to get votes?

There's a discussion going on about this on Pharyngula [Progressives put pressure on Obama] but most readers are avoiding the real question. One commenter (Amplexus) said,

My fellow godless hedonists,

Obama is totally on our side. He's just hiding some of his feelings to get elected. We cannot take a stand on principle, we cannot afford to. Obama is blurring his position to win over independents that he sure as hell is going to shake off when he gets elected.

In other words, Obama is a liar and a hypocrite but that's okay because we all know that deep down he's a true believer.

Is that the common point of view among liberal Americans? Won't John McCain exploit this hypocrisy during the campaign?

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Evolutionary Psychology: The Capacity for Religion

 
Allen MacNeill has started a new blog called Evolutionary Psychology. Allen teaches introductory biology and evolution at Cornell University (New York, USA). This could be a good addition to the blogosphere since he intends to defend the field. (Good luck!)

The first posting on the new blog is The Capacity for Religious Experience is an Evolutionary Adaptation for Warfare. It starts out well with ...

Recent work on the evolutionary dynamics of religion have converged on a "standard model" in which religions and the supernatural entities which populate them are treated as epiphenomena of human cognitive processes dealing with the detection of and reaction to agents under conditions of stress, anxiety, and perceived threat.

I agree with this. There has been selection in the primate lineages for intelligence and one of the reasons for the fitness advantage may well be the ability to cope with external threats. I think that religion, and many other human behaviors, are epiphenomena that are indirect consequences of intelligent brains.

Unfortunately, this does not seem to be what MacNeill really means. He goes on to describe behaviors such as religion and warfare as though they were individually selected. He seems to be implying that there are genes for religious behavior and for engaging in warfare. This isn't the same as the "standard" model—unless my interpretation is completely wrong.

Here's how religion evolved, according to MacNeill ...

Wilson (2002) has proposed that the capacity for religion has evolved among humans as the result of selection at the level of groups, rather than individuals. Specifically, he argues that benefits that accrue to groups as the result of individual sacrifices can result in increased group fitness, and this can explain what is otherwise difficult to explain: religiously motivated behaviors (such as celibacy and self-sacrifice) that apparently lower individual fitness as they benefit the group.

At first glance, Wilson's argument seems compelling. Consider the most horrific manifestation of religious warfare: the suicide bomber. A person who blows him or herself up in order to kill his or her opponents has lowered his or her individual fitness. Doesn't this mean that such behavior must be explainable only at the level of group selection? Not at all: the solution to this conundrum is implicit in the basic principles of population genetics. Recall that one of Darwin's requirements for evolution by natural selection was the existence of variation between the individuals in a population. (Darwin, 1859, pp. 7 - 59) Variation within populations is a universal characteristic of life, an inevitable outcome of the imperfect mechanism of genetic replication. Therefore, it follows that if the capacity for religious experience is an evolutionary adaptation, then there will be variation between individuals in the degree to which they express such a capacity.

Furthermore, it is not necessarily true that when an individual sacrifices his or her life in the context of a struggle, the underlying genotype that induced that sacrifice will be eliminated by that act. Hamilton's principle of kin selection (Hamilton, 1964) has already been mentioned as one mechanism, acting at the level of individuals (or, more precisely, at the level of genotypes), by which individual self-sacrifice can result in the increase in frequency of the genotype that facilitated such sacrifice. Trivers (1971) has proposed a mechanism by which apparently altruistic acts on the part of genetically unrelated individuals may evolve by means of reciprocal altruism.

Given these two mechanisms, all that is necessary for the capacity for religious behavior, including extreme forms of self-sacrifice, to evolve is that as the result of such behaviors, the tendency (and ability) to perform them would be propagated throughout a population. The removal of some individuals as the result of suicide would merely lower the frequency of such tendencies and abilities in the population, not eliminate them altogether. If by making the ultimate sacrifice, an individual who shares his or her genotype with those who benefit by that sacrifice will, at the level of his or her genes, become more common over time. (Wilson, 1975, p. 4)

I take issue with this description. When an evolutionary psychologist says that "all that is necessary" for the evolution of a behavior is that it confers some advantage, your adaptationist bullshit detector should hit the red line. That's not all that is necessary. Another, very important, requirement is that there be a genetic component to the behavior. In other words, we need to show that suicide bombers (for example) have different alleles in their genomes than atheists.

I don't believe there's any evidence that such alleles exist.

The idea that there's a specific genetic propensity for religion is difficult to reconcile with our history. If religion alleles have been selected for thousand of years then how come European countries have been becoming secular in the past century? Are Europeans just learning to override the dictates of thei genes?

Or, is religion just an epiphenomenon—one of many cultural ways that a society can encourage cohesiveness? As a way of creating unity—and identifying strangers—religion is no different than patriotism or irrational devotion to a charismatic political leader (Obama as a religion? ). As a matter of fact, it's probably no different than the cliques formed by adolescent girls or the street gangs of teenage boys. They all serve the same purpose, albeit on different scales. They are all learned behaviors. In my opinion, religion is a product of nurture, not nature.

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Has Darwinism Been Rejected?

 
A number of misconceptions about evolution are described on the website Understanding Evolution for Teachers. One of them is Misconception: “Most biologists have rejected ‘Darwinism’ (i.e., no longer really agree with the ideas put forth by Darwin and Wallace).

Response: Darwin’s idea that evolution generally proceeds at a slow, deliberate pace has been modified to include the idea that evolution can proceed at a relatively rapid pace under some circumstances. In this sense, “Darwinism” is continually being modified. Modification of theories to make them more representative of how things work is the role of scientists and of science itself.

Thus far, however, there have been no credible challenges to the basic Darwinian principles that evolution proceeds primarily by the mechanism of natural selection acting upon variation in populations and that different species share common ancestors. Scientists have not rejected Darwin’s natural selection, but have improved and expanded it as more information has become available. For example, we now know (although Darwin did not) that genetic mutations are the source of variation acted on by natural selection, but we haven’t rejected Darwin’s idea of natural selection—we’ve just added to it.

Here's how I would re-word the first sentence of the second paragraph.

We now know that natural selection is just one of several mechanisms of evolution. One of the others is random genetic drift where variants can become established in a species purely by chance. There is clear evidence that variants that are neither harmful or beneficial can contribute to evolution and, in fact, the evidence suggests strongly that this is the most common form of evolution. However, there have been no credible challenges to the basic Darwinian principles that adaptive evolution proceeds exclusively by the mechanism of natural selection acting upon variation in populations and that different species share common ancestors.

I realize that my version is more complicated but it is also more accurate. This is a case where over-simplification comes at the expense of accuracy and I don't think the spin framing version is worth the sacrifice. There's nothing wrong with informing the general public (and teachers) that Darwinism remains true even though modern evolutionary theory covers much more than just Darwin's central ideas.

Ironically, the Understanding Evolution website has a good description of Genetic Drift, which they describe as "one of the basic mechanisms of evolution." I don't know why don't mention these other mechanisms on the page where they discuss Darwinism.

Now, look at the first paragraph of the website version. I think they're referring to punctuated equilibria. In this case, the extra complication isn't worthwhile because it doesn't really represent a significant change from Darwin's idea of evolution by natural selection. As a matter of fact, the description is downright misleading. The key concept in punctuated equilibria is that evolutionary change is associated with speciation by cladogenesis and the idea that evolution can occur rapidly isn't all that significant.

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Missing Pieces of the Puzzle

 
Understanding Evolution for Teachers is a website run by the University of California Museum of Paleontology (UCMP) in Berkeley.

Part of the website addresses a number of misconceptions about evolution and one of them is: Misconception: “Evolutionary theory is incomplete and is currently unable to give a total explanation of life”.

What I particularly like about their explanation is the "jigsaw puzzle analogy" that they use to illustrate the concept. Looking at the figure, you can immediately see the relevance—the fact that a few pieces are missing does not mean that we can't see the big picture.

There is no doubt about the general structure of evolutionary theory in spite of the fact that some pieces of the puzzle haven't been put in their proper place. There is no doubt about the fact that neither creationism nor any other explanation fits the scientific data.

I don't know who first came up with the jigsaw puzzle analogy. I first heard about it on talkorigins many years ago but I've forgotten who the author was. Please let me know if you remember. This figure needs to be widely disseminated because it makes an important point. I hope the University of California and the Understanding Evolution website won't object as long as we attribute it to them.

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[Hat Tip: John Dennehy]

Tangled Bank #111

 
The latest issue of Tangled Bank has been published on denialism blog [Tangled Bank #111].

Welcome to Tangled Bank #111! Today's entries are presented without comment, but with poetry, a truly remarkable natural, albeit human, phenomenon, or to quote Love and Rockets:

You can't go against nature
Because when you do
Go against nature
It's part of nature too.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.