Daniel Belden and the Deerfield Massacre

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

William Beldon married Thomasine Sherwood (1615-1655) and they had the following children.

1. Samuel Beldon (1647-1737)
2. Daniel Belden (Belding) (1648-1732)
3. John Belden (1650-1713)
4. Susannah Beldon (1651-1706)
5. Mary Beldon (1653-1724)
6. Nathaniel Beldon (1654- )

I descend from John Belden (1650-1713) and his wife Ruth (Hale) Hayes (1646-1700). But this is a story about his brother, Daniel Beldon (sometimes known as Daniel Belding).

More than a Blog?

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

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

The author of the EMBO Reports article is Howard Wolinsky, an American journalist. I want to address one part of his article. Wolinsky writes,

This incident, like a handful before it and probably more to come, has raised the profile of science blogging and the freedom that the Internet offers to express an opinion and reach a broad audience. Yet it also raises questions about the validity of unfettered opinion and personal bias, and the ability to publish online with little editorial oversight and few checks and balances.

It's true that there's no editorial oversight on science blogs. It's not quite true that there are no checks and balances since most science bloggers read and comment on each other's posts and bad science bloggers are easily exposed (e.g. creationist sites).

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

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

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

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

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

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

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

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

Junk & Jonathan: Part 13—Chapter 10

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

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The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.

In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).

Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)

Better Biochemistry: Near-Equilibrium Reactions

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

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

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

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

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

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

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

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

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

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

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

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

Here's an example of bad teaching from a 2003 textbook!

Although the cleavage of fructose-1,6-bisphosphate is frequently unfavorable (ΔG'° = +23.8 kJ/mol), the reaction proceeds because the products are rapidly removed.

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

Monday's Molecule #145

 

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

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

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

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

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

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Kevin O'Leary Is a Jerk

 

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

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

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

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

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

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

Is Intelligent Design Creationism a Scientific Theory?

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

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...

ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

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

A Twofer

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

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

A Reason to Doubt the IDiots

 

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

Klinghoffer's latest posting is: A Reason to Doubt the Real, Rather than Pretended, Confidence of Darwin Advocates.

Much of the debate about Darwinian evolution is conducted in public online forums. If interpreted with some care, these give a convenient way of measuring the real confidence of leading spokesmen on the Darwin side. I don't mean the level of bluster -- they're all full of bluster -- but rather what they really must feel at some level deep down.

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

Uh, no, thank you!

It's quite a contrast with intelligent-design advocates who, like them or not, wrestle with the top scientists and thinkers on the other side, while ignoring the small timers.

I really don't think this merits further comment by me.¹ I'll let the words stand for themselves. I hope you were as amused as I am.

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

Image Credit: conservababes

Junk & Jonathan: Part 12—Chapter 9

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

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

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

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

Who Owns the Information in Your Genome?

 

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

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

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

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

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

Razib focuses the issue by asking whether an identical twin has the right to publish their genome over the objections of the other twin. Do you have the right to publish your genome sequence over the objections of your non-identical siblings and your parents? Razib says yes.

For that matter, people who put their genotypes in the public domain are partially exposing their whole families. Do they have to go ask for permission? Obviously I don’t think so. I didn’t ask my siblings or my parents.

This is one of those cases where "rights" and the "law" might conflict with social responsibility. I think Razib is dead wrong. I think he had to ask his sibling and his parents for permission and, if they refused, he should not have published his genome sequence. That's the ethical way to behave.

A few days later, Rasmus Nielsen posted a response to Razib Khan on his (Nielson's) blog: Evolutionary Genomics Blog. Nielson defended the decision to get permission from the tribal council and he also criticized Razib for not consulting his siblings before publicizing his genome information. Here's what Rasmus Nielson said .... [Do the genes belong to the tribal council?]

I cannot help but worry about the issues regarding disclosure of genetic information. As long as the public has faith in the geneticists ability to predict phenotypes, the implications of disclosing genetic information are enormous. When my brother in a few years are being considered for a position as CEO for a major company, I am sure he wouldn’t appreciate if I disclose that I carry a mutation that disposes me to early onset of Alzheimer’s disease. He might after all then also carry the mutation with 50% chance. Even if we wouldn’t want to ban me from disclosing information about myself, the nice thing for me to do would nonetheless be to talk with my brother before making the disclosure.

Again, it's the "nice thing to do," that should determine your behavior and not whether you have the legal "right" to do something. Nielson attributes the difference between him and Razib to an American preference for individualism.

Razib Khan responded to the criticism [Decency not by law alone].

Going back to Nielsen’s post he contends that it would be the “nice thing” for him to do to consult his sibling if he was going to disclose genetic information which might have broader impact upon him (in this case, the potential presence of a gene predisposing someone to Alzheimer’s). I think that’s key: I don’t have much of an issue with scientists who follow their conscience, and try to be decent human beings. Scientists are people too; not just analytic computation machines. The problem is when a legal framework emerges which regulates what science is, and isn’t, done. Obviously at the boundary I totally agree with the idea that science has some ethical constraints. We wouldn’t want a thousand Mengele’s to bloom. But I think the legal threshold should be set rather high. If governmental bodies begin to regulate the bounds of scientific inquiry at a fine-grained level that’s a pretty strong incentive for aspiring Leon Kass’ to take over such agencies.

I'm not sure what to make of that response. Rasmus Nielson was not proposing a law that says you can't publish your genome information without the permission of your family members. He was merely saying, as am I, that Razib behaved badly by not consulting his family. I don't have much respect for people who behave like that even if the law allows it.

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

There's a long list of prescriptions and warnings for those who want to participate in the Personal Genomes Project run by George Church. Here's what it says about consulting your family ...

Your publicly available DNA sequence data, trait data and other information will include certain information that applies to your family members. Some people may draw conclusions from your publicly available information, including speculating about what such information might reveal about you and your family members. As a result, the PGP cannot predict all of the risks, or the severity of the risks, that the public availability of this information may pose to you and your relatives. You are strongly encouraged to discuss this study and its potential risks, including the fact that not all of the risks are known, with your immediate family members.

Is this strong enough or should participants actually have to obtain written permission from their immediate family members? (They do have to get written permission from an identical twin.)

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Image Credit: The Spittoon.

Ancient Plants

 

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

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

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

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Carnival of Evolution #40

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

There are 25 articles. Read them all!

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

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Canada's Office of Religious Freedom

 

John Baird is the Minister for Foreign Affairs in Canada's federal government under our Conservative Prime Minister, Stephen Harper. A few days ago he announced the establishment of an Office for Religious Freedom [Rights and freedoms and religion].

Societies that protect religious freedom are more likely to protect all other fundamental freedoms. They are typically more stable and more prosperous societies. This view has been reinforced in consultations I’ve had around the world so far.

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

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

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

....

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

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

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

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

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

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

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

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

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

Through our combined efforts, I am confident that the Office of Religious Freedom can help do just that.

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

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

That is what John Baird meant, right?

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An Ugly Little Fact

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

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

So how do the knowledgeable scientists deal with this ugly little fact"? Are they ready to abandon general relativity? No, they aren't. The typical response is skepticism combined with a "wait and see" attitude while the result is confirmed. Chad Orzel of Uncertain Principles has a nice analysis of the experiment: Faster Than a Speeding Photon: "Measurement of the neutrino velocity with the OPERA detector in the CNGS beam". Chad concludes with,

So, if you had money to bet on it, bet that this result is wrong. But these guys aren't complete chumps, and if something is wrong with their experiment, it's something pretty subtle, because they've checked all the obvious problem areas carefully.

Victor Stenger expresses similar skepticism in an article published on Huff Post [No Cause to Dispute Einstein].

As someone who worked in neutrino physics for thirty years before retiring from research in 2000, I should be more excited than most by the report from CERN that neutrinos have been observed moving faster than light. And I am. The experiment looks very well done and the scientists involved are saying all the right things -- that their result is very preliminary and must be independently replicated before accepting it as scientific fact. If the observation is confirmed, it may be the most important discovery in science in the last 100 years.

However, a big fly in the ointment is the supernova in the Large Magellanic Cloud, which sits just outside our galaxy 168,000 light-years from Earth. It was first seen by the naked eye on February 24, 1987. Three hours before the visible light reached Earth, a handful of neutrinos were detected in three independent underground detectors. If the CERN result is correct, they should have arrived in 1982. So, if I were a wagering man, I would bet the effect will go away because of some systematic error no one has yet been able to think of.

These responses are typical. Instead of immediately rewriting the textbooks in light of a new discovery, scientists initially express skepticism of results that conflict with well-established models. They do this because history has convinced them that most of those discoveries will never be confirmed and the standard model remains intact. [See alos Sean Carroll: Can Neutrinos Kill Their Own Grandfathers?]

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