A Politically Incorrect Commercial

 
This is bad form on the part of Mercedes-Benz. Somebody forgot to tell them that it's only men who are supposed to be stupid in TV commercials.

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[Hat Tip: Pretty shaved ape at Canadian Cynic

The Nitrogen Cycle

From Horton et al. (2006).

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The nitrogen needed for amino acids (and for the heterocyclic bases of nucleotides) comes from two major sources: nitrogen gas in the atmosphere and nitrate (NO₃^⊖) in soil and water. Atmospheric N₂ which constitutes about 80% of the atmosphere, is the ultimate source of biological nitrogen. This molecule can be metabolized, or fixed, by only a few species of bacteria. N₂ and NO₃^⊖ must be reduced to ammonia in order to be used in metabolism. The ammonia produced is incorporated into amino acids via glutamate, glutamine, and carbamoyl phosphate.

N₂ is chemically unreactive because of the great strength of the triple bond (N≡N). Some bacteria have a very specific, sophisticated enzyme—nitrogenase¹—that can catalyze the reduction of N₂ to ammonia in a process called nitrogen fixation. In addition to biological nitrogen fixation there are two additional nitrogen-converting processes. During lightning storms, high-voltage discharges cause the oxidation of N₂ to nitrate and nitrite (NO₂^⊖). Industrially, nitrogen is converted to ammonia for use in plant fertilizers by an energetically expensive process that requires high temperature and pressure as well as special catalysts to drive the reduction of N₂ by H₂. The availability of biologically useful nitrogen is often a limiting factor for plant growth, and the application of nitrogenous fertilizers is important for obtaining high crop yields. Although only a small percentage of the nitrogen undergoing metabolism comes directly from nitrogen fixation, this process is the only way that organisms can use the huge pool of atmospheric N₂.

The overall scheme for the interconversion of the major nitrogen-containing compounds is shown in Figure 17.1. The flow of nitrogen from N₂ to nitrogen oxides, ammonia, and nitrogenous biomolecules and then back to N₂ is called the nitrogen cycle. Most of the nitrogen shuttles between ammonia and nitrate. Ammonia from decayed organisms is oxidized by soil bacteria to nitrate. This formation of nitrate is called nitrification. Some anaerobic bacteria can reduce nitrate or nitrite to N₂ (denitrification). Most green plants and some microorganisms contain nitrate reductase and nitrite reductase, enzymes that together catalyze the reduction of nitrogen oxides to ammonia.
This ammonia is used by plants, which supply amino acids to animals. Reduced ferredoxin (formed in the light reactions of photosynthesis) is the source of the reducing power in plants and photosynthetic bacteria.

Let’s examine the enzymatic reduction of N₂. Most nitrogen fixation in the biosphere is carried out by bacteria that synthesize the enzyme nitrogenase. This multisubunit protein catalyzes the conversion of each molecule of N₂ to two molecules of NH₃ (ammonia). Nitrogenase is present in various species of Rhizobium and Bradyrhizobium that live symbiotically in root nodules of many leguminous plants, including soybeans, peas, alfalfa, and clover (Figure 17.2). N₂ is also fixed by freeliving soil bacteria such as Agrobacteria, Azotobacter, Klebsiella, and Clostridium and by cyanobacteria (mostly Trichodesmium spp.) found in the ocean. Most plants require a supply of fixed nitrogen from sources such as decayed animal and plant tissue, nitrogen compounds excreted by bacteria, and fertilizers. Vertebrates obtain fixed nitrogen by ingesting plant and animal matter.

Nitrogenase is a protein complex that consists of two different polypeptide subunits with a relatively complicated electron-transport system. One polypeptide (called iron protein) contains a [4 Fe–4 S] cluster, and the other (called iron–molybdenum protein) has two oxidation–reduction centers, one containing iron in an [8 Fe–7 S] cluster, and the other containing both iron and molybdenum. Nitrogenases must be protected from oxygen because the metalloproteins are highly susceptible to inactivation by O₂. For example, strict anaerobes carry out nitrogen fixation only in the absence of O₂. Within the root nodules of leguminous plants, the protein leghemoglobin (a homolog of vertebrate myoglobin) binds and thereby keeps its concentration sufficiently low in the immediate environment of the nitrogen-fixing enzymes of rhizobia. Nitrogen fixation in cyanobacteria is carried out in specialized cells (heterocysts) whose thick membranes inhibit entry of O₂.


A strong reducing agent—either reduced ferredoxin or reduced flavodoxin (a flavoprotein electron carrier in microorganisms)—is required for the enzymatic reduction of N₂ to NH₃. An obligatory reduction of 2 H^⊕ to H₂ accompanies the reduction of N₂. For each electron transferred by nitrogenase, at least two ATP molecules must be converted to ADP and P_i (inorganic phosphate) so the six-electron reduction of a single molecule of N₂ (plus the two-electron reduction of 2 H^⊕) consumes a minimum of 16 ATP.


In order to obtain the reducing power and ATP required for this process, symbiotic nitrogen-fixing microorganisms rely on nutrients obtained through photosynthesis carried out by the plants with which they are associated.

©Laurence A. Moran and Pearson/Prentice Hall

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1. Monday's Molecule #66

[Nitrogenase Image Credit: Dixon and Kahn (2004) based on the structure PDB 1n2c by Schindelin et al. (1997)]

Dixon, R. and Kahn, D. (2004) Genetic regulation of biological nitrogen fixation. Nature Reviews Microbiology 2, 621-631. doi:10.1038/nrmicro954

Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)

Schindelin, H., Kisker, C., Schlessman, J.L., Howard, J.B. and Rees, D.C. (1997) Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Nature 387: 370-376 [PubMed]

Tales from a New Encyclopedia

 
Centre for Inquiry's CELEBRATION OF SCIENCE AND FREETHOUGHT

ATHEISTS, HERETICS and UNBELIEVERS have fought at the forefront of every major civil rights movement of that last 300 years, including the Enlightenment, universal suffrage, abolitionism and minority civil rights. As the aggressive 'New Atheists' make headlines, the public tends to forget the legacy from which they stem.

In celebration we present:

TALES FROM A NEW ENCYCLOPEDIA

A presentation by Tom Flynn, Fri, April 4, 7pm
Tom Flynn, editor of FREE INQUIRY, leading secular humanist magazine, discusses the challenges he faced - and some of the surprising things he learned - during his five years editing THE NEW ENCYCLOPEDIA OF UNBELIEF. It covers in unprecedented detail the freethought, atheist, and humanist traditions and histories across the world. Flynn will share insights from research unearthing a once-vibrant freethought tradition in Toronto.

$5 general, $4 students, FREE for Friends of the Centre of Inquiry.
Join today ($60 regular, $20 students & low income)

The event is at CFI located just south of St. George & College at 216 Beverley St.-Canada's first home for those whose worldview is based on science, secularism and rationality. All are invited

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Send Email Back in Time

 

Google announced a new service starting today. You can now send email messages back in time using your gmail account. Unfortunately you can only go back four years to the day that gmail was launched. See Gmail Custom Time.

Is there a limit to how far back I can send email?

Yes. You'll only be able to send email back until April 1, 2004, the day we launched Gmail. If we were to let you send an email from Gmail before Gmail existed, well, that would be like hanging out with your parents before you were born -- crazy talk.

Think carefully before using this new feature. Each person only gets ten messages.

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For Once, Chris Mooney Talks Sense

 
Read Chris Mooney's latest posting on The Intersection where he addresses the framing controversy [A Dialogue on Framing, the F-Word, and the Future of ScienceBlogs, Part I: Framer Culpa].

When I teamed up with Matthew Nisbet a year ago to talk about the subject of framing science--which I still believe to be a very important one--it was not my goal to alienate or outrage a group that I consider one of my most important audiences, namely, ScienceBlogs bloggers and readers. And yet when you look at the latest blowup over what I have posted, Sheril has posted, and Nisbet has posted about Expelled, it's undeniable that there is now an audience that reacts very negatively even to any basic mention of the concept of framing.

And there's just no other way to spin it--this is a painfully ironic communication failure on the part of those of us who wanted to introduce what I view as a very important communication tool to the science world. If we can't explain something so useful to an important segment of our own audience, how can we possibly hope to use it to counter the other side?

Good for you Chris. The irony has been apparent to many of us and it's really good to see you confess to having created the problem. My respect for you just went up several notches.

Let me just correct one little thing. There are plenty of science bloggers out there who don't like your views on framing science. Not all of us belong to the ScienceBlogs^TM consortium.

Now, to be sure, the concept of framing has been quite influential already for many people who care about science, but who are not seemingly well represented on ScienceBlogs. When I go around lecturing with Matt Nisbet, we constantly encounter enthusiastic, receptive scientist-laden audiences at universities. There is simply nothing like the response that we've seen here over the last week. Indeed, I believe the reactions at lectures may have skewed my perceptions, and made me neglect or dismiss, to a significant extent, the way our ideas were faring in the science blogosphere.

But no success on the lecture circuit can change the fact that somehow--and I'll have ideas about how it happened in later posts--the concept of framing has been blackened on Scienceblogs, which I consider a truly tragic occurrence. And while I'm hardly the only guilty party here, I certainly played a role in that, whether actively or by omission.

It's very common for people on the lecture circuit to get an exaggerated—and false—impression of their message. This is because the only people who come to your talks are the true believers. When dissenters do show up it's often hard for them to debate the speaker just by posing questions from the audience.

I'm not surprised that the Nisbet/Mooney road show fooled you into thinking that your ideas were widely accepted in the scientific community. The other way of fooling yourself is to organize a conference where the only people invited are those who agree with you. This is what Nisbet did at AAAS.

Allow me to re-iterate the point I made earlier. It's not just on ScienceBlogs^TM that the concept of framing has been blackened. I've met many scientists who think that your views on framing¹ are an unacceptable way to teach science. A good many of those scientists have never read a single posting on any ScienceBlogs^TM blog and, furthermore, they have never even heard of Seed and the group it supports.

I admire the fact that you confess to poor framing of your ideas. Now. how about discussing whether they are even correct? Up to now all you've done is reject any criticism on the ground that we don't really understand framing. Maybe we do, but we're still opposed. Have you ever thought of that?

Your message still seems to be that you just made the mistake of not presenting your ideas correctly. In other words, you didn't frame properly. I hope that subsequent postings won't continue in that vein. It's time to realize that it was not only the medium that was flawed but also the message.

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1. Framing is deliberately altering what you want to say in order to make it more acceptable to your audience.

Is Faith Inevitable?

 
Last Thursday evening I watched a panel discuss the question "Is Faith Inevitable?" Unlike previous shows on TV Ontario, this one had a balance of believers and non-believers.

Two of the non-believers, Robert Buckman and Ronald de Sousa, are well-known in Canada (see below). You can watch the entire show at The Agenda.

I agree with the comments made by an undergraduate here at the University of Toronto when he says that the discussion got sidetracked [The Unexamined Life ...]. The real question is not whether faith is valuable, it's whether there is a God that you should have faith in.

Furthermore, I was very disappointed in Buckman and de Sousa because both of them bought into the line that we have evolved a need for religion. This is ridiculous. There is no gene for believing in supernatural beings and there's no reason to think that atheists need to overcome their genetic makeup in order to reject the notion of God. I wish we could put an end to this silly meme before it spreads any further.

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Gene Genie #28

 
The 28th edition of Gene Genie has been posted at Greg Laden's Blog [Gene Genie #24]. (It really is number 28, in spite of what Greg says. See Gene Genie.)

Welcome to Gene Genie #24: with a heavy emphasis on Personal Genetics.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

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Canada Wins World Championship!

 
I'm sure you've already heard the news. The Canadian women's team of Dawn Askin (lead), Jill Officer (second), Cathy Overton-Clapham (third) and Jennifer Jones (skip) beat China yesterday to win the World¹ Women's Curling Championship.

Most of you were probably watching the game so I don't need to remind you how exciting it was.

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1. Just to clarify for my American friends ... this was not a tournament where only teenagers in colleges like UNC could play and it was not a tournament confined to a single country. This is a world title. The USA didn't even make the playoffs.

[Photo Credit: Ford World Women's Curling Championship]

Stuff White People Like

 
Check out the blog Stuff White People Like, especially, Paris, San Francisco, and Having Gay Friends.

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[Hat Tip: Jane at Beer with Chocolate.]

Monday's Molecule #66

 
This is a very important enzyme. Most living organisms on this planet could not survive if this enzyme didn't do its job. Very few species have this enzyme but we depend on those few species for our very existence.

Your task for today is to identify the enzyme (1) and the species from which this particular enzyme was isolated (2). You also have to write out the complete reaction that is catalyzed by this enzyme (3).

In addition you have to identify the Nobel Laureate who is associated with the reaction that is catalyzed by the enzyme. (Hint: the Nobel Laureate studied the chemical reaction, not the biological one.)

The first person to correctly identify the enzyme and species, write the chemical equation, and name the Nobel Laureate. wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There is only one ineligible candidate for this week's reward.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly answers the questions and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner! The enzyme is nitrogenase from Azotobacter vinelandii. It fixes atmospheric nitrogen into ammonia by catalyzing the following reaction ...

The Nobel Laureate is Fritz Haber (1918) who worked out a chemical method of synthesizing ammonia from nitrogen.

Bryant Ing of the University of Toronto was the first person to get it right.

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[Image Credit: Dixon and Kahn (2004) based on the structure PDB 1n2c by Schindelin et al. (1997)]

Dixon, R. and Kahn, D. (2004) Genetic regulation of biological nitrogen fixation. Nature Reviews Microbiology 2, 621-631. doi:10.1038/nrmicro954

Schindelin, H., Kisker, C., Schlessman, J.L., Howard, J.B. and Rees, D.C. (1997) Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Nature 387: 370-376 [PubMed]

Make Your Own Phylogenetic Tree

 
Sandra Porter at Discovering Biology in a Digital World has prepared a short video presentation on how to make your very own phylogenetic tree from DNA sequences [A beginner's guide to making a phylogenetic tree].

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Nisbet Reveals His True Colors

 
Framing is about spin, censorship, and, above all, it's about agreeing with Matt Nisbet and Chris Mooney. If you don't agree with them then it's because you just don't understand framing.

It's about time we started to ignore Nisbet and Mooney. Fortunately, they are making it easy by posting drivel like Why the PZ Myers Affair is Really, Really Bad for Science and PZ Myers, Mind Your Manners (see comments).

I'm opposed to censorship of any kind but I really wish Matt Nisbet and Chris Mooney would voluntarily decide to keep their stupid mouths shut for a few years. I'm with PZ Myers on this one [I'm supposed to sit down and shut up?].

If anyone is really interested in seeing exactly what the blogosphere thinks of Matt Nisbet and Chris Mooney you need only check the links that Greg Laden has posted at The Framing Critique (Dawkins-Myers-Expelled! -Gate). I really hope this spells the beginning of the end for the Nisbet/Mooney tag team.

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Wells Takes a Rain Check on Apology

 
The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Evolution News & ViewsI challenged Jonathan Wells to agree to a simple statement that, I believe, might reflect his true beliefs about evolution [A Challenge to Jonathan Wells].

In one of the biggest surprises of the 21st century (not!) Wells has backed off [What’s in a Word?].

Darn. I guess I’ll have to take a rain check on that apology – because I don’t agree with this – and not just because Maurice et al. (2008) are cited incorrectly. Here’s why.

"Evolution" has many meanings. It can mean simply "change over time." The present is different from the past. The cosmos evolves. Technology evolves. No sane person denies evolution in this sense.

Biological evolution never means just change over time, but that's not the real problem with Wells' post. You're going to have to scoot on over to Evolution News & Views and read the whole thing.

I can't make head nor tail of it. I wonder if Wells actually thinks it makes sense?

John Pieret takes on the task of dissecting the Wells definition of evolution on Thoughts in a Haystack [Falling in the Wells]. He's a braver man that I.

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Watch and Weep

 
ABC News follows a group of home-schooled Christian children on a museum tour. The tour leaders are interviewed. They attempt to defend the lies they are telling the children.

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[HatTip: Friendly Atheist: How to Ruin a Trip to the Museuam.]

Evil and Sin

 
Yesterday's issue of the Toronto Star had an article on The fundamentalist atheists.

I'm getting real tired of hearing this phrase but I haven't completely given up trying to understand what people mean when they use it. In this case, the article is by Stuart Laidlaw, who is billed as the "faith and ethics" reporter. Laidlaw is commenting on a recent talk by Chris Hedges. Hedges seems to be one of those "sophisticated" Christians who have all the answers.¹ Naturally, he denigrates the "new atheists" like Richard Dawkins because they just don't understand serious Christianity.

Serious Christians seem to be very concerned about evil and sin.

Hedges, in Toronto recently to promote his book, attacks both fundamentalists and the new breed of atheists as not only intolerant, but wrong about both the Jesus story and the nature of sin.

Sin, he says, is a personal thing that will always be with us. Humans will never outgrow it through evolution, as the atheist authors contend, nor can anyone (Jesus included) relieve us of it, as fundamentalist Christians believe, Hedges says.

The best we can do, he says, is try to mitigate evil by living a good life, and having democratic institutions in place to ensure that we can get rid of bad leaders from time to time.

Sin, as I understand it, is when you violate a moral rule of some kind. It usually means you are disobeying the wishes of supernatural beings. It's not a word used by atheists.

Evil is something I can understand. People do bad things. Religious people do bad things and atheists do bad things. No atheist that I know would ever claim that humans will evolve to the point where they don't do bad things. What a ridiculous idea. What in the world is Hedges thinking?

For fundamentalists, evil and sin are an external force – often represented by Satan – to be vanquished by giving yourself over to Jesus. For the new atheists, evil and sin are the fault of religion, and can be defeated by getting rid of all religion and giving yourself over to scientific, reasoned thought.

For Hedges, it's the same argument: People are basically good, but external forces make us do bad things. Get rid of those forces, and people will be good.

No more effort is needed to achieve utopia, he says.

Just because religions can be evil does not mean that all evil is due to religion. No atheist believes this, as far as I know.

I believe that people are basically good but they still do bad things and they don't need external forces to do them. People are quite capable of being evil all by themselves. What in the world motivates people like Hedges to make up false stories about athiests? It makes him look very silly.

The question of evil and sin seems to be so intertwined with the existence of God that religious people (Christians?) seem to have difficulty untangling them. They seem to think that atheists are as obsessed about evil and sin as they are when, in fact, most of us don't give it much thought. Perhaps that's because we don't have to deal with the paradox of a good God who allows evil and sin?

Hedges draws a distinction between the new breed of atheists and such past non-believers as Albert Camus or scientists of the Enlightenment, whose skepticism he says helped drive human knowledge and understanding.

But Hedges has few such hopes for the new atheists. Where atheists of the past used their disbelief as a stepping off point to find something else to believe in, the new atheists claim to have already found it in what he calls a "cult of science."

Anything that can't be proved scientifically is simply discounted, Hedges says, warning that such a narrow approach to study thwarts the pursuit of knowledge by denying a voice to those who disagree.

The "new atheists" claim there are no supernatural beings because there's no evidence of such beings. This has nothing to do with evil and sin. When are these sophisticated Christians going to address the real question instead of going off on weird tangents? If they have a good argument for the existence of god then let's hear it. Otherwise, their "sophistication" looks more like "obfuscation" to me. (Or like The Emperor's New Clothes and the Courtier's Reply.)

It's time to stop whining and face up to the real question. Is there a god? Questions about evil and sin are irrelevant until that question is settled.

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1. In spite of his confusion about religion, he seems to be a pretty good guy. He was right about Iraq, for example.