Buy This Book!!!

 
Carl Zimmer is among the very best—possibly the best—of the modern science writers. His new book Microcosm: E. coli and the New Science of Life is going to be on sale May 6, 2008. Buy it, now. I just did.

Here's a synopsis from Publishers Weekly.

When most readers hear the words E. coli, they think tainted hamburger or toxic spinach. Noted science writer Zimmer says there are in fact many different strains of E. coli, some coexisting quite happily with us in our digestive tracts. These rod-shaped bacteria were among the first organisms to have their genome mapped, and today they are the toolbox of the genetic engineering industry and even of high school scientists. Zimmer (Evolution: The Triumph of an Idea) explains that by scrutinizing the bacteria's genome, scientists have discovered that genes can jump from one species to another and how virus DNA has become tightly intertwined with the genes of living creatures all the way up the tree of life to humans. Studying starving E. coli has taught us about how our own cells age. Advocates of intelligent design often produce the E. coli flagellum as Exhibit A, but the author shows how new research has shed light on the possible evolutionary arc of the flagellum. Zimmer devotes a chapter to the ethical debates surrounding genetic engineering. Written in elegant, even poetic prose, Zimmer's well-crafted exploration should be required reading for all well-educated readers. (May 6)

Copyright © Reed Business Information, a division of Reed Elsevier Inc. All rights reserved.

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Having a Wife Creates More Housework for Men

 
A newly released study looks at the amount of house work done by men and women in different living situations. Like most of these surveys, the data is based on interviews and on diaries kept by men and women. The most remarkable results are reported in a press release from the University of Michigan [Exactly how much housework does a husband create?].

Here's how they describe the data collection process.

For the study, researchers analyzed data from time diaries, considered the most accurate way to assess how people spend their time. They supplemented the analysis with data from questionnaires asking both men and women to recall how much time they spent on basic housework in an average week, including time spent cooking, cleaning and doing other basic work around the house. Excluded from these "core" housework hours were tasks like gardening, home repairs, or washing the car.

Assuming that this is a reliable way of accessing workload, the study published a chart showing the amount of housework done by maried and single men and women.


The 2005 results show that when women get married they end up doing 7 hours more housework per week but when men get married they end up doing 8 hours more housework per week. The take-home message is clear. Women are a lot more costly than men. Women do more to mess up a house than men do.

Pay attention, men. It may not be worth the effort to get married.

The title of the press release is interesting: Exactly how much housework does a husband create?. Here are the opening paragraphs.

ANN ARBOR, Mich.---Having a husband creates an extra seven hours a week of housework for women, according to a University of Michigan study of a nationally representative sample of U.S. families.

For men, the picture is very different: A wife saves men from about an hour of housework a week.

The findings are part of a detailed study of housework trends, based on 2005 time-diary data from the federally-funded Panel Study of Income Dynamics, conducted since 1968 at the U-M Institute for Social Research (ISR).

Is it just me or does there seem to be a disconnect between the statements in the press release and the chart that's published on the same page?

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Toronto Diversity

 
According to the latest census results, visible minorities make up 46.9% of the population of Toronto and 42.9% of the greater Toronto area. Check out the story in The Toronto Star and watch a video showing the change in precentage of visible minorities fro 1951 to 2006 [Visible minorities gaining].

How does this compare with other cities around the world? My impression is that Toronto is one of the more diverse cities in the world.

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Ramachandran Plots

THEME:

More posts on
Protein Structure
The peptide bond has considerable double-bond character and this prevents rotation around that bond in the polypeptide chain. Adjacent amino acids can adopt different configurations by rotation around the two other bonds in the backbone. The angle of the bond between the nitrogen atom (blue) and the α-carbon atom (black) is &Phi (phi) and the angle of the bond between the α-carbon atom and the carbonyl carbon atom (grey) is Ψ (psi) [The Peptide Bond]. These angles are measured in degrees where 180° is the angle of the bonds when all of the atoms of both residues lie in the most extended conformation. Rotation in one direction is positive so the values go from 0° to 180° and in the other direction they go from 0° to -180°. (180° = -180° in this notation.)

Most of the amino acid residues in a given protein are found in some form of secondary structure such as α helix, β strands, or turns.

The Φ and Ψ bond angles for each residue in the α-helical structure are very similar as shown on the left. This is why the structure is so regular. Similarly, the Φ and Ψ bond angles for every residue in a β strand are similar. Since the residues in a β stand are in an extended form, the Φ and Ψ angles in this conformation are close to 180°.

For any given protein, you can plot all of the bond angles for every pair of residues. These can be plotted on a diagram called a Ramachandran plot, named after the biophysicist G.N. Ramachandran (1922 - 2001). Such a plot shows that most of the residues in β strands have similar bond angles that cluster in a region near the top left-hand corner of the diagram. Similarly, residues in a right-handed α helix have very similar bond angles around Ψ=-45°, Φ=+45°.

The residues in Type II turns also have very characteristic bond angles. Some regions of the Ramachandran plot will be empty because of steric clashes between the oxygen atoms [see The Peptide Bond]. These regions are mostly located in the lower right-hand corner of the plot.


Let's look at some specific examples. One of the proteins we saw in the slideshow was an all-α protein called human serum albumin [PDB 1BJ5]. Another was an all-β protein called Jack bean conconavalin A [PDB 1CON].


If you click on the PDB numbers of these proteins you will be directed to the Protein DataBase (PDB) entry for these proteins. Click on "Structural Analysis" then "Geometry" in the left-hand sidebar of these PDB entries to see the link to "Ramachandran plot." This will take you to the two diagrams shown below for Human serum albumin (left) and Jack bean conconavalin A (right).

The Ψ and Φ angles of every residue in the protein are plotted. Note that for the all-α protein (left) almost all the angles cluster around the region identified as α helix. Similarly, for the all-β proteins (right) the angles cluster in the upper left-hand corner of the plot where you expect to find residues in β strands.

Large regions of the plot are empty indicating that many conformations are disallowed for steric or thermodynamic reasons. The point is that the number of conformations of polypeptides in solution is not infinitely large. Most residues cluster in regions of secondary structure (α helix, β strands, turns). These are thermodynamically stable structures and polypeptides will spontaneously adopt these secondary structures very rapidly.

The overall conformation of a polypeptide then depends on the arrangement of secondary structure motifs relative to each other. Even at this level, there are preferred motifs such as β barrels and α helix bundles.

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Come to Our Birthday Party!!

 
Click on Birthday Party for sharper images.

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Get a Job!!

Position	Assistant Professor (2)
Location	Department of Biochemistry, University of Toronto
Position Description	The Department of Biochemistry, University of Toronto invites applications for two tenure-track positions at the rank of Assistant Professor commencing on July 1, 2008. The Department is interested in individuals who employ modern molecular approaches in studies of macromolecular complexes, membrane protein structure, lipid-protein interactions and dynamics, single molecule visualization and dynamics in living cells, non-coding RNA, or chromatin. Successful applicants will be expected to establish an independent research program, compete effectively for external funding, and contribute actively to the undergraduate and graduate teaching programs in the Department. Salary will be commensurate with qualifications and experience. Applicants should arrange to have three letters of reference sent directly to the mailing address below. In addition, applicants should send their curriculum vitae, copies of significant publications, and a 2-3 page description of their research plans either by e.mail to: chair.biochemistry@utoronto.ca or by mail to the address below. Closing date for applications is April 30, 2008, or until the positions are filled. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.
Eligibility	We seek candidates with a Ph.D. in biochemistry, biophysics, cell biology or a related discipline. Candidates must also have at least two years post-doctoral training and have an excellent publication record.
Contact	Interested candidates are encouraged to apply to: Chair, Department of Biochemistry Room 5205, Medical Sciences Building University of Toronto Toronto, Ontario, M5S 1A8, Canada.
Posted	March 13, 2008

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The Peptide Bond

THEME:

More posts on
Protein Structure
Proteins consist of one or more strings of amino acids joined end-to-end to produce a polypeptide. The characteristics of each protein are due to the different amino acids that are combined to make the polpeptide(s). Each of the 20 or so common amino acids has a different side chain but the basic structure is common to all amino acids.

Amino acids have a central α-carbon atom, a carboxylate group (—COO^⊖), and an amino group (—NH₃^⊕). The fourth group attached to the α-carbon is the side chain (The third group is —H). Side chains can be as simple as —H (= glycine), or —CH3 (= alanine). In the example shown on the right, the side chain is —CH₂OH (= serine).

Proteins are synthesized by the translation machinery consisting of ribosomes , aminoacyl-tRNAs, and various translation factors. The template for synthesis is messenger RNA (mRNA) copied from the gene. Amino acids are strung together in a particular order specified by the mRNA codons.

The biosynthesis reaction is complex. It is coupled to hydrolysis of at least three ATP equivalents because the joining of two amino acids is thermodynamically unfavorable. The actual chain elongation reaction is catalyzed by the peptidyl transferase activity of the ribosome. The new bond that is created is called a peptide bond.


In the reaction shown above, the carboxylate group of the amino acid alanine is joined to the amino group of the amino acid serine to create a dipeptide with a peptide bond. Water is eliminated in this reaction. During protein synthesis the reaction continues as the mRNA is translated and long strings of several hundred amino acid residues are made.

The peptide bond has some interesting properties that play an important role in determining the three-dimensional structure of proteins. Look at the traditional depiction of the peptide bond in part (a) (top) of the figure on the left. It shows the actual peptide bond as a single bond and the bond between the carbon atom and the oxygen atom as a double bond. Note that the nitrogen atom has a pair of unshared electrons represented by the two red dots.

The middle structure shows that one electron from the nitrogen and carbon atoms can redistribute to form a double bond between C and N. This leaves an unshared pair of electrons on the oxygen atom. The actual bonding pattern is a mixture of these two resonance forms as shown in the bottom structure.

The partial double bond nature of the peptide bond has important consequences since it inhibits rotation around this bond. With a single bond there is free rotation so the groups on either side can adopt many different conformations. With a double bond there is very little rotation and the groups on either side are locked into the conformation that was formed when the bond is created.

The peptide bond has enough of a double bond characteristic to prevent rotation of the two newly joined amino acid residues. Thus, the O—C—N—H atoms around the peptide bond lie in a single plane shown in blue in the figure on the right.

What this means is the polypeptide chain is somewhat stiff and rigid. It can only adopt conformations that result from rotation around the other bonds in the chain. There are only two of these other bonds that can rotate. Looking at the central α₂ carbon atom above, you can see that there can be rotation around the N—C_α bond and around the C_α—C bond.

The angle of rotation around the N—C_α bond is called Φ (phi) and the angle around the C_α—C bond is called Ψ (psi). For each pair of amino acid residues, these two angles are all that's needed to specify the three-dimensional shape of the polypeptide backbone of the protein.

Not all angles are possible as shown on the left. If the two negatively charged oxygen atoms are too close together they will repel one another. This clash is called steric hindrance and it further limits the number of possible conformations of the polypeptide chain.

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Spring Is in the Air

 
The days are getting warmer and the snow is melting away. Spring is the time when a young person's fancy turns to .... poster presentations.

Every year at this time the lobby of my building fills up with poster presentations from undergraduate courses. Today it's the turn of a course called HMB322H "Human Diseases in our Society." This course is part of our "Human Biology" program. One of the assignments in the course is to shadow a health care professional (usually a researcher) and report on the kinds of things he/she does in a typical week.

The posters are supposed to explain the research/professional activity. Grades for the assignment are based on the quality of the poster as well as the explanation given by the student as the judges question them about their project.

The idea behind this assignment is to make 3rd year students familiar with the activities of a health care worker and provide them with an opportunity to practice their skills at presenting their findings to fellow students.

The Human Biology program¹ is run by a colleague of mine, Valerie Watt, and I'm a big fan of the innovative ideas she's trying out in the courses. Not all of them are going to work but at least she's trying to find new ways of teaching. The students I talked to seemed pretty excited about their shadowing experiences.

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1. I'm not a fan of the program, especially the sub-specialty called "Health & Disease" that these students are taking. I don't think that's an appropriate area of concentration for an Honors B.Sc. degree from the University of Toronto. I'd prefer to have them concentrate on basic fundamental science.

Tangled Bank #102

 
The latest issue of Tangled Bank is #102. It's hosted at Further Thoughts [Tangled Bank #102].

Welcome to the latest issue of The Tangled Bank, the blog carnival dedicated to the world of biology, medicine, natural history…and Sarah Silverman.

We’re all getting older. And as we get older, we lose the ability to hear some frequencies. Diane Kelly of Science Made Cool offers Is That…A Dog Whistle? – a tale of a test that lets you know just how much damage you did to your hearing back in your clubbing days…or will do when you finally finish grad school and are able to emerge onto the social scene ....

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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.

Botany Photo of the Day and the Nitrogen Cycle

 
Check out the Botany Photo of the Day and learn what this plant has to do with Australia, Argentina, Uruguay and The Nitrogen Cycle.

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The Guelph Creationists

 
The University of Guelph is located in southern Ontario (Canada) about 2 hours west of Toronto. It has recently gotten a lot of attention because of the presence of several Intelligent Design Creationists among its staff and students.

Here are the main players.

David K.Y. Chiu is Professor of Computing and Information Science and Professor of Biophysics Interdepartmental Group. He has a Ph.D. in Systems Design Engineering from the University of Waterloo (Canada).

Professor Chiu is head of the Pattern Learning Research Group. Most of his recent papers have to do with recognizing patterns in bioinformatics data.

Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins", Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]

Chiu, D.K.Y. and K. Zhang (2007) Biomolecular data analysis: a post-genomic reflection. Biomolecular Engineering, 24:319-320.

Chiu, D.K.Y. and Y. Wang (2006) Multipattern consensus regions in multiple aligned protein sequences and their segmentation. EURASIP Journal on Bioinformatics and Systems Biology, Vol.2006:1-8.

Ma, P.C.H., K.C.C. Chan, X. Yao and Chiu, D.K.Y. (2006) An evolutionary clustering algorithm for gene expression microarray data analysis. IEEE Trans. on Evolutionary Computation 10:296-314.

Hwang, C., Chiu, D.K.Y. and Sohn, I. (2005) Analysis of exon structure using PCA and ICA of short-time Fourier transform. L. Wang, K. Chen, and Y.S. Ong (Eds.): ICNC LNCS 3611, pp.306-315, 2005, Springer-Verlag Berlin Heidelberg 2005.(also Second Intern. Conf. on Fuzzy Systems and Knowledge Discovery, joint ICNC'05-FSKD'05, 27-29 Aug. 2005, Changsha, China.)

Durston, K. and Chiu, D.K.Y. (2005) A functional entropy model for biological sequences. in supplementary volume of the journal, Dynamics of Continuous, Discrete and Impulsive Systems, Series B, 2005 (also Proc. 4th Intern. Conf. on Engineering Applications and Computational Algorithms), pp.722-725.

Professor Chiu is a Fellow of the International Society for Complexity, Information, and Design. Other fellows include Michael Behe, Paul Nelson, Guillermo Gonzalez, William Dembski, Jonathan Wells and Scott Minnich.

Kirk Durston is National Director of the New Scholars Society whose aim is to "be a resource to those faculty and scholars who have an interest in developing the spiritual area of their lives from a Christian perspective." Durston has a B.Sc. in Physics from the University of Manitoba (Canada), a B.Sc. in Mechanical Engineering from the University of Manitoba (Canada) and an M.A. in Philosophy from the University of Manitoba (Canada). He is currently a Ph.D. candidate in the Biophysics Interdepartmental Group at the University of Guelph [Kirk Durston].

Durston's supervisor is David Chiu (see above). This is not a simple case of a graduate student falling under the influence of his supervisor since Durston was a well-known creationist even before he joined Chiu's group. It's just a coincidence that student and supervisor share the same views on religion and evolution since to suggest otherwise would be like accusing Chiu of selecting a student based on his religious views and not on the normal criteria. Intelligent Design Creationists are vehemently opposed to that kind of discrimination.

I'm sure Durston's previous degrees in physics, mechanical engineering, and philosphy made him well qualified to do Ph.D. research on the evolution of proteins in a bioinformatics lab.

Jack Trevors is a Professor in the Dept. of Environmental Biology [Jack Trevors] and he's also a member of the Biophysics Interdepartmental Group [Jack Trevors].

Professor Trevors has a B.Sc. and an M.Sc. from Acadia University (Canada) and a Ph.D. from the University of Waterloo (Canada). Most of his many publications are on various aspects of microbiology diversity and industrial applications but he is also interested in "Bacterial evolution with an emphasis on the origin and of the first bacterial cells and functional genetic instructions."

Trevors is famous in creationist circles for two papers he has published with David Abel, Director of The Gene Emergence Project at The Origin-of-Life Foundation, Inc. in Greenbelt, MD (USA). These papers are widely quoted as evidence that the origin of life cannot be explained by natural processes.

Abel and Trevors have also just published a paper with creationists Durston and Chiu.

Abel, D.L. and J.T. Trevors. (2006) Self-organization vs. self-ordering events in life-origin models. Physics of Life Reviews 3:211-228. [doi:10.1186/1742-4682-2-29]

Trevors, J.T. and Abel, D.L. (2004) Chance and necessity do not explain the origin of life. Cell Biology International 28:729-739. [doi:10.1016/j.cellbi.2004.06.006]

Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins. Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]

Jack Trevors is not a creationist according to this profile at the University of Guelph. He's a "self-proclaimed atheist."

Take that question about the origins of life. It's hardly a new line of inquiry for Trevors, who was about 10 when he began wondering about the existence of God. He's still wondering. Indeed, it's a question that has consumed a fair amount of his own life recently, albeit now voiced in the language of a professional scientist: Where and how did the genetic code and its instructions arise?

No small question. “The origin of genetic instructions in the DNA is the most pressing question in science,” he says. “Genetic instructions don't write themselves, any more than a software program writes itself.”

He adds that the issue goes far beyond deciphering the recipes for making proteins. Given that our genetic material constitutes the stuff of our own identity, “it's the search for ourselves, our origins,” he says.

Call it looking for God in our DNA — or at least that's how a person of faith might phrase it. Trevors, a self-proclaimed atheist, is more circumspect. “If you're a religious person, you say God. If you're an evolutionist, you say evolution.”

He notes, however, that not even evolution deigns to tell us where or how life itself first came about or how DNA's instructions came to be. Perhaps the birthplace of those instructions — like the very creation of the universe itself — is, in Trevors' words, both “unknowable and ‘undecidable' at this point in time.”

The same profile article describes his association with David Abel ...

It's a million-dollar question, literally. That's the size of the prize in a contest being run by the Origin-of-Life Foundation based near NASA's Goddard Space Flight Centre in Maryland. All the winner needs to do to claim the reward — actually annual instalments of $50,000 for 20 years — is to explain how the initial genetic code arose — or, in the words of the contest rules, provide "a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life."

The Gene Emergence Project is a program of the foundation, a scientific and educational body of about 200 scientists in 40 countries.

"We want the international scientific community to help us prove that genetic instructions don't write themselves," says Trevors, who got involved by contacting David Abel, the project's program director, two years ago.

"Jack relentlessly looks for evolutionary explanations for everything we observe in biology," says Abel, adding that his Guelph colleague helps ensure that "life-origin theory" remains empirically responsible, or answerable to the test of repeated observation. "He likes to include the full gamut of microbiological phenomena to make sure our models are explaining all aspects of genetic control."

Trevors has written on the topic, including a paper last year with Abel called: "Chance and Necessity Do Not Explain the Origin of Life." There and in a more recent piece, they frame the genesis-of-life discussion in terms that might resonate with a computer programmer, including referring to genes as linear strings of digital instructions and describing DNA's four nucleotide building blocks as four-way switches. If genes are merely algorithms, albeit highly sophisticated ones, another obvious question occurs, says Trevors. “Computer programs don't write themselves. Why would scientists or anyone else think genetic programs write themselves? The question has to be asked and examined from a scientific perspective.”

I don't know about the rest of you but I don't often hear atheists say things like that. Maybe he's thinking of aliens who write genetic programs? I also don't know too many atheists who would publish papers with known creationists who use the data to support their religious agenda.

The Origin-of-Life Prize has a complicated set of rules that must be followed in order to claim victory. The organization has posted a list of suggested texts that candidates should be familiar with (see sidebar on their website). That list is very revealing. There are books by well-known scientists like Michael Behe, Hubert P. Yockey, Walter James ReMine, William Dembski, and David Berlinski.

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First Sex?

 
Here's the opening paragraphs from a news item on the National Geographic website ["First Sex" Found in Australian Fossils?].

Sex is part of the "oldest profession" and often called the subject of the "world's oldest joke." Now scientists think they've found evidence of the oldest known creatures to engage in sexual reproduction.

A new study suggests that nature's first sexual encounter took place among tubular invertebrates called Funisia dorothea, which lived about 565 million years ago.

This is an example of bad science writing. Sexual reproduction is a phenomenon seen in many bacteria and in all eukaryotes (with minor exceptions). Animals are not the only eukaryotes that have sex. Plants, do it; fungi do it; and so do all single-cell eukaryotes.

The ancestors of these tube worms were having sex for at least a billion years before the Neoproterozoic. The idea that these organisms were "nature's first sexual encounter" is silly.

Who is responsible for this misrepresentation of the evolution of sex? The paper by Droser and Gehling (2008) was published in Science last week. The only reference to sex in the peer-reviewed paper is the following ....

The branching patterns and rarity of branching of Funisia is consistent with metazoan asexual budding. The consistency of tube widths on individual bedding surfaces (Fig. 1, A, I, and J), the densely packed nature of the attachment structures, and the clustering pattern of developmental stages of attachment structures on individual bedding planes suggests that the juveniles settled as aggregates in a series of limited cohorts.

These solitary organisms thus exhibit growth by addition of serial units to tubes and by the division of tubes, and dispersed propagation by the production of spats. Among living organisms, spat production is almost ubiquitously the result of sexual reproduction but is known to occur rarely in association with asexual reproduction (8). Hence, despite its morphological simplicity the Neoproterozoic F. dorothea provides evidence of a variety of growth modes and a complex arrangement for the propagation of new individuals. In living organisms, synchronous aggregate growth may result from a variety of factors—including response to competition, sediment disturbance, and heterogeneity of the substrate—and has the advantage of reducing competition for space between clones and can also decrease gamete wastage (9, 10).

There's nothing in the paper about these organisms being the first to reproduce sexually—that wouldn't have survived the reviews. The only remaining question is why did the author (Droser) allow herself to be quoted in a press release when she must have known that it was misrepresenting the paper?

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Droser, M.L. and Gehling, J.G. (2008) Synchronous Aggregate Growth in an Abundant New Ediacaran Tubular Organism. Science 319:1660-1662. DOI: 10.1126/science.1152595

Nobel Laureate: Fritz Haber

 

The Nobel Prize in Chemistry 1918.

"for the synthesis of ammonia from its elements"


Fritz Haber (1868 - 1934) was awarded the 1918 Nobel Prize in Chemistry for working out a method to synthesize ammonia (NH₃) from nitrogen (N₂) and hydrogen (H₂). This process, now known as the Haber-Bosch process, is an essential step in the production of artificial fertilizer. At the time, it was not known how long the natural sources of nitrogen such as Chile saltpetre (sodium nitrate) would last. Harber worked at the Kaiser-Wilhelm-Institut (now Fritz-Haber-Institut) für physikalische Chemie und Electrochemie in Berlin-Dahlem, Germany

Many species of bacteria can fix nitrogen into ammonia in a reaction catalyzed by the enzyme nitrogenase [The Nitrogen Cycle]. The Haber-Bosch process involves heating nitrogen and hydrogen to a temperature of 450°C under 200 atm of pressure in the presence of an iron catalyst. Bacteria do it at 20°C or less at atmospheric pressure.

The 1918 prize was announced in November 1919 and the prize wasn't awarded until June 1920. Part of the delay was due to the fact that Fritz Haber was head of the German Chemical Warfare Service during the war. He was responsible for initiating mustard gas attacks on the allied lines.

The presentation speech was delivered by Doctor Å.G. Ekstrand, President of the Royal Swedish Academy of Sciences. No member of the Swedish Royal family was present at the ceremony because of the death of crown-princess Margaret.THEME:

Nobel Laureates

The Royal Swedish Academy of Sciences has decided to confer the Nobel Prize in Chemistry for 1918 upon the Director of the Kaiser Wilhelm Institute at Dahlem near Berlin, Geheimrat Professor Dr. Fritz Haber, for his method of synthesizing ammonia from its elements, nitrogen and hydrogen.

In accordance with Nature's plan of economy, soil fertility under normal circumstances is maintained at an even level if the waste products from the crop are returned to the soil; if, however, substantially increased productivity is required from the soil, then additional fertilizer must be used. Since meanwhile a large proportion of the annual harvest is consumed by the yearly increasing population of towns, and since the towns' waste products are returned to land under cultivation only to a very incomplete extent, the inevitable consequence is that the soil becomes exhausted and the harvest yield diminishes. This has, in turn, led to the manufacture of artificial fertilizers which has also increased year by year in importance to such an extent that, at least in Europe, hardly a country exists which can do entirely without them.

Among these substances nitrogenous compounds occupy an important position, since usually the soil does not possess a large store of these to be released to suit the plants' needs by weathering as in the case of phosphoric acid and potash; added to which there is the fact that part of the effective nitrogen turns into inactive atmospheric nitrogen during the cyclic process. Admittedly a part of this loss is compensated by rainfall and through the activity of bacteria, but so far experience has shown that intensive cultivation cannot be maintained without artificial nitrogenous fertilizers. This applies, above all, to one of today's most important crops, sugar-beet.

For many years only two artificial nitrogenous compounds existed, namely potassium nitrate and ammonium chloride. The older methods by which these were made, however, ceased to play a part, at least in Europe and America, when Chile saltpetre (sodium nitrate) came into the picture and use was made of the by-products from dry distillation of mineral coal for this purpose.

The consumption of Chile saltpetre, calculated in terms of nitrogen, amounts to about 500,000 or more tons per annum. Under normal circumstances the vast majority of this saltpetre is used for fertilizer purposes. The burning question, therefore, has long been: how long will the saltpetre deposits in Chile last? The Chilean authorities give very widely varying estimates, and experts in Europe are of the opinion that at current production rates the deposits will be exhausted within the foreseeable future.

Be that as it may. The protracted World War has sufficiently demonstrated to every country the need of organizing, wherever possible, production of essential commodities within its own borders in sufficient quantities to meet its own needs.

Now, since saltpetre is among the most important of these substances, particularly in those countries which possess neither large mineral coal deposits nor cheap hydro-electric power, the artificial production of ammonia and nitric acid has reached an unprecedented degree of importance.

A substance on the borderline between natural and artificial products is the ammonia obtained by dry distillation of bituminous and brown coal. This ammonia comes from the nitrogen content of these minerals, amounting to approximately 1.3 % by weight, of which however the largest portion (around 85%) remains behind in the coke or is liberated as nitrogen during distillation.

During the first ten years of this century several methods were published, based on binding the nitrogen from the air, but few of these survived the trial stage. The first of these was Frank-Caro's cyanamide method. Indeed it appears that calcium cyanamide did not come fully up to expectations as a fertilizer, but since its nitrogen content can be converted to ammonia relatively easily, this has not so far proved to be an obstacle to the application of the method to an ever-increasing extent.

Using the main principles of thermodynamics every quantitative condition with regard to the combustion of atmospheric nitrogen to produce nitric oxide can be calculated. Birkeland and Eyde were, of course, the first to apply this technically with successful results.

Until 1904 nobody had been able to bring about a direct combination of nitrogen and hydrogen to form ammonia without the help of dark electrical discharge, although the experiments of Berthelot and Thomson proved that the combination occurred exothermically. With the experience we now have we can easily see that this negative result was due to the slowness of the reaction at low temperatures, and unfavourable equilibrium conditions at high temperatures. Admittedly, in 1884 Ramsay and Young had conducted some experiments on this, using iron fillings as a catalyst, but these yielded only uncertain results.

In 1904 Haber and van Oordt began a methodical study of this relevant field, based on modern physico-chemical methods, after a single previous experiment had given Haber a hope of finding a technical solution to the problem. They worked at a temperature of about 1,000° C and normal pressure, using iron as a catalyst. From these experiments it emerged that from red heat onwards, and also at higher pressures, only traces of ammonia could be formed.

During this work it was also shown experimentally for the first time that a real state of equilibrium existed in the system
N2+ 3H2 → NH3, which is in fact the real basis for the synthesis of ammonia.

In the "Zeitschrift für Elektrochemie" of 1913 can be found the treatment of this question, by Haber and Le Rossignol which has the most important practical meaning: "Über die technische Darstellung von Ammoniak aus Elementen" (On the technical production of ammonia from the elements). This treatise provided the groundwork for the development of the method on a factory scale at the "Badische Anilin- und Sodafabrik" in Ludwigshafen, the main development occurring under the guidance of Dr. C. Bosch.

Earlier experiments had shown the pointlessness of exceeding dark red heat, i.e. about 600° C. On the other hand, the reaction formula showed that combination occurs with a contraction of from 4 to 2 volumes.

From the law of equilibrium it follows that the higher the pressure is the more the equilibrium must shift to the ammonia side. This provided the basic principles. A temperature of about 500° C had to be used at the highest possible pressure, which in practice meant at about 150-200 atmospheres. It could also be assumed that this high pressure speeded up the reaction. But work with a flow of gas in a circulation system at such high pressure and at a temperature approaching red heat posed very severe difficulties and up to then had never been tried. It was, however, completely successful. The treatise in question contains detailed drawings of the equipment used with which, using iron as a catalyst, about 250 grams of ammonia were produced per hour and per litre of contact volume; with uranium or osmium as a catalyst considerably more was produced.

The heating is done electrically. Since however the heat escaping from the equipment is largely regenerated in the entrant gases the required temperature can largely be maintained by the regenerated heat and by the heat liberated during the formation of ammonia. A very important point in Haber's observations is that the gases can be given a greater flow rate during the reaction which of course substantially increases the amount of ammonia produced per unit of time.

Haber found the best catalyst to be osmium, followed by uranium or uranium carbide. According to tests conducted mostly at the factories of the "Badische", the activity of the catalyst may be increased by oxides or certain salts of alkalis and alkaline earth metals, just as it may be decreased by catalytic poisons. Gradually more active catalysts have been discovered, and by this means it has been found possible to reduce substantially the pressure in the chamber.

In 1910 construction work was begun on the first large factory near Oppau in the neighbourhood of Frankfurt am Main, with an estimated annual output of 30,000 tons of ammonia.

The basic materials, nitrogen and hydrogen, are produced by standard methods.

Power consumption in the ammonia process is very low, amounting to no more than 0.5 kilowatt-hours per kilogram of ammonia. Per kilowattyear, therefore, no less than 10,000 kilograms of nitrogen are bound.

Since the position of the equilibrium of the reaction depends, among other things, upon the heat of formation of ammonia and its specific heat, Haber in a series of seven articles in the "Zeitschrift für Elektrochemie" of 1914-1915, has extensively described experiments carried out to confirm these figures with the greatest possible accuracy.

As, according to Ostwald's modified method, ammonia can be converted into nitric acid and the latter into calcium nitrate, the ratio between the overall costs of producing calcium nitrate is, according to the available calculations, approximately as follows:

Norwegian Hydro: 100
Haber: 103
Frank-Caro: 117

in other words, they are the same for the first two methods but approximately 15% higher for the last.

Since, however, of the three existing nitrogen methods, Haber's is the only one capable of operating independently of any available source of cheap hydroelectric power it can in future be applied in all countries; since furthermore it can be utilized on any convenient scale and because it can produce ammonia very much more cheaply and nitrate equally as cheaply as any other method, as explained above, it is of universal significance for the improvement of human nutrition and so of the greatest benefit to mankind.

German Haber factories, especially the recently built Leuna Works near Merseburg, are also in full production, providing the vast majority of all nitrogenous fertilizers obtainable in Germany. Moreover, the method has already been extensively applied in the United States of America.

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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]