Good Science Writers: Albert Lehninger

 
Albert Lehninger (1917 - 1986) was a biochemist whose main research interest was the production of energy by mitochondria. His second book, Bioenergetics was published by W.A. Benjamin Inc. in 1965 as part of a series of biochemistry books by well-known scientists. One of the other books in the series was Molecular Biology of the Gene by James D. Watson. Neil Paterson of W.A. Benjamin was the man behind getting these scientists to write books for the general public and students.

Later, when Neil Patterson had moved to Worth Publishers, he persuaded Lehninger to write a textbook and the first edition of Biochemistry was published by Worth in 1970. Following Lehninger's death in 1986, the book, now called Lehninger Principles of Biochemistry was taken over by David Nelson and Michael Cox and the current publisher is W.H. Freeman and Company.

Lehninger's writing was characterized by an emphasis on basic chemical principles and his style was crisp and unapologetic. He is not mentioned by Richard Dawkins in his book: The Oxford Book of Modern Science Writing but that's no surprise because many well-known textbook authors are not recognized as good science writers.

The first excerpt comes from Bioenergetics )pp. 18-20).

The First Law [of thermodynamics] tells us that energy is conserved; every physical or chemical change must satisfy this principle. However, there is another fundamental aspect of energy exchange which is not explained by the First Law. A simple example will serve to illustrate the problem.

Suppose we place two blocks of copper together, one hot and one cold, and seal them in an insulated container. The temperature of the hot block will fall and that of the cold block will rise until they both reach some intermediate temperature, which at equilibrium will be uniform throughout both blocks. The flow of heat and thus of energy from the hot block to the cold is spontaneous. However, if we put two identical blocks of copper, both at the same temperature, into such a container, we know that they will remain at the same temperature; we would never expect the temperature of one block to rise spontaneously and that of the other to fall. However, if this should happen, it would not violate the First Law because the energy lost by one block would be gained by the other; the total energy of the two blocks would remain the same.

It is quite clear from considering this example ... that spontaneous physical or chemical changes have a direction which cannot be explained by the First Law. In brief, all systems tend to approach equilibrium states in which temperature, pressure, and all other measurable parameters of state become uniform throughout. Once they reach such an equilibrium they no longer change back spontaneously to the nonuniform or nonrandom state. When the two blocks of copper in our model have reached exactly the same temperature, all the heat energy originally contained in the two blocks has been maximally randomized, and we know that it will never by itself "unrandomize." The Second Law of thermodynamics provides us with a new yardstick or criterion for predicting the tendency of a physical process to occur and the direction in which it will occur. First, it defines entropy as a randomized state of energy that is unavailable to do work. Second, it states that all physical and chemical processes proceed in such a way that the entropy of the system becomes the maximum possible. At this point there is equilibrium.

The second excerpt is from the first edition of Biochemistry (1970) pp. 276-278. (The second edition is shown in the figure.)

Complex organic molecules such as glucose, contain much potential energy because of their high degree of structural order; they have relatively little randomness, or entropy. When the glucose molecule is oxidized by molecular oxygen to form six molecules of CO₂ and six of water, its atoms undergo an increase in randomness; they become separated from each other and may assume different locations in relation to each other. As a result of this transformation, the glucose molecule undergoes a loss of free energy, which is useful energy capable of doing work at constant temperature and pressure.

The free energy of glucose so released is harnessed by the cell to do work. Biological oxidations are in essence flameless or low-temperature combustions. As we have seen, heat cannot be used as energy source by living organisms, which are essentially isothermal, since heat can do work at constant pressure only when it can flow from a warmer to a cooler body. Instead, the free energy of cellular fuels is conserved as chemical energy, specifically the phosphate-bond energy of adenosine triphosphate (ATP). ATP is enzymatically generated from adenosine diphosphate (ADP) and inorganic phosphate in enzymatic phosphate-group transfer reactions that are coupled to specific oxidation steps during catabolism. Since the ATP so formed can now diffuse to those sites in the cell where its energy is required, it is thus also a transport form of energy. The chemical energy of ATP is then released during transfer of its terminal phosphate group(s) to certain specific acceptor molecules, which become energized and can do work.

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[Photo Credit: Mitochondria and Neuroprotection—In Memory of Albert L. Lehninger]

ATP Is a Coenzyme

 
ATP (adenosine 5′-triphosphate) is the main energy currency in living cells. It undergoes a type of reaction called hydrolysis where one or two of the terminal phosphate groups are released.


These reactions are accompanied by a considerable release of energy and that's why ATP is such an important molecule. It is synthesized by a special reaction that is not the reverse of the hydrolysis reaction. Instead it utilizes the energy of a proton gradient across a membrane to make ATP [How Cells Make ATP: ATP Synthase]. Since ATP is very stable inside the cells it can serve as an energy storage molecule until it is ready to be used.

One of the important features of enzymes is their ability to couple reactions that would otherwise not occur. One of the ways that enzymes do this is by bringing together two different substrates to form a reactive intermediate. There are dozens of molecules that can be used in a wide variety of different reactions and these are referred to as coenzymes or cofactors. ATP is one of them.¹

Here's an example of how ATP can be used to make a reaction proceed when it would otherwise not take place because it requires too much energy. The formation of glutamine from glutamate requires the attachment of an ammonia group to glutamate. This reaction will not take place inside the cell because the direct energy requirement is too high.

Instead, the enzyme glutamine synthetase utilizes the energy of ATP to make the reaction go in two steps.


In the first step, ATP is hydrolyzed to ADP and the phosphate group is attached to glutamate to make a "high energy" intermediate called γ-glutamyl phosphate. The enzyme does not release this product; it holds on to it until a molecule of ammonia enters the active site to displace the phosphate group and create glutamine. In this way the overall reaction can proceed because each of the intermediate steps is favorable. (Hydrolysis of ATP in step one and hydrolysis of γ-glutamyl phosphate in step two.)

The enzyme has coupled the overall hydrolysis of ATP to ADP + P_i to the formation of glutamine from glutamate. ADP will be used to synthesize another molecule of ATP so that the store of energy currency remains constant inside the cell.

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1. ATP was first discovered as an essential factor in fermentation and muscle contraction. Hans von Euler-Chelpin received the Nobel Prize in 1929 for recognizing the importance of adenosine phosphate "cozymases."

Nobel Laureate: Hans von Euler-Chelpin

 

The Nobel Prize in Chemistry 1929.

"for their investigations on the fermentation of sugar and fermentative enzymes"



Hans Karl August Simon von Euler-Chelpin (1873 - 1964) received the 1929 Nobel Prize in Chemistry for his work on fermentation, especially the recognition of a phosphorylated nucleoside as an important cofactor (cozymase). We now know that the most important cofactor is ATP.

Here's how von Eular-Chelpin describes the work in his Nobel Lecture.

By a long series of purification processes a preparation was obtained with a maximum activity - expressed in rational units - of ACo = 85,000, the starting material being characterized by ACo = 200. It was possible to convert this preparation into salts - salts of the alkaloids and of the alkaline-earth metals were used for the isolation - and cozymase can be recovered therefrom with practically unchanged activity4. The composition of the most highly purified product corresponds approximately to a so-called nucleotide, for it contains a sugar residue, a purine residue and phosphoric acid, and everything points to a close relationship with a substance occurring in muscle in small quantities, adenylic acid.

Hans von Euler-Chelpin was recognized by the Nobel Committee but he rarely gets credit in the textbooks for discovering ATP.

von Euler-Chelpin shared the 1929 Nobel Prize with last week's Nobel Laureate, Arthur Harden.

THEME:
Nobel LaureatesThe presentation speech was delivered on December 10, 1929 by Professor H.G. Söderbaum, Chairman of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences. (All award ceremonies are held on Dec. 10th because Dec. 10, 1896 was the day Alfred Nobel died.)

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The fermentation of liquids containing sugar - there we have a chemical reaction older than all chemical science. The point of time when men first began to take this reaction into their service is really lost in the mists of antiquity, before the beginning of history. The peculiar and apparently self-caused process by which an innocent fruit juice is transformed with the active formation of scum, into a drink which is either stimulating or intoxicating according to the quantity partaken, attracted attention in the very earliest times; and to many peoples it appeared so wonderful that nothing less than the cooperation of a divinity seemed to them possible as an explanation.

Our enlightened time has scarcely the right to marvel at this, when we take into consideration how long a time science has since required to obtain an acceptable conception of the nature of fermentation. Here we stand face to face with one of the most complicated and difficult problems of chemical research. Little more than a couple of centuries separate us from the time when men first began to perceive that the fermenting substance was sugar, which under the influence of a certain something was decomposed, with carbonic acid and ethyl alcohol as the final products of the decomposition.

But what this "something" was, and how it worked, still remained unsolved questions, long defying the most penetrating attempts at interpretation. It was not until our own days that it has been vouchsafed to us to have a fairly satisfactory answer to these questions, but even here the process of development has been slow, toilsome, and it took place, so to speak, in several instalments.

In carrying out the provisions of Alfred Nobel's Will, the Swedish Academy of Sciences has already once before had its attention directed to this sphere of research. That was in 1907, when Eduard Buchner was awarded the Nobel Prize in Chemistry for his discovery of non-cellular fermentation. At the time complaints were raised in certain quarters against this award as being insufficiently justified. Seen in the perspective of distance in time, however, Buchner's discovery has more and more stood out as a line of demarcation between two different epochs, pointing the way to a new phase in the history of the chemistry of fermentation.

Buchner's discovery marked the final decision in a long struggle between two distinct schools - one, the older one, represented by Justus von Liebig the other, the younger one, represented by Louis Pasteur. According to the former school, fermentation was a purely chemical process, evoked by an unorganized ferment with unstable properties, which were imparted to the fermenting substance and thereby brought about its decomposition. According to the latter school, it was rather a physiological process, inseparably connected with the vital act of a microorganism known as the "fungus of fermentation". Buchner's discovery made it evident that to some extent both were right, but also to some extent both were wrong, and, consequently, that the truth lay between the two.

But the value of the discovery makes itself known in a still more definite way through the impulse it has given to later research. In fact, during the last three decades that research has made such great advances, has given such an enlarged insight into the mechanism of the process of fermentation, that the Academy of Sciences has found the time ripe once again to award a Nobel Prize in this department. In so doing the Academy has deemed it right to divide equally the Nobel Prize in Chemistry for the present year between Professor Arthur Harden and Professor Hans von Euler.

Buchner assumed in the yeast juice the presence of a uniform ferment or enzyme, known as "zymase".

When, however, Harden and his fellow-workers filtered a quantity of Buchner's yeast-juice through a gelatine filter, known as an "ultrafilter", and thereby split it up into two fractions (a filtrate and a sediment that did not pass through the filter), the curious state of things occurred that neither of these fractions was any longer able to bring about fermentation, but that after being mixed with one another they recovered that capacity.

Harden explained this by saying that a high-molecular enzyme, the zymase proper, was left on the filter, which let through a low-molecular complementary enzyme, which for the sake of brevity was called co-enzyme or co-zymase.

Another no less important advance is made in Harden's demonstration of the hitherto neglected part played by phosphoric acid in the process of fermentation. It has been found that a certain addition of phosphate gives rise to an equivalent amount of carbonic acid and ethyl alcohol. This effect is associated with the formation of one or more definite compounds between sugar and phosphoric acid - known as the "zymo-phosphates", amongst which a glucose monophosphate and a glucose diphosphate are to be regarded as the most important.

In the same measure as research in this department has made new conquests, a clearer and clearer insight has been gained into the importance of this discovery. In particular the work of von Euler and his pupils during the last few years greatly contributed to the unravelling of the mechanism of phosphorization.

The primary function of phosphoric acid in fermentation consists, according to von Euler, in the fact that in cooperation with an enzyme it gives rise to glucose monophosphate, identical with the monophosphate discovered by Harden and Robison. This phosphate afterwards undergoes a mutation in the presence of co-zymase, inasmuch as a glucose diphosphate and an active glucose are formed, after which the latter yields the necessary material for the subsequent stages of the fermentation.

This demonstration of the part of mutase played by the co-zymase, or in other words of the identity of co-zymase and co-mutase, is of fundamental importance, for it has fully revealed the central position in the process of fermentation of the complementary enzyme in question.

The researches of von Euler and his pupils have further led to the concentration of the co-zymase and to a far more exact study of its properties than had been previously possible. They have been able to determine approximately its molecular weight, which has been found to be about 490; and they have also been able to draw certain definite conclusions concerning its chemical nature, which make it highly probable that we have here what the chemists call a pentosenucleoside. The production of a co-zymase with a high activity has also shown in a brilliant manner the character of that enzyme as a specific activator.

Finally, what gives special interest to the study to the complicated reaction mechanism of the fermentation of sugar is that it has been possible to draw from it important conclusions concerning carbohydrate metabolism in general in both the vegetable and the animal organism.

The brief summary which has now been given, and which, in view of the scanty time allowed, has necessarily been extremely fragmentary, will in any case probably have shown that there is an extremely intimate connection between the researches of Harden and von Euler in this field. On the one hand, the fundamental discoveries of Harden have formed the precondition and point of departure for the various work of von Euler; and on the other hand, it is only the work of the latter that has made fully evident the importance of Harden's discovery.

Under such circumstances the Academy of Sciences has not hesitated this time to avail itself of the expedient that is offered by the Statutes of the Nobel Foundation of dividing the prize between two equally meritorious scientists.

Professor Harden. When the Royal Swedish Academy of Sciences resolved to adjudge to you, together with Professor von Euler, this year's Nobel Prize in Chemistry on account of your important contributions to our knowledge of alcoholic fermentation, the Academy had let herself guided by a firm conviction that these contributions had opened indeed a new chapter in the investigation of that very complicated matter.

It is with the most sincere gratification that I have the honour of conveying to you the congratulations of the Academy on this distinction, the outward signs of which you are now about to receive.

Professor von Euler. It is a great pleasure to the Swedish Academy of Sciences to be able to award this time the Alfred Nobel's Prize also to one of her members, and so much more since during a long series of years we have been in the position to follow from nearby your energetic, persevering, and systematic investigations. The Academy is also firmly convinced that the distinction which has fallen upon you today, will not contain for you the temptation to rest on laurels already obtained, but that on the contrary it will mean a stimulus to continued and, as we all hope, successful work in the service of biochemistry.

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Evolution in Ontario Schools

 
The United Church Observer comments on the deficiencies of Canada's education system when it comes to teaching evolution Where's Darwin?].

“Nothing in biology makes sense except in the light of evolution,” wrote the late Ukrainian geneticist Theodosius Dobzhansky, who found evidence for evolution by studying the genetic varietals of fruit flies. To most scientists, Darwinian evolution is the unifying principle of biology, as solid and significant as Newtonian gravity or Copernican heliocentrism. But you wouldn’t guess it from its place in Canada’s school system.

In all but one provincial science curriculum, evolution is relegated to a single unit in a Grade 11 or 12 elective course taken by a sliver of each graduating class. It would not be a stretch to say the majority of Canadian high school students graduate without ever encountering Darwin’s theory of natural selection.

The situation in Ontario is a little more complicated than this statement suggests. There's plenty of opportunities in Grades 1-8 to learn about diversity, change and adaptation but unfortunately it's true that the word "evolution" isn't mentioned [The Ontario Curriculum Grades 1-8: Science and Technology, 2007]. I'm told by several teachers that they frequently talk about evolution even though it's not specifically mentioned in the curriculum guidelines. It would be much better to put the fundamental concept of biology in the provincial curriculum.

Evolution is only covered specifically in Grade 12 Biology [The Ontario Curriculum Grades 11 and 12: Science]. As mentioned in the United Church of Canada article, this course is only taken by a small percentage of students in Ontario high schools.

The curriculum looks pretty good (see below). I wonder how it compares with the curricula in typical American high schools? Does anyone know?

The fact that this material is required in Grade 12 Biology suggests that high school science teachers will probably be familiar with the basic concepts of evolution and I'd be surprised if it doesn't get brought up in other courses. After all, the same teachers that teach Grade 12 Biology are often teaching other courses as well.

The fact that the Province of Ontario curriculum is so strongly supportive of evolution in the Grade 12 curriculum indicates that the government doesn't have any doubts about the validity of evolution even though they may be a bit wishy-washy about mentioning it in the primary grades.

Evolution
Overall Expectations
By the end of this course, students will:
• analyse evolutionary mechanisms, and the processes and products of evolution;
• evaluate the scientific evidence that supports the theory of evolution;
• analyse how the science of evolution can be related to current areas of biological study, and how technological development has extended or modified knowledge in the field of evolution.

Specific Expectations
Understanding Basic Concepts
By the end of this course, students will:
– define the concept of speciation and explain the mechanisms of speciation;
– describe, and put in historical and cultural context, some scientists’ contributions that have changed evolutionary concepts (e.g., describe the contributions – and the prevailing beliefs of their time – of Lyell, Malthus, Lamarck,Darwin, and Gould and Eldridge);
– analyse evolutionary mechanisms (e.g., natural selection, sexual selection, genetic variation, genetic drift, artificial selection, biotechnology) and their effects on biodiversity and extinction (e.g., describe examples that illustrate current theories of evolution, such as the darkening over time, in polluted areas, of the pigment of the peppered moth, an example of industrial melanism);
– explain, using examples, the process of adaptation of individual organisms to their environment (e.g., explain the significance of a short life cycle in the development of antibiotic-resistant bacteria populations).
– formulate and weigh hypotheses that reflect the various perspectives that have influenced the development of the theory of evolution (e.g., apply different theoretical models for interpreting evidence).

Developing Skills of Inquiry and Communication
By the end of this course, students will:
– outline evidence and arguments pertaining to the origin, development, and diversity of living organisms on Earth (e.g., evaluate current evidence that supports the theory of evolution and that feeds the debate on gradualism and punctuated equilibrium);
– identify questions to investigate that arise from concepts of evolution and diversity (e.g.,Why do micro-organisms evolve so quickly? What factors have contributed to the dilemma that pharmaceutical companies face in trying to develop new antibiotics because so many micro-organisms are resistant to existing antibiotics?);
– solve problems related to evolution using the Hardy-Weinberg equation;
– develop and use appropriate sampling procedures to conduct investigations into questions related to evolution (e.g., to determine the incidence of various hereditary characteristics in a given population), and record data and information;

Relating Science to Technology, Society, and the Environment
By the end of this course, students will:
– relate present-day research and theories on the mechanisms of evolution to current ideas in molecular genetics (e.g., relate current thinking about adaptations to ideas about genetic mutations);
– describe and analyse examples of technology that have extended or modified the scientific understanding of evolution (e.g., the contribution of radiometric dating to the palaeontological analysis of fossils).

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[Hat Tip: John Pieret "Refried Great Northern Beans" who loves finding examples where other countries are as bad as his. ]

University of Toronto Secular Alliance

 

Please consider joining the University of Toronto Secular Alliance. Visit the University of Toronto Secular Alliance (UTSA) website for more information.

Meetings will be held every second Wednesday beginning Wednesday, Sept. 10th. Meetings last from 7pm-10pm in the All-Purpose Room at the Multi-Faith Centre (2nd floor, 569 Spadina Ave. entrance from Bancroft Ave.)

All interested students are invited to a welcome party at CFI.

CFI STUDENT WELCOME PIZZA PARTY
Thursday, September 4th at 11:00 am - 3:00pm
Come to 216 Beverley st (just south of College at St. George) to meet other students interested in science, secularism and freethought. There will be information on the center's activities and student groups. Several universities will be represented including York University, The University of Toronto and Ryerson University.

There will be stimulating discussions and activities to introduce you to the centre's goals and mandate. We'll also have pizza, drinks and lots of fun games - including gaming consoles (with Guitar Hero! woo!) and board games (like Risk! awesome.) We are also inviting all CFI volunteers to join us for this event.

Drop in between 11 am - 3 pm.  $3 donation for BBQ - $1 for drinks; *FREE* to Friends of the Centre.

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Spore and Evolution

 
Spore is a computer game that let's you "evolve" organisms beginning with a simple cell and moving "upwards" to creatures that can build spaceships. The game is designed by Will Wright whose previous credits include SimCity and The Sims.

Wright and his company have been heavily promoting the game as a way of learning about evolution. As part of this promotion they have distributed free copies to many scientists in advance of the opening day of sales in retail stores. Here's how it's described on the Spore Website.

How will you create the universe?

With Spore you can nurture your creature through five stages of evolution: Cell, Creature, Tribe, Civilization, and Space. Or if you prefer, spend as much time as you like making creatures, vehicles, buildings and spaceships with Spore’s unique Creator tools.

CREATE Your Universe from Microscopic to Macrocosmic - From tide pool amoebas to thriving civilizations to intergalactic starships, everything is in your hands.

EVOLVE Your Creature through Five Stages - It’s survival of the funnest as your choices reverberate through generations and ultimately decide the fate of your civilization.

Time for a reality check. Spore is a computer game. It's purpose is to make bundles of money for Will Wright and his company. It may be an excellent game but it is NOT a way of learning about evolution. Evolution does not have a purpose or a direction.

Carl Zimmer has just published an article in The New York Times about Spore and computer simulations [Gaming Evolves]. Some scientists don't think the game reflects evolution.

Unlike the typical shoot-them-till-they’re-all-dead video game, Spore was strongly influenced by science, and in particular by evolutionary biology. Mr. Wright will appear in a documentary next Tuesday on the National Geographic Channel, sharing his new game with leading evolutionary biologists and talking with them about the evolution of complex life.

Evolutionary biologists like Dr. Near and Dr. Prum, who have had a chance to try the game, like it a great deal. But they also have some serious reservations. The step-by-step process by which Spore’s creatures change does not have much to do with real evolution. “The mechanism is severely messed up,” Dr. Prum said.

Nevertheless, Dr. Prum admires the way Spore touches on some of the big questions that evolutionary biologists ask. What is the origin of complexity? How contingent is evolution on flukes and quirks? “If it compels people to ask these questions, that would be great,” he said.

The object of the game is to "evolve" advanced creatures that the player "designs." What are the chances that the average player is going to appreciate the roles of contingency, and quirks? Probably so close to zero that it's not worth discussing.

I have a problem when we talk about games like Spore and real evolution in the same breath. I have a problem when someone like Will Wright is promoted on the National Geographic TV channel. The press release from National Geographic sounds ominous ..

(WASHINGTON, D.C. — AUGUST 21, 2008) In the newest creation from Electronic Arts Inc. (EA) and video game pioneer and "The Sims" mastermind Will Wright, Spore™ enables players to design a virtual galaxy of new life, such as a one-eyed web-footed creature with a snout, and then control their species' evolution. But how much real-world science is behind this groundbreaking new game? And what genetic connections do people share with a universe of strange organisms?

On Tuesday, Sept. 9, at 10:00 p.m. ET/PT, National Geographic Channel (NGC) presents the premiere of How to Build a Better Being, the companion documentary to the highly anticipated new video game Spore, which will be released nationally on Sunday, Sept. 7. The show, which is also included in the limited run of the collectable "Spore Galactic Edition," joins Wright and leading scientists in exploring the genetic information we share with all animals — even creatures we could never have envisioned. From prehistoric fish with wrists to 8-ton elephants with trunks, get powerful new insight into the origin of species and how our prized parts came to be. Then see how evolutionary creature-making is translated into a brave new world of gaming.

"What are the things that evolution has at its disposal to define a creature, to mix and match the parts, and eventually come up with a unique organism that's going to live its life and try to reproduce?" — Will Wright, gaming innovator

Some would argue that anything that promotes evolution is a step in the right direction. It's a valid point.

But why can't we have our cake and eat it too? Why can't we promote evolution but do it in a scientifically accurate manner? It's abundantly clear to all scientists that the general public knows little about evolution and what little they know is mostly wrong. Do we have to cater to those false impressions?

What effect is it going to have in the long run if we misrepresent science by pretending that evolution is progressive and ladder-like and leads eventually to us—or at least leads to intelligent animals? Is anyone else concerned about this?

The video clip below doesn't mention Spore. It looks like the same old evo-devo emphasis on semi-conserved regulatory genes and regulation of animal development as keys to understanding how humans evolved.


The Spore advertisement exploits the National Geographic connection.

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Comment Policy on Sandwalk

 
I think it's time to re-state my policy on comments. I don't like censorship. That's why my policy is close to the one mockingly described at Draft Blogger's Code of Conduct.

We also decided we needed an "anything goes" badge for sites that want to warn possible commenters that they are entering a free-for-all zone. The text to accompany that badge might go something like this:

"This is an open, uncensored forum. We are not responsible for the comments of any poster, and when discussions get heated, crude language, insults and other "off color" comments may be encountered. Participate in this site at your own risk."

As a consequence of this policy, there are several very annoying people making comments on Sandwalk. I don't respond to comments from those people but others are free to do so.

There are two types of comments that will be removed from Sandwalk. These are cases where censorship is justified, in my opinion.

The first is outright spam of the sort that we all have to tolerate from time to time. If your comment serves no other purpose than to direct people to 30 different "free" travel websites, for example, then these comments will be quickly removed.

The second is blatant promotion of commercial products on the pretext that they are relevant to the content of a posting. An example of the second type is the posting of a website for collagen creme in the comments section of an article about the biochemistry of collagen.

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Alternating Generations

 
Check out When Ferns Don't Look Like Ferns by Christopher Taylor on Catalogue of Organisms. The concept of alternating generations is an important concept that everyone should understand.

All plants undergo alternation of generation to a greater or lesser degree. Here's an interesting way to think about the concept from the Biology course notes at the University of Miami.

If animals were to undergo alternation of generations, then imagine that you are the diploid individual (sporophyte). Your mother, the gametophyte, would be haploid, and would look completely different from you (maybe like a SmurfTM). Your grandmother would be diploid, and look like you. Your own offspring would look like your mama the SmurfTM, your grandchildren would look like you, and so on.

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[Image Credit: Lewis & Clark]

Genes and Geography

 
Your DNA tells you who you are related to. This has led to projects that can trace your ancestors. Your DNA can also tell you where you've come from. This is because most of our ancestors didn't get out much. They tended to marry their cousins and close neighbors. Over many generations the people in a particular region came to resemble each other much more closely than they resembled people in other countries.

Razib at Gene Expression has been discussing the evolutionary implications of this kind of population genetics. See his latest posting and learn how to interpret the map shown below [Genetic map of Europe; genes vary as a function of distance].

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Monday's Molecule #86

 
In honor of all those students who are returning to college this week's molecule is another simple one that should be familiar to every undergraduate taking an introductory biochemistry course. Your task is to identify the molecule and give me its correct common name—the one required on an exam—and the complete, correct IUPAC name.

There's a direct connection between today's molecule and a Nobel Prize. We are looking for the single person most responsible for identifying this molecule as an important part of a metabolic pathway. This person didn't know the exact structure but got the basic chemistry correct. Be careful, there are several possible candidates who haven't already been featured on Sandalk. I want the one person who best meets the criterion.

The first person to correctly identify the molecule 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 are four ineligible candidates for this week's reward. You know who you are.

THEME:

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

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are no open.

UPDATE: The molecule is ATP of adenosine 5′-triphosphate. Lots of people got the molecule but nobody guessed the Nobel Laureate (Hans von Euler-Chelpin). There are no winners this week.

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What the Heck?

 
Coturnix posted a video on A Blog Around the Clock. His posting, entitled Just replace '9/11' with 'POW'..., was critical of McCain and his running mate Sarah Palin. The main issue in the election, according to Coturnix and others, is race. If true, that's sad.

I tried to watch the video that Coturnix embedded in his blog and this is what I get ...


Isn't that interesting? Is this a joke or has the server at hulu has been set up to recognize and block IP numbers that are registered outside of the USA? Why?

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Why Is Canada in Afghanistan?

 
The Toronto Star asked this question a few days ago. Here's the entire article from Our Man in Afghanistan. I've chosen to accompany it with a photograph of the Prime Minister of Canada shaking hands with Hamid Karzai. This is the same photo that Canadian Cynic used in Sorry ... why exactly are we over there again?.

My words fail. So here's Britain's The Independent:

"The Afghan president, Hamid Karzai, has pardoned three men who had been found guilty of gang raping a woman in the northern province of Samangan.

The woman, Sara, and her family found out about the pardon only when they saw the rapists back in their village.

“Everyone was shocked,” said Sara’s husband, Dilawar, who like many Afghans uses only one name. “These were men who had been sentenced and found guilty by the Supreme Court, walking around freely.”

Sara’s case highlights concerns about the close relationship between the Afghan president and men accused of war crimes and human rights abuses.

The men were freed discreetly but the rape itself was public and brutal. It took place in September 2005, in the run up to Afghanistan’s first democratic parliamentary elections.

The most powerful local commander, Mawlawi Islam, was running for office despite being accused of scores of murders committed while he had been a mujahedeen commander in the 1980s and a Taliban governor in the 1990s, and since the fall of the Taliban in 2001. Sara said one of his sub-commanders and body guards had been looking for young men to help in the election campaign.

“It was evening, around the time for the last prayer, when armed men came and took my son, Islamuddin, by force. I have eye-witness statements from nine people that he was there. From that niGht until now, my son has never been seen.”

Dilawar said his wife publicly harangued the commander twice about their missing son. After the second time, he said, they came for her. “The commander and three of his fighters came and took my wife out of our home and took her to their house about 200 metres away and, in front of these witnesses, raped her.”

Dilawar has a sheaf of legal papers, including a doctors’ report, which said she had a 17mm wound in her private parts cut with a bayonet. Sara was left to stumble home, bleeding and without her trousers."

Remind me again what Canadians are getting killed and mutilated for?

Exactly. All we're doing is propping up a government that's as corrupt as the group we are fighting. We are caught in the middle of a civil war and the best thing to do is to get the heck out and let the Afghans sort it out for themselves.

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Science and Public Relations

 

I have come to this conclusion: the greatest tragedy of public polity, in science and without, in the democratic nations, one that looks very likely to me to be the major proximal cause of the ultimate failure of democracy, is the invention of public relations.

Read more from John Wilkins at Spin versus framing: the tragedy of PR.

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Barack Obama Answers Science Questions

 
An organization called Science Debate 2008 has crafted 14 questions about science for the US Presidential candidates. Barack Obama has submitted his answers [Presidential answers to the top 14 science questions facing America].

1. Innovation. Science and technology have been responsible for half of the growth of the American economy since WWII. But several recent reports question America’s continued leadership in these vital areas. What policies will you support to ensure that America remains the world leader in innovation?

... My administration will increase funding for basic research in physical and life sciences, mathematics, and engineering at a rate that would double basic research budgets over the next decade. We will increase research grants for early-career researchers to keep young scientists entering these fields. We will increase support for high-risk, high-payoff research portfolios at our science agencies. And we will invest in the breakthrough research we need to meet our energy challenges and to transform our defense programs.

I'm a little confused about how the American system of government works. I think the answer means the following: "My administration will submit to Congress a proposal to increase funding ..." Is that correct? Is it just campaign rhetoric when a Presidential candidate talks like this or does the President really have more power to make laws than I imagine?

The second part of his answer suggests that the office of the President will somehow influence the granting agencies to direct more of their funds to early-career researchers and to "high-risk, high-payoff" grant applications. Can the White House make NIH, for example, distribute money differently or does that require legislation to enact?

I don't think anyone believes that Barack Obama wrote these answers, although I'm certain that he approved them. It would be interesting to know who did write the response and how much influence that person(s) will have if Obama wins the election in November. Does anyone know who his advisers are?

The answers don't seem to be much different than those I would have expected from most other Democratic candidates, or from John Kerry in 2004, or Al Gore in 2000. Am I missing something or is there some radical change in the way things are going to be done in Washington that escapes me?¹

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1. Doubling of research funding in 10 years means a yearly increase of 8%. While this is better than an increase that doesn't match inflation, it doesn't strike me as a very radical proposal to fix the funding situation.

[Hat Tip: Jim Lippard]

Genomics and Darwinism!?

 
The scientific research journal Genome Research is proposing to publish a special issue on "Genomics and Darwinism" to coincide with Darwin's 200th birthday [Genome Research].

Genome Research is now accepting submissions for a special issue, entitled Genomics and Darwinism, devoted to comparative and evolutionary genomics, including primary research reporting novel insights in large-scale quantitative and population genetics, genome evolution, and natural and sexual selection.

The deadline for submissions is September 1 and the issue is expected to coordinate with Darwin's 200th birthday (and 150th anniversary of the publication of On the Origin of Species) in February 2009.

The creationists have already jumped on this as evidence that "Darwinism" is the proper terminology when referring to evolution: see DaveScot's post on Uncommon Descent entitled Is “Darwinism” a term only used by creationists?.

I wish that Genome Research had used "Genomics and Evolution" as their theme. Or, even better, "Genomics: Beyond Darwinism." Is this what Carl Zimmer warned us about when he said that he feared an over-emphasis on Darwin [Carl Zimmer at Chautauqua]? I think Carl is right and I think we need to push back. I'll be sending a letter to the editors of Genome Research.

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Dealing With the Controversy

 
Here's an exercise for those of you who are truly interested in teaching accurate science. Go to the recent posting by Casey Luskin on Evolution: News & Views and figure out how to respond to his challenge. He's claiming that a great deal of evolution is "random" but that's not what the "Darwinists" are saying ["Random" Samples of Media and Textbook Descriptions of Darwinian Evolution].

Is he right?¹ What should we teach in school?

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1. Yes, and no. As usual Casey Luskin has only a superficial understanding of evolution and a very weak grasp of reality. However, from time to time he accidentally stumbles onto an important point. Let's set aside the fact that he has no idea what he's talking about and address how we should respond to such criticisms. My view is here: [Evolution by Accident].

Tangled Bank #112

 
The latest issue of Tangled Bank has been published on Science Notes [Tangled Bank #112].

Welcome, science readers, to Tangled Bank 112. It’s a privilege to host so much good science writing. Today’s entries are presented mainly with only the authors’ comments because it’s late and I want to get them published.

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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.

Connie Barlow and Michael Dowd at Chautauqua

 
One of the many highlights of my week at Chautauqua was meeting Connie Barlow and her husband Michael Dowd. Michael is the author of Thank God for Evolution. His blog, The Evolutionary Evangelist promotes the concept of Evolution Theology ....

As I and others are now using the term, Evolution Theology, or Religion 2.0, refers to those whose position on the science vs. religion controversy tends toward reconciliation or synthesis. The term points broadly to those who do not see themselves at either end of the polarized debate as it is currently framed (either anti-evolutionary creationism and intelligent design at one end, or anti-religious atheism at the other). Theistic evolutionists, religious naturalists, evolutionary humanists, emergentists, pantheists, panentheists, theosophists, and the 11,000+ signers of the Clergy Letter Project may differ in how they integrate evolution and theology , but they all do.

The short Wikipedia article on Michael Dowd refers to him as an itinerant Pentecostal preacher. He and his wife travel around America promoting evolution and Christianity. Michael and Connie sat in on a class that I took (Evolution and Christianity). Michael's version of Christianity is very confusing to me, as was the instructor's version. It's part of the so-called "sophisticated" Christianity that seems to deny any scientifically detectable evidence of God's intervention in affairs of the natural world. Undetectable, that is, unless you are a person of faith. People of faith can see the hand of God in events such as the breakup of the Soviet Union and the tearing down of the Berlin wall whereas the rest of us see these as entirely natural events. People who hold this position often go as far as saying that they really don't believe in supernatural beings because God is everywhere in nature.

I had never heard of Michael Dowd before last week but I have been a fan of Connie Barlow for fifteen years. She is the author of two books that I consult frequently when discussing evolution. The first one is From Gaia to Selfish Genes: Selected Writings in the Life Sciences published in 1991 and the second is Evolution Extended: Biological Debates on the Meaning of Life published in 1995.


The books are collections of excerpts from publications by leading thinkers about evolution. The selection is excellent. All the important ideas are there. In some cases this is my primary source because I haven't been able to find the original works; for example, I don't have a copy of The Logic of Life by François Jacob.

It was a delight to finally meet Connie Barlow (and you, too, Michael!). I wish I had known that she would be in Chautatuqua so I could have brought my books for her to sign. As you might have guessed, Connie is the "evolution" part of the team while Michael is the "theology" part. The unusual part of this relationship is that Connie doesn't necessarily buy into religion in the same way as her husband.

Connie published another book in 2002 called The Ghosts Of Evolution Nonsensical Fruit, Missing Partners, And Other Ecological Anachronisms. I'm not familiar with this book but I think I'll buy it.

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Useful RNAs?

The latest issue of Nature contains a news feature by Anna Petherick [Genetics: The production line]. The article is mostly about a new regulatory RNA called HOTAIR but it's the implications of this discovery that bother me.

Let's look at the question being posed ...

If more than 90% of the genome is 'junk' then why do cells make so much RNA from it?

One of the answers being promoted by many molecular biologists is that this RNA is mostly functional and it represents a massive new level of control that has hitherto gone unnoticed. That doesn't mean that we never knew about regulatory RNAs because, in fact, we've known about them for over three decades. The important point of this opinion is that these RNAs are abundant and it "explains" the presence of so much non-coding DNA in eukaryotic genomes.

The other answer to the question is that transcription is sloppy and it frequently makes mistakes. That's why there's a very low level of transcription from all parts of the genome. It's junk RNA. This explanation seems to be widespread in the molecular biology community but it doesn't get much press because there are few papers that discuss this hypothesis [What is a gene, post-ENCODE?] [Junk RNA].

The probem in this field is that it's difficult to publish a paper that proves a negative (but see Brosius (2005)) and it's easy to publish a paper showing that a particular non-coding RNA has a function. The rare examples of those with function get all the publicity and obscure the fact that 99% of these transcripts may not have a function.

The article continues with ...

It is hard to comprehend the upheaval that RNA has been causing in molecular biology over the past few years. Once viewed as a passive intermediary, it was thought to faithfully carry genetic messages from the DNA sequence to the protein-making machinery, where things were made that actually got things done. Biologists were comfortable in the knowledge that only 1–2% of the human genome made protein-coding RNA in this way, and most of the rest was filler. So when, in 2005, geneticist Thomas Gingeras announced that some cells churn out RNA molecules from about 80% of their DNA, he astonished scientists attending the Biology of Genomes meeting at Cold Spring Harbor Laboratory in New York. Why should cells bother with so much manufacturing if, as it seemed, such a tiny fraction was involved in the important business of protein-making?

I wasn't at this meeting but I'd be very surprised if the scientists were "astonished." I'm pretty sure most of them thought that this was an artifact of some kind, probably due to accidental transcription.

This is a case where the author of the article could have benefited from interviewing more of the skeptics.

Over the past three years or so the case for this 'pervasive transcription' has strengthened. The phenomenon has now been ascribed to mice, fruitflies, nematode worms and yeast. These studies, and Gingeras's original reports, came from microarrays — a technology that relies on the tendency of nucleic acids to find their complementary cousins in a solution. Gingeras works for the microarray manufacturer Affymetrix in Santa Clara, California. But not everyone has been persuaded of the extent of pervasive transcription, in part because microarrays are subject to background 'noise'. Even using no RNA, control chips will give off some signals, and results can be a matter of interpretation.

Yes, false positives may account for some of the observations but I think most scientists recognize that the microchips are actually detecting rare transcripts. The question is whether these rare transcripts are biologically significant or whether they are artifacts like most of the alternative splice variants that made all the headlines a few years ago.

If the transcripts are accidental and nonfunctional then the fact that we see this in mice, fruit flies, nematodes, and yeast isn't a surprise. It is not evidence that the transcripts are functional. We would like to see evidence that most of these transcripts are (1) evolutionarily conserved, (2) reproducibly synthesized from a functional promoter, and (3) abundant enough in vivo to make a difference,

John Mattick, the director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia, has no such qualms. He is a long-time advocate of non-coding RNA's importance. The doubters, he says, "keep regressing to the most orthodox explanation [that the long RNAs are junk]. But they can't just sit on their intellectual backsides and tell us to prove it."

John Mattick is one of the most vocal cheerleaders for non-coding RNA. He maintains that huge amounts of it are biologically functional. His statement is a tacit confession that he has no proof of his claims. What in the world is wrong with asking for "proof" (evidence) whether sitting on our backsides or standing?

Is Mattick advocating science by assertion? It certainly seems that way in many of his papers.

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Brosius, J. (2005) Waste not, want not – transcript excess in multicellular eukaryotes. Trends in Genetics 21:287-288 [DOI: 10.1016/j.tig.2005.02.014]

Everyone Must Read this Paper

 
Christopher Taylor writes on Catalogue of Organisms ...

Nearly thirty years ago, a paper was published that almost every student of evolutionary science will end up reading at some point in their career. Despite being only eighteen pages long and containing no original research, many people see it as marking something of a revolution in biology.

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Spencer Wells at Chautauqua

 
Spencer Wells is Explorer in Residence at the National Geographic Society. He has impeccable credentials: Ph.D. with Richard Lewontin, and postdoc with Luigi Luca Cavalli-Sforza and Sir Walter Bodmer. Wells heads the The Genographic Project, a project that collects and analyzes DNA samples from individuals around the world in an attempt to understand human evolution and migration.

Wells spoke last Wednesday morning in the amphitheater. He gave an interesting and informative lecture on "Deep Ancestry: Inside the Genographic Project." Most Sandwalk readers are familiar with the basic results of these studies. They indicate that modern humans originated in Africa and rapidly spread from there to all other continents. The controversy is about timing. Wells promoted the view that the last migration out of Africa took place only about 50,000 years ago.

Before the lecture, I explained to my students that this type of DNA sequence analysis relies on the fact that different human populations are genetically distinguishable. What this means is that scientists are able to tell what group you belong to by looking at your DNA. This establishes that there is a biological difference between races/populations. That's why you can trace migration routes.

Wells explained this very well without using the "race" word. Africans split from the groups on all other continents less than 100,000 years ago. Later on the migrating population subdivided into Europeans, Asians, and native Americans (+ others). In response to a question after the lecture he made the standard politically correct statement ...

Listen, I’m a scientist, and to the extent that people listen to scientists, I would like them to absorb this message, that scientifically speaking, races have no biological basis.

This got the expected round of applause from the audience. (They love that stuff at Chautauqua.) Nobody seemed to notice the discrepancy between what he said in his lecture and the idea that "races have no biological basis."

Aside from that minor glitch, Wells did a fine job of explaining the science behind these studies. The Genographic kits were on sale at the Chautauqua bookstore and I suspect they sold a lot of kits last week. According to Wells, the Genographic Project is the largest DNA typing program in the world and the information it returns to you on your ancestry is much more reliable—and cheaper—than many of the for-profit companies that have sprung up recently.

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[Photo Credit: Chautauquan Daily]

Nobel Laureate: Arthur Harden

 

The Nobel Prize in Chemistry 1929.

"for their investigations on the fermentation of sugar and fermentative enzymes"



Arthur Harden (1865 - 1940) received the 1929 Nobel Prize in Chemistry for his work on the basic metabolic pathway of fermentation. As we now know, this is the glycolytic pathway whereby sugars such as glucose are converted to pyruvate. In yeast extracts the conversion of glucose to alcohol can be studied in vitro and this led to the discovery of enzymes and pathways.

Much of the basic work on biochemical pathways was done in the early part of the 2oth century. It was recognized that proteins (zymogens) were responsible for the conversion. Harden's contribution was the discovery that there were phosphorylated sugar intermediates in the pathway. He characterized two of these sugars; glucose phosphate and fructose diphosphate [Monday's Molecule #85]. This was a big step towards figuring out how the pathway operated.

Harden shared the 1929 Nobel Prize with Hans Karl August Simon von Euler-Chelpin.

THEME:
Nobel LaureatesThe presentation speech was delivered on December 10, 1929 by Professor H.G. Söderbaum, Chairman of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences. (All award ceremonies are held on Dec. 10th because Dec. 10, 1896 was the day Alfred Nobel died.)

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

The fermentation of liquids containing sugar - there we have a chemical reaction older than all chemical science. The point of time when men first began to take this reaction into their service is really lost in the mists of antiquity, before the beginning of history. The peculiar and apparently self-caused process by which an innocent fruit juice is transformed with the active formation of scum, into a drink which is either stimulating or intoxicating according to the quantity partaken, attracted attention in the very earliest times; and to many peoples it appeared so wonderful that nothing less than the cooperation of a divinity seemed to them possible as an explanation.

Our enlightened time has scarcely the right to marvel at this, when we take into consideration how long a time science has since required to obtain an acceptable conception of the nature of fermentation. Here we stand face to face with one of the most complicated and difficult problems of chemical research. Little more than a couple of centuries separate us from the time when men first began to perceive that the fermenting substance was sugar, which under the influence of a certain something was decomposed, with carbonic acid and ethyl alcohol as the final products of the decomposition.

But what this "something" was, and how it worked, still remained unsolved questions, long defying the most penetrating attempts at interpretation. It was not until our own days that it has been vouchsafed to us to have a fairly satisfactory answer to these questions, but even here the process of development has been slow, toilsome, and it took place, so to speak, in several instalments.

In carrying out the provisions of Alfred Nobel's Will, the Swedish Academy of Sciences has already once before had its attention directed to this sphere of research. That was in 1907, when Eduard Buchner was awarded the Nobel Prize in Chemistry for his discovery of non-cellular fermentation. At the time complaints were raised in certain quarters against this award as being insufficiently justified. Seen in the perspective of distance in time, however, Buchner's discovery has more and more stood out as a line of demarcation between two different epochs, pointing the way to a new phase in the history of the chemistry of fermentation.

Buchner's discovery marked the final decision in a long struggle between two distinct schools - one, the older one, represented by Justus von Liebig the other, the younger one, represented by Louis Pasteur. According to the former school, fermentation was a purely chemical process, evoked by an unorganized ferment with unstable properties, which were imparted to the fermenting substance and thereby brought about its decomposition. According to the latter school, it was rather a physiological process, inseparably connected with the vital act of a microorganism known as the "fungus of fermentation". Buchner's discovery made it evident that to some extent both were right, but also to some extent both were wrong, and, consequently, that the truth lay between the two.

But the value of the discovery makes itself known in a still more definite way through the impulse it has given to later research. In fact, during the last three decades that research has made such great advances, has given such an enlarged insight into the mechanism of the process of fermentation, that the Academy of Sciences has found the time ripe once again to award a Nobel Prize in this department. In so doing the Academy has deemed it right to divide equally the Nobel Prize in Chemistry for the present year between Professor Arthur Harden and Professor Hans von Euler.

Buchner assumed in the yeast juice the presence of a uniform ferment or enzyme, known as "zymase".

When, however, Harden and his fellow-workers filtered a quantity of Buchner's yeast-juice through a gelatine filter, known as an "ultrafilter", and thereby split it up into two fractions (a filtrate and a sediment that did not pass through the filter), the curious state of things occurred that neither of these fractions was any longer able to bring about fermentation, but that after being mixed with one another they recovered that capacity.

Harden explained this by saying that a high-molecular enzyme, the zymase proper, was left on the filter, which let through a low-molecular complementary enzyme, which for the sake of brevity was called co-enzyme or co-zymase.

Another no less important advance is made in Harden's demonstration of the hitherto neglected part played by phosphoric acid in the process of fermentation. It has been found that a certain addition of phosphate gives rise to an equivalent amount of carbonic acid and ethyl alcohol. This effect is associated with the formation of one or more definite compounds between sugar and phosphoric acid - known as the "zymo-phosphates", amongst which a glucose monophosphate and a glucose diphosphate are to be regarded as the most important.

In the same measure as research in this department has made new conquests, a clearer and clearer insight has been gained into the importance of this discovery. In particular the work of von Euler and his pupils during the last few years greatly contributed to the unravelling of the mechanism of phosphorization.

The primary function of phosphoric acid in fermentation consists, according to von Euler, in the fact that in cooperation with an enzyme it gives rise to glucose monophosphate, identical with the monophosphate discovered by Harden and Robison. This phosphate afterwards undergoes a mutation in the presence of co-zymase, inasmuch as a glucose diphosphate and an active glucose are formed, after which the latter yields the necessary material for the subsequent stages of the fermentation.

This demonstration of the part of mutase played by the co-zymase, or in other words of the identity of co-zymase and co-mutase, is of fundamental importance, for it has fully revealed the central position in the process of fermentation of the complementary enzyme in question.

The researches of von Euler and his pupils have further led to the concentration of the co-zymase and to a far more exact study of its properties than had been previously possible. They have been able to determine approximately its molecular weight, which has been found to be about 490; and they have also been able to draw certain definite conclusions concerning its chemical nature, which make it highly probable that we have here what the chemists call a pentosenucleoside. The production of a co-zymase with a high activity has also shown in a brilliant manner the character of that enzyme as a specific activator.

Finally, what gives special interest to the study to the complicated reaction mechanism of the fermentation of sugar is that it has been possible to draw from it important conclusions concerning carbohydrate metabolism in general in both the vegetable and the animal organism.

The brief summary which has now been given, and which, in view of the scanty time allowed, has necessarily been extremely fragmentary, will in any case probably have shown that there is an extremely intimate connection between the researches of Harden and von Euler in this field. On the one hand, the fundamental discoveries of Harden have formed the precondition and point of departure for the various work of von Euler; and on the other hand, it is only the work of the latter that has made fully evident the importance of Harden's discovery.

Under such circumstances the Academy of Sciences has not hesitated this time to avail itself of the expedient that is offered by the Statutes of the Nobel Foundation of dividing the prize between two equally meritorious scientists.

Professor Harden. When the Royal Swedish Academy of Sciences resolved to adjudge to you, together with Professor von Euler, this year's Nobel Prize in Chemistry on account of your important contributions to our knowledge of alcoholic fermentation, the Academy had let herself guided by a firm conviction that these contributions had opened indeed a new chapter in the investigation of that very complicated matter.

It is with the most sincere gratification that I have the honour of conveying to you the congratulations of the Academy on this distinction, the outward signs of which you are now about to receive.

Professor von Euler. It is a great pleasure to the Swedish Academy of Sciences to be able to award this time the Alfred Nobel's Prize also to one of her members, and so much more since during a long series of years we have been in the position to follow from nearby your energetic, persevering, and systematic investigations. The Academy is also firmly convinced that the distinction which has fallen upon you today, will not contain for you the temptation to rest on laurels already obtained, but that on the contrary it will mean a stimulus to continued and, as we all hope, successful work in the service of biochemistry.

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Barbara King Replies

 
Barbara King sent me the following email message in response to my posting on her talk at Chautauqua [Barbara King at Chautauqua]. When people take the time to send me an email message my policy is to post such rebuttals without comment.

Hi, Larry Moran.

I think it's not too helpful to your readers to take a definition out of context from my book, and link it to my Chautauqua talk. At Chautauqua, I did not cite or employ Geertz's definition of religion.

Rather, I mentioned that I would focus on two aspects of religion (necessary but not sufficient aspects, as I put it), 1) the expression of empathy and compassion (which exist in balance with violence and cruelty, of course) and 2) symbolic rituals that in some way seem to go beyond the here-and-now, for example, burial rituals that go beyond hygenic disposal of the dead to include grave good and ritual processes that may embrace the sacred. I think the Chautauqua audience was more than capable of following that sort of framework, laced with a lot of examples from primate studies and archaeology that speak to those two particular aspects (of course, explaining too the inevitable risks in using great apes of today to model early human evolution.... that's an enjoyable point to debate, and I do enjoy conversations where people disagree on such things).

I'm not too sure how you could know what "most" of the audience of hundreds thought of my talk, unless you polled them? Your characterization of confused people doesn't fit with my experience of interacting with people there, at all....

I spoke at AAAS in Boston last winter and made a stand: I won't answer questions about my personal beliefs. The reason is really simpler than any you indicated (I surely don't remember saying what you said I said!): I'm a scientist, and want to keep focus on the science. Seems like a reasonable enough point. I don't understand this peculiar drive to know what scientists' personal beliefs might be! I was pleased that the Chautauqua audience applauded (literally) my answer.

I often enjoy your blog (some days more than others, clearly). I'd appreciate your posting this, if you're open to doing so.

Best wishes,

Barbara King

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What Is a Scientist?

 
The question has come up in the discussion of the AAAS video on Panda's Thumb [The AAAS responds to “Expelled”]. The video highlights several people who claim that science and religion are compatible. Since AAAS is a scientific organization, it makes sense that the people being interviewed are scientists. However, many of them are not—at least not by my understanding of what a scientist is.

For example, some of the people being interviewed are high school teachers in Dover. One of them, Jennifer Miller, is participating in the comments. Is she a scientist? Yes, according to some people because she got an undergraduate degree in biology. According to PvM that's all it takes.

Is this sufficient? I don't think so. I think that a scientist has to be an "expert" in some area of science and I think that having an undergraduate degree isn't enough. This doesn't mean that the testimony of high school science teachers is irrelevant to the discussion about compatibility of science and religion. It just means that they aren't really expert enough in science to be called scientists.

This issue also came up last week when I was talking about it to a fellow evolutionist. That person made the claim that Richard Dawkins isn't a scientist any more. That's going too far, in my opinion. Just because he may not have a grant and may not be publishing papers in the scientific literature does not mean that he has lost his claim to scientific expertise. If we try to stick to a definition like that then not only are high school teachers eliminated but also a great many real scientists.

Why do you think? Can you be a scientist if all you have is an undergraduate degree? Can you be a scientist if you don't publish in scientific journals?

Here's a challenging test of your definition of a scientist. The photograph below is from the April 30, 2008 edition of The Daily Mail in the UK [Calamari for 500: Scientists defrost giant squid with 10.8 inch eyes]. The caption reads, "A technician sits in the tank with the carcass as scientists examine the squid."

Surely these people aren't real scientists?

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[Image Credit: The scientist cartoon is from Jacks of Science]