Monday's Molecule #81

 
Today's molecule is not a specific molecule but rather a type of molecule. You have to identify the type of molecule shown here.

There's a connection between today's molecule and a Nobel Prize. The clue is the red "P" atom in the molecule. The Nobel Prize was awarded for discovering where that red "P" came from and how quickly this type of molecule was produced. Similar studies were done with many other "P"-containing molecules. This was the beginning of a whole new field of study in biochemistry.

The first person to correctly identify the type of molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are 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 may select multiple winners if several people get it right.

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

UPDATE: The molecule is a phosphatidate. It's an intermediate in the synthesis of triacylglycerols or glycerophospholipids. The R₁ and R₂ groups represent strings of -CH₂- groups, usually sixteen or eighteen carbons.

The phosphorus (P) atom is derived indirectly from inorganic phosphate and the incorporation of radioactive phosphorus as phosphate (³²PO₄^2-) into phosphatides was first studied by George de Hevesy. He received the Nobel Prize in 1943 for his work on using radioisotopes to study the synthesis of biological molecules such as phosphatides.

Lots of people knew that the molecule was a phosphatidate but nobody got the Nobel Laureate so there are no winners this week.

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Gene Genie #34

 
The 34th edition of Gene Genie has been posted at ScienceRoll [Gene Genie 34: Summertime].

This is the first time I host Gene Genie since January. Gene Genie is the blog carnival of clinical genetics and personalized medicine. Enjoy the numerous posts and articles focusing on these interesting fields of medicine.

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

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

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health
33. Neurophilosophy
34. ScienceRoll

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Species-Scape

 
This is a snapshot of an animated picture of a "species-scape." The size of the organisms represent their relative abundance on Earth. See Species-Scape on the Cornell University website.

Another version is shown on Christopher Taylor's blog Catalogue of Organisms [The Species-Scape Picture].

Notice how insignificant mammals are, yet one particular species of mammal has the potential to ruin the entire planet for all other species.

Some groups seem to be missing, bryophytes (moss) for example. Can you find any others?

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Nobel Laureate: George Palade

 

The Nobel Prize in Physiology or Medicine 1974.

"for their discoveries concerning the structural and functional organization of the cell"

George E. Palade (1912 - ) received the Nobel Prize in Physiology or Medicine for his contribution to understanding how proteins are synthesized and secreted in eukaryotic cells. He worked mostly on the secretory (exocrine) cells of guinea pig pancreas using a combination of cytological and cell fractionation techniques. As he says in his Nobel lecture, he was fascinated by the organization of these cells with their complex endoplasmic reticulum studded with ribosomes. Palade was among the first to get good electron micrographs of these structures [see below].

The idea was to track the route of newly synthesized proteins from the ribosomes to the exterior of the cell. Part of the solution came from developing techniques for EM autoradiography. This allowed Palade and his group to show that new proteins were first made by ribosomes sitting on the surface of the endoplasmic reticulum (ER). The labelled proteins were immediately seen to enter into the lumen of the ER. Subsequently they passed through internal vesicles and the Golgi until they reached the plasma membrane.

The photographs below show the results of a typical pulse-chase experiment. In the first panel (A) you can see that that with only a short pulse of radioactive amino acids the radioactive proteins—identified by the black squiggles—are localized to the endoplasmic reticulum. For a complete description of the photograph see The American Society for Cell Biology.

The pathway worked out in the 1950s and '60s is now known to be correct and it's a universal pathway found in all eukaryotes.

Palade is credited with being the first one to describe the small particles that later came to be known as ribosomes.

Palade was born in Romania where he obtained his M.D. degree in 1940. He joined the Rockefeller University shortly after World War II and remained there until he took up a position at Yale in 1973. In 1990 he moved to the University of California, San Diego.

Palade shared the 1974 prize with Albert Claude and Christian De Duve.

The presentation speech was delivered in Swedish by Professor Jan- Erik Edström of the Karolinska Medico-Chirurgical Institute


THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen,

The 1974 Nobel Prize in Physiology or Medicine concerns the fine structure and the function of the cell, a subject designated Cell Biology. There are no earlier Prize Winners in this field, simply because it is one that has been newly created, largely by the Prize Winners themselves. It is necessary to go back to 1906 to find Prize Winners who are to some extent forerunners. In that year Golgi and Cajal were awarded the Prize for studies of cells with the light microscope. Although the light microscope certainly opened a door to a new world during the 19th century, it had obvious limitations. The components of the cell are so small that it was not possible to study their inner structure, their mutual relations or their different roles. To take a metaphor from an earlier Prize Winner, the cell was like a mother's work basket, in that it contained objects strewn about in no discernible order and evidently, for him, with no recognizable functions.

But, if the cell is a work basket, it is one on a very tiny scale indeed, having a volume corresponding to a millionth of that of a pinshead. The various components responsible for the functions of the cell correspond in their turn to a millionth of this millionth, and are far below the resolving powers of the light microscope. Nor would it have helped if researchers had used larger experimental animals: the cells of the elephant are not larger than those of the mouse.

Progress was quite simply at a standstill during the first few decades of this century, but then in 1938, the electron microscope became available, an innovation that held out great promise. The difference between this microscope and the ordinary light microscope is enormous, like being able to read a book instead of just the title. With such an instrument it should now be possible to see components almost down to the dimensions of single molecules. But the early hopes were succeeded by disappointment. It was found impossible to prepare the cells in such a way that they could be used. The book remained obstinately shut, even though it would have been possible to read it.

Albert Claude and coworkers were the first to get a glance inside the book. In the mid-forties they made a break-through and succeeded in preparing cells for electron microscopy. I say a glance, because much technical development still remained to be done, and George Palade should be mentioned foremost among those who developed electron microscopy further, to the highest degree of artistry.

In addition to form and structure it is necessary to know the chemical composition of the cell components in order to understand their functions. It was hardly possible to analyse whole cells or tissues since these consist of so many different components, and so, one would get a confused picture. Each component has to be studied separately and obviously this is difficult when the components are so small. Here a new art was developed, and again Claude was the pioneer. He showed how one could first grind the cells into fragments and then sort out the different components on a large scale with the aid of the centrifuge. This was an important beginning. Palade made further contributions, but it was above all Christian de Duve who introduced brilliant developments within this field.

The functions of the cell could now be mapped with this armoury of methodology. Palade has taught us which components function when the cell grows and secretes. The Prize Winner of 1906, Camillo Golgi, discovered a cell component, the Golgi complex. Palade has demonstrated its role and he discovered the small bodies, ribosomes, in which cellular protein is produced.

Production of organic material must be balanced by scavenging and combustion of waste, even in the tiny world of the cell. de Duve discovered small components, lysosomes, which can engulf and dissolve, e.g., attacking bacteria or parts of the cell itself which are old and worn out. These are real acid baths, but the cell itself is normally protected by its surrounding membranes. Sometimes, however, the lysosomes are converted into veritable suicide pills for the cells. This occurs when the surrounding membranes are damaged, e.g. by ionizing radiation. The lysosomes play a role in many clinically important conditions and the foundations laid by de Duve are of the greatest significance for the interpretation of these states, and, thus, also for prophylactic and therapeutic measure.

To sum up, the 1974 Prize Winners have by their discoveries elucidated cellular functions that are of basic biological and clinical importance. Thus, they cover both aspects of the Prize, Physiology as well as Medicine.

Albert Claude, Christian de Duve and George Palade. During the last 30 years a new subject has been created, Cell Biology. You have been largely responsible for this development both by creating the basic methodology and by exploiting it to gain insight into the functional machinery of the cell. On behalf of the Karolinska Institute, I wish to convey to you our warmest congratulations, and I now ask you to receive the prize from the hands of his Majesty the King.

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The Ethical Frontiers of Science

 
I'm at the Chautauqua Institution this week where the theme is The Ethical Frontiers of Science.

Today's speaker was Arthur Caplan Professor of Bioethics at the University of Pennsylvania. His topic was "Is it Immoral to Want to Live Longer, Be Smarter and Look Better?" The answer is no, it is not immoral. There's nothing wrong with wanting to take advantage of modern scientific advances to prolong life, enhance intelligence, and look better." I agreed with everything he said.

Caplan looked over the speakers for the rest of the week. Many of them are his friends and he's very familiar with their views. That's why he was able to congratulate us for coming to the first lecture. "It will be the highlight of the entire week," he said, "because all the other speakers are wrong." I suspect he's right but it will be fun, nevertheless, hearing what some of them have to say.

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Monday's Molecule #80

 
Today's molecules are the little black blobs in the photograph. One of them is circled in the lower left-hand corner.

There's a direct connection between today's molecule and a Nobel Prize. In fact, the photograph was lifted directly from the Nobel lecture of the prize winner. The prize was awarded for determining the role of those little black blobs in the type of cell shown in the photo.

The first person to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are 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 may select multiple winners if several people get it right.

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

UPDATE: The photograph is rough ER and the black blobs are ribosomes. George Palade won the Nobel Prize for working out the pathway of protein secretion from the ribosomes on the surface of the ER to the plasma membrane. Many of you got it right but the first one was Charles Peterson of Hofstra University.

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Good Science Writers: Sean B. Carroll

 
Sean B. Carroll is Professor of Molecular Biology and Genetics at the University of Wisconsin in Madison, Wisconsin (USA).¹ His research interests focus on evolution and development, mostly in fruit flies and other insect. Carroll is one of the leading advocates of a new approach to evolution arising out of what we have learned from animal development ("evo-devo"). (See the official Sean B. Caroll website.)

He is co-author on two textbooks: From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (2nd ed, 2005) with Jen Grenier and Scott Weatherbee; and Introduction to Genetic Analysis (9th ed., 2007) with Anthony Griffiths, Richard Lewontin, and Susan Wessler. Sean B. Carroll has written two trade books: Endless Forms Most Beautiful: The New Science of Evo Devo (2005) and The Making of the Fittest (2006).

Sean B. Carrol was not included in Richard Dawkins' book: The Oxford Book of Modern Science Writing

The excerpts below are from The Making of the Fittest. This is a book that emphasizes the role of natural selection in evolution.

It may be the most remote place on Earth.

Tiny Bouvet Island is a lone speck in the vast South Atlantic, some 1600 miles southwest of the Cape of Good Hope (Africa) and almost 3000 miles east of Cape Horn (South America). The great Captain James Cook, commanding the HMS Resolution, tried to find it on his voyages through the Southern Ocean in the 1770s, but failed both times. Covered by an ice sheet several hundred feet thick that ends in sheer cliffs, which in turn drop to black volcanic beaches, and with an average temperature below freezing, it still doesn't get many visitors.

Fortunately, for both my story and natural history, the Norwegian research ship Norvegia made it to Bouvet Island in 1928, with the principle purpose of establishing a shelter and a cache of provisions for shipwrecked sailors. While on Bouvet, the ship's biologist, Ditlef Rustad, a zoology student, caught some very curious-looking fish. They looked like any other fish in most respects—they had big eyes, large pectoral and tail fins, and a long protruding jaw full of teeth. But they were utterly pale, almost transparent. When examined more closely, Rustad noticed that what he called "white crocodile fish" had blood that was completely colorless.

Johan Ruud, a fellow student, traveled to the Antarctic two years later on the factory whaling ship Vikingen. He thought the crew was pulling his leg when one flenser (a man who stripped the blubber and skin from the whale) said to him, "Do you know there are fishes here that have no blood?"

Playing along, he replied, "Oh, yes? Please bring some back with you."

A good student of animal physiology, Ruud was perfectly sure that no such fish could exist, as textbooks stated firmly that all vertebrates (fish, amphibians, reptiles, birds, and mammals) possess red cells in their blood that contained the pigment hemoglobin. This is as fundamental as, well, breathing oxygen. So when the flenser and his friends returned from a day's efforts without any blodlaus-fisk, Ruud dismissed the idea as shipboard lore.

Of all the scientists in the world today, there is no one with whom Charles Darwin would rather spend an evening than Sean Carroll.

         Michael Ruse

He wasn't looking for a new kingdom.

Microbiologist Tom Brock and his student Hudson Freeze were prowling around the geysers and hot springs of Yellowstone National Park one day late in the summer of 1966. They were interested in finding out what kinds of microbes lived around the pools and were drawn to the orange mats that colored the outflows of several springs.

They collected samples of microbes from Mushroom Spring, a large pool in the Lower Geyser Basin whose source was exactly 163 degreed F, thought at the time to be the upper temperature limit for life. They were able to isolate a new bacterium from this site, a species that thrived in hot water. In fact, its optimal growth temperature was right around that of the hot spring. They dubbed this "thermophilic" creature Thermus aquaticus. Brock also noticed some pink filaments around some even hotter springs, which raised his suspicion that life might occur at even higher temperatures.

The next year, Brock tried a new approach to "fishing" for microbes in the hot springs of Yellowstone. His fishing tackle was simple: he tied one or two microscope slides to a piece of string, dropped it in the pool, and tied the other end to a log or a rock (don't try this on your own—you will be arrested and quite likely scalded or worse). Days later, upon retrieving the slides, he could see heavy growth, sometimes so much that the slides had a visible film. Brock was right that organisms were living at higher temperatures than had previously been thought, but he did not imagine that they were living in boiling water. And they weren't just tolerating 200 degrees F or more—these organisms were thriving in smoky, acidic, boiling pots such as Sulpur Cauldron, in the Mud Volcano area of the park. Brock's Yellowstone explorations opened eyes and minds to the extraordinary range of life's adaptability, identified bizarre but important new species such as Sulfolobus and Thermoplasma, and launched the scientific study of what he called "hyperthermophiles," lovers of superheat.

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1. Sean B. Carroll is the biologist. Sean Carroll is the physicist at the California Institute of Technology and one of the authors on the blog Cosmic Variance.

The Fluctuation Test

John Dennehy of The Evilutionary Biologist continues his almost perfect¹ record of picking important papers for his Citation Classic.

This week's paper is the classic 1943 paper by Luria and Delbrück on the fluctuation test [The Fluctuation test]. This was the paper that proved that mutations arise randomly with respect to their phenotype. As John says, it is one of the most important experiments in biology.

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1. For the exception see It Happens to all of Us Eventually.

Good Science Writers: Eugenie Scott

 
Eugenie C. Scott has been the Executive Director of the National Center for Science Education (NCSE) since 1987. She is a physical anthropologist who taught at several universities prior to becoming director of NCSE.

Scot has published dozens of articles on evolution and creationism in the popular press and she is a frequent guest on television and radio broadcasts. She is one of the world's leading experts on explaining evolution to the general public (and to other scientists).

Although she meets all the qualifications, she was not included in Richard Dawkins' book: The Oxford Book of Modern Science Writing.

The following excepts are taken from her latest book Evolution vs. Creationism: An Introduction.

If a population at the end of a geographic range of a species is cut off from the rest of the species, through time it may become different from other populations. Perhaps natural selection is operating differently in its environment than it is in the rest of the species range, or perhaps the population has a somewhat different set of genes than other populations of the species. Just by the rules of probability, a small, peripheral population is not likely to have all the variants of genes that are present in the whole species, which might result in its future evolution taking a different turn.

No longer exchanging genes with other populations of the species, and diverging genetically through time from them, members of a peripheral, isolated population might reach the stage where, were they to have the opportunity to mate with a member of the "parent" species, they would not be able to produce offspring. Isolating mechanisms, most of which are genetic but some of which are behavioral, can arise to prevent reproduction between organisms from different populations. Some isolating mechanisms prevent two individuals from mating at all: in some insects, for example, the sexual parts of males and females of related species are so different in shape and size that copulation can't take place. Other isolating mechanisms come into effect when sperm and egg cannot fuse for biochemical or structural reasons. An isolating mechanism could take the form of the prevention of implantation of the egg or of disruption of the growth of the embryo after a few divisions. Or the isolating mechanism could kick in later: mules, which result from crossing horses and donkeys are healthy but sterile. Donkey genes thus are inhibited from entering into the horse species and vice versa. When member of two groups aren't able to share genes because of isolating mechanisms, we can say that speciation between them has occurred. (Outside of the laboratory, it may be difficult to determine whether two species that no longer live in the same environment are reproductively isolated.)

The new species would of course be very similar to the old one—in fact, it might not be possible to tell them apart. Over time, though, if the new species manages successfully to adapt to its environment, it might also expand and bud off new species, which would be yet more different from the parent—now "grandparent"—species. This branching and splitting has, through time, given us the variety of species that we see today.

... common to all ID [intelligent design] proponents is the rejection of "Darwinism." In ID literature, "Darwinism" becomes an epithet, though it is not always clear in any given passage exactly what is meant by "Darwinism." In evolutionary biology, "Darwinism" usually refers to the ideas held by Darwin in the nineteenth century. Usually the term is not used for modern evolutionary theory, which, because it goes well beyond Darwin to include subsequent discoveries and understandings, is more frequently referred to as "neo-Darwinism," or just "evolutionary theory." Evolutionary biologists hardly ever use "Darwinism" as a synonym for evolution, though it occasionally is used this way by historians and philosophers of science. In ID literature, however, "Darwinism" can mean Darwin's ideas, natural selection, neo-Darwinism, post-neo-Darwinian evolutionary theory, evolution itself, or materialist ideology inspired by "Godless evolution."

The public, on the other hand, is unlikely to make these distinctions, instead equating "Darwinism" with evolution (common descent). For decades, Creation Science proponents have cited the controversies among scientist over how evolution occured—including the specific role of natural selection—in their attempts to persuade the public that evolution itself—the thesis of common ancestry—was not accepted by scientists, or at least was in dispute. Within the scientific community, of course, there are lively controversies, including over how much of evolution is explained by natural selection and how much by additional mechanisms such as those being discovered in evolutionary developmental biology ("evo-devo"). No one says natural selection is unimportant; no one says that additional mechanisms are categorically ruled out. But these technical arguments go well beyond the understanding of laypeople and are easily used to promote confusion over whether evolution occurred. Intelligent Design proponents similarly exploit public confusion about "Darwinism" to promote doubt about evolution.

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Was Charles Darwin a Good Science Writer?

 
Olivia Judson is a research fellow at Imperial College in London (UK). She studies evolution. Judson is a former pupil of W.D. Hamilton. She is also the daughter of Horace Freeland Judson.¹

Judson writes a weekly article for the New York Times website. This week she tackles the heretical question of whether Charles Darwin was a good science writer [An Original Confession]. Here's a treaser ...

It always happens the same way. A glance around the room to make sure no one else is listening. A clearing of the throat. A lowering of the voice to a conspiratorial tone. Then, the confession.

“I’ve never read ‘On the Origin of Species.’ I tried, but I thought it was boring.”

Thus, a number of eminent scientists — biologists all — have spoken. Or rather, whispered.

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1. Author of The Eighth Day of Creation, the definitive history of the early days of molecular biology.

[Hat Tip: RichardDawkins.net]

Tangled Bank #109

 
The latest issue of Tangled Bank is up at Greg Laden's Blog [The Tangled Bank #109: LOL Evolution!].

Welcome to the One Hundred and Ninth Edition of The Tangled Bank, the Weblog Carnival of Evolutionary Biology. This is the LOL edition of the Tangled Bank....

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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.

A Gene Wiki

 
The prevalence of errors and omissions in sequence databases is one of the ugly little secrets of molecular biology [Errors in Sequence Databases]. We know how to fix the problem; it requires careful annotation by knowledgeable experts. Unfortunately, this is time-consuming and expensive since you have to hire annotators. One other possibility is to allow open access to all existing records in databases such as GenBank, RefSeq, or PDB. This ain't gonna happen because here's no way to verify the changes to make sure they are valid. The people who control these databases are very reluctant to allow open access and the authors of the database entries are uneasy about allowing others to insert annotations into their records.

But there are other models that might work. A recent paper by Huss et al. (2008) in PLoS Biology describes a possible solution. They point out that Wikipedia seems to be a successful model of collaborative effort to ensure accuracy. Why not adopt this model for gene annotation?

Some examples of human genes already had Wikipedia entries and these entries were updated and annotated by various users. In order to stimulate and encourage this process, Huss et al. (2008) created stub entries on Wikipedia for every human gene. Here's how they describe it in their paper.

In principle, a comprehensive gene wiki could have naturally evolved out of the existing Wikipedia framework, and as described above, the beginnings of this process were already underway. However, we hypothesized that growth could be greatly accelerated by systematic creation of gene page stubs, each of which would contain a basal level of gene annotation harvested from authoritative sources. Here we describe an effort to automatically create such a foundation for a comprehensive gene wiki. Moreover, we demonstrate that this effort has begun the positive-feedback loop between readers, contributors, and page utility, which will promote its long-term success.

Today, anyone with access to Wikipedia can contribute to annotating human genes. Two examples of well annotated genes are HSP90 and NF-κB.

Let's look at some examples of stub entries to see how the process might work. I've chosen the human members of the HSP70 multigene family because I'm familiar with these genes. All members of the family function as molecular chaperones, helping to ensure that proteins are properly folded [Heat Shock and Molecular Chaperones].

There are two major inducible genes called HSPA1A and HSPA1B. They are adjacent to one another on chromosome 6. The database entries for these genes are confusing and in most cases it's almost impossible to discern which gene is being referred to.

Here's the Wikipedia stub for HSPA1A. Clearly there's an opportunity to modify this entry in order to make it clear that there are two very similar genes and to point to the proper sequence records for this gene. The second gene, HSPA1B, has its own entry in EntrezGene so I was expecting to find it on Wikipedia. Unfortunately, it's not there. A search for HSPA1B redirects you to HSPA1A. So right away we have a problem. Someone made a decision to merge these entries on Wikipedia making it very difficult to correctly annotate the separate genes.

HSPA1L is an intronless gene closely linked to HSPA1A and HSPA1B. HSPA1L is not heat shock inducible, instead it is developmentally regulated. The gene is expressed exclusively in the testes. The stub entry for this gene [HSPA1L] includes an RNA expression profile that beautifully illustrates the developmental regulation but there's nothing in the annotations that mentions this. This is an excellent opportunity to correct an omission in the existing databases.

Let's look at one more example to see how useful the Wikipedia effort might be. The HSPA4 gene is identified on all databases as a member of the HSP70 gene family. It's usually called "Heat shock 70kDa protein 4." The Wikipedia stub reflects the GenBank annotation [HSPA4]. However, it has been known for a long time that this gene is NOT a member of the HSP70 gene family. The annotation is incorrect. Instead, this gene is Apg-2 an HSP100 homologue not related to HSP70. The original error is due to Fathallah et al. (1993) who sequenced the first example. They mistakenly called it a novel hsp70 gene due, in part, to sequencing errors and partly to an overactive imagination. Mistakes such as these are extremely difficult to remove from the database but we now have an opportunity to correct the error on the Wikipedia entry.

Putting the human genes on Wikipedia is almost as good as allowing open access to the primary sequence databases. The effort will only be successful if scientists make the effort to edit the Wikipedia entries. It's unlikely that most gene entries will be modified but even if only a subset is annotated, it's better than none at all. It would be nice if the RefSeq records could point to the Wikipedia records. That will encourage people to make comments on Wikipedia.

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Huss III, J.W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T.J., Valafar, F., and Su, A.I. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biol 6(7): e175 [doi:10.1371/journal.pbio.0060175]

Flatfish

 
Flatfish are strange looking animals that live sideways. One of their eyes has migrated to one side of the fish so that when it lies on its "side" at the bottom of the ocean both eyes point upwards. This is an interesting example of the evolution of a change in development.

Fossil relatives of modern flatfish have recently been described and they confirm much of what was surmised about the evolution of these strange creatures. Several bloggers have written about this and it's well worth the effort to read their postings.

Christopher Taylor at Catalogue of Organisms wrote The Ugly Stick in Action.

Ed Yong at Not Exactly Rocket Science wrote 'Missing link' flatfish has eye that's moved halfway across its head.

GrrlScientist at Living the Scientific Life wrote The Mysterious Origin of the Wandering Eye.

Carl Zimmer at The Loom wrote Dawn of the Picasso Fish.

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[Image Credit: The drawings are by Georgi Pchelarov from The Classification of Fishes.]

Good Science Writers: G. Brent Dalrymple

 
G. Brent Dalrymple is a geologist at Oregon State University (now retired). He received the National Science Medal in 2005. This is the USA's highest award for scientific achievement.

Dalrymple has published two books on the age of the Earth: The Age of the Earth (1991), and Ancient Earth, Ancient Skies: The Age of Earth and Its Cosmic Surroundings (2004). The first book grew out of his preparation for the 1981 creationist trial in Arkansas that resulted in overthrowing the "equal time" law. Michael Ruse writes of his testimony at that trial [in Science and Creationism, see NCSE Supporter Dalrymple receives National Medal of Science]

Rounding out the science witnesses was G. Brent Dalrymple of the U.S. Geological Survey. He gave a quite brilliant disquisition on methods of dating the earth. One would not think that such a topic could be all that intrinsically interesting, but Dalrymple gave this assumption the total lie. He held us absolutely spellbound as he talked of various dating techniques and how geologists compensate for weaknesses in one direction by strengths from another. My sense was that Dalrymple was so good and so firm that he rather broke the back of the State's case. He had checked all of the Creationist arguments and showed in devastating detail the trail of misquotations, computational errors, out-of-date references, and sheer blind stupidity which allows the Creationists to assign the earth an age of 6000 years. After Dalrymple, the State seemed far less ready to tangle with witnesses.

The following except is from The Age of the Earth. It can only give a bit of the flavor of Dalrymple's writing. In my opinion this book is one of the classic science books of the 2oth century. Richard Dawkins did not include G. Brent Dalrymple in The Oxford Book of Modern Science Writing.

Four and one-half billion years. That figure, which represents the current estimate of the age of the Earth, is so large, so far outside of our normal everyday experience that it is difficult to comprehend its true scope and meaning. Even scientists who deal with numbers of that magnitude on a daily basis often find it difficult to grasp the full significance of that span of time. If a piece of string 2.4 cm long (about an inch) represents one year, for example, then a 183-cm length (about 6 feet) is equivalent to the average lifetime of a person living in the United States. A string representing all of recorded human history would be fully a kilometer long, but a piece representing 4.5 billion years would be 114,280 km long! Four and one-half billion quarters would form a stack nearly 8,000 km high. Can anyone fully visualize a string that would wrap around the Earth nearly three times, or a stack of quarters that would reach from here to the center of the Earth and halfway to the other side? ...

As staggering as these numbers may seem, the evidence clearly shows that the Earth's age is, indeed, 4.5 Ga, and the universe is probably three to four times older. Yet humans are relatively recent inhabitants of our planet and have witnessed only an infinitesimally small percentage of Earth's history. No man, no creature, no plant was present when Earth, her sister planets, and the Sun condensed from a shapeless cloud of primordial matter. How then can we peer back into these seemingly infinite reaches of time and calculate an age for the Earth that requires ten digits?

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Good Science Writers: Jacques Monod

 
Jacques Monod (1910 - 1976) received the Nobel Prize in Physiology or Medicine (1965) for his work on the regulation of the lac operon (with François Jacob). While best known as a biochemist, Monod was also well respected for his many articles on politics and philosophy.

Dawkins didn't select anything from Monod for The Oxford Book of Modern Science Writing because his selections were limited to books written initially in English. Monod's most famous work is Le Hasard et la Nécessité first published in France in 1970. It is well known in the English version: Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (1971). The excepts below are from the translation by Austryn Wainhouse.

Various mutations have been identified as due to

1. The substitution of a single pair of nucleotides for another pair;
2. The deletion of addition of one or several pairs of nucleotides, and
3. Various kinds of "scrambling" of the genetic text by inversion, duplication, or fusion of more or less extended segments.

We call these events accidental; we say that they are random occurrences. And since they constitute the only possible source of modification in the genetic text, itself the sole repository of the organism's hereditary structures, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is ever likely to be revised.

I believe we can assert today that a universal theory, however completely successful in other domains, could never encompass the biosphere, its structure, and its evolution as phenomena deducible from first principles....

In a general manner the theory would anticipate the existence, the properties, the interrelations of certain classes of objects or events, but would obviously not be able to foresee the existence or the distinctive characteristics of any particular object or event.

The thesis that I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles, and therefore essentially unpredictable.

Let there be no misunderstanding here. In saying that as a class living beings are not predictable upon the basis of first principles, I by no means intend to suggest that they are not explicable through these principles—that they transcend them in some way, and that other principles, applicable to living systems alone, must be invoked. In my view the biosphere is unpredictable for the very same reason—neither more nor less—that the particular configuration of atoms constituting this pebble I have in my hand is unpredictable. No one will find fault with a universal theory for not affirming and foreseeing the existence of this particular configuration of atoms; it is enough for us that this actual object, unique and real, be compatible with the theory. This object, according to the theory, is under no obligation to exist; but it has the right to.

That is enough for us as concerns the pebble, but not as concerns ourselves. We would like to think ourselves necessary, inevitable, ordained from all eternity. All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency.

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