A field guide to misunderstandings about open access

 
Want to find out what Open Access is really all about? Read A field guide to misunderstandings about open access.

Do you think that articles in open access journals aren't peer reviewed? Think again.

Do you think that all open access journals charge huge publication fees? Wrong.

Do you think that open access journals are lower quality? Nope.

---

[Hat Tip: Bora Zivkovic: A Blog Around the Clock]

Dynamic Genomes

There may have been a time in the past when scientists imagined a static genome that only changed slowly over millions of years. However, beginning in the 1960's we began to see the genome as a much more dynamic entity. The first evidence of this kind of genome came with the discovery of huge amounts of variation between individuals in a species.

This was followed by the discovery of transposons and junk DNA. We began to see genomes as rather sloppy DNA molecules with lots of pieces hopping in and out on a timescales of generations. We began to realize that many genomes were full of pseudogenes.

Chromosomal rearrangements such as inversions, duplications, and translocations were documented. In mammals, many of them were associated with cancer, thalassemias, and other diseases but the general impression was that these rearrangements of genetic material were quite common. Indeed, some non-disease examples began to accumulate in the literature. Clear evidence of normal rearrangements associated with regulation and development—including mating type switching in yeast, immunoglobulin rearrangements in mammals, chorion gene amplification in Drosophila, and antigenic variation in trypanosomes—reinforced the idea that the genome was not static.

Most of this information was incorporated into the textbooks. For example, by the early 1980's Benjamin Lewin' textbook Genes had an entire group of chapters under the heading "The Dynamic Genome: DNA in Flux."

We soon learned about the expansion and contraction of repetitive sequences in the human genome. These observations eventually gave rise to DNA fingerprinting whereby every individual could be uniquely identified by variations in the genome.

By the early 1990's the concept of the dynamic genome had become so widely entrenched among molecular biologists that when Singer and Berg published "Genes and Genomes" they felt obliged to inject a note of caution. While genomes are dynamic at the scale of species evolution, the typical genome of an individual is not subject to significant rearrangements.

Outside of molecular biology, the idea that genomes were flexible never seemed to catch on. Most people thought of genomes as relatively static entities that didn't change much over millions of years. In part, they adopted this position because they still placed a great deal of emphasis on the power of natural selection. If genomes were well-adapted then why would they change? Part of the skepticism about junk DNA stems from the belief that selection will eliminate useless DNA.

Recent developments have stirred many people to re-think their concept of genomes. For example, Sandra Porter of Discovering Biology in a Digital World recently asked, "What if everything you thought you knew about the genome was wrong?."

To the extent that such questions acquaint people with the concept of a dynamic genome, they are good. On the other hand, if such questions lead to the unthinking acceptance of alternative splicing, superabundant transcription, and a plethora ot RNAs, they are bad.

---

Handel's Messiah

 
One year Ms. Sandwalk took the entire family to see a full performance of Handel's Messiah. It was agony, except for one brief part of the performance where we all got to stand up. Ms. Sandwalk thought it was wonderful but, remember, she also likes some country music.

My children still talk about it. I guess it's one of those "experiences" that contribute to character building, or something.

Now there's an explanation in New Scientist: How misery inspired Handel's Messiah. I knew there had to be a reason.

---

Monday's Molecule #115: Winners

 
UPDATE: The molecule is indigotin or indigo dye [2,2’-Bis(2,3-dihydro-3- oxoindolyliden)]. The Nobel Laureate is Johann Friedrich Wilhelm Adolf von Baeyer.

This week's only winner is Alex Ling from the University of Toronto.

The winners this week are Pete Horwich from Dalhousie University and Devin Trudeau from the University of Toronto.

---

Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.

I'm looking for the Nobel Laureate whose name is associated with this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.

Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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 Prizes 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 now open.

---

Nobel Laureate: Adolf von Baeyer

 

The Nobel Prize in Chemistry 1905.

"in recognition of his services in the advancement of organic chemistry and the chemical industry, through his work on organic dyes and hydroaromatic compounds"


Johann Friedrich Wilhelm Adolf von Baeyer (1835 - 1917) won the Nobel Prize in Chemistry for his work on the preparation of organic dyes from coal tar.

His most notable achievement was the synthesis of indigo dye and determination of its structure. A cheap industrial synthesis of indigo was soon developed, freeing Europe from its dependence on indigo from India.

He was also the first person to synthesize phenolphthalein, the well-known acid or base indicator.

The presentation speech highlights the importance of the relationship between basic science and industry.
THEME:
Nobel Laureates

The complex and unique composition of indigo, however, made this also one of the hardest of tasks. Here there could be no question of one of those casual discoveries, which by happy accident seem to achieve half the work. Years of work were required for even von Baeyer's acumen and experimental skill to achieve the necessary insight into the pigment's chemical composition and to be able to manufacture it from simpler constituents. Even after the purely scientific part of the work had been completed it still took a number of years to make the results obtained from research applicable to technology.

Von Baeyer succeeded in producing indigo synthetically in three principal ways, namely from ortho-nitrophenylacetic acid, from ortho-nitrocinnamic acid and from ortho-nitrobenzaldehyde and acetone. This paved the way for the reproduction of indigo from raw material obtainable without much difficulty from coal tar. And if the problem of producing indigo industrially has now been solved from the technical as well as the economic point of view, this is entirely due to von Baeyer's basic work in the fields in question.

---

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

2,296,911 visits?

 
It's April 1st and PZ Myers tells us that Pharyngula had 2,296,911 visits last month [What are all you people doing here?].

Problem is, I don't think this is an April Fool's joke.¹

There are already 225 comments to that posting, which is probably what PZ means when he asks what everyone is doing there. Now he knows—they're posting comments!

---

Sandwalk had 107,747 visits or less than 5% of the number that visited Pharyngula.

Nobel Laureate: Michael Behe

 

The Nobel Prize in Biochemistry 2009.

"for his contributions to understanding complex biological systems"


Michael Behe (1952 - ) wins the Nobel Prize in Biochemistry for his amazing work on complex biological systems, especially the concept of irreducible complexity.

Beginning with the publication of his first book, Darwin's Black Box, Behe has written numerous articles on the organization of molecular machines such as the snare complex of Mus musculus and the bacterial flagellum. He has shown that these systems exhibit a fundamental property that previous biochemists overlooked—they are so well integrated that their origin cannot be explained by the older naturalistic theory of natural selection.

His later work, The Edge of Evolution, is a seminal contribution to modern evolutionary theory. In that book he explains how previous versions of evolution are incapable of explaining the origin of protein-protein interaction sites.

The presentation speech highlights the importance of this work.
THEME:
Nobel Laureates

The development of protein features, such as protein-protein binding sites, that require the participation of multiple amino acid residues is a profound, fundamental problem that has stumped the evolutionary biology community until the present day (and continues to do so, as I explain below). It is a fundamental problem because all proteins exert their effects by physically binding to something else, such as a small metabolite or DNA or other protein, and require multiple residues to do so. The problem is especially acute for protein-protein interactions, since most proteins in the cell are now known to act as teams of a half-dozen or more, rather than individually. Yet if one can’t explain how specific protein-protein interactions developed, then it is delusional to claim that we can explain how anything that depends on them developed, such as the molecular machinery of the cell. It’s like saying “we understand perfectly well how a car could evolve; we just don’t know how the pieces could get fit together.” If such a basic requirement for putting together complex systems is not understood, nothing is understood. Keep this in mind the next time you hear a blithe Darwinian tale about the undirected evolution of the cilium or bacterial flagellum.

---

Posted on April 1st, 2009.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Advice for Women: What to Do When You Discover He's an Atheist

 
Friendly Atheist found the answer on YouTube.

---

Sean Eddy on "Open Education"

 
I've been thinking a lot lately about how to get my textbook online without asking everyone involved to work for free. It's not an easy problem.

There's a myth out there that some places like MIT are putting up all kinds of useful information for free. The Open Courseware project sounds really exciting until you realize that they can't publish any of the slides they use in their powerpoint presentations because they're all copyrighted. It also doesn't take much perusal to realize that many MIT professors don't know as much about their subjects as you might imagine.

There's a new book advocating the concept of "Open Education" ("Opening Up Education" T. IIyoshi and M.S.V. Kumar eds. MIT Press). The book is reviewed by Sean Eddy on PLoS Biology [Open Revolution].

Sean Eddy used to be an active participant on the talk.origins newsgroup back when he was a graduate student so I eagerly followed the link to his review. I wasn't disappointed. It's the same Sean Eddy that I knew 12 years ago. He can still recognize bullshit when he sees it.

So, while I like storming the establishment with pitchforks and torches as much as anyone, when I picked up Opening Up Education (or rather, when I downloaded the PDF to my Kindle), I was looking for pragmatism, not utopianism. After 500 pages of “the silos we all know about in higher education are under assault in the new world,” the “hated textbook publishers,” the “epistemological hegemony of higher education,” and the “noble philosophy” of making everything free—“traitors” and “patriots” and “communists,” oh my!—my hopes were beaten down. Many of the 30 essays in this collection are more manifesto than explanation, and many of the 38 authors are writing more for their fellow revolutionary comrades than for us.

Life is never as simple as the Web 2.0 fans make out. Somebody is going to have to do a lot of work before the quality of a website matches what's in the best introductory textbooks. And it's extremely naive to think that all that work is just going to be given away for free.

I'm not just talking about authors. There's a whole team of people involved in publishing my textbooks. This includes editors who correct my spelling and grammar—an onerous task in my case. It includes artists who make the figures and editors who obtain permissions and copyrights for photographs. Then there's the staff at the publishers who receive and mail out manuscripts for review and editing and who handle all the paperwork/electrons associated with a major project.

Are we going to ask all of them to work for free by putting everything on the web? Of course not.

Sean does an excellent job of bursting the bubble.

“Remix,” “collective wisdom,” “Web 2.0”—many of these essays ride a bubble of popular digital punditry enthusiastically but too uncritically. Many technologists today are infected with an idea that “community is king,” that high-quality content will rain down freely merely because we connect digital communities openly. This confuses ways of sharing ideas with ways of creating ideas. It is a kind of magical thinking that has much in common with the cargo cults that cut landing strips in the jungle and carved radios from sticks in hope that more sophisticated beings would parachute technological artifacts down upon them. With all respect to the passionate and pioneering initiatives described in this collection, building landing strips to receive open educational content will not be enough. More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.

I have some ideas. I'd like to put my book on the web so that everyone can read it but nobody can download it or print out the figures and text. If you need a printed version you can sign on to the server and print out a chapter for $3. The pages would come with your name and email address printed in the header and footer—or perhaps as a watermark. The idea is to make the material available at minimal cost to an individual user while inhibiting the distribution of photocopies.

No matter how easy it is to read something online, I think there's still a market for a printed version of the material. I know from personal experience that highlighting and scribbling in the margins on my computer monitor doesn't work.

Online textbooks have several advantages such as hyperlinks, frequent revisions and updates, and interactive learning. But we need to find a way to pay for it. If you think the work is going to be given away for free then you are living in a dream world. Check out the MIT Open Courseware site under Biology to see what the cargo cult version of Web 2.0 gets you.

---

[Photo Credit: Nature]

[Hat Tip: Jonathan Eisen at The Tree of Life]

Religion and Child Abuse

 
I don't think that religious indoctrination is always an example of child abuse. However, there are other ways that count as clear examples of abuse [Taliban blocks UN polio treatment in Pakistan].

Militants had reportedly agreed to allow the [polio] vaccination program to take place as part of the peace agreements.

However, the militants had reneged on their word and despite assiduous efforts made by the increasingly irrelevant local administration, no vaccinations have taken place.

“It’s a US tool to cut the population of the Muslims. It is against Islam that you take a medicine before the disease”, said, Muslim Khan, Swat’s Taliban spokesman, speaking by telephone.

---

[Photo Credit: daylife/Reuters: "A man holds his twins as he waits for them to receive polio vaccines in the southern province of Kandahar September 21, 2007. Afghan health officials said on Friday they had brokered a deal with Taliban leaders to allow the immunization of children against polio in rebel-held areas in a rare sign of cooperation between the warring sides."]

[Hat Tip: RichardDawkins.net]

Way too Sensitive?

 
The techniques for detecting DNA and RNA are extremely sensitive. This sensitivity often leads to misinterpretations because it become difficult to separate signal from noise. The idea that 90% of our genome may be transcribed into functional RNA, for example, may be due to the sensitivity of an assay that can easily detect tiny amounts of accidental transcription.

Similarly, the often proclaimed ubiquity of alternative splicing may be due to the easy detection of splicing mistakes. Other examples of problems with noise might be the presumed abundance of small regulatory RNAs and the frequency of transcription factor binding sites.

The problem is acute when it comes to analyzing DNA from fossils. There, tiny amounts of contamination can really screw things up. That's why John Hawks is also interested in this problem of over-sensitive DNA assays.

Just how sensitive is the technology? Hawks has found a very interesting and informative example [The trouble with contamination]. This example is about contamination but keep in mind that it also applies to the detection of noise in transcription, DNA binding, and splicing.

Here's the original report from the BBC ['DNA bungle' haunts German police]. Over the past few years German police have been on the lookout for a mysterious woman who was linked to several murders. Her DNA was found at over 40 different crime scenes. This woman became one of the most wanted people in Europe but nothing was known about her aside from her DNA.

Finally someone became suspicious and started to look closely at the way they were collecting and analyzing DNA. To make a long story short, the alleged murderer is a factory worker in Bavaria who works in a factory that manufactures cotton swabs. The same swabs that are used to collect samples at a crime scene. Those swabs were contaminated with her DNA.

There's a lesson here. Any technology that can detect the DNA from a factory worker on a cotton swap is quite capable of detecting tiny insignificant amounts of nucleic acids inside a cell.

---

1,2,3 ... What Are We Fighting for?

 
President Obama wants to sacrifice more American in Afghanistan and Canada's Prime Minister, Stephen Harper, is suggesting that this might be something that Canada should support. This is in spite of the fact that there are times when he seems to know the right answer to the question; Can We Win in Afghanistan?.

Let's make sure everyone knows what we're fighting for: 'Worse than the Taliban' - new law rolls back rights for Afghan women.

Hamid Karzai has been accused of trying to win votes in Afghanistan's presidential election by backing a law the UN says legalises rape within marriage and bans wives from stepping outside their homes without their husbands' permission.

The Afghan president signed the law earlier this month, despite condemnation by human rights activists and some MPs that it flouts the constitution's equal rights provisions.

The final document has not been published, but the law is believed to contain articles that rule women cannot leave the house without their husbands' permission, that they can only seek work, education or visit the doctor with their husbands' permission, and that they cannot refuse their husband sex.

---

Glass Knives

 
One of the best labs I ever took as an undergraduate was an advanced cytology lab where we learned to use the electron microscope.¹ Part of the process was preparing thin sectioned material and that involved making our own glass knife that would cut very thin slices from wax-embedded tissue.

Here's a video from Leica showing how it's done today.²



I was reminded of this recently when I had occasion to refer to an electron micrograph taken by Harrison Latta. Latta invented the glass knife back in 1949. You can read about his discovery in this tribute to him on the University of California, Los Angeles, website.

This is one of those simple technological innovations that made a huge difference but would never have been recognized by the Nobel Prize committee.

---

1. Yes, they had electron microscopes back in those days!
2. You can also buy diamond knives but that's a lot less fun.

YouTube Suspends the Account of the James Randi Education Foundation

 

If you have a YouTube account, follow these instructions.

To complain to youtube follow this link;
http://www.google.com/support/youtube...

Scroll to the very bottom and click on "new issue"

Select "suspended account" from the options and express your opinion.

The mediafire link is;
http://www.mediafire.com/?sharekey=4d...

UPDATE: I was astonished to learn that some readers don't know who James Randi is or what the James Randi educational foundation is all about.

Randi is a former magician ("The Amazing Randi") from Toronto, Ontario (Canada). He is best known for investigating claims of the paranormal and for his one million dollar challenge. He has appeared on television many times and often writes columns and article debunking paranormal claims.

The goal of the James Randi Educational Foundation is ...

The James Randi Educational Foundation is a not-for-profit organization founded in 1996. Its aim is to promote critical thinking by reaching out to the public and media with reliable information about paranormal and supernatural ideas so widespread in our society today.

The Foundation's goals include:

* Creating a new generation of critical thinkers through lively classroom demonstrations and by reaching out to the next generation in the form of scholarships and awards.
* Demonstrating to the public and the media, through educational seminars, the consequences of accepting paranormal and supernatural claims without questioning.
* Supporting and conducting research into paranormal claims through well-designed experiments utilizing "the scientific method" and by publishing the findings in the JREF official newsletter, Swift, and other periodicals. Also providing reliable information on paranormal and pseudoscientific claims by maintaining a comprehensive library of books, videos, journals, and archival resources open to the public.
* Assisting those who are being attacked as a result of their investigations and criticism of people who make paranormal claims, by maintaining a legal defense fund available to assist these individuals.

To raise public awareness of these issues, the Foundation offers a $1,000,000 prize to any person or persons who can demonstrate any psychic, supernatural or paranormal ability of any kind under mutually agreed upon scientific conditions. This prize money is held in a special account which cannot be accessed for any purpose other than the awarding of the prize.

Located in Fort Lauderdale, Florida, the Foundation is funded through member contributions, grants, sales of books and videos, seminars, and conferences.

The current President of the foundation is Phil Plait of Bad Astronomy.

---

Monday's Molecule #115

 
Identify this molecule and explain why it is useful. You must supply the common name and the formal IUPAC name.

I'm looking for the Nobel Laureate whose name is associated with this molecule.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, David Schuller of Cornell University, Adam Santoro of the University of Toronto, Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, and Elvis Cela from the University of Toronto.

Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

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 Prizes 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.

---