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Thursday, October 30, 2008

Citing Blogs

 
Some of my students have been asking how to cite blogs and other internet sources. I found a set of instructions on the NCBI website and I thought Id share them with you [26. Electronic Mail and Discussion Forums].

According to those instructions, you should cite Pharyngula like this:
Myers PZ (University of Minnesota, Morris, MN). Pharyngula [blog on the Internet]. New York: ScienceBlogs LLC. [2006 Jan] - [cited 2007 May 16]. Available from: http://scienceblogs.com/pharyngula/.
I'm not sure I agree with everything that's there. For example, I don't think it's useful to have the date when the blog started (2006, Jan). I don't think we need the affiliation of the author, or where the blog is published—unless it's part of a collective. I think it's important to cite a specific posting if that's what you're referring to.

Here's how I would cite today's posting on worshiping golden cows.
Myers, P.Z. (2008) Pharyngula [Internet blog] - "Where's Charlton Heston when you need him?" (Oct. 29, 2008) [cited Oct. 30, 2008]. ScienceBlogs LLC, New York. Available from: http://scienceblogs.com/pharyngula/2008/10/wheres_charlton_heston_when_yo.php
Here are some examples of how to cite comments on blogs [Examples of Citations to Blogs]. In the first example the author is unknown. In the second example the comment author is identified by affiliation.
Teresa. Comment on: "Flo's pledge: deal or no deal?" 2007 May 12 [cited 2007 May 16]. In: Kim. Emergiblog: The Life & Times of an ER Nurse [Internet]. San Francisco: Emergiblog. c2005-2007 - . [about 1 screen]. Available from: http://www.emergiblog.com/2007/05/flos-pledge-deal-or-no-deal.html scroll down to comments.

Lanard J (Western Pacific Regional Office of the World Health Organization, Manila, Philippines). Comment on: "This blog can save your life!" and "Health Communication: Science and Art." 2006 Oct 15 [cited 2007 May 17]. In: Bernhardt JM. Director's Blog [Internet]. Atlanta: Centers for Disease Control and Prevention (US), National Center for Health Marketing. [2006 Jul 13] - . [about 2 screens]. Available from: http://www.cdc.gov/healthmarketing/blog_101106.htm scroll down to locate comment.


Wednesday, October 29, 2008

The Meat-Robots Are Stirring

 
The mind-body problem is one of the more serious problems in philosophy. At the risk of over-simplifying, the two main camps can be described as dualism and monism. A dualist thinks that there's more to the mind than just neurons—the word that comes up most often is consciousness. The monist rejects the idea that there is some vitalist component to the mind. It can all be explained by the structure of the brain and the laws of physics and chemistry.

Monists are materialists, for the most part. Dualists often believe in supernatural beings.

Michael Egnor writes articles on Intelligent Design Creationism for the Evolution News & Views website at the Discovery Institute. He thinks the materialists have been winning but it's time for the zombies meat-robots to strike back.

As a general anti-science strategy, it's easy to see why the mind-body problem is resurfacing. The IDiots have lost the battle over evolution so they have to look around for something else to attack. We (scientists) don't understand exactly how the mind works. That's a perfect gap to shove God into, for now.
The materialist project to explain the mind reads less like a compendium of scientific and philosophical investigation than like a psychiatrist’s case log. Succinctly, the materialist project is batsh*t. The mind is a catastrophe for materialism. Materialism doesn’t explain the mind, and it probably can’t explain the mind. Materialism flounders on the hard problem of consciousness — the problem of understanding how it is that we are subjects and not just objects. Now a number of scientists and other academics are challenging this repellent materialist nonsense. There’s no scientific or even logical justification for the inference that the mind is merely the brain, without remainder, and the philosophical and sociological implications of the materialist view of the mind are abhorrent. Now there’s a reality-based push-back to materialist superstition, and the materialists have an insurrection on their hands.

The meat-robots are stirring.
I wonder if the meat-robots have something substantial to contribute to the discussion or whether they'll just be complaining about science, as they always do?


Voting Machines

 
We just had a Federal Election in Canada. We used paper ballots and the results were in by midnight. I had only one choice to make.

This isn't possible in the USA because American vote for many different candidates when they have an election. The ballots can be very complicated but you can always vote "straight Republican" or "straight Democrat" to simplify the process. Here's how voting machines work .... or not.




[Hat Tip: Mike the Mad Biologist]

Nobel Laureate: Albrecht Kossel

 

The Nobel Prize in Physiology or Medicine 1910.
"in recognition of the contributions to our knowledge of cell chemistry made through his work on proteins, including the nucleic substances"

Albrecht Kossel (1853 - 1927) won the Noble Prize for his studies on proteins, especially those proteins that bind to nucleic acids. He was the first to characterize protamines and histones.

The significance of Kossel's work was not fully appreciated because at the time proteins were thought to be the information carrying molecules and nucleic acids were merely structural components of the nucleus. One gets the impression that the simplicity of the protamines, and to a lesser extent, the histones, was a disappointment.

The flavor of thinking in 1910 is captured by the presentation speech on the Nobel rize website.

THEME:
Nobel Laureates
There are several kinds of proteins. One group which is included here are the so-called protamines obtained from the milt of fish. Kossel has made a detailed study of these. For these a relatively simple structure has been discovered inasmuch as the number of dissimilar atom groups in them is not very great. They therefore present simpler relationships than proteins in general, and consist mainly of substances belonging to the group which I have just called basic breakdown products of protein. For certain protamines Kossel, thanks to his methods of determination, has in fact been able to establish the quantitative relationships of the building blocks making up these protamines, a goal which we seem to be far from attaining where the other proteins are concerned.

Work on these most simple protein bodies, i.e. the protamines, is however not only of great importance because it has explained the structure of such protein bodies. The protamines are also of direct interest for the knowledge of certain cells and their life, because they are in fact characteristic of certain transformation products of the cells and are formed from ordinary protein.

One protein group, first observed by Kossel, consists of the so-called histones. They stand between the protamines and what is termed ordinary protein. This group, again, is important because of its occurrence as a component of certain cells, and has also been studied in detail by Kossel.

Professor Kossel has made an extensive and important study of the problem of the protein compounds in cells. As we have already mentioned, the proteins are very complex bodies. Within the cells the relationships are further complicated by the fact that the proteins there are combined in varying degrees with other substances such as those grouped under the name of «nucleic acids.
It is clear from Kossel's Nobel Lecture that he recognized the importance of chromatin in heredity but was unclear about which component corresponded to genes.
If we now summarize the results of the investigations of loosely bound nuclein substances, the result is a follows: A composition of the chromatin substance of the cell nucleus from two components, the one rich in bound phosphoric acid and having the qualities of an acid; the second showing a protein with the qualities of a base. In their chemical structure both components show a notable similarity based on the remarkable accumulation of nitrogen atoms and because of this chemical structure the chromatin formations can be sharply differentiated from the remaining cell components; and this quality must obviously be associated with the function of the chromatin substances. These atom groups rich in nitrogen and containing phosphorus are those whose deposits in the chromosomes are first set in motion during cell division and whose transmission to other cells forms an essential part of the reproductive process.


Tuesday, October 28, 2008

Translation at CSH

 
My co-author, Marc Perry, is at the Cold Spring Harbor Laboratories on Long Island (NY, USA). He sent me this photograph. I think it may be a Henry Moore.





This Book Don't Need Reviews

 
Book Description (from Dembski at Uncommon Descent):
Although atheism might have been logically tenable before Darwin, writes Richard Dawkins, Darwin made it possible to be an intellectually fulfilled atheist. This little book shows that atheism must seek intellectual fulfillment elsewhere decisively demonstrating the need for intelligence in explaining life’s origin. This is the best overview of why traditional origin-of-life research has crashed and burned and why intelligent design is necessary to explain the high-tech engineering inside the cell.

Author William A. Dembski worked closely as an advisor with the producers of the Spring 2008 documentary Expelled: No Intelligence Allowed starring Ben Stein. How to Be an Intellectually Fulfilled Atheist (Or Not) is the intellectual argument that helped inform significant elements of the movie. This controversial feature-length documentary film about researchers, professors, and academics who claim to have been marginalized, silenced, or threatened with academic expulsion because of their challenges to some or all parts of Darwin’s theory of evolution is one of the top twelve highest grossing documentary’s of all time. It has attracted both praise and controversy in its challenge against Darwinism.
If you liked the previous books by Jonathan Wells and William Dembski then you'll love this one. If you didn't, then you won't.

Did he really say "Ben Stein" and "intellectual argument" in the same sentence?


Junk DNA Opponents Are at It Again

 
Nils Reinton has just posted a provocative piece on Sciphu entitled Hammering nails in the “junk-DNA” coffin. Here's what he says,
Below you will find a list of references that I hope will contribute to the fall of the term “junk-DNA“, - some of it may (currently) lack a known function, but it is not junk !!!

Disclaimer: This is a list of useful references when arguing against the common overestimation of the amount of “junk”-DNA. By listing these I am not claiming anything beyond what I have already posted on this blog or in a comment somewhere. Also and importantly, I have not myself had the time to review these articles as thoroughly as I would have wanted to, - some have been read carefully, others lightly and yet others just skimmed through. Thus, you are more than welcome to comment on these references if you have opinions on any of them, or find them unsuited for this list.
You are more than welcome to visit Sciphu and make comments. I can't be bothered.

The articles are just the same-old, same-old, litany of occasional discoveries of functional bits of DNA coupled with a fanatical belief in the biological significance of every single transcript that has ever been reported in the literature.

Oh yes, I almost forgot. Nils also throws in some papers about the number of binding sites for transcription factors. I guess he hasn't read any of my postings on the importance of non-specific binding [see Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm].

THEME

Genomes & Junk DNA

Total Junk so far

    54%
I think there's good reason to assume that up to 90% of our genomes consist of junk DNA where the word "junk" means that it does not have a biological function. I haven't been able to keep up my series of postings analyzing the human genome but so far there's very good reason to believe that more than half is junk.

I've never seen an anti-junkie address the genetic load argument. Has anyone else? I wonder how they think we can survive if a substantial amount of our DNA is essential?


Schizophyllum commune Has 28,000 Distinct Sexes

 
This is the Botany Photo of the Day from The University of British Columbia Botanical Garden and Centre for Plant Research. The organism is the fungus Schizophyllum commune which is reported to have 28,000 sexes according to Tom Volk's Fungus of the Month for February 2000. Check out the Botany Photo of the Day blog for a much better picture.

In some parts of the world sex is legally restricted to arrangements involving single members of specified gender. I wonder which sexes of Schizophyllum commune would qualify? Personally, I think that members of sex 408 should be allowed to marry members of sex 12,105 but all other marriages are immoral and should be illegal.





Definitions Matter: Negative Selection and Postive Selection

 
In recent issues of the Proceedings of the National Academy of Sciences (USA) we have an interesting example of misuse of a key term in evolution.

The paper in question is by Sun et al. (2008a) of the University of California, San Francisco. The title of the paper is important: "Experimental evidence for negative selection in the evolution of a Yersinia pestis pseudogene." Here's how they describe this negative selection in the abstract,
Yersinia pestis, the agent of bubonic plague, evolved from the enteric pathogen Yersinia pseudotuberculosis within the past 20,000 years. Because ancestor and descendant both exist, it is possible to infer steps in molecular evolution by direct experimental approaches. The Y. pestis life cycle includes establishment of a biofilm within its vector, the flea. Although Y. pseudotuberculosis makes biofilms in other environments, it fails to do so in the insect. We show that rcsA, a negative regulator of biofilms that is functional in Y. pseudotuberculosis, is a pseudogene in Y. pestis. Replacement of the pseudogene with the functional Y. pseudotuberculosis rcsA allele strongly represses biofilm formation and essentially abolishes flea biofilms. The conversion of rcsA to a pseudogene during Y. pestis evolution, therefore, was a case of negative selection rather than neutral genetic drift.
Hmmm ... something about this form of "negative selection" seems puzzling. Does anyone see what it is?

The article was published online on June 3, 2008 and appeared in the June 10, 2008 issue of PNAS. It was communicated by National Academy member Stanley Falkow of Stanford University.

In this week's issue (Oct. 21, 2008) we see a letter from Jianzhi Zhang of the Department of Ecology and Evolutionary Biology, University of Michigan (Zhang, 2008).
There are two types of natural selection in biological evolution: Positive (Darwinian) selection promotes the spread of beneficial alleles, and negative (or purifying) selection hinders the spread of deleterious alleles (1). Pseudogenization is normally detrimental and prevented by negative selection. However, changes in genetic background or environment may render a formerly useful gene worthless, leading to the relaxation of the negative selection. Consequently, mutations disrupting the gene are fixed by genetic drift, and the gene becomes a pseudogene. This is the common type of pseudogenization by neutral evolution. Sometimes, however, a previously useful gene may become harmful to an organism. In this case, mutations destroying the gene would be beneficial and would be fixed by positive selection. Thus, pseudogenization can be adaptive (2). Recently, Sun et al. (3) reported an excellent example of adaptive pseudogenization, convincingly demonstrating that gene loss can also serve as an “engine” of evolution (4). Nevertheless, instead of calling it “positive selection,” they mistakenly used “negative selection.” The case involves Yersinia pestis, the agent of bubonic plague that is frequently transmitted by fleas. The authors found that the rcsA gene of Y. pestis became a pseudogene in the last 20,000 years (3). Replacing the rcsA pseudogene with its functional version represses the formation of biofilms in fleas (3), which would reduce the transmission rate of the bacteria. That is, the pseudogenization of rcsA allowed the formation of Y. pestis biofilms, which enhances the transmission of the bacteria, and hence was likely driven by positive selection.
That looks like a pretty devastating criticism to me. I'm convinced that the title of the paper was inaccurate. They were publishing an example of positive selection and not negative selection as claimed.

The authors replied in the same issue (Sun et al., 2008b).
In our article (1) we used “negative selection” to succinctly convey that a previously functional allele became deleterious and therefore was removed by natural selection. However, Zhang (2) is correct that our usage was contrary to the usual meaning. Olson's term, “adaptive gene loss” (3), would have been more appropriate. We are gratified that Zhang agrees with our conclusion that the pseudogenization of rcsA was adaptive.
Translation: "We really screwed up."

How did this happen? Normally, before a paper is published the work is presented at meetings and in lab group meetings. Was there nobody who recognized that the authors were using the wrong term? Clearly the authors themselves (all three) never questioned what they were putting into the title. Clearly the person who communicated the article didn't either, and neither did any of the reviewers.

What's happening to science these days? Now, don't get me wrong. These sorts of things happened in the "olden days" as well but I'm convinced that the problem is much more serious today. There is too much stuff being published that should never have made it past the lab group, let alone past reviewers.

Here's a question for everyone who has read this far. What should be done with the original paper? The title is wrong. How do we alert people to the fact that the authors have agreed that they made an error?



Sun, Y-C., Hinnebusch, J.B. and Darby, C. (2008a) Experimental evidence for negative selection in the evolution of a Yersinia pestis pseudogene. Proc. Natl. Acad. Sci. (USA) 105:8097-8101. [DOI: 10.1073/pnas.0803525105]

Sun, Y-C., Hinnebusch, J.B. and Darby, C. (2008b) Reply to Zhang: Adaptive gene loss in Yersinia pestis rcsA pseudogenization. Proc. Natl. Acad. Sci. (USA) 105:E70; published ahead of print October 15, 2008. [doi:10.1073/pnas.0807434105]

Zhang, J. (2008) Positive selection, not negative selection, in the pseudogenization of rcsA in Yersinia pestis. Proc. Natl. Acad. Sci. (USA) 105:E69; published ahead of print October 15, 2008 [doi:10.1073/pnas.0806419105]

Guns and Kids Don't Mix

 
From an Associated Press report: Boy, 8, shoots himself to death at Mass. gun show.
WESTFIELD, Mass. (AP) — With an instructor watching, an 8-year-old boy at a gun fair aimed an Uzi at a pumpkin and pulled the trigger as his dad reached for a camera.

It was his first time shooting a fully automatic machine gun, and the recoil of the weapon was too much for him. He lost control and fatally shooting himself in the head.
I'm mostly interested in the comment further down in the press release.
"This accident was truly a mystery to me," said Bizilj, director of emergency medicine at Johnson Memorial Hospital in Stafford, Conn. "This is a horrible event, a horrible travesty, and I really don't know why it happened."
Canadian Cynic says exactly what we all must be thinking.
Yeah, it's a puzzler, all right. A real stumper. Children and fully automatic weapons -- what could possibly go wrong?
This is why I love Canadian Cynic!





Monday, October 27, 2008

A Rainy Day in Toronto

 
The large white building is part of the MaRS complex of research buildings. It houses the labs of my colleagues who are based in the Hospital Research Institutes. Many of them are in my Department. I wonder if a pot of gold has appeared in one of their offices?




Gene Genie #39

 
The 39th edition of Gene Genie has been posted at Genetics & Health [Gene Genie #39: Personal genomics, health and evolution].
Welcome to the 39th edition of Gene Genie, the carnival of clinical genetics and personalized medicine.

Personalized genomics are all over the news lately, so let’s jump right and see what’s going on.
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
  35. Microbiology Bytes
  36. Human Genetic Disordrs
  37. The Genetic Genealogist
  38. ScienceRoll
  39. Genetics & Health



The Spaghetti Harvest

 
The Spaghetti Harvest in Switzerland was first broadcast by the BBC on April 1, 1957. I'm old enough to have seen it on television in 1957—it was on the The Tonight Show with Jack Parr [On This Day].



I'm not sure that you could broadcast something like this today in North America. Most people wouldn't understand. New Scientist lists it as one of Seven of the greatest scientific hoaxes.



Monday's Molecule #94

 
Most of you should recognize this molecule. You must describe both parts of the molecule, making sure to state clearly what you are seeing. As an extra challenge, you have to specifically mention something that is not shown even though it might be normally considered part of the complex.

It's a short step from there to this week's Nobel Laureate(s) but you need to be careful. There are two possible answers and one of them has already been chosen. You have to pick the other one.

The first one 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 three ineligible candidates for this week's reward: Alex Ling of the University of Toronto, Haruhiko Ishii, and Bill Chaney of the University of Nebraska.

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 now open.

UPDATE: Several people recognized that the molecule is a nucleosome. The figure on the left show the conformation of the histone core consisting of histones H2A, H2B, H3 and H4. The figure on the right shows the same protein core (rotated) with DNA wrapped around it to form the nucleosome core particle. The fifth histone, H1, is part of the linker region and it isn't shown.

Nobody guessed the Noel Laureate. It is Albrecht Kossel. There is no winner this week.


Final Notice: PZ Myers in Toronto and Guelph

 
The Center for Inquiry, Toronto and The University of Toronto Secular Alliance are sponsoring a lecture by PZ Myers this Friday evening (Halloween). Contact me if you want to meet PZ.

From the CFI press release ...

Fri, Oct 31, 2008, 7:30pm at University of Toronto, J.J.R. MacLeod Auditorium. A catered reception with PZ exclusively for Friends of the Centre will take place from 6:00 - 7:00 pm at the Centre For Inquiry.

Partnered with the University of Toronto Secular Alliance the Centre for Inquiry - Ontario presents the popular biologist and author of the stimulating blog Pharyngula. Dr. Myers is an associate professor of biology at the University of Minnesota, Morris. He obtained his B.S in zoology from the university of Washington and his Ph.D. in biology from the Institute of Neuroscience, University of Oregon. His blog is the most widely read science blog on the internet with topics ranging from octopus, religion and getting kicked out of Expelled.

Note:  On Sat, Nov 1, 2008, 2-4pm Guelph Campus Skeptics will host a more informal interactive discussion with PZ Myers at the University of Guelph, A.A. Thornbrough Building, Rm. 1200 (click THRN on the map). There will be refreshments available from 1 - 2pm. The cost is $3 and free for members of CFI.

PZ Myers Presents: Science Education: caught in the middle of the war between science and religion

Friday, October 31, 7:30 pm - 9:30 pm
MacLeod Auditorium
2158-1 King's College Circle,
Room 2158, Toronto, ON, M5S1A8
See the PZ Myers Visit website for more information, including how to get tickets and how to get to the MacLeod Auditorium.