The Blue Watermelon Theory

 
A reader sent me the link to this video with the following comment ...

I came across this movie. It's amazing!!
Please make time to watch it. It'll blow your mind.

We can turn it into a contest.

Question 1: What is the IQ of Shawn? and where did he learn to talk so fast?

Question 2: How many times are the words "false," "falisfiy" and "falsification" used in the video?

Question 3: How come nobody ever told me that evolution has been falsified?


Question 4: Why do we call them IDiots?

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Apologies to those who have seen this video before.

An Amazing Photograph

 
This is an amazing photograph. Phil Plait of Bad Astronomy explains why [Phoenix Descending].

Phil is an excitable guy but you've rarely seen him this excited in a video.

He has good reason ...

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Tobacco Mosaic Virus

 

Monday's Molecule #73 is tobacco mosaic virus (TMV). As its name implies, TMV is a plant virus that infects tobacco and related species. It was one of the first viruses to be identified and one of the first to be purified.

A large number of studies have been done with TMV because it is so easy to purify and because of its simple structure. The virus is composed of 2130 copies of a small coat protein (158 amino acids) wrapped around a single-stranded RNA molecule of 6000 nucleotides.

Stanley won the Nobel Prize in 1946 for crystallizing TMV—a result that was widely interpreted as evidence that proteins were the genetic material (the RNA component wasn't recognized). Watson studied TMV crystals in order to learn about helices. Later on Rosalind Franklin worked on the structure of TMA with Stanley. Aaron Klug worked out the mechanism of assembly based on the demonstration by Fraenkel-Conrat and Williams (1955) that purified coat protein and purified RNA could be mixed and spontaneously reassembled to form active virus particles [See Citation Classic from Oct. 26, 2007].

Later, Fraenkel-Conrat mixed and matched coat protein and RNA from different viruses and used the hybrids to infect plant cells. He showed that the new viruses always had the properties of the RNA and not the coat protein, demonstrating that the genetic material was the RNA and not the protein.

Early workers on in vitro translation uses TMV RNA as a template since it was one of the few examples of pure mRNA.

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[Image Credits: The figures are from Alberts et al. (2002) Figure 3-33.]

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002) The Molecular Biology of the Cell 4th ed., Garland Science, New York (USA)

Making Rudyard Kipling Proud

 
We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm.
S.J. Gould & R.C. Lewontin (1979) p. 584A typical just-so story has two components. First, it postulates the existence of an allele "for" some trait in the absence of evidence that the gene(s) actually exist (or even that such genes are possible). Second, it postulates that the allele "for" the trait was selected in the past so that now it has become fixed in the population. The attractiveness of most just-so stories lies in the creation of an elaborate, but plausible, adaptive advantage for the postulated allele.

The field of evolutionary psychology seems to have been largely taken over by those who can create the most elaborate just-so stories to "explain" modern society. For example, the avoidance of incest in most (but not all) societies is due to fixation of an anti-incest gene in our ancestors [Another Boring Just-so Story]. As with most just-so stories, there is no evidence for the existence of multiple alleles of a gene where one allele confers incest avoidance while the other allele confers acceptance of incestuous relationships. (The problem becomes even more difficult if it's a trait due to multiple alleles at different loci.)

There's a trendy extension of just-so storytelling that looks superficially like evidence. It's the creation of a computer program to simulate one's just-so story. Naturally, these programs always work as expected since that's the nature of a just-so story. You have a postulated beneficial allele with a postulated selective advantage and, presto!, the allele becomes fixed in your simulated population. It doesn't prove a thing. If your program doesn't work as expected, then all you have to do is fiddle with the selective advantage (s) until it does.

This year's fad in just-so stories is the religion gene. Here's one of the latest from NewScientist, which should know better [Religion is a product of evolution, software suggests]. The article reviews the speculations of James Dow, an Emeritus Professor of evolutionary anthropology at Oakland University in Michigan.

To simplify matters, Dow picked a defining trait of religion: the desire to proclaim religious information to others, such as a belief in the afterlife. He assumed that this trait was genetic.

The model assumes, in other words, that a small number of people have a genetic predisposition to communicate unverifiable information to others. They passed on that trait to their children, but they also interacted with people who didn't spread unreal information.

The model looks at the reproductive success of the two sorts of people – those who pass on real information, and those who pass on unreal information.

Under most scenarios, "believers in the unreal" went extinct. But when Dow included the assumption that non-believers would be attracted to religious people because of some clear, but arbitrary, signal, religion flourished.

"Somehow the communicators of unreal information are attracting others to communicate real information to them," Dow says, speculating that perhaps the non-believers are touched by the faith of the religious.

Make no mistake. This is bad science. It does not meet any of the criteria of good science.

From time to time we challenge the veracity of press releases so it's always wise to check the source to see if the views of the author have been misrepresented. In this case, the original paper is online at The Jounral of Artificial Societies and Social Simulation website [Is Religion an Evolutionary Adaptation?]. Here's the abstract. You can read the article and decide for yourself whether you think this is a worthwhile contribution to the literature on evolution.

Religious people talk about things that cannot be seen, stories that cannot be verified, and beings and forces beyond the ordinary. Perhaps their gods are truly at work, or perhaps in human nature there is an impulse to proclaim religious knowledge. If so, it would have to have arisen by natural selection. It is hard to imagine how natural selection could have produced such an impulse. There is a debate among evolutionary scientists about whether or not there is any adaptive advantage to religion at all (Bulbulia 2004a; Atran and Norenzayan 2004). Some believe that it has no adaptive value itself and that it is just a hodge podge of of behaviors that have evolved because they are adaptive in other non-religious contexts. The agent-based simulation described in this article shows that a central unifying feature of religion, a belief in an unverifiable world, could have evolved along side of verifiable knowledge. The simulation makes use of an agent-based communication model with two types of information: verifiable information (real information) about a real world and unverifiable information (unreal information) about about an imaginary world. It examines the conditions necessary for the communication of unreal information to have evolved along side the communication of real information. It offers support for the theory that religion is an adaptive complex and it disputes the theory that religion is a byproduct of unrelated adaptive processes.

How many of you think that this work supports the just-so story and refutes other possibilities?

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Centromere DNA

During mitosis in eukaryotic cells the chromosomes are duplicated and the two sister chromosomes separate and move to opposite ends of the dividing cell. This segregation is controlled by spindle microtubules that attach to specific regions of the chromsomes called centromeres.

Centromeres are easily seen in the light microscope following chromosome condensation. They appear as a constricted region where the daughter chromosomes remain attached to each other. In non-dividing cells the centromere region is heterochromatic, which means that it remains relatively condensed compared to the rest of the chromatin that contains active genes (euchromatin).

Yeast centromeres are very simple but mammalian centromere DNA has not been extensively characterized because it consists largely of multiple repeats of simple sequence DNA. Because of the repetitive nature of centromeric DNA these region are difficult to clone. They are missing from the human genome database.

THEME

Genomes & Junk DNA

Total Junk so far

    54%
Nevertheless, we have a pretty good idea of the organization of centromere DNA from the few centromeres that have been sequenced. In humans the dominant repeat is α satellite DNA, a 171 bp sequence that is repeated about 18,000 times at an average centromere. Kinetochore proteins bind to the central region of the centrosome and the spindle microtubules attach to the kinetochore (Cheeseman and Desai, 2008).

Fluorescent hybridization studies with α satellite DNA light up all centromeres on human chromosome indicating an abundance of α satellite DNA at all centromeres. We don't know how much of this DNA is essential for chromosome segregation. There are rare examples of neocentromeres (newly formed centromeres) that have very little α satellite DNA suggesting that much of it is non-essential. Artificial human chromosomes segregate at mitosis with only a few copies of α satellite DNA at their centromeres.

Not all α satellite DNA is associated with functional centromeres since the presence of inactive, nonfunctional centromere sequences in the human genome is well known. (Such as one of the ancestral centromeres associated with the formation of human chromosome 2 from a fusion of two separate primate chromosomes. See Stanyon et al. (2008) for a review of the evolution of primate chromosomes with an emphasis on the formation of new centromeres and the loss of ancient ones.)

There are also at least 68,214 monomeric α satellite sequences in the human genome (Alkan et al. 2007).

Human centromeres range from 0.3Mb to 5Mb in size (Cleveland et al. 2003). If the average centromeric region is 3Mb (3,000 kb) in size then 23 centromeres represents 2% of the entire genome sequence. Not all of this DNA is essential because, among other reasons, there is considerable variation between individuals in the length of a given centromere. Nevertheless, lets assume for the sake of our junk DNA calculation that all of it is essential.

Monomeric α satellite sequences make up about 0.3% of the genome (Alkan et al. 2007). These bits of DNA are almost certainly non-essential "escapees" from centromeric regions or fossil centromeres. The total amount of α satellite DNA in the human genome is between 2% and 5%. The vast majority of these sequences are not in the databases. If we add in the fossil centromeres we can estimate that the total amount of junk α satellite DNA comes to about 1% of the genome.

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[Image Credits: The drawing of a centromere is from Alberts et al. (2002) Figure 4-50. The photograph of chromosomes is from Hunt Willard (Schueler et al. (2001)]

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002) The Molecular Biology of the Cell 4th ed., Garland Science, New York (USA)

Alkan, C., Ventura, M., Archidiacono, N., Rocchi, M., Sahinalp, S.C., et al. (2007) Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Comput Biol 3: e181. [doi:10.1371/journal.pcbi.0030181]

Cheeseman, I.M. and Desai, A. (2008) Molecular architecture of the kinetochore–microtubule interface. Nature Reviews Molecular Cell Biology 9:33-46. [doi:10.1038/nrm2310]

Cleveland, D.W., Mao, Y., and Sullivan, K.S. (2003) Centromeres and Kinetochores From Epigenetics to Mitotic Checkpoint Signaling. Cell 112:407-421. [doi:10.1016/S0092-8674(03)00115-6 ]

Schueler, M.G., Higgins, A.W., Rudd, M.K., Gustashaw, K. & Willard, H.F. (2001) Genomic and genetic definition of a functional human centromere. Science 294:109-115.

Stanyon, R., Rocchi, M., Capozzi, O., Roberto, R., Misceo, D., Ventura, M., Cardone, M.F., Bigoni, F., and Archidiacono, N. (2008) Primate chromosome evolution: Ancestral karyotypes, marker order and neocentromeres. Chromosome Research 16:17-39. [doi: 10:1007/s10577-007-1209-z]

An inordinate fondness for systematics

 
The title of this posting is from the blog Catalogue of Organisms. Some of you may think it's a bit weird to be interested in taxonomy in the 21st century. If you think that way then you haven't been paying attention to what's going on in biology these days.

Christopher Taylor, the blogger at Catalogue of Organisms, has just posted an article about why it's important to pay attention to systematics [Poor Taxonomic Practice takes some F****ing Liberties!]. Read what he has to say.¹ You can tell from the title of his posting that he feels strongly about the subject.

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1. Especially the part about the botched attempt to save a native American species, Spartina foliosa.

Monday's Molecule #73

 
Today's molecule is rather large but it's made up of only two different macromolecules. It has been a favorite molecule of many famous scientists. Several fundamental advances in our understanding of biochemistry and molecular biology have come from studies of this molecules and its components.

You need to identify the molecule and give its correct common name. We don't need the formal IUPAC name in this case, because there isn't one!. Pay attention to the correct common name—you may not be able to guess it just by looking at the molecule but you should be able to deduce it knowing that it is connected to a Nobel Prize.

There's an direct connection between today's molecule and a Nobel Prize. The prize was awarded for purifying the molecule and determining its composition. 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.

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 tobacco mosaic virus (TMV). The Noble Laureate is Wendell Meredith Stanley (Chemistry 1946). There were quite a few readers who got it right but the first one was John Dennehy of CUNY New York (USA). Congratulations John! He has already declined my offer of lunch on Thursday and taken a rain check to be cashed the next time he's in Toronto.

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A Canadian Biochemist

 
This week's citation classic on The Evilutionary Biologist is really a classic. It's the Journal of Biological Chemistry paper on site-directed mutagenesis from Michael Smith's lab at the University of British Columbia.

Michael Smith, who died in 2000, won the Nobel Prize in 1993 for his work on site-directed mutagenesis.

A couple of weeks ago I pooked fun at John Dennehy's selection of a Richard Dawkins paper for his citation classic series [It Happens to All of Us Eventually]. This week John writes,

Any connection between a recent Sandwalk post, the fact that Smith is Canadian and that this article is biochemical in bent is purely coincidental.

I think we can all appreciate that this is just a coincidence. We expect you to recognize all outstanding Canadian biochemists on the grounds that they are truly excellent scientists and not just because you are pandering to your neighbors up north.¹

I'll assume that the last citation classic was just a temporary moment of insanity.

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1. Although a little pandering never hurt anyone. You never know when you might have to emigrate.

Gene Genie #32

 
The 32nd edition of Gene Genie has been posted at Highlight Health [Gene Genie #32 - Googling the Genie].

Welcome to the 32nd edition of Gene Genie, a blog carnival devoted to genes and genetic conditions. This edition includes some excellent articles on genes and gene-related diseases, genetics, genomics and personalized genetics.

Google Health launched publicly this week and to recognize the event, the last section of the carnival is devoted to articles specifically about the service. Google, financial backer of 23andMe, also funds the Personal Genome Project, which plans to unlock the secrets of common diseases by decoding the DNA of 100,000 people in the world’s biggest gene sequencing project [1]. With the vast number of genetic data points collected for each genome sequenced, a digital system for the movement and storage of personal health information is critical for the widespread use of individualized healthcare. Google’s entrance into the online personal health records market may thus help to accelerate the era of personalized medicine.

With these thoughts in mind, let’s get to to this month’s edition of the Genie.

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

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Good Science Writing

 
In case you haven't noticed, there's a debate going on about the quality of science writing. Many scientists—I am one—think that the quality of science journalism is not as good as it could be.

I maintain that the top three criteria for good science writing are: 1) accuracy, 2) accuracy, and 3) accuracy. Everything else is much less important. Scientists tend to score high in accuracy when they write about science, especially if it's their field. (There are many exceptions.)

Professional science journalists tend to score high in other categories such as readability and style. These are very important features of good science writing and no scientist can be considered a good science writer without being a good writer as well as a good scientist.

What about the non-professional who writes a good story that is not scientifically accurate? Can such a person be awarded kudos for good science writing? If the awards are handed out by other journalists, and not by scientists, is accuracy of information going to count for very much?

All these questions come up in a posting on Thomas Levensen's Blog The Inverse Square Blog [More on Richard Dawkins’ Peculiar View of Science Writing]. Levensen is upset about the fact that Dawkins only selected articles by scientists in his recently published anthology The Oxford Book of Modern Science Writing.

Read Levensen's posting to see the point of view that I dispute. Note that Levinsen refers to some very popular books by science writers who were not scientists. Some of these books may be popular but they do not score high in the category of scientific accuracy. How would Levensen know this? He's turned on by a good read and not by whether or not the information is correct. Other books by science writers are excellent. They are well written and scientifically accurate. Nobody disputes that. The question we're addressing is the general quality of science writing and not the obvious counter-examples.

As a general rule, do you think that science journalists are doing a good job of presenting accurate scientific information in their books and articles? Do you think that professional scientists do a better job?

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[Hat Tip: John Wilkins]

Rating Science Blogs

 
I received the following message this morning from Amy Liu of Blogged,com.

Dear Larry Moran,

Our editors recently reviewed your blog and have given it an 8.0 score out of (10) in the Education/Science category of Blogged.com.

This is quite an achievement!

Blogged.com: Science

We evaluated your blog based on the following criteria: Frequency of Updates, Relevance of Content, Site Design, and Writing Style.

After carefully reviewing each of these criteria, your site was given its 8.0 score.

... Please accept my congratulations on a blog well-done!!

Sandwalk ranks 190th out of 822 science blogs. The top blog is Centauri Dreams an astronomy blog with a 9.8 rating. Bad Astronomy ranks 94th with an 8.9 rating.

I only recognized two blogs in the top 20: Science Blog (2nd 9.8), and Cosmic Variance (5th 9.8). In my opinion, Cosmic Variance deserves a high ranking, but so does Bad Astronomy for slightly different reasons. Science Blog is a joke, it just copies press releases.

Pharyngula (36th 9.1), The Genetic Geneologist (38th 9.0) and Aetiology (39th 9.0) make the top 40. Molecule of the Day (42nd 9.0), Discovering biology in a digital world (46th 9.0), Biocurious (47th 9.0), The Evilutionary Biologist (48th 9.0), and Sex, Genes & Evolution (49th 9.0) are in the next 20 top science blogs.

There are other ways of ranking science blogs. For example, they could be ranked by popularity as on Wilko [The Top 100 Science Blogs]. The problem with that ranking is that some of the best science blogs aren't even listed as science blogs (e.g. Bad Astrononmy).

I'm not under any illusions about the rankings of science blogs. They don't count for much in my book and I can't imagine that anyone is going to make a decision based on what Blogged.com reviewers say about a blog. But it does raise an important point. The world wide web is a mess. There's lots of inaccurate information out there and lots of blogs and web sites with hidden agendas that are not obvious. (See OpenCourseWare for one aspect of this bigger problem.)

The question is whether anything can be done about it. Is there any way to provide web users with a reliable way of determining what is accurate scientific information and what isn't? In the case of blogs, I suppose that forming clusters of blogs such as ScienceBlogs^TM or Nature Network is one way.

Both of those groups are run by for-profit science magazines. It seems a shame that we have to rely on the private sector to put their stamp of approval on good science blogs. Besides, that's only going to work if the quality of blogs on such sites is maintained at a high level so that outsiders can trust them as authorities. So far, it seems to work reasonably well although there are a few mistakes now and then (cough, Framing Science, cough).

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Fugu, Pharyngula, and Junk

 
PZ Myers writes about Random Acts of Evolution in the latest issue of Seed magazine. The subtitle says it all.

The idea of humankind as a paragon of design is called into question by the puffer fish genome—the smallest, tidiest vertebrate genome of all.

The genome of the puffer fish (Takifugu rubripes or Fugu rubripes) has about the same number of genes as other vertebrates (20,000) but its genome is only 400 Mb in size [Fugu Genome Project]. This is about 12.5% of the size of mammalian genomes.

THEME

Genomes & Junk DNA

Total Junk so far

    53%
The Fugu Genome Project was initiated by workers who wanted to sequence a vertebrate genome with as little junk DNA as possible in order to determine which sequences are essential in vertebrate genomes. The small size of the fugu genome suggests that more than 80% of our genome is non-essential junk.

Many of you might recall the results of my Junk DNA Poll from last January. In case you've forgotten the results, I'll post them again. The question was: "How much of our genome could be deleted without having any significant effect on our species?" The question was designed to find out whether Sandwalk readers believed in junk DNA or whether they were being persuaded by some scientists to think that most of our genome was essential. (Modern creationists are also promoting the death of junk DNA.) There was some dispute about the interpretation of the question but most readers took it to be a question about the amount of junk DNA.




Astonishingly, almost half of Sandwalk readers think that we need more than half of our genome to survive. This would be a surprise to a puffer fish.

I began a series of postings in order to explain what our genome actually looks like. So far we've determined that about 2.5% is essential and 53% is junk. Now it's time to finish off this particular theme and have another vote.

PZ points out that most of what we call junk DNA is not controversial. It consists of LINEs and SINES, which are (mostly) defective transposons. The pufferfish genome has a lot less of this kind of junk DNA than we do. This accounts for a good deal of the reduction n genome size that we see in modern pufferfish.

PZ also points out that we need to think differently about evolution ...

In the world of genomic housekeeping, the puffer fish is a neatnik who keeps the trash under control, while the rest of us are pack rats hoarding junk DNA.

There's a lot of thought these days going into trying to figure out some adaptive reason for such a sorry state of affairs. None of it is particularly convincing. We'd be better off reconciling ourselves to the notion that much of evolution is random, and that nothing prevents nonfunctional complexity from simply accumulating.

Well said PZ!!¹

Watch for a few more postings on the remaining 45% of our genome then get ready to vote again. I'm hoping for a better result next time!

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1. I used to know someone named Paul Myers who would never had said such a thing on talk.origins. Any relation?

[Image Credit: The junk DNA icon is from the creationist website Evolution News & Views.]

Congratulations Janet Stemwedel

 
Janet Stemwedel has just been promoted to Associate Professor with tenure at San Jose State University [The letter].

Congratulations Janet.


Here's a picture of me congratulating her in advance. Wait 'till she learns what it's really like to be a tenured Professor. She won't be smiling for long!

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Botany Photo of the Day

 
This is green green ixia or Ixia viridiflora. Go to Botany Photo of the Day to find out where it grows.

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A Chip Bus in Ottawa

 
Chip buses in Ottawa and Quebec are almost as common as Tim Horton's. You haven't really tasted poutine until you've bought it at a chip bus.

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