Science Fiction and Intelligent Design

 
Peter Kazmaier (photo, left) is a research scientist for some private company. He is also an Adjunct Professor of Chemistry at Queen’s University in Kingston, ON (Canada). Kazmaier is the author of a science fiction novel called The Halcyon Dislocation.

Peter Kazmaier has a blog. He recently posted some comments that were picked up by Denyse O'Leary. Here's what Kazmaier says on Who is ‘Galileo’ in 2008? Limitations of Science II.

Recently a film has been released Expelled! No Intelligence Allowed. In it Ben Stein and the producers argue that this very process of suppression is operating in the area of investigation into Intelligent Design. An excellent interview of Ben Stein and others can be found on the website for ListenUp tv.

I have listed the way in which 2008 science is even more susceptible to suppression than science in Galileo’s time. Are there any advantages on the side of those who believe they are being blocked? Yes there are. Through the democratization of knowledge, it is much easier to disseminate ideas today than in Galileo’s time. One can circumvent the journal refereeing process and publish the information directly through books, movies, or the internet.

So what are the personal messages for me to take away from this? First of all I need to understand and follow up the claims made by Expelled. Secondly, as I referee articles, I need to be aware of my own prejudices and biases and not allow them to influence my comments. Finally, at every turn I need to oppose suppression of free discussion of scientific ideas, whatever their source.

I really hope he will follow up on the claims made by Ben Stein in the movie Expelled. I look forward to seeing another post in the next few days where Kazmaier admits that he has been duped by the IDiots. That's what I expect from a Professor at Queen's.

It's true that we need to avoid suppression of good scientific ideas. That's always a given in science. On the other hand, the importance of free expression and skepticism is only manifest if we are able to freely speak out against bad science and bad ideas. There's no rule that says we have to praise every idea just because it claims to be science.

The mark of a good scientist is to be able to separate the potentially good ideas from those that are just plain silly. Offering tacit support to Ben Stein is not a good beginning.

In addition to being a scientist and a writer of science fiction, Peter Kazmaier is also a member of The Word Guild. Here's their mission statement.

Our goal is to impact the Canadian culture through the words of Canadian writers and editors with a Christian worldview. We will do this by connecting, developing and promoting Canadian writers and editors who are Christian.

Hmm ... I see why Kazmaier is so worried about bais when he says, "I need to be aware of my own prejudices and biases and not allow them to influence my comments."

Denyse O'Leary is on the Board of Directors of The Word Guild. Now I see why she promotes Kazmaier on her blog(s). I bet it has something to do with prejudices and biases.

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Nobel Laureate: Wendell Stanley

 

The Nobel Prize in Chemistry 1946.

"for their preparation of enzymes and virus proteins in a pure form"


Wendell Meredith Stanley (1904 - 1971) was awarded the 1946 Nobel Prize in Chemistry for purifying and crystallizing tobacco mosaic virus (TMV). Stanley shared the Nobel Prize with James Sumner and John Northrop who purified and crystallized the enzymes urease and pepsin, respectively.

Stanley's work seemed to indicate that the infectious agent in TMV was a protein, in spite of the fact that TMV was known to contain RNA. You can see from the presentation speech below that back in 1946 the prevailing consensus favored protein as the genetic material. We now know that in 1946 there was a small group of scientists who were thinking that nucleic acid was the genetic material and not protein.

The presentation speech was delivered by Professor A. Tiselius, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Science.THEME: Nobel Laureates

Your Majesty, Royal Highnesses, Ladies and Gentlemen.

In 1897 Eduard Buchner, the German research worker, discovered that sugar can be made to ferment, not only with ordinary yeast, but also with the help of the expressed juices of yeast which contain none of the cells of the Saccharomyces. The discovery was considered so important that in 1907 Buchner was awarded the Nobel Prize for Chemistry.

Why was this apparently somewhat trivial experiment considered to be of such significance? The answer to this question is self-evident, if the development within the research work directed on the elucidation of the chemical nature of the vital processes is followed. Here, as in other fields of research, progress has taken place step by step, and the conquest of new fields has often been very laborious. But there, more than in most fields, a tendency has showed itself to consider the unexplained as inexplicable - which is actually not strange where problems of life and the vital processes are concerned. Thus ordinary yeast consists of living cells, and fermentation was considered by the majority of research workers - among them Pasteur - to be a manifestation of life, i.e. to be inextricably associated with the vital processes in these cells. Buchner's discovery showed that this was not the case. It may be said that thereby, at a blow, an important class of vital processes was removed from the cells into the chemists' laboratories, to be studied there by the chemists' methods. It proved, too, that, apart from fermentation, combustion and respiration, the splitting up of protein substances, fats and carbohydrates, and many other similar reactions which characterise the living cell, could be imitated in the test tube without any cooperation at all from the cells, and that on the whole the same laws held for these reactions as for ordinary chemical processes. But - and this is a very important reservation - this was only possible if extracts or expressed juices of such cells were added to the solution in the test tube. It was then natural to assume that these cell juices or cell extracts contained some substance which had the capacity of initiating and maintaining the reactions and guiding them into the paths they follow in the cell. These unknown active substances were called enzymes or ferments, and the investigation of their effects became one of the principal problems of chemistry during the first decades of this century, which for the rest it still is.

The important question of the nature of the enzymes remained unsolved, however, in spite of the energetic efforts of the research workers. It is manifestly a question of substances of complicated structures, which are present in such extremely small amounts that they, so to speak, slip through the fingers when one tries to grasp them. It is really remarkable to see how far it was possible to get in the study of the effects of the enzymes and the course of the enzymatic reactions, without knowing anything definite about the nature of these very active substances, nay, even without even being quite clear that they were substances which could be isolated in the pure form at all.

In 1926, however, in connection with his studies of a special enzyme "urease", James B. Sumner of Cornell University, Ithaca, U.S.A. succeeded in producing crystals which exhibited strikingly great activity. The basic material was the bean of a South American plant, Canavalia ensiformis, in America called the "jack bean", and the crystals had an activity that was about 700 times as great as that of bean flour. What was still more important was that it was possible to dissolve the substance and re-crystallize it several times without its activity being affected. The crystals proved to consist of a protein substance. Sumner expressed the opinion that in reality this protein substance was the pure enzyme.

As is so often the case with important discoveries, this result will probably to a certain degree have "been in the air", in that at the time it had been assumed in many quarters that the enzymes were protein substances of quite a special nature. On the other hand, Willstätter, the German chemist and Nobel Prize winner, had carried out far-reaching purifying experiments with enzymes and had arrived at results which caused him to doubt whether it was a question of protein substances or carbohydrates at all. We know now that this was due to the fact that Willstätter's purifying methods yielded solutions which were all too weak for it to be possible for chemical reactions to give a definite result.

For the chemist crystallization is the final goal in the preparation of a substance in pure form. Even though crystallizability is not such a reliable criterion of purity in the case of protein substances as in that of simpler substances, nevertheless Sumner's results have now been accepted as verified and thus also accepted as the pioneer work which first convinced research workers that the enzymes are substances which can be purified and isolated in tangible quantities. Thereby the foundation was laid for a more detailed penetration of the chemical nature of these substances, on which an understanding of the reactions taking place in living cells must finally depend.

Sumner's pioneer work was not immediately followed by similar work in other quarters, which might perhaps have been expected. About three years after Sumner's work had been published, however, Dr John Northrop of the Rockefeller Institute at Princeton began to work on the purification of the protein-splitting enzymes met with in the digestive apparatus and gradually succeeded in obtaining a number of them in crystallized form, e.g. the pepsin met with in the gastric juice and the trypsin and chymotrypsin in the pancreas. Northrop and his collaborators, among whom should be mentioned in the first place Kunitz, also made extremely comprehensive studies of the homogeneity and purity of these purified enzymes, and in that connection gave further proof of their nature as protein substances. Exceedingly interesting results were attained also in the isolation of some protein substances which appeared to be the mother substances of these enzymes. On the whole Northrop used his purified material for detailed chemical studies to a greater extent than did Sumner, and his contributions in the matter of working out the most satisfactory conditions for the crystallization of enzymes have been of the greatest importance for subsequent research workers.

This year's third Nobel Prize winner in Chemistry, Dr Wendell Stanley, first worked at the Rockefeller Institute in New York but moved in 1932 to the department of that Institute at Princeton. The problem which attracted his attention, namely the chemical nature of the viruses, was to a certain degree analogous to the problem of the enzyme just mentioned. As is well known, viruses are contagia which give rise to a large number of the best known illnesses in man, animals and plants, e.g. smallpox, infantile paralysis, influenza, foot-and-mouth disease, mosaic disease (on tobacco plants), etc. The virus particles are invisible in the microscope, and when Stanley began his work, they could only be identified by the symptoms of disease which they occasioned. Thus the problem was more difficult, inasmuch as the effect of the virus could not be as easily measured as that of an enzyme, where an exactly known chemical reaction can be employed. Stanley first tried to show the protein nature of viruses by studying how the virus of the tobacco mosaic disease was attacked by protein-splitting enzymes, but in 1934 he passed on to attempting to purify that virus by methods similar to those which Sumner and Northrop had employed so successfully for enzymes. In 1945, by using large quantities of infected tobacco leaves, he did succeed in producing small amounts of crystals which were extremely active, and which, after detailed investigation, proved to be the bearers of the virus's activity. Here, too, it was a matter of active protein substances. Subsequently it has been proved that nucleic acid also forms an important constituent of the latter.

It seems as though Stanley's discovery may take us another long step forward along the road towards a closer understanding of the chemical nature of the vital processes, for apart from the fact that in extremely small quantities they can give rise to diseases, the virus substances, like the bacteria, have the capacity to reproduce themselves. It was remarkable enough when Buchner found that certain of the functions of the living cell can be separated out from it and are to be found in the expressed juice, but it appears still more remarkable that the capacity to reproduce - this unique characteristic of life - can also be exhibited by certain molecules, thus by dead substances. It must be borne in mind, however, that, as far as we know now, this capacity is only possessed by the virus molecule when it is in contact with the living cell, and that probably the latter is materially responsible for the reproduction of the virus substance.

Investigations both by Stanley and by other research workers show that many kinds of viruses, e.g. the smallpox virus, are considerably more complicated in structure. It is conceivable that the "molecular virus" which Stanley isolated represents the simplest type in a long series of different kinds of viruses which gradually approach the living bacteria. An extraordinarily fascinating field is hereby opened up to research workers, and it is not improbable that development will lead to a closer scrutiny of the border-line between living and dead matter.

Even among scientists we sometimes hear the assumption expressed that the innermost secrets of the vital processes will always be hidden from us, that there is a wall through which we cannot penetrate. Today we do not know whether that be correct, but we know that this wall - if there is one - is considerably farther away than one had dared to believe earlier. That this is so is to an appreciable degree the result of the discoveries which have been rewarded with the 1946 Nobel Prize for Chemistry.

...

Doctor Wendell Stanley. We owe to you one of the most striking discoveries in modern chemistry and biology. The demonstration of the fact that a virus can be crystallized in the same way as many proteins and enzymes, and that it actually is a protein, at once opened up an almost unlimited field of research with fascinating possibilities. You have not only thrown open the portals to this domain, but you are yourself successfully exploring its possibilities, and rich fruits have already been harvested, thanks to your own work and that of your school.

Gentlemen. The fundamental problems which you have attacked and solved with such remarkable success are closely related, and the methods used have much in common. The more recent achievements have added to the significance of the earlier advances in this field. Your work and your discoveries deserve the gratitude of mankind. The award to you of the Nobel Prize in Chemistry for 1946 is an expression of this gratitude.

Doctor James Sumner, Doctor John Northrop, Doctor Wendell Stanley. With the warmest congratulations of the Academy I now ask you to receive your awards from the hands of His Majesty the King.

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Browser Wars: What Browser Do You Use?

 
I started using Netscape about 15 years ago when it first evolved from Mosaic. I kept using the latest versions until just a few years ago when I switched to Firefox—the offspring of Netscape (they use similar Mozilla engines). I never liked Microsoft's Internet Explorer (IE) because it didn't work well on some of the scientific websites. Safari is okay but not as easy to use as Firefox, in my opinion. I'm not that familiar with Opera. (Most bloggers have to have several different browsers in order to make sure their blogs look good for all readers.)

Firefox is about to release a new version and this event is covered on the Scientific American website [The latest version of the Firefox Web browser: Fast and secure]. It's interesting that Scientific American would consider this a newsworthy event. I assume it's because so many scientists are using Firefox?

Anyway, that's not what I want to talk about today. Here's part of the SciAm article.

Where would we be without the ubiquitous Web browser? More than a decade ago, Netscape, AOL and its ilk helped transform the Internet from simply a network of networks to the backbone of modern society by giving users access to anything and everything that was searchable. In typical fashion, Microsoft soon took hold of the Web browser market with Internet Explorer, which chased its competitors down to single-digit market share and borderline irrelevance.

That's the way it was until 1998, when Netscape (battered by Microsoft in the browser wars) decided to share its Mozilla browser software with the public for free. To make a long story short, the public tweaked and improved the software over time until, in 2003, the Firefox Web browser was born. Today, there are about 180 million people using Firefox to navigate the Web, according to Mozilla Corp., formed three years ago to oversee a number of public software projects.

With the Firefox version 3.0 (the latest) only a few weeks away from launching, the Web browser poses a serious threat to Internet Explorer's dominance. As of April, about 40 percent of Web surfers were using Firefox compared with 55 percent relying on Internet Explorer to navigate the Web, according to W3Schools, a Web site that tracks browser usage. Not bad, considering Microsoft held nearly 69 percent of the market at the end of 2005, the first year Firefox started its rise to prominence. (Firefox, which runs on the Windows, Linux and Mac operating systems, was used by about 24 percent of Web surfers at that time.)

One of the advantages of Firefox is that there are many second party add-ons because of the open source nature of the browser engine. Some of these widgets are pretty useful.

I'm not too excited about the upcoming changes in the new version of Firefox but it looks like other people might be more impressed. The trend is clear. Firefox is on the verge of displacing IE from it's dominant position.

Here's the question. What browser do you use? You can answer in the poll found at the top of the left sidebar. Why do you like your browser?

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What's the Difference Between Female DNA and Male DNA?

 
Answer: The "female" DNA sequence is incomplete because it lack DNA from the Y chromosome.

A recent press release from the Leiden University (Netherlands) proclaims Leiden scientists sequence first female DNA.

This is a well-deserved winner of Jonathan Eisen's second Genomics by Press Release Award [Genomics By Press Release Award #2: Lieden University and the First "Female" Genome]. Read the award persentation speech on his blog The Tree of Life.

Congratulations to Leiden University¹ for showing us how science should not be done and how science journalism is taking over from peer review publication.^2.

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1. "Leiden University is the oldest university in the Netherlands. It was founded in February 1575, as a gift from William of Orange to the citizens of Leiden who had withstood a long siege by the Spaniards."

2. We look forward to more press releases when the data is actually published in the peer reviewed literature.

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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