New Seven Wonders of the World

 

One of my colleagues just got back from Rio de Janeiro where he visited one of the New Seven Wonders of the World. It got me thinking about the others that were recently voted in. It's not a bad list but I think the Eiffel Tower and Stonehenge should have been on the list instead of Christ the Redeemer and the Colosseum.

And what about this? When it's finished it will be one of the most impressive structures that humans have ever made—especially when you consider the location. A somewhat greater challenge than Macchu Picchu, don't you think?

The international space station may turn out to be not very useful but then the Great Wall of China, the Eiffel Tower, and Christ the Redeemer weren't very useful either.

Blog Spam: What's the Point?

 


There must be some advantage to spammers who litter the comments section with spurious messages. They usually have a name that links to something. For example, today there was a poster named "Viagra" who put several comments on my blog. If you click on "Viagra" it takes you to a webpage (search2.site.io/index.html) with a list of Viagra related items.

Can someone explain the point of all this? What advantage to spammers get out of polluting blogs?

I left an example of this spam in the comments of the thread Science Policy Forum: Framing Science.

Monday's Molecule #40

 

Name this molecule. There's a short common name but it's not sufficient. You have to supply the complete IUPAC name in order to win the prize. There's a direct connection between this Monday's Molecule and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this Wednesday's reward. Both of them are waiting to collect their prize when September rolls around. The prize is a free lunch at the Faculty Club.

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 the Nobel Laureate. Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.


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

Francis Collin on CBC Radio

 
CBC Radio recently interviewed Francis Collins. The interview was conducted by Mary Hynes a woman who shows herself to be completely ignorant of atheism [Tapestry: Interview with Francis Collins].

You can listen to the entire interview if you dare but there's nothing new here. For the most part, Collins repeats the same old tired arguments we saw in his book The Language of God [Theistic Evolution According to Francis Collins]. One of the things he says is that when he was an atheist he began to question his lack of belief. All of his questions about God were answered on reading the first few pages of Mere Christianity by C.S. Lewis! I bet you didn't realize how easy it is to become a Christian! Neither did PZ Myers so he posted the first chapter of Mere Christianity on his blog [Get Ready fo Become a Christian]. Atheists beware, read it at your peril. You might fall down on your knees and be converted to Christianity.

Collins believes that one of the strongest arguments for the existence of God is our sense of what's right and wrong. He calls this the Moral Law. Somehow we seem to know the difference between good and evil. Collins also thinks that the concept of altruism is a major stumbling block for atheists. Here's how he puts it in the radio interview.

... because if you pursue the socio-biological explanation of altruism to its ultimate conclusion, and you say that it's really just evolution that is responsible for this sense of right and wrong, you can't get away from what that means, That means that good and evil have no absolute significance at all. They're purely arbitrary. They're evolutionary contrivances. The idea that we have in our head about something being right or wrong is just a complete illusion. And for people who want to adopt that view you have to go all the way there and embrace that. And something about that, in people I talk to, even those who .. consider themselves to be atheists or agnostics, that really troubles them. And it should.

Now many people seem to think that C.S. Lewis and Francis Collins have a very sophisticated view of religion—one that Dawkins fails to grasp when he criticizes religion. But as far as I'm concerned, if this is the best they can do then theists deserve all the criticism they get.

Evolution has given us brains and we have learned how to use them. Over thousands of years we have developed rules of behavior designed to improve our security and well-being and promote an orderly society. Accordingly, it is "bad" to take something that doesn't belong to you and it is "good" to help your neighbor. It is "bad" to lie and it is "good" to tell the truth. In the long run, if everyone does "good" things your society will be better off. Nobody like thieves and liars. They can't be trusted.

"Good" and "bad" are not arbitrary and they are not the direct product of evolution. They have "absolute signficance"—they promote social interactions and humans can achieve much more collectively than they can as individuals. Collins is way off base here. I don't know of any atheists who are troubled by this. I can't imagine who he's talking to.

Denyse O'Leary and the Blogosphere

 
Denyse certainly got my attention when she announced on her blog that she had some nice things to say about me and some "almost-nice" things about PZ Myers [Podcast: Why I think the blogosphere beats legacy media cold, plus heartfelt regards to Larry Moran and PZ Myers]. Listen to Casey Luskin interviewing Denyse O'Leary and decide for yourselves. The relevant questions come at 12 minutes and 45 seconds into the podcast when she's asked about PZ Myers and me [Blogophile: Denyse O'Leary and the Blogosphere]. If you don't want to follow the link to a podcast where you can skip to the end then listen to the whole thing below.


Click here to get your own player.

The Purpose of Graduate Education

 
There has been considerable debate about the real purpose of a graduate education. Is it just a way of training students to become university Professors? [Job Propsects for Graduate Students]. Is it true that graduate students are just indentured labour as a recent article in Nature implied?

These are interesting questions. One of the issues that often comes up in these debates is the "pressure" to publish. Supervisors will often try to persuade their graduate students to publish papers. Is this a good thing or a bad thing?

It's a good thing, in spite of what most people believe. Here's how Ryan Gregory sets up the question ...

At the base of this discussion is the assumption that most advisors actually do encourage/pressure their students to publish -- an assumption with which I will not disagree here. What remains open is the interpretation of why this might occur. There are several possibilities:

Read his blog to see why graduate students should publish papers and why this doesn't necessarily mean that the advisor is treating them like slave labor [Why would advisors encourage students to publish?].

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[Photo Credit: Graduate students in the Dept. of Biochemistry, University of Toronto.]

Gene Genie #14

 

The 14th edition of Gene Genie has just been published on Microbiology Bytes [Gene Genie #14: Bugs and Beyond].

Top Five Dead Scientists

 
Robin Ince lists his top five scientists in the video. It's obviously intended to be a farce since he doesn't mention Charles Darwin. Some bloggers have asked for serious submissions. For example Peter Mc at The Beagle Project Blog wants to know who you would name for the other four spots [Top five dead scientists: list 'em]. So does James Randerson at the Guardian [Top five dead scientists].

So who would I choose besides Charles Darwin at #1? How about Isaac Newton (#2) and Albert Einstein (#3). They seem pretty obvious. I'm tempted to go with Ibn al-Haytham (965-1039) for the #4 position although I don't know as much about him as I should. At #5 I'll pick Thomas Hunt Morgan (1866 - 1945) the first geneticist to win a Nobel Prize and the founder of modern genetics. (And because nobody else has named him yet.)

Honorable mentions to Max Planck, Niels Bohr, Francis Crick and Louis Pasteur. Some of those mentioned by others don't even make the top 100 on my list.



[Hat Tip: Coturnix]

Six Days 'Till the Poll Closes

 
Get on over to the left-hand margin and vote for your view of evolution. The poll closes at the end of August. When it does, I'll explain the errors of your ways!

Sam Harris Gets It Right (Again)

 
Sam Harris has a letter in this week's Natrue where he takes the editors to task for their accommodationist approach to the fight between rationalism and superstition [Scientists should unite against threat from religion].

The immediate object of Harris' letter is a recent commentary praising Islam as an "intrinsically rational world view" that is "perfectly in harmony with scientific naturalism." Harris points out the fallacy of such a position then goes on to raise questions about a review of Francis Collin's book The Language of God. According to Harris, the review, entitled "Building Bridges," ...

... represents another instance of high-minded squeamishness in addressing the incompatibility of faith and reason. Nature praises Collins, a devout Christian, for engaging "with people of faith to explore how science — both in its mode of thought and its results — is consistent with their religious beliefs".

I agree with Harris that the Theistic Evolution version of Christianity promoted by Collins is not compatible with reason and science. I agree with Harris that Nature should be ashamed of itself for suggesting otherwise. This is an area where the editors of Nature should either avoid comment or, preferably, defend science.

Harris closes his letter with a nice jab.

There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference.

People Living Today Outnumber all Those Who Have Died in the Past

 
Friday's Urban Legend: DEFINITELY FALSE

This month's issue of Scientific American addresses this popular myth [Fact or Fiction?: Living People Outnumber the Dead].

The human population has swelled so much that people alive today outnumber all those who have ever lived, says a factoid whose roots stretch back to the 1970s. Some versions of this widely circulating rumor claim that 75 percent of all people ever born are currently alive. Yet, despite a quadrupling of the population in the past century, the number of people alive today is still dwarfed by the number of people who have ever lived.

The data is supplied by Carl Haub, an expect on world demographics at the Population Reference Bureau in Washington DC (USA) [How Many People Have Ever Lived on Earth?].

The myth isn't as outlandish as it seems. If you look at the chart above it's not difficult to imagine that the area under the curve from 1950 - 1998 might be close to the area under the rest of the curve. (The start point—Adam & Eve in 5,000 BC is meant as a joke.) Nevertheless, Carl Haub points out that it just doesn't make sense once you start to think about it seriously. But, and this is a serious "but", nobody really knows how many people were alive in the past.

Any such exercise can be only a highly speculative enterprise, to be undertaken with far less seriousness than most demographic inquiries. Nonetheless, it is a somewhat intriguing idea that can be approached on at least a semi-scientific basis.

And semi-scientific it must be, because there are, of course, absolutely no demographic data available for 99 percent of the span of the human stay on Earth. Still, with some speculation concerning prehistoric populations, we can at least approach a guesstimate of this elusive number.

The guesstimate begins with a decision about when to start counting. Haub picks 50,000 BC as a somewhat arbitrary beginning of the human population. As it turns out, the exact start point may not matter very much since the human population was probably small for many tens of thousands of years.

The growth in human population can only be estimated by making guesses about the average life expectancy and birth rate at different points in time. Carl Haub is about as knowledgeable in this field as anyone so we can assume that his guesstimate is as good as it gets. Remember that we are interested in how many people have ever lived and this has to include children who died young as well as adults who lived to be 40 or 50 years old.

There are estimates of the number of people alive in 1AD based on the population of the Roman Empire and China. The consensus is about 300 million (45 million in the Roman Empire). By 1650 the world's population may have been close to 500 million even when you take into account the ravages of the Black Death.

Here's the bottom line. The people alive today represent about 6% of all the people who have ever lived.

The Rings of Uranus Viewed Edge-on

 
The photograph and caption from SciencDaily says it all [Astronomers Get First Look At Uranus's Rings As They Swing Edge-on To Earth].

This series of images from NASA's Hubble Space Telescope shows how the ring system around the distant planet Uranus appears at ever more oblique (shallower) tilts as viewed from Earth - culminating in the rings being seen edge-on in three observing opportunities in 2007. The best of these events appears in the far right image taken with Hubble's Wide Field Planetary Camera 2 on August 14, 2007. (Credit: NASA, ESA, and M. Showalter (SETI Institute))

As expected, Phil Plait of Bad Astronomy has much more information and lots of spectacular photographs [Yes, yes, rings around Uranus, haha]. Where does he get them?

Do You Support Our Troops?

 
A. Whitney Brown explains why he supports the brave American troops fighting in Iraq. His talk applies to my support of brave Canadian troops fighting in Afghanistan—or at least it raises the same questions.



[Hat Tip: Canadian Cynic]

Job Prospects for Graduate Students

 

This week's issue of Nature has two short articles on the future of science in the USA. The first one refers to Indentured Labour. It talks about the fact that the number of life science researchers in the universities (tenure and tenure-track) has leveled off at about 30,000 while the number of students earning degrees in the life sciences has doubled. The pejorative reference to graduate students as indentured labour is quite unnecessary. It declares a bias and prevents rational discussion.

The second article makes a similar point [More biologists but tenure stays static] about the job prospects of Ph.D. students.

Both Nature articles are based on statistics compiled by the Federation of American Societies for Experimental Biology (FASED). The original study can be found at [Education and Employment of Biological and Medical Scientists: Data from National Surveys]. The Nature articles have stimulated considerable debate on the blogosphere, See PZ's posting and the comments [The most daunting numbers I've seen yet].

Most of the postings have failed to ask the really hard questions so that's what I'm going to do. But first, let's look at the data from the powerpoint presentation on the FASEB site.

The first graph shows the number of Ph.D. graduates in life sciences over the past 40 years. The rate was about 4,000 per year throughout most of the 1980's then jumped up to about 6,000 per year in the late 1990's. Lately there has been a further increase to about 7,000 per year. Much of the increase is due to foreign students.


The second graph shows the increase in positions for researchers with a Ph.D. in life sciences. The number of jobs has almost tripled from 1973 to 2003. Most of the increase has been in industry as a result of the expansion of biotech firms. Most of the fuss is because the number of academic jobs seems to have flattened out at about 60,000. Of these, only 30,000 are tenure or tenure-stream positions. At our university the number of positions in hospital research institutes (non-tenured) has vastly outpaced the number on the campus (tenured) so this isn't a surprise to me.


One of the questions being debated is whether we should continue to graduate far more Ph.D's than the number of academic positions that need to be filled. The answer is yes and here's why.

Assuming (incorrectly) that our primary purpose in graduate education is to train our replacements and assuming (incorrectly) that all graduates want an academic position, we should still graduate more candidates than there are positions because we will want to choose the best candidates for a position and this means that there has to be a larger supply than the demand. How large should this supply be if we were to treat graduate students as a commodity? I don't know, maybe five or ten times the number of jobs?

Now, don't get me wrong. I'm not advocating that we behave this way. I'm simply pointing out to those who do want us to adopt this point of view that there should be many more Ph.D.'s than jobs. That's something that most people don't seem to understand. They seem to think that the number of Ph.D. graduate should approximate the number of jobs available. What this would mean in practice is that the selection for tenure-stream Professors would take place mostly on admission to graduate school and whatever happens afterwards is hardly relevant (i.e., no weeding out). (Some people even think that the candidates for tenure-stream positions are chosen from graduates of their own institutions. Those people are really out of touch.)

Is the "crisis" as serious as most people think? I don't believe it is for several reasons. First, many of the foreign students will return to their native countries. This means that the graduate students who are getting Ph.D.'s in America won't all be looking for jobs in America. Second, many students want to take jobs in industry because they pay better. They won't be competing for academic positions. Third, there's a considerable lag between the expansion of student numbers and the expansions of faculty. Many universities have plans for faculty expansion in the near future. Fourth, the steady-state level of faculty positions disguises the fact that faculty hired in the 1970's expansions are now retiring. Thus, for the short term there will be more new hiring than the graphs indicate.

But behind all this debate and discussion is a more serious issue. Why do students go to graduate school? Is it only because they want to be trained for a future job? Should Professors look upon every graduate student as a job trainee and behave accordingly? I'd like to think that there are still students out there who go to graduate school for the love of science. I did.

The graduate school experience is an end all by itself and not always a means to an end. Sure, it would be nice if things work out and the student gets a nice post-doc and an academic position—if that's what they want—but there's other things to do after graduate school. I've known lots of students who went into teaching, medicine, or law for example. I've known students who choose to be full-time parents even though they did well in graduate school and enjoyed the experience.

I'm very reluctant to fall into the mindset where I view every graduate student as a trainee for a job in industry and academia and not as a young inquisitive scientist. If Professors adopt the former mindset, and some do, then the goal of graduate research is not to answer important scientific questions but to churn out enough papers in respectable journals to ensure you get a good post-doc. The fact that this goal is sometimes compatible with the ambitions of the P.I. (more papers) makes for a deadly combination.

Hugh McLachlan on Cloning Humans

 
Last week I posted an article on cloning humans. It was a reference to a piece in New Scientist by Hugh McLachlan, a Professor of ethics at Glasgow Caledonian University in Scotland (UK). McLachlan does not oppose the cloning of humans and neither do I.

Here are some other articles on the same topic [Ignore The Boys from Brazil - say Yes to human cloning], [Poor reasons for making human cloning illegal].

McLachlan sent me the following message in response to some of his critics. It addresses some of the issues that have come up in the comments on Sandwalk. He has given me permission to post it.

I think that the risks to the embryos are irrelevant to the issue of whether or not human cloning should be illegal. (Whether public money should be spent on human cloning if it is a very inefficient technique is another matter.) The potential mothers should be informed about the known risks and they must, of course, give their consent. The risk to the mothers is not a justification for making the technique illegal in my view.

Consider an analogy. Imagine that 100 people were trapped, unconscious in a building. They might, for instance, be hostages. A bomb might be primed to explode shortly. If they are not rescued fairly soon they will die. Suppose that the only way they could be rescued is if they were snatched by SAS. The snatch might kill them all. It might result in some being injured, impaired and disabled. It might even result in some living a life that was not worth living. However, there is a chance that one or more might survive to live a normal life. Should we take the chance and snatch them? If we are thinking only about the interests of those 100 people, we must do it even if the chances are remote that any will be saved.

To say that it should be illegal to make the snatch because of the risk to the hostages would be absurd. It is similarly absurd to say that, because of the risks to the embryos involved, human cloning should be illegal.

There is a risk to the soldiers. However, since people volunteer to be soldiers and might even volunteer for particular dangerous missions it is generally judged acceptable that soldiers are exposed to such risks. I can see no reason why we should not allow potential mothers to accept the risks of delivering clones if that is what they want to do.

The objection about the risks to the embryos/clones involved looks at the issue of risk and uncertainly the wrong way round. Suppose that some technique or other were devised to reduce the suffering of those people who had some particular relatively minor ailment. The question of the risk of the technique to these potential patients might be relevant particularly if we assume that to live with the ailment is still pleasant and worthwhile even if not as pleasant and worthwhile as life without the ailment. Suppose that, with the technique, the likelihood is that X% of the patients will be cured completely of the ailment, Y% will end up with a worse case of the condition and that Z% will die in the course of treatment.

In a situation such as this, it is important to know what numbers X, Y and Z stand for to try to judge whether the risk involved in worth taking. Ideally, we would tell the patients and let them decide for themselves. However, human cloning is quite different from this imagined scenario. For the people who might be born as a result of cloning - whether, in the event, they actually are born - cloning is their only chance of birth and life. In the absence of cloning, they will not be born. Hence, cloning is not a risk for them but an opportunity - their only opportunity. To make cloning illegal in their interests on the grounds that, in the course of the technique, not all implanted embryos will become healthy mature human bodies is absurd.

Fool me once .... shame on you ...

 
See Can You Hear the Drums Beating?, Bush Flubs the Message and A Prelude to War.

There's an old saying in Tennessee — I know it's in Texas, probably in Tennessee — that says, fool me once, shame on — shame on you. Fool me — you can't get fooled again.
                                                   George W. Bush 2002

[Hat Tip: John Lynch]

Rationalism vs. Superstition: The Enemies of Reason (Part 2)

 
Here's part 2 of Enemies of Reason, Richard Dawkins' attack on superstition. This episode focuses on medical quacks and kooks. It's very entertaining. You'll certainly like the segment on how to increase the number of strands in your DNA!

Read Orac's review at Respectful Insolence. The point to remember is that the battle is between rationalism and superstition and the atheism vs. religion controversy is only a subset of the bigger battle. And evolution vs. creationism is an even smaller subset. You are missing the point when you ask people like Richard Dawkins to align themselves with moderate theists in order to combat the extreme versions of creationism.

Justice, Texas Style

 
Reuters is reporting that the State of Texas has just executed it's 400th convicted criminal since 1982 [Texas executes 400th person since 1982].

The Governor's office issued a statement in response to criticism of the large number of executions in Texas.

Texans long ago decided that the death penalty is a just and appropriate punishment for the most horrible crimes committed against our citizens.

I suspect this is true. Texans probably do support the death penalty. That's not the point. The point is why are there are so many more executions in Texas compared to other states with the death penalty and why is the USA one of the few "civilized" nations to permit executions of their own citizens?

I don't know the answers to these questions. Does anyone else?

Nobel Laureate: Earl W. Sutherland, Jr.

 

The Nobel Prize in Physiology or Medicine 1971.

"for his discoveries concerning the mechanisms of the action of hormones"

Earl W. Sutherland, Jr. (1915-1974) received the Nobel Prize in Physiology or Medicine for his work on the mechanism of action of hormones, particularly epinephrine. Sutherland was very much influenced by Carl Cori [Nobel Laureates: Carl Ferdinand Cori and Gerty Theresa Cori] who worked on the pathways of glycogen breakdown and glucose synthesis in mammalian liver cells. Sutherland is responsible for discovering how the hormone epinephrine regulates glycogen synthesis [Regulating Glycogen Metabolism]. Along the way, Sutherland discovered the second messenger cyclic AMP (cAMP), which was Monday's Molecule #39.

The presentation speech was delivered by Peter Reichard of the Karolinska Medico-Chirurgical Institute. Note the opening line that refers to Monod's famous quote"What is true of E. coli is also true of the elephant." It was 1971 and Chance and Necessity had just come out. For years scientists had thought that the action of hormones demonstrated that so-called "higher" organisms used higher-level processes to regulate metabolism. Hormones needed whole tissues and organs to show an effect. What Sutherland proved was that hormones work at the cellular and molecular level just like the molecules that regulated activity in bacteria.

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen,

What applies to bacteria also applies to elephants. This free quotation after the French Nobel prize winner, Jacques Monod, illustrates with some exaggeration one important principle of biology: that of the identity of the fundamental life processes.

Yet one need not be a Nobel prize winner to know the difference between bacteria and an elephant. The latter is not only much larger. The decisive difference lies in the fact that bacteria are unicellular organisms and that all the functions of life are contained in a single cell. In higher organisms on the other hand, there occurs a division of labor between different types of highly specialized cells. Nevertheless, the elephant must function as an integrated unity. The cells in the different organs must be coordinated in such a way that they rapidly adapt to the changing requirements of the environment.

The hormones form part of such a coordinating system. Among other things, the difference between a bacterium and an elephant lies in the fact that the latter - as well as all of us here - for the sustainment of his life is completely dependent of the proper function of hormones, while bacteria can do without them.

What then is the function of hormones? Ever since the first hormone was discovered about 70 years ago this has been a central theme of research for many scientists. This question is also of considerable medical importance. Many diseases are hormone diseases, amongst them diabetes. In spite of this the mechanism of hormone action remained a complete mystery until recently. The answer did not come until Earl Sutherland started his investigations on the function of the hormone epinephrine.

This hormone is produced in the adrenal glands and is transported to different organs of the body by the blood. It is formed in increased amounts during stress and adapts the individual to new situations. One of its important functions lies in the liberation of glucose inside the cells for the production of energy. Epinephrine serves as a chemical signal, as a messenger, which is sent out from the adrenals to activate different organs essential for the defense of the individual.

Sutherland investigated the effect of epinephrine on the formation of glucose in liver and muscle cells. He discovered a new chemical substance which serves as an intermediate during the function of the hormone. This substance is called cyclic AMP. It transmits the signal from epinephrine to the machinery of the cell, and Sutherland therefore called it a "second messenger". Furthermore, Sutherland made the important discovery that cyclic AMP is formed in the cell membrane. This means that epinephrine never enters the cell. We may visualize the hormone as a messenger which arrives at the door of the house and there rings the bell. The messenger is not allowed to enter the house. Instead the message is given to a servant, cyclic AMP, which then carries it to the interior of the house.

Sutherland suggested already around 1960 that cyclic AMP participates as a second messenger in many hormone mediated reactions, and that its effect thus is not limited to the action of epinephrine. First this generalization was not willingly accepted by the scientific community, since it was difficult to visualize how a single chemical substance could give rise to all the diverse effects mediated by various hormones. By now Sutherland and many other scientists have provided convincing evidence, however, that many hormones exert their effects by giving rise to the formation of cyclic AMP in the cell membrane. Sutherland had discovered a new biological principle, a general mechanism for the action of many hormones.

How can one then explain the specificity of different hormones? A good part of the explanation lies in the fact that different cells in their membranes possess specific receptors for various hormones. The different messengers thus must find their way to the right door in order to deliver their messages.

Cyclic AMP was discovered in connection with investigations concerning the function of hormones. It came therefore as a big surprise when Sutherland in 1965 reported that cyclic AMP also occurred in bacteria which apparently had no use for hormones. It was soon found that cyclic AMP was produced by other unicellular organisms, too. In all these cases cyclic AMP was shown to have important regulatory functions which aid the cells in their adaptation to the environment. Maybe we can look upon cyclic AMP as the first primitive hormone, regulating the behaviour of unicellular organisms. We then may look upon the true hormones of higher organisms as components of an overriding principle which was added during the course of evolution. Thus the difference between uni- and multicellular organisms does not, after all, appear to be so great, and with respect to cyclic AMP we can turn around Monod's dictum and say that what applies to elephants also applies to bacteria.

Dr. Sutherland,

Hormones were known in biology and medicine for a long time. The mechanism for hormone action remained a mystery, however, until you discovered cyclic AMP and its function as a second messenger. In recent years it has become apparent that cyclic AMP also serves as an important regulatory signal in microorganisms, and that its action thus is not limited to the function of hormones. When you discovered cyclic AMP you discovered one of the fundamental principles involved in the regulation of essentially all life processes. For this you have been awarded this year's Nobel prize in physiology or medicine. On behalf of the Karolinska Institute I wish to convey to you our warmest congratulations, and I now ask you to receive the prize from the hands of his Majesty the King.

Google Sky

 
If you haven't updated your copy of Google Earth then you should do so right now. A new feature called "Sky" has been added [Celestial add-on points Google Earth at the stars.

The image on the right shows us what the sky will look like tomorrow night when Mercury, Saturn, and Venus are close together in Leo. Saturn is going to be very close to Regulus. Unfortunately, the program won't tell me if I can see this from where I live. I don't know if this feature is missing or if I just can't find it.

You can click on the galaxy icons to get more information and you can click on each star to find out it's name, distance, spectral type etc.

Pretty cool. I wonder if Phil Plait of Bad Astronomy will comment? I'd like to know what he thinks of the program.

Identity of the Product of Mendel's Green Cotyledon Gene

 
This posting has been replaced by Identity of the Product of Mendel's Green Cotyledon Gene (Update).


Another of Mendel's seven genes has been identified. This one is described in his 1865 paper Experiments in Plant Hybridization [MendelWeb] as character number 2.

2. To the difference in the color of the seed albumen (endosperm). The albumen of the ripe seeds is either pale yellow, bright yellow and orange colored, or it possesses a more or less intense green tint. This difference of color is easily seen in the seeds as their coats are transparent.

Mendel's reference to the color of albumin, or endosperm, is inaccurate. He was actually observing the color of the cotyledons—the "seed leaves" that surround the embryo in the pea seed. These tiny leaves are covered by a seed coat that is partially transparent.

In wild-type peas the seeds turn yellow as they mature (i) but certain mutants exhibit a "stay-green" phenotype where the peas retain their green color (I). The figure shows seeds from a plant with the II genotype (top) and the ii genotype (bottom). The seed coat has been removed from the lower pair of each group of four peas.

In a paper just published in the Proceedings of the National Academy of Sciences (USA) a group in Japan has identified the "stay green" gene that Mendel worked with (Sato et al., 2007). It turns out that the gene, called SGR (stay-green), encodes an enzyme that is localized to chloroplasts and plays a role in the degradation of chlorophyll during senescence and maturation of seeds. When the enzyme is defective chlorophyll isn't broken down and the tissue stays green.

This brings to three the number of Mendel's genes that have a known function. The wrinkled pea phenotype is caused by a defect in the gene for starch branching enzyme (Bhattacharya et al., 1990) [Biochemist Gregor Mendel Studied Starch Synthesis]. The tall/short phenotypes are caused by defects in the gene for gibberellin 3β-hydroxylase (Martin et al., 1997). Gibberellins are plant growth hormones.

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[Photo Credit: The photograph of mutant and wild-type pea seeds is taken from Figure 1 of Sato et al. (2007)]

Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C., and Martin, C. (1990) The wrinkled-seed character of a pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60:115-122.

Martin D.N., Proebsting W.M., Hedden P. (1997) Mendel's dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins. Proc. Natl. Acad. Sci. (USA) 94:8907–8911.

Sato Y., Morita R., Nishimura M., Yamaguchi H., and Kusaba M. (2007) Mendel’s green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway. Proc. Natl. Acad. Sci. (USA) (early publication, [August 20, 2007]).

Monday's Molecule #39

 
Today's molecule is complex but it has a very simple common name. The common name is not sufficient—you must supply the formal IUPAC name to win the prize. There's a direct connection between this Monday's Molecule and Wednesday's Nobel Laureate.

The reward (free lunch) goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There's only one (Marc) ineligible candidate for this Wednesday's reward since many recent winners haven't collected their prize. The prize is a free lunch at the Faculty Club.

In preparation for the beginning of classes in three weeks I'm going to start requesting email responses. 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 the Nobel Laureate. All responses will be posted tomorrow along with the time that their message was received on my server. This way I may select multiple winners if several people get it right.

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

Like a Broken Record ...

 
Matt Nisbet is at it again. His particular spin frame on the rationalism vs. superstition debate is that the rationalists are making too much noise. According to Nisbet, we atheists are hurting the "cause" (what cause?) by speaking out loudly against superstition in the form of religion. Apparently it would be better to tone down the rhetoric in order to avoid offending those who believe in superstition. This is the strategy that has been followed by Americans for the last 100 years or so. No matter how stupid the religious extremists are, whether from the pulpit or on talk radio, we mustn't say that they are stupid because that would hurt their feelings. Or rather, it would hurt the feelings of the moderate believers who tolerate and support the religious extremists.

Of course Matt doesn't recognize that this is just his personal opinion. Oh no, that wouldn't be right, would it? If you are going to attack Dawkins, Hitchins, and Harris then you'd better frame it make it sound like an attack based on solid scientific reasoning. Here's what Matt Nisbet says in his latest posting [Why the New Atheist Noise Machine Fails].

Everything we know from social science research on attitude formation and beliefs predicts that the communication strategy of the New Atheist noise machine will only further alienate moderately religious Americans, the very same publics who might otherwise agree with secularists on many social issues.

Everything we know from history predicts that social change is often stimulated and led by vocal "extremists" who dare to speak out even if it offends those who prefer the status quo. This was true of the women's movement, the civil rights movement, and the gay rights movement. In those cases it was the moderate male chauvinists, the moderate racists, and the moderate homophobes who were initially offended. They didn't like being told that their long-held beliefs were wrong. In all those cases I suspect there were Matt Nisbets who tried to silence the outspoken leaders because they were offending the average moderate citizen.

If social science "research" says that the cause of outspoken individuals always fails then that says a lot more about the so-called "research" of social scientists than it does about reality.

The Dawkins/Hitchens PR campaign provides emotional sustenance and talking points for many atheists, but when it comes to selling the public on either non-belief or science, the campaign is likely to boomerang in disastrous ways.

The experiment is under way. Up until 2005, atheism was pretty much hidden under a bushel and religious superstition was rarely confronted in public. The result is that America is the most religious country in the industrialized world and evolution isn't taught in schools. Let's see if there's any change in the status quo over the next decade as the Dawkins/Hitchens framing PR campaign continues. According the Nisbet, the country will become even more religious because of the backlash. I'm betting that religion will become less important to Americans when they realize that there are other options.

There are times when I wonder which side Nisbet is on. It sounds to me like he's perfectly happy with the way things have been for the past several decades.

Don't Mess with Canadians

 
I recently returned from spending a week in a foreign country. I did not behave like the Canadian in this video although there were times ...



[Hat Tip: Canadian Cynic]

The Cause of Variation in a Population

John Dennehy of The Evilutionary Biologist has posted a wonderful article on This Week's Citation Classic. The classics are two back-to-back papers on genetic variation in fruit flies (Hubby and Lewontin (1966), Lewontin and Hubby (1966)). That's Lewontin on the left.

Please get on over to The Evilutionary Biologist and read what John has to say. These were very important and groundbreaking papers when they came out and everyone needs to know why.

Here's some background.

In the olden days there were two competing theories to explain variation (heterozygosity) in a population. The classical theory said that mutations are constantly being removed from the population by positive natural selection or purifying selection. Variation is a transient phenomenon that would disappear entirely if it weren’t for new mutations that arise at a significant rate.

The balance theory maintains that variation in a population is often due to balancing selection. The best known example of balancing selection is the allele for sickle cell disease. In the heterozygous state it confers resistance to malaria but in the homozygous state it is often lethal. Both the sickle cell allele and the wild type allele are maintained in the human population by balancing selection.

Hubby and Lewontin (1966) discovered that there was a huge amount of genetic variation in fruit flies. Their data suggested that 50% of all loci had multiple alleles. This is difficult to reconcile with the balance theory and it was also a big surprise to those who supported the classic theory. It seemed unlikely that at any given point in the evolutionary history of a species that so many genes could be undergoing selection. Further work confirmed that other species contained a huge amount of variation.

The solution to this surprising observation was the recognition that most of the alleles were neutral. The variation is explained by fact that fixation by random genetic drift is much slower than fixation by natural selection. Thus, while the variation is transient in the sense that it is a snapshot of an ongoing process, the process is not selection but drift.

The results of Hubby and Lewontin (1966) led directly to Neutral Theory.

The neutral theory also asserts that most intraspecific variability at the molecular level (including DNA and protein polymorphisms) is selectively neutral, and is maintained in the species by the balance between mutational input and random extinction. In other words, the neutral theory regards protein and DNA polymorphisms as a transient phase of molecular evolution and rejects the notion that the majority of such polymorphisms are adaptive and actively maintained in the species by some form of balancing selection.
                M. Kimura

This explanation is also known as the Neoclassical Theory. Balancing selection is now thought to play only a minor and insignificant role in the cause of variation in a population.

... the neoclassical theory is not refuted by occasional observations of overdominance for fitness, because the theory does not deny that cases exist but only that they are common and explain a significant proportion of natural variation. So it is no use trotting out that tired old Bucephalus, sickle-cell anemia, as a proof that single-locus heterosis can exist. Anyone who has taught genetics for a number of years is tired of sickle-cell anemia and embarrassed by the fact that it is the only authenticated case of overdominace available. “If balancing selection is so common," the neoclassicists say, "why do you always end up talking about sickle-cell anemia?"
                R. Lewontin

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[Photo credit: The photograph of Richard Lewontin is from (Photographs of Participants in the Molecular Evolution Workshop)]

Where's the Evidence for Intelligent Design Creationism?

 
Denyse O'Leary has friend named David Warren. Warren writes articles for newspapers and he and Denyse are friends because they both worship at the church of anti-Darwinism. Over on Post-Darwinist Denyse brags about the latest article written by her friend [ Another Toronto journalist takes swat at Darwinists (or Darwinoids)]. Note the title of the blog article. It's more of the same old, same old, "Darwinist" baiting. Turns out that 99.9% of the IDiot movement is about attacking evolution (their version) and 0.1% is about presenting evidence for intelligent design. (And even that tiny amount of evidence has been refuted or shown to be irrelevant.)

So what about David Warren? Is he any different—don't hold your breath. Here's the article that he wrote for some Canadian newspapers [Panspermianism]. The main point of the article is supposed to be that panspermia is ruled out because scientists have shown that DNA won't survive in outer space (*yawn*). But the real purpose of the article is to whine about the evil atheist materialists and how they are suppressing the IDiots.

Much of the “star chamber” atmosphere, that has accompanied the public invigilation of microbiologists such as Michael J. Behe, and other very qualified scientists working on questions of design in organisms and natural systems, can only be explained in this way. The establishment wants such research to be stopped, because it challenges the received religious order, of atheist materialism. Any attempt, or suspected attempt, to acknowledge God in scientific proceedings, must be exposed and punished to the limit of the law; or by other ruthless means where the law does not suffice.

There's more, but you get the idea. The IDiot movement is scientifically bankrupt. They have no scientific evidence to back them up so the only thing they can do is lash out at their opponents. When is the last time you've seen an article from an IDiot that explains any evidence for the existence of an Intelligent Designer? That's right, hardly ever. Is there a reason why they don't support their case with real data? Yep, you bet there is. And that's exactly why they have to stoop to attacking "Darwinism" at every chance they get. They don't have any other option. Pathetic, isn't it?

[Image credit: The photograph is from one of my students, Zarna. That's her in the picture. She took it last December in India (Oh My God)]

Should Cloning Humans Be Legal?

 
In the July 21 issue of New Scientist, Hugh McLachlan thinks that we should legalize cloning of humans [Let's legalise cloning].

But why are we so against the idea of cloned human babies? As a bioethicist specialising in reproductive issues, I believe it has more to do with an irrational fear of cloning than any logical reason. All the arguments in favour of a ban describe risks that we accept quite easily and naturally in other areas of reproduction.

One argument against human cloning is the idea that it is morally wrong or undesirable to create replicas of people. But although a clone has the same gene set as the adult from which it was cloned, environmental factors will ensure that the resulting individual is not an identical copy, either psychologically or physically. What's more, we accept genetically identical people in the form of twins. If anything, clones would be less alike than twins because they would be different ages and be brought up in different contexts. Objecting to cloning on these grounds makes no sense.

I agree with McLachlan. Aside from the safety issue, there doesn't seem to be any good reason to forbid the cloning of humans.

This is a topic that's frequently discussed in "ethics" classes. I've never really understood what "ethics" actually means—but I'm working on it. The cloning of humans isn't an ethical issue for me personally because there isn't a conflict between two versions of what I think I ought to do. However, maybe it's an ethical issue for society as a whole because there are some people who think that it is unethical to clone people. Is that right? What's unethical about it?

Do we define "ethical" issues in terms of conflict between different groups? If so, is there a way of distinguishing between issues where the two sides are almost equally represented and those where one side has an overwhelming majority? For example, is the cloning of humans still an ethical issue in a society where 99% of the population is opposed? Does it cease to be an ethical issue if 99% are persuaded to accept human cloning?

Amazing Grace

 
Last night we saw a screening of the film Amazing Grace in a small cozy theater. At the end of the movie there was a fascinating talk by one of the producers Ken Wales. We learned a lot about how the film was made.

The film follows the efforts of William Wilberforce to abolish slavery in the British Empire at the end of the eighteenth century. Wilberforce and his close friend William Pitt the Younger, who became Prime Minister in 1783, finally succeeded in eliminating slavery by 1807.

There's mention of the fact that Wilberforce was a Christian and some of his allies were preachers but this isn't an important theme. The movie makes it clear that Pitt, who was a prime mover in social change, did not share Wilberforce's beliefs. During the discussion afterward it was clear that the religious motivation was important to some people.

The title of the movie comes from the song Amazing Grace whose words were composed by John Newton, an ex-slave trader who converted to Christianity. Newton, who has a significant part in the movie, influenced Wilberforce and served as his mentor.

One interesting scene depicts a debate in the House of Commons in 1778. The newly elected Wilberforce is advocating the withdrawal of British forces from America, thus abandoning the attempt to put down the rebellion. Wilberforce is attacked and challenged to distinguish between appeasement and surrender. "It's merely a question of timing," he says.

This scene, and many others, reveal that Great Britain was a functioning democracy at the time of the American Revolution. It contrasts markedly with the general impression of Americans who tend to think that this sort of representative democracy was invented by them in 1776.

William Wilberforce's third son was Samuel Wilberforce ("Soapy Sam") who became the Bishop of Oxford and debated evolution with Thomas Huxley in 1860.

Tangled Bank #86

 

The 86th issue of the Tangled Bank has been posted on Fish Feet [Tangled Bank #86].

Peter Lawrence on What's Wrong with Science

 
Peter Lawrence is a Professor at the University of Cambridge in Cambridge, UK. He has worked on various aspects of fruit fly development for almost 40 years. Readers may know him as one of the authors of Wolpert's Principles of Development or as the author of The Making of a Fly.

Peter is a very smart guy. He thinks a lot about the "big picture" and not just the minutiae of day-to-day work in a competitive environment. That's why his article in this month's issue of Current Biology is worth reading. Lawrence writes about what's wrong with modern science [The Mismeasure of Science].

For most scientists, there won't be any revelations in the article but it's put together well and covers all the bases. The main point is that today's scientists have to worry far too much about "productivity" in order to get funded. The system is geared towards artificial measurements of research success that may, or may not, reward creativity and innovation.

Modern science, particularly biomedicine, is being damaged by attempts to measure the quantity and quality of research. Scientists are ranked according to these measures, a ranking that impacts on funding of grants, competition for posts and promotion. The measures seemed, at first rather harmless, but, like cuckoos in a nest, they have grown into monsters that threaten science itself. Already, they have produced an “audit society” [2] in which scientists aim, and indeed are forced, to put meeting the measures above trying to understand nature and disease.

The journals are evaluated according to impact factors, and scientists and departments assessed according to the impact factors of the journals they publish in. Consequently, over the last twenty years a scientist's primary aim has been downgraded from doing science to producing papers and contriving to get them into the “best” journals they can [3]. Now there is a new trend: the idea is to rank scientists by the numbers of citations their papers receive. Consequently, I predict that citation-fishing and citation-bartering will become major pursuits.

You need to read the full article to get all the details.

So, what can we do about it? It's an old complaint, one that's been openly discussed even since I first met Peter Lawrence back in the mid-1970's. If a bunch of (relatively) smart scientists can't figure out how to fix the problem then maybe it's unfixable.

Here's where I think Lawrence drops the ball. He proposes the same tired old "remedies" that we've never adopted in the past in spite of the fact that we all pay lip service to their benefits. He wants us all to pay attention to "quality" and "originality" over quantity. He wants us to be more careful about putting authors names on a paper. He wants a code of ethics for scientists. He wants to reform the peer review process in the leading journals. None of this is going to happen as long as money is tight and the granting agencies have to come up with defensible policies for turning down 75% of grant applications.

The short term solution is to put more money into the grant system and to stop hiring more scientists. The long term solution is to look for better ways of funding. I like the idea of giving large block grants to departments and letting the researchers divide it up as they see fit. This would have worked well in any department I've been in but I hear horror stories about other departments.

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[Photo Credit: The photograph of Peter Lawrence is from his website at the University of Cambridge (Peter A. Lawrence]

Lawrence, P.A. (2007) The mismeasurement of science. Current Biology 17:R583-R585.

Half-Truths in Sicko?

 
Jim Giles reviewed Michael Moore's Sicko in the July 14th issue of New Scientist [Review: Sicko, directed by Michael Moore]. Like many reviews, this one conceded that Moore has a point about the shape of health care in the USA but was reluctant to admit that other countries are doing better. One paragraph mentioned "half-truths."

For the most part, Moore makes his case by absenting himself from the screen and allowing those who have been let down by the system to do the talking. Then he travels to the UK and France and finds that what conservatives in the US damn as "socialised medicine" actually works well. He does the same in Cuba, ferrying ill Americans to the island where they receive excellent healthcare at almost no cost. The result is a moving, funny and shocking film. It is a powerful call for change, despite its half-truths.

In last week's issue of New Scientist, a letter writer challenged Giles to produce his "half-truths," pointing out that the Sicko website documents every claim in the movie.

Here's how Jim Giles responded ...

The most obvious half-truths were the slanted depictions of the healthcare systems in the UK, France, and Cuba. The British NHS can be great, but waiting lists are often long and access to certain drugs can depend on where a patient lives. France's system is indeed highly rated, but Moore did not mention the very high taxes there. Cuba's public health is far above what would be expected for a country with limited resources and suffering the consequences of the US trade embargo, but it also restricts access to certain drugs and technologies.

Some of these sound very much like half-truths to me. Yes, waiting lists for non-lifethreatening procedures are often longer in countries with socialized medicine. That is, they are longer than the wait for similar procedures in a fully private system where people can afford to pay for it. On the other hand, the waiting time in the UK is a lot shorter than it is for Americans who can't afford decent health insurance, isn't it?

Access to certain drugs is restricted in all socialized medicine systems. For example, the system won't pay for drugs that don't work and haven't been approved. This is bad news for quacks who generally do much better under a private system. Socialized medicine often won't pay for expensive drugs if a cheaper alternative is available. Is this what Giles meant?

It's true that taxes are higher in countries that provide universal access to medical treatments. This isn't a half-truth in Sicko. As I recall, it's one of the main points. The US system is more expensive in spite of the fact that it's run by the private sector.

Gene Genie #13

 




Gene Genie #13 has been posted on The Genetic Geneologist [Gene Genie #13: Into the Future].

The Hominid Bush

 
Brian Switek of Laelaps has posted a wonderful essay on Homo sapiens: The Evolution of What We Think About Who We Are. Read it.

In a just world, the IDiots like Jonathan Wells would read what Brian, and others, have to say and stop spreading lies about what scientists think.

[Photo Credit: The photograph of Hamlet is from The Young Shakespeare Workshop]

Jim Watson on the Discovery of the Double Helix

 
THEME

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Deoxyribonucleic acid (DNA)
This is a nice addition to my earlier postings on the story of DNA [The Story of DNA (Part 1)][The Story of DNA (Part 2)]. This story (below) is straight from the horse's mouth.



[Hat Tip:Shalini].

University of Toronto Professor in Space

 
That's astronaut Dave Williams on the right. He's a University of Toronto adjunct professor of surgery. According the the University of Toronto press release,Williams was a Professor here in emergency medicine until he was selected for the astronaut training program in 1992 [U of T professor to walk in space].

Chautauqua Institution

 
Today we're off to the Chautauqua Institution for an entire week of learning and fun. I'm really looking forward to hearing Judy Collins on Tuesday.

This week's program is Music: Heart, Soul and Dollar. Last year it was Global Climate Change with Al Gore.

Next year we'll be attending the week on Darwin and Linnaeus: Their Impact on Our View of the Natural World. In 2009 it's a full week on Darwin again as we celebrate the 150th anniversary of something important. I'm hoping to offer courses on evolution next year and in 2009 so book now. :-)

Chautauqua is one of my favorite places in the USA. If you've never been there, you are missing some of the best that America has to offer. See the Wikipedia entry [Chautauqua Institution] for a brief description.

This is a great opportunity to mingle with people of various faiths and to attend discussions and debates about the intersection between faith and society. But it's not all about religion—there's a significant percentage of the guests who are non-religious and we don't have to hide it.

Misanthropic Principle

 
In the June 30th issue of New Scientist Paul Davies discussed the anthropic principle [The flexi-laws of physics]. He says,

If the universe came with any old rag-bag of laws, life would almost certainly be ruled out. Indeed, changing the existing laws by even a scintilla could have lethal consequences. For example, if protons were 0.1 per cent heavier than neutrons, rather than the other way about, all the protons coughed out of the big bang would soon have decayed into neutrons. Without protons and their crucial electric charge, atoms could not exist and chemistry would be impossible.

Physicists and cosmologists know many such examples of uncanny bio-friendly "coincidences" and fortuitous fine-tuned properties in the laws of physics. Like Baby Bear's porridge in the story of Goldilocks, our universe seems "just right" for life. It looks, to use astronomer Fred Hoyle's dramatic description, as if "a super-intellect has been monkeying with physics". So what is going on?

As far as we know, life exists on one small planet orbiting an insignificant star in an unremarkable galaxy off in one small corner of the known universe. This reminds me of a famous Mark Twain quotation [Mark Twain and the Eiffel Tower].

I really like the letter from Nathaniel Hellerstein that appeared in the July 21st issue of New Scientist.

If Paul Davies says that the universe is bio-friendly, then I say he hasn't taken a good look at it (30 June, p 30). The universe is bio-tolerant, maybe, or better yet bio-indifferent. Looking at the night sky, I do not see a cosmos optimised for producing life. It appears to be optimised for producing vacuum.

Even if the universe somehow "needs" life, it evidently doesn't need very much of it. Perhaps, from the cosmic point of view, life is a necessary evil, to be tolerated and limited.

I call this the misanthropic principle - it certainly fits the facts better than the anthropic principle does.

Cody on the Sandwalk

 


Here's a picture of Cody from 90% True on the Sandwalk.

Ethidium Bromide Is a Dangerous Chemical

 
Friday's Urban Legend: PROBABLY FALSE

Monday's Molecule #35 from last month was ethidium. The salt, ethidium bromide, is used as a dye to stain DNA [Ethidium Bromide Binds to DNA].

Most of us have heard that ethidium is a potent mutagen so you need to be very careful when using it in the lab. Wear gloves at all times and dispose of any excess ethidium solutions in the proper containers.

According to Rosie Redfield, a microbiologist at the University of British Columbia (Canada), this may have been an overreaction to the presumed dangers of ethidium bromide [Heresy about Ethidium Bromide].

THEME

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Deoxyrobonucleic Acid (DNA)Apparently ethidium is regularly used as a drug to treat African Sleeping Sickness and it shows no significant ill effects when used at doses that are 1000 times what we use in a typical laboratory.