The Terror of Risk

It seems that the media is like the creepy Nazi from The Marathon Man who sorrowfully remarks that in the previous days torture they had killed the nerve in the tooth that he was using to cause the Dustin Hoffman character pain. He then continues that they would have to drill into a healthy tooth to expose the nerve so they could continue the torture.

What I mean is that the media is constantly bringing some low risk, next to impossible event or complication and hitting us with it so that we will a) pay attention so that we can avoid the horrible fate and b) advocate the removal of all risk of this ever happening.

Now there are some campaigns that make a lot of sense. I can remember when pretty much everyone drove around in cars without wearing seatbelts while smoking. The causality and probability of both seatbelts and smoking were pretty much well established. On the other hand the fear of terrorists, contaminants in our drinking water and food is pretty much a fabrication created by exposing the incredibly improbable as possibly happening to you.

The latest is toxic epidermal necrolysis and its association with fairly common medications. What they do not tell you is that the necrolysis only happens once in a trillion prescriptions. No, fear sells almost as good a sex. In this case there is an incredibly small risk when you take certain medications that your skin will fall off in a horribly debilitating and quite often fatal drug reaction (LINK TO STORY) . There is no doubt that the people who suffer this reaction deserve our support and sympathy but they should not be used as a fear tactic to remove perfectly good medications from circulation.

This is in fact the reason why so many drugs fail in trials. There are many drugs that have been tested and have worked well for common conditions. The problem is that one in a thousand or one in five hundred patients will have an adverse reaction so the drug is withdrawn. We need our medical societies to step forward and set or recommend proper regulations for drugs so that as long as adverse reactions fall below a certain threshold (I'd say one in a thousand would be OK as long as I am not the one) the pharmaceutical manufacturers would be protected.

I don't know that pretty soon we will be chewing on willow branches and rubbing eels on our warts if we don't start accepting a certain level of risk.

LINK TO WIKIPEDIA PAGE
.

Trust the French: Natural Recycling

Found on the internet ... it made me smile. I like the paradox of using the highest level of animation to produce a minimalist video with no real dialogue and simple plotlines. This reminded me of the Skrat clips from the Ice Age videos (which also made me smile) and the amazing introduction to Wall-E (which left me stunned with its brilliance).

The editors at Boing Boing make the excellent point that although Miniscule video clips are spread all over the internet the French animators are trying to make a living at this and we should feel motivated to purchase their products.

OK, Now this Guy wins the Crystal Growing Competition

I am not a big fan of post-modernist art. I just don't get performance art and don't like dissonance and abstraction.

This I get.

This guy turned an entire apartment into a crystal growing experiment and called it "Seizure". A number of students at the end of the crystal growing competition looked at the bottom of their beakers and commented on the thick pad of well formed crystals that covered the bottom. Now imagene a whole apartment covered with those crystals.

I would have some concerns about exposure to the crystalline dust by going into the apartment and there is such a thing as copper poisoning but on a cool scale this is way cool.

LINK TO ARTIST WEB SITE

New Brunswick in the News: Tungsten

The CBC is reporting that a company in New Brunswick has found a mineable ore body that it proposes to work for tungsten. It would appear that the most important user for the product is the nation of China. In fact the company homepage has a Chinese language link about the project. I knew about zinc and copper (and in fact antimony but we don't mine it anymore) but this is the first that I had heard about tungsten in New Brunswick.

LINK to GeoDex

Tungsten has a number of uses that relate to its physical and chemical properties of high density, hardness and relative inertness. It seems to be an important component of speciality steels where performance at high temperatures is important. There is an alloy called high speed steel that can be up to 18% tungsten. Of course, the feasibility of the mine is related to the demand for the metal and the cost of mining in New Brunswick.

Once again we will need to carry out the dreadful algebra to determine if the upheaval of our environment (and probably public financial support) will equal 250 resource based jobs. just look at the GeoDex webpage picture of the mine sight and it just looks like New Brunswick. Of course you could argue that NB has lots of scrub forest and could easily live with a couple hundred acres less if it meant real jobs. I am glad however that a full environmental impact statement is going to be done. I would also like to know if this is simply an ore extraction or if there will be some processing of the ore before it leaves Canada.

Environmental Chemistry Experiment in Fredericton

This is the basis for an ongoing environmental nightmare in Fredericton.

First you spill some chemicals (LINK to story): namely 2,700 litres of chromium trioxide spilled by Custom Machine & Hardchrome.

Second you MAIL the following notice to the affected people (LINK to announcement): "The Department of Health continues to advise about a dozen homeowners and several businesses in the Evergreen Park area outside Fredericton not to consume their well water, or use it for cooking, bathing or any other use which would bring it into contact with their body."

Third you ignore the affected people so that an older couple ends up drinking the rainwater from their roof downspout. (LINK to story).

This is really as bad as it gets environmentally speaking. This is a citation from the Wikipedia page on CrO3:

"Chromium trioxide is highly toxic, corrosive, and carcinogenic. Chromium trioxide may cause cancer and/or heritable genetic damage. It is explosive when mixed with combustible material. It is toxic in contact with skin and if swallowed and very toxic by inhalation. CrO3 causes severe burns and may cause sensitisation by inhalation and skin contact. It is also toxic: danger of serious damage to health by prolonged exposure through inhalation. There is a possible risk of impaired fertility. CrO3 is very toxic to aquatic organisms may cause long-term adverse effects in the aquatic environment."

This is the stuff that made Erin Brokovitch famous. I just hope that Custom Machine & Hardchrome has very very good insurance and that this won't just be a case where the company just folds up and the province is left with the clean-up. I do however wish that someone would offer the old couple a cup of cold water in Jesus' name.

X-rays in your life

I love this paper on X-rays generated from unrolling Scotch tape in a vacuum. They even proved it by using the X-rays to take a picture of a researchers finger. To do that the researcher would have to have his hand in a vacuum chamber long enough to expose the film. That is loving your research. This is the kind of work I would love to be involved in. Absolute genius.

LINK to Article

National Chemistry Week Crystal Growing

It is National Chemistry Week (LINK) and the highpoint of the week will be Mole Day (October 23 ... 10.23 ... you know .... Avogadro's Number ... 6.02 x 10(23) ... man, it kills the mood when you have to explain everything).

So, in the first year chemistry class we tried growing crystals of Potassium Aluminum Sulphate ...


And Copper (II) sulphate.

All in all the crystals were very nice. The class set of crystals can be seen by following the link below.

2008-10-21(CH1013XL)

ABU Riverkeepers

So, the ABU Biology Society and their faculty sponsor Penny Humby got us all up on a rainy Saturday morning to drag other people's garbage out of a nameless brook we had never really noticed before. This professor took his camera and whenever he took a photo the students would all look sad and feign intense interest in gum wrappers.

From 2008-09-27(BI3513Riverkeepr)

So I passed the camera off to a student and suddenly the other students were posing like models for the Eatons catalogue (go figure).

From 2008-09-27(BI3513Riverkeepr)

So they took my camera and wandered off to play Riverkeeper in their own 'hood and they even formed a gang called the Keypurz .. here they are with their peeps flashing their gang signs. ]

From 2008-09-27(BI3513Riverkeepr)

Some people took Riverkeeping to a whole new level of personal participation.

From 2008-09-27(BI3513Riverkeepr)

Finally at the end of a long wet morning the students met a hillbilly and his pet snake.

From 2008-09-27(BI3513Riverkeepr)

This is a slideshow of the rest of the photos:

Thanks to all the students that participated and for the Biology Society for getting us together. And thanks to Somer for taking the photos of students with smiles.

Things that Make Me Laugh: Science Ads

Chemists get a reputation as humourless, soul-destroying trolls that hide under bridges and kill any hope that wanders by. It is therefore quite pleasing to see a thin layer chromatography firm depart from the stereotype and show a sense of humour in this clip that is in fact an extension of a famous Monty Python skit. The cinematography and acting are very good for this sort of thing so it must have been a labour of love for the owners of the company.

LINK TO VIDEO

Internet Serendipity

Came across both of these on the same day and the serendipity of it all it made me laugh ...

"The Scriptures are so chop'd and minc'd, and as they are now so Printed, stand so broken and divided, that not only the Common People take the Verses usually for distinct Aphorisms, but even Men of more advanc'd Knowledge in reading them, lose much of the strength and force of Coherence, and the Light that depends on it" John Locke

CHEM 1013 Lab 2 Penny Data

So we have been working in the penny library for a fortnight now and we have counted and measured pennies ....

And boiled pennies in acid ...

All in the name of science. So now it is time for us to collect our data as a class. Use the comments section of this post to give the densities that you measured. Give them as YEAR (Density gcm-3) [so you should report them as 1993 (7.8 gcm-3)]. This way you will be able to compare your data in your formal report with the data from the class.

Charles We Hardly Knew Ye

Science is done by human beings and we as humans share much that is mundane about our lives. There is a new book out now that explores the real, human side of scientists that loom large in our minds and imaginations. Check out this description ...



"He suffered from incessant retching or vomiting, usually brought on by fatigue; and from painful bouts of wind that churned around after meals and obliged him to sit quietly in a private room until his body behaved more politely. Reading between the lines, his guts were noisy and smelly. "I feel nearly sure that the air is generated somewhere lower down than stomach," he told one doctor plaintively in 1865, "and as soon as it regurgitates into the stomach the discomfort comes on." He was equally forthright with his cousin...: "all excitement & fatigue brings on such dreadful flatulence that in fact I can go nowhere." When he did go somewhere, he needed privacy after meals, "for, as you know, my odious stomach requires that."He also had trouble with his bowels, frequently suffering from constipation and vulnerable to the obsession with regularity that stalked most Victorians. He developed crops of boils in what he called "perfectly devilish attacks" on his backside, making it impossible to sit upright, and occasional eczema. There were headaches and giddiness. He probably had piles as well."

Sort of makes you see Charles Darwin in a whole new way don't you think?

LINK TO BOOK

Five Days to Get Your Life in Order

It would appear that they are about to switch on the Large Hadron Collider. You may remember this installation for the initial word that it would be able to find the "God particle" and later on that when the thing was turned on it would cause the existing universe to wink out of existence. It would appear that someone has corrected the math on that issue.

I especially like the calming reassurance: "As the Safety Assessment Group writes, “Each collision of a pair of protons in the LHC will release an amount of energy comparable to that of two colliding mosquitoes, so any black hole produced would be much smaller than those known to astrophysicists.” "

LINK TO ARTICLE

So if you have anyone to apologize to or to show some love you have until September 10th.

It still makes me think of this cartoon:

LINK TO LARGER IMAGE

CHEM 2113 Lab #1 Class Data

This is the post for the class to combine it's data collected in the first lab. I want everyone to log into the comments section of this post and leave any data that you have on the compounds.

for example;

Compound E: m.p. 123.5 - 125.0 oC
Compound E: TLC (CH2Cl2) Rf = 0.123
Compound E: TLC (acetone) Rf = 0.789

Welcome Back: Questions for Prof. H.

1. Why blog?

Three reasons really: ego, access and anonymity

Ego: The nature of the internet ensures that this is a public forum with a memory. People throw stuff on the internet without thinking about it much but it all gets stored somewhere. With that in mind a person has to believe that they have something to say that other people need to read.

Access: This blog will pretty much be "active" 24/7 which means that it can function as a forum for the courses anytime that a student has opportunity to work on the course. Perhaps I will not be signed on but a message can be left that another student might be able to read and help.

Anonymity: Some students just do not do the "face-to face thing" very well. They may come to my office with specific goals and questions and then let the stress of the encounter cut the meeting short or incomplete. A blog gives a student a chance to think things through and make sure that they get what they need (or at least they have the opportunity). The anonymity is important in that it is possible for the student to participate without me or their peers developing a negative opinion of them.

2. How would this blog be different from other online forums?

This could be done internal to the university computer system. I noticed that when Union University had a tornado tear apart their campus they had an off-site blog ready to go (LINK) and that reinforced in my mind the importance of having multiple lines of communication.

I see that some courses are supported by Facebook pages and that has two problems in my mind: a loss of anonymity and Facebook contact with the professor (both of which can have their problems if you tend to be a bit wild on Facebook).

3. What will you use this blog for?

If you look over the posts prior to this one you will see that there are three basic types of post:

a) Course information / discussion quick announcements especially for students that may have missed something, I might be able to emphasize here. I will also routinely post links and comments to information on the internet that relates to concepts taught in the course.

b) Course assignments: This is something that I have tried before and I don't think I have it quite right yet but would like to try again. I will post a problem and the class will work together to post a solution to the problem in the comment section of the post and only students that log in and post will share in the marks.

c) Commentary: Sometimes a professor just has to vent.

And a Tree Shall Lead Them

As if we needed more reasons to love trees there is a science story out today that not only are trees our only proven hope to sequester atmospheric CO2 it would appear that trees are also able to remove airborne pollutants and convert them to amino acids.

LINK TO ARTICLE

So it would appear that the trees are important to us for a number a reasons. It would make for an interesting social and cultural study to look at populations that have extensive wood supplies and compare them with similar groups that do not. I bet that wooded societies are healthier and happier and probably wealthier. The anthropologists talk to us about Stone Age and Bronze Age societies but there must be a Wooden Age in there somewhere. I would guess that our complex master - slave relationship with our cellulosic neighbours must be an important part of our development.

In our own little corner of the world we have a property here at ABU where the campus sits on a much larger parcel of land that was clear-cut in the early 1970's. That is our best bet for the photo below. Notice that the highway has not been twinned and the old farm property that was here before ABU is still intact. In terms of the clear cut it makes for an interesting comment that the parts that were not clear cut are the high ground between Gorge Road and the Gorge Brook, the Gorge Brook area itself and a boggy area in the North - East sector of the property.

What I like about this early view of the property is that it clearly shows the property borders since I am sure the woodcutters would have cut right to the border with the neighbours. It also clearly shows where the logging roads are and that might be useful for access to the woods today.

If we now look at the 2005 Google Earth view of the ABU property we can see that the scrub forest has covered the property again. Up close it is a nasty tangle of poplar, birch and swamp maple with a seasoning of conifers. But it is treed and starting the natural process of succession from cleared land to conifer forest. What is also clear is the gaping hole in the property that is the surface pit for fill that worked the property from the time of the last clear cut and left about a quarter of the property stripped down below the subsoil leaving an almost Mordor like blasted moonscape of scum, slime and tufts of mis-begotten grass.



Well, it looks like we are going to be here for a while and it is clear that the good Lord gave us trees to save us from ourselves so I think we had better start planting some trees.

"Recycled" Water ... It's About Time

I love this article in today's New York Times.

LINK TO NYT ARTICLE

I have been lecturing for years that it is the mark of the civilized Western society that we can urinate, defecate and dump chemical waste into our own drinking water and not suffer for it. We can directly connect the success of urbanization with municiple water treatment systems. I always say that more people are alive today because of municiple water treatment than modern medicine ... but no one listens.

The author (not journalist in this case) visits a new water treatment plant and realizes that the purpose of the plant is to treat sewerage and return it to the city drinking water reservoir. The first response is "Yuck" but there is some really well developed science and chemistry here.

What really gets me cranking are the self righteous rural folk that claim that they have their own well and will not "pollute" their bodies with treated water. In most rural settings your well is down stream from someones septic field ... or a cemetery. At least with municple water someone is responsible for monitoring the water quality.

There is one line in the article that I really like and it shows the two objective and subjective sides of the science involved:

"You could argue that in coming to terms with wastewater as a resource, we’ll take better care of our water. At long last, the “everything is connected” message, the bedrock of the environmental movement, will hit home. In this view, once a community is forced to process and drink its toilet water, those who must drink it will rise up and change their ways. Floor moppers will switch to biodegradable cleaning products. Industry will use nontoxic material. Factory farms will cut their use of antibiotics. Maybe we’ll even stop building homes in the desert."

I think I am going to get a copy of the authors book.

LINK TO AMAZON BOOK LISTING

Physical Science in the Olympics: Air Quality

There is a fight going on right now between the BBC

LINK TO BBC STORY ON AIR QUALITY

And the Beijing Olympic Organizing Committee

LINK TO OFFICIAL OLYMPICS SITE ON AIR QUALITY

In essence the BBC is saying that the air quality is bad and anyone can see that it is bad. In fact they have been measuring it and the numbers confirm that it is bad. For example, today (08.08.08) they obtained a reading of 191 micrograms per cubic meter of the worst kind of solid particle pollution called PM10 pollution. The WHO cites 50 micrograms per cubic meter as the the criteria for acceptable air but raised that to 150 for Beijing.

On the other side, the organizers of the Beijing Olympics are saying:

" Du said in the past seven days the Air Pollutant Index (API), an indicator of the air quality, in Beijing has been all below Level II, indicating excellent or good air quality.
"Maybe the fog makes it not a nice picture to look at the Bird's Nest or the Water Cube, but the monitor south of the two stadiums reads the API at 80 today. It conveyed a strong message that our efforts had paid off since August," he said. An API rating of 51-100 (level II) means good quality. "

What it comes down to is the number and how it was determined. It is amazing that scientists are capable of using modern technology to measure the same physical phenomenon and get such dramatically different numbers. Physical science is supposed to be above this sort of thing. If the data are distorted then who is distorting them? Is it more likely that the BBC is knowingly publishing false or skewed numbers to support a story and embarrass the host city and country or that the Olympic organizers have "adjusted" their numbers to look better. At least the BBC admits to a 20% error in their measurements. There is another possibility that both sets of numbers are false. We cannot know but there is a third voice on the issue from within China and on that blog this is a picture of the air quality today.

LINK TO BLOG

What we can know is how well the athletes respond to the air. According to the SOURCE OF ALL KNOWLEDGE (Wikipedia) an average human has a deep breath volume of about 5 liters. An adult will make about 40 deep respiration's per minute during physical exertion. So that is about 200 L of Beijing air a minute or one cubic meter of air every five minutes. You have to believe that even elite athletes pulling that kind of air into their lungs for that period of time will have to see an effect. This is the reverse of what high altitude training does to prepare and athlete. At high altitude the air pressure is lower so there is less oxygen, in response the body increases lung capacity and the number of red blood cells to capture as much oxygen as possible. When the athlete returns to sea level there is a short term benefit that can improve performance. In this case however what we are looking at are athletes that can perform well in bad air. I do believe that China may well have an advantage here.

As a post script to this issue there is also a bit of discussion about the air quality of these Olympics compared to air quality in previous Olympic cities such as Athens and Mexico City. According to the BBC this is what athletes faced in previous Olympics.

Other Olympic cities on the opening day of the Olympics:

London (United Kingdom) 21
Athens (Greece) 43
Sydney (Australia) 20
Seoul (Korea) 41

Beijing (China) 191

Source: World Bank 2004 and BBC 2008

Liberal Arts Science: Opposing the Darkness

Teaching Science in a liberal arts university one often loses a bit of perspective. The reality is that we as a society have to come to some sort of agreement as to what basic level of science knowledge is necessary for functional adults. This is especially true for educated adults since we live in a world largely defined by its relationship with the products of science and technology. That is why we have science requirements for arts students ... the question haw effective a single isolated science credit is in a fourty credit degree. I don't know but I would hope our students would avoid the problem demonstrated in this video. One might even hope that their religious studies courses would explain mystery.

What is endearing about the video below is the completely unashamed attitude that personal assertion is equal to truth.

Christians Behaving Badly

Pound for pound I would say that the weirdest person in the Old Testament is Elisha. Weird stuff just happened around him.

"Elisha Is Jeered 23 From there Elisha went up to Bethel. As he was walking along the road, some youths came out of the town and jeered at him. "Go on up, you baldhead!" they said. "Go on up, you baldhead!" 24 He turned around, looked at them and called down a curse on them in the name of the LORD. Then two bears came out of the woods and mauled forty-two of the youths. 25 And he went on to Mount Carmel and from there returned to Samaria."

What I find striking about this passage is the commonplace almost mundane reporting style. If we were blogging about a trip between Fredericton and Moncton we might mention the high price of corn at roadside vegetable stands in the same tone that our faithful biblical reporter indicates that 42 men get mauled by two bears (OK, I know the plausibility sensors are ringing on this incident but you must remember that people back then were addicted to cheap Kung Fu movies where the bad guys would willingly line up to get their faces smacked).

It would, as well, appear that Christians that travel are not always on their best behaviour. I, of course, like you all have been tailgated and passed dangerously by a maniacal person with "Honk if you love Jesus" bumperstickers (which is actually a quite clever way of making you NOT honk at a bad driver). It would appear that more recently the standards of Travelling Christians Behaving Badly has been raised by Victoria Osteen who apparently struck a flight attendant that got in her way down with hemorrhoids. It looks to me like a strange cross between Career Barbie and Harry Potter. What is that worship song we sing ... "Just Like in the Days of Elisha"?

LINK TO COMPLETE STORY

Science Under Your Skin

Carl Zimmer is an author and writer that I enjoy reading. He is strongly anti-Creationist but writes in an even-handed rationalist way that avoids the mean spirited positions of Dawkins and his disciples. In fact he makes me think of Stephen Jay Gould.

For whatever reason, Carl took an interest in people who have science tattoos and has now collected images of these tattoos at the link below. I have to admit that I would never get a tattoo myself due to 1) a defining abhorrence of the idea of exposing more of my skin than absolutely necessary, 2) lack of faith in the hygiene practices in most tattoo parlours that I have seen and 3) no easy gloss that escapes this clear statement: Ye shall not make any cuttings in your flesh for the dead, nor print any marks upon you: I am the LORD. Leviticus 19:28
Nevertheless I am impressed that some people would go to the expense and pain of having these ink drawings pushed under their skin. An amazing number are chemical in nature.

LINK

Something New I am Playing With

I have found a program called CamStudio which is an open source facility that allows capture of audio along with screen capture. I am still working out how to use it but I am currently playing with the idea of posting a series of "videos" that show me solve a problem in real time and record my comments about logic and value. My first attempt is really choppy but I think I can see some promise as I hopefully get better at it.

There is a series of popular videos called "You Suck at Photoshop" that are really quite funny so for lack of a better name I have called this series "USuk@Chemistry" (LINK). That is also a bit of a shout out to a blog that used to exist about ABU Science called "Chem Sucks". I think that in this case my attempt to be funny might send the wrong message so I will probably give them some name like ChemPosts or ChemChats or DrMelHoldsYourHandWhileYouMeltDownatHomeStudyingForTomorrowsTest, you know something like that. Anyway, for those of you that are missing your Dr. Mel fix, here you go.

National Geographic Publishes Worlds Most Disturbing Photo

A couple of posts ago I was on about how we regard some animals as different from others and the fads of the day dictate if we consider them as appropriate for food or commercial exploitation. In the same vein I think the people at National Geographic wanted to publish a photo that would shock people to make a point. It is a very disturbing image concerning the bush meat industry in Africa. It seems that the appearance of oil money in some parts of Africa has resulted in a demand for bush meat and apes appear high on the menu.

This image shows the body of an ape being prepared for market. It seems that the value of the meat is increased if the hair is removed before sale but the skin is intact so they burn it off with a blowtorch. That is the image below.

LINK TO ARTICLE

This image is disturbing to me on a number of levels and I think that the National Geographic Society is going to get a lot of outrage going over this. I hope their gamble pays off. The trade in bush meat that results in these kinds of images needs to stop. But then again I wonder how much meat we would eat if we could see the killing floors of the industrial slaughterhouses of North America. Perhaps it is time for the National Geographic to point it's lens at our own culture before it ignites outrage over other cultures even if it is justified.

Mentos and Diet Coke Blurs Physics and Chemistry

You know, when it comes down to it Chemistry calls itself "The Central Science" because when you draw all of science as a Venn Diagram it overlaps with more sciences it than any other. For all that Chemistry is the most insecure science as well. Very few universities are creating pure chemistry departments now and are in fact rolling them into other disciplines such as biology and physics.

The line between Chemistry and the other sciences gets blurrier all the time. Take for example this recent publication by the American Journal of Physics ...

LINK TO ARTICLE

This is of course the famous reaction that spawned a 1000 YouTube videos and made these guys famous.

LINK TO EepyBird

The article has even been reviewed by the news magazine for the American Chemical Society [LINK] and it turns out that there are a number of factors that combine to make the Mentos / Diet Coke reaction explosive. It appears that the gum arabic used in the composition of the Mentos make the foam more stable and frothier. A microscopic analysis of the surface of the Mentos reveal that it is covered with gas bubble nucleation sites and that the density of the mint meant that it falls to the bottom of the bottle of pop. All useful insights.

But it is not physics. Indeed what exactly do the authors mean in their title when they say "physical reaction". Now I have a little physics in my background and as I remember my terminology a physical reaction is a response to a force (you know ... Newton's Laws and such). I think they are just trying to avoid the word "Chemical" as if it were a dirty word.

I think chemists need to protect their turf while it is still ours and this is not a physics paper. The problem is how do we protest? I mean, we all know the hierarchy ... if you are not smart enough to do math you do physics, if you are not smart enough to do physics you do chemistry, if you are not smart enough to do chemistry ... well you know how it goes etc. We will need to be careful and bide our time but we can't let them walk over OUR turf and pretend to own our ideas. Wait for the right time and remember the codeword (stoichiometry (it is the only science word that chemistry truely owns)).

Welcome to My World in Metaphor

There is a remarkable passage in Mark Twain's "The Adventures of Huckleberry Finn" that goes:

"Sometimes we'd have that whole river all to ourselves for the longest time. Yonder was the banks and the islands, across the water; and maybe a spark--which was a candle in a cabin window; and sometimes on the water you could see a spark or two--on a raft or a scow, you know; and maybe you could hear a fiddle or a song coming over from one of them crafts. It's lovely to live on a raft. We had the sky up there, all speckled with stars, and we used to lay on our backs and look up at them, and discuss about whether they was made or only just happened. Jim he allowed they was made, but I allowed they happened."

My intellectual world occurs at a level far below our technical ability to "see" what we are doing. Oh yes, we can use some very elaborate methods , such as atomic force spectroscopy, to visualise the positions of atoms but only in crystals of heavy atoms.


Any so, if we want to "see" what we are doing in chemistry and biochemistry we sink to metaphor and simile. Whenever we reduce macroscopic objects and even ideas to the microscopic level we lose important information in the simplifications. I don't know how many times I have tried to use a simplified simile to explain a chemical reaction only to end up fighting with students that cannot get past the simile to the concepts taught.



With that all said as a preamble I see a new company has entered the market for industrial animation of science - biochemical - chemical processes. They have a sampler / demo reel at this site:

LINK TO DEMO REEL

There are some moments captured in the demo that I like. Such as the moment when an micelle / vesicle carrying a drug molecule contacts a cell wall and submerges like an asteroid into the ocean.

Or this moment that shows a fist full of pills dropping out of the pyloric sphincter an into the acid bath that is your stomach (thankfully a clear colourless liquid in this image, I know I have seen stomach contents in my life and it does not look like this). The pills begin to disintegrate as they travel leaving a drug plume.


And this image captures the moment in time just before a protein touches a glyco-protein receptor on a cell surface.


It is not my intention to get drawn into the whole irreducible complexity debate. I do however appreciate how these kind of images place an accessible window on the microscopic world of biochemistry that exists in my head. We are all large, salty bags of water with amazing and complex chemistry going on in our cells all the time. These images are nothing like what really happens but until we can see with our own eyes they will have to do.

It does not matter if you believe it was made or just happened. It is astonishing how little we know about the complexity of what happens below our skin. Every step towards humility in our discussions on complexity is a step forward.

Made me Laugh

What can I say? Both of these made me laugh but one of them shouldn't have I suppose ... I guess on second thought one of these isn't funny ... can you guess which one?

They Shoot Elephants Don't They?

It seems everytime you turn around some poor country in Africa is being over run by herds of elephants and the whole discussion of herd culls occur. Most recently, Kruger National Park is thinking of reducing the size of its herd. Link to Article. The issue is that 100 years ago there were about 6000 elephants left in Africa and a century of conservation means that there are currently about 600,000 and they are straining available resources.

Of course there is a very emotional response, the elephant is iconic for Africa in the same sense that the polar bear is iconic for Canada. There is also a real appreciation that elephants are long lived mammals with strong family ties and apparently real emotions. No one would say they are sentient or conscious but some would argue their intelligence.

The question needs to be asked though, what makes an animal off limits for killing? It would appear that a human emotional response to the animal (kittens and puppies which we kill by the thousands each year) scarcity due to human activity (whooping cranes) and perceived intelligence or kinship (the great apes) all mean that an animal should not be killed.

That brings us to the whales. If I understand the biology, whales are huge, long lived mammals (altho Herman Melville calls them fish and he saw a lot of them) that for the most part we hunted to edge of extinction. And yet, just like the elephants, we left them alone for a century and I tell you, you could walk around the island of Newfoundland on the backs of the whales and not get your feet wet. They are everywhere and are responsible for almost any positive news in tourism for the Atlantic Provinces.

We allowed the elephants to recover and their numbers justify both hunting and culling now. We allowed the buffalo to recover and if you go out west you can get a buffalo burger. We have allowed the whales to recover and some populations could easily accommodate a profitable "fishery" (doesn't it bug you to hear of the fur seal "fishery" each spring but "mammalry" sounds too similar to something else).

Link to Cartoon

Now, I like the cartoon "The Other Coast" it is gentle humour with a social and environmental consciousness. I am sure that they would be appalled to find that I have linked their cartoon to this discussion. But it was their cartoon today that got my mind thinking on this topic.

But I have to ask, if the biologists tell us that the populations are large enough and stable enough to allow a monitored whale hunt then why not? What is special about the whales as a species that puts them in the same class as the great apes? It would seem to me that Canada has a significant potential natural resource off its shores that it could be exploiting.

This is a photo I took a while ago when we lived in Newfoundland, a friend had taken us out in his boat and this is a whale in the mouth of St. John's harbour. The towers that you see on the horizon are the St. John's Basilica. What is strange about this is that St. John's harbour is essentially a huge sewer and if you go out at the right tide the water coming out of the harbour is brown with "suspended solids". Even so, there you have a whale frolicking in the harbour. Indeed, you can get an often spectacular live view of the harbour from the other side at this link.

And this one is waving good-bye from the waters of Freshwater Bay close to Cape Spear. Like I say, unless we can articulate a reasoned argument for continued protection I fail to see why limited hunts similar to the ones we have for polar bears, elephants and buffalo should not be allowed.

I have no idea where this came from. It is horrifically hot and muggy here and I guess I am feeling a bit like a beached whale and had to release a conservative rant or start biting people.

Summer Internet Surfing

I stumbled across this website that made me laugh ...


Created by OnePlusYou

and these are questions that have been bugging me as well ...


Created by OnePlusYou

$5190.00The Cadaver Calculator - Find out how much your body is worth.

Created by OnePlusYou

POSTSCRIPT

So it turned out that this site is not as benign as I first thought. I came across the link in a theology blog that I monitor and just went to the widget site. It figures that the link embedded in the images above in FACT sends you to a Russian "dating" website. I have told these people how old I am, my height and weight and some of my personal preferences in filling out the "questionnaire" to determine how many cannibals I could feed or how much my body is worth. I would assume that the email associated with this website is currently being bombed by "offers" of companionship by busty ladies named Svetlana. I have disabled the links as best I can now and all I can say is that I am glad that I use an Internet pseudonym for this blog. If any of you managed to get caught in this before I posted this warning you have my apologies.

Now, I have all these new email messages from Nadya to read ...

Something New Under the Sun

Every now and then you see something that just makes you go hmmm.

There is an abstract for a paper published in the Journal of the American Chemical Society that just pokes you in the eye and says "Not only is this amazing chemistry but traditional publishing just doesn't fully show the awesomeness of the reaction".

LINK TO ABSTRACT

At it's simplest level they created a molecule that reversibly breaks a bond when exposed to light. What is cool is the video that goes along with the paper.

Now, photochromic bond dissociation is the cornerstone of the whole discipline of photochemistry (essentially the whole area can be summarized by the statement "Look! We took expensive pure starting materials and shone harsh UV light on them to make complex sewage, we then spent years extracting components from the sewage"). What makes us chemists all giggly about this molecule is the speed of UV capture, bond dissociation and re-association and the fact that the molecule does NOT degrade to sewage. That and the fact that there is the uber cool video showing the whole process.

Why do you care? You know that irritating commercial with the smug near future family that walks outside and their sunglasses immediately turn dark? Now connect the dots and see the bunny. The future is now.

Let the Bitter Howling Begin

If there are any students out there that monitor this blog ... this message is for you. I have decided to allow cheat sheets for my tests and exams in first year chemistry. I know, I know, I fought you guys long and hard on this issue. Our debate always went:

Arguments for Pro -Cheat Sheets:

1) chemistry should be about understanding not memorization
2) memory aids would lower the stress of testing so that the student can do his/her best work
3) creation of the summary sheet is itself an excellent learning process

Arguments for Anti-Cheat Sheets:

1) this course is not a democracy so if I say you need to memorize some basic formulae and logical problem solving sequences suck it up and march like a soldier ... you know what? When I was a student we had to memorize the entire periodic table AND the isotopic masses IN LATIN. I don't care what the professors in OTHER universities are doing, if all the other chemistry professors jumped off a cliff would you expect me to as well? Hmm? Why are you smiling? Did that image make you happy in some way? Well, just for that smarty pants the formal report is due tomorrow ... hand it in just before the unscheduled mid-term.

And at some point in the debate the two sides would descend to childish name calling and secret scheming for retaliation.

So, I have decided to roll over like an old dog. The kicker was a low key investigation at the recent conferences that I attended where the dominant logic was that cheat sheets give the illusion of help but if the student doesn't know the chemistry they will fail anyway.

By the way, I came across this link to a spectacular online periodic table:

LINK TO PERIODIC TABLE

I like this quote for the way it makes the causal link between philiosophy and morality:

"To say that a man is made up of certain chemical elements is a satisfactory description only for those who intend to use him as a fertilizer."
Hermann Joseph Muller

And as I have discovered while on sabbatical ... Jesus may take the wheel but He doesn't do paperwork. My office is a disaster and the lab looks like a combination yard sale - toxic waste dump. I am trying to get things back to "Normal" and I like the attitude in this cartoon:

A Sunday Quote

I came across this quote today in an article that I was reading and I thought a paraphrase to change "poet" to "scientist" would actually be more an accurate reflection of the goal of science in the liberal arts tradition.

"To a poet, nothing can be useless. Whatever is beautiful, and whatever is dreadful, must be familiar to his imagination: he must be conversant with all that is awfully vast and elegantly little."

Samuel Johnson

A Very Odd Chiral Separation

There are symmetry laws written into the basic code of the Universe that we live it. If indeed Nature abhors a vacuum it is positively fanatical about breaking symmetry. The more one reads about them the more one is amazed by how basic symmetry rules control so much of what we know about anything.

Simply put breaking symmetry in any fundamental kind of way is strictly forbidden. When symmetry is broken the consequences are pretty amazing. Indeed, if you read Singh's "Big Bang" it is argued that the Universe itself is the result of a symmetry breaking event.

That said, in my discipline of chemistry the most important symmetry rules are written into the nature of tetrahedral molecular substructures in a phenomenon we call chirality. In terms of geometry, if you have a molecule with any point in it where there are four unique molecular bonds to the same atom there are two distinct spatial arrangements that are possible. For simplicity we call them left handed and right handed. It just so happens that the proteins in our bodies are, in fact, long chains of substructures that all have these tetrahedral atoms (pretty much each one an amino acid). What is remarkable (and amazingly improbable) is that each one of these atoms is the left handed version.

McMurry, 5th Ed.

Why is this amazing or improbable? The universal symmetry laws say that when molecules or atoms that are not left handed or right handed form a tetrahedral atom that there must be a 50:50 mix of left and right handed products. That is why scientists and chemists in particular are obsessed with Escher prints. Escher was an artist that made his money creating images where left and right handed images generated each other ...

In fact the only way we can separate handed molecules is with another handed molecule. The question of course is where the broken symmetry comes from but that is an issue for another day. Suffice it to say that chemists have a unique interest in any sort of process that is capable of sorting left and right handed objects.

Well a new one has surfaced.

It was in the Globe and Mail today that another right sneaker has washed up on a beach in British Columbia. What makes that odd is that the foot was still in it. What makes it odder still is that this is the fourth right foot sneaker with a foot still in it to wash up in recent days.

LINK TO GLOBE AND MAIL ARTICLE

In the absence of a real twisted murderer loose on the West Coast it would appear that this is the result of a natural process of some kind where accidents or suicides result in bodies washing down river and out into the ocean where natural dismemberment results in the feet separating from the bodies but that the right handed foot / sneaker combination follow a different path than the left handed sneakers. The importance of the sneaker is to provide protection for the foot so it stays intact and the natural buoyancy of the sneaker makes the dismembered foot float.

All in all it would appear that a right handed object floating in the ocean is somehow polarized and separated from an equivalent left handed object. The proof of this theory would be to go back to the river source of the bodies and examine the coast in the opposite direction from where the right handed sneakers were found. If this theory is right there should be a stretch of BC coastline where the left footed sneakers accumulate. You heard it here first.

I'm just sayin'.