Pharyngula still going strong. Especially in Minnesota!

According to a November 2007 poll, the Weblog awards, P.Z. Myers' Pharyngula is the second best (most popular) science blog after Steve McIntyre's Climate Audit and Phil Plait's Bad Astronomy Blog. Why second? Actually there are three very popular blogs but Climate Audit and Bad Astronomy Blogs had the exact same number of votes...so P.Z. is second. I wanted to use Google Trends to compare the traffic on these three sites and it seems, according to this tool, that Pharyngula is in fact quite ahead when Google searches are used as a comparison.

Lately, there's been a small slip in Pharyngula's traffic but I guess it is only temporary (students on vacation) But there is one thing I find quite odd, most of Pharyngula's traffic, comes from Minneapolis, MN. Humm....Are you "Googling" yourself that often P.Z.???

Boris the Cat can walk again!

I like stories like this (From The Vancouver Sun)
Boris the cat is found at a construction with a broken back in Mission but, thanks to hydrotherapy at K9H2O in Abbostford Boris can walk again......makes me believe in the human race again!

See Boris during hydrotherapy and Boris walking again

K9H2O's photostream on Flickr

YOU CAN ADOPT BORIS (before June 20th)

Energy, Pyramids, Wine and DNA

I am in Kelowna, Canada's closest thing to the Napa Valley. I like wine, I like to taste it and I like to smell it. I just like wine...just enough! Last Friday I went on a wine tour and I have been looking forward to this. Imagine, the sun, the vines and that wonderful liquid.

We went to Summerhill Pyramid Winery, one of the most visited winery in Canada. Why? I have absolutely no idea...for one thing I did not like their wine ! The special thing about this winery is that they have this tacky pyramid where their wine ages. What? They age their wine in a pyramid? Absolutely! This pyramid has the same proportions as the great pyramid of Kheops. Our guide even told us:

"It has been scientifically proven that wine ages better in a pyramid, milk will turn to yogurt when put in a pyramid"....are you kidding me? Scientifically proven? Has he was saying that I looked around me to see if our group (about 40 people) were buying this....NO ONE SAID ANYTHING, they just had fish eyes not really listening to what was being said. It seems so easy to fool people, all you need is to mention a few buzzwords such as Energy, Science, Proof and voilà! Doing a bit of research on the net about pyramids and their powers I found this list (with some of my comments beside them...)

ref: http://www.geocities.com/undergsci/pyramideffects.html

• Sharpen razor blades (Sure...Gillette will hate that!)
  
• Restore the lustre to tarnished jewellery and coins
  
• Purify water (Hey, build a pyramid in Myanmar...)
  
• Mummify and dehydrate meat, eggs and other food stuffs (Mummies...of course)
  
• Help keep milk fresh and prevent souring without refrigeration (and yogurt...)
  
• Dehydrate flowers without losing their form or colour
• Increase the growth rate of plants (a pyramid will activate transcription factors just like that)
  
• Help attain increased relaxation
  
• Improves the taste of coffee, wine and certain fruit juices (taste is relative, is it?)
  
• Promotes healing of cuts, bruises and burns, as well as reduces pain from toothaches and headaches (Sure.....!)
  

Here's what I think...people are so gullible because they:

1. Lack scientific knowledge
2. Lack critical thinking
3. Trust anyone that seem to "know what they are talking about"

This is sad. Very sad!

A company even claims that they can activate some of your junk DNA...just go there, read their biological blurb and tell me if you understand anything!

Via Sandwalk

Good point!

I need to vent......

Habacuc could have saved this dog in his exhibition, he could have shown that one person can make a difference and that we can not remove ourselves from our environment. He could have shown that human compassion can triumph. He decided to let this dog die while everybody watched in silence. This does NOT surprise me (see next video below), it reminds me that Homo sapiens can be a real parasite to this planet and that we, in fact, do not live in harmony with other species. We belong to no ecosystem, we are part of the problem. I wouild like to believe that someday things will get better...I do not. I will keep on doing my random acts of kindness....

Q: How many available free ribosomes in E.coli? R: 500 nM

I like trivia and I always wonder about how many of "whatever" per cell...or, wait, how fast a specific process is...This kind of data is usually a pain to find...Well not anymore, I found this site: B1ONUMB3R5. Even better, click on the topic you are interested in and get the reference....Now you have data you can use to impress people at conference cocktails.

Via: http://neurodudes.com/

I want to learn...and remember what I learned!

To all of you interested in teaching/learning, I urge you to read THIS ARTICLE from Macleans. Teaching behavior will influence learning habits and retention. After all, that's our goal, teach something the students will apply! Isn't it?

Image source: Flickr CC

Device to Root Out Evil

Ah...controversy finally got the best of it! Art is sometimes supposed to challenge our minds and our souls. I guess this was too much for some people...just too bad! I am surprized this sculpture will move to Alberta (Calgary), a more conservative province. Oh well....all the best little church!


Read the story HERE

Image source: Flickr CC

Tornado in a bank.....

Languages and genomes

While looking through Technorati I stumbled on this blog post..."Litterature - Can languages be understood by treating them like genomes?". That caught my attention because a few years ago, while teaching population genetics at Carleton University in Ottawa I told my students about this tribe on Vancouver Island: The Nuu-Chah-Nulth. I have great respect for the first nations and I wanted my students to learn from an anthropological point of view, not just through a stretch of nucleotides. While doing my research for my course I found a few articles including this one: Gene flow across linguistic boundaries in native North American populations.

Using statistical methods and mtDNA analysis, the authors found that language can in fact be replaced (or modified) faster than mutations can occur because language can be transmitted in a vertical fashion (just like DNA) as well as horizontally between unrelated people. Because first nations have been subjected to tremendous pressures through the centuries it is plausible to think that at times DNA might have evolved at different speeds when compared to language evolution depending on the tribe.


A few highlights:

• The Navajo and Apache, who reside in the Southwest, have high nucleotide diversities, in the range of nucleotide diversities in populations classified as Amerind speaking.
• Several sites were polymorphic only in populations classified as Amerind-speaking, but none occurred in all populations attributed to Amerind.
• With respect to Greenberg’s three language families, the average nucleotide diversity within populations is low in Eskimo-Aleut populations and high in Amerind populations. However, nucleotide diversity varies considerably among the populations classified as Na-Dene-speaking.
• The Alaskan Athabascan and Haida populations, who reside in the North, have low
  nucleotide diversities, in the range of nucleotide diversities in the Eskimo-Aleut-speaking populations.

When reading through the blog, I slowly realize that the author is a believer of intelligent design** and that, like all ID proponents, he decides to include some no-so-objective-god-related-stuff in his blog. Here's what he states while trying to explain why languages can not be understood the same way a DNA sequence can:

"The problem is that languages are fully teleological, whereas the tools of molecular phylogeny do not acknowledge teleology in genomes."

In other words...God created the languages...so do not even try to study them with objective techniques!

**Silly me...the title of the Blog site is: Literature - A discussion of ID-relating reading

Alien design.....Intelligent design? (PART 2)

After writing my last blog posting I was interested to see is UFO sightings were recorded before the camera was invented...actually I knew it was but I wanted to document it. What better than a YouTube video? Well there it is. Actually very interesting. When I think about it, people at that time could not imagine such technology and therefore anything unusual, especially something flying would have been associated with some god or superior entity. Watch the following video and notice that the design of the "flying saucers" has not changed.

Alien design.....Intelligent design?

Reading a recent blog post from my favorite graduate bunch (see Alien Autopsy - Bayblab) I thought of something that bugged me for a long time: Alien Design.

Before you continue: first, lets agree on a few things.

1) be open minded BUT....
2) be critical at the same time

OK...If aliens exist they are probably advanced and the popular belief is that they are way more advanced than we are. If they really are that advanced and if they travel through some wormhole (interesting blog post here), the perception of time is not the same. Therefore design should be quite the same and TIME should not have any effect on the appearance of the extraterrestrial vehicles. When we compare pictures of ufos taken through the years one can only admit one thing....they are very, very similar (there are exceptions of course). If these pictures were bogus, or if the "flying saucers" were man made (a hoax) the design would probably evolve as years go by as we are all influenced by imaginary and not so-imaginary Stealth spy planes.



The ufos all look the same despite their location and year....puzzling isn't it?

Image source: The image was assembled from pictures that can be found on THIS SITE.

Gr8t news! SMS and english language...

Here is on for the purists. It seems "texting" (SMS) and instant messaging (IM) is not as damaging to the language of Shakespeare as previously thought. After studying 1.5 million words taken from SMS and IM (72 subjects), University of Toronto researchers have found that only 3% of the words were abbreviated. Moreover, the word YOU was preferred over U nine times out of ten. Surprising isn't it?

"Contrary to popular belief that IM is breaking down English language, we found that online shorthand is actually not detrimental. Our study shows that while kids use words like 'gotta' and 'gonna' in IM, they do use 'shall' and 'will' while communicating formally. I would encourage my child to use IM simply because it means using a fluid language. This automatically hones their skill with English."

Reference: The Times of India
Image source: Filckr CC

So...what is going to happen to them?

Selling the war then...now selling a book. Ouch!

Please forgive me, this has absolutely nothing to do with biology and I know I am not very original with this posting but this is just too funny....Am I dreaming?

If you want more of this comedy, you can read the transcript of an interview Scott McClellan had with Anderson Cooper. He is a real master of spin, he was hired by W. for this specific talent!

In all fairness, I added the next video where McClellan has a chance to explain his book and views to Katie Couric

Peru and the economy of bird poop

Guano is a great mix and there is a market for it, once again. So what the heck is guano? After all, even Captain Haddock, a seasoned sailor did not know what it was (See Tintin, Prisoners of the Sun). Could it be the latest coffee fad from Starbucks? Not really! While the phrase "I would like a Tall Guano Latté to go" might sound realistic, it is quite unlikely that guano will end up in your favorite beverage! This term is used in Peru to differentiate between useless bird waste and the nutrient-rich waste of cormorants, pelicans among others. Guano is dung!

Now that you are aware of that fact lets see what is the hype about this complex substance. Guano, especially Peruvian guano is very rich in phosphorus and nitrogen in the form of ammonia. Before synthetic fertilizers were made available, natural sources were an important part of the economy of producing countries including Peru. Peruvian even fought with Spain to preserve it during the so-called "guano boom" in the 19th century. Starting in 1840 and for 30 years, 12 million tons were exported to America and Europe and then the "guano boom" busted.

Today, soaring prices for synthetic fertilizers ($600/ton last year) are rejuvenating the demand for guano and the Peruvian Island Isla de Asia has plenty of it....well not as much as before, but at least enough to sustain a 10 to 20-year demand. Peru exports it guano to Israel, France and The United States at a price close to $500/ton. The problem is that it is not a sustainable source because that the bird population is declining. The numbers have declined substantially from what it was in the 19th century (60 million birds compared to 4 million today). The seabird population is declining because of overfishing....because you see seabirds live on fish and guano, to be produced, needs food to be digested by someone....good Peruvian guano might not be around for very long.





References:
http://countrystudies.us/peru/12.htm
NY Times
Click here to access a great slideshow

Physics rules the world

One of my college professor used to tell us that physics was the MOST important science to understand life because all the other ones rely on physical concepts. I did not like physics too much and decided to pursue a career involving biology. Soon enough I realized that physics was indeed at the core of almost everything. From the aqueous solutions to the cell membrane physics define what really happens.

Protein folding is no exception. Physical forces influence the interaction of thousands of atoms and shape polypeptides. No structure...no function! The problem with a physical approach to understand and model protein folding resides in the fact that femtosecond calculations have to be made. As Ken Dill (UCSF) puts it, it is all about timing:

"You need to be faithful to the atomic dynamics from one instant to the next, otherwise you violate Newton's laws"

Kenneth Dill is part of a group that participated in a protein-folding competition: CASP7 (Critical Assessment of Techniques for Protein Structure Prediction) held in november 2006 in California (Pacific Grove). Basically, each team (there were 250 teams) had to predict the structure of 6 proteins...in three months! To do so, many, including Dill, used supercomputers such as Tungsten at NCSA. To predict protein folding, Dill and his group used the ZAM model (Zip And Assembly), once a few amino acids find their position, the rest of the amino acids in the polypeptide interact with each other in a Zipper fashion.

Fig 1: ZAM predictions in CASP7 compared with experimental PDB structures. The GDT (CASP's Global Distance Test) gives the percentage of residues (x-axis) whose alpha carbon coordinates lie within a given cutoff distance (y-axis) from the native structure, for predictions by all participants in CASP7 (orange colors). The best predictions correspond to lines in the lower-right quadrant of the graph. The five ZAM models are shown for each target in gray, with the best model highlighted in red. (click here to access original Website)

The physical approach allowed adequate prediction for 4 of the 6 proteins (see figure 1) and Dill thinks his group did at least as good, if not better, that other groups using bioinformatics.

Yes...I have to admit, physics still has a very bright future!

For a list of NCSA projects click HERE

Image source: http://www.flickr.com/photos/mscolly/145052885/

World-O-Meters

Stats in real time. Anything wrong with this picture?

SHAGYA BLOG: British Columbia Government Attacks Freedom of Speech

SHAGYA BLOG: British Columbia Government Attacks Freedom of Speech

W.A.C. Bennett, Gordon Campbell and the end of a dream

I am new to the West Coast and I hope I never lose my constant amazement about the natural wonders of British Columbia and the quality of life here. But this could change.

The BC government is now selling rivers to private companies so that they can produce cheap electricity they will sell at a high price. This is exactly what W.A.C. Bennett did...but in reverse! Bennett, a former BC premier, brought power generation and electricity production to the people of BC. The Campbell government is now reversing the tide....a very interesting video can be found HERE

Not surprizingly, they also slashed the budgets of post-secondary institutions. A pro-business government? You better believe it! Oh...before I forget, Gordon Campbell's new election gag law imposes extreme limits on any organization who wants to talk about many topics from December of this year until the May, 2009 provincial election. What are these topics? Here is a list just fro you (from the Just Shut Up BC website)

• Climate change, health care, public schools, the Olympics, child care, transit, fish farms,affordable housing, run of river private power projects, carbon taxes, raw log exports,resource-dependent communities, public private partnerships, minimum wage, free trade, mental health services, offshore oil drilling, public power, electoral reform, the gateway project, post-secondary education, taxes, clean air, First Nations treaties, public safety, seniors’ care, harm reduction, poverty...and more

Other blog interested in this topic:
Shagya-blog

How to become a genius

Being a genius has a lot to do with perception...either you perceive yourself as a genius and nobody else does or you think you are just a regular person and everybody thinks you are a genius. Sometimes you might be a real genius and everybody knows it, including you...but that is quite rare. It seems there are ways to "become" a genius and it has little to do with a gift from mother Nature (or God for that matter) rather than being able, or lucky enough, to "see" something nobody else saw or even bothered looking at.

Here is a paper published in PLOS Computational Biology that just might help you. I decided to bring the highlights to you...read on genius....

1) Nobody cares about your age, especially if you are young and, it gets even better....if you are a "nobody", nobody really cares. You can imagine very controversial concepts and maybe you will be lucky enough (and smart enough) to be right on target. The most important thing is to keep your mind open to new ideas and concepts....people once thought planet Earth was flat!

2) Look out for the weird....something unusual happens? You can do two things...you can trash the results that would screw up your error bars or you can try to replicate these "weird"result. By the way, if you need to refresh your statistical knowledge, the Bayblab guys have something for you.

"This should be encouraging news for those of us who don't consider ourselves geniuses. The best way to promote scientific success may be to maximize exposure to chance occurrence and events—especially those that have more upside than downside potential. So, don't just ignore those little inconsistencies that arise in your work, give them some room for consideration. This is something anyone can do, though it takes time and courage"

3) Take risks....ah...risks! Calculated risks maybe but risks are an important part of it. I suggest you buy a Magic 8 Ball if you are too scared. Chances are you will come up with news ways of analysing the situation!

4)Enjoy your work....nuf said!

5) Learn to say NO!...that is difficult. Here is a way to look at it: Saying NO is actually saying YES to other things! Ah...logic!

6) Learn the joy of writing and presenting. Open an account on Blogger and try to say things that make you look like a genius....Expose your ideas to other ones. CONFRONTATION!!!! Eventually, you will have to present something, so remember that practice makes perfect...just like your mother tells you (or used to tell you)

7) See the big picture. You are going somewhere with this new concept...right? Remember and, most importantly, understand the WHY...WHY is this important, WHY should someone listen to you for more than 5 minutes (or 5 seconds)...WHY????

You are now on your way to become the very best scientist this planet ever had.


Reference:
Giddings MC (2008) On the Process of Becoming a Great Scientist. PLoS Comput Biol 4(2): e33. doi:10.1371/journal.pcbi.0040033

Seen in Port Angeles, WA

Of course I was expecting exceptions....To us, Canadians, that seems out of this world!

Should we be surprized?

Found today...in PLOS Biology

"Community pressures place significant stress on teachers as they try to teach evolution, stresses that can lead them to de-emphasize, downplay,or ignore the topic."

Panties, superstition and Myanmar

I was reading this on Radio-Canada's website today...interesting. Very briefly, this SITE ask women to send their panties to the Myanmar ambassador in Ottawa.
WHY? Because, according to a popular belief, men lose all power when they touch a piece of feminine garment that was worn under the belt...especially panties. Ladies, get rid of these old underwear for a good cause.....

Image source: http://www.flickr.com/photos/lopezpastor/347989165/

Scratch my back and I'll scratch yours

An editorial published today in PLOS medicine brought to light something many of us (read "science literate") already know. "GOOD news", especially medical "GOOD news", come with a price tag.

Medical good news are fabulous because most are concerned about health-related issues. To no surprise, when a medical breakthrough is released we listen and watch, almost captive. When these news are "sponsored" without our own knowledge this becomes a problem. Why? Simply because the public is generally uninformed (or misinformed) about their own bodies and the alternatives presented through these "GOOD news" seem to be the only ones because the sponsor, usually a big pharma company, pays for a powerful release in prime time TV. These, folks, are not news...they are advertisement!

Image source: http://www.flickr.com/photos/monkeyiron/392510021/

See the big picture?

I had this idea on a smaller scale and not as an autoportrait....argh! Got to fire up the right side of my brain! Creativity man...creativity!

See for yourself...click HERE!




PS: Not the most eco-friendly art on the planet.....hummm!

Let's get serious!

LOOK !!!

I do not normally post political things but I recently read: "London has 10,000 crime-fighting CCTV cameras which cost £200 million...". This makes me think in biological terms.

You are being watched, you adapt....but you can't watch the watchers
http://current.com/items/88856223_you_can_t_picture_this

Some become creative....a niche for everyone! Wonderful world!


Via http://curry.podshow.com/

Human 2.0 Olympics

Oscar Pistorius is a double-amputee South African athlete. I admire anyone that rises above life's challenges. I admire anyone that becomes a model for others. I admire anyone that decides they can do anything they want to. I really do! Oscar Pistorius is one of these humans that decides an obstacle is just that...an obstacle! I admire that! So much, you have no idea.

Despite this admiration I could only agree with The International Association of Athletics Federations (IAAF) decision to not allow him to compete in the Olympics. I really think his prosthetics give him an unfair advantage over the other athletes. Although I agree with that decision, I find it quite ironic that he has an "unfair" advantage....interesting when you think many of these athletes are using performance-enhancing drugs....so much for fairness!

This decision was overturned by the The Court of Arbitration for Sport (CAS). I think this is a mistake and lack of courage from the CAS. How far will that go? The door is now open to Human 2.0 Olympics where genetically-modified cyborgs will compete. The Olympics will now become an ideal that is even farther than it ever was before for kids.

To get a spot on the start line in Beijing, Pistorius has to qualify but many doubt he will make it, apparently he is not in the shape he should be for that ultimate racing exerience. This does not matter wheter he makes it or not....the damage is done!

Also published on my other blog: Darwinslegacy.blogspot.com

Reach out!

OK..I am coming out of the closet...

Well....I have something to tell you! I am....well......I am confused about.....about my.....well...I am confused about where my right is! YES! I am one of those persons that do not know their left from their right! Tell me to turn right....my body always wants to turn left! Tell me to turn left....well I will turn left! Sometimes I am totally convinced left is right! Does that make any sense? Is there a name for a condition like mine? Does that mean I have no right hemisphere? Well.....Bayblab dudes.....now you know! I am a leftie that knows nothing but left! It's like right does not exist....Seriously!

A-M-A-Z-I-N-G !!!!!

I LOVE THE WEB....it's full of those little gems! Take for example these tow sites about the art of the Mandala...

The Mandala is truly a work of patience! It is a representation of the Universe....so many grains of sand! Look HERE first....and then HERE (choose Nanomandala at LACMA). I promise you the ride of your life - at nanoscale!

Bacteria as tools....

After you watch this....go to this amazing site:
WWW.TED.com

Tippi !!!

As much as I hate animal abuse and their abusers, I like to see animal-loving humans...almost makes me like the human race....Click HERE!

Mmmm....brain soup!

The microscopic world of protists is so diverse. From the cute and swift Paramecium caudatum to the diarrhea-causing Giardia lamblia. A colleague recently sent me an email with a story of the brain eating amoeba Naegleria fowleri....I had to investigate!

First, lets say that infection are rare but more common when heat waves are present....since these heat waves are likely to be longer and more prevalent, this story is of public interest. This interesting organism enters through the nose and makes its way to the central nervous system by crossing the olfactory neuroepithelium. From 1995 to 2004 only 23 infections have been documented but the recent death a of a 14 year-old boy sparked fear in Arizona.

When you look at the way this parasite travels, we find that the strategies are almost always the same: ENZYMES! How do you get into a cell...easy! First break the membrane with a specialized key known as a phospholipase (phospholipase A2). Then attack proteins with a specialized protease. By attacking the cellular cement holding the tissues together you end up liquifying them. The angry amoeba can then phagocytose the remaining fragments and voilà....you are history!

With only a few cases in the last decade chances are that you can die of many other things....and if you smoke...well....do not even bother about this story, your relative risks are virtually "0"!

For a list of publications on the infective mechanisms click HERE

Image source: http://upload.wikimedia.org/wikipedia/en/b/ba/Free-living_amebic_infections.png

YOU MAKE ME SICK!!!!!

I do not hate many things....but I do hate some things....I REALLY DO! I am sick and tired of animal cruelty. I am mad as hell! Tonight I came back home after teaching a late lab. Exhausted from a very busy day I sat down with a bowl of cereal at my kitchen table. The Oak Bay Newspaper is on the table...so I start to look at it, without really reading. But then THIS STORY.

The goose had been shot in the bay at close range through the back with a Tru-flite, hunting-grade practice arrow. Unable to fly, the adult bird was paddling close to the bay’s western rocks when Waddell caught up with it. She picked up the compliant bird and tucked it beside her into the kayak.

So someone shot a Canada goose with an arrow at close range in Oak Bay...the animal must have been left for dead. Who the hell does a thing like that? Do we need to kill geese right here? Do we need it for food? NO! This was done by a sick person that needs to see what suffering is. Just for the kick of it! This is a totally gratuitous and cowardly thing to do. WHY? WHY? WHY? What are you trying to prove? So you got a bow...and an arrow...hey....what not try a big bird...RIGHT? Does a stupid gesture like that make YOU a better person? Are you helping anyone with this? What are you trying to prove???

There was the highly publicized case of Michael Vick and dog fighting charges....wow...what an athlete! What a role model!

To all of you who are harming animals, and I am not talking about hunting for food, I am talking to those who take a sick pride in harming animals...YOU MAKE ME SICK...for all that is worth to you!

Deadly space bugs

It is known that microgravity (MG) affects the way cells react. For example, astronauts coming back to Earth after a long time spent under very low gravity show signs of bone resorption and muscle mass loss. Bacteria react to low gravity too. In a paper published in 2002, Dr. Cheryl Nickerson and her team (see reference and link to pdf file below) discovered that the expression of many genes is in fact affected by MG (Figure on right). As can be seen, some genes are expressedm or not under normal gravity (1xg) but this expression pattern can be almost completely reversed under MG (or LSMMG - Low Shear Modeled Micro Gravity). Because gene expression seems to be influenced by microgravity, the obvious experiment was now to determine if the virulence of bacteria is increased un der MG...in other words are microbes susceptible to become "superbugs" in space? The answer, sadly, seems to be YES! In another study, to be published in PNAS, Dickerson and fisrt author James Wilson show that some virulence genes are in fact turned on by microgravity. In a mere 12 days in september, during spaceflight STS-115, Salmonella tiphymurium became more virulent. According to the authors, the shape of bacteria did not change but they seem to form a biofilm which is more difficult to eliminate by the immune system. In fact, when these "spacebugs" were fed to mice, they show a 3-times increase in virulence. Space is definitively a weird place to be...even for bacteria! Astronauts beware...bring your Purell!

For audio of this story follow this link

References:

1) James W. Wilson, Rajee Ramamurthy, Steffen Porwollik, Michael McClelland, Timothy Hammond, Pat Allen, C. Mark Ott, Duane L. Pierson, and Cheryl A. Nickerson. Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon PNAS 2002 99: 13807-13812

2) Wilson et al. Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq. PNAS doi/10/1073/pnas.0707155104.

Are we evolving?

Bacteria evolve right before our eyes. Hospital acquired diseases are a very good example. Overexpose bacteria to some antibiotic, toxins, metals etc...they will change in a matter of days, adapting to their new environment. Unicellular organisms have absolute freedom to change because their own evolution, as individuals, can only benefit the population. If they fail to adapt, some individuals will be eliminated BUT those who are successful will become the ancestors of a resistant colony.

Why is it that this principle can not be applied to our own cells? Simply put, because the fate of our own cells is interconnected, a small change in the genome could mean disaster for the other ones. The reason why our own cells do not evolve in our lifetime (under normal circumstances) is discussed in an article by Pepper et al., soon to be published in PLoS computational biology. An article on the Nature website (september 21, 2007)explain why evolution within our own cells is unlikely and not desirable. Our tissues simply DO NOT evolve!

It is known that epithelial tissues have a rather high turnover...old cells are replaced on a constant basis. The speed at which they grow could suggest that these cells are more prone to mutations. This is not the case. As Philip Ball explains in its news feature (Nature): "Why a person doesn't evolve in one lifetime" epithelial cells take a long walk on the way to differentiation. Epithelial stem cells divide just a little before they commit to their final state. Mutations can occur within these cells but since they do not compete against each other because these mutations make differentiation of these stem cells more difficult.

On the other hand, the immune system is made to evolve, it has to adapt to new pathogens every single day but there is a price we pay for this: a higher incidence for cancer!

Reference: http://www.nature.com/news/2007/070917/full/070917-11.html
Image source: http://www.digitalapoptosis.com/archives/science/cells2.jpg

Too funny or too pathetic...hummm...good question!

Lynn (AKA Babybluezephyr) wrote this in her blog:

"So I get a friend request from someone today that is a teacher at camosun, and is wanting to start a group for everyone in the class. Which in itself is pathetic."

I think I just might be the "pathetic one"...the culprit. Why ??? Well let me tell you that I teach at Camosun and that,on the 24th of August, I sent a request to my students to join a group that I created in Facebook. Why in the world an instructor like me would like to get students to join a Facebook group ? Because I need friends ?.....well...it's true that I just moved from Québec and that I left my very good friends behind...but no, it is not the reason. Because I want to be a cool instructor ? Well, I want to reach students but mostly, I want them to work together. The group I created in Facebook (for BIOL 124) is a study group that, I hope, the students will use to solve problems and understand that Web 2.0 tools are there to be used for learning and not just because to show funny pictures and talk about drinking habits - of course I exagerate a bit here. Are my intentions pathetic? Are they that funny? Well maybe for some...

Yesterday, I talked with one of my colleagues that is also a blogger. He wrote this:

Facebook is not where they go to learn. It’s where they go to socialize, relax and throw virtual food at each other.

After talking to him and reading his post I almost regret having created this Facebook group. I understand that students might not want me in their space but still many students replied to my request. When I think about it, with such a perspective, when I was 20-26 I just might have found a request to facebook pathetic....but maybe not....

Health Canada and the FDA have to regulate chicken soup!

Chicken soup....YUM. Especially my wifes chicken soup...sublime and soothing after a day of ski. Some of you were told by your grandmothers...."chicken soup is good when you have a cold". This amazing meal has health virtues that have been published in very serious journals...CHEST for instance. A quick search on Pubmed with the keywords "chicken" and "soup" gave me 77 hits...hey...not bad at all!!! Some of those studies use qui sophisticated instruments, jusst look at this one:

Measurement of the radical scavenging activity of chicken jelly soup, a part of the medicated diet, 'Yakuzen', made from gelatin gel food 'Nikogori', using chemiluminescence and electron spin resonance methods.International journal of molecular medicine. 2006 18(1): 107-111

Another publication offers a list of conditiions treated with chicken soup or soup made with other fowl. As an example here is a table from an article published in CHEST: Fred Rosner, MD (1980)Therapeutic efficacy of chicken soup. Chest, 78(4): 672-674.


Furthermore, it seems that using certain parts of chicken or fowl can have adverse effects:



Now...what do you (as a serious scientist) think of this abstract???

"A case is reported in which a previously healthy individual, having received an inadequate course of chicken soup in treatment of mild pneumococcal pneumonia, experienced a severe relapse, refractory to all medical treatment and eventually requiring thoracotomy. The pharmacology of chicken soup is reviewed and the dangers of abrupt termination of therapy are stressed"

Caroline, NL et Schwartz, H. 1975. Chicken soup rebound and relapse of pneumonia: report of a case. Chest, 67 (2) 215-216.

Finally, for your own pleasure here is a study of "sipping soup through a straw" and its effects on nasal mucus velocity...that's a gem!

Saketkhoo et al. 1978. Effects of drinking hot water, cold water, and chicken soup on nasal mucus velocity and nasal airflow resistance. Chest, 74(4) 408-410

Here is my very last question....how am I suppose to pronounce the first authors name? Is it...SAK-ATCHOO???

What are the odds?

Some people are sooo lucky! Just try to calculate the odds of this considering

1) Windspeed
2) Air moisture
3) Rotation of the Earth
4) Geographical position of the house
5) What happened a few million years back...
6) Angle of entry in atmosphere...etc...

I think you can sleep tight tonight...the odds are slim that you are going to get killed by a meteorite in your sleep...but it's still plausible...
Photo credit: http://www.flickr.com/search/?q=meteorite&l=4

Look mom....no hands!

I just hope that people using the games with this GADGET have enough brain cells left!

Photo credit: http://www.flickr.com/photos/evert-jan/72570274/

Can math and PCR save the elephants?

Ivory trade from elephant tusks is still going on despite its ban in 1989. Last year it is estimated that 3,000 elephants were killed. Between August 2005 and August 2006, 23,461 kg of ivory has been seized but the identification of poachers is difficult, partly because there is no way of telling where the ivory is coming from in Africa...until now!

In order to adress this issue and provide a better monitoring, Samuel Wasser and its team have demonstrated that DNA extracted from elephant tusks allows to determine if the elephant is from the savannah or the forest. These studies are based on microsatellite and mitochondrial DNA (Wasser et al., 2004, PNAS, 101: 14847-14852). In order to further identify the region where the elephants were killed, this same team designed a genetic and probalistic approach based Voronoi tesselation (Wasser et al. 2007, PNAS, 104: 4228-4233). These analysis allowed to identify a common region in Africa: most likely Zambia. Now, let's hope that Zambia will be monitored more closely and that the poachers, that decimated between 50 and 90% of the elephant population will be caught...

Another way to put a stop to elephant killing does not involve genetics or statistics knowledge...STOP BUYING IVORY!!!!

Traffic on the bridge...

Attention: Virus crossing ahead! Found this on Nature Cell Biology site. Absolutely amazing! Never heard of anything like that. Click here for a video of this remarquable finding!

Photo credit: http://www.flickr.com/photos/ryanpmurphy/363818292/

Paris Hilton's phenotype

Brain researchers have identified an enzyme apparently responsible for neuronal connections. It seems that glycogen synthase kinase-3 (GSK3) prevents memory loss. This finding could lead to interesting research leads in neuroscience and Alzheimer's disease. It could also explains Paris Hilton's peculiar phenotype, a lack of GSK3? She recently forgot to renew her drivers license...and
Associated Press decided to ban the publication of this amazingly important news.

Photo credit:
http://www.flickr.com/photos/laszlo-photo/149047693/

Isectomycology ?

Absolutely beautiful. Never heard of this before....silly of me not to know this existed! Natures is just perfect...unless you are the victim!

Fed up with hypocrits???

Unbelievable! I am so fed up with people saying one thing but doing the opposite... ARRGGH!!!!!





See for yourself here:
http://www.cbc.ca/world/story/2007/02/28/gore-electricity.html?ref=rss

Photo credit:http://www.flickr.com/photos/jetalone/378293806/

A well-rounded champion!

Can you draw a perfect circle in less than a second? This Ottawa teacher, Alexander Overwijk, surely can!

Modern art, Britney Spears hair and Brad Pitt's facial tissue...

I love art, especially contemporary art. One of my favorite painters is Barnett Newman and the National Gallery in Ottawa has one of its paintings...Voice of Fire (the title)...and it is just splendid! This special painting is nothing more that two vertical lines surrounding a red one (you can see it here). The museum purchased it in 1989 for 1.8 million (CDN). Is that too much for such a simple painting (although it is 18 feet tall)?

Maybe yes....but...maybe not! It depends! Some people would not spend a dime for it. After all, all this money could have been used for social housing, homeless people, shelters....biomedical research! On the other hand, this is the price to pay for a "Barnett Newman". Why? Because there is a market for it! Still not convinced?

Let me give you a little (and disgusting) example!

You follow someone and that person blows its nose and throws the facial tissue on the ground as he walks...are you going to touch that dirty facial tissue? Chances are, you are going to stay clear of that piece of softened cellulose with goo in it. BUT WAIT....that person in front of you is...YES...Brad Pitt! If you have just a bit of marketing brains, you are going to sell it on eBay (if you can prove it comes from Brad...maybe you can extract DNA from it). That SAME facial tissue now has a market potential! You understand? Sure you do! That is probably why you are not surprized by the fact that poor Britney's (boo-hoo) hair is now on sale on the internet...for a million bucks MINIMUM.

That's a lot of money for some keratin that grew in a head full of water....but that's just me!

Picture: http://www.flickr.com/photos/russelljsmith/9658510/

And...what about YOU?

Frequently I posts teaching tips and my feelings about teaching. I am interested in sharing experiences! Anyone with good stories are VERY WELCOME to write about them. Just tell me about them and I will create a link to you blog! I just want to create an exchange blog...but not just about me! So...what about YOU????

Photo credit: this image was modified and can be found at this site: http://www.flickr.com/photos/assbach/136040511/

Teaching tip #6: Open door

An open door is so much more than just a door. An open door invites for discussion, creativity and thinking. An open door is really telling your students that you care. An open door creates an opportunity for you to recall what you were then....just a kid with questions and, maybe, fear of the future! Now, there you are...a teacher, a professor, a parent or maybe.....a student! Remember where you come from. Just remember!

Photo credit: http://www.flickr.com/photos/yewenyi/

Distance Learning...wonderful!

I started to teach a course with some students in the classroom and some in another city. It works perfectly well for several reasons:

• I am aware that the distant students are AS IMPORTANT as the students are in the class room
• I am aware that distant students need 2 to 3 seconds before they can hear me and I have to patient for their feedback
• I refer to them just as much as I refer to the students in the classroom (see first comment)
• Technical staff is ESSENTIAL for successful distance learning
• I am using tools that make sure students see where I am going...no laser pointers here!

Picture credits: http://www.flickr.com/photos/philipyk/

Teaching tip #5 - a quick survey tells you where they fell

You are a good teacher...not doubt about it! You care and your students know that! But did they get everything you wanted them to get? Did they reach YOUR objectives? After class, ask them to write on a sheet of paper what THEY think was the most important message of your lecture. If it was in line with your own objectives...bulls eye! If not...next time make sure to come back on the last lecture. Easy!!!

A new nail in the intelligent design's coffin!

A new paper published in Nature indicates that an increase in atmospheric oxygen levels might have "stimulated the evolution of macroscopic multicellular animals and the oxygenation of deep oceans".

This new oxygenation is considered as a very stressful event in our planet natural history because oxygen usage means free radicals production and protein (and DNA) damage. It would be very interesting to compare phylogenetic data from anti oxidant and DNA repair proteins. If this theory is right, we should be able to correlate atmospheric/ocean oxygen increase with cellular molecular protection.

Reference: Fike, D.A., et al. (2006) Oxidation of the Ediacaran Ocean. Nature, December 2006, p 744-747.

Teaching tip #4 - DO YOU CARE ENOUGH?

I read this somewhere:

"People do not care about what you know until they know how much you care".

Caring is the MOST important thing when it comes to teaching. It does not matter if you are a seasoned professor or a novice...if you do not care, it shows or it will show very quickly. Students are not idiots and they will not care either. If you should ever stop caring, take a break. You might be burned out, or begin to be. If after that break you still do not care, your flame is out......choose another career...for the students sake!

Nanotechnology as pollution?

Nanotechnology holds big promises. Nanotechnology could even, a day, revolutionize the way we treat or prevent disease, the way we look, the way we think and even the way we go to war.

Nanotechnology is as inspiring as year 2000 was, back in the 50's. It is far away but still it is already here. The problem is this, nanotechnology could, one day, be a very big problem. How do we get rid of microscopic things that do not respond to medication, antibiotics or antivirals. We already thought of creating new devices that seem promising, but have we thought of poential solution to real future problems? Some particles could be so small, there is a potential for them to be endocytosed by some tissues. They could gain access to vital organs like the brain, kidneys or liver. Günter Oberdörster is a researcher in the field of nanotoxicology and his studies prove that nanoparticles can gain access inside the body through inhalation.

At the cell level, those nanoparticles can be ingested by specialized cells called macrophages. These cells, that have evolved to destroy microorganisms, can move from blood circulation to tissues and back to blood. This way, they can transport nanoparticles to tissues. These cells, when they die, will spill this nanopollution. Nanoparticles, many of them, have a very stable form. Bucky tubes and bucky balls are made of carbon and their molecular configuration makes them as stable as diamond (which is also carbon). Once in the tissues, they could stay there for a very long time and nobody can predict what can happen.

We, humans, have this problem....we create problems to which we have no solutions. Silly human race....