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um… I am not a big fan of fuel cells (explained elsewhere) since they are electrical based and the amount of pollutions created during the manufacturing of its reactants is equally if not worse than burning diesel fuel. 

A major break through was announced today on the potential of using switchgrass (yeah the weed that grows on marginal farm land) to make ethanol.  The effort was led by Kenneth Vogel, a geneticist with the U.S. Department of Agriculture in Lincoln, Nebraska.  Vogel and his colleagues basically enlisted 10 farms and demonstrated the following.
1. Ethanols produced from switchgrass is as much as 540% efficient than the total energies (diesel trucks fuels etc).
2. The carbon pollution emitted to the atmosphere upon combustion is equivalent to the amount of greenhouse gases (CO2) absorbed.  i.e.  it’s carbon neutral.

Reference:

On a recent literature scan, I couldn’t help but notice that Paris Hilton has been mentioned in the notoriously popular Science magazine.  A recent study from the McGill university in Toronto has found that male mice stops licking their painful site of injection when a cardboard cutout of Paris Hilton is present!!  Whatever the conclusion, I wondered who would fund such project.  Turned out, since the US dollar is weaker than the CA dollar, the Canadians could finally start to do some cool experiments.  The results suggests that mice actually use their eyes in addition to olfactory system in determining whether they’re in danger or not. 

Credit: Greg Miller
ScienceNOW Daily News
5 November 2007

Recently I joined this public opinion forum and one of the first topic I saw was on the genetics of homosexuality.  Are these folks homosexual because they choose to? or it’s genetics?

So, while currently this topic is still being debated,
we can first look at several lines of evidence on whether genetics may
be at least partially contributing to the final outcome (homosexual/or
not).

Hypothesis 1:  If there is a strong genetics component in determining
sexual orientation, then it must be heritable.  It means parents are
passing it from one generation to the next.  Therefore, individuals who
share large percentages of their genome with one another would have
higher probability (risk in other context) of having the phenotype
(homosexual).  Heritability is defined as the proportions of phenotypes
that could be accounted for by the genotypes.  In nature, no one is
more similar to each other than his or her own maternal/identical twin.  It would be the perfect natural experiment!  The goal then is to ask
given that two individuals are identical in their DNA, what is the
probability of one twin becoming homosexual if the other twin is
already homosexual?  Several studies have looked at exactly this topic
and it is found that this trait is highly heritable (50-60% explained
just by DNA alone) in female and modestly heritable in males (~30%).
Some of you may think WOA this is actually saying if the DNA between
two peons are identical there is ONLY 50% chance that the other twin is
homosexual? that’s like tossing a coin right? 
(ref: Kirk et al Behavior Genetics 2000 Jul;30(4):345-56.)

Well to put things in perspective… many disease we consider highly
heritable actually have a modest to small genetic component.  For
instance, we think if one family member has cancer then the chance of
having cancer in other family members, especially twins, is VERY
high… well how high? actually ~ 10% if lucky.  Thus, you can see,
that explaining 50% of the homosexuality cases by genetics is actually
quite high (vs 10% in cancer)!

Some may argue the mere fact that homosexuality produces no offspring,
its genetically unsuccessful nature, would not favor its very own
existence because the genes do not get passed down to the next
generation.  He he he… well we can explain this phenomenon by using
the magic words "complex genetic traits" or "quantitative traits."
These terms basically suggest the underlying genetic cause(s) may
involve many many genes and while each gene may produce a favorable
outcome (reproduction of the offspring), a certain combination of gene
variants may produce a homosexual individual (I could provide a solid
example, but please think about it first).

Hypothesis 2: If Sexuality is determined by genetics, the underlying
physiology should also be different?  Do we have any evidence for a
physiological differences between homosexuals and heterosexuals?

Recently, the brain images of homosexuals versus non-homosexuals were
obtained (with heterosexual women as control) using functional Magnetic
Resonance Imaging (fMRI).  The study basically studied two pheromones,
4,16-androstadien-3-one (AND) and the estrogen-like steroid
estra-1,3,5(10),16-tetraen-3-ol (EST).  AND is detected
primarily in male sweat, whereas EST has been found in female
urine. They compared the pattern of activation induced by AND and
EST among homosexual men, heterosexual men,
and heterosexual women. Interestingly, in contrast to heterosexual men, and in
congruence with heterosexual women, homosexual men displayed
hypothalamic activation in response to AND. The authors noted that
maximal activation was observed in the medial preoptic area
anterior
hypothalamus,
which, according to animal studies, is highly involved in sexual
behavior. These findings show that our brain reacts
differently to the two putative pheromones compared with common
odors, and suggest a link between sexual orientation and
hypothalamic neuronal processes.  So again, underlying genetics control
how the brain developed, and we now know for a fact that homosexual
brains functionally are different.  Sorry to the lesbians, no similar
studies have been done on lesbian brains.
(Ref: Savik et al, Proceedings of National Academy of Sciences of the USA, 2005)

The public often have this preconceived notion about stem cell research, that we owe to kill the embryo in order to harvest the embryonic stem cells, right? NO!! well yes just until recently when a group of scientist led by Robert Lanza of Advanced Cell Technology in Worcester, Massachusetts announced this week that they have successfully established embryonic stem (ES) cell lines without having to destroy the embryo.

The trick is to remove a single cell (blastomere) from an early cell mass known as a blastocyst (an
eight-cell human embryo).  The same technique, known as preimplantation genetic
diagnosis, is used to biopsy laboratory-made embryos for genetic
abnormalities. After the single blastomere is removed, the seven-cell
embryo goes on to develop normally. The even trickier part is that by suspending this extracted single cell close to the 7-cell mass, it received the proper signals and guidance to continue to proliferate. 

Eventually, the blastomeres were removed to a group of mouse support
cells that helped maintain the human cells as ES cells. Meanwhile, the
original blastocyst embryo was safely returned to the freezer. "These
are the first human embryonic stem cells in existence to be made
without destroying an embryo," said Lanza, whose team is preparing the
findings for publication.

With this breakthrough, congress(and especially the white house) really owe to rethink the possible therapeutic benefits of Stem Cell research and regenerative medicine.  Now that we have bypass the ethical and legal issues dealing with a human being, the next step should be asking what sort of signals are being passed onto the blastomere that would eventually turn into a pleuripotent ES cell line?  I hope, in our life time, we could achieve regenerating livers at least.

So all you alcoholics, praise stem cell research please.

Source: ScienceNOW Daily News, June 19th, 2007

It’s been awhile since the last attempt to clone primates.  Recently at an international stem cell research conference a team of US researchers reported the success in cloning embryonic stem cell from rhesus monkey.  They were able to remove the chromosomes from the primate eggs, and replace them with the chromosomes of skin cells.

about ~8% success rate was reported (21/278) in producing a hollow embryonic ball (called blastocyst), with the right polor axis and orientation.  Eventually, 2 embryonic stem cell lines were created.  This means the cells in the cell line could  be "told" to turn into specific tissues/organs/organisims later.  The work was carried out by
Shoukhrat Mitalipov of the Oregon National Primate Research Center in
Portland and colleagues.

source: Nature 447, 891      (21 June 2007)

Crocodiles, Fairies, Pirates, and Indians… how do you re-conjure up
the lost memory of childhood from these old, stubborn, and just acerbic
adult bodies of ours?
I find it increasing difficult for grown-ups to even think near the
edge of box, let alone outside the box and beyond the box.  How could
we ever free our mind?

In the world of often pressing daily annoyances, fights, deaths, and quarrels, our minds are constantly either jaded, drugged, or empty.  Duties and tasks become so mechanical and methodical, we became no different than machines, the breathing, walking…brain dead.

In my recently found past time, I find this movie amusing and could relate somewhat closely with it.  In the movie Finding Neverland, Academy acclaimed actor Johhny Depp is
the child who never wanted to grow up, who tried everything in his
power NOT to be a star (well… good try).  While he constantly struggled to make peace with the society, he could not find even find peace with his family.  Equally mesmerizing, Kate Winslet played a
widowed mother with four children who longed for this magically place called
Neverland. Eventually, she could toss away the stifling struggle of life and live to believe in fairytale.  Equally painful is the process of growing up, the children must face the death of their mother.  But how do they come to a consensus between their imagination and reality?  Where do they find the tipping equilibrium?  Without giving anything further away, I think this movie is one of the best I’ve seen.  it’s a story about the original author of Peter Pan, how he struggled in life to help a poor widow and an old mother to start believing in Neverland again. 

Interestingly, Neverland is a vague psychological symbol, it is a
place that is different depending on who you talk to.  Some would say
it’s a place where your imagination is unlimited, others would tell you
it’s a place where you never die…etc  It’s amorphous enough
where we could make it anything we want to be.

The bottom line, however, which I think is also the most beloved key of this movie, is perhaps the fact that Neverland promised one would find limitless possibilities with no rules and boundaries in this Uptoia of free minds!  Depp is just a fascinating character. When
you watch him in the film he’s unbelievably under the age of twenty! 

So where do we find peace? Does it represent that bit of complacency we find in ourselves when we die?  or we could live to see Neverland?

The major banks and security agencies currently use what’s call an RSA 1024bit encryption for secure transaction etc.  Basically, the server has a public key which is freely transmitted via the net while the client holds a private key which are the prime numbers (non-divisible factors) of the public key.  Only client hold the private keys.  The trick on hackinginto the system is to decipher or brute-forcely firgure out the prime numbers by factoring a large number.  Recently, a team of mathematicians has set a new record for factoring a large
number into primes, breaking a massive 307-digit number into its three
indivisible factors and beating the previous record by 30 digits.  When translated into bits (1s and 0s), it’s an astounding 1017-bit encryption, meaning if you got anything less than 1024 encryption, their algorithm will break it. 

The new trick/breakthrough is at the distributed computing level, by taking advantage of computers NOT all at the same facility but anywhere on the planet.  One could easily see if a hacker could gain control of large number of computing power across the globe, he/she could almost break into anything.  Specifically, the gaming consoles such as the late PlayStation3 are optimized for number crunching and the fact that they’re networked make them easy targets. A quick "borrowing" of  a swarm of PS3s would crack open a secure network within minutes. 

It took the team of scientists 95 CPU years to crack open the 1017-bit number, which  is equivalent to 3Billion CPU floating operations (flops) seconds.  The latest tally suggests over 5Million PS3s sold and assuming about 3 millions are networked, it would only take about 16-20 minutes to crack open any secure connection!
But… don’t be too worried, it’s easy to up the encryption number. In fact, the 1024 encryption was upgraded from the previous 512-bit encryption when a similar algorithm was developed in 1999.

Reference: http://sciencenow.sciencemag.org/cgi/content/full/2007/523/1

While the title of this post suggests a focus on microbiology, disciplines in medical science are so intricately woven together, it is hard to define one specific topic without touching its relevance in other fields. 

If you ever worked or visited large hospitals, you’d know what I am talking about.  Imagine a cancer patient.  Because he/she often received large dosage of radiation or chemo-therapy, there is a general lack of strong immune system, giving plenty opportunities for bacteria infections.  Also, the late over-use of anti-microbial agents have resulted in massive development of antibiotic-resistant bacteria IN or AROUND hospitals.  One common germ we find around us (even as we speak now) is a bug call Staphylococcus aureus.  Staphylococcus for it’s round shape and aureus for it’s golden color.  It’s usually harmlessly living in the nose or skin of a healthy person (remember that first hand-shake?? hehehe).   Complications arise when the skin-barrier has been broken, which allows the bacteria to sneak in and attack. S. aureus can cause a wide range of infections from common pimples to pneumonia etc.   Also, this bug could withstand hydrogen peroxide and form blood clots!!  So your normal Sav-on/Long’s drug H2O2 would have no effect here.  Even worst, an immuno-suppressed person who is more susceptible to bacterial infection often resides within the hospital where antibiotic-resistant S. aureus may likely to share the same residence! Giving medications (antibiotics) without knowing what strains of the bug a patient may have often accelerates the infection and exacerbates the condition. 

Recently, a "crystal structure" of a critical enzyme called Extracellular Fibrinogen -binding protein (Efb-C), produced S. aureus was solved, meaning we now know what this enzyme "looks" like, thus could infer how it may function.  This enzyme helps the bug evade our common defense against the microbial community, called the complement system.  The complement system is basically a set of reactions (cascade) that generates a large sticky ball around the bug, engulfing and neutralizing it (them).  Efb-C basically blocks this cascade from occurring, thus rendering our primary defense useless.  Once the crystal structure of Efb-C is solved, we could design novel small molecules to target this protein, thus creating a NEW kind of antibiotic! 


Let’s now go back to the hospital scenario.  Once a person has been identified of carrying antibiotic resistant S. aureus, we could administer this new drug and save the patient from potentially life-threatening complications (meningitis, Pneumonia etc).  What’s the moral of the story? um… wash your hands and stop touching yourself the whole day.  Oh yeah, for those internet cafe goers, wipe the keyboard and mouse or wash your hands after an evening of CS or Doom!

Credit: Michal Hammel, Georgia Sfyroera, Daniel Ricklin, Paola Magotti, John D Lambris, Brian V Geisbrecht Nature Immunology
8, 430 - 437
(01 Apr 2007)
 

The retinas of most non-primate mammals contain only two classes vision cells that support dual-colored vision. In human and other primates, a duplication occurred on the x-chromosome, allowing for trichromatic vision(!!!!)- and hello to RBG color.

Obviously, having the peripheral sensory perception such as being able to see tri-color goes hand-in-hand with having the proper neuronal circuitry (the wires) to interpret it.  Interestingly, New World Monkeys do not have this x-chromosome duplication of the photoreceptors.  They were able to see color vision via changes in their single gene.  And something called an X-linked inactivation (similar mechanism that produces the Calico cat) could produce patches of color R, color B, and color G.  So, scientists thought may be the hardware is in place long before we had the physical traits to see color.  Nature is waiting for this one last step before committing to full color vision!

Recently, scientists at the Neuroscience research institute at UC, Santa Barbara and the Departments of Opthalmology, medicine, and genetics at Johns Hopkins University were able to insert a color rod receptor gene into mouse.  Their initial result shows the mouse do seem to respond to color now!! They ask can the brain have enough plasticity (a fancy word for being flexible) in interpreting this new dimension of color discrimination? 
It turns out that mouse with newly acquired skill have changed physiological behavior and were able to discriminate along the axis of this new color dimension.  This means, these animals do have the neuronal capacity but not yet the proper physiological/genetic endowment.  Imagine inserting a gene that allows the mouse to talk!! hehehe

Reference: Jacobs et al, Science 23 March 2007:Vol. 315. no. 5819, pp. 1723 - 1725

One of my most sought-after question is what makes us (Homo sapiens) human? We often associate humans with a species who knows how to make tools, how to commit murder (or genocide), and get high on some psychedelic mushrooms/drugs.  Yet, recently a report from Senegal (March issue of Current Biology) showed a picture of a chimpanzee (7 millions away from humans) making a spear and jabbed out a bush baby from a tree trunk!!  Prior to this discovery, making lethal weapons for hunting was exclusively humanly feature!!

Some of you may wonder what is a bush baby?? because I did well… here it is.

LOL

Chimpanzee killing bush baby~

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Okay… that was just a joke.  Here is a real picture of the bush baby

Courtesy from David Haring’s website www.haringphoto.com/about

And appeared in Science the images of chimpanzee shooting a spear.

Courtesy P. BERTOLANI/CAMBRIDGE (PHOTO AND INSET)

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Well… survival of the fittest at work here… we need to tell Bush to stop teaching chimps how to make high-tech weapons!