My scientific world is probably best defined as medium-to-small.  Because there’s usually a tie-in to a molecule, my conceptual world operates somewhere between the slightly sub-nanometer to human sizes of meters and kilometers. Except for my occasional forays into astronomy, I don’t often stretch my mind to light-years or cram it down to subatomic particles. But even then I’m often writing about the chemical stuff in cosmic clouds or the composition of Mars dust. But even the molecular world is maddening when trying to talk about size.

Science writers– particularly when we delve into the abstract– depend on reliable size comparisons. We can spend hours trying to come up with an appropriate size analogy as we desperately dodge  cliches.

But the internet is wonderful, and I’m continually amazed by its power to illustrate. Yesterday, via Amy Rice Doetsch, a science educator friend, I found out about this amazing web resource that bridges the wilds of biological sizes from coffee bean to carbon atom. In this case, a very slick set of graphics provide the equivalent of paragraphs of size perspective.

Then I went looking for even broader comparisons, and found this one– not quite as graphically refined– but one that goes all the way from cosmos to quark. I’d love to hear of other examples. In the meantime, enjoy!

ASU O-Chem Dude

This particular chem project (written report) wanted drawings, so I took full advantage!  And it’s easier to draw my own than figure out how to cite photos!!  The chemical drawn is caffeine, if you were curious.

An article was published in the scientific magazine “Nature” called “Cells go fractal” on September 4th. The article reported on the findings of research done at the European Molecular Biology Laboratory (EMBL) as it was published at the ‘2009 European Molecular Biology Organization (EMBO) conference’ held in Amsterdam.

Experiments done by Sebastien Huet and Aurélien Bancaud in a research group led by Jan Ellenberg at the EMBL in Heidelberg, Germany, tracked the movement of molecules within cells, this was then compared the pattern of movement against mathematical models. It was found that, large molecules moved according to the same rules as small molecules, suggesting that their environment was therefor fractal.

The researches were able to track the behaviour of the cells by means of injecting live mouse cells in a lab dish with fluorescent molecules. They were able to track the molecules with this special type of imaging in microbiology called fluorescence microsopy. The study focused on how cells can keep track of gene activity or gene expression through chromatins in the cell nucleus.  Basically this process takes place to ensure the right molecules interact with each other at the right time and in the right place in the cells. Huet and Bancaud found that the molecules moved as if they were having to navigate obstacles (but there are no barriers, as they exist in other parts of the cell) to navigate around in the cell nucleus. When the team looked at the behaviour of different sized molecules, they saw that large molecules were obstructed to the same degree as small molecules in the cell nucleus.

It was furthermore discovered by studying how proteins, bound to different kinds of chromatin (namely Euchromatin and Heterochromatin), moved around in the cells and found that the different types of chromatin were fractal in different ways. Meaning molecules behaved differently for each type of chromatin with its own distinct fractal characteristics. All this information could be used to learn exactly how cells use a fractal structure to change the behaviour of proteins to change particular DNA sequences and skip whole other parts of the DNA sequence. It’s also expected that with insight into these fractal structures researches can learn how to better target certain areas of DNA for study or perhaps in the future even for new types of treatment for disease.

Links:
http://www.nature.com/news/2009/090904/full/news.2009.880.html
http://www.nature.com/
http://fractuality.wordpress.com/files/2009/10/cells-go-fractal.pdf

http://www.embl.de/
http://www.embo.org/

http://www.embl.de/research/units/cbb/ellenberg/members/index.php?s_personId=4421
http://www.embl.de/ExternalInfo/ellenberg/homepage/bancaud.html
http://www.embl.de/research/units/cbb/ellenberg/members/index.php?s_personId=939
http://www.embl.de/ExternalInfo/ellenberg/homepage/labmembers.html

http://en.wikipedia.org/wiki/Microbiology
http://en.wikipedia.org/wiki/Cell_(biology)
http://en.wikipedia.org/wiki/Molecule
http://en.wikipedia.org/wiki/Fluorescence_microscopy
http://en.wikipedia.org/wiki/Gene_expression
http://en.wikipedia.org/wiki/Cell_nucleus
http://en.wikipedia.org/wiki/Chromatin
http://en.wikipedia.org/wiki/Euchromatin
http://en.wikipedia.org/wiki/Heterochromatin
http://en.wikipedia.org/wiki/Protein
http://en.wikipedia.org/wiki/DNA_sequence

Glucose

Fred l’un de mes anciens collègues de travail vient de me soumettre ce lien que je trouve fort instructif.

Il nous permet de découvrir ce qui nous entoure avec la découverte du monde de l’infiniment petit.

Il ne s’agit pas d’une application très récente, ni très poussée, mais elle permet d’apprendre en famille de façon originale.

En utilisant le curseur on accède à un univers qui parfois nous échappe.

Ludique cela permet à tout à chacun d’avoir une idée de la taille des cellules, atomes, virus et autre molécule d’eau…

Bonne découverte ou redécouverte!

Two American Alligators (Photo/Matthew Field)

Oh alligator love, it’s not as fickle as you might think. Get on a gator’s good side and you may just have found a friend for life, if you’re another alligator of course.

In a study that combines field science with molecular biology, researchers from the Savannah River Ecology Laboratory found that alligators were surprisingly loyal partners and akin to birds in their mating habits. The discovery offers new insights into evolutionary links and behavior of crocodilians, birds and dinosaurs – and certainly, at least where one science writer is concerned, proving there is a lot more going on behind those alligator eyes than a cold reptilian stare.

Researchers trapped and re-trapped alligators at Louisiana’s Rockefeller Wildlife Refuge, 76,000 acres of alligator dream real estate bordering the Gulf of Mexico. “Given how incredibly open and dense the alligator population is at RWR, we didn’t expect to find fidelity,” said researcher Stacey Lance. “I don’t think any of us expected that the same pair of alligators that bred together in 1997 would still be breeding together in 2005 and may still be producing nests together to this day.”

Crocodilians have already proven to be more invested in the care of their offspring than most other reptiles, actively nurturing young and defending nests. Crocodiles are even known as considerate egg-layers. As a female drops the egg, she will blindly catch it with a hind leg before it hits the ground and gently place it in the nest. But up until now alligators were thought to be polygamous, mating with several different partners and leading to many fathers for a single nest.

After ten years of following alligators at the refuge, scientists Lance, Travis Glenn, Ruth Elsey and Tracey Tuberville discovered that 70 percent of female alligators stick with who they like. Even if they have multiple partners, the same bachelors get picked year after year, regardless of whether females encounter a new slew of potential suitors.

The study marks the first time fidelity has been observed in any crocodilian species. “In this study, by combining molecular techniques with field studies, we were able to figure something out about a species that we never would have known otherwise,” said Lance. “Hopefully future studies will also lead to some unexpected and equally fascinating results.”

Results of the study were published in the October 7 issue of Molecular Ecology.

Smallest to Largest

Have you ever looked around at everyday objects and wondered what they are made of? Easy some may say, wood for a desk, rubber for a tube, but then what is the wood and rubber made of? It is like an infinite path down the road of no return. But for everything as we know it, there is a beginning and an end – life and death. In this article I shall increment from the smallest proven known, and I emphasize on the words known and proven, particle, the photon, to the largest known proven object in existence, the universe. It turns out that this topic is more complicated that can be imagined and will be left open for discussion and review, and please note not all these particles and objects can be measure on the same scale system.

Photon: size 0
This is the beginning of our journey. A photon is an elementary particle, the quantum of the electromagnetic field and the basic “unit” of light and all other forms of electromagnetic radiation. The mass of a proton is zero but yet can still be observed at both microscopic and macroscopic level due to it not having a rest mass. They exhibit properties of both waves and particles in the sense that they can bump off each other yet behave normally like waves and are diffracted. The photon is massless, has no electric charge, and does not decay spontaneously in empty space. During a molecular, atomic or nuclear transition to a lower energy level, photons of various energy will be emitted, from infrared light to gamma rays with a speed of ‘c’ (speed of light) in open space. There is however a theorized smaller particle, namely the Higgs boson, aka the God particle. But we shall not divulged into that just yet until the folks at CERN make a hopeful discovery.

Neutrino: close to 0
Closely followed to the photon is the neutrino which as well has a mass of near 0. These particles are created as a result of radioactive decay or nuclear reactions such as those in the sun. Neutrinos are very difficult to discover as they pass through objects nearly unnoticeable. Only experiments deep underground where nothing can interfere have scientists observed these particles. Heres a fun fact, more than 50 trillion solar electron neutrinos pass through the human body every second.

Electron: 9.11 × 10^−31 kg
An electron is a subatomic particle that carries a negative electric charge. It has no known substructure and is believed to be a point particle with a mass that is approximately 1836 times less than that of our next particle, the proton. Electrons also have quantum mechanical properties of both a particle and a wave, so they can collide with other particles and be diffracted like light. Electrons are the particles that circulate around the nucleus of an atom. The electron has a mass of just 9.11 × 10^−31 kg.

Quark: < 1.67 × 10^−27 kg
The quark is a fundamental constituent of matter making up stable particles namely hadrons such as protons and neutrons.

Protons/Neutrons: ~1.67 × 10^−27 kg
Protons and neutrons usually form the nucleus of an atom and the majority of an atom’s weight (99.9%). They have a mass of around 1.67×10^−27 kg. The two particles are bound by nuclear force into atomic nuclei.

Atom: 1.67 × 10^−27 to 4.52 × 10^−25 kg
The atom is a basic unit of matter consisting of a dense, central nucleus surrounded by a cloud of negatively charged electrons and a mix of positively charged protons and electrically neutral neutrons at the centre. The masses of atoms range from 1.67 × 10^−27 to 4.52 × 10^−25 kg. More information can be seen in a periodic table.

Molecule: > 1.67 × 10^−27
A molecule, the smallest particle of a substance that retains all the properties of the substance, is composed of one or more atoms. A molecule may consist of atoms of a single chemical element, as with oxygen (O2), or of different elements, as with water (H2O). Most molecules are far too small to be seen with the naked eye, but there are exceptions such as DNA, a macromolecule, that can reach macroscopic sizes. Single molecules cannot usually be observed by light (as noted above), but small molecules and even the outlines of individual atoms may be traced in some circumstances by use of an atomic force microscope.

Red Blood Cells: 6-8μm
Red blood cells are the most common type of blood cell and the vertebrate body’s principal means of delivering oxygen to the body tissues via the blood. They take up oxygen in the lungs or gills and release it while squeezing through the body’s capillaries. There is no standard size for them, but average estimates put them at standard size of about 6-8μm.

Home Sapien: 100µm to 2.72m
The great home sapien, oh what a wonderful creature, James Sweitzer once said: “As much as we have progressed in science, we are still finite creatures with limited conceptual abilities and imperfect observational tools – but add one thing, we are curious at that”. We as a creature are the most highly evolved that lives on this planet Earth. What makes us is our highly developed brains, capable of abstract reasoning, language, introspection, and problem solving. We humans range in size, but the minimum and maximum is ambiguous, for at what stage do we become human once the little sperm enter the egg. Or are we only human once we are born? If we begin at the stage of the egg then we are 100 and 200 µm in diameter so to speak. The tallest human to determined was a man in USA namely Robert Pershing Wadlow at 2.72 m (8 ft 11.1 inches), but of course who knows, there could have been taller people back in the days.

Great Pyramid of Giza: 3.8 million metric tons
Located outside Cairo, Egypt, the great pyramid of Giza is the oldest and largest of the three pyramids located in the vicinity. Construction began around 2540BC and concluded around 20 years after. The pyramid was once 146.6 meters (480.97 feet) tall, but due to erosion is shrank down to a still impressive 138.8 m (455 feet). It is roughly 2,500,000 cubic meters. With an estimated weight of 3.8 million metric tons.

Three Gorges Dam: 34 million metric tons
Next on our list is the Three Gorges Dam, spanning the Yangtze River in China. The dam weighs about 34 million metric tons, has a length of 2,335 meters (7,661 ft) a height of 185 m (607 ft), and width (at the base) of 115 m (377.3 ft). The dams main structure was completed in 2006 for an estimated us$39 billion.

Mount Everest: 3.04 x 10^5kg
Mount Everest is the highest mountain on Earth, and the highest point on the Earth’s crust, as measured by the height above sea level of its summit, 8,848 meters (29,029 ft). The mass is estimated as 3.04 x 10^5kg. The mountain, which is part of the Himalaya range in Asia, is located on the border between Sagarmatha Zone, Nepal, and Tibet, China. Everest has claimed 210 lives, including eight who perished during a 1996 storm high on the mountain. Conditions are so difficult in the death zone that most corpses have been left where they fell. Some of them are visible from standard climbing routes.

Earth: 5.97 × 10^24 kg
Earth is the third planet from the Sun. It is the fifth largest of the eight planets in the solar system, and the largest of the terrestrial planets (non-gas planets) in the Solar System in terms of diameter, mass and density. Its Mean radius is 6,371.0 km and has an estimated mass of Mass 5.97 × 10^24 kg.

Jupiter: 1.90 × 10^27 kg
The next heaviest planet in our solar system is Jupiter with a mass of 317 Earths (1.90 × 10^27 kg). It is the fifth planet from the Sun and the largest planet within the Solar System. It is a gas giant with a mass slightly less than one-thousandth that of the Sun but is two and a half times the mass of all of the other planets in our Solar System combined.

Star: 2100 solar radii or 7 quadrillion Earths
I have groups all stars as one as they vary dramatically in size, our sun is a star and is in fact tiny compared to all others which really does get you thinking, first have a look at this image (notice the sun in that image is not even a pixel!) and then this video – that video should really get you thinking. Our sun has a diameter of 1.39×10^9 m with an estimated mass of 1.99×10^30 kg (332,900 Earths). Now to put that into perspective, the largest known star is VY Canis Majoris with a size between 1,800 and 2,100 solar radii (basically 1800 of our suns can fit in its radius). Assuming the upper size limit of 2100 solar radii, light would take more than 8 hours to travel around the star’s circumference, compared to 14.5 seconds for the sun. It would take over 7,000,000,000,000,000 (7 quadrillion) Earths to fill the volume of VY Canis Majoris.

Galaxy: 200 million LY
A galaxy is a massive, gravitationally bound system that consists of stars and stellar remnants, an interstellar medium of gas and dust, and an important but poorly understood component tentatively dubbed dark matter. Typical galaxies range from dwarfs with as few as ten million  stars up to giants with one trillion stars, all orbiting the galaxy’s center of mass. These galaxies each consist of million to trillions of solar system, which makes you wonder, we cannot possible be alone, especially taking into account that fact that there are 100 billion observable galaxies. In 1961, Dr. Frank Drake developed an equation that estimates the number of technologically advanced civilizations that might exist in our Galaxy alone. Frank Drake’s own current solution to the Drake Equation estimates 10,000 communicative civilizations in the Milky Way.

In 2005, Japanese astronomers have discovered what they call the largest object in the universe: a colossal structure 200 million light-years wide that resembles a swarm of giant green jellyfish. This young galactic blob could reveal how and when the earliest galaxies formed.

Universe: 46.5 billion LY
The universe is the theoretical limit, the all encompassing region that holds everything together. The age of the Universe is about 13.7 billion years, but due to the expansion of space we are now observing objects that are now considerably farther away than a static 13.7 billion light-years distance. The edge of the observable universe is now located about 46.5 billion light-years away. It contains about 10^80 atoms, with the vast majority of the energy density contributed by the mysterious dark matter and dark energy. Some theories however state that the ‘World (meaning everything possible in this context)’ consists of many galaxies. Picture them as sheets of paper next to each other flowing in the wind. A theory developed from this was that two of these papers struck each other and started off the development of out universe from the big bang.

What really got me thinking is that atoms are somewhat like solar systems, with the sun as the nucleus and planets as electrons. Now atoms make up molecules in the same way that solar systems make up galaxies. Galaxies compose the universe along with the mysterious dark matter the same way that quarks and electrons, protons and neutrons make up atoms. So from this sort of ratio the universe contains all the galaxies and solar systems etc. what if the so called God particle is a universe?

The upper and lower boundaries of this list are not static and are just known facts we currently have. So lets summarize the scale line:
Photon – Neutrino – Electron – Quark – Proton/Neutron – Atom – Molecule – Red Blood Cell – Homo Sapien – Three Gorges Dam – Mount Everest – Earth – Jupiter – Star – Galaxy – Universe.

–openpit

Ordinea găsită în viaţă constă, pentru scopurile noastre prezente, în două tipuri principale. Primul este acel tip de ordine găsit în ondulaţiile de pe ţărmul mării; acesta este tipul de ordine care se găseşte în bio-monomerii care stau la baza întregii ordini materiale ce întreţine viaţa. Al doilea tip este cel găsit în informaţia codificată înscrisă în filamentele şi spiralele moleculelor de ADN şi ARN. Deoarece această a doua ordine conţine ordinea succesivă sintactică a unui tip, adunând codul într-o propoziţie scrisă.

Moleculele de ADN şi ARN sunt nişte fire lungi, formate din lanţuri spirale de bio-monomeri secvenţializaţi . Secvenţele ascund un cod care oferă informaţie şi instrucţiuni pentru sinteza proteinelor pe care se clădeşte viaţa. Informaţia este conţinută sub forma unui limbaj de patru litere, de tipul „abcacddcabaacdbbcad” etc., care se continuă cu mii de litere. La fel ca ţi în alfabetul real, succesiunea este cea care dă semnificaţia (succesiunea literelor d, a şi n: dan – nume, dna – adn în engleză).

De aceea, este clar că literele rămân aceleaşi, însă informaţia transmisă este determinată de succesiunea literelor din acest tip de ordine. Sinteza fiecărei proteine în organism este controlată de gena ei care este o porţiune a filamentului de ADN care conţine secvenţa ordinii genetice, care se comportă ca un şablon pentru sinteza secvenţelor moleculare specifice ale proteinelor.Aceasta înseamnă că secvenţele aminoacizilor bio-monomeri care apar ăntr-o proteină sunt decise de secvenţele limbajului de patru litere din filamentul de genă. Sunt necesare trei „litere” de ADN în succesiune pentru fiecare aminoacid bio-monomer dintr-o secvenţă proteică. Aceasta înseamnă că sunt necesare 300 (trei sute) de „litere” de ADN pentru a da instrucţiunile pentru sinteza unei secvenţe proteice de 100 (o sută) de litere.
Din aceste fapte rezultă clar că metoda prin care noi ne scriem numele pe nisip folosind secvenţe ale unui alfabet de 26 de litere pentru a transmite o informaţie cum ar fi cea despre identitatea noastră, este destul de similară în principiu cu metoda folosită de celulă pentru a transmite informaţie către ribozomi (unde este îndeplinit procesul de sinteză în celulă), pentru a se asigura că sintezele specifice de proteine sunt realizate. Analogia dintre scrierea numelor noastre pe nisip şi scrierea informaţiei în gene este apropiată. Ambele implică codarea informaţiei prin mijlocirea secvenţelor.
Astfel, ar fi tot atât de şocant pentru cei mai mulţi dintre noi să fim întrebaţi dacă credem că mişcarea întâmplătoare a moleculelor şi atomilor, cauzată de energia întâmplătoare, a scris codul genetic în secvenţa filamentelor moleculare de ADN, pe cât de şocant ar fi dacă ni s-ar cere să credem că numele noastre au fost scrise pe nisip de acţiunea întâmplătoare a mării şi a vântului. Şi mesajul scris pe ţărmul mării şi codul genetic al genelor sunt, cel puţin pentru omul lipsit de prejudecăţi, mai presus de orice îndoială, nişte coduri. În mod sigur, ordinea oricărui cod sugerează oricărei persoane receptive semnele clare ale inteligenţei sau raţiunii! Pe cât de sigur este că orice persoană fără prejudecăţi este condusă sătre postularea unei inteligenţe de către un nume neaşteptat scris pe nisipul unei plaje, tot atât de sigur este că un înscris în filamentele genelor ne obligă să presupunem o raţiune în spatele lor. Aceasta pentru că informaţia codată este o formă de raţiune. Ea exprimă raţiunea. Codurile de orice tip sunt de neconceput pe orice bază aleatoare, deoarece raţiunea nu este aleatoare în natura ei.

Un mic calcul

Pentru a clarifica şi mai mult acest lucru, să facem un mic calcul. Să ne imaginăm probabilitatea implicată în presupunerea unei explicaţii întâmplătoare a codului. Închipuie-ţi o genă simplă de 400 de litere şi să presupunem că o maimuţă este este pusă să bată la o maşină de scris genetică, într-o încercare de a scrie gena noastră codată de 400 de litere, folosind numai întâmplarea oarbă pentru acest lucru. Ea are la dispoziţie numai simplul alfabet genetic de patru litere. Şansele ca ea să obţină ordinea corectă pentru prima secvenţă sunt de 1 la 4. Şansele ca ea să obţină a doua secvenţă corectă sunt de 1 la 16. Şansele ca ea să obţină primele trei secvenţe corecte sunt de i la 64. Cineva poate să calculeze şansel pentru obţinerea celorlalte 397 secvenţe corecte. Pentru o simplă genă de numai 300 de secvenţe, „şansele împotrivă” au fost calculate la 1 urmat de 130 zerouri la 1.
De aceea, este de mică mirarea faptul că cei mai mulţi oameni de ştiinţă au ajuns la concluzia că secvenţele ADN-ului şi proteinelor nu pot fi atribuite doar purei întâmplări. Direcţia trebuie să fie aranjată dinainte într-un fel sau altul.

Will your D.N.A. be the new barcode?

George Orwell couldn’t have dreamed this up

IBM scientists are working on ambitious research where nano-sized holes will be drilled into computer chips and DNA passed through to create a ‘genetic code reader’.

IBM said that experts from nanofabrication, microelectronics, physics and biology are working together to master a technique where a long DNA molecule passes through a three nanometer wide hole (a nanopore).

As the molecule passes through the nanopore one unit of DNA at a time, an electrical sensor can ‘read’ the DNA.

The challenge of the silicon-based ‘DNA Transistor’ would be to slow and control the motion of the DNA through the hole so the reader could decode what is inside it.

IBM claimed that if the project was successful it could make personalized genome analysis as cheap as $100 to $1,000, and compared it to the first ever sequencing done for the Human Genome Project, which cost $3 billion.

For any doubter out there, ‘Big Blue’ has released a video of its own discussing the possible implications, and some of the processes involved:

Interesting, and slightly scary, stuff.
from Ken Eakins

Mandalas:  The art of centering

“There exists no circle in the world which is not made from within a single point which is located in the center…and this point, which is located in the center, receives all the light, illuminates the body, and all is enlightened.”  From the Zohar

Mandala is a Sanskrit word for circle or wheel that signifies beginnings with no ends.  The variations of patterns are endless, but each has a specific center, and concentric rings that emanate from that center.  Every culture and spiritual practice has their own representation of the circle, evident in their art, architecture and rituals.  In ancient Britain the Druids told time and performed rituals within their circles of large boulders. The circular Aztec calendar was also a time keeping device as well as a vehicle for religious expression.  The 12^th century Christian nun Hildegard von Bigen created mandalas to express her visions and beliefs.  The mandala is a recurrent Christian image: the rosary, halo, Celtic cross, crown of thorns, rose windows, floor of Chartres Cathedral and more.  In Islam the entire building of the mosque becomes a mandala as the dome of the roof represents the arch of the heavens and turns the worshippers’ atttention towards Allah.  The Star of David is a Hebrew spiritual symbol.  Natives of North America create and use medicine wheels and dream catchers.  Navajo Indians spend days or weeks creating sand mandalas. Indigenous Australians have bora rings, and the Amish have hex signs on their barns. Some cultures regard the mandala as an eye of God, or of the Goddess.

Zen Buddhist monks also spend days or weeks creating a sand mandala, only to sweep it up and disperse it into flowing water, to demonstrate the impermanence of life.   According to Buddhist scripture sand mandalas transmit positive energy to the environment and to the people who view them, even after they are swept away. The circle with a center pattern is the basic structure of nature, from the smallest molecule to the conceptual circles of family, friends and community, to the seeming endless Milky Way galaxy.

Psychotherapist Carl Jung created mandalas for his own growth and with his patients and said that a mandala symbolizes “a safe refuge of inner reconciliation and wholeness.” Whatever your belief systems are, creating your own mandala design, or coloring one, lets you express yourself. Flowers, rings found in tree trunks, and snowflakes can be your inspiration.  The act of creating the mandala – with crayons, markers, paint, collage or stones — is relaxing and centering.  When you have completed it, look at what you have created.  Notice where your eyes land, and where they travel.  Then go to the center of the mandala and focus on it as you become aware of your own center.

Cottonweed Pokemon Totally Looks Like CH3 Functional Group

» Think you can do better? Make your own!

Pictures by: dunno source, dunno source Look-Alike by: suonwong1124 via Totally Looks Like Builder

Today my Physical Science students and I were discussing atoms and molecules.  The point of the lessons was not simply that a molecule is a combination of different atoms, but really understanding that these combinations then make up unique substances with characteristics of their own.  We started with water, a great starting point because kids are familiar with it, and are most often familiar with the chemical equation for water..H2O. They can observe that water is different than oxygen or hydrogen and has it’s own unique characteristics.

We explored these concepts with a simple experiment.  (This experiment does use electricity, so use commonsense safety precautions.) We took two copper wires with their ends exposed and attached one end of each wire to the top of a 9 Volt battery, using electrical tape to secure it.  Do not let the wires touch each other, and do not use a stronger battery.  We then put the other  end of each wire into a glass with a solution of water and baking soda.  As soon as the wires were immersed we were able to observe the breaking down of water molecules into their atoms of hydrogen and oxygen.  As the students watched, the gases bubbled away from the ends of the wire and  we were able to discuss the concepts involved.  So, in this first phase we observed a molecule breaking down into atoms.

After a few minutes of observation the students began to observe another change.  The end of one of the wires was turning a bluish green.  Baking soda contains carbon atoms and when you combine hydrogen, oxygen, carbon, and copper (from the wires) you get hydroxycarbonate.  Hydroxycarbonate is that bluish green substance that we find on the Statue of Liberty which is made of copper.  In this phase of the experiment  we can watch as new molecules are formed.

Most science concepts can be taught with common household items…this one came from our textbook, love Dr. Wile, but there are experiments for just about everything online.

If the findings mentioned in this article turns out to be true, this puts a whole new spin on human prehistory and migration. Here is the gist of the importance:

The skulls, jawbones and fragments of limb bones suggest that our ancient human ancestors migrated out of Africa far earlier than previously thought and spent a long evolutionary interlude in Eurasia – before moving back into Africa to complete the story of man.

While on the topic of sciences, I may as well put up this: a photo of the structure of a s single molecule.

Am I at UVM or Hogwarts? From http://harrypotter.wikia.com

Here it is, the first big rush. Our second class, Cell and Molecular Biology (CMB) is a four-week long course, with exams at the beginning of just about every week, including this week’s. (More on that later.) “It goes by quickly,” Dr. Fiekers says at the beginning of Monday’s introductory lecture.

This is another class that’s “review that should have been review”. I always assumed med school would throw us right into the detailed classes. Now I realize that they have to do this because everyone’s science background is very different. My biology classes were extremely intense and detailed. It may not be that way at other schools, or perhaps they emphasized different things. The school HAS to do this to make sure everyone’s on the same playing field going in.

For the science majors, here’s what we covered in one week: Genetics and diseases, genome organization and chromatin structure, the 20 amino acids, protein structure and purification methods, globular and fibrous proteins, membranes, purine and pyrimidine biosynthesis, metabolism, glycolysis, enzymes, enzyme kinetics, replication, transcription, translation, and two clinical talks on sickle cell and XP.

For the non-science majors: Imagine seeing several months of your life fly by in one lecture. Now imagine having around twenty of these lectures in five days. It’s like one of those movie fights with a bunch of ninjas. You take down the first ninja with only a little hassle. Then the second one comes. It’s just as hard as the first one, so you take it down. Then the third one comes, and the fourth…Basically, it’s a fight to maintain your stamina so you don’t get taken down.

 ***

One of our first lecturers is Dr. Everse, who gave us the chemistry review lecture during Orientation. He’s like an excited kid when he lectures, constantly moving around the lecture hall, asking questions to the students and talking at high energy. “Did your Mom ever buy you new tennis shoes before school started?” he asks at the beginning of his first Monday lecture. “Well, I continued the tradition. I bought new tennis shoes. So if I’m running up and down, I’m just breaking them in.” He’s awesome. I highly recommend him.

Then there’s Dr. Wallace, who reviews the biology of DNA replication, transcription and translation. During her second lecture, one of my fellow students emails me. Paraphrase: “Have you noticed Dr. Wallace’s uncanny resemblance to Professor Trelawney from Harry Potter?” (pictured above) Hahaha. Dr. Wallace is also awesome.

And I can’t forget Dr. Tracy. Dear Dr. Tracy. When she lectures, it’s like your sweet, loving Mommy is teaching you the details of biochemistry. I hear she’s also really cool to work for.  

 *** 

In MSLG,  we had a reading about the cultural history behind sickle cell. The part that stuck out to me was Linus Pauling’s comment that perhaps sickle cell carriers should have a mark on their forehead so they could know who not to have children with. I’m sure he meant that innocuously with the best intentions. It’s still horrific for me to contemplate.

We had another reading about an American anthropologist’s analysis of people from Nacirema. Here’s a riddle: How many medical students (besides me) can figure out who the people of Nacirema really are? The answer might be surprisingly low.

***

We had an exam on Monday. Yes, even though we had a final on Friday, we had a Readiness exam on Monday from 1 to 2 PM. It only counts for 5% of our grade, but it’s meant to test our competency with the biological material. Thankfully they gave us review modules for it during Orientation.

On Tuesday, we have a Student Activities Fair for student groups to showcase themselves and get people to sign up on their listserves. The Christian Medical and Dental Association (CMDA) is also there, as well as a girl who’s trying to get a group together to do salsa dancing. I hit those both up.

There are tables for the AMSA (American Medical Student Association) and the AMA (American Medical Association). I ask them what the difference is between the two in terms of what they do. I don’t get a straight answer. Even the girl at the AMA table admits she’s in both.

The best was the Orthopedic Surgery interest table. Just about every other table had fancy signs, goodies, candy or freebies. Theirs only had a sign-up sheet. I ask them if the two people behind the table if they have freebies. “Nope. Here’s a pen.” I am impressed by their straight-to-business, non-gimmicky approach. I sign up immediately.  

 On Wednesday, the teachers bring us free donut holes. Overheard: “What’s a donut hole?” The person was being serious. Another student: “There’s a whole world of donuts I’ve never heard of before. At the end of the day,  our teachers and the dean serve us Ben & Jerry’s ice cream cones. Awesome. I then go meet with my MD/PhD advisor, who’s great and puts me  in touch with some people who’d be awesome to work for in terms of my research interests. 

Thursday was a long day. We had our first COMET session, which is meant to give us some interactive learning. Today we visualized several protein structures. I didn’t think this was too bad, but it went from 2:30 to 4, and since we’d had lectures since 8 AM, this really drained us. I went back home and tried to do work, with little success.

On Friday, I find out I easily passed my Introductory to Clinical Decision Making class. Woo hoo!

***

Highlight of the Week: Friday’s  Clinical Correlations lecture on XP disease, a disease where people can’t tolerate ANY amount of sunlight because it will cause them to break out into cancer.

This was taught by Dr. Schwarzenberger, a dermatologist. ”I am here as your comic relief,” she tells us. Apparently she was going into internal medicine, and she ended up giving a talk on skin cancer. One thing led to another, and she ended up in dermatology. “Be careful with what you give talks on. It can have life-long implications.”

We learn how bad the sun is for our skin, in terms of causing wrinkles and skin cancer. But it converts Vitamin D! “Actually, you can get that easily from a capsule.” So how much sun is safe to expose yourself to? Currently, given the increased incidence of skin cancer, the current position is “none”. In fact, it’s been suggested that sunlight should be placed up with tobacco in terms of risk of causing cancer.

After that, I was afraid to go outside. But I can’t deny it was absolutely an entertaining and highly engrossing lecture.

News

• Space Shuttle Discovery finally headed off into space over the weekend (to refuel the international space station).
• Disney buys Marvel for $4bn.
• The California fires get worse.

Health care

• FactCheck points out 26 lies about H.R. 3200.

Miscellaneous

• Paul Krugman addresses the debt outlook.
• Cathleen Falsani’s tribute to Ted Kennedy, "So Much More Than His Mistakes."
• A molecule is imaged for the first time.
• Liz writes about why she loves LA–I have many of the same reasons.

One million of these, they say…

Would fit into one of these…

The first photograph of the atomic structure of a single molecule. There is much to wax poetic on here…

“Researchers at IBM Zurich have managed to image a single molecule in detail for the first time.

In these images of a pentacene molecule, the bonds between the carbon atoms are visible as five linked rings.”

READ MORE…

Da doamnelor si domnilor. S-a Reusit. S-a fotografiat structura chimica a unei molecule.

Sunt sigur ca muti dintre voi intotdeauna v-ati intrebat cum arata o molecula sau un atom? Iata ca imposibilul de ieri, devine azi din ce in ce mai posibil, iar pasul catre urmatorul nivel de detalii este chiar dupa colt.

Articolul complet cu explicatii il puteti gasi pe StiintaAzi sau varianta in engleza pe BBC News.

For this week’s photos, I ventured into surrealism. The first is a series from Romain Laurent – he has crafted photos all around the city where everyone is 45 degrees. (the montage can be found at Like Cool)

This was a lot more successful than Laurent’s last photo series, in which everyone was 98 degrees.

Although these posts are supposed to be about photography, I came across something on Flickr that isn’t, but was worth sharing. My sister once had a friend named Griffin, but as far as I could tell, he was not half lion, half eagle. Click to enlarge. (h/t Flickr user Preshaa)

Finally, in a pretty interesting development, the BBC is reporting that for the first time, an individual molecule has been photographed. This is incredible to even think about. From the article:

The detailed chemical structure of a single molecule has been imaged for the first time, say researchers.

The physical shape of single carbon nanotubes has been outlined before, using similar techniques – but the new method even shows up chemical bonds.

Understanding structure on this scale could help in the design of many things on the molecular scale, particularly electronics or even drugs.

Anyway, here’s the picture:

For more info on Friday photos, click here.

The above picture was taken by scientists at IBM, and it’s of a single molecule. If you’re having a bit of trouble picturing it, here’s the more recognizable artists’s rendition:

From the article:

Like the venerable electron microscope, but more powerful and with an eye for the third dimension, the AFM [Atomic Force Microscope] is able to make the nano world something we humans can appreciate visually. Using a silicon microscale cantilever coated in carbon dioxide (tiny, tiny needle), lasers, an “ultrahigh vacuum” and temperatures that hovered around 5 Kelvin, the AFM imaged the pentacene in nanometers. It did this while sitting a mere 0.5 nanometers above the surface and its previously invisible bonds for 20 long, unmoving hours. The length of time is noteworthy, said IBM scientist Leo Goss in statement from IBM, because any movement whatsoever would have disrupted the delicate atomic bonds and ruined the image.And that’s the real beauty of this image. For the first time ever we can see where each of those carbon and hydrogen atoms line up, and the overall symmetrical shape they create. In 3D.

My favourite part of the article was where it mentioned that atoms have no colour. Which makes perfect sence once you think about it…

IBM Takes First 3D Image of Atomic Bonds [Gizmodo]