News from Granada
Traveling in the desolate landscape of Iberia is truly eye opening. Instead of lush green, you find dry harsh environments, desolate of inhabitants. The cities are dense, crowded full of life - late into the night. The culture here is a big mix ... not the usual cosmopolitan mix of New York, London or Paris but a mix of European, Arab, Jewish and of course Gypsy who have all lived together and mixed for a thousand years (well the Gypsies are still a bit distinct). Cordoba, while lacking in the many tourist attractions of Granada (except the fabulous Mezquita), feels more authentic than the big Granada. Cordoba was also the largest city in Europe 1000 years ago and at the time was the center of knowledge in this part of the world. Some great thinkers and scientists originated from Cordoba (e.g. the Roman philosopher Seneca, the Islamic Philosopher Averroes and the Jewish Philosopher Maimonides). Funny how things change. To read more on Cordoba's history, click here.

One amazing feature of Granada is the Alhambra ...

I will update later with more info and photos.

[Update 8/8/05]

Here are my travel companions in the Plaza de la Corredera in the center of Cordoba's old city. Later we visited la Mezquita (see pics below), it was first a Visigothic Cathedral that was destroyed by the Moors, then a giant Mosque (3rd biggest in the world). Where Cordoba was reconquered by the Christians in the 1200s, a giant Cathedral (see pic #4) was built in the center of the Mosque.

After the Muslims fled Cordoba, they installed their new capital in the fortress on a hill overlooking Granada. Here are pictures from this fortress, the Alhambra.

And if you think that Moorish influence was restricted to Spain, there are plenty of examples in Portugal, such as the fantastic photo seen bellow of a fountain in Sintra Portugal (summer residence of the Portuguese Royal family - when Portugal had a Royal Family). Also the use of ceramic tiles to decorate the outside of buildings is much more prominent in Portugal than in Spain, as you can see from this fantastic city-scape painting (on ceramic tiles) from the Alfama neighborhood of Lisbon (see bellow).

Off to Europe
So today, we're getting ready to leave for Portugal and southern Spain, to visit and to attend a good friend's wedding.

Last night another at another friend's place we had an intense discussion of recent events. We are living in trying times. I've also gobbled up Thomas Frank's What's the Matter with Kansas in a couple of days. Scary stuff.

So what do all these events have in common? From the WTC to the underground in London, to the resorts in Egypt ... from the small towns in Kansas to the madrasas in Peshawar - I feel that free western society (or is it moderation) is under siege. From all sides, the knives of ideologiocal conflict are being sharpened. Each group is pointing towards its leopard - and often they are pointing at us.

We're not there yet, but it would seem that we are heading down the path to ... I don't know what. What can we do? I guess we need to stand up - not to fight, but to try to bring reason - but how do you reason with individuals that are full of irrational ideas? We need to fight paranoia in others and ourselves.

There is no "Zionist Conspiracy" and there is no "Liberal Conspiracy".

I think that this vacation is well needed - I've been working too hard ... and thinking and worrying too much about where western society, and the world in general are headed.

The Descent of Woman
Last week I picked up Elaine Morgan's The Descent of Woman. Morgan has an entertaining conversational style that makes her book not only informative, but quite a pleasure to read. She makes quite a good case for the Aquatic Ape Theory (see previous post), and how evolutionary logic should explain how unique human traits in men and women, developed.

Also she has a great passage I'd like to share with you:

[explaining baboon behavior] As soon as an outside enemy appears, hostile encounters between members of the male cohort cease. All aggression is directed outward, against the enemy. And the rewarding sensation of hostile arousal against the enemy is deepened and enriched by the warmer and more rewarding sensation of love for, and solidarity with, the brother in arms.

... Because the most disturbing thing about the primate male bond is that it works only when the leopard [or enemy] comes. And if it is rewarding for all the male cohort, it is especially so for the leader, who knows that the leopard's arrival is the signal for all rivals to cease challenging, for unruly subordinates to step into line, for all the strength of the pack to be subservient to his will. An alpha-male baboon only tastes this heady sensation at the approach of a real enemy, but an alpha Homo sapiens with enough ingenuity can invent his own leopard.

... The whole business of politics and government as conducted by males hinges around the process of identifying or inventing the kind of leopard that will unite the greatest possible number of men in the tightest possible bond.

In wartime it is easy: they have territorialism and xenophobia on their side, and the other tribe, or the other nation, constitutes the leopard. But as nation states grow larger and administration more complex, men have to be given the drive to exert themselves, and cooperate, and carry out orders, for long periods when there is no war. They subdivide into factions and cliques: the Whigs are the leopard, or the Republicans, or the abolitionists; and if bond shows sign of weakening they bring on a sabre-tooth tiger: Popish Plot, International Jewry, Yellow Peril, Bolsevik Conspiracy, capitalist lackeys. It is a curious way to run a society, but this is the way men are built, and this is the psychological mechanism that powers most of their political systems.

Eye Candy & Quiz
Topic: Biology
Well I was taking some phase pictures of hepatocytes (liver cells) that we plated on a collagen coated coverslip - nice cells, if I do say so myself. To the left is an image of a hepathocyte (or part of a hepathocyte), all those lines and squiggles being organelles ... compartments where specialized cellular functions take place.

So here is your quiz ...

What is organelle A (the big round slightly out-of-focus thing)?
What is organelle B (the dark dots)?
What is organelle C (the long squiggles)?

And finally, which of these organelles contains DNA?

Funny thing is that I just noticed the question mark in side of organelle A ...

Good luck!

Global Warming Witch Hunt
Topic: Science and Culture
On July 6th President Bush declared:

I recognize the surface of the earth is warmer and that an increase in greenhouse gases caused by humans is contributing to the problem ...

So why is a certain member of congress on a witch hunt after climatologists?

From the Houston Chronicle:

Late last month, Barton requested mounds of documents from three scientists known for studying global warming. As chairman of the House Committee on Energy and Commerce, Barton demanded detailed documentation of almost every aspect of hundreds of studies the scientists had penned.

He made a similar request to the head of the National Science Foundation, writing, "The term 'records' is to be construed in the broadest sense ... whether printed or recorded electronically or magnetically or stored in any type of data bank, including, but not limited to ... summaries of personal conversations or interviews ... diaries ... checks and canceled checks ... bank statements."

Barton gave the scientists 18 days to comply with the request, which he has the power to convert into a subpoena.

And why would this Texas Republican try to discredit scientific research that points to a drastic increase in the global temperature? I wonder.

Even the house Science Committee chair, Republican Sherwood Boehlert is calling for an end to this idiotic crusade, stating to Barton:

My primary concern about your investigation is that its purpose seems to be to intimidate scientists rather than to learn from them.

The way science is evaluated is not through politics, but through peer review. I guess we live in a time when people believe only convenient facts, while anything that does not justify our prejudices (or our wishes) is simply thrown out the window.

Flying Snakes!
Topic: Biology
(Well maybe they just glide.)

I saw an interesting article in the current issue of Science on these curious serpents.

Apparently there are five related species (of the genus Chrysopelea) that jump out of trees and glide. To find out more visit http://www.flyingsnake.org, a website maintained by Jake Soka who studies these snakes at the University of Chicago.

Paperless Notebooks?
Topic: Science Workplace
As a scientist I spend a large chunk of time putting to paper all the things that happen in the lab everyday. But in the lab of the future, instead of notebooks, perhaps scientists will be keeping electronic notebooks ... OK confession, I've been keeping an electronic notebook for a year and a half using Microsoft Word.

But I just read in the July edition of Nature that spurred on by pharmaceutical companies, the time of electronic notebooks is at hand!

So are there any e-notebook programs, beside typical word processing programs? There are a couple of commercially available programs and at least one free one.

From a personal experience, I can tell you that the biggest plus is that my enotebook is neat, easy to search and is flexible enough to readily incorporate data straight into my notes (as long as it's digital data). Also the cut and paste feature allows one to easily incorporate info from the web or often used protocols.

I'll experiment with the freeware (see above) and update you on how it compares to MS Word.

Bug Tampers with Fly Sex
Topic: Biology
I was just alerted about an interesting "News item" in the July 7th edition of Nature that describes how a small bacterial parasite, Wolbachia, drastically alters how flies respond to genetic changes. This bacterium seems to be able switch the sex of infected embryos. In certain cases, the parasite actually rescued the viability of flies harboring lethal genetic mutations.

When looking at a large collections of mutant fly colonies housed at the Bloomington Stock Center at Indiana University, researchers identified that about 30% of the strains were infected with the bug!

This bug could cause problems for fly geneticists ... and others who read their papers!

So how many published results are just wrong? Well labs that study sex determination must be extra vigilant, and this field may be the most affected. I also wonder how many other unknown parasites exist out there that can drastically affect how our biological subjects respond to our experimental protocols?

End of Religion
Topic: Bookclub Meeting
Last night we finally watched the last two episodes of the Decalogue and discussed our current book, The Satanic Verses.

The Decalogue is a great set of films about people (in this case living in a huge Warsaw complex) coping with their flaws, or committed sins. These individuals have to deal with the consequences of their actions as a mysterious guy (or "Jesus figure") watched over them (incidentally we really liked looking for this "Jesus figure" guy ... he always gave a brief appearance with some condescending scowl and never said anything). Each Decalogue deals with one of the Ten Commandments, although often it is hard to tell exactly which Commandment a particular episode focuses on. This series was aired on Polish TV at the end of the 80s when Communism was collapsing and religious freedom was rising in Eastern Europe. It demonstrates how potent a force religion became in guiding the Poles out of their decaying social system.

Now the Satanic Verses ... It has always been a puzzle why certain Islamic clerics declared a fatwa (or religious proclamation), condemning Salaman Rushdie to death, when the novel he wrote deals with Indian immigrants in London, who are trapped between their traditions, their religion and modernity. Very prescient stuff considering recent world events. Any how we figured out that we had enough of religion ... for now. Our new bookclub book is Coetzee's Disgrace.

Using the Nuclear Bomb to Test the Age of Neurons
Topic: Biology
Well some people are smart, and others are really clever.

In today's issue of Cell, researchers use the C14, released in the environment during the atom bomb testing (1943-1963), to determine the age of neurons.

This type of experiment is known as a pulse-chase experiment where a pulse of labeled chemical is added to a biological sample. To figure out how fast the sample is being replaced, researchers measure the amount of labeled sample remaining after different intervals. Thus in the 1943-1963 period, every human born incorporated trace amounts of C14 into their newly formed bodies. Then after 1963, the levels of C14 drooped ... thus anytime after 1963 the newly made proteins, lipids, sugars or DNA had less C14 in them. So to find out how fast a cell was replaced, all you need to do is to measure the amount of cells with labeled DNA (since DNA is only made at the "birth" of a cell).

Now in normal experiments researchers add radiolabeled chemicals to laboratory samples ... but in this case these clever researchers used a natural pulse of C14 (caused by atom bomb testing) to date long lived cells such as neurons ... pretty ingenious.

Ref: Kirsty L. Spalding, Ratan D. Bhardwaj, Bruce A. Buchholz, Henrik Druid, and Jonas Frisen. Retrospective Birth Dating of Cells in Humans. Cell (2005) 122:133-143

Catholic Church and Evolution
Topic: Science and Culture
OK there has been a lot of talk about the "new" stance that the Catholic Church has expressed on evolution.

See this entry on the Panda's Thumb, and these entries on Pharyngula: one, two.

If you missed it, here is the OpEd that sparked it off (see below). Now what do I say? Is it even worth replying to this? I do want to point out how Cardinal Schonborn reffers to ... us(?) ... as neo-Darwinists ... I guess it makes us sound evil, like neo-nazis (or the out-of-fashion neo-cons). Anyway ... here it is:

July 7, 2005
Finding Design in Nature
By CHRISTOPH SCHONBORN

Viena

EVER since 1996, when Pope John Paul II said that evolution (a term he did not define) was "more than just a hypothesis," defenders of neo-Darwinian dogma have often invoked the supposed acceptance - or at least acquiescence - of the Roman Catholic Church when they defend their theory as somehow compatible with Christian faith.

But this is not true. The Catholic Church, while leaving to science many details about the history of life on earth, proclaims that by the light of reason the human intellect can readily and clearly discern purpose and design in the natural world, including the world of living things.

Evolution in the sense of common ancestry might be true, but evolution in the neo-Darwinian sense - an unguided, unplanned process of random variation and natural selection - is not. Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.

Consider the real teaching of our beloved John Paul. While his rather vague and unimportant 1996 letter about evolution is always and everywhere cited, we see no one discussing these comments from a 1985 general audience that represents his robust teaching on nature:

"All the observations concerning the development of life lead to a similar conclusion. The evolution of living beings, of which science seeks to determine the stages and to discern the mechanism, presents an internal finality which arouses admiration. This finality which directs beings in a direction for which they are not responsible or in charge, obliges one to suppose a Mind which is its inventor, its creator."

He went on: "To all these indications of the existence of God the Creator, some oppose the power of chance or of the proper mechanisms of matter. To speak of chance for a universe which presents such a complex organization in its elements and such marvelous finality in its life would be equivalent to giving up the search for an explanation of the world as it appears to us. In fact, this would be equivalent to admitting effects without a cause. It would be to abdicate human intelligence, which would thus refuse to think and to seek a solution for its problems."

Note that in this quotation the word "finality" is a philosophical term synonymous with final cause, purpose or design. In comments at another general audience a year later, John Paul concludes, "It is clear that the truth of faith about creation is radically opposed to the theories of materialistic philosophy. These view the cosmos as the result of an evolution of matter reducible to pure chance and necessity."

Naturally, the authoritative Catechism of the Catholic Church agrees: "Human intelligence is surely already capable of finding a response to the question of origins. The existence of God the Creator can be known with certainty through his works, by the light of human reason." It adds: "We believe that God created the world according to his wisdom. It is not the product of any necessity whatever, nor of blind fate or chance."

In an unfortunate new twist on this old controversy, neo-Darwinists recently have sought to portray our new pope, Benedict XVI, as a satisfied evolutionist. They have quoted a sentence about common ancestry from a 2004 document of the International Theological Commission, pointed out that Benedict was at the time head of the commission, and concluded that the Catholic Church has no problem with the notion of "evolution" as used by mainstream biologists - that is, synonymous with neo-Darwinism.

The commission's document, however, reaffirms the perennial teaching of the Catholic Church about the reality of design in nature. Commenting on the widespread abuse of John Paul's 1996 letter on evolution, the commission cautions that "the letter cannot be read as a blanket approbation of all theories of evolution, including those of a neo-Darwinian provenance which explicitly deny to divine providence any truly causal role in the development of life in the universe."

Furthermore, according to the commission, "An unguided evolutionary process - one that falls outside the bounds of divine providence - simply cannot exist."

Indeed, in the homily at his installation just a few weeks ago, Benedict proclaimed: "We are not some casual and meaningless product of evolution. Each of us is the result of a thought of God. Each of us is willed, each of us is loved, each of us is necessary."

Throughout history the church has defended the truths of faith given by Jesus Christ. But in the modern era, the Catholic Church is in the odd position of standing in firm defense of reason as well. In the 19th century, the First Vatican Council taught a world newly enthralled by the "death of God" that by the use of reason alone mankind could come to know the reality of the Uncaused Cause, the First Mover, the God of the philosophers.

Now at the beginning of the 21st century, faced with scientific claims like neo-Darwinism and the multiverse hypothesis in cosmology invented to avoid the overwhelming evidence for purpose and design found in modern science, the Catholic Church will again defend human reason by proclaiming that the immanent design evident in nature is real. Scientific theories that try to explain away the appearance of design as the result of "chance and necessity" are not scientific at all, but, as John Paul put it, an abdication of human intelligence.

Christoph Schonborn, the Roman Catholic cardinal archbishop of Vienna, was the lead editor of the official 1992 Catechism of the Catholic Church.

Stem Cell Legislation
Topic: Science and Culture
Illinois became the 4th state to provide funding for stem cell research. They'll be providing $10 million the first year for this type of research. The other three states are:

-California with $3 billion over 10 years
-Connecticut with $100 million over 10 years
-New Jersey with $150 million over 10 years

Other state legislatures that have bills in the works are Maryland, Missouri, Wisconsin, New York and Massachusetts.

So what's cooking on the federal level?

Well the GOP, just doesn't get it! In order to counter a bill sponsored by Senators Specter and Harken, Frist and company came up with an alternative bill. They propose that at the 8 cell stage of development (so after fertilization, the zygote [fertilized egg] divides 3 times to produce an 8 cell embryo) at this stage the cells can be artificially separated to form embryonic stem cells (ES cells). Now what the GOP senators are proposing is that rather than use whole in vitro fertilized embryos that are going to be discarded anyway, researcher will carve cells off of an in vitro fertilized egg. Some cells will be used to produce stem cells and other cells will then be implanted in a woman ... I guess to save the embryo's soul???

OK I've heard crazy ideas ... but this is nuts. Imagine you go to an in vitro fertilization clinic and the doctor tells you "we've in vitro fertilized a dozen eggs, we'll carve a chunk out of one and implant that one into you (or into your wife)." I bet that you would exclaim "are you out of your mind!" as specially when other embryos are siting there and will one day BE DISCARDED.

To the GOP, here is some advice: wake up folks.

Terrorism
Topic: Science and Culture
Sorry about the delay in the posts. I've been busy planning a wedding. Incidentally I was back in NY City over the weekend. Being back in the big town, and hearing about the London Bombings brought back terrible memories. In the summer of 2001, Jenni was working at the Federal Building on Church street, just north of the World Trade Center Plaza. We spent much of the summer in this neighborhood (although I confess that I never really liked the twin towers). Fortunately for us when the towers were hit, Jenni was back in Law School, and away from the disaster, although we do know some people who worked in the area (all of them were OK).

So why are they doing this?

This question has been thrown around a lot. And I'm afraid that the answer may not be simple. I'm also dismayed that it's examination from both sides of the political spectrum is flawed.

On much of the left, there are many who claim that much of the hate towards America has been due to our lousy reputation in the world. By mistreating the 3rd world and indirectly enslaving people we foster hate and resentment. There is a kernel of truth to this. Among Osama bin Laden's greatest supporters are the poor. But if one examines those that flew into the planes into the towers, most were educated in the west, and they were middle class, not poor. As for the US international relations, it's true that the US government has had cozy relations with most of their tyrannical dictators, mainly due to our need for oil. It's also true that our biased siding with the hardliners in Israel has not helped us ... but I think that we suffer from not interacting enough (economically) with the Middle-east. If you look at the world map, all the parts of the world that produce terrorists are the parts of the world that are not taking part in global trade. Besides terrorists, all that those countries export is oil. They are not educating or preparing their citizens for international trade. Economic prosperity and the increase in education that comes along with trade produces a middle class, which in turn drives for political moderation and a stomping out of irrational, religious extremism. These ideas are discussed greatly in a fantastic book by Fareed Zakaria, The Future of Freedom: Illiberal Democracy at Home and Abroad (right).

On the right, the "neo-conservatives" have been advocating that terrorism stems from a lack of democracy. As our president likes to say, tyranny and repression breeds "an ideology of hate". And to a certain extent, they are right. But how do we fix this? The conservatives believe that these people should get there own elected government so that they can blame themselves and not the west. To do so the west has to exterminate the dictators. One problem with this line of thought is that by acting irrationally (i.e. bombing one Muslim country because a group of unrelated Muslim fanatics terrorize you) the US fuels resentment. From the beginning the right has made the simple minded mistake of grouping all their "enemies" in one camp. But that's what you get when you see the world in black and white (instead of trying to understand the complexity of the situation).

A second problem is that, you can't bomb people into democracy! Democracy requires a stable society. What does a stable society require? Well people have to be educated, they have to be economically viable, they need rules (i.e. laws), and confidence that the rules are to be followed by others too, and they need infrastructure (i.e. hospitals, fire departments, roads, electricity, water ...). Unfortunately although we recked the country, the US government has been unwilling to fix it. Resentment towards the US in Iraq grows. What the middle east now sees more than ever is that after NYC was attacked, the US got revenge on all Muslims. The ranks of the extremists grow...

One problem that both sides have payed little attention, but is probably the greatest factor in instigating terrorism is ... religion. Yes, I've said it, and it's about time that this country has this discussion. Religion is not a force of good (or evil) IT'S A FORCE OF IRRATIONALISM. It alters your mind so that your view of the world is skewed, and so that you cannot properly evaluate the situation. It forces you to be selfish in your beliefs - in other words you believe in what is convenient and not what is true. Thus religious fanatics in the Islamic world see the US as a big Satan, and certain extremist elements in the west see Islam as a great evil (and see the advent of the Rapture). Do we get any nearer to a solution? No. We get closer to religious WAR.

What made the west prosperous and peaceful was not religion ... it was the Enlightenment. Before the enlightenment, Europe was the bloodiest place on the planet. Religious strife was everywhere, and an uneducated populace was manipulated to fight wars to make their rich overlords more powerful. But economic prosperity and secular institutions undermined this system. Rational science helped the leaders of these countries to develop industry, science filtered into society and help to promote questioning and innovation. So Europe ceased it's internal wars and focused it's energies on industrialization. It then basically overwhelmed the rest of the world with it's political, economic and military might(unfortunately often through bloodshed). From an OpEd in the NY Times by Suketu Metha:

Of course I feel a loyalty to America: it gave my parents a new life and my sons were born here. I have a vested interest in seeing America prosper. But I am here because the country of my ancestors didn't understand the changing world; it couldn't change its technology and its philosophy and its notions of social mobility fast enough to fight off the European colonists, who won not so much with the might of advanced weaponry as with the clear logical philosophy of the Enlightenment. Their systems of thinking conquered our own. So, since independence, Indians have had to learn; we have had to slog for long hours in the classroom while the children of other countries went out to play.

But once countries like India get educated and build a middle class, that's when they prosper economically and become more educated and brush off irrationality that holds back societies and promotes hate war and other foolish endeavors. All these four factors go hand in hand. Economics, rationality, education and peace. The left and the right in America don't seem to get this - and the Islamic world is not headed there. Religion is part of the problem! (can I yell it any louder?) And so I still fear what is to come abroad and at home.

Lipid Rafts Seen (Again) at Last
Topic: Biology
One controversial field in cell biology, is the study of how different types of lipids segregate from the bulk lipids in biological membranes.

OK ... lets step back a bit. In 1972, a model of how lipids form a membrane was proposed by Singer and Nicolson ... the fluid mosaic model. The famous cartoon from their paper is seen here (right). In this model, biological membranes were composed of two layers (or a bilayer) of lipids. The membrane is stable as the lipid's hydrophilic (water loving) heads (circles in the pic on the right) are exposed to the solution and their hydrophobic (water fearing) acyl side chain (squiggles in the pic on the right) are buried in the membrane core. Membrane bound proteins (big blobs in the pic) would float in the plane of the membrane.

So membranes are simple ... right?

Well some weird results started to appear. The very next year John Yu et al. publish a paper describing how a fraction of membranes were resistant to being solubilized with cold detergent. This was eventually seen in cells by Deborah Brown who also copurified proteins that seem to like these "membrane microdomains". These enigmatic membranes acquired other names such as "lipid rafts" and DRMs for Detergent Resistant Membranes ... however it would seem like the more names they gave it the less they knew about it. Many thought that these microdomains were artifacts of cooling trhe samples. Others refered to them (with contempt) as oil slicks.

But this is all very controversial - most researchers are weary of these microdomains as they can be only isolated at low temperatures. However, researchers (such as John Silvius) have shown that you can create this partitioning of lipid domains in artificial vesicles (or liposomes). In these rafts, the lipids tend to be ordered and kick out any lipids that do not compress well. The ability of these ordered membrane patches to form is dependent on cholesterol. So do these rafts exist in cells (or as us biologists say, in vivo)? Well rafts turn out are too small to see with the light microscope ... but despite this fact, Schutz et al. saw them by labeling single lipids and adding just the right amount of these labeled molecules to muscle cells. Others have observed that in polarized cells raft components localize to the site of polarity (for more on polarity, click here).

Now in a recent issue of the Journal Cell (see cover left), Adam Douglass, from the Vale Lab, observed single protein molecules going in and out of microdomains on the surface of white blood cells. In fact they trick the white blood cell into polarize towards the coverslip and use TIRF Microscopy to visualize the polarized membrane with all it's lipid rafts. (I'll post something on TIRF some other day). Very cool. And check out the movies!

Ref:

Singer SJ, and Nicolson GL. The fluid mosaic model of the structure of cell membranes. Science (1972) 175:720-731

Yu J, Fischman DA, Steck TL. Selective solubilization of proteins and phospholipids from red blood cell membranes by nonionic detergents. Journal Of Supramolecular Structure (1973) 1:233-248

Brown DA, Rose JK. Sorting of GPI-anchored proteins to glycolipid-enriched membrane subdomains during transport to the apical cell surface. Cell (1992) 68:533-44

Schutz GJ, Kada G, Pastushenko V, and Schindler H. Properties of lipid microdomains in a muscle cell membrane visualized by single molecule microscopy. EMBO (2000) 19:892-901

Douglass AD, and Vale RD. Single-Molecule Microscopy Reveals Plasma Membrane Microdomains Created by Protein-Protein Networks that Exclude or Trap Signaling Molecules in T Cells. Cell (2005) 121:937-950

July 4th Bang
Topic: Physics
So remember the Comet Crater Contest? Well yesterday Deep Impact collided with Comet Temple 1 and hopefully soon we'll have a look at the inside of a comet!

Follow this link to NASA's Jet Propulsion Laboratory to see pics and movies of the big event.

Acidic Oceans - Need Time to Evolve
Topic: Science and Culture
A new report in Nature documents how the Oceans are getting more acidic.

(Update)

Someone asked me, how is this happening? Basically as CO2 levels rise, some of this excess CO2, is dissolving into the ocean. In water CO2 reacts with H2O to give HCO3- (carbonate) and H+ (e.i. acid levels rise).

(end of update)

Now there are many out there who pooh-pooh climate change. Often the argument against the importance of rising temperatures (from some in the media's eye) goes along the lines of "one degree, that's nothing!", but it's not how much the environment changes but how fast. If the change is too rapid, species can't evolve to adapt to the change, leading to a collapse of the deck of cards. In other words if the change happens over generations, it give the gene pools time to adapt - but if the genetic complement of a species can't catch up with the change, then whole species are left in the lurch and that's when a whole ecosystem can collapse.

Speaking of evolution and collapse, I saw a link on the Panda's Thumb (blog) about the cartoon, Tom the Dancing Bug that regularly appears in Salon.com.

Enjoy.

Alternative Energy
Looks like the first prototype fusion reactor plant will be built in France. Read the article in yesterday's NY Times.

This is a big (baby) step into solving the world's current energy needs. Although there is lots of coal to go around for years, the amount of toxic byproduct (in carbon dioxide and sulfur dioxide) is unsustainable. Natural gas and oil reserves are cleaner, but much lower than coal. As for hydroelectric energy, well there are only so many dams you can build. Solar and Wind energy? It's viable for small communities like the Boston harbor island (right) but the amount of space these take up is tremendous.

In contrast fission energy (where radioactive nuclei are broken apart to produce energy) is cheap, takes up almost no space and actually releases less nuclear waste into the environment than burning coal! There is trace amounts of radioactive uranium and thorium in coal. From a government web site:

... coal-fired power plants throughout the world are the major sources of radioactive materials released to the environment ...

But even better than fission is fusion. This energy is a byproduct of the drop in mass resulting from the fusion of hydrogen nuclei together to form helium (Energy=[change in mass][speed of light squared]). This process drives radiation release from stars like our own sun. For more on the solar fusion cycle - first described by Hans Bethe click here. (Hans Bethe bio from the Nobel site.)

How clean is fusion energy?

From the same NY Times article:

Gates Foundation Awards
Topic: Science Workplace
As much as people love to hate Microsoft, we should all thank the Gates Foundation for spurring on technological advance to help the Developing World.

From an article in today's Science section of the NY Times:

... 43 projects were the winners of a competition announced by Mr. Gates two years ago to find new ways to attack the greatest health challenges facing people in poor countries; the contest attracted 1,500 proposals from 70 countries.

The projects, which will get five-year grants of up to $20 million each, are "very visionary and very, very high risk," said Dr. Richard D. Klausner, a former director of the National Cancer Institute who now runs the Gates Foundation's global health program. "But if any of them are successful, it will be well worth the investment."

In total $437 million in grants were awarded. So what kind of research are they funding? Well David Baltimore (head of Cal Tech ... where this guy is starting a lab) won a grant to develop stem cells that when injected into an individual can generate a super immune system, capable of fighting many diseases.

To see a complete list of the projects funded by the Gates Foundation, click here.

Educated Educators
Topic: Science and Culture
As a Canadian living in the US (for almost 8 years now), I've gotten over most of my Canadian-inferiority-complex (not that Canadians are inferior, but most Canadians in the US have the unconscious need to prove the reverse). However, seeing the two sides of the border does give you some greater perspective. So as a pontificating Canadian my biggest complaint about the US is the education system.

From a good Op-Ed piece in today's NY Times:

Not counting those who teach summer school, about 20 percent of the country's teachers have second jobs (often during the school year, too), and the majority of those jobs could not be construed as enhancing universal respect for those who teach.

In Canada, provincial money is distributed to schools equally (based on how many pupils a particular school district has). The US school funding system, where property taxes fund local schools, results in the segregation of society, with wealthy families clustering in certain school districts and poorer school districts holding classes in closets. As a result the disparity between the best schools and worse schools is smaller in Canada than in the US.

In Canada, a teaching position in an elementary, middle or high school is a true career. The pay is high enough to provide for a good standard of living, and thus attracts teachers with high levels of education. How do I know this? In my family alone, my father and mother were teachers; in addition, I have two aunts and an uncle who taught as well. They were all comfortably middle class: my father even had a masters (and almost a PhD) in nuclear physics and still opted to become a high-school (and later an elementary-school) teacher. Due to his love of science, he was a great high-school teacher. On several occasions, I remember as a kid, we would bump into former students who thanked my dad for really explaining physics and giving an appreciation of science to his students, leading them to careers in high skilled areas. When I was a kid, my father would spend the time to answer my million and one questions, not only in physics, but in history, philosophy and millions of other subjects he had read up on. I ended up as a researcher. In Canada, people of his stature (knowledge professionals) are respected and well paid and contribute greatly to society. This is contrary to the situation here in the US.

Here education is paid lip service by elected officials. In addressing educational issues, the local, state and federal governments always look for quick fixes (testing, the latest trendy way of teaching etc...). But what is needed is a fundamental change in how we treat education, and this has to do with educators. This career choice can't be treated as a "last resort job" as it is by many here today. In New York, Jenni and I knew a lawyer(?) who quit her job to become a New York City teacher - not for money, or security, but more as a public service - as if teaching were doing charity work!

We need to pay our teachers more, we need to get people with higher degrees teaching, we need to equalize funding to school districts, and we need to start respecting teachers (and other knowledge workers). Richard Feynman onced remarked that there are many Jewish scientists because Jewish culture respects knowledge. This is true for Asian cultures as well. Will this be ever be true in the US as a whole? If not, the US (and I'm part of this country now) will eventually fall behind Asia scientifically and economically.

Richard Axel
Topic: Biology
Two days ago I was talking to a rotation student in the lab about the Nobel laureate and Columbia Professor Richard Axel, then last night at another BBQ (this time at Ben's place), the biology of olfactory was brought up, and finally this morning flipping through the Columbia University Magazine, there was an article on ... Richard Axel.

My first recollection of Dr. Axel was in a graduate student class I attended at Columbia. A bald, tall, and lanky individual in a suit walked into the room, sat down on the front desk, crossed his legs and said "So what do you want me to talk about?" He gives the paradoxical appearance of aloofness mixed with intense concentration.

Apparently in high school (Stuyvesant High) he played center for the school basketball team ... and once faced-off against against Lew Alcindor (who later renamed himself Kareem Abdul-Jabar). Apparently Alcindor taunted him by calling him Einstein. Once in college (at Columbia University) he was hired to wash dishes for Bernie Weinstein's lab. Since he asked many questions but broke much or the glassware they fired him after the first day, and rehired him as a research assistant.

He originally wanted to study English or Biology, then the Vietnam War arrived. To avoid the draft he applied to med school - but then spent his entire subsequent career as a researcher as he disliked dealing with patients (and as a pathologist disliked dealing with corpses). Although he is now famous for his discovery (with his then postdoctoral fellow, Linda Buck) that the human genome contains about a thousand or so odorant receptors (all belonging to the G-couple receptor protein family), he was involved in many serendipitous but key scientific findings.

He cloned one of the key proteins involved in Cell Polarity, Rho (for Ras Homologue). What is strange is that he cloned it from Aplasia, the giant slug with giant neurons, first popularized by another Columbia Nobel Laureate. Dr. Axel was also an author on the paper that first described how to introduce foreign DNA into cells using lipid. From this paper, Columbia patented DNA transfection, the single most profitable Biotechnology patent to date (for you lab rats, think about that every time you use lipofectamine and other related products). His lab is currently investigating olfactory perception as a model of brain function.

There are many other Axel stories, but you can read up about some of them at the Nobel Site.

Ref:

Buck, L., and Axel, R., A Novel Multi gene Family May Encode Odorant Receptors: A Molecular Basis for Odor Recognition, Cell (1991) 65:175-187

Wigler, M., Pellicer, A., Silverstein, S. and Axel, R. Biochemical transfer of single-copy eukaryotic genes using total cellular DNA as donor. Cell (1978)14:725?731

Madaule, P. and Axel, R. A novel Ras-related gene family. Cell (1985) 41:31?40