Reales Alcázares

This year I attended the VII European Congress of Protistology which was held in Seville in early September, and planned some travel afterwards. On Wednesday, the day before the conference ended, we all had a private tour of the Real Alcazar, which means Royal Palace. "Alcazar" comes from the Latin castra, meaning castle or fortress, which the Moors then adapted to Al-ksar, which became "Alcazar" in Spanish. 

An outside view of the palace's architecture

The Moors ruled in Southern Spain for a few hundred years, and they build this fortress initially, but later generations of Christian Spanish rulers kept using it and adding on to it. When the Christian King Pedro I ordered his palace built in the Alcazar, he hired local craftsmen to decorate it in the mudejar style, which was sort of a Christian-Islamic hybrid style that drew heavily on influence from Moorish art and architecture. 

Facade in the Mudejar style

Below is an image of the courtyard which served as the public courtyard. There was water in the center and a sunken garden containing orange trees, providing some shade in the hot summer. Some of you may also recognize this as the Water Gardens of Sunspear in Game of Thrones, which was indeed filmed here.

The Courtyard of the Maidens

And speaking of gardens, we also toured the outer palace gardens which are still very well landscaped and taken care of. 

I also really enjoyed being able to think of a time in 14th-century Spain when the Christians could live together with the Muslims and Jews, before the Reconquista of 1492 after which the Jews and Muslims were all forcibly expelled from Spain by Queen Isabella and King Ferdinand, and the Spanish Inquisition began. But on a brighter note, this palace was also a nice prelude to my next stop on this trip, Granada, which holds the Alhambra, another beautiful example of muslim architecture but on a much greater scale. 

Non-fiction: Pattern Formation

Pattern Formation: Ciliate studies and models
Joseph Frankel
1989

I finally finished reading this book, about pattern formation in ciliate systems. The ciliates are a phylum of protozoa (single celled life forms that are organized more like animal cells than like bacteria), but the evolutionary distance between ciliates and animals and ciliates and plants are very great. For unicellular organisms ciliates tend to be quite large with a highly organized cell cortex, which make them very amenable to studies on a microscope. The beginning of the book does a very nice job of presenting a comparative cell biology of different ciliate species and outlining the characteristics that set them apart from other cells.

Image of the ciliate Tetrahymena thermophila from
a fluorescence microscope. The rows of cilia that
run the length of the cell are highly regular, and the
asymmetrical oral apparatus is in red at the top. Image © 
2014 Galati et al. from the cover of J. Cell Biol. 27(6).

Ciliates are so named for their high numbers of cilia, which are sometimes described as "hair-like projections" that the cell beats in order to move and sense its environment. On the cell cortex, all ciliates possess several rows of cilia, as well as an oral apparatus (also made up largely of cilia) and a contractile vacuole pore, which they can use to regulate the amount of water inside the cell. The ciliate body plan also tends to be asymmetrical, and possess handedness - in normal cells, you always see these structures organized in one way and not the mirror image.

Many experiments are described in detail, involving random mutation and micro-surgical dissections, where biologists have been able to perturb the structure of the cell cortex in ciliates and even to generate cell doublets and mirror-image versions of cells. We know that in these cases, the molecular building blocks that comprise these cellular structures possess the same handedness and asymmetry as normal cells, and that it is only the larger scale assembly of these structures that is mirrored compared to normal. Close microscope studies of how cells grow and adjust their structure after manual manipulation with needles, and how they duplicate and either divide. revert to normal, or die in cases of doublets and mirror image cells, all give us valuable insights into the rules that govern pattern formation in biological systems, and how cells know where to place specific structures.

Mutants that are "doubled" versions of cells can help us 
figure out how cells decide where specific structures are
supposed to go. Image from J. Frankel (2008) Euk Cell 7(10).

Most of these observations are still not out-dated today, partly because ciliates have not received the
vast amount of attention that model organisms like mice, flies, and yeast have. But it's particularly exciting to read this book in the age of genomics, when we are much more easily able to sequence genomes and silence genes to study their phenotypes. Genetic studies on these organisms should be able to shed much more light into the precise molecular mechanisms that govern pattern formation at the cellular level.

Additionally, we tend to think of the cell's DNA as the hereditary component. But in cells like these its important to consider the structural organization of the cell and its cortex, and to ask whether all of the positional information needed to create and maintain a normal cell is all hard-coded into the genome, or whether the already-established structure of the cell contributes to heredity as well. If we were able to remove the cell's entire cortex, would the genetic material be sufficient to faithfully reproduce the exact same pattern as the
original cortex? Or is the pattern present on the cortex required to guide new structures to the correct place?

Topkapi Palace

On my last full day in Istanbul I visited Topkapi palace, where the Ottoman sultans lived until 1856. Sultan Mehmed II ordered its construction and it was finished in 1465. When I was 15 I remember taking a tour of Charlottenburg Palace in Berlin. Walking through Topkapi Palace, I caught myself thinking, "Now this is what I call a palace." The grounds are really massive.

The bright colors of the tiling that adorns the walls is a welcome contrast
to the architecture and decor that's common in Europe.

If you ever visit Topkapi Palace, make sure you pay the extra to see the harem apartments - it's worth it. When most people hear the word "harem" they think of the sultan's concubines, but it was also where the Sultan and the princes lived, in addition to wives and concubines, plus other slave girls and female relatives. They also employed eunuchs who lived there too. The eunuchs who were around the women were mostly black eunuchs, often from Sudan, and this was because the black eunuchs tended to have more of their genitalia removed so they were considered the least threatening. The Valide Sultan, the sultan's mother, was in charge of the rest of the women and for the most part they weren't allowed to leave the apartments. Harem means "forbidden".

There were fountains all over the place inside the harem apartments - water, especially running water, was a sign of wealth.

Later that day I went to get some dinner at a place near my hostel. Across the street was an old stone wall that was no longer in use by anyone else, so one of the nearby shopkeepers hung some of his rugs and scarfs up there to advertise. Well, it turns out that there is a family of stray cats that lives on the other side of the wall, and the kittens came out to play. One of the kittens started playing with the rugs and the shopkeeper came over and tried to get him to stop. Later he went into the restaurant and came out with a bunch of leftover chicken that he gave to the cats.

Stray cats are everywhere in Turkey, but the locals seem to take care of them.

Later that night I went out with some of the people from my hostel, and we ended up at one of the restaurants under Galata bridge, which mostly sell fish. I had already eaten and wasn't hungry enough to eat again, but the view was fantastic.

Bosphorus at night

Hagia Sophia

One of the most famous historical buildings in Istanbul is the Hagia Sophia, known as the Aya Sofya in Turkish. This was a basilica built in the 6th century when Istanbul was Constantinople and the empire was Christian. After the Ottoman Turks invaded in the 15th century and Constantinople because the muslim Istanbul, the basilica was turned into a mosque. Now it has been turned into a museum, and some of the original Christian mosaics and paintings that had been covered up are again displayed.

The Virgin Mary with Jesus in the middle, with Justinian I on the left, and Constantine I on the right.

Several of the mosaics display historical figures, including Constantine I, Justinian I, and Empress Zoe. Some are in better shape than others - a couple were missing large portions from the bottom.

Juxtaposition of two religions: seraph in the middle
with arabic on the top and bottom.

Some of the Christian paintings that had been covered up during the basilica's use as a mosque are now visible again, and a couple of these are of seraphim. Seraphim are the type of things that you see in these old cathedrals but never in any modern churches. It makes me think about how the common conceptions of angels seem to have changed over the centuries. Nowadays we usually see angels depicted as blonde white women with white fluffy wings and long white robes and golden halos. But I remember reading the Gospels and other parts of the Bible when I was younger and whenever an angel comes to speak to someone, like one of the shepherds tending a flock, the angel always has to say "Do not be afraid" - and I remember wondering why someone would be afraid of an angel. But I think it's because angels used to be thought of as fearsome and powerful, and perhaps this image has changed over time. Certainly there exist old descriptions of different types of angels. The seraphim in particular, which are the highest ranking angels in some schools of thought, were supposed to have 6 wings: two covering the face, two covering the feet, and two for flying. They are said to fly around the throne of God crying "Holy, holy, holy" and are sometimes described  as burning with fiery passion for serving God. Stranger angels exist too - the ophanim from the jewish angelic hierarchy are described as looking like a wheel-within-a-wheel, covered with hundreds of eyes.

Also on the grounds of the Aya Sofya were buildings housing the tombs of some of the Ottoman rulers. I was wearing a tank top at the time and was told I had to cover up, but I had come prepared with a scarf, which I just wrapped around my shoulders. Inside these buildings were beautiful vibrant tiling and stained glass, similar in style to what you find in Topkapi palace, but the actual tombs weren't what I was expecting. I guess as a WASP when I think of "tomb" I think of a stone sarcophagus or something similar, but the tombs in these buildings looked like green tents of different sizes, some of which were crowned with a white turban-looking object. Later on I read that the tent structures of the sarcophagi are supposed to symbolize the nomadic nature of the early Ottomans, and the turbans are indeed turbans and are sometimes placed on poles above sarcophagi of men.

Tomb of Sultan Murat III.

Both the cistern and the Aya Sofya I did on my first full day in Istanbul. The following day I went on a Bosphorus cruise, almost all the way to the Black Sea, and the following day I visited Topkapi palace. Aya Sofya didn't take nearly as long as the palace, but I did end up wishing I had bought an audio guide - I was wanting to save money at the time, but I think the extra pieces of history and other information would have been worth it, in retrospect. I was also told that there are some people, referred to as neo-ottomanists, who want the Aya Sofya back in use as a mosque and have organized protests around it. Personally I hope it stays as a museum so that the Christian art on the walls is kept displayed and people can visit and learn about its history.

The Basilica Cisterns

Now I'm finally getting around to starting to write about my trip to Istanbul. Istanbul has several great historical buildings that have been turned into museums, like Topkapi palace and Aya Sofya, but one of my favorites was the basilica cisterns, which is also listed here in Travel + Leisure's 25 Coolest Underground Wonders. It certainly didn't take as long to walk around in the cisterns as it did in Topkapi palace, which was huge, but it's dark and creepy which gives it a unique ambience. There is now a walkway so that visitors can walk around it, and many of the columns are lit which give the cisterns limited visibility. There are also carp in the water, which you can faintly see, which adds just a little bit more to the spectral quality of the place.

The lights on the columns reflect into the water.

The cistern is over 100,000 square feet and contains 12 rows of 28 columns. It was built in the 6th century during the reign of Emperor Justinian I, and provided water to the palace in Constantinople back then. Even in more recent times it provided water to Topkapi palace after the Ottomans built it in the 15th century. It is said the the construction of the cistern took 7,000 slaves. One of the columns inside is different than the others and is called a Hen's Eye column - the designs on it in tear shapes are said to honor the slaves who died while building it.

Hen's Eye column

There are two more unique columns in the cistern, which are similar to the others except that at the base of each is a Medusa head. One is sideways, and one is upside down. It possible that the sideways one was turned that way so that it would fit the size of the column, but the upside down one is the same width whether upside down or right side up, so it must have been placed like that on purpose. One possibility is that they turned it upside down in order to negate the effects of the gorgon's gaze. The Medusa heads were probably originally from a Roman temple or other structure, but no one knows where they actually came from.

Sideways Medusa head at the base of a column.

Though the visit doesn't take long, I loved the slightly eerie atmosphere that was unlike any of the other attractions you'll find in Istanbul. I've since read that there are supposedly several hundred ancient cisterns lying beneath Istanbul, which is fun to think about.

Pamukkale

The day after I went to Ephesus, I took a day trip to Pamukkale, which is a few hours away from Kusadasi so it really took the whole day. Pamukkale means "cotton castle" and is named for the travertines. Because there are so many minerals in the water some people say it has healing properties and actually the Greek city Hierapolis, which was built at the top, was originally a hospital. The carbonate in the water give the terraces its white color and get deposited as limestone.

Limestone terraces at Pamukkale

The tour dropped us off at the top and we got to look around for two hours. The first thing I did was to go "swim" in the travertines - really they're not deep enough to swim, but you can sit/lie down and relax. It's very refreshing. At the bottom of the pools and a bit around the pools the calcium carbonate deposits turn into white mud which is fun to walk in. There's also a hot springs there, but it's closed off and you have to pay to get in - the price didn't seem worth it at the time when the pools were free.

The pools were relaxing and
also fun to walk around in.

Hierapolis is also on the top of the hill - it is almost all in ruins but in one spot there was an archway with Greek letter carved across the top. While I never studied Greek, as a scientist I've learned some of the Greek letters so I could make out "...MNASIO" which was the remnants of "GYMNASION" or the gymnasium (and baths). There's also an amphitheater in the ruins - its not as large at the one at Ephesus, but the one at Ephesus has been largely reconstructed, and the one here was 90% original.

The amphitheater at Hierapolis is in the background.

The weather was probably just as scorching as the previous day had been, but because I got to dip in the water it felt much milder. I was glad I had gotten to see some of the natural landmarks of Turkey rather than just historical buildings - human history is fascinating but I like having a bit of both. Cappadocia didn't make it on my itinerary this time, though, unfortunately - maybe someday.

The Basilica of St. John

Ephesus is also famous in Christianity for being one of the seven churches of Asia as mentioned in the book of Revelation, as well as for being the place where John spent time living. I was raised Protestant, and every Sunday in Sunday school I used to learn about things in the Bible, knowing it all happened in the Middle East on the Mediterranean, so it was neat to be able to see an actual place where some of the Bible was supposedly written nearly 2000 years ago when the major language of the region was Greek.

Before going to the Basilica and the citadel surrounding it, I visited one of the mosques nearby, known as the Isa Bey Mosque. 

Isa Bey Mosque

Isa Bey Mosque was built in the 14th century. The courtyard is still nicely landscaped. There were two minarets originally - one totally collapsed, and one partially remains.

The storks of Selcuk taking over more ruins

Next I walked up to the Basilica of St. John, commissioned by Justinian I in the 6th century. It is located on the hill where John the Apostle was said to have written the gospel of John and died, according to Christian tradition. In reality it is unlikely that the Gospel of John was actually written by an individual named John, but John is also credited with writing a few other books of the New Testament, including the book of Revelation, which he wrote while he was exiled to the Isle of Patmos. Some Christians take Revelation to be literal and about how the world is going to end, but some Biblical scholars say that John likely wrote it about Emperor Nero and concurrent events.

Ruins of the Basilica of St. John

A turtle in the ruins tries to hide behind a
fallen column to get away from the tourists.

Next to the ruins of the Basilica is the Ayasoluk citadel, originally a Byzantine castle, later rebuilt and added to by the Ottoman Turks. What's left of the citadel contains several cisterns, a byzantine church, and a mosque. I had read that recently the citadel had been closed to the public, but now it is open and you are free to walk around inside.

The Byzantine church, which they say is where St. John spent his time while alive.
I didn't end up getting a good picture of the citadel walls.

It was neat to see a little Christian history while in Turkey - the Aya Sofya is another great example, which I may write about later on. In both cases though you end up with a juxtaposition of Ottoman muslim history on top of Byzantine christian history, which reminds you how drastically a single place can change over time.

Ephesus, Turkey

A week and a half ago I just got back from my trip to Italy and Turkey - wonderful trip but it also feels good to be back. I may put up some more posts about the trip in the coming days/weeks.

As someone who is not very well versed in world history, one of the really interesting things about Turkey for me was how much history it spans, both in terms of years and number of empires. The southeastern part of Turkey has the Tigris and the Euphrates running through it, and was once part of Mesopotamia known as the cradle of civilization and the part of the world where agriculture was born more than 10,000 years ago. Parts of Turkey later became part of the Greek Empire and then the Roman Empire. The ancient Greek city of Byzantium was renamed by the Roman emperor Constantine I to Constantinople and played an important part in the history of the Christian religion. Constantinople remained Christian for about one thousand years until it fell to the Ottoman Turks and became the capital of the muslim Ottoman Empire as Istanbul. The Ottoman Empire then collapsed and become Turkey after World War I.

One of the highlights of the trip was the ruined city of Ephesus, an ancient Greek city built in the 10th century B.C. What's left of Ephesus (now known as Efes in Turkish) is on a hilltop outside the town of Selçuk near the Aegean coast. Turkey is very hot in July, and the sun beating down at this site was intensified by all of the marble that it could reflect off of. I ended up getting burnt even though I'd put on sunscreen that morning.

One some of the columns and structures you can
still make out inscriptions in Ancient Greek.

Most of the city has now crumbled to ruin, but there are a few places of interest that are still standing or have been reconstructed. One of these is the Library of Celsus, which was destroyed by earthquakes, but whose facade was re-erected in the 1970s.

This view looking up at the entrance of the Library of Celsus
shows some of the intricate stonework.

The Library of Celsus was a Roman building that was completed in 135 AD to honor Tiberius Julius Celsus Polemaeanus, the Roman senator. It housed 12,000 scrolls and there was a mausoleum for Celsus underneath. The front of the facade also contains statues with Greek labels underneath - I could recognize enough greek letters to make out "EPISTEME", the personification of knowledge.

Another of the major sites at Ephesus was the amphitheater. Though much of it has been reconstructed and may not be original, this amphitheater is the largest in Anatolia. It was originally built in the 3rd century B.C. during the Hellenistic Period, but then enlarged during the Roman period.

Amphitheaters like this one were used for events like plays as well as gladiator fights.

Of course one of the things that set Ancient Rome apart from other civilizations were the aqueducts and the plumbing, so no Roman city would be complete without its public bathrooms -

Public toilets in Ephesus

Away from the rest of the ruins of Ephesus, closer to the outskirts of Selçuk, is the ruins of the Temple of Artemis, which was one of the seven wonders of the ancient world. It was built in the Bronze Age and was destroyed and rebuilt three times before its final destruction in 401. Almost nothing is left of it now, and when I visited the area seemed to be a little flooded and now looks marshy.

The Temple of Artemis: once one of the seven wonders of the ancient world,
now home to storks. as well as geese and ducks.

Those who study biblical history also know Ephesus as one of the seven churches of Asia and the place where John was said to have written his gospel - I did visit the basilica of St. John as well but that will probably be saved for another post.

Lemon drinks

Springtime in the bay area means lots of beautiful weather. My neighborhood gets a fair bit of sun and the heavy drooping branches of our backyard lemon tree made me  want to harvest some to use for refreshments.

Lemon tree at right. In the foreground, an extremely tall dandelion.

I picked ten very yellow and very fat lemons and washed them inside. I peeled them with a vegetable peeler and poured vodka over the peels in order to make this limoncello recipe (note: I don't bother to trim the pith, it turns out just fine). The vodka and peels need to steep for 4 days, so I let that pitcher sit and now I had 10 peeled lemons left over so decided to look up some recipes that require lemon juice.

I didn't really feel like major baking so at first I was mostly looking at recipes for things like lemon vinagrette, but then a ginger lemonade recipe caught my eye. I compared a bunch of recipes and ended up coming up with the one below. After juicing all ten lemons I had 2 2/3 cups of lemon juice, so I scaled up the recipe which is written out for 1 cup of lemon juice.

Ingredients:
2 cups water
1 cup honey
2 tbsp minced fresh ginger
several mint leaves
1 cup fresh-squeezed lemon juice
2 cups club soda

Directions:
Bring honey, water, ginger and mint leaves to a boil, then remove from heat and cover for 10 minutes. Strain the ginger and mint out of the liquid, and then add the lemon juice and club soda. Refrigerate.

I'll also note that it tasted a little heavy on the honey, and light on the ginger, so at the end I threw some more sliced ginger and mint leaves into the container in the fridge which will hopefully add a little more flavor over time. 3/4 cup honey instead of 1 cup might not be a bad idea as well. But all in all, it was a pretty easy recipe and tastes very refreshing on a sunny afternoon!

Athens, GA represent!

New Years Resolutions

It's common to think about resolutions when the New Year begins so I thought I'd throw mine on here.

1. Eat less meat

I've been thinking about this more mainly because of the environmental effects of raising livestock. Raising cattle typically requires lots of grain to feed them, and growing all that grain requires lots of water - I heard someone say recently that the amount of water required to produce one beef patty is the amount of water a human will drink in 4.5 years. Not to mention that cattle and other livestock produce a lot of greenhouse gases, which is also bad for the environment. I saw a really neat infographic about it awhile ago, but I can no longer find it. Here's another one:

I'm perfectly happy to eat GMOs so I don't care about that part of it, but it does reflect the carbon footprint that different types of meat have.

Now I don't think I really have the motivation to become fully vegetarian, but I do want to strive for a few things:
1) make vegetarian sandwiches instead of with cold cuts, and pick a good vegetarian option at restaurants instead of a meat option
2) when I do eat meat, choose to eat fish or pork more than beef or mutton
3) opt for game when possible, or wild fish

And then it would probably be a good idea to eat more of things like nuts and peanut butter to get more protein. Of course, even if I stop eating beef entirely, I do consume lots of dairy: cheese, cream, milk, yogurt. I eat LOTS of cheese. And dairy is also produced by cows. But dairy cows are usually different from beef cows, and a cow used for milk can make it for a long time, as opposed to a beef cow being butchered once and producing a finite quantity of meat.

2. Drink less sugar

By now, everyone knows that sugar is bad for you. Places like Whole Foods prides itself on not carrying food that contains high fructose corn syrup, but what the public doesn't seem to realize is that sucrose (sugar, table sugar, cane sugar, natural raw cane sugar, or whatever they want to call it) is pretty much just as bad for you. So if you go to drink a Mexican coke, don't fool yourself into thinking its any better health-wise.

So here's how I want to accomplish this one:
1) Stop drinking soda (by itself at least, i'll probably still allow myself cocktails with soda in them, or the occasional indie root beer)
2) Drink less cranberry juice - I drink a LOT of cranberry juice. It has lots of vitamins, but also lots of sugar. I'll try to drink water instead, or flavor the water if I crave the sweetness too much with an alternative.
3) Cut back on Starbucks - I've started going to Starbucks almost every morning. This is totally unnecessary, and should also help my wallet.

3. Pack lunches for work

This is pretty simple - I go out to lunch almost every day, and probably end up spending a lot of extra money because of it. This mainly happens because I'm lazy and never feel like packing lunch. Or, I make a small sandwich to bring to work, but get hungry again after eating it. I'm going to try to force myself to bring a full lunch almost every day and hopefully this will help me save money.

4. Create (and finish!) a solo choreography

I've been taking belly dance classes on and off for 3-4 years, but I still have never finished creating my own choreography. I'm not particularly creative naturally, and trying to make choreographies is something that I have struggled with when I've tried. But it is something that I want to accomplish and I feel is my next step in my development as a dancer. After all, ideally dance is a form of self-expression.

Those are the big ones - I have high hopes for 2015 and am hoping this summer to have a chance to travel to the Mediterranean and the middle east! That would be my first time outside of North America or Europe! Happy New Year.