Malawi: Dave joins the Trials of Excellence for Southern Africa

When I moved to South Africa, I hoped to maximize the impact I could make with the remaining years of my career. I was grateful, then, to discover many networks were already in place to enable South African scientists to engage researchers in other African nations! In 2018, I connected with a team in Malawi to contribute lectures to a bioinformatics training workshop. I had taken my first steps into the Trials of Excellence for Southern Africa (TESA II).

The African partners of TESA-II. Uganda is the singleton up north, while Malawi is the one that closely follows the west edge of the rift valley lake. Created via

TESA is one of four regional networks launched by the European and Developing Countries Clinical Trials Partnership in 2015 to improve collaboration among biomedical researchers in different African nations. The other partnerships are located in west, central, and east Africa. In its second round of funding, TESA II includes institutions from Angola, Botswana, Malawi, Mozambique, Namibia, South Africa, Uganda, Zambia, and Zimbabwe with European partners in France, the Netherlands, Spain, and the United Kingdom. South Africa is represented by three institutions: Stellenbosch University, University of Cape Town Lung Institute, and LT Clinical Research.

My renewed involvement in TESA came about through a request from Dr. Elizabeth Kampira. Two M.Sc. Bioinformatics students funded by TESA were completing their classwork for the first year of their training, and it was time for them to frame their project proposals. I offered to help them assemble their projects. For Osborne, I suggested a project based on the homology of sequences among members of the Mycobacterium tuberculosis complex. For Temwani, I looked instead to tobacco, the major export crop of Malawi, in a project that draws new lessons from repository data sets. The department liked the projects, and they decided to name me as co-Supervisor to both students. I needed to plan a trip up there!

Dr. Kampira, Osborne, Prof. Newton Kumwenda, me, and Temwani

My flight to Malawi reinforced in my mind just how large a country South Africa is. The flight to Johannesburg from Cape Town took essentially the same amount of time (two hours) as the flight to Blantyre, Malawi, from Johannesburg. I was a bit worried about the flight to Blantyre because South African Airways had temporary halted its flights to Chileka International Airport early in 2019 due to safety compliance issues. My arrival was without any major events. As an American, though, I was required to buy a visa ($75 USD) upon arrival, but finding the right form and getting in the right line got me a bit scrambled. My taxi driver was standing at the exit, and we drove for around twenty minutes to reach the city center.

Main offices of the Leslie Lodge

I was delighted by the Leslie Lodge, a comfortable bed and breakfast just a couple of blocks from the College of Medicine campus. The gardens surrounding the main building were lovely, from little flowers to birds of paradise bushes. Even on my first day there, I spotted a couple of bushbucks enjoying the grounds!

I did require the telephoto to get this close…

I spent most of my three full days at the Blantyre Health Research and Training Trust. The BHRTT is the Malawian participant in TESA II. Osborne, Temwani and I spent time in the conference room working with their new bioinformatics workstation. I also quizzed them about their knowledge of molecular biology and genetics. Like many students, connecting their earlier biology and biochemistry classwork to standard techniques in bioinformatics is a bit of a challenge. Why, for example, is a six-frame translation necessary to evaluate all possible translations of a messenger RNA sequence? I hope that I was able to help show the relevance of that earlier material.

We also spent quite a lot of time detailing the requirements of their projects. Installing software is part of it, of course, but being able to understand the outputs is going to be an even bigger deal. Osborne began testing the ProteinOrtho software, and Temwani was happy to get his hands on gigabytes of RAW data from tandem mass spectrometry experiments in tobacco. My hope is that the students can both “run the numbers” and understand the implications of what comes out the other end.

The College of Medicine Library

I was also very grateful for the chance to talk about some of the research that I have found most interesting during my time at Stellenbosch University. The dean of the College of Medicine helped publicize my talk for Friday, and we had a good turnout at the conference room on the top floor of the library. I spoke about proteogenomics, an emerging field that tries to combine the best of proteomics and genomics for new insights. The group asked interesting questions, and I think some new collaborations might be coming my way soon. It is always good to encounter curious people, no matter the country!

Some of my new friends in Malawi!

Depression and recovery, one year on — Rachel Strohm

Almost a year ago, I shared a blog post by Rachel Strohm about grappling with depression as she continues her graduate studies. In a post uploaded today (see below), she wrote more about her experience of actively recovering from depression. Is there a moment where the red light of depression winks out, when we can proclaim ourselves “cured?” Are there golden habits we can cultivate that work for everyone in moving past this debilitating condition? Sadly, no. I am pleased to see that she has taken an active approach to resolving her depression rather than surrendering to it. I hope that her journey helps others (like me) who have struggled against anxiety and depression in handling a stressful career. I hope you find her post as interesting as I did.

Morning journaling Almost a year after my earlier post about my experience of depression in grad school, I wanted to discuss some of what I’ve learned about recovering from depression. I expected that recovery would be nonlinear, with good days and bad, and that’s been accurate. I also expected that at some point, I would […]

Depression and recovery, one year on — Rachel Strohm

Farrar’s striped SIMD Smith/Waterman

Have you ever found yourself thinking “it doesn’t really matter what license I use with the source code I develop?” This post from Sean Eddy reveals the interesting story of code to accelerate local alignment of two biological sequences. In it, Michael Farrar made it possible to accelerate this core process of bioinformatics using “SIMD” parallel execution. He published his approach in 2007 and then suddenly died in 2010. His approach has only now been issued under a proper open source license. I think you will find Dr. Eddy’s tale quite enlightening!


Michael Farrar’s striped SIMD Smith/Waterman source code [swsse2; Bioinformatics, 2007], is now available under an open source license for the first time. You can download it [here].

View original post 416 more words

Teaching bioinformatics for the “wet bench”

Early in 2019, my friend Dr. Bronwyn Kirby came to me with a request. She organizes the B.Sc. Honours program at the University of the Western Cape Department of Biotechnology. Each year the compulsory “MBP” unit includes a one-week bioinformatics unit, but for 2019 the Honours program was without an instructor for this segment. Could I offer these students a program that mixed lectures with hands-on “practical” materials?

I resolved to do it, and as my plan evolved, I created a fair amount of new material to fit the program. This post will explain some of the decisions that I’ve made and share the end products of that work!

The big picture

I must start by explaining that these five days are far from the only teaching I will do for UWC Biotechnology this year. I usually teach a lecture on protein identification for Ashwil Klein in the Proteomics Module (BTY718), and this year I hope to add one on quantitation for biological MS. Most of my bioinformatics lectures from prior years, though, have been in the Next-Generation Sequencing Module (BTY722) that Dr. Kirby herself teaches (I generally prefer the phrase “massively parallel sequencing”). I present three topics for her: Assembly and Annotation, Amplicon Sequencing, and Differential Gene Expression. When I first offered these lectures in 2017, I had to look up just what she meant by “amplicon sequencing!” (In the end, I settled on a mix of PCR primer design, 16S rRNA sequencing, operational taxonomic units, deleteriousness of variants, and quantification.) I am pleased that I have been able to migrate the last two of these to YouTube playlists of several short (~15 minutes) segments. I have produced any number of hour-plus lectures on YouTube, but I think that more people would be receptive to the material if it is subdivided into digestible segments like these two.

There’s one more teaching commitment I have to UWC this year. In 2018, Dr. Caroline Beltran and I created a seven-day “Special Topic” in Clinical Biomarkers for the department. I am ridiculously proud of how it turned out. You can watch the videos we produced of each lecture at that link. I have not seen another university in the continent of Africa offering such a course!

The sage on the stage

Half of the new bioinformatics week was built around a very old-school format. Each morning at 9:00 AM, I opted for an hour-long lecture, leveraging a fair bit of material I already had on hand but adding some new topics:

Over the years, I have watched as the sequencing-driven core of bioinformatics has steadily gained new auxiliary fields, frequently with little relationship to primary sequence. My own field, identifying tandem mass spectra to peptide sequences, is already an example. I felt that exposing students to imaging informatics, exploring ab initio protein structure estimation, and evaluating the relationships among different genes and/or proteins would be a good sampling of this growing diversity.

I was very pleased this week to see how the UWC Biotechnology students responded to this advanced material. They asked excellent questions, and they seem to absorb quite a lot of what I had to say (we will find out for sure after the assessment next week!). I always appreciate a room that laughs at my jokes, too! The videos from the five lectures can be watched as a YouTube playlist. The slides from the lectures appear in a Google Drive folder.

A practical in programming

For the hands-on element of bioinformatics week, I decided to introduce the UWC Biotechnology students to programming, using the R statistical environment. I particularly valued the encouragement of Eugenia D’Amato, a population geneticist, who brought many of her students to each of my teaching sessions.

I made my first attempt to teach R programming at Kumasi in Ghana. At the time, it was a last-minute replacement for the bioinformatics practical I planned, which made liberal use of web servers (the wifi was a problem at the teaching hall). This time I would have enough lead time to frame my lessons a bit more carefully! Because I have been a computer programmer through many years and many languages, I had to be cautious about blasting past our students with advanced topics. I settled on what seemed like a relatively modest set of topics:

I must say that I am proud of the students rallying to follow along. I am sure it was very disorienting to many of them, and some are probably still asking, “why did we do that?” Some were tempted to give up at the first syntax error from a mis-typed line, but I encouraged them to keep peppering me with questions until the examples worked on their computers. My hope is that a quarter of the students will some day face a problem in their research that they can circumnavigate because they know just a little bit of coding. Perhaps another half of them will need to make use of statistical methods from R, and I am sure that they will be better positioned to carry out (or at least understand) the data analysis.

I have grown accustomed to recording video of my lectures with my Canon full-HD camcorder. For the programming demonstration, though, I resolved to do a “screen recording” (using what was happening on the computer screen as the video rather than my charming face). I was delighted to discover that Microsoft PowerPoint has a screen recorder feature on the “Insert” page of its interface. At the start of each class, I would start the recorder with Windows-shift-F (record the full screen) and Windows-shift-R (start recording). At the end of class, I stopped the recording with Windows-shift-Q. After a few seconds, a recording image would appear on that slide, and I could save the presentation (around a gigabyte for one hour).

It’s all fine and good to have the video on a slide, but I wanted it on YouTube with all the other bits! For this, I used a trick that applies across the DOCX, XLSX, and PPTX formats; they’re actually zip files! If you simply change the extension to ZIP, you can navigate into the directory structure of the file to pull out any piece you like, including the 10fps MP4 file created by the recorder. Then, as fast as fibre, I had my video on YouTube! The playlist appears here. The scripts I created to support my lessons appear in a Google Drive folder.

I hope that my little tale helps you when you’re thinking about ways to incorporate more bioinformatics content in your classes!

Madrid: the Royal Palace and an Egyptian surprise

An index to blog posts from our Spain trip can be found on the first entry.

January 7, 2019

We had just one day remaining to us in Spain, closing with an overnight flight to Johannesburg. We stowed our baggage at “Lock and Be Free” on Calle de Toledo in the morning chill. We then hoped to find a shop that could serve a gluten-free breakfast. I am afraid we wandered quite a long time. At last we seated ourselves at a diner. The young staff read Natasha’s celiac disease card (in Spanish), and they looked perplexedly at its detailed descriptions. At length they settled on eggs and potatoes, with coffee for her and tea for me. Life was wonderful once more!

Madrid Town Centre

A panorama of Plaza de la Villa

We had soon wandered into Plaza de la Villa, a medieval square that features some very lovely architecture. On our Monday morning, however, all the surrounding buildings seemed closed for business. It’s a shame, since it appears the Casa de Cisneros offers some Mudejar design elements (yes, even this far north!).

We had hoped to visit the Museum of the History of the Jewish Community of Madrid, next door. When we arrived, however, all entrances to the building were closed. I think it would have been an interesting visit, since I don’t know much about the Jewish community’s efforts to re-establish itself in Spain after founding a synagogue at Madrid in 1917.

The Cathedral Church of the Armed Forces has been adorned by an anarchy symbol!

We had a couple of opportunities to see the Cathedral Church of the Armed Forces, and both times we stopped to gaze. I wonder what it is about the facade that makes it seem so prototypically Spanish?

The seat of the archbishop is beautiful!

Of course, just a few more steps west brought us to Catedral de la Almudena, the seat of the Archbishop of Madrid. I was interested to learn that this church only began construction in 1879. The mosque that once stood on this site, however was demolished in 1083, the year when Alfonso VI reconquered Madrid in the aftermath of the fall of the Caliphate of Cordoba. Again, it would have been nice to see the museum there, but now we were quite close to our main destination for the day!

Royal Palace

The Royal Palace at Madrid was built during 1738-1751. The first king to occupy the palace was Carlos III.

One of the first exhibits we visited was Cartas al Rey, a temporary exhibition about Spain’s role in World War I. Of course, Spain was neutral, so one might mistakenly think it was doing nothing. The exhibit showed that the nation played a key role in communications among the belligerent powers. A great many of the exhibits, however, were more personal in nature; individuals throughout the world wrote to Spain to request help in locating prisoners of war and determining whether loved ones were alive or dead. It was touching.

Of course, a majestic entrance hall is a requirement!

From there, we passed into the castle proper. The grand staircase and mural ceilings of entrance hall were truly lovely. The passage then led in a circuit of the second floor. Bronze statues of Greek gods standing in muster room had been re-homed from the Seville Alcazar. In another room, I loved a massive clock and aimed my camera. Immediately, a guard was there with “No Photos.” Another room featured the current royal family portrait. It seemed almost photographic, though it had taken a decade to produce!

At least it’s not gold lamé, am I right?

The rooms grew progressively more grand. I particularly loved the porcelain room. When we reached the grand dining room, I joked that the mirror at the end was entirely unnecessary to create a deeper look to the room. Natasha whispered back, “There’s no mirror,” and of course she was right! The silver and gilt place settings over the centuries were beautiful, though of more interest to my companion. We came out of the suites to courtyard balcony, and I felt a sense of relief at being in a more open space. I saw a pair of stone renderings of a royal duo at a distance. Natasha was sure it was the Catholic Monarchs at a glance. From there we entered the royal chapel. How beautiful! I felt that while the throne room was enormous, with lovely frescoes on the ceiling, the thrones themselves seemed less impressive.

It’s good to be the king.

Once we returned to the parade facing the cathedral, we enjoyed a view of the gardens, woods, and distant suburbs from the overlook of the palace.

Egyptian Temple, Peruvian food, and an English Court

We continued to a park north of the palace, where Natasha was delighted to see a skein of ice covering a shallow pool. She was discouraged to see young people throwing pebbles to try breaking the ice.

Temple of Debod at Madrid

We continued to another park, where we ascended a long flight of stairs (murderous on Natasha’s ankle) to the top of a high platform. Even thought we knew what we would find, it was still a bit of a shock. Two centuries before Jesus, Egyptians constructed a temple to Amun and Isis. Subsequent generations expanded the temple with additional rooms. The Temple of Debod was eventually completed by Romans. When modern Egypt built the Aswan Dam, however, the temple would have been inundated, so the nation gifted the structure to Spain. It was rebuilt in 1972, the year of my brother’s birth! As we circumnavigated the temple, Natasha tried to discern which blocks were original and which represented replacements. She was excited to see a cartouche at its back. Madrid has struggled to keep this site secured, though, and that’s probably why we couldn’t see the inside.

From there we took a very long walk. We passed the Conde Duque Cultural Centre. We had walked for quite a while when we were surprised to encounter Leon the Baker, a chain of shops that are entirely gluten-free. We acquired three muffins and a chocolate chip cookie for me to keep my spirits high. We pushed up to the marketplace that contained a gluten-free restaurant, but the marketplace was closed, sadly. We back-tracked to a Peruvian restaurant for a lovely though expensive farewell meal. I had a cream sauce chicken with fruity, peppery overtones.

From there, we paused to visit the El Corte Ingles, a large shopping store, for some last-minute purchases, and then we descended to the subway for a run down to the luggage locker place. We had a lovely chat with the attendant, and then we strapped ourselves to the bags. With my heavier roller bag and Natasha’s large hiking backpack strapped to me, I was really struggling to make forward progress. Just the same, we managed to make our way down to Tirso de Molina and descend to the trains. Two exchanges later, we were on the subway spur to the airport, taking it all the way to the end for the international terminal. We paid the extra fee for air travelers, and we were on our way to the check-in desk.

Our honeymoon had finally come to an end, but Natasha and I are both over the moon to spend our lives together!

Madrid: Prado in a hurry!

An index to blog posts from our Spain trip can be found on the first entry.

January 6, 2019

Who knew January 6th was a holiday? Apparently Spain, a Catholic country, has strong feelings about the arrival of the Three Magi. Given that the city came to a standstill, Natasha and I were very lucky that the Prado museum was open from 10-2, albeit at full price!

We saw a lovely fountain of Neptune and knew we had come to the right place. Natasha’s long-ago training in art history prepared her somewhat better for the onslaught of religious, historical, and mythological creations we were soon to behold. It couldn’t hurt that she once binge-watched “Fake or Fortune.”

This photo comes from Astral Traveller. The building was under renovation on our visit.

I prepared myself by flipping open the museum guide brochure to the full-page grid of thumbnails showing the most widely-sought masterpieces on offer. I drew mental circles around pieces by Bosch, Durer, and Titian. Natasha added a host of others, including Raphael, Caravaggio, El Greco, Rubens, and finally Goya. We were ready to play Museum Bingo! Of 54 listed masterpieces, we eventually visited 30, frequently moving at “trot.”

Art images have been downscaled from bitmaps made available through the Prado website.

I was interested in seeing artist portrayals of the historical figures we met in our tour of Al-Andalus. “Queen Isabella the Catholic dictating her will” naturally emphasized the queen, with the assembled nobles nearly sketched in comparison to her finely-detailed face. Her son-in-law Philip the Fair fared worse, since medieval artists liked the drama of portraying the grief of his wife Joanna the Mad at his death!

Carlos V befriended Titian, and a heroic image emerged!

Charles V has shown up many times across our last three weeks, usually in the context of “and Charles V destroyed this priceless Muslim architecture…” His friendship with the artist Titian, however, produced some lovely visuals, such as his rendering of the monarch as a knight for Christ.

This sixteenth century bronze by Leone Leoni put Charles V in a mythological context.

The statue of Charles V destroying a fury has the remarkable property that his clothes may be unscrewed from the nude statue underneath!

This adoration by the shepherds may be the last of El Greco’s creations.

Natasha had a lot to say about El Greco, an artist I only knew by name. Doménikos Theotokópoulos was born in Greece in 1541 and moved to Toledo at age 36. I am a big fan of Impressionism, and in many ways, El Greco’s style prefigures that movement. I loved the evocative images on display.

Bosch could see a different world by closing his eyes!

For me, the opportunity to see “The Garden of Earthly Delights” by Hieronymus Bosch was the highlight of my day. The work is an amazing fantasy, and the room was perpetually crowded. I waited my turn to get a closer look and knelt down to gaze. The creativity and caprice that Bosch allowed himself must have been quite the shock to his contemporaries.

Goya knew who he considered the heroes.

Natasha and I were one room away from the display of “The Executions” by Goya when the guards began turning everyone back to the exits. I did not really know the story behind the painting. In my discussion of Alhambra I mentioned that the French army occupied Spain during the Napoleonic era. The second of May uprising represented a dramatic turn when the Spanish demonstrated that they no longer perceived the French troops as allies. The executions represent the French response on the following day.

The afternoon sun felt awfully nice as we emerged from the museum. We paused on a concrete bench, and I began scribbling notes for this post in my little green notebook. Natasha surprised me by recording a short video!

Granada: Multifaceted Alhambra

An index to blog posts from our Spain trip can be found on the first entry.

January 4, 2019

The “Red Fort” atop Sabika Hill has spawned more stories per square foot than almost any other place I could imagine. Was it a mansion constructed by an ambitious Jewish vizier? Was it an outpost of “Oriental” civilization, filled with chivalry and fright? Is it a concrete expression of complex geometries? Was it all intended as a sumptuous playground for the sultan? Alhambra may have elements from all of these stories in its multilayered history.

Dave botches something important in honeymoon planning.

Our last day in Granada promised to take us inside Europe’s most touristed attraction, Alhambra! We had been advised to buy our tickets long in advance, and yet I had found it difficult even to determine which site was the “official” place to buy tickets. Then we had to pin down which days we would be in which city. Then we needed to pin down what type of pass we wanted, given that different tickets corresponded to different parts of the massive site. Amidst all these ambiguities, we never acquired the tickets until our trip had begun. When we looked at the purchase site after arriving at Seville, the 14 euro tickets had no availability for a couple before January 10th, and the last singleton vanished from sight before our eyes.

This map of the Alhambra complex, from D. Fairchild Ruggles, will be helpful.

We discovered an uncomfortable phenomenon. Tour guides are buying such large blocs of tickets that individuals cannot acquire them. We bit the bullet and booked two “seats” in a Low Cost Tours Europe visit to Alhambra for January 4th. For the privilege, we paid 50 euros each. With the purchase complete, we discovered that the tour was to be conducted in Spanish. Neither Natasha nor I speak the language.

The Arab Fort or Alcazaba has the oldest “bones” in Alhambra.

How did Alhambra come to exist in the first place?

Antonio Fernández-Puertas made a useful resource to understand how this fortress-palace-city evolved when he detailed the lives of three Nasrid sultans who ruled between 1314 and 1391. I introduced Yusuf I and Mohammed V in the preceding post. Ismail I was the father of Yusuf I and thus the grandfather of Mohammed V. To read the lives of these three sultans is to become witness to a Game of Thrones-style bloodbath. Ismail I ruled Granada during the time of the last significant victory by the Moors against the Christian kingdoms, the Battle of Vega in 1319. I could easily imagine a movie structured around the dramatic 1359 coup against Muhammad V in which a hundred conspirators scaled the Alhambra walls to murder vizier Ridwan in his bed and narrowly miss the capture of the sultan!

This map, also from Ruggles, diagrams the “famous part” of Alhambra.

To return to the history of Alhambra, though, I would try to assemble a small timeline:

  • 1013-1090: During the Zirid dynasty, Jewish vizier Yusuf ibn Naghrila builds the first residence next to the Alcazaba (fortress) atop Sabika Hill.
  • 1314-1325: Reign of Ismail I, who creates the Alcazar del Genil after his victory in battle. He remodeled the summer palace (Generalife) and constructed the Puerta de la Armas. He began a new palace complex where Palacio de Comares would stand and constructed a cistern where Palacio del Riyad (later called Palace of the Lions) would stand.
  • 1333–1354: Reign of Yusuf I, who constructed the 45m Torre de Comares , which houses the Salón de los Embajadores (considered by many to be the masterpiece of Nasrid architecture). He also built the Gate of the Esplanade and the Torre del Cadi and Torre Quebrada.
  • 1362-1391: Second reign of Muhammad V, who began by rebuilding the Mexuar, the public area of the palace. His reign saw considerable creative design, including the Puerta el Vino, the Sala de la Barca, as well as the patio and facade of the Palacio de Comares. Later in his reign, he initiated the Palacio del Riyad (called the Palace of Lions by the Christians after Reconquista) and created the Palacio de los Alijares (later leveled).
  • 1492: The city of Granada surrenders to the forces of Isabella of Castile and Ferdinand II of Aragon.
  • 1525: Carlos V (Holy Roman Emperor) decides to construct a Renaissance Palace and several residential rooms next to the Nasrid Palaces.
  • 1533-1637: The Carlos V Palace is under construction for a century without completion.
  • 1581-1618: St. Mary Church is constructed on the site of Alhambra’s Great Mosque.
  • 1810-1812: The French Army occupies Alhambra, building their fortifications on and around the medieval fortress. Eastern walls were demolished as the troops departed.
  • 1923-1928: Leopoldo Torres Balbas implements a plan to finalize the Carlos V Palace.
Behind the fortifications of Alcazaba, there’s not much to see. These are barracks wall footings, capped in concrete.

I have mentioned quite a lot of Muslim architecture from Al-Andalus, so it might help to put them in context. The Caliph of Cordoba set a distinctly Andalusian design to the architecture he introduced in Madinat al-Zahra (begun 936-940 A.D.). The Nasrid rulers of Granada echoed that design aesthetic in construction of their palaces (1314-1391). Muhammad V may have transmitted these possibilities to Pedro I during his time in Seville, and Pedro I (who reigned 1350-1369) certainly incorporated a lot of Andalusian ideas in the “mudejar” style of his palace at Sevilla.

From Alhambra’s viewing platforms, you have an unrivaled view of Granada. At the upper left is the cathedral, and centered at the bottom you can see the Royal Chancery.

How well do English speakers fare on a Spanish tour?

We spent our morning shopping for gifts, and then we enjoyed a happy lunch at an authentic Mexican restaurant close to our lodgings. From there we popped over to Plaza Nueva, and then we started the slog up the hill to Alhambra. In brief, it is a heavy slope, especially at first. Natasha paused at a ceramics shop to acquire some pretty Christmas tree ornaments. Soon thereafter, we passed through an archway into a pretty green-belt. The sunlight was dappled from its passage through the trees. It was thoroughly lovely.

Even though it was never finished and is a totally different style than its neighbors, Carlos V looks lovely as sunset approaches.

Our guidebook suggested that the main entrance was at the Puerta Vino, but it seems to have moved to a spot further east, where the hilltop divides into the Alhambra to the west and Generalife to the east. We met with out guide and group, and we received our previous tickets to the sites within the complex. I tried the earpiece for the first part of the tour, but I picked up few words, and they were all out of context. The guide did not attempt to keep his English-speaking pair apprised of what was going on or what we were seeing. His first comment to us, in fact, was to specify that we were on a bathroom break.

I believe this capital was from the mexuar, the public areas of the Nasrid Palaces.
The tile work was outstanding throughout. I believe this was also from the mexuar.

We had another problem, too. Natasha’s Christmas ankle sprain was aggravated by the uneven footing of the site, and the guide seemed to be accelerating as the day went by! My own legs were not feeling great from the treatment. Before we entered the Nasrid Palaces, Natasha and I handed back the audio equipment in case we were left behind. We did part ways with the group just as they jetted off to the summer palace and Generalife. The tour guide did not seem sad we split.

Looking south in Court of the Myrtles
Looking north in the Court of the Myrtles. This tower is Yusuf I’s creation.

My experience of the pinnacle

So how about that Alhambra? Let me start by saying it is not all one thing. The bit that everyone raves about is the Nasrid Palaces, and as I’ll share below, it’s truly glorious. The Arab Fort, on the other hand, is the oldest, most ruinous part. I don’t think I understand its history at all. The Renaissance palace of Carlos V is in nice condition, but then it is half the age of the oldest parts! Other areas include the massive gardens and summer palace in the Generalife. One should not leave out the Medina; at some points, 40,000 citizens have called this town home.

The astonishing ceiling of the Hall of the Abencerrajes
Everyone realizes when they have reached the Patio of Lions.

Our tour guide assaulted the Arab Fort at Caesar-speed. We entered through a cavalry ramp and we passed by cement-capped wall footings of soldier barracks with barely the time to snap a photo. Our guide lingered for a moment atop a viewing deck that afforded a fantastic view of the city below. I would have enjoyed a few moments with my zoom lens, but i was just starting to realize the extent of Natasha’s ankle damage, and I had no clues from the guide’s monologue whether or not I would have time to switch lenses! In moments, he pulled us from the platform, back through the ruins to the other side, where he pointed to the snowy mountains in the distance and talked about the climate and North Africa, which is really not so very far away. Gibraltar is only 113 miles from Granada, as the crow flies.

Layers upon layers of decoration
The Tower of the Ladies comes with its own reflecting pool.

Our look at the Carlos V palace was very brief, taking us into the central atrium, ringed by Romanesque columns. Natasha and I returned to the building later to visit its Alhambra museum, and I am very glad we did. We got the chance to see beautifully-carved rafters that had been pulled from the earliest parts of Arabic Alcazar at Cordoba (not Alcazar of the Christian Kings). A gorgeous marble basin that had been plundered from the Madinat Al-Zahra by Berbers was there, too, showing the caliph as a mighty lion devouring prey. They even featured a yamur (top spire) of the Mezquita at Almonzara that had been appropriated by Christians to stand atop Iglesia Santa Ana (on Plaza Nueva in Granada). If we had stayed with out tour group, we would never have seen these artifacts. As matters stood, we did not have much time in the museum since its winter hours end at 6 P.M. We entirely missed our chance to see the Fine Arts Museum in the same building, and no photos were allowed in the Alhambra museum.

This Summer Palace is entirely unlike the one in Beijing!
These wall footings of the medina would once have been next door to the mosque. St. Mary’s put an end to that!

Naturally, Natasha and I have seen quite a lot of Mudejar and Andalusian interior decorating in our visits to Cordoba, Seville, and Granada. I would particularly point to the Mezquita at Cordoba, the Alcazar at Seville (though created for a Christian king), and the Nasrid Palace at Granada. The last two of these sites have the most in common, but Alhambra’s Nasrid Palace is on a grander scale and in better condition than Seville’s Alcaazar. The vivid patios and powerful ceremonial spaces of the Alhambra Nasrid Palaces speak to an artistic sensibility that hangs together through this part of the complex. All too soon, however, our tour moved into the royal living spaces, and they no longer bear walls of carved plaster, painted wood, or amazing crenelated ceilings. The tour takes one through many elegant and even astonishing chambers, but only a small part of the Sabika hilltop is the mind-blowing beauty that we associate with the name “Alhambra.”