HUPO-PSI 2018: Dave’s takeaways

I have now attended three HUPO-PSI (Human Proteome Organization Proteomics Standards Initiative) meetings: Ghent, Beijing, and Heidelberg.  As an early skeptic about the standard data formats for mass spectrometry, I confess I have substantially revised my opinion on the usefulness of HUPO-PSI.  I have now served as the Quality Control Working Group chair for two full years, and I feel I understand quite a lot more of what these meetings accomplish.

Who is HUPO-PSI?

HUPO-PSI may receive less name recognition than the formats that they have made possible.  Thousands of biological mass spectrometrists have used the mzML format, frequently employing ProteoWizard software to produce it.  The mzML format, then is probably HUPO-PSI’s most conspicuous success.  This format, though, was not the first XML-based attempt to capture proteomics data.  We would probably point to mzXML for that.  Actually, mzML wasn’t even the first file format canonized by HUPO-PSI for this purpose!  We would point to mzData for that.  Because HUPO-PSI was humble enough to seek the input of the mzXML team, a far more fully-fledged format, mzML, could be produced by merging the best aspects of mzData and mzXML.  I also see a huge splash from the Molecular Interactions side of HUPO-PSI, though I have always associated with the mass spectrometry side instead.

HUPO-PSI has its share of detractors, as well.  The group has placed quite a lot of emphasis on XML as the preferred “persistence” (mode of long-term information storage), though its formats have occasionally been translated to other strategies for long-term storage, such as the HDF5 scalable technology suite.  A consequence of embracing XML is that researchers see their data storage needs increase significantly; we frequently see that the mzML produced from a Thermo RAW file increases in size even as it reduces the amount of information it contains through “peaklisting.”  As a consequence, some of the groups within HUPO-PSI have invested effort in more streamlined options for data storage, such as the tab-delimited “mzTab” format, now undergoing an expansion to a wide variety of analyte types.  The team of which I am part, the Quality Control Working Group, is looking at another structural strategy called JavaScript Object Notation or “JSON” for compactly relating information.

Two topics have mystified me more than any others about the operation of HUPO-PSI.  The first is the reliance on a “CV” and “ontology.”  Controlled Vocabularies are essentially sets of terms that have been rigorously defined for use in reporting a kind of information.  An ontology relates these terms together, for example through “IS_A”, “PART_OF,” “HAS_PART,” and “REGULATES” relationships employed in the Gene Ontology.  HUPO-PSI makes use of ontologies that have been defined for other efforts, such as the Units of Measurement Ontology created by European Bioinformatics Institute and Phenotype and Trait Ontology.  It also maintains its own set of controlled vocabularies, such as the PSI-MS.  For my quality control to create a HUPO-PSI compatible format means connecting into these information resources rather than “reinventing the wheel” with an altogether new ontology.

The second topic that mystifies me is the “Document Process.”  Once a working group has beaten all the problems they can find from a proposed file type (a schema, or format to store the information, along with a CV that defines key terms for that file type), they submit the package to the document process, wherein more experienced standards creators draw attention to potential problems and external reviewers evaluate the extent to which that format meets the needs of the community for which it is intended.  I will learn a lot more about the Document Process when our proposal is ready for this group!

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Despite his expression, Bunsen would certainly approve!

Meeting Outcomes

The mzML format seems very stable and very capable in its version 1.1.0.  Mass spectrometry technologies, however, are always improving!  For the last decade and more, ion mobility technology has been maturing in technology development laboratories, and a few mass spectrometry vendors now offer instruments that incorporate this separation technology.  The mzML CV and schema, however, has had somewhat patchy support for the information from this separation.  At this year’s meeting, Eric Deutsch convened a small group of people to discuss the best way to support this technology within mzML, ideally without forcing a major update in the format.  Hans Visser of Waters Corporation has made a lot of contributions on this score, and Matt Chambers (a wunderkind whose company I enjoyed during my decade at Vanderbilt) had offered some feedback on how to incorporate this information.  Our meeting at HUPO-PSI helped set us on a course for formal support for ion mobility!

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I am grateful for the Ph.D. students and recent grads supporting our effort!

The HUPO-PSI Quality Control Working Group

I was really proud of the Quality Control Working Group.  I assigned us all a bit of homework for this meeting.  Three committee members create tools that generate quality metrics; all of us were assigned the task of creating a mock-up of the qcML we thought our software should produce.  One of us produced a database for storage of quality metrics; he was tasked to demonstrate what a qcML holding an analysis of these metrics should look like.  As a result, this meeting was far more concrete about what we need to do to finalize this format.  In particular, we grappled with the challenges of embedding information in JSON format within an XML wrapper.  Our consideration of complex data structures for particular metrics, such as three-dimensional matrices, is now much more applied in nature.

The field of proteomics needs to improve its ability to communicate issues of quality control.  There’s a perception of irreproducibility that hangs over the field.  While there is some basis in reality for these reproducibility claims, a fair bit of the problem is that researchers shy away from discussing quality issues in their papers.  A Ph.D. student in Shanghai has been heading the Quality Control Working Group recommendations for “MIAPE-QC:” the Minimal Information About a Proteomics Experiment for Quality Control.  I was sad that she could not attend the meeting due to grad school requirements, but a colleague of hers from Beijing presented the current state of the MIAPE-QC document.  We had a really good conversation about it, but I think our recommendations were a bit garbled on their way back to her; she was discouraged by our feedback and felt we were arguing for her to start over.  We’re working to clear up the confusion.  We will support her valuable efforts in educating our community.

Next stop: Cape Town?

As the meeting drew to a close, I put on my presenter hat one last time.  It was time to state my case for hosting the next HUPO-PSI at Cape Town!  Several different sites are bidding to host: Adelaide, Tokyo, San Diego, and Cape Town are all in the mix.  I started by taking the bull by the horns.  Cape Town may seem very far away, but it is actually in the same time zone as Heidelberg!  Flying from New York City is pretty rough, though, with a flight time of almost 15 hours.  My friend Eric Deutsch would have one of the worst routes since he is coming from Seattle.  Still, South Africa is seeing good growth in mass spectrometry, and we would love to see more of its laboratories corresponding with HUPO-PSI.  I highlighted some of the lovely attractions and hosting sites that we might visit as a group.  Hopefully, the steering committee will see its way to Cape Town in the near future!

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The HUPO-PSI Steering Committee enjoys dinner.

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My experience with depression in academia

Graduate school is grueling, and it represents the nadir of many people’s emotional lives. A great many of my friends have struggled during these painful years. I needed counseling to remain on target while completing my Ph.D., and I know I am in good company on that score.

In this brave and insightful post, Rachel Strohm explains the process that led her to realize that depression was weighing her down and the therapy that helped her to rediscover herself. If you find that several of these warning signs sound familiar, remember that there are many people nearby who want to help!

Rachel Strohm

A painting that is almost entirely a deep turquoise blue, divided by a horizontal line of lighter blue in the middle

Mark Rothko, Untitled (Blue Divided by Blue)

And now for a post on a more personal matter.  I haven’t said much about this publicly, but for the last several years of my PhD studies, I’ve been dealing with a severe case of depression.  I missed major deadlines, failed in my teaching obligations, and thought seriously about dropping out at various points.  For most of that time, I didn’t really understand that I was ill, or that treatment was an option.  Once I did understand that and opened up about how I was feeling, I made enormous progress towards feeling happy and productive again.  I’d like to talk about this experience, and how some common narratives about academic success can make it particularly difficult for graduate students to identify when they’re depressed and get help.  Depression is a very common experience for graduate students, with nearly 40% of students in a…

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Strolling the Heidelberg Altstadt

To visit a city with as much history as Heidelberg only to spend 100% of one’s time at a conference would be a great injustice. Between my wanderings on my arrival day and this evening, I have really come to appreciate the beauty that this city presents at unexpected moments.

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The lovely banks of the Neckar River

Heidelberg architecture begins its ascent in the twelfth century, with a local Benedictine monastery dating to 1130; the name “Heidelberg” didn’t appear in writing until 1196, though. Over a period of five hundred years, the Counts of the Palatinate and the Prince Electors resided in this city. A fortification on a hill overlooking the Neckar River was mentioned as early as 1303; today, this site is dominated by the ruins of a majestic castle!

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A schloss by any other name…

In many respects, though, Heidelberg gained fame as a center of learning. Prince Elector Ruprecht I founded the “Ruperto Carola University” in 1386, making it the oldest university in Germany. After an early 19th century reorganization, the institution came to play an even greater role, with luminaries such as Hegel advancing philosophy while Robert Bunsen invented gas-analytical methods (and inventing the Bunsen Burner) and Hermann von Helmholtz investigated visual perception.

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The old university plaza, featuring a tower from the nearby Jesuit church, was an ideal place to read a book!

For two decades in the early 19th century, Heidelberg became the focus of the “High Romanticism” literary movement. At the opening of the 20th century, the city constructed a palatial university library in the heart of its old town. In December 2014, UNESCO named Heidelberg as its tenth “City of Literature.”

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The library in the old town is tremendously impressive!

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Peterskirche

The churches of the city are really striking, as well. Peterskirche, the oldest, was originally constructed in the 12th century. Its tower almost seems like a post-modern deconstruction of a Gothic chapel, with flat faces in each cardinal direction and shuttered windows flush to the surfaces below its clock dials. I would have loved to explore its insides, but its doors were shut late on Tuesday afternoon when I visited.

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No nave is complete without a giant, reflective cross!

I also loved the Jesuitenkirche and its accompanying college. The church encompasses three parallel naves of equal height. I stepped inside and was delighted to see all the light pouring into the nave from the setting sun. I listened surreptitiously to an organist rehearsing for a service. I tried to set my phone down on a large table at the back so I could make an audio recording, only to realize that it was a fountain of holy water! I pulled it out of its damp case and got the recorder working properly.

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Springtime on Philosopher’s Walk

Learning that the “Philosopher’s Walk” led to a beautiful vista of the castle and old city from above on the opposite bank of the Neckar River, I began my walk up the slope. What I hadn’t seen mentioned is that the Philosopher’s Walk is steep. This middle-aged professor huffed and puffed, particularly on the initial parts of the ascent. After a while, the slope calmed down and I only needed to take care of the sun, which was beating down pretty well for a day in early spring!

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The Church of the Holy Spirit, as seen from Philosopher’s Walk

The climb was definitely worth it! I found a lovely flower garden at one scenic overlook, and the vision of the old city below was astonishing. To see the churches standing tall among the surrounding buildings helped separate them from the background. The castle’s architecture makes it seem like a fantasy rather than anything brooding. As I looked to the west, I saw modern Heidelberg spilling out along the riverbank. Heidelberg’s history, its legacy, and its charm make it a very appealing package.

The first leg of the triangle: from Cape Town to Heidelberg

April 17, 2018

When my travel itinerary gets too intense, some of the plates I am always spinning may slip away and smash. Almost everything was right for this journey to Heidelberg, Germany, but I left something rather important out of my plan!

My journey started with a pleasant taxi ride. The driver was the same fellow who had carried me to the airport for my Russian adventure last year, and he remembered my ambitious plan to tour three cities there. It was nice that he had taken the time to listen and remember. I was at the airport in plenty of time, which was helpful when we encountered a logjam behind a completely burned car in the approach road to the drop-off site.

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My JNB-FRA flight used a Boeing 747-8.

My flights to reach Frankfurt started with a quick dog-leg to Johannesburg.  I had initially thought I would be flying from JNB during the first part of my planned sabbatical at the Human Metabolomics Centre, so the dog-leg was a late addition. Happily my Visa card lets me use the Bidvest lounge at both CPT and JNB airports. With a well-fed belly, I boarded the ten-hour flight to Frankfurt. I was happy to watch “The Last Jedi” for my third time, and I enjoyed “The Shape of Water” after a fitful patch of sleep. An hour later, (just after 5AM) we touched down in Frankfurt!

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Your life will be easier if you learn to read these diagrams!

My next task was to make the run south to Heidelberg, the site of this year’s HUPO-PSI workshop. The train station at the airport, however, is not the same as the hauptbahnoff at Frankfurt, and that added some complexity. In the end, I used the S8 subway to get to Niederrad and then caught a stopping train to Mannheim. After that I had just another fifteen minutes south on a final train to Heidelberg. Not so bad for 23 Euro!

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Alas that I could not also visit Worms!

To be honest, I was hoping for someone holding a sign at the train station, directing me to the conference destination. I had come to understand that EMBL was quite a bit off the beaten path. As things were, I waited a couple minutes for the tourist information center to open at 9AM. I learned that city bus number 39 would run directly to EMBL, but I’d need to catch it at Bismarckplatz, the central point for the bus network. Since it was a “twenty minute” walk to reach the site, I set out with my backpack and 26 inch roller bag in train.

Have I mentioned spring is my favorite season? Tired dirt suddenly springs forward bits of green, and trees burst out with unexpected sprites of color. Breathing the air along my road hike was just the inspiration I needed to get past my night on the plane. I was able to walk directly to the bus stop where I could catch bus 39 away from the madding crowd. I was a bit disoriented when I realized the bus was chock-full of American accents! Yes, many of the researchers doing their work at EMBL are American or set their English accent in the United States. I funneled off the bus at the same place as they did.

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Route 39 (purple) gets you from the center of Heidelberg to EMBL. The lower star is the train station. The upper star is where I found lodgings!

I should mention that I have gotten spoiled by the HUPO-PSI meeting in the last two years (Ghent and Beijing). In last year’s meeting, the Phoenix Center hosts set me up with a lovely suite knowing that the lovely Natasha was joining me on the trip. I had misunderstood a couple of comments on the HUPO-PSI Steering Committee phone calls and mailing lists to suggest that at least the Steering Committee would be housed at EMBL. Imagine my shock when I learned that EMBL has zero housing on-site at its training center! I had no place to stay for these four nights!

I went into damage control mode. I hit up my favorite hotel booking website to see what lodgings I could find for four nights starting with TODAY. Understandably, the pickings were pretty poor. Badly-located cots did not appeal, and paying more than $1000 USD for a hotel seemed a bit extreme. I decided on the youth hostel next to the zoo. It was on the wrong side of the river, but one bus would bring me back to the central hub for the buses, and another would bring me to EMBL.

On a trip already featuring a taxi, two planes, a subway, two trains, and now two different buses, I was relieved to pay my 2.60 Euro to retire to my hostel room, shared with five other men. I took a “Hollywood shower,” lingering under the steamy water for longer than strictly necessary. It was my first proper boiler in months, since Cape Town’s water crisis prevents this luxury.

In my next post, I’ll talk about my experiences walking around the lovely, historic city of Heidelberg!

Arniston: a Town with three names

April 1, 2018

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It’s a tricky descent.

Our stay at Bredasdorp gave us good access to Arniston, a coastal town with good things on offer. Happily the R316 road that brought us there was paved and smooth rather than compelling us to bounce down a gravel path! We arrived easily within a half hour. On our jaunt to the southeast, we were reminded that the military has a significant presence in the area. Much of the zone between De Hoop Reserve and Arniston is used as a test range. We passed Air Force Base Overberg and base housing not long before reaching the town itself.

Our first stop in the area brought us to a lovely public beach. Our goal, however, required a bit of a hike over sand dunes, over a hill, and down sandstone steps to a field of smoothed stones. We were headed to Waenhuiskrans, “Wagon House Cliff,” and its fascinating sea cave. The cave contributed the first name for the town in this area. Natasha and I checked the tide tables to be sure that we would get the chance to see the cave, since it cannot be visited when the tide is in!

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The sea’s entrance to Waenhuiskrans Cave is dramatic!

The path to the cave, however, leads along the water front, and Natasha had sighted many inviting tidal pools. I missed the entrance to the cave, at first, and walked further along the rock face than I meant to. I could see into the cave from the water side, but I had no path to walk in. I had to double back to a small cave and crouch through an archway at its rear to enter the Waenhuiskrans Cave.

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The cave interior is delightfully ripply.

Once you’re inside, no more crouching is required! The cave was reputed to be big enough to turn an ox team inside; this is similar to the traditional requirement for the width of streets in Salt Lake City. While one can find both historical and modern graffiti inside, the cave is mostly in its natural state. The floor was a bit treacherous at first, especially before my eyes had adjusted to the darkness inside. After a while I was striding about without a problem. This natural feature provided the first of the names for the towns at this site.

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Sea urchins!

I came back outside the cave to catch up with Natasha. She had been investigating the tidal pools with joy. The lovely red anemones were pretty sizable, and the fish caught in the pools were doing well to stay clear. Natasha taught me how to recognize a limpet; their remains were everywhere to be found on the rocks projecting into the sea. She really hoped to find an octopus, but we didn’t want to run ourselves onto rocks from which we couldn’t return!

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Stones in a hollow

She and I ventured from one beach to the next by hopping across the rocks. The waves were crashing with a lot of energy, though, and I decided to head back up the bluff after I had to sidestep a wave to save my camera from a dousing. We dodged trucks driving up the walking path to return to Strawberry, our car. This time on the path, we looked around a bit more, and I realized that the sand dune separating the land from the beach at Armiston were just about as large as the ones we had seen at De Hoop! Kids were trying to slide down the slopes on their “boogie boards.” It looked like fun.

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Who doesn’t love a good cairn?

We drove the car into the town proper. Arniston takes its English name from an 1815 shipwreck in this area of an East Indiaman. For lack of a chronometer, the Arniston ran into a reef offshore here, and the wreck killed 372 people onboard, mostly wounded English soldiers. Only six people survived! The mourning parents of four children killed in the wreck built a memorial near the wreck site, and a replica was emplaced on the site in 2010.

As we drove along the main road, we encountered one of the biggest businesses in the area. The Arniston Spa Hotel is easily the largest building in the area. Its position on the beach gives a commanding view of Kassiesbaai, with lines of sand dunes stretching to the northeast for miles. The name of the bay is yet another name for the town.

Kassiesbaai is the set of buildings on the hill just north of the Hotel. The narrow streets and white-washed buildings of the old fishing town seem quite distinct from the vacation homes to its south. In trying to navigate Kassiesbaai, we found ourselves turned around in an adjoining area that featured a fair number of shacks. When we encountered a person transacting business with people in a passing vehicle, Natasha reminded me that the fishing industry has an entangled history with the drug trade. Poachers sometimes exchange their catch for “tik,” or crystal meth, and the drugs can ravage these coastal towns.

With our short tour complete, Natasha and I headed back to Bredasdorp for lunch.

Jackalopes Return to Yellowstone Ecosystem

In my mind, salamanders will always be born in fire, drop-bears are a menace throughout the Southern Hemisphere, and jackalopes are a traditional feature of the Mountain West.

GEOGRAPHY EDUCATION

After a 93 year hiatus, the elusive Jackalope has returned to the greater Yellowstone ecosystem! These beautiful, yet frightening, creatures were once widely collected by tourists, but better management practices have allowed a re-introduced pack to thrive again. These guys have been sporadically spotted all around the west, including Wyoming, Montana, Colorado, and New Mexico. Idaho allowed a ?shoot on sight? policy for jackalopes, so they have not been seen there in quite a while.

Source: jellostone.com

Long live the Jackalope!! May the majestic creature once again flourish in the West.

Tags: biogeography, environment,ecology, fun.

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Testing the waters at De Hoop Nature Reserve

March 31, 2018

South Africa features a promontory just east of Cape Town that points down toward Antarctica. This area, reached by climbing Sir Lowry’s Pass over the Hotentots-Holland mountains, combines the high Overberg plateau with l’Agulhas peninsula. Natasha and I set our sights on visiting “De Hoop” Nature Reserve to the east of this peninsula, using the historic town of Bredasdorp as our base camp.

De Hoop is centered on a massive brackish body of water fed by the Sout River that has been cut off from the Indian Ocean by 2.5 kilometers of sand dunes. It draws its name from a farm established in 1739 by Frederick de Jager, a free burgher, on lands granted by the Dutch East India Company. De Jager had “the hope” that this sandy, rocky soil could be coaxed to produce good crops.

Driving to De Hoop, however, is a bit of a challenge. On the map, it seemed straightforward. We would follow R319 east from Bredasdorp and then diverge to the east on the road to Malgas (pronounce the ‘g’ with a good throat-clearing). Finding R319 was fine (it’s the same thing as “All Saints”), and we followed it for a couple of miles before finding our sign for Malgas. We were less than thrilled to discover that our path from that point forward was entirely gravel and rock, leading from one dusty sheep farm to another. Forty cautious minutes on the Malgas spur brought us to the sign for De Hoop, and we followed a rougher road still to the entrance gate.

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The view of the reception area from the bluff

I must say, at this point, that I was skeptical of the claims that De Hoop was a beautiful pearl. Natasha’s report that the reserve had been closed for a period in the early 2000s due to a fire, combined with our area’s historic drought, did not fill me with confidence. Just the same, we paid our 80 Rand to a charismatic gate guard, and over the hill we went. As soon as we began our descent from the 200m bluff to the coast, the variegated greens of this coastal plain became apparent.

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Bontebok

Natasha and I both caught the thrill of the place as we drove down a side road to the reception area. It lies between two plains, and each featured quite a few groups of animals. The most common type we saw was the bontebok, an antelope that was generally outnumbered by springboks when we visited the Northern Cape. We were particularly excited to see a Cape mountain zebra, but we didn’t have the camera handy until we reached the parking lot. Natasha spied an eland at a distance, too!

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We walked on a shelf that mirrored this one.

The reception office had a handy and well-executed booklet available for 20 Rand that supplied a historical, geographic, and biological appraisal of the area. We grabbed a copy since it documented the points of interest on the 3km hike that we elected to follow along the vlei (like “flay,” frequently meaning marsh, but here meaning the body of water). In no time we had started our walk. For much of the path, we were striding along a limestone and sandstone conglomerate shelf, approximately eight meters above the water’s surface, though we did occasionally dip down to meet it.

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Melkkamer

Where fuzzy creatures were concerned, our hike was something of a bust. The dassies were MIA, though their droppings were not, and our much-anticipated visit with the Cape clawless otter was fruitless, though we did see evidence of their dinners of crab. We did enjoy the little blooms along our path, though. The area is part of the UNESCO World Heritage Site spanning to Cape Point due to its wildly diverse fynbos plants. We also enjoyed the touch with the area’s history as “Die Melkkamer” (the “Milk Room”) mansion complex came into sight on the opposite side of the water. The earliest building dates from 1872.

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Not a beach for swimming

Eventually, the path dumped us onto a pebbly beach that was covered in some sort of salt-tolerant grass. We didn’t dip a hand in to feel the water. Instead, we turned back to the north to return to the reception center. We passed a long-dusty watering hole, along with a tree that we eyed warily, since it looked like it might serve as a home for baboons. As we approached the reception center, more bonteboks came into view. A scout from the herd kept a watchful eye on us. We loved the massive fig trees (brought here from KwaZulu-Natal) that have graced that drive since the 1950s.

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Fynbos, dunes, and tidal pools, oh my!

One must be careful when using the phrase “tidal pool” near Natasha. She was intent on seeing the Koppie Alleen (“Lonely Hill”) Rocky Shores. We drove toward the beach and took the side road heading east to the site. We had once again found a long gravel road stretching into the distance. For an added bonus, this one was limited to half its width for traffic in both directions since the park is paving a new road with strong bricks. We puttered along for half an hour at 20 kph until we found the Koppie Alleen parking lot in good repair.

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Looking southwest from the top of the dune wall

Just as De Hoop is separated from the rest of the region by a 200m wall of hills, the hills and plain of De Hoop are separated from the beach by a range of sand dunes. At Koppie Alleen, one can follow the right fork of the path to the to nearest dune top, or one can follow the left fork down to the beach.

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Sandstone beach

We started on the beach. We arrived with the tide already high and rising. Many of the pools in which Natasha might play with stars, anemones, coral-worms, and limpets were already submerged by the waves. The rocks were fun to climb on though, and the sandy beaches were as near unspoiled as one can imagine. I shot a few moments of video to remind me of their crash.

I saw some odd bubbles enclosed in a blue membrane in the sands though. Natasha warned me off the “blue bottles” right away. Portuguese man-of-war jellyfish are quite prone to stinging the unwary finger.

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Dave, moments before succumbing to sunstroke

At this point, I fell into a bit of a swoon. Natasha coaxed back up the walkway to the food trailer and poured a Diet Coke into me. I had touched too much sun and not enough water today! From there, we climbed to the dune top to get one last look at the beautiful coast.

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Ostrich!

As Natasha drove us along the endless gravel road back to Bredasdorp, she spotted a female ostrich, outlined beautifully by the declining sun. We paused for one last snapshot.