Blog from the Sea of Cortez: Baja Coastal Institute

Last Saturday marked our third visit to La Paz — but this trip was different. Instead of hosting public showings, we focused on a series of research and educational events organized in collaboration with our partners at the Baja Coastal Institute (BCI).

BCI is deeply concerned about the future of southern Baja California. They've witnessed the unchecked spread of resorts and condominiums along the coast between Cabo San Lucas and San José del Cabo. Now that this stretch is nearly saturated, developers are setting their sights on the next frontier: the coastline north toward Cabo Pulmo.

When you've built up everything between Cabo San Lucas and San Jose del Cabo, where do you go next? Why you keep going towards Cabo Pulmo!

A powerful "hospitality-industrial complex" is entrenched in the region. Children are often steered toward careers in hotels and casinos, and many local communities have come to see those jobs as the only viable economic future. BCI is working to change that narrative — to give communities a more informed and empowered voice in this imbalanced conversation. They’re doing it through research, education, and outreach.

Their research program is focused on water and fisheries — essential but finite resources. One recent white paper revealed a troubling fact: the region’s aquifers are recharged annually with about 47 million cubic meters of water, yet existing permits allow for 51 million cubic meters of extraction — and that’s without factoring in new hotels or golf courses. The risk of overexploiting water is real, and it could severely limit the future of these communities.

Their education program brings these insights directly into schools. While hospitality will likely remain part of the region’s economy, BCI wants the next generation to understand the tradeoffs and consider broader possibilities for their future. Their message: it’s okay to dream bigger.

This mission aligns closely with the goals of our Foundation. 

One moment stands out: one of their leaders was thanking us for the use of our microscopes so their students could see what was literally in the waters around them. Even this simple instrument is lacking in these rural schools. She grew quite emotional as she told us that not only can the schools not afford them, but with they didn't even want them. When a child’s future is assumed to lie in the hospitality sector, who needs to study plankton?

The idea that children are locked into limited futures before they even begin — that hit home.

We started the week with an exploratory mission into the mangroves on the south side of El Magote, the sand spit across the bay from La Paz.

Looking at a nudibranch, found in the mangroves of El Magote.
Marcos, the instructor, had an amazing ability to keep even jaded teenagers spellbound.

We then took two groups of high school teachers out on day trips on the boat, doing some research and education activities in the area north of El Magote, the big sandspit across from La Paz. There had been a fish kill there a few weeks earlier and we wanted to see if there was any causal evidence left behind. We looked at some plankton samples and did some ROV surveys, but by the time we got there, we were way too late for a forensics analysis.

Using a refractometer to measure salinity.

Plankton tow off El Magote

We also had two "docked" programs at the wharf in La Paz. BCI students traveled from their remote schools to the boat to enjoy 2 hours of hands-on experience.

A "Docked" program in La Paz with rural high school students.

Blog from the Sea of Cortez: Squid

William ("Gilly") Gilly, is one of the scientists on board, as well as a Foundation board member and Stanford professor at Hopkins Marine Lab. He is also an expert on the Humboldt Squid. He first got interested in them because of their unusually long and accessible axon, which allows experimentation on how nerves work. Since then, he's gotten interested in their natural history, including the boom and bust nature of squid fisheries.

Through 2008 it was a huge fishery, the fourth largest in Mexico. Then with the arrival of El Nino in 2009-2010, and the higher temperatures it brought, the fishery collapsed. Squid that used to grow to well over 4kg sexually matured at a small size (<1kg). The fishermen in their small pangas and using a jig, simply couldn't collect enough to make a living.

This is not the first time this has happened, but when previous El Ninos relaxed and cooler water came, the squid always returned to their former jumbo size. Unfortunately, this time the squid stayed small. The waterfront in Santa Rosalia that used to support ice plants, packing houses, and a huge fleet of pangas disappeared with the squid. 

Until this year.

On Tuesday (29 Apr), we intended to anchor in San Lucas Cove for the night after a long passage from La Paz. Ahead on the radar we could see dozens of small radar signals. It was very calm, so our first thought was that they might be pelicans resting on the surface (our X-Band radar is that sensitive), but as we got closer we realized it was a huge fleet of pangas heading out from Santa Rosalia looking for squid.

As mysteriously as it disappeared, the squid were back.

When we got to Santa Rosalia yesterday afternoon, Gilly, Unai, and I wandered over to the fishing docks to see what was going on. Walking with Gilly, it was clear that he is a local rock star. He is well known for unraveling the mystery of why squid disappeared 15 year ago and for not giving up hope that they would someday return. It's as if they figured he had engineered something for the good times they were now enjoying.

The place was a madhouse. Hundreds of people were launching pangas, filling them up with gas, charging batteries (used for lights to attract the squid) and getting ready for a night on the water. 

We talked to some of the locals and it turns out that the squid are now large enough (2-4 kg), that a skilled jigger can catch 2,000 lbs or more, making it once again profitable. Prices are also high. Unfortunately for the locals, so are costs. Because the local squid infrastructure is long gone, the fishermen have to clean their own catch, then arrange to have it trucked to Ensenada for shipment to China. 

Still, after a 15 year hiatus, the fishery is viable again. 

Gilly negotiated with a fisherman to buy 20 squid early in the morning (0500) so he could dissect them and see if they were sexually mature. Despite their mid-size, most were not, meaning that if they were left alone, they would grow still bigger. The small phenotype that dominated for so long has mysteriously disappeared.

Is it sustainable? Who knows? The fleet here in Santa Rosalia is exclusively small pangas, so they don't have the impact of the large trawlers out of Peru or China. Previous busts have been driven by the coming and going of El Nino, not overfishing.

But, as this old boat can attest, every fishery has its limits.

Getting ready to head out

Some of the 65+ pangas that headed out last night, looking for squid.

Blog from the Sea of Cortez: Exploring Isla San Marcos

Over the last few weeks we have done a lot of science: re-occupation of old CTD sites, eDNA sampling, fish surveys, etc. But it's all been pretty structured.

Today was different. It occurred to me that this was our first real day of pure exploration --- just going wherever out scientific instincts took us, with no particular agenda. Finally, 45 years after I got my PhD, I get to be a gentleman oceanographer.

The morning was spent looking for octopus. Gilly, a Stanford scientist and board member, had seen octopus kill a mollusk, then move into its shell. Once it got too big, it went looking for a bigger victim and so on up the housing chain. A few octopus were found, but they were just living under rocks, not in a victim's shell. We'll keep looking.

For the afternoon, we decided to explore an area north of Isla San Marcos. The charts of the area are not very good and some of them suggested that the ridge was actually two ridges or, possibly, seamounts, with a valley between them. The ridge is of interest because it is relatively shallow, often less than 40m, surrounded by deeper water, so it is likely to attract a lot of wildlife. We had also seen a few local fishermen out there. We decided to take a look with our echosounder and, possibly, ROV.

And, indeed, the area was incredibly abundant with wildlife. We saw hundreds of birds (mostly Elegant Tern, Yellow-footed Gull, Brown Pelican) and several humpback whales. There was a pod of about 100 dolphins swimming energetically around us all day --- occasionally they'd wander over for a closer look if we brought out a new piece of equipment.

We also saw many dense schools of fish on the echosounder, usually pressed up against the bottom, presumably hiding from the dolphins above.

The two seamounts turned out to be one long, continuous ridge trending to the NNW. Much of it was relatively shallow --- 40-60 m.

We collected enough echosounder data that we should be able to make a decent map of the area. That will require one of us mastering Echoview, a sophisticated piece of software, which will take a little time.

The day felt very "Steinbeck and Ricketts". We were out in the sun poking around all day, then retired to an anchorage in the evening for beers and talking.

Maddie taking a turn at the wheel of the ROV.

A pod of dolphins hung around the area all day.

Transect across the ridge, west to east. The lines SM1 and SM2 mark the location of two CTD casts. Note the "fish balls" above the ridge. Also, the deep scattering layer, located at 200m on the west, 350m on the east.

CTD cast "SM2". This shape is typical of the area: temperature, salinity, oxygen, and chlorophyll all decrease with depth. The thermal gradient is strong enough to overcome the haline gradient. Deep water tends to be hypoxic or even anoxic.

After a CTD cast, the line must be brought in and "level wound." That means laying the wraps hard against each other to get nice even layers. Captain Paul nails it every time with his Jedi-like focus.  Oh, and he does it with his bare hands. When it's my turn, it looks like spaghetti.

A reef just off Isla San Jose.

Isla San Marcos. I found its starkness beautiful, but then I've always loved deserts.

An evening of chatting and enjoying a cold beer.

Blog from the Sea of Cortez: Electrical woes

Flyer has a unique hybrid system. She can run as a conventional diesel, but she also has two 100 kW motor / generators that can be clutched in, allowing her to run as a pure electric boat. It's truly delightful being in electric mode --- something like a sailboat, with just a light background hum. 

This propulsion trick requires some truly massive batteries --- almost 400 kWh worth (compare to 50-80 kWh for a Tesla model 3). All that power has to run through a set of inverters --- two for the propulsion motors, one for the rest of the boat's electrical loads. Most of the time, the system works great.

But then there are the other times.

Yesterday was one of those times. The inverter used to run the house loads tripped five times in the afternoon until we finally gave up and started up our Bollard 32 kW genset. It's been running since.

We're not sure exactly what the problem is, but we do know that it doesn't like La Paz. I'm not just being flippant: the water here is at least 8°C warmer than in the northern Gulf, where the unit ran for days without any problems. My theory is that there is an airlock in the inverter cooling system, which allows just enough water to get through most of the time, but not enough when the water heats up. Unfortunately, clearing the lock is not a simple matter as the unit has meters of small cooling hoses running through it, all of which have to be independently cleared.

There also seems to be an issue with the hybrid system's many CAN bus connectors.

Right now, we're heading to Agua Verde where we have a busy schedule with local fishing groups and school children. I'm hoping to get a few quiet hours on Monday to take the cooling system apart.

Life on the bleeding edge...

Blog from the Sea of Cortez: Farewall to Safari Voyager!

Western Flyer is licensed by the US Coast Guard as a Research Vessel. That means that, as much as we'd like to, we cannot carry passengers for hire. So, to help pay the cost of our 3 month voyage through the Gulf of California we have partnered with someone who can: Uncruise, an adventure cruise company. 

For the last 10 days their ship, Safari Voyager, a 174 foot, 66 passenger adventure cruise ship, has been shadowing us. Guests have been participating in many of our research activities, such as CTD casts, and intertidal surveys, but then retiring to Voyager for meals and to sleep. In the late afternoons Susan Shillinglaw, one of our board members and a John Steinbeck expert, has been leading the group in reading passages from Log from the Sea of Cortez. 

The results were fantastic. There was something special about reading about an area from the book, say Puerto Refugio, then visiting the actual site with Flyer close at hand. We would compare what Steinbeck and Ricketts saw with what we were seeing. It was also hard not to notice the parallels between the backdrop of war in 1940, to our world today, all of which led to some interesting discussions. 

Take this passage:

We take a tiny colony of soft corals from a rock in a little water world. And that isn’t terribly important to the tide pool. Fifty miles away the Japanese shrimp boats are dredging with overlapping scoops, bringing up tons of shrimps, rapidly destroying the species so that it may never come back, and with the species destroying the ecological balance of the whole region. That isn’t very important in the world. And thousands of miles away the great bombs are falling and the stars are not moved thereby. None of it is important or all of it is.

--- Steinbeck, John. The Log from the Sea of Cortez (Penguin Classics) (p. 4). 

Is this the dawn of a new environmental awareness? Or, is it a nihilistic view of the world where evolution grinds on, indifferent to its outcome? Much of the book discusses "non-teleological thinking," the idea that nature has no purpose, it just "is". Man may do foolish things, but there it is.

With such heady topics, it would have been easy for the group to chase down a rabbit hole, but Susan kept things going and on-topic.

I first read Log from the Sea of Cortez as a late teenager. At the time, it read as an adventure story to me, with vivid descriptions of days and nights at sea. With so few years under the belt, the philosophical musings went over my head and I skipped a lot of them. This time, we all slowed down and thought a bit more deeply about the book. I got so much more out of it.

Still confused, but at a higher level.

--- Popular saying around RWS. 

Blog from the Sea of Cortez: Santa Rosalia

Some blog entries just write themself. This is one of them.

This morning, we pulled into Santa Rosalía, and old French mining town. It was founded in 1884, and for 70 years, millions of dollars worth of copper was extracted until the mines played out. After that, they were never profitable, and the town has tried to reinvent itself as a tourist town. 

Of particular pride is the opening of Instituto Tecnológico Superior de Mulegé (ITESME) in 2005. Since then, it has come a long way as a technical college, offering programs in electrics, renewable energy, hospitality, IT, and mining. 

An old steam shovel where it dropped.

The old refractory furnace.

Lots of colorful architecture.

The town was not visited by Steinbeck and Ricketts, probably because they were deterred by the very active smelter at the time and all the smoke it created, but we were eager to visit. One of our board members, Dr. William Gilly, has been to the town many times, and has been working to introduce a marine sciences program at ITESME, so the town already knew about Flyer.

Once again, our local partneers, this time ITESME and Hagamos Más, came through. The welcome the town gave us was humbling. 

The town turned out!

Local Yaqui dancers performing
a traditional dance.

Imagine our astonishment when we were presented with
this model of the Flyer! Even the doors open!

Even more astonishing was the fleet of 70
tiny Flyers, one for each guest.

Me with my little Flyer.

One of the Yaqui dancers in our engine room.

It wasn't too long ago that
Western Flyer looked like this.

Blog from the Sea of Cortez: eDNA

Marine Environmental DNA (eDNA) is the study of the genetic material shed by passing marine life. Once sequenced, a scientist can determine which species were present. 

Previously, the only way to do this would be to send a trained observer overboard in SCUBA gear. Even then, there were limits to how deep a study could be done, and there's always the problem that a human garbed in SCUBA gear, with its Darth Vader-like sounds, could send a shy fish fleeing. By contrast eDNA can see everything at every depth. The tool is so powerful that it frequently indicates the presence of salmonid DNA in the Gulf of California, even though there is none in the area. Where does that DNA come from? I leave it to your imagination. 

However, there are limits. There are millions of species on the planet, but only a fraction have had their genetic material sequenced, so a scientist has to rely on libraries of known genomes. Because many species are very closely related, their genomes may have slight differences, so differentiation down to the species level can be difficult (but frequently unnecessary).

For Leg 2, we have Dr. Adrian Munguia-Vega, an eDNA scientist with an appointment at the University of Arizona. He also has a small lab in La Paz that specializes in genetic population studies. He has been taking eDNA samples everytime we put a CTD package over the side, so we will have genetic information along with basic oceanographic information.

While the technology is incredible, the process is actually a pretty simple one.

Adrian with his Niskin Bottle.
It's used to collect a water sample at a specific depth.

Sterilizing the tools. Without sterilization, the sample
is vulnerable to being contaminated by any passing life,
including humans. It was a windy day, so
a towel was used to shield the butane lighter.

Extracting a single filter sheet.

Putting the sheet in the vacuum extractor.

Pulling a vacuum on the water.
What's left behind is what is sequenced.

We won't know what Adrian will find until he takes the samples back to the lab to be sequenced.

BONUS PICTURE

Flyer at Punta Trinidad in the rarely visited Reserva de la Biosfera El Vizcaíno.
The nearest road is about 40 miles away.

Blog from the Sea of Cortez: Santomar

At the invitation of iAllumbra, we visited a Red Snapper and Totoaba fish hatchery owned and managed by Santomar, located near La Paz.

Totoaba? Isn't that the endangered fish coveted by the Chinese for their swim bladder? The one whose demise has also caused the inevitable extinction of the diminutive porpoise, the Vaquita? Yes, it is. While they are under a lot of pressure in the wild, it turns they are well suited for being grown in a fish farm. The facility we visited, located about 20 minutes away in industrial Pichilingue seemed like an unlikely place for a hatchery, but inside, it is a truly remarkable high-tech place.

Under one roof, the hatchery replicates the entire food chain of Totoaba fingerlings, from algae to copepod. There are hundreds of details that must be mastered. For example, algae is grown under artificial light because the sun would make the water too hot, which would require more energy to cool down than the electricity used by LEDs. Because totoaba only spawns in the spring, the facility needs to mimic all four seasons to ensure a year-round product --- the intensity and duration of sunlight varies accordingly.

Winter season at the hatchery.
Eggs will be harvested from these fish.

Spring. The adults are slightly larger,
and a lot more active. This is the stage at
which the eggs are harvested.

Tanks used to grow the larvae into fry.
The red lights keep the fish calm.

All these details must be mastered, but what matters most is the yield of fingerlings. Once they are moved into the open ocean pens, the process gets a lot more straightforward.

I asked them whether they sell the swim bladder. After all, if the hatchery could put more on the market, that would reduce demand for wild totoaba, reducing pressure on the few remaining as well as the hapless vaquita. Unfortunately, Mexican law doesn't allow them to do that. The law is simple: you cannot sell totoaba swim bladders. Anything more nuanced could create a cover for the already lucrative black market. 

La Paz is a lovely, charming town, but I didn't expect to see something so high-tech in it. I really enjoyed our visit and learned a ton. Thanks to our hosts, Santomar!

 

Blog from the Sea of Cortez: La Paz

Today was our big day in La Paz: Regreso del Western Flyer a La Paz --- an open house for the city of La Paz, celebrating the return of the Flyer after an 85 year absence. The weather forecast promised hot temperatures (90+) with little wind, so we weren't sure how many people would show up. We need not have worried: our local partners had done their jobs. Hundreds of people stood in that hot sun, in some cases for nearly 2 hours, just to have a chance for a quick tour of the boat. 

The "Flyer advertising the Flyer"

To handle that many people we had arranged for about a dozen local high school students to act as bilingual docents. They accepted the job with enthusiasm and even showed up on Friday for a 90 minute crash course on the boat. We simply could not have done the job without them.

Local students Mariana and Daniel
explaining the science program on Flyer.

A hard-earned ice cream after a
hot day wrangling the crowds.

To me, the students made the day not only because of their energy and good cheer, but because it reminded me why we do this. Many of them told me what a fantastic time they had and that it encouraged them to continue their studies. In particular, one young man was toying with a career in electrical engineering, but wasn't sure whether he would be working for money, or because he loved the job. Today convinced him that he could have both.

I think it's safe to say that we left a lot of goodwill behind at a time when both nations need it.

Damn, what a photogenic boat.
Flyer never takes a bad picture.

Blog from the Sea of Cortez: The Steinbeck Head

After 50+ years of neglect and 6 months underwater, large parts of the Flyer were totally rotten and had to be replaced, but there is one part that is almost 100% original: the "Steinbeck Head." Yes, you too can sit where John Steinbeck sat 85 years ago!

The Steinbeck Toilet after 6 months on the bottom
and a bit of cleanup. Photo by Susan Shillinglaw.

Both the head and the toilet were in surprisingly good shape. The toilet was filthy, there was a crack in the porcelain base, the flapper valve was not functional, and some of the floor tiles were missing, but everything else was in excellent condition.

Captain Paul spend coutless hours cleaning the sludge from inside and outside of the toilet. The base was repaired with a bit of epoxy. 

The flapper valve assembly was replaced with a modern one, although the lever is original.

The original lever, cleaned up and still in use.
Photo by Phil Sconce.

The insides after cleaning. The float is not original,
but it has the same soldered construction. Photo by Phil Sconce.

The missing tiles were more of a challenge. We couldn't find exact replacements, but then Phil noticed that the toilet was actually sitting on top of some untouched tiles. He took the toilet off, carefully chiseled out enough of these hidden tiles to replace the missing tiles, bedded them in concrete, then put the toilet back on. 

The results are striking: the head looks pretty much exactly as it did 85 years ago! It's one of the favorite attractions on the boat.

The head as it looks today.
Photo by Sherry Flumerfelt

Despite the extensive restoration, hidden here and there are some
nearly untouched spots. Here's one: you can still see the barnacle marks on the
window from when Flyer was underwater. Perhaps you can find some others?

Blog from the Sea of Cortez: 17 March 2025

The weather for most of our sendoff on Sunday was very pleasant: sunny, warm, and calm. But an hour before departure, it started blowing hard --- about 20 kn, gusting to 25 kn from the south. Once we rounded Point Pinos, we felt the full sea state. Maybe 8-9' seas.

Unfortunately, shortly afterwards, we had our first accident: me. I was climbing up out of the fish hold, having just posted the blog before this one.  The companionway is covered by a heavy sliding hatch, which often sticks. Knowing this, I gingerly gave it a pull, then again, this time more forcefully. The hatch slid open suddenly, just as the boat took a roll to port. My left thumb got scissored between the frame and the hatch itself, leaving a cut down to the bone and blood everywhere.

Andrea, our Captain, and I had a brief discussion about whether to keep going or head back.After a lot of staring at the wound, she summarized the situation well: "The use of your hand is worth more than an hour of our time." So back we went. I ended up spending Sunday evening at CHOMP, the Monterey hospital, while the boat continued down the coast. Diagnosis is that I will need to see a hand surgeon in a week. Meanwhile, the risk of an infection is great, so I'm to be on antibiotics, while changing the bandage twice a day.

Bandaged and good to go.

After getting patched up, John Gregg (our founder) and I drove down the coast the next day and I rejoined Flyer in Santa Barbara.

Sherry, our Executive Director, says that every great trip starts with a disaster. If so, I took one for the team and got that out of the way.

Blog from the Sea of Cortez: 16 March 2025

“It would be good to live in a perpetual state of leave-taking, never to go nor to stay, but to remain suspended in that golden emotion of love and longing; to be loved without satiety."

--- Log from the Sea of Cortez

We had a good and proper send off! We spent 3 hours offering public tours of the boat and hundreds showed up. We were on a hard deadline to leave not only because that was what the crowds expected, but because a foul squall line was fast approaching with big southerlies associated with it. We knew we were in for a possibly rough passage past Big Sur, but if we got out quickly, the fetch wouldn't have time to build and maybe we'd get out of the worst of it.

That deadline meant that we had to rush people through the boat, perhaps a little faster than they were prepared to move. For the first time, we opened up the engine compartment, so that took a little longer. Still, in the end, everyone got a good and proper, albeit occasionally rushed, tour.

We were looking good for our 1500 departure, but then crisis hit. There were 9 people on board, but only 8 immersion suits. Fortunately, relief skipper Brian had one on his boat. He completed the round trip journey to Moss Landing in record time, probably breaking more than a few laws on the way, but we had our suit and it was time to go.

Despite the nearly one hour delay, hundreds of people hung in there to say good bye. As we cast off the lines, a cheer ripped through the crowd. I must admit to feeling more than a little emotional about being on the receiving end of all that good will.

And, so we are off!

The Fishwives Sea Shanty band sings from the top of the deckhouse.

Some of the many people wishing us Bon Voyage!

Blog from the Sea of Cortez: 15 March 2025

Western Flyer is the boat that took John Steinbeck and Ed Ricketts to the Gulf of California in the spring of 1940, after which they published Sea of Cortez: A Leisurely Journal of Travel and Research. Steinbeck's better known, and very influential, book Log from the Sea of Cortez is the narrative part of Sea of Cortez. It's a very readable travelogue about the voyage --- a heady mix of science, philosophy, environmentalism, and adventure. It heavily influenced me to get into a career in oceanography.

The boat was nearly lost to history, but thanks to John Gregg and the Western Flyer Foundation, it was saved and meticulously restored over the last 8 years. She is now fully seaworthy and kitted out as a research and educational platform. More at the Foundation's website.

I've been involved with the Foundation for about 7 years now, first as a groupie, later on the Board, and for the last 5 years, as President of the Board. 

Tomorrow (Sunday) we leave from Monterey to recreate parts of the voyage. More here. I don't think it's an exaggeration to say that I'm giddy with excitement! I intend to publish updates as we go along. 

But, before that moment when you shove off, there's always a mad time getting the boat ready. We have a lot of equipment --- scientific equipment (x2 for spares), boat spare parts, crew gear, provisions, a dinghy, gangway --- it all has to be securely stowed for a long voyage. In particular, we are expecting rough seas on Sunday night, so we have to be ready from the very start.

Flyer the night before departure from Moss Landing

Just a small portion of the provisions. This will only get us to Santa Barbara!

If all goes well, we will reach Santa Barbara late on Monday night (17 March).