55 Music Concourse Dr.
Golden Gate Park
San Francisco CA
Regular Hours:


9:30 am – 5:00 pm


11:00 am – 5:00 pm
Members' Hours:


8:30 – 9:30 am


10:00 – 11:00 am

The Academy will be closed on Thanksgiving and Christmas Day.

Planetarium will be closed Sep. 22, 23, 24

Birds and Mammals Research 

June 23, 2014

The rediscovery of a “missing” New Guinea bat, and the value of collecting and documenting modern biodiversity.

Scientific museum specimens were often collected for one reason, and then used in studies that were not even imagined by the original field collector.  This is easy to understand for collections made 100 years ago for taxonomic purposes and that are now used for studies of stable isotopes, ancient DNA, environmental toxicology, and evidence of global climate change. And these are just a few of the many modern high tech uses of museum specimens.


But recent work on bats in New Guinea has turned this around.  Collections made for modern studies of logging impact have uncovered an important specimen valuable for basic taxonomy – and for recognizing a species that has not been definitively documented in over 120 years.


In a report just published in the Australian Museum Scientific Publications, a group of researchers from Australia’s University of Queensland were mist-netting in Central Province Papua New Guinea, as part of a larger study to investigate the impacts of logging and to compile a reference library of ultrasonic bat recordings.  They had only a couple mist nets and harp traps set up in the forest, and they captured 42 specimens of 10 species, and the vast majority of captures were of a single species, the Common Blossom Bat. But there was one specimen that was unusual and the team could not identify it in the field.


The unknown specimen was collected and it took many months of research and the specimen being loaned to the Australian museum before it could be positively identified, based on a number of obscure characteristics.  It turned out to be Thomas’s big eared bat, Pharotis imogene, previously known definitively from only one locality – Kamali village in Central Province, Papua New Guinea. This species is the only representative of its genus, Pharotis, and has the largest ears of any of the New Guinea big-eared bats.

Pharotis Live Photo

Thomas’ big-eared bat from near Oio Village, Photo Catherine Hughes

Because it had not been documented or collected in over 100 years, many people presumed it was extinct. But many regions of the world are biologically very poorly known and poorly documented.  According to The Bats of Papua New Guinea by Frank Bonaccorso, “the species probably still exists, yet remains difficult to survey by routine collecting methods. Surveying with harp traps near potential roost trees or caves in the Kamali and Tuman River areas of Central Province may prove effective in the study of this species.” In fact, this study that used a single harp trap extended the known range by over 120 km to the east.

The harp trap set along a logging track in the Abau District, Central Province, Papua New Guinea

The harp trap used to collect the Pharotis specimen, set along a logging track in the Abau District, Central Province, Papua New Guinea

Bats are notoriously difficult to identify even by experts, especially in a place like Papua New Guinea where there is so much diversity.  Although Pharotis is known from a small series of specimens (mostly collected in 1890), all are old and there is no preserved tissue available or barcode data available for comparison.  Even the authors of the report found it quite difficult to figure out what they had, and they would never had been able to (or even persisted in trying) without the specimen in hand. This new modern specimen could be extremely valuable in documenting this species, developing new diagnostic tools such as DNA barcoding, and for creating better morphological keys.


Image of Thomas’ big-eared bats from the field guide, The Bats of Papua New Guinea by Frank Bonaccorso

Sadly, most of the previously collected specimens of Pharotis have been lost.  Luckily some early specimens were distributed to the American Museum, the Australian Museum and the British Museum of Natural History, but others were lost due to a flooded Italian museum and to poor collections management elsewhere.


This study highlights the value of museum specimens in modern research, and the importance of taking specimens in modern field studies. Ironically, these studies were undertaken to assess the impacts of selective logging.  The biggest threat to lowland forest in PNG is due to habitat loss from logging, mining, and oil palm conversion.  One of the few things that might slow habitat loss is the fact that one little poorly known female bat was recently collected there.

Filed under: Uncategorized — jdumbacher @ 9:00 pm

April 5, 2012

On the Roof


“What’s our time?” Logan asks moving along the rock paths that crisscross the roof of the CAS.

“Two minutes.” Ore, a graduate student, checks his stopwatch. It’s raining and cold and my second bird survey experience has been unexpectedly lucrative.

Half an hour earlier, winding our way through the halls of the research department, I was expecting 30 wet minutes of cloud spotting. Up on the roof in our yellow vests, the team, shielding our binoculars from the downpour, noted the temperature, weather, and wind direction. Logan was already looking around. ‘Can we start yet?’ his impatient hands said as he waited for Ore to set the timer. As soon as Ore gave the go ahead, Logan, a fourteen-year-old volunteer and bird expert, was leading us around the roof spewing names of bird species too fast for me to document.

We moved in a line, with Logan in the front shouting numbers, species, and the species codes of the birds he saw and heard. “It’s actually prime season for bird watching,” Logan explained to me later as he typed in the day’s data. “Lots of spring arrivals and the gulls haven’t left yet. Twenty one species, could have been twenty three if we hadn’t run out of time; good diversity.” He nods. Just seconds after the clock had run out, Logan had pointed straight up, shouting, “Oh man, that was a Mew Gull.” He shook his head, disappointed, and headed off the roof. Once the survey is over no additional birds can be added to the day’s data.

Ore has Logan name all the gulls; he knows the group particularly well. “Gulls, I love them.” Logan laughs and explains that they are a very over-looked group with a lot of rarities.

After a little over a year of conducting the Tuesday morning roof surveys, the CAS team is very familiar with the local birds. I was shocked to see two pairs of Red-tailed Hawks circling the area. Ore pointed to some tall pines, “Oh, that pair of Red-tailed Hawks nest in those trees over there.” The birds were behaving differently in the rain, a lot more vocally active and many were using the roof for shelter. As we made our way around the Dr. Seuss-like domes we heard three Downy Woodpeckers call.


Moe Flannery, the collections manager of the Ornithology and Mammalogy department, started the roof survey to learn which bird species were   utilizing the green roof. The data collected by the CAS team is posted on eBird, an international bird sighting website, used by birders around the world.

The survey has shown that the CAS building has, in many ways, been successfully integrated into the park environment and the green roof is a      huge part of that effort. The roof has provided important winter habitat for migrating birds resting and feeding. Last winter a flock of seventy plus  Kildeer made use of the green roof for at least three weeks. Kildeer need big open areas of vegetation and seemed quite content in Golden Gate   Park. Recently, the team spotted an Oregon Junco flying with nesting material, exciting evidence that the Juncos are back to nest on the roof for a third year. Oregon Juncos are ground nesters and the roof provides a safe haven from predators and people that also occupy the park.

In line with the mission of the CAS to explore, explain and protect, the survey team continues to monitor action on the roof, not just to share information about our local bird species, but also because of their commitment to improve the world we live in.

- Page McCargo

Filed under: Uncategorized — sstebick @ 1:09 pm

February 5, 2012

Casual Sunday birding in Golden Gate Park… With the camera

Well, it’s a sunny Sunday in Golden Gate Park.  The weather was warm and pleasant, and the winter birds were active.  My wife Tiffany and I took a stroll up the hill and into the park near Lloyd Lake, where there are often plenty of ducks, gulls, coots, and even a grebe or two.  I had my camera with me since I needed a little practice using my long lens on birds. Although none of these are great photos, they show some of the common species that you can see here in the park:


A couple Song Sparrows (Melospiza melodia) were skulking in the underbrush near Stow Lake.  They are difficult to see, but have a very distinctive pattern of banding on the chest which come to a spot in the center.


Here you can see the Song Sparrow’s streaking pattern very nicely.


And of course, the Dark-eyed Juncos (Junco hyemalis) are common around many footpaths.  This junco was in a group of 4-5 others and feeding on bread and bird feed scraps left on the ground by some earlier hikers.  The Song Sparrows were also with them, but the sparrows were more skiddish and more quickly jumped into the thicket behind them while I got these photos.


Several Ring-necked Ducks (Aythya collaris) have been hanging out in Lloyd Lake, near the 25th Avenue north entrance to the park.  Although the Mallards are still slightly more abundant, the Ring-neck Ducks have been common here this year with over 20 in the lake today.


The Hooded Mergansers (Lophodytes cucullatus) were my favorite sighting today.  They are always very spectacular (the male is above), and are great divers.  We often see a pair here on Lloyd Lake, and today there was one male and two females.  The male was pretty cheeky, and allowed us to get a pretty close look and some decent photos.  He aggressively chased two male Mallards away from a patch of weeds where he was diving, despite the fact that he was only a fraction of the Mallards’ size.


Here is a male Hooded Merganser swimming alongside a female.  They stayed closely together most of the time.


I was surprised by how few gulls I saw this morning.  Lloyd Lake is a great place to see Mew Gulls (Larus canus) this time of year, and we got great looks at several.  They are smaller than the Ring-billed or Western Gulls, and have almost no visible marking on the bill.


The much larger Western Gull (Larus occidentalis) was also present (although I took this photo on the Stow Lake boat dock).  These tend to be a little more aggressive than the Mew Gulls, and they respond quickly to the many people who bring bread to feed the ducks.


My wife Tiffany told me that there were Widgeon here too, and this is one of the reasons that we walked up to the lake.  Here is a male American Widgeon (Anas americana) in non-breeding plumage, with the obvious white forehead.  There were only about 3-4 pairs, but they too were relatively easy to see and came pretty close.


We looked for the Wood Ducks (Aix sponsa)  that we often see on the western side of the lake, but we failed to spot them today.  I still haven’t photographed them, and I was hoping to get a nice photo of their head pattern in the sun.  Instead, we saw a lone male Green-winged Teal (Anas crecca) sleeping with its bill tucked into its back feathers.


American Coots (Fulica americana) were common on all of the bodies of water in the park (as usual),

And we got great looks at Pied-billed Grebes (Podilymbus podiceps) on both Lloyd Lake and Stow Lake.


Last but not least (unless you are talking about size) were Anna’s Hummingbirds (Calypte anna).  We saw several out servicing the flowers.  I understand that the Academy is working on upcoming pollination exhibits which will most certainly feature hummingbirds.  Anna’s Hummingbird is a year-round resident that survives well on the parks many flowers, which provide a great source of nectar and pollen.

Another unphotographed highlight would have to be the California Quail (Callipepla californica) that we heard just north of Lloyd Lake.  As we approached the lake, we could hear some scraping in the underbrush, but I was unable to see what was in there.  I figured a junco, towhee, or even a squirrel, and walked on without working too hard to see it.  But later, when we were across the lake, we heard multiple clear “Chi-ca-go” calls of California Quail.  We walked back hoping to photograph one, but alas we were unable to see or even hear them again.  The quail are noteworthy, as I learned at a recent Golden Gate Audubon Conservation Committee Meeting, because California Quail were all but extirpated from the city limits.  There are believed to be only a single family group or “covey” that still lives around the Botanical Garden and Arboretum.  At first I suspected that this could be the same group that had just moved deeper into the park.  But as we walked toward the Academy, we heard another group of quail at the northeast end of Stow Lake – just across Martin Luther King Drive from the Arboretum.  I would still like to get a good look at the covey at Lloyd’s Lake, but it is tentatively great news to me that there may be another group settling there.

Why are the quail disappearing in the city?  It is believed that off-leash dogs are probably the major threat to ground-nesting birds in the city.  As the population rises and as people in the city want dogs for companionship, the impact on ground nesting birds is increasing.  Dogs are also a huge threat to shorebirds – especially the endangered Snowy Plover (Charadrius alexandrinus).  So please do your part and keep your dog on a leash unless you are in a designated off-leash area!

It was nice to get the camera out and shoot a few of the common local species.  In just a couple weeks, Gary Sharlow and I will be taking a group of photographers to Crissy Field to teach and practice some tricks for photographing birds in the field.  This will be a part of the adult programming that Gary has been developing, and a potential source of data and images for citizen science projects.

Filed under: Uncategorized — jdumbacher @ 4:44 pm

December 15, 2011

Surveying birds in Milne Bay Province, Papua New Guinea


We recently spent a very successful 2-month field trip in the island province of Milne Bay, Papua New Guinea surveying birds and collecting samples to screen for various avian diseases.  We had an amazing crew – collaborator David Mindell, Post-doctoral researcher Jerome Fuchs, Berkeley PhD student Zachary Hanna, San Francisco State University Masters Student Molly Dodge, PNG National Museum researcher Bulisa Iova, and the amazing artist Isabella Kirkland.  We spent two months sailing on the SV Dalai, a French-build sloop owned and operated by Bruno and Carmen Montel.

This ship was an excellent way to get around, and the crew and field team were amazing.  We departed from Alotau, Milne Bay Province in September, and returned in November after sailing to Normanby Island, the Amphlet Group, Dawson Island, BudiBudi Atoll, Woodlark Island, Ginetu Island, Gawa Island, and the Trobriand Islands, just to name a few of the key islands.


We captured and sampled over 500 birds, including this Emerald Ground Dove (Chalcophaps indica), and the Collared Kingfisher (Halcyon chloris) below.

Collared Kingfisher, Halcyon chloris.

Although it may look like I’ve not blogged for a while, this is not so.  We were invited by the New York Times to blog in their very excellent series, Scientist At Work, and this link should direct you to most of our posts from the recent field trip:


Feel free to post comments or questions here, and enjoy!

Filed under: Uncategorized — jdumbacher @ 11:01 pm

February 17, 2011

A sick gopher from Golden Gate Park…

A couple weeks ago, I got a call because there was a gopher outside staggering around, obviously disoriented, even falling over onto its side. When I found it, it was lethargic and easy to approach and I picked it up and carried it inside without any struggle or fight. It was loaded with fleas. The folks that called suggested that it may have been poisoned. Since catching this one, friends and colleagues have mentioned seeing other sick or dead gophers around this part of Golden Gate Park, suggesting that this may not be an isolated case.  A couple people even suggested that the city may be putting out poison baits to reduce the huge numbers of gophers in the park.

So we did a little asking around to find out whether anyone is using poison in Golden Gate Park, and the answer appears to be an emphatic, “no.” No one in the Academy is using poisons, not even around our precious collections spaces. In fact, the entire park is off limits to toxic herbicides, fungicides, and rodenticides. So we

spoke with our veterinary doctor in the Steinhart Aquarium, Freeland Dunker.

Freeland is very knowledgeable about animal diseases of all sorts, and almost immediately suspected raccoon roundworm, or Baylisascaris procyonis. This is a common roundworm found in a large percentage of raccoons (between 70-100% of west coast urban raccoons are infected with these worms!), and is very likely endemic to the huge population of raccoons in Golden Gate Park and nearby Sunset and Richmond neighborhoods. The worms normally live in raccoon intestinal tracts, and raccoons can shed thousands of eggs in their feces. The eggs are robust in the environment, and can live for a long time in the soil or in a raccoon latrine.

When other species ingest the eggs, the eggs hatch in their intestines and try to find a good place to settle. But since the larvae are not in a raccoon, they don’t find an acceptable place to settle, and they burrow through the intestinal walls and wander around inside the body looking for a place to settle. These wandering larvae cause a disease called larval migrans, or literally, migrating larvae. As these worms burrow through the body of the host, they leave a trail of destruction. Worms often migrate to the eye, brain, and meninges, causing encephalitis, neuroretinitis, central nervous system damage, and death. Our recent sick gopher was likely an advanced case, and probably had the worms in its brain and spinal column.

Baylisascaris LarvaeBaylisascaris larvae, which move through the body of its host leaving a trail of destruction and causing the disease condition known as “larval migrans.”

Although it is extremely rare, cases of Baylisascaris are known in humans. The CDC has a website that discusses Baylisascaris as a potential emerging human disease. Note that 4 of 11 known human cases were from California. All of the human cases were severe or fatal, and often most aggressive in young children. The damage done by migrating worms can be permanent, and neurological damage to the brain and eyes is usually the first sign of infection, and by then, it is usually too late to do anything but prevent additional damage.

Next time we find one of these gophers, we will try to confirm the diagnosis, and report back. Unless you’re a gopher, there’s really not much to worry about.  You can’t catch this directly from gophers, as they are not typical hosts and probably do not shed eggs (but you could catch it from eating gophers…) But it is worthwhile to keep an eye on your small kids and definitely don’t let them play near raccoon feces.

Filed under: Uncategorized — jdumbacher @ 7:41 pm

February 1, 2011

Avian Pox moves through Galapagos, 100 years ago…

Diseases can have significant effects on bird populations, especially populations that have never been exposed to them. Avian pox is a disease that was presumably moved around by humans, and has been introduced to Galapagos – as well as Hawaii – where the disease has had a significant effect on birds.

Recent work by Patty Parker (from University of Missouri) and her team of researchers has learned where the pox came from, where and when it was introduced, and some details about how it spread across the archipelago. In CSI style, they visited collections (especially ours here at California Academy of Sciences), and examined literally thousands of birds that have been collected over the last century and that are now held in public research collections.

Every bird in the collection has a label that includes information on where and when the bird was collected, and by whom. By looking for external pox lesions, they could get a rough estimate of which birds had pox, where and when.

Photos of pox lesions from Galapagos birds(This photo shows pox lesions preserved in 100-year old specimens collected on the Galapagos during the 1899 Snodgrass and Heller Expedition and the 1905-06 California Academy of Sciences Expedition).

But they didn’t stop there – on birds with large lesions or multiple lesions, they used tiny scalpel blades and cut minute pieces off the lesions. These tissue samples were then used to confirm that the disease was actually pox. Two techniques were employed – first, they did histopathology studies (basically looking at the lesions under a microscope to confirm their external appearance as pox-like), and second, they extracted DNA and amplified and sequenced poxvirus DNA. Together, these two tests not only confirmed pox as the culprit, they actually identified the pox strain as being nearly identical to known strains of Canary Pox.

With this information on the pox strain as well as the information on where and when the pox lesions first showed up, they could unravel how and when the virus first came to the Galapagos. No specimens from 1891 and 1897 contained any pox-like lesions. found that samples collected prior to 1900 never showed pox lesions.

Canarypox virus (CNVP) is a form of avipoxvirus that attacks wild and captive passerine birds, and can cause significant mortality. It is double-stranded DNA virus in the family Poxviridae. Externally, it causes lesions on feet, head, bill, and around the eyes, and can impede sight, feeding, and movement. It can also affect respiratory and digestive tracts inhibiting breathing and digestion. Because the virus contains a double-stranded DNA molecule as genetic material, it is hardy enough to persist in the environment longer than many other viruses.

Check out their full research article at PLoS One

Filed under: Uncategorized — jdumbacher @ 2:14 pm

December 14, 2009

The Sailors

Traditional sailing proas still sail around remote Milne Bay, much as they have for centuries. I’ve heard about this from colleagues and have seen some small sailing canoes off Normanby Island on previous trips, but I was dying to see some of these boats up close and learn more about the traditional sailors. This blog is devoted to a bit of anthropology, and specifically the skills of sailing and boatbuilding that are so well developed – and preserved – in the region.


We saw our first sailing canoe tacking off Byron Island on our way to TubeTube Island. The boat was beautiful, and the sailors seemed at home on the water, but it was still far away and difficult to see how they were sailing.

Papua New Guinea Fall 2009 Trip; Milne Bay Province aboard Dalai

On TubeTube Island, we saw our first sailing proa up close. The boat had several men who had been to Alotau, and were on their way back to their village with supplies purchased from town. While they were on shore resting, they peddled some beetle nut.


Bruno talked to the sailors, and they gave him a quick tour of the boat. They introduced us to the parts of the boat and showed us how they sailed it.

Carvings on the hull

Carvings on the stern

The boat had incredible detail in the bow and stern plates and nice carvings on the hull. The rigging used modern ropes and plastic for sails, but otherwise the structure followed the traditional local sailing rig.

Loading trade store goods on the proa
Later, they loaded trade store goods on the boat, opened the sail and headed off.

Setting Sail in the Local Proa

Once they set sail, it was obvious that it takes tremendous knowledge and skill to rig these boats. Although it may look like these are cheap plastic tarps tacked together, the stitching and shaping of the sail are highly engineered for strength and performance. The sail is carefully shaped, and sewn to maintain proper sail shape. Ropes are sewn into the sail margins so that they can be lashed to spars and raised and lowered.

foot of the sail, lashed to a spar with ropes

Here you can see some of the sewing and lashing on the foot of the sail. We had little time with these folks before they were on their way, but we were headed to the islands of Panapompom and Panaete, where boatbuilding was their main craft. These islands built and supplied most of the finest sailing boats used in this part of Milne Bay Province, and we were excited to see more of these boats in Panapompom.

A small proa built just for a young boy

On our way east toward Panapompom Island, we worked on the islands of Hummock and Haszard, and we anchored in their lagoon. Here we also encountered many sailors, including young boys who sailed smaller, single-boy versions of the larger sailing canoes.

Aladin sailing with the local boys of Hummock Island

Aladin went for a spin on some of these small canoes. Aladin has been building boats since he was a toddler, and so he exchanged notes with the local young sailors on design and technique.


The men and boys of Hummock Island also build and test scale models of their sailing canoes, as does Aladin. They worked together with models as well as larger sailing canoes. At times like these I wished that I wasn’t so busy with the biological research, and I wished that I had more time to learn and write about the local sailing knowledge.

Medium proa, reaching downwind

Larger proa with many passengers and much cargo

As we pressed eastward, we saw more and more sailing canoes, some larger, some with many passengers, and some with slightly different designs.

Very large canoe off Hummock Island

Boat on the shore on Watts (Kwaraiwa) Island

Two sailing canoes "parked" on the beach at Hummock Island

We sailed to Panapompom in early November. Our main goal was, of course, to study the birds of the Deboyne Island Group, but we were all excited to be in the archipelago of the great sailing canoe architects and builders. The lagoon between Panapompom and Panaete is very shallow near Panaete – too shallow for Dalai, which has a 2.5 meter draft – so we anchored off the northeast side of Panapompom Island. This was an excellent decision for the birds, as Panapompom Island was higher and had more variation in habitats and geology, so there were many diverse birds. And we were close to Panaete – just a short sailing canoe ride away. While we studied birds, Bruno and Aladin studied canoe-building with some of the knowledgeable men, and they sailed to Panaete to meet some of the other builders. The photos that follow were taken by Bruno and Aladin during their sail to Panaete on a sailing canoe.

Sailing on the sailing canoe, "Coins" with Jimmy

They sailed with Jimmy, one of our hired helpers, but also a master sail-stitcher and sailor. They raised and lowered the sail, and showed Bruno and Aladin how to use the steering board rudder at the stern to steer the canoe.

Sailing canoe outrigger cutting through the water

The water in the lagoon was crystal clear, so it was easy to see the coral and rocks under the surface. The sailing canoes had a shallow draft, so it was easy to avoid hazards, and they were able to move very quickly through the water.

A sailing canoe being built, and stored under thatched roof

Once on Panaete, they visited several boat builders and saw boats in the process of construction, such as this one that is nearly completed.

nearly finished boat under thatch roof cover

It is quite easy to see that these are not merely dugout canoes. The bottom of the hull is constructed of a dug-out tree trunk, and a particularly strong wood is chosen for this. Then side planking is added for extra buoyancy and to protect the boat in heavy seas, and internal reinforcements are needed to secure these parts to the bottom of the hull. In earlier times, all of the pieces would be carved to fit exactly and then lashed together with fiber ropes.

Decking on "coins"

The outrigger is made of a heavy solid wood that can counterbalance the force of the wind on the sail. The canoe always tacks with the outrigger on the windward side of the boat. The decking is made of wooden saplings or bamboo, and can be made thick enough to support a lot of cargo or people, as needed. The mast rests at the bottom of the main hull and is supported off a large armature that spreads the force over the decking platform.

carving from the bow or stern of the sailing canoe

Although every part of the sailing canoe was functional in some way, some parts were elaborated decorated and embellished with carvings like this bow or stern plate. Bruno also worked with Jimmy and the boat builders to photograph and record the names of many of the ship’s parts. Like sailors anywhere in the world, the New Guineans had specialized names for every part of the boat.

Boat with coconuts on rack

Once back on Panapompom, on our last evening we tried to visit one of the boat builders living there who was famous for building small replicas of the large sailing canoes.

Aladin holding a scale replica of a Panapompom sailing canoe

These little boats were only a few inches long, but they had every functional working part of the larger boats. We weren’t lucky enough to find the model-maker (he was out working in his fields) but we did get to see one of his small models.

22 people riding in an outboard "banana boat"

Increasingly, these sailing canoes are being replaced by fiberglass boats with 40-50 horsepower engines, like this standard commuter boat. One can only wonder how many more years the traditional sailing canoes will be used. Throughout the Pacific, very few islands or island groups still use the traditional sailing canoes. The next time I come to these islands I would love to try to make a documentary film about these amazing seafaring people and try to record some of this knowledge before it is lost.

Filed under: Uncategorized — jdumbacher @ 10:32 am

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