Journal archives for May 2019

May 07, 2019

Behind the power of iNaturalist

In past bio-blurbs we introduced project participants to individuals who are assisting in the Australasian Fishes project. In this edition, we introduce, not a person, but a key element in the success of the project, the software used to collect the research data, iNaturalist.
Imagine that NASA contacted you for advice. They said they were launching a space probe, designed to travel beyond the Solar System, and wanted to include data which illustrated all natural life on Earth. Assuming that once you were over the initial surprise that NASA had your contact details, you might ponder the options available before giving them advice. Perhaps many of you would suggest launching a complete, digitised, set of David Attenborough’s wildlife documentaries, which would provide a beautiful and amazing cross section of our planet’s natural environment. On the other hand, you might suggest storing aboard the spacecraft, a digitised set of all National Geographic (NatGeo) issues, since its founding in 1888, as a way to provide a photo collection of some of the best wildlife images on our planet. Both would provide any interested extra-terrestrial with a broad view of the diversity of natural wildlife found on Earth, however, we know that both views would be limited. In spite of the fact that both David Attenborough’s work and the entire NatGeo collection have given mankind an excellent perspective of the planet over the years, we know there are still a lot of images of our rich natural life, laying on the cutting room floor at both institutions. Each entity recording the natural environment exists not only to provide documentary evidence of life on the planet, but must also entertain and enthral their respective audiences. The view they give us is heavily edited, designed to interest as well as document. Although graphic and attractive, both sources have gone through the filter of numerous editors, who have shaped the final product we are viewing.
I would suggest you should nominate the iNaturalist database. iNaturalist is the software used by Australasian Fishes, and would provide as a truer representation of what our planet has to offer in terms of flora and fauna diversity and uniqueness. A copy of the iNaturalist database, destined to travel beyond the Void, if downloaded today, would contain 19.7 million observations of life on Earth, covering more than 210,000 different species. The alien viewers would learn that over 1,4 million Earthlings have contributed to this project, submitting millions of images with quality ranging from amateur to NatGeo cover, in richness and colour.
The view provided would be an unvarnished, scientific database of what life looks like at a particular point in time, across the entire planet, collected by people with passion for their subjects and without the need to meet any commercial objectives. It is quite a collection as iNaturalist is the leading citizen science software in the world and worthy of the space flight.
That’s quite an accomplishment for an 11 year old piece of software, but as participants in Australasian Fishes know, this is not a regular piece of software. iNaturalist was first developed in 2008, placing it’s founding between the birth of Facebook (2004) and the release UBER (2009). It started life as a group Master’s Degree project at the University of California’s Berkley School of Information. Three Berkley students, Nate Agrin, Jessica Kline and Ken-ichi Ueda worked together to create the earliest version of this citizen science software. Once it was produced, both Agrin and Ueda continued working on the platform, collaborating, and seeking help from others along the way. By 2014, the project merged with the California Academy of Sciences, and since 2017, it has been a joint initiative between the Academy and the National Geographic Society.
iNaturalist needs no real introduction as all of us in the project are aware of the features of the software and how its design and utility has been a strong catalyst for growth of the Australasian Fishes (AF) project. You are using the software to read this article. It serves the project, free of charge, as a very serious and robust platform for crowdsourcing information on individual organisms (like a fish) at a particular time and place. Once recorded the observation becomes part of a global network of data on Nature, incorporated in to other online databases such as the Global Biodiversity Information Facility (https://en.wikipedia.org/wiki/Global_Biodiversity_Information_Facility). We have seen this process in Australasian Fishes, and the software has been a catalyst for project growth and engagement.
Participants would be encouraged by the growth in iNaturalist powered projects as illustrated by the amazing growth of observations in our project. We have over 50,000 observations of 2,194 different species. This growth is driven by our project’s 1,500+ observers submitting their images and geolocating their fish photos. The software makes creating research grade observations easy and fun because of the unique design of the platform. It is far more than just a database of life on the planet. There is also another dimension to its growth and that is “spin-off” projects or other initiatives which are using iNaturalist for their own research. Since established, iNaturalist has been the backbone of numerous citizen science initiatives such Bio Blitz’s, school projects, wildlife surveys and special interest groups. An example would be the City Nature Challenge (https://en.wikipedia.org/wiki/City_Nature_Challenge) which annually focuses on urban, biodiversity. There are projects for subjects like roadkill, animal tracks and fish catches, as well as the type of data collected by Australasian Fishes. The software can handle all such varied uses, creating a diverse but comprehensive picture of natural life on this planet. Frequent users of Australasian Fishes will know of the growth in projects founded by project participants. To illustrate, you have read in the Journal section, for example, about Shelly Ocean Swimmers (https://www.inaturalist.org/projects/australasian-fishes/journal/16962-member-profile-lucy-smiechura) which began as an ocean swimming group, but using the power of iNaturalist, its members have grown to be avid citizen scientists, recording almost 4,000 observations the diverse marine life in their area for all. There are other projects, which are dedicated to singular locations such as Shiprock in Sutherland Shire (https://www.inaturalist.org/projects/shiprock) collects images of the diversity of marine life at one local area. There are also projects dedicated to individual classes of flora and fauna, such as Sea Slugs of the World (https://www.inaturalist.org/projects/seaslugs-of-the-world) which was set up by Sascha Schultz in 2017, to carry on the earlier work of the Sea slug Forum. So, from a very local focus to the global collection of data, iNaturalist has been the successful engine of this scientific endeavour. I would guess many participants in AF belong to more than one iNaturalist projects.
What has made iNaturalist so successful is its fusion of two elements of citizen science: the citizen and the science. To support the science the software is well designed with artificial intelligence supported scientific tools including automated species identification (providing either genus or family, if the AI cannot decide on a species), easy to use geolocation software, easy data downloading, taxa guides, video tutorials, a comprehensive app, and even Teacher’s Guides on how to use the software for education. It is what you’d expect from advanced scientific software.
It is the “citizen” component which has driven its current success. Aside from its scientific grunt, the true power of the iNaturalist, however, is its integration of social medial tools for the purpose of advancing knowledge. Everyone knows the power of social media. Its power to capture (or addict?) the attention and time of people has occupied much space in the media, which has focused on the downside of social media. Research has shown it does have negative impacts such as its addictive qualities, anxiety issues resulting from fear of missing out, sleep deprivation and the decrease in communication skills for those who seem to reside in the cyber-verse for much of their waking hours. iNaturalist, however, illustrates how the addictive tools of social media can be used for positive outcomes. The social media components of the program works to connect people who share common interests, motivating and inspiring people who wish to learn and creating a virtual community of like-minded citizens, all focusing on achieving a scientific outcome or objective. There are several ways to communicate in the project, allowing group and private discussions on observations. There are leader boards recognising the contribution of project leaders in numbers of observations and identifications, a strong motivation which work to put you in contact with experts, at the touch of a button.
In summary, the iNaturalist data base would make an excellent record of life on Earth, because of people like you and the software upon which we operate. Our database is gaining notoriety in the scientific community and through your assistance and the iNaturalist platform we are helping to create to facilitate future research on the natural environment.
This journal post was written by Australasian Fishes member, Harry Rosenthal.
Thank you as always Harry! :).
Posted on May 07, 2019 10:25 by markmcg markmcg | 16 comments | Leave a comment

May 30, 2019

Andrew Trevor-Jones - Member profile

To many of us in the Australasian Fishes project, underwater photography has been a great personal challenge. As a hobby it can be both a provider of immense frustration and personal satisfaction, often at the same time. While the core business of the Australasian Fishes project is the capturing, identifying and geolocation of various fish species inhabiting Australia and New Zealand, it is more than simply a collection of fish snaps. Readers need only look at the Journal section for the regular reports of discoveries and unique observations the project produces each month so see some of the contributions the project is making.
A brief examination of observations further reveals that some participants are using their digital photography tools to create images which are underwater “art”. Several members take underwater photography seriously, and from their work, we gain both enjoyment and insight into the marine environment. In their work we not only see the fish, but also gaze the underwater environment in its enchanting and amazing best.
One project participant whose images reflect the unique world of macro-size fish is Andrew Trevor-Jones. His macro images, not only capture the region’s strangest fish but also gives us a view into a unique world which most of us rarely recognise. Andrew is ranked at #16 in the project, submitting almost 800 images so far. Through his lens, he allows you to enter a world of colour and sharp detail. Andrew gives us a window to the universe of the tiny, intricate and beautiful.
Like many in the project, Andrew’s interest in fish began at a very young age. His Dad was an avid freshwater aquarist but Andrew became interested in marine fishes by catching juvenile tropical marine fishes around Sydney and keeping them in his own aquaria. This sparked his interest, in particular, of tropical species. He recalls being a young member of the Marine Aquarium Research Institute of Australia for a number of years and was mentored by the likes of Rudie Kuiter. His interest in fishes and most things marine led to studies in Marine Biology at UNSW. He followed this interest to learn to SCUBA through the UNSW dive club. Once he experienced SCUBA he rarely snorkelled, except on holidays to pass the time between dives preferring to stay down with the fish and other organisms rather than just taking brief visits.
Andrew currently works in the Herpetology department at the Australian Museum validating frog calls for the FrogID app (another citizen science project). Before that he was working in the Museum’s Search & Discover area interacting with visitors and answering questions about wildlife, following a career in IT for 30 years.
Andrew has owned many cameras and now uses a Nikon D500. He shoots exclusively with Nikon cameras and lenses, both above and below the water, and is very pleased with the results. For housings, he has also been a loyal Ikelite customer, as he found them inexpensive and he needs to upgrade his housings each time he upgrades his camera.
An important driver of his upgrades has been to reduce shutter lag. With an SLR, there is almost no lag between the times you press the shutter button until the photograph is taken. Andrew notes early P & S cameras had terrible shutter lag telling us, “I used to joke that I’d press the shutter button and the fish would find a mate, they’d spawn and the eggs would hatch before the camera took the photograph.” Andrew admits that many of today’s P&S cameras have almost no shutter lag and the quality of the photographs is equal to that of an SLR.
Another driver for upgrading regards eyesight. In his world of the micro, eyesight is critical. Like many of us, Andrew first needed reading glasses in his early 40s and P&S cameras often require the photographer to frame the photograph by looking at the LCD on the back of the camera. He noted with an SLR you look through the viewfinder and see what the lens sees, and most SLR viewfinders have a diopter adjustment so he could adjust for his eyes.
Andrew has tried various eyesight magnification solutions, such as a “gauge reader” facemask, a bifocal type of mask, inexpensive hydrostatic lenses that were “stuck” on to the inside of the mask, at the lower part of the mask so vision straight head was not affected. These were good but if water got into the mask, they’d fall off. He next discovered that Mares made a mask you could order with lenses at the bottom in any diopter you wanted settling on +2.5 which worked best. He later learned about Oz Bob, an optometrist in Dee Why (Sydney) specialising in adding custom lenses to masks. He is currently using an Oz Bob mask with +2.5 magnification. His work demonstrate its effectiveness.
Today Andrew almost always shoots macro and uses a 60mm lens in a flat port. He shoots with dual strobes as he likes being in control of the lighting, especially the colour of the light. Shooting macro with strobes means that he not only has a small distance between the subject and the lens, so less water to absorb light, but there is also a short distance between the strobes and the subject so the light is barely changed by the water. Andrew advises that it is critical to get close to your tiny subjects, which means not only having the right equipment, and properly corrected vision, but also requires you to develop an understanding of the organisms you seek, and how they interact with their habitat.
Many years of hunting for newly settled tropical marine fish uniquely prepared Andrew for finding small and often cryptic subjects for photography. He thoroughly enjoys locating difficult to spot animals, in particular species of his favourite fish family, the Syngnathidae (seahorses, pipefishes and their relatives). His favourites include Leafy Seadragons and Pygmy Pipehorse, Idiotropiscis lumnitzeri. These fish are small (up to 55mm total length) and are rarely seen by divers because they can be quite cryptic. In fact, they were only first found in the late 1990s and described in 2004. Andrew's skill has allowed him to see as many as 25 on a single dive!
Andrew warns us that finding pygmy pipehorses, and pretty much any cryptic animal, takes practice and experience. He advises, “If you I have never seen one before, it is unlikely you will find one without assistance. The best way to learn how to find them is to dive with someone that can show them to you. The more you see, the better your eyes (and brain) become at spotting them. A lot of it comes down to non-conscious pattern recognition in your brain. I’m to the point now where I can spot one just by seeing its tail wrapped around an alga or just an eye looking out at me.
Another skill Andrew possess is recognising individual fish, over long periods of time. He says, “The more often you see a particular species the more familiar it becomes to your brain and the easier it is to spot. It works in much the same way as recognising people. The more often you see them, the more familiar they become to the point you don’t even have to think about who they are.” As a result, he develops long term relationships with his subjects, for example he has photographed an individual female Bigbelly Seahorse, who has occupied the same rock at Kurnell for the past seven years.
The project has benefited from Andrew’s focus on the small and unique. For example he has amassed a collection of long term photos of individual Weedy Seadragons. When he sees an individual he takes head shots from both sides to determine which individual he’s seen, due to the dot patterns on the snout. He also takes flank shots from both sides, as the flank pattern can be used for identification using software. Identifying individuals allows him to track them over time and especially following males with eggs, including length and number of broods.
This skill has importance to marine science as another favourite fish of Andrew’s is the Red-fingered Anglerfish, Porophryne erythrodactylus. This is another species that was only recently described (2014) and is rarely seen because its camouflage (shape and colour) resembles sponges. Like pygmy pipehorses, there is the thrill of finding them but an equal thrill of finding the same individual on subsequent dives. While an individual can sit it the same spot for weeks and even months they can move overnight to a spot 10s of metres away.
Andrew never dives without his camera and it is very rare that he takes no photographs. As a result he has accumulated many photographs. While time is an issue he tries to identify all images at least genus level. He uses Lightroom and uses the scientific name as a keyword. While he recognises most species, he has numerous reference books with the most commonly used book is “Coastal Fishes of South-Eastern Australia” by Rudie Kuiter. For unusual syngnathids he likes “Seahorses and Their Relatives” by Rudie Kuiter. Recognising that both books are a little old so he is careful to check for taxonomic changes using World Register of Marine Species, Australian Faunal Directory or even iNaturalist.
We encourage all participants to examine the current body of work Andrew has contributed to the project, as you will see creatures which you have never seen, but who have probably seen you. To really appreciate challenge, art and science of Andrew’s work, try to find images which also includes Andrew’s finger in the frame. From that you will gain some insight in to the degree of difficulty which had to be surmounted to deliver these images to Australasia Fishes.
This journal post was written by Australasian Fishes member, Harry Rosenthal.
Posted on May 30, 2019 04:36 by markmcg markmcg | 3 comments | Leave a comment

May 15, 2019

How you can contribute to World Oceans Week

Last year, a group in Halifax, Nova Scotia set up an iNaturalist project, World Oceans Week 2018, and is issuing a challenge once again to divers and others to contribute to the count for 2019.
This year, World Oceans Week runs from June 1-9. A new iNaturalist project, World Oceans Week 2019, has been set up to document a snapshot of the world’s ocean life during the days surrounding the U.N. Oceans Day (June 8).
The Australasian Fishes community can play our part to make this initiative a success. I strongly encourage you all to make a big effort to record new observations during the first week of June. As always, please upload your observations to Australasian Fishes but in addition, add them to the World Oceans Week 2019 project. Your observations will then be included in the World Oceans Week 2019 count. We can provide excellent information on our part of the world and showcase the strength of our Australasian Fishes community. The information below has been copied from the World Oceans Week 2019 project page.
Thanks everyone,
Mark 🙂

World Oceans Week project overview

In recognition of Oceans Week, a group from Halifax, Nova Scotia would like to once again challenge the global iNaturalist community to make this an opportunity to explore our coastal areas, our oceans, seas, rivers, and lakes. Observations of marine flora and fauna shared through iNaturalist will help fill gaps in temporal, spatial and taxonomic coverage around the world.
The objective of the World Oceans Week 2019 iNaturalist project is simple – we wish to encourage people to accept the challenge to record and share their own personal observations. From June 1-9 set aside time to explore our coastal areas, oceans and seas. If you don’t have an opportunity to visit these areas perhaps explore a local river or lake or use this opportunity to go through old photos and select images of plants and animals taken when on vacation at the beach.
On June 8th each year, we celebrate the ocean, its importance in our lives, and how we can protect it - World Oceans Day helps raise the profile of the ocean and inspire more involvement in helping to conserve this amazing resource we all depend on. During Oceans Week all around the globe events and activities are organized and all are encouraged to participate as it is up to each one of us to help ensure that our ocean is healthy for future generations.
For those of us who are lucky to live/play along the coast or work at sea or have opportunities to partake in ecotourism on the high seas we would like to encourage getting out and exploring nature. Recording and sharing our observations will help create research grade data for scientists working to better understand and protect nature. This is the vision of iNaturalist.
It is fitting that this Oceans Week challenge to share coastal and marine observations originates from Atlantic Canada as it was a group located in Nova Scotia, the Oceans Institute of Canada (OIC), located at Dalhousie University and led by its Director, Dr. Judith Swan, and supported and counseled by Haligonian, Elisabeth Mann Borgese, the founder of the International Ocean Institute, who first introduced at the United Nations (UN) Earth Summit in 1992, the concept of World Oceans Day (WOD) on behalf of the Government of Canada.
Oceans Week this year is June 1-9th.
For more information on the history of WOD see http://www.worldoceansday.org/history
Posted on May 15, 2019 02:53 by markmcg markmcg | 0 comments | Leave a comment