Mapping Data With Google. Awsome!

Everglades Ark now has an interactive map method based as described earlier in the post “Harnessing the Power of Epicollect and Google Maps”. This allows you to see the geographic interconnections of all of the observations as they are updated.

Link to the interactive map through this link: Everglades Ark Map Link

This is a simple illustration of a small portion of the area under observation. In this map the criteria selected are marked in colors. Red are animals; green are plants.

Observations are recorded in the data base. Criteria are then selected and filtered in Excel. The data are then added to the map. The updated map is posted for your review in the linked site. Using this method the maps will become increasingly sophisticated as observations are made and interest is developed.

Here is what you can see:

You will see maps as they are updated. You are encouraged to make comments or open a discussion or simply follow discussions that the author feels are relevant.

Here is what you can do:

Open the map and select the layers that you wish to correlate. If available, the map matching your criteria will then appear. You may request posting of specific criteria for mapping to meet a particular need. You may also go to the Epicollect5 data file directly and make your own map to match your own needs by following the guide already posted as mentioned above.

Click to Link to the interactive map at: Everglades Ark Map Link

Please engage in a discussion through the comments link below:

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#maps #mapping #google maps #data #correlations #geography #connections #

Half a Day at the Everglades National Park 

GPS 25.785710, -81.415130

I took some friends, Brenda and Dave, and their friends from Canada on a trip of exploration to Chokoloskee at the southernmost entrance of the Everglades National Park. The entire Federal and contiguous State park and reserve areas comprise 3 million acres of park land. For more than three hours we went on a guided excursion in an open flat bottom motorboat to tour a small area of the Ten Thousand Island region near the entrance. We crossed Chokoloskee Bay into Indian Key Pass and boated through some of the mangrove islands of Everglades National Park.

At the bottom end of the blue line on the map is the entry point.

The early January morning was cool and overcast but gradually warmed over the next three hours. It was spectacular! The water was flat and the guide was pleasant, knowledgeable, and navigated the tricky waters well. We started at low tide and departed the area as the tide waters returned.

One of many sandy islands covered by Red Mangrove trees seen here at low tide.

At first glance it was still, silent, and not especially interesting. As we moved along toward the Gulf there was more to see. Five species of animals were obvious. Mangrove covered sandy islands were always within easy sight. Then the guide started to point out the highlights. 

Below are photos of the five most interesting things to see.

Racoons: Perhaps an otherwise unclassified small, salt tolerant raccoon are unique to this area.

This little salt tolerant raccoon was foraging for muscles at low tide on the exposed marshes.
Here is what the raccoon is hunting

Pelicans: Juvenile yearlings

We know this to be a Brown Pelican

Osprey: Nesting male and female

Mated couple tending to their nest. Full flaps and slats and landing gear down
Wide wing span on landing
Departing into the wind
Drying the wings after a wet fishing trip.

Dolphins: The bottle-nosed dolphin (Tursiops truncatus), were seen throughout the trip but were most visible as the group of four rode the boat’s bow wave on the return leg of our trip. This was the most interesting part of the trip for our guests because the animals were very close, active, and seemed to enjoy the playful moment. The dolphins often live together in family packs who share company, work and play together.

Just playing in the waves together
Missed the wave
Perfect jump with the classic roll to right.

Eagles: One seen in a nest but were too far to photograph as were cormorants.

We did walk onto one of the islands where some of the First Nations People lived and worked. There was evidence that they fished, hunted, made pottery goods, and traded in the area. 

It is time to explore more of this immense parkland right in our backyard ! 

We had an excellent lunch of fresh caught Stone Crab Claws at the Havana Café of the Everglades. No the crabs are not killed and they released to regenerate the lost claw. GPS 25.81672, -81.35971


US national park size comparison

If you go in your own use these NOAA charts

#Everglades National Park #Everglades #Raccoon #Pelican #Osprey #Dolphins #mangroves #islands #Stone Crabs

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Harness the Power of Epicollect5 + Google Maps

We started to collect GPS locations for specific findings using Epicollect5 about a year ago. Now what? In a previous blog we discussed distance measuring using tape and compass measurements and GPS locations. This method exceeds that technology by light years.

A general map plot of all of our findings is available on the Epicollect5 data site. If you want to see something specific you can make a custom map to see where all of our areas of special interest are located using Google Maps! Even though the project is public you must create a login to access the epicollect5 site to download data. Go to Epicollect5 and log-in.

Epicollect5-Everglades Ark, generic map of the SWFL observation sites. Dots show what is in the area.

In Epicollect5 the data comes in two forms. The first is the data Table. The second is a Map of all of the sightings. You can see it by clicking on the word map located in the upper right side of the site banner. The third is a data file available through Download. If you want to map a specific set of data you can do this by some manipulation of the data. You will use two types of software. Use Excel for data manipulation and Google Maps for custom mapping. You must have a Google identity. Follow these steps:


Selected screenshot from Everglades Ark data base on epicollect5
  • In your web browser search for Epicollect5
  • On its home page upper right of the navigation banner click on FIND
  • Enter the name Everglades Ark the query box
  • When the image of the site appears click on VIEW DATA on the right side
  • View data opens the data page the Epicollect5 for the Everglades Ark
  • In the left of the view data navigation banner click on Survey and Catalogue
  • The table of the collection will appear
  • On the right side of the navigation bar there are three choices click on Download
  • A new drop down menu will open on the left side with several selections
  • Select EC_Auto, Select your Timeframe, Select CSV. CSV (comma delimited) works well for Excel.
  • Click on Download. The entire file will appear in your downloaded files folder.
  • Once downloaded you will find several data sets in the folder. These folders contain the sets named in the headings of the Epicollect5 folders
  • Click on the data set appropriate for your interest
  • To use the data, select Open the download with the Microsoft Excel. Your manipulation of the Excel date does not effect the Epicollect master data file.


Screen shot of Excel file. For the non Excel users it looks intimidating but it is not.
  • In Excel open file called “1-survey_and_catalogue.cvs”
  • Sort the desired new data sets for the selected criteria. Be sure to lock the appropriate fields. For mapping, always include the GPS columns and any mix of data columns to match your interest criteria.
  • Make a new Excel file with an appropriate title (like December flowering plants.cvs) and paste the data into a new sheet.
  • Save this to your computer desktop as a .cvs file


This example of a simple map has bright red markers to show locations of observed flowering trees from 10- 2021 to 1-2022

The goal is to plot a specific selection of the data for characterization of a set of the collection. For this we can use google maps through their portal at: Visualize your data on a custom map using Google My Maps

  • Log in to your Google account
  • Go to Google My Maps:
  • In the welcome pop-up, select Create a new map:
  • In the text Untitled map, edit the map title and description in the Map title dialog box:
  • In the Description dialog box enter a description of your map
  • In the menu, select Import:
  • Select your saved data sheet from your desktop. This will be the first data layer we upload. Drag and drop your GPS data file on your desk top to the Import Your Data into Google Earth. Following the instructions at Visualize your data on a custom map using Google My Maps. After uploading your data, you’ll be asked to select the column(s) with location information, so that your data will be correctly placed on the map (e.g. columns with latitude and longitude information). For this example, select the Lat and _ Long columns_, and hit Continue. You can hover over the question marks to see sample data from that column.
  • Pick the column you’d like to use to title your markers. For this example, select the Date column and click Finish:


The Google map function is very versatile and very powerful. You can enter multiple layers of data on the same map. The maps can be enhanced with colors, icons, add titles, search for types, collaborate with colleagues, all available in the instructions on the GoogleMap instruction site. For example on one map you could overlay flowering undergrowth plants, blooming in the month of February, where observations of Monarch butterflies were recorded. Different symbols and colors could be used to separate the two types of data for easier visualization. You can measure distances, map directions, chart changes in observation patterns, estimate rate of spread of changing conditions… it is almost endless!

It is just that easy ! Try it out using the technique described. You will be amazed !



Visualize your data on a custom map using Google My Maps

Please send comments and let us know what you discover.

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#Google #map #excel #database #create map #custom map #GPS

Ode to Eko

Eko, Malayan tiger, Naples Zoo (Dec.)

Ode to Eko

Eko Eko burning bright
In thy heart beats delight.
So quiet and calm, hold your power
Waiting for the rightful hour.

That immoral hand comes to spy.
I cannot ask the question why.
All I know is that I must bite
And I do with all my might!

Through the cage comes a shot.
The pain is great, searing hot.
Man kills me, He makes his choice
Species die without a voice.

Eko Eko eyes were bright.
Now they're dark as the night.
What loss we have no more to see.
What have we lost for you and me.

By John Knapp with inspiration from: Bill Blake, David Attenborough and the late Eko, Malayan tiger, Nalpes Zoo. 

Please donate to support the excellent work of the Naples Zoo Donation

# Eko #tiger #Naples #zoo #shot


Naples Daily News

Naples Zoo


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Does Reef Green Fluorescence Point To the Cause of Stony Coral Tissue Loss Disease?

Green Fluoresence Protein

I’ve seen this green color in the past. It seems relatively obvious now that the green color that we are looking at in the reefs is wild Green Fluorescing Protein (GFP)1. It is one of the most important biologic markers used today. It was initially discovered in a jellyfish, Aequoria Victoria, and reef polyps. Its development as a synthesized reagent was awarded the Nobel prize. It is one of a class of reagents that radiate fluorescent green, red, yellow and blue when exposed to special wavelengths of light. They are used as bioluminescent markers in biochemistry and cell biology in a wide array of research and industry. I used this marker some years ago when using molecular imaging to search for circulating tumor cells (CTC) at the Barbara Ann Karmanos Cancer Institute, Tumor Biology and Microenvironment Program, the School of Medicine and the Bioengineering departments of Wayne State University and the associated NIH National Cancer Institute in Detroit.

Here are two examples of green and blue fluorescent proteins seen in two different coral species as they respond differently to the same blue light. Note that the GFP reef corals are stricken with SCTPD while the red fluorescent protein (RFP) reef coral seems to be unaffected.

Fig 1. GFP polyp in coral
Fig. 2. RFP polyp in coral as seen in Marine life could be like this in South West Florida, 3/3

The colorful green bioluminescence occurs when the GFP is exposed to a particular energy of blue light. The light excites electrons in the molecule which, when they return to their rest state, emit green light. In this case blue light exposure radiates green fluorescence. Cells continually manufacture the florescent protein for replacement as it matures.

Wouldn’t it be ironic to think that the polyps that gave us the GFP may help us to understand the cause of their disease?

I’ll make this very clear. This is just my conjecture. I am not an expert in any of the following issues. This is the realm of highly sophisticated experts in multiple specialized fields.

Thoughts on tracing down an idea for cause and effect

There may be a relation between protein structure and spectroscopic function. Loss of fluorescence may indicate that the GFP molecule is misfolded, split or destroyed. There are some things that can cause these molecules to stop performing including: insufficient molecular oxygen, increase in temperature above 70 degrees Celsius (158 F); exposure to an acid with a pH less than 5.4, age degradation, or protein modification. Some of these are not likely because the water temperature, acidity, and the rate of aging of the reef in the ocean are relatively constant. Temperature, acidity and aging is not what is at work in the polyps or in the reef. What is not constant is a biologic process which may alter the GFP. An virus could invade a cell and change a proteins including GFP. Lack of fluorescence may be a direct symptom of a disease. GFP labels living cells therefore it can be used to monitor infectious processes in plants and animals.3 GFP behavior part of a larger process causing death of the polyp complex

Problem statement:

Is there a direct correlation between the lack of the GFP and the cause of SCTLD?


Establishing a causal relationship. Is the disease infectious:

In an earlier posts Fluorescent Photos to Measure Reef Viability (2) and Hunting the Cause of Stony Coral Tissue Loss. Looking at the Reefs with Scientific Vigor (3) I suggested a test of infection showing a controlled method of applying the diminished green polyps or BFP (blue fluorescing protein) polyps to GFP polyps. If the trial infection works then the cause is either a bacteria or a virus. This may depend upon identification and use of a vector organism which may be critical for the test to work.

If there were a virus in a polyp or associated zooxanthellae, a comparison of DNA before, during and after exposure could be made. Sample both at various stages of the disease using the GFP as an indicator of the staging. Additionally, special techniques of microscopic dissection, staining and a variety of light and electron microscopy should show some evidence. The polyps and the zooxanthellae are higher level organisms and their DNA should to be decoded. If the disease is virus specific, PCR testing may be done to discover it. DNA sequencing and Crisper technology might be used to find a place in the DNA where a lethal virus could attach.

Discussion of findings:

Crisper technology could be used to modify the DNA to engineer a resistant strain of stony coral. The strain could be cloned and reproduced in vast colonies. Multiple coral polyp types could be added to make a more representative colony. The harvested viral resistant polyp strains could be explanted back onto the dead wild coral reefs that were cleaned of dead coral tissue, algae and debris. These are all untried technologies.

Spread of the disease:

Polyps are filter feeders. They harvest their sustenance from the organisms in the float of water of the ocean directly into their gut. This sounds like a combination of opportunity: portal of entry, susceptible host, and an obviously virulent pathogen. Viruses are frequently carried by arthropods (insects) that can spread the virus in the viral particle of their bodies. They inject the particle into host cells using their sharp, piercing or cutting anatomy as do mosquitos, ticks, flees and others. Examples of this include Zika, West Nile fever, Deer Tick fever. Viruses can also spread by contact through the air in water droplets. (Such as the Corona virus). An arthropodal nymph acting as a vector could easily be carried by currents, ships and wind for hundreds or even thousands of miles where it could start another colonial infection.

There may be a number of contributing factors such as rising water temperatures, pollution, habitat destruction, water depth, invasive species, symbiotic species relationships which may exacerbate the process.

Search for complicating factors:

  • How long does GFP continue to fluoresce without replacement
  • Discover the virus pathogen and its structure
  • Unravel the complexities of the method of action of the pathogen
  • Geographically locate areas of afflicted coral
  • Calculate the rate of spread, rate of infection, time from onset to death
  • Identify the origin of the disease and the vector
  • Identify potential causes of increased susceptibility of the reefs
  • Search geological and anthropological history for episodes of similar reef diseases

Discussion on actions:

  • Consider possible unintended consequences of well intended actions
  • Search for other possible causes such as prions, rickettsiae and other outliers.

Next step:

  • Form a team of experts in the necessary fields
  • Estimate the cost of the project in stages
  • Form a group of interested parties of influence
  • Promote the idea seeking funding and permission to act on findings.
  • Begin the search for the cause and form an action plan
  • Begin at a fixed base location with relative separation from recreational or commercial activity
  • Start small with two isolated sites each with differing characteristics in reef health
  • Engage in work to slow or stop SDTLD


Not much is known about reef ecosystems, polyps and their physiology, diseases, and pathogens. Additionally, they are part of a larger oceanic system of which we have limited knowledge. The current blog is biased by knowledge of land based diseases. There may be causes of which we are completely unaware. It is a voyage of discovery aboard Everglades Ark.

I am very interested in your thoughts on the subject of reefs, polyps, fluorescence, viral biology, or any of the topics which are presented. Additionally, if you are interested in helping or would like to report on your findings please contact me.

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  1. The GFP page
  2. Fluorescent Proteins
  3. Split green fluorescent protein as a tool to study infection with a plant pathogen, Cauliflower mosaic virusFluorescent protein microscopy
  4. Algorithms and Datasets for Colour Science
  5. Spectrum or excitation and emission of protein fluorescence microscopy

#RFP #GFP #fluorescing protein #vector #SDTLD #stony coral tissue loss disease #virus #crisper #spectroscopy #polyp #crisper #DNA

Hunting the Cause of Stony Coral Tissue Loss. Looking at the Reefs with Scientific Vigor (3)

Stony Coral Tissue Loss Disease in Florida Is Associated With Disruption of Host–Zooxanthellae Physiology is a must read for those who seek more in-depth information 1

This blog is a continuance of previous blogs Death in Paradise and Fluorescent Photos to Measure Reef Viability. In this post I’m looking at two things: 1. Possible SCTL by infection and 2. Genetic engineering a replacement polyp to grow new SC surface tissue. Here is what can be done with fluorescent lighting.

Night photo of reef UB light(with false color brightening). Bright green fluorescent protein shows viable stony coral (SC) polyps. Magenta areas are viable algae. Blue areas are soft coral. Black are non viable surfaces.


Expose a fixed area to white light and with UB light. Photograph the area with the appropriate light filter. Similarily, expose variations of coral varieties, stages of disease, seasons, depth and other variables. Compare data among and between them.

In Figs. 1 and 2 look at the condition of the coral. They are suffering Stony Coral Tissue Loss Disease (SCTLD) with accumulation of dirt and covered with algae. This was typical of many areas of the reefs.

Fig. 1. Waiting for the night to start work
Fig. 2. Time to select the location and set up

In the previous blog , a fixed area was photographed with illumination to near ultraviolet (UB) light. Data of light, hue, chroma, luminance (CieLab. color space) was recorded. This can be seen in Fig. 3.

Fig. 3. Identification of fluorescence of specific locations or areas of a small sample showing multifocal Lytic Necrosis (LN) seen as black.

Identification of stages of SCTLD:

Fluorescence may facilitate a systematic description of SCTLD at the gross and microscopic levels. Photoshop CieLab, combined with white light examination may provide a better description of the disease stages.

Further research to be done to test infection-by-transference hypothesis:

A section of the coral with healthy and distressed polyps could be easily identified and biopsied as described by Woodly This identified area would look like the amber outlined section in Fig. 5.

Fig. 5. Use fluorophotography to select the area for biopsy and microscopic examination. This loss of Green Fluorescent Protein (GFP) may be the stage where the disruption of a host–symbiont physiology takes place. This may be the opportune stage to identify the DNA of a causative agent. Knowledge of this area could be helpful in future attempts at reengineering.

Method to rule out the infection-by-transference hypothesis:

  1. Isolation of healthy SC GFP polyps
    • Propagation of healthy polyps in sheet form
  2. Isolation of distressed polyps
  3. Application of distressed polyps to surface of healthy polyps
  4. Examination of time-lapsed photographs to determine if application causes distress and/or death of healthy polyps.
  5. Repeat
  6. Evaluate results
  7. Refine method and repeat

Method to detect the source of the infection hypothesis:

  • Select the healthy GFP polyps and their associated Zooxanthella 
  • Extract the DNA2
  • Select the BFP polyps
    • Extract the DNA2
  • Contrast and compare the two samples
  • Identify the point of difference.

Further research to be done:

  • Reengineering from knowledge of this area as shown above is a path not yet reported. Replacements for a variety of SC polyps might be engineered with the purpose of replacing the currently susceptible species.
  • Consider a new infective agent that is otherwise undescribed pathogen (prion?)

Reef Quality Assurance:

In order to determine the changes in large areas of a reef wall, fluorophotography may be applied for a quick scan. Large scale examination of a reef wall could be done using the photographic method described below. Fig 6. shows an area low in expectation for SC polyps. Fig. 7 shows the same area using UB lighting confirming that expectation.

Fig. 6. Determining the viability of a questionable location. White light illumination.
Fig. 7. UB illumination shows no green and no red. This is the best evidence of no viable SC polyps.

A wide angle view can show an area which fluoresces. This photograph shows an area of coral reef with heads illuminated with UB light that brightly reflect GFP. Estimates of the viability of an entire reef can be determined based on a percentage of an area which is bright.

This view of a reef wall shows the examples of a 3 X 4 M area using fluorophotography.


From the previous blog it was shown that coral fluoresence shows viable stony coral polyps. Reefs do vary in terms of variables mentioned above. Reef color value does indicate viability across all species. CIE Lab values do indicate the progress of SCTLD.

At least one method of reef biome intervention may be possible. Reef interventions can be measured at a large scale.

What measures should be initiated:

  • Pursue testing and rule out an infection hypothesis
  • Test genomic differentiations searching for causative agent
  • Systematize wide angle, macro and micro fluorophotography methods for quality assurance purposes
    • Use high resolution macro photographic camera
    • Use microscopic dissection and photography with UB lighting
    • Use variable blue to ultraviolet wavelength light sources in photography

Help is needed in this effort. If you have comments, questions or greater interests in the investigation and fight against SCTL disease please leave remarks and comments.


  1. SCTLD in Florida
  2. A genomic view of the reef-building coral Porites lutea and its microbial symbionts

#Fluorescent photography #SCTLD #stony coral #green fluorescing protein #GFP #BFP #DNA #Zooxanthella #polyps #coral #Caribbean #Lab


Fluorescent Photos to Measure Reef Viability (2)

The condition of the Caribbean reefs has been observed for decades thanks to dedicated marine biologists and experienced scuba divers. I wanted to observe, document, and inform others about the disease which is unseen and under-appreciated by most during this time of our human Covid epidemic. The disease is called Stony Coral Tissue Loss Disease (SCTLD). See previous post Death in Paradise. Also see Marine Life Could Be Like This In SWFL.

I believed that for the observation of reef polyp viability an adjunct to visible light one should consider a non-invasive test using reef fluorescence observation to determine SCTLD extent and its progress. The green fluorescent proteins (GFP) of many living reef polyps can fluoresce in response to exposure to specific light wavelengths.1 They exhibit variations in fluorescence in terms of wavelength (color) and intensity (brightness).2 We will call this reef temperature. Non-viable reef polyps and plant forms appear to differ significantly in fluorescent wavelength and dimmer luminance or appear black.7

Examples of observations and photographs that I made made between December 12 and December 14, 2012 in the Caribbean Site #16. The light sources were: White light from Nikonos S1B flash and Blue light (Ultra Blue UB) source from SeaLife FluroDive gear which generates Ultra Blue (UB) light.3,4 No GPS or location descriptions are provided. Imbedded in the images are CieLab* notations.

Fig. 1a shows an area of coral with damage probably a result of SCTLD. Fig. 1b shows a similar area with UB lighting where the damage has lost the polyp layer and the accompanying protein of those polyps is missing. Since the polyps are the source of the fluorescence when dead they do not reflect.

Fig. 1a. White light
Fig 1b. UB light

This small area shown in Figs. 2a and b may show the advancement of the process where mottled dark areas without fluorescence are present. Green areas circled in amber are not yet afflicted. The circled blue areas show disease in progress and black areas are dead. The different spectrum shows compromised surface. The amber circled areas were color sampled via Photoshop. The blue area sampled is smaller than the green area. The blue area L.a.b. is 54,-48,-33. The green area L.A.B. is 15,20,26. This is a remarkable difference in light values.

Fig 2a. White light
Fig. 2b. UB light

These color extracted areas in Figs. 2ac and 2d permit visualization of the percentage of healthy and compromised polyps.

Fig. 2c. UB light green extract
Fig. 2d. UB blue extract

The Fig. 3 series of photos show another reef area.

Figs. 3a through 3d show a different variety of stony coral which is not suffering any apparent SCTLD but is surrounded by areas that are dead coral overgrown with algae.

Fig. 3a. UB light unaltered.
Fig. 3b. False UB light enhanced to show the context of the site.
Fig. 3c. UB and white combined.
Fig. 3d. UB light alone with selected CieL.a.b. readings in amber areas.


CieLab5 is a photometric method of describing a three dimensional color space. It is more comprehensive than RGB, Panatone, CMYK or HSB.

Three dimensional graphic representation of CieLab color space. From Prospector

This appears to be a useful method for assessing reef viability. Here is what I propose:

The Important question (null-hypothesis):

Why aren’t reefs all the same color temperature?


Expose a fixed area to white light and the same area with the UB light and photograph each using an appropriate filter. Similarily, photograph variations in coral species and other variables and photograph them. Compare the photos using Photoshop to interpret the light of the ultra blue photograph. Record the data of light hue, chroma, luminance (CieLab. color space )


  • UW camera with filter (SeaLife)
  • UW fluorescent blue light lamps aimed for even distribution of light
  • Plastic pipe square frame 1 meter X 1.5 M with fixed 1.5 M legs to support camera
  • Software (Photoshop and Excel)

Exposure technique:

Establish a standard normal site. Select an ideal healthy reef area and use this as a basis. Photograph it using the method listed above with the camera at the center of a standard square. Mark GPS location (Drop a weighted line from dive boat). Include other very pertinent information like temperature, current flow and other variables as noted below.

Select a typical affected reef test site and use this as a basis. Photograph it using the method listed above with the camera at the center of the square. Mark GPS location (Drop a weighted line from dive boat). Repeat additional test sites.

Data collection technique using Photoshop for each photo:

Data is collected in a selected photo area as numeric readings in CieL.a.b.. Include a standard sample (B&W and Color). Collect CieL.a.b. data in photo as a fraction or total picture.

Number of sites

The number of sites depends on the area of interest and existing information. Examples include proximity or remoteness to areas of traffic or resort, city, sewage effluent, runoff’s, windward, and leeward sides of island . Ten to one hundred sites are conceivable.


Seasons, lunar cycles, temperature, months, storms, rise in water level, toxic products, population growth, recreational usage, associated life forms and structures.


Findings could be collected in an Epicollect5 data base in a standard fashion6. This would be available to the public for observation or assessment and downloadable in a cd file. The file could be manipulated in Excel at the discretion of interested parties. At this time I have included a simple table for data presentation.

Num.Subject GPSTimeDateTempe CSourcePhoto #Pic AreaLa.b.Observer
Typical but incomplete data file structure UB=Ultra Blue, W=White sc=stony coral, ag=algae

Data manipulation in Excel:

Statistical analysis of findings by comparing normal to test site data will be done when an adequate number of observations are gathered. This could imply what is happening to the reef by comparing measures between and among species and locations. Measurement may make possible knowledge based judgements.


Given this limited data base all conclusions are still speculative. In image Fig. 2b area G exhibits a Luminance value 54%, 48% green value, and a 33% blue value. In image 2d area B L is 15%, 20% green value, 24% red value. This suggests that viable polyps in this image are 34% more luminescent, 28% more green and 57% more blue than their counter parts in the blue areas. In image Fig 3d area G is very polyp viable and area R appears to have little or no polyp viability. Areas G in both Fig 2b and 3d are remarkable similar. They may have similar GFP. Better controls and more numerous observations may provide improved accuracy.8


UW Fluorophotography seems to have the ability to distinguish viable from absent, unhealthy or dead coral polyps.


This pilot study suggests that the null-hypothesis may be refuted. The answers to some important questions can be implied from the data. All of the reefs are not the same color temperature. This may point to answers for these questions. Reefs do vary in terms of variables mentioned above. Reef color values indicate viability across all species. Color does indicate the progress of SCTLD. At a larger level; there is a general trend in reef viability, measures taken can show an improvement, stabilization, or degradation the reef in size, viability, or level of SCTLD. This answers can be substantiated in a more controlled test with measures mentioned in the statement of method noted below.

This trial test suggests that there may be additional documentable methods for judging the reef system. These important questions need to be addressed. Should intervention of reef life be done? How do you know if interventions are effective?

These measures should be initiated:

  • Expanded use of communal data base
  • Expanded data collection to multiple data collectors.
  • Improved method;
    • Photo fluoro-microscopy of sectons of coral polyp growth
    • Differentiation of CieLab images of coral species
    • Inclusion of a photo standard B&W and Color into photos
    • Stabilization of position of UW camera
  • Further infrastructure development;
    • Capacity of shores and islands to continue development
    • Sustainability measures
      • Water supply, sewage treatment, electricity supply, 
  • What is the expectation for the future?
  • Can information of effectiveness of measures be transferred to other locations?

The motivations are critical to the stakeholders of the entire Caribbean:

  • Should further research be done? 
  • Will reef conditions effect resort business?
  • Should reef recreation and fishing business models be modified?

My hope is to continue to help in the management of this problem and that you, too, are willing to help. Please let me know of your interest and comments. Please look for the next post in this series to see plans for further work in marine biology.


  1. Applying new methods to diagnose coral disease.
  2. Fluorescence-Based Classification of Caribbean Coral Reef Organisms and Substrates David G.
  3. Fluorphotorgaphy Zawada , Charles H. Mazel
  4. SeaLife
  5. Three dimensional representation of CieLab space
  6. Epicollect5
  7. Fluorphotorgaphy
  8. Fluorescence-Based Classification of Caribbean Coral Reef Organisms and Substrates David G. Zawada , Charles H. Mazel

Important supporting references:

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#fluorophotography #green fluorescent protein #CieLab #color temperature #research #marine biology #Caribbean

Death In Paradise

This is not a British mystery drama. In fact, it is a serious very real mystery story with life and death consequences that will affect all of us. Earlier I posted three blogs titled Florida Reefs Could Be Like This. This blog is about a more likely scenario for our reefs and coastline. The scenario is affecting all of the Caribbean as we watch.

I had an eye opening under water SCUBA trip a week ago. I visited a place where I had been before and enjoyed very much. I dove in 20 widely separated reef locations. I was intentionally looking to see the condition of the reef system. I had an excellent trip but an extraordinarily disturbing finding. I took photographs of the reefs during the day and at night with white light. I also took photographs of the same sections of the reef at night with high energy blue light. The images might make you more aware of an advancing, worrisome problem. Previously I saw gorgeous, colorful panoramas of reefs teaming with all imaginable genus and species of marine life. Now many are completely or partially dead; covered with algae, decayed plants and a dirty mixture of sand plant detritus and broken coral. The larger fish were gone; tunicates not seen; smaller life forms missing, fewer small fish were present.

Fig. 1 Healthy brain coral with colorful, well defined ridge anatomy,
Fig. 2 Dead brain coral covered with algae, sand and debris.
Fig. 3 Pillar coral which took decades to grow is now dead along with all of the other stony coral in this area.

The pillar coral in the center of this image shows the relative indiscriminate action of the problem. It affects most of the stony (hard) coral of the reef. The soft coral and sponges are not directly effected, however, without the hard coral anchorage they don’t survive long.

Fig. 4 Detail of Stony Coral Tissue Loss Disease in process. The algae is not the cause but the consequence of the dead coral.
Fig. 5 After the coral dies it can’t reproduce and continue to build after a storm. The soft coral and sponges don’t resist storm surges. The reef is just a pile of random small pieces, blocks of larger dead coral heads, strands of surviving soft coral all overgrown by algae.

Here is the mystery.

What is causing the problem? How big is the problem? Where did it come from? What if anything can or should we do about it? These topics will be discussed in the following blogs. Your thoughts are not only welcome but encouraged.


Race to stop stony coral disease

Rapid spread of stony coral disease in the Mexican Caribbean

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#coral #stony coral #soft coral #sponges #tunicates #brain coral #pillar coral #dead coral

Trees of Christmas

Did I tell you that I love Christmas trees? 

These are the flowering trees of Christmas that I found while bicycling in the surrounding area here in SW Florida. They are so remarkable. It is difficult to imaging the range of chroma and combinations of hues. Some of these are so spectacular that the photographs simply cannot capture the full essence of the visual impact. When I stopped to admire them, I was surprised to find the pleasant aroma that added to the sensory experience.

When we decorate our Christmas trees, they may be very beautiful and have a significant personal context, but these trees are naturally decorated for all to enjoy during this holiday season.

Orchid tree (Bauhinia purpurea)
Silk floss tree (red blossom)
Silk floss tree (white blossom)
Mexican Wild Olive tree
Pink Plumeria (Hawaiian frangipani)
African tulip tree (Spathodea campanulata)
Dwarf Powderpuff Bush (calliandra haematocephala)

I’m tempted to have a monthly blog showing the flowers of the month. I’m sure that you will want to see the Jacaranda and the Flamboyant Royal Poinciana Please comment and let me know what you think.

Many of these trees are originally derived from other continents. They are not classified as invasive or ecologically advantaged here in Florida. In some areas the streets are lined with them resulting in a magnificent display of brilliant colors. Some are rarely found and may be in private landscaped gardens. When I see them, it is like discovering a hidden treasure. 

On occasion we may visit some of these plants and discuss them in greater detail, but today this is just fun for the eyes.


Urban Tropicals

University of Florida Gardening Solutions

#December flowering trees #flowering trees #Bauhinia #Powder puff #Tulip tree #frangipani tree #silk floss tree #wild olive tree #pliumeria #

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Beauty and the Beast

Alligator resting at GPS location 26.340647. -81822001. “Apex Allie” is the beast of the lake.

The apex alligator in photo #6436 described in the Alligator post is the Keystone animal for the Bird Island lake. Its behavior allows all of this balanced ecosystem to survive. Alligators are very territorial. There are only one or two and rarely three alligators that patrol the Bird Island lake. They feast on the other animals which attempt crossing the lake. The size of Apex Allie reflects the size, diversity and health of the system. The mass of the alligator pales in comparison to the mass of all of the birds, secondary predator animals and vegetation.

Three islands with the GPS location of a favorite sunning spot for the apex alligator at the point opposite the South island

There are three potential access points that could allow an invasion of the predator animals onto the islands. The shallow areas close to the mainland which are overgrown with vegetation make two islands vulnerable. These are indicated at points listed on the map as A., B., and C. Human intervention is necessary to maintain the security of these vulnerable points. They need to be cut back on a regular schedule to prevent crossing by land or arboreal bridges through the overhanging vegetation. Note that Apex Allie is resting at a promontory of the mainland (See GPS location) that provides easy access to three sides of the South Island. It is a really big, well fed monster of an animal.

The birds seek out the areas that are protected by the alligators. Bird droppings are rich in nitrogen and other plant nutrients, therefore these areas have lush growth of native plants. The plants provide shelter for the birds. The secondary predators are attracted to the birds like a magnet, the alligators are attracted to the secondary predators. The alligators which eat the second level predators grow to substantial size.

Predator pyramid showing the interdependence of all subordinates.

If one of the layers such as the bird population collapses then the system is unsustainable. The isolation of the islands provided by the alligator shows their Keystone role in this collaborative circular economy.

Graphic showing the interactions of resources and animals in the Bird Islands

In this schematic are four environments which are interconnected by bridges. These include air, water mainland and island. The two bridges shown here are soil and trees which support the bird populations. The water environment is dominated by the alligator. The alligator cannot climb the trees to threaten the wetland bird population. So they are safe if an alligator enters the island because the reptiles can’t climb trees. The aquatic birds are threatened by the alligator if they stay in close proximity to the island shore. If they move inland or from the shore to the undergrowth then they are at less risk. If a land bridge (shown in dotted amber line in the schematic) becomes available to the raccoon or other land based predators then the ecosystem will collapse. If the rats, snakes and especially the raccoons gain land access to the islands the birds and eggs will be eaten or the birds will abandon the islands. Raccoons are especially dangerous because they are prehensile and clever.

Characterizing the population of the Bird Islands. The island is populated by water birds many of which are moderate to large, big winged, long legged, migratory birds that roost and nest in the trees. There are many others. They typically feed on fish, insects, seeds, frogs, and anole. The overgrowth of trees provides perches and nesting areas for the birds. The interior has nests for the lower dwelling birds and some of the larger birds. There is nothing on the islands to feed on except for smaller birds. The population may be self limiting as determined by space.

AlligatorFoodControls aqua populationPredator
BirdShelter and foodNitrogen and nutrientsPredator
RaccoonFoodControls terra populationPredator
TreeNitrogen and nutrientsShelter, FoodMutualist
Table to show the give and take aspects of the major players in the Bird Island ecosystem

The combination of these predators results in a stable system controlled by limitations imposed mostly by the animal niche behavior. This mutualist system is characterized by the cross predatory behavior.

This young 5 foot alligator (about 4 years old)* is the new dominant apex predator just outside my door. It is staying warm in the sun. The iguana in the foreground is in a standoff because his path to his favorite hibiscus in my flower garden is blocked.

If you look at the Bird Island apex alligator and compare it to this alligator you can see that it is at best one third of the size of the Bird Island lake alligator. True to the concept, the pond in which it resides is approximately one third of the size of the other lake. The pond also has no island. The iguana is a herbivore and the alligator is a carnivore. Mr. Iguana is very fast, climbs trees and is a very capable swimmer. He walked to the screen right. Thanks to Mr. Alligator my hibiscus survives for another day.

Naturally we can appreciate the beauty of the birds of the islands. Here are some busy birds on the island.

Blue heron with blue eggs
Showing off
Taking off
Blue is my favorite color. The chicks below are white

Birds are level 4 predators and not the keystone. Yes, that is a fish in the mouth of the bird.

People provide the ultimate ecologic advantage to the species which satisfy their interests at the time. Human intervention provides an ecologic advantage to the birds by controlling the bridges to the islands, thus favoring the birds. Sometimes intervention can have unintended consequences.


* Alligator Biology

Wetland Bird environments

Florida water bird Colony locator

#Alligator #balance #ecosystem #interdependence #interactions #predator #mutualist #barrier #bridge #niche #keystone #balance #ecologic advantage

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