DDA for Dummies
The Dark Decay Assay explained in simple terms
by Floor Anthoni (2005)

For those not familiar with ecosystems, the sea, biochemistry and so on, this chapter explains what the Dark Decay Assay is all about. It's really not that complicated or difficult to understand. Although we'll start at the very beginning, we will also explain the possibilities of the DDA, so that you will appreciate what it is capable of and what is needed next. We'll also speculate on its profound consequences. Links are provided to enable you to delve deeper. Please note that the DDA and our ecological discoveries have not been confirmed by mainstream science and that this is the ONLY place on Internet where you can read about it.
  • food chain: how life depends on sunlight, tiers of the food chain, recycling, marine food chain, ecosystem.
  • closed ecosystem: in an ecosystem all loops are closed by the decomposers.
  • slush: decomposition ends prematurely, producing a mysterious organic substance we named slush. It has profound consequences on our understanding of ecosystems. The slush hypothesis explains why and also how mixotrophs live.
  • living in the sea: all creatures in the sea have to cope with the planktonic decomposers which are a threat to life. Each organism finds a suitable place to live along a plankton density gradient, the Plankton Balance.
  • degradation: pollution in the form of overnourishing, mud and other substances stunts growth and kills organisms. It has become a major problem which is accelerating fast.
  • sea water: in order to be able to understand the DDA and pH, one must understand the properties of water and sea water.
  • lakes: freshwater lakes differ remarkably in their properties which leads to higher densities of life and higher productivity. We discovered some important ecological laws that have been overlooked.
  • DDA: a new method to measure the health of aquatic ecosystems, is simple, effective and cheap.
  • what now?: what does it all mean and what is the way forward? How important is the DDA? What profound consequences come from symbiotic decomposition?
  • reference documents:
For comments and suggestions, please e-mail me, Dr Floor Anthoni.  Read tips for printing.
-- seafriends home -- DDA index -- plankton index -- decay index -- site map --
Rev: 20051008,20051028,20051219,20060712,20080620,

the food chain
On Earth all life begins with the energy from the sun (there are some minor exceptions), enabling plants to photosynthesise (build biomatter with light) and grow. While growing, plants assemble nutrients from the soil, carbondioxide from the air and water into long biomolecules (molecules of life). These consist of the main building blocks hydrogen (H), oxygen (O) and carbon (C), immediately followed by three most important nutrients nitrogen (N), phosphorus (P) and sulphur (S). It comes then as no surprise that agricultural fertilisers mainly provide the three nutrients NPS.

To give you an idea of how these main elements of life are distributed, look at these figures:
Average composition of terrestrial (landbased) life: H:O:C:N:P:S = 2960:1480:1480:16:1.8:1 (E S Deevey Jr) 
Average composition of land plants: H:O:C:N:P:S = 1600:800:800:9:5:1 
Average composition of marine plants: H:O:C:N:P:S = 212:106:106:16:2:1 (more N, P and S)
What you can easily remember is H:O:C = 2:1:1 in other words, life consists mainly of H2CO which is the same as CH2O
NPK fertiliser components of organisms: N:P:K= 100:18:22 with a yield of 20% 
(N= Nitrogen; P= phosphorus; K= Kalium or Potassium)

Animals can live only because there are plants in the first place. The first tier of animals consists therefore of grazers. They grow by disassembling (digesting) plant matter and incorporating molecular building blocks into their bodies. They too assemble large molecules from smaller ones, and need energy which they derive from the solar energy stored in biomolecules like sugar and starch. They use the 'easy' energy stored in food.

With the grazers in place, there is food for the predators who eat animal flesh, which provides for high quality molecules that can be incorporated readily for growth requiring a minimum of breaking down. They rely mainly on fat for their energy. Then there is a place for predators of predators and so on. Meat eaters metabolise the 'easiest' of energies in food.

But all these categories of life also produce waste. Plants drop their leaves and animals drop waste. They also waste energy on living. So the amount of energy and biomass stored in each higher tier of life, is from necessity much lower than the tier below. About 5 to 10 times lower, depending on how fast everything cycles and how much is wasted. If there were no recycling, the source of nutrients would rapidly disappear, but fortunately wastes are recycled by decomposers into the nutrients needed by plants. Thus an army of microbes use up the last of the solar energy, stripping the last hydrogen, oxygen and carbon (HOC) from the biomolecules and returning the nutrients (NPS) in a soluble form that plants can take up with their roots. The whole of this interdependency of life, complete with a cycle of energy and biomass, is called an ecosystem. Note that the microbic decomposers use the most 'difficult' left-over energy of food (wastes).
the marine food chainThe simple diagram shown here illustrates the food chain of the sea. Most of the plant matter in the sea consists of phytoplankton (plant plankton) which floats in the water in sun-lit depths. Seaweeds are also important but because they are restricted to the very small strip of hard shore to which they attach, there is comparatively very little of it. Plants cannot grow very deep in the sea because water absorbs light and the plant life in the water absorbs light too. So we find plants no deeper than 15m along the coast and 35m in clear water. Phytoplankton lives somewhat deeper because currents and eddies move it up and down the water column.
The diagram shows how life begins with a large amount of phytoplankton, which keeps a much smaller amount of zooplankton (animal plankton) alive. This is then eaten by larger animals like fish fry and shrimps, which get eaten by larger fish and so on, but each tier is 5-10 times smaller than the previous. Because all these organisms are cold blooded, they do not waste energy on heat, which is one of the reasons that the ocean food chain has many tiers. It is interesting to note here that sea creatures are very wasteful in their reproduction. A mature snapper for instance, produces millions of eggs just to make one adult fish. But this waste is necessary to produce the many small animals in the food chain, which make the packets of solar energy larger and larger until finally the mature snapper can eat it too. Sea creatures thus produce eggs mainly for food (99.99%) rather than reproduction (0.01%). It is indeed a strange fish-eat-fish world.
closed ecosystem
the plankton food chainA food chain is not an ecosystem until all loops are closed and the nutrients of life returned to the plants. In this diagram the marine food chain has been simplified to three tiers and three new components added. Small waste particles are decomposed in mid water by the planktonic decomposers and the resulting nutrients dissolved so that seaweeds and phytoplankton can reassemble them again into molecules of life. Larger waste particles and dead bodies sink to the sea bottom (sea soil) where the sea soil decomposers do the same. Notice that solar energy is locked up in all the coloured circles, except for the pink one, the nutrients which do not contain any usable energy.
The main differences between the two guilds of decomposers are:

Scientists have never made a conscious distinction between the planktonic decomposers and the phytoplankton, as the two are indistinguishable under a microscope apart from their sizes, and furthermore because some weird organisms make up the phytoplankton. Many are both animal and plant. So it came as a bit of a surprise that sea water contains very small organisms (bacteria) and even smaller ones (viruses), together making up the smallest of plankton particles (pico and femto plankton). It was even more surprising to find that their numbers and their biomass is actually quite high. But from the above diagram and the fat arrows connecting them, one can see that these findings were entirely predictable.
As self-evident as it may seem, the planktonic decomposers were our first discovery that led to the Plankton Balance hypothesis. Quite surprisingly, this guild of decomposers is not mentioned in any textbooks, is not taught at University and has no references in the scientific literature. It is an entirely new discovery.

Decomposition connects all trophic levels in an ecosystem - Floor Anthoni

Another principle that was entirely predictable but not discovered until shown by the DDA method, is that decomposition cannot easily complete. This is because all energy conversions are accompanied by losses and that all energy eventually ends up at its lowest state as heat (the laws of thermodynamics). Thus a car battery needs more energy to be charged than it can hold, and when discharging it, can deliver even less usable energy. Treat the molecules of life as batteries of solar energy, and they need more energy to be built than they can store, and likewise, cannot be decomposed fully using only the energy within. Thus decomposition stops prematurely, resulting in some usable nutrients and a class of unusable organic molecules that we have named slush, like incompletely molten snow. Slush is of no use to plants and neither can it be eaten by animals. Only bacteria can decompose it further if they receive an additional energy in the form of a high energy fuel like sugar, or in the case of the DDA method, alcohol.

Slush is not a new invention by nature and has been around as long as life existed. Naturally, nature has found a way of decomposing it, or else the oceans and lakes would contain only slush and life as we know it would not be possible. Scientists have just not been aware of it and how it functions. It is a remarkable substance because it is entirely transparent and invisible and can reach high densities without affecting the clarity of the water. It is also difficult to measure.

Our slush hypothesis or symbiotic decomposition hypothesis explains how plants use bacteria to obtain benefit from slush. By excreting slime with sugars and algins, algae create an incubation mat for bacteria on their skins. The additional energy food enables the bacteria to fully decompose slush from the water around, a great benefit to the host who not only receives the desired nutrients, but also carbondioxide and hydrogen ions, all products of decomposition. It enables seaweeds to be more productive than they could otherwise be. It is plants' interest to make more slime and sugars and to slough (sweat) them off, because, detached from the plant, they still continue their important role in decomposition.
We'll see later that another discovery by the DDA is that the availability of hydrogen ions is of major influence to aquatic productivity. It so happens that these hydrogen ions are very scarce indeed in sea water, as measured by its pH. So, obtaining them through symbiotic decomposition is of great benefit to sea plants (algae, phytoplankton and even corals). More about this later.
ecosystem with symbiotic decomposersThus the aquatic ecosystem diagram above now needs to be modified as shown here. The food chain essentially remains unchanged, but in the return path of decomposition, a new guild of decomposers, the symbiotic decomposers, has been drawn. They live on the skins of aquatic plants and convert slush to nutrients (and carbondioxide with hydrogen ions). With these additions we're now getting a step closer to how the sea and lakes work.
One would think that slush remains a small part of the biomass in the oceans, but our measurements showed the opposite. 
Remember that the world's oceans are very large and very deep so that most of the sea column never sees light. Symbiotic decomposition in this underworld is thus not possible, resulting in a high production of slush that slowly finds its way to the surface. Only in the presence of light and plants can slush be decomposed further. In the island state of Niue, which is surrounded by a gin-clear blue ocean, we found that although phytoplankton biodensity there is nearly ten times less than around a continent, the biodensity of the slush is so high (8 times) that this very clear water contains half the biodensity of that around continents.

The thermodynamic conversion deficit is so essential a principle, that it must apply to all ecosystems found on Earth. It explains why fruits are sweet because their sugars need to assist decomposition in the soil. Many plants sacrifice their roots to further decomposition in the soil, and they also supply energy food (sugars, slime) through their roots to the soil.

The oak tree and the aphids
In our garden stands an oak tree which rains sticky sugars down onto the decking and chairs. It is a nuisance caused by thousands of aphids sucking its sap and wasting sugars. I often wondered why the oak tree had no defences against these little sapsuckers. Now I know that the rain of sugar is needed for the soil decomposers to complete the decomposition of fallen leaves from the previous season for the oak tree to get the nutrients and minerals it craves for. The oak tree does not make sweet fruits, you see?

The slush hypothesis also explains how corals live. A long time ago scientists discovered that corals can live in seas with very little zooplankton (the normal food of polyps) because they have symbiotic algal cells (zooxanthella, a primitive dinoflagellate) inside their tissues. These symbiotic plants, it was thought, convert sunlight to food using the scarce nutrients around, and if the animal shares its wastes with the plant cells, it becomes a self-contained ecosystem, able to live from sunlight. Our slush hypothesis changes this somewhat by postulating that these mixotrophs (mixed-feeders) have decomposing bacteria on their slimy skins. The sugars produced by the plant cells are passed through the skin to the decomposers which enables them to decompose the slush of which there is vastly more than nutrients (and also invisible). Also the polyp's wastes are passed to these decomposers living on their skins. Because there exists so much slush in the blue oceans, the hypothesis also predicts that many more organisms in several phyla have adapted to this mixotrophic way of life, waiting to be discovered.

living in the sea
Living conditions in the sea are so entirely different from those on land, that you must read the chapter on biodiversity/marine which discusses this, and the introduction to habitats of the sea. If you don't know these differences, you will be unprepared and most likely have the wrong ideas about how the sea works and how to save it. Not surprisingly, most scientists including marine scientists, are also insufficiently aware.
One of the main differences between living on the land and living in the sea is that food is drifting around as a thin soup. Those creatures able to catch it (filterfeeders like sponges), don't need to move because the food is moved past them by currents. But what scientists have overlooked is that the decomposing bacteria are designed to break biomolecules apart, and they are not particularly choosy about whether they attack dead or living creatures. On living creatures they cause infection and disease, eventually resulting in death. Thus every organism in the sea lives in the balance between the good (food) and the bad (disease) influences of the plankton. Creatures want to live where there is more food, but that also brings more threat of disease, resulting in early death. So the long-lived ones end up living close to starvation. Of course various defence mechanisms have evolved.

Our newly discovered plankton balance hypothesis explains this and its consequences. This too should have been entirely predictable, but remained unrecognised until we discovered it as a major missing ecological factor that has been overlooked. Read more about it in the plankton balance chapter.

In the sea there exists a gradient (gradual change) in the density of the plankton soup, being densest in estuaries where rivers bring new nutrients, freshwater plankton and mud, and thinnest at outlying islands near the edge of the continental shelf where the water is much clearer. Along this gradient, the sea creatures (both plants and animals) find the best place to live, and this explains their general distribution. But what happens when the gradient changes, as for instance when people pollute the sea?

Then every creature has to pack up and move to a new place. But the sessile (sitting) ones can't do this, so they die as their offspring establish in more suitable places. Thus a changing gradient results in widespread death, which is what we have observed in recent times. If gradients keep moving (sometimes to and fro), this results in an overall scarcity of life and variety, as if the sea is dying. This in turn creates much open territory, which can then be occupied by foreign species that are more suitable to the new conditions. In a country like New Zealand which over eons of time has enjoyed clear seas, degradation of the marine environment and invasion by new species has become quite prominent.

Biodiversity in the sea
The plankton balance hypothesis explains another mysterious paradox why coral seas are so rich. When we talk about biodiversity, we mean the diversity in species, not particularly counting microbes and bacteria. Biodiversity can be high only if species grow old. For an organism to grow old, it must reduce the risk of disease, and thus teeter on the balance of starvation. This explains why biodiversity in the sea is highest where food is scarcest: in the clear coral seas and the deep sea bottom.
But the slush hypothesis adds another dimension: living from slush is healthier than living from phytoplankton because the bacteria that decompose slush are all locked up on the skins of other organisms, whereas the bacteria in the phytoplankton are on the loose, being 'breathed' by all water breathers.
Deep sea organisms (gorgoneans and corals) do not live from phytoplankton or slush because there is no sunlight. In their environment food is very scarce indeed, but so are bacteria, because these are all locked up inside the sea soil. This can also be observed in shallow lakes. In other words, the soil bacteria then out-compete the planktonic ones.

Wherever humans live, they changed the environment around them to suit themselves. They converted forests into arable lands and pastures, and their sheer numbers and their livestock produce vast quantities of nutrients that all end up in the sea. But pollution is no more than the wrong substances in the wrong place in the wrong quantities. Thus a small amount of pollution does not need to be harmful, and indeed due to natural erosion, the coastal seas have for eons been receiving the fertility they need.
causes and effects of pollutionThe amount of pollution in seas and lakes has become very harmful, but where does it come from and what harm is done? The diagram shows on left what humans do, then what substances are produced, and on right what these substances do to the sea. It looks rather complicated, and indeed it is, but the words are familiar and you can follow each of the arrows from left to right. For a complete description, read the chapter on marine conservation/causes&effects. If we want to save the sea, we have to reduce every arrow in this diagram.

Quite understandably, scientists have concentrated on the visible side of degradation, mainly the harm caused by mud (sedimentation, deposition) but we discovered that the invisible decomposers (bacteria) are the main factor in degradation. The decomposers are associated with death, such as dead phytoplankton, their main food source. When the density of the phytoplankton increases, their decomposers follow suit, but then suddenly the baddies take over and the plankton becomes dangerously sick when equally suddenly its food value diminishes as simultaneously its threat to life increases. So the plankton balance  factor plays a major role inside the plankton. In this manner even killer plankton can emerge, which has no practical food value because the phytoplankton (the solar energy) is consumed in its entirety by very aggressive bacteria. To our surprise, the first major change in the quality of the plankton with its accompanying degradation, happens when the water is still considered 'healthy', between 15 and 10 metres visibility. This agrees with our observations of widespread death to underwater life.

If you want to see what degradation looks like, visit the decay section.


sea water
Water is one of the most amazing substances on planet Earth as it makes life possible. It is amazing that it exists as a liquid and a solid (ice) since really, it should exist only in gas form (at Earth's surface temperatures). Consider its close relative hydrogen sulphide (H.S.H) which is a larger and heavier molecule (molecular weight= 1+1+32) as opposed to water (H.O.H) with molecular weight =1+1+16. Yet hydrogen sulphide exists only as a gas. The reason for this anomaly is that the shape of the water molecule is like a boomerang with a negative charge in the middle and a positive charge at its ends. This attracts other water boomerangs to click into place, forming tiny islands of liquid water. This cohesion of water particles also makes water condense easily from a gas back into liquid state.

From a chemical perspective, water is unique because it is the only known substance that is both an acid (with an excess of hydrogen ions H+) and a lye (with an excess in hydroxyl ions OH-). Thus it is attractive to many kinds of substance (acids, lyes, salts) that because of this, dissolve easily. Water is therefore the perfect carrier for the molecules of life and the minerals and nutrients associated with life.

The balance between hydrogen and hydroxyl ions is measured with a pH meter, which essentially only measures the concentration of hydrogen ions. In neutral pure water not all water molecules are dissociated (split) into ions, but only one in every 600,000,000 which is very scarce. (concentration at pH=7 = 10^-7 mol/litre = 1E-7 x 18/ 1000 = 1.8E-9)  By comparison, carbondioxide is so scarce in air (320ppm by molecules) that it limits plant growth on Earth. Yet one in about 3000 molecules is carbondioxide.
The concentration of hydrogen ions can be measured with a pH meter and neutral pure water corresponds to a pH of 7. Every step on the pH scale corresponds to a ten-fold increase or decrease in hydrogen ion concentrations. The pH or the availability of hydrogen ions, is what the DDA method measures while a plankton sample is decomposed. To read more about pH and how a pH meter works, read the pH chapter.

The salt molecule sodiumchloride (NaCl) is of all salts, perhaps the easiest to dissolve in water, again because of its small size and shape which locks in perfectly with the water boomerangs. In doing so, it forms larger islands of liquid water, which leaves less space for other substances to dissolve into. Salt water is therefore much less solvent than fresh water, reason why soaps won't  foam or lather (other minerals in seawater are also responsible).

Sea water contains many salts (see the composition of sea water), which altogether raise the pH to about 8.1 (the pH of pure water is 7.0; rain water which is saturated with CO2, has a pH of 5.5), compared to that of lakes which is between 6.0 and 7.0. Thus hydrogen ions are much less readily available in the sea, which as we discovered, is of major importance to productivity and maximum attainable biodensity.

ocean alkalinity mapped
The Woods Hole Oceanographic institution has been studying the acidity of the sea for a long time, resulting in this map. The acidity of the ocean is not constant as it changes from place to place, from a low of 7.8 to a high of 8.2. Low pH (but still alkaline) is associated with upwelling areas of high productivity. In a given place, it is not constant either as it is higher at the end of the day compared with the end of the night. Areas with intense eutrophication are relatively more acidic.

There exists a very large difference between a lake and the sea, not only because lakes are not salty but also because they are more acidic (more hydrogen ions) than the sea. Because many lakes are not interconnected by the same rivers, they have properties that are unique to each, unlike the sea where all waters are interconnected. Furthermore, the planktonic ecosystems in fresh water are much simpler, counting far fewer species and phyla (main shape groups) than those of the sea. Thus lakes offer an excellent opportunity for the study of aquatic ecosystems.
With the DDA we made some spectacular and basic discoveries in lakes. We discovered that the natural pH (without any influences from living organisms) is characteristic and that the maximum biodensity as well as the maximum growth rate of phytoplankton depends on pH, proving that the availability of hydrogen ions is a major ecological factor in aquatic ecosystems that has so far been overlooked. The lower the pH (more hydrogen ions available), the higher a lake's productivity and maximum biodensity can be.

We also discovered that high productivity is mainly consumed by bacteria and that the clarity of a lake can be very deceptive, since bacteria remain invisible. To our surprise, the sea with its high pH fitted well within the newly discovered laws of productivity, which means that the sea is disadvantaged by its low availability of hydrogen ions (high pH). Fortunately, the newly discovered slush and symbiotic decomposition come to the rescue as these provide for the missing hydrogen ions. It appears as if marine algae thrive in a thin cocoon of slime that lowers the pH (providing hydrogen ions). But having decomposers so close also means that marine algae live in a risky situation that can easily be disturbed. It is not surprising therefore, that they are so sensitive to degradation and very difficult to keep in aquariums.

DDA, Dark Decay Assay
oversimplification of an ecosystemThe Dark Decay Assay is a newly discovered test method to get a grip on how degradation works. From extensive observations we postulated that the planktonic bacteria were the main ingredient of degradation but we needed a way to prove this. Research of plankton is severely hampered by the difficulty of collecting (straining) it, its many players in a very large range of sizes and the fact that it changes rapidly. Plankton biodensity is also very low, which excludes many scientific instruments as they are not sensitive enough. We then knew that we needed to simplify the planktonic ecosystem to its most basic form, as shown here.
As plants synthesise (build) biomolecules from nutrients, they also scavenge from the water carbondioxide (CO2) and hydrogen ions (H+) which therefore become scarce (the pH increases). One could not put it simpler than this, even though a great number of complex biochemical reactions are involved. The green arrow goes upward symbolising the increase in pH.

The zooplankton eats the plant plankton and digests it but they breathe oxygen ('burning') and the pH does not change much. Besides, the biodensity of the entire food chain is much less than that of the phytoplankton, so we can safely ignore the whole orange arrows. Note the small side loop which we thought necessary in case phytoplankton respires (breathes) like plants at night. But we have not been able to measure this.

Wastes and dead bodies are decomposed by the planktonic decomposers (brown arrow) who break all the chemical bonds, including hydrogen bonds, and return hydrogen ions to the water (pH goes down). Notice the small side loop direct from the green plants to the bacteria, which represents how dead phytoplankton feeds the decomposers direct. This arrow can become very prominent as plankton becomes sick, attacking live phytoplankton as well.

With this simple understanding of an oversimplified ecosystem, we thought that a pH meter made a good chance, as it is extremely sensitive. Fortunately for us, high precision (three-digit) pH meters had recently become affordable.

The pH one measures at any time (in light) is the result of algae pushing the pH up and at the same time decomposers pulling it down. In order to measure the behaviour of the decomposers therefore, the plants had to be disabled by simply placing the sea water sample in the dark and measuring how pH behaved. Because the samples are hermetically sealed, gases cannot escape and hydrogen ions remain in solution. We then postulated that these would be a good measure (proxy) of biodensity because hydrogen atoms are an essential and predictable part of living matter. Thus the change in pH represents the amount of biomatter decomposed, and when decomposition halts, the total biomass in the sample. Because a pH meter measures densities, the method does not measure biomass but biodensity (biomass per litre). Now a new biodensity unit was needed and we posited (proposed) the hion as new unit of biodensity, which is 1 for the hydrogen ion concentration at a pH of 9.00. One day this unit will be equated to actual biodensity (grams biomatter per litre) but for the moment this is not strictly necessary since all comparisons are made using the same hion unit. Because the pH scale is logarithmic, the hion scale shown alongside it, is also logarithmic.

Please note that pH measures acidity only and not biodensity. But when decomposing an organic sample in a closed container, the increase in acidity or decrease in pH corresponds to the number of hydrogen bonds broken and hydrogen ions released into the water. The drop in pH then becomes a measure of biodensity. Also note that some hydrogen bonds remain such as in hydrogensulphide H2S, ammonia compounds NH4+ and the natural gas methane CH4. Thus biodensity cannot be calculated exactly from the change in pH and an average formula for algae like H:O:C:N:P:S = 212:106:106:16:2:1.

results with the DDAThis graph shows two groups of DDA measurements. They originate from a long coastal trip following a 40 nautical mile (75km) transect to the edge of the continental shelf (S-E-C-D). Notice how accurate the DDA is and how the curves flow smoothly along without much criss-crossing. The total biodensity of the phytoplankton is represented by the top group which measures around 30-80 hion, a range from good to medium quality water. The first drop in pH over the first 48 hours is representative of decomposer activity and it is measured with the red 48-hour rectangle. So we end up with two essential measurements: total biodensity and bacterial attack or rate of attack (RoA). This roughly corresponds with the good side and the bad side of plankton as postulated by the plankton balance hypothesis. We'll come to the second group later (slush).

autumn seawater qualityThe simple DDA method now enables us to objectively measure the quality of the water in units that make sense to the environment, while also representing the two most important qualities of the plankton. The idea is simple: one cannot have a healthy environment in a sick sea. When the plankton becomes sick, the marine environment suffers proportionally. But there remains a problem. Our measurements are but snapshots in time and the water quality changes daily, seasonally and annually. This is why underwater observations remain important.
The most important figure is the red rate of attack, which should not exceed 10 for healthy plankton. What we see is that there are distinctly different bodies of water. One of the key findings was the very high rates of attack in the top-right for the famous Poor Knights marine reserve where both healthy and very sick water is found, and this at the best time of year (autumn). It confirms recent observations of extreme degradation.

chronic decline of fish in a marine reserveEven extreme degrees of degradation have not been noticed by divers and scientists alike. This graph shows chronic decline of non-fished species in a non-fished marine reserve, the Poor Knights in New Zealand. The data was measured by marine scientists who studied how the reserve improved after total closure in 1998. Most of the fish graphed here have never been fished, some because they are plant eaters and others because they have not been targeted by floating fishing lines. The curves were gleaned from a scientific report that did not mention a word about it. The graph clearly shows the chronic decline of fish, which we have observed for over a decade before 1998. Only one fish species increased, sweep (Scorpis lineolatus) which is a near-coastal fish tolerant of poor quality water. This decline agrees with the DDA observations in the map above, as well as with our own observations.

Honest answers to painful questions
Although the data of the decline of fish at the Poor Knights was included in the scientific report to the Department of Conservation, not a word was mentioned about it, as if the scientists had not noticed or did not want to draw attention to the bad news. Science is all about being honest, even when results are disappointing. What are the honest answers to the following painful questions?
  • Does the Poor Knights marine reserve protect biodiversity? [NO]
  • Knowing that this is NZ's best coastal marine reserve by far, how would the other marine reserves fare? [FAR WORSE]
  • The graph shows non-commercial fish species but would commercial fish be exempted from this mysterious disease? [NO]
  • If these curves represented commercial fish stocks, would we call it a fishery collapse? [YES]
  • Knowing that this is happening 20km out in sea at the edge of the continental shelf, how would the situation be close inshore? [FAR WORSE].
Only by being strictly honest will we be able to find the right cure for the ills in the sea. Note that NZ is now going through a period of rapid degradation of its seas, an era that other nations have gone through several decades or even centuries ago. Even so, degradation may still be the main cause of present-day fishery collapses elsewhere.

We have now brought together an overwhelming mass of evidence that shows that marine reserves cannot work where degradation reigns and the above graph is living proof of that. Read the war for marine reserves for more. But if non-commercial non-fished species are affected, would the commercially fished species somehow be exempted? Of course not. Whereas fishermen affect the adult fish, degradation mainly affects their larvae, resulting in recruitment failure. New Zealand has now entered a new era with fishery collapses where fish stocks are determined by degradation. But elsewhere in the world, this has been going on for quite some time.

Going back to the coloured graph above (Leigh to Mokohinau), the second group of curves was obtained by adding a tiny amount of ethyl alcohol (as in an alcoholic drink) at day five. As you can see, this provided enough energy food for the bacteria to continue decomposition of what remained as slush. Adding more alcohol was not able to decompose any further and we believe that the end of the curves represents the total biodensity including slush. We understand why slush is dense as one nears the blue waters (because it arrives from the deep sea bottom), but it also occurs in areas where treated or untreated sewage is discharged. We observed that sewage may have a much worse effect on the marine environment than we have suspected but much more work needs to be done.

The DDA is an exciting technique that because of its simplicity, can be done by amateurs at a very low cost. It allows them to measure objectively the health of the sea, rivers and lakes and it bring us a step closer towards saving the sea. The measurements are stable and accurate, such that they can be compared with other places in other times.

The Dark Decay Assay is done with a 3-digit pH meter which also happens to be waterproof. The vial contains only 30ml of sea water, which makes the DDA perhaps also the most sensitive plankton test available. The vials are standard Fuji 35mm film canisters made from High Density Polyethylene HDPE.
In order to be able to compare results from place to place and time to time, the temperature needs to be stabilised, in this case with a modified car fridge for a six-pack of beer. Two trays contain 24 vials each. The whole laboratory is portable and works at home, in the car or on board, and even on a plane.


what now?
Our many discoveries did not happen by accident or in a lucky moment, but they were born from conflict. Existing scientific knowledge could not explain the distribution of organisms along the shore or out towards remote islands. It could not explain why so many organisms were disappearing over such large areas. It could not explain why we were losing so much so fast and why now and why we find less life where there is more food and why organisms of all phyla are affected and why the young ones are more affected and so on. Some very important ecological factors must have been overlooked and fortunately we had the courage to investigate this all alone.

On the Seafriends web site we have now brought together a coherent and harmonious set of theories (which remain hypotheses until proven beyond doubt) which explain how the sea really works and which also have predictive power. We have brought together the science needed to understand how the soil degrades and erodes, how this affects the sea and how degradation in the sea works. We now even have the tool needed to assess how sick our seas and fresh waters are, a tool that can also be used to measure progress while turning the tide. Everything we need to combat degradation, all the answers are here. We now need to assess their relative importance and cost. Then we need to act.

We now need scientists to become engaged and attempt to prove us either right or wrong. With their much better facilities they will be able to carry our humble beginnings further. In the meantime we can still progress the DDA by improving its accuracy, doing more seasonal studies and mapping the health of the sea. We are interested in developing several scatter diagrams further such that each body of water on this planet can be placed on these diagrams as a single dot, representing an objective measure of their health.

We are particularly interested in assessing the damage caused by sewage alone, because this can be turned into an advantage so easily and so quickly by shipping it out to sea, outside the continental shelf. Here swaths of ocean can be fertilised with it and monitored by satellite. As a new fishery is created there, we are also salvaging the old coastal fishery, resulting in a double benefit and it is cheaper in many cases than treating the sewage.

We need strategically placed conscientious amateurs who are willing to give some time for the sake of a better future for all. They must be able to obtain samples from the seas, lakes and rivers where they live or that they visit frequently. They must be able to deliver consistent and high quality measurements. We must have government departments with vision, able to place resources into the hands of amateurs at the lowest possible hindrance. Is that too much to ask for?

Increased DMS could cause heavier rainsCould degradation make hurricanes more destructive?
What an outrageous thought! Of course not! However, let's follow this idea through. Recently there have been more hurricanes and stronger ones too. There have also been more torrential rains. Hurricanes feed off warm water that allows more water to evaporate more quickly, resulting in more water droplets and bigger ones, feeding hurricanes with their thermal energy. Global warming could do this but not so suddenly and so soon. 
We've seen that the gas dimethyl sulphide (DMS) is produced by decomposers and that the sea can quite suddenly become sick, feeding the solar energy to these decomposers, thereby suddenly producing more DMS. This makes more cloud more quickly and with bigger droplets, as if the sea was warmed by a few degrees, resulting in more powerful hurricanes and more of them. Crazy as it sounds, we can't dismiss this idea, as the example shows how the planet's processes are interlinked in mysterious ways.
The diagram shows how much the DMS molecule resembles that of water. Together with their negative and positive polarities, transparent water vapour molecules attach to the DMS molecule, forming water droplets. So DMS promotes cloud formation and heavier droplets, which could cause heavier rains and hurricanes. Cloud formation also cools the planet, thereby counteracting the warming effect of greenhouse gases.
How important is the DDA and the discoveries made with it?
Many pH measurements led to the discovery of half a dozen elementary ecological laws that, if confirmed, would turn the way we understand the sea on its head. It would in fact send many publications on this subject to the dustbin. So let's review what these discoveries are about:
  • The most important ecological factor in the sea has been overlooked: the guild of decomposing bacteria. They are very active and cause disease and infection. The health of sea water depends on their numbers as all marine organisms live directly (eating it) or indirectly (eating those who eat it) in a delicate balance between the food that plankton brings (soup) and the chance of dying from decomposing bacteria (sewage). Each sea organism thus lives in a precarious balance between the good life (thick soup) and a long life (thin sewage), which are in conflict with one another. This is what I named the plankton balance. The Plankton Balance fills an important gap in our understanding of life in the sea.
  • Alkalinity in the ocean depends substantially on the plankton balance in which the pH results from autotrophs (plants) using hydrogen ions and driving the pH up, while decomposers return hydrogen ions, thus driving the pH down. The daily rhythm can amount to 0.4pH units (250%), and the difference between estuaries and the open sea as much as 1-2 units (1000-10,000%). Degraded seas due to eutrophication have reduced pH. Scientists measure ocean pH without taking account of this effect.
  • The most important limiting factor in aquatic ecosystem is the dearth of hydrogen ions (H+), which has also been overlooked. The more acidic the water, the higher biological productivity becomes, and the denser the amount of life. In the sea this is borne out by the observed fact that highly productive upwelling areas are more acidic. In other words, 'acidic' seas are a good thing. This could well be a very serious omission of mainstream science.
  • A serious scientific mistake was not recognising that decomposition cannot completely break organic matter down into inorganic salts. There are conversion losses and the second law of thermodynamics forbids this. So there is an intermediate organic molecule that is neither a nutrient for plants (dissolved salts), nor food for bacteria. My measurements showed that the sea is awash in this mysterious substance that I named slush. In fact the biomass in slush is far larger than all life on Earth combined. Reader please note that this is a very serious omission by mainstream science, and cannot be disproved! The other 5 laws tie in closely with this.
  • Life on this planet would never have been possible, if slush could not be decomposed further. The only way for this to happen is when plants team up with decomposing bacteria in the act of symbiotic decomposition, where the missing energy is supplied by the plant to allow decomposers to complete the last step in decomposition. This explains how corals can grow where nutrients are severely limited, and it explains why seaweeds are more productive with symbiotic decomposition than without. Symbiotic decomposition may well be the main source of growth for plants.
  • The most important benefit obtained from symbiotic decomposition is firstly hydrogen ions, since these are in shortest supply, and secondly nutrients, and finally CO2 in a form ready to use. The hydrogen ions lower pH on the skins of marine plants (and some phytoplankton), as well as on the skins of coral polyps. In this cocoon of reduced pH, these organisms can be more productive than without.
The above discoveries are not trivial as they affect everything we know about the sea, the soil and the planet. Once confirmed, they could well add up to the biggest scientific blunder ever, also because one could have predicted these one hundred years ago, when also the technology was adequate for their discovery.

Profound consequences
Many studies have found that land plants are severely limited by the amount of carbon dioxide they can extract from air, since they are all competing for the same resource (air). Not surprisingly, the air in glasshouses is enriched by carbondioxide in the process of warming them (as in Holland), which leads to a 30-40% increase in productivity for a three-fold (300%) increase in carbon dioxide (1200ppm). However, for a limiting factor, this does not make sense, since one would have expected at least 300% higher productivity, since nutrients, moisture and temperature are no longer limiting.
We showed that the thermodynamic conversion deficit stops decomposition prematurely. If conversion efficiency were akin to that of a motor running on a low temperature, one could expect that less than 30% ends up in nutrients (dissolved salts), leaving perhaps as much as 3/4 in slush (dissolved organic molecules). Thus symbiotic decomposition is likely the most productive part of any plant, where a tiny sacrifice in sugars produces a huge supply of hydrogen ions, carbon dioxide and nutrients. This also means that a plant's highest uptake of carbondioxide happens through its roots rather than through its leaves. It explains wy organic farming (which supplies large amounts of decomposable mulch), is more successful than expected, whereas greenhouse hydroponics (roots in nutrient solutions) is not.
Symbiotic decomposition has profound consequences for horticulture and agriculture and for how we should treat the world's soils.

Reader please note that these discoveries were first published in September 2005 and two years later
have not received the necessary scientific attention. We've written over 400 personal e-mails to
scientists working in related fields and have not received a single reply. What does that say?