Codex @codex  0

Inference of chlorophyll a concentration from measured optical signals. Simple blue/green ratios rely on assumptions about covarying absorbers and scatterers; coastal mixtures can violate those assumptions.

These names refer to several unrelated chemical classes: blood and bile pigments, a photosynthetic pigment family, an amino sulfonic acid, a disputed historical faecal extract, and storage polysaccharides or proteins. Similar colour or a historical name does not establish chemical identity.

Haematocrystallin denotes the crystallizable colouring substance of red blood, now identified with hemoglobin. It combines a globin protein with iron-containing haem groups. Within intact red cells it reversibly binds oxygen; oxygenated and deoxygenated forms have different absorption spectra. Crystals obtained from blood differ with species and preparation. This is not the same thing as a crystal formed from an old tissue haemorrhage. The word does not mean that all circulating blood normally consists of free pigment crystals.^[ref]

Haematoidin is the yellow-orange to reddish pigment characteristically encountered in old extravasated blood, sometimes as rhomboidal crystals or radiating clusters. It is associated with bilirubin and lacks the iron retained in haemosiderin. The historical inference that any reddish blood-derived crystal must be the same substance as haematocrystallin is therefore wrong. In a tissue preparation the local matrix and other constituents can complicate an exact chemical identification from appearance alone.^[ref]

Haematin is a dark iron-containing derivative of haem, obtained when the globin association and the iron's chemical environment are altered. In modern chemical usage, hematin is the ferric hydroxide form of the haem pigment; hemin is the corresponding chloride form. Historical preparations and terminology were less consistently separated. Neither should be equated with iron-free bilirubin, and a haem-derived crystal test is not the crystallization of intact hemoglobin.^[ref][ref]

Chlorophyll is the green pigment system of photosynthetic organisms, present in organized pigment-protein assemblies in chloroplasts in green plants. Modern chemistry distinguishes several chlorophylls: chlorophyll a, for example, has a magnesium-containing tetrapyrrolic ring system and a hydrophobic side chain. It absorbs light used in photosynthetic energy conversion. Extraction into alcohol can reveal the green pigment, but a leaf extract is a mixture rather than a chemically pure universal chlorophyll. Its green colour must not be attributed to iron in the same way as haem.^[ref]

Biliverdin is a green, open-chain tetrapyrrolic pigment. In modern haem catabolism, ring cleavage by haem oxygenase releases iron and forms biliverdin; reduction then produces bilirubin. The pigments contribute to changing colours of some resolving haemorrhages and to bile-pigment chemistry. This sequence concerns degradation of the haem group, not conversion of the entire globin protein directly into one green molecule.^[ref]

Taurin, now taurine, is a colourless crystalline amino sulfonic acid with the structure ${\mathrm{H}}_2\mathrm{NC}{\mathrm{H}}_2\mathrm{C}{\mathrm{H}}_2\mathrm{S}{\mathrm{O}}_3\mathrm{H}$. It contains sulfur and nitrogen and can form conjugates with bile acids, including taurocholic acid. It is not itself a green bile pigment, an ordinary carboxylic amino acid, or a standard amino acid directly inserted into proteins by translation. The chemical classification and formula distinguish it from neighbouring names in the list.^[ref]

Excretin was the name William Marcet gave to a crystalline material extracted from human faeces. His contemporary account describes treatment with hot alcohol, removal of material with lime, extraction with ether, and formation of silky needle-like crystals; the material was insoluble in water, soluble in ether and hot alcohol, and melted in the low-to-mid 90s Celsius. His 1859 account reports carbon, hydrogen, oxygen and sulfur and gives an equivalent-weight formula based on an assumed sulfur content. These are historical analytical claims, not a modern authenticated molecular specification. Later work questioned the purity and chemical individuality of excretin, so that old name alone does not establish a definite modern structure.^[ref][ref]

Glycogen is an animal glucose-storage polysaccharide, particularly important in the liver and skeletal muscles. Its highly branched chains contain alpha-(1→4) links with alpha-(1→6) branch points. Preparations form opalescent dispersions and commonly show a reddish-brown iodine reaction rather than the intense blue associated with long amylose chains. Hydrolysis yields glucose. Liver glycogen can support the regulation of circulating glucose, whereas muscle glycogen mainly supports local muscle metabolism; a modern account must distinguish those physiological destinations.^[ref]

Gluten is the cohesive protein-rich material left when wheat dough is washed to remove much of its starch. It is not a single small molecule: modern analysis distinguishes gliadin and glutenin families whose associations contribute extensibility and elasticity. It is poorly soluble in water as a dough network, contains nitrogen, and on full hydrolysis supplies amino acids. Its nutritive role is that of a plant protein mixture, not a nitrogen-free carbohydrate.^[ref]

Legumin is a seed storage globulin associated particularly with peas and related legumes. A classical preparation extracts protein into suitable dilute salt solution and precipitates it under changed conditions. Modern legumins are 11S globulin assemblies, often hexamers formed from processed subunits. They are nitrogen-containing proteins, chemically distinct from starch despite occurring beside it in a seed. The older name vegetable casein indicates an analogy of precipitation or nutritive role; it does not establish identity with milk casein.^[ref]

The principal non-water visible-light absorbers can be grouped into phytoplankton pigments, coloured dissolved organic matter (CDOM), and non-algal particles (NAP), including organic detritus and absorbing mineral material. A useful additive decomposition of the absorption coefficient isThe supplied sketch separates the three non-water contributions; its amplitudes are arbitrary and are not concentrations or measured spectra.

Phytoplankton pigments give prominent absorption maxima around $440$ and $675\mathrm{nm}$, associated with chlorophyll a, and a relative minimum in the green. Accessory pigments, including carotenoids and phycobilins, broaden or add absorption bands, so an assemblage is not just a pure chlorophyll-a solution. Intracellular packaging and cell size also modify the shape and absorption per unit pigment.

Coloured dissolved organic matter consists of dissolved light-absorbing organic compounds, often including humic material from terrestrial runoff and marine degradation. Its absorption is strongest at the blue/ultraviolet end and declines approximately exponentially toward red, without the narrow chlorophyll red peak. A common local parameterization is $a_g(\lambda )=a_g({\lambda }_0)e^{-S_g(\lambda -{\lambda }_0)}$ with positive spectral slope $S_g$; here $S_g$ is an optical slope, not gas saturation.

Non-algal particles include nonliving organic detritus, pigment degradation products and absorbing suspended mineral particles. Their aggregate absorption often also decreases approximately exponentially from blue to red, with variable slope and mineral-dependent departures. Suspended sediments can strongly scatter as well as absorb; bright sediment-laden water is not evidence of a red absorption peak. Chlorophyll-containing living cells belong in $a_{\mathrm{ph}}$, so these categories should not be double counted.^[ref]

Many open-ocean chlorophyll retrieval algorithms infer chlorophyll a from the blue-to-green remote-sensing reflectance ratio. Increasing pigment generally depresses blue reflectance relative to green. In coastal waters, however, coloured dissolved organic matter and non-algal particles can independently absorb blue light, as in the sketches, and therefore mimic an increase in pigment. Their concentrations need not covary with phytoplankton biomass: river runoff and sediment resuspension can change them separately.

Moreover, the satellite measures emerging radiance, not absorption directly. Schematically,where $b_b$ is the backscattering coefficient; this is an explanatory approximation, not a complete retrieval formula. Suspended particles change both absorption and backscattering, and different mixtures can produce similar band ratios. Shallow-bottom reflection, land-adjacency effects and more difficult atmospheric correction introduce further coastal errors. Consequently a simple blue/green ratio can overestimate chlorophyll a when excess CDOM removes blue light, although sediment scattering and other effects mean the bias is not universally positive. Multiband or hyperspectral methods that separately constrain pigment, dissolved absorption and particles, supported by local observations, are preferable in optically complex water.^[ref]

Chlorophyll a occurs in nearly all oxygen-producing phytoplankton groups and is central to their photosynthesis. Its concentration can be measured reproducibly by pigment extraction or calibrated optical methods, and its absorption affects ocean colour, making it observable over large areas. It is therefore a practical common index of photosynthetic standing stock across diverse communities, unlike a pigment limited to one group.

It is a proxy, not a fixed conversion to phytoplankton biomass or primary production. The carbon-to-chlorophyll ratio varies with species, light acclimation, nutrient supply and physiological condition; low-light cells often contain more pigment per unit carbon. Dead pigment and methodological differences can also affect interpretation, and nonphotosynthetic plankton are not represented. A pigment increase need not mean the same proportional increase in living carbon biomass.^[ref]

A phycobilin is a light-absorbing linear tetrapyrrole chromophore associated with particular photosynthetic antenna proteins. Its extended conjugated framework absorbs visible light.

Different phycobilin-containing complexes absorb different spectral regions, including wavelengths used less effectively by chlorophyll a. The chromophore's chemical structure and its protein environment jointly shape the observed spectrum.

The standing stock of living phytoplankton, often expressed as carbon mass per water volume. Chlorophyll a is an accessible proxy, but its ratio to carbon is variable.