Month: March 2018

Bryophytes : Seeking The Root(less) Origins of Mud

Bryophytes : Seeking The Root(less) Origins of Mud

Reading Time: 9 minutes

For 90% of its existence, planet Earth (mostly) lacked the one thing that cradled civilizations and made millions for detergent companies : mud. Then, sometime around 458 million years ago, it suddenly began seeing a lot more of Mr Mud. Why the sudden rise? How the sudden rise? What in the sodden rice is mud, anyway? And where exactly do those rootless plants called  bryophytes fit in? The Nerd Druid investigates the root(less) cause behind this muddy mystery.

India and farmers

It is March, spring in the Northern Hemisphere. In East India, along the hot dusty flyovers of Kolkata, crimson Rudropolash flowers bloom, giving the speedway a red bannister. Thousands of kilometers away, tens of thousands of impoverished farmers march 180 km barefoot from Nashik to Mumbai to make the government hear their plight. Their red headdress contrast and clash with the saffron of the Indian summer like a tide of Rudropolash, reminding ideologies and ideologues that governments are, ultimately, of, for, and by the people. It is time for the Indian spring [Note:IndianSpring].

Image of impoverished Indian farmers marching 180 km from Nashik to Mumbai to voice their grievances. Their red turbans, headdresses, and flags give the illusion of red Rudropolash flower in full bloom.
Indian Spring

This is not a political blog. However, science and politics sometimes seem rather (unhappily) closely entwined. In this particular article, we shall have no opportunity to explore said entwinement.

A very brief history of farming

Instead, we come to the basic reason why farmers are. Given arable land, farmers grow food. Without farming and agriculture, civilisation as we know it (and as we clearly are very not aware of) would not have existed. Primitive hunter-gatherers, perhaps exhausted with having to chase after or pluck food all day, decided, about ten thousand years ago, that enough was enough. Here be river. Here be fertile land. Here be seed. Where be hammock?

And that is how modern civilisation arose. Through extremely sturdy king-sized hammocks.

Of course, just like you can’t make fire without fuel, or babies without incredibly strong storks, you need a proper substrate for good crops to grow. Luckily, riverbeds and its frequently flooded adjoining areas provided such substrates. The Indo-Gangetic plains in India, Pakistan and Bangladesh, and the North China plains are one of the largest such alluvial plains, as also one of the most fertile in the world.

Map of the Indo-Gangetic Plains. A large percentage of the world's alluvium deposits are found here.
The Indo-Gangetic Plains


Alluvium (from the Latin alluvius, from alluere, “to wash against”) is loose soil or sediments that have been eroded and deposited by water on land, and which has not yet compacted into rock. Alluvium comprises fine particles of silt and clay, as also larger particles of sand and gravel. Agriculturally, alluvium is gold. The high mineral content, optimal water-retention capacity, and optimal breathing room for plant roots make it ideal for a successful harvest. Unsurprising then, that a third of the world’s population now lives in the two largest alluvial plains I spoke of a minute ago.

Geologically, alluvium is quite young, with most deposits in the world having formed in the Quaternary Period of the Cenozoic Era.

Wait. The what period of the what era?

Earth’s geological eras

Well, Earth’s geological timeline is divided into several time-sections, for lack of a better word. The largest sections are called Eons. There are four of them, though for all intents and purposes, especially for the intent and purpose of this article, we’ll talk about two : the Precambrian [Note:Precambrian], and the Phanerozoic. The boundary between the two, situated 542 millions years in the past, is approximately when complex life (such as trilobites or corals) began appearing on Earth. The name phanerozoic, from the Ancient Greek words φανερός (phanerós) meaning visible and ζωή (zōḗ) meaning life, is quite apt.

A cartoon schematic of Earth’s geological timeline, designed by Ray Troll. It shows the geological ages stacked up like a pyramid.
Earth’s geological timeline, in cartoon version. Designed by Ray Troll.

Actually, I lied. I’m not going to talk about the Precambrian, not in this article anyway.

Back to the classification systems. Eons are divided into Eras; the Phanerozoic Eon has three Eras — the Paleozoic (paleo = old, ancient), the Mesozoic (meso = middle), and the Cenozoic (ceno = recent, new). We live in the Cenozoic Era, in the Quaternary Period, in the Holocene Epoch. Epochs can be further subdivided into Ages, though the Holocene hasn’t been long enough to admit such a division.

Eons > Eras > Periods > Epochs > Ages

There. That should clear things up.

The Paleozoic Era

We are, today, more interested in the Paleozoic Era. Beginning 542 mya (mya = million years ago) with the appearance of complex life, the Paleozoic Era ends 251 mya and gives way to the Triassic Period of the Mesozoic Era.

Hold on. Triassic? Does that mean the Mesozoic Era…?

Yep. The Mesozoic Era has three Periods : Triassic (251 – 200 mya), Jurassic (200 – 145.5 mya), and the Cretaceous (145.5 – 65.5 mya). The Mesozoic is the “Age of the Dinosaurs”!

Which (a) makes no sense, it should have been the “Era of the Dinosaurs” and (b) makes no sense, because we ain’t talking about dinos today. Curse you Michael Crichton [Note:Crichton].

Rewind. Back to the Paleozoic.

Schematic of Earth’s geological timeline, in all its detailed glory. This is the International Chronostratigraphic chart, updated February 2017.
Earth’s geological timeline, in all its detailed glory/

Incorporating 291 million years of Earth history, the Paleozoic Era is divided into six Periods : Cambrian, Ordovician, Silurian, Devonian, Carboniferous, and Permian. The Cambrian saw the greatest number of species evolve in a single Period, in an evolutionary event called the Cambrian Explosion. The animals, or rather, the fauna of this Period was dominated by the hard-shelled trilobites. Fish, coral and cephalopods (octopuses and squids, among others) evolved in the Ordovician, though fauna were dominated by trilobites, snails and shellfish. The Cambrian Explosion was balanced out by the Ordovician-Silurian extinction event, where almost half of all marine life disappeared. Things warmed up in the Silurian Period, which saw an explosion in the evolution of fish (both jawed and jawless), as well as the rise of vascular plants on land.

Vascular plants

Most plants and trees that we see today have a highly evolved, though simply explained, mechanism of life. Roots burrow deep into the soil, providing support and extracting water and minerals. These raw materials are then transported throughout the plant body via the rigid xylem tissues. Leaves “cook” these raw materials using sunlight to photosynthesize “plant food”, which is then transported via the less rigid phloem tissues to other parts of the plant body. Plants that have the xylem-phloem (XP) transport structure are vascular plants. The earliest such plants, Cooksonia being a wonderful representative, were the earliest precursors to such XP plants. Nowadays, ferns, conifers, and angiosperms (flowering plants) are all vascular, and all have XP.

Photographs showing xylem elements in the shoot of a fig tree (Ficus alba): crushed in hydrochloric acid, between slides and cover slips
Photographs showing xylem elements in the shoot of a fig tree (Ficus alba): crushed in hydrochloric acid, between slides and cover slips

Which shouldn’t be surprising. All those millions of years gives one lots of experience [Note:XP].

Roots, of course, do more than support and feed the plant. In rocky terrain, they sneak into crevices and break the rock apart into stones and pebbles, enabling wind and water and sun to break them further into finer particles of sand, silt, and clay. Thus, soil! In plain land, or mountain slopes, they hold onto the topsoil, preventing rainwater and wind from blowing it away. Roots are thus both friend and foe to Sir Erosion, and are quite critical for Sirs Environment and Ecology.

Classifying soil and rocks

Since we are on a classification spree today, would we like to try and classify rocks, pebbles, and soil based on how large or tiny the particles are? Bet we would. The Wentworth scale will help immensely.

Image of the Wentworth scale of classifying soil particles
The Wentworth scale of classifying soil particles

Anything above 256 mm (diameter) are boulders. 64 – 256 mm are cobbles, 2 – 64 mm are gravel (4 – 64 mm are pebbles), 62.5 µm – 2 mm is sand, 3.9 – 62.5 µm is silt, and 0.98 – 3.9 µm is clay [Note:Wentworth]. Silt and clay together make up what is usually called mud.

That takes care of one question. Two more to go.

The rise of mud is a bit of a chicken-and-egg problem. Rooted plants break apart rocks which are then eroded into silt and clay; thus, mud. Therefore, rooted plants must have come first, right? However, rooted plants also need mud for the roots to carry out their primary functions. You can’t leach water and minerals from hard rock, can you, Mr Joe Root [Note:JoeRoot]?

Houston, we seem to have a problem.


Which is where bryophytes come in.

The term bryophyte comes from Greek βρύον (bryon), meaning tree-moss or oyster-green and φυτόν (phyton), meaning plant. Bryophytes are land plants and include various species of liverworts, hornworts, and mosses. Bryophytes arose in the Ordovician Period, sometime around 470 – 460 mya. Around 458 mya, they began to proliferate.

Image of a bryophyte. This is Marchantia, an example of a liverwort.
Bryophyte. This is Marchantia, an example of a liverwort.


But was there mud at that time? Yes, mud was present at that time, mostly in ancient river deposits. This mud originated from the action of non-biotic erosional agents (wind, rain, water, sun) as well as biotic ones (microbes and fungi). However, the percentage of mud (silt+clay, remember?) with respect to the coarser and larger sand and gravel was woefully small.

How small?

William McMahon and Neil Davies, both geologists from the University of Cambridge, decided to find out. They trawled through nearly 1200 published papers for data on mud rock in 704 ancient river deposits. As if that wasn’t enough, they themselves collected new data from 125 ancient river outcrops. Then they calculated, based on relative thickness of mud layers and sand+gravel layers, the percentage of mud (PoM), 458 mya. Their median result?


Woeful doesn’t even begin to describe it.

However, McMahon and Davies weren’t done yet. They went ahead and calculated the median PoM of times after 458 mya. And they found that, over the next 100 million years or so, the PoM kept on increasing until, at about the end of the Devonian Period (359 mya), the PoM had reached 26%!

This was, of course, good news for rooted vasculars, which arrived in mid-Siluria around 430 mya. Given mud to grow on, rooted vasculars would be further able to make more mud. And the chain was established.

Except, what happened between 458 – 430 mya? How did the PoM increase from 1% to about 10% in the intervening 28 millions years? Do we have someone to blame?

Graph showing the percentage of mud and the proliferation of microbes and plants in the Paleozoic Era. Bryophytes start thriving around mid-Ordovician, about 470 mya. The percentage of mud begins to rise from late Ordovician and early Silurian, about 460-440 mya.
Percentage of mud and the proliferation of microbes and plants in the Paleozoic Era

Bryophytes and the origin of mud

I can see the tiny bryophytic child jumping about at the end of the classroom, raising her hand and trying desperately to say,

“It was me! It was me! I made mud.”

To which the geology teacher would inevitably ask, “How?”

Well, to start with, even tiny scrappy little green mats are, in large enough numbers, enough to stop wind and water wash away existing mud into the river and then the sea, ensuring enough mud stays on riverbanks. By stabilising riverbanks such, they might have even altered the paths of rivers and streams, thus changing the landscape towards a state conducive to more plant growth. Finally, organic acids secreted by the bryophytes during photosynthesis would have altered soil chemistry and led to the actual creation of mud.

So, basically, to recap, bryophytes (liverworts, hornworts, and mosses)

  1. Made mud
  2. Made sure the mud stayed
  3. Which led to the rise of the rooted plants
  4. Which led to more mud
  5. And more rooted plants
  6. And thus, agriculture!

Moss are the Boss!

Image of the evolution of plants. Bryophytes such as mosses, liverworts, and hornworts feature prominently.
The evolution of plants



Note:IndianSpring : Or not. As of today, March 13 2018, the Maharashtra government, which was inclined to acquiesce to the farmers’ demands, has indeed acceded to said demands, and have arranged for special trains to put the farmers back in their places.

Note:Precambrian : Well, technically, the Precambrian is a super-Eon, further divisible into three Eons : Hadean, Archaen, and Proterozoic. However, as papa Feynman used to say, what’s the point of learnin’ names if ya don’t know what they do?

Note:Crichton : Actually, no, bless you. You, sir, single-handedly made people fall in love with the prehistoric (more precisely, the mesozoic). Dinosaurs became cool, thanks to you. Scary, too. As The Nerd Druidess loves singing (in perfect rhyme and rhythm)

Oh Michael Crichton

Your dinosaurs

They so wonderfully frighten

Note:XP : XP, in roleplaying game (rpg) lingo, means Experience Points. Given that Dungeons and Dragons was one of the first popular rpgs, it is entirely possible Gary Gygax came up with the name. I wonder how many XP a Nerd Druid class might accumulate.

Note:Wentworth :  Humans speak in decimal. That is, (most of) our activities are carried out in powers of 10. We have ten fingers (101). A hundred meter (102) race is the most exciting, now that Bolt has retired. A thousand kilos (103) makes a ton(ne), though cricket commentators seem to think a century is a ton. Blame the Brits for that. Agriculture arose ten thousand years ago (104), a hundred thousand (105) is called a lakh in India, while a million (106) is probably the most used word in this article.

Computers, however, speak in binary (or octal, or hexadecimal, but never mind). Powers of 2. The method of classification of grain sizes, that is, the Wentworth Scale, also uses powers of 2. Rewriting the paragraph in the main text in terms of powers of 2 and millimeters, we have

Anything above 28 mm (diameter) are boulders. 26 – 28 mm are cobbles, 21 – 26 mm are gravel (22 – 28 mm are pebbles), 2-4 – 21 mm is sand, 2-8 – 2-4 mm is silt, and 2-10 – 2-8 mm is clay.

Binary rules!

Note:JoeRoot : Absolutely no intention of evoking the fine English batter here. Although, truth be told, Root is definitely no average Joe.


  1. McMahon, William J. and Davies, Neil S. : Evolution of alluvial mudrock forced by early land plants, Science (2018) [doi : 10.1126/science.aan4660]
  2. Fischer, Woodward W. : Early plants and the rise of mud, Science Commentary (2018) [doi : 10.1126/science.aas9886]
  3. Yirka, Bob : Ancient rootless plants linked to increase in production of mud rock, (2018)
  4. Gramling, Caroline : Early land plants led to the rise of mud, ScienceNews (2018)


Billy Perkin : The Boy Who Dyed

Billy Perkin : The Boy Who Dyed

Reading Time: 7 minutes

William Henry Perkin was born this day, in London, 180 years ago. His accidental invention revolutionised the fashion and textile industry and, in what is infinitely more important, ensured that another Nil Darpan may never need be written. Also, he probably saved a lot of innocent snails from slaughter. As Google honours Perkin with a doodle (header image), the Nerd Druid delves into the life and times of Billy Perkin [Note:BPerkin], the father of the synthetic dye.


A simple word, six letters, three syllables. Nowadays, in India, it is most associated with a certain brand of budget airline. So much so, that a google search this morning yielded a full first page of IndiGo (the airline) results, and none whatsoever of either the colour or the dye, both of which have seen their fair share of history.

Indigo, historical dye collection of the Technical University of Dresden, Germany

Indigo, as a dye, has ancient origins. According to Pliny the Elder, the Harappans extracted the dye from a certain plant (Indigofera tinctoria) that grew in the Indus valley. The Ancient Greek term for the dye was Ἰνδικὸν φάρμακον (Indikon farmakon). This later became indicum in Latin and later indigo in Portuguese. The Silk Route brought indigo to Europe, when Marco Polo reported about it in 1289. However, a further three centuries went by before the European textile landscape realised the potential of the dye, and started large-scale manufacture. The process was not easy, for indigo is a tricky dye, and tends to oxidise easily on contact with air. Once oxidised, it takes its familiar dark blue hue, is insoluble in water, and is then quite permanent. As such, before use, it needs to be reduced to its leuco or white form, and kept in this form, unoxidised, until it is ready to be used. Medieval European technology did ultimately figure out how to tame it, but it was still a laborious and often dangerous process to extract it. Wordsworth has written many a worthy word about the plight of indigo farmers in England [Note:Wordsworth], as has Dinabandhu Mitra about their Indian cousins.

About the time Nil Darpan was being written, that is, about the latter half of the 1850s, a young, talented and precocious chemist was hard at work at his ramshackle hut-lab in London, trying hard to extract quinine from aniline.

Malaria is one of the greatest human killers in history. Each year, more than 200 million people are infected worldwide, of whom more than 700,000 do not make it. Malaria is endemic in many areas of Africa and Asia, and is a primary cause of poverty and a major hindrance to economic development. Malaria has been around since the time agriculture began, ten thousand years ago. While never as singularly destructive as the Black Death, the American smallpox epidemics or the Spanish flu epidemic of 1918, malaria has always been around, whether in civilised urban centres (ancient Rome) or in battlefields (medieval Europe).

19th-century illustration of Cinchona calisaya

The Quechua were the first to find an effective remedy for malaria. Indigenous to Peru, Bolivia and Ecuador, the Quechua would prepare and use a tincture of the bark of the cinchona tree to control the fever to a large extent. Jesuit monks brought the treatment to Europe in the middle of the seventeenth century. In 1820, French chemists Pelletier and Caventou extracted the active ingredient from cinchona bark and named it quinine. For more than a century hence, quinine would prove to be the most miraculous drug human beings had come across.

In spite of its great usefulness, there remained, in the middle of the nineteenth century, no sure way of synthesising quinine in the laboratory. The only source of quinine was the bark of the cinchona tree. In the early nineteenth century, in an attempt to maintain their monopoly over cinchona bark, Peru and adjoining countries began preventing the export of cinchona saplings and seeds. Although the Dutch did manage to smuggle seeds outside South America and grow cinchona in Indonesia, the need for synthetic quinine was acutely felt. This is where August Wilhelm Hofmann, later von Hofmann, came in.

August Wilhelm von Hofmann (1818 – 1892), German chemist

Hofmann was an exceedingly talented German chemist who, at the young age of 28, had been appointed the first director of the Royal College of Chemistry in London. The year was 1845. The appointment was not without merit. Just two years previously, Hofmann had shown that the substances crystallin, kyanol (or cyanol), benzidam, and oil of anil, synthesized independently from different sources, were all actually the same substance. Crystallin had been synthesised by Unverdorben in 1826 when he carried out destructive distillation of a certain naturally occurring dye. Fourteen years later, in 1840, Fritzsche had treated the same dye with caustic potash (potassium hydroxide, KOH) and obtained oil of anil. Six years earlier, in 1834, Runge had obtained the beautiful blue coloured substance kyanol by treating an isolate of coal tar with chloride of lime (Calcium hypochlorite, Ca(ClO)2). Finally, in 1842, Zinin had obtained benzidam by reducing nitrobenzene. After Hofmann’s affirmation, this substance came to be known as aniline.

And the dye used by Unverdorben and Fritzsche?


Hofmann and Perkin were a good match. Both were young, highly talented, and had a tendency to think outside the box. Perkin’s father, himself a builder, wanted him to be an architect. Billy Perkin point-blank refused to join the family business and instead, in 1853 at the age of fifteen, joined the Royal College of Chemistry, under Hofmann. In two years he had impressed his boss enough to be made assistant. Given the desperate need to synthesize quinine, and based on his own hypothesis, Hofmann had the perfect project for his precocious assistant : synthesize quinine from aniline.

2D structure of aniline

Aniline is a rather simple organic molecule, and can be thought of as the organic equivalent of ammonia, with one hydrogen atom replaced by a benzene ring (C6H5NH2). Quinine, on the other hand, is rather more complicated (C20H24N2O2). It was Easter, Hofmann had gone home, leaving Perkin to muck about in his own ramshackle lab. Following Hofmann’s idea, Perkin decided to attack the problem by dissolving aniline in sulphuric acid and then oxidising it with potassium dichromate (K2Cr2O7). What he got instead was a black precipitate. Thinking he had failed, he tried washing it out with alcohol.

Scientific discoveries are often serendipitous. While detailed planned experiments do often bear fruit, a very large and recent example being the detection of the Higgs boson by the LHC and the detection of gravitational waves by LIGO, accidental discoveries tend to be…miraculous.

What Perkin (probably) did not know was that the dichromate he used was impure. In it was mixed isomers of toluidine (C6H5NH2CH3) [Note:Toluidine] which reacted with the aniline and the alcohol to form a beautiful purple compound. Perkin had an interest in painting and photography, and his expert eye soon told him that he had something amazing in his hand.

While extracting indigo dye was complicated and laborious, extracting purple dye was far more so. In Perkin’s time, purple one of the rarest and most expensive dyes in the world. Extraction and manufacture of Tyrian purple was a lengthy and expensive process, involving glandular secretions of murex sea-snails, a rare species of molluscs [Note:TyrianPurple]. Which is why it was deemed a royal colour, fit for personages such as Alexander and Justinian I

Byzantine Emperor Justinian I clad in Tyrian purple, 6th-century mosaic at Basilica of San Vitale

Perkin’s mauveine made Tyrian purple, and its naturally occurring cousins, obsolete. Not only did mauveine have a rich and vibrant purple colour, tests on silk and other fabrics showed that it was quite durable too. Perkin sent off a sample to the dye works in Perth, Scotland, and received very favourable replies. In August of that year, Perkin, still 18, filed for a patent for the dye mauveine. With capital from his reluctant father and on-field help from his brothers, Perkin slowly built up his business. The Industrial Revolution helped him, and so did the adoption of purple dresses by Empresses Victoria of England and Eugénie of France. It became both a fashion statement and a matter of prestige to own purple dresses, especially crinolines (hooped skirts). Perkin’s Mauve provided a cheap way to own purple. Thus, with a little help from history, hard work, and sometimes luck, William Henry Perkin built the first synthetic dyeing industry in the world.

Sir William Henry Perkin (1838 – 1907), English chemist

And in doing so, he saved the lives not only of humans labouring in dyeing factories, but also of the uncountable number of murex sea-snails that would no longer have to be sacrificed for Tyrian purple.


Note:BPerkin The Nerd Druid is not certain that Sir William Henry Perkin was actually ever referred to as Hey Billy Perkin/There’s snot in yer muffin. However, within the field of probabilities and plausibilities, one might not be, presumably, too far off the mark herein should one deign to, er, presume certain presumptuous presumptions about young Billy. I mean Sir William.

Note:Wordsworth In his autobiographical poem The Prelude, William Wordsworth speaks of the plight of the indigo dye workers in his hometown of Cockermouth thus

Doubtless, I should have then made common cause

With some who perished; haply perished too

A poor mistaken and bewildered offering

Unknown to those bare souls of miller blue

Note:Toluidine Toluidine (C6H5NH2CH3) is basically aniline plus a methyl (CH3) group. Depending upon the position of the methyl group with respect to the amine group, toluidine has three isomers : o-toluidine, m-toluidine, and p-toluidine. In the ortho-isomer, the amine and methyl groups sit next to each other (2-methylaniline); in the meta-isomer, they are one space apart (3-methylaniline); while in the para-isomer, they are two spaces apart (4-methylaniline). Perkin’s dichromate had the ortho and para varieties, the former being a dye itself. 

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Caption : 2D structures of the three isomers of toluidine

Note:TyrianPurple The following passage has been taken directly from Wikipedia :

The process of making the dye was long, difficult and expensive. Thousands of the tiny snails had to be found, their shells cracked, the snail removed. Mountains of empty shells have been found at the ancient sites of Sidon and Tyre. The snails were left to soak, then a tiny gland was removed and the juice extracted and put in a basin, which was placed in the sunlight. There a remarkable transformation took place. In the sunlight the juice turned white, then yellow-green, then green, then violet, then a red which turned darker and darker. The process had to be stopped at exactly the right time to obtain the desired color, which could range from a bright crimson to a dark purple, the color of dried blood. Then either wool, linen or silk would be dyed. The exact hue varied between crimson and violet, but it was always rich, bright and lasting.