Field of Science

Microbial Phylomon and friends

I'm currently running low on ideas for what bacteria/fungi/protists/viruses/archaea I should convert to phylomon next. If you have any suggestions, please leave them in the comments.

History of Scarlet Fever: Witches, The Occult and The Renaissance

In the last installment, we looked back to the time of Hippocrates, and his description of a streptococcal disease in 430 BCE. We continue with the story some two thousand years later.
It has been a turbulent era, with empires falling, fiefdoms rising and a decline of scientific thought in the western world. The era described by Petrarch as the "Dark Ages" was coming to an end, with sparks of the enlightenment appearing over europe. The fruits of Arabic golden age philosophers such as Avicenna, al-Razi were reaching various libraries and scholars.
It was the time of Heinrich Cornelius Agrippa, who was famous for his works on magic. It was these that often attracted ire from the religious orthodoxy that dominated Europe. He is an intriguing historical figure, but not the focus of this piece. the focus is on his student, Johann Weyer. Regrettably, Agrippa died before Weyer could finish his training with him. At a loss, Weyer ended up attending medical school in France. It was these experiences which moulded Weyer into an expert in both medicine, and magic.
It was these two skills which became useful to him when he encountered the "Malleus Maleficarum". For those of you not up to date on hysteria inducing books of the 15th century, let me explain. This book consisted of the "evidence" that witchcraft existed, the forms it took, and advice on how to catch them. Endorsed by the church, copies of this book spread throughout europe, and fuelled the hysteria that lead to Witch hunts.
Johann Weyer :Extra points if you can spot the optical illusion

Weyer however, debunked the Malleus Maleficarum  in his own book "De praestigiis daemonum".
 In it, he presented evidence that these women were afflicted with mental issues, and should handled by physicians, not law courts and angry mobs.
 Whilst he never doubted the existence of supernatural entities such as demons and angels, he was sceptical of the degree to which these beings interracted in human affairs. As he got older, he moved away from magic, and concentrated more on the study of medicine.
 In the winter of 1563,  Weyer recorded the outbreak in lower germany referred to as "The Great Plague" . In his account , he states that this disease had spread to various cities in Europe, such as Danzig, Vienna, Cologne and even London.
In the region of the lower rhine, A disease appeared that caused swelling of glands in the throat, which was associated with a characteristic rash. This pestilence proliferated throughout the winter, travelling up the rhine all the way to Basel. The plague claimed the lives of many children, and was a cause of childbed sickness in young mothers. Various authors have speculated that this disease could have been scarlet fever. However, as with the previous post in greece, the descriptions for this disease are relatively vague.
The problem with these descriptions are the same as the ones I described in my previous post on hippocrates and the ancient Greeks. For nearly two thousand years, there had been little or no advances in the description and the treatments for this disease. However, had Johann Weyer been aware of advances in medical science occurring in Italy, he may have provided a far more rigourous identification of the plague of which he had been a witness.

The Renaissance had reached Italy nearly a century before northern Europe. Italy was the trade hub of europe, importing goods from the east to sell on to the west. And with these goods came various artisans and scholars, who helped to translate many works from Islamic scholars, as well as lost works from Ancient Greece.
Works of Galen reached Italy, and were taught in various schools of medicine. However, due to prohibitive laws on human dissection in Galen's time, much of his works were based on what he gleaned from dissecting barbary apes. Such was his repute that many of his claims on anatomy went unexamined for many years.
One man, Andries Van Wesel would change this. He approached anatomy from a more practical standpoint.  He is known better by the latinized name he published under, Andreas Vesalius.
He was among the first people to perform human dissections. He pioneered a practical approach to teaching whilst he held a post at the  University of Padua. He would get students involved in dissections. He is probably best know for the detailed images of human anatomy that populate his medical works. It was this culture of detail that he impressed upon his students, one of whom was a man from Palermo named Giovanni Filippo Ingrassia. Ingrassia already possessed a wealth of experience in the art of animal dissection, and had travelled to further his studies into human anatomy.
 Vesalius's attention to anatomical detail is a lesson that Giovanni Ingrassius took to heart. After his studies, he returned to sicily, where he would work as a physician and lecturer, eventually contributing much to the literature. It was in 1553 whilst he was working as a physician that he published a book which contains a description of a disease he called “rossalia”. His detailed description of the etiology of this disorder indiciated beyond reasonable doubt that he was the first person to produce a stringent identification of the disease we now know as scarlet fever. Using his method of identification, it became possible to look at this as one disease, and distinguish it from others with similar symptoms, such as measles.
He eventually attained became  the "protomedicus" of Sicily, placing him in charge of public health for the region. When the "Great Plague" described by Weyer reached the shores of Sicily, they were lucky to have a man as experienced as Ingrassius in charge. He recognised the contagious nature of disease, and frequently used isolation as a means of bringing it under control.
However, there was still yet more to be revealed about Ingrassia's rossalia, which we shall return to in the next post.


"An historical account of the plague and other pestilential distempers which have appear'd in Europe ..." - 1722 Richard. Brookes

"An account of the sore throat, attended with ulcers: a disease which hath of late years appeared in this city, and in several parts of the nation" - 1748 John Fothergill

Journal articles:

Rolleston, J. (1928). THE HISTORY OF SCARLET FEVER BMJ, 2 (3542), 926-929 DOI: 10.1136/bmj.2.3542.926

Cappello F, Gerbino A, & Zummo G (2010). Giovanni Filippo Ingrassia: A five-hundred year-long lesson. Clinical anatomy (New York, N.Y.) PMID: 20803570

We are Doomed- London Riots Edition

I alluded to many causes of our destruction in my comic of doom. I missed out the collapse of civilization, which is a shame considering that it is particularly apt for my current situation. London is burning as I write this.
Police have been unable to deal with the chaos.
People will tell you that it's been set off by the death of father of two Mark Duggan, who may or may not have been in possession of a converted replica gun, and may or may not have shot at police officers who definitely shot their own radio in the process. But this is by no means the whole story, which involves a lost youth with nothing to lose, an underfunded and demoralised police service and an economy in turmoil.

I'm currently aggregating news stories at my friend's non-science blog Ihatethisf**kingcity, and will write a better post on the London Riots once I can tie up the notes into a story, and once the fires have died down.

But if there is one thing I want to say at this minute, it's not a riot, it's the collapse of civil society.
to reiterate:

I'll be updating here. Its going to be a long night, and thankfully it's quiet where I am at the moment, and they haven't looted my coffee yet.

9/8/11- new updates can be found here. Better preparation,bigger police presence, should have more time to write a post on the origins of this catastrophe.

A History of Scarlet Fever: Beware of Ancient Greeks Bearing Diagnoses

Regular readers may notice that I have a favourite bacterium, that I post on more than any other. This bacterium is known as Streptococcus pyogenes. My interest stems not only from the interesting ways in which it evades and bamboozles the immune system. It also comes from the weird diversity of infections that it causes. Not to mention that it once tried to kill me, and that I now study it for a living to get REVENGE.
I've decided to explore the history of the diseases caused by this bacteria, and how our understanding of them have changed over time. So let's start right to the beginning, in Ancient Greece.

The year is 430 B.C. and Athens was in the grip of war with its rival city state, Sparta. The war had reached its second year. Their leader, Pericles, had realised early on that facing Spartans on the battlefield would be suicidal. 
Instead, he goaded them into attacking the city of Attica. When the Spartans took control of the city, they found it empty of people. They had all been evacuated to Athens, and whilst the Spartans had wasted their time securing the empty city of Attica, Pericles was pillaging unprotected spartan territory. Pericles strategy was a success, but there was one factor he didn't account for in his strategy. And this factor may have changed the outcome of the war. 

An epidemic that had been proliferating in Ethiopia and Egypt had reached Greece. It probably started out as a few isolated cases in the countryside. However, when Pericles evacuated the inhabitants of cities into Athens, this changed. The city rapidly became overcrowded, and soon it was the perfect incubator for this plague.
"...people in good health were all of a sudden attacked by violent heats in the head, and redness and inflammation in the eyes, the inward parts, such as the throat or tongue, becoming bloody and emitting an unnatural and fetid breath.
"These symptoms were followed by sneezing and hoarseness, after which the pain soon reached the chest, and produced a hard cough. When it fixed in the stomach, it upset it; and discharges of bile of every kind...
Those who were ill were often abandoned, as carers would themselves be at high risk from contagion.  Pericles himself was brought low by this disease. It had killed both of his sons, his wife, until eventually the plague killed him.
As the numbers of the dead increased, hundreds were piled into mass graves, whilst more were burned on funeral pyres.
The Spartan army, seeing the smoke from these pyres of Athens, pulled back. Whilst  unassailable against any human foe, they knew better than to attack an infested city.

It is because of the writings of Thucydides that we know so much about this plague. He was one of the first writers to describe events based on facts alone, without invoking supernatural entities, or warping events to make a moral point. His detailed descriptions of the plague have lead many to speculate on the disease that caused it.
In the original first draft of this post, I was going to suggest that it may have been caused by a strain of scarlet fever, as others have in the past. Whilst this may have been the case, it is not the only suspect. Others have concluded that it was caused by some variant of the Ebola virus, whilst many believe it to have been an epidemic typhus.
The "plague of Athens" is the "Jack the ripper" case for epidemiology. This plague may have caused Athens to lose the Peloponnesian war, and the outcome of this war itself is blamed for the decline of Greece as a major power in the ancient world. This plague occupies an important place in history. Yet we can only speculate on the disease that caused it. The diversity of the diseases blamed for the plague indicates the true reason for this mystery. Thucydides descriptions of this plague are woefully insufficient to diagnose what caused it. However, had one of his contemporaries been present, it might have.

 There had been schools of medicine in Greece for around two hundred years before Hippocrates was born. They borrowed from more ancient medical traditions in Egypt and Mesopotamia. These traditions were heavily based on superstition, with prayer to a divine entity forming a keystone of their treatment paradigm.
It was Hippocrates who changed this. Like Thucydides, he did not see the hands of the gods in every day events. He described diseases as natural phenomena, divorced from the supernatural. He and his students had a disciplined approach to medicine, which involved taking detailed observations on patients and their diseases.
During his life, and for some time afterwards he and his followers created the Hippocratic corpus, a collection of works and case studies that laid the foundation for modern medicine.
At sometime between 410-400 BC, the first in a series of works known simply as "Epidemics" were written. These consisted mostly of case studies, which contemporary physicians could use as reference to determine the prognosis for their patients.
Within these records, there is a description of an outbreak of a disease that caused a severe skin rash, along with a sore throat and fever. But these symptoms in themselves do not outright indicate that this was indeed scarlet fever. During this outbreaks, some of these patients experienced complications which are somewhat unique to Scarlet fever.
"in the most of them abscessed ended in suppurations, and there were great fallings off (sloughing) of the flesh, tendons, and bones;
The symptoms described here are very similar to necrotizing fasciitis
However, he descriptions written down in "epidemics" became the main reference for later generations of physicians when they described incidences of scarlet fever as they arose.
This legacy would persist for nearly two thousand years after. That is where I'll pick up the story in the next post

Hippocrates Epidemics Part 2 -


Rolleston, J. (1928). THE HISTORY OF SCARLET FEVER BMJ, 2 (3542), 926-929 DOI: 10.1136/bmj.2.3542.926

Descamps V, Aitken J, &; Lee MG (1994). Hippocrates on necrotising fasciitis. Lancet, 344 (8921) PMID: 7914656

Microbial Phylomon

Picking up on a post on Lab Rat, I decided to quickly doodle some bacterial phylomon of my own for fun. Thus, I present GFAJ-1Streptococcus pyogenes, Bacillus anthracis,