Microbial Phylomon: It came from beneath the Petri Dish !

A special halloween edition of microbial phylomon.

First up, the Brain Eating Bug

The frankenstein bug !

And finally the beast with five genomes !

A special thanks goes to BruceDSTaylor on reddit for their suggetsions.
I haven't been posting much recently, although I am still working on a couple of posts and phylomon, my time has been taken up with writing papers and getting my stuff sorted out for PhD. So the posting is going to suffer for a fair bit.

Have a spooky halloween ! Whatever you are -ah-ah-ah

History of Scarlet Fever : Werewolves, Sennert and Scarlet Fever

 I have previously talked about Johann Weyer, a prominent medic with an interest in witchcraft and magic. In the early renaissance, superstition still ruled, and there were a number of scholars  at the time who maintained an interest in the occult. Weyer was one of these. I've already talked about his work with respect to witchcraft, but I did not however talk about his work on Lycanthropy. That is, Werewolves.
The werewolf legend specifically refers to people who can turn into wolves on the full moon, or simply at will. These people were the undead, cursed individuals who roamed the earth to do the devil's work.
The Lycanthropic* legends can be found in various cultures and iterations, but it boils down to one thing: an individual who can, at will, turn into an animal.

During the witch hysteria of the middle ages, people in general were on high alert for supernatural activity of any sort. As well as women bieng convicted as witches, there were men who were tried as werewolves.
Weyer met with a number of them, including a man in Padua who could not be convinced that he wasn't a werewolf (Despite the threat of being burned alive). another man, a spaniard, held the belief that he could turn into a bear. Weyer's conclusion was that these people, like the witches he had previously encountered, were deluded, and should be put into asylums, as opposed to being executed.
 But Weyer didn't have the last word on this, and there were many who speculated on the source of this peculiar malady.
Ten years after Weyer made his observations on a scarlet fever outbreak, Daniel Sennert was born in the city of Breslau, at that time controlled by the Hapsburg's.
Sennert wrote extensively on topics ranging from medicine to science. It has been evinced by some that he came up with "corpuscular theory", which is the theory that all matter can be divided into small particles, which in turn could be subdivided into smaller ones and allow materials to change form. But at the same time, he also seemed to believe in the competing theory, atomism, in which the world is made of indivisible spheres of varying sizes that cannot be broken down.
Sennert, like Weyer , grew up in a superstitious atmosphere. Despite Weyer's many travails, werewolf and witch hysteria still permeated the public consciousness.
In one of Sennert's books , he writes of a mythical creature known as the Baslisk.
A basilisk is a strange creature that is born from athe egg of a rooster, or a hens egg hatched under a toad, depending on who you ask. It also looks different depending on who you decide is your source. However, what is shared in all of it's legends is how it kills ; a lethal gaze.
Sennert writes of an incident in Warsaw in 1587, where a basilisk was believed to be lurking in a cellar.  Two children and their nurse went into this cellar, and did not leave alive. The local inhabitants came up with an interesting solution to this situation.
They took a condemned criminal, and cut him a deal. He could go down into the cellar and face the basilisk, and should he survive, his sentence would be commuted.
He accepted, and was kitted out in protective coveralls, and a suit of mirrors, to ensure the basilisk's fatal gaze would be focused on it's own reflection, thus causing it to kill itself. The man descended into the cellar, and when he came out, he announced that the basilisk had been killed. He described a strange creature that had the "figure of a fowl, eyes and extra feet like a toad and highly coloured with spots".

Behold, the most terrifying Basilisk !

This account shows the fundamental differences between Sennert and Weyer, that become all the more startling when you look more closely. Sennert attended the University of Hittenberg  Wittenberg where he studied chemistry and medicine. But as he became more well regarded, he showed more credulity to the practice of magic. In contrast, Weyer was trained by a magician in the occult in his early years, and developed into a more sceptical physician.
Whilst Weyer's assessment of werewolves and witches was that they were mentally ill, Sennert took a different approach. Whilst he acknowledged in some cases that "natural Lycanthropy" can occur, which matches Weyer, he also believed in "Diabolical Lycanthropy"  which was caused by the Devil.
This was not to say that Sennert did not make any useful contributions to the science.
As a practical chemist, he performed many experiments which helped him formulate his opinions on corpuscularianism.
 Sennert also read a lot and widely about science, philosophy and alchemy, a fact that is reflected in his many writings. it is because of this that he was familiar with the work of Giovanni Fillippo Ingrassia. So when there was an disease outbreak in Wittenberg, he recognised the characteristic "Rubiolae" described by the eminent Sicilian.
  Sennert not only diagnosed these patients, but took it upon himself to study them as the disease developed.
He noticed that when scarlet fever subsides, the extensive skin rashes damage the skin and cause it to flake off. This characteristic "desquamation" had never been recorded before. But this was not all he found.
Recovering patients would also experience swelling in their joints and arthritis. He believed that there was a connection between these symptoms and the preceding scarlet fever. That these were "sequels" to scarlet fever.
This finding would still be controversial for nearly two hundred years afterwards. Part fo the reason for this is that these sequels did not necessarily occur immediately after the disease.
It is because of this that Sennert is not remembered for his belief in basilisks, or for his ideas on werewolves. He is remembered for what he got right about scarlet fever; not what he got wrong about the supernatural.

*despite the greek language roots, the word "Lycanthropy" can be used generally to describe any form of animal/man hybrid.

References:
 Books (accessible via Google Books)
Chapter 7 , History of Magic and Experimental Science Part 12 by Lynn Thorndike, reprint 2003

Anatomy of Melancholy Part 1 by Robert Burton 2002 reprint

Journals

Michael, E. (1997). Daniel Sennert On Matter and Form: At the Juncture of the Old and the New1 Early Science and Medicine, 2 (3), 272-299 DOI: 10.1163/157338297X00159

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

In which I attempt to review "The Psychopath Test"

When I first saw him, he was in the queue to see The Infinite Monkey Cage (Prof Brian Cox's Radio show)  at the Cheltenham science festival. I noticed him immediately, in the queue, carrying a laptop under his arm.
In the cluttered teenage bedroom that is my brain, I tried to work out where I recognised him from.  He wasn't my year 7 biology teacher, although they look strangely similar. Then it clicked. After 10 whole seconds of staring at him, and him smiling back.
 But at this point it was irrelevant. If I stared for a second longer, I'm pretty sure I would look like a gormless psychopath. I didn't want to offend one of my favourite scientists, so I peeled off quickly, trying not to be more of an embarrassment than I already was.
I spent all of 5 minutes wondering what I would have said to him, and cursing myself for not being quick or bold enough to start a conversation. But at ChelSci there really isn't much time to dwell on things like that, and soon I was off to the next talk. I probably wouldn't get another chance to meet him, so it was best not to dwell.
However, after one of the lectures I decided to get some reading material for the 3 hour journey back to London from Cheltenham. Luckily, they had opened up a Waterstones at the science festival, so I could go in and get a copy of a book that I'd heard a lot of good publicity about.
And right by the entrance, I saw the man I had accidentally glared at earlier.

 PZ myers was in waterstones, peering at a shelf of books. For those of you who don't know, PZ is probably the best blogger still remaining at scienceblogs.com and an outspoken proponent for atheism.
And now was my chance to have a conversation with him, a golden opportunity, although probably not as good as when he was bored waiting in a queue. But still, I'll take what I could. I wouldn't squander this opportunity like I had with Richard Dawkins.
When I was a lowly undergraduate in my first year of study, there was an interesting event happening at the museum adjacent to my campus. There was a discussion over the full extent of evolution in our daily lives, which I thought would be fascinating. I tried to get my friends to go, but they didn't really go for it.
At the end of the discussion, I bumped into Richard Dawkins whilst he was waiting for his cab.  He had been one of the speakers, and had talked a fair bit about stuff from his book, the extended phenotype. However, at this point in time, I had little or no idea who Sir Richard Dawkins was. All I knew was that one of his books was listed on the syllabus (the selfish gene) and that he was an inspiring speaker. I knew he was an important person, but i didn't quite grasp why. It was because of this that I had a conversation with Sir Richard Dawkins about.... the english weather.
when I got back to halls, and mentioned this, I was met with uproar and hand wringing.  firstly, how come I didn't tell them that Richard Dawkins was part of this talk, and secondly how I wasted an opportunity to talk to him.
But this time would be oh so different. and it was, I knew exactly who PZ myers was, and I'm sure I would have something interesting to talk with him about. Inside my brain, a little homunculus was putting together all of the folders marked "pharyngula" together with an aim to put everything together for a conversation.
"Hi are you PZ myers? "
"yes"
"I read your blog"
"oh, and who are you?" he said raising an inquisitive eyebrow. The tiny homunculus in my brain frantically attempts to find intelligent responses, but defaulted to the truth
"[--insert name here--]" there was a silence "I am a PhD student studying infection" i didn't know what that information contributed, except another short pause, which I dutifully filled with more words. The homunculus pressed the stream of consciousness emergency button, which is always a tricky manoeuvre.
"I'm not sure the right way to introduce myself, or whether i should define myself by my qualifications"
"oh, don't worry about that"
Great, now the initial awkwardness is out the way , conversation can start. The homunculus proudly opens the "pharyngula" folder of conversation topics. Funny, I thought there would be more stuff in here. Ah, PZ is an american. My prejudices tell me that americans don't often leave america. let's go with that.
"oh, I didn't expect to see you in england"
"Oh well, I've been doing talks in glasgow and other places. I'm just taking some time off and enjoying the sites"
My internal homunculus realises that almost all of the pharyngula facts strewn over then floor of the office of my brain. "Stall for time whilst I get these together," it would have told me if it existed.
"Oh, did you catch  the Infinite monkey Cage" I said, wryly accessing my short term memory.
"Oh yes" PZ replied "a little too much physics for my liking, not enough biology"
"Well" I improvised " Biology is the language of love "
Jesus, where did I get that corny line from ? Was I coming on to him?  I definitely didn't want to come on to him. I didn't want to frighten the old gent.
"oh" PZ responded " I never thought about it like that"
"oh, and it's responsible for hate and other emotions "
Well on the bright side he definitely knew I wasn't coming on to him. On the downside I was failing to conceal my lunacy.
"Oh, well I'd better get back"
"Oh yes, of course" Thank god. Who knows what bullshit I'd've said next.
"Nice meeting you" he said
"you too, and thank you for blogging"
To which he smiled and gave a polite reply, before taking his place in front of the books. Perhaps I should have opened with that, but never mind, the moment had passed.
I walked off glad the pressure of the conversation was over. I was about to walk out, but then I remembered that I still needed to get that book.  It was the psychopath test by Jon Ronson. He was speaking later in the conference, and I had read a bit of the publicity spiel for it, and it seemed like it would be a good read. I turned back and saw that it was on the very same shelf PZ was looking at.  Having already said my goodbyes , I didn't want to invading his personal space once again, or worse get into another painful conversation.
 I could have waited until he left. But wouldn't that be even more suspicious, wringing my hands and glaring just on the periphery of his vision ? I'd probably get arrested.
 Instead I decided to go past and grab the book as quickly as I could hopefully without him noticing. In my mind I was a book grabbing ninja, but in reality I was the twat who barged past PZ myers to get a book. My escape may not have been graceful, or cunning but it was hasty.

And this was how I ended up with a copy of The Psychopath Test by Jon Ronson. In retrospect, my odd behaviour around PZ myers left me in the perfect state of mind to read this book, for it was about how craziness, ranging form the mild to the severe, affects each of us and how it affects society on a larger scale.
It was one of those books that I simply could not put down.  It begins with a simple story of the author investigating the erratic behaviour of one individual, and how that behaviour affected a number of different people in interesting ways. From there, he diligently investigates people with personality disorders, and how the treatment and diagnoses of these individuals have affected us.
Through his research, he met an individual who faked madness to avoid prison, and ended up indefinitely detained in broadmoor. Funnily enough, most of his doctors knew he faked psychosis, but determined that this was a symptom of psychopathy. And through this story we enter the strange kafkaesque world of the madness industry.
It was at this point in reading the book on the way from London to cheltenham that I finally give in. You see, a large part of the time I spent reading this book on the train, a loud mob of cricket fans have sat next to me in the carriage. In particular, a very inebriated individual whom I would come to know as "Nobby" sat down next to me, with a half pint still in his hand. From his red features and slurred speech, I presumed that this was not his first one. The train guard had noticed that Nobby was carrying a beer on public transport, but wisely didn't harass him about it when he wasn't making a fuss. In fact, none of these events were enough to tear me away from the book. The fascinating story of Emmanuel "toto" constant, a Haitian mass murderer inexplicably living with his mother in a New York suburb verged on the unbelievable.
However, for around half an hour, "Nobby" had been loudly announcing to the train carriage that he needed to go take a piss. He went to the train loos, and found that all of them were locked. Still I read the book.
Nobby then started complaining that he'd piss himself, and he needed a bottle. It was when one of his friends suggested that he should take this opportunity to"top up his pint" that I cracked up. And that was how I got into a conversation with "Nobby".
admittedly, all I could really get out of him was how incredibly desperate he was for the loo, and how he couldn't believe that not only both the loos were occupied, but that they were occupied for so long. He was right not to, so it transpired. The train guard eventually noted the mans distress, and unlocked the lavatories. The were empty all of this time.
Apparently, the policy of british rail is to lock all lavatories on some local journeys to stop vandals from destroying them. And that was why Nobby nearly pissed himself.  And it was why, a notably more relieved nobby, was still furious with the train guard.  The train guard to his credit took the verbal abuse with good humour, and did his best to not inflame the situation.
Eventually nobby cools down a bit, and notices that I'm reading a book. I say that it's about madness. He looks straight at where I presume he thought my face was,  winked blearily and said "well, everyones a bit mad. I'm mad. I'm definitely mad, but I guess you've noticed that. Everyone's a bit mad"
Which is funnily enough, one of the conclusions you can take from the psychopath test. In the book, the author, Jon Ronson learns the art of diagnosing psychopaths. And he meets a number of characters, from a ruthless corporate executive, to an overly rude concierge, each of whom are described on the psychopathic spectrum. He demonstrates the old adage that a hammer wielder sees a world made of nails. Once armed with the "psychopath test" he sees madness everywhere. And so will you.

The point is that when you have these tests, one tends to extrapolate from the most extreme bits of behaviour. Nobby was not a lunatic, despite behaving like one. In this extreme situation, where he was both too drunk to stand, and suffering from a strained bladder, and surrounded by equally drunk (if more restrained) friends, he behaved like an impulsive mad man. But I am only observing him at his most extreme edge. I have no idea what he's like the rest of the time, so I can't make a solid diagnosis based on this.

Having finished this book , I went into a joint session on the human mind, with Richard Wiseman and Jon Ronson. Anyway, it was nearing the end of the question and answer session that a distressed lady came up to the microphone. She had not read the book, but had read in various reviews that it took a light hearted and comical view of mental disorders. Having suffered from mental disorders herself, she was not happy with what she saw as the trivialisation of these diseases.
It was for this reason I hung out at waterstones afterwards, so that if she turned up to attack him, I'd at least get a good view.
Whilst I was waiting for this event to occur (It didn't) I thought a bit more about her statement. Evidently, it was never the authors intention to trivialise mental disease. He references cases of people who genuinely suffered terribly from psychiatric disorders, and how doctors struggled to find ways to "cure" them. But this book isn't just about psychopaths, and those who we regard as mad. It is how we respond to madness in the modern era, and how this response affects us and our society as a whole.

What I'm saying is that I highly recommend that people read this book. In fact I would recommend you read it as I did, fumbling through a conversation with a personal idol, and then whilst absently consoling a drunken yob whose only real desire was a working lavatory.

Even More Microbial Phylomon !

Even more Microbial Phylomon as requested by you the readers!

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.

References:

Books:
"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

More Microbial phylomon

More microbial phylomon !