Pretty simple, huh?

http://tinyurl.com/6a2baeh

The Telegraph today may be showing pretty pictures of bacteria but they display OLD-STYLE  microbiology when we know at a molecular level now that these matters are far more complex than pinpointing the great big "bruisers" of microbes like E coli and helicobacter pylori.


This study "provokes reexamination of the traditional view of killing strategies against bacteria" and contains some far more challenging actual shots of bacteria. And this paper points out the seriousness of microbiologists ignoring the need to research cell-wall-deficient bacteria.

The ridiculousness of showing the public computerised pictures of the fearsome "bogeyman" pathogens that can be easily named is particularly evidenced by recent papers on nanobacteria and others that have long shown a link between these incredibly tiny  microbes and calcifying human conditions, like artery or kidney disease.

All this research (which does not receive media coverage) indicates it is this increased depth of knowledge we need to seek if we are ever going to get to grips with chronic illness.

Our fossilized beauty

The recent unearthing of my childhood fossils and stones collection has resonated with my belief in the gradual structuring and reinvention of our human body over time.

I do not believe that we consist only of our isolated selves, our personal lifelong genes. We are not self-contained, pure and untainted within our skins; and current developments in microbiology and genetics give me encouragement in believing this.

What if each of us, when we were tapped with a little fossil hammer, broke open to reveal complex beauty? The beauty created by additional beings within us that have gifted their pattern to our make-up.

Maybe we have many quiet contributors within us that will not be revealed for a very long time, despite how clever we think we are in scientific terms. Until the relevant patch of earth cracks and crumbles, the true face of the stone will not be exposed to examination and awe.

What I am suggesting is that we are the sum of many people - past and present - and also many other things, so that our physiology and health may get a little improved, or a little worsened over a period of our lives; or maybe both of these possible actions, in one lifelong balancing act.

The possibility that some creature could slip a few genes in to another unrelated creature simply by living with them was once thought to be extremely rare. Recent studies on intracellular bacteria and their hosts seriously question this view

When I look at the magnificent tracery of ancient fossils within my stone collection I'm excited about what we can learn in the near future about the greater complexity of our human body - if we are prepared to think inside and outside ourselves.

Naming names

What's in a name? Well, if someone called you by the wrong name you wouldn't hesitate to correct them.
And humans do so love the naming of things. Whole books are written about those individuals who have come up with naming systems for different scientific areas such as Carolus Linnaeus for botany. 


Much effort is spent these days in testing and identifying the name of the bacteria that may have caused an infection. Once the doctor knows what it is then s/he feels able to prescribe the correct antibiotic. Or that's the theory.


But a new paper has shown how difficult it can be to put a name on something as shape-shifting as microbes. 
The genes from one microbe may be quite useful to another nearby microbe - especially if they convey antibiotic resistance - so they parcel it out in a generous way apparently. This is called horizontal gene transfer.


In Nature News magazine this week they reported on the important discovery of the mechanism by which microbes do this, and also revealed how amazingly quick it can happen. Overnight 47 per cent of marine bacteria had taken the genetic make-up of an introduced modified microbe in to their own genetic make-up. Now that makes naming microbes a bit tricky.


Evolutionary biologist Jeffrey Townsend at Yale University in New Haven, Connecticut, told the magazine: "In order to understand antibiotic resistance, pathogenicity, or the beneficial things that bacteria do for us, we need to understand how they evolve through horizontal gene transfer — knowing about this process can help us live in a world full of microbes."

And most of us want to carry on living in this microbe-crammed world, don't we? I think we need to pay less attention to naming things, and start applying our knowledge to understanding important processes in and around us.

Working in harmony

I have so missed singing in a choir! I finally got to a community choir rehearsal this week and loved it, despite my tiredness afterwards.
Voices training up and down the scales with fun exercises, learning new musical parts and words, having a laugh with friends and people I hadn't met before.
It involved a lot of concentration for me but, oh, when our choir leader's hand counted us in and our voices wove together - the beauty of that connected sound thrilled me.


So much in our society today separates.
And there is a lot in scientific practice that separates everyone out to their specialisms. Often the system, or social norms, keep us firmly apart from others with a scientific perspective that comes from a slightly different discipline.
But I have found that some barriers have been brought down gradually over the last few years, for those who seek out connections. 


Now hear some encouraging words for patients from distinguished professor emeritus of microbiology and immunology, University of Michegan Medical School Fred Neidhardt:"Not uncommonly, investigations of infectious disease proceeded largely in medical school departments of internal medicine or pediatrics, while explorations of the intricacies of microbial growth processes were pursued at the same schools in basic science microbiology departments. 
"That situation has been changing in the past couple of decades, and finally the frontiers of bacterial physiology and of virulence (molecular pathogenesis) have virtually fused."


In a post-antibiotic age where microbes are the focus of close attention in acute and chronic medical processes, that is a good thing to know - the scientists, whose combined knowledge may understand the problem better together, are now talking to each other!
Prof Neidhardt says the science has undergone a "seachange" because their differently wise voices are now "intertwined".


To all of my friends and acquaintances with more know-how than I: please, share the knowledge you have across professional boundaries, listen to people you haven't listened to before, join your wisdom to others' wisdom. The rising chorus will produce something connected and more wonderful that will benefit us all.

Coalition thinking

Wow, what a week it's been for the English! Our first exciting experience of creating a real political coalition.
For it to continue, and work effectively, I believe we will have to change ourthinking. Maybe in the same way that microbiology experts have had to change their thinking recently about the human body and why it gets ill.
For so long we have talked of a sealed and protected physical body that has to wage war against any pathogens that threaten to infect us from the outside.
At the same time people have started to understand now that there are a lot of friendly bacteria on the inside (mainly because of that advert for a certain mini-drink).

So here we have a model depicting two tribes of bacteria, which suits our traditional way of thinking:there are these friendly, helpful bacteria that understand the needs of the human body; and there are those BAD bacteria (boo!) that we must never allow to have control over our body.
Suddenly we have a new third set of bacteria being mentioned and people are starting to say "D'you know, I never realised that they could look like that, or how they work exactly?" A bit like Nick Clegg.

Some microbiologists have named these bacteria existing inside our bodies pathobionts - a combination of pathogen and symbiont. A symbiont is a helpful organism which works in perfect synergy with its host.
Other experts are describing the human body now as a "superorganism" and conclude that the newly discovered microbes provide "metabolic functions far beyond the scope of our own physiological capabilities".
So how can we be sure if these pathobionts are going to work well together for our good, or if they might harm us instead?

We simply can't be sure.
That's right, we just have to try to get along with them.
We have to provide the right structure to work together in our body (a healthy immune system, well exercised muscles).
We have to limit the jobs that they do in our body to the ones we want them quietly to get on with (by not overfeeding them with any processed foods).
And we have to promise that we won't suddenly attack their tribal group (antibiotics are a dangerous weapon).

We are going to have to learn to live and work together with our pathobionts, otherwise we will see an even greater increase in chronic illness than we have already.
If you think my analogy is a bit far fetched then have a look at this scientific article (which focuses particularly on fungal infections like candida). University of North Carolina microbiologist William E. Goldman says that the infections are "not very good at causing disease in normal hosts with normal immune systems".
"But a growing population of people have not-so normal immune systems. Fungal infections are so deadly in part because most patients who become seriously ill are already weakened by AIDS, cancer, transplants or medications that handicap the body’s ability to mount a strong defense.
"More and more of these patients have taken high doses of anti biotics to prevent other infections, fundamentally changing the body’s ecology and allowing unnatural fungal growths to take over. More patients are also undergoing medical procedures that breach normal immune barriers with catheters and other devices."
He mentions catheters because we all have three parts to our immune system: the largest organ in our body, our skin; then our innate immune system which provides 24/7 security guards; and our adaptive system which attacks when danger is identified.
In these interesting times please give the microbial coalition a chance - a strong and stable agreement is the best option for your body's long term health.

Cancer and bacteria

Have you noticed recently how there is increasing talk of vaccines against cancer?
As lay people, this might seem rather confusing. We know that the medical establishment have urged us for a long time to have all our immunisations for infectious diseases.
We are also made aware that cancer organisations have worked for decades, putting millions of pounds in to cancer research which is increasingly complex and often focused on inherited genetic causes.
Cancer Research UK makes its opinion crystal clear on its website: 'Cancer is not in any sense an infectious disease.'
So how come the major research breakthroughs (setting to one side more effective drugs to slow down, but not cure, cancers) have been in cancers like cervical or liver cancer, where the cause is shown to be a specific virus.
Cancer Research UK, while relaying some helpful virus-specific advice on its website, still plays this down incredibly by saying: 'Cancer...represents a very rare accident of long-term infection with such a virus.'
But now lets hear from Paul Ewald, evolutionary biologist and the first recipient of the George R. Burch Fellowship in Theoretic Medicine and Affiliated Sciences:'Back in 1975, mainstream medicine agreed that about 0.1% of human cancer cases were caused by pathogens. When it came to the rest of cases, their view was that they were probably caused by a combination of inherited predispositions and mutagens.
'Then in 1985, the percentage of cancer cases they tied to pathogens was 3%, and they continued to make the same argument about the remaining cases. In 1995 the percent of pathogen-induced cancer cases was accepted to be around 10%.
'Now, we’re at 20%. Still, mainstream medicine contends that the other 80% of cases do not have an infectious cause, but the question is – do you believe them anymore?'
Another very recent and conclusive addition to this crowd of infectious connections to cancer came in a study published in May by the Institute of Genetics and Molecular Medicine at the University of Edinburgh (Attaching and Effacing Escherichia Coli downregulate DNA Mismatch Repair Protein In Vitro and are associated with colorectal adenocarcinomas in humans: Oliver D.K. Maddocks et al).
In a brilliant paper, worthy of a Crystal Mark from the Plain English Campaign, it persuasively 'demonstrates for the first time' the link between cancer of the colon and bacteria able to attach themselves firmly to cells inside the colon. Up to 100 were found hiding in a single cell.
Not only that, but the research scientists also say their study has uncovered the mechanism the bacteria uses to shut off the colon cells' ability to protect themselves against dangerous genetic mutation. This may be how the bacteria possibly causes colon cancer, but proof will only come from further study.
Interestingly, they note a 'striking similarity' with the bacteria helicobacter pylori, which also interferes with the mechanisms of gastric cells and causes stomach cancer. For a long time H.pylori as the known cause of stomach ulcers was ignored by the medical establishment too, while doctors still hector patients about helping themselves by avoiding stress (for pity's sake!).
With more and more research like University of Edinburgh's study coming to light - but repeatedly ignored by frontline medical staff - how long do we have to wait in pain and ill health before our doctors take a closer look at the infections we have each collected in our bodies? Until it's too late?

Life too complicated?

I always appreciate the news according to The World Tonight, especially on Robin Lustig's watch. It is vital that we take in a broad sweep of the issues which are important to our everyday lives.
And I think The World Tonight is often the best at this - by miles, in comparison with other BBC news output for the UK. Lustig has recently posted on his blog his theories about why the current swine flu is a 'flu scare'. Of course, most of his concerns about scaring people lie with how it is presented by health experts and the media.
But he makes this point: 'We live in a complex, confusing, technologically-challenging world.... We lie awake at night and worry: do I know enough, understand enough, to make the right decisions for myself and my family?...But the answers are usually as confused as the questions.'
Lustig may have noted that people are generally less willing these days to accept what they are told by officialdom, but something is else is also going on.
Because the modern world - particularly medical science - has advanced to such a detailed state, we as humans have an overwhelming urge for someone to tell us 'it's OK - we know what's happening'. And we invariably turn to an expert in the particular area of concern, whether it be a cancer doctor or an infectious disease specialist, for that essential reassurance.
So what would be the result if a virology expert turned round and admitted about the current H1N1 flu strain:'Actually this is so globally complex and new that we don't have any idea how this will develop or how to effectively protect ourselves.'
Panic!!
And, though we do have a few pointers for how the pandemic may move and change, it seems true to say the experts have little idea where this may all be heading, or why it is happening now.
But it is 'only flu' as Lustig and others protest. 'Just wash your hands!'
Again that heartcry for simplicity and reassurance erupts.
The official advice that people with 'underlying health conditions' need to be careful about coming in to contact with the virus is a simplistic message masking a whole new world of unknown factors.
Evidence is emerging from international biomedical expertise of even greater complexities in our bodies than we have ever imagined, involving a community of many more genomes than our human genome!
The Human Microbiome Project states that 'within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. These communities, however, remain largely unstudied, leaving almost entirely unknown their influence upon human development, physiology, immunity, and nutrition' (my emphasis).
Please - take a deep breath and don't panic.
Yes, we still have some way to go to understanding what it is happening at a bacterial and virological level.
But, if we as patients - as well as that lumbering medical establishment, so slow to adjust - take a step back from the detail of our bodies then we may start to observe a few patterns in the complex mesh of human metabolic processes.
Too often we rush to doctors who prescribe the necessary treatment for the current complaint - stop that pain, cut that part of the body out, try this prophylactic treatment.
But how come several different symptoms, noted in different parts of the body by different specialists,are happening in the same body?
Should I be considered so dilettanteish for mentioning that, for example: an infected wound requiring amputation is attached to a diabetic body with increasing vision defects; or gastroenteritis suddenly occurs in a person with a heart condition given antibiotics for pneumonia; or a teenager with early onset arthritis in their joints also suffers with chronic fatigue and acne?
Surely if we push and pull our bodies around in a blinkered manner, as specialist doctors tend to, the microbial communities within will break out in to a fist fight too - and may enlist some viral thugs to join forces.

Which bacteria = which illness?

In bed in the dark of night but not asleep.

This can be a curse for those with chronic low level illness or constant pain. My personal suggestion to help relieve this is listening to the radio (using an earpiece if you don't sleep alone!)

To my delight when I was tuning in overnight two weeks ago I got to hear the world-renowned geneticist Jane Peterson on the incredible Human Microbiome Project which will investigate the links between bacteria and illness.

The format of the BBC World Service programme The Forum was perfect for the weaving discussion about the trillions of microorganisms that live on or in our bodies.

The project will link microbiologists worldwide as they plan to genetically analyse and name every new microbe they find!

All this is possible because of new techniques for identifying hard-to-detect bacteria such as mycoplasma. Previous in-vitro techniques were far too outdated to detect such intelligent microbes which naturally thrive in-vivo, that is, in a living being.

Intelligent? I hear you scoffing at that description of an organism as small as a fungal spore. Of course, we all believe the tag-line, don't we? - Kills 99% of all known germs! Gotcha microbe!

But the Human Microbiome Project is about identifying bacteria that we have never known! And they are intelligent critters.

One of the points Dr Peterson made was that we have only just begun to understand how bacteria in human hosts live in "microbial communities". Medical science is "a little bit behind" she admitted, in comparison to environmental science which already understands the interconnectiveness of microbes.

For example, donors of swab samples to studies within the project will be given clear instructions on which soap to use on their skin. Absolutely not any of those anti-microbial products! Why? Because some bacteria adore clean skin. And some microbes are more persistent than others. If you kill one species then a stronger one will take their place.

Which makes me wonder...why is it that when I have taken a short course of antibiotics, say for a chest infection, then my digestive tract reacts very badly, or I get other pains?

The NHS - even if it is "a little bit behind" - is surely right to shift towards a policy of specifically targeted antibiotic use. Hopefully we will soon know the reason why in much more detail.

The Human Microbiome Project has just announced $42 million funding for studies in to microbes involved in ulcerative colitis, Crohn's Disease, psoriasis, bacterial vaginosis, obesity, sexually transmitted diseases, esophageal cancer, paediatric irritable bowel syndrome and more. Quite a lot of interesting investigations to be going on with, I think.

A modern parable for the chronically ill

A security guard is sitting at his desk, a couple of token CCTV screens in front of him. In this very quiet building the security desk is tucked to one side, away from the gaze of people passing by.
Not much happens so it is unsurprising that occasionally the bored security guard puts his feet up and nods off.
On one of these occasions some brazen robbers take advantage of his nap and creep past the desk. They invade the inner office and tie up the staff.
They steal everything they can get their hands on and get access to the valuables in the safe - but the security guard is none the wiser.

Once the robbers have stolen everything and decided to set up their own illegal business there, they are a bit hungry. They call up a pizza firm and a bakery and impersonate the office manager to order some take-aways.
The pizzas and doughnuts arrive, but the security guard doesn't think this is suspicious and lets the delivery men deliver to the inner office.
The robbers are enjoying their new crime base and the free facilities but eventually get fed up with having to fool the security guard outside in the lobby. So they devise a way of sealing up the security guard's mouth.
Once they have attacked him, he is forced to remain at his desk as if he is on guard, but all he can do is shriek and groan through his sealed mouth. Now the security guard is aware of what’s happening but unable to tell anyone.

He is a conscientious guy so he decides to risk contacting the main security centre to call for help. But at the other end of the phone line the operator is alarmed and confused to receive several calls and hear nothing but a terrible moaning sound.
The security centre operators become quite distressed when the muffled screeches are repeated over and over again as the security guard keeps phoning.
Eventually the controller of the security centre takes a decision to stop these calls that are distressing his staff so much. He sends round a telephone engineer to the nearest exchange.

Soon the telephone line to the office security guard has been cut and they are no longer troubled by the awful calls.
They assume that the office staff and valuables are safe but the security centre has in fact let the robbers get away with the crime. The business originally operating from that sleepy office is now totally wiped out.

Have you noticed how modern Western medicine is devoted to describing what your main symptoms are and then prescribing specific medication to reduce or stop each symptom?
But consider the word ‘symptom’. When we experience pain or joint aches or digestive problems, what are these symptoms of?
Our bodies are complex organisms able to send us messages to tell us that something is wrong. If we remove these messages – these symptoms – then we don’t know anything dangerous is happening.
The security guards in our body are called Vitamin D Receptors. These form the major part of the body’s innate immune system. This is different from the adaptive immune system which moves to destroy any bacterial or viral ‘robbers’.
In our nice clean society the Vitamin D Receptors get sleepy because they don’t have much danger to look out for. But there are some very clever bacterial ‘robbers’ out there who know how to get past them.
Around one hundred of them can fit inside one human cell. They also produce a ‘slime’ which eventually can coat the Vitamin D Receptors and stop them communicating.

If your body seems to be sending you alarming and painful messages – symptoms - then it may be better for your long term health to listen to them, rather than cut them off at source with medication.
For that you don’t need a specialist. You need to have a holistic view of how the body works. In the past this may have been an area left to ‘alternative’ medicine but now some scientists are beginning to uncover how the body works as a whole mesh of complex metabolisms.
Why not make some further investigations to help yourself out of chronic illness and back in to health?