Bio suit…

HOW human do you think you are?

100% ?

90% ?

Well, let’s play a numbers game: in terms of cell numbers, you have in the order of a trillion cells in your body, though this value varies greatly between people and is constantly changing within each of us. However, you have some ten times this number of bacterial cells within (and on) your body 1. So at one level at least, you are only 10% human.

Of course, bacterial cells are quite a bit smaller than your cells, so there’s room for the both of you, in you.

bladder lactobacillus mouth1_scale_final
Images of human epithelial (tissue surface) cells coated with bacteria.

In terms of genes, the instructions that make you you, humans have about 30,000. Again, there are in the order of a hundred times this number of bacterial genes operating within and on your body 2. So at another level you are only 1% human.

Don’t worry though, of course you’re 100% human. Instead, we need to consider the extent of what being human actually is. Being human comes part and parcel with being a super-organism. We live in a symbiotic relationship with hundreds of different species of bacteria, without which we could not survive. Think of them as an invisible extension of your body’s innate defences, occupying every external surface, your skin, your gut, your eyes, ear, nose, and various other orifices.

There is mounting evidence to suggest that they influence our development; our physiology; our nutrition and metabolism; and immunity, where they play an important role from birth in educating our immune systems. They are your interactive suit of armour, both part of the environment and part of you. These communities of bacteria are referred to as the microbiome, and they are being investigated as part of the Human Microbiome Project, an effort by many research labs coordinated by the National Institute of Health.

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Targeting antibiotics…

rb1INHERITANCE, the process by which some of your parents DNA is repackaged in the agreeable form of you, can be described as ‘vertical gene transfer’, i.e. the passage of information down a lineage. However, this is not the only means by which DNA information can travel.

I once spent six years conducting research into the mechanisms by which resistance to antibiotics can be spread within, and between, bacterial species. Much of this focussed on horizontal gene transfer (HGT), specifically the transfer between bacteria of DNA packages called ‘plasmids’, which can contain a full set of instructions on how to resist an antibiotic. Unlike inheritance, HGT is more akin to you reaching out and placing your hand on your cousin and acquiring their ginger hair, or nose shape.

This is of course a very serious issue, in fact it has never been more serious. The subject of HGT is a key topic in many aspects of biological sciences, and I’ve blogged about some of the interesting aspects of such DNA information transfer before.

In the past 10 years or so, an oft’ discussed topic of conversation at the scientific conferences I’ve attended has been the development of targeted antimicrobials. This is a move towards being able to ‘take-out’ (in the mafia sense) those specific bacterial species that are causing a particular infection/disease, but without providing a selective pressure to develop resistance to the drug on this, and neighbouring, bacterial species.

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Amalgam fillings are safe…

AMALGAM, a compound of mercury with another metal, has been used for fillings for 200 years. A ScienceDaily news article says, ‘Amalgam fillings are safe, but sceptics still claim controversy’.

Speaking at the 87th General Session of the International Association for Dental Research in Miami, Dr Rod Mackert, of the Medical College of Georgia, points out that someone would need 265 – 310 amalgam fillings before even slight symptoms of mercury toxicity could be felt. The reason being that when mercury is mixed with the other metals used in fillings (silver, tin and copper), the compound produced contains no free mercury. A poison is only a poison when it is at the right dose; a fact that has been appreciated for hundreds of years. You may absorb only 1 micrograms (1/1millionth of a gram) of mercury a day from a mouthful of fillings, yet consume around 6 micrograms from food, water and air, according to the US Environmental Protection Agency.

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Life in Dr Jim’s lab (part 1)

AS promised, I have finally found some time to start documenting some of the things we’re doing in my lab.

However, I’m starting small. Very small.

I’m going to tell you about some of the toys tools we use in the lab; no, not hammers and nails, and not even the fancy equipment you’ve seen on CSI*, rather, some of the simple and time saving technologies that make our lives easier.

So, we’re going to have some fun with superparamagnetic beads. That’s a mouthful! Superparaganetic beads are basically beads that are attracted to magnets, but which don’t become magnetic as a result +.

Caitlin (200) Nature Methods 2: 71 - 77

Our magnetic beads are tiny. In fact, each one is just 100 nm (nanometers), which is about 1/10,000th of a millimetre on a ruler (smaller than those in the image to the left, which are microparticles). These beads have a number of uses, but their main use is to bind to something you want to purify, and drag it out of a mixture of hundreds of other things that you don’t want. This mixture could be a biological sample, like blood, urine or liquefied poo; it could be a sample of contaminated food, or it could be an environmental sample, such as soil or seawater. In each case, there may be one thing you want to extract, a particular protein, a piece of DNA, or even a whole cell (human or harmful bacteria), but how do you get at it?

All you need is some basic knowledge of what the thing you’re after might like to bind to, some sort of molecular glue. Some proteins bind to other proteins, or DNA. For example, antibodies are used in your body to bind specifically to different types of foreign materials in your blood, a different antibody for each foreign material; they then alert your immune system. If you coat each bead with a particular antibody, say one that binds to a particular harmful bacterial cell like Salmonella, then you can add your beads to a mushed up sample of biological material, and use magnets to drag the beads (and the cells attached to the beads) away from the rest of the mush. You can then wash your beads a few times in a fresh solution and start your experiments.

Here is a video of some beads in action – though my sample is a salt solution, rather than poo!

My soundtrack (when it activates!) reminds me of my favourite film, ‘Sideways’.

Uses of magnetic beads:

  • Finding binding partners of your molecule of interest.
  • Deliberately pulling out a known molecule of interest from a mixed salad of other chemicals.
  • Pulling whole cells (human or harmful bacteria) out of a biological sample.
  • Having fun with magnetic beads.

* Whom, I should add, have managed to get DNA sequences out of a centrifuge – a piece of kit for spinning things to the bottom of a tube – in the time it takes to say, ‘Well, it seems to be our guy’s blood on the a paint sample matching a 1979 B-Body Dodge Charger’, which is clearly ridiculous**)

** Dodge didn’t make a B-Body Charger in 1979.

+ Remember your school physics, where you scraped an iron nail against a strong magnet, and the nail then becomes magnetic? If you went a step further, as I did, you would take you now magnetised nail into the woods with you, and when you got lost, you would find a clear and stagnant pool, upon which you would set your nail, atop a leaf, and float it on the water. The nail should then align itself North-South. Unfortunately, I could never remember which end of the nail point North, so it was a little fun, but pointless. The point being, your beads won’t just start floating towards any iron that happens to be near by.

Bad Science excerpt: The Doctor Will Sue You Now

bad-scienceBen Goldacre has released the infamous chapter that was missing from the original ‘trade’ paperback edition of his book, ‘Bad Science’. He recently posted the chapter on his Bad Science blog, under a Creative Commons license; this means ‘You are free to copy it, paste it, bake it, reprint it, read it aloud, as long as you don’t change it – including this bit – so that people know that they can find more ideas for free at

I have reposted the article in full, but you can just as well read it on Ben’s blog, or hell, you could even go spend a few quid and buy his book!

This is an extract from
BAD SCIENCE by Ben Goldacre
Published by Harper Perennial 2009.

The Doctor Will Sue You Now

This chapter did not appear in the original edition of this book, because for fifteen months leading up to September 2008 the vitamin-pill entrepreneur Matthias Rath was suing me personally, and the Guardian, for libel. This strategy brought only mixed success. For all that nutritionists may fantasise in public that any critic is somehow a pawn of big pharma, in private they would do well to remember that, like many my age who work in the public sector, I don’t own a flat. The Guardian generously paid for the lawyers, and in September 2008 Rath dropped his case, which had cost in excess of £500,000 to defend. Rath has paid £220,000 already, and the rest will hopefully follow.

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Writing time…

So the university has afforded me some free time for the next five days, which gives me the perfect opportunity to get caught up on some of the science blogging I’ve been planning. In the next few days I will be posting some pictures and video that fall into the broad category, ‘Life in the lab’. In this I will be discussing topics, in no particular order, such as:

‘I’m just running a gel…’, – what does this line, often used by lab scientists, actually mean?

‘Using biology as a scaffold for building nano-electronic circuits…’ – this is some of the research I am involved in.

‘Toy’s for science boys (and girls)…’ – Yes, there are geeky tool kits (I call them toys) that we use in molecular biology. Most people won’t know the point of using them, let alone that they exist; I’ll attempt to explain why they’re cool.

Finally, I will be doing a research blog on ‘Targeted antibiotics…’ – new approaches to make antibiotics more useful, and that take out the ‘bad’ bugs, but leave the ‘good’.

Bionic eye…

This is just the sort of grass-roots level innovation that has made science and technology great; interested people doing interesting things. This is a video by Canadian film maker Rob Spence and is from his ‘Eyeborg‘ project website.

You can keep apace with their current progress via their blog.