This post may be a little inelegantly structured: the direction I wanted to take it in changed twice while writing it, and it wasn’t even intended for a lay audience when I started, so there are a few definitions shoved in parenthesis, and the occasional rambling sentence where I attempt to make a point that I think is interesting, but which requires quite a bit of background knowledge to understand. Cancers are a group of diseases characterised by the loss of control of the proliferation of a cell line, leading to invasion and destruction of tissues. The disease generally begins with a genetic transformation – a mutation, or chromosomal aberration – and further genetic changes accumulate as the disease progresses. Such mutations cause inappropriate proliferation by disrupting regulators of the cell cycle and programmed cell death, or the upstream signals of these. Risk factors for developing cancers can be divided into exposure to carcinogens – substances in the environment which damage DNA – and inborn genetic variation, particularly in the effectiveness of DNA damage detection and repair systems.

Those genes which lead to tumourigenesis when mutated can be roughly classified as oncogenes, which promote the cycle cycle, and tumour suppressor genes, which halt the cell cycle. Their effect on the cell cycle may be proximal, or distal. The retinoblastoma (Rb) tumour suppressor, for example, directly inhibits progression of the cell cycle into the synthesis phase by inhibiting the transcription of genes such as DNA polymerases, which are required for duplicating the DNA. Several oncogenes have a more distal effect as upstream signals. The oncogenes ER, HER2, Ras, and Raf all signal to, amongst others, Rb, and in cancers they permanently inhibit its activity.^[1]

There are many different ways in which a gene can be disrupted, and different types of DNA damage can have different effects on the same gene. A gene product can be lost, for example by mutation to its promoter regions, or may be left unable to efficiently perform its role, for example by a missense mutation. The effect may be knock out an entire signalling or DNA repair pathway, the downstream effect being inappropriate promotion of the cell cycle, inappropriate gene expression, inability to trigger apoptosis, or accumulation of DNA damage. It is not just loss of a signal or inappropriate under-expression of a gene which causes problems: over-expression or activation of signalling may also be problematic. Short substitutions, deletions or missense mutations may knock out a single domain (section of the protein with a distinct function), which may be especially problematic if it is a regulatory domain: the protein will always be “switched on”. The signalling component RAS, for example, is found in about 20% of tumours to have lost the GTPase activity (if that means nothing to you, just think of it as a switch) which changes its structure, thus halting downstream signalling; it is left in a permanently “on” state, causing inappropriate transcription and cell cycle promotion.^[2] Over-expression of signalling components can also be a cause of cancer: HER2, for example, is a receptor involved in the transduction of signalling from growth factors circulating in the blood, to pathways inside the cell. In around a quarter of breast cancers it is over expressed, thus inappropriate activation of downstream signals occurs (amongst them, RAS and Rb).^[3] HER2 is the target of the drug Herceptin, which any British person who follows the news should recognise the name of.

In addition to small scale mutations, the majority of tumours acquire chromosomal abnormalities, and in some cases these are the initial cause of tumourigenesis. These can be in the form of deletions which knock out several genes; and insertions, inversions and translocations which create fusion genes.^[4] Fusion genes may be problematic because they can combine the active regions of one gene with the promoters or regulatory sites of another, or because the resultant product looses some of its functionality. Chromosomal aberrations are commonly associated with inherited chromosomal instabilities, such as the breakpoint cluster region (Bcr). The breakpoint cluster region is on the long arm of chromosome 22 (22q), in a gene usually expressed in leukocytes (white blood cells) which produces a receptor involved in signalling. Translocation of a region around 22q11.2 frequently involves another unstable region, on chromosome 9 (9q34.1), in the abl proto-oncogene. The result of this is a fusion gene, including the bcr promoter (a section of DNA near the gene which assists in regulating when the gene should be expressed), and the domains of abl involved in signalling (the kinase domain – and some when I’ll write a post explaining what kinases do), ultimately leading to leukaemia.^[5] Other chromosome aberrations occur in cancers, including aneuploidy – loss or gain or a chromosome (monosomy and triploidy respectively). Our normal compliment of chromosomes is in duplicate (actually, it’s more complicated than that with the sex chromosomes), so loss of a chromosome, does not necessarily mean complete loss of genes, but the remaining chromosome may carry defective genes which cause problems in the absence of fully functional copies. Many biological processes depend not just on the all-or-nothing expression of a gene, but on the finely balanced relative concentrations of a group of gene products, which can easily be knocked out of balance by euploidy.^[6]

Tumour suppressors, the brakes of the cell cycle, and oncogenes, the accelerators of the cell cycle, are amongst the most important subjects of cancer research. The traditional methods of treating cancer involve surgery and killing cells in a crudely targeted fashion with radiation and toxic chemicals, and a good chance of failure. Advances in the pharmaceutical treatment of cancer are being made thanks to an understanding of the molecular aspects of the disease. This includes the targeting of oncogenes and tumour suppressors, as in the case of HER2 and Herceptin (and estrogen receptors and Tamoxifen) in breast cancer. Recent developments also include techniques for targeting radio- and chemotherapies which exploit the fact that, due to the many mutations that build up as a tumour develops, the more advanced tumours express many unique antigens, which can be targeted with tailor made antibodies. The field is moving forward fast at the moment, especially thanks to applications from genomics, including the genome project, and the development of high throughput methods of analysing genomes, finding mutations, and comparing expression patterns over time, between normal and diseased tissues, and in response to drug treatments. It’s a shame that the extent of the mainstream media’s coverage of biomedical issues runs to headlines like “Aspirin cuts risk of dying by 25%,” “New alert over dangers in our fruit,” and “Scientists find food that stops us getting fat,” (all in the Daily Express in the past couple of weeks^[7]) entertaining though they are. Fascinating news and advances come out of the cancer molecular/cell biology field each week, but either the interesting stories pass under the radar of the newspaper editors, or by the time the story makes it to print it has been mangled beyond recognition.

References

1. ^ Halaban, R. 2005. Rb/E2F: A two edged sword in the melanocytic system. Cancer and metastasis reviews 24:339-356. Full Text
2. ^ Rajalingama, K., R. Schrecka, U.R. Rappa and Š. Albert. 2007. Ras oncogenes and their downstream targets. BBA Molecular Cell Research Article in Press. Full Text
3. ^ Olayioye, M.A., 2001. Intracellular signaling pathways of ErbB2/HER-2 and family members. Breast Cancer Res 3:385-389 Full Text
4. ^ Mitelman F., B. Johansson, and F. Mertens. 2007. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7(4):233-45. Full Text
5. ^ Alvarez, R.H., H. Kantarjian, and J.E. Cortes. 2007. The biology of chronic myelogenous leukemia. Semin Hematol. 44(1):S4-14.
6. ^ reviewed in Weavera, B.A.A. and D.W. Cleveland. 2006. Does aneuploidy cause cancer? Current Opinion in Cell Biology 18(6):658-667 doi
7. ^ Daily Mail Watch, April 2007 archives

So I was rummaging around in my desk draw the other day, when I found this early draft from a famous novelist. Obviously, any resemblance between the characters in this story and real people, alive or dead, would be entirely coincidental.

Fact:

Chiropractic — a Global profession founded by D.D. Palmer in Iowa in 1890 — is a system of medicine. In 2009, bloggers uncovered documents identifying numerous medical conditions being treated by chiropractic, despite a lack of evidence for efficacy, including colic, earache, masturbation, and racist personality disorder.

The academic discipline known as Science is a deeply obsessive system of acquiring knowledge about the natural world that has been the topic of recent controversy due to reports of its fanatical insistence on hypothesis testing, empirical evidence, and the abandonment of traditional ideas when these are shown to be false.

All descriptions of experiments, medical procedures, documents and secret rituals depicted in this novel are accurate.

Prologue

The Royal Homeopathic Hospital,

London 10:46 P.M.

Renowned homeopath Professor Sir Paul Angler staggered through the Royal Homeopathic Hospital’s store room, pulling cabinets and shelves from the walls as he went. Suddenly the light from the corridor was blocked, and a man stood silhouetted in the doorway. The sixty-four-year-old homeopath could see that his attacker was tall and slim, with pale skin, unkempt hair, thick framed spectacles and two weeks’ beard on his face. He wore a knitted tank-top over his shirt, and a stethoscope around his neck. The pale-skinned man screamed silently with laughter. He raised his eyebrows. “What are you running from, Professor?”, he asked. “I only want to give you your… medicine.”

Angler froze, and tried to crawl beneath a desk as his attacker leaped briskly over the wreckage of cabinets and medicine jars. The cowering homeopath looked up as the pale-faced man stood loomingly, stroking his beard with the little finger of his left hand, while tapping a shelf with his right hand.

“Sulphur!”, he declared, sharply. “Quinine! Zinc! Arsenic!” Then, slowly, “aha!”

“No!”, Angler pleaded.

“Arnica,” declared his attacker, raising his eyebrows. “30C dilution. ‘Good for physical overwork and jet lag.’” He looked down at the shivering heap of lab coat on the floor. “You do look like you’ve been doing a little too much ‘work’, Professor. You know that this is bad for your health. Let me help you… rest.”

The pale-faced man suddenly dropped to his knees beside the homeopath and grabbed his jaw. Single-handed, he expertly removed the safety lid from the jar of pills, raised his eyebrows and paused. Then he swung his arm down at Angler’s face, stopped an inch from the man’s nose, and slowly tapped the jar. A single white sugar pill dropped into Angler’s open mouth, and his attacker slammed it shut. Angler gulped with fear and the pill went down. His attacker’s eyes, as shallow as his philosophy, shone with glee. “One,” he counted.

Angler was sweating and panting, his skull aching from the repeated impact of his own jaw, by the time his attacker had counted to five.

“Alright,” he moaned. “Please. I’ll tell you the secret.”

The pale-faced man paused, and then lowered the jar of pills. “Good,” he said. “Now we are getting somewhere.”

The homeopath’s speech was physically wearing, but he performed his fiction with ease. This lie was well rehearsed, though he had prayed that the curtain would never rise on this act. He lectured for twelve minutes before stopping to catch his breath. He fancied he felt drowsy.

“That will do,” said the pale faced man. “Yes, that will do very nicely. Almost exactly what the others said.”

The homeopath looked startled. The others?

“Yes,” chuckled his attacker. “The others. All three of them. They blabbed even quicker than you did.” He paused again, staring into Angler’s terrified eyes. He lifted his arm again. “And so, when you drift off to Bedfordshire,” he continued, “I will be the only one who knows the truth.”

The truth. The Truth. The true horror of this situation dawned on the homeopath. If the others are dead, the Truth dies with me. He panicked and struggled against his captor, who cackled with laughter.

“Professor!,” he said, sarcastically. “Please! I don’t want to have to tell the nurses that you would not take your medicine. Be a big brave boy for me now. Doctor knows best.” And he squeezed the homeopath’s cheeks to force his mouth open. He emptied the bottle into Angler’s mouth, and slammed his jaw shut one last time, causing the homeopath to splutter, and send pills clattering across the floor. His attacker watched them roll under benches and cabinets. But when he removed his hand from Angler’s mouth, and saw the drooping eyelids, he knew that his work was done. For five minutes he might survive, before drifting into a sleep from which he would not awake.

The pale faced man rose, chuckled to himself, and was gone.

Alone, Paul Angler surveyed the wreckage of his pharmacy, fighting the urge to lie down and close his eyes. A drive greater than the desire to live drove him.

If I die, all this will be lost. All that we have have worked for, all that we have fought for all these years. I must pass on the secret.

He rose with great effort and began crawling towards the exit. Shivering, he staggered through the great echoing corridor to the top of the great marble staircase. He thought of his murdered colleagues, their teachers and the teachers before them, smiling down on him from their great portraits. He thought of the secret that they had been entrusted to guard.

He summoned the last of his strength, and cleared his mind. He knew what he must do.

To be continued…

I thought about how badly the story reflected on The Independent. I don’t read The Independent very often (does anybody?) but it wasn’t the first time this year that I’d noticed The Independent taking a bizarro line, and in a news piece, supporting the government or libertorian lobbies on issues that seemed contrary to their traditional stance. I briefly wondered whether there had been a proprietorially-engineered shift in editorial position while I wasn’t paying attention these past few years, or whether maybe the staff cuts were taking their toll, and then I forgot about it all because I don’t really care.

Then Chester Cycling found and satirised this amazing comment piece.

So I took a look at The Indy comment pages for the first time in years.

The first article is a sub-Delingpole Telegraph Blogs-style piece: “Is catastrophic global warming, like the Millenium Bug, a mistake?”. Pure link bait and comment trolling. The most delightful thing is the illustration, still watermarked:

The second article is Daily Express-style capture-the-audience-with-fear fiction piece: “Michael Gove could be prime minister”.

I was a bit surprised to see The Independent publishing this sort of crap. Although I’ve hardly read anything from it in years (has anybody?) I still had a vague idea that it was a quality paper. But it seems that the well-documented link baiting and comment trolling practices, pioneered by Spiked! Magazine and familiar from the likes of Telegraph Blogs can not be stopped. The Independent has jumped the shark.

If you have ever worked in a molecular or medical biology research laboratory, chances are one of the first things you learnt was tissue culture (or the microbiology equivalents). Even if you know nothing about biology, you’ve probably heard mentions of “cell culture” on the news, or at the very least heard about the results of studies in tissue culture. If you hear about “cell lines”, you’ve got culture. If you hear about a “laboratory study” showing that your favourite chemical is carcinogenic, you’ve probably got culture. If you hear about new trials on a miracle cancer cure that has been shown to be effective in “preliminary laboratory tests”, you’ve probably got culture. Everything from zombie epidemics to £10,000 animal-free beef is cell culture. Knowing a little bit about what tissue culture is, and what its uses and limitations are, is therefore important when answering such questions as “is my baby’s bottle poisonous?”, “is stem-cell research ethical?” and “is vitamin C an effective cure for colds/cancer/HIV?”

So. What is tissue culture (TC)? It’s when you take specific cells from a multi-cellular animal and grow them in a dish full of nutrients (a mimic of your blood serum). The point of doing this is to create a system on which to experiment which does not require growing and killing lots of individuals — something that is, for some reason, considered unethical. Especially when it’s humans you propose using. Typically, human or other mammalian tissues are used — especially “model organisms” such as mice. You can use healthy or diseased cell lines from all sorts of different organs. Once you’ve grown up a nice batch of cells in your dish, you can see how they respond to your cancer drug, environmental contaminant, or new junk food ingredient. You can see exactly how the behaviour of your cells changes over the minutes, hours and days of exposure; how they recover after the chemical has been flushed away; how your cancer drug works in dozens of different tumours; how your junk food ingredient works in the old and young, male and female, fit and fat; and how your environmental contaminant interacts with other environmental contaminants. It’s great. If you work hard enough, you can know everything you want to know about your chemical within a week. Wipe out cancer and save the world by next Monday. At least, that’s what the animal-rights movement would have you believe. And the tabloid press fall for it daily.

Trouble is, it’s very easy to get superficially interesting answers using TC. Which makes it very easy to convince a journalist that you have important results, but very difficult to convince a scientist. That’s not to say that TC is not important. But everything that we measure in TC is an estimate of what happens in real life situations. It’s a model that uses surrogate measures from which we can develop hypotheses about what happens in reality. A bad analogy is in order, I think. Suppose you are building a car. You want to protect your future drivers from side-on impacts. Very early on in the design process, you have an engineer conduct strength tests on different materials and designs for doors. From this, you can narrow down the field of designs, and make hypotheses about which designs will perform best on the road. But you can not be sure that the strongest material will provide the best protection against injury and death. You would want play with the crash test dummies, before putting the car on the road. And once the car is on the market, you would analyse incidents. Because when the door is attached to the car and put on the road, a huge number of other variables comes into play. And so it is with, er… what was the topic again? Tissue culture.

Cells did not evolve for growth in a dish. They evolved in the context of cooperation with a vast number of other specialist cells in a body. They are not fine-tuned for survival in the absence of skin, an immune system, a digestive system, liver and kidneys. They are not supposed to live like barnacles on plastic. But if you’ve worked with research quality cell lines, you’ll know that it’s surprisingly easy to make them grow in a dish. Feed them every couple of days, and they’ll happily live for many months. Well go and say that to the post-docs and technicians who made it that way. They were up until midnight processing disgusting lumps of freshly excised tumour. They spent months trying out different combinations of nutrients and fungicides in an attempt to make the cells survive longer than a week. They may be easy to grow now, but don’t think there wasn’t any effort involved. Billions of cells died in the process of making those few grow. Under these circumstances, you can hardly expect the cells not have evolved a little. You are introducing them to a vast number of novel mutagens by taking them away from the protection of skin. And putting anything into a new environment is going to mean new selection pressures. When you finally manage to immortalise your cell line, is it because you’ve perfectly adapted the conditions to the cells, or because the cells have adapted to the conditions?

So. There are all sorts of reasons why TC can not be anything more than an approximation of what is happening in real life. A useful approximation, but unreliable in the absence confirmatory evidence from in vivo and population studies. But these are only the intrinsic limitations of TC. When judging the merits of TC based research, you must also take into the account the fact that TC is easily misused and misrepresented, and that charlatans are doing it all the time. TC is a favourite of cargo-cult healers and nutritionists — those who like to keep up a superficial appearance of having a scientific basis for their quackery. Take, for example, the shamen who pedal vitamin C as an HIV/AIDS drug (Patrick Holford, for example) or as a cancer therapy. They will tell you that in TC, vitamin C has been shown to kill tumour cells, or those cells that are infected with HIV. Therefore, the reasoning goes, we should abandon proven therapies, in favour of taking some vitamin supplements. Trouble is, you can chuck a big lump of any chemical in a dish of cells and the cells will die. I could pour a bag of vitamin C into a dish of healthy cells. They will die. Conclusion: those vitamin supplements are deadly poisonous. Except that your cells will never be exposed to a bag of vitamin C, because you have skin, a digestive system, and kidneys. And because people just don’t go around pouring bags of vitamin C down their throats. I could spit in a dish of cells and tell you that spit is a killer. It’s not.

But it’s not just charlatans that abuse TC. Many legitimate scientists bend the rules a little. They may not even be aware that they are doing it. Take the case of Bisphenol A (BPA), something I did a little work on a couple of years ago. BPA is a component of some plastics, notably bottles. It is known to very slowly leach out of the bottles and into your drink. There is a little bit of evidence (mostly from rats) to show that consuming BPA may be harmful. And there are a lot of TC experiments on the chemical. BPA is a xenoestrogen, meaning that it mimics the activity of estrogens. Estrogen, of course, regulates prolactin release, and cell division (particularly in the breasts). We know that BPA mimics estrogens because when we put some in our dish of tumour cells, we see that within seconds the estrogen receptors have been activated, and all the other effects of estrogen follow. There are loads of results to confirm this because there are a lot of experiments into the effect of estrogen (there’s plenty of money in breast cancer research). If you’re doing the experiment anyway, it’s hardly any more effort to look at BPA. And you can pretend that your research has another potential medical application. Since it’s not the primary aim of your research, the journal’s reviewers won’t notice that you’re using it at a thousand times the concentration that you would find it in the body. So even if enough BPA does leach out of your bottle, and even if BPA does do interesting things in the body, a large proportion of the TC studies will be irrelevant to understanding how it does those things, because they look at inappropriately large concentrations and inappropriately small timescales.

So, next time you are flicking through the health pages of the Daily Mail — which I know all of you like to do — engage healthy skepticism when they update the list of miracle cures and carcinogens. Like statistics, tissue culture is incredibly useful — whether you’re searching for the truth, or a convincing lie.

Continue reading at At War With The Motorist…

Continue reading at At War With The Motorist…

Continue reading at At War With The Motorist…

This time around, Rubberknickers Pickles is ending The War by lifting restrictions on how much of our town centres can be given over to car parking. The idea is nothing new, of course, but it is assumed that most will have forgotten the previous occasions when it was announced. The “news” is that the paperwork has gone through: the new version of the government’s planning rules are complete.

Continue reading at At War With The Motorist…

In 2000, London’s previous mayor, Ken Livingstone, began the process of fixing forty years of mistakes that had been made in the pursuit of the impossible — the comfortable accommodation of mass motor vehicle use in a dense city centre. He recognised that cities are supposed to be places for people and returned key locations like Trafalgar Square to use as more than mere traffic gyratories.

Continue reading at cotch dot net…

Continue reading at At War With The Motorist…