What would you prefer, a colonoscopy or an autopsy? 

This question may not have crossed the mind of the middle-aged man who'd put off seeking medical attention for his pain. When he eventually decided to take action, it was too late – he died on the way to the health facility. Instead of going up to a hospital ward, he went down to the mortuary. That's how I came to be performing an autopsy on him, to determine the cause of his unexpected death.

An autopsy is the most intimate diagnostic procedure. At least if you're having a colonoscopy, you get to wear one of those silly gowns that tie up behind, even though it doesn't cover your behind adequately. For an autopsy, the subject lies completely naked on a cold steel trolley and scrutiny is not limited.

You have to be prepared for a colonoscopy by clearing out your guts. Most people find this purging unpleasant. But if your bowels aren't empty, the very abnormalities that are being searched for could be missed.

The autopsy room is fitted with industrial strength extraction fans to reduce the noxious odours that may emanate from the deceased subject who is undergoing a post mortem examination. The smell is usually due to the contents of the bowels, rather than the effects of putrefaction, though there might be a general sort of raw flesh aroma beyond that ordinary toilet vibe. I know it sounds gross, but I'm trying to point out the benefits of not letting bodily problems go too far.

I have publicly posed the choice between autopsy and colonoscopy before, trying to encourage people to use the kit that our tax dollars pay to be sent to every Australian between the ages of 45 and 74 every two years as part of the National Bowel Cancer Screening Program.

Like most public health strategies, detecting and dealing with diseases early in their course is cheaper than waiting until obvious symptoms occur.

The Faecal Occult Blood Test (FOBT) detects microscopic blood in the poo. Although the cause of such invisible bleeding from the bowel can be due to diseases other than cancer, the big C is why screening is done and where the greatest economic losses can be reduced.

Having a colonoscopy to investigate a positive FOBT may be uncomfortable. But you are given a relaxing sedative which usually results in amnesia for the event. An autopsy does not cause pain to the body but there is much pain for the loved ones who have lost the person who requires an autopsy.

When I was a country doctor in regional Western Australia, a special activity of mine was getting to the bottom of sudden unexpected deaths presumed due to a disease (rather than something unnatural like an accident or homicide). For me, it was a more straight-forward proposition than ferreting out the cause of undifferentiated symptoms in a living patient, which was my usual job in daylight hours and on-call after hours.

It is no simple feat to make a diagnosis. It includes taking a thorough history of the problem, performing a physical examination of the patient, choosing the right tests, interpreting the results and wrangling all the information into coherent sense. Statistics influence a diagnostic algorithm, but relying on probabilities doesn't always work when dealing with one person. Years of training and experience are critical factors enabling a doctor to pick the outliers from an apparently recognisable pattern. Individuals are so … individual. They don't always fit in the box.Less qualified health advisers working to a protocol might seem a useful addition to service provision, but such doctor-substitutes may not be able to deliver the safest option for medical care at the beginning of the disease journey.

An autopsy may come at the end.

Routine hospital post mortem examinations are now rare. Most autopsies these days are instigated by the legal system, which is how I came to be a 'death detective', doing in the rural zone what a forensic pathologist does in the city for cases where the person's demise is unexplained.

When the local police had deemed the circumstances of any particular case here were not suspicious, the coroner could authorise a post mortem examination to determine the cause of death when necessary. During my time performing autopsies, a few unexpected things turned up. The patient mentioned at the start of this story was one example.

At his autopsy, I was confronted by hard clumps of abnormal white tumour tissue marching throughout his abdominal cavity, the cancerous claws invading his normal organs, causing angry inflammation and bleeding everywhere it went. He had the most violent-looking bowel cancer I ever saw, not only locally aggressive, but spreading through blood and lymphatic channels to distant parts of his body. These poisonous seeds grew destructively where they lodged while the cancer continued to conquer the original site in his colon.

This wasn't the only person who I discovered had died from a bowel cancer not diagnosed in life. An older gentleman, whose death was expected to be due to the usual coronary artery disease, had actually died from a blood clot to the lungs, caused by a hidden bowel cancer no one had previously detected.Cancers of the intestinal tract continue to be in the top seven causes of death and years of potential life lost in Australia. But it's not just lack of enthusiasm about having a fibre-optic tube poked up your bottom.

Timely access to this procedure, when it is required, is an issue that affects rural and regional Australians disproportionately compared to urban dwellers. These geographically-based obstructions and social determinants of health are a problem for the diagnosis and treatment of other diseases, not just cancers. They result in lower life expectancy and crappier health statistics overall, in direct parallel to the degree of remoteness from the major cities.

Don't get too depressed if you live in a country area. Dwelling on epidemiology and population patterns neglects the individual. Too broad a view is not always the best way of looking at a topic. Narrowing the focus to what can be achieved at a personal level yields the greatest effect and the best results.

Genetics have a significant impact on health and longevity. We can't do much about changing genes at present and all genomes are deteriorating. Most bowel cancers are not due to inheritable defects. On a optimistic note, you can have some influence over what you eat and what you do with your body, whatever your environmental context. And don't underestimate the involvement that your thoughts and emotions have on your health and well being. Use your imagination positively!

What would I prefer, an autopsy or a colonoscopy?

I've not performed colonoscopies, though I've assisted and observed them being done. I appropriately referred plenty of my own patients to those doctors who were skilled at this operation. Most of the punters gained benefit from the adventure, though a few eventually died of their colo-rectal cancer despite treatment, perhaps because the timing wasn't optimal.

Performing autopsies for the coroner, however, was one of the highlights of my medical career. It was a useful service to my rural community, while there was still an autopsy room in the regional hospital. This specialised activity came to an end when the hospital was rebuilt. Facility upgrades don't always increase every service. The opportunity was taken to remove what was deemed to be unnecessary, centralising expertise in the capital city.

What can compare to the full sensory experience of delving into the amazing human body, to admire its intricacies and reveal its secrets? Although such a thorough investigation might seem too late, knowledge is expanded. And an autopsy can ease the suffering of those left behind by providing the reason for an otherwise unaccountable death.But I wish you all a long, healthy and happy life with need for neither colonoscopy nor autopsy.