In which I present a new outlook

I'm trying to get back into blogging about my research. The truth is, I don't have the time. I'm exhausted - truly - physically and mentally exhausted. I've worked pretty much 6.0-6.5 days a week since Christmas and I've had one day of annual leave since July apart from when the University was actually closed...and I'm just about keeping afloat.

So, to try and get myself to blog a bit more often, I've moved from Tumblr to Blogspot - the reason? I'm sick of Tumblr putting my website offline over 50% of the time due to their shit servers, thus meaning when I finally do get 5 minutes to write something, I find that I can't do it. Blogspot is far more reliable and has many more options to allow me to write things on the fly.

This theme/template isn't permanent - it's a space-filler until my custom design is finished (outsourced - I don't have the time to do it myself!). It'll do for now, I think!

In which I praise a kinder, changing world

From mid-November until mid-January, I had to do something extremely unpleasant. I did not want to do it but I did not have any choice. No one forced me to do it per se but there was no real option. I had to watch someone I work very closely with become very ill over a period of two months, peaking in January. For one reason and another, he had been working very, very hard in November - long hours, little time off - and, as so often happens, tiredness gives way to fatigue and fatigue to exhaustion and exhaustion opens the body to all manner of ills. I watched him become more tired and weary by the day and I watched him gradually starting to look off colour but watched him totter on with no thought for himself, continuing to work like a Phoenician until the point came when he got so ill that he couldn’t work any more. He wasn’t gravely ill (though it’s an illness that can and does kill) and he wasn’t hospitalised (though that often happens too) though by the time he finally sought medical attention, he was so ill that he was incapable of working or having any kind of life and was bedbound much of the time. He managed to get medical help just in time and I was very, very relieved when the doctors told him that he’d caught it just in time and that it was unlikely to be fatal but it would take his body quite some time to recover, even with the best medicines available.

I’m pleased to say that within two weeks, he was looking much better and the colour had quite literally returned to his cheeks. He was no longer bedbound and was back at work again and, as very often happens when someone has suffered a serious illness, his life had a bit of a reboot and a few epiphanies occurred as he put his life into order. The illness that he is now thankfully in remission from is caused by a defect in the metabolism of a compound central to a wide range of metabolic processes called 5-hydroxytryptamine, which is formed in the intestines. Without it, blood doesn’t clot properly, appetite vanishes, the body can’t tell if it needs nutrients, the small intestine doesn’t respond properly to food so nutrients don’t absorb into the blood properly leading to the beginnings of malnourishment, sex drives and desires for intimacy vanish, changes in the brain give rise to a constant feeling of fear and pains in the joints and abdomen start to occur. If this 5-hydroxytryptamine deficiency is left unchecked, it is fatal in about 4% of patients, but it can be treated in many cases using a straightforward course of tablets. No one really knows why this metabolic defect occurs that stops the body producing it but it’s actually a very common illness with just under 5% of the population having it at any time. 5-hydroxytryptamine is also known as serotonin and its deficiency is also known as clinical depression.

I know from my own experiences (which I have written about here) that 5-hydroxytryptamine deficiency can be a very misunderstood illness. Unlike similar illnesses in which the body stops producing something necessary, like insulin in diabetes, many people who have yet to suffer from it seem to think that the patient is faking it or is in some way “weird” or even “dangerous”. This is of course sheer stupidity and prejudice on the part of the uneducated, inexperienced people passing this judgement. As with all illnesses, one of the biggest hurdles can be telling one’s colleagues, family and friends. Their response can be very variable, particularly if they don’t understand it and any serious illness can be a very good test of who your friends are. When I experienced this myself (which I wrote about here), I found that a surprising number of my so-called friends were very judgemental, treated me like a leper and were far from understanding. None of them are now my friends. I realised therefore that my colleague needed support and I felt that I could simply not let him go through it alone. He knew I had suffered from it in the past as I am always very open about my period of 5-hydroxytryptamine deficiency in 2006. The reason I am open about it is because I feel it helps people suffering from it feel less alone and helps to reduce the idiotic stigma around this disease. I am pleased to say that my intentions paid off as he came to talk to me when he realised that he was ill and I was able to offer practical advice on getting through the illness itself and the side-effects of medication as well as to help him realise that he was not alone. When you are that unwell, the lack of 5-hydroxytryptamine in your blood makes you unable to form normal social interactions with others and as such renders you very alone. He took himself off to the GP in January and started a course of treatment with medication and I’m very pleased to say that he did very well on it and began to recover within weeks. He will continue to recover for the next 6 months before he can truly be declared as in remission. I have been in remission for 6 years now and I know that it could come back at any time.

Having told me, he had to then face the task of telling his friends and family and I spent a good deal of time explaining that they may not be very understanding as it’s a very misunderstood illness. I was completely taken aback that out of the dozens of people that he had to tell, only one has been remotely unkind. Everyone else has offered him nothing but support, kindness and love and has helped him to recover. One person who clearly doesn’t understand 5-hydroxytryptamine deficiency has been very cruel and seems to think he can “snap out of it”…yes because that’s how it works - just like how diabetics can snap out of it and get their insulin back. I am amazed that in the 6 years I have been in remission, the world has changed. People are clearly better educated now and understand 5-hydroxytryptamine depression a lot more well than they did 7 years ago.

I mentioned that serious illness often helps one put live into perspective and can have oddly positive outcomes as I’m sure many reading this will understand. In my colleague’s case, he accepted the fact that he was gay having been unsure for some time. Just as I am open about my experiences with 5-hydroxytryptamine deficiency, I am also, of course, open about my sexuality. In the workplace, I feel that this can benefit others who are less comfortable about it as it can give them confidence. As such, my colleague came to me when he realised this and we had a number of discussions about it including practical aspects (well, sex education in schools in the UK doesn’t include same-sex sex-education, which is criminal in my view, so there were gaps to fill!). Some reading this would not understand the need for this but imagine that when you were at school, during every biology or PSE lesson that covered sex or relationships, you were taken out of the class and put in a separate room and taught nothing. Imagine that when all your friends were enjoying their first kiss/fumble behind the bike sheds/school prom/first date/etc that you were taken off and put in a room alone and not allowed to experience it. That is what the UK educational system has been doing to LBGT teenagers for years and continues to do, unfortunately.

For many years, I did not understand the concept of “the gay community”. I thought it meant a lot of very camp men who lived in Soho and were very cliquey. I now realise it means something else. When I was in my late teens, an older friend (I shall call him Harry) who was in his mid-30s and much more worldly wise than I and who I just sort of met and got on very well with gave me a lot of very good advice - both emotional and practical - re: getting my head around my sexuality and going on to actually do something about what I had been feeling for many years but had been too scared to admit, even to myself. Harry and I were very close friends for about 2 years which isn’t long but he passed on the wisdom of the ages during that time and I must stress that our friendship was only even platonic - there was no unrequited love or anything smutty - just friendship. I realise now, some 15+ years later, as I pass on the same information and wisdom to the next generation, just has Harry did for me and someone else in turn did for Harry that this is the “gay community” - the passing on of the wisdom of the ages. The folk wisdom learnt through experience that gets passed on. Filling those gaps in knowledge and emotional development have been the duty of the older, more experienced man in the gay community for generations. Nothing smutty, nothing sordid, just guidance and passing on of information - just as fathers do to sons, traditionally. I hope that this tradition will end within my lifetime and that schools will teach these things properly and parents will raise their children to understand both opposite gender sex and same gender sex, since they don’t know which one will be relevant to their child (or perhaps both will?).

So, again, my colleague had to tell people and, again, I spent a good deal of time preparing him for the way it often was. Some people would not want to be friends with you any more. I lost of a lot of “friends” who could not/would not accept my sexuality. Others were shocked that after 20 or so years of seeing me one way would then have to see me another and learn to love me all over again. Others felt I had deceived them and could not handle that. I prepared my colleague for all of the above and for any rejection he might face from his family. But the outcome was beyond belief.

Not a single person said anything other than “oh ok”. No one was angry, upset or confused by it. Everyone accepted it and everyone probably now loves him more than they did before. Total, 100% acceptance. I could not have predicted that.

And thus it is now that I praise this kinder, changing world. A world in which the stigma of being LGBT is fading by the year and in which true equality to live our lives with the same standing as others is finally starting to happen. A world in which the stigma of 5-hydroxytryptamine deficiency is STARTING to fade, but we’re still getting there on that one. It staggers me that anyone would give someone a hard time because they are ill but some people are scarcely human, I feel.

As for my colleague, he is now happier than I’ve ever known him, and he has written about his experiences here. Read about them. His strength and energy are inspirational.

In which I lament due process in science

In science, we have a very simple process for taking data from the laboratory to becoming a “result” in the public domain. The work is written up in the form of a manuscript for a scientific journal, submitted to said journal and the editor thereof will send the manuscript out to 2-10 peer reviewers (other scientists in the field) who criticise it, evaluate it, decide if it can be published (a) at all or (b) as-is with no changes [very rare!] or (c) with minor modifications [pretty common] or (d) with major modifications. Until a discovery has been through peer-review and published in a journal, it is not a valid discovery as it lacks any independent validation. Twice in the last month have “discoveries” been released to the press without any publication in a scientific journal. This is major jumping of the gun and very misleading - what if there is a major flaw in the study that renders it invalid? Will the authors retract the press release? No - they’ll just quietly move on to other things. Nothing should be released to the press without due process taking place and I do not understand why scientists see fit to jump the gun - many journals even embargo press releases prior to publication and for a very good reason!

The latest piece of unpublished data released to the press concerns bacteriology and “new bacterial life”. This makes out that some amazing new form of life has been found…what the authors have actually found is a microbe from a novel genus (assuming their data are valid and pass review, of course). To put this into context, in 2012 the International Journal of Systematic and Evolutionary Microbiology published over 137 genera novae (new genera)* - just shy of 3 per week. That does not include genera novae published in other journals and then put into the IJSEM’s Validation List system. So, 3 novel genera within the Bacteria per week. In 2012, how many of these warranted an article on the BBC website? Zero**. Not one. The last article on bacterial taxonomy on the BBC website was in 2010 and concerned a species nova (new species) within the genus Halomonas and had been published in a peer reviewed journal prior to the press release.

My point? 

1. This is not a major discovery by any means - yes it’s interesting but genera novae are almost 3-per-week - really not a groundbreaking discovery in that alone. Yes, it’s from a fascinating location and the evolution will no doubt be fascinating but just the novel organism alone is nothing interesting really.

2. It has not been peer reviewed or independently verified by deposit into two international culture collections in accordance with the Bacteriological Code. It is worth noting that a large number of DNA sequences can be found in the GenBank database regarding an apparent species nova that is then never published - presumably stumbling at the Collection or peer-review stage.

Press-releases should not be issued prior to peer-review and should not go out on mundane aspects of a discovery just to get there first - wait for the whole story to be clear and release THAT - it’s bound to have more impact.

* Using the search string “gen. nov.” as an exact phrase from Jan 2012 - Dec 2012 on the IJSEM website.

** Using the search strings “novel bacteria” and “new species bacteria” and “new genus bacteria” over all time on the BBC website.