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Tuesday, 20 November 2012

Jasper's miracle spinal cure...

Blog on the "Spinal Repair" Jasper Dog story on the BBC
The full paper is open access and available here.
A nice commentary by James Guest is available here, (but you may have to pay for that!).

I have been told that some of my tweets looked a bit negative?  ...that is totally wrong, this is an exciting area of research and I believe it is very possible that, eventually, we will have some treatments start to appear.  But the rub is in the word "eventually" :-(
My negativity is in the reporting. The media are building the work up beyond its own conclusions and really should keep calm and take the opportunity to educate the public, not dumb it all down.
I first heard about this work many years ago (a talk with one of these authors in fact) and it's authors are smart and thoughtful scientists.  Pretty much any limitation you would think of, they are perfectly aware of... but they are doing their best!

Some points, feel free to correct me in the comments if I have something wrong!:
(1) Long tract function failed to improve.  I.e., there is basically a set of "master neurones" in the CNS which project all the way from the brain to the level of the hind limbs, bladder etc.  I would be pretty delighted to see paralysed dogs walk again too (obviously!)... but if we are to have paraplegic humans walk again we would probably need these neurones repaired.  Sadly there was no evidence of this.  That's not surprising of course.  If you chop a motor nerve... I would have expected that whilst the top end may survive, the bottom end (below the damage) will just shrivel up and die... (so you have an obvious worm analogy here) therefore, what is the poor old implanted cell supposed to do?  It doesn't really just need to bridge a little gap... it would have to cause an entirely new "end bit" to grow.  That's a tougher ask of course.  So if the damage is way up the cord... it would have to grow down several inches.  If you are lucky... the lesion is right at the point where the descending neurones synapse (connect to) the final neurone. The final neurones then head straight out of the cord and innervate (connect to) the actual muscle.  If that was the case... it may be possible for the new "growth" to simply make a new connection within the spinal cord.
(2) So what did improve?  Co-ordination between front and hind limbs.  This is a more tricky parameter to assess......  to start with... motor movements of a hind limb (of a dog/cat) on a treadmill will actually be generate locally?  i..e., if you pull the leg back it will, to a certain degree spring back and forth by reflex actions .  This is sometimes referred to as "spinal walking" (Spinal walking physiology paper).  It is not real walking [video]. So it looks like walking although it isn't.  So the co-ordination is actually quite a subtle thing to measure.  It isn't really even understood exactly how it works either, but there are various nerves which run between each of the four limbs and it appears that these are the ones, if any, which have improved.
(3) Could the statistics be flawed I hear you ask....  Well of course there is one way in which trials easily can be fudged, but that won't be the case here!!  ...if you ran enough trials, by pure chance you could expect that one trial would throw up an apparently statistically significant result.  You could just then publish that one and say nothing about the others!  ...I'm sure that this is not the case with this this one (well I'm not sure, but I simply can't believe that would be the case!!!!)

Final thoughts....    Jasper was lovely!!!  I wish him well and I sure hope he has a long and spritely life!
Olfactory ensheathing cells on Wikipedia
Neurone  = the individual cell
Nerve = the whole nerve bundle
CNS = central nervous system.

Thursday, 11 October 2012

How to be cool at the posters...

A lovely blog on rules for poster presentations here:
...but I have done my own amended set here....


Well naturally, I agree with the bad breath thing:
So BO and bad breath are both non ideal for poster presenters... But of course your neuroscience will tell you that many olfactory receptors desensitise pretty rapidly and thus you CANNOT smell your own smell for all that long... Thus everyone else knows you smell EXCEPT you!
Clothes? Remember many people will only see you from the wrong side of the board so think about how you look from the knees down. May be don't wear shoes with left and right written on... Or if you do be sure to get them the right way around.


Stake out your poster from some distance away... Maybe from the wrong side of the board. Do the knees and shoes of any "customers" look friendly or not? If not keep clear... Are are THEY wearing those shoes with left and right written on them... Could be a long discussion...

Being special

Please remember having a PhD may impress people in the local 7-Eleven but it does NOT make you an expert at a science conference... And I never want to hear a phd/grad student describe themselves as an "expert" on Wikipedia either... Yuk!

Questions anyone?

Don't ask if your viewers have questions: Obviously if they have questions, they will ask!! Asking if people have questions looks naive and desperate... Just leave us to wander about in peace and think about science, NFL, your font, our dinner or whatever!! If we have questions we will ask...

If someone does ask you a question... Just answer the question, don't subject them to 15mins on your entire poster!

Be Cool

Take a book and assume no one is interested in your poster. It's special to you but probably not special to the vast majority of delegates. Don't be offended or disheartened if people are not particularly interested. It's just life, we are all interested in different stuff!

Get there early and grab a chair... Chairs are often scarce so take a stick and people may offer you theirs.

...but give your chair up if you see someone else with a stick, they are probably not cheating!

Be relaxed and check out good places to eat from the local poster presenters!

Friday, 31 August 2012

Lie detector

Any scientist who thinks that a lie detector detects lies is an idiot. A lie detector detects stress pure and simple. If you are clever enough, it is possible to devise a series of questions which COULD be stressful for the criminal, but not for an innocent, but that still does not mean it detects lies... It is still just detecting stress.

So you have a dead tomato found in you kitchen. What did you have for breakfast... No stress no response... Ask did you throw the tomato = stress.

For it to work, you would have to ask a question that only the perp new was contentious... The experts probably do just that, but it is incredibly hairy... And I just wish they would call it a stress test, not a lie detection test.

Thursday, 23 August 2012


Why channelomics is a naff term, but why it is useful...

It's a term which is being used more and more these days:
Why it's naff is obvious? Omic this omic that it's getting really irritating! Proteome, transcriptome, metabolome, membranome, interactome....

But the trouble is, these areas are able to claim to be areas of research which are self standing.... I have been personally told that you can't just study ion channels... It's too marginal a subject..

So my calculation is that if everyone who works on ion channels and ion channel diseases can bandy about the terms channelopathy, channelome, channelomics.. We might be able to defend the subjects as valuable.

Wednesday, 20 June 2012

Research Excellence Framework

This post could only conceivably be of interest to a professional scientist of one sort or another...
Few subjects have probably been blogged on more by UK scientists than the Research Excellence Framework... otherwise known as REF ...otherwise known as "Son of RAE".
Anyway, this post is about the issue of "metrics" vs "impact".  Making some attempt to quantify research excellence.  Now currently, metrics are out.  Journal Impact Factors are lambasted and Citations (i.e., H-indexes) are out the window.  The accepted feeling is that someone can just read through your paper and make an objective judgement on it. This person will almost certainly not be an expert in your field and if they are they will either be your buddy or your rival!! Mmmm.
Now if it were me I would just stick to the metrics.  It is flawed of course, but if you are going to be judging people, at least a metric system allows people to see where they are at openly.
My feeling is that the reason metrics are being abandoned is because it is too difficult to control, i.e., it doesn't necessarily give the right answer.  So what is the "right" answer.  Well someone once Tweeted:  "The secret of any assessment exercise is to find criterion which put ones self at the top"... oh I think that was me...  Anyway.  I think it is true.  You are a god of research, massive reputation, influence, sit on all the best University Committees and the BBSRC... BUT, once you have split your "output" between a couple of junior academics... and excluded your own funding... your CV may not look any better than a junior academic any more.  Perhaps someone has gotten to their 4 reasonable papers before you and you have 50 papers, but none are really any more than reasonable.  So bingo: "IMPACT"...  now you can look at yours and theirs and say, theirs was in the same journal and has got the same citations, but mine has "impact" and there's doesn't.  Not only that, but "I" will be at the meeting where that totally arbritary judgement is made and the junior academic won't be. QED. "Impact" it is.  I can sit around with my new friends and we can all decide why "our" papers are better than "their" papers.

Now lets give a numerical example.  I know nothing about football.  But there are two teams I want to compare which is best.  Aston Villa and Accrington Stanley.  OK here is the metric approach.  Aston Villa are in the premiership (publish in high impact factor journals and have a have a lot of citations)... Accrington Stanley are in league division 2 (as or writing, which is a kind of lower impact factor journal and a fewer cites type of division).  I conclude Aston Villa are a better "team".  Now without metrics.  I have watch AS play and they seem to play with high intensity.  When they kick the ball they make a lot of noise and they all seem to pass well and run about a lot.  Aston Villa, well their kits seem to stay cleaner and they have a pretty neat organisation at the back.  They don't seem to run about so fast or kick the ball so hard.  However, since I live down the road from AS's home ground and all my friends follow them I amd going to give them the nod.....