Girl, Interrupting

November 26, 2010

Brief thoughts about academic honesty

Filed under: Academic dishonesty,science ethics — sylviamclain @ 12:32 pm
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Always tell the truth – they tell you when you are a kid – I think I quickly learned that ALWAYS telling the truth is not always the best idea – lies of omission (especially to my mother) save a lot of pain all around and are sometimes diplomatically the best way forward.

Recently an academic at Duke, Anil Potti, resigned and retracted several science papers because his work couldn’t be reproduced by himself or other scientists in his field. Potti also had apparently lied on his CV saying he was a Rhodes scholar when he wasn’t although he later explained he was a Finalist as a Rhodes scholar.

What I wonder about this story is if this is a combination of overselling your scientific results and spinning your CV too much or actual academic misconduct. I think the results are out still, but this incident is worrying none the less.

When I think about the lovely art of CV writing, and that bit of grant writing in that distressing section where you basically have to convince the reviewers you are the greatest thing since sliced bread, I always have a little shudder. I hate writing those things, largely because sometimes when you write them down they don’t sound quite right. For example, I was a fisheries feild technician when I was 22, which sounds a whole lot better to me than the actual job of hauling around heavy equipment in the woods and counting fish.

OK so you obviously can’t lie as in I have 50 papers in Nature that all have been cited at least 400 times (though some people do this, and actually get away with it (at least in the short term)) but where do you draw the line?

For instance, I held a grant where I was the PI, however the post-doc on the grant was almost entirely supervised by the co-PI. While I had a central role with supervision of our student, do I say I supervised the post-doc? Do I give some lengthy boring explanation about how our management structure works? The opposite also happens, you may not be a *formal* supervisor but turn into one through the course of a collaboration. Do you list this? Keep in mind you only have 2 pages (at most) to list how wonderful you are.

I realize that these are boring examples and this isn’t really dishonesty per se but this is where the hard part lies sometimes. Do you make it sound better or worse? One of the problems I believe is that as an academic your specific roles aren’t always clear – lots of us interact and collaborate with alot of people and writing it down on paper isn’t necessarily always easy. And if you try to be humble and under sale yourself – you probably won’t get funded. Its like getting a house, its hard to make that first step onto the ladder these days, and hard to get funded (its getting harder). And though I have held a few grants, I don’t currently have one and as a result I don’t currently have any of my very own students or post-docs but I desperately need some if I want my research career to continue.

And this is part of the problem – desperation to get funded, while MOST academics (I believe) don’t intentionally lie, someone might disagree with your assessment of something so dull as ‘she didn’t really supervise that post-doc’ – and then if you make a mistake in your scientific research years later would it come out as “Charlatan scientists claims control over other people’s resources” ?

I have a feeling that Potti’s case is probably more complex than this, given that he has made the news in the New York Times and has actually resigned. Scientists do make mistakes and do own up to them and retract papers without loosing their jobs. Most famous example I can think of is Stephen Hawking – so something seems strange about Potti’s story.

But as @DrAustPHD said on twitter: Pressure system enough: people will short cut (& worse).

This is a frightening thought in some respects but I think on the whole most people DON’T fudget their results (though they do make mistakes) and most people are honest about what they say about themselves. And the good news is, if you out and out lie? You often get found out in the end….

November 16, 2010

The dangers of unconscious bias

Filed under: rational thinking,science ethics — sylviamclain @ 12:55 pm
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Its around us everywhere, unconscious bias, in the media, in the government infrastructure, in academia.

I have read several articles lately about bias and inequalities in academic science – such as a blog post “What women think” by Athene Donald which highlights, amongst other things that academic women might be less likely to be supported by their line managers and have a harder time getting promoted in a male dominated environment. Similarly, Imran Kahn has written an online article in which he expresses concern about higher education cuts leading to a decrease in diversity in scientific fields which are already predominantly ‘Pale, male and stale’.

In a seemingly non-related article – the Home office has announced a new ‘stop and search’ plan allowing the police to stop people based on what really seems to amount to racial profiling.

So could the new Conservative ‘Big Society’ in the UK, which is supposed to mean we all love each other, really signify an increase in gender and racial inequalities across all government departments?

Perhaps, but I also think that the people making these decisions probably don’t think they are doing anything of the kind. They probably think that this is just ‘common sense’ and has nothing to do with racial profiling or any sort of discriminatory bent. What it more likely signifies is unconscious bias. And everybody has unconscious bias, it is part of being human.

I was born during civil rights era in the not so deep South in the US, Martin Luther King Jr. was assassinated when I was about 6 months old. Growing up in the post-civil rights era, I learned that racism was uniformly bad, and a thing that was apparently perpetrated by many of my ancestors. This is a horrifying realization as a kid and you vow to yourself you will NEVER be a racist and I sincerely hope that in actual fact I am not.

But the other thing I learned is that legalities certainly don’t make racism just magically disappear. Just because the Civil Rights Acts (1965 and 1968) said ALL men (and women, but here I use men as these are the historical words ) are created equal and have certain unalienable rights to life, liberty and the pursuit of happiness, didn’t necessarily mean that racism evaporated in a puff a smoke, that there were group hugs all around and it was over. It’s much more complex than that.

In many people’s minds, racism is the KKK and sexism is people who just think women are dumber than men. Even though people that think and say things like this obviously do exist (such as Professor Richard Lynn), it is not very often we hear things this overt from day to day. It is worth noting that Prof. Lynn himself thinks he is just ‘observing the facts’ and talking common sense in a sort of ‘some of my best friends are women but…’ kind of way.

It is rare for us to see bias in ourselves, and most people I think would say they are decidedly NOT racist (or any other ist). Because unconscious bias is unconscious.

I think most people that consider themselves rational, evidence-based, scientific, humanitarians believe that they are well free from any sort of unconscious bias. If you are trained as a scientist, you are trained to try and look at the facts as objectively as you can. This is easier said than done. Have you ever had to let go of a pet theory because it was wrong? This ain’t easy.

But what I find myself seeing over and over again in science blogs and rationalist thinking articles is lots of unconscious bias – against the very things that the authors believe are biased and intolerant themselves.

For instance, I saw recently in an article about atheism embedded in a science blog the following statement:

“One thing that always surprises and disgusts me about so-called christians is their willingness to hate those who have different beliefs than they; those with other faiths or (especially) no faith at all.”

In my mind, this is a pretty vitriolic statement about hatred and it is also not a universal truth, even though it is stated as if it is, which is a prime example of unconscious bias. I know plenty of Christians who do not ‘hate’ people with other beliefs but simply think that they are wrong and are rather more tolerant of different beliefs than some ‘rational-thinkers’ I know.

I have deliberately NOT included a link to this article because I don’t believe the author is being consciously overtly biased, and I am sure they don’t believe that they are. I am also certain that they have frustrations with many of the christians they have met.

I have to admit, I have a fear of fundamental foot-washing Baptists, the minute someone tells me they are a Baptist I not only want to run screaming but also have a full-set of preconceptions about what kind of person I think they are (some of it not so nice). But a healthy part of this reaction is my very own bias AGAINST people that have a particular belief I don’t agree with.

Bias is almost never overt, it is almost always covert and I think we should all take the time to stop and see where it comes from in ourselves before we condemn others for the very beliefs we have and often hate in ourselves.

September 1, 2010

On women in science

Filed under: science ethics,women,women in science — sylviamclain @ 10:44 am
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I am always in 2 minds about Women in Science. There is something about that title that reminds me of the Muppet Show and I can hear the announcement line sounding like ‘Pigs in Space’ – and it just sounds silly..

I am, after all, a woman in science though I haven’t really ever thought of myself as that. I don’t mean I think I am not a scientist (I am) and I am pretty clear that I am a woman, but those things don’t seem like they should be mutually exclusive to me. The term Woman in Science actually points out that that subject (women) in Science is something somehow different.

I have always thought, in my job why does (should) it matter that I am a woman? Other than I obviously use different washroom facilities. My position on this as a graduate student was a follows: I am training to be a scientist, and I am just as good (or bad) as the next guy or gal, I should be judged on my merits not on my reproductive equipment. So I was adamantly against participating in any society which highlights the fact I am different – I didn’t want to be a part of women in science groups, full stop, which to me seemed divisive and separates women even further from a male dominated profession.

It is true that women are under-represented in many sciences, especially the physical sciences, and they did not participate in professional science (except on the sly) until fairly recently. There are some pretty amazing stories about women who worked in science against all of the odds. There are amazing individual stories about Rosalind Franklin, Caroline Hershel and so many others that worked in science before they were really ‘allowed’ and yes it really was ‘allowed’.

And we love these stories! I do, they are great, and impressive. In the UK they love an underdog, and in the US they love the pioneer American dream spirit – against all odds! These amazing forerunners fought the system and won. Individually this is powerful stuff. But should you really have to fight against the odds just to have a job in science? And what about all of the women who probably fought the good fight and still failed, or had to give it up, or quit to have children (as a lot of people did, as it was “normal”) who knows about them? My mother (who is a social worker) always told me that if she had it to do all over again she would be a wildlife biologist, or a park ranger. But my mother was born in the 30’s in Southern US and as she said – that’s just the way it was, women were either nurse’s, teachers or social workers – so she didn’t even KNOW she had a choice, really.

And some of the women, I am sad to say, who have succeeded against all odds are the worst about repressing other women, just like some of the most conservative people about social equality are the very ones that could have used a leg up, simply because they themselves fought ‘against the odds’ and therefore think ‘why can’t everyone else?’

I really don’t want to be and hope I am not like that, not that I have a startling Nobel prize winning career, but I don’t want to be intolerant of people with different backgrounds (be they women or whatever under-represented portion of the population) who didn’t do what I did. No one’s life is the same. I also think by excluding people you cut your base, you necessarily limit what can be done, just like only funding the elite. And while —– (insert whatever under-represented group you like) aren’t ‘excluded’ in any formal sense these days, they may well be excluded in an unconscious manner, unconscious bias – and this can sting, and in some instances be so discouraging, people just think – forget it, I can’t (or don’t want to) deal with this.

I think about some of the things that have been said to me in my scientific career, for instance:

When I got my first independent fellowship from NSF, I was ultra-excited, and a senior (male) professor told me –
“You only got it because you are a woman” ?!?!

When I was on an interview panel with a male colleague who said (in response to a question I asked the candidate)
” She just thinks that because she is a woman”

Thankfully, these instances, at least in my career, have been rare. Most people don’t think or at least don’t say things like this.

So here is the two minds bit – bias still exists, and I truely believe that all people, regardless of race, gender, etc. should be encouraged not discouraged, so maybe a women in science group is the way to do this? But I still don’t want to be a member, because I don’t want to classify myself as different, but I think, as I didn’t used to think, there is a place for this, whether or not I want to participate myself.

So if you want to join a women in science (or whatever group) I have one thing to say –

you go girl!

August 20, 2010

It is damn hard to admit you are wrong

And I don’t mean when you get the facts unequivocally wrong like in a pub quiz, you kind of have to say you were wrong when you find out Sylvia Plath wrote the Bell Jar after you claimed it was Charles Darwin.

What is hard to see – really hard to see – is when you only might be wrong. For instance you think X, someone asks you have you thought about Y? which might make you change your mind about X. Lots of us just a) choose to ignore Y, b) spend a long time justifying why really Y doesn’t matter or c) get really angry and argue more about X.

Its the standard criticism people a large portion of the scientific community have about Homeopathy. Practitioners of homeopathy say it works, scientific evidence says it doesn’t. Homeopaths ignore scientific evidence, so the story goes.

What is true is that data is data, data doesn’t lie – but the interpretation of data, and this is what scientists spend, arguably, most of their time doing, is an entirely different matter. Even though we don’t like to admit it, especially in science (because, after all scientists are supposed to be entirely rational), its hard to alter your pet theory when the data doesn’t quite match up, when it is not obvious that you might be wrong.

BUT, even though this is difficult, it is also part of the job. You must to try to weigh the evidence rationally, and when your theory is wrong just say it is wrong.

The Ben Goldacre/Samira Ahmed twitter ‘debate’ is a good example of this – Goldacre said he was wrong, but not without a flood of excuses…
(see here and here)

So Ben Goldacre tweeted that an upcoming news show (which included maths formula, he assumed was not kosher) was ‘bollocks’ on Twitter and invited heckler’s from the Twitter community to reiterate this point. Turns out, he was wrong, so admitting his mistake he tweeted:

BenGoldacre: @samiraahmedc4 humblest apologies, all the outward signs of bullshit were there, and was impossible to tell from PA report. sorry!

and quoting Suw Charman-Anderson:
It was entirely unsurprising that he should see Samira’s tweets and dismiss them out of hand, given the PR industry’s history of producing bunkum formulae to promote their own brands.

Maybe so, we all have reasons why we are wrong, but and here is the point… its a not easy to say what probably should be said. In this case something like – “I was wrong because I didn’t read the evidence and just had a knee-jerk reaction, even though most of my articles are about gathering evidence and in this case I didn’t bother before I reacted” – would have maybe been more appropriate. And more difficult.

Its much easier when you make a mistake to blame it on other stuff, rather than just saying ‘that was stupid, sorry’
I have caught myself doing this, and even with regard to my research, but in my job there is a standard I have to live up to. If I want to be worth my salt as scientist I have to try to read and collect the evidence before I just decide something is crap.

I think this is a good lesson, for lack of a better word, about what ‘evidence-based’ should mean. It means actually listening to the evidence, reading the evidence, before you say anything, even if it is from sources you don’t always respect. Evidence is not about the people or venue its reported in, it is about the evidence. This is not always so easy, but it is an ideal we should strive for.

June 17, 2010

Persevering against all odds is NOT the way forward

Beware of the hype..

Most of us love a good old perseverance, against all odds, pulling yourself up by your boot straps story.

And there are thousands of them about scientific people – some apocryphal, some mythological and some of them are even true.

Are most great scientists like this? Should we take these stories to heart during these difficult financial times? Definitely not.

So many people love to talk about Einstein and how he merely worked as a lowly patent officer and then miraculously launched into cutting edge world physics – apocryphally on his own, where he was anti-establishment, beyond the realm of normal stuffy academics.
But the man had a PhD in Physics and worked hard, incredibly hard, and importantly always maintained access to the library at University of Vienna, where he read alot. And his job at the patent office, wasn’t exacly, what most people probably think it was. They weren’t paper pushing bored bureaucrats at Einstein’s patent office, like the driver’s license offices of today. Nope, they were scientists trying to prove if what was being patented was actually scientifically sound. Intellectually, it was a fabulous place to be.

Then we have the mythological – the Good Will Hunting model, where the poor Boston working-class boy who sweeps the floor is actually a mathematical genius and can solve things just by well, you know, gazing at numbers on the wall knowing what they mean – with NO training. Which would be akin to learning to speak Chinese by just looking at the characters, which I have tried – it doesn’t work ( but maybe I am just not a genius).

But, really. This just doesn’t happen. Almost every story like this, when you behind this veneer of idiot savant, there is usually some training, sometimes autodiadectic, hard work and some pre-exposure to the subject at hand.

Then there are the stories about women – how against all odds they overcame adversity to do the scientific research they were passionate about and always wanted to do. Rosalind Franklin is a good example – she was shunned, ousted, and eventually (posthumously in fact) given credit for her contributions to science. This is cool, don’t get me wrong, against-all-odds stories usually puts a tear even in my crusty eye.

But think how much MORE Dr. Franklin could have done with more support and more funding!

And while these are great stories, they are also really dangerous stories.

Why? Because sometimes it leads people to believe that ALL science is conducted, or rather all science COULD be best conducted against the odds by people so passionate they don’t care about things like, getting paid! AND this gives governments a good excuse NOT to fund science or higher education under the idea the adversity is the mother of invention. The real quote, as you know, is necessity is the mother of invention.

But a mother is not the only parent – whether you are single parented or not, it takes two – in some capacity. And what I am getting at is the other parent is almost always SCHOOL and TRAINING. Thinking, and thinking well, takes an awful lot of reading, grist to the mill and work.

So should we give up on science funding and vainly hope that all of the researchers and geniuses out there will just beat the odds and discover what they were going to discover anyway?

Perhaps some would say – yes, sure, why not? If Einstein can do it so can anyone else (I think it is worth mentioning here, Einstein was a theorist… back in the day when they didn’t need computers, but now to be a theorist you really need them, and they cost money).

On the surface this might seem sort of viable.

For instance, the UK, per capita, has a higher scientific publication rate and a higher citation rate from those publications compared to the rest of the world, second only to the US, despite spending a smaller proportion of their GDP, on the average, on science funding than most countries (the US actually spends a lower proportion of their GDP, but the US has a much bigger GDP than Britain).

Now in the current funding climate, this should give us a warm fuzzy smug feeling in the UK, we can pump ourselves up know that we can achieve so much with ‘so little’ and persevere despite the lack of funding.

It really isn’t much solace however, largely because it is NOT TRUE.

These are statistics from 2004, AFTER the UK has increased its R&D budget over a 10 year period from 1992 to 2003, under Labour, to be close to the highest in Europe by the end of 10 the year period. However, NOW, the science, R&D and Higher educations budgets are decreasing, so these publication statistics will undoubtedly get worse, the UK won’t be soaring at #2 after all of the budget cuts.

When you are close to the top of research and innovation is when you want to put in MORE money to keep up the momentum, not slide back into wartime austerity measures, and start bringing up stories about those who persevered without.

This is true especially now, when most UK-based industries are failing and new ‘technologically based industries’ are needed. ALL of the candidates in the recent UK general election were in agreement about this, during the election anyway, though not apparently any more.

A ‘make do and mend’ mentality, persevering against the odds are admirable individual qualities and of course help with research, teaching and reading science. But relying on these qualities to emerge from underfunded science and education sectors is not simply less than ideal, it is the death toll for science, innovation and higher education en masse.

But I guess we will get some good stories out of it.

June 13, 2010

Facts shmacts

Filed under: bad science,random,science ethics — sylviamclain @ 12:54 pm
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in support of Dr. Goldacre…

There is a recent controversy between Ben Goldacre and Jeremy Laurance concerning Goldacre’s ‘attack’ on health journalists. Laurance, doesn’t like it, and one of the points he brings up is that Goldacre doesn’t know the pressure journalists are under with deadlines and etc. Which presumably means we should be forgiving about him not checking the facts.

Well cry me a damn river …

We as scientists are under greater and greater pressure to do the same thing that journalists are doing according to Jeremy Laurance, namely, in order to keep our jobs in research we need – grants, publications, high-impact papers, etc. Where there is obvious pressure to pubish faster than we maybe normally would.

I feel this pressure, I need papers, I have several which are ‘almost there’ but I don’t think are good enough to publish. I have a fair amount of research experience, have written a fair number research publications (admittedly not inthe 100’s) and at this stage I have a pretty good idea when I might need to publish something, and when I need to hold off and do some more work.

So you might be thinking, yeah but you don’t have a deadline. REALLY? Scientists have deadlines just like anyone else (I am sure Ben Goldacre has deadlines too – he is after all a journalist). We give talks, go up for probation (and these days redundancy boards thanks to budget cuts), write grants (where your track record is assessed partly on your number of publications), have to get students (who don’t want to work for you if you aren’t well published) and all while teaching and doing administration.

But is anyone, ANYONE, going to feel sorry for me in the literature just because I had to publish my research quickly? And say, well, its ok that the facts weren’t checked, because scientists are under too much pressure these days? I sincerely doubt it.

And what kind of scientist would I be if I just shoved half-baked research out?
A really, really bad one is what I would be.

Whatever you think about his methods, it should be remembered that Ben Goldacre’s column is called BAD SCIENCE, and not ALL JOURNALISTS ARE CRAP – and this is actually important. There are bad scientists just as there are bad scientific journalists. And both are similar in that they either don’t check their facts or they don’t finish their job. And I think all Dr. Goldacre is pointing out is, they should have checked the facts.

May 23, 2010

Science takes time and we are not all going to die…

Filed under: genetic technology,morality,science,science ethics — sylviamclain @ 1:00 pm
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well we are, but not by a world taken over by synthetic beings in the near future…

Science isn’t very fast, even though it often seems like it especially when we read media reports about ‘new’ scientific breakthroughs…

Last week, Genetic entrepreneur Craig Venter who established the genetic tech company the Venter group, published a paper in Science where they took a chemically synthesized genome and created a bacteria cell. They synthetically reproduced the genome of bacterium A, then they put this genome into bacterium B (different species) and the host bacterium B produced bacterium A cells.

Replicating synthetic DNA using bacteria or just enzymes from bacteria has been happening for a long time, its what is used in recombinant DNA technology, invented by Stanley Cohen and Herbert Boyer in the 1970’s. It is, for instance, how we can use DNA for crime cases, by replicating bits of real DNA synthetically. What is different in the Venter paper is that this technique used synthetic, man-made DNA to replace the natural DNA of a bacteria to form a new living cell, which is entirely ‘run (and can replicate itself)’ from this synthetic DNA, this is kind of cool.

And technologically this is an enormous step, the Venter group had to develop a new methodology and techniques for this to work, which again is a large-scale significant feat, but there is no new underpinning scientific discovery in all of this. Or more simply put its a small scientific step and a huge technological breakthrough.

So why is this distinction between science and technology important?
Science and technology are not the same thing (even though there is sometimes a fuzzy line between the two), we have forgotten this…
and the science bit, well it takes a lot of time.

Technology development can be fast – but science isn’t necessarily fast, in fact it is almost never fast… but it is science that underpins any technology, and technology is one outcome of science which has been built up by years of research, which has evolved over a long period of time.

This result has also sparked a debate about ethics ,‘playing god’ – eventually wiping out humanity á la ‘I am Legend’ – and even a warning from the Holy See. This genetic ethics debate is not exactly new, I remember having it as an undergraduate in the late 1980’s and it also arose when Dolly was created…

But are we in any kind of imminent danger of synthetic humans taking over the planet? I don’t think so – why? Because science takes a long time.

For instance think about how long has it taken to get to the point of making a bacteria? and Venter reproduced an already known species of bacteria, they didn’t create a super bacteria which can say jump tall buildings in a single bound and this is a really important point….

Well its taken years and pretty quick years by the normal scientific standard.
In 1868 DNA was first found by Friedrick Miescher who called it nuclein.
In the 1910’s X-ray diffraction was discovered by Max von Laue and the father and son team, William (not Billy) Lawrence Bragg.
In 1953 James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin discovered the structure of DNA using X-ray diffraction techniques.

Incidentally the von Laue and Bragg’s were physicists. Who didn’t probably care (or know) about Miescher’s nuclein when they were watching atoms scattering X-rays from minerals.

The point of all of this – that science takes time. It also takes us on paths we CANNOT predict no matter how much we DO try to predict. So just because we can technologically make a known bacteria from reproducing and ‘watermarking’ an already existing bunch of DNA, doesn’t necessarily mean we are on a linear path to creating some kind of superhuman…

If you read Venter’s Science paper he says this:

No single cellular system has all of its genes understood in terms of their biological roles. Even in simple bacterial cells, do the chromosomes contain the entire genetic repertoire? If so, can a complete genetic system be reproduced by chemical synthesis starting with only the digitized DNA sequence contained in a computer?

So they answered the last question, but not the first one…. Meaning, they know they can reproduce a bacteria, by reproducing its DNA, but they still cannot explain at an intimate level the totality of gene function and again

No single cellular system has all of its genes understood in terms of their biological roles.

We are still a pretty long way from understanding this, even though we can now reproduce something that is already in existence, Venter’s bacteria A is a known species, we don’t know which bits of the genetic code to change to make say a hippo from a bacteria. And when is this going to happen? Who knows? And this is a scientific question that is likely going to take a long time to answer, and may even involve a scientific revolution on the order of Copernicus or quantum physics…

Technologically Venter has made a huge leap, but scientifically it really is just the next obvious step in some already known science, there is no new scientific discovery and the science bit, well it takes time…

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