When flickr introduced video functionality, the community was divided. To a certain type of purist it was the beginning of the end, or the last straw; the big coporate takeover ignoring the wishes of a passionate established community in favour of mass appeal. A certain type of purist flouced off and cancelled their membership.

To the rest of us, flickr videos are just moving photographs: just another way to capture the light and landscape, the streets and streams of changing scenes.

more moving photographs...

Spam mail. I don't mean your regular crap. Professional spam mail from the professional spammers: PR. Somebody put me on a list and now all kinds of companies and individuals are paying all kinds of PR agencies lots of money so that the PR agencies can pay the mailing list compiler a load of that money to send me spam about their crap photography competitions. And then I laugh at them in public. Money and time well spent all round, I think.

Last week, for instance, Rebecca at AppleJupp could hardly contain her excitement to be announcing to me the totally new "mobile phone photography course" being organised by "Photography Made Simple". For just forty pounds, this unique course will, for the first time ever in the UK, teach you how to take photos with your Blackberry. But where do you go to become a qualified cameraphoner? Crystal Palace.

Sadly, as it was last Saturday, I was too late to make an anonymous tip-off.

I used to work on Cleveland Street in central London. Our next-door-neighbours at "The Tower, 60 Cleveland Street", were one British Telecom. Their offices were designed for some old fashioned method of telecommunications routing involving microwaves, and so it just happens to be one of the most distinctive -- most noticeable -- buildings in the country, being as it is, a narrow cylindrical building of 620 feet, covered in antennae and dishes, in an otherwise low-rise and conventional section of the centre of a major world city. Legend has it that, because of the potential military importance of the communications networks, the tower was only officially revealed to exist in 1993 by an MP responding to the persistent rumours -- conspiracy theories! -- that there might possibly be a large and unusual shaped top secret skyscraper somewhere in the vicinity of the Totenham Court Road. These days, the tower is largely redundant: the idea of using microwave technology as the backbone to a communications network didn't really have time to catch on before fibre-optics became the in thing. These days, most of those antennae and dishes are decoration, unplugged and silent, protected from removal by a grade II listing. The building is nothing more than heritage. It just sits there looking pretty, counting down the days to the Olympic games in LED lights that can be seen from miles around.

At the same time as working in Cleveland Street, I was living in the shadow of another transmitter, the more mundane but equally difficult to miss Crystal Palace Transmitter, which rises 720ft above the chalk hills eight miles south of the city centre. Though only the second tallest structure in the capital, once its 360 foot base height is factored in, it becomes the highest, and is prominent on the horizon from around the city. It is the main transmitter of television and radio -- local and national, BBC and independent, analogue and digital -- for the whole city.

In february 2008 I photographed the transmitter from the public park below it and was issued with a stop-and-search by the metropolitan police. A pair of officers drive a patrol car around Crystal Palace all day specifically for this purpose (at least, this was the case in 2008). I think they were probably just bored and wanted something to do -- somebody to talk to -- for five minutes. They explained the reason for their constant zealous and jealous vigilance: the transmitter hosts the emergency services radio system (I have subsequently been unable to verify this fact) and is known to be a terrorist target. One of the officers said, "nah, it's fine, just, like, you shouldn't put the photographs on the internet or whatever, cos they might be used by terrorists in planning an attack."

There are 418 flickr photographs tagged "Crystal Palace Transmitter", and approximately 38,000 google image hits, alongside the usual detailed Wikipedia article and fine google earth coverage. Its existence is not one of London's better kept secrets.

The point I want to make about all this is not about whether the things the policeman said are true or lawful, or to bitch about the general behaviour of individuals in the metropolitan police (these two might have been a bit dim, but they were perfectly nice), nor is it really about the need to stand-up for our civil liberties (you're familiar enough with that argument already). Because the idea of stopping and searching photographers in the name of keeping London safe fails at a much more fundamental level than the civil liberties argument: terrorists don't go around photographing the crystal palace transmitter. And piles of money -- our money -- are being spent to act upon the absurd idea that they do.

There are two main reasons why terrorists don't go around photographing the Crystal Palace transmitter -- apart from the fact that it's easier to look the photos up on Google Earth. Firstly, it's because terrorists aren't photographers. I don't simply mean that, like almost 100% of people, almost 100% photographers are not terrorists. I mean that terrorists aren't photographers. Perhaps in cheap TV dramas, where one can't illustrate that a character is shady by showing that he is thinking shady thoughts, terrorists go around with their expensive SLR equipment taking photographs of their targets. In the real world, they don't. When asked for evidence to support the efficacy of their activity, the best the police can do is point to one guy who went around filming stations with a phonecam and who was successfully prosecuted for, er, fraud and immigration offences. He could, perhaps, theoretically, be linked to terrorism, though, they say. And apparently that's good enough evidence for police in London.

Secondly, terrorists don't go around photographing the Crystal Palace transmitter because terrorists aren't interested in the Crystal Palace transmitter. Not unless they are shit terrorists. I'm not an expert on the way terrorists think, but I understand that Terrorism Studies 101 teaches that the goal of the terrorist is to make a scene: to get into the headlines and get into people's heads; to spread their message and to spread fear. Toppling a tower in a suburban park and depriving a few million people of Celebrity Big Brother for the five minutes that it takes the engineers to switch on the backup signals is somewhere down in the thousands on the list of the most effective ways one could achieve that goal. Toppling an iconic piece of architecture in a busy central business district -- even if the tower was functionally redundant -- would have a far higher impact. Which is exactly why terrorists did target the BT Tower: the IRA exploded a bomb there in 1971. But I never did get a stop-and-search on Cleveland Street.

Some of us still cling to the unfashionable idea that if one wants one's actions to be effective, they need to have some basis in reality and be informed by evidence about how the world works. The Home Office told us what they think of that idea back in October. If there's one thing the Home Office can be commended for, it's being consistent in ignoring the inconvenient complications of the real world as they instead throw our money away on absurd ineffective solutions to serious social and security problems.

I have been quiet here for a couple of weeks while getting my blogging in order. Over the past couple of years I've been blogging here sporadically on a random assortment of topics from photography to publishing via skepticism and hardcore science. Because that combination of interests is rather unique and few of you care to read my uninformed thoughts about all of them, but because I can not decide on any particular topic to give up writing about, the blog is therefore being broken up and the parts sold to the highest bidders. So from now on, you can find me blogging in these places:

• On the nature of science, skepticism and bad arguments at Lay Science
• On science publishing, open data, and the future of the scientific paper at Journalology
• On hardcore cancer biology at a location yet to be announced
• and the stuff that I just made up off the top of my head -- the LabLit and Skepticism Lit -- at another location yet to be announced

Leaving this site to become a dedicated photography site. That doesn't mean I won't be writing much here. I'm going to be stepping up the blogging about photography and about being a photographer in London and the UK, and about some of the photogenic and not-so photogenic locations that I stumble upon. You may also have noticed that the site has just been reskinned ready for its new photography focus -- do take a look around at the updated galleries!

But what if you do happen to have all of the same interests as me and do want to hear my uninformed views on all of them? That's OK! I've made another little site to amalgamate them all -- you just need to subscribe to that!

Thanks to everyone who subscribes, and please take a moment to update your subscriptions -- unless you were only ever here for the photography talk.

Here are a couple of short extracts from a piece I started writing in the summer on the subject of research fraud. One day I will find the time to pick up work on it again. By this stage in the story is has been established that the narrator is a European student, the setting is the Midwestern United States, and "Jeff" is the narrator's boss, an Assistant Professor.

It is a banal coincidence that Sabriena and I celebrate the anniversary of our birthdays on the same day of the year.  The day happens to fall in the second week of August, nine days after Kate and my arrival.  Aside from Sabrina herself, the only person who wished me a happy birthday on that occasion was the large bored desk clerk at the Social Security Administration.  Kate and I had taken the afternoon off and the bus downtown to queue up for an hour in order to receive the magic number that opens up the exciting possibilities of bank accounts, pensions, and legitimate salaries.

And so I turned twenty standing in a queue just so that a clerk could fill in some forms on my behalf.  Afterwards, Kate went out to spend the evening exploring the downtown area of the city; for me, however, finding out just how soulless and depressing that city centre is would have to wait for another day.  I had to ride the bus back up the hill to the university.  I had been asked to.  Well, not exactly asked to.  It was simply assumed that I would.  Jeff had already given me the work to do.

When I arrived back, shortly after five, Sabrina was still working too.  Working rapidly but with great skill.  Transferring micro-quantities of liquids between millilitre Eppendorf tubes with a speed and accuracy that was thrilling to watch -- a skill that I would soon acquire myself.  Sabrina had two young children and a birthday dinner appointment that she couldn't miss.

I had no such excuses.  That would be the first day that I would work through to eight, and it would not take long for this to become normal.  Jeff seemed like a nice enough guy, just a little hard working, hard driving, and ambitious.  I was fine with that; I might have to learn to say "no" if ever I found myself with other things to do, I thought, but otherwise I didn't mind the work.  And he was friendly and jolly with everybody.  He shared jokes about the latest publications with the professor emeritus who sometimes toured the building in his wheelchair.  He shared jokes about last night's basketball with the cleaner.  The kind of person who, when he asks you how you are, you don't even notice that he couldn't care less.

So I found myself spending an evening in the cramped and crowded culture room, one of several small rooms that doubled as a partition between our half of the wing and our neighbouring lab.  This room, ten feet by eight, was stuffed with two incubators, similar in size and design to the standard upright fridge-freezer, and two great laminar flow cabinets. These latter devices provide a a metre by half-metre working space with a glass screen and aperture to insert one's arms, surrounded by an array of bulky nineteen-eighties machinery for maintaining the correct pressure and airflow for sterile technique.

I wasn't alone, of course.  Often I would find myself last to leave the laboratory, but as often there would be somebody still to bid goodnight to at seven, eight, nine o'clock.  On this occasion it was the post-doc Earl.  He was occupying one of the cabinets, processing fresh surgical explants ready for his experiments.  I silently gave thanks to be working with a long immortalised population of cells, happily growing suspended in nutrients in a jar, free from the grisly details of life in a complex multicellular organism.  I settled down where the fresh flesh -- the bloody fatty cancerous lump -- would be out of sight.

Over those three hours or so of repetitive mixing of liquids, swirling of dishes, counting of cells and centrifuging of tubes, Earl and I chatted.  About our projects and our governments, the places and the people that we knew.  He was a proper American, from Biloxi Mississippi.  Wide and freckled, bald and bearded and southern-accented.  An educated liberal, of course – everyone was.

And we talked about the lab and its people, past and present.  We talked about the prof, Adam, who had been born Adolf in 1930s Germany; the other post-doc, John, from Oregon, who rose at four each morning to ensure that he could always be home for dinner with his daughters; the students, Sabriena and Tanya, and Kara and Billy who had married in Vegas; Pam the laboratory manager; and Jeff.  It wasn't the first time that I had heard stories about Jeff.  But up until then the advice had been vague, delivered with a smile and a wink.

Earl took no such trouble.  He was never rude to Jeff, but he was the only person I had seen return Jeff's charm with a blank face that asked "why the fuck is this guy still talking to me?” Jeff and Earl talked about politics in exchanges that would be described as "robust".  As a reaction to his Chinese upbringing, Jeff had fallen to the opposite extreme of American libertarianism, and he was probably the only academic in the building who had supported the war.  But Earl didn't hate Jeff for his politics.  He could handle robust exchanges.

It was hypocrisy and shallow charm that Earl hated.  The way Jeff talked to Sabrina when an experiment failed.  The pressure that he put on her to work late and not see her children, when he was driving home to his own.  And it was the loss of the previous laboratory manager, Joannie, who had been under Jeff's management.  She had quit without giving notice after only a few months of it, and nobody ever found out the exact reason.  A straw just broke the camel's back, they supposed.  Despite his distance from those events, Adam had at least had the sense to take direct responsibility for Pam when she was hired in Joannie's place. "Don't let him bully you," Earl said.

--

By the end of August, I was largely left to manage experiments and get on with them myself.  I had been taught all of the basic procedures and scribbled notes in a file labeled “Joannie's Protocols”, so Jeff disappeared to his office.  He would occasionally come down to the lab to look at some results, declare them unsatisfactory, and give orders for a repeat experiment, or some variation with a different drug or concentration.  Cell culture experiments take some time.  Not because the procedures are complicated and intensive -- though they can be -- but because cells need to be grown for several days, exposed to drugs for hours and given a day or more for the effect of the chemicals to become apparent; proteins separated on paper need to be incubated with antibodies overnight; photographic films left for hours to pick up faint sources of luminescence; and stocks of cells need feeding at three day intervals – no more, and no less.

The job of the cell biologist is therefore not a nine to five monday to friday affair.  Working at weekends -- just the essential tasks as part of ongoing projects -- is normal.  Everybody does it sometimes.  It was the last saturday in august that I got on my new bicycle and rode off into the heatwave at ten in the morning.  There was an hour of essential tasks to see to, and perhaps some less essential ones, which could really wait until monday, but which involved results that people were very keen to see.

When I wondered in, Adam was making a rare visit to the shop floor.  He stood at the edge of a very large puddle almost shouting at the man in the sleeveless shirt and tool belt who stood beside him staring at the water.  Jeff and Earl were moving soggy cardboard boxes up onto shelves.  Billy had headphones on and was standing in the puddle working and ignoring everything that was happening around him.  Ten minutes later Adam and the facilities guy were joined by Karen, head of the neighbouring lab, who had come to collect her barrel of distilled water from the water distillery that we shared with the rest of the wing.

It transpired that the second-year undergraduate student who did odd-jobs in Karen's lab several evenings each week had set the distillery running the previous evening.  Only that day returned from the summer break, by the time he had completed his other chores he had forgotten about the machine and went home.  Overnight, a gallon of water each hour bubbled over the top of the barrel, tumbled down the sides of its trolley, and slowly spread across the watertight black linoleum floor.  Most of it had accumulated in the little tissue culture room, whose wooden furniture would still be damp and beginning to smell on Monday.

On the Monday morning I saw that undergraduate for the first time. Karen led him in to make an apology to Adam.  Short and shy, he was trying to disappear behind her, but she pushed him out to stand in front of everybody and speak.  I didn't care what damage his flood might have done.  I was far too distracted by his blue eyes, scruffy hair, hint of beard, and the nerdy pun on his t-shirt.  I lent on a bench and tipped a jar crashing over the floor before he could finish his apology. But by then nobody else really cared what damage his flood might have done either.  Reports of the first levee breaches were on the radio and eastern New Orleans was already under water.

Hurricane Katrina destroyed Biloxi Mississippi, and the fungal contamination that grew in the damp tissue culture room destroyed hundreds of hours of carefully prepared surgical explants.  Three days later, while Earl threw piles of flasks and dishes into a biohazard bag, Jeff stood in the doorway of the tissue culture room complaining about the sudden rise in gas prices.  Earl broke his nose, walked out, and never came back.

I should remind the reader that this is a personal blog and it doesn't represent any organisation or company I might be employed by affiliated with.

A friend of mine once told me how much she hated "the proliferation of these bioinformatics papers." All these simulations and models of what happens in real life. All of it utterly useless -- since when was the stuff that comes out of a computer worth anything? None of it even remotely reflects anything that happens in real life. And the methodology papers -- the endless methodology papers. They're making yet another neural network and modifying a bayesian something-or-other, when they haven't even found where they left the markov models yet! How can you have so many of these methodology papers? Clearly they can be no more than incremental advances. (Of course, BLAST is an exception -- it's old enough to have been around and heard of when we were undergrads, and is therefore a perfectly legitimate and mainstream molecular biology tool.)

Similarly, some people still voice their skepticism about the need for open access. Access isn't really a problem, is it? These open access advocates are just making facile arguments about the how the people who pay for scientific research should have some kind of say regarding its dissemination.^[1] Come on, really, show me, who is in want of access? Everyone (everyone who matters) already has subscriptions, right? Access isn't a problem. And the open access "movement" isn't an ideology. It's just another business model.

And then, yesterday afternoon m'colleague shouted for advice handling an author of a scientific manuscript who was questioning the need to deposit her not inextensive collection of genomes in a database. I don't blame the author for wanting to get out of the chore—she had a lot of data, and depositing it will be a dull repetitive task. M'colleage was trying to write a letter and struggling to put into words the reason why we mandate deposition of sequence data, and why merely including them as supplementary MS Word files isn't good enough.

These attitudes, you will have noticed, have one particular thing in common: they all completely miss the fact that the biomedical sciences have moved on in the past quarter century. In almost every field (lets not wake the poor taxonomists) the science being done and the science being published today are not quite like that of 25 years ago. Even if the science of today were like that of 25 years ago the case for open data sharing would be strong enough; as it is, it's simply absurd to think that open sharing of data isn't worth doing.

--

Individual scientific papers -- the basic units of scientific research -- are rarely exciting; rarely even interesting. Where nerds get excited about science, it's where science offers a beautiful explanation for how the world works. And scientific papers don't do that. They offer some speculative interpretations of data on obscure problems in obscure systems. It is the literature as a whole -- hundreds of dull papers put together -- which tells a complete and exciting story. The sum is more than the parts -- the theory is more than the data.

In the field I know best -- cancer cell biology -- 99 in 100 papers published are tedious details, discovered with a science-by-numbers formula. The (anti-)proliferative effect of one abbreviation interacting with another abbreviation in three-letter-acronym-and-a-number cells, concluding with a suggestion that the authors' work might have implications for cancer treatment and a note that further work is necessary. Or even better, the complete lack of anything interesting at all happening when the first abbreviation interacts with the second. The abbreviations and their effects have been studied, in combination with others, in all of the most widely used three-letter-acronym-and-a-number cell-types, and somebody is scraping the barrel.

But the tedious details put together add up to an understanding of how the cell works and how it goes wrong. The details could be put together by a human, going through the thousands of papers on the topic, assembling the facts and finding the trends. Or, more plausibly, given the amount of tedious details out there, they could be assembled by a computer, with a database and a clever algorithm. Except that four in every five of those tedious details, discovered at great expense to taxpayers, will be inaccessible to that clever algorithm. They will be locked away in the basements of university libraries, hidden in human-readable prose that humans will never read. The results of billions of pounds of work searching for an understanding of cancer and a better chance at defeating it will be worthless, because they will never be amongst the parts that add up to the greater whole.

So I told m'colleague to explain to her author that unless she deposits her genome sequences, the last three years of her professional life will ultimately have been wasted. An average paper in a high-volume mid-tier journal that will be glanced at by a few colleagues when published. Another bullet point on a CV. They will never further science beyond that. They won't contribute any important discovery or real advance to the field. They will be forgotten. Nobody will seek them out when the time comes to make the leap forward.

That's just where biology is at these days: lots of tiny fragments of data, spread thin through the literature. The most interesting and important unanswered questions will require the synthesis of that work. The most interesting and important questions can't be answered without the heap of data that has already been produced, but which is locked away.

On machine readable data, Mike Ellis says, "at some point in the future, you'll want to do "something else" with your content. Right now you have no idea whatsoever what that something else might be." This is especially true in science: at some point in the future, tedious data obtained at great expensive, as part of the bigger picture, will finally be important and valuable. Right now, you can have no idea how important.

Publishers are allowed to get away with keeping science closed, holding it back, and wasting public money because there are still sufficient numbers of scientists who let them -- who have themselves failed to grasp that the world and science have changed.

Since sequencing the human genome, the Sanger Institute in the UK and the US National Human Genome Research Institute have turned their sights -- and their vast sequencing capacities -- to cancer. Cancers can be thought of as genomic diseases, caused by somatic mutations, and progressing by the accumulation of further mutations. Last week, Nature published online the papers describing two new cancer genomes,^[1][2] bringing the total number of human cancer genome sequences published to five. Pleasance et al sequenced a malignant melanoma and a lung cancer cell line, comparing them to the genomes of healthy cells from the same individuals. Melanoma and lung cancer are good choices, since each has a very strong association with a specific cause -- UV radiation and tobacco smoke respectively -- and their causes are as different as two carcinogens can get, so comparison of the genomes of such tumours could tell us interesting things about the types of genes and chromosomal regions susceptible to physical versus chemical carcinogenesis.

These publications are more important as a symbol of where cancer biology is going than for the actual results that they report, though. Because they report on the genomes of one individual tumour each, we can draw from them little in the way new conclusions about cancer in general. In each case, the genome sequence was derived from a metastasis, meaning that the cancer was at an advanced stage: its cells would likely have been subjected to many stresses, may have lost many of the mechanisms that protect the genome against further damage, and would therefore have picked up a large number of mutations and chromosomal rearrangements long after the initial carcinogenic transformation event.

To further complicate matters, both the cancer cells and the control cells taken from the same individuals were established cell culture lines. Cells do not naturally find themselves in petri-dishes, and do not tend to grow very well outside of the body. In establishing cell culture lines, therefore, cells are subjected to all sorts of additional stresses, and natural selection means that the cells which survive in a dish may not be entirely representative of the starting population of cells.

These genome sequences, then, show us that these cancer cell lines contain tens of thousands of mutations, but it's difficult to say which of those might have been caused by the original carcinogenic attack and could have had a role in the cancerous transformation; which were picked up as the tumour grew, its cells competed, and further adaptations -- like invasion and metastasis -- were acquired; and which were produced by the act of establishing cell lines.^[3] The authors do a little preliminary bioinformatic analysis using software which seeks mutations in functional sequences, but here the original limitation of the papers -- that they have a sample size of one -- prevents us concluding much that we didn't already know.

That's not to say this isn't exciting. These papers herald the truly important results of the cancer genome projects that will emerge when the sample size is in the hundreds or thousands, when we have sequences of sequences showing how tumour genomes evolve as they progress, and comparative cancer genomics potentially revealing signatures common to all examples of a particular cancer, or tumour sub-types that react to different treatments. We've taken the first steps into cancer genomics over the past decade -- from genome-wide association studies and high-throughput comparative genomics with technology like microarrays, to the first trickle of whole-genome sequences. It'll be thrilling to see where it goes over the next -- what it reveals about basic biology, and how far it advances personalised medicine.

References

1. ^  Pleasance, E., Stephens, P., O’Meara, S., McBride, D., Meynert, A., Jones, D., Lin, M., Beare, D., Lau, K., Greenman, C., Varela, I., Nik-Zainal, S., Davies, H., Ordoñez, G., Mudie, L., Latimer, C., Edkins, S., Stebbings, L., Chen, L., Jia, M., Leroy, C., Marshall, J., Menzies, A., Butler, A., Teague, J., Mangion, J., Sun, Y., McLaughlin, S., Peckham, H., Tsung, E., Costa, G., Lee, C., Minna, J., Gazdar, A., Birney, E., Rhodes, M., McKernan, K., Stratton, M., Futreal, P., & Campbell, P. (2009). A small-cell lung cancer genome with complex signatures of tobacco exposure Nature DOI: 10.1038/nature08629 full text
2. ^  Pleasance et al, 2009. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature advance online publication 16 December 2009, doi:10.1038/nature08658 full text
3. ^  The authors say: "If the majority of mutations derive from the mélange of mutagens present in tobacco smoke, the clone of cells that ultimately becomes cancerous would acquire, over its lifetime, an average of one mutation for every 15 cigarettes smoked." I suspect that this could be a slightly misleading picture of cancer biology, and it would be interesting to know whether it really is true that the majority of mutations in an advanced lung cancer cell line are related to the original carcinogens rather than stresses in the progressing tumour and cell culture.

Skepticism -- the movement and the everyday scientific method -- is about vetting the new ideas that want to take up residence in our minds. It's a critical thinking toolkit that is there to prevent us getting fooled. It's not cynicism or stubborn disbelief, just a cautious and questioning approach to the claims of others. It's knowing the fallibility of the human mind; it's the opposite of gullibility.

The gold standard that a skeptic seeks in an argument is to be able to see and evaluate and understand the original science and data and statistical analyses that supposedly support the claims of that argument's proponents. But one doesn't always have the time or expertise to go around making such rigorous examinations of complicated arguments. In those situations it's common to tentatively accept the conclusions of experts in the field who you believe to have made those rigorous examinations themselves and who you trust to have got those examinations right. Accepting the consensus of the experts without having rigorously examined their evidence yourself is an argument from authority -- a "trick", if you like, but one that is not entirely unacceptable.

But for an issue as important as climate change, where we're talking about big risks and being asked to make big sacrifices, one wants to make a more rigorous examination of the arguments and evidence and to be more confident about the science than one would for matters of less consequence. But proponents and opponents of anthropogenic global warming (AGW) both claim to have the science and the data and the statistics on their side -- they both claim to have applied skepticism and the scientific method -- and the lay person perhaps doesn't have the dozens of hours required to learn the maths and chemistry and physics behind the arguments. All they're left with is picking the side with the most PhDs in climate-related sciences, right?

But the AGW proponents have one other important thing going for them: even if the skeptical lay person can't independently evaluate the claims of the proponents, they can easily see the absurdity of the claims of the opponents.

For example, on this week's Little Atoms, Johnny Ball embarrassed himself with this series of arguments:

1. According to Ball, there is a scientific controversy because: "would you consider a qualified engineer to be a scientist? I think I would, and the majority of engineers don't believe that we're changing the climate.^{[citation needed]}" Well, no, engineers are not scientists. Some engineers -- a small minority -- happen to also be scientists, but engineering is not a science, at least, not in the sense that matters. Many engineers know much about how physics and chemistry work, and most probably know more mathematics than the average scientist. They can apply some scientific facts about the way the world works. But they are not doing science. Science is a body of facts and theories about the way the world works, but far more importantly, it is a way of studying the world. Science is a process and a tool, a method of empiricism, critical thinking and skepticism. Engineering and science share facts about the world, but they are very different processes and very different tools. The two professions think in different ways, and are rarely taught anything about each-other's way of working.
2. Climate scientists are "cooking the books for grant money". Yeah. It's the scam of the century in which tens of thousands of individuals have abandoned their scientific principles to cooperate in successfully defrauding all the governments and funding agencies of the world. Also, did I mention that they are Reptilians? Dudes, have you still not realised how absurd you look making this claim?
3. Ball points out that climate scientists ignore the sun-spots -- we keep shouting "sun-spots" and they keep ignoring us! Uh. Except, he forgets that somebody went and invented Google. We can all now google about sun-spots and climate change, see just how climate scientists have ignored them by, er, studying them and incorporating them into their theories and models and papers and reports, and we can read the lay summaries of climatologists and astronomers explaining why sun-spots aren't -- and can't be -- more than a minor detail in climate.
4. Finally, Ball compares climate change "sceptics" to Darwin and Faraday and Copernicus, while climate scientists are like eugenicists: when Darwin proposed evolution, the scientific consensus was against him, and it took a few decades for the rest of the scientific community to catch up. Ball seems to be proposing that, er, climate change scepticism is, uhm, a new science that the rest of the scientific community will catch up with over time. Did he somehow miss the last thirty years of climate scientists slowly convincing the scientific community into consensus?

The lay person can have some confidence that the climate scientists are right about AGW not merely by weighing PhDs and picking the authoritative argument. They just need to look at the sheer amount of money and effort poured into the argument by the denialists, and snigger at how embarrassingly piss-poor are the claims that effort buys. Zombie arguments and absurd conspiracies. The climate scientists might be giving us data and graphs and theories that we couldn't possibly independently verify, but when the best the denialists can buy is a "rah rah rah look at the sun-spots" and a "help help, we're being oppressed, like Copernicus", I know which argument my skeptical mind is more persuaded by.

And this is also why Greenpeace need to shut up and let the grown-ups put the case for AGW.

I caught the first fifteen minutes of Radio 4's Start The Week before leaving the house. Andrew Dalby was on, promoting his book The World and Wikipedia: How We Are Editing Reality. It was actually Amanda Goodall, author of Socrates in the Boardroom, who made the most interesting comment. I paraphrase from my hastily scribbled note:

... we feel guilty about using it, and nobody 'fesses up to using it, perhaps because we feel it doesn't have any legitimacy -- because it doesn't look like it has any legitimacy. Perhaps it's time to introduce, say, a small fee for use, to introduce some legitimacy.

Of course. That's exactly the problem with the "free" model that the internet -- by cutting materials costs to nearly nothing -- makes possible. Because you're not paying, directly and openly, for a product or service or content, it doesn't look legitimate.

It's the same dilemma that we had with walks in the park. These are clearly illegitimate as forms of exercise or leisure, and so we rightly built (on those parks, appropriately) gyms, which, by charging just a small monthly fee, made walking legitimate. Or free education. I am unfortunate enough to be amongst those who spent several years studying for a worthless sheet of paper from an illegitimate "back-street" university. This government deserves great praise for bringing the back-street universities into the mainstream by allowing them to charge students a small fee for their use. And what is the oldest profession but the welcome legitimisation of an act that, without the direct and open exchange of a small fee, just doesn't feel legitimate?

--

Goodall was not alone in providing refreshing insight into the Wikipedia "problem". Social media expert (got that? social media expert. I bet the BBC blurb writer copied that right out of his twitter profile. I know, twitter, right?) Evgeny Morozov had this additional suggestion to help Wikipedia to gain legitimacy:

It's time for Wikipedia to get an editorial board, because all newspapers have editorial boards, so why shouldn't Wikipedia?

Yes! Newspapers are exactly the great model of success in reliability and verifiability and legitimacy that we should be replicating. Certainly they would not, say, let a self-declared "expert" go around making the embarrassing comments of a novice in the field. You wouldn't find newspapers editing reality.

IanVisits notes the irony of the Docklands Light Railway, famous for their absurd private policing of passengers' photography, launching a photography competition and inviting you to send in photographs taken at their stations, even though their security patrols stop people from taking photographs at their stations. Obviously the scheme was dreamt up by the PR and marketing department, who think that they can get hundreds of publicity photos, some of which are bound to be quite good, for a single payment of £150 (or nothing at all if the prize was in turn given to them free by the manufacturer's marketing department) -- a tiny fraction of the cost of hiring a photographer.

It's a trick that marketing departments and PR companies everywhere seem to have really caught on to this year. Don't pay a professional photographer a grand to get the shot you need, make people do it for free! Offer a cheap prize as bait, call it a competition, and make sure the small print gives you unlimited rights to the catch. Then, target your spam at a few good photographers, and hope that some of them fall for it.

Here are just a couple of the more surreal competition subjects that PR agencies have pestered me with lately:

• Media Consulta PR agency send unsolicited mail on behalf of the EU Safety and Health at Work Agency, who seem to think that it would be exciting to share "my image of Safety and Health at Work." Ironically, their unsolicited bulk mail appears to break theEU's rules on unsolicited bulk mail. But at least the EU were offering a whole €1,000.
• Ceres PR send unsolicited mail on behalf of the HGCA -- the cereal farmers' marketing board. They've created "Annual Farmhouse Breakfast Week", and think that you might want to hand over your photography in exchange for a mid-range kitchenware set. Hey, why not also get a mathematics student to write the formula for a perfect breakfast?

Sadly, the DLR competition seems to have made a schoolboy error -- not in asking members of the public to do something that another department is using all the intimidation it can muster to stop the public doing, but in its offering of a prize. A cheap compact digital camera. Who would want a cheap compact digital camera? Hint: not the brilliant photographers you want to give you fantastic free marketing shots.

People love a good argument with Richard Dawkins. So many people are so desperately seeking reassurance that he is wrong, and book shop shelves groan under the output of writers who are happy to provide that reassurance, in big words and glossy covers, with referenciness aplenty and a friendly review from an Oxbridge theologian. Dawkins calls them his fleas: the hastily bashed out "Dawkins Delusions" and "God Solutions" that claim to refute Dawkins' writings on God, while presenting the same old pitiful arguments for His existence. Parasites on his name, contributing nothing, and not even worth the effort to crush.

Into this environment steps The Selfish Genius, in which Fern Elsdon-Baker sets out to explain why Richard Dawkins is wrong on almost everything he has ever written about. Elsdon-Baker is not a conservative preacher or obscure amateur theologian trying to convince us of God's greatness, though. She's a historian of science who, though she can't keep herself from commenting on Dawkins' religious work, is interesting for spending three quarters of her book arguing that Dawkins has his history of science wrong, his philosophy of science wrong, and, uniquely for the current plague of anti-Dawkins books, his science wrong.

Elsdon-Baker was the guest at the Royal Institution's October Cafe Scientifique, and I and some other curious biology nerds went along -- without having read the book -- to find out whether this flea had a bite. The jaws moved. The jaws moved a lot. But the teeth are missing. To convey the full humiliating extent of this book's failure to break flesh is going to take a little bit of history of evolutionary biology, and some fascinating and exciting contemporary molecular biology. Biology nerds can skip the history, but should be amused by the science.

Continue reading under the fold...

This week, the shocking private emails of a group of senior scientists were leaked after one of the scientists placed his laptop in the line-of-sight of the dozen or so nosy people who were sat behind him at a rather dull public lecture in London.*

Secreted in a back corner of the lecture theatre, Charles Quackenbush strains to hear the next facile question tumble and stumble in "uhms" and "ahs" from the eager humanities student in the front row. He briefly exchanges a look with a fellow from the department (the wednesday evening public lectures are always a source of great amusement for the department's old boys) before returning to his emails, leaving Sir Frederick to try explaining again the very basics of natural selection to the sociologists of science.

Dear Charles, Just to confirm, as per our earlier conversation, that the recording will be Thursday at nine -- my BA will meet you in BH reception. Could you send your press photo for the listings? I don't think we have one on file. Melvin.

Charles taps out a quick content-free response about "looking forward to it", and drags in a file from close at hand. Archives the email.

Dear Prof Charles Quackenbush, I am a MA Science Communication student at City Univ--

Are you sure you want to delete this email? OK Cancel

And then another new arrival; the latest episode in the great ongoing saga that was tearing the department in two. A short episode.

chaz, those are mighty hateful hurtful words. i can't believe you would say such things about collins, after that nice book he wrote about me and science not being incompatible. cheers, God.

Charles frowns, looks up and glances over to his right. At the far end of the row Professor Goddard Z Bumsted O'Higgins leans forward and grins at him, iPhone in hand. Charles doesn't stop frowning. Hits reply, but he's too slow. There's already another new entry. Its author, Professor Elisabeth Penelope Ditherley de Pelet, a row in front to the left, is now staring, stern face and unfocused eyes illuminated by the light from her netbook, at another of Sir Frederick's amusingly captioned slides of his golden retriever.

Shut up, Bumsted, the grown-ups are trying to talk here. Charles, I'm afraid your argument is utter utter cock. It would be by *not* inviting Collins to speak that the university would look like it had the agenda. Obviously you're free to publicly say whatever you like about the guy, but the fourth best university in the world can't snub the head of the NIH without anybody noticing. You know how these things work. When people of his standing announce that they're coming to town, an invitation is expected from us. If you succeed in blocking this, the headline will be "fundamentalist atheists go out of their way to be rude," and I couldn't blame anybody for running it--

Charles thinks about replying with "yawn", and yawns.

--frankly, I'd have thought you'd have more important things to be doing than preaching to the rest of the department. You can't have failed to hear the *gossip*, even stuck in your own fantasy land? -Betty x

Charles frowns some more. Sends a blank email to Goddard, subject "what's the gossip?" Continues through the dregs of his inbox.

Dear valued reader, We are pleased to announce that there is still time to register your place at the first annual International Conference of Gastropodcomparativesystematicsemiquantitativetemporalnuclearmisinteractomics, to be held in Las Vegas, 18-21 March 2010...

Charles hits the spam button.

heheh. betty's post-doc has been telling everyone what she walked in on in the darkroom the other day. your students were in there, *kissing*. from what i've heard, they've been doing a lot of that lately. heh. they're probably in there *now*. I say, though, old chap, I'd have thought you'd have been wanting to put a stop to that sort of thing? cheers, God

The colour drains from Charles and his hands begin to shake with horror. Kissing. How awful. Charles had read that kissing could lead to friendship and a social life, even marriage, or children. Charles couldn't afford for his people to be rushing around all over the place having children. There was science to be attended to, and they were already behind on delivering it.

Charles stares at Sir Frederick's "science kitteh" slide, tapping his feet manically, wondering desperately what he can do to contain the situation. Eventually, the solution comes to him.

Hi All, I stand by everything I've said and will still vote in the 'no' camp, but I have no interest in wasting any more of my time arguing with those of you who apparently don't care for reality, rationalism or academic integrity. Invite him if you like. *I* will make sure that I am well out of it. There's an interesting looking conference in Las Vegas that weekend. I think I might take the whole lab. A good dry conference should get those students back in line. Regards, Chaz.

 * Obviously, any resemblance to real people, events, or email exchanges is entirely coincidental.

Charles Quackenbush stands at the far end of the platform, away from the crowds around the shelter at the platform steps; positioned well over the tactile paving and the yellow line.

"The train now approaching platform... one... is the... oh nine... oh four... service to... London Victoria... calling at... Herne Hill... Brixton... and... London Victoria."

The rails begin to sing their high-pitched wail. Charles takes a deep breath and closes his eyes. The rain rolls down his cheeks.

And the train pulls up, beside him, past him, coming to a stop twenty seconds later with Charles stood, eyes still closed, beside the final set of doors. The doors open, and the eyes open, and Charles doesn't really have much choice but to step on board. He'll just have to get off at the next stop and try again.

"Any unchecked tickets please," comes an abrupt shout. "Good morning, sir, could I see your ticket, please?" Charles, of course, has not purchased a ticket. His intention had not been to go anywhere today. At least, not via Herne Hill. He pays the penalty fare and is given his ticket.

Charles steps off the train with the few dozen passengers changing to the Blackfriars line, and casually wonders across the platform as the Victoria train continues on its way. On the Blackfriars platform, the electronic display scrolls a long list of destinations for the train through to Bedford, the reflected lights creating a psychedelic show on a warped and battered advertising display case.

"I'm sorry to announce that the... oh nine... twelve... service to... Bedford... is delayed by approximately... nine... minutes."

Two empty paper coffee cups are caught by the wind. They roll around in circles, catch on the corner and break dance through the eddies, colliding, bouncing violently apart, and hurl themselves from the platform edge. Charles sits on a cold metal bench and stares through the rain, across the track, over the scruffy scrub of the embankment, and out to the twin beige concrete tower blocks looming over them from across the road. "Open doors other side," reads a helpful sign placed high on the chain-link fence between the tracks and bank.

"Open doors other side," thinks Charles. The doors are open for the post-doc on the other side of the lab, whose experiments work, whose papers get published in Cell and Nature, whose smile charms committees and conference rooms. The doors were always open for the guy he lived with during his PhD, who, despite his obvious brilliance, never bothered looking for a post-doc position but within a year of graduating had already accumulated an MBA and a small but cool hi-tech company. Or his friends at Oxford -- the lawyers and bankers; and his friends from school, who had travelled the world, published novels, and were already sending children of their own to the same school. And here was Charles, at the end of a second post-doc, penniless -- personally and professionally -- and not a datum that any sane person would want to publish. His career was over. They would make him take the walk of shame.

"I'm sorry to announce that the... oh nine... twelve... service to... Bedford... is delayed by approximately... seventeen... minutes."

Charles sighs and sits back in the seat, folding his arms and tilting his head. And he sees it. The damp mouldy rope, hanging from the station canopy; one end tied securely around a beam, the other looped and slipknotted . Why? What purpose could such a thing serve? Charles stares at it for a few minutes, wondering how strong it might be. The estimated time of arrival on the electronic display revises itself. Charles hadn't considered this method. Hadn't done his research. It couldn't be a bad way, though, could it?

Charles stands purposefully, steps up onto the bench and balances with one foot on the arm rest. He reaches out and grabs at the rope. A few of the fifty-or-so people on the platform notice the performance, and wander quietly and casually away, so as not to see the finale. Charles places the loop around his neck, takes a deep breath, and steps onto nothing. He swings forward, out over the coffee cups and cracked tactile paving and faded yellow line. The rope creaks, the beam cracks, and Charles falls, pursued by the station canopy onto the tracks, knocking his head on the lip of the platform and rolling onto the dead third rail. Somebody on the platform looks up from their newspaper and screams. A distant voice rings out,

"I'm sorry to announce that the... oh nine... twelve... service to... Bedford... has been cancelled."

Charles lies on the track for a while, panting, while the stars fade. His eyes focus on a solitary white flower in the fence. Bind weed climbing the wire links. His phone rings, and he sits up with effort, loosening the rope that still hangs from his neck. There are some "yeses" and "of courses" and "thank yous" from Charles, and the occasional dizzy and vacant nod. An offer. Not science. Something about writing and publishing and online media; a startup doing something new, something interesting, perhaps. Not science, but an offer; an invitation to do the walk with purpose and a destination and his head held as high as a head could be. A fresh breeze blows down the tracks, drying his face. He nods to himself, and smiles.

Charles slowly rises to kneel, rubbing his neck and knees and brushing dirt from his damp clothes. He pulls himself up onto the crowded platform with some effort; the broken section of station canopy clattering after him. He stands there, staring blankly at the arrival of the oh-nine twenty-seven. Steps aboard, still lost in his thoughts, and squeezes himself in, with his feet awkwardly arranged around somebody's briefcase, and his face shoved into the armpit of a Metro-reading old man. Then he snaps back into the world as lightning strikes a concrete tower and thunder cracks. The train slows. "Apologies for this delay, ladies and gentlemen. Due to a broken train at Farringdon we are being held in a queue outside Elephant and Castle."

Charles takes a deep breath of armpit, turns around, and starts pounding on the doors.

I think I've mentioned before that I keep a copy of Burkhardt's Selected Letters of Charles Darwin handy in the smallest room ("for fun"). In this letter to Asa Gray in November 1857, a load is lifted from Chaz's mind...

By the way I must tell you what I heard yesterday, though not in your line, but on subject of the crossing of individuals. Barnacles (Balanus) are hermaphrodite & with their well shut up shell offer as great a difficulty to crossing as can well be conceived: I found an individual with a monstrous & imperforate penis, but yet with fertilised ova; but I did not know whether it might not be case of parthogenesis or a strange accident of some floating spermatozoa. Well yesterday I had an account by a man who, watching some shells, saw one protrude its long probosciformed penis, & insert it in the shell of an adjoining individual! So here is a load off my mind.

On Thursday, I fly off to the temperate rainforests and volcanoes of Los Lagos, in Chile. I and some colleagues will be cycling a few hundred miles up and down the hills, and observing some of the work done by Computer Aid International, a charity which refurbishes and upgrades old PCs for use by schools, universities, and hospitals who otherwise wouldn't be able to afford such infrastructure. Computer Aid's work is the kind of charity work that really enables independent development, personal and national: computers enable education and vital locally relevant research.

As you may already know, I've been raising funds for a Computer Aid project to help the development of computer resources at Nairobi's Kenyatta University, which, already in need of research resources, has been the victim of recent troubles. In light of my own bicycle having had a non-consensual change of ownership while locked outside a pub in Fitzrovia on friday night (for which there is an outstanding punch in the face due and waiting on my desk, if the new owner would like to inform me where to send it), I have decided to embark on a gruelling sponsored challenge. Yes, on monday, tuesday, and wednesday this week, I will be riding the tube to and from work.

This is not a simple and relaxing task. I assure you, it is not going to be a holiday. I will be setting my alarm and getting out of bed a full hour earlier than usual, with no training, in order to stand on a street corner waiting for a rare chance to see the elusive number 3 bus. Should I be lucky enough to find one, I might find somewhere to stand on it, while it embarks on its migration through the traffic jams and roadworks to Brixton high street. There I will see one of nature's great spectacles: the herding of literally tens of thousands of humans. I will get to join them as they surge across at the traffic lights, and then stop abruptly and chaotically outside of my first major milestone: Brixton station. There they will wave their Oyster cards with superstitious flourishes at the automatic barriers, and stand two deep on the one working escalator, reading their free newspapers. Then, for half-an-hour, I will be conveyed in a real historical nineteen-sixties tube train through stations that have been stripped and "undergoing refurbishment" for three years. I will bounce around the carriage, held up by the dense mass of armpits, attempting to read a book. The train will stop outside of Victoria Station, in the stuffy tunnel, waiting for the train ahead to clear the platform. The same at Oxford Circus and King's Cross, where I will finally be deposited in a network of tunnels whose configuration seems to change every week, presumably due to the great concentration of magic at platform 9 ¾ above. The last exhausting leg of the journey is the five minute walk across the Euston Road and down the Grays Inn Road, past the snooker halls and the vomit puddles outside the kebab shops, to arrive at work ten minutes late, despite rising an hour earlier than is usually considered civilised. In the evening I will do the reverse. Where signal is available, I will give live updates on my progress via twitter.

So please, please, please, sponsor me on my great tube ride this week. Just a few quid. A bus fare's worth will help advance humanity. Links and tweets also appreciated. I assure you, this isn't going to me: I'll be paying all of my own tube fares out of my own pocket. Here's how you can contribute:

Make a donation through Just Giving.

or...

Buy some prints.

Thanks.

On my recent post, what is wrong with the scientific paper?, Steve Hitchcock said that the most important problem with the paper is access, and that when we solve the problem with access, everything else will follow. I agree that access is hugely important, I recognise that we haven't won everyone over yet, and I know we do have to continue working away at the access problem, so I will devote a future post to reviewing that topic. But having thought about it a little longer, I am more convinced than ever that it is not access that is the big problem which is holding back the paper and journal, and open access is not the solution from which all others follow and fall into place.

There is one big problem, a single great big problem from which all others follow. The great ultimate cause is not, as I said last week, the journal. It is more basic than that. It is the impact factor. The journal is the problem with disseminating science, but the reason it has become the problem, the reason people let the problem continue is the impact factor. The impact factor is a greater problem than the access problem, because the former stands in the way of solving the latter. The impact factor is a great big competition killer; by far the greatest barrier to innovation and development in the dissemination of science.

Scientists can look at all of the problems with disseminating science, and they can look at us proposing all of these creative and extravagant solutions. They might agree entirely with our assessment of the state of the scientific paper and of the journal, and they can get as excited as us at the possibilities the flow from new technologies. But blogs and wikis are mere hobbies, to be abandoned when real work starts piling up; databases a dull chore, hoops to jump through when preparing a paper. So long as academics can get credit for little else besides publishing in a journal — a journal with an impact factor — any solution to publishing science outside of the journal will never be anything more than a gimmick, a hobby that takes precious time away from career development.

In a worse position than blogs and wikis, where cheap easy products are available, are the wonderful but complicated ideas that would benefit from financial backing to implement — the databases, and open lab notebooks, and the like — but which are currently artificially rendered unviable because no scientist could ever afford to waste time and money on a product that isn't a journal with an impact factor. No scientist can try something new; no business can offer anything new. Even such an obviously good idea as open access to the scientific paper has taken over a decade to get as far as it has in part because it takes so long for start-up publishers with a novel business model to develop a portfolio of new journals with attractive impact factors.

I am not a research scientist. I don't have to play the publish-or-perish game. So I have no personal grudge; no career destroyed or grant lost by rejection from a top-tier journal. It doesn't bother me how much agony, absurdity, and arbitrary hoop-jumping research scientists have to go through in their assessments and applications. But it bothers me greatly that, by putting such weight on the publication record — not actual quantity and quality of science done, but a specific proprietary measure of the average impact of the journals (and journals alone) that it's published in — public institutions across the world are distorting markets, propping up big established publishers, and destroying innovation in the dissemination of science. End the malignant metric and everything else will follow.