Category: science

A kilogram of beef is responsible for more greenhouse gas emissions and other pollution than driving for 3 hours while leaving all the lights on back home.

New Scientist, 18 July 2007

In the pub on friday night Dan showed me his boids – virtual creatures that evolve in a virtual world according to a genetic algorithm (yes, these are the sorts of friends I have!). He told me that when he made mistakes in the code, the boids seems to evolve to take advantage of it. So there was a bug that meant that predator boids moved quicker when they were with other predator boids. What happened was that the boids exploited this bug and learnt to hunt in packs.

What I found was interesting was my reaction to this – “Cripes!” I thought “How the hell did they work out how to do that?!”. Even though, as a programmer, I knew exactly how much intelligence and autonomy these boids had (none). Even though, as a dyed-in-the-wool evolutionist, I could understand the directionless-logic of a genetic algorithm, some part of me leaped at the chance to ascribe intention to those little coloured triangles as they floated around the screen. Despite years of thinking about evolution, despite knowing that an evolutionary algorithm was an undirected process, that no boid made any decisions, that all that happened was that those boids which had some simple rule that made them associate with other boids moved faster and this made them more likely to be reproduced in the next ‘generation’ and that this meant that pack-like behaviour became more prevalent – despite all this, my instinct was still to ask “Why did they decide to hunt in packs and how did they see it would work”.

It made me realise just how alien the logic of evolution is, that someone like me who is theologically and intellectually predisposed to want to understand it still fails to grasp it instinctively.

The wikipedia article on Criticisms of Wikipedia

The comparison to the Encyclopædia Britannica runs throughout, and the issue of authority/reliability:

The main problem is the lack of authority. With printed publications, the publishers have to ensure that their data is reliable, as their livelihood depends on it. But with something like this, all that goes out the window. (Philip Bradley)

Now I don’t believe that printed publications are all that reliable, having read a bunch myself and even written a few, but it seems that there is another important difference between Wikipedia and Encyclopædia Britannica. This is not a difference concerning the writing and writers, but a difference in the readers, or at least a difference in the tacit view of the readers the two encyclopaedia’s have. From the Wikipedia Criticisms article:

to the ordinary user, the turmoil and uncertainty that may lurk beneath the surface of a Wikipedia article are invisible. He or she arrives at a Wikipedia article via Google, perhaps, and sees that it is part of what claims to be an “encyclopedia”. This is a word that carries a powerful connotation of reliability. The typical user doesn’t know how conventional encyclopedias achieve reliability, only that they do. (Robert McHenry, former editor in chief EB)

Wikipedia’s detractors imply that readers are defenceless, passive – I imagine them arriving in the shining halls of Wikipedia like wide-eyed children stumbling first time into some emporer’s Palace. Like children they are easy prey for the court tricksters and schemers with their silver tongues, beautiful clothes and easy, cosmopolitan ways.

The view of the readers is made more explicit in this quote from the former editor in chief of EB:

The user who visits Wikipedia to learn about some subject, to confirm some matter of fact, is rather in the position of a visitor to a public restroom. It may be obviously dirty, so that he knows to exercise great care, or it may seem fairly clean, so that he may be lulled into a false sense of security. What he certainly does not know is who has used the facilities before him.

Again passivity, but the second theme here is clear – infection. Innocent children’s mind, polluted by wikipedia’s unsanitised intellectual bugs.

Do we believe that people are that stupid, that they are this weak? With the EB model where a cannon of knowledge is prepared centrally and distributed to a passive audience this model of the reader is appropriate. For Wikipedia, based on the idea of a community of dual writers-readers, it is not so clear that it is.

Question: if you want to falsify a theory, do you need a plausible alternative theory?

Toy-examples of falsification suggest not, but I think they mislead. For example: my theory is “there is a fairy in my cupboard”. Potentially falsificatory test of this theory: open cupboard – is there a fairy there? Ignoring for the moment the problem of the impossibility of hard falsification, it looks fairly straight forward. That was the theory, there was the test.

However, this toy example is so simple it allows us to leave implicit the plausible alternative, namely there is no fairy in the cupboard. If no plausible alternative is to hand, I don’t think identifying a potentially falsifying test is so straightforward.

I arrived at this train of thought via a discussion last night about vegetarianism. I was trying to convince people that we have have an evolved disposition to obsess about and ritualise our food behaviours, so that any food habit, however arbitrary or initially unideologically – for example not eating meat just because you happen to live with vegetarians – can quickly and easily embed itself in our psychological preferences and become the subject of purity rituals and taboos (“Don’t cook my vegeburger in your bacon fat!” sort of thing).

I’ve been trying to think of a way to test/falsify this theory and can’t. This either means that the information content of the theory is actually minimal – i.e. it isn’t actually saying anything – or it means (my best guess for the truth) that my scientific imagination isn’t very good. And I think the missing link in my chain of thought it the lack of any apparent plausible alternative. Simple negating the theory (“food behaviours are not subject to purity obsessive behaviour”) doesn’t produce an interesting theory, and the tests that it suggests would, i feel, be passed without actually providing evidence that my theory is any good at all, just better than nothing. In other words, I think I would find people are obsessive about food behaviours, some of which are pretty arbitrary, but I don’t think this would allow me to convince anyone that what I am saying is true.

The problem may be with the nature of the theory (an evolutionary ‘just so’ story?) rather than with falsficiation.

If we knew what we were doing, it wouldn’t be called research, would it?

Albert Einstein (attrib.)

The British Centre for Science Education is a single issue pressure group dedicated solely to keeping creationism and intelligent design out of the science classroom in publicly-funded schools in the United Kingdom.

Truth is Science is a Creationist front that recently sent power point presentations and DVDs to every secondary school in the country, in attempt to promote teaching Creationism as part of the national science curriculum.

Richard Buggs, of Truth in Science, had a piece in today’s Guardian saying that Intelligent Design (i.e Creationism) is science. He is wrong, and the online comments to the article here explain why

Thinking about Creationism, after seeing Steve Jones from UCL give a talk in Sheffield last week called ‘Why Creationism is Wrong and Evolution is Right’. He didn’t really talk about why Creationism is wrong, which was probably wise. I don’t think you’ll ever win an argument with Creationists talking about the evidence – they’ve got a comeback for every contradiction to Creationism you can think of. It doesn’t matter if the comebacks are nonsensical, you get involved in an endless chase of facts, intepretation and reinterpretation. The only way to really finish an argument is to talk about meta-theory: what counts as evidence? what could convince you the world was one way instead of another? Do you, fundamentally, just believe that your imaginary friend is more important to you than anything i can ever say or do?

The so called ‘Creationism-Evolution debate’ is totally asymmetrical. Creationism isn’t a theory, it doesn’t suggest a process by which things come to be. It is equivalent to ‘they just got that way’. Okay, fine. Now lets talk about how they got that way, and what an answer to that question would look like.

Steven Jones, on whether Creationism should get 50% of teaching time is schools, said it would be just as sensible to give 50% of sex education classes to the theory that babies are brought by storks. This highlights the asymmetry of the supposed debate nicely, I thought.

The foundation of Creationism is disbelief in the possibility of design without a designer (an ‘argument from failure of the imagination’). I wonder if exposure to a few basic or common examples of emergent order (traffic jams, the BZ reaction, embryological development (!)) would help a believer loosen the conviction that the only possible or sane explanation for complexity is Creation?

Update: Gallery of Belousov-Zhabotinsky reaction images

Hemmingway : Always do sober what you said you’d do drunk.

A scientific version of this maxim: Always work out a test of whatever wild speculations you make

This is absolutely key

The most important difference between evolutionists and creationists, Prof Jones concluded, is that scientists are always prepared to say, “I don’t know”.

“If there weren’t any unknown parts of evolution, bits we don’t understand, it wouldn’t be a science,” he said, “That’s one thing that believers never say, because it’s all written down in a big book.”

(Steve Jones speaking at the Hay Festival)

The crucial difference between creationism and evolution is not that one provides a better fit of the data than the other. The difference is that one is a generative, empirically-driven, scientific theory and the other isn’t. As a research programme, Creationism isn’t even wrong. Science helps you work out what you don’t know, and how you’re going to move into a position of knowing it. Creationism has no account of what isn’t known or of how to go about finding it out.

Perhaps this defines science in psychology: does your investigation (be it questionnaire, cell recording, computational modelling work, whatever) have the capacity to provide you with a surprise?

If this does everything it says on the tin [abstract] then it’s very exciting indeed. I shall put it here in lieu of actually having time to read it right now. If anyone does, let me know how it goes

Social Cognitive Maps, Swarm Perception and Distributed Search on Dynamic Landscapes, CVRM-IST 127E-2005 technical report, final draft submitted to Brains, Minds & Media, Journal of New Media in Neural and Cognitive Science, NRW, Germany, 2005.

http://alfa.ist.utl.pt/~cvrm/staff/vramos/Vramos-BMM.pdf

ABSTRACT: Swarm Intelligence (SI) is the property of a systems whereby the collective behaviors of (unsophisticated) entities interacting locally with their environment cause coherent functional global patterns to emerge. SI provides a basis with which it is possible to explore collective (or distributed) problem solving without centralized control or the provision of a global model. To tackle the formation of a coherent social collective intelligence from individual behaviors, we discuss several concepts related to self-organization, stigmergy and social foraging in animals. Then, in a more abstract level we suggest and stress the role played not only by the environmental media as a driving force for societal learning, as well as by positive and negative feedbacks produced by the many interactions among agents. Finally, presenting a simple model based on the above features, we will address the collective adaptation of a social community to a cultural (environmental, contextual) or media informational dynamical landscape, represented here – for the purpose of different experiments – by several three-dimensional mathematical functions that suddenly change over time. Results indicate that the collective intelligence is able to cope and quickly adapt to unforeseen situations even when over the same cooperative foraging period, the community is requested to deal with two different and contradictory purposes.

We are so often drawn to describe the world, we are so comfortable with this, we enjoy good descriptions so much, that we can believe that we have explained things. Descriptions explain nothing. Descriptions are not understanding. Many descriptions can be true of the same thing. Explainations are exclusive. Many things might be true. Science is finding out what things definitely are and aren’t true.

If i’ve got this right, the Coriolis Force is a correction physicists use when calculating equations of motion – it isn’t a real force but a factor used to correct for the relative shift in coordinate frames. While the standard (newtonian) laws of motion can predict, for example, where a cannonball will land if fired with a certain force in a certain direction, they don’t take account that, while the thing is in flight, the reference frame (ie where the earth below is) is changing. So, you have to add a correction in – the coriolis effect.

It’s not an insignificant effect – for example nineteenth century gunnery tables, which the navy used to calculate the direction and force of cannon fire, took into account the coriolis effect. When, in the first world war, the British navy fought a battle in the falklands they found all their shot landed 100 yards to the left. Their calculations took account of the coliolis effect, but only as it works in the northern hemisphere. In the southern hemisphere the effect is reversed (which is why the water goes the other way down the plug-hole) and so all the aim of the cannon was by a factor of twice the anticipated coliosis effect.

I hope i’ve got it right – i’m not a physicist, so apologies, I’m writing this from memory from an otherwise unremarkable lecture i went to last night – but, basically, how cool is that?

In Nature, last week, a review of the role of long-distance running in the evolution of the human form. I guess the importance of endurance-based running in human evolution explains the popularity of jogging…

Endurance running and the evolution of Homo. Dennis M. Bramble & Daniel E. Lieberman. Nature 432, 345 – 352 (18 November 2004)
Abstract: Striding bipedalism is a key derived behaviour of hominids that possibly originated soon after the divergence of the chimpanzee and human lineages. Although bipedal gaits include walking and running, running is generally considered to have played no major role in human evolution because humans, like apes, are poor sprinters compared to most quadrupeds. Here we assess how well humans perform at sustained long-distance running, and review the physiological and anatomical bases of endurance running capabilities in humans and other mammals. Judged by several criteria, humans perform remarkably well at endurance running, thanks to a diverse array of features, many of which leave traces in the skeleton. The fossil evidence of these features suggests that endurance running is a derived capability of the genus Homo, originating about 2 million years ago, and may have been instrumental in the evolution of the human body form.

Quoting selectively, for your enjoyment…

The ER [Endurance Running] capabilities of Homo raise several additional questions, the first being whether long-distance running was an important behaviour in human evolution or merely the by-product of enhanced walking capabilities. Traditional arguments have favoured the latter hypothesis;

…

Yet walking alone cannot account for many of the other derived features in Table 1 because the mass-spring mechanics of running, which differ fundamentally from the pendular mechanics of walking, require structural specializations for energy storage and stabilization that have little role in walking

…

Considering all the evidence together, it is reasonable to hypothesize that Homo evolved to travel long distances by both walking and running.

…

ER may have helped hunters get close enough to throw projectiles, or perhaps even to run some mammals to exhaustion in the heat. Although such demanding strategies have been occasionally documented among modern foragers (see ref. 61), they might have been too energetically expensive and low-yield for the benefits to have outweighed the costs.

..

Another hypothesis to explore is that ER was initially useful for effective scavenging in the open, semi-arid environments apparently inhabited by early Homo. If early hominids were regularly scavenging marrow, brain and other tissues from carcasses, then ER would have helped hominids to compete more effectively for these scattered and ephemeral resources.

…

Today, ER is primarily a form of exercise and recreation, but its roots may be as ancient as the origin of the human genus, and its demands a major contributing factor to the human body form.

And just a couple more comments which arrived by email, on the filing problem, and solutions

GP Says:

I opt for the ‘disorganised piles in boxes’ approach, and a brain which alway knows that ‘I’ve read something about that somewhere, now what was it and what did I do with it…’. It doesn’t work very well, but neither has it ever crashed…
If you come up with a good system let me know!

JS Says (in ps)

PS. My colleague, Dan, (who’s very into data visualisation) mentioned http://websom.hut.fi/websom/ – which probably doesn’t help too much, but is quite cool. Dan says “if your brother wants to talk about self organising maps, I’m more than willing”.

Just a few responses i had to my post about the filing problem. I’m still interested to hear from any one else who has good advice on information management systems

MD said:

You know you’re having a frustrated day when you reply quickly to emails about filing. Nonetheless:

All my bibliography stuff is handled by something called BibTeX which is part of a typesetting system called LaTeX. Maybe you’ve come across it? (It’s all very open source and free etc..)

You essentially have a text-based database that stores all your referebces, with as much or as little meta-info as you want. Then you write all your writing in LaTeX which is a mark-up language useful for mathsy documents (but I reckon dead useful in general) which can include citations. The LaTeX document looks at your BibTeX file and pulls out and formats the appropriate references.

LaTeX is generally great, especially when you want to combine two documents and you don’t want to re-number everything (sections, figures, equations etc). So my thesis will be a cut-and-paste job of my articles/reports, and I’ll not have to re-format everything. Plus it looks good.

LaTeX might represent an over the top learngin curve for non-maths stuff, I don’t know. Have no idea how to keep track of paper stuff.

RS said:

Personally I would just build a small access database. Each discrete item gets several properties: format, keywords, location etc. for hard copies you can then just have a numerical index linked to a database entry. For soft copies each item could be hyperlinked or embedded in the database. You would then find it easy to generate search queries based on keywords. You could easily flag sources that are referenced in individual papers you are working on and if laid out correctly you could then auto-generate a list of bibliographic references. Whilst I don’t know how you could exactly do it I think it should also be possible to link references within a document to the database entry. Whilst it would take a while to build I think it would be quite a powerful tool.

You could store notes separately and cross reference papers within the database directly. It would mean entering a bunch of data each time you read a paper but it would probably repay the time invested.

WJ, displaying an uncharacteristic lack of rigour, said:

Disorganisation is the key to innovative academic research 😉

I’m not a good example…. hard copies are rare…. pdfs are by
subject mainly (and with replications for when i’m writing a
particular paper)…. format is always of the type “Jennings (2004)
The Politics of Celebration.pdf” [i.e. name (date) short title for own
personal reference].

have a few articles stored by author. but only a few.

KG said:

M$ Access all the way. I’d love to know if there is a GPU licenced alternative with similar functionality, but last time I asked a free software geek he suggested that if you want a graphic interface you’re stuffed.

Access cos flexible, hyperlinkable, searchable, expandable and webable (if your really keen). I store references to all my info in one integrated database, (split according to source type: authored book, edited book, journal, web, other) including a section for notes on each. I store a list of things to read there too, and can search titles and authors in the whole lot in one go, but filter unread if you just want something you’ve actually seen. My bibliography creation is pretty clunky (read: doesn’t work) but will be sortable by the time I’ve got a thesis to add a bibliography to.

There’s also the potential bonus that if you’ve got a bunch of friendly academics or research team all using access on the same network you could actually use the same db and choose to just see your references or the whole project’s, including notes they’ve made on readings – if you trust x and he says paper y is crap, then thats one less to read!

Anyways, come round for a test drive, and you can have the shell of mine to play with if you like.

I am back in academia, and now i must decide how i’m going to sort out my papers. I’ve been avoiding the problem, but the rate at which i’m accumulating paper, and PDFs, means I’ve now got to settle on some method for keeping track of everything. Whatever the system is, it needs to facilitate the these things for me:

1. Keeping track of my paper copies of journal articles (which ones i have, where they are)

2. Keeping track of my PDF copies of journal articles (which ones i have, where they are)

3. Searching both paper and electronic copies of journal articles

4. Easily inserting (auto-formatted) journal references into manuscripts

5. Organising and searching of non-journal bits of paper (newspaper cuttings, unpublished manuscripts, miscellaneous text, etc).
[Or, at least, those are what I think my needs are]

I’m interested in how everyone else does this. I presume that all academics (and most informational professionals, for that matter) have to deal with the overwhelming amount of information it is possible to accumulate. I feel/hope there’s a good solution out there, but I’m struggling to reconcile all the different types of information i want to keep and use, and the different purposes for which I want to use them.

One solution I’ve seen is to keep all the papers in topic-organised folders, and a list of what you’ve got in something like Endnote. Problem with this is that I’m never very comfortable with topic-based organisation. I’ve never managed to specialise (read: focus) on one field, so there isn’t really the coherence in my papers that makes organising my topic natural. Papers speak to several topics, or don’t fit neatly into any.

My PhD supervisor uses biblioscape to keep a record of what he’s got on paper, and he organises the hard-copies by accession number – ie as he gets a paper he puts a number in the top corner and stores them all in numerical order. It’s a neat way of getting round issues with deciding how to store the papers. It means that recent papers are on top (so to speak), but it does mean you lose any other implicit organisation that might arise from, say, storing by first author or topic. Plus he’s dependent on his electronic index working (and by most reports biblioscape is a bit flakey. And the reference insertion add-on i never got to work perfectly too).

One other guy in the research group writes short pieces of text which reference each paper he’s got. It’s a good way or giving more coherence to papers he has read before filing them away. I don’t know how he keeps track of the actual paper (and PDFs as well).

Other people (including my co-author on the book) use a self-authored web-app to keep track of their notes, hyperlinks and documents. This has the advantage of being accessible anywhere, and – since it’s web based – there’s lots of cross-referencing and search functionality already ‘built in’. In fact, after the book, I was so taken with how useful wikis are, that i’ve started my own to keep my notes and hyperlinks – but it doesn’t seem ideal for organising my bits of paper. I’m happy storing my own short notes, memos and links on a combination of this blog and my personal wiki, but i’m still left with the paper problem (ie items 1 through 5 on my wish list).

This is the system I adopted during my PhD: A filing cabinet with all journal papers organised by author; Using Endnote to keep track of what is in the filing cabinet, with a keyword to indicate if it was in electronic form rather than paper form. PDFs stored all in the same folder on the harddisk with the name in form for [First Author’s Surname] + [Year of publication] (ie Brown04.pdf). This meant that i had to put paper copies back in the right place (which could be fiddly) and also download their details from Web of Science or Pubmed when i acquired them.

This all seemed to work okay, but it was quite high maintenance, and didn’t give me any good way of organising things that aren’t journal papers. So, at this point in time, i have ten years worth of random bits of paper i thought were interesting at the time, with no idea what is where or how they should be organised (they’re all in different piles by when i acquired them, and i acquired them usually on the impulse that the information felt important, but i didn’t know why – or i knew why but didn’t have anything to do with it). What do i do with all this paper information? And is there a way i can integrate the way I organise it with my academic paper collection?

I’ve started a new academic project as part of my post-doc, and am facing the need to do something with all the new journal articles i’m acquiring, as well as the feeling that i really should organise all the papers I acquired while writing the book, and papers from four years of research in boxes somewhere – and all under the knowledge-shadow that everything will interconnect with everything else, so there’s no good way to keep paper separate by project (and who would want to lose out on the serendipity of accidental cross-links anyway?).

Has anyone got any good advice?

Thanks to Kat for this, from oztam.com

People ? often do not have a good sense of the limitations of sample-based research. Warren Cordell, chief statistical officer at Nielsen for many years, devised a wonderful visual explanation for [the United States] Congress, which went as follows. The picture (below) is comprised of several hundred thousand tiny dots (the population).

The three smaller pictures contain 250, 1,000 and 2,000 dots (the samples). They are ‘area probability’ samples of the original picture, because the dots are distributed in proportion to their distribution in the picture. If we think of homes [or persons, consumers] instead of dots, this is the sampling method used for most media research studies.

Now move back 30 inches or so. When the eye stops trying to read the dots, even the smallest sample provides a recognisable picture (you can use top-line data). But you would have trouble picking her out of a group of women based on the 250-dot sample (do not try reading demographic breaks). At 1,000 dots, if you squint to read the pattern of light and dark, you would recognise her in a group (now you can read major demographics). At 2,000 dots, you see her more clearly – but the real improvement is between 250 and 1,000 – an important point. In sampling, the ability to see greater detail is a ‘squared function’ – it takes four times as large a sample to see twice the detail. This is the strength and weakness of sample-based research. You get the general picture cheap, but precision costs a bundle.

UpdateYour metabolic rate while watching TV may not be less than while unconscious, but in children it is less than other resting activities (less fidgiting):

Ref:

Effects of television on metabolic rate: potential implications for childhood obesity.

The young sea squirt swims the oceans. When it finds a comfortable rock to settle down on it attaches to it by the head and proceeds to digest its own brain – a brain which would be of no further use during an uneventful future of filter-feeding.

Sea Squirts, aka tunicates, also aka urochordata, are more than just a curio from marine biology. Sea squirts are more closely related to humans than any other invertebrate group – evolutionary biologists reckon that they resemble the ancient last common ancestors of all vertebrates.

The brains they have in the larval form are really just a rod of nerve cells, a notochord. But it’s this notochord, found in its most primitive form in the sea squirts, which defines the phylum to which all birds, fishes and mammals belong. We humans could, ultimately, be just a development on the larval form of these slimy plankton eaters.

Nicol suggested to me that this means there might be a genetic switch which could still be flipped in humans, and would give us a strong urge to press our heads to the nearest rock face, digest our brains and move no more.

I think maybe it’s already happened, except that the switch is memetic, not genetic. The rock is a sofa and the digestive juices responsible for atrophying our brains are the emissions from the TV.

An additional curious note about tunicates is that they use a rare metal, vanadium, to bind oxygen in their blood, rather than iron (like humans) or copper (like squid). What this means for the sofa/TV/brain digestion analogy I don’t know.

It’s definitely an anomaly, but what kind of anomaly is it? In the British Journal of Psychology this month there is a meta-analysis of studies of electrodermal response to being stared at – or, to put it another way, a review of the evidence on whether we have a sixth sense to detect when people are looking at us. The review looked at two different paradigms and, quoting the conclusion:

We conclude that for both data sets that there is a small, but significant effect. This result corresponds to the recent findings of studies on distant healing and the `feeling of being stared at?. Therefore, the existence of some anomaly related to distant intentions cannot be ruled out. The lack of methodological rigour in the existing database prohibits final conclusions and calls for further research, especially for independent replications on larger data sets. There is no specific theoretical conception we know of that can incorporate this phenomenon into the current body of scientific knowledge. Thus, theoretical research allowing for and describing plausible mechanisms for such effects is necessary. [My emphasis].

So that’s okay then – just casually suggest that the entire physicalist basis of western science may be in error. Surely this result should either be better supported and in a better journal, or not published at all.

Thoughts anyone?

Ref:
Schmidt, S., Schneider, R., Utts, J. & Walach, H. (2004). Distant intentionality and the feeling of being stared at: two meta-analyses. British Journal of Psychology, 95, 235-247

One of the markers of pseudoscience is unrestrained endorsement. If you don’t have the resources or motivation to engage critical facilities, then you have to simply embrace everything that is suggested that doesn’t offend your broader instincts.

Example: New-Age eclecticism. Example the second: psychobabble; as long as it has the words ‘neuro’ (for a business audience) or ‘psychodynamic’ (for a therapeutic audience) in it, you can probably get away with it.

I shall add this to my heuristic-toolkit for the ‘how to deal with too much information’ problem…