The tree of life

What Darwin Didn't Know on BBC 4 tonight presents a very neat picture of evolution - including 'The tree of life". Concludes with (if I heard and remember correctly) "...we'll complete Darwin's great project. We'll explain life itself."

Meanwhile in the current New Scientist:

Why Darwin was wrong about the tree of life

The tree-of-life concept was absolutely central to Darwin's thinking, equal in importance to natural selection, according to biologist W. Ford Doolittle of Dalhousie University in Halifax, Nova Scotia, Canada. [...]

For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. [...] today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

The New Scientist is - rightly IMHO - at pains to point out that the problems it highlights with the "tree of life" provide no ammunition for the creationists or other opponents of science.

Personally, I think it is the BBC 4 programme that provides ammunition to the opponents of science. Over-simplification and excessive claims in the long run undermine trust in science.

(There's an obvious information angle to this in 'bio-informatics', but I also think that what's emerging in the New Scientist article links to David Weinberger's 'Everything is miscellaneous', in the sense that the 'tree of life' was an 'old style' categorisation. Real evolution is much more miscellaneous...")

Playing with Graphviz

Tony Hirst put me on to Graphviz, in particular the neat way of assembling the data in a spreadsheet and then exporting it to a text file in order to get the required xxxx.dot input file.

I'm playing with this as a way of looking at the relationship between the different authors, the different academic fields (philosophy, physics, semiotics...), and the different topics (knowledge, entropy, signs...) relevant to information. Of course, all these categories are problematic for all sorts of reasons (what's the difference between an academic field and a topic being one that jumps out at you) but nevertheless it seems useful to try different categories out and see where it leads.

One particularly handy feature is that it is easy to associate web links with nodes in the graphs, so you can have further information 'behind' any node.

Here's where I've got to. Names in red text are clickable - I would have underlined them, but it seems Graphviz have not inplemented an underlined style.

OK, so there's some way to go before it is really anything useful, but I think it shows promise.

OU C and S department bloggers

My blog posts are currently appearing on the front page of the Open University's Department of Communication and Systems' website. That is not at all what my blog was intended for and will, I hope, change soon. In the meantime, though, I'd better deliberately write posts more suited to being read in that context.

For example, here are some personal thoughts on blogs of some other members of the department.

John Naughton's 'Memex 1.2'. Probably our most prolific blogger (in terms of number of posts that is - Tony Hirst and Ray Corrigan do fewer but longer posts), John is Professor of the Public Understanding of Technology in the Systems Group of the Department. There are far too many posts for me to keep up with, but those I read I invariably find interesting and often provocative.

Tony Hirst's 'OUseful'. Tony is in the ICT Group of the department, and an acknowledged expert in Web 2.0. I often find his posts fascinating and learn how to do new things from them, but I hope Tony won't be offended if I also say that sometimes I can't understand a word he's saying... but that's because he's just so far ahead of me in understanding the web! And he really does understand the web.

Ray Corrigan's 'B2fxxx'. Ray, also in the Systems Group, says his blog is "Random thoughts on law, the Internet and society." Ray's posts invariably draw attention to 'difficult' areas of the web - intellectual property rights, privacy and the like - and he has the knowledge and understanding to provide invaluable insight into the issues.

Chris Blackmore's 'Random Ramblings'. Chris, another member of the Systems Group*, says of herself "I'm an Open University academic, teaching and researching environmental decision making and systems. I also have a deep love of nature and being outdoors" and this is reflected in the content of her blog posts. Chris hasn't posted anything on her blog since November, which is a shame since I'd always enjoyed reading her posts, but I know she has been exceptionally busy recently.

*I don't know if there is any significance in the fact that three of our bloggers are in the Systems Group. I'm in the ICT group like Tony, and there is a third group, Technology Management. Until October 2007 these were three separate departments but were brought together in a reorganisation.

Water into Watts

Another story of someone finding a way of getting unlimited power from water - but this one's backed by $60 million! I saw it in a paper in IEEE Spectrum:

Imagine that you could make hydrogen atoms do something that quantum mechanics says they can’t: slip into an energy state below the ground state, the collapse releasing 100 times as much energy as you’d get by just burning the hydrogen. If you could harness the heat to produce power, using hydrogen from water as fuel, you’d consume no oil, create no fumes, and solve the problems of energy and global warming forever.

Of course, first you’d have to overturn a century’s worth of physical theory, prove your point experimentally, and demonstrate its feasibility in a prototype power-producing system. Yet this is precisely what a company called BlackLight Power says it has done. The company, based near Princeton, N.J., has raised US $60 million, equipped massive labs, hired two dozen employees, gotten some high-profile executives to serve on its board, and attracted a devoted following of fans to online discussion boards.

Unlimited power from water (like 'the car that runs on water') is a staple of the popular press and a favourite of DIY 'inventors'. By and large, I think these claims are nuts. (We touch on this in the block on power for digital media in the new course T325: Technologies for digital media in the context of fuel cells for portable products such as laptops - there have been claims of cells that 'run on water'. In fact these cells do work and you do add water to keep them going, it is just that the energy isn't coming from the water, it is chemical potential energy in something else already in the cell. Saying it runs on water is sort of true but misleading.)

Anyway, back to the $60 million funding of something that requires the last 100 years of physics to be wrong for it to succeed. What I am wondering, is why I simply do not believe it, whereas clearly lots of people do. I'm quite confident in NOT believing it, and find the $60 million funding depressing. I have an undergraduate degree in physics but I don't claim that makes me an expert - I know I have pretty much no grasp of string theory, to take one example. So, it is not that I can honestly say that I, personally, can prove that the Hydrino theory is wrong.

Meadow says:

How do you come to have faith in a source or in a scientific test or procedure? Generally, you have learned from experience that a person, publication, or a broadcaster tells the truth or because someone that you trust encouraged you to believe in the source.

I suppose that is it: I have developed trust in the sources that tell me quantum mechanics is true (sort of), but I have no reason to trust Randell Mills of BlackLight Power. Most of the people I know would, I believe, instinctively agree with me. Indeed, I think a lot would wonder why I'm wondering about it at all: it is clearly rubbish and so what if a load of daft-but-rich people in America support it? But, I don't know, that seems like evasion. There are things taken as conventional wisdom that I don't want to sign up to, so how do I decide?

Messages, meaning, and symbols

While reading Messages, Meaning, and Symbols by Charles Meadow, I have made notes and put them on a wiki here http://intropy.wikispaces.com/Meadow2006.

I did this:

a) as a way of making my reading more active
b) to experiment with the use of a wiki
c) to have somewhere to store notes for future reference

Some general comments on the book.

In the preface, Meadow says

The assumed readers are undergraduates in information science and general readers, anyone from age fourteen or fifteen up.

I think the age 'fourteen or fifteen up' is reasonable, since it has a very simple writing style. It reads to me a bit like 'Dorling Kindersley' encyclopaedias. That's not a criticism, but it did seem a bit odd, since it felt as though maybe there was a mismatch between the topics and the style.

The coverage is very broad, and it would seem to me that it would work very well as 'an introductory text to undergraduates in information science' as it says in the blurb on the back cover.