He found this paper in Nature:
Georgy Koentges (2008). Evolution of anatomy and gene control. Nature 451, 658-663. doi:10.1038/451658a

and decided to “blog” about it. This consisted of excerpting a few quotes, without any commentary or indication where he had cut the text. In all he took about 20% of the full article so it looks like he’s breaching copyright, the naughty boy. This might be excusable if he’s accurately representing the article. Well, let’s take a look and see (you can guess the result, can’t you?).

idnet.com.au (or ‘Noel’ as I’ll call him) starts off badly. This is the first quote:

Since Darwin we know that we must explain organisms not only in mechanistic terms (of mutation, selection and adaptation on the population level) but also in historical terms, as ‘descent with modification’, evolution in phylogeny. Because phylogeny is the outcome of developmental processes in populations, all heritable morphological changes derive from developmental changes in molecular control hierarchies and networks.

The start is from the third paragraph of the paper:

Since Darwin we know that we must explain the elephant not only in mechanistic terms (of mutation, selection and adaptation on the population level) but also in historical terms, as ‘descent with modification’, evolution in phylogeny. Molecular changes hundreds of millions of years ago constrain the possibility of change here and now. Not everything is possible, and evolutionary history is as much a story of constraint as functionality. Leonardo’s ‘flying machines’ didn’t just fail because bodies of a human size and weight fall under physical scaling laws limiting how big muscles could become. The evolutionary history that led to our present body size also stops us acquiring wings, either now or any time soon.

OK, so he’s changes “the elephant” into “organisms”, which is forgivable as “the elephant” only makes sense with the first two paragraphs. But where is the “Because…” sentence? Oh, the middle of the next paragraph.

So it goes on.. Noel picks out sentences and makes small changes as he sees fit. We can see his intentions when, for example, he takes this sentence:

This idea has been refined over the years in cogent discussions of ‘evolvability’, but there are few specific examples in metazoans where we can assign major structural changes to specific gene-regulatory causes.

and changes it into this:

There are few specific examples in metazoans where we can assign major structural changes to specific gene-regulatory causes.

Hey, let’s leave out the positive work that’s been done, and leave the negative in. Another nice example. Noel writes:

Recent studies on vertebrates suggest that only a fraction of ‘ultra-conserved’ CRMs are active and absolutely required for the animal to survive. Some CRMs might modulate the activities of others, so their effects might not be apparent.

Oh noes!! We poor biologists are clueless about how ‘ultra-conserved’ CRMs are conserved. But in the original the first sentence is followed by

As CRMs were assayed at only a few embryonic time points, the absence of regulatory information cannot be construed as a lack of function. It is not clear when, and in which cell types, organ-system specific CRMs are expected to be active, so inferences from such studies should be treated with great caution.

The sentence Noel leaves us with is further down the paragraph, in a discussion of the effects of deleting CRMs – it’s explaining why we might not see a big effect if we do simple knock-out experiments. (Ha! It implies that development is not be irreducibly complex, so I can see why he might want to leave that out).

I could give more other examples, but I think the point is clear. Noel has picked out the comments about how we are uncertain, whilst ignoring all the parts which explain what has been done, or pointing to areas of future research. The whole article is actually positive, in that it’s showing the sorts of things that could be done in the near future, with as the new technology and levels of inquiry they allow become applied to evo-devo. But UDites only get a partially copied, mis-represented version of the paper, which might interest Nature’s Lawyers as well.

Ah well, it could be worse for Noel. He might have used the “Blogging About Peer-Reviewed Research” icon.

EDIT: 1. Added Mister DNA’s spiffy graphic, 2. The original post has been on a heavy diet: it’s only a third the size it was, and makes even less sense. Some of the quotes highlighted above have disappeared. So now this post makes even less sense.

BBC NEWS | UK | Probe into police ‘bugging’ of MP

An MP is unhappy that his discussions with a constituent was being bugged. Hey, it’s all part of the War On Terror, designed to Keep Us Safe.

I think an argument can be defended that this sort of surveillance is a good idea, in which case MPs shouldn’t be exempt – the security services are no doubt picking up all sorts of information that is more important personally than anything the MP could say (I’m sure the only reason they can have such a grand building is that they pay for its upkeep with money from betting and insider dealing). I’m sure politicians don’t like being spied upon, so perhaps they should indulge in a bit of empathy with the rest of us.

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The reaction of the professional IDers was, apparently, to not enter. Bill Dembski posted the challenge at Uncommon Descent, but went no further (at least publically). Casey Luskin, attack-mouse of the Disco Institute (Casey, any chance of you sending mea signed photo I can put up here?) told us in the UD thread

Dembski’s methods of design detection can discriminate between informational patterns that are produced by chance/law, or alternatively were produced by intelligence. When there is real design to be detected, Dembski’s methods of design detection can work regardless of whether the designer was human or non-human.

and then complained that the other sequences might be of non-human design, so the method won’t work. Of course, he doesn’t actually try to apply the method, and then note that there might be false positives. Neither are apparently prepared to use Dembski’s explanatory filter for anything other than making divine coffee.

One of the amateur IDers, Patrick, did some detective work. He discovered that four of the six sequences are found in the synthetic bacterium Mycoplasma genitalium. The rest of the UD crowd are ecstatic and declare victory. Oh, and complain about how it’s an awful challenge. Even funnier, when Musgrave clarifies the challenge, they really pile on, claiming total victory using an appalling cricket analogy (my conclusion is that Patrick didn’t read the final delivery and was undone by the wrong’un).

Now, before Musgrave reveals all, I’ll try and make an intelligently designed prediction, based on my extensive research (5 minutes BLASTing the sequences). BLAST is an algorithm for efficiently searching DNA sequences for close matches – you give it a sequence, and it tells you what sequences are similar. There is a huge database called GenBank, which should contain all publically available sequences. If you plug in Ian Musgrave’s sequences in (as the ironically named Teleological has also done), you find that the same four sequences as Patrick are in there as coming from the synthetic bacterium. But, the final sequence, number 6, is also found in a natural M. genitalium, so it isn’t artificially designed. Nobody at UD seems to have noticed this yet.

Two points amused me. Firstly, I was not surprised that there was a little trap – what’s the point in setting a challenge like this if you make it easy? The second one is the way Patrick found the solution. Before his post, DLH had pointed to Venter’s work on making an artificial bacterium. Patrick acknowledges that he has to use extra information to decide which is designed, and indeed argues that he needs to have this extra information. In other words he needs to know the identity of the designer. This is not good because ID claims that it is possible to detect design without knowing anything about the designer. There is a strong insistence that one shouldn’t say anything about the identity of the designer. A cynical interpretation of this is that it is an attempt to avoid admitting that the designer is their Christian God, so that ID is creationism, and hence religion. So, Patrick has demonstrated an important point – in practical design detection one immediately tries to use as much information as one has about the putative designers. And why not?

Oh, silly me. Politics.

Yes, the beast will soon send off the description of his project on Integrated Pest Management For The Removal of the Coarse-haired Wombat (Vombatus ursinus) from Finland.

35% is a reasonable proportion of the grant for me to charge as an overhead, don’t you think?

This was all started by a group of biologists who have been working at NCEAS on publication biases in ecology (the biggest bias is, of course, that not enough of my papers get accepted straight away). They managed to get their latest results published in TREE.

The received wisdom is that there is a bias against women in science. One area where this might be seen is in acceptance of papers for publication – referees and editors might have a bias (conscious or subconscious) against women. If this is true, the proportion of papers published by women should be higher in journals where the gender of the author is not known.

For this and other reasons there have been suggestions floating around that journals shift to a system of double-blind reviews. At the moment most journals have single blinding: the authors’ identities are known to the referees, but the referees’ identities are not revealed to the authors (unless the referees wish to do so). In double blinding, the referee doesn’t know the identity of the author. Hence, any bias due to gender of the author should be removed. So, if a journal shifts from single blinding to double blinding, the proportion of papers by female authors should increase.

In 2001 the journal Behavioural Ecology moved to double blinding. But did this change the proportion of female authors? Or, more exactly, was there a bias against women that was removed? After all, the proportion of female authors might be changing in the rest of science – the null expectation is that the change in Behavioural Ecology should be the same as in similar journal, rather than there should be no change. So, the group gathered data on the number of papers by male and female first authors from before and after Behavioural Ecology switched to double blinding for five similar journals too. And then they compared the change in proportion of female authors in Behavioural Ecology to that in the other journals.

Err, no.

What they did was to compare the change in the proportion of female authors in each journal to zero. They found was that Behavioural Ecology and Biological Conservation. had increases that were significantly different, but not the other journals. They therefore concluded that there was an effect of double blinding, and that the increase in Biological Conservation must have been due to other factors. Oddly, though, at no point did they seem to make a direct comparison. It is not clear that they looked at the data either. Had they done so, they would have seen this:

The lines show the change from before Behavioural Ecology went double blind to afterwards. The vertical lines are the standard errors. Behavioural Ecology is the thick black line. We see that the proportion of female authors increases in all of the journals, but also that it is greatest in Behavioural Ecology. But is that increase significantly (in any sense) greater than in the other journals? Well, comparing it to zero obviously inflates the estimate of significance, because the other journals are all also increasing.

We can get an idea about if the data show anything with a more focussed analysis. This is also simplified, but I an ignoring some variation, and a more sophisticated analysis (=too much hassle to explain) comes to the same conclusion (and yes, for those who have read the paper, so does including the “don’t knows”).

What we can do is calculate the difference between the before and after proportions of female authors for the “control group”, and estimate the distribution of differences that would be expected if there was no double blinding implemented. Then we can ask if the difference in the proportion for Behavioural Ecology falls so far outside this distribution that it would be unlikely to explain the change.

These are the differences:

Journal	Percentage Before	Percentage After	Difference (%)
Behavioural Ecology	23.7	31.6	7.9
Behavioral Ecology & Sociobiology	25.1	26.3	1.3
Animal Behaviour	27.4	31.6	4.2
Biological Conservation	13.8	20.6	6.8
Journal of Biogeography	14.4	16.5	2.0
Landscape Ecology	19.5	23.4	3.9

For the journals in black, the mean difference is 3.65%, with a standard deviation of 2.15%. If these were exact, then there would be a 95% chance that the change for another, similar, journal would be between -0.6% and 7.9%. So, Behavioural Ecology is right on the edge.

But it assumes that the variance is known. In reality it is estimated, and only estimated from 5 data points (i.e. not a lot). If we take this into account, we find that the prediction for a journal would fall between -2.3% and 9.6% (with 95% probability). Now Behavioural Ecology is reasonably well inside the limits. Even someone wanting to do a one-sided test will find it inside.

So, the analysis shows little evidence for any effect of double blinding. But there are a couple of caveats, which could have opposite effects. The first is simply that there is not a lot of data – only 6 data points. We would really need more journals to be able to come to any conclusion. In particular, there may have been some other changes at Behavioural Ecology that could have had an effect.

The second caveat is more subtle. Suppose you were a journal editor, and you introduce a rule that authors have to admit that statisticians are the highest form of life in their acknowledgements. After a couple of years, you notice that the proportion of authors called Fisher has increased. You wonder if this is because of the new rule. So, you compare it with other journals, and find no increase. You therefore declare that Coxes appreciate statisticians, but other people don’t. But what about all those other effects you didn’t see? What about the changes in numbers of Boxes, Coxes, and Nelders? Humans are very good at detecting patterns, but very bad at judging whether they are random. And using the same data from which you spotted a pattern to assess whether it is real is naughty – of course you’re going to see an effect, because you’ve already noticed it in the mass of all possible things that could happen. Now, I don’t know if the authors are guilty here – they don’t say how they came to decide to examine this particular aspect of the data, but the introduction is a bit arm-wavy about the effect of double-blinding on sex ratio.

Of course, the solution to both caveats is simple – get more data. Anyone fancy trawling through the literature this weekend?

EDIT: Oops. I should have hat-tipped Grrlscientist for her post, which encouraged me to write this. Hedwig – I’m sorry. Please don’t set Orpheus onto me…

Reference
BUDDEN, A., TREGENZA, T., AARSSEN, L., KORICHEVA, J., LEIMU, R., LORTIE, C. (2008). Double-blind review favours increased representation of female authors. Trends in Ecology & Evolution, 23(1), 4-6. DOI: 10.1016/j.tree.2007.07.008

Isn’t this just great? You too can find out what the Afrikaans is for heteroscedasticity.

Seriously, this is the sort of resource that is really useful for a small number of people. The web is ideal for it. If only it was easy to find with Google.

I wanted to use the site to find out what the Finnish for “ordinal regression” is. Of course, it’s one of the few terms they don’t have. So, please tell me! Or tell me what it is in any other language that might be useful – help the ISI!

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In reality, of course, what happens is that you get sucked into it more and more, until you realise that there is no way you or anyone else will understand it. If you’re lucky, that’s after you have retired from a successful career as a theoretical physicist. But then the truth hit me…

One of the points they make about quantum mechanics is that it happens at very small scales, so we can never see it directly. Hence, they have to use instruments to measure the effects. With these, all sorts of bizarre and counter-intuitive result are found. But they are never observed directly. Perhaps this is no accident. Perhaps it was designed.

Here’s my just-so story theory. Everyone knew that physicists were the only real scientists, finding Great Truths, and telling us that philately will get us nowhere (*). So, as a joke some poor technician decided to set up the latest instrument they were toiling away at to produce non-sensical results. The experiment was performed, and the results published. Thus was quantum mechanics began.

Of course, the technician couldn’t admit to it, but that didn’t matter. He just persuaded his friends and colleagues to play along with the joke, and build ever bigger instruments to produce nonsense and allow them to laugh behind the backs of these great Nobel-winning scientists. Then, someone must have mockingly suggested digging out the inside of a Swiss alp. And they even fell for that.

So, now we have a whole subject that makes absolutely no sense, because it is a fiction brought about by a conspiracy of instrumentalists. They can’t admit it, because they have invested too much in the scam (as, come to that, have several governments). Instead, they go on building their machines to produce random results, safe in the knowledge that whatever odd squiggle is seen as an output, some theoretical physicist will be able to explain it with some weird theory (just stringing us along, eh?).

Of course, biologists would never fall for something like this, would they? After all, what could we be given by a technician? A machine that magically produces all the DNA we want? Who would fall for that?

(*) There. Two obscure references for the price of one.