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Wow, a slow news day, eh? The BBC, shunning predictable Chinese military aggression, another turn of the tides in Iraq, and yet more boring news about the economy, lead with “Brown criticised over embryo bill“. Somebody at BBC News is clearly a fan of Cardinal Keith O’Brien. ‘Keith who?’ I hear you ask. What do you mean you’ve never heard of the leader of the Roman Catholic church in Scotland? The big news is that O’Brien is making a fuss over the Human Fertilisation and Embryology Bill. The bill, currently in parliament, will, amongst other things, make it easier for researchers to develop methods of growing tissues and organs that are genetically identical to those who require transplants or grafts, and is likely to help solve the problem of transplant rejection and the need for immunosuppressive drugs after transplants. Then there’s cancer, Alzheimer’s, HIV, blah, blah. This is, I’m sure you’ll agree, a terrible thing. I couldn’t put it better than O’Brien himself:

“This Bill represents a monstrous attack on human rights, human dignity and human life.”

The reason, of course, is that this bill enables the use of hybrid embryos. Putting little bits of reprogrammed adult human DNA into animal zygote cells. This presents all sorts of obvious problems for the Roman Catholic Church. It suggests the clearly impossible: that humans are animals, evolved like all other animals, and following the same developmental rules as our neighbours. The Cardinal is, I am sure, confident that hybrid embryos will never work, because of the obvious fact that cows, pigs and mice are not created in God’s image. That’s elementary stuff. Comes right at the beginning, in Genesis 1:27. It’s almost embarrassing that these biologists don’t know that.

Then there is the problem that this bill mentions embryology. The Roman Catholic church has, for the past few decades, tried to convince the world that it knows all about embryology. And don’t they just. Is it not the case that human embryos are human beings? Is it not so that fertilised eggs can think and feel, recite their twelve times tables, and lead missions into pagan lands? O’Brien is privileged with an intimate knowledge of God’s colossal mind, and he knows that God loves zygotes. So of course the Roman Catholic church must oppose a bill that makes such absurd claims as development being mind bogglingly complicated, life having fuzzy boundaries, or that you are infinitely more valuable and important than the half dozen skin cells that have fallen off your right index finger during your current browsing session.

Of course, it’s not just the mind of God that O’Brien knows intimately. God knows what you and I think, and he has spilled the beans to O’Brien:

“I can say that the government has no mandate for these changes: they were not in any election manifesto, nor do they enjoy widespread public support.”

Yes of course. Who is better placed to judge the beliefs, feelings and fears of the public on this matter than Cardinal Keith O’Brien? And he’s the perfect candidate to head this “single permanent national bioethics commission” that he proposes, too, what with his deep knowledge of developmental biology and reproductive medicine, and his profound understanding of the national mood. Not to mention that direct line to God. You couldn’t find a more representative candidate in the land.

Indeed, people were talking of nothing but the Human Fertilisation and Embryology bill on the crowded train home yesterday, and I can tell you, they’re not too happy about the army of monsters that are coming our way. “Haven’t these scientists ever heard of zombies,” one of them asked? Another was concerned that the convergence of reprogrammed human nuclear DNA with bovine mitochondrial DNA within the same cell membrane could just be the final straw that breaks the camel’s back and leads God to break his promise never again to commit genocide by flooding the earth. One gabbling mouthbreather even pointed out that such an untested and unprecedented confluence of incompatible nucleotide sequences could, for all he knew, flip the earth’s magnetic poles and precipitate the fiery conclusion of the universe.

Oh wait, have I got that right? Now I think about it, perhaps Britain is not the reactionary backwater that O’Brien thinks it is. Perhaps the senile and simple individuals who pray for the souls of cells do not make more than an entertaining but tiny minority of people in this country. Perhaps, just maybe, O’Brien’s series of non-sequiturs have led him to a confused and offensively hyperbolic fantasy about morality that he is pretending is representative of a universal hallucination of the British public. Sure, this bill does not have widespread popular support. But that is because parliamentary bills get only widespread popular obliviousness and apathy. The cardinal is dreaming if he believes that there is widespread popular opposition to it.

How about a front page science story that doesn’t give 99% of the coverage to absurd ideas?

From the World Health Organisation’s Multi-Sectoral Forum on Road Safety in China (March 2008), on driving in a country where over a quarter of a million die on the roads each year:

Both lack of awareness to risks and inexperience means that people all over the world, not just in China, are more likely to engage in dangerous behaviour such as speeding, driving without a seatbelt or a helmet, and drink driving. Without action, the road injury toll will only worsen, because it is a well know fact that basic road safety measures like seatbelts and helmets save lives. The more commonplace they become in China, the more lives will be saved on the roads.

I was shocked by the reckless behaviour of Beijing’s 5 million car drivers and their passengers: I did not see a single one of them wearing a helmet.  Were they to be involved in a collision, a helmet might mean the difference between life and death.

More interestingly, while seatbelts are compulsory in China, most Beijing taxis halve the cost of seatbelts by only installing one half of the belt per seat — either the belt or the socket is present; rarely both.  More interesting still is the curious and bizarre fact that a third of Beijing taxi drivers only pretend to wear their seatbelt.

The most shocking thing of all, though, is that Beijing has provided the visitor to the city with a fleet of convenient taxis — but where were the helmets for passengers to use?

The BBC reports that a 62 mile long standstill on a motorway just north-west of Beijing has entered its tenth day.  Motorists on the road between Jining and Huai’an, including hundreds of trucks from the coal fields of Inner Mongolia, have spent the week playing chess and being fleeced by the entrepreneurial locals who are bringing them food and water.  The problem is roadworks.  (And bad drivers who keep crashing.)  It’s always the way.  Congestion is always caused by roadworks.

Continue reading at At War With The Motorist…

Not in the television programme — well, I don’t know, I haven’t seen it yet due to pesky tennis fans capturing the remote control — but in the Simon Mayo interview (page liable to expire, but I guess everyone has heard the podcast). The statement to which I refer, made by David Attenborough on Radio 5 on Friday, concerns that old question of whether human evolution has “stopped”. A lot of people like to comment on this issue, and I can see why. It’s a quirky question that does not appear to be of great consequence, but which appeals to our collective ego; and it’s a question that has an obvious answer. Obviously evolution has stopped: advances in agriculture, medicine, and technology mean that we are no longer subject to natural selection pressures. As Sir D puts it, “the Darwinian survival of the fittest has now been largely negated.”

Trouble is, the obvious answer is wrong. It would be correct if we redefined evolution to fit a definition of “fittest” as being adaptation to a pre -agrarian culture. But that is not what evolution means. Lets take the oft-quoted definition of evolution as “change in allele frequencies over time” — that is, gene variants becoming more or less common in a population. Now think about it: humans have been taken from their previous hunter-gatherer niche — where evolution would be stabilising good hunter-gatherer adaptations in the population — and put into a whole different niche, where many hunter-gatherer adaptations are superfluous, or even unhelpful. Under such circumstances, you can bet that some allele frequencies are changing. Stabilising selection has been lifted, and now genetic drift and mutation of those genes can occur freely, eroding the now superfluous adaptations.

There are several reasons why this error is so attractive. I suppose it comes from viewing evolution as a progressive process striving for perfection. Evolution and natural selection are seen as being about creating new adaptations, and one forgets the roles of genetic drift, and stabilising selection. Certainly, if one can’t see the creation of something new and interesting and obviously adaptive, it’s easy to overlook the fact that evolution is happening all the same. If an improvement to a body part becomes more common in a population, we instantly recognise evolution; but we don’t recognise evolution in the loss of such a feature, or the gain of a genetic disorder. I’m sure Sir David is aware of all of this, but it’s easy to lapse into popular but wrong ways of thinking — we’ve all done it.

But on the question of whether humans are evolving, there’s a second reason why the error is not easily forgiven. It is always asserted that the reason for human evolution having stopped is that technological, agricultural, and medical advances have put an end to famine, pestilence, infant mortality, and the other natural selection pressures. And, however many times I have heard the claim, I still haven’t gotten over the astonishment that such a bad argument can be made by such great intellects. If the claim were true, what conclusions can we draw about evolution in the population of Zimbabwe, where famine is setting in, HIV/AIDS has halved life expectancy to the early thirties, and infant mortality is one in ten? The simple fact is that the human species does not have advanced agriculture, technology, and medicine.

People like Fiona Hudson-Kelly, whose incompetent spam for training workshops in “professionally managed email marketing” sparked a lengthy rant about the fact that public money is being wasted on crap management consultants and social media training workshops.

More of that sort of thing can be found on Hey, look at this social media clown.

Somebody called Dawn Foster writes in The Grauniad Bike Blog today about her latest blog, A Hundred and One Wankers, a rigorous academic exercise mapping London’s wankers — specifically, the wankers who just can’t control themselves when confronted with all the provocatively sweaty sexy ladies riding their bicycles on London’s streets.  Be they cabbies, white van drivers, special branch in their pimped range rovers, politicians’ chauffeurs, or even pedestrians, the male half of London’s non-cycling population seem to break down when confronted with those of us cool enough to have a bicycle.  If it’s a gentleman cyclist, they break down with jealousy and try to use the advanced stop lane in the hope that some of our awesomeness might rub off.  And with lady cyclists they break down with desire, become temporarily delirious, and do or say something embarrassing.

You can participate in the fascinating study of this phenomenon by filling in the survey on the Guardian article’s comment thread; and by subscribing to 101 Wankers.

I’ve been following CBC’s How To Think About Science series, and caught the Evelyn Fox Keller episode the other day. It was interesting, but there were a couple of issues that I just can’t let pass. Keller talks about the hype of genomics ten years ago — during the human (and other) genome projects, when huge amounts of a new kind of raw data were piling up, and everyone was speculating about the interesting things we could do with it. Leaving aside the fact that many of the claims about genomics have and are coming true (albeit, over a longer time-frame than mainstream media imagined it would), I have a problem with Keller’s own bit of hype.

It’s epigenetics, of course — reversible and heritable changes (both between generations of cells and generations of individuals) in gene expression patterns which do not alter the DNA sequence itself. Epigenetics is where all the hype is in biology at the moment. Don’t get me wrong: I think the field is interesting and exciting. But as the hottest newest branch of biology, everybody knows the name, and few know the details. It’s cited as the mechanism of faith healing, mind reading, and homeopathy. In Keller’s case, epigenetics is cited as a problem for theneo-Darwinian view of evolution. By “neo-Darwinism”, Keller particularly means the gene-centered view of evolution. The name “Dawkins” may have arisen once or twice. The problem that Keller thinks that epigenetics has for mainstream modern evolutionary biology is that organisms may be able to control their mutation rates in response to changes in environmental conditions, and thus alter the rate of evolution.

Keller is referring, I suppose, to the checkpoints and DNA repair mechanisms that spot and fix errors in DNA replication during gametogenesis (the production of sperm and eggs). It’s difficult to make a copy of three billion base pairs without making a few mistakes, and too many mistakes in too many important genes add up to a miscarriage. So there are some molecular machines which follow the copiers around, checking that they got it right. The machines do their best to fix the typos, and in extreme circumstances, will kill the cell if the mistakes are too big. Where epigenetics comes in is in the regulation of those molecular machines. Epigenetics hires and fires the copyeditors. Specifically, there are epigenetic mechanisms which pack away genes — wrap them around proteins called histones, to form structures called chromatin. Locked away in these packages, the genes can not be switched on, and no new copyediting machines can be produced.

The hypothesis that mutation rates may be under control by some mechanism which recognises changes in the environmental conditions and responds by altering the expression levels of the copyeditors is, I’m sure you’ll agree, a fascinating one. But a problem for the neo-Darwinian picture of evolution? I’m not sure I see the connection, there. Here is how I imagine such a mechanism working: in the cells producing sperm and eggs, a set of receptors monitor environmental conditions; when environmental conditions change, those receptors pass the message on to the nucleus, where a set of machines make the appropriate changes to gene expression. Why do I propose such a mechanism? Because just such mechanisms coordinate development, transmit the messages of hormones, detect pain smell light taste, determine the activity of drugs, and do a-hundred-and-one other things in the cell. They are the default way of getting a cellular response to an external stimulus. And it has already been empirically determined that such a mechanism exists in the case of DNAcopyeditors. The DNA copyeditors are not switched on 24/7 — after all, they are needed primarily during cell division. The mechanism which switches them on was discovered by researchers interested in cancers, who found that this mechanism is often damaged in tumours, leaving thecopyeditors in a permanent ‘off’ state.

Perhaps it doesn’t work this way. Whatever. My point is that it is very easy to imagine a mechanism by which environmental changes lead to heritable changes in mutation rates — a mechanism which can be created by the simple modification of another very similar mechanism. That modification? Orthodox neo-Darwinian evolution. The receptors and signals, the gene expression machinery and the chromatin re-modellers are all the product of orthodox neo-Darwinian evolution. And the system no doubt remains at the whim of natural selection. The idea that evolution itself evolves is fascinating, but it does not appear problematic or revolutionary to me.

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I said I had a second issue with the programme, didn’t I? Ah, yes, still on the topic of Dawkins and the idea of the selfish gene. Keller suggests that the ideas expressed by Dawkins have been surpassed and overturned by the modern developments of molecular biologists. Developments such as the fact that genes have complicated networks of interactions with each other. Gosh. It’s almost as though Keller hasn’t read The Selfish Gene. In TSG (Or was it The Extended Phenotype?), Dawkins is very careful to point out the fact that the “genes” of population geneticists — Mendelian particles of inheritance, and the “genes” for which the word “gene” was coined a century ago — are not quite the same thing as the “genes” of molecular and developmental biologists. Dawkins’ selfish genes need not be defined by start and stop codons, upstream promoters, or discreet messenger RNA products. Which makes Keller’s criticism largely irrelevant.

Whatever. Who cares? Somebody slightly mischaracterised an obscure academic problem, buried in an obscure podcast. Well, the main reason I care is that Keller is herself telling us that we should be more precise when talking about genes. When first used, the term “gene” was just a placeholder for a phenomenon we understood little about, she reminds us. Over time, we’ve filled in the details. The problem is, the population geneticists and evolutionary biologists have filled in different details to the molecular geneticists and developmental biologists. They’ve all continued to use the term “gene”, but they’re now using it to mean different things to each other. Oh, wait, haven’t I heard this somewhere before?

I guess it’s just that Richard Dawkins is so shrill and screechy that it’s impossible to read him carefully.

Filipe V. Jacinto and Manel Esteller, 2007. Mutator pathways unleashed by epigenetic silencing in human cancer. Mutagenesis 22(4):247-253; Free full text