weblog photography photoblog contact site map
Login Login


RSS feeds Syndicate

Subscribe to the weblog:

RSS 2.0 Atom

Subscribe with Bloglines

Subscribe to the photoblog:

RSS Atom

Subscribe with Bloglines

List of RSS feeds

[Comments icon] Recent Comments
  • Lies, Damn Lies, and Tissue Culture by jdc
  • Bristol, England by Farah El-Jarad
  • George the creationist by JBoyd
  • George the creationist by Joe
  • George the creationist by JBoyd
  • George the creationist by Joe
  • George the creationist by JBoyd
  • George the creationist by Joe
  • George the creationist by JBoyd
  • George the creationist by Joe
  • George the creationist by JBoyd
  • Bristol, England by mvanes
  • Hampshire, England by Rosemary Reavell
  • Simple rules by Joe
  • Simple rules by Martin

All comments

Photoblog Photoblog



Archive - RSS

[blogroll icon] Blogroll
  • The Panda's Thumb
  • Pharyngula
  • On The Nature Of Things
  • Dispatches From The Culture Wars
  • The Loom
  • Stranger Fruit
  • The Personal Genome
  • My Lab Is On Fire
  • The Living Code
  • Brain Waves
  • Evolving Thoughts
  • EvoWiki's list of Evolution blogs
  • Gene Expression
  • Sandwalk
  • The Cheerful Oncologist
  • Free Association
  • Migrations
  • Epigenetics News
  • Spoonful og Medicine
  • Seven Stones
  • Evilutionary Biologist
  • A Trip Down To The Shops
  • Improbable Research
  • Jesus and Mo
  • Over Compensating
  • Russell's Teapot
  • xkcd
  • Cectic
  • Boing Boing
  • Stephen Fry
  • Butterflies and Wheels
  • The Raving Atheist
  • Richard Dawkins
  • Nigel Warburton
Sci & Tech
  • The Science Blog
  • The Intersection
  • Real Climate
  • The Scientific Indian
  • Whitedust
  • Bad Science
  • SciAm
  • Bad Astronomy
  • Badscience Blogs
  • Panda Bear MD
  • Sue Blackmore
  • Nature Journal Club

Things that made me laugh, cry, nod approvingly, spit tea on the keyboard, turn red with rage, or most importantly, learn something this week.

Dear UK, If forty lashes for a teddy bear gets you angry, what is the appropriate response to death for reading a webpage?

Behind the scenes I've been ranting at my Scienceblog neighbours. Since I've been busy writing my k99 grant and have little energy to write ...

10 January: A baby planet, magnetic monopoles, how Down's syndrome protects against cancer and a potential drug target for parasitic disease...

Found in an old manuscript in the ruins of an old university: Well this year has been pretty much the same as those that went before. We pla...

Yale has started putting course material online in a systematic way, following in the grand tradition of MIT‚€™s OpenCourseWare. Among the ...

Benazir Bhutto has been assassinated, probably by Islamist extremists. While no saint, she clearly stood for democratisation in Pakistan, a...

Coming to this cold it is by no means obvious that Mario Anzuoni has not recorded a scene of unspeakable violence. In fact far from being...

A famous example of the troubles involved in Biblical translation is the expression ‚€œlamb of God.‚€ How do you convey the idea ‚€” the c...

Max Planck Institute for Infection Biology, Berlin, Germany. A microbiologist wonders how antimicrobial peptides beat infection. My group is...

When Answers in Genesis says it?s design And not just a matter of fitness I know they?re not fibbing?right there, number...

This one deserves another outing, this week.

I‚€™ve found the answer. You can stop looking now. It‚€™s really simpler than we‚€™d thought. You see, if the fundamental constants or the...

"I'm angry ... " (cont. p 94)

"I phoned Camelot and they fobbed me off with some story that -6 is higher, not lower, than -8, but I'm not having it."

Ben Goldacre The Guardian Saturday October 20 2007 Let‚€™s imagine that we live in an exotic parallel universe where I am able to use an amu...

Boy with retinoblastoma uses echolocation to ride bike.

Oh, no ‚€¶ we've almost missed it! Now we have to make a mad scrabble for birthday hats and noisemakers and cake and ice cream. It's...

We have to unpick exactly what was objectionable in what he said and what was acceptable debate.

 This Watson dust-up is going to get very interesting. First we have all those people who were quick to condemn Jim Watson as a low-life ra...

Ben Goldacre The Guardian Saturday October 20 2007 Let‚€™s imagine that we live in an exotic parallel universe where I am able to use an amu...

For if I said what I was quoted as saying, then I can only admit that I am bewildered by it.

Some people on the internet can't help turning into schoolyard bullies.

A spokesman for Stonewall added: "It shows that there's no limit to what gay and lesbian people can do, even being a wizard headmaster."

Modelling effort uses mass computing power to make breakthrough.

Checking the literature in preparation for our monthly News & Views meeting, my colleague Clare Thomas spotted this recent paper from PL...

?What is the purpose of publications??[The] purpose of data is to support, directly or indirectly, the marketing of our product....

"For a bunch of people who claim their truth is being suppressed by a corporate conspiracy..."

Today is an International Blog Action Day, when more than 15000 bloggers are blogging about single common issue - environment (and hi-tech j...

From “This Modern World,” a brilliant cartoon on Intelligent Design (hat tip: Noodle Food):...

Cancer kills. I know, big surprise. But the average layperson probably have no clue that 90% of cancer deaths are associated with metastas...

‚€œWater undoubtedly is the most important chemical substance in the world,‚€ explained Elmar Fuchs and colleagues from the Graz University...

 PhilipJ has posted the latest "Molecule of the Month" on Biocurious [Molecule of the Month: Superoxide Dismutase]. The molecule ...

Activity AP 3.22 requires students to role-play the different processes in using nuclear power to generate electricity.

The answer to the anti-bloggers in the mainstream press: we can do your job better than you.

Why do women, in contrast to our closest relatives, stop giving birth while they are still relatively young and healthy? This week's pap...

This afternoon, the webhosts of Tim Ireland's Bloggerheads, and of Craig Murray's website, pulled the plug. The background, according to Tor...

(Disclaimer: this is not my field but the paper looked interesting so here goes ...)Promoters, enhancers and other DNA regulatory elements t...

If watches could but timely watchlings breed, Their hatchlings on minutest clocksprings feed, And win their loves by telling truest time, Of...

I've written much about the Nuclear Pore Complex (NPC). This large molecular gate controls the flow of molecules into and out of the nucleus...

I have a daughter of marriageable age, and here is a useful service:Marry Our Daughter is an introduction service assisting those following ...

Background: Social environmental influences on human health are well established in the epidemiology literature, but their functional genomi...

We have the capability to rebuild him. Better, stronger, faster‚€¶ He may not have been given a Nobel Prize yet, but at least Stephen Hawki...

[Courtesy of Ricardo Vidal] Foreword: It is my pleasure to release #15 edition of blog carnival Gene-Genie, a carnival about genes and gene-...

You've got to read this account of the intelligence that led to the Iraq war.On April 23, 2006, CBS's "60 Minutes" interviewed Tyler Drumh...

Read the comments on this post...

What do you think? Can I use this video clip in my introductory biology course? It explains everything you need to know about DNA.Read the c...

Viruses found in the River Cam in Cambridge, famous as a haunt of students in their punts on long, lazy summer days, could become the next g...

Want one. bookmark this on del.icio.us - posted by bengoldacre - more about this bookmark...

Eukaryotic genomes are chimeras of sequences from many different sources. There are the genes responsible for the normal functioning of the ...

[click on image for full-size; from Science, v317: 1029-1031.] From the pages of last week‚€™s Science Magazine comes an article from Jean M...

Page: 1 2 3 4 5 6 7 8 9 10

What skepticism is

I was watching the TANK vodcast the other day. They had a short feature: "what is skepticism?" It had a series of vox pops shot in Sydney. People told us what they think skepticism is. It's all about being stubborn, close minded and refusing to believe the things that everybody else believes, apparently. The programme makers didn't answer the question themselves -- after all, "you and I know what it is". Well, I do know what skepticism is, but how would I explain it to those who don't? Skepbitch has managed to get in with an answer before me, but I'd like to add my own way of describing what it means to be a skeptic.

Skepticism is the opposite of naivety. Being a skeptic means being aware of all of the ways you can be deceived. It means knowing the methods that other people use to deceive you -- the propaganda and rhetoric techniques, and the fallacies in their own thinking. It means knowing the limitations of your senses, and designing ways to get around those limitations. And it means knowing the appropriate volume of evidence to demand for claims about the world. A skeptic does not have a closed mind, but their mind is not a free-for-all. Skepticism is the doorman who checks for fraudsters.

When I was very young, ghosts were fashionable in the UK. I loved the ghost stories on television -- Fortean TV on Channel 4, and an ITV programme whose name I forget, hosted by a man with large dusty book and a candle. Though the stories were transparent fiction, the ten year-old me believed them. He was naive. He got fooled, and one can chuckle at his expense. If more people realised that the antonym of "skeptical" is "naive", they might be a little less inclined to use it as a derogatory term. There is nothing to celebrate about being gullible and exploitable.

Keywords: epistemology, philosophy of science, science

Permalink | Comment | By Joe Dunckley, 2008-02-06 22:36:45 | Viewed 2620 times

Lies, Damn Lies, and Tissue Culture

If you have ever worked in a molecular or medical biology research laboratory, chances are one of the first things you learnt was tissue culture (or the microbiology equivalents). Even if you know nothing about biology, you've probably heard mentions of "cell culture" on the news, or at the very least heard about the results of studies in tissue culture. If you hear about "cell lines", you've got culture. If you hear about a "laboratory study" showing that your favourite chemical is carcinogenic, you've probably got culture. If you hear about new trials on a miracle cancer cure that has been shown to be effective in "preliminary laboratory tests", you've probably got culture. Everything from zombie epidemics to £10,000 animal-free beef is cell culture. Knowing a little bit about what tissue culture is, and what its uses and limitations are, is therefore important when answering such questions as "is my baby's bottle poisonous?", "is stem-cell research ethical?" and "is vitamin C an effective cure for colds/cancer/HIV?"

So. What is tissue culture (TC)? It's when you take specific cells from a multi-cellular animal and grow them in a dish full of nutrients (a mimic of your blood serum). The point of doing this is to create a system on which to experiment which does not require growing and killing lots of individuals -- something that is, for some reason, considered unethical. Especially when it's humans you propose using. Typically, human or other mammalian tissues are used -- especially "model organisms" such as mice. You can use healthy or diseased cell lines from all sorts of different organs. Once you've grown up a nice batch of cells in your dish, you can see how they respond to your cancer drug, environmental contaminant, or new junk food ingredient. You can see exactly how the behaviour of your cells changes over the minutes, hours and days of exposure; how they recover after the chemical has been flushed away; how your cancer drug works in dozens of different tumours; how your junk food ingredient works in the old and young, male and female, fit and fat; and how your environmental contaminant interacts with other environmental contaminants. It's great. If you work hard enough, you can know everything you want to know about your chemical within a week. Wipe out cancer and save the world by next Monday. At least, that's what the animal-rights movement would have you believe. And the tabloid press fall for it daily.

Trouble is, it's very easy to get superficially interesting answers using TC. Which makes it very easy to convince a journalist that you have important results, but very difficult to convince a scientist. That's not to say that TC is not important. But everything that we measure in TC is an estimate of what happens in real life situations. It's a model that uses surrogate measures from which we can develop hypotheses about what happens in reality. A bad analogy is in order, I think. Suppose you are building a car. You want to protect your future drivers from side-on impacts. Very early on in the design process, you have an engineer conduct strength tests on different materials and designs for doors. From this, you can narrow down the field of designs, and make hypotheses about which designs will perform best on the road. But you can not be sure that the strongest material will provide the best protection against injury and death. You would want play with the crash test dummies, before putting the car on the road. And once the car is on the market, you would analyse incidents. Because when the door is attached to the car and put on the road, a huge number of other variables comes into play. And so it is with, er... what was the topic again? Tissue culture.

Cells did not evolve for growth in a dish. They evolved in the context of cooperation with a vast number of other specialist cells in a body. They are not fine tuned for survival in the absence of skin, an immune system, a digestive system, liver and kidneys. They are not supposed to live like barnacles on plastic. But if you've worked with research quality cell lines, you'll know that it's surprisingly easy to make them grow in a dish. Feed them every couple of days, and they'll happily live for many months. Well go and say that to the post-docs and technicians who made it that way. They were up until midnight processing disgusting lumps of freshly excised tumour. They spent months trying out different combinations of nutrients and fungicides in an attempt to make the cells survive longer than a week. They may be easy to grow now, but don't think there wasn't any effort involved. Under these circumstances, you can hardly expect the cells not have evolved a little. You are introducing them to a vast number of novel mutagens by taking them away from the protection of skin. And putting anything into a new environment is going to mean new selection pressures. When you finally manage to immortalise your cell line, is it because you've perfectly adapted the conditions to the cells, or because the cells have adapted to the conditions?

So. There are all sorts of reasons why TC can not be anything more than an approximation of what is happening in real life. A useful approximation, but unreliable in the absence confirmatory evidence from in vivo and population studies. But these are only the intrinsic limitations of TC. When judging the merits of TC based research, you must also take into the account the fact that TC is easily misused and misrepresented, and that charlatans are doing it all the time. TC is a favourite of cargo-cult healers and nutritionists -- those who like to keep up a superficial appearance of having a scientific basis for their quackery. Take, for example, the shamen who pedal vitamin C as an HIV/AIDS drug (Patrick Holford, for example) or as a cancer therapy. They will tell you that in TC, vitamin C has been shown to kill tumour cells, or those cells that are infected with HIV. Therefore, the reasoning goes, we should abandon proven therapies, in favour of taking some vitamin supplements. Trouble is, you can chuck a big lump of any chemical in a dish of cells and the cells will die. I could pour a bag of vitamin C into a dish of healthy cells. They will die. Conclusion: those vitamin supplements are deadly poisonous. Except that your cells will never be exposed to a bag of vitamin C, because you have skin, a digestive system, and kidneys. And because people just don't go around pouring bags of vitamin C down their throats. I could spit in a dish of cells and tell you that spit is a killer. It's not.

But it's not just charlatans that abuse TC. Many legitimate scientists bend the rules a little. They may not even be aware that they are doing it. Take the case of Bisphenol A (BPA), something I did a little work on a couple of years ago. BPA is a component of some plastics, notably bottles. It is known to very slowly leach out of the bottles and into your drink. There is a little bit of evidence (mostly from rats) to show that consuming BPA may be harmful. And there are a lot of TC experiments on the chemical. BPA is a xenoestrogen, meaning that it mimics the activity of estrogens. Estrogen, of course, regulates prolactin release, and cell division (particularly in the breasts). We know that BPA mimics estrogens because when we put some in our dish of tumour cells, we see that within seconds the estrogen receptors have been activated, and all the other effects of estrogen follow. There are loads of results to confirm this because there are a lot of experiments into the effect of estrogen (there's plenty of money in breast cancer research). If you're doing the experiment anyway, it's hardly any more effort to look at BPA. And you can pretend that your research has another potential medical application. Since it's not the primary aim of your research, the journal's reviewers won't notice that you're using it at a thousand times the concentration that you would find it in the body. So even if enough BPA does leach out of your bottle, and even if BPA does do interesting things in the body, a large proportion of the TC studies will be irrelevant to understanding how it does those things, because they look at inappropriately large concentrations and inappropriately small timescales.

So, next time you are flicking through the health pages of the Daily Mail -- which I know all of you like to do -- engage healthy skepticism when they update the list of miracle cures and carcinogens. Like statistics, tissue culture is incredibly useful -- whether you're searching for the truth, or a convincing lie.

Keywords: HIV, badscience, biology, cancer, cell biology, medicine, molecular biology, science, tissue culture

Permalink | Comment | By Joe Dunckley, 2008-02-05 01:55:12 | Viewed 3834 times

Delete your myspace account

Go on. If you haven't already. Have you got an old account lying around, that you'd forgotten about? It's really very easy:

  1. Log in
  2. Click "home" (top left)
  3. Click "account settings" (top right)
  4. Click "cancel account"
  5. In the box put "Your persecution of atheists disgusts me, and your aesthetic values offend me."
  6. Check your inbox.

While you're waiting for the email to arrive, you can watch this short moving picture presentation from Messers Fry and Laurie:

Keywords: Rupert Murdoch, atheism, free speach, from the web, religion

Permalink | Comment | By Joe Dunckley, 2008-01-30 23:37:50 | Viewed 5350 times

Sunday syndrome #6: Welcome to life

This post is part six in a series. The series so far can be found here.

Cogito, ergo sum.

Renť Descartes, 1637.

I've given five posts and several thousand words over to introductions to principles in development, evolution and molecular biology. I won't be dropping those topics altogether, but it's time to explore new territories in the Sunday syndrome, including the philosophical and political. Things should be a little more digestible from here on. Chromosomal aberrations -- that is, large scale mutations in which so much genetic material is deleted or duplicated that a difference is visible under the light microscope -- have serious effects on development. We have discussed a few examples of syndromes which arise in individuals which carry these aberrations, but the individuals we see are the exceptions. In each case, I have given the frequency of the disease in terms of live births, but the frequencies are much higher in conceptions. The deletions that we see in live births are a relatively small proportion of the genome, and we rarely see live births in which both of the two copies of the genome are affected. More extreme deletions do occur, but the individuals carrying them never make it to birth. The rule is miscarriage.

Perhaps the most extreme syndrome that we see surviving to term is anencephaly. And yet, paradoxically, anencephaly has the smallest number of symptoms and directly affected organs of any of the syndromes that I have so far discussed. In most cases, physical development is largely normal, with the exception of one particular system: the nervous system. Anencephaly is classified as a neural tube defect, alongside spina bifida, and is caused by an error during the developmental process of neurulation.

Neurulation starts on day 18 of development, and is complete by day 30. The cells along the centre of the back fold in to form a grove, which then closes over to form the neural tube, the precursor of the central nervous system. With a frequency above one in every 500 births, closure of the neutral tube fails to complete. If this occurs towards the posterior,spina bifida arises, and the individual is physically disabled. When this occurs at the head, the skull does not form properly, and the amniotic fluid destroys the developing brain. Those individuals which survive to term are born without a brain. All will die within hours of birth. The reason anencephaly is the most extreme of our syndromes is because it affects those parts of us that are most uniquely human, and raises important questions about medical ethics, and the fuzzy boundaries of humanity.

This is one of the great social functions of science: to free people from superstition.

Steven Weinberg

Last year, a court case was brought in Ireland to determine whether a woman whose foetus had been diagnosed with anencephaly could travel to the UK for abortion. A French website exists solely to oppose the abortion of anencephalics . It is murder. Despite the fact that these individuals will never have a life. Never have a thought or feeling, either of pain or joy. Never know that they exist or will cease to exist. Never, no matter what the anti-abortionists may tell you, "know God". There is no they.

I am not willing to believe that the anti-abortion movement is solely about the control of women -- though that is undoubtedly a motivation for cynically manipulative church elders. Rather, it is about simple rules. When faced with difficult moral decisions some people are just too cowardly to give important decisions the time and thought that they deserve, and would rather follow an easy formula. Why take the time to make an informed and reasoned decision on an important issue, when you can have somebody else make an uninformed one for you? Why waste paper on a law library when there's a handy single volume that never needs revising? Why test competing ideas when yours comes straight from the Lord? Why examine his world when his world is so stubbornly rebellious? Sweep aside the complicating details that five hundred years of discovery have burdened us with, and go for the simple answer.

Physiology, psychology and neuroscience, with a little help from physics and philosophy, have destroyed simple dualism. Developmental biology has destroyed the simple boundaries of life and consciousness. Evolutionary biology has destroyed the simple boundary between species. Biochemistry has destroyed the simple boundary between life and non-life. Astronomy has put us in our place and physics has overturned our understanding of that place. It's time to stop pretending that there are simple rules.

Keywords: abortion, anencephaly, biology, developmental biology, ethics, medical genetics, medicine, neurulation, philosophy, politics, religion, science, sunday syndrome

Permalink | Comment | By Joe Dunckley, 2008-01-28 00:47:50 | Viewed 6744 times

What immunity isn't

I seem to have become a full time critic of Radio 4. Recently, the station has been running trails for a documentary looking at how rats have developed immunity to all common rat poisons. Erm. Is that right? I didn't catch the documentary and I'm no immunologist, but I'm pretty sure that rats are not immune to poisons. They are, perhaps, tolerant or resistant to the poisons. The difference illustrates an interesting principle of animal evolution.

Tolerance (or resistance) is a direct product of selection: the poison kills all those individuals that are not tolerant, while those individuals which just happen to carry a mutation that makes them at least partially tolerant -- e.g. by flushing the poison out of the body, breaking it up into harmless components, or by modifying those biological molecules with which the poison interacts -- survive, and pass on their tolerance. Tolerance is the result, therefore, of long-term exposure to the single poison, and is specific to that single poison (though it may rely on some general principles, like having a liver and kidney to clean up the body).

Evolution is a fantastically powerful way of producing systems capable of performing complex tasks, like pumping nasty things out of the body. But those systems are made the hard way: through the deaths of those which do not possess them. Every time a novel killer arrives on the scene, a new catastrophe unfolds. This is especially a problem with pathogens, because pathogens evolve much faster than we ever could. An individual who is capable of adjusting to new threats would have an enormous advantage over those who play the lottery with them. The immune system provides just such a capability.

Immunity, then, is not a direct result of evolution, but is produced by an immune system; and unlike resistance, it is not hard wired. Once you have an immune system, you can gain immunity to new threats throughout your life. But the immune system has an interesting evolutionary tale of its own. The adaptive immune system -- that part which learns and remembers specific threats -- works by utilising evolutionary processes within individuals, rather than over multiple generations. B-lymphocyte cells produce receptors -- proteins that stick out from the cell surface -- that allow them to recognise foreign cells, and it is these receptors that are the subject of this internal evolution. The genes that encode these proteins undergo a process of "somatic hyper-mutation": they are deliberately damaged. Thus a population of B-cells contains a huge variety of these proteins, and between them, are capable of recognising most potential threats, at least hazily. But evolution is, of course, more than just mutation: what about selection? Well, selection events take place when a B-cell actually encounters a pathogen that it recognises. At this point, it proliferates, producing lots of copies, which because of hyper-mutation, exhibit slight variation in their ability to recognise the pathogen.

Thus, while the immune system is something that, like resistance, has evolved the hard way over hundreds of generations, through the deaths of those that don't have one; immunity is something that is evolving within each of us at a rate that allows us to keep up with fast evolving threats.

Keywords: Radio 4, biology, evolution, genetics, immunology, medical genetics, science

Permalink | Comment | By Joe Dunckley, 2008-01-23 17:45:47 | Viewed 8765 times

In which I get violent

Tina Beattie was on Start The Week this morning, talking about the New AtheismTM. I only caught little bits of it, but I've managed to find the time to flick through the podcast. You can guess the angle taken just from the use of the ridiculous term "New Atheists", but you probably won't guess the argument that Beattie was out to make. Really, it deserves an award of some kind. Most creative non-sequitur of the week, perhaps. The New Atheism, we learn, is a "smokescreen for a withering of democracy," and we are engaging in a "projection onto religion of the failures of society and democracy since 9/11."

Things don't start too well. Beattie struggles out of the starting blocks with this essentially meaningless stream of babble*:

TB: Demonisation of religion that is perpetuated by a certain very dull kind of Anglo-American atheist materialism allows us to escape our own responsibilities for a burgeoning global climate of violent confrontation.

More so than having a cup of tea, going to the gym, spending Sunday in church? All sorts of things take up time that could be spent doing other things. So what? Andrew Marr, the host, does his best to steer the conversation back into the realms of reality. Beattie continues:

TB: But I think that just as we are very aware that the rhetoric of militant religiosity can produce acts of violence, we should not sever the connection between the very real acts of violence which we are carrying out in the world in the name of democracy, in the name of the anti-religious rhetoric produced by some of our influential members of the intellectual classes to fuel that violence.

Oh. Right. It sounds awfully like you're making a jaw-droppingly silly argument there. Could you clarify that for us?

AM: So it's as much Western intellectual smugness that you're going on at as atheism pure and simple?

TB: Yes... well... atheism pure and simple is as complex as religion.

Oh. OK. "Atheism (n). Western intellectual smugness. Product of democracy, and therefore sibling of violence." (Bizarro English Dictionary. Bizarro University Press, 2008). Gotcha.

Edward Lucas, another guest on the programme chips in, starting with the necessary swipes at our dear leader, Richard Dawkins, in order to establish his credentials:

EL: ... they're using science for questions that it isn't suited for ...


EL: ... they also display quite spectacular ignorance sometimes in their attack of religion.

Boring. It's almost as if you haven't actually read any of the work that you describe. Almost like a quite spectacular display of ignorance of your subject, one could say. But, anyway, petty back-and-forth attacks aside, what does Lucas have to say about Beattie's thesis? Well, even with his sympathies, he's struggling to follow her unique logic. A bit more clarification, might be in order.

TB: When we support a rhetoric which condemns probably the vast majority of the world's people as uniformly ignorant, irrational, dangerous, and immoral -- which is what new atheism does -- at the same time as we are fighting a sort of war on terror ... we are involved in military struggles that real human beings with a different belief to our own are being killed.

Gosh. An Islamicist act of mass murder, and an illegal invasion initiated by the most religious Western leaders of their time -- born-again Bush and recently-baptised Blair. Now I see that it was all the fault of us bloody atheists for being so damned talkative. It's all so clear now. Poly Toynbee should have just told us all to follow the Pope, and shut up about the UN. And what on Earth did Richard Dawkins think he was doing preaching peace, when he knows very well that such ideas are far to sophisticated for those who have a different belief to our own, and will only make them violent as they struggle to understand.

Since we New Atheists, alongside Western DemocracyTM, are fighting a sort-of-war-on-terror here, isn't it about time we incorporated it into our holy book? It's awfully embarrassing to have our most prominent spokespeople constantly rambling off-message, spouting nonsense about peace, international law, and perhaps just, you know, like getting along with each other. We're militants, for God's sake. Well, not for God's sake. Cthulhu's perhaps.

TB: Now I know, there's enormous political effort goes into saying that this is not a war of the west against Islam, but at the same time, it's not coincidental that when there's a very popular movement of antagonism to religion, there's also a lot of political violence against communities often identified as being religious.

Of course. What the new atheists have to do is just shut up and let everyone else get on with it, because, you know, the proles are simple minded, and will get lairy. What do you expect when you go and say that somebody else believes something that isn't true? Isn't it obvious that unnamed persons will then go and rough them up? It's our fault that other people get violent when we criticise ideas that are untrue and undesirable. The idea is too dangerous for the common man.

If the argument were not so transparently batty, it would be offensive. If the argument of the New Atheists is that clinging to irrational ideas can cause one to become violent (actually, the argument of atheists goes "God: probably not real." An elementary mistake, that one, but we'll let it go.), then the argument of Beattie seems to be that questioning irrational ideas can cause those who cling to them to become violent. Somehow, I just can't see how the atheist fits the role of bad-guy in that situation.

* Apologies for incomplete or badly transcribed quotes: these are taken from my shorthand notes as there is no official transcript. Listen to the podcast for the full quotes.

Keywords: Radio 4, Start The Week, Tina Beattie, atheism, bad arguments, religion, reviews

Permalink | Comment | By Joe Dunckley, 2008-01-21 20:16:04 | Viewed 9550 times

In which I'm happy to invoke Godwin's law

Night of Shame

Night of Shame

This is a repost of something that I posted to flickr earlier today.

This is Bebelplatz. On the 10th of May 1933, Propaganda Minister Joseph Goebbels, with the aid of brownshirts and Nazi Youth, held the first of the Nazi book burnings here. Twenty-thousand volumes were destroyed that evening. The plaque nearby reads: "where they burn books, they will also burn humans in the end."

I wasn't going to post this image -- there are technical flaws. But doing the rounds on the immoral, godless, liberal nightmare that is the reality based blogging community is the wonderful "Family Bookstore" at Abunga.com. Abunga allows you to Empower Decency! by "blocking" books. If enough people "block", they won't stock the book. This marvelous feature is here to prevent our families from being corrupted by violence and pornography. And to prove it, the first book to be banned is The Golden Compass. They have produced a press release in celebration of this triumph of family values over filth. It's good to know that those voting to ban the book have not themselves been corrupted by actually reading the book: the other two books in the series remain on sale.

You can sign up and do your bit for Empowering Decency! I myself have banned Fahrenheit 451 and Markus Zusak's The Book Thief. Banning Fundamentalism and Evangelicals was also rather satisfying. Let us pray for their success!

This is not a small business moulding supply to demand or a specialist merchant picking only the relevant stock. This is a demonstration of the tyranny of the majority that is never more than a vote away.

Keywords: book burning, books, fascism, history, politics, religion

Permalink | Comment | By Joe Dunckley, 2008-01-21 16:08:47 | Viewed 9574 times

Experiment avoidance: a short history

I've been reading John Gribbin's In Search of SchrŲdinger's Cat. He casually mentions the atomic (or, rather, 'atomistic') theories of the ancients -- in particular Democritus. Gribbin accuses historians of science and popular writers of attributing too much to Democritus, whose ideas about the world do not resemble modern physics. I've been consuming quite a bit of history of science and pop-physics lately and can't say I've ever been given the impression that Democritus (or any ancient philosopher scientists) founded particle physics. The historians do credit the atomists -- notably Leucippus, Democritus and Epicurus -- with being unusually modern in their science. But science is not just a body of knowledge; it is a method for discovering how the world works. It is the atomists' approach to understanding the world that is unusually modern.

Rather than looking at the atomists in terms of modern particle physicists, compare them to the other ancient philosopher scientists. The Athenians generally shunned experimentation: though Aristotle is noted for his taxonomic observations, the Athenians were generally happiest with reason and rational thought, and were unaccomplished empiricists. Those in the Pythogorean tradition valued logic and mathematics, but they turned their study into a cult of mathematical superstitions in which the proles were defended from the subversive facts like irrational numbers and dodecahedrons. The approach to science taken by the atomists was one which valued both the rational (what Democritus called "legitimate thought") and the empirical -- though Democritus was aware of the limitations of the senses, and described the empirical as "bastard thought," noting that it must be applied with care. By advocating an empirical and a reductionist approach, the atomists are the intellectual ancestors of the most exciting and productive modern sciences.

This approach to understanding the world was to a large extent forgotten. The Romans picked over the remains of the Athenians, and they synthesised that with Christianity to produce the received wisdom of a millennium and a half. Religion ascended and the endarkenment closed in. The power of science was rediscovered, eventually, and began once again to free people from superstition. But as Carl Sagan asks: where might humankind be today had it never been forgotten?

Keywords: Aristotle, Carl Sagan, Democritus, Epicurus, Leucippus, Pythagoras, ancients, atomists, empiricism, epistemology, history of science, philosophy of science, religion, science

Permalink | Comment | By Joe Dunckley, 2008-01-19 23:59:45 | Viewed 10439 times

J. Bronowski, 18 January 1908 - 22 August 1974

Buy the whole series. Go on.

Keywords: Jacob Bronowski, history of science, in memoriam, science, television

Permalink | Comment | By Joe Dunckley, 2008-01-18 23:24:49 | Viewed 11123 times

Review: Extreme Pilgrim

I caught the last couple of minutes of Extreme Pilgrim (BBC 2, Friday 9pm) and was intrigued, so fired up the iPlayer to watch the whole thing. It's Vicar of Dibley meets Ray Mears' Extreme Survival, all done in the style of an American college student movie. The main character presenter is Peter Owen Jones, a Sussex parish priest who defies the law that Anglican priests may speak no louder than a whisper. His accent is very 1960s public-school, though it also reminded me a little of this Fry and Laurie sketch, which begins to make sense when you learn that before joining the priesthood he was in marketing. There is marvelous rhythm in the way he pronounces "Him-ah-lee-ahs". It made for a slightly surreal programme when combined with the Alan Davies haircut and constant bewildered/stoned facial expressions.

Jones goes "seeking the spiritual enlightenment that Britain once had" in India. He joins some Sadus at the Kumbh Mela, the massive Hindu festival on the Ganges. The first half of the programme is given over to Jones getting stoned and staying up 'till five in the morning. I wonder what Stephen Green or Mary Whitehouse would make of nice Anglican vicars smoking weed on the BBC. After a wadge of notes has changed hands, the group sit around the camp fire talking of how we should not be seeking rewards in this life, and of how the modern world is too concerned with the economic at the expense of the spiritual. In a marvelous scene with a cross-legged old guru, subtitles pop up to say "give me a hundred rupees"; this is translated for Jones, however, as a stream of spiritual babble about giving up material possessions. Another marvelous scene shows Jones, having been fast-tracked into the job of a Sadu, dressed in the full orange robes and still looking rather spaced. He stands in silence for twenty seconds before wondering aloud "where am I?" When the festival is over Jones sets off for a cave in the mountains with the objective of "purifying your parts with austerity". Fnarr fnarr.

It's all very nice. We meet lots of amicable characters preaching peace and charity. But it's the perfect advert for why peaceful, liberal, friendly, wishy-washy "spiritual" religion is not universally harmless. This is the eastern spiritual utopia that so many Westerners look to as the solution to the problems of our materialist lives in the West? A skeletal shaman runs back and forth across a busy road to kiss the tarmac: "he's making the energy meet -- that's his philosophy." In his mountain cave, Jones is visited by the village chief, who comes with offerings and a request for blessings of his daughter's marriage. Jones is very upset one morning as he confesses to battering a scorpion with a saucepan: "I was a guest on his territory." The programme closes with Jones observing that he is "a product of a society that values economic well-being as much as spiritual well-being." Uhuh. And your society has running water, an absence of open-pit latrines in the street, and a distinct lack of amoebic dysentery. I would call that a good thing. And that is the problem with peaceful, liberal, friendly religion: to value "spiritual needs" means to value the next life and the invisible friend above the needs of real people in the one life that they get. A "philosophy" that values disease and starvation does not indicate a care for man's real spiritual needs.

So while the programme ended up as Vicar of Dibley meets Ray Mears, deep down it was trying to combine the Jesus complex of the git-wizard David Blaine with the philosophical power of rocket scientologist Tom Cruise. The programme thinks that it is making a profound insight into society and nature (the same "profound insights" of stoned hippies everywhere), but utterly fails to make the case. Still, it makes for entertaining television.

Keywords: Extreme Pilgrim, Peter Owen Jones, religion, reviews, spirituality, television

Permalink | Comment | By Joe Dunckley, 2008-01-17 17:07:06 | Viewed 11928 times

Model splicing
Blogging on Peer-Reviewed Research

The central dogma of molecular biology, first described by Francis Crick in 1958, describes the flow of information between DNA, RNA, and proteins.[1] The central dogma is interesting, but I believe that its use in teaching is somewhat misleading and gives it undue importance. If you've come across the central dogma before, it was probably in an undergraduate or perhaps high-school lecture, where it was casually mentioned when explaining that gene expression involves the flow of information from DNA sequence to messenger RNA, and from there to protein sequence and structure. Because we think of gene expression in terms of the information carrying molecule, introductory biology teaches gene expression in those terms: we think of it as a two step process of transcription (DNA to RNA) and translation (RNA to protein).

Gene expression is not a two step process, and of all the steps involved, transcription and translation are not necessarily the most interesting. This week's Thursday paper is "Pre-mRNA Secondary Structures Influence Exon Recognition",[2] by Hiller, Zhang, Backofen, and Stamm, and it looks at a particular aspect of one of the lesser known steps: alternative splicing. The story as told by introductory biology is that DNA is transcribed into messenger RNA (mRNA): a carbon copy of the information in DNA whose sole purpose is to convey the information from the precious DNA archive, which is kept safely in the nucleus, out to the sites where the proteins are produced. In fact, the result of transcription is "pre-mRNA" (or "primary transcript"), which undergoes a series of modifications before it is ready for translation. One such modification is splicing.

When researchers started examining the human genome, they were surprised at how many genes they found -- eventually coming down from an estimate of hundreds of thousands, to something around 25,000. But they were sure there were far more proteins than that. The reason proteins outnumber genes is that evolution has stumbled upon an efficient way organising things: make several proteins with a single gene. Thus most genes (in "higher" organisms, anyway) are split into many "exons", each specifying a different section of the protein sequence, and "introns" (non-coding sequences which contain metadata). Thus the protein coding sequence may be split into sections A, B, and C, and the gene may have, say, three alternative versions of each; the protein can be constructed with A1, B1, and C1, or A1, B2, and C3, or A1 and C1 alone, and so on. Splicing is the process that organises the exons. WhatHiller at al are asking is: how does the gene expression machinery know which exons to pick for the protein desired?

Continue reading under the fold...

Keywords: alternative splicing, biology, gene expression, genetics, molecular biology, reviews, science, splicing, thursday paper

Permalink | Comment | By Joe Dunckley, 2008-01-10 15:25:31 | Viewed 14596 times

Radio roundup: the blasphemy edition

Many people in Britain have been campaigning for a repeal of the blasphemy laws, which have had a bit of bad PR since they were used in an attempt to censor Jerry Springer: The Opera a few years ago, and since we saw how other countries use their blasphemy laws. The issue has come to the fore this morning because it will be discussed in parliament today and may be included in the current criminal justice bill. On Today (go to Weds 07:53), Don Horrocks of the Evangelical Alliance attempted to argue against the repeal of these laws:

We shouldn't be doing it at this time and this place ... everybody knows that it will never be successfully used again ... setting new legislation or repealing existing legislation sends out a signal to society about what is important ... [this has been] part of the culture and the history of our country for many hundreds of years.

Oh yes. The culture and history card. I'm not aware of anybody -- certainly no atheist or secularist -- arguing for a ban on the innocuous features of our history and culture; indeed, you'll find plenty of atheists admiring religious art or singing Christmas carols. But culture and history are not a good enough argument alone. Tuberculosis , capital punishment and death in childbirth are very much part of history and, thanks to Dickens and the heritage industry, our culture. That executing people for rebelling against the Church of England is part of history and culture does not convince me that it is something worth preserving. Horrocks went on to play the "Jesus is a very real friend to many people" card.

How about the claim that repealing the blasphemy laws would send out a signal to society about what we consider to be important values in Britain today? I hope so. It would say that British people value freedom of speech and put individuals before religious authorities. It would set a precedent which says that imaginary invisible friends do not have greater rights than real living people. The signal would say that organisations can not consolidate their power by intimidating dissenters into silence: a signal that seems rather timely, given the current trend of Western governments to restrict freedoms, and of Islamicist movements to intimidate individuals.

But what of the claim that this law itself is harmless? Horrocks claims (unless I have misunderstood him) that the last successful prosecution of the law was in 1922, but so far as I can tell, that is wrong. On Monday evening (Jan 6), Tom Robinson presented a brief history of the British gay liberation movement, in The Sex Lives Of Us, and talked about one of the few invocations of the law which have made it to court since the previous successful prosecution in 1921. Mary Whitehouse sued the Gay Times for "vilifying" Christ by publishing a poem about a gay and promiscuous Jesus. This was a case that was raised more than fifty years after the previous successful prosecution and long after Lord Denning had described the law as a "dead letter" that would never be successfully used again. It was a case which had nothing to do with defending a "very real friend" and everything to do with prejudice and homophobia. And that is the threat that this law poses today: the court may have rejected the case brought against Jerry Springer: The Opera, but the time and money that was lost means that it will be difficult for artists to fund even remotely controversial productions in future. The blasphemy law is a license to intimidate and discriminate, whether it can be prosecuted or not.

Fortunately, this law is in its last days. I have no doubt that only a tiny minority in this country are even remotely opposed to its repeal, and a lot more are in favour. Parliament seems to like modernising things when government gives it the chance, just so long as it remembers that it is not the US congress and does not need to pander to the extremists. You can read more about this at MediaWatch.

Keywords: Radio 4, blasphemy, politics, religion

Permalink | Comment | By Joe Dunckley, 2008-01-09 14:08:02 | Viewed 14742 times

Pulp parodies

"Does Anything Eat Shit?" by Sarah Herman. Summersdale, £7.99 (0.49 in January sales).

A peculiar British Christmas tradition is that of the "humorous" stocking filler book. Produced by a team of Ed Reardons at four days a piece, the most laughs they are likely to provoke are at the Publisher's christmas party when they see just how many people have fallen for them. That's not to say that cheap stocking filler tat is universally dreadful: a friend recently introduced me to Matthew Parris ' marvelous "Scorn" series of insult anthologies, for example. But there is one genre that never fails to displease: the "parody". You know the ones I'm talking about: from the loathsome Barry Trotter to the simply pointless Eats, Shites & Leaves, we've all received at least one copy of each. Does Anything Eat Shit? is a parody of the New Scientist's "Last Word" column, and associated books. (You probably have several of those too, especially since New Scientist stumbled upon the marvelous marketing trick of selling them under several different titles, such that you can find two copies of the same book under the tree.) Lets start with the things that I like about this book: it's shorter than it looks.

Now, on to the things that aren't so likable. We'll start with the cover and work our way in. The blurb lies. "...if you've learnt absolutely nothing useful by the time you've finished this book, at least you'll be laughing." I'd like a money-back guarantee on that, please. At least the subtitle is honest: "101 crap questions and answers." The author, according to blurb, has a "twisted mind". I'm imagining her with a "you don't have to be mad to work here..." sign above her desk. Dive inside to the acknowledgments and the picture crystallises. "Big back-slapping thanks..." go to all her currrazy friends, with such hilarious names as "Captain Lucy 'Pevs'" (the pirate) and "Page Master Rob". I'm reminded of The Fast Show's Colin Hunt: office joker. Oh, and while we're here: pirates. Everyone loves pirates, and everyone makes "arrrr, I'm a pirate" jokes in the pub. But I think most people are aware of the fact that such banter is not funny or original, and that putting it into print is an insult to dead trees.

Well, what about the actual content of this book? Mercifully, it is in a large and widely spaced type with lots of blank spaces (at least half of the book is empty space), so there isn't too much of it. It's not funny. I can't even see any evidence of it trying to be funny. The author seems to think that merely saying things that aren't true, in the style of the Last Word column, is enough to make the reader laugh. The situations are dull: a mix of questions that might raise a giggle from six-year-olds ("wouldn't it be useful if our arms were longer?"), and situations designed to set up jokes about current affairs ("if sea levels are rising, what measures are being taken to prevent us from drowning?"), most of which are a poor retelling of the throwaway jokes you get from stand up, Radio 4, or BBC2 comedies, and which sound rather dated already. Fortunately, the punchlines are given away in the questions ("do we keep goldfish imprisoned in tanks because of the threat their intelligence poses to national security?") so there is no need to read the answers.

The book does not even accurately mimic the style of the Last Word, because it misses the point of the column, and the reason it is so popular: the Last Word is interesting not because the answers are a list of random "facts", but because they bring a synthesis of disparate fields so that the bulb lights and you realise how elegant and simple scientific explanations of everyday phenomena are when put in context. For the same reason, great science fiction works when it bends a single rule in order to make a point, or to create a scenario in which to ask "what if?"; science fiction that abandons science altogether is lazy pulp fiction. Brave New World is a classic; Star Trek is mocked. Does Anything Eat Shit? is of the cheap and lazy variety: rather than bend a rule to set up an original and imaginative joke, the author abandons reality altogether, and expects that to be enough to make us laugh.

Perhaps this is just a case of satire being dead: on one side is real science, which is just as bizarre as Herman's fictional science, but with the benefit of being true, interesting, and sometimes even presenting genuinely funny situations; on the other side is a plethora of pseudosciences -- from traditional medicine to perpetual motion -- which use the language of science to disguise their own bizarre and laughable fictions. It's an issue I wrote about three years ago in the context of April fools jokes. Creating bizarre and amusing situations to parody science doesn't work because nature is far more imaginative than any human could ever be, and already has her own stock of bizarre and amusing situations.

Judge for yourself at myspace.

Keywords: books, humour, reviews, science

Permalink | Comment | By Joe Dunckley, 2008-01-08 12:40:26 | Viewed 15088 times

Experiment avoidance syndrome

This morning's Taking A Stand on BBC Radio 4 featured twins who were adopted by separate families at birth. The twins had then been enrolled in a psychiatric study -- indeed, they state that the "experiment" was the reason for the separation. For much of the programme it was implied that the purpose of the study was to characterise the various contributions of biology and upbringing in development. That the study was unethical went unquestioned.

Well, no. When the programme actually got around to talking about the study itself, to which it devoted a minute or so (fair enough, they had lots to fit in the half-hour programme), "nature versus nurture" did not seem to be its purpose at all. The study was in fact trying to determine whether it is better for twins to be adopted together or separately, in terms of their development, education and psychiatric health. This was still considered an unethical thing to do -- the guests spoke of their meeting with the principal investigator and his refusal to apologise -- and again no supporting arguments were made. Perhaps the study was unethical -- there are a series of examples of improper doctors and drug companies through history. But I can not judge this one because the details were not described and the programme gave us no pointers for further reading. But I don't think it's adequate just to give us a brief summary and tell us that it was unethical, when actually, it's not at all obvious that it was.

It reminded me of a story that Skrabanek and McCormick tell in Follies and Fallacies in Medicine (they in turn attribute it to the great champion of evidence based medicine, Archie Cochrane ). The story tells of an early randomised controlled trial which was comparing hospital versus home treatment of heart attacks. It was generally assumed that hospital treatment was the effective way to treat heart attacks, and there were only a few maverick specialists arguing otherwise. At a meeting half-way through the trial the results so far were discussed: eight had died at home and four had died in the hospital. "Well, we told you so, and now it would clearly be unethical to continue the trial!" Oops! On closer inspection, it turned out that the opposite was true: four had died at home and eight had died in the hospital! Some tumbleweed blew past, a cough was stifled, and a distant church bell clanged. It was decided that the numbers so far were too small to draw any conclusions from, and the trial went on.[1]

I was also reminded of last year's "Durham Fish Trials". Supplement pill manufacturers Equazen conducted a "trial" with GCSE students (15 year-olds) in County Durham which looked at the effect of taking fish oil pills on exam performance. The study did not use control groups, and as far as I know, it was never peer reviewed, though it did generate plenty of (mostly favourable) publicity for the company. Parents were arguing that it would not be ethical to have a control group: students in the control group would loose out in their exams. Clearly they had already decided on the efficacy of the pills in advance, and apparently hadn't considered the possibility that fish oil was harmful in terms of exam results.[2]

Do we have/need a name for this sort of thing? Perhaps the "mind-made-up fallacy", "objection to evidence fallacy", "unethical control fallacy", or the "gut conclusion fallacy".

Continue reading under the fold...

Keywords: Durham fish trials, Radio 4, badscience, ethics, medicine, philosophy of science, randomised control trials

Permalink | Comment | By Joe Dunckley, 2008-01-07 11:16:33 | Viewed 15593 times

Sunday syndrome #5: The anarchist that wasn't

This post is part five in a series. The series so far can be found here.

In the first installment of Sunday Syndrome I used the example of Prader-Willi Syndrome. This week we'll bring in a very different disorder, Angelman's Syndrome (OMIM:#105830), whose surprising connection to Prader-Willi gives us some interesting insights into how inheritance, evolution and development work -- insights whose application to medicine includes everything from understanding cancer to developing stem-cell therapies. Angelman's syndrome is also known as "Happy Puppet syndrome", because of its symptoms: severe mental retardation with limited language ability and a habit of laughing; and abnormal movement, a little bit like the jerky movements of the puppets in Thunderbirds. The interesting thing about Angelman's is how it is inherited: the most common culprit is a deletion of bands 11-13 in the long arm of chromosome 15 (15q11-q13): the same region as Prader-Willi.

But Angelman's and Prader-Willi, if they are deletions of exactly the same piece of DNA, should surely be one syndrome, combining the symptoms of each and always co-occurring? And yet we only ever see one or the other, never both. The clue to why this should be comes from a closer inspection of the inheritance pattern. We inherit two copies of each of our chromosomes: one from each parent (with the exception of the sex-chromosomes). A deletion on the paternally inherited chromosome 15 causes Prader-Willi, but never causes Angelman's. A deletion on the maternally inherited version causes Angelman's, but never causes Prader-Willi. Actually, it's not quite that simple: "uniparental inheritance", in which one parent contributes two copies of a chromosome, while the other parent contributes none (an improbable coincidence of errors, but with some documented cases). Two copies from the father and the child has Angelman's, two copies from the mother and the child has Prader-Willi. Conclusion: an intact paternally inherited copy of chromosome 15 is required to prevent the child developing Prader-Willi, and an intact maternally inherited version is required to prevent the child developing Angelman's.

It can't just be a coincidence that the syndromes correlate so perfectly with the parent in every one of the thousands of documented cases, nor can it be some simple historical accident: during gametogenesis (sperm and egg production) homologous chromosomes pair up and sections are shuffled between them. Therefore, Y chromosome aside, no chromosome follows an all male or an all female line: the relevant section of the paternal chromosome 15 may be a part of your grandmother's chromosome 15, for example. Something must be being done to the chromosome duringgametogenesis , something that males and females do differently, but which is ubiquitous throughout the species. The solution to this riddle is a marvelous quirk of inheritance called "genomic imprinting". During gametogenesis chemical modifications are made to a selection of genes. These modifications do not change the gene sequence, but they do alter gene expression (time, place, quantity, and so on) -- sometimes effectively switching a gene off altogether.

This raises the question: why should such a mechanism arise? It could be purely the result of neutral evolutionary mechanisms, of course, but this seems unlikely: a layer of complexity that carries risks such as Prader-Willi and Angelman's suggests something more complicated is going on. Deducing how and why something evolved is difficult -- even when one has fossils or comparative genomics with which to test hypotheses. Still, we can make hypotheses, and we can build models to test their plausibility -- so long as we don't put too much weight on mere hypotheses and models. One of the more plausible and interesting models proposed for imprinting is Tom Moore and David Haig's 1991 "parental conflict" model.[1] This model follows from the fact that mothers and fathers do not invest an equal amount of their resources in a child: the mother invests in the pregnancy, with a considerable risk of death, followed by protection of the child during vulnerable early life; the investment of the father depends on the species, but in all mammals it is less than the mother. An additional important fact is that mothers can be certain which children are their own, while it is possible for fathers to be deceived.

In such situations, mothers and fathers are predicted to evolve different strategies for maximising the survival of their genes. The mother's strategy is to value her long term fertility above the survival of any one child. The father has less interest in his partner's long-term fertility -- after all, the relationship may not last -- so he values a child's survival above the ability of the mother to bear children in the future. These are not conscious strategies or values, of course, and for the purpose of this post, we are only interested in their physiological rather than behavioural manifestations. Moore and Haig's model proposes that we should expect fathers to encourage maximum growth rate of the child in order to minimise the length of the most vulnerable stage of the child's life, and to give the child a head-start against all those children of other fathers. The mother should fight back against this: rapid growth could damage her body and her chances of future offspring, or may put her other children in danger.

Whatever the reasons for imprinting having evolved, the process itself need not have been especially complicated: the mechanisms for heritable modification of gene expression are not used for imprinting alone, and are likely far more ancient than imprinting. The steps involved in setting up an imbalance in imprinting may be relatively small, and once initiated could canalise evolution into reinforcing the imbalance (and I may elaborate on that topic another day). Imprinting is just one of several examples of epigenetics: the heritable (either in terms of parent to child, or in terms of cell division within an individual) modification of gene expression. One of the most important mechanisms of epigenetics is chromatin modification. Chromatin is a protein structure associated with DNA, and which can control access to genes by tightly packing the DNA and preventing it associating with the transcription machinery. Some of the other roles of epigenetics include X-inactivation, the process by which the extra X chromosome is silenced in females, in order to equalise gene expression with males, who have a single X; the silencing of some of the junk DNA in the genome, such as pseudogenes and parasitic DNA acquired from viruses; and most interestingly, with the differentiation of cells into their specialised roles.

This latter function, sometimes described as "cellular memory", brings us back to our tale of development. Development is to a large extent about cells taking specialised jobs in different tissues, organs and systems. To do this, cells remodel their genome by changing the pattern of repression by chromatin in response to external signals (such as the concentration gradients discussed at the end of the last entry). Differentiation by chromatin remodeling of the genome allows different cells to produce unique sets of metabolic enzymes, receptors and cellular structures, and to respond differently to events outside of the cell. Not all such modifications are permanent, however, and chromatin remodeling goes on throughout the life of the cell -- in response to external events, or in order to control cell division, for example -- as a contributor to short- and medium-term control of gene expression. It is tempting to think of chromatin as being in control of genes because of this role it plays. Yet the opposite is just as true: the way in which chromatin remodeling responds to signals is just as much a product of genes, and ultimately evolution.

Just as the genome is vulnerable to damage, leading to diseases, so the epigenome is vulnerable to damage. Cancers, for example, occur when there is a loss of regulation of the cell cycle. We talk of tumour suppressor genes (which slow down the cell cycle) and oncogenes (which speed up the cell cycle) picking up a mutation that jams them in an always-on or always-off state. But the genes themselves need not be mutated: abnormal control of transcription will have the same outcome, and we commonly see cancers in whichepigenetic abnormalities lead to an over- or under-expression of important genes.[2] Additionally, our knowledge of epigenetics is enabling the development of cancer drugs which target those genes which have become jammed, whether by epigenetic or genetic mutation. Epigenetics has another important medical application: induced pluripotent stem cells (IPS), which were the big science news of November, when the first human IPS cells were produced. The production of IPS cells essentially involves the de-differentiation of an adult cell into a mimic of early embryonic stem cells, which have the potential to develop into any other adult cell. An important part of this process is to reverse all of those changes in chromatin structure that have been made during development. This, it turns out, can be done by switching on a few specialised genes which have already evolved to do that job.[3]

With such a diverse range of important applications epigenetics is set to be a newsworthy field. This leads on to my final point about epigenetics. As the youthful epigenetics begins to break through to the mainstream it has begun also to pick up quacks and cranks. The religious-in-crisis, afraid of the advances that are explaining consciousness, have cited epigenetics as the source of free will. Faith healers and quacks jump on epigenetics as the mechanism by which one can alter gene expression with "mind energy" (which also has something to do with quantum physics, I'm told).[4] Others cite imprinting as a mechanism for the inheritance of acquired characteristics.[5] Epigenetics is important and exciting, but it is not the revolution that these groups have been so desperately seeking. Epigenetics does not break up the rules of biology, and it does not mean that any old failed ideas suddenly become true; it does not support the claims of alternative medicine practitioners or eastern mysticists any more than quantum mechanics does (that is: not at all). Epigenetics fits comfortably in mainstream biology: it is no less a product of evolution than any other aspect of our heredity; and in common with the rest of molecular biology, it is a product of and a servant to genetics, not just a master over it.

Continue reading under the fold...

Keywords: Angelman's syndrome. Prader-Willi, biology, cancer, chromatin remodelling, epigenetics, genetics, imprinting, medical genetics, medicine, pseudoscience, science, stem cells, sunday syndrome

Permalink | Comment | By Joe Dunckley, 2008-01-06 20:18:55 | Viewed 16191 times

George the creationist

Read about member of parliament George Galloway in any British newspaper, no matter what its editorial policy or political situation, and you will read about corrupt, self-serving Stalinist dullard on an ego-trip. But I hardly have any sympathy for British newspapers to begin with, and since the Telegraph was sued for faking the documents linking him to oil-for-food fraud,[1] I can hardly trust them to behave themselves and paint a true picture of the man. Just look at the faces of the assembled US Senate as Galloway puts on the full war-crimes indictment, and tell me you didn't grin a little? Similarly, he's not afraid to savage the likes of Sky News.[2] He asks difficult questions and makes a scene, which is a good thing, especially in the current political climate. And he has a record of liberalism on most social issues.[3]

And yet, I can't help thinking that participating in a reality television show is deserving of a good solid punch in the face alone. Engaging young people in politics? What a wanker. And Galloway does seem to have associated with a variety of unsavoury characters over the years, with some rather illiberal ideas -- from Stalinists to Islamic fundamentalists via the anti-abortion movement -- which perhaps qualify him for extremist crank status, verging on the religious fundamentalist himself.[4][5] (Though other fundamentalists have denounced him as a "false prophet", apparently.[6]) The perception of Galloway as an ego-maniac with no real interest in doing the job that voters have given him is difficult to deny when you see the man's record of attendance in parliament (11% of votes) and his constituency, even when you take into account reporting bias.[3] And yet, through all of this, I have never been quite willing to dismiss the man entirely when it's so difficult to get a clear picture of his opinions and activities.

But while I was away, Galloway broke the camel's back with this little parcel of wisdom, broadcast on national talk radio:?

"I was looking at my little six month old baby today beginning to take his first steps crawling across the hall of the Methodist Central Hall today, and it doesn?t look like an accident to me. He doesn?t look like an accident of evolutionary chance to me. I?m not really prepared to believe that from the bottom-dwelling slugs of the pond came the voice of Pavarotti. I?m not really prepared to believe that Albert Einstein and a spider are really the same thing, that they just took a different evolutionary path."[7]

Oh yes. Well done, George. That would be a scientific literacy age of.. what? Eleven? I'll give you a clue: Darwin did not write a famous book titled On The Origin Of Species By Means Of Chance. Seriously, even the famously bat-shit insane and reality-hostile organisation Answers in Genesis know that natural selection is not "chance". Everything in this quote betrays the fact that Galloway knows less about science and natural history than the average six year old. Such ignorance of science is itself sufficient reason to question a member's ability to make decisions in parliament, considering the sort of issues that parliament is asked to consider. But coupled with the other assembled charges against him, it's pretty good evidence that Galloway is simply not qualified for any career beyond sitting around in leotard pretending to be a cat.[8] Preferably with no television cameras present. There are long arguments under way regarding whether Galloway is actually a Creationist, and if that is how he would describe himself. It's irrelevant. Either way, he has displayed ignorance of a magnitude that is worrying in a member of parliament.

Continue reading under the fold...

Keywords: George Galloway, creationism, evolution, politics, science

Permalink | Comment | By Joe Dunckley, 2007-12-31 12:14:36 | Viewed 18706 times

Page: 1 2 3 4 5 6 7 8 9 10

Creative Commons License Best Viewed With Any Browser! Valid HTML 4.0 Valid CSS Powered by Apache Powered by Powered by mySQL

All text on this site is © Joe Dunckley 2001-08, except where stated, see this page for conditions of use.

0.19622802734375 secs