Wednesday, November 30, 2005

Men are ... what's that word for illegitimate offspring?

Sorry, not terribly polite - and this is quite a blunt post. But I've just heard too many stories this week of men messing up women's lives.

There's the ex-husband who banned his wife from wearing slippers around the house because "they weren't sexy enough".

There's the ex-husband who rang his wife continually when she was away from home in an attempt to prevent her from doing anything socially.

There's the ex-partner who pushed his girlfriend down the stairs and then kicked her in the head.

There's the ex-lover who for a year refused to allow his woman to describe herself as "his girlfriend" - she came to the conclusion eventually that she was his "bit on the side".

There's the guy who got involved with a woman whose lover had relatively recently died when he already had a steady girlfriend.

There's the guy who rang his wife up whilst she was doing a presentation to say: "The baby won't eat her food. What should I do?"

That's just stories that I have heard in the last week. What is it with men?

Well, here are two suggestions. The first is the sexual "liberation" of women, and the casualisation of sexual relationships. Women are now considered free by society to sleep with whomever they want to. What this actually means is that, in most cases, if they want to get the attention of men, they have to sleep with them. So the big biological motivator for men is now being offered them in most relationships, to actually get them into the relationship in the first place.

Of course, this is miles removed from the "slavish" "Victorian" Christian morality that prevailed even until about 30 years ago. I would suggest that, within this paradigm, "living together" - in the sense of sexual relationships which were beyond the most casual encounters - was basically something that, if it existed outside marriage, was something which marked the most committed relationships. So if men were to get their biological "payoff" (as one might coarsely put it) they already had to be pretty committed to their women. Women weren't expected to become sexually involved with somebody before they were pretty sure that they were "the right sort of person". Nowadays, in most cases, the relationship is built the other way round - sex in many cases comes pretty early on, and you find out what the person is like later. So women can easily find themselves involved with men who, with more than five minutes thought and a few milligrams less hormones, they know are basically not the sort of person they want to be involved with. And whereas men - in biological terms - don't seem to care who they sleep with, women - in biological terms - are designed to want sexual relationships to be of the stable, child-rearing (i.e. years rather than minutes) kind.

The second phenomenon is the breakdown of families. This has impacts in all sorts of areas. In many cases, the dads of teenage girls are no longer around. This takes away a huge source of tension, of course - how many slammed doors are directed from the teenager to her dad? how many shouts are directed from the dad to his teenage daughter? But the reason for this tension in many homes is the fact that the dad is trying to protect his daughter - something that, in many cases in later teenage years (and particularly when a girl leaves home), she comes to see and appreciate. (At least, I hope!) And even if the girl is frustrated and tries to break away from the straitjacket that she perceives her parents protection to be, it still places some constraints on her, and no matter how much she rejects her parents' attitudes, she will still be affected by their opinions of different boys that wander in and out of her life. I suspect that fathers, in particular, will indicate the sort of boy/man that they think is appropriate for their daughters - and this will, regardless of her protestations, shape her thoughts.

It also has an impact on men when they are growing. Dads who stay around are role models for sons. How does a man know how to respond to the woman he is in love with? Well, the most likely role models will be the men he has seen relating to women that they love. If his dad showed love, care and affection for his mum, then as like as not, he will see that this is good, and will treat the women he loves in the same way.

These aren't cast iron conclusions - people can overcome all sorts of different backgrounds to become good at relationships - and people who have had everything good can still be lousy at them. But I wonder to what extent these factors do have an impact.

As Jon Mackenzie says at the bottom of his posts, "Go on, disagree. See if I care."

Tuesday, November 29, 2005

After some thought, (part of) a poem

Scott Adams has continued his explorations of issues related to intelligent design on his blog. It is hard to tell whether he is trolling or genuinely curious - after all, he is 'only' a cartoonist.

His latest post, which has (so far) garnered a mere 300 comments (sigh - have I had that many since I started?!) reminded me of a poem by Steve Turner - here's the last verse.

If Jesus was thirty-two today we'd have to
end it all. Heretic, fundamentalist, literalist,
puritan, pacifist, non-conformist, we'd take Him
away and quietly end the argument.
But the argument would rumble in the ground
at the end of three days and would break out
and walk around as though death was some bug,
saying 'I am the resurrection and the life . . .
No man cometh to the Father but by me'.
While the magicians researched new explanations
and the semanticists wondered exactly what
He meant by 'I' and 'No man' there would be those
who stand around amused, asking for something
called proof.

Steve Turner, "If Jesus was born today", Nice and Nasty

Anybody familiar with any of my poems will probably immediately recognise the influence that Turner has had on me, but that's not important right now.

Sunday, November 27, 2005

Technological evolution competition

Bill Dembski, at Uncommon Descent, has a few days to run on a competition to demonstrate gradual development/co-option in the technological realm.

When I had a connection with the RAF, they had standard issue sunglasses which were known as "Mark 14's". What interested me about this was how something as inherently simple conceptually as sunglasses should have gone through 13 previous design iterations prior to arriving at its current state of sophistication. It led me to construct stories akin to the evolutionary just-so stories that people suggest in nature as to what, exactly, the previous 13 "marks" might have looked like. For example, I wondered whether Mark 6's had been abandoned when they ripped off the ears of a fast jet pilot who ejected when wearing them, on account of the fact that the arms of the glasses were made out of cast iron and weighed five kilograms each. Or whether the primitive Mark 3's had been rejected when it was determined that plywood, although cheap, didn't make acceptable lenses for sunglasses.

Wednesday, November 23, 2005

Government's double standards?

The UK government failed in its attempt to push through legislation that would allow people to be detained for 90 days without being charged. Tony Blair emphasised over and over again that he was being asked for this by the police, that people shouldn't second-guess what the professionals thought - and there was a kerfuffle when police forces apparently made representation of these opinions to local MP's.

In the case of the legislation to extend licencing hours which comes into force in the next day or so, the opinions of the police seem (where expressed) to have been against the changes - extended opening hours and potential round-the-clock drinking are hardly going to make a policeman's lot a more happy one.

But whereas the opinions of the police seem to have led to Tony Blair placing his credibility on the line in the case of 90 day detention without charge, the government don't seem to have given a hoot for their opinions over licencing. And the funny thing is, whilst the potential threat from terrorists is doubtless greater, nobody has been able to make a coherent case for 90 day detention reducing the threat of terrorism (although plenty have pointed out the risks to civil liberties of such detention). But plenty of people know the impact that late night drinking has in turning city centres into no-go zones, and its relationship with anti-social behaviour.

So why is Tony Blair so concerned about the opinions of the police in one case - being prepared to alienate most of his party to fulfil their wishes - and so indifferent in the other case? Might it be that there are other issues at stake? ITWSBT

Tuesday, November 22, 2005

The Catholic position on Intelligent Design

Here, the Vatican's chief astronomer (! - the implication being that they have a whole department of astronomy!) says that ID isn't science:
According to the Italian news agency, ANSA, Father Coyne was speaking informally at a conference in Florence when he said that intelligent design "isn't science, even though it pretends to be."

This has been cited with glee in several places. What has not attracted so much attention in such places has been the opinion of the Pope, and a close associate of his, Cardinal Schonborn, who both argue that the universe requires intelligent agency (see here for Denyse O'Leary's analysis of this in English). Well, one would hope so!

Doubtless people will say something along the lines of, "Well, are they scientists?" But this isn't relevant, firstly because one's belief or otherwise in the supernatural is a matter of presuppositions, not evidence. Any and all observations are accommodated by people who believe in evolutionary explanations for all life - even when the evolutionary explanations are contradictory. This may partly be a symptom of a psychological phenomenon - called "confirmation bias" - evidence is fitted into one's existing mental framework rather than jettisoning the framework and adopting a new one. The same happened with the Aristotelian view of the universe with its epicycles; the same happened with phlogiston; the same happens with creationists for that matter - and the same happens to all of us when we are faced with odd circumstances that we need to find an explanation for.

Secondly, whilst Benedict and Schonborn may not be scientists, they aren't stupid - any more than Scott Adams is (despite his disingenuous blog to the contrary), or Denyse O'Leary was when she started researching "By Design or By Chance?", or Michael Behe was when he realised that there were weaknesses in evolutionary theory before he started writing "Darwin's Black Box". And unlike many scientists, Benedict and Schonborn also know the dangers of "unprofessional" intervention in science because they have a sense of history. Just because people aren't scientists doesn't mean that they are incapable of comprehending scientific arguments, and coming to their own conclusions about it.

Saturday, November 19, 2005

Hello, Phoebe

who are you,little i

(five or six years old)
peering from some high

window;at the gold

of november sunset

(and feeling:that if day
has to become night

this is a beautiful way)

e.e.cummings, "73 poems", 52
Actually, it wasn't evening - perhaps "if autumn has to become winter" would be more appropriate.

Wednesday, November 16, 2005

Our family - 3,500 years old.

One of the arguments against creationism and ID is that they tend to be funded by organisations that have a religious agenda.

Ateleological organisations have the advantage that in some settings, philosophical naturalism is considered to be inherent in the definition of science. As I have mentioned before, this is incorrect - most of the people who shaped modern science weren't philosophical naturalists, and in fact they believed that the pursuit of science was possible because the order in the universe had been put there by God. But because a naturalistic approach has been accepted as inherent to science, it is now possible for an organisation to adopt a "neutral" sounding name - Scientific American, American Association for the Advancement of Science, New Scientist - and pursue an agenda which excludes the possibility of ID by definition. Not because work in ID is not science - but because a narrow definition of science is being used specifically to exclude this as an option.

Any organisation that doesn't exclude a priori the possibility that there may be such a thing as an "external other" can be defined as "religious" - because it doesn't presuppose philosophical naturalism. In fact, it is impossible to have an organisation which accepts the possibility of teleology which won't be considered religious. Even an organisation which remained agnostic on the issue would be effectively being open to the possibility - which is not a naturalist position, and could therefore be classed as religious.

However, cast it the other way. Think about the (US) National Center for Science Education - which is actually about "Defending the Teaching of Evolution in the Public Schools", rather than about science education in general (nice neutral title). It's supported by people who have an anti-teleological agenda - they want to make sure that no form of teleology is promoted in public schools. Do we deconstruct their comments because they have a prior commitment to the teaching of evolution? Do we say that their opinions are invalid because they are seeking to oppose presentation of a teleological perspective in public schools? No. We accept that they are going to present material that is consistent with their foundation - but then we deal with that material on its merits.

In the same way, it isn't valid to dismiss the arguments of ID or creationist proponents on the basis of their worldview - or even the worldview of the people who are funding their research. People are bound to present research that they believe in. The way of refuting research isn't to say that the author doesn't share your worldview - no matter how invalid you think the other worldview is - that is postmodernism, not science. It's to show that their methods or conclusions are flawed. You can show that people haven't made a scientific case for their position - and that's what I was trying to do by interacting with the Avida and AFGP papers (see the side bar). Forget the fact that they wrote those papers because they didn't believe that ID or creationism was necessary - the papers simply don't show what it's claimed that they show. In the same way, criticisms of ID or creationist work has no need to look at how the work was funded. It should be able to show that the work is just scientifically wrong.

Aaaanyway, whilst trying to find out more about Charles Simonyi, who endowed Richard Dawkins' professorship (which is used more to "bash religion" than to promote the public understanding of science - I have talked about the upcoming TV shows that Dawkins is preparing below) I happened across this paper, which I thought was interesting.
Abstract: Questions concerning the common ancestors of all present-day humans have received considerable attention of late in both the scientific and lay communities. Principally, this attention has focused on `Mitochondrial Eve,' defined to be the woman who lies at the confluence of our maternal ancestry lines, and who is believed to have lived 100,000-200,000 years ago. More recent attention has been given to our common paternal ancestor, `Y Chromosome Adam,' who may have lived 35,000–-89,000 years ago. However, if we consider not just our all-female and all-male lines, but our ancestors along all parental lines, it turns out that everyone on earth may share a common ancestor who is remarkably recent. This study introduces a large-scale, detailed computer model of recent human history which suggests that the common ancestor of everyone alive today very likely lived between 2,000 and 5,000 years ago. Furthermore, the model indicates that nearly everyone living a few thousand years prior to that time is either the ancestor of no one or of all living humans.

I don't remember the media making much of this, but what is interesting is that the common ancestor would thus be comfortably in the era after the biblical flood.

P.S. Thinking about it, doesn't research that show we share a common ancestor 3500 years ago rather undermine research that shows we share common ancestors tens to hundreds of thousands of years ago? Doesn't it suggest that maybe the accuracy of their findings was the odd order of magnitude out? Or that their methodology was flawed? ITWSBT.

Monday, November 14, 2005

To which race of Middle Earth do you belong?

Apparently, I am ...


brought to you by Quizilla

(... though it ought to be observed that 40% of the people who took it got this result as well)

Saturday, November 12, 2005

Scott Adams and GROGGS

I plugged the Dilbert Blog (which perhaps, in the spirit of the strip, ought to be called the Dilblog) a little while ago. This was based on my experience of Scott Adams' insightful cartoon strips.

I have been startled at how thought-provoking his posts have been, and I was particularly startled by this recent post, which demonstrated a really keen analysis of many of the issues in the debate between evolution and ID.

Which is more than I can say for some ex-university acquaintances of mine, who are still convinced that:
a) ID is "God of the Gaps"
As a scientist, I see things every day that we can't yet explain. We tend not to put in papers `because we don't understand this, we conclude that someone designed it this way' not because `someone designed it this way' is a logically impossible conclusion, but because it raises far more questions than it answers.

b) ID has a political/religious agenda
discussion of the designer is deliberately discouraged by ID proponents, as part of the strategy to sidestep the US ban on teaching creationism in schools and to mask the religious motivation of most of those who support ID

c) ID should 'fess up to who the designer is
Doesn't ID rather beg the question of who the "intelligent designer" is? Given the lack of verifiable data, that strikes me as a rather religious question.

d) ID is the same as young earth creationism
Creationism is scientifically foolish because, in its strong form (God created everything just like it is now, just after having his breakfast on Sunday 23 October 4004 BC), it contradicts things that are observed, and in its weak form (created everything), it tells us nothing. Believe it, if you like, it may even be right, but it is not scientific.

... none of which errors Scott Adams falls into. Guess they must be too highly trained, or something ....

Friday, November 11, 2005


You gave me Christopher Robin, and then
You breathed new life in Pooh.
Whatever of each has left my pen
Goes homing back to you.
My book is ready, and comes to greet
The mother it longs to see -
It would be my present to you, my sweet,
If it weren't your gift to me.
A.A.Milne, Winnie-The-Pooh

Sometimes it's hard when, as a parent, you are lost in the chaos of messy rooms, a hectic round of children's activities, and children themselves who are permanently non-compliant, to remember the most amazing thing - that you are part of a unique family, and the interdependencies between the people within it are so tangled as to be inextricable.

The Winnie-The-Pooh stories are magical - I am just working through the series with my four year old. But what is even more magical is that they have their roots in a real (albeit now old-fashioned) family, where the son wanted his dad to tell him stories, and was spellbound when they turned out to be about him and his toys - and where the dad realised that there would be no magic were it not for his wife - who is, other than the dedication, completely invisible in the stories themselves.

Tuesday, November 08, 2005

Dawkins - religion is "the root of all evil"

In the new year, Richard Dawkins, Professor of Atheism - sorry, that should be Charles Simonyi Professor of the Public Understanding of Science - at Oxford University, will be airing a "provocative" two part documentary addressing this subject. In particular, he apparently wishes to point out the destructive force that the three monotheistic religions - Christianity, Muslim and Judaism - have been in Western civilisation.

Surprising? Hardly. His views on religion are well-known - he considers bringing children up within a religious tradition to be a form of child-abuse - see here for commentary - and he considers anybody who doubts darwinism (which "allows one to be an intellectually-fulfilled atheist") to be either mad, stupid, ignorant or evil. And the mainstream media in the UK are slanted against the expression of orthodox religious belief. So it was overwhelmingly likely that Dawkins would get the opportunity to continue what he started in the Royal Institution Christmas Lectures some years ago.

Neither is the theme likely to be surprising to most Christians who seek to present their beliefs in a public forum. "Look at all the suffering caused by religion" is probably in the top three intellectual objections to Christianity.

However, at risk of stealing his thunder, I have a couple of wonders. Firstly, is he going to address the fact that the twentieth century - the most bloody in human history (so far) - was so bloody because of anti-religious regimes? Stalin's Russia; Mao's China; Hitler's Germany; Pol Pot's Kampuchea. Of course, organised religion has wickedness to answer for - yes, there were the Crusades; yes, there has been sectarian violence in Northern Ireland for many decades; yes, there was the Inquisition, the Salem Witch Trials and the Counter Reformation. But do any of these compare with the systematic extermination of millions of Jews in Hitler's final solution? Or the Killing Fields?

Secondly, since I have no doubt that his focus will be on Christianity (being branded as anti-semitic is not what he would want, and it is always dangerous to publically condemn Islam), will he draw a distinction between the powerful organised religion represented by institutions such as the Catholic Church and the message of Jesus, which was the antithesis of power? Or will his research be as lazy as Robert Winston's was when he was preparing his "insightful, provocative" book on religion?

More scientific iconoclasm

I am writing with reference to: Chen et al. 1997. “Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish.” Proc. Natl. Acad. Sci. USA 94.
Here is a link to the full paper, and this is the abstract.
Freezing avoidance conferred by different types of antifreeze proteins in various polar and subpolar fishes represents a remarkable example of cold adaptation, but how these unique proteins arose is unknown. We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process by which this occurred through characterization and analyses of notothenioid AFGP and trypsinogen genes. The primordial AFGP gene apparently arose through recruitment of the 5 and 3 ends of an ancestral trypsinogen gene, which provided the secretory signal and the 3 untranslated region, respectively, plus de novo amplification of a 9-nt Thr-Ala-Ala coding element from the trypsinogen progenitor to create a new protein coding region for the repetitive tripeptide backbone of the antifreeze protein. The small sequence divergence (4-7%) between notothenioid AFGP and trypsinogen genes indicates that the transformation of the proteinase gene into the novel ice-binding protein gene occurred quite recently, about 5-14 million years ago (mya), which is highly consistent with the estimated times of the freezing of the Antarctic Ocean at 10-14 mya, and of the main phyletic divergence of the AFGP-bearing notothenioid families at 7-15 mya. The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function. It also represents a rare instance in which protein evolution, organismal adaptation, and environmental conditions can be linked directly.

Firstly, I would like to say that this is a good paper. It is well-researched; the paper itself doesn’t make too strong claims for itself; and it is an example of exactly the sort of paper that darwinism needs to present if it is to move from the realm of story-telling to being on a solid scientific footing.
What I do not agree with, however, is the iconic status that this paper has in the darwinist community. Like the Avida paper that I discuss below, this paper crops up over and over again as a demonstration of how darwinism can – nay, has – solved all the problems that challenge it.

For example: it is cited here in a comment on a post by William Dembski; it is presented here on the NAS website as a “cool tale in molecular evolution”; and it is effectively the framework of one of the objections to the Meyer paper that Panda’s Thumb are reacting against to in Meyer’s Hopeless Monster.

If AFGPs arose in this way, this is a significant example of new – and highly useful – functionality arising. However, let’s think about the evolutionary process that has taken place, if this account of how AFGPs appeared is correct.

Firstly, presumably (since the trypsinogen gene continues to be used by the organism) the gene was duplicated. In organismal terms, this is a necessary first step; however, it is basically an evolutionarily neutral step. Then, a large section of the functional part of the trypsinogen gene was deleted – again, following duplication, this is a neutral step. Then comes the insertion or deletion of a couple of nucleotides to induce a frame shift within the gene that has lost its original functionality. This is analogous to where the computer model, Avida, mutates the genomes of its digital organisms. These are the evolutionarily significant steps. Then, having established the AFGP functionality, it was amplified. Once the functionality is there, it is possible to select for increased expression of the functionality. The significant step, then – to establish the functionality – requires only a couple of changes. Of course, the first neutral steps were significant in terms of evolution – but the likelihood is that these don’t provide anything that can be selected for.

It is significant that, even in this simple example of a beneficial process, all of the “difficult” evolution has happened elsewhere. The 5’ sequence of 67 nucleotides and the 3’ sequence of a couple of hundred nucleotides, is preserved in the AFGP gene from the trypsinogen gene. The 1.7 kbp insert in the AFGP gene is irrelevant to the gene. The spacer sequence is almost identical to an existing sequence that has undergone a frameshift. The backbone sequence has also been recruited from an already specified sequence. And the gene is highly repetitive, containing tens of copies of functionally identical sub-genes.

The fish breeding mechanism is also significant. The fish certainly aren’t sexually mature for many years. My reference books didn’t provide a definitive answer on this, but is it the case that these fish breed in the conventional fishy way – by mixing milt and roe? So many thousands of baby fish are released – presumably fully biochemically functional – but without the investment of huge amounts of energetic resources on the part of the parents. The significance of this is that this means of reproduction gives many opportunities for “beneficial mutations” to be present - and also tested - in every generation (compare mammals with litters or calves, birds or amphibians with a clutch of eggs). Furthermore, with sexual reproduction (compare bacteria) it is possible for beneficial mutations to spread through the population, rather than simply following one genetic line. This form of reproduction provides about the best possible framework within the animal kingdom for evolution.

So to summarize: this papers provides a coherent explanation of how the AFGP functionality might appear, and this is a significant evolutionary change. However, it is a long way removed from the appearance of complex polypeptides, and it is an evolutionary change that takes place in the reproductive environment which is most suited to evolution. Also, it is not a complicated evolutionary step – most of the complex evolution has already taken place elsewhere, and to use the analogy of “climbing Mount Improbable”, this evolutionary step represents climbing onto the trig point at the top of the mountain once the mountain itself has already been scaled. So it is presumptuous to argue – as many darwinists seem to think – that this paper suggests that darwinist explanations of all biological features are just around the corner.

Thursday, November 03, 2005

Visitors' book

I know that I have had hits on this blog from all around the world - every continent with the exception of Antarctica. I would love you to say "hi" when you stop by. I have just added a link to a frappr map in the sidebar. If you like, you can pin yourself onto the map, and leave a comment.

Wednesday, November 02, 2005

Some implications of probability bounds

It is argued that ID has little impact on anything in the world of “real science”. However, to consider at least one issue, there are some conclusions that can be drawn on the basis of work on probability bounds. The bounds place constraints on the starting point for evolution, and would perhaps assist in showing how evolution might happen – and also establishing whether evolutionary explanations are plausible.

For example, take as a starting point a random sequence of DNA bases. It is unclear from literature whether this is assumed to be a basis of evolutionary progress – whether having a random sequence of bases would be a starting point for natural selection. Actual proposed mechanisms by which novel proteins might appear is rarely addressed. But let's assume, for the sake of argument, that the engine of evolution is random DNA sequences which are then modified by natural selection.

However, three out of 64 of the DNA base codons code the STOP sequence – that is, if one of these codons is found, they will terminate a protein chain. Now, the probability of three bases NOT coding for STOP is thence 61/64 – or 0.953. The probability of two lots of three bases NOT coding for STOP is 0.953 squared – 0.908. The significance of the universal probability bound is that we can exclude chance as a reasonable explanation for an event if the probability of an event is less than this bound. And it turns out that the probability of 7000 lots of three bases NOT coding for stop is close to Dembski's conservative value for the universal probability bound of 10 to the power of -150.

In other words, we can exclude the possibility that a protein with a chain of over 7000 amino acids arose on its own. The likelihood of a DNA sequence of the required length arising at random can be excluded, using the universal probability bound – such a protein would have to arise by other mechanisms - perhaps as a consequence of adding together smaller components. Obviously, if as I suggested in an earlier post, higher probability bounds ought to apply to biological systems, then the maximum number of amino acids that could be present in a protein as a starting point for natural selection would be consequently smaller.

I would like to explore some further implications of the probability bounds in future posts.