God Agrees With Darwin, Immodest Deists damned

Very recently, New Scientist (one of my daily science reads) headlined "Darwin Was Wrong"" on the cover. Inside, the article "Why Darwin was wrong about the Tree of Life" explained, quite reasonably that the simple evolutionary relationships between organisms implied by the tree structure that Darwin envisaged was rather more complicated.

Now that DNA sequencing is a standard tool of molecular biology we are able to examine the genomes of an extremely wide variety and great number of organisms. We can inspect the plasmids of bacteria, the chromosomes (and plasmids) of yeast, the circular DNA of of mitochondria or any other organelle (such as the photosynthetic chloroplasts of plants) that contains genetic material, and having done so we find that bits of DNA have moved around rather more than can be explained by simple "vertical transfer" from parent to offspring.

The existence of an alternate route - "horizontal gene transfer", or HGT - should come as little surprise: the very existence of organelles such as mitochondria and chloroplasts points to a "Tree of Life" with hidden convergences in its branches: what are now organelles are descended from once independent organisms that were somehow absorbed. Such endosymbionts (internally symbiotic organisms) are however only the tip of the iceberg.

Thanks to the publicity concerning the possibility of an Avian Flu pandemic we are all aware that viruses are not necessarily limited to infecting a single host species - they can "jump" species. DNA replication, although remarkably accurate is not perfect: shit happens, genetically speaking, from time to time. When errors occur, they may be so disastrous that nothing works properly at all, but they may be more subtle, allowing an organism to survive but with some new capability (such as antibiotic resistance) or they might be a minor variation on a theme that nonetheless allows previously inaccessible niches to be exploited.

If two or more viruses happen to infect an organism at the same time there is considerable potential for genetic information to be well and truly shuffled between viruses. For example, something lethal could be transferred from a virus that can't easily infect people to another hitherto innocuous virus that we all live with without worry, thereby creating a dangerous and infections new virus. In the case of Avian Flu the fear is that although it is difficult for a human to be infected with native Avian Flu, it can happen through, for example, a cut; if this should happen in an individual also infected with human flu something very nasty could happen indeed.

HGT is therefore a "very real" factor in our consideration of evolution. The New Scientist article gives many more specifics, but the upshot is that Darwin's nice neat Tree of Life isn't so neat any more.

Unfortunately - and this is where I think New Scientist somewhat lost the plot in pursuit of journalistic celebrity - not even trees are trees. The simple branching tree is an ideal, our concept of tree embodies the idea of branching stems that, having parted, remain apart. Nature is not so constrained by idealism. After a bit of digging, I found the correct name for the phenomenon I knew existed: the merging of branches within and between trees - even between trees of different species occasionally; it's called inosculation.

Thus with a greater appreciation of the many and varied ways in which genetic material can migrate between organisms, we should see that Darwin's Tree of Life is in fact more truly tree-like than ever before.

But no, "Darwin Was Right! Tree of Life Truly Tree-like!" isn't going to create the brouhaha that "Darwin Was Wrong!" does. So what everyone sees at first, and even at a second unthinking glance at New Scientist is simply: Darwin Was Wrong!

Oh dear. Darwin was wrong? Consternation all round necessarily arises since all such assertions are necessarily true (I think you'll find I am at least self-consistent there), especially when they are printed - or vomited all over the internet. It follows logically from the premise that Darwin was wrong (if you use the correct sort of logic) that anyone who disagreed or disagrees with Darwin must have been or is right! This obviously includes creationists and proponents of Intelligent Design; ID'ers - the covert operatives of Creationism trained in the use of pseudo-scientific camouflage.

Intelligent Design attempts to appear scientific in promoting or defending an unscientific world-view, and so I thought it would be fun to be if not wholly scientific at least as scientific as I could be in a short blog piece, and to examine the whole Darwin and Evolution thing from the theistic, Creationist and Intelligent Design perspectives - making explicit the implicit axioms and reasoning reasonably from them with logical logic to see what we might reasonably, logically conclude.

In other words, I'm going to take the idea behind Creationism and Intelligent Design as givens and see what follows. The conclusion is surprising.

Firstly though, let's deal briefly with the questions What is Science? and What does it mean to be Scientific? Of course there are whole library sections devoted to philosophy and the philosophy of science in particular, so don't expect this to be exhaustive, complete or perfect.

Science is an art - the art creatively explaining the world as it presents to us. Science is axiomatically founded on data, observations, evidence - what we can describe and measure of the world. Scientists seek to explain their findings - they theorise, they hypothesise and then they ask"what if...?" and follow up on their ideas with predictions based on them, predictions that they can then test by gathering more data.

In doing so practicality plays an important role: Occam's Razor is an expedient, it says not that the simplest explanation is, or is mostly likely, to be right, merely that the simplest explanation is to be preferred, since if it turns out to be wrong the next simplest explanation can be examined and least effort is wasted. Science multiplies entities when it is necessary so to do. But in addition to practicality, logic and usually mathematics apply. This is not the place to discuss the "unreasonable effectiveness of mathematics" in the sciences (though I will comment in passing that it should be less of a surprise than it seems to be) so we shall accept pro tem the idea that mathematics can tell us a great deal about the world - even when it appears at first sight to be at best tangential.

At which point I should like to introduce Algorithmic Information Theory (AIT) and the work of Gregory Chaitin (discoverer (?) of Chaitin's Number)...

Chaitin's work is essentially about randomness, undecidability and unknowability in mathematics. The fundamental idea of AIT is that a program is "elegant" if it is the smallest possible program that produces a particular output; such a program is elegant because it cannot be compressed - it contains all the information necessary for its particular and no more. An elegant program is a very paragon of mathematical beauty. Alas proving a program to be elegant is not, if I recall correctly, possible - but in principle there must be such a program... and it should be a characteristic of a perfect omnipotent being that they would write only elegant programs.

Let us now consider a complex, multicellular organism. All cells are derived from one original; they share the same DNA. The DNA may have been "modified" by e.g. methylation, but the DNA is very highly conserved. Thus in information terms, such an organism contains a lot of redundant information, it should be highly compressible, indeed one could look upon embyrogenesis and subsequent maturation as the great unfolding of a highly compressed "program".

And finally I can introduce God (God this is my reader, reader this is God) as I think he might be seen by the devout monotheist, particularly one who is committed to the literal truth of the Bible. The monotheist's deity is omniscient and omnipotent, he is the alpha and omega of geekdom. He can create anything with a word. Right first time.

Let us assume that he did so. Fiat Lux! Et Lux Erat! God created the world, placed every atom, subatomic particle, every photon in its proper place and then rested. The evidence of great age seen in the rocks is illusory because He mixed His isotopes just right to give the appearance of radioactive decay over billions of years; the fossilised bones of long dead dinosaurs were created as they were found, they aren't fossils at all - they were never alive. There may be suggestions of the passage of geological time, but Darwin misinterpreted them as signs of evolution, not as he should have done - as signs of divine potency.

God is great. His work is beautiful. We are - apart from being beloved of him and created in his image - insignificant. We cannot understand the mind of God; to attempt to do so would be at best hubris, to claim to have done so would be blasphemy. So I think the devout ought to reason.

Yet creationists - and ID'ers have done precisely this, and in doing so they make their of their belief a vanity beyond compare, they vaunt and flaunt their ignorance and they choose to turn their backs upon the very questions they themselves raise

Even if the Bible is taken literally, and the world was created in six days (whatever limits should be placed on the extent "the world"), how do we know how long a day of God is?

How can an omnipresent being "move upon the face of the waters" anything other than metaphorically - unless there was some place that he was previously not, in stark contradiction of our assumption of omnipresence.

The interpretation of a story that cannot possibly be exact, being necessarily only a part of the truth, is take as the one thing it cannot be: the literal, exact and complete truth. The sin of pride is everywhere in fundamentalism of any hue.

But the key point is this: if God is, by definition, perfect and infallible, and his works of paramount beauty, why would he have created the world in such a plodding way, placing each component part individually in the places we find them? Of course he could have done; he may choose to move in mysterious ways as he pleases - he may have created in infinite multiverse in which each variation of creation was played out. The question is: should we not consider his design in the terms that it is presented to us, on the basis that, if he wanted to present something else he would have done so.

And if it is not miraculous to consider the creation of a universe and fully formed creatures ex nihilo, would it not be miraculum mirabile to to create everything from the least possible, the most informationally dense "seed"? It might be complex to create a great oak tree, but would it not be even more demanding to see how to encode the form of the tree into a seed and to let time effect the transformation. And since God has the freedom to choose, why would he not choose the most beautiful, elegant approach, which would be to start with some microscopic seed encoding everything that should spring forth without redundancy. And where in the Bible does it say that this is not how it was done?

And as if creating a single seed were not marvellous enough, consider creating the conditions in which a rocky planet would come to be, a planet on which conditions would so combine as to create life and allow for the whole biosphere to unfold, for life to emerge from lifeless matter.

And then consider the universe, and a Big Bang from which everything comes to be. How could such marvelry be exceeded! If the religiously inclined truly believed in being humble before God they would look upon science as the tool by which our preconceptions, misunderstandings and pride are progressively stripped from us.

This was the inspiration of the Renaissance, the idea that examination of the world was the way to the fullest possible appreciation of the beauty of God's creation - and hence to inspired worship of Him.

Every new discovery brings awe, every failure to understand demonstrates the incomprehensible richness of the world, every theory and hypothesis, being merely our latest attempt to make sense of the evidence, is destined to be refined and ultimately replaced by a better idea; and does not knowledge of our inability to perfectly comprehend creation do anything other than laud and magnify the creator?

Apparently not. The course of human history is the history of intellectual humiliation, yet still humility escapes us. The Earth was the centre of a limited universe, and around it circled the sun and the planets. And then they didn't. Copernicus demoted Earth from pride of place to being merely another planet circling the sun. Then the stars of heaven were discovered to be not fixed to some perfect crystalline sphere but scattered through space like dust. We discovered our galaxy, and we are not at the centre of it: our sun is undistinguished in kind or place without our galaxy. Our galaxy is but one of billions we can see; our universe may be only one in infinity.

But, if out location and matter is not special, at least humanity remained special. We were separately created. But then we find that we share much with primates, a lot with apes, plenty with mammals, reptiles, birds, fishes, insects, sponges, amoebae... in fact all life is interwoven. We are not special. Over the course of history our self-appointed privileges have been progressively stripped from us by scientific progress; science should be the believers' hair shirt or lash - let them take it up and bear the contumely of creation.

The one thing we can still do that, as far as we know no other entity can, is think. Of all the things that supposedly distinguish us, mind - the capacity for reason and free will - remains unchallenged - yet the fundamentally inclined seem ungracious in their refusal to apply their God given gifts.

If the the creationists and ID'ers claim to believe in a creator God of unsurpassable power whose works are necessarily possessed of beauty and elegance forever beyond our capacity to fully appreciate and our limited appreciation of those works can only gro - and grow without limit - are we not proud, vain, disrespectful if we turn our backs on them? If we choose to believe that the world came to be in 4004 BC pretty much as it is, are we not underestimating God's power to efficiently encode his creation in the most elegant way possible?

To create man, in his own metaphorical image or not (for would not a God of human size and form be a diminishment), God would have relied upon evolution.

God created evolution - and in doing so he would knew he would be giving us Charles Darwin to enlighten us as to the beauty of the process.

What we have instead of a continuation of the Renaissance is an incipient De-naissance, the celebration of ignorance and a hubristic reluctance to seek understanding.

Yes, believe that God made the world, but don't you dare claim to know how he did it, and don't you dare disparage the powers of mind he gave us to investigate it.

Evolutionist do not claim to know everything - evolution is "just" a theory, but it's not "just a theory"; the details will change, the theory will grow and we will understand more and more - and learn how much more we have yet to learn... and that's the beauty of science and the world.

God and Darwin in perfect harmony... there's got to be a musical - a song at least - in there somewhere.

Amen (Theological Stuff)

Relatedness?

I was won over watching Crout's KazooKeylele - Ukulele - The final countdown (hmmm... there's creativity for you) on YouTube, so I followed up... and watched Dorkbot Alba's Waldflöte vs Kazookeylele - dueling banjo's only to spot that Roundest Objects in the World Created was a "related" video. The latter is about incredibly precise spheres of silicon intended as possible replacements for the standard metric kilogram.

And the relationship is?

Doh! The Quantum Zeno Effect

"Doh!" as in, beaten to it again!

A long time ago (though I doubt as far back as 1977) I humorously proposed what is apparently called the Quantum Zeno Effect - a way of inhibiting state changes by obsessive observation.

I say humorously because I was proposing it as a way of handling nuclear waste - and one that is not as far as I can see at all practical (Worried about radioactive decay? Just keep an eye on it - and it won't! How one could appropriately "observe" a large mass of diverse composition I wasn't - and still amn't - sure).

And, as this is the way of things, I find out today (thanks of course to the New Scientist article here - subscription required to read the whole article online) that George Sudarshan and Baidyanaith Misra of the University of Texas apparently described this phenomenon way back when I was 16. It's since been established experimentally too.

The reason it works is that for small t, the probability of a transition is proportional to t squared...

I found a nice demonstration of the idea here (a pdf of a presentation by Wayne Itano of NIST) but, for those of you impatient for the Technical Stuff the maths bit looks like this...

So, there you have it: a watched superposition never decays.

(Of course in practice you can't make the absolutely necessary infinite number of observations to completely stop decay, but you ought to be able to slow things right down)

A Poke in the Eye/The Pain of Prawns?

[Irony On] Another triumph of experimental science: living things respond to stimuli.

This is the truly staggering insight I glean from this report in New Scientist. The fact that living things respond to stimuli I find to be a substantial development on the basic ideas of cause and effect. [Irony Off]

(Just to be fair, the original paper - enticingly entitled "Nociception or pain in a decapod crustacean?" - might well be more intelligent... but I have my doubts.)

I quote...

Robert Elwood at Queen's University Belfast in the UK and his colleagues claim they have found convincing evidence that prawns do feel pain. When they dabbed an irritant - acetic acid - onto one of 144 prawns' two antennae, the creatures reacted by grooming and rubbing the affected antenna for up to 5 minutes. This focused reaction is similar to that seen in mammals exposed to a noxious stimulant...

(NB "one of 144 prawns' two antennae"? Poor prawns! How do they share them? Perhaps they meant "one of the two antennae of each of 144 prawns"?)

Anyway, according to New Scientist he (Elwood) then goes on to say:

The prolonged, specifically directed rubbing and grooming is consistent with an interpretation of pain experience.

Which is not, by any stretch of the imagination - and mine stretches quite a lot - "convincing evidence that prawns do feel pain".

By this reasoning I would have to conclude that some modern cars with "smart" wipers also feel pain as evidenced by the "prolonged, specifically directed" wiping the windscreen receives when it gets wet.

And now I think about it, I have personally observed mud washing down hills when it rains - clearly even hills must suffer mightily from the elements so "specifically" do they endeavour to rid themselves of all that water by sloughing their skin.

At least Lynne Sneddon (University of Liverpool) has some common-sense, "You could argue the shrimp is simply trying to clean the antenna rather than showing a pain response, " she is reported as saying.

However, in response to this - and other alternative explanations - "Elwood insists such comparisons are flawed":

Using the same analogy, one could argue crabs do not have vision because they lack the visual centres of humans.

which is such an aggravatingly stupid remark that I just had to write this damn posting to express the pain of my cognitive dissonance!

No, no, no, no no! Pain is an instance of the sort of thing that drives Philosophers and Artificial Intelligence workers round the bend - the problem of qualia. In a philosophical nutshell, what we sense and what we feel about our sensory experiences (what we perceive perhaps) are two different things. If we were to (correctly!) use the same meta-analogy one could argue perhaps that crabs don't recognise their friends - not that they don't see or respond to light.

If I poke you in the eye with a sharp stick you will probably say "Ow!", and I grant that you experience pain, though I could - philosophically - perfectly reasonably doubt it: I feel pain, you make strange noises when poked - how and why should I connect behaviour with feelings?

Rub a cat's fur the wrong way and it will groom it back into place; is the cat in pain, is it perhaps mildly irritated, is it vain? Even once we solve the problem with respect to other "people" it remains to be seen how we extend the concept of pain to other organisms.

And of course there is pain and there is suffering. If I experience brief - but possibly intense pain - it is, by definition all over quickly; if I know it is going to happen again I will anticipate - and suffer. If I endure prolonged pain I have long enough to wish it would end, and so suffer when it does not - particularly if I don't know when it might end (I might suppose it is going to go on forever).

Obviously if you avoid inflicting pain you avoid inflicting pain-related suffering; but what if pain can be inflicted without suffering?

Discuss.

Nuff said.

Thiotimoline.dll

Some years ago (back in 1999 apparently - whatever happened to Moonbase Alpha?) I sent an email to Xircom's technical support service and received the surprising response that my message was received "tomorrow" (I sent it to New Scientist's Feedback column- the original item is here)

Eight years on and I am (partially) delighted to announce that whatever the underlying technology was/is/will be it has been/is being/will be developed to undreamed of heights of sophistication by none other than Microsoft and has been implemented as some sort of precognition extension to Windows Explorer.

Last night, I thought I was editing some photos - but I suspect now that this was merely paramnesia: when I looked at my photo folder I found this...


Not only did Vista know that I would be editing these images, it knew precisely how I would edit them - and most helpfully actually provided the resulting files, which could have saved me considerable effort if I had only known about this feature beforehand.

Unless of course, now that I have seen these files I do in fact modify them myself and Vista didn't do the work for me and is merely telling me that I am going to do some more editing...

Suddenly I realise that I can now test one of the good-old-fashioned paradoxes of time-travel (without the aid of a black-hole): now that I know I am going to edit these files today, what will happen if I don't?

Apologies if, as some fear, this results in the complete collapse of space and time as we know it and the banishment of the entire universe into neverness.

Actually, this is now a "very real" (as opposed to merely slightly real) fear: using the Windows "Start"button search I typed "modified: today" and, as expected, received a list of all the files I have worked on today... but searching instead for "modified: tomorrow" there is... nothing.

Oops!

Woah! The two files that were, yesterday, to be modified "tomorrow" are listed as modified "today" even though I haven't touched them - so there's no fiddling with time after all! I am truly impressed! Vista was right all along!

And on the further-up-side, if Vista seems not to keep your files where you think they are, let it search more widely - it may tell you where they will be, and then of course you can look them up there.

PS You can read more about Thiotimoline here. It makes a very good screen cleaner in solution - effectively removing tomorrow's grubby finger marks today! (Reapply every 24 hours for optimum results)

Counterproductive Advertising

New Scientist is running some ads on for Channel 4 in the UK - specifically for a programme called "Dumped".

Now, I don't mind advertising as long as the advert is designed to catch my eye rather than to reach out and grab me by the gonads.

This particular ad is unfortunately of the latter kind. It's not just a static ad it animates on "roll-over", i.e. when the cursor passes over the ad rectangle, and in this case illustrates the issue one presumes is to be addressed in the program, that of rubbish spilling all over the place and spoiling the environment. Like this...

Congratulations! You succeeded beyond your wildest dreams: online advertising rubbish is a menace. Every time I drag the cursor to the scroll bar I get the animation; and once the rubbish has been dumped all over my screen clicking anywhere in the bounding rectangle (the red box) - such as to click a blog link - opens a Channel 4 web page.

Even when it just ate my screen space it was so infuriating that I complained to New Scientist about them accepting and running the ad, Channel 4 for approving it and whoever designed it.

But when I discovered that it also caught clicks too more drastic action was required. Enter AdBlock Plus (0.7.5.1) for Firefox.

A short while later, after digging around in the page source code to find the right URL's to block the ad is gone... and so are all the other ads!

So the solution to online ad rubbish is simply an online bin man/refuse collector/waste management executive... but what a good job it doesn't all accumulate in some internent "landfill" site. Maybe it should though - what fun to be had. Let's build a garbage heap in Second Life and send all these ads there.

In concluding irony: brilliant! Annoy your target audience so much you lose all advertising benefits! Is that what you would call a successful ad campaign?

Inexplicable "Inflatable Planets" - Hot Saturns

Back in September 2006 New Scientist ran an article on "The riddle of the inflatable planets" in which Dimitar Sasselov said that the newly discovered planet HAT-P-1 was so light that it would float on water "like a beach ball."

Now New Scientist has reported today that another group The Trans-atlantic Exoplanet Survey (TrES) has found another particularly anomalous planet designated TrES-4, this one being "about the density of balsawood" [Balsawood! Does it have any uses other than model aircraft construction?]

Apparently, according to New Scientist, Travis Barman, a theoretician at Lowell Observatory, said, "This planet cannot exist.", i.e. there's no good explanation for how it could have become so large.

However, here's a hypothesis: the planet is not as large as it appears - the apparent size of the planet suggested by the observed dimming during transit could be due to a set of sufficiently dense rings. Saturn's rings are considerably wider than the planet, and they scatter quite a lot of light (though I'm not sure how much... I may be a geek but I'm not actually doing this research!)

I see two basic possibilities for the existence of rings around such "Hot Jupiters" (planets of Jupiter mass very close to their parent stars)

1. There could be a stable ring system. Intuitively this seems unlikely given, amongst other things, the considerable radiation pressure likely to be experienced so close to a star - dust would be driven off

2. There is a temporary ring system - it would wouldn't need to be stable, it could be recently formed. Perhaps if the planet had one or more moons, additional tidal heating from stellar proximity etc. might have expedited its disintegration and the formation of rings, in which case extended observation might record progressive dissipation of the rings and decrease in the dimming observed.

In either case, what would have been observed would be a "Hot Saturn" rather than a "Hot Jupiter", and the abnormally low density would be explained by the mis-estimation of the planet's size, i.e. mistaking the attenuation due to the ring system for attenuation due to the planet itself.

I wonder how this hypothesis could be observationally tested - actually I wonder whether it is viable at all... but that's what a bare hypothesis is: an idea for exploration...