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Welcome to The Lotus Position, an intermittent collection of extempore navel gazings, ponderings, whinges, whines, pontifications and diatribes.

Everything is based on a Sample of One: these are my views, my experiences... caveat lector... read the Disclaimer

The Budapest Office - Castro Bisztro, Madach ter

The Budapest Office - Castro Bisztro, Madach ter
Ponder, Scribble, Ponder (Photo Erdotahi Aron)

Guest Nutter/Kindred Soul: Bill Bailey

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Friday, 30 January 2009

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)

Monday, 12 January 2009

Google Desktop Review

I finally got fed up with Vista's built in indexing and thought who better to index my files than the Masters of the Search Universe, i.e. Google.

So I installed Google Desktop (5.8.0809.23506) and what an eye opening experience it has been.

I was aware of potential security/privacy issues and so made very sure not to enable the "Search Across Computers" option that transfers my data to Google so that it can be accessed elsewhere - if if only ostensibly by me. I also very carefully avoided enabling
the "
Enable Enhanced Content Indexing" check-box: all I wanted was basic content indexing, not the "backup and view previous versions", web-history search "and more", or thumbnails of images. Just the basic index my data files stuff please Mr Google.

I was surprised at what wasn't found... and then I discovered that unless "Enhanced Context Indexing" is enabled Google Desktop doesn't seem to index at all! On Vista it uses the built in (if enabled) Microsoft Index - so, of course, when I turned off Vista's indexing I got nothing at all! Even when it was on I would get results like this...

I searched for "LQG" and got 10 results; by summary at the top they were described as "1 email... 1 file... 1 other... no chats... etc.", but looking at the list itself it showed 10 items which by icon were: 1 pdf, 2 zip, 7 emails... despite the fact that I had told Google Dekstop NOT to index emails. In other words, when it's not doing its own indexing it doesn't know which way's up.

Because I couldn't find files I knew existed, I of course referred to the online help. Here it says:







But look at the prefs...

Do you see an item called "Enable content indexing..." No, of course not. They can't keep their Help (sic) aligned with the application. No wonder I couldn't find the right thing to enable to actually get my files indexed.

But do you also notice that I said don't index C:? You can tell Google Desktop not to index certain locations - and you can specifically tell it to index others.

But what is not clear is that the Don't overrides the Do... so when I wanted to index only Documents, which has been relocated to another partition (say, X:) I said "don't index X:" "do index X:\Documents" - and of course got nothing. I then had to specifically NOT index lots of other folders on X: to leave, by omission, only Documents. Not clever.

However, I did in the end enable "Enhanced" indexing. But now I discover so many other things that are inadequate to appalling I am going to remove it, but I thought you should know the (further) gory details.

Firstly, if you want to rebuild the indexes you have to Uninstall and Reinstall Google Desktop. Yes, that's what it says here. That's mind bogglingly antediluvian for starters.

I also have lots of very long documents - in the case of "IT", the book, currently running to over half a million words if you include all the annotations etc. - but does Google Desktop index them properly? Does it hell! "Up to 10,000 words" - usually less "to save space" are indexed. That is utterly useless. I have the space, I want an index! Do I get a choice about trading space for completeness? No. Obviously they've taken a leaf out of Microsoft's book and decided that's not a choice I could sensibly want. Unfortunately, the limitation on document sizing is buried in the Help (sic) file so I doubt that many people are aware of just how incomplete their searches might be. Thanks to Mark Russinovich for bring the partial indexing to my attention, but since his blog entry was written in 2005 I thought I'd check - and the answer is still the same. Three years later, storage getting cheaper and bigger every day and still Google Desktop does not do what it says on the imagined tin.

With regards to the privacy concerns etc., Google Desktop does apparently have some sort of facility to encrypt the indexes but the check-box doesn't seem to be enabled and there's nothing here about why that may be. Anyway, I have cunningly redirected (using Tweak GDS, or a simple registry hack) the Google Desktop index location to place it on a TrueCrypt encrypted drive... taking care of course that the encrypted drive is mounted before Google Desktop starts - otherwise it reverts back to its default location without any notification or "please locate" dialog.

However, while trying to work out why Windows Defender is suddenly taking so long to scan the system I looked in C:\Users\Me.MyMachine\AppData\Local\Temp and found gigabytes of what looked like temporary ZIP extractions. Yes, I had told Google Desktop to search Zip files but I didn't know it was going to dump the contents back onto disk (and not delete them when finished) in what I suspect is an unencrypted location even if Index Encryption could be turned on.

Other miscellaneous shortcomings:
  • There's no filename option, so you can't restrict your search to documents of known name.
  • There's no "OR" or "NOT" operator for boolean searches, though you can prefix a search terms with "-" to exclude it
  • oh, I give up, it just isn't good enough
In other words, unless you just want to index lots of personal type emails and you're not concerned about privacy don't waste your time with Google Desktop: it only does partial searches, you can't filter by filename, its not well documented, and for a "product" now several years old and, strangely for Google no longer in beta, it still feels like an early beta product.

Google Searching on the Web: Hero
Google Desktop Search: Zero

I wonder if that old Outlook add-on... what was it called... LookOut is still around? I actually used that on a TB RAID server at work a few years back and it indexed EVERYTHING (that it could read)

Google Desktop: Time Wasting Stuff (the time I spent downloading, installing, trying to configure, debug, test, etc. etc. etc. before giving up.)