Friday, 13 June 2014

Undesigned information

Supplementary material

For a few decades, now, a creationist mathematician called William Dembski has been quite vocal about the concept of "irreducible complexity", which in a nutshell is something (some natural object or phenomenon) that is so complex that it could never, ever have developed without the assistance of magic. Needless to say, the proponents of such a concept usually say that their argument is based solely on science and not on, say, their religious beliefs, but by a coincidence that is even more astonishing that the spontaneous appearance of life, all of them happen to be religious. Dembski himself has a degree in divinity, even! (As a lapsed catholic, I have no precise idea what that is. It is not a degree in theology, and in the U.S. I believe that it is given by church-related institutions (and often as a honorary title). Not to make light of it, but to me it's akin to a degree in Pokémon studies; it means that someone has talked a lot about something that doesn't exist).

What a creationist biochemist like Michael Behe sees as irreducible complexity that proves the need for a supernatural engineer, all other scientists see as systems that may look very complex indeed but that don't require magic to be understood. The famous case of the bacterial flagellum is a good example of irreducible complexity that is after all quite reducible. It is a complex biochemical machine that bacteria use to move about, and although it's true that it is unlikely for each piece of this complex apparatus to have evolved independently until *shazam!* all were ready to be assembled to form a fully-functional flagellum, it is far less flabbergasting when we realize that most of these pieces were already present in bacteria, and used for other purposes. A sandwich appears less impressive in its final form when you know that the fridge contained ham and cheese and mayo and that there is bread in the pantry and a tomato on the kitchen counter.

"If you can't dazzle them with data, baffle them with bullshit". In my case, that would be very easy to do if the speaker was a mathematician, because my math-fu is weak. So when a mathematician says things like "information can neither be created nor destroyed", I simply wouldn't know where to start looking if Google didn't exist. Many creationists, who are as bad as I in mathematics and decidedly worse in biology, often refer to that line from Dembski as if his views on information theory were accepted by the scientific community, clearly thinking that they are as sound as Newton's laws of thermodynamics. Equating the succession of nucleotides in a DNA sequence with information, these enthusiasts readily quote their champion: "neither algorithms nor natural laws are capable of producing information."

That DNA contains information, I have no problem with. Obviously, the succession of nucleotides forms a code (it's called the genetic code, after all!) that directs the assembly of proteins, which in turn help living cells function. On top of that, the shorthand way to describe a succession of nucleotides is to drop the phoshoribosyl backbone of DNA and just focus on the first letter of each nucleotide's name: A, C, G or T. To a casual reader, it really looks as if DNA is "written" in some fashion. Like a message in morse code, or a computer line written with 1s and 0s. But that's where the analogy goes too far.

Take the following line from Shakespeare: "There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy". It is clearly information, and this information is carried by a totally arbitrary system of communication: certain signs arranged in a certain order, and the message itself is totally independent of the communication system used. You could write that sentence in Chinese or Korean and the information itself would not change.

Not so with the genetic code. Each nucleotide is more than a symbol; it is a molecule whose very shape will determine its possible interaction with other molecules. In that sense, it is more like a cog in a machine that a letter in a sentence. But even the cog analogy is abusive; a cog in a machine is placed just so, and other cogs are likewise finely positioned; no matter what William Paley might elegantly argue, a watch does not contain a bucketload of useless or broken cogs. The human genome, by contrast, is full of parasitic transposons and of integrated retrovirus remains, not to mention thousands of pseudogenes.

But there is information anyway in our DNA, even if this information is mechanistic in nature more than based in an abstract code. Does the statement "neither algorithms nor natural laws are capable of producing information" apply, then? Well, no, I beg to differ. As the cartoon above illustrates, a mindless flow of water subject to purely natural laws can certainly create information. Looking at a dry river bed, it is clear where the water will flow during the next flash flood. This information is a lot like the genetic code, which instead of directing water in one direction will direct how a transfer RNA will sit next to another during the process of assembling amino acids into proteins. Information can definitely originate from mindless, undirected and clearly not supernatural sources.

Thursday, 5 June 2014

Slender man

Supplementary material

Slender man is a modern version of the bogeyman; a fantastic creature straight out of nightmare meant to send chills down our collective spine. He was first seen in 2009 on the internet forum Something awful in two edited photos showing children at play being observed by a preternaturally thin and out of focus figure; an apparition guaranteed to scare the beejebus out of me. The photos were accompanied by a note saying the children had disappeared soon after the photos were taken, and that the photographer was also missing. An excellent spooky creation, if you ask me.

Slender man joins the ranks of a long series of scary pop culture figures that are all the more frightening for never being actually seen: the bogeyman, the sack man, Baba Yaga and the like.

The character became quite popular and inspired many stories, games and attempted film productions. Unfortunately, he was apparently also the inspiration for a failed murder attempt committed by two 12-year old kids. Thankfully, for once, reality did not catch up with fiction.

Tuesday, 3 June 2014

Fecal graft

Supplementary material

Certain therapeutic approaches may be shocking when we first learn about them. The idea of using leeches for any medical treatment certainly sounds counter-intuitive, mostly because of its very high yuck factor of the damn things. And yet, these antipathetic invertebrates have been used for practically ever by members of the medical corpus, and an archaic word for a physician in English is leech. Even setting aside the medieval principle of the four humours (justifying the use of a blood-sucking animal, helping reduce the level of blood when it is overabundant relative to phlegm, yellow bile and black bile), leeches secrete anticoagulants which even today work wonders in the treatment of people who had a finger severed and reattached (or even a nose)!

Another approach whose basis could only be charitably defined as dubious is fecal bacteriotherapy, which can be summarily described as poop grafting. More accurately, it is a technique that replaces an intestinal bacteriome that has been thrown off-kilter by some factor or other, resulting in nefarious effects, by a one more closely resembling that of the patient before they were ill.

Oddly enough, this has been done with animals for quite a long while. It is only recently that we have started truly appreciating what stool transplant could do for human health. It has had, among other effects, a spectacular rate of success in dealing with hard-to-treat infections with Clostridium difficile, and this is good news indeed as this opportunistic invader has grown more and more resistant to anbtibiotherapy as time went by. (Resistant C. difficile nosocomial infections in hospitals have become a big public health issue in recent years).

The human body contains a vast number of cells, but roughly one in ten is an actual human cell. The bacterial population we carry with us (what is sometimes referred to as the bacteriome) outnumber our cells by an order of magnitude! Is it any wonder that our health would depend in large measure on the harmonious relationship between our body and these trillions of partners? If we consider the human body, bugs and all, as an ecosystem, we'll have a good idea of the importance of maintaining our homeostasis. And just like any good ecosystem will contain bacteria, fungi and other creepy-crawlies that play a crucial role for the welfare of all, so does it go for us.