Friday, 15 August 2014

Evaluating ID

   One thing I noticed is that, it is far easier to attack ideas than to defend them. Often its because defending is in response to an attack, which the defender needs time to think through, carefully deduce the opponents argument, point out flaws and do his or her own research to rebut the attacker. So, I will play a little game, if you may, engaging in back-and-forth arguments for and against design, throwing in some specific examples. This is going to be a long post though, composed over several days.

A note though: I am only familiar with general arguments for ID. If anyone knows more refined points, please inform me and I will take them into consideration.

So what is the concept for intelligent design? At the Intelligent Design homepage, it states "
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection

  In the recent years, the Discovery Institute has come under fire for being religiously motivated, but I ll move past that and take a closer look at their arguments. Coming from a physics/engineering background, I can see how design can be appealing, regularly dealing with concrete, specific answers. And although non-religious, I lean towards the Rare Earth Hypothesis that Earth-like planets are a special and unique occurrence.

One of the key features of DI's theory is that the designer is not identified. In other words, you could replace the designer with anyone (God, aliens, the Matrix etc) and the theory remains just as valid.

The first problem immediately becomes apparent. You see, the Discovery Institute doesnt just insist biological systems are designed, even the Earth was designed to accommodate complex, intelligent life. (Check out their documentary the Privileged Planet for example.) What is the problem with this?

It immediately points to the exclusion of certain designers (sorry Cthulhu, you couldn't have created Earth) and very strongly towards God. Their article rebutting the idea of panspermia (life from other planets) heavily implies this. Do they have a religious agenda? Actually it couldnt be less obvious that they are religiously motivated.

 However, ID lends support to deism, which is a philosophical, not religious position. Fair enough, lets focus on biological systems first, since arguments for/against fine-tuning of the Universe are wandering into the realm of the un-falsifiable.

First, let me offer credit to intelligent design. There exists other scientific fields that do attempt to detect the presence of deliberate tinkering. Richard Deem of, aside from criticising the general push of ID, has an interesting list of points:

  1. Archaeology: Is that rock formation natural or due to intelligent design?
  2. Anthropology: Do sharp, pointed rocks occur naturally or are they designed by intelligent beings?
  3. Forensics: Intelligent cause of death or natural circumstances?
  4. SETI: Are those radio signals natural or caused by intelligent beings?
This is actually quite a good argument. We look for signs, "motifs" if you may, that indicates a particular biological system is designed. However, the first difference one would notice between ID and these other scientific fields is this: we know what features to look for, because we know that natural processes cannot produce certain features, where-else

Take the study of stone tools by archaeologists and anthropologists. How would one know if a stone was designed, or simply occurring in nature? Of course, arrow-heads would be a dead giveaway - shapes like that dont occur naturally, written records and observations of arrow-making further back this up. For more obscure, primitive artifacts, we look for systematic flaking i.e. a stone with numerous flake scars is unlikely to have been the result of natural breakage. Natural rocks may have flake scars, but its unlikely they would have so many. See here for more.

This same principle (to me at least) cannot applied to intelligent design. This is because:
a) We do not know the mechanisms the un-identified designer could have used;
b) Our minds may be too primitive to comprehend design, if life was indeed designed.
(In fact some primitive tribes thought cameras could steal your soul. What if we are tribesmen, gazing upon some vastly incomprehensible design?)

Lets go a little into details and revisit William Paley's famous watchmaker analogy. He says that, if we find a watch in the field, we can easily discern that it had a designer.  This argument, while compelling, does not work upon closer inspection. First of all, we know a watch is designed because watches dont simply appear as random products of nature. We can even observe them being designed and manufactured!

Is this beautfiul snowflake intelligently designed?

 Well, a counter-rebuttal would be you could say we dont see apes evolve into man either, so how can we know evolution occurred either? I will discuss this further detail in the near future, but we will get to the basics by giving an evolutionary counter-example to the "common design, common designer" argument. It means that common designs that function effectively are re-used by the designer because it works.

In evolutionary theory, two similar biological structures (anatomical or genomic) can be homologous or analogous. The former means that two particular organisms inherited the structure from a common ancestor(common descent theory), while the latter implies the process of convergent evolution i.e. two unrelated organisms gaining a very similar biological structure.

What happens is that organisms with homologous  structures slowly attain morphological differences over time, while organisms with analogous structures actually grow more to resemble each other.

One important point is organisms with homologous structures often bear remarkable similarities in genome sequence. In contrast, organisms that arrived at a trait via convergent evolution bear little or no resemblance in genome sequence to each other. A good example would be bats and birds, which diverged all the way back from the age of dinosaurs.

How does this challenge ID? Well I now take "common design, common designer" to its extreme conclusion via reductio ad absurdum. If birds and bats had a common designer implementing a common design for flight into of their wings then wouldnt it follow that they have anatomical and genetic similarities as well? They don't!

You can see from this picture that bats and birds have different anatomical structures for their wings. Notably bats have the mammalian "five finger" structure. Well you could then say "this is an example of the Designer exerting creative power", but how are we even going to test that?

   I ll illustrate this again by a not-completely original example of convergent evolution, first posted at the evolution blog the Panda's Thumb here, by a former YEC.

The Arctic cod and Antarctic nothothenioid are notable in possessing anti-freeze proteins to prevent their blood from coagulating. But the unique thing about them is that their protein structures do not resemble each other. Each evolved their traits independently! If you are interested, please read the original research paper, first published in PNAS here for more information. (Also note that the nothothenioid antifreeze protein is very similar structurally to fibrinogen - a protein involved in blood clotting).

Evolutionary theory produces a unique feature known as a fitness landscape. Taking one particular environmental condition, there are several ways evolution by natural selection can act to produce a population with an average phenotype which is well adapted to its present condition. This is represented by the local "peaks" A, B and C. However if an organism is at the top of a local maxima, say A, it will have to experience a decrease in fitness before being able to climb the highest peak B. (this is a very layman explanation of a complex science, so apologies).

There's more than one way to adapt

Lets look further at more of the points the Discovery Institute makes.

Another fundamental concept of a scientific theory is that it must be:

a) produce testable hypotheses
b) falsifiable

The IDEA center has a good intro to the testability of ID.

The Short Answer: Yes. Intelligent design theory predicts: 1) that we will find specified complexity in biology. One special easily detectable form of specified complexity is irreducible complexity. We can test design by trying to reverse engineer biological structures to determine if there is an "irreducible core." Intelligent design also makes other predictions, such as 2) rapid appearance of complexity in the fossil record, 3) re-usage of similar parts in different organisms, and 4) function for biological structures. Each of these predictions may be tested--and have been confirmed through testing!

I will be taking a look at them, from 1 to 4. I have already challenged point 3 and will briefly skim through the others.

1) We will find specified complexity in biology. The problem is specified complexity needs to be defined more specifically so to speak. Proteins, although generally complex and carry out specific tasks, are actually less specific than people like to think. Lets look at enzymes, proteins meant to catalyze chemical reactions. Although hundreds of amino acids long, the only real important parts are at the active site which consists of only several amino acids. THOSE are the complex specified parts. Want proof? Go on wikipedia and look up the range of protein structures. Note how many "protein folds" are re-used for different proteins (particularly the alpha helix and beta pleated sheets).

 Ah, irreducible complexity. This is actually  a very interesting point, because oftentimes evolution that increases complexity proceeds by stepwise transitions until a complex organ/organelle is formed. The logic goes: if an ancestral component protein or anatomical structure is removed, then the whole system would cease functioning, then prior steps would have no function and would be useless according to evolutionary theory.

On the Uncommon Descent blog you can see the icon for ID - the bacterial flagellum. In fact, they should actively testing for its irreducible complexity! Take apart the bacterial flagellum by deleting part by part. See if the flagellum still functions. Experiment on other biological systems too.

A caveat though. Just because a system is irreducibly complex, doesn't mean it couldn't have evolved. Do you know why?

  a) Mutations could act upon existing genes, deleting and removing parts of a system. If the parts that have been deleted or pseudogenized only carry out secondary, unimportant functions then the system would still be working. Hence an "irreducibly complex" core - that has lost certain original working parts, but losing more would render the system unusable. A good analogy would be how natural arches form - underlying rocks are eroded until the arch is left. The arch is now irreducibly complex!

b) Exaptation - this is a very important part of evolutionary theory that intelligent design proponents overlook when criticising evolution. What happems is that a prior anatomical structure / gene is co-opted to perform a different function. A cogent example is the fish-tetrapod transition. For a transitional form like Tiktaalik, it is able to use its fins for walking on land as well as swimming in water.

2) Rapid appearance of complexity in the fossil record This is probably referring to the Cambrian explosion. I lack the credentials to properly analyze it, but remember  The Cambrian explosion shows a trend of increasing complexity, although a relatively rapid one. Please read this very detailed critique of Darwin's Doubt here to understand the nuts and bolts.

One more note about it is that the Cambrian seas were actually very volatile because oxygen levels were constantly fluctuating, resulting in several extinction events that wiped out many genera. Well maybe the Designer didnt mind watching many newly designed species bite the dust after all......

4) Function for biological structures - Well most biological structures already have a function but i think people are jumping to conclusions by proclaiming it intelligently designed. The problem is there are huge swathes of non-coding DNA in the genome. A general trend of biological complexity goes like this - the larger the fraction of non-coding DNA, the more complex the organism. Take the human genome, which appears as mostly junk. Yes, some of these non-coding DNA have important functions but others don't, and may even be harmful. (See retrotransposons - jumping genes that copy their sequences all over the human genome. Really).


For now ID appears too much to be a philosophical than a scientific one. It needs a greater testability and predictive quality before it can be considered science. Funny enough I don't really mind if they actually do find genuine evidence for design (and its implications) but who knows? Next up I will discuss falsifiability of evolution and intelligent design, as well as more points listed on the IDEA centre.