Tuesday, 9 December 2014

Tokyo Ghoul

Just thought I should share this awesome anime music video(AMV). I started watching Tokyo Ghoul last month and now Im hooked.

There's just something about the pure psychoticness of it.....

On Transitional Fossils & Imperfect Design

Note: I am a novice in many of the established sciences I often advocate for. if one wants a more comprehensive assessment, please visit some of the established sites, such as Understanding Evolution or Talk Origins. I will attempt to give my own view of the information contained in these sciences, while linking interested readers to more.

 When we talk about evolution spanning many millions of years, the sheer number of organisms living and dying, we simply cannot observe these changes in real time. Thats why we need to indirectly infer these changes by studying the fossils themselves to construct a detailed view of its evolutionary history.

This is the first hiccup that creationists will always attack. So we cant observe macro-evolution? Then doesnt it rely on faith to believe in it?

This is heavily mistaken on several levels.

 You see, if we only rely on direct observations (the philosophy known as empiricism), we would miss out on a whole new level of science. As a matter of fact, valence bond theory, molecular orbital theory (something Im much more familiar with) and even Einstein's theory of relativity were vindicated by indirect inferences!

Did you think we could observe gravity actually bending time? Or actually see the electron shells of atoms? Of course not. However, these scientific theories explained a lot of what we could observe. The process of science doesnt rely on empiricism alone, but also rationalism. We make rational inferences and formulate theories based on available evidence, then find further evidence to test them.

Let us turn back to Darwin's Theory of Evolution. Nevermind that there have been observed instances of speciation before, or that it was found that bacteria had evolved the capability to digest nylon (note that nylon is a synthetic polymer invented in the 1930s). Nevermind the evolution of antifreeze proteins in Arctic and Antarctic fish. Lets look at transitional fossils.

So, what is a transitional fossil? A transitional fossil is simply a fossil organism which has features intermediate of its ancestor and progeny. Often, paleontologists group fossils with particularly striking intermediate features under the term "transitional fossils". In fact, there are a huge number of them!

It could even be argued that all fossils are transitional (this is not entirely true, rather "intermediate" more accurately describes the situation). Mainly because life, as a whole is in a constant state of flux. Speciation events continuously occur.

No other analogue of common ancestry comes closer when we look at the evolution of languages. Consider the Spanish and Italian languages. Did you know that they actually share common ancestry with Latin? Over time, they were adopted and modified by their respective cultures until they are completely distinct languages from each other. Then look at the Mandarin language:

From http://www.omniglot.com/chinese/evolution.htm
This is going off on a tangent, but note how Chinese characters slowly evolved from simple sketches of the objects they were supposed to represent? (All the characters are arguably transitional forms).

I would now like to address a fellow blogger (and someone I respect) who wrote recently that transitional fossils probably don't exist here. Hopefully I can fairly represent his argument by picking his main points. So he writes:

Logically we have to qualify what a transitional is. I defined it as a species between designs. For example an ape, whether extinct or extant is designed to be arboreal, and thereby dwell in trees, but a human is a bipedal designed to walk uprightly on two legs. So to transition you need to go through many imperfect stages in between the two states of being.

Logically, just now think, given there are millions of species on earth, how many organisms should look anatomically CLUMSY, because they are transitioning, in an 'imperfect stage' between what they were and what they're becoming?
This point in particular, was what inspired to write this post. So he asks, if evolution were true shouldn't we expect to see hundreds of awkward, transitioning organisms in the animal kingdom?

Further down, he concludes:

 I expect to see 'transitionals' everywhere, if evolution is so prevailent in nature. I see none. Furthermore I see that every species is a whole design, viable, with all of the tools needed to do it's job, perfect for it's specific job.

I feel that to address his points we need to consider several factors. First of all, a transitional form does not "need" to imperfect. Its unfair to imagine a "real" transitional form to be some awkward, mutated, crocoduckian abomination.  While it is true there are often fitness "trade-offs" when a species is evolving towards a particular trait, this does not accurately portray the situation.
I ll summarize a few points.

1. First, when design proponents argue that "everything is well-designed" one would point out this is not necessarily so.

Look at the flying squirrel. It is not capable of true, powered flight like birds or bats are, and could be considered "inferior" tp them. It has a much cruder design for its "wings" (the patagium) yet it soars gracefully through the trees by gliding.

Its even possible that the flying squirrel is a "transitional" precursor to true winged squirrels in the future. Who knows?

 I will try to illustrate this further by pointing out a very famous transitional fossil of the evolution of birds from flying dinosaurs.

Consider Archaeopteryx.

Image courtesy of Livescience here
(Again slightly off-topic).
I am continuously saddened when creationists constantly accuse scientists of deceiving the masses. It seems their only purpose is to slander evolution and accuse evolutionary biologists of being deceitful, capricious liars.

Even worse is when you realise that creationists cant even agree on whether Archaeopteryx is a dinosaur or a bird. You have one site which implies that fraudulent scientists have claimed Archaeopteryx is a bird (later revising the hoax to a dinosaur).

Then you have Jonathan Sarfati correcting them and claiming that Archaeopteryx is indeed a bird and NOT a hoax. Really.....(at least Sarfati has the integrity to prevent the promulgation of lies though....)

Enough of that, lets ignore the debate entirely and focus on Archaeopteryx itself. If it was a genuine bird, then it wouldnt have been a very good one.

First, Archaeopteryx has asymmetrical flight feathers. Second, it does NOT have a sturdy breastbone. It would have been an inferior flyer compared to modern day birds.

There are also subtle, tell-tale signs that it is distinctly reptilian. First, its "beak" (if it can even be considered a beak) has teeth. It also has a long, bony tail. If we saw Archaeopteryx, it would probably be a freak.

Then consider the giant panda, which feeds on bamboo. As a matter of fact, it seems largely maladapted to its environment. It has a carnivorous digestive system and lacks the ruminant gut most herbivores have to properly digest cellulose. Thats why it has to consumer prodigious amounts of bamboo to survive!

 By the way, there are actually a lot of "freaks" in the animal kingdom even today. (See these freaks and  these giant animals). Oh, check out this fish with transparent blood and  this worm-like amphibian too.

Of course, just because they arent particulary well designed doesnt mean that they are simple. (More on that later).

2. How does one know that modern species aren't transitional forms?

The fish-tetrapod transition occurred in the distant past, during the Devonian, but why not we look at some modern species of amphibious fish that can give us vital clues of how the transition might have occurred?

Consider the mudskipper.

Image courtesy of NatGeo

It is truly a fish adapted to live on land. It uses its pectoral fins to walk on land. It can propel itself forward by flexing its muscles.

It breathes air through its skin and pharynx (but only when its wet). It can store water in its gill chambers as extra oxygen supply. Its entirely possible that fish like these are precursors to new species of amphibians in the distant future wouldnt it?

3. Exaptation and Jury-Rigged Design
So what is exaptation? It simply means a shift in function of a trait during the evolution of a particular species. What happens is that a trait originally used for one purpose is eventually adapted for another.

In the aforementioned example, I glossed over briefly, the evolution of birds from theropod dinosaurs. Why would theropods possess feathers, one might ask? Well, feathers might have originally kept theropods warm. They might also served to increase running speed when hunting prey.

This is a re-constructed skeleton of a "terror bird". Note how similar its anatomy is to dinosaurs. Image is from Wikipedia
These designs, are then in essence, "jury-rigged" and co-opted from prior forms, often with very subtle weaknesses. (See some at Talk Origins here).

I ll lay out some more evidence for imperfect design, particularly in the cellular respiratory and photosynthetic processes. Its very likely they evolved from putative metabolic processes.

The RubisCO enzyme is crucial in the carbon fixation process (for photosynthesis) as it catalyzes the carboxylation of RuBP. But one major problem with this enzyme is that it cannot differentiate between carbon dioxide and oxygen. So if there is a significant amount of oxygen, the activity of this enzyme is severely affected.

Above all, we have even succeeded in creating variants of RubisCO which are more effective than the ones in nature that does not have this weakness!

Even the cellular aerobic respiratory process (in combination of glycolysis, the Kreb's cycle and the electron transport chain) are only about 34.5% efficient. That means they only succeed in metabolizing about 34.5% of the energy from glucose. Would you consider this effective?

4.   Punctuated Equilibrium 

I wont go into too much into this. But first theorized by Stephen Jay Gould, it posits that species are often at an equilibrium, at a local fitness peak (I alluded to this in my previous post). Only when drastic changes in environment or ecology occur, then selective pressures favour rapid evolution of certain traits.

This probably means that many of the organisms we see today are at the top of a local "peak" and hence are optimized to the environment they are in, thanks to millions of years of evolution.


 Nature is very complex, and it would be surprising if it wasnt.  But just because nature trumps human design doesnt then necessitate a better designer for it.

This is simply because of our limited understanding and ingenuity, such that we require to draw inspiration from what we can observe. Consider modern designs as compared to primitive ones. The former is clearly much more complex than the latter. But it doesn't necessarily mean people today are much smarter than people in the past, it just means we have much more information and build upon the successes of our forebears.

 The laws of physics are very complex, does that require a designer too?

I suppose for Christians (and other adherents of monotheistic religions) they would say: yes.

But that is a discussion for another time.

Thursday, 4 December 2014

Some stuff

Ah, its been a while since I posted, but just finished exams, so expect posting frequency to rise until sometime in January.

I might delve deeper into philosophical stuff this time round though. There's some stuff I wanna discuss....