Sunday, September 27, 2009

The probabilistic nature of life

Life is probabilistic not deterministic. That is one of the toughest things for the human mind to grasp in my opinion. Growing up our numerous experiences that can be explained by Newtonian physics and our tendency to engage in pattern matching creates a mental model of the universe that does not reflect reality. What happens in any given instance, with any particular species, and in any biological or physical system will fall within some range of behaviors but predicting the exact behavior is impossible.

There is also the issue of never being able to prove something beyond a shadow of a doubt. This also is difficult to incorporate into an understanding of the universe when trained in a deterministic manner. However, the way that science works is to accept the model or theory that best fits the data until a better theory comes along. The problem with creationism and intelligent design is that it refutes the theory of evolution based on the fact that not all of the pieces are explained at this point. Resorting to god as a hypothesis is a non-explanation because none of the workings of the system are addressed. It is analogous to trying to reverse engineer a car. During the process all of the pieces are catalogued, the engineering drawings are made, and the manufacturers of all of the parts are identified. At a certain point in the process it is still an unknown where the screws that hold the taillights on are made. Therefore the team throws their hands in the air, trashes all of the parts lists and engineering drawings, and declares that there is no way Ford could have manufactured the vehicle but god must have magically created the car.

Similarly evolution explains the preponderance of the evidence now available. The knowledge base will continue to grow and expand and the theory will be tweaked. However, the theory of evolution is not likely to be thrown out and adjustments to the theory do not negate the overarching concept or most of the pieces.

In summary it is necessary in my opinion to become comfortable with uncertainty, probability, and chaos theory at various levels to be able to incorporate evolution into a world view. We will never know for sure but the statistical probability of being correct increases as the theories are argued, studied, and tested.

A few answers to common questions about and critiques of evolution

Criticism: The truth is that, just as there is evidence for evolution there is also evidence against it. Evolution teaches that things evolve from simple to complex. And this is supposed to be true for all living things. But there is stacks of evidence against that hypothesis. A few examples from an interesting book called "The Crumbling Theory of Evolution," by J. W. G. Johnson.: "Among the dead bones of the past, we find no fossil links, no evolution.

Response: There are many intermediate species found within the fossil record. The fossil record is particularly telling because a VERY tiny percentage of organisms have been fossilized. Additionally the geological strata provide a nice smooth progression from single celled organisms roughly 3.5 billion years ago through the complex organisms today. There are no instances of any organisms grossly more complex than their predecessors merely appearing ex nihilo.

The fossil record is corroborated in terms of dating via numerous forms of radiometric dating. A wide range of dates can be tested with various forms of radioactive decay including Uranium 238-Lead 206 (4.5 billion year half life), Uranium 235-Lead 207 (704 million), Thorium 232-Lead 208 (14 billion), Rubidium 87-Strontium 87 (48.8 billion), and Potassium 40-Argon 40 (1.3 billion). All of these tests are very robust and have very tight error bars.

Then, if we look at the living world of the present, again we find no inter-mediates between living kinds.

Every species in existence is an intermediate. All species will follow what came before and will be replaced by what precedes them. That is a very elementary concept. Good examples are the many breeds of dogs that have been produced through selective pressures provided by humans. Can these breeds still reproduce? Sure, for the time being anyway. If you keep breeds separated for a long enough time genetic drift will generally make them unable to interbreed.

Living creatures prove that kinds do not change no matter how long the time span. For example, using the evolutionist's supposed ages (later I will talk a bit on this particular issue as well), there is a dragon-fly species still with us after sixty-million years. The Australian lung-fish should have evolution in its blood, but it has not changed in 220 million years. Spiders remain unchanged after 300 million years. Cockroaches and silverfish unchanged in 350 million years. "Turtles have been turtles for 250 million years of evolutionary time.

All that means is these few species the author cherry picked have not mutated significantly in the amount of time chosen. There is nothing in the workings of evolution that would indicate change MUST occur. It does tend to occur as seen from the fact that the dragonfly, lung-fish, spiders, and turtles evolved from prokaryotic cyanobacteria over the course of three billion years. Additional many other species were mutating into forms that were more appropriate for the changing ecological niches that ebb and flow with climatic changes and with the ever changing balance with other species. However with any system it should not be surprising if a few components/species remain viable and near optimal for their particular niche or their niche has not been subjected to pressures for a relatively lengthy period of time.

Turtles have an incredible skeleton. They live inside boxes; and their girdles are inside the rib cage. That should mean a lot of evolving. We should find millions of quarter-turtles, then half-turtles, and so on. But we don't. The very first turtles were perfect turtles. There is no fossil of something pre-turtle, nearly-turtle. "The hard fact is that every kind of creature living today which appears in the fossil record, appears there in form similar to its present form.

He is cherry picking the data again. The entire fossil record is a collection of simpler forms followed by small mutations over vast time spans. The first fish sans fins were followed by fish with first very subtle fins followed by more complex fins, then by fins that doubled as legs, then true legs, etc. This is evidenced by the mutations evidenced by Eusthenopteron, Panderichthys, Ticktaalik, Ichthyostega, and Acanthostega over the roughly 25 million year time span from 380-365mya.

This was dramatically confirmed by the Coelacanth fish. This fish, through one of its relatives, was credited as being the ancestor of amphibians, a vigorous evolutor. It was regarded as extinct for seventy million years. But in 1939, a fisherman hauled up a Coelacanth very much alive. To an evolutionist, this was just as upsetting as if a dinosaur had walked up the street. Since then, several more living Coelacanths have been caught, all of them exactly as they were when the last Coelacanth fossil was laid down seventy million mythical years ago."

This was not upsetting at all to evolutionists. In fact quite the opposite was the case. This was a very exciting finding for evolutionists. Again there is nothing within the workings of evolution and natural selection that precludes well adapted species from continuing for millions of years. Furthermore because this living fossil in the form of Coelacanth is so readily available morphological, bio-behavioral, and genetic studies can and have greatly enhanced our understanding of evolution.

Then there is another interesting law of science called The Second Law of Thermodynamics. ... "It would hardly be possible to conceive of two more opposite principles than this principle of entropy (mass-energy loss) and the principle of evolution. Each is precisely the converse of the other. (Henry M. Morris, The Twilight of Evolution., p.35).

This is a VERY old and worn out argument against evolution. The earth is not a closed system. Entropy works when you have a finite amount of energy in a system that is sealed off from all outside inputs. The earth has had a constant supply of external energy for the last 4.6 billion years in the form of the sun. It is very analogous to the continued creation of complexity in a car factory. If you close and lock the doors on the factory then yes things will begin to decay and nothing will ever come out the doors in the way of products. However, if you continually provide electricity, raw materials, and food for the workers then complex systems will be generated. It is quite possible that entropy will eventually lead to the darkening and dissipating of the matter in the universe over many trillions of years. However the big bang infused all of the matter in the universe including what is included in the stars with massive amounts of energy. Complexity can increase in the local subsystems around stars because there is a massive energy imbalance between the star and the surrounding matter.

Evolutionists will say that different layers of rock formations will show different periods of the evolutionary process, in other words, the simple becoming more complex as you get closer to the surface of the rock formations. This sounds very good and fine except that fossil remains don't always appear in that order. In fact, fossils are found in all kinds of order contrary to the evolutionary ladder. Many caves and canyons that appear to be millions of years old can indeed have been formed over a very short period of time. A simple example. Some years ago a volcanic mountain blew up and left a huge deep gorge that looked like a prehistoric canyon. Of course it wasn't as it had just been formed. So things are not always as they appear.

Small differences in a local area are taken into account by paleogeologists and paleontologists. Taking a very small difference in a localized area does not negate the findings that are rigorously compared across the planet. Also see my comments on radiometric dating above. The various forms of radiometric, stratigraphic, and paleomagnetic data fit very tightly together and provide an incredibly robust picture of the ages of the many and varied fossil finds.

There's no question that genes determine what a foetus is and what it will grow into. Here also manipulation plays a big part. We know that we can develop better breeds of cows, flowers, etc. But still a cow is always a cow; a flower is always a flower, etc. We may be able to change the colour and the size of something but the specie itself always remains true to its own kind. So here once again evolution falls flat.

That is over a VERY short period of time. Selective breeding has only been around for thousands of years whereas evolution works over hundreds of millions of years. The difference is so many orders of magnitude apart that the author's comparison falls flat. As I mentioned above, if you keep the breeds completely separated for a long enough period of time the differences will generally continue to build until interbreeding cannot occur.

So the improvements of the spontaneous type (just going back to the Second Law of Thermodynamics for one minute) hypothesised by the devotees of the current theory of evolution who suggests that cosmic radiation caused genetic changes which resulted in a higher order of off-spring survivability than the parent possessed, and also a change in the genetic makeup have not been found to support that theory.

This is only one very small cause of genetic change. There is massive amount of evidence that shows genetic changes are incredibly common and most of these changes happen because of transcription errors that randomly/accidently occur when genes are replicated within each organism. The fact that this has been happening for hundreds of millions of years is evidenced by the "junk" DNA found in every organism. Most changes that occur randomly are neither beneficial nor nefarious. Thus there are no selection pressures that would eliminate organisms that carry these random mutations.

In simple words, scientists may be able to work with genetic engineering and indeed have made wondrous advances, but that's not creating life, it's simply meddling with life that already exists. Even cloning is not creating life but is simply taking from already existing life.

This argument is what is called ignoratio elenchi or a red herring. While it is true that current genetic engineering is only altering current life forms this has nothing to do with the mechanisms that drive evolutionary change necessarily.

Because of all the millions of creatures that exist on the earth, only humans think in terms of logic, good and evil, can invent incredible devices and machinery, understands and is in a constant learning process and development, etc.

Another red herring and he is also begging the question. He is assuming that there must be an intelligent designer without providing a rationale for why that is so. Self organization and increases in complexity driven solely by the laws of physics are observed in the lab and throughout the universe on a regular basis. One example is the creation of new stellar and associated planetary systems from the remnants of previous systems.

The evolutionists say that we are related to the apes. Yet we are separated by a gulf so wide that it seems to defy all logic.

The genetic differences between Homo sapiens and the various other hominids are actually very small with our genetic code being comfortably over 95% identical. We actually share a tremendous amount of DNA with all other living organisms including things like pine trees and fruit flies.

The evidence for evolution is immense and volumes of data are added each year that provide additional support. There is no theory that fits the massive amounts of evidence better than evolution while the theory of evolution becomes more robust with every passing discovery.

Steps toward the formation of RNA

A recent article in Nature reports another possibility in the steps toward the formation of RNA. In short science is slowly closing in on the pathways that could have led to the first replicating polymers and then to the first cells. All of the answers are not available and we will probably never know exactly how the first life formed but some of the plausible pathways are being discovered.

Nature 459, 239-242 (14 May 2009)
Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions

Matthew W. Powner, Béatrice Gerland & John D. Sutherland


At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis—cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate—are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.