Sunday, March 2, 2008

What Do Our Chromosomes Tell Us About Our Distant Relatives?

(Note: I recommend reading the previous posts 1 and 2 first)

In this post I will reveal some striking observations about our chromosomes that may come as a surprise for many, specially the religious. Basically, chromosomes are sub-cellular components of organized DNA structures that hold individual instructions. These instructions are called genes and are necessary for developing and maintaining a healthy body. In every cell in the human body there are between 20,000 to 25,000 genes located in 46 chromosomes (except for the sperm and egg cells which only have 23 chromosomes each). These 46 chromosomes appear in 23 pairs, one of each pair from the mother's egg and the other of each pair from the father's sperm. The great apes (i.e. chimpanzees, gorillas and orangutans), on the other hand, have 48 chromosomes in their cells which occur in 24 pairs.

Each chromosome has a short arm and a long arm which are separated by a specific repetitive DNA sequence called centromere. Chromosomes are protected from destruction, rearranging and fusing with each other by a specific repetitive DNA sequence at the end of each chromosome called telomere. The whole heredity information encoded in the DNA is known as the genome. An actual photograph of the chromosomes from one cell is called a karyotype. The following figure shows a normal male karyotype.

When the human genome was compared with those of great apes some interesting observations emerged. Almost half the human chromosome 5 is a reversed end to end rearrangement of the chimpanzee chromosome 4. This means that almost half of human chromosome 5 has the same linear sequence of genes as those of the chimpanzee chromosome 4, but in a reverse order[*]. There are similar segment inversions on human chromosomes 1, 4, 9, 12, 15, 16, 17, and 18 when compared to their analogous chromosomes of the chimpanzee[*].

However, more striking observations emerged when the human chromosome 2 was closely observed and compared to some chromosomes of the great apes. First, when the chimpanzee chromosomes 2p and 2q were laid end to end it created an almost identical banding structure to the human chromosome 2[*]. This can be shown in the following figure.

Second, the remains of telomere was found in the middle of the human chromosome 2. The DNA sequence of this region is exactly the DNA sequence of two head-to-head fused telomeres [*]. Third, at the place where we would expect centromere on the human chromosome 2 we find the remnants of a centromere pattern of a chimpanzee chromosome (namely chromosome 2q). Fourth, the centromere of human chromosome 2 lines up with the centromere of the chimpanzee chromosome 2q[*].

The scientific explanation for these observations is based on the theory that humans and chimpanzees shared a common ancestor who had 48 chromosomes. In the case of human chromosome 5, an inversion of a segment of chromosome 4 occurred in one of our primate ancestor. This inversion falls into well-studied class of mutations called chromosomal inversion. Incidentally, the inversion did not cause any abnormalities because the rearrangement was balanced with no extra or missing genetic information and, therefore, could have spread through the population of our ancestors. Similar mutations happened to the inverted segments of the chromosomes 1, 4, 9, 12, 15, 16, 17, and 18 during the course of human evolution.

On the other hand, the scientific explanation for human chromosome 2, as explained to me by Professor Kenneth Miller, is more complicated. A fusion between primate chromosomes 2p and 2q occurred in one of our primate ancestors. The cell in which this took place was in the germ line (the reproductive organs) or in the early embryo, so that many tissues were affected. Such a fusion, incidentally, falls into well-studied class of mutations known as Robertsonian Translocation. The individual possessing the fused chromosome would have 47 chromosomes in their reproductive tissues. In a male, this would mean that about half of his sperm would have 24 chromosome and about the other half would have 23 chromosomes. Children born by fertilization with the 23-chromosome sperm with a normal 24-chromosome egg would themselves have carried 47 chromosomes. Since the fused chromosome trait is genetically neutral, it could have spread through small population of humans or human ancestors. Eventually, two individuals with 47 chromosomes each would have met and had offspring. Half their children would carry 47 chromosomes, quarter would carry 48 chromosomes and quarter would carry 46 chromosomes that we have today. It is important to note that the same sort of change in chromosomes has also occurred in horses and (many times) in mice. The last remaining species of Asian wild horses have 66 chromosomes while domestic horses have 64 chromosomes yet they can freely interbreed.

Despite the overwhelming scientific evidence in favor of the common ancestor theory, religious people offer alternative hypotheses for explaining these chromosomal observations. One of their favorite explanation is that the fused chromosome 2 can also indicates a human ancestor who had 48 chromosome rather than a primate common ancestor. They argue that the human-chimpanzee chromosomal relationship is simply a reflection of the vast similarity in the physical characteristics between humans and chimpanzees. Put it simply, a designer (Allah) may have reused designs.

However, this explanation only focuses on the fusion issue and totally ignores other mounting evidence in favor of the common ancestor theory. Also, the assumption that Allah may have reused huge amount of the genetic material of the chimpanzees in the design of human does not fit well with the central theistic assumption that humans are very special creatures of Allah. Moreover, an omnipotent all-powerful creator can not simply reuse old designs for his final special creation and then asks us to reject all the evidence His special creation entails in favor of the common ancestor. Yet, to the contrary, He wants us to accept without evidence the creation claim. This very act can only be described as deception. Finally, by applying Occam razor to the "design re-using" hypothesis, one can simply shaves off the extra designer part thus resulting with the scientific natural explanation.

Other explanations for the above chromosomal observations are less impressive and are mainly based on fallacies. Some religious people say that whatever the evidence says, Allah is the creator of everything; human and apes are totally two distinct creatures. Clearly, this is an example of "appeal to authority" fallacy. Other religious people claim that these chromosomal observations are not correct (an "appeal to ignorance" fallacy) or fake (a "conspiracy theory"). Others fear that the scientific explanation can raise racial conflicts (an "appeal to fear" fallacy) while others say that most of the people, despite of their different religious beliefs, do not accept the theory of evolution (an "appeal to common practice" fallacy). Strangely, some people still argue that the theory of evolution is a theory, not a fact. This is a common misconception that has been thoroughly explained in a previous post.

On the other extreme of the religious explanations, theistic scientists, such as our Kenneth Miller (who is a Roman Catholic) and Francis Collins (who is the director of the National Human Genome Research Institute and also a devout Christian), provide a compromise. They accept the theory of evolution but believe that it was the way God did his creation. They, therefore, accept the that humans and apes have a common ancestor. This form of believe is usually referred to as theistic evolution. I shall not argue against this assumption in this post but would emphasize the fact that by accepting the theory of a common ancestor yet more authority is taken from God (or Allah). I shall return to argue their theistic evolution claim in later posts.

Finally, I would like to share the following clip (of Professor Kenneth Miller's distinguished presentation) with you.

Saturday, February 2, 2008

The Scientific Knowledge

In this post I will explain the concept of "scientific knowledge" and demonstrate some important principles that can be used to evaluate scientific claims.

Basically, science refers to the systematic objective approach of acquiring knowledge, and to the organized body of knowledge gained through such research. The "objective systematic approach" is known as the scientific method and it consists of the collection of data through observation and experimentation, and the formulation and testing of models or hypotheses. The process must be objective in the sense that observations, experimentation and reasoning must not be altered or biased by a particular belief. Those with a particular belief will often see things as reinforcing their belief, even if they do not.

Scientific researchers are driven by their curiosity, intuition or interest in particular phenomena or interrelationships within previous knowledge. They propose hypotheses as explanations of phenomena, and perform experiments to test these hypotheses.

Generally, scientific research follows a certain structural process. The steps in this process must be repeatable in order to predict, dependably, any future results. Arguments are made to present reasons for a particular claim or interpretation being put forward in the hypothesis using non-fallacious reasoning methods. A hypothesis is rejected if an inconsistency occurs between the observed outcome of an experiment and that hypothesis. However, a hypothesis can never be proven, but rather only supported by surviving rounds of scientific experiments. Therefore, a hypothesis is a claim that has been neither well supported nor yet ruled out by experiment. If substantial experimentation and observations support a hypothesis then it eventually become an accepted theory.

We now define the "Scientific Knowledge" as the accumulated body of facts, concepts, principles, laws theories and model gained through the scientific method.

Researchers may test and reject several hypotheses for a particular phenomenon. When they compare alternative hypotheses they take into consideration the apparent application of the hypothesis to multiple cases of phenomena (i.e. it's scope), the prospect that a hypothesis may explain further phenomena in the future (i.e. it's fruitfulness) and the degree of fits with existing recognized knowledge (i.e. it's conservatism). But more importantly, the testability and the simplicity principles are very critical for evaluating scientific knowledge and therefore will be explained in more details.

Testability is important to retain or falsify the scientific status of hypotheses. Hypotheses are tested by performing experiments. However, due to the inductive nature of experiments, "no amount of experimentation can ever prove me right; a single experiment can prove me wrong", as Albert Einstein once said. Therefore, some philosophers and scientists have asserted that a "hypothesis or a theory is scientific only if it can be shown false by an observation or a physical experiment". This principle is known as the falsifiability principle. Being falsifiable does not mean false; rather, it means capability of being criticized by observational reports. For example, "the existence of Allah" is unfalsifiable because it can not be shown false by an observation or physical experiment. Falsifiability principle is very important in science and the philosophy in science because it provides us with an understanding on how one might assess a theory or a hypothesis. It may also save us from attempting to falsify a non-falsifiable claim. Unfalsifiable claims say nothing about either their validity or truth. If evidence cannot be presented to support a hypothesis, and yet the hypothesis cannot be shown to be indeed false, not much credence can be given to such a hypothesis.

The second important principle to assess and compare alternative hypotheses and theories is their simplicity. In science, there is preference for the least complex explanation for an observation and when judging hypotheses. The explanation of any phenomenon should make as few assumptions as possible, eliminating those that make no difference in the observable predictions of the explanatory hypothesis or theory. This principle is known as Occam's razor and is often paraphrased as "All other things being equal, the simplest solution is the best". Therefore, when multiple competing theories or hypotheses are "equal in other respects", the principle recommends selecting the theory or the hypothesis that introduces the fewest assumptions and postulates the fewest entities. For example, in Pathology, infectious diseases are clinically evident diseases resulting from the presence of pathogenic microbial agent such as viruses and bacteria in the infected individual. A religious pathologist adds to the previous explanation the assumption that diseases are caused by Allah as a sort of punishment or for testing the faith of the infected people. Because the theistic explanation makes one extra assumption (i.e. Allah's divine will) to explain the same phenomenon, Occam's razor shaves off this extra assumption and therefore the first explanation is preferred. Yet in the Islamic world, Allah's divine will is postulated in explaining all natural phenomena along with natural scientifically-proven explanations.

By considering the concept of scientific knowledge and the principles of evaluating (scientific) claims, especially the falsifiability principle and Occam's razor, and by becoming aware of the common scientific misconceptions, that were explained in the previous post, we shall start our journey to the scientific critical thinking of Islam from the next post.

Thursday, January 10, 2008

Common Misconceptions

In this post I present the notion of "misconception". This is because most Islamic writings that describe the relationship between Islam and modern science are mainly based on misconceptions.

Basically, a concept is an abstract or general idea inferred or derived from specific instances and is typically labeled or designated by a corresponding term. For example, in Physics, we have concepts like motion, velocity, force and mass. Concepts help to integrate apparently unrelated observations and phenomena into theories and laws, which are the basic ingredients of science. For example, the concept of motion is described using the concepts of velocity, acceleration, displacement and time, and the relationship between motion and force is described in Newton's laws of motion. The ability to form or understand mental concepts and abstractions is called conception. A misconception is an incorrect conception which happens when a person believes in a concept that is objectively false. For example, in the theory of evolution, the idea that humans evolved from monkeys is a popular scientific misconception of the idea that humans and the monkeys simply share a common ancestor. A list of some common misconceptions and their corresponding clarifications can be found here.

A misconception may result from incorrect information (aka erroneous belief) or from incorrect reasoning (aka logical fallacy). When a misconception is favorable to the person who holds it is called self-deception. But when a person strongly holds a false belief in spite of invalidating evidence then it is called delusion.

One of the critical erroneous belief misconception in science is to believe that science is about proving anything. Proving something does not make it true. Nothing in science is ever proved true, it is only confirmed by observation and/or experiment. Regardless of how well or how long something has been confirmed, it is always subject to falsification or correction by new observations or experiments. For example, Newton's laws of motion and classical mechanics were verified by experiment and observation for over 200 years but they later were modified when the Special Theory of Relativity was introduced and showed that the laws would be wrong at very high speeds.

Another common misconception is the
confusion over the meanings of the terms "fact", "law" and "theory" by suggesting that "fact" means "truth," and "theory" means "speculation" or that a "law" is more certain than a "theory". Scientific facts, laws and theories are three very different types of statements. Scientific facts are controlled, repeatable and verified scientific observation or phenomena. A scientific law is a description of an observed regularity among facts, often expressible as a simple mathematical formula. A theory is an integrated conceptual framework for explaining and reasoning about the events that have been observed and if a lot of evidence is collected to support the theory, it will probably be considered as a good explanation. It may, given even more testing and verification of its predictions, become an accepted theory. The notions of "fact", "law" and "theory" can be illustrated by considering the "gravity" concept:
It is a scientific observed fact that if we drop anything heavier than air then it will fall. This fact is described by Newton's "law of Universal Gravitation". Newton described the behavior of the gravity by this law but he did not (actually could not) explain why gravity did it. Einstein developed a theory of gravity, called the "General Theory of Relativity", which explained how gravity works. This theory is widely accepted as most of its predictions have been verified in many experimental observations.
Apart from factual misconceptions, a reasoning misconception, or a fallacy, is a component of an argument that is evidently flawed in its logic or structure thus restating the whole argument to become incorrect. Fallacious arguments are very common and can be quite persuasive. A careful look at newspapers, advertisements, and religious and political propaganda can reveal many fallacious reasoning and arguments. But it is sometimes hard to evaluate whether an argument is fallacious depending on the complexity of its strcuture.

A very common fallacy is known as the appeal to authority. Here, a person accepts a claim because he erroneously believe that the claimant is a legitimate source or an expert on the field of that claim. For example, a person believes that the universe was created in 6 days because the Quran said so and he believes that the Quran is a ligitimate divine source of knowledge.
Other common fallacies are the regression fallacy, cherry picking and appeal to emotion. A detailed list of common fallacies can be found here and here.

On the other hand, misrepresentation of a concept, though not a misconception in itself, may produce a misconception. For example, the misrepresentation of the theory of evolution as presented by a creationist produces a misconception which can be revealed by considering a corresponding presentation by a theistic pro-Darwin biologist.

Many people have difficulty challenging their misconceptions. This is due to several reasons. Some people have long adopted misconceptions and they become deeply ingrained in their minds. Other people lack the will or ability to gain new information or re-evaluate old information and therefore they don't like to be proven wrong even in the face of evidence to the contrary. Some people may purposely embrace and propagate misconceptions to achieve some personal, religious or political goals. It is necessary to mention that due to the objective nature of conceptions and the subjective nature of being human, it is likely that everyone has some kind of misconception.

Wednesday, January 9, 2008

Perspectives on Islam and Modern Science

The majority of Muslims today believe that Islam is in complete harmony with modern science and that the relationship between Islam and science is very strong. This belief is based on many claimed observations. There are many references in the Quran and the Sunnah that encourage the act of seeking knowledge and that appreciate and glorify science and scientists. Also, many Muslims are convinced that modern science was first developed in the Muslim world by Muslim scientists under the Islamic civilization. Moreover, there is a strong focus in the Muslim world nowadays to claim a divine inspiration for Islam by showing that it is a dispenser of scientific truth. This is done by interpreting particular verses of the Quran (and sometimes particular elements from the Sunnah) and claim to show that these verses make prescient statements about the nature of the universe and many other phenomena recently confirmed or discovered through scientific research. This field is widely known as the scientific miracles in the Quran (or Sunnah) and is widely presented by many Islamic scholars as a proof of the divine nature of the revealed Quran and therefore the divine nature of Islam itself. On the other hand, the term "religion scientists" is widely used in the Muslim world, from the layman to the highly educated individual, to refer to the Muslim priests who are specialized in issuing Fatwas or to the Muslim scholars who are involved in "Islamic studies"; which is an umbrella term for traditional Islamic academic research, such as Islamic theology, Islamic history, Islamic economics and Islamic jurisprudence.

However, this claimed association between Islam and modern science raises the following questions:
  1. Are the above claimed observations correct?
  2. Are they sufficient to claim a strong association between Islam and modern science?
  3. Do they reflect the reality of the scientific understanding in the Muslim world today?
The answers to these questions will be demonstrated in the following posts. So stay tuned!