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.


Anonymous said...

i hate to be the one to post religious material, but:
from koran: [71:14] "He is the One who created you in stages."

science and religion are compatible, however, most scientists tend to rage against metaphysics and reject the spiritual side of things, even today scientists acknowledge that chances of our planet's existence is over, 1/33 billion.

to conclude the main side of atheism that i detest most is the sheer arrogance and ego-centricity - no offense, but atheists i meet always look down upon others and consider their views to be the only possible truth - a bit like religious extremists...

Atheist Mohammed said...

Thank you for your comment. My respond to you will be slightly detailed.
First, not everybody has faith in the Quran. Second, the verse you've quoted above would present an irony: the word "atwar=stages" in the Arabic text of the verse you've quoted above means "developing or evolving stages". In one hand, it can be interpreted as the developed stages of the human embryo from conception to death. But it can also be interpreted (as you have implied) to indicate the notion of evolution. I shall discuss the first interpretation of this and other verses (which reflect the embryology claim) in the next post. However, if you proclaim that this verse indicates the theory of evolution then prepare yourself for the blasphemy accusations. Not a single Islamic scholar accepts the theory of evolution.

Basically, there is a huge gap between science and faith: belief in science is based on evidence while faith is a belief that does not rest on logical proof or material evidence (see ). So, what are the criteria you employ to distinguish scientific and metaphysical phenomena? I personally believe that the answer to this question is "ignorance of the evidence for a natural explanation". Unfortunately, many people prefer junk explanations to no explanation and conspiracy theories to no theory at all. Simply go back in history and see how many phenomena were considered divine or metaphysical or spiritual but are now well-established well-studied facts in science? Many, take some weather phenomena (such as the lightning, clouds or the rain) and compare the respective religious and scientific explanations.

Religious people believe that they have the absolute knowledge while scientists are always skeptical and this is the beauty of science. So who is the fundamental here?

Regarding your claim that chances of our planet's existence is over, 1/33 billion. I will accept this claim. Yet, our galaxy contains 200-400 billion stars ( . If we assume that every star has only one planet then the chances of earth-like planets in our galaxy, still according to your claim, is between 6-12 planets. NASA estimates 500 billion galaxies in the universe ( . So, a humble estimate gives us 3000 billions to 6000 billions earth-like planets!! This estimates is based on one planet per star, imagine how much earth-like planets are possibly there in our universe.

Regarding your claim of atheists' sheer arrogance and ego-centricity. Tell me please, what kind of respect you will show to a scientist who make a particular claim and asks us to believe it without giving any material evidence because he claims that he only says the truth? What if he added that only the members of his lab/group can understand his claim or that the foundation of his claim are divine or is based on spiritual power? what if he said that human mind has limited capabilities to understand his magnificent claim?
You would disrespect this scientist but would you pay the same disrespect if the same claims and explanations are given by a priest or a mullah?

I would suggest that you read more and more about the beauty of science and the foundation of spiritual and metaphysical claims first. This blog is a good beginning, I believe.

Take care.
Mohammed (James).

Anonymous said...

an example of what i meant by arrogance is dawkins famous bashing at students who ask him questions (search youtube for videos ) and james watson's claim that white men are genetically superior...
obviously clerics everywhere would not accept new theories, it is only natural for their fear of changes, however, many islamic scholars accepted - and discovered - new theories, especially in mathematics:ūsā_al-Khwārizmī , philosophyū_Alī_ibn_Sīnā, logic, astrology and medicineū_Alī_ibn_Sīnā, even evolution has been suggested by al biruni and al jahiz before darwin:ū_Rayhān_al-Bīrūnī

please note im not only arguing for islam, but for all religions, i have read many books from atheist authors the best one yet was dawkins, although not yet convincing, bases his argument that god is not needed, because his existence would be "inefficiency", and who is to say that efficient is better than in-efficient ? how is one superior ?
is attention to detail inefficiency ? why is there no appreciation of complexity ? of taking one's time ?
a common anti-natural selection argument is that it eliminates beauty, this is refuted by suggesting that beauty is still there because of sexual attraction, but why isnt the need for beauty not eliminated in the process of sexual attraction, would that not be 'efficient' ?
i do appreciate your quest for finding the truth, but i think you ought to look more at your reasons...

Atheist Mohammed said...

Well, Dawkins' approach in the school is not much different than the Islamic indoctrination in mosques, school, universities and satellite channels programs (fatwa calls). It is one way out of many to approach the audience. Dawkins in his approach has also authored many books, gave many talks, produced several tv programs and participated in debates. Talking with school children is one of his way, which as you know is part of his profession as a biology scientist.

Also, science is not responsible for those who misuse it or mis-interpret it. Watson's claims is his own and has nothing to do with the credibility of the theory of evolution or the morality questions. If evolution is a well-established theory then any bad consequences (if any) does not undermine the establishment of the argument for the theory itself.

Dawkins' argument against God's efficiency and necessity is based on his scientific background (mainly on Occam's razor). We can still freely postulate other explanations (and also other Gods or goddesses) as we wish but it wont make the argument more appealing from a scientific point of view.

Again, presenting the contributions of Islamic scholars in science say nothing about the truth of Islam. Their contributions are based on their intellectual abilities plus the accumulated scientific knowledge from India, Persia and Greek. Remember that Talis was the first to talk about all living beings came from water yet this does not make Zeus the true God.

Regarding your argument of beauty, what is your alternative evolutionary more-efficient way for competing for sexual partners?

Finally, I would like to add that I was a devout well-versed Muslim. I find the reasons I'm posting (and going to post) in this blog were sufficient to me to renounce Islam. My blog is about posting "my own experience" and this is why you will see "my reasons". Yet I'm very flexible regarding my approach if I find a more-suitable alternative.

Thank you for your valuable links. Take care. Mohammed (james).

Anonymous said...

I was raised Muslim and now i'm a proud Atheist, Its good to see many Arab Atheists speaking out. stay strong.

Anonymous said...

"science is not responsible for those who misuse it or mis-interpret it"

but religion is ?

again, efficiency is not everything, 'while linux is efficient and stable, i use a mac' i have yet to see any concrete proof that a supreme being cannot exist, and while his existence cannot be proven either, that is rather the point of hell and heaven, now some evolutionists like francis collins argue that evolution and the concept of god can exist perfectly together, btw the point of mentioning those scholars was that religion and science can coexist, and that religion doesn't hinder scientific spirit, not that they made those discoveries because they were muslims (which is what you seem to have understood).

"Religion and science are two ways to reach the same truth" - Averroes

Anonymous said...

one more point i would like to make (and one that you seem to be dwelling on) is the 'islamic indoctrination' and 'closed minded clergy'.

now i think we all agree that many things that are done in the name of God (and science, as you mentioned above) do not represent him (or it) necessarily.

i think you know that more than i.

Atheist Mohammed said...

Well, First, the point I was trying to make is that misuse of something has nothing to do with the truth and credibility of that thing. I was not talking about the misuse of religion but about the credibility of religion itself as faith-based doctrine which does not rest on evidence. These are two different things. Second, Francis Collins did not give any evidence for his religious views. Yet, Collins believes in the theory of evolution literally but adds that it was the way "the Lord" employed to make his creations. Well, if Collins had the same intellectual knowledge but was raised as Muslim, then he would say "Allah" instead of "the Lord". If he was raised as Hindu then "Vishnu " and so on (did you get my point?). Scientifically, using Occam's Razor, we simply ignore the God hypothesis and evolution would still be valid without any divine intervention.

Well, you said that science and religion can co-exist, but your example of aljahiz and albiruni were not successful. Aljahiz was Moutazil, a person who put the mind in front of the religious text, and for many Muslim schools (specially Salafi and Hanbali schools) they are considered Heretics. Albiruni, on contrary to what you've said, announced that "[the Qur'an] does not interfere in the business of science nor does it infringe on the realm of science", see

Again, you can always make many contributions but then add the God hypothesis as an extra redundant cause which can still be eliminated without affecting the scientific part(did you read my previous posts about misconceptions and scientific knowledge?).

Averros's quote you've mentioned above was his own view and does not have any power without evidence even if Averos was the greatest philosopher in the history. Note that Watson was alienated in the scientific community when he made his claims about Whites superiority. His contributions in Genetic and DNA did not give him any protection specially that his opinions was not supported by any evidence.

Finally, remember that my main message is that religions have no evidence and therefore should not be indoctrinated to the young. Science is totally different.

Take care,
Mohammed (james)

ryan said...

i'm a proud atheist too,
stay strong!

greetings from singapore :)

Kaisa said...


I’m working on my Master’s Thesis at the University of Helsinki and my thesis is about leaving Islam. In particular, I’m interested in how the social pressure affects the process of leaving Islam and what the actual consequences for apostates are in today’s world.

As you can imagine, it is extremely difficult to find interviewees on this subject. I have interviewed some people in Finland, but I’d definitely like to hear from more. The testimonials on websites are also an important source, but they don’t always answer my particular questions. Therefore, I’m hoping I could e-mail you my questionnaire and you could take the time to answer the questions with as few or many sentences as you like.

Best regards,

Wahhabi Backward Mullah said...

LOL. I can do nothing but laugh at what I perceive to be the narrow-mindedness of intellect, and rational suicide of one's self. But, the darwinian human that I am, I will not offer any help to you. Each to his own in this mechanized life.

By the way, the reality of life outside of earth is 0, despite all the mathematical possibilities, because you are using the lack-of-evidence-to-fill-the-loop argument to argue that "ooh, even though we have not detected intelligent life elsewhere, mathematical probabilities estimate our earth-like planets to be around 4000 billion." Bring positive evidence, not speculation and conjecture, no matter how much refined.

Masato Matsuo said...

Hey Mohammed,

It's good that you're challenging and modifying your belief system using science, but I feel that you are in danger of slipping into an equally extreme opposition to religion that you say exists within religion against science.

Don't misunderstand me here. I don't follow a particular religion myself and know very little of Islam so my comments should be taken in light of this.

There are two points I'd like you to consider:

1. You imply that because religion does not align with science it has no value or relevance. Many people find comfort in religion/belief and whether they can scientifically prove what they believe is irrelevant to them. Religion should, in my view, be taken as a moral guideline by which you can live your life. Problems occur where fundamentalism arises but remember that fundamentalism can exist in science as well as religion.

2. On the issue of faith, I would like you to think about what faith means. If I read you correctly you equate faith with belief and perhaps that is what most people do. To me faith is something you have tested and found to be true for yourself.
For example, if we take the basic Buddhist teachings of the Four Noble Truths: (1) there is suffering (2) suffering has a cause (3) suffering can cease (4) there is a way to end suffering.
I place great faith in these teachings. Not because Buddha said so but because I have tested them and found that they work for me. I know these things to be true and yet I probably cannot scientifically prove them to you.
This does not mean that they are invalid. There is no mention of religion or God, nor is there any need for it, and yet there is faith.

I have enjoyed reading you blog posts so far and I do hope you continue in your own quest to find the truth. I have faith that you will get there! :-)
I expect that you will get a lot criticism from those with strong religious beliefs and I admire you for having the courage to post as you do. I would however ask that you consider the balance of science/religion in your posts so that they don't become entirely anti-religion. The middle way is always the best.


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