The Origin of Life

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Since I am related to medical profession I will have to agree with saad on ``Origin of Life`` issue.But I would like to warn both the Evolutionist and the creationist not to jump to conclusions and start interpreting the information to prove their point.If they dont stop they will have to take multiple falls and one of them is going to cripple one or both of them.The creationist are already using Big bang theory to their advantage but regecting the evolution theory.I would like to caution them not to use Quranic text to corraborate the scientific findings.The Big Bang theory is not without doubts and defects,according to stephan Hawkings who came up with this theory now says that if ``imaginary time`` theory were to be entertained then the Big bang is not required(dont want to give details ).According Lerner the age of large number of galaxies is so old that they predate the time of the Big bang(dont want to give details).And the Evolutionist are also to quick to grab on something.I agree that the darwin theory works for prokaryotes but in eukaryotes it gives a blurry vision.The race from Apes to man is a long one I agree but from prokayotes to eukaryotes is not decided yet.The Evolutionist should also consider the fact that it was the creationist who coined the concept of evolution first.The text recovered from Iraq early this century ``Babylonian Text`` from the ruins of Asurbanypals library tells of the story of creation in which God after creating the universe used to reside in the waters.In the waters He created life and Himself took his place in the havens.This was written some 5000-7000 yrs ago.Well Quran has the same story also.

I want both to see that there are plenty of issues untouched by either one.Would be glad to expand on it if interested.

Salman Qadeer

p.s, Hello Saad remember me.

As this article is about setoff of the Chowk horizon (quite limited that is, I might add :)) and the debate is chilled, I have several thoughts but not a coherent mind to put them into writing after all day of working. So I am going to copy following excerpt which is the closing paragraph of ``The Mind of God`` by Paul Davies and which say pretty much what I wanted to say:

What does it mean? What is Man that we might be party to such privilege? I cannot believe that our existence in this universe is a mere quirk of fate, an accident of history, an incidental blip in the great cosmic drama. Our involvement is too intimate. The physical species // *Homo *// may count for nothing, but the existence of mind in some organisms on some planet in the universe is surely a fact of fundamental significance. Through conscious beings the universe has generated self-awareness. This can be no trivial detail, no minor byproduct of mindless, purposeless. We are truly meant to be here.

(Paul Davies, ``The Mind of God`` p. 232)

Re: Saad Shafqat

I hope you are proud of yourself!

One of my American friends, who once spotted me on Chowk, has surfed the Chowk recently. He was really interested by Chowk and things related to Pakistan. He is presently reading this article and is getting ready to talk evolution with me. He is a creationist.

He is being reading Dawn and Friday Times and in general, just pestering me with questions! His comment was that Pakistani newspapers are just like the American ones - same topics; economy, nuclear etc!

He is really, really into the political-religious scene of Pakistan.

Thanks for nothing bud! :)

Re: Wasiq

You say ``I guess then I am clearly in the camp of those who believe that we arose out of a configuration of molecules that by chance (though the probabilities themselves may be helped tremendously by the properties of the molecules in question) led to a set of molecules that could replicate themselves with great accuracy. I believe fundamentally that there is no qualitative difference between the living and the non-living elements in the universe``.

Wasiq, this is precisely what I am trying to say - that ultimately, in our current state of knowledge, reductionism (materialism) is just as much a BELIEF as vitalism is. Neither has been proven or falsified. This is not to say that
reductionism hasn’t been a spectacular success as a framework within which to explain biological and physicochemical phenomenon - just that it hasn’t delivered the goods yet, as far as explaining what constitutes life and how it all began.

About the origin of life, the devil continues to be in the details. Abstract theorizing can only get one so far. This is why biology is so much more tedious and boring than physics! In this vein, some great questions from you about error-correcting mechanisms in RNA replication.

The best way to explain this, I think, is to look at contemporary organisms in which RNA to RNA replication takes place. This to my knowledge only happens in RNA viruses such as rhinoviruses (common cold virus) and influenza. The replication of these viruses is characterized by very high error rates because their replicases (enzymes) have NO proofreading ability. The error rate is in the order of 1/2500 to 1/10000 nucleotides synthesized. Such a high misincorporation rate results in greater than 99% of viral progeny being defective, despite the fact that these RNA viruses are very small (only a few thousand bases). It also means that no virus can exist as a free agent and depends on parasitizing a cell that can provide the necessary proteins (and error-correcting mechanisms) from the host DNA synthesis machinery. This of course puts a damper on our thinking that RNA viruses could have been the first living organisms - because even modern RNA viruses cannot exist without much outside support. Also, it seems highly improbable that RNA would have during evolution lost self-correcting mechanisms, because a strain that had these would have had a huge survival advantage over the others, in its accurate and independent self-replicating ability.

As for the sense of purpose in replication of genes, and extrapolating to humans I have some half-baked ideas that will take a while to pen down. Am in a hurry, so later.

regards,

A

Re: Wasiq.

``If one were to state that the living matter is fundamentally and physically different from non-living matter, then one has to explain how during the ambiguous phase of transition between ``non-living`` and ``living`` a foetus suddenly switches from one set of physical laws to another.``

Actually, the only instance in which the transition between `living` and `non-living` needs to be explained is the origin of life. Except for that initial event, living matter has always come from other living matter. The cellular origins of the human fetus are always `alive` - everything starts from the sperm in the male testis and the egg in the female ovary. The sperm and ovary get together to form a zygote, which then matures into a fetus. So the stream of life is never interrupted.

Of course there are many problems with classical vitalism. On the other hand, the notion of higher properties emerging from specific combinatorial complexities has rational appeal. This is really what I, too, am trying to say. Do not be distracted by my use of the term `vitalism`. As you have also said, I think that there is some fundamental property in living matter that is more than just its component atoms. You can call this property a `vital spark` or `combinatorial complexity` - point is non-living things don`t have it.

To my mind, to define this special property, life needs to be successfully synthesized. If life is simply molecules in the right combination, the combination should be reproducible. As we know, this hasn`t happened. Interestingly, there is an article on this in the latest Newsweek (Feb. 22 issue, page 50), in which a group of scientists have specifically set out to synthesize life. They are armed with entire genome sequences from several bacteria and the experiment will investigate the minimum number of genes necessary for something to be `alive`. The team is led by Craig Venter, a maverick NIH-trained biologist who`s developed a neat trick for rapid gene sequencing. (Since these are just claims yet, the reference is in Newsweek and not some academic journal.)

I am open to all possibilities and would be happy with either result in this experiment. It is certainly possible that living organisms may at some point be synthesized from off-the-shelf chemicals. But unless that happens, don`t you think it remains possible that life is its own elementary particle ?

Also, life on other planets is entirely plausible. That would indeed be a fascinating discovery, but I don`t think it would answer the point we are discussing. The question would not be whether life arose but how it arose. We already know life arises naturally - it happened here on Earth :-). Naturally, but exactly HOW ? That is the question. And I think only the successful creation of life from non-life can settle this.

I remain intrigued by Richard Fortey`s analogy of aspiring life-synthesizers and the alchemists who insisted, unsuccessfully, on turning base metals into gold.

Saad

Re: goga (23)

``Men, at least among the developed nations, have lower life expectancy than women. It is because of the male hormones that make them more prone to infections and heart decease. So even male population succumbs prematurely because of self-replication.``

Goga: well, that is one way of looking at it, especially since testosterone is linked to aggressive behavior and risk-taking, the most common cause of death in young men (violence and accidents), which has a substantial effect on reducing average male life expectancy.

However, what I was referring to was the suggestion (from this paper in Nature) that ``aristocratic`` women from Britain who were childless lived much longer than women with children who had survived the dangers of childbirth. For men, I think it would be hard to show a difference between childless men and men who became fathers. In fact, I suspect that we would find that men who are fathers tend to live longer, so that reproduction confers a survival advantage.

Anita

Anita (17):

Men, at least among the developed nations, have lower life expectancy than women. It is because of the male hormones that make them more prone to infections and heart decease. So even male population succumbs prematurely because of self-replication.

Wasiq (10):

I do not think there is any way of de-coupling cause from effect. Bayes` theorem formulates that in the probabilistic sense. In estimation theory, mathematical expressions are written the violate causality for calculation purposes or to gain some insight and one can also get away with `f(n) approximately equal to f(n+1).` Because of the iterative nature of these calculations, these approximations work when the time steps are not very large.

There are several problems in asking questions about existence of the universe. First, there is the problem of self-reference. It has been proved that there are decidable and undecidable propositions in mathematics. Furthermore, it is impossible to formulate an algorithmic approach for a given statement to decide whether it is decidable or undecidable. It will take an infinite amount of time to do that on, for example, a Turing machine. An example of self-reference is a statement like: `This sentence is not true.` A sort of a statement that a clever Star Track captain would give a wicked computer which would lead to its selfdemise. Interestingly human mind has the capability to avoid such loopholes and function robustly in a complex environment (most of the time).

We are living inside the universe and it might not be possible to accept answers to question like why the universe exist and what is the purpose of the existence of the universe. And this would be due to the problem of self- reference. To somebody independent of the universe, the existence of the universe might make perfect sense.

The other is the problem of language. Many philosophers have thought that human language is inadequate for formulizing the fundamental questions of existence and hence there is no hope for finding the answers.

Wasiq (13):

As I understand, the multi-universe theory is one way of interpreting the quantum mechanical events. According to quantum mechanic, a system is fuzzily occupying all possible states until an observation is made. The multi-universe interpretation says that when the observations made the universe splits into other universes each containing a possible outcome. For example, when the spin of the electron is measured (which is either -1/2 or +1/2) the universe actually splits into two--in one the spin of the electron is -1/2 and in the other the spin of the electron is +1/2). If this is true then soon after big bang the universe started to split into other universes every time a quantum state was selected.

This idea is not widely accepted. One criticism is that we do not notice the splitting. The other is that this interpretation gives rise to highly complex view of reality which, according to Occum`s Razor, has a little chance of being true. In any case, I think that this interpertation might be useful in doing some calculation like Feymann`s path integral in which all possible histories of a partical are considered.

Wasiq (16):

Yeah, I got a bit carried away there but not a bad idea for a science fiction. :)

Re: the effect of reproduction on female life span.

Sorry, it wasn`t in Science, it was in Nature. Longevity and the Barren Aristocrat. Nature, vol 396, December 24/31 1998 issue (just in case you were looking Aamina).

Anita

temporal:

Tashreeh ka shukriya. Looks like chacha Ghalib is posing the same question as Rene Descartes. Descartes asked if an all-powerful magician could fool him into believing in the existence of things that did not exist. He decided that he could be fooled into falsely believing the existence of anything, except the fact of his own existence (hence, `I think, therefore I am`). Ghalib, being the philosopher and mystic, seems to have left it open-ended, which of course makes it much more interesting.

Saad

Wasiq & Goga, re: edge of the universe.

Thank you for your tremendous comments. False vacuums, worm-holes, 4-dimensional space, create-space-as-you-go, a bubble with an edge yet no edge ... much too much. Seems to me the edge of the universe is also the edge of human comprehension.

Saad

Wasiq:

I see your point about the spontaneous generation of order in crystals. However, while crystal formation can be readily reproduced, emergence of life has never been. The point about the powerful effects of selection is well taken.

To my mind, at the core of all origin-of-life thinking is the great vitalist versus mechanist debate. This is the question of whether there is something special about life that makes it qualitatively and fundamentally different from non-living matter. Since the mechanistic approach has enjoyed tremendous intellectual and experimental success, the answer is believed to be a resounding `no`.

I don`t buy it.

I think there is something qualitatively different about living matter. Living organisms must be more than just particles of matter arranged in the right configuration, which is why one cannot pull chemicals off a shelf and create life in a bottle.

Karl Popper has said that hypotheses cannot be verified, only falsified. The way I see it, because life has not been synthesized, the hypothesis of vitalism has not yet been falsified.

Erwin Schrodinger says in ``What is Life ?`` (Cambridge University Press):

``From all we have learnt about the structure of living matter, we must be prepared to find it working in a manner that cannot be reduced to the ordinary laws of physics.``

So if we concede that there may be something to vitalism, does that mean we have to invoke incomprehensible divine intervention (ie, `God`) in the origin of life ? I don`t think so. In Schrodinger`s statement, the qualification `ordinary` is the escape hatch that keeps the argument alive. It is conceivable that the property of life is one of the fundamental building blocks of our universe, like matter, energy, space and time, and, like the rest, is governed by observable rules and laws.

Saad

Re: Wasiq

The paradigm of life originating as a set of non-enzymatically assembled, self-replicating polynucleotides, somehow recognized by surrounding amino acids as a primitive genetic code, is as you say - an extraordinarily improbable event. The odds certainly boggle the mind.

To my mind, questions with no easy answers are (its not as simple as saying it was just a chemical reaction that happened under the right conditions - we just have not been able to create the right conditions).

1. Its almost impossible to see how polynucleotides formed spontaneously. A veritable army of chemists have for over 40 years been trying to synthesize nucleotides from elementary molecules (ribose sugars, bases, phosphates) with limited success. It certainly doesn’t happen under the postulated conditions of the ‘hot primordial soup’. For one, nucleotides are unstable in water and tend to dissolve in their component parts. For another, they do not stick together very well under hot conditions - cold would be much better. One would have to postulate extremely high levels of generation of nucleotides and polymerization to overcome these dissociation tendencies. Further, the fact that Miller-Urey and Eigen type experiments yield low levels of amino acids and nucleotides does not support this theorization too well.

2. Even if primitive RNA was able to solve the proverbial which came first, chicken or egg (gene or protein) scenario by having extraordinary self-catalytic activity to function as its own enzyme in the self-replicating process, it would have to contend with very high error rates (in the order of 1 in 100), with no correction mechanism in sight. This limits our postulated primitive RNA nucleotide size to approximately 100 bases to have any fidelity in replication. Primitive RNA would very quickly have to come up with a genetic code and synthesize the necessary error-correcting proteins (enzymes), but it can’t do that with just a 100 bases, it needs more like 500 to a 1000. So its a bad Catch-22 situation for our primitive RNA.

Also, what is life anyway? Are self-replicating polynucleotides alive? Is a piece of DNA alive in a PCR reaction of template, primer, and polymerase? Is life possible without nucleic acid (e.g. prions)? Where do we draw the line?

Unfortunately for us scientist types, if we stick to the line of reasoning that says that the origin of life on Earth was a unique one-time only event, wouldn’t we then have to admit that this is beyond what we would usually think of as scientific theory - since we cannot use this theory to explain 1)observed phenomena, and 2) we cannot test it by further experimentation. We know how evolution happened, and can easily explain it by invoking (what Goga rightly points out) are Bayesian conditional probabilities and natural selection. However, as far as origin of life is concerned, we are on very shaky ground. I think it would be fair to say that at present no theory comes close to adequately explaining how life arose.

So what do you personally think Wasiq - was God playing organic chemist, or are we a configuration of molecules arranged by chance in just the right way - not fundamentally different from non-living matter? Or are you among the ‘I don’t know yet’ crowd?

As for what the sense of deep purpose is, for any organism to replicate itself (Reply #8) - what a fascinating question that is for humans - the only species that can control it, yet continues to replicate itself, albeit, the more in control, the less the replication. Have you seen a recent interesting Science piece (within the last 2 months I think) on what the cost of reproduction may be to women, in terms of years of life lost?

Anita

Saad:

Although you did not put the question to me but here is what I think. It depends on the particular theory of the existence of the universe that whether the universe has an edge or not. For example, an old theory, the steady state theory says that there is no edge of the universe since there is not beginning or the end of the universe.

Big bang theory, on the other hand says that there was particular instance, although a fuzzy one due to constrains of quantum mechanics, when the universe was born and it is expanding. This is backed up by the observation that galaxies are moving away and faint background radiation, a left over of big band. Hence, it is widely accepted. Now modern physics also tells us that matter and time space are not separable. So wherever there is matter, time-space exists as a consequence. So a simple answer would be that the universe is extended to wherever you can find any amount of matter and hence time-space. A person looking for the edge of the universe may never find it since he is carrying his material body everywhere he goes and hence creates time and space around him.

But the answer would not be that simple. The universe was born under very special circumstances that`s why we have the laws of physics as we know them. This might not have been possible without some sort of boundary conditions on the universe. One kind of boundary conditions might be that the universe is wrapped round in time and space at its edges. That is, the edge of the universe is littered with wormholes. Anything trying to escape the universe would be transported to some other point in the universe through one of the wormholes. So nothing could escape the universe. But that might not be the whole story. These boundary conditions might not fit the observations since we do not get electromagnetic emissions from the wormholes at the edge of the universe. Other boundary conditions might give rise to forces and particles not ordinarily found elsewhere in the universe. Let see what Wasiq has to say.

Saad:

hasb-e-hukm tashreeh haazir hai:

Aa-gahee.........taqrir ka


Yusuf Husain says:
Howsoever awareness spreads out
Its net of hearing,
Like the soaring Phoenix,
The meaning of the speech escapes

My spin:
No matter how wide and deep a network of antennaes AWARENESS spreads (ostensibly to receive communication) the substance of our speech escapes the net(work)like the elusive phoenix.

Hastee kay-----khayal hay.

Yusuf Husain says:
O Asad, be not deceived
By this existence,
The whole universe is nothing
but a noose of the snare of thought.


My version:

O Asad don`t be fooled by the mirage of EXISTENCE It is but a creation of the fertile imagination.

Hope this helps.

regards

RE: Goga.

Your point about the definition of `reductionism` is well-taken.

RE: Afrasiyab.

Thanks, yaar. Tum to kafi jaldi convince ho gaye :-). I`d love to talk cricket, but given Pakistan`s mutant batsmen, speculating on life`s beginnings is much less taxing!

RE: temporal.

Qibla, tashreeh - please!

RE: Adeel.

It isn`t really a question of where the energy would come from. There is abundant energy from the sun (which continues to maintain all the life in Earth`s biosphere today), the Earth has its own internal heat (which would have been much greater 3.8 billions years ago), and there is always energy from electric discharges in the form of lightning. The problem to be explained is how all this abundant energy directed the spontaneous assembly of carbon, hydrogen, oxygen, nitrogen and water into a living cell. As I said earlier, my understanding of the second law of thermodynamics is that the spontaneous generation of order from disorder is a physical impossibility (but lets see what Wasiq says).

RE: FerozK.

On the matter of the mother of all headaches, couldnt agree with you more ;-).

Saad

RE: Wasiq.

Interesting comments. A few points:

1. Is it not correct that the spontaneous creation of order out of disorder is not something improbable, it is impossible (ie, the odds are zero) ? At least that is how I understand the second law of thermodynamics.

2. Unlike you, I am quite concerned that life has not been synthesized in a lab. If it were `just a question of chemistry`, this should have been done by now. True that we cannot be certain of the initial conditions on Earth when this happened, but is that so conceptually challenging ? We can be certain that it involved carbon, hydrogen, oxygen, nitrogen, water and some form of energy. Indeed, if you take apart a living cell, that is what you`ll get. Yet we can`t take these ingredients from a shelf and reassemble them into life. In a world where human intelligence has split the atom and discovered quantum mechanics, this anomaly strikes me as very serious.

3. If life is just a question of chemistry, it seems odd that all known life can be traced to one common origin. The basic molecular machinery of all living things is identical, right down to the enzymes of self-replication and the process of electron transfer in the respiratory chain. Also, all life forms can only use L-amino acids although their optical isomers - the D-amino acids - could theoretically have done just as well. If life is something that spontaneously pops out of the right kind of brew at the right temperature, should we not expect more variation in the basic template of life ? Indeed, all of life seen on Earth is of only one kind; should there not have been more than one kind of `life` ?

Saad

PS: On an unrelated note, on the subject of cosomology, please indulge me with a question that I cannot find an answer to. Is there an edge to the universe ?

Wasiq (8):

Many of the argument that you have presented are such: something depends on something else and that something else depends on something else--an infinite chain so to speak in which every member is explained by the next member. It would be jusified for someone to ask why some chain exists or why any chain exists at all. ``Leibniz made this point by inviting us to consider an infinite collection of books, each one copied from a previous one. To say that content of the book is thereby explained is absurd. We are still justified in asking who the author was.`` (``The Mind of God``, Paul Davies. p. 171)

As for the conditional probabilities, a similar chain exists if you consider the Bayes` Law. Because you are now shifting the question from calculating the probability of occurrence of an event to the probability of obtaining some fantastically specific conditions for that event to occur. According to Leibniz, you have not gained any ground.

Saad:

You are quite a prolific writer, indeed. Although there are many things to be discussed, I disagree with your definition of reductionism that: ``...the scientific approach that reduces all observed phenomena to physics and chemistry...`` A more precise definition is: ``...the method of reductionism, whereby the properties of a complicated system are understood by studying the behavior of its component parts.`` (Paul Davies, ``The Mind of God``, p. 77)

Such an assumption renders this method to be attacked not only from a religious point of view but also from a philosophical point of view.

To all:

Those who are unhappy that others disagree at least with some of evolutionary ideas, following anecdote might be of some consolation:

... Dr. Peebles was troubled that inflation theory was being so readily accepted without being tested, mainly in the absence of a viable alternative. ``I find that distasteful.`` he said.

Dr. Peebles`s skeptical tone did not seem to upset cosmologists. ``He is half enthusiastic, half curmudgeon who wants to keep us honest,`` said Dr. Turner of Chicago. He wants us to slow down the train before it gets over some cliff.`` (Science Times, Feb. 9, 1999)

I don`t get it. Why is this editing not working the way that it should.

I meant to say well written, and the character you had mentioned.

Re: Saad Shafqat

Excellent intro to the topic...I agree, ``...how delicious to contemplate...``, but only concern is, here we go again... and round and round we go!

The debate on creationism v. evolution always boils down to a matter of personal choice believes, what ever they may be, and there is no scientific data, or corpus of research which will convince its detractors either ways. Trust me on this Saad, trying to prove evolution to a creationist is like trying to demolish a brick wall with your head! The wall will still be there, but you will have a mother of all headaches!

Saad:

Sorry yaar, the pc insulted Chucha Ghalib:

The line should read``


Aagahi daam-e-shunaidan jis qadr chahay bichai
mood`dua anka hay apnay aalam-e-taqreer kaa

Saad:

(inside of a tall serene church, candles lit in some corner, blue eyed non middle-eastern blondish fellow with halo around the head staring or in meditation on the walls, some kiosks to the side with naked dusty bulbs----enters temporal ---makes a three pronged movement with his right hand----- to confirm that his wallet,pen and car keys are firmly where they should be-- there is rustle behind the partition--a hoarse voice speaks---temporal clears his throat---silence--- silence for three or four seconds and then says)

Aaagahee daam-e-shunaidan jis qadr chahay bichai mood`dua ankaa hay apnay aalam-e-taqrir kaa

(priest takes this for Latin, makes rustling noises, adjusts his collar, fiddles with his fingers)

Hastee kay mat faraib maiN aajaaiou Asad
aalam tamam halqa-e-daam-e-khayaal hay

(as the priest straightens up to receive the confession in a more familiar language, temporal walks out of the kiosk without looking back).

regards

Saad ji, Saad ji, I am convinced yaar, no more convincing required.

Your play was very informative but I did not want to reply to it untill I had checked all the sources that you have metnioned in your play through your character Omar.

Well write yet again.

Now lets get back to the good stuff called cricket. I know you are an avid fan.

So, when is that match in Calcutta.

It may so that the misssing link that gave ``birth`` to life from inanimate was a tremendous amount of external energy - so much energy that is incomprehensible by us at this time. That could have been the ``big bang``. This burst of energy ``aligned`` complex inorganic and organic molecules into an organized protoplasmic form.

What do you think Saad?

Adeel.