On The Beginning And The End Of Life

13 thoughts on “On The Beginning And The End Of Life”

1. SmartLX: The question how did it happen. What caused the change? And one other thing. You talk as if you were there at the beginning. That these processes were seen by you. How do you know anything was there? Or what was there? And, and, it seems that if any thing had been left out the process that led to the life of any kind, then it would have failed. Everything would have needed to be have been just right, lets call it the ” Goldilocks theory ” just right for life as fickle and fragile as it is needed to be pampered and cogiled to sustain it until everything else was put in place to maintain. Then using some imagination, how would it know to reproduce, to eat, to recognize danger, for that matter, what caused it to have the sensors implanted within, to be able to sense or know, its needs and especially, the dangers.
   Would it not be safer and more reasonable to assume that an intelligence provided it all, and not some freak accident.

   1. Gerald writes: [The question how did it happen. What caused the change?]

      Nothing changed. There are molecules in this universe that self replicate. They aren’t alive in any sense of the word, but they make copies of themselves. It’s a chemical property they have. Life is just built upon such molecules. We are nothing more than huge conglomerations of molecules that can self replicate. If you want to credit something for the start of life, credit the laws of chemistry. That’s what makes life possible.

      Your argument, by the way, is entirely self defeating. You keep talking about how life couldn’t possibly have started on its own, so therefore some god creature made it all happen. A god creature that is, of course, also alive. So if life can’t begin on its own, what created the god creature that created us? Of course this is where you invoke the magic – the god creature just always existed and didn’t need creating. But now you’ve admitted that life does not HAVE to be created. Therefore your statement that life can’t have started on its own is obviously false, isn’t it.

      You don’t have a logical argument, Gerald. You just can’t fathom that your being is temporary and that life is a result of the laws of chemistry, so you use god creatures to avoid thinking about the finite existence that is life and the harsh reality of the universe…

      1. Discovery InstituteCenter for Science and Culture
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         Discovery Institute > Center for Science and Culture > Articles > Evidence for Intelligent Design from Biochemistry
         Evidence for Intelligent Design from Biochemistry
         From a speech delivered at Discovery Institute’s
         God & Culture Conference

         Michael J. Behe
         Discovery Institute
         August 10, 1996
         Print ArticleA Series of Eyes

         How do we see? In the 19th century the anatomy of the eye was known in great detail, and its sophisticated features astounded everyone who was familiar with them. Scientists of the time correctly observed that if a person were so unfortunate as to be missing one of the eye’s many integrated features, such as the lens, or iris, or ocular muscles, the inevitable result would be a severe loss of vision or outright blindness. So it was concluded that the eye could only function if it were nearly intact.

         Charles Darwin knew about the eye too. In the Origin of Species, Darwin dealt with many objections to his theory of evolution by natural selection. He discussed the problem of the eye in a section of the book appropriately entitled “Organs of extreme perfection and complication.” Somehow, for evolution to be believable, Darwin had to convince the public that complex organs could be formed gradually, in a step-by-step process.

         He succeeded brilliantly. Cleverly, Darwin didn’t try to discover a real pathway that evolution might have used to make the eye. Instead, he pointed to modern animals with different kinds of eyes, ranging from the simple to the complex, and suggested that the evolution of the human eye might have involved similar organs as intermediates.

         Here is a paraphrase of Darwin’s argument. Although humans have complex camera-type eyes, many animals get by with less. Some tiny creatures have just a simple group of pigmented cells, or not much more than a light sensitive spot. That simple arrangement can hardly be said to confer vision, but it can sense light and dark, and so it meets the creature’s needs. The light-sensing organ of some starfishes is somewhat more sophisticated. Their eye is located in a depressed region. This allows the animal to sense which direction the light is coming from, since the curvature of the depression blocks off light from some directions. If the curvature becomes more pronounced, the directional sense of the eye improves. But more curvature lessens the amount of light that enters the eye, decreasing its sensitivity. The sensitivity can be increased by placement of gelatinous material in the cavity to act as a lens. Some modern animals have eyes with such crude lenses. Gradual improvements in the lens could then provide an image of increasing sharpness, as the requirements of the animal’s environment dictated.

         Using reasoning like this, Darwin convinced many of his readers that an evolutionary pathway leads from the simplest light sensitive spot to the sophisticated camera-eye of man. But the question remains, how did vision begin? Darwin persuaded much of the world that a modern eye evolved gradually from a simpler structure, but he did not even try to explain where his starting point for the simple light sensitive spot came from. On the contrary, Darwin dismissed the question of the eye’s ultimate origin:

         How a nerve comes to be sensitive to light hardly concerns us more than how life itself originated. He had an excellent reason for declining the question: it was completely beyond nineteenth century science. How the eye works; that is, what happens when a photon of light first hits the retina simply could not be answered at that time. As a matter of fact, no question about the underlying mechanisms of life could be answered. How did animal muscles cause movement? How did photosynthesis work? How was energy extracted from food? How did the body fight infection? No one knew.

         To Darwin vision was a black box, but today, after the hard, cumulative work of many biochemists, we are approaching answers to the question of sight. Here is a brief overview of the biochemistry of vision. When light first strikes the retina, a photon interacts with a molecule called 11-cis-retinal, which rearranges within picoseconds to trans-retinal. The change in the shape of retinal forces a change in the shape of the protein, rhodopsin, to which the retinal is tightly bound. The protein’s metamorphosis alters its behavior, making it stick to another protein called transducin. Before bumping into activated rhodopsin, transducin had tightly bound a small molecule called GDP. But when transducin interacts with activated rhodopsin, the GDP falls off and a molecule called GTP binds to transducin. (GTP is closely related to, but critically different from, GDP.)

         GTP-transducin-activated rhodopsin now binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When attached to activated rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cut a molecule called cGMP (a chemical relative of both GDP and GTP). Initially there are a lot of cGMP molecules in the cell, but the phosphodiesterase lowers its concentration, like a pulled plug lowers the water level in a bathtub.

         Another membrane protein that binds cGMP is called an ion channel. It acts as a gateway that regulates the number of sodium ions in the cell. Normally the ion channel allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump keeps the level of sodium ions in the cell within a narrow range. When the amount of cGMP is reduced because of cleavage by the phosphodiesterase, the ion channel closes, causing the cellular concentration of positively charged sodium ions to be reduced. This causes an imbalance of charge across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain. The result, when interpreted by the brain, is vision.

         My explanation is just a sketchy overview of the biochemistry of vision. Ultimately, though, this is what it means to “explain” vision. This is the level of explanation for which biological science must aim. In order to truly understand a function, one must understand in detail every relevant step in the process. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as vision, or digestion, or immunity must include its molecular explanation.

         Now that the black box of vision has been opened it is no longer enough for an “evolutionary explanation” of that power to consider only the anatomical structures of whole eyes, as Darwin did in the nineteenth century, and as popularizers of evolution continue to do today. Each of the anatomical steps and structures that Darwin thought were so simple actually involves staggeringly complicated biochemical processes that cannot be papered over with rhetoric. Darwin’s simple steps are now revealed to be huge leaps between carefully tailored machines. Thus biochemistry offers a Lilliputian challenge to Darwin. Now the black box of the cell has been opened and a Lilliputian world of staggering complexity stands revealed. It must be explained.

         Irreducible Complexity

         How can we decide if Darwin’s theory can account for the complexity of molecular life? It turns out that Darwin himself set the standard. He acknowledged that:

         If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But what type of biological system could not be formed by “numerous, successive, slight modifications”?

         Well, for starters, a system that is irreducibly complex. Irreducible complexity is just a fancy phrase I use to mean a single system which is composed of several interacting parts, and where the removal of any one of the parts causes the system to cease functioning.

         Let’s consider an everyday example of irreducible complexity: the humble mousetrap. The mousetraps that my family uses consist of a number of parts. There are: 1) a flat wooden platform to act as a base; 2) a metal hammer, which does the actual job of crushing the little mouse; 3) a spring with extended ends to press against the platform and the hammer when the trap is charged; 4) a sensitive catch which releases when slight pressure is applied, and 5) a metal bar which connects to the catch and holds the hammer back when the trap is charged. Now you can’t catch a few mice with just a platform, add a spring and catch a few more mice, add a holding bar and catch a few more. All the pieces of the mousetrap have to be in place before you catch any mice. Therefore the mousetrap is irreducibly complex.

         An irreducibly complex system cannot be produced directly by numerous, successive, slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.

         Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can’t be produced directly, one can’t definitively rule out the possibility of an indirect, circuitous route. However, as the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met skyrockets toward the maximum that science allows.

         The Cilium

         Now, are any biochemical systems irreducibly complex? Yes, it turns out that many are. A good example is the cilium. Cilia are hairlike structures on the surfaces of many animal and lower plant cells that can move fluid over the cell’s surface or “row” single cells through a fluid. Inhumans, for example, cells lining the respiratory tract each have about 200 cilia that beat in synchrony to sweep mucus towards the throat for elimination. What is the structure of a cilium? A cilium consists of bundle of fibers called an axoneme. An axoneme contains a ring of 9 double “microtubules” surrounding two central single microtubules. Each outer doublet consists of a ring of 13 filaments (subfiber A) fused to an assembly of 10 filaments (subfiber B). The filaments of the microtubules are composedof two proteins called alpha and beta tubulin. The 11 microtubules forming an axoneme are held together by three types of connectors: subfibers A are joined to the central microtubules by radial spokes; adjacent outer doublets are joined by linkers of a highly elastic protein called nexin; and the central microtubules are joined by a connecting bridge. Finally, every subfiber A bears two arms, an inner arm and an outer arm, both containing a protein called dynein.

         But how does a cilium work? Experiments have shown that ciliary motion results from the chemically-powered “walking” of the dynein arms on one microtubule up a second microtubule so that the two microtubules slide past each other. The protein cross-links between microtubules in a cilium prevent neighboring microtubules from sliding past each other by more than a short distance. These cross-links, therefore, convert the dynein-induced sliding motion to a bending motion of the entire axoneme.

         Now, let us consider what this implies. What components are needed for a cilium to work? Ciliary motion certainly requires microtubules; otherwise, there would be no strands to slide. Additionally we require a motor, or else the microtubules of the cilium would lie stiff and motionless. Furthermore, we require linkers to tug on neighboring strands, converting the sliding motion into a bending motion, and preventing the structure from falling apart. All of these parts are required to perform one function: ciliary motion. Just as a mousetrap does not work unless all of its constituent parts are present, ciliary motion simply does not exist in the absence of microtubules, connectors, and motors. Therefore, we can conclude that the cilium is irreducibly complex; an enormous monkey wrench thrown into its presumed gradual, Darwinian evolution.

         Blood Clotting

         Now let’s talk about a different biochemical system of blood clotting. Amusingly, the way in which the blood clotting system works is reminiscent of a Rube Goldberg machine.

         The name of Rube Goldberg; the great cartoonist who entertained America with his silly machines, lives on in our culture, but the man himself has pretty much faded from view. Here’s a typical example of his humor. In this cartoon Goldberg imagined a system where water from a drain-pipe fills a flask, causing a cork with attached needle to rise and puncture a paper cup containing beer, which sprinkles on a bird. The intoxicated bird falls onto a spring, bounces up to a platform, and pulls a string thinking it’s a worm. The string triggers a cannon which frightens a dog. The dog flips over, and his rapid breathing raises and lowers a scratcher over a mosquito bite, causing no embarrassment while talking to a lady.

         When you think about it for a moment you realize that the Rube Goldberg machine is irreducibly complex. It is a single system which is composed of several interacting parts, and where the removal of any one of the parts causes the system to break down. If the dog is missing the machine doesn’t work; if the needle hasn’t been put on the cork, the whole system is useless.

         It turns out that we all have Rube Goldberg in our blood. Here’s a picture of a cell trapped in a clot. The meshwork is formed from a protein called fibrin. But what controls blood clotting? Why does blood clot when you cut yourself, but not at other times when a clot would cause a stroke or heart attack? Here’s a diagram of what’s called the blood clotting cascade. Let’s go through just some of the reactions of clotting.

         When an animal is cut a protein called Hageman factor sticks to the surface of cells near the wound. Bound Hageman factor is then cleaved by a protein called HMK to yield activated Hageman factor. Immediately the activated Hageman factor converts another protein, called prekallikrein, to its active form, kallikrein. Kallikrein helps HMK speed up the conversion of more Hageman factor to its active form. Activated Hageman factor and HMK then together transform another protein, called PTA, to its active form. Activated PTA in turn, together with the activated form of another protein (discussed below) called convertin, switch a protein called Christmas factor to its active form. Activated Christmas factor, together with antihemophilic factor (which is itself activated by thrombin in a manner similar to that of proaccelerin) changes Stuart factor to its active form. Stuart f

         1. Behe testified in a court of law about the cilium in the 2005 Kitsmiller v Dover lawsuit. He was thoroughly embarrassed and his claims about irreducible complexity were shown to be false. That was 11 years ago. Yet your creationist masters at the discovery institute still put that on their website as if it is valid. Why would they need to you, Gerald? Why would they need to use debunked garbage?

            You are being lied to, Gerald. More like brainwashed actually. You believe what you read there, and you don’t even know that it’s utter nonsense. How many things have you posted over the years here that have been exposed for their fraudulent and irrational basis? You need to start researching both sides of every topic, and see how ludicrous religion based pseudoscience is…

2. but if you apply energy to the brain it will not reform the cells and restore the connections that existed previously. That information is lost forever, and trying to zap the brain would probably only speed up the process of degradation. It would be like smashing Michaelangelo’s David and then trying to fix it merely by pouring crushed marble on top of it. The amount of matter or energy is far less important than the precise arrangement of it.
   Precisely my point. Everything had to have been prepared just right.
   Yet, many ignore the most obvious answer. God

   1. Gerald – You seem to have a basic misunderstanding of biology. Once those connections degrade, simply zapping them with electricity isn’t going to rebuild them. Using electricity to restart the heart is simple chemistry – it’s electrical impulses that tell the muscle that is the heart to contract in the first place. So that’s why defibrillators work. The synapses and neurons in the brain produce the electricity however, and sending an electric charge into them doesn’t do squat.

      Since there is no way to repair trillions of neurons in the brain, there is no way to reverse the degrading process.

      You credit your flavor of god because you lack knowledge about the human body and how it works….

3. That was uncannily fast, Gerald.

   I did pose my explanation as an “if”, precisely because I don’t know the specifics. Evidence does suggest a great deal about what was present, though, so we didn’t have to be there. If the whole Answers in Genesis “Were you there?” thing were a valid counter to an argument, the police would never be able to solve any murder without a direct witness. The nature of evidence is otherwise, happily. As for the specifics of how various features of living beings came about, take this video about the evolution of eyes as an example. Something small changes and has some minor benefit, and is therefore selected for because those with it are more likely to survive. Any improvements are rewarded the same way, so a light-sensitive patch becomes a light-sensitive divot becomes a pinhole camera. No imagination is necessary to the process, only to an understanding of the process.

   Michaelangelo’s David was deliberately sculpted by Michaelangelo. There are direct accounts from the time of its creation, like the one about the man who criticised its nose. By contrast, we watch brains form from a single cell as part of a body which organically assembles according to a set of genetic instructions we observe being constantly rewritten to this day. Even if the original instructions were deliberately written somehow, there’s probably nothing left of them now.

   1. Understood and accepted. But it was sculpted. No one would have looked at it and said that some one pulled it out of the earth just like it was. No they would have said some ones hand formed it. So comparing this with the mastery of of the real Adam, there can be no doubt but some one else’s hand with much more expertise not only sculpted “The Adam” but made him a living sculpture.

      1. That would make sense if there wasn’t a literal mountain of evidence that all life springs from a common ancestor that was very small and simple. That’s why the Bible writers (and other creation story tellers in other religions) came up with the Adam and Eve scenario. It was the best their imagination could come up with.

         By the way, you actually come from air for the most part, not soil. Your lack of education in biology continues to haunt you.

   2. About the original instructions He has them backed up on His hard drive for when all is made new.

   3. SmartLX brings up a very important point with his ‘were you there’ comment. Many of the arguments used by theists in favour of a god-like entity might work reasonably well in isolation but are effectively contradictory when considered in tandem.

      Take fine-tuning, for example. Basically, the argument goes that certain physical parameters are fine-tuned to such a zillionth of a degree that even the slightest imaginable perturbation would render the universe uninhabitable for any life-form or even tear the whole fabric of the universe apart. Then we learn (often from the very same people, like Gerald) how common miracles are. Unbelievably, there’s even an ‘Argument from Miracles’. That’ll be the miracles that require fine-tuning to change to such a large degree that the universe would………

      It’s the same with the bunkum notion of ‘historical’ and ‘observational’ science. On another thread I mentioned how when we view astronomical phenomena we are, in actuality, directly observing history, up to 13+ billion years ago. Of course creationist ‘science’, in the guise of Ken Ham has an answer to that:

      “When we hear the term light-year, we need to realize it is not a measure of time but a measure of distance, telling us how far away something is. Distant stars and galaxies might be millions of light-years away, but that doesn’t mean that it took millions of years for the light to get here, it just means it is really far away!”

      But let’s put such obvious stupidity aside: if ‘historical’ science really is useless, then ‘natural theology’ too is equally as useless. When Rev. Paley imagined happening upon a watch while walking on a heath, what particular line of thought did he pursue? Err, that would be ‘historical science’……….but “was he there” when the watch was manufactured? What’s good for the goose is good for the gander.

      Even though I obviously don’t agree with his overall conclusions, Paley’s reasoning was perfectly sound, in this regard, especially given the year he wrote his epic work. It’s the ‘historical’ vs. ‘observational’ dichotomy that’s completely fatuous. For example, we can directly observe the history of the evolution of the eye for the simple reason that every imaginable stage in the evolution of the eye (that’s all 40 separate kinds of evolution of the eye, mind you) can be directly observed today in different organisms, and the genetic differences between those organisms at all stages of all eye evolution can be directly compared.

      Creationists appear to happily accept genetic evidence when it convicts a criminal who murdered someone 50 years ago, but if the same lab using the same methodology tells us that humans share a gene with a chimpanzee, it suddenly becomes “where you there”?

4. Hi Tushar, some food for thought:

   “if we talk about evolution in a scientific way then the Bible of that would be “Origin of Species” by Charles Darwin”

   There’s a problem with that analogy. The ‘modern synthesis’ of evolutionary biology has little in common with what used to be called ‘Darwinism’. The vast majority of biologists today have never read ‘Origin of Species’ and have no need to, other than for historical interest. It’s certainly not required reading in most university biology courses, any more than Newton is required reading for a physics course.

   “what made the association of these chemicals to “think” that we have to exist and survive and hence “adapt””

   There’s now a great deal of evidence that ’emergence’ is a fundamental phenomenon; i.e., when particular combinations of ‘things’ reach certain levels of complexity, they can exhibit characteristics above and beyond their constituents, which then may further ‘evolve’ according to their ability to adapt to external pressures. This is not merely a biological phenomenon, it’s readily observed in computer algorithms which are free to evolve, which has led some researchers to voice serious concerns about the potential for a future ‘singularity’ in which artificial intelligence develops something akin to a ‘consciousness’ and starts acting in its own interest.

   We could equally ask why, if neither hydrogen nor oxygen molecules are ‘wet’, how come when they’re combined in a particular way, they become ‘wet’? So, is water ‘intelligently’ wet in the same way that organisms ‘intelligently’ adapt and computer algorithms ‘evolve’ to ‘intelligently’ compute better? Or, is their nothing particularly special about ‘intelligence’? It being merely another kind of emergent phenomenon in the same way that ‘wetness’ is, albeit as a species we certainly find it useful and kind of interesting (and, remember, we aren’t naturally intelligent all the time; psychology courses spend a great deal of time teaching students to recognise the cognitive biases and irrationalities inherent to human thinking). Bear in mind that by a country mile, the most numerous, successfully adaptive and longest living kinds of organisms on this planet are the simplest examples (viruses, viroids and unicellular organisms), notable by their never having evolved ‘intelligence’.

5. Tushar … from a casual reading of your question, I think you may probably want to revisit evolution.
   Here’s a link http://nptel.ac.in/courses/121106008/

   Lectures 2 & 3 on origin & evolution of life are decent, though somewhat basic.

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