The Secret Diary of Darwin

[Mary Ann Gilmore]

Hi John,
I appreciate your taking the time to answer. I have been asking people these questions for years, including many, many college professors. I have added my comments and questions again. I know you are busy as are most people, but as you said, these questions get to the heart of things. I wanted to add a lot of questions but only selected a few. Please let me be clear. Without getting into a philosophical discussion of truth I am not arguing for any position here, but rather discussing the process of arriving at the truth of a matter. Here we are talking about using the scientific method for arriving at conclusions and developing a theory. I appreciate your logic, which is always glowingly obvious [as in in your previous posts on other subjects] and which is one of the most sorely lacking in most substantive discussions. However, I am looking for, not how a theory can be toggled together, or just the logic used, but a factual, solid foundation which would provide the evidence needed for a theory to have validity. I am trying to get beyond terms like illustrate [although if the evidence is there first I would accept it], chance, blind luck, imagine, serendipity, etc. and terms like this which, to me, do not have any place in an objective scientific discussion. When nothing is known at a particular point, can one just say, the hypothesis breaks down here and there is a blank? Doesn't the conclusion come from following the evidence? Otherwise it is credulity (as opposed to belief or faith) is it not? I have concluded that you appreciate a straightforward discussion so if any of my comments seem too straightforward, please let me know. It does eliminate confusion though, does it not?
Sincerely,
Mary Ann Gilmore
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The predictive power of some of the hypotheses that the Darwinian theory ties together can be illustrated in this way:
Is there any way to get to an actual predictive power without illustrating? Some of the examples below can be used by others not espousing Darwinian evolutionary theory but other evolutionary theories as well?
(a) intergenerational differences
• No offspring of a sexual union is, if you look closely enough, an exact copy of either parent; and even amongst organisms that reproduce asexually, random mutations occur due to background radiation.
Yes, mutations occur, but how often? Even though they can occur due to, as you say, background radiation, or chemicals, are there reliable numbers as to how often they occur? My questioning throughout the years has not yielded any really solid answers as to any reliable frequency being predictable. And even if they were predictable, the vast majority of mutations are harmful. In fact, some say that for every useful mutation there are many, many, maybe even thousands which are harmful. Carl Sagan said "Most [mutations] are harmful or lethal." In fact mutations are said to be responsible for hundreds of diseases that are genetically determined. On top of all that mutations can result in a variation of a trait which is already present but does not change into something else.
(b) exponential population growth
• Take any population of bacteria and give it sufficient suitable growth medium (which may be agar agar, or meat, or something else), water, and room in which to grow, and in a certain period its population will double; after a second such period, it will double again; and after a third, it will double again.
• Take any population of animals or plants free of resource constraints and free of predation, and you will see the same phenomenon. What keeps a population stable is, most commonly, a relatively stable limit on some resource essential to successful reproduction, which may be nesting sites, mates, food, space, or something else.
(c) resource competition
• Beyond replacement of parents (e.g. two offspring to replace two parents), reproductive success is relative. Successful reproduction of just three offspring by two parents in every generation would result in a 25,000-fold increase in population in just 25 generations (the 25th power of 1.5 25 > 25,250). The offspring of just two or three couples would fill most local habitats quite quickly. The offspring of many more would fill them within a few generations. And what then?
What occurs then is that, on average, every mating pair can only replace itself; offspring in excess of what the habitat can support will not live long enough to reproduce, or they will survive at the cost of their parents' or grandparents' earlier demise. One way or another, the exponential tendency of reproduction will be constrained to replacement reproduction and a stable population. This inexorably sets up competition.
(d) differential reproductive success
• With competition established through resource constraints, any trait conferring upon its possessor an advantage over others in reproductive success will lead (if its possessor does not also possess some equally disadvantageous trait) to a slightly greater than average (i.e. replacement, zero-growth) reproductive success of that trait, and others will experience slightly less than average reproductive success. Whatever that trait may be -- say, big muscles or a big smile -- it is advantageous only because it results in greater than average access to resources essential to reproductive success, such as superior senses of smell, balance, or treachery, or others' generosity, lust, or trust.
The breeding of dogs illustrates nicely, if artificially, the process by which natural selection may differentiate members of the formerly one species so much that they become incapable of interbreeding. Dogs have been bred so large and so small that direct interbreeding between the smallest and the largest is physically impossible. We can confirm that the smallest and the largest are members of a single species only by a chain of reproductive successes between animals of intermediate sizes.
Sufficiently prolonged division between two populations of animals or plants has the potential to enable a gradual divergence in habit or signalling behaviour sufficient to make the two populations behaviourally incompatible. Beyond this point, even without further geographic isolation, the two populations will continue to diverge, becaues their newfound habits and behaviours find slight advantages in slightly different habitats and reduce food competition between the populations. Birds that eat one type of seed, for instance, will peck perfectly happily alongside birds of another species that eat a different type of seed, though they will chase away members of their own species.
For any pair of animals or plants to reproduce sexually, a gamete of one must pair, chromosome by chromosome, with a gamete of the other. Increasing divergence between two populations, in habits, signalling, and attraction, eventually reflects differences between their genomes sufficient to render chromosomal pairing between gametes from the two simply impossible. At that point, there is no argument: the two populations can by no stretch be considered populations of the one species.
All this occurs gradually and through several different processes, so the point at which two populations become two species is not necessarily easy to put a finger on. There are four four clearly distinct species of more rat living beneath the Israeli desert, incapable of interbreeding. Yet they look identical -- hairless, blind, and of similar size -- and it would be very easy to mistake them for one species.
The actual likelihood of such apparently unlikely events as an eye's formation by pure chance is causally similar to, and perhaps easier to see in, the actual likelihood of the apparently unlikely construction of a complex protein -- but the protein may be in some ways an easier example to grasp hold of and shake the sense from. So let's look at that.
Any biologist will give the odds of a particular group of atoms' randomly combining into the shape of a certain protein by chance as being vanishingly small. Yet no biologist will see that as an obstacle to the Darwinian theory. To others, this may be paradoxical; but the reasons for a biologist's ability to accept both of those things are overwhelming.
First, there are many, many atoms in what is now the biosphere, involved in a great many chance encounters, often stimulated by the input of significant energies, and this alone accounts for a great many opportunities for even fairly unlikely chance events to occur. Just as the "one in a million" likelihood of Three Mile Island accidents has been found to occur many times over due to the number of reactors and the length of time for which they've been on line, leaving some 10 to the 30 or 10 to 50 atoms lying around on the surface of the Earth to interact for sufficiently long in environments rich in sunlight, lightning, and pounding climatic effects does increase your odds somewhat.
When you say 'fairly unlikely', can you give me some probabilities please? I tried to do that in my response. In fact, some probabilities are so vanishingly small that they are outside the boundaries of even being possible, never mind probable, as I mentioned previously. So how could any scientist accept that?
In fact, when, in the 1960s, two scientists, Miller and Urey, mixed together a few substances present in the early Earth's atmosphere -- methane, ammonia, water, and hydrogen -- and exposed that mixture to artifical lightning, and found at the end of just one week that amino acids had been produced by it, including glycine and alanine. Other researchers replicated this and even succeeded without lightning, simply using heat. One week!
Yes, I understand this, but it took human intelligence, knowledge and planning to set the experiments in motion in the first place. Would the experiments have taken place in their laboratories if they just shut the door and waited for it to happen? What was necessary under prelife conditions for this to occur? And how long would it take? Again, probabilities?
Second, though a certain element of luck is required in order to generate a range of amino acids by chemical serendipity, the building of a protein from amino acids is not so great a step as to be unimaginable, and I understand that the mechanisms by which amino acids may chain together are fairly simple. Of course, some proteins will be more stable than others, or to exhibit other properties that make them more common. And so it goes. In other words, there's likely to be a type of selective force at work here, favouring certain amino acids and certain combinations of them.
I took many biology classes in college, in fact, wanting to major in it, and never once had a professor teach me something or have me set up any experiments based upon a certain element of luck or discuss chemical serendipity??? What is the likely selective force here? There are no Urey-Millers that we can see setting up the experiment. And what is the selective force based upon? And what would be the "reasons" that a selective force would have for favoring certain amino acids or combinations over others?
Third, the creation of the majority of proteins (including enzymes) of life as we know it is not dependent upon random interactions as described above; it is instead an emergent property of life itself, and even, preceding life, of chemical factories.
What I mean by this is that once you have some kind of reproducible coordinated chemical factory such a simple precursor to a virus, you have the potential for that factory to be retooled to produce chemicals that would never occur otherwise -- and most of the proteins we depend upon are themselves manufactured. What this implies is that the unlikely complexity of living things does not occur by some unimaginable concurrence of pure chance events but as the result of a series of successes (surrounded by many, many failures), each building on the last.
How did you get to the point of "once having a kind of reproducible coordinated chemical factory? That seems to me to be the biggest leap of all? I then could see your analogy more clearly. And I agree with your implication that the unlikely complexity of living things does not occur by ... pure chance events, etc?
If you can imagine a small manufacturing robot designed to build more like itself and to capable of forming coordinated robot "colonies" that together manufacture further robot "colonies" with chance variations, you will see the potential for increasing complexity. If you add to this the element of competition between robot colonies, and the survival of those with the most sophisticated survival mechanisms, then you have a fair analogy to the mechanism that drives increasing sophistication of the design of organisms from the relative simplicity of small organelles to the almost unmatched complexity of a lettuce, with humans and other apes perhaps falling somewhere between.
You use the word 'design' here. How does one imagine design when the whole thing supposedly was either by chance or by some probabilities outside even the range of chance, or an undefinable 'selective force'?
It is not possible, at present anyway, to look back at those early moments of the Earth's prehistory and to follow exactly which chemical paths led, through increasing sophistication; increasing competition; promiscuous mutation; and remorseless selection, to the first structure we would recognise as living. But it is possible to follow the nature of the mechanisms involved and to see that the chances of the occurrence of events such as we understand are not at all vanishingly small but increasingly likely once they have a foothold; and that the foothold may have taken, in the right atmosphere, just a week. That the exact mechanisms are not known and may never be known, and that the odds of creating a self-replicating molecule to begin with may not be exactly calculable are not the strengths of Darwinian theory; but neither are they its weaknesses, as the theory does not seek to explain or predict such matters but rather to explain and predict what occurs once we do have something we recognise as living.
In discussing odds and chances, what we have to recognise is that they are references to hypothetical alternative universes. If I say that the chance of your blind-drawing the black ball from a bag containing a black ball and a similar white ball is one in two, I mean much more than "I don't know which one you will draw"; what I mean is that in every second universe, you will draw the black one. This is a crucial concept to grasp in any discussion of probabilities.
With reference to the formation of eyes, of nucleotides, or even of proteins, a probability represents, of all alternative possible worlds, the fraction in which the event occurs in which we're interested. Probabilities are calculated with certain assumptions of randomness, though. If I calculate that in every second universe you will draw the black ball rather than the white one, I will be incorrect if it turns out that, in every universe, white balls lose their heat faster than black ones and for that reason contract further than black ones and become harder to grasp.
Similarly, in calculating that the probability is low that the mutation of a particular gene will result in front teeth that cut rather than grind, the apparently resultant unlikelihood that humans should develop incisors convenient for cutting food is illusory if it overlooks that, of the hundreds of alternative mutations affecting the shape of those teeth, only the mutation producing cutting teeth will allow its recipient to get twice as much nutrition from the available food.
What appears to be mere probability (and therefore unlikelihood) , can, then, actually be more than likely, due to what are termed selective pressures.
Selective pressures imply some sort of 'selective' process or at least choices, does it not? What is the process or what is the basis for the choices?
This is analogous to the "probability" of building proteins and nucleotides. Yes, if it required random rearrangement of atoms in random soups, the probability would be low. But in fact it is possibly much more easily for proteins and more-complex molecules to form once there are certain precursors in place, and the probabilities turn increasingly in favour of one kind of complexity or another until certain steps become all but certainties. When we produce a new human being from a mere 46 chromosomes, we don't imagine it to be an unimaginably small chance that a complex human being, complete with thousands of proteins and even two completely formed eyes, should result. We understand that from the simple recipe instructions contained in the long recipes lining the strands of those 46 chromosomes, that complexity is built up, step by step.

As it is in an individual organism's development, so it is in evolution. The sophistication of the most complex molecules, organs, and organisms is hardly subject to the rules of chance, being for the most part under the control of, and an emergent property of, slightly less sophisticated molecules, themselves the result of slightly less sophisticated ones still: it is an emergent property, not visible in the simple rules of the game but nevertheless flowering from them. Accidents will of course happen. In such sophisticated factories as we are, they will happen a lot. It is estimated that 90% of all human embryos abort. Of those developmental accidents that are not fatal, some, the majority, are distinctly disadvantageous. Every so often, though, one must provide some advantage. In this way, those living in extremely cold climates tend to successfully reproduce offspring with short, thick limbs, and those living on lactose-containing milk tend to successfully reproduce offspring producing a lactose-digesting enzyme. The success and spread of each advantageous trait is not a chance event any more than is the abortion or failure to reproduce successfully of organisms with highly disadvantageous ones; it is in fact a highly probably emergent result of the mechanisms involved.
What do you think -- does it start to make sense when you realise that the construction of any complexity in an organism is the end result not of a chance event but of a process of many steps, each step not at all unlikely but merely one successful small mutation amongst many, most of which end up carried by few offspring and eventually lost altogether?
Please see above remarks re mutations. I agree with you totally that things should make sense especially when one realizes that the construction of any complexity in an organism is the end result of a process of many steps. That is what I have been trying to find out about this theory for decades. Your logic as I said is great, but I see mostly illustrations, imagines, etc. when I want to see is real, verifiable evidence for claims made. Is it possible that there are so many theories of evolutions because every time something is unprovable another mechanism must be 'created' to explain the 'unprovable' and thus deviations lead away from Darwin? Looking forward to hearing your response.
Cheers --
John
Mary Ann Gilmore