Minutus

Darwin's discovery of the mechanism of evolution is called a theory rather than a hypothesis because there is no doubt (at least, none in the minds of those who've understood how he arrived at his conclusions) that it adequately and most plausibly explains and ties together all the known facts of evolution. Darwin at no point imagined, by the way, that his theory accounted for the beginning of life; only for how it evolves. The individual changes in that process of evolution occur by chance, but the fact of that evolution's direction (e.g. the gradual evolution -- many times over -- of an eye from a light-sensitive patch to an enclosed lensed imaging organ, and the evolution of legs into fins in cetaceans and into wings in dinosaurs) is controlled by the differences each small change makes in the degree of its possessor's adaptedness to his or her habitat.

Hi John,
If the evolution of life develops by chance, but not necessarily the beginning, at what point does chance take over? Closer to the beginning but at what point, if not at the beginning? Was it when molecules began clustering together? or some other point? If so, what point? I know that there are 'theories' of evolution' around today, depending upon whom one reads or talks to, but which 'theory' is being talked about here? Thanks for your lively and straightforward approach.
Sincerely,
Mary Ann Gilmore
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From: John Harvey
To: minutus@yahoogroups.com
Sent: Mon, November 2, 2009 2:12:08 AM
Subject: Re: [Minutus] The secret diary of Drawin ( was Charles Darwin and his homeopathic doctor!)
Dear Venkat,
Sivasiva Palani's "The Secret Diary of Charles Darwin" is not quite what it appears to be at first blush. The author gives the clues to what this article actually is, one after another, right here:
"Seeking answers to these queries, I stumbled upon Charles Darwin's lost chronicles and discovered, to my utter astonishment, validation of the Indian TODD theory and a verdict against the TOE. Here then, is an excerpt from the authentically spurious and chimerical diary of the father of the theory of evolution."
If not for the clues, the article would be a massive fraud. But the author, clearly not any sort of historian, stumbled upon Darwin's hitherto undiscovered diary? And this incredibly important discovery is nevertheless still unavailable to anybody else to read? And Darwin went to the trouble to keep a second set of private diaries, and wrote conflicting accounts in the two private sets? And he wrote in such ignorance of his own discoveries? These suggestions are worth a chuckle, but are not worth being hoodwinked by.
Of course, the biggest clue is the one that follows right after that passage: "Charles wrote: 'It is a muggy April first day in 1835.'"
The article was an April Fool's Day hoax, and was probably sent to the editors on 1 April 1991.
If the joke were in any further doubt, it's a matter of historical record (see >) that on 1 April 1835, Darwin was not departing Calcutta but trekking through the Andes, in South America, as far from Calcutta as he could possibly be. And there appears to be no record that the Beagle ever visited any part of India, with or without Charles Darwin.
Neither "apes are our ancestors" nor "the ascent of man from lesser life forms" appears in Darwin's work as contentions that he argued for. Darwin's argument was not that evolution occurs; that was fairly well accepted already by many natural scientists and could be seen in everyday breeding of, for instance, pigeons, cattle, dogs, and many crops. What was at issue was the mechanism of evolution not under artificial control. The spectacularly prolific evidence that Darwin amassed on his Beagle voyage and through his further studies of the evolution of barnacles, pigeons, and other creatures led him, step by step, to what became the inescapably obvious conclusion as to evolution's key mechanisms.
What Darwin came to realise is, fundamentally:
(1) that the traits of the particular members of a species best-adapted to their habitat will lead to greater numbers of their offspring than of others to survive long enough to reproduce;
(2) that there is always resource competition (principally for food and for suitable mates) between members of a species, because populations given unlimited resources always increase exponentially; and
(3) that resources are not unlimited.
These three facts together led him to conclude that once, due to their inheritable traits, some individuals have greater reproductive success than others, natural selection (i.e. differential reproductive success) of those heritable traits will, through the generations, make them increasingly common in that population. (This is the same process that dog breeders have used for thousands of years to create breeds with the traits that they preferred a dog to have.)
When Darwin had to sum up this process in a phrase, he did so not in the practically useless "survival of the fittest" but in the far more descriptive "descent with modification by means of natural selection".
That is of course a mere snippet summary of Darwin's contribution to the understanding of how evolution occurs, and doesn't do justice to the man's genius in perceiving what he did and in overcoming his own religious prejudices to understand it, or to the amount of work he put in to test whether it really explained all that was known about evolution.
Darwin's discovery of the mechanism of evolution is called a theory rather than a hypothesis because there is no doubt (at least, none in the minds of those who've understood how he arrived at his conclusions) that it adequately and most plausibly explains and ties together all the known facts of evolution. Darwin at no point imagined, by the way, that his theory accounted for the beginning of life; only for how it evolves. The individual changes in that process of evolution occur by chance, but the fact of that evolution's direction (e.g. the gradual evolution -- many times over -- of an eye from a light-sensitive patch to an enclosed lensed imaging organ, and the evolution of legs into fins in cetaceans and into wings in dinosaurs) is controlled by the differences each small change makes in the degree of its possessor's adaptedness to his or her habitat.
It's again a matter of historical record that Darwin did not rush home to publish a theory he thought would prove acceptable, some theory that humans descended from apes. (Unlike some today, he was perfectly aware that humans are apes!) Neither did he rush home to publish any nonsense about man's ascent. Rather, he kept his discovery of descent with modification by natural selection fairly quiet for decades, and for at least two very good reasons. One is that, had he publicly shown the evidence for the heresy of the "transmutation of species" upon his return, he might have been executed. Such was the power of religion in a "civilised" country in 1835. Another is that he knew that his wife would be greatly upset by his unambiguous loss of faith in an omnipotent deity's every-sparrowfall control, and he was most reluctant to cause her that hurt.
Cheers!
John
2009/11/2 Venkat >
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"The mind is not a vessel to be filled but a fire to be kindled."

— Plutarch

Hi John,
I have more questions and some thoughts. See below please. This is a very wide as well as deep subject so I did not address all of my questions but some relevant ones as time allowed. Thanks. I don't use Cheers but I love your use of it!

Sincerely,

Mary Ann Gilmore
________________________________

From: John Harvey
To: minutus@yahoogroups.com
Sent: Wed, November 4, 2009 5:03:24 AM
Subject: Re: [Minutus] The secret diary of Drawin ( was Charles Darwin and his homeopathic doctor!)
Hi, Mary Ann --
Good questions! And many thanks for your feedback. Always good to have at least one reader.
"The theory of evolution", since Darwin's time, has come to refer to the Darwinian theory. Other ideas do float around, but they don't have the status of a theory; many are not even hypotheses, as they don't attempt to explain and predict, but merely to explain. The hypothetical components of Darwin's theory each has predictive power: intergenerational differences, exponential population growth, resource limits, resource competition, differential reproductive success. And each predicted outcome of these simple hypotheses is there to confirm.

Can you give examples, more than one to establish a pattern, of any absolutely accurate predicted outcome of any one of the above mentioned components, or of any perhaps not mentioned?
The greater significance of the theory is that it offers even stronger predictive power than do its components, allowing the prediction of change in population proportions of traits from generation to generation, even to extinction of once-common characteristics in favour of those that have outbred them -- even to the point of such changes that the new population can no longer interbreed with the population it derived from or that spawning population's other founder colonies.

This, of course, is the process of speciation, the creation of new species. And one of the practical results of applying the theory's predictive power is the (non-GM) breeding of new varieties and breeds by selection and interbreeding of stock most strongly exhibiting the characteristics the breeder wishes to emphasise. (In dogs, such a characteristic may be largeness, or smallness, or a propensity for gentleness, or a propensity to exert dominance behaviour or to hunt rats or to point at game or to recognise certain unique smells.)

How does the example of dogs developing new characteristics relate to the creation of an entirely new species? Are they not still dogs with different characteristics? Please explain.
The theory of electromagnetism too is but a theory. Yet it allowed the prediction of the existence of radio waves, which led to their discovery and the invention of, for instance, radios, television, and microwave transmission.
Not knowing an upper limit to the frequency of electromagnetism did not in any way invalidate the theory. Nor did not knowing that x-rays and cosmic rays existed invalidate it. When we discover a completely different phenomenon of "communication" between two atoms that is faster than light and does not consist of electromagnetic resonance -- such as occurs in quantum entanglement -- the discovery cannot in any invalidate that the theory of electromagnetism is well understood, successful in its predictions, and to that extent fully correct; it simply adds a new thing to be understood in the universe.
Just so is it unnecessary for us to know at exactly what point reproduction of complex molecules became the positive-feedback loop of self-selecting molecules. All the evolutionary change we're able to detect, in vivo or in the fossil record, is explained and can be predicted very nicely by the theory of evolution by descent with modification by means of natural selection: Darwinian evolution. It's clear that even a colony of bacteria, for instance, is subject to the same evolutionary forces as any other organism: in perhaps a hundred generations, possibly far fewer, a large colony of 0.1% penicillin-resistan t bacteria will, when faced with the selective force of penicillin, become an equally large colony comprising entirely penicillin-resistan t bacteria.

I do not understand how not understanding the upper limits of a theory is the same as having a solid foundation for a theory. For example, what is the probability of a complex molecule forming at some unknown previous time? I know there are various different hypotheses about this but the proteins needed for life have very complex molecules and the chance of even a simple protein molecule forming at random has been acknowledged by some scientists to be only 1 in 10 (to the 113th power). Excuse me or my computer, since I have never been able to get the power attached to a number!) but mathematicians dismiss any event of 1 in 10 (to the 50th power) as never happening. An idea of the odds involved is seen in the fact that 10 to the 113th power is larger than the estimated total number of all atoms in the universe. Also what is the probability of obtaining the proteins which serve as enzymes (of which some 2,000 are needed for cellular activity) at random? 1 chance in 10 to the 40,000 power. If one were using the organic soup hypothesis for the origin of life, this number would be larger than if the whole universe were an organic soup.
It's almost a given that the first molecules to self-replicate must have done so due to some new or unusual circumstance -- otherwise they wouldn't have been the first. Let's call that luck, or chance. Whether those first ones continued to replicate, or replicated with substitutions (i.e. changes), or simply fizzled out, we cannot know. But it's again almost a given that, at some point, another such first occurred -- and limped into a self-perpetuating process.

See above question and comments on probability, please.
Again, it doesn't matter whether it was from the beginning of this that selective forces culled certain molecules in favour of certain others. For all we know, there may be many parallel "colonies" even now of various self-replicating molecules in hot springs, in clay riverbanks, in deep-sea fissures, in volanic calderas. They may be there; they may not. They may replicate using some mechanism tending toward exponential growth in numbers; they may not. They may be subject to selective pressures; they may all coexist without particular competition. What we do know is that all the species of living organisms of which we have any evidence tend to reproduce to outstrip natural resources, and we understand that this by necessity means selection of some over others to survive to reproductive age and selection of some of these over others to have second-generation descendants. Unless all alternative characteristics were equal in reproductive value, all else must follow from these simple observable facts: alteration in population characteristics best adapted to the population's habitat; speciation; even mate choice on the basis of those characteristics that have proven successful.

I also have another question regarding using chance. I think that chance is a completely different topic and needs comprehensive definition if it is to be used in the context of any scientific discussion. It seems to me it becomes a nebulous catchall for evidence not available. Another example, nucleotides are even more difficult to obtain. The chance of forming even the simplest histone is said to be 20 to the 100th power, another huge number according to Hoyle and Wickramisinghe"larger than the total of all the atoms in all the stars and galaxies visible in the largest astronomical telescopes."How can probabilities like these be addressed or can they?
We evolved into four-limbed apes, and other land mammals evolved into four-limbed whales, not by blind chance but by the competitive pressures of the success of certain design characteristics in particular habitats, tropical and coastal. These pressures made those characteristics increasingly common through the generations and offered further success to exaggeration of most such advantages. In this way did our hind limbs grow significantly longer than those of our forebears while whales' hind limbs grew significantly shorter than their forebears'. And in this way, in various orders of animals, did a complex organ enabling interpretation of easily refractable electromagnetic radiations through lensed imaging -- an eye -- develop four or five times over independently, in small steps, each offering an advantage over the last, from a light-sensitive patch to a patch with some shielding offering directionality, to a pinhole imager, to a lensed imager.
I'm sure it's evident by now that at what point chance took over is not quite the right question. Chance favoured some kind of self-replication and favoured some variations in that replication. Eventually -- and this may have taken minutes or centuries -- that replication outstripped either the sites or the raw materials necessary for all such self-replicative molecules to succeed.
The relevant timing question, if you enjoy watching this kind of thing occur today and understanding it fully, may be at what point the role of chance variation is drowned out by the role of the sheer numbers of that variety in its differential success over others. Chance merely produces a new variety. Its suitability to its habitat in comparison with others determines its success.
Or, if you prefer prehistory, the question may be at what point blind luck became superfluous in kickstarting evolution. Evidently the answer to that question is: very early. Whenever it was that replication with variation commenced, and whether the resource shortages that imposed selective pressures on that process altered replication of simple or complex molecules, both evidently occurred well before creation of all known fossil records.
The date and the stage of replication at which selective pressures began to operate in selecting the relative numbers of replicant variants certainly don't affect the relevance or accuracy of the theory's predictive capabilities concerning all known life. But the transformation from a process of simple replication to one of the natural selection of variants amongst modified replicants would be kind of fun to watch, wouldn't it.
Cheers --
John
2009/11/4 Mary Ann Gilmore >
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"The mind is not a vessel to be filled but a fire to be kindled."

— Plutarch