Darwin, Darwinism and Neo-Darwinism

G. Richard Jansen
Colorado State University
Fort Collins, Colorado, 80521
May 1, 2010, Revised September 6, 2011

In the beginning God created the heaven and the earth.

And the earth was without form, and void;

and darkness was upon the face of the deep.

And the Spirit of God moved upon the face of the waters.

Introduction

            Darwin participated in the famous voyage of HMS Beagle from 1831-35 as a geologist not as a naturalist. In his article on the voyage his comments about the Galapagos Islands dealt primarily with the geology with a few comments about the reptiles. He also commented that the flora and fauna on the separate islands, especially the birds were distinctly different.

             It is the theory of mutability that informs almost the whole of this first notebook. The questions to which Darwin addressed himself were those later to appear in the Origin. Why are individual plants and animals sufficiently alike to group themselves into species, and yet sufficiently different to vary among themselves within species? Why do modem species resemble the extinct ones in any area, and why have the extinct ones become extinct? Why are some species born while others die? And finally, the ultimate question: Why are species related to each other, and what is the chain of their relationship? His answers to these questions were groping, tentative, highly speculative, yet invariably derived from the hypothesis of mutability. The notebook deserves to be quoted at length, partly because much of it is not available in print and also because it is only by extensive quotation that it can be seen how readily Darwin took to his theory and how bold and elaborate his speculations were, even at this early stage. He speculated about the most fundamental facts, the facts of life and death, of generation and variation:

            "Why is life short. Why such high object generation. Why is generation so high an object?] We know world subject to cycle of change, temperature and all circumstances which influence living beings. We see the young of living beings become permanently changed or subject to variety, according to circumstances ... Hence we see generation here seems a means to vary or adaptation ••• There may be unknown difficulties with full grown individual with fixed organization thus being modified Therefore generation [is designed] to adapt and alter the race to changing world On other hand, generation destroys the effect of accidental injuries, which if animals lived for ever would be endless (that is with our present system of body and universe), Therefore final cause of life.

            Why does individual die? To perpetuate certain peculiarities (therefore adaptation), and obliterate accidental varieties, and to accommodate itself to change (for, of course, change, even in varieties, is accommodation). Now this argument applies to species. If individual cannot propagate he has no issue with species. If species generate other species, their race is not utterly cut off-like golden pippins, if produced by seed, go on otherwise all die.

            The fossil horse generated, in South Africa, zebra and continued-perished in America. There is nothing stranger in death of species than individuals. Absolute knowledge that species die and others replace them.

            With respect to extinction, we can easily see that variety of ostrich (Petise), may not be well adapted, and thus perish out; or, on the other hand, like Orpheus, being favourable, many might be produced This requires principle that the permanent variations produced by confined breeding and changing circumstances are continued and produced according to the adaptation of such circumstances, and therefore that death of species is a consequence (contrary to what would appear from America) of non-adaptation of circumstances.

            With this tendency to vary of generations, why are species constant over whole country. Beautiful law of intermarriages partaking of characters of both parents, and these infinite in number •••. According to this view animals on separate islands right to become different if kept long enough apart ... Now Galapagos tortoises ...

            A species, as soon as once formed by separation or change in part of country, repugnance to intermarriage settles it. Propagation explains why modem animals same type as extinct, which is law almost proved We can see why structure is common in certain countries when we can hardly believe necessary, but if it was necessary to one forefather, the result would be as it is. This view supposes that in course of ages and therefore changes, every animal has tendency to change. This difficult to prove.'

            The different intellects of man and animals not so great as between living things without thought (plants), and living things with thought (animals).

            Organized beings represent tree irregularly branched The tree of life should perhaps be called the coral of life, base of branches dead; so that passages cannot be seen. The bottom of the tree of life is utterly rotten and obliterated in the course of ages .It leads you to believe the world older than geologists think. '

Erasmus Darwin 1731-1802

            Erasmus Darwin conjectured that all living things are ultimately descended from a single microscopic ancestor (which is the modern scientific orthodoxy). Beyond that, he argued, evolution has been driven by 'the three great objects of desire' - sexual lust, hunger and security. To a greater or lesser extent, depending on the species, lust leads to the dominant males propagating the species, thus improving it. This is the essence of natural selection. The need for food has led different species to develop different characteristics, adapted to their preferred diet, and here he cites as examples the elephant's trunk or the hard beaks that some birds have developed. Considerations of security have similarly led to different adaptations, such as flight, speed, camouflage or protective shells. He summed all this up in the following passage:

            Would  it be too bold to imagine, that in the great length of time since the earth began to exist, perhaps millions of ages before the commencement of the history of mankind, ... that all warm-blooded animals have arisen from one living filament, which THE GREAT FIRST CAUSE endued with animality, with the power of acquiring new parts, attended with new propensities, directed by irritations, sensations, volitions and associations, and thus possessing the faculty of continuing to improve by its own inherent activity, and of delivering down those improvements by generations to its posterity .. !'  

          Erasmus Darwin's last work, a great book-length poem published posthumously in 1803, The Temple of Nature, expanded on the views published in Zoonomia on the development of life on earth, telling in verse the story of the evolution of life from primitive beginnings to the present day:z

Origin of the Species by Means of Natural Selection

Charles Darwin 1809-1882

            The first edition was published in 1859, twenty-one years after Darwin returned to England after the five year voyage of HMS Beagle. In the first part of the book Darwin points out that most, but by no means all, naturalists believed in the immutability of the species. However the concept of the mutability of species was increasing among naturalists. Among these Darwin cites Buffon, Lamarck, Saint Hillaire, Wells, Wallace, Spencer, Hooker and a number of others. In fact, Wallace's paper and Darwin's paper on the origin of species were published together in the same issue of the Journal of the Linnean Society. It was surely out of a sense of decorum that he didn't mention his Grandfather Erasmus Darwin who, as we have seen, antedated in writings much of what Charles came to believe. He should have included his friend and colleague Charles Lyell whose similar views on the origin of the species predated Darwin's. The concept of evolution was in the very air Darwin was breathing. Darwin made the strong point that the origin of species and natural selection are inter-dependent and can't be separated. They are joined at the hip., so to speak.

            In chapter I Darwin discussed variation and selection occurring under domestication, things that were well known in the England of his time. For example, breeds of high milk yielding dairy cows such as Holsteins were developed considerable before Darwin's book. Chapters II through chapter V are the center and core of Darwin's hypothesis on the origin of the species. Bear in mind that these ideas Darwin developed before Gregor Mendel and before anything was known about genes, genetics, inheritance and mutations.

            In chapter II Darwin discussed the variations that occur in nature, varieties changing into species so imperceptively that they barely can be distinguished. It was very clear from the evidence that species are not immutable but are changeable over time. Darwin later speculated that over time new varieties coalesced into new genera, new families and so on.

            Chapter III points out that life is involved in a struggle for existence and survival. This was of course obvious to most people. Darwin's grandfather Erasmus Darwin summarized this struggle thusly: "The world would seem to be one great slaughterhouse whose first rule might be expressed eat or be eaten."
            Herbert Spencer coined the term "survival of the fittest" which is a tautology with fitness being defined as surviving.

            Chapter IV "Natural Selection" is the heart of Darwin's hypothesis which he defined in the title of his book as "The Origin of the Species by Means of Natural Selection." Darwin argues from the reality that man has been able through the known variability of animals and plants under cultivation or domestication to select favorable variants and perpetuate them as new strains or varieties. He argued that with the known variability occurring in nature and million of years of time selection pressures, which he termed "natural selection" selected those variants best able to survive and have progeny. This was aided by the normal biological processes of sexual selection, intercrosses, geographical isolation of varieties and extinction of species due to failure to compete successfully in the struggle for existence.

            After summarizing laws of variability Darwin forthrightly discussed and listed difficulties with his theory: 1) absence or rarity of transitional species, 2) species with habits widely different from those of their allies, 3) organs of extreme perfection, 4) "natura on facit saltum" (nature makes no leaps), 5) organs not in all cases absolutely perfect. In his final chapter Darwin expressed his confidence that his theory would eventually surmount all these difficulties.

            The three areas where Darwin's theory on the origin of species have been brought up to date are origin of life, the fossils record and molecular genetics. The National Academy of Sciences in its report on Science and Creationism conveniently has summarized these matters for us.

Origin of Life

            "Experiments conducted under conditions intended to resemble those present on primitive Earth have resulted in the production of some of the chemical components of proteins, DNA, and RNA. Some of these molecules also have been detected in meteorites from outer space and in interstellar space by astronomers using radiotelescopes. Scientists have concluded that the "building blocks of life" could have been available early in Earth's history.

            An important new research avenue has opened with the discovery that certain molecules made of RNA, called ribozymes, can act as catalysts in modem cells. It previously had been thought that only proteins could serve as the catalysts required to carry out specific biochemical functions. Thus, in the early prebiotic world, RNA molecules could have been "autocatalytic"--that is, they could have replicated themselves well before there were any protein catalysts (called enzymes). Laboratory experiments demonstrate that replicating autocatalytic RNA molecules undergo spontaneous changes and that the variants of RNA molecules with the greatest autocatalytic activity come to prevail in their environments. Some scientists favor the hypothesis that there was an early "RNA world," and they are testing models that lead from RNA to the synthesis of simple DNA and protein molecules. These assemblages of molecules eventually could have become packaged within membranes, thus making up "protocells"--early versions of very simple cells.

            For those who are studying the origin of life, the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells.

            Will we ever be able to identify the path of chemical evolution that succeeded in initiating life on Earth? Scientists are designing experiments and speculating about how early Earth could have provided a hospitable site for the segregation of molecules in units that might have been the first living systems. The recent speculation includes the possibility that the first living cells might have arisen on Mars, seeding Earth via the many meteorites that are known to travel from Mars to our planet.

            The report on Science and Creationism made this statement in regard to Darwin's theory of the origin of the species through natural selection, the fossil record and molecular mechanisms:

            "Darwin's original hypothesis has undergone extensive modification and expansion, but the central concepts stand firm. Studies in genetics and molecular biology--fields unknown in Darwin's time--have explained the occurrence of the hereditary variations that are essential to natural selection. Genetic variations result from changes, or mutations, in the nucleotide sequence of DNA, the molecule that genes are made from. Such changes in DNA now can be detected and described with great precision.

            Genetic mutations arise by chance. They may or may not equip the organism with better means for surviving in its environment. But if a gene variant improves adaptation to the environment (for example, by allowing an organism to make better use of an available nutrient, or to escape predators more effectively--such as through stronger legs or disguising coloration), the organisms carrying that gene are more likely to survive and reproduce than those without it. Over time, their descendants will tend to increase, changing the average characteristics of the population. Although the genetic variation on which natural selection works is based on random or chance elements, natural selection itself produces "adaptive" change--the very opposite of chance.

             Scientists also have gained an understanding of the processes by which new species originate. A new species is one in which the individuals cannot mate and produce viable descendants with individuals of a preexisting species. The split of one species into two often starts because a group of individuals becomes geographically separated from the rest. This is particularly apparent in distant remote islands, such as the Galápagos and the Hawaiian archipelago, whose great distance from the Americas and Asia means that arriving colonizers will have little or no opportunity to mate with individuals remaining on those continents. Mountains, rivers, lakes, and other natural barriers also account for geographic separation between populations that once belonged to the same species."

                So many intermediate forms have been discovered between fish and amphibians, between amphibians and reptiles, between reptiles and mammals, and along the primate lines of descent that it often is difficult to identify categorically when the transition occurs from one to another particular species. Actually, nearly all fossils can be regarded as intermediates in some sense; they are life forms that come between the forms that preceded them and those that followed.

The fossil record thus provides consistent evidence of systematic change through time--of  descent with modification. From this huge body of evidence, it can be predicted that no reversals will be found in future paleontological studies. That is, amphibians will not appear before fishes, nor mammals before reptiles, and no complex life will occur in the geological record before the oldest eucaryotic cells. This prediction has been upheld by the evidence that has accumulated until now: no reversals have been found.

Discussion of Specific Aspects of Evolution

Origin of Life

            The National Academy of Sciences report Science and Creationism made this assertion:

            "For those who are studying the origin of life, the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells. Will we ever be able to identify the path of chemical evolution that succeeded in initiating life on Earth? Scientists are designing experiments and speculating about how early Earth could have provided a hospitable site for the segregation of molecules in units that might have been the first living systems. The recent speculation includes the possibility that the first living cells might have arisen on Mars, seeding Earth via the many meteorites that are known to travel from Mars to our planet."

            It is disappointing to see an organization that should be devoted to the highest standards of scientific investigation and reason make such a statement based on speculation and wishful thinking. Included is a speculation that life could have originated on Mars and been delivered to earth on a meteor. This is of course nonsense, and merely begs the question as to how life originated on the rather inhospitable planet Mars.

            The conditions on earth three to four and a half billion years ago are, of course, not known, nor is there even the remotest consensus on what these conditions might have been. There is no knowledge as to what molecules were present, at what temperature, and with what atmosphere .  If water was indeed present what were the concentrations of the substrates for life formation.  How could even the most primitive cell  formed be able to replicate itself ?`          
          A so-called "RNA world" has been proposed. All life, as far as is known is based on the genetic code present in DNA and RNA. Both molecules include in their structures ribose, purines and pyrimidines. Larralde, Robertson and Miller (PNAS 92: 8158-8160 (1995)) studied the stability of ribose under varying conditions of ph and temperature. Based on their results these workers concluded because of the instability of ribose early genetic material, if indeed there was any, could not have been RNA or DNA. Levy and Miller (PNAS 95: 7933-7938 (1998)) also concluded that early genetic material could not have included the purine cytosine because of instability, thus not have either DNA or RNA been created. In addition there is no known mechanism how either RNA or DNA with a replicable genetic code could have arisen and been transcribed and translated without  all  the needed enzymatic machinery unfortunately also not present. A purely chemical origin of life without some form of design is exceedingly unlikely. 

            The statement cited above in the National Academy of Sciences publication Science and Creationism is the heart and soul of Darwin;  natural selection by Mutations happen. Ones that improve survivability are selected from and contribute to progeny. The progeny become geographically separated, as for example the varieties of Finches on the Galapagos Islands resulting in new species. This is, however, a hypothesis that remains unproven to this date.

            Darwin considered that the origin of species and natural selection were inextricably linked, each depending on the other for validation. After his book was published Darwin started to realize the significant limitation of natural selection in explaining the origin of the species. In 1863 he wrote this to a friend: "In fact the belief in Natural Selection must at present be grounded entirely on general considerations. When we descend to details, we can prove that no one species has changed [i.e., we cannot prove that anyone species has changed]; nor can we prove that the supposed changes are beneficial, which is the groundwork of the theory. Nor can we explain why some species have changed and others have not." By 1875 Darwin attributed more and more to Lamarck's theory of the inheritance of characteristics acquired through use and disuse and less to natural selection.

            With time and especially after the publication of Darwin's book on the descent of man Darwin's "bulldog" Thomas Huxley came to understand better the full moral and ethical implications of Darwin's ideas that he had been so vigorously defending and said this in the Romanes lecture. He himself described the Romanes lecture as an orthodox discourse on the text, II Satan, the Prince of this world," and he declared the superiority of the best theologians
over most of their opponents to be their recognition of the realities of evil:

            "The doctrines of predestination, of original sin, of the innate depravity of man and the evil fate of the greater part of the race, of the primacy of Satan in this world, of the essential vileness of matter, of malevolent Demiurgus subordinate to a benevolent Almighty, who has only lately revealed himself, faulty as they are, appear to me to be vastly nearer the truth than the "liberal" popular illusions that babies are all born good, and that the example of a corrupt society is responsible for their failure to remain so; that it is given to everybody to reach the ethical ideal if he will only try; that all partial evil is universal good, and other optimistic figments".

            Stephen J Gould's theory of punctuated equilibria casts additional doubt on the idea that evolution happens through a series of incremental small steps. Instead, according to Gould, the fossil record shows bursts of change occurring between long periods of stasis.

             In 1954 in the Journal Nature The British zoologist J. Gray put it this way in reviewing the book Evolution in Action by Julian Huxley  
(Nature, 173,227( 1954)):

            Darwinian orthodoxy demands implicit faith in the efficacy of natural selection operating on chance mutations. Subscribe to this and all doubts and hesitations disappear; question it and be forever lost. The case for orthodoxy can seldom have been stated with greater cogency and enthusiasm than by Dr. Julian Huxley in "Evolution in Action". A few readers, perhaps rather pagan in their outlook. may think it a little strange that, if the Case is quite so strong as they are asked to believe, it should still be necessary to argue the merits of natural selection with almost evangelistic vigour.

            On one point all biologists are agreed: the basic concept of organic evolution has, for a century, stood unrivalled as a contribution to biological thought. As a working hypothesis it opened up and exploited vast new fields of paleontological, anatomical and embryological inquiry. The status of natural selection is not quite so high. True, it is the only theory we have; but when judged as a working hypothesis it is disappointing to find so little advance in a hundred years. What new facts have been brought to light ? How far can it be shown to have elaborated the pageantry of animal life since 1859? A century is a fantastically short period of cosmic time, and all sorts of queer, exciting and improbable things may happen in five hundred million years; so, if we accept 'possibility' as a basis for scientific thought, why worry! Dr. Huxley admits quite frankly: "No one would bet on anything so improbable happening; and yet it has happened. It has happened thanks to the workings of Natural Selection and the properties of living substance which make Natural Selection inevitable" . What more can be said, except possibly to suggest that there may be a slight difference between something that 'has happened' and one which 'may have happened'. No amount of argument, or clever epigram, can disguise the inherent improbability of orthodox theory; but most biologists feel it is better to think in terms of improbable events than not to think at all; there will always be a few who feel in their bones a sneaking sympathy with Samuel Butler's scepticism " ••• there must have been a little cheating somewhere with these accidental variations [mutations} before the eagle could have become so great a winner". How far the heathen will be converted by Dr. Huxley is difficult to say.

            The theory of natural selection implies the survival of organisms possessing functional advantages over their predecessors or rivals. Strange as it may seem one immediate effect of the "Origin" was a marked recession in the study of animal function. There was, and still is. a tendency for morphologists to ascribe to organs and structures functional significance for which there was, or is. little observational evidence. In this respect "Evolution in Action" is by no means guiltless ; it goes a considerable way beyond the physiological facts. Is Dr. Huxley quite sure that the loss of the lateral digits by the ancestors of the horse gave them an "additional turn of speed"! And. is he certain that the parallel between increasing complexity of anatomical structure (so clearly displayed throughout vertebrate evolution) and increasing complexity or versatility of behaviour is quite so obvious as he suggests! In what ways is the behaviour of a "frog, a lizard, or even a sheep, an 'advance' on that of a stickleback? What about the hoary old story of snakes walking by their ribs.

            To lay readers the more exciting part of "Evolution in Action" deals with the position of man in relationship to the rest of the animal world. To Dr. Huxley, man is an organism in a class apart from all others. In many ways man is more distinguished; but most readers will be sorry to read that "the human species to-day is burdened with many more deleterious mutant genes than can possibly exist in any species of wild creature", It seems a great pity that natural selection should have met its 'Waterloo just when it was most needed. In the jungles of the past Nature guards her secrets with particular care, and it is a brave man who ventures far from the recognized tracks; it is so much easier to sit and criticize more adventurous spirits. Dr. Huxley's aim is not to comfort the despondent but to hit the dragons of Improbability stoutly on the nose and to give the world a real feeling of the unity and sweep of evolution • • . as a self-transforming process •.• building its future by transcending its past". He has succeeded.

             At the outset he writes: "Darwinian orthodoxy demands implicit faith in the efficacy of natural selection operating on chance mutations. Subscribe to this and all doubts and hesitations disappear; question it and be forever lost". After saying that I state "the case for orthodoxy", he continues: "A few readers, perhaps rather pagan in their outlook, may think it a little strange that, if the case is quite so strong as they are asked to believe, it should still be necessary to argue the merits of natural selection with almost evangelistic fervour". Later, he states, "No amount of argument, or clever epigram, can disguise the inherent improbability of orthodox theory; ... there will always be a few [biologists] who feel in their bones a sneaking sympathy with Samuel Butler's scepticism".

            These allegations from one of our leading biologists demand an answer. First, I repudiate" (and I am sure that other biologists will agree) the idea that there is any such thing as a "Darwinian orthodoxy" which "demands implicit faith in natural selection" -or in anything else. I venture to remind Sir James Gray of Sir Ronald Fisher's "Genetical Theory of Natural Selection". In that remarkable book, Fisher demonstrated conclusively: (1) that gradual evolutionary change, BB postulated by Darwin and later established by the paleontologists, could have been brought about by selection acting on small mutations, on the basis of a particulate (Mendelian) mechanism of inheritance; but could not have been brought about on the basis of a mechanism of blending inheritance; (2) that, given the observed facts concerning heritable variations and their origin, neither orthogenesis (in the sense of inherently determined and directional variation) nor Lamarckism in any of its forms could have played any but the most trivial part in effecting evolutionary change , (3) that selection, acting upon small mutations and their recombinations, is capable of producing an extremely high degree of apparent improbability; and (4) that natural selection does not have to await the precise mutations needed to produce desirable adaptation, but operates on the stored variance made possible by the particulate mechanism of heredity, eliciting from it the required recombinations. (Gray's statement about selection "operating on chance mutations" obscures this essential point, and neglects the fact that the effect of genes are gradually adjusted by selection operating on the gene complex.)

            These are not dogmatic statements, but scientific conclusions; and the resultant neo-Darwinian or selectionist theory of evolution is no more an 'orthodoxy' than is the atomic theory of matter or the Mendelian theory of inheritance. Evolutionary biologists support it, not because they would be "forever lost" and excluded from an orthodox fold if they questioned it, but because it--and so far, it alone--is able to account for the facts.

            Finally, the reason why it is still necessary, especially in a semi-popular book, to argue the case for natural selection so vigorously is that, unfortunately, a certain number of prominent biologists still publicly evince "a sneaking sympathy", to use Gray's own words, with Samuel Butler, or other vitalists or Lamarckians.

            That my review of Dr. Huxley's book should be regarded as a matter of "major concern to general biological theory" is a sobering thought. It just shows how careful one must be in approaching the preserves of evolutionary genetics. I can only say that none of the works to which Prof. Huxley refers, or appears to have in mind, gives me reason to believe that a 'conclusive demonstration' of the fact that certain things can happen is necessarily proof that they have happened. A demonstration that Dr. Huxley might conceivably make a mistake is no proof that he has, in fact, done so. Not' does a feeling of disappointment in natural selection as a working hypothesis during the past hundred years prove that biologists-prominent or otherwise are either  vitalists or Lamarckian fellow-travellers.

            The Fossil Record

            The number of intermediate forms that have seen in the fossil record are few compared to realistic expectations from a common descent followed by natural selection. One school of thought holds that mammals derived from reptiles.  Another view held especially strongly by Prothero holds that mammals arose from Synapsids totally separately from reptiles. There are many intermediate forms in the fossil record but many of these didn't survive. The fossil record shows most species arising from no ancestor and leaving no progeny.

              Human evolution is the term used to refer to the origin  of Homo sapiens as a species distinct from other hominids. The term "human" in the context of human evolution refers to the genus Homo but studies of the descent of humans with modifications  usually include other Hominids such as the Australopithicines from which the genus Homo had diverged by about 2.3 to 2.4 million years ago in Africa. Scientists have estimated that hominids and chimpanzees branched off from their common ancestor about 5–7 million years ago. That estimate itself is amazing since the first fossil of a Chimpanzee wasn't discovered until 2005 and consisted of  several teeth.

Comparative table of Homo species (From Wikipedia)

Comparative table of Homo species

Species	Lived when (Ma)	Lived where	Adult height	Adult mass	Cranial capacity (cm³)	Fossil record	Discovery / publication of name
H. habilis	2.3 – 1.4	Africa	1.0–1.5 m (3.3–4.9 ft)	33–55 kg (73–120 lb)	510–660	Many	1960/1964
H. rudolfensis	1.9	Kenya				1 skull	1972/1986
H. ergaster	1.9 – 1.4	Eastern and Southern Africa	1.9 m (6.2 ft)		700–850	Many	1975
H. georgicus	1.8	Georgia			600	4 individuals	1999/2002
H. erectus	1.5 – 0.2	Africa, Eurasia (Java, China, India, Caucasus)	1.8 m (5.9 ft)	60 kg (130 lb)	850 (early) – 1,100 (late)	Many	1891/1892
H. antecessor	1.2 – 0.8	Spain	1.75 m (5.7 ft)	90 kg (200 lb)	1,000	2 sites	1997
H. cepranensis	0.9 – 0.8?	Italy			1,000	1 skull cap	1994/2003
H. heidelbergensis	0.6 – 0.35	Europe, Africa, China	1.8 m (5.9 ft)	60 kg (130 lb)	1,100–1,400	Many	1908
H. neanderthalensis	0.35 – 0.03	Europe, Western Asia	1.6 m (5.2 ft)	55–70 kg (120–150 lb) (heavily built)	1,200–1,900	Many	(1829)/1864
H. rhodesiensis	0.3 – 0.12	Zambia			1,300	Very few	1921
H. sapiens sapiens (modern humans)	0.2 – present	Worldwide	1.4–1.9 m (4.6–6.2 ft)	50–100 kg (110–220 lb)	1,000–1,850	Still living	—/1758
H. sapiens idaltu	0.16 – 0.15	Ethiopia			1,450	3 craniums	1997/2003
H. floresiensis	0.10? – 0.012	Indonesia	1.0 m (3.3 ft)	25 kg (55 lb)	400	7 individuals	2003/2004

            The knowledge about genetics, especially at the molecular level, has increased exponentially since Darwin's time. When Darwin was alive Gregor Mendel's work on plant genetics, which initiated genetics as a scientific discipline, was still essentially unknown in Europe. Those who were initially aware of the work failed to appreciate its significance.

            At the molecular level it is now known that all of life shares the same "genetic code" which is the mechanism by which genetic information is transmitted from one generation to the next generation. The code is located in the molecule deoxyribonucleic acid (DNA).

            DNA is a double stranded  chain each consisting of two nucleotide pyrimidine bases, adenine and thymine, and two nucleotide purine bases, cytosine and guanine, each linked to ribose as nucleosides and all phosphate linked to each other in two long chains, base paired with each other.  . In the human genome, for example there are three billion base pairs. The DNA chain is wrapped around histone proteins resulting in what is called chromatin. The code is a triplet code consisting of three adjacent nucleotide bases.

            The two stranded DNA is unzipped and a single strand transcribed to messenger  RNA, mRNA, again by base pairing. The mRNA is translated to protein on ribosomes of rRNA and transfer RNA, tRNA, each tRNA molecule attached to a single amino acid and base paired with the mRNA. All of these steps require specific enzymes to be carried out. The regions of the DNA transcribed are  called  exons and the regions not transcribed are called introns. It is not yet completely clear how much of the DNA is transcribed.  The regions not transcribed are sometimes called "junk DNA" but this reflects more ignorance than knowledge.

            The unit of inheritance is called a gene and after being transcribed and translated results in a single protein. This is a very brief summary of what is a very complicated process that includes regulatory genes and regulatory proteins. There occur insertions and deletions of DNA strands called indels and rearrangements and recombinations of the DNA molecule. There also are point mutations consisted of a single loss of change of a nucleotide base. Indels of insertion or deletion can consist of strands of DNA up to 50 or more nucleotide bases. It is clear that since the code is a triplet of adjacent nucleotide bases mutations and indels can play havoc with the accurate transcription and translation of the genetic code.

            Mutations and indels are a degradation of the genome and sometimes the phenotype as well.  They rarely improve the information in the genetic code. There are many thousands more deleterious than beneficial mutations or indels. As a result the overwhelming percentage of random mutations destroy information and lead to increased disorder in the genome. Most of the deleterious mutations are only very slightly deleterious and are retained in the genome and are inherited by the next generation. It is difficult to see how mutations can lead to increased survivability, new species, new classes and new phyla. It is much easier to see how deleterious mutations can lead to less fitness and less survivability.

            The mutation rate in humans is estimated to be 100-200  mutations per zygote per generation Lynch has looked recently on the implications of the human mutation rate on the fitness of Homo sapiens over many generations (Proc. Nat. Acad. Sci. 107(3) 961-968 (2010)).

Lynch estimated that the loss of fitness of humans is likely to be 1-3%  in a generation. He speculate further that the decline in fitness could be as high as 60% in 200 years.  These are interesting suggestions but they raise an even more interesting question as to how the human genus has done so well over several million years and how Homo Sapiens has done so remarkably well over the past 150 thousand years.  Something is not consistent here. It would have been helpful if author Lynch had looked backwards in time as well as trying to predict the future.
       

        An interesting article authored by Freiman and Tijan entitled Regulating the Regulators: Lysine Modifications Make their Mark was published in Cell 112: 11-17 (2003).  The authors' concluding remarks are worth quoting in full: "The recent completion of several animal genome sequences has revealed that the number of expressed genes is considerably lower than expected. Consequently, the vast differences in cell types, signal transduction pathways, and complex behaviors characteristic of different species cannot be easily explained by increased gene number (i.e., worms, 19K and humans, 30K) alone but, rather, how a relatively limited number of genes (roughly 10–30K) are differentially expressed and utilized. In other words, the dramatic phenotypic differences between a worm and a mammal can at least partially be rationalized by differences in the complexity of the regulatory code and not merely gene content. The discovery of multiple covalent modifications of the regulatory apparatus discussed here suggests that organisms have evolved various mechanisms to maximize the usage of a relatively limited number of genes and transcription factors. By utilizing multiple distinct mechanisms to modify and control the transcriptional machinery, organisms have evolved much greater potential for directing diverse expression profiles by a finite number of transcription factors. Taking advantage of multiple covalent modifications of transcription factors organisms have effectively gained the ability to utilize the same regulatory factor in different ways and thus expand their range of gene expression patterns. Regulation by modification not only enhances the functional potential of each individual transcription factor but also provides an effective means of greatly amplifying the functional plasticity of the transcriptional machinery required for combinatorial diversity. This quantum increase in the repertoire of regulatory events ultimately provides the rich tapestry of molecular interactions necessary to direct the diverse arrays of gene expression programs that define complex organisms."

                While many components of the transcriptional machinery are conserved through evolution, we suspect that some modification networks may be specific to individual organisms, resulting in different gene expression outcomes depending on the species. For example, the transcription factor TFIID is largely conserved from yeast to humans; however, the diverse programs of gene expression regulated by this multiprotein coactivator complex in unicellular and multicellular organisms have diverged substantially. Therefore, it is possible that covalent modification of transcription factors, like TFIID, may occur in a species-specific manner, thereby allowing these factors to evolve specialized functions related to their evolutionary niche. For example, TFIID derived from animal cells containing cell type-specific subunits may be modified by specific mechanisms specialized to function in certain tissue types. Clearly, transcription is exquisitely regulated in all organisms, and one mechanism utilized to achieve such regulation is covalent modification of the transcriptional machinery. Future studies in diverse organisms and specialized regulatory pathways should further illuminate how transcription factor modification contributes to the elaborate mechanisms of gene regulation.

            It has long been appreciated that although all cells in an organism, for example a human, contain the same DNA the DNA is expressed very differently in the different tissues of the body. This comes about through the regulation of gene expression. Freiman and Tjian extend this understanding to the possibility that the difference in phenotype between, for example a worm and a human, results similarly from differences in the regulatory code and not merely gene content. There is still much we don't know about life processes and still more we don't even know we don't know.

            Fay and Wittkopp recently evaluated the role of natural selection in the evolution of gene regulation (Heredity 100: 191-199 (2008)). They start from the premise that evolution happened through natural selection but provide no evidence or even an argument that this is the case or that natural selection is involved in the evolution of gene expression.  They end their paper on a hopeful note: "We are still at the early stages of understanding the molecular, genetic and evolutionary forces underlying gene expression.  Over the next few years it will be exciting to discover how natural selection has shaped patterns of gene expression within and between species on a genomic scale. With regulatory diversity now documented in many systems future studies can begin dissecting the genetic basis and biological functions of adaptive changes in gene expression."  Of course. Future studies.  It is worth noting that these workers cited well over one hundred references but did not cite the above cited important article by Freiman and Tjian. They did cite Darwin's 1959 book on the origin of the species.

            There were many difficulties with his theory at the time that Darwin himself noted.  One was and still is the sudden appearance of most animal phyla over a 10-20 million year period during the Cambrian with no pre-existing fossils in the pre-Cambrian period, i.e. no apparent ancestors. Another problem was and still is the lack of the number and variety of intermediate fossils that would be expected from evolution over time through many small changes.  Descent with modification undoubtedly happened at the level of species, genera and family. All horse genera and species in the fossil record and living are in the same family, Eqiudae. Reptiles evolving into mammals appears to be an example of evolution at the level of class. Archaeopteryx is thought to be a transistional link between reptiles and birds.There is no evidence of phyletic evolution.

          This should come as no surprise to anyone since it has always been the underlying issue.  Darwin lost his belief in God at the same time he started to develop his ideas on the origin of the species. The full implication he himself saw was that man is just another animal common with all the other animals and not made in the image of God since there is no God. Darwin's colleagues Wallace and Lyell both intuitively  rejected this implication. In their mind man is not just another animal. The most interesting epiphany of all was that of Thomas Huxley, Darwin's "Bulldog".  After railing against the hidebound views of cleric and others who opposed Darwin's theory Huxley later said this in his Romanes lecture:

"The doctrines of predestination, of original sin, of the innate depravity of man and the evil fate of the greater part of the race, of the primacy of Satan in this world, of the essential vileness of matter, of malevolent Demiurgus subordinate to a benevolent Almighty, who has only lately revealed himself, faulty as they are, appear to me to be vastly nearer the truth than the "liberal" popular illusions that babies are all born good, and that the example of a corrupt society is responsible for their failure to remain so; that it is given to everybody to reach the ethical ideal if he will only try; that all partial evil is universal good, and other optimistic figments".

1. Life began on earth, according to the geological fossil record 3-4 billion years ago. There is no credible scientific theory as to how life originated.

2. It is  unlikely that life originated by strictly chemical and physical processes without pre-existing information or design.

3. No fossils of multicellular animal phyla except sponges were observed before the Cambrian period which is estimated as beginning 550 million years ago. All living animal phyla, except two, were present by 520 million years ago.  None had prior  ancestors in the pre-Cambrian period.

4. All life, including the simplest single cell prokaryotes, have within them a design.  The design is at a minimum DNA, but obviously much more must have been involved.  There is no credible scientific theory as to how DNA could have originated.

5.  The fossil record shows clearly that the very great majority of species appeared without an  ancestor and disappeared without  progeny. The exceptions are few.

6. The theory that all phyla and species originated solely or even predominately,as a result of random mutations followed by natural selection is not only unproven, it is unlikely.

7 Descent with modifications happened since the beginning of life. This happened within species, genera, and family. It is not understood how this happened .There are at most several examples at the level of class.   There is no evidence of phyletic evolution. Special creation of all species also is not likely.

8.  We do not know how or why our universe came into being. There is a credible scientific theory, the so-called "Big Bang", in which the  universe came into being at a singularity but it is a theory far from certain.

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