Re: Question from a curious student

AN

[Graphic: Rod & Rhodopsin (`simple' eye molecular machinery), Bellarmine College.]

Thank you for your message. As is my usual practice when I receive a private message on a creation/evolution/design topic, I am copying my reply (minus your personally identifying information) to my blog, CreationEvolutionDesign, that others may benefit.

----- Original Message -----
From: AN
To: Stephen E. Jones
Sent: Tuesday, May 30, 2006 12:35 PM
Subject: Question from a curious student

>Mr. Jones,
>
>I recently read an article about you and had a few questions.

I am not aware of any article about me. I would appreciate more details about it, including its URL if it is webbed. In fact, from your questions, you may have me confused with an evolutionist, perhaps London genetics professor Steve Jones? But as my blog's title block says, " I am an Australian Christian old-Earth creationist/IDist biologist who accepts common ancestry."

>In school, I have been debating a few of my friends on the question of creationism and evolution and which, or both, is correct.

You have fallen into the first trap, accepting that the question is between "creationism" (my emphasis) and "evolution." As Professor Phillip E. Johnson pointed out, a "the debate is set up as pitting creationism (that is, an ideology) against evolution (no ism, therefore a fact)" and therefore "No matter what the evidence may be, an ideology (especially a religious ideology) can never beat a `fact' in a debate":

"The essay by National Academy of Sciences President Bruce Alberts, `Evolution Versus Creationism: Don't Pit Science Against Religion,' was published in The Denver Post, September 10, 1996, p. B9. The essay is a compendium of the usual spin-doctor arguments that official science organizations rely on to stop any serious questioning of evolution or materialism before it can get started. I recommend that teachers look for essays of this kind and use them for critical-thinking exercises ... One thing to notice right away is the title: the debate is set up as pitting creationism (that is, an ideology) against evolution (no ism, therefore a fact). No matter what the evidence may be, an ideology (especially a religious ideology) can never beat a `fact' in a debate conducted under scientific rules. Scientific materialists actually see the issue that way and so they naturally frame the debate in those terms. I always insist that an ism be put on both words or neither. Let the debate be between the competing facts (creation and evolution) or the competing ideologies (creationism and evolutionism). Better still, let it be between theism and materialism. What was present and active in the beginning, God or matter? That frames the question correctly and levels the playing field." (Johnson P.E., "Defeating Darwinism by Opening Minds," InterVarsity Press: Downers Grove IL, 1997, pp.124-125. Emphasis original).

So the first thing to do in debating your friends is for them and you to define your terms. What do you each mean by "creation" and "evolution"? The "standard scientific theory" meaning of "evolution" is that "human beings have developed over millions of years from less advanced forms of life, but God had no part in this process":

"Facing such a reality, perhaps we should not be surprised at the results of a 2001 Gallup poll confirming that 45 percent of Americans believe `God created human beings pretty much in their present form at one time within the last 10,000 years or so'; 37 percent prefer a blended belief that `human beings have developed over millions of years from less advanced forms of life, but God guided this process'; and a paltry 12 percent accept the standard scientific theory that `human beings have developed over millions of years from less advanced forms of life, but God had no part in this process.'" (Shermer, M.B., "The Gradual Illumination of the Mind," Scientific American, February 2002. My emphasis)

Note that it is not merely "human beings have developed over millions of years from less advanced forms of life" because if "God guided this process" then that would not be "evolution" in the "standard scientific theory" meaning of the term.

This is confirmed by the leading evolutionist, Richard Dawkins, citing Charles Darwin, that "any evolution that had to be helped over the jumps by God was not evolution at all" (my emphasis):

"Darwin ... wrote in a letter to Sir Charles Lyell, the leading geologist of his day: `If I were convinced that I required such additions to the theory of natural selection, I would reject it as rubbish...I would give nothing for the theory of Natural selection, if it requires miraculous additions at any one stage of descent.' [Darwin, C.R., letter to C. Lyell, October 11, 1859, in Darwin, F., ed., "The Life and Letters of Charles Darwin," [1898], Basic Books: New York NY, Vol. II., 1959, reprint, pp.6-7]. This is no petty matter. In Darwin's view, the whole point of the theory of evolution by natural selection was that it provided a non-miraculous account of the existence of complex adaptations. For what it is worth, it is also the whole point of this book. For Darwin, any evolution that had to be helped over the jumps by God was not evolution at all." (Dawkins, R., "The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design," W.W Norton & Co: New York NY, 1986, pp.248-249. Emphasis original)

>Do you agree with the possibility that at one point a greater being could have set the world in motion and evolution naturally took hold from there?

This is why it is important to define your terms. The point is that if "a greater being" (e.g. God) "set the world in motion and evolution naturally took hold from there" then that is not "evolution" in the scientific sense of the term.

>After a bit of research, I have not found any information regarding how the first life, which we all evolved from was created in the first place.

See above on clarifying your terms. Your sentence "which we all evolved from was created in the first place" requires clarification. What do you mean by "evolved" and "created"?

I am not asking you to answer this question to me (since my long-standing policy is not to get involved in private discussions about creation/evolution/design issues), but to answer it to yourself.

But if your statement is, "I have not found any information regarding how the first life" originated by a fully naturalistic process (which is what "God had no part in this process" means) then there is no such information.

Perhaps the easiest way to demonstrate that is the case of leading atheist philosopher, Antony Flew, author of a book, "Darwinian Evolution," who, based on the inordinate difficulty of "even to begin to think about constructing a naturalistic theory of the evolution of that first reproducing organism" and "the almost unbelievable complexity of the arrangements which are needed to produce (life)," concluded that "intelligence must have been involved":

"A British philosophy professor who has been a leading champion of atheism for more than a half-century has changed his mind. He now believes in God -- more or less -- based on scientific evidence, and says so on a video released Thursday. At age 81, after decades of insisting belief is a mistake, Antony Flew has concluded that some sort of intelligence or first cause must have created the universe. A super-intelligence is the only good explanation for the origin of life and the complexity of nature, Flew said in a telephone interview from England. Flew said he's best labeled a deist like Thomas Jefferson, whose God was not actively involved in people's lives. ...,' he said. `It could be a person in the sense of a being that has intelligence and a purpose, I suppose.' ... Over the years, Flew proclaimed the lack of evidence for God while teaching at Oxford, Aberdeen, Keele, and Reading universities in Britain, in visits to numerous U.S. and Canadian campuses and in books, articles, lectures and debates. There was no one moment of change but a gradual conclusion over recent months for Flew, a spry man who still does not believe in an afterlife. Yet biologists' investigation of DNA `has shown, by the almost unbelievable complexity of the arrangements which are needed to produce (life), that intelligence must have been involved,' Flew says in the new video, `Has Science Discovered God?' .... The first hint of Flew's turn was a letter to the August-September issue of Britain's Philosophy Now magazine. `It has become inordinately difficult even to begin to think about constructing a naturalistic theory of the evolution of that first reproducing organism,' he wrote. ... if his belief upsets people, well `that's too bad,' Flew said. `My whole life has been guided by the principle of Plato's Socrates: Follow the evidence, wherever it leads.' ... Flew told The Associated Press his current ideas have some similarity with American `intelligent design' theorists, who see evidence for a guiding force in the construction of the universe. He accepts Darwinian evolution but doubts it can explain the ultimate origins of life." (Ostling, R.N., "Atheist Philosopher, 81, Now Believes in God," Livescience/Associated Press, 10 December 2004)

>The shakiness of current published studies on this does not impress me.

I would be surprised it it impresses anyone! It certainly did not impress Antony Flew.

>Also, how do you react to the criticism of evolution that it does not explain how complex structures, such as the eyeball, could have evolved in a single genetic mutation because if it evolved over a period of time, it would have no use until complete?

This is what made me suspect that you might have me confused with an evolutionist. I don't "react to the criticism of evolution." I make "criticism of evolution"! I am currently taking a one-year detour from writing a book, "Problems of Evolution," to compile an `Evolution Quotes Book' being an ebook of my ~10,000 online evolution quotes classified into topics.

The problem for evolution is not to "explain how complex structures, such as the eyeball, could have evolved in a single genetic mutation" since: 1) evolutionist don't claim that it did; and 2) the problem that needs explaining is not just any part of the eye, but the entire visual system.

As R.L. Gregory, Professor of Neuropsychology at the Brain and Perception Laboratory, University of Bristol, pointed out, the problem is not just "what use is a half-made lens?" but "What use is a lens giving an image, if there is no nervous system to interpret the information?" and "How could a visual nervous system come about before there was an eye to give it information?" given that "In evolution there can be no master plan, no looking ahead to form structures which, though useless now, will come to have importance when other structures are sufficiently developed":

"The problem of how eyes have developed has presented a major challenge to the Darwinian theory of evolution by Natural Selection. We can make many entirely useless experimental models when designing a new instrument, but this was impossible for Natural Selection, for each step must confer some advantage upon its owner, to be selected and transmitted through the generations. But what use is a half-made lens? What use is a lens giving an image, if there is no nervous system to interpret the information ? How could a visual nervous system come about before there was an eye to give it information? In evolution there can be no master plan, no looking ahead to form structures which, though useless now, will come to have importance when other structures are sufficiently developed. And yet the human eye and brain have come about through slow painful trial and error." (Gregory, R.L., "Eye and Brain: The Psychology of Seeing," [1966], Weidenfeld & Nicolson: London, Second edition, 1972, p.25)

But note that being an evolutionist, Prof. Gregory just assumes that "the human eye and brain have come about through slow painful trial and error," since: 1) they exist; and 2) `blind watchmaker' evolution is the only explanation remaining for their origin, given that intelligent design and/or creation by God are ruled out in advance as possibilities.

>I hope that you will engage me directly, as I am just a high school student seeking perspective on this issue, not some raving religious fanatic who will only see things one way. Thanks for your insight!!

Sorry, but I just don't have the time to "engage ... directly" anyone and everyone who wants me to. As I said, my long-standing policy is not to get involved in private discussions about creation/ evolution/design issues. I will usually answer only the first email (copying it to my blog), but not any subsequent emails. If you read my blog (and others listed in its side-pane) you will find over time that most of your questions will be addressed.

[...]

AN

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

Big Bang may have been a Big Bounce #1

Big Bang may have been a Big Bounce, ABC / Discovery News, Larry O'Hanlon, 24 May 2006 ...

[Graphic & legend see PhysOrg.com]

The Big Bang may have been a Big Bounce, say theorists searching for what preceded the birth of our own universe. [See also PhysOrg.com and the original at Discovery News.

I have split this post into two parts because I want to add some more comments from a Christian perspective about the Big Bang and what if there was a "before" it.]

... If their new mathematical simulations are correct, what came before the Big Bang was a previous universe a lot like our own. [And Oh, what a big "if"! How could any cosmologist know that his/her "mathematical simulations are correct" of what happened "before the Big Bang" (assuming there even can be such a `time' - see below) in "a previous universe"? There is no way to re-run the origin of the Universe to experimentally test such simulations. All that such simulations could do is be tweaked until they are consistent with the known evidence.

But then there are many cosmologists who each have their own, mutually exclusive, "mathematical simulations" that have been tweaked until they are consistent with the known evidence. The problem they all have is something that affects all historical sciences (i.e. sciences of past unique and unrepeatable events), and that is, "the problem of equifinality," namely "the fact that different processes can lead to similar end-forms":

"The problems of explanation in physical geography caused by the number of factors involved and their interaction, by the difficulties of scale, by the frequency of change and by the problem of deciphering the role of man as against that of nature are heightened by the fact that different processes can lead to similar end-forms - the problem of equifinality. When seeking an explanation for a particular phenomenon it is important to remember that, although certain phenomena appear to be broadly similar in type, their form may be an inadequate guide to their origin. One should not be dogmatic as to the origins of many natural phenomena. ... When conducting one's own fields investigations, therefore, it is necessary to adopt the principal of multiple working hypotheses, seeking to formulate and test as many explanations as possible." (Goudie A., "The Nature of the Environment," [1984], Basil Blackwell: Oxford UK, 1989, Second edition, 1990, reprint, p.340. Emphasis in original)

So there is simply no way that cosmologists could ever know that their particular theory of "what came before the Big Bang" was what actually happened.

That is assuming that there even can be a "before the Big Bang," which would be a time before time, a self-contradictory absurdity. Paul Davies points out that "it is not possible to extend space and time through ... a singularity" and therefore "the big bang must be the origin of time itself," therefore "there was no `before' for anything to happen in":

"Clearly, if the universe is growing bigger, it must have been smaller in the past. We can imagine running the great cosmic movie backwards until all the galaxies are squashed together. This compressed state corresponds to the time of the big bang, and in a certain sense the expansion of the universe can be considered as a vestige of that initial explosion. Today it is normal for cosmologists to claim that the universe began with the big bang. This weighty conclusion follows if you trace the expansion back in time to some idealized point of origin at which all the matter of the universe is concentrated in one place. Such a state of infinite density represents an infinite gravitational field and infinite spacetime curvature -i.e., a singularity. The big-bang singularity is similar to the situation at the center of a black hole that I described in the previous chapter, but lying in the past rather than the future. As it is not possible to extend space and time through such a singularity, it follows that the big bang must be the origin of time itself. People, especially journalists who get angry about scientists explaining everything, often ask: What happened before the big bang? If this theory is correct, the answer is simple: nothing. If time itself began with the big bang, there was no `before' for anything to happen in. Although the concept of time being abruptly `switched on' at some singular first event is a hard one to grasp, it is by no means new. Already in the fifth century, Augustine proclaimed that: `The world was made, not in time, but simultaneously with time.' [Augustine, "Confessions," Penguin, 1961, p.294] Keen to counter jibes about what God was doing before he made the universe, Augustine placed God outside of time altogether, making him the creator of time itself. ... the idea of time coming into being with the universe therefore fits very naturally into Christian theology. ... we shall see that recent ideas in quantum physics have changed our picture of the origin of time somewhat, but the essential conclusion remains the same: time did not exist before the big bang." (Davies, P.C.W., "About Time: Einstein's Unfinished Revolution", Penguin Books: London, 1995, pp.131-132. Emphasis original)

And Stephen Hawking noted that, "even if there were events before the big bang, one could not use them to determine what would happen afterward, because predictability would break down at the big bang" and so "we could not determine what happened beforehand" and "events before the big bang ... should not form part of a scientific model of the universe":

"All of the Friedmann solutions have the feature that at some time in the past (between ten and twenty thousand million-years ago) the distance between neighboring galaxies must have been zero. At that time, which we call the big bang, the density of the universe and the curvature of spacetime would have been infinite. Because mathematics cannot really handle infinite numbers, this means that the general theory of relativity (on which Friedmann's solutions are based) predicts that there is a point in the universe where the theory itself breaks down. Such a point is an example of what mathematicians call a singularity. In fact, all our theories of science are formulated on the assumption that space-time is smooth and nearly flat, so they break down at the big bang singularity, where the curvature of space-time is infinite. This means that even if there were events before the big bang, one could not use them to determine what would happen afterward, because predictability would break down at the big bang. Correspondingly, if, as is the case, we know only what has happened since the big bang, we could not determine what happened beforehand. As far as we are concerned, events before the big bang can have no consequences, so they should not form part of a scientific model of the universe. We should therefore cut them out of the model and say that time had a beginning at the big bang. Many people do not like the idea that time has a beginning, probably because it smacks of divine intervention. ... There were therefore a number of attempts to avoid the conclusion that there had been a big bang." (Hawking, S.W., "A Brief History of Time: From the Big Bang to Black Holes," [1988], Bantam: London, 1991, reprint, p.50) ]

It collapsed on itself, then some weird physics caused it to inflate into the universe we have today. Physicist Dr Abhay Ashtekar of Pennsylvania State University and team publish their results in a recent issue of Physical Review Letters. .... To peer into that unimaginable crush, Ashtekar and colleagues started again without assuming that the "fabric" of space-time continuum existed in the earliest moments of the universe. "The general belief is that the continuum may be just an approximation," says Ashtekar. ...[So their entire theory depends on that assumption, that there was no "space-time continuum" existing at "the earliest moments of the universe." But then how can they meaningfully speak of "space" and 'time" if there was none?]

Instead, the team applied what's called loop quantum gravity, a strategy that has been developed to join quantum physics with Einstein's General Relativity. ... Using this concept, the researchers concluded that a previous universe collapsed in on itself in a gigantic gravitational Big Crunch. Then, when the density of that crunch reached super astronomical values, gravity flipped into a repulsive force - another weird outcome of this physics - and inflated the new universe in which we live. [It sounds like this "loop quantum gravity ... strategy" just an excercise in circular reasoning? That is, it is hand-crafted' to get around the singularity? If so, it cannot non-circularly be used to prove that there was no singularity.]

"It's long been speculated that as you get to the Big Bang, quantum theory was going to be important," says physicist Dr Jorge Pullin of Louisiana State University. It's also been speculated that if you could work out the equations, you'd probably see that the Big Bang was a Big Bounce, he says. But this is the first time that anyone has actually done a thorough job working through the physics back through the Big Bang, he says. ... As for what it tells us about the previous universe, it's not much, says Pullin. [This is because of astrophysicist Robert Jastrow's point that, "in the first moments of its existence the Universe was compressed to an extraordinary degree" and "The shock of that instant must have destroyed every particle of evidence that could have yielded a clue to the cause" and even if something "may have existed before our Universe appeared" (assuming that there can be a "before") "if it did, science cannot tell what ... it was":

"Consider the enormity of the problem. Science has proven that the Universe exploded into being at a certain moment. It asks, What cause produced this effect? Who or what put the matter and energy into the Universe? Was the Universe created out of nothing, or was it gathered together out of preexisting materials? And science cannot answer these questions because, according to the astronomers, in the first moments of its existence the Universe was compressed to an extraordinary degree, and consumed by the heat of a fire beyond human imagination. The shock of that instant must have destroyed every particle of evidence that could have yielded a clue to the cause of the great explosion. An entire world, rich in structure and history, may have existed before our Universe appeared; but if it did, science cannot tell what kind of world it was. A sound explanation may exist for the explosive birth of our Universe; but if it does, science cannot find out what the explanation is. The scientist's pursuit of the past ends in the moment of creation. This is an exceedingly strange development, unexpected by all but the theologians. They have always accepted the word of the Bible: In the beginning God created heaven and earth." (Jastrow, R., "God and the Astronomers," [1978], W.W. Norton: New York NY, Second edition, 1992, p.106) ]

"The only thing you can conclude is that the bounce occurs," he says. [No - one cannot "conclude ... that the bounce occurs" if that is a starting assumption of the theory, and of the "loop quantum gravity ... strategy." In that case it would just be circular reasoning, concluding to be true what one had already assumed to be true in the premises. To be continued in part #2.]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book

Re: Progressive Creation & common descent #3

Craig (copy to my blog, CreationEvolutionDesign, as agreed).

Thanks for the opportunity to comment on your draft paper, Similarities and Differences between Old-Earth Views: Progressive Creation & Evolutionary Creation . I will comment [bold and in square brackets] only on those sections that mention me ... .

[Continued from part #2]

Scientific Questions about Evolution
The previous three sections, beginning with Peter Ruest in Evolutionary Creation with Intelligent Design, ask questions about unguided naturalistic evolution. For example,
According to Peter Ruest a process of unguided evolution would be, "for lack of time, unsuccessful in mere random-walk trials; ... random mutations, followed by natural selection, cannot produce all biological functions and an entire biosphere [due to] the huge size of the possibility space; ... specific direction is required. (2001)" and "in two respects, it is still unknown whether the known mechanisms of evolution are adequate: First, the origin of life... Second, the evolutionary emergence of novel functions... (2005)" Stephen Jones claims "a fully naturalistic mechanism [is] the weakest part of their position," and I think we should ask "important questions about rates of change, irreducible complexity,..." [Agreed. As the quotes of Behe and Dawkins citing Darwin (in part #1) showed, common ancestry is not essential for evolution. What "evolution" requires is a fully naturalistic mechanism.

---

In fact, single common ancestry is the worst-case scenario for evolution, as per this new section of my "Why I (a Creationist) Accept Common Ancestry" page:

Single common ancestry is the worst-case scenario for evolution!

By that I mean that all life descending from one origin of life is evolutionists least preferred option. Evolutions would not have been falsified if life had turned out to be polyphyletic, i.e. deriving from multiple, separate, original ancestors. In fact evolutionists would be delighted if they found an entirely different form of life on Earth that could not possibly have arisen from a common ancestor of all other forms of life (e.g. based on D-amino acids, an entirely different genetic code, etc). That is in fact what they are trying to find extraterrestrially, in order to "transform the origin of life from a miracle to a statistic":

"Nevertheless, the application of this method to areas where we have little knowledge is essentially an act of faith. For example, one exercise which we shall later carry through is to estimate the likelihoods of the origin of life in a suitable planetary system, the origin of intelligence, the origin of technical civilization, etc. Such estimates are, either implicitly or explicitly, based upon terrestrial experience. But it is dangerous to extrapolate from one example. This is why, for example, the discovery of life on one other planet-e.g., Mars-can, in the words of the American physicist Philip Morrison, of the Massachusetts Institute of Technology, `transform the origin of life from a miracle to a statistic.'" (Shklovskii, I.S. & Sagan, C.E., "Intelligent Life in the Universe," [1966], Picador: London, 1977, p.358)

Darwin himself in his Origin of Species was ambivalent whether life originated in "a few forms or ... one":

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." (Darwin C.R., "The Origin of Species by Means of Natural Selection: Or The Preservation of Favoured Races in the Struggle for Life," [1859], First Edition, Penguin: London, 1985, reprint, p.459. My emphasis)

The creationist theologian Floyd E. Hamilton observed that "a world order in which every species was different from every other species [would] be far harder to attribute to one God":

"It is the habit of some evolutionists to sneer at such a line of argument and to inquire why an omnipotent God should be obliged to create so many animals on the same general plan. Such statements seem to assume that God could not or would not create individuals with common points of similarity and with their bodies built on the same general scheme, but that if He created at all He must have created every separate individual species of plant and animal with no points of similarity with other species! We might with justice reply to such an objection with the question as to why He should not create them similar? As a matter of fact, however, would not a world order in which every species was different from every other species be far harder to attribute to one God than the world order with its similarities such as we see around us?" (Hamilton, F.E., "The Basis of Evolutionary Faith: A Critique of the Theory of Evolution," James Clarke & Co: London, 1931, pp.149-150)

Similarly, the creationist "biotic message" theorist Walter ReMine points out that life exhibits "The Unifying Message," that "This system of living objects was constructed by a single source (e.g., a common designer)" (my emphasis):

"Why would a designer create life to look like evolution? What possible motive could a designer have to be misleading? Is the designer trying to trick us? This is now the evolutionists' standard argument. This book responds by showing they do not truly know their own theory. Life was designed to look unlike evolution, and to see this, one must understand evolutionary theory deeply. ... message theory ... claims that life was intentionally designed to communicate a message. .... Life was made by no ordinary designer, but by one with unusual intentions. Identifying these intentions resolves the difficulties. Features of life that seemed inexplicable become understandable once the designer's goal is recognized. That goal was consistently pursued by the designer. Throughout nature it guided design choices and shaped the pattern of life. The data admit to no other solution. The pattern is intricate, yet so consistent it could not result from thoughtlessness. The pattern was premeditated. It was designed intentionally to meet a single-minded goal. The designer's goal was a reasonable one, carried out in a reasonable way and with meticulous care. Ironically, evolution is central to that goal. Life was designed to thwart evolutionary explanation. ... Life could have looked like an art gallery with many artists - yet it does not. This is not happenstance. It is premeditated design. It is a major factor in message theory. All life is linked together by a complex web of similarities. Life looks like the product of a single designer. ... Message theory says nature was intentionally constructed to look this way. ... The biotic message is the sum of the unifying and non-naturalistic messages. The Unifying Message: `This system of living objects was constructed by a single source (e.g., a common designer).' ... The Non-naturalistic Message: `This system of living objects did not result from a naturalistic (evolutionary) process.'" (ReMine, W.J., "The Biotic Message: Evolution Versus Message Theory," St. Paul Science: Saint Paul MN, 1993, pp.17-19, 22. Emphasis original)

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

Re: Progressive Creation & common descent #2

Craig (copy to my blog, CreationEvolutionDesign, as agreed).

Thanks for the opportunity to comment on your draft paper, Similarities and Differences between Old-Earth Views: Progressive Creation & Evolutionary Creation . I will comment [bold and in square brackets] only on those sections that mention me ... .

[Continued from part #1]

Scientific Evidence for Common Descent
Peter Ruest says, "The strongest evidence for common descent of different species consists of shared errors, like certain mobile genetic elements inserted at exactly corresponding positions in their DNAs. ... As a consequence of the extensive genome sequencing efforts of the last few years, the 'fact of evolution," which has been touted for almost one hundred fifty years without stringent support, now at last has become virtually incontrovertible. (Sep 2005 in PSCF, not yet available on the web)"
Dick Fischer: "It is one thing to suggest that God may have modeled our DNA along the same lines as lower animals, such that similarities are due to like genes ordering a protein sequence serving a like function. It is quite another to assert that God also incorporated all the excess nonfunctioning baggage. (source available later)" [The source and quote is on my page, "Why I (a Creationist) Accept Common Ancestry " page, under "Evidence and arguments that lead me to accept common ancestry ," "Vitamin C pseudogene ":

"An examination of the human DNA molecule, the genetic blueprint of man, shows that many of the same sorts of genes and gene sequences are found in lower animals. Some creationists would say this is not surprising. Since man has many of the same physiological functions as lower animals, our DNA naturally would carry comparable information. Thus the argument has been made that any resemblances in DNA mean only that God used similar gene sequences to order similar functions. Although there may be a commonality of design, as the argument goes, that does not prove common descent. ... The case for common design but no common descent becomes suspect when the entire human DNA sequence is analyzed, and copying errors are found in the same places in the DNA of non-humans. In addition to genes that function normally, we have nonfunctioning genes as well, called `pseudogenes.' Our DNA sequence is a complicated set of instructions that appears to have a long history of replications, and therefore contains an abundance of pseudogenes. Humans have pseudogenes incorporated along the entire DNA sequence that can also be found in other animals, i.e., the chimpanzee and gorilla. It is one thing to suggest that God may have modeled our DNA along the same lines as lower animals, such that similarities are due to like genes ordering a protein sequence serving a like function. It is quite another to assert that God also incorporated all the excess nonfunctioning baggage too ." (Fischer, D., "The Origins Solution: An Answer in the Creation-Evolution Debate ," Fairway Press: Lima OH, 1996, pp.64-65)]

Stephen Jones: With progressive independent creations, "'God also incorporated all the excess nonfunctioning baggage' in each separate creation from scratch, to deliberately create an appearance of descent, that never actually happened. But this is the same `appearance of age' problem of Philip Gosse's Omphalos , which claimed (in effect) that each separate creation, object bore false witness to past processes, which had never taken place. (from Section 8)" {more about Creation with Appearance of Age} Evidence for common descent "is a tie-breaker between the two possible creationist/intelligent design positions: design without descent, i.e. separate ex nihilo and de novo creations; and design with descent (or descent with design), i.e. mediate creations." [I later added under the same "Vitamin C pseudogene " heading, this quote by the late Colin Patterson, which points out that "in tracing the texts of ancient authors, the best evidence that two versions are copies one from another or from the same original is when both contain the same errors":

"Darwin could not possibly have predicted that the hereditary material (of which he knew nothing) would turn out to be littered with ... meaningless repeated sequences like the shared Alu sequences in apes and humans ... An interesting argument is that in the law courts (where proof `beyond reasonable doubt' is required), cases of plagiarism or breach of copyright will be settled in the plaintiff's favour if it can be shown that the text (or whatever) is supposed to have been copied contains errors present in the original. Similarly, in tracing the texts of ancient authors, the best evidence that two versions are copies one from another or from the same original is when both contain the same errors. A charming example is an intrusive colon within a phrase in two fourteenth-century texts of Euripides: one colon turned out to be a scrap of straw embedded in the paper, proving that the other text was a later copy. Shared pseudogenes, or shared Alu sequences, may have the same significance - like shared misprints they can have come about only by shared descent." (Patterson, C., "Evolution ," [1978], Cornell University Press: Ithaca NY, Second edition, 1999, p.117).

With progressive creation by modification, a new species is created by genetic modification but most of the original genetic material is not modified, and the parent/offspring relationships are retained. This is consistent with evidence for common descent - such as a shared genetic code (in most species), structures that seem vestigial, homologous structures (like bat wings, whale flippers, dog paws, and panda thumbs) that seem to be "variations on a theme" derived from previously existing structures, similarities in gene sequences (ranging from essential developmental genes to nonfunctional pseudogenes) in different species, and "molecular clock" correlations - that is often claimed as evidence against progressive creation. With independent creations, sometimes there might be a logical reason for a designer to re-use functional components (including genes) from an existing organism in a newly created organism. But in most cases, especially with pseudogenes and genetic errors, a more plausible explanation is a history of common descent, which is consistent with either natural evolution or progressive creation by modification. [Agreed. I distinguish between Progressive (Fiat) Creation, as advocated by Hugh Ross, where `basic kinds' are created ex nihilo (out of nothing) or de novo (new, out of existing material with no genealogical continuity); and Progressive (Mediate) Creation, where all taxa (in the Bible the original Hebrew word min which is translated "kind," - e.g. Genesis 1:11-12,21,24 - has the same broad meaning as "kind" has in English, and can therefore correspond to any taxonomic category, from species upwards) are created (either naturally or supernaturally) by modification, and therefore out of existing material with genealogical continuity.

I obtained the term from this quote of the great 19th century evangelical Presbyterian theologian, Charles Hodge (a contemporary of Darwin and perhaps his greatest theologian critic), who distinguished between an "immediate creation," where "God created the universe out of nothing by the word of his power, which creation was instantaneous" and a "mediate , progressive creation," where God "form[ed] out of preexisting material" and "working in union with second causes":

"Mediate and Immediate Creation. But while it has ever been the doctrine of the Church that God created the universe out of nothing by the word of his power, which creation was instantaneous and immediate, i. e., without the intervention of any second causes; yet it has generally been admitted that this is to be understood only of the original call of matter into existence. Theologians have, therefore, distinguished between a first and second, or immediate and mediate creation. The one was instantaneous, the other gradual; the one precludes the idea of any preexisting substance, and of cooperation, the other admits and implies both. There is evident ground for this distinction in the Mosaic account of the creation. ... It thus appears that forming out of preexisting material comes within the Scriptural idea of creating. ... There is, therefore, according to the Scriptures, not only an immediate, instantaneous creation ex nihilo by the simple word of God, but a mediate, progressive creation; the power of God working in union with second causes." (Hodge, C., "Systematic Theology ," [1892], James Clark & Co: London, Vol. I, 1960, reprint, pp.556-557. Emphasis original)]

A theory proposing creations by genetic modification (instead of independent creations) increases the credibility of questions about naturalistic evolution:
In Logical Principles for Evaluating Evolutions I explain that "full common descent is only one component of naturalistic evolution, which could be false even if common descent was true... because a discontinuity in descent is only one of several possible ways that evolution might be false. ... Logical scientific evaluation provides support for the plausibility of a full common descent, so arguing against descent is counter-productive (in building a case for design) because this will focus attention on aspects of biology where the evidence is consistent with neo-Darwinian theory, and will distract attention from important questions - about rates of change, irreducible complexity,... - where evidence indicates that a theory of 100%- Natural Total Macro-E may be incorrect."

Stephen Jones, consistent with logical principles of evaluation, says: "I have myself found from a decade of debating evolutionists, that what really rattles them is a creationist like me who accepts common ancestry (the strongest part of their position), and challenges that it was always and everywhere a fully naturalistic mechanism (the weakest part of their position)." [Agreed. This is consistent with the evolutionists' antagonism to Behe, even though he accepts common ancestry. On a personal note, after I accepted common ancestry in 1995 , it made no difference to the evolutionists-they still regarded me as a creationist, as I did myself.]

[Continued in part #3]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

Re: Progressive Creation & common descent #1

Craig (copy to my blog, CreationEvolutionDesign, as agreed).

Thanks for the opportunity to comment on your draft paper, Similarities and Differences between Old-Earth Views: Progressive Creation & Evolutionary Creation . I will comment [bold and in square brackets] only on those sections that mention me, i.e. I won't comment on "Evolutionary Creation". The comprehensiveness of my response and the pedantic inclusion of hyperlinks and quotes is mainly for the benefit of readers of my blog (some of whom I assume are just starting in this controversy and are therefore unfamiliar with some terms and names). I don't expect you to include any of it in your page, but you are welcome to do so. Because of its length, I will break this post into two or more parts on my blog. It will require some conversion before it can be posted to my blog, so it may not appear there until tomorrow.

---

Similarities and Differences between Old-Earth Views :
Progressive Creation & Evolutionary Creation
by Craig Rusbult, Ph.D.

[...]

Progressive Creation and Common Descent
How should we define evolution and creation? evolutionary creation is an old-earth view of creation, so how does it differ from what is usually called old-earth creation or progressive creation? Two possible differences are full common descent and totally natural process.

Stephen Jones accepts full common descent [I prefer the term "universal common ancestry" or " universal common descent " because they are terms I am more familiar with in the scientific literature. By that I mean that I accept (as Mike Behe does) that "all organisms share a common ancestor":

"Evolution is a controversial topic, so it is necessary to address a few basic questions at the beginning of the book. Many people think that questioning Darwinian evolution must be equivalent to espousing creationism. As commonly understood, creationism involves belief in an earth formed only about ten thousand years ago, an interpretation of the Bible that is still very popular. For the record, I have no reason to doubt that the universe is the billions of years old that physicists say it is. Further, I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it. I greatly respect the work of my colleagues who study the development and behavior of organisms within an evolutionary framework, and I think that evolutionary biologists have contributed enormously to our understanding of the world. Although Darwin's mechanism-natural selection working on variation- might explain many things, however, I do not believe it explains molecular life. I also do not think it surprising that the new science of the very small might change the way we view the less small." (Behe, M.J., "Darwin's Black Box : The Biochemical Challenge to Evolution," Free Press: New York NY, 1996, pp.5-6)]

but he doesn't think the creation process was totally natural. [That's correct. Although I accepted universal common ancestry in 1995 , my thinking was clarified by the following 1996 quote from Christian philosopher Del Ratzsch , showing that common ancestry and supernatural intervention by God are not mutually exclusive:

"Suppose contemporary evolutionary theory had blind chance built into it so firmly that there was simply no way of reconciling it with any sort of divine guidance. It would still be perfectly possible for theists to reject that theory of evolution and accept instead a theory according to which natural processes and laws drove most of evolution, but God on occasion abridged those laws and inserted some crucial mutation into the course of events. Even were God to intervene directly to suspend natural law and inject essential new genetic material at various points in order to facilitate the emergence of new traits and, eventually, new species, that miraculous and deliberate divine intervention would by itself leave unchallenged such key theses of evolutionary theory as that all species derive ultimately from some common ancestor. Descent with genetic intervention is still descent-it is just descent with nonnatural elements in the process." (Ratzsch, D.L., "The Battle of Beginnings : Why Neither Side is Winning the Creation-Evolution Debate," InterVarsity Press: Downers Grove IL, 1996, pp.187-188)]

He calls himself an old-earth progressive creationist because "common ancestry [common descent] is not uniquely evolution" and "does not preclude supernatural intervention" and "if there has been any supernatural intervention then it is not evolution but creation" so (and here he cites Phillip Johnson) [Perhaps more to the point, I also cite Dawkins quoting Darwin, that "miraculous additions at any one stage of descent," i.e. "any evolution that had to be helped over the jumps by God was not evolution at all ." (my emphasis):

"The Duke of Argyll, for instance, accepted the evidence that evolution had happened, but he wanted to smuggle divine creation in by the back door. He wasn't alone. Instead of a single, once and for all creation in the Garden of Eden, many Victorians thought that the deity had intervened repeatedly, at crucial points in evolution. Complex organs like eyes, instead of evolving from simpler ones by slow degrees as Darwin had it, were thought to have sprung into existence in a single instant. Such people rightly perceived that such instant 'evolution', if it occurred, would imply supernatural intervention: that is what they believed in. .... Darwin perceived this too. He wrote in a letter to Sir Charles Lyell, the leading geologist of his day: `If I were convinced that I required such additions to the theory of natural selection, I would reject it as rubbish...I would give nothing for the theory of Natural selection, if it requires miraculous additions at any one stage of descent.' [Darwin C.R., letter to C. Lyell, October 11, 1859, in Darwin F., ed., "The Life and Letters of Charles Darwin," [1898], Basic Books: New York NY, Vol. II., 1959, reprint, pp.6-7]. This is no petty matter. In Darwin's view, the whole point of the theory of evolution by natural selection was that it provided a non -miraculous account of the existence of complex adaptations. For what it is worth, it is also the whole point of this book. For Darwin, any evolution that had to be helped over the jumps by God was not evolution at all." (Dawkins R., "The Blind Watchmaker ," W.W. Norton, 1986, pp.248-249. Emphasis Dawkins')]

"creationists can believe in common ancestry." He also quotes "evolutionists [who] regard those who accept common ancestry as creationists, if they don't accept that the mechanism was fully naturalistic. For example, leading Intelligent Design theorist, Michael Behe accepts 'that all organisms share a common ancestor,' but he is regarded by evolutionists as a creationist, because he argues that natural processes alone were insufficient to explain life." [For example, Darwinist philosopher Robert Pennock classifies Behe among the "creationists":

"A more powerful movement is gaining strength within the Tower and is beginning to take the lead in the battles against evolution in the field. This is the group of creationists that advocates `theistic science' and promotes what they call -intelligent-design theory.' Creationism-watchers have called the advance guard of intelligent-design creationism (IDC) the `upper tier' of creationists because, unlike their earlier counterparts, they carry advanced degrees from major institutions, often hold positions in higher education, and are typically more knowledgeable, more articulate, and far more savvy. ... Among the more well-known names to sign on to the crusade are Michael Behe (Lehigh University) ... " (Pennock, R.T., "Tower of Babel: The Evidence Against the New Creationism," The MIT Press: Cambridge MA, 1999, p.29)

even though Pennock knows that Behe accepts common ancestry:

"Intelligent-design theorist Michael Behe has said that he has no reason to doubt the truth of common descent, but he does doubt the power of natural selection to shape the full range of biological complexities. In Darwin's Black Box he claims to have found a number of such `complex organs' to prove his case. This is clearly an important claim. ... So what does Behe have to say? We already have a fairly clear idea given our earlier discussions of critical passages from Darwin's Black Box Behe hopes to show the impotence of Darwinism by pointing out purportedly profound explanatory gaps. Trying to do this is nothing new. ICR's Duane Gish has tried to do this by pointing out gaps in the fossil record. ... Indeed, as we saw, almost every creationist attack proceeds in the same way, by citing something that Darwinism supposedly cannot explain." (Pennock, 1999, p.264)

So to the Darwinists, Behe, even though he "has said that he has no reason to doubt the truth of common descent," is lumped into the same category as the "ICR's Duane Gish "! The decisive factor that makes one a creationist in Darwinst eyes is not acceptance or reejction of common ancestry, but whether one maintains that the process has not been fully naturalistic.]

{more about the views of Jones }
I also question a common definition of evolution: "Advocates of naturalistic evolution... often define the essence of evolution as full common descent. But full descent is accepted by Michael Behe, so why is there such a strong reaction against Behe... if the essence of evolution is descent, rather than a history that is 100% natural?"

My view of biological development by progressive creation, which is similar to the view of Jones, differs from proposals for independent creations "from scratch" so a new species would not necessarily have any relationships with previously existing species. Instead, I propose creations by modification of the genetic material (by changing, adding, or deleting it) for one or more members of an existing species. These two theories are similar, since both propose miraculous-appearing creations (independent or by modification) occurring progressively through time; but there are important scientific differences, and I think the scientific evidence strongly favors creation by modification. [I would add that the Biblical evidence favours it too. After the original creation ex nihilo (out of nothing) of the raw materials of the universe in Genesis 1:1 , God thereafter creates, makes and forms, ex materia (out of existing material). Even Adam and Eve were not made out of nothing, but out of the ground (Genesis 2:7) and Adam's body (Genesis 2:22), respectively].

[Continued in part #2]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

Comments moderation has been turned on

About a month or so ago, I became aware of a new Blogger feature of comments moderation:

[Graphic: "It's the law," University of Wisconsin- Parkside]

Blogger Comments Moderation to Control Spam Blogger has now introduced the ability to moderate comments on your blog. This is a wonderful way to control comment spam on your blog and a much desired feature. Now you can approve or reject posted comments before it goes live on your blog. And catch any comment spam before it reaches your page. You can choose to moderate your comments via either email or from blogger.com. The feature needs to be enabled from the Settings | Comment tab. Comments that have already been published or rejected are removed from the moderation list. Rejected comments are deleted and cannot be recovered. Only blog administrators will be able to moderate comments.

I decided at the time that I would switch that on, if another time-wasting or abnoxious comments poster turned up on CED. Such a time-wasting (not necessarily obnoxious) poster (who is well-known to me, and I to him, from our previous debates on a number of discussion groups) has turned up on CED (see comments here, here, and here). I have therefore now turned comment moderation on.

I have accordingly modified CED's one and only policy as follows:

1) Anyone can comment, but comment moderation has been turned on. Low-quality, time-wasting, off-topic, spam, nasty, or defamatory comments will be rejected.

PS: the following long quote, which I have posted before, expresses very well my view of the difference between comments on a blog and replies on a discussion group, i.e. "The word comment for weblogs implies that the author does not need further participation to reach a goal - comment if you want."

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

---

"Worlds are colliding, people. Your friendly neighborhood message board is not alone in the online community world any longer. This year we are celebrating the 25th anniversary of the message board. Since that time, interfaces have improved, email has been integrated, but comparatively little has changed regarding the basic structure and intent of the message board. However, in the last few years, we've seen the arrival of a new set of tools and processes that offer additional opportunities for message board-based online communities. The appearance of weblogs have left many observers, including me, wondering about the differences between the two technologies and how they will be used inside online communities. Are weblogs really that different from message boards? How? Note: Below I make assumptions and generalizations about message board and weblog design. My goal is to discuss what I think are standard practices across the technologies. I realize that the assumptions below may or may not match with your experiences and I present them as suggestions. .... First, I believe that weblogs and message boards are different .... Perhaps the most compelling difference in weblogs and message boards is the locus of control. Weblogs are individual or small group resources- the control of content and value is driven by a single person or small group. Message Boards are group resources- the control of content and value is shared equally across all users. ... The locus of control matters most in defining who can post new topics, which drive the content of the resource. In weblogs, this role is centralized, with new topics being presented by a defined and focused person or small group. This centralization facilitates focus and direction on behalf of the webloggers. In many message boards, all members usually have the ability to create new topics. This decentralization allows for more emergent and unpredictable directions that may reflect the group's desires as a whole. ... The centralized vs. decentralized nature of the technologies fit nicely into two distinct intentions. With weblog authorship being centralized inside a community, they can easily become news sources, where trusted individuals provide accounts of events and information. The decentralized nature of message boards works well to accumulate group input and facilitate collaboration and group decision making. ... Weblogs and Message Boards both allow for responses from the community - new topics can be responded-to by others. Weblog topics have comments and message board topics have replies. This subtle difference in syntax reveals a difference in the roles. The word comment for weblogs implies that the author does not need further participation to reach a goal - comment if you want. Reply, on the other hand, implies that participation is explicitly requested by the poster. A discussion is not a discussion without a reply. ... The order and presentation of topics across message boards and weblogs relate another difference. Weblogs are consistently arranged with the most recently posted topics at the top of the page, regardless of new comments. With a message board, the posting of replies can govern the presentation of the originating topic - topics with new replies are often presented at the top (but not always, of course). This illustrates the relative importance of replies in message board discussions. Replies can keep a discussion alive and at the top of the page for months or even years in some cases. ... Since a weblog depends on a single person or select group, the likelihood of off- topic or inappropriate topics (or responses) is greatly reduced. Further, as discussed previously, weblogs do not depend on responses to provide value. So, in situations where spam or flame wars are a problem, weblogs can turn-off comments and depend on new topics from the webloggers for value. Being group resources, message boards do not have the luxury to turn off replies, but do prevent problems with moderation of each new topic or response. ... How topics are archived and organized provides another look at the differences. Often, each new topic in a weblog is assigned to a category that is used to organize the topics for future reference. A single weblog may have many categories that archive and organize posts that were originally presented on the weblogs' front page. Message boards are often presented with multiple starting points for creating a new discussion. The member chooses the appropriate location to post a new topic, depending on subject matter. In this way, message boards create multiple "front pages", spreading the presentation of new topics across locations/content buckets in the community." (LeFever, L., "What are the Differences Between Message Boards and Weblogs?," Common Craft weblog, August 24, 2004. Emphasis in original)

Planets Found in Potentially Habitable Setup?

Planets Found in Potentially Habitable Setup, SPACE.com, Ker Than, 17 May 2006 ...

[Graphic: "HD 69830/HR 3259," Sol Company.]

Three medium-sized planets of roughly the same mass as Neptune have been discovered around a nearby Sun-like star, scientists announced today. [See also ABC/Discovery, National Geographic, New Scientist, USA Today, etc.] The planets were discovered around HD 69830, a star slightly less massive than the Sun located 41 light-years away in the constellation Puppis (the Stern), using the ultra-precise HARPS spectrograph on the European Southern Observatory's 3.6-meter La Silla telescope in Chile. The finding, detailed in the May 18 issue of the journal Nature, marks a first for astronomers because previously discovered multi-planet solar systems besides our own contain at least one giant, Jupiter-sized planet. "For the first time, we have discovered a planetary system composed of several Neptune-mass planets," said study team member Christophe Lovis of the Geneva Observatory in Switzerland. The setup is similar to our own solar system in many ways: The outermost planets is located just within the star's habitable zone, where temperatures are moderate enough for liquid water to form, and the system also contains an asteroid belt. The newly discovered planets have masses of about 10, 12 and 18 times that of Earth and they zip around the star in rapid orbits of about 9, 32 and 197 days, respectively ... [It is absurd (if not dishonest) to claim that a "planetary system composed of several Neptune-mass planets" which have "masses of about 10, 12 and 18 times that of Earth" and "zip around the star in rapid orbits of about 9, 32 and 197 days, respectively" is "similar to our own solar system" and is a "Potentially habitable set-up"!]

... In the early years of planet hunting, the wobble technique was sensitive enough to spot only large, massive planets because they produce more significant stellar wobbles. However, the technique has since been refined to the point where lower-mass planets can now be detected. [Well, astronomers have not yet found any truly Earth-size exoplanets, as yet. That could be because either: 1) they are there but not yet detected; 2) they are rare; or 3) they don't exist.]

I have scanned and placed on my website an amazing chapter out of a slim book I bought at a remainder stall, Professor Stuart Ross Taylor, "The Solar System: An Environment For Life?," in Walter, M., ed., et al., "To Mars and Beyond: Search for the Origins of Life," Art Exhibitions Australia: Sydney & National Museum of Australia: Canberra, Australia, 2001, pp.57-67. It reads like something out of The Privileged Planet, not by an Emeritus Professor of Planetary Science at the Australian National University! I intend to quote from that chapter as appropriate. However, I will quote Prof. Taylor's conclusion first, as it is appropriate to this post:

"These new discoveries reinforce the message from our own system. Nothing resembling our Solar System has been discovered. The conditions that existed to make our set of planets are not easily reproduced elsewhere. Indeed, no two planets in the Solar System are alike. Likewise, the 80-odd moons are also odd characters that defy efforts to put them into pigeonholes. So it should have come as no surprise that when nature tried elsewhere to build planets the end result was different. We are left with the conclusion that attempts to find some general formulae for recreating the detail of the Solar System are likely to be on the wrong track. Local accidents have predominated over general theories, just as some overlooked detail of the landscape may ruin the course of a battle that was planned according to the best principles of military strategy." (Taylor, S.R., "The Solar System: An Environment For Life?," in Walter, M., ed., et al., "To Mars and Beyond: Search for the Origins of Life," Art Exhibitions Australia: Sydney & National Museum of Australia: Canberra, Australia, 2001, p.67)

As will be seen by reading the online chapter, or when I post further quotes from it, it is increasingly likely that our Solar System, the Earth and life on it, are unique in the entire Universe!

Prof. Taylor seems to agree with that (or at least the unlikeihood of disproving it), because he said in 1999:

"When the remote chances of developing a habitable planet are added to the chances of developing both high intelligence and a technically advanced civilization, the odds of finding 'little green men' elsewhere in the universe decline to zero." (Taylor, S.R., in "Other stars, other worlds, other Life?," Holoscience, Views, 15 December 1999)

and discoveries since then have given him no reason to change his mind.]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

Massive duplication of genes may solve Darwin's 'abominable mystery', etc

Two different stories only six days apart, about the sudden origin of the Angiosperms (flowering plants), which was Darwin's "abominable mystery":

"The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery." (Darwin, C.R., Letter to J.D. Hooker, July 22nd 1879, in Darwin F. & Seward A.C., eds., "More Letters of Charles Darwin: A Record of His Work in a Series of Hitherto Unpublished Papers," John Murray: London, 1903, Vol. II, pp.20-21).]

[Graphic: The yellow water lily (Nuphar advena), Yi Hu, Penn State.]

Massive duplication of genes may solve Darwin's 'abominable mystery' about flowering plants, EurekAlert, 11-May-2006, Barbara K. Kennedy, Penn State ... [Also at ScienceDaily & PhysOrg.com.] The yellow water lily (Nuphar advena) shows evidence of an ancient genome duplication that may have been a key event in the evolution of flowering plants. Researchers from the Floral Genome Project at Penn State University, with an international team of collaborators, have proposed an answer to Charles Darwin's "abominable mystery": the inexplicably rapid evolution of flowering plants immediately after their first appearance some 140 million years ago. [If the origin of the angiosperms (a plant division - Anthophyta - equivalent to an animal phylum):

"Classification of Plants Plant biologists use the term division for the major plant groups within the plant kingdom. This taxonomic category corresponds to phylum, the highest unit of classification within the animal kingdom. Divisions, like phyla, are further subdivided into classes, orders, families, and genera ... Angiosperms: Division Anthophyta: Flowering plants" (Campbell, N.A., Reece, J.B. & Mitchell, L.G., "Biology," [1987], Benjamin/Cummings: Menlo Park CA, Fifth Edition, 1999, pp.549-550. Emphasis original)

one of the "four major periods of plant evolution":

"The fossil record chronicles four major periods of plant evolution, which are also evident in the diversity of modern plants ... Each period was an adaptive radiation that followed the evolution of structures that opened new opportunities on the land ... The fourth major episode in the evolutionary history of plants was the emergence of flowering plants during the early Cretaceous period in the Mesozoic era, about 130 million years ago. The flower is a complex reproductive structure that bears seeds within protective chambers called ovaries. This contrasts with the bearing of naked seeds by gymnosperms. The great majority of modern-day plants are flowering plants, or angiosperms (Gr. angion, `container,' referring to the ovary, and sperma, `seed')." (Campbell, et al., 1999, p.548. Emphasis original)

arose as the result of a "Massive duplication of genes," then it would not "solve Darwin's 'abominable mystery' about flowering plants" - it would confirm it! And indeed, falsify Darwin's theory (as a general theory), since: 1) this was a major new chapter in life's history; 2) which did not arise "by accumulating slight, successive, favourable variations" but by a "great or sudden modification":

"As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great or sudden modifications; it can act only by short and slow steps. Hence the canon of `Natura non facit saltum,' [nature does not make leaps] which every fresh addition to our knowledge tends to confirm, is on this theory intelligible." (Darwin, C.R., "The Origin of Species By Means of Natural Selection," 1872, Sixth Edition, Senate: London, 1994, pp.413-414. Parenthesis mine)]

By developing new statistical methods to analyze incomplete DNA sequences from thirteen strategically selected plant species, the researchers uncovered a previously hidden "paleopolyploidy" [i.e. ancient polyploidy] event, an ancient whole-genome duplication that preceded the appearance of the ancestral flowering plant. The results will appear in the June issue of Genome Research. Claude dePamphilis, associate professor of biology at Penn State, is the principal investigator of the Floral Genome Project and the senior author of the paper. "We found a concentration of duplicated genes that suggests a whole-genome duplication event in the earliest flowering plants," he says. "A polyploidy event early in the history of flowering plants could explain their sudden evolution." ... [This may not be completely new. I remember doing a genetics assignment on polyploidy (i.e. the duplication of an entire genome) in 2002, and in at least one of the journal articles I drew upon said that the reason there is so much polyploidy in angiosperm species (~70%) is probably because of ancestral polyploid events.

But while polyploidy has been an important factor in generating new species of plants (it is comparatively rare in animals for several reasons), despite an entire genome being duplicated, the resulting new species is still within the same genus. Harvard botanist and Neo-Darwinism co-founder G. Ledyard Stebbins pointed out that "polyploidy has contributed little to progressive evolution":

"Polyploidy is a very common method of evolution in higher plants. Between one-fourth and one-third of the species of flowering plants are polyploid with reference to their nearest relatives. Familiar examples among crop plants are wheat, oats, potato, tobacco, cotton, alfalfa, and most species of pasture grasses. Familiar weeds and wild flowers which are polyploid are the eastern blue flag (Iris versicolor), meadow rue (Thalictrum spp.), some species of wild rose, chickweed (Stellaria media), miner's lettuce (Montia perfoliata), yarrow (Achillea spp.), and various species of violets and asters. Furthermore, there is evidence that polyploidy in the remote past has given rise to many genera and groups of genera such as the apples, olives, willows, poplars, and many genera of ferns. Nevertheless, polyploidy has contributed little to progressive evolution. In genera which contain both diploids and polyploids, the major trends of evolution are all represented by diploid species, and the polyploids serve merely to multiply the variations on certain particular adaptive `themes.' This is probably because the large amount of gene duplication dilutes the effects of new mutations and gene combinations to such an extent that polyploids have great difficulty evolving truly new adaptive gene complexes." (Stebbins, G.L., "Processes of Organic Evolution," Prentice-Hall: Englewood Cliffs NJ, 1966, Second printing, p.129)]

The reason is that two genomes (like two copies of the same edition of a book or newspaper) don't have any new information. It would take a very special (to put it mildly) duplication event to produce a new phylum!

South Pacific plant may be missing link in evolution of flowering plants: Novel reproductive process may point to ancestors of angiosperms, says University of Colorado study, EurekAlert!, 17-May-2006, Ned Friedman ...

[Graphic: Amborella leaves, University of Colorado, Boulder.]

A new University of Colorado at Boulder study involving a "living fossil plant" that has survived on Earth for 130 million years suggests its novel reproductive structure may be a "missing link" between flowering plants and their ancestors. The Amborella plant, found in the rain forests of New Caledonia in the South Pacific [It is significant that this plant occurs only in New Caledonia, because that island "is a fragment of the ancient continent of Gondwana."] has a unique way of forming eggs that may represent a critical link between the remarkably diverse flowering plants, known as angiosperms, and their yet to be identified extinct ancestors, said CU-Boulder Professor William "Ned" Friedman. Angiosperms are thought to have diverged from gymnosperms -- the dominant land plants when dinosaurs reigned in the Cretaceous and Jurassic periods -- roughly 130 million years ago and have become the dominant plants on Earth today. "One of the biggest challenges for evolutionary biologists is understanding how these flowering plants arose on Earth," said Friedman, a professor in CU-Boulder's ecology and evolutionary biology department, whose study appears in the May 18 issue of Nature. "The study shows that the structure that houses the egg in Amborella is different from every other flowering plant known, and may be the potential missing link between flowering plants and their progenitors."... [No doubt this is a `vestigial organ' (Amborella is itself an angiosperm) and therefore further evidence that angiosperms arose from gymnosperms (non-flowering seed plants like conifers), which I accept. But as Friedman correctly observed, below, that that does not change the fact that "The mystery remains abominable":

Ancient shrub unlocks a clue to Darwin's 'abominable mystery'. Christian Science Monitor, May 18, 2006, Peter N. Spotts ... To millions of moms, the Mother's Day bouquet still gracing the dining room table symbolizes gratitude and love. To Charles Darwin, however, they also would stand as colorful characters in what he called an "abominable mystery" - the origin of flowering plants. "It's no different now," sighs biologist William Friedman. The mystery remains abominable. .... [The reason is that, as would be expected in a new phylum, angiosperms have many "unique characteristics" that gynosperms lack, including "flowers, closed carpels, double fertilization ... and ... sieve tubes and companion cells in the phloem":

"The unique characteristics of the angiosperms include flowers, closed carpels, double fertilization leading to endosperm formation, a three-nucleate microgametophyte and an eight-nucleate megagametophyte, stamens with two pairs of pollen sacs, and the presence of sieve tubes and companion cells in the phloem ... . These similarities clearly indicate that the members of this phylum were derived from a single common ancestor. This common ancestor of the angiosperms ultimately would have been derived from a seed plant that lacked flowers, closed carpels, and fruits. The earliest known, clearly identifiable fossils of angiosperms are flowers and pollen grains up to 130 million years old, from the Early Cretaceous period ... . There are intriguing suggestions that much older fossils-up to 200 million years old-may have had some, but perhaps not all, of the characteristic features of angiosperms. Currently the interpretation of these fossils is enigmatic, and it appears most likely that the phylum did in fact originate in the Early Cretaceous (or perhaps uppermost Jurassic) period." (Raven, P.H., Evert, R.F. & Eichhorn, S.E., "Biology of Plants," [1971], W.H. Freeman and Co/Worth Publishers: New York NY, Sixth Edition, 1999, p.519)

For all these to arise from one "Massive duplication of genes" would be indistinguishable from a miracle (which I expect it was)!]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book'

Flores hobbit was sick human: scientists, etc

Because of lack of time, now that I am working full-time on my `Evolution Quotes Book', I am reverting to normally posting brief excerpts and comments in shorter, hopefully daily, composite posts.

[Graphic: "Homo Floresiensis, Left, and Homo Sapiens", Discovery Channel]

Flores hobbit was sick human: scientists, ABC, May 19, 2006, Anna Salleh ... Scientists who argue the "hobbit" is really just a modern human with a small brain have published evidence for the first time in a major scientific journal. Today's issue of the journal Science carries a paper led by primate evolution expert, Dr Bob Martin of the Field Museum in Chicago. It says Homo floresiensis is likely to have been a modern human, who suffered from microcephaly - a condition that causes a small brain. This reignites the debate about whether the remains of the small hominid from the Indonesian island of Flores is really H. sapiens or a dwarf version of H. erectus that evolved after becoming isolated on the island, as was originally suggested. ... [Martin has been a longtime proponent of H. floresiensis being a microencephalic H. sapiens. However, I think Martin, and indeed the dwarf H. erectus proponents, are both wrong! As previously posted, my view is that H. floresiensis is a direct descendent species from Australopithecus via a lineage separate from H. erectus and H. sapiens.

But if Martin is right, it will be a public relations disaster for Human Evolution, so confident have been the claims via the media that this `Hobbit' was a dwarf species of Homo erectus . This is the problem of transacting science via the media and not through scientific journals. Every time the claim turns out to be wrong, on the principle of "The Boy Who Cried Wolf," the public will further distrust science.]

Apes prove to be forward thinking, ABC, May 19, 2006, Helen Carter ... Apes plan for the future, according to new research that questions whether humans are the only animals to think ahead. German research published today in the journal Science says apes can choose an appropriate tool to reach a treat and save the tool for the future instead of using it immediately. The researchers, from the Max Planck Institute for Evolutionary Anthropology, say that planning for future, not just current, needs is one of the most formidable human cognitive achievements. This is because it imposes a long delay between performing an action and being rewarded for it. The researchers let bonobo chimpanzees and orangutans select tools to reach grapes and juice bottles. They chose appropriate tools half of the time, took them to their sleeping rooms then used them up to 14 hours later when retrieving the treats. Both species show the skill, the researchers say, suggesting it evolved at least 14 million years ago, when all great ape species shared a common ancestor. "Our results suggest that future planning is not a uniquely human ability, contradicting the notion that it emerged in hominids only within the past 2.5 to 1.6 million years," they write. ... [Note that "They chose appropriate tools" only "half of the time"! Sounds like that is what would be expected to happen randomly? Anyway, it doesn't say much for these apes' "forward planning"! How do the researchers know that the apes haven't merely formed a weak conditioned association between the tools and the treats?

More generally I regard these attempts to prove that "X ... is not a uniquely human ability" as flawed (if not delusional) because it compares the highest of a particular ape's (or other animal's) ability with the lowest human ability. That way they could `prove', as Betrand Russell pointed out, that there should be "Votes for Oysters":

"There is a further consequence of the theory of evolution, which is independent of the particular mechanism suggested by Darwin. If men and animals have a common ancestry, and if men developed by such slow stages that there were creatures which we should not know whether to classify as human or not, the question arises: at what stage in evolution did men, or their semi-human ancestors begin to be all equal? Would Pithecanthropus erectus , if he had been properly educated, have done work as good as Newton's? Would the Piltdown Man have written Shakespeare's poetry if there had been anybody to convict him of poaching? A resolute egalitarian who answers these questions in the affirmative will find himself forced to regard apes as the equals of human beings. And why stop with apes? I do not see how he is to resist an argument in favour of Votes for Oysters. An adherent of evolution should maintain that not only the doctrine of the equality of all men, but also that of the rights of man, must be condemned as unbiological since it makes too emphatic a distinction between men and other animals." (Russell, B., "History of Western Philosophy," George Allen & Unwin: London, 1961, pp.697-698)

They should compare `apples with apples', i.e. the highest ability in both apes and humans. Then it will be seen that there is a vast gulf between ape and human forward planning.

Another, related, problem is the vague terminology. What is "forward planning" and "thinking ahead"? One could argue that a dog which buries a bone and later digs it up and eats it, is planning ahead. Is that "forward planning"? If not, why not (without committing the fallacy of special pleading)? But if so, then what is so special about apes chosing "appropriate tools half of the time" taking "them to their sleeping rooms" and then using "them up to 14 hours later when retrieving the treats" (my emphasis)?

And also why, on Darwinian principles, is human forward planning and thinking ahead so vastly superior to that of apes, given that: "Natural selection" (i.e. the differential reproduction of random micromutations) "tends only to make each organic being as perfect as, or slightly more perfect than, the other inhabitants of the same country with which it comes into competition" (my emphasis):

"Natural selection tends only to make each organic being as perfect as, or slightly more perfect than, the other inhabitants of the same country with which it comes into competition. And we see that this is the standard of perfection attained under nature." (Darwin, C.R., "The Origin of Species by Means of Natural Selection" 1872, Sixth Edition, 1994, Senate: London, pp.162-163)]

Stephen E. Jones, BSc (Biol).
`Evolution Quotes Book,'

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"Of course, there have been many who have clearly shown that they are not Darwinians. Bateson, in 1914, wrote: `We go to Darwin for his incomparable collection of facts. But to us he speaks no more with philosophical authority. We read his scheme of evolution as we would that of Lucretius, or of Lamarck, delighting in their simplicity and their courage.' Watson, in 1929, wrote: `The only two ` theories of evolution ' which have gained any currency, those of Lamarck and of Darwin, rest on a most insecure basis ; the validity of the assumptions on which they rest has seldom been seriously examined, and they do not interest most of the younger zoologists.' J.B.S. Haldane wrote of Darwinism in 1925: `This is still only a working 'hypothesis.' Many probably hold the opinion of Sir D'Arcy Thompson, who wrote in 1925 : `How species are actually produced remains an unsolved riddle, it is a great mystery.' It is rather interesting to note that T.H. Huxley, who fought the battle for Natural Selection and came out victorious, while an enthusiastic evolutionist, was never an out-and-out Darwinian. Poulton, in 1908, wrote: `Huxley was at no time a convinced believer in the theory he protected." (Broom R., "Finding the Missing Link," [1950], Greenwood Press: Westport CT, Second edition, 1951, Reprinted, 1975, p.103)