Saturday, August 06, 2005

Common ancestry and common city

AN (copy to CED blog, minus personal identifying information and with minor changes)

Thanks for your message. When I was running my recently terminated Internet discussion list, CreationEvolutionDesign I used to `kill two birds with one stone' and copy private messages I received on creation, evolution and design topics to my list, after removing the sender's personal identifying information and replacing his/her name with "AN" (for ANonymous). I had thought that would not work with my blog of the same name that replaced my list, but I have had second thoughts and will give it a try. I imagine that a lot of readers could be interested in basic questions. You are welcome to make comments to the blog post, anonymously if you wish.

On Sat, 6 Aug 2005 14:45:35 +0800, AN wrote:

AN>Hi Stephen
>
>My name is AN, I came across your internet article on common ancestory while I was doing a Google search for something else. I was very interested in your views. It's still an open question for me, but I do appreciate the distinction you make between common ancestry and naturalistic evolution. I wonder if there were muliple ancestors, as opposed to a single common ancester, which were the precursors to the Biblical kinds.

And an especial thanks that you can see "the distinction" that I "make between common ancestry and naturalistic evolution." Most (both creationist and evolutionist) in my experience cannot (or will not) see that distinction.

As for "Biblical kinds" , the Bible doesn't means anything scientific by it. The Hebrew word "min" just means kinds, like someone would say in English (e.g. "there are different kinds of trees and flowers in that forest"), without meaning anything about their taxonomic classification:
"min. Kind. The word min occurs in thirty-one passages (chiefly Gen 1, 6, 7; Lev 11; Deut 14), thirty of which belong to Moses' Pentateuch. The other one is Ezk 47:10. The etymology of min cannot be established with certainty. ... Some have argued that when God created min, he thereby fixed the `species.' This is a gratuitous assumption because a link between the word min with the biologist's descriptive term species cannot be substantiated, and because there are as many definitions of species as there are biologists. In light of the distinctions made in Gen 1, such as the distinction between herbs and grasses which are, however, members of the same class (Angiosperms), it is possible that in some cases the biblical term min may indicate a broader group, such as an order. Elsewhere, in Lev 11:14, 15, 16, 19, 22 (four times), min appears consistently as equivalent to nothing broader than genus. However, Lev 11:4 `the falcon after its kind,' and 11:16 `the hawk after its kind,' refer to divisions within the order Falconiformes, yet both have subdivisions called min. Likewise, as Payne points out, the locust, bald locust, cricket*, and grasshopper all belong to the order Orthoptera and the locust, bald locust, and grasshopper belong to the family Acridiidae, but again each has its subdivisions called min (genus?). God created the basic forms of life called min which can be classified according to modern biologists and zoologists as sometimes species, sometimes genus, sometimes family or order." (Kaiser W.C., "min. Kind," in Harris R.L., Archer G.L. & Waltke B.K., eds, "Theological Wordbook of the Old Testament," [1980], Moody Press: Chicago IL, 1992, Twelfth Printing, Vol. I, pp.503-504).
* This does not make it clear that while they are in the same order (Orthoptera) of insects (class Insecta of phylum Arthropoda) as locusts and grasshoppers, crickets are in a different family (Gryllidae) from them.

AN>I was quite surprised to find that you are a fellow Perth resident. I live in […] and fellowship at [church] in […]. I've been a YECer most of my Christian life until a few years ago when I got involved on the discussions boards at [...]. Needless to say I was greatly challenged and a lot of my thinking changed. I would now describe myself as OEC with ID as a key foundation of my scientific understanding of origins.

OK. I have never been a YEC, even though I was converted to Christ (at age 20) in a fairly conservative evangelical Baptist church. I think there are yecs and there are YECs. The former (yecs) are those who believe the days of Genesis 1 are literal 24-hours as a default position, because they know of little or no scientific evidence to the contrary. That would describe the vast majority of Christians up to the 18th-19th century. The latter (YECs) are those who believe the days of Genesis 1 are literal 24-hours, *despite* knowing the evidence to the contrary.

Denyse O'Leary, of the Post-Darwinist blog makes this point (see tagline quote).

AN>A few months ago I was considering whether I should/could do a science degree so that I could have some credible input into the creation/evolution debate. I was encouraged by the fact that you have done that. I still don't know when or how I will be able to do this, but your example has encouraged my to keep it before God in prayer and to trust him for whatever his will is.

I would heartily recommend creationists doing "a science degree so that [they] ... could have some credible input into the creation/evolution debate." However, it is a big (and expensive) commitment and you probably would need strong motivation to do it. In my case it was a combination of: 1) wanting to know the truth; 2) feeling the need for credibility to write a book on the problems of evolution; 3) a vague idea about getting a job as a science teacher (which I later decided against); 4) not being able to think of anything better to do! and 5) a feeling that that is what God wanted me to do. I nearly forgot 6) an excuse to buy great books!

>Regards
>
>AN

PS: Again, thanks for your message, but my long-standing policy is not to get involved in extensive private discussions about creation/evolution/design topics as: 1) I don't have the time; and 2) I believe that such discussions should be public. So if you have any follow-up questions, please make them as comments to my blog posts. Thanks.

Steve

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"Were the famous scientists of long ago young earth creationists? William Provine; a prominent Darwinist, thinks so. In a recent online review, he complained that a National Academy of Sciences publication on how teach evolution is flawed. He questioned the Academy's decision to cite Copernicus, Kepler, Galileo, and Newton as examples of thinkers whose views on physics and astronomy were vindicated because, as be put it: `Why would the National Academy have chosen this example in a book about evolution when all four were young-earth creationists? 34 Well, prior to about 1750, everyone was, in one sense, a young earth creationist! For example, the Venerable Bede (672?-735) wrote a history of the world, and so did Sir Walter Raleigh. (1554?-1618}. Both men began with `Creation,' the origin of the universe, as described in Genesis 1 and 2. They assumed that Creation took place about 6000 years ago. But the two men could hardly have been more different! Bede was an English monk in the Dark Ages, and Raleigh was a skeptical English adventurer who lived nearly a thousand years later in the Elizabethan Renaissance. Raleigh was rumored to be an atheist, holding forth in taverns, but his religious views had no impact on where he would begin his account of history. Prior to the development of geology as a scientific discipline in the 18th century, there was no widely accepted source of information about cosmic or human origins apart from the Bible. Raleigh would have to either begin with Genesis, or take the risk of resurrecting an account of origins written by a classical Greek philosopher. But the philosophers' accounts were not science-based; they were simply accounts that were not based on a Christian understanding of the universe. So Copernicus and the others were not young earth creationists in the sense that Provine assumes. They accepted a traditional account of origins as an alternative to no account." (O'Leary D., "By Design or by Chance?: The Growing Controversy on the Origins of Life in the Universe," 2004, p.129)
Stephen E. Jones, BSc (Biol). "Problems of Evolution"

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12 comments:

Anonymous said...

Simon Conway Morris in his article, "Evolution: Bringing Molecules into the Fold" states that:

Constructing that this animal is the most primitive living chordate,
phylogenies is central to the evolutionary enterprise, yet rival schemes are often strongly contradictory.


If this is the case then would that not undermine the validity of common ancestry

Anonymous said...

Simon Conway Morris in his article, "Evolution: Bringing Molecules into the Fold" states that:

Constructing phylogenies is central to the evolutionary enterprise, yet rival schemes are often strongly contradictory.

If this is the case then would that not that undermine the validity of common ancestry?

Stephen E. Jones said...

Anonymous

I assume this is not from Paul K., because he has begun signing "Paul" at the end of his comments. While it is not mandatory for those making comments to give their name, it would be appreciated if they to gave their given name and surname initial, or just their initials, or at least a pseudonym, so I can tell if it is a different person making comments.

First, thanks to Anonymous for his/her high-quality, non-nasty comment. I have for the first time implemented my policy stated at the foot of CED blog's front page:

"Policy note: Nasty or low-quality comments will be deleted or ignored."

by deleting a number of nasty comments from the one person. In future I will do that routinely. As a guide to what I consider "nasty" or "low quality", see the rules on the front page of my now terminated list CED: http://groups.yahoo.com/group/creationevolutiondesign/

AN>Simon Conway Morris in his article, "Evolution: Bringing Molecules into the Fold" states that:
>
>Constructing phylogenies is central to the evolutionary enterprise, yet rival schemes are often strongly contradictory.

Indeed, Conway Morris, S., "Evolution: Bringing Molecules into the Fold," Cell, Vol. 100, pp.1-11, January 7, 2000, p.11.

AN>If this is the case then would that not that undermine the validity of common ancestry?

Not really. As I have said a number of times on my now terminated list CED, this sort of argument (which is popular with YECs) where one: 1) keeps one's own position out of the ring; 2) attacks the position(s) in the ring, and then 3) when the other position(s) in the ring have problems (as all positions do-see tagline), declaring that one's own position as the winner, is fallacious.

In such cases what one should do (if one is interested in getting at the truth of what *really* happened-as opposed to what one would have *liked* to have happened), is put one's own position in the ring too, and compare *in parallel* the competing positions.

In the case of "common ancestry", as Darwin (citing Plato) correctly pointed out, "if species were not created separately they must have descended from other species":

"Lastly, you refer repeatedly to my view as a modification of Lamarck's doctrine of development and progression. If this is your deliberate opinion there is nothing to be said, but it does not seem so to me. Plato, Buffon, my grandfather before Lamarck, and others, propounded the obvious views that if species were not created separately they must have descended from other species, and I can see nothing else in common between the 'Origin' and Lamarck." (Darwin C.R., letter to Charles Lyell, 12 March, 1863, in Darwin F., ed., "The Life and Letters of Charles Darwin," [1898], Basic Books: New York NY, Vol. II., 1959, reprint, pp.198-199)

That is, there are really only two alternatives, either: 1) common ancestry (all organisms share a common ancestor); or 2) separate creations (organisms were created separately ex nihilo/de novo).

So when one says something like, "Constructing phylogenies is central to the evolutionary enterprise, yet rival schemes are often strongly contradictory" and "If this is the case then would that not that undermine the validity of common ancestry?" then one should put on the table for parallel consideration one's separate creations alternative.

As I say in my "Why I (a Creationist) Accept Common Ancestry" page, "I have found from a decade of debates, that those who oppose common ancestry are very reluctant to put on the table for criticism their separate creations alternative,":

-----------------------------------http://members.iinet.net.au/~sejones/cmnctsry.html#ltrntvsprtcrtns
Stephen E. Jones
Why I (a Creationist) Accept Common Ancestry […]
The only alternative to common ancestry is separate creations
As Darwin rightly observed, as had been pointed out by Plato, "if species were not created separately they must have descended from other species" ... I have found from a decade of debates, that those who oppose common ancestry are very reluctant to put on the table for criticism their separate creations alternative. […]
-----------------------------------

I will wait and see if Anonymous is a rare exception and will put on the table for discussion, *his* (or *her*) alternative to common ancestry.

Steve

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"TO SAY that orthodoxy is true does not mean that it has no difficulties. Orthodoxy *has* difficulties, and the apologist does not try to conceal them. To affect omniscience is cultic. Plato set an example of right procedure. First he defended the world of Ideas; then he reviewed the difficulties. He did not fear the difficulties because he believed that the substance of his philosophy was true. No other system could answer the question, How is knowledge possible? In a similar way, orthodoxy does not fear the difficulties because it believes that the substance of Christianity is true. Christianity is consistent with itself and consistent with the things signified. No other system can answer the question, How can a sinner be just before God? If a person withholds belief until all difficulties are resolved, he will go to his grave in unbelief, for difficulties are only a sign that we are men and not God. Plato was confined to a cave, while the Christian sees in a mirror dimly. " For our knowledge is imperfect ... " (I Cor. 13:9) To confuse a system with its difficulties betrays a want of education." (Carnell E.J., "The Case for Orthodox Theology," Westminster Press: Philadelphia PA, 1959, p.92. Emphasis in original)
Stephen E. Jones, BSc (Biol)
http://members.iinet.net.au/~sejones
http://creationevolutiondesign.blogspot.com/
http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
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Anonymous said...

I apologise for not signing my previous post where I quoted from Simon Conway Morris.

That is, there are really only two alternatives, either: 1) common ancestry (all organisms share a common ancestor); or 2) separate creations (organisms were created separately ex nihilo/de novo).


Then if I disprove common ancestry, separate creations must be true. While this approach works well in mathematics, science tends to work by inference to best explanation.

My original question merely probes whether common ancestry is the best explanation.

It seems to me that the evidence is conflicting. I would agree that the example of Vitamin C pseudogene you give in your article on common ancestry is good evidence for common ancestry. However the more general argument from homologies is mitigated by the ubiquity of convergence. See the previous article by Conway Morris I cited. Of course Conway Morris doesn't interpret it that. I imagine he would see convergence as merely as difficulty not a major problem. The same could be argued for the conflicting phylogenetic trees.

In other words when does a "difficulty" become a major problem? I don't have a fully developed argument for either separate creation or common descent. Just questions.

orion

Stephen E. Jones said...

Orion

Thanks for signing your name (which I assume is a pseudonym). I will preface your comments with "OR>".

OR>Anonymous said...
>I apologise for not signing my previous post where I quoted from Simon Conway Morris.

No problem.

>SJ>That is, there are really only two alternatives, either: 1) common ancestry (all organisms share a common ancestor); or 2) separate creations (organisms were created separately ex nihilo/de novo).

OR>Then if I disprove common ancestry, separate creations must be true. While this approach works well in mathematics, science tends to work by inference to best explanation.

My point was that *all* explanations have to be on the table. There is no point in making an "inference to best explanation" when the only alternative "explanation" is left off the table.

It is also a mark of good science to start with "multiple working hypotheses":

"Spin more than one hypothesis. If there's something to be explained, think of all the different ways in which it *could* be explained. Then think of tests by which you might systematically disprove each of the alternatives. What survives, the hypothesis that resists disproof in this Darwinian selection among 'multiple working hypotheses', has a much better chance of being the right answer than if you had simply run with the first idea that caught your fancy." (Sagan C., "The Demon-Haunted World: Science as a Candle in the Dark," [1996], Headline: London, 1997, reprint, p.197. Emphasis in original)

The reason is that "If we operate with a single hypothesis, especially one we favor … the correct explanation may not even be included":

"Multiple hypotheses should be proposed whenever possible. Proposing alternative explanations that can answer a question is good science. If we operate with a single hypothesis, especially one we favor, we may direct our investigation toward a hunt for evidence in support of this hypothesis. ... Of the many hypotheses proposed to answer a particular question, the correct explanation may not even be included." (Campbell N.A., Reece J.B. & Mitchell L.G., "Biology," [1987], Benjamin/Cummings: Menlo Park CA, Fifth Edition, 1999, pp.14-15)

OR>My original question merely probes whether common ancestry is the best explanation.

And my point was that "best" implies that *all* alternative explanations are on the table. It is meaningless to consider "whether common ancestry is the best explanation" without considering what it is the "best" *of*.

OR>It seems to me that the evidence is conflicting.

Remember that Morris is talking about "conflicting" phylogenies that are far deeper than ape-human common ancestry (which is what separate creationists are most concerned about). There are no major problems (that I am aware of) with "the [phylogenetic] evidence" for common ancestry at that comparatively low level, which is just within a family, Hominidae (humans and apes).

OR>I would agree that the example of Vitamin C pseudogene you give in your article on common ancestry is good evidence for common ancestry.

Agreed [see http://members.iinet.net.au/~sejones/cmnctsry.html#vtmncpsdgn].

And what about "Common chimp-human DNA endogenous retroviral (ERV) sequences" [http://members.iinet.net.au/~sejones/cmnctsry.html#cmphmnrvs]:

"Further evidence of genetic linkage between man and other higher primates can be derived from an endogenous retroviral sequence imbedded in our DNA that is also found at the same point in the DNA of chimpanzees. Retroviruses are a particular class of virus, which includes the HIV virus that causes AIDS, for example. These viral agents have the ability to annex themselves directly into a DNA sequence, and an ancient virus apparently did. The entire genetic code was then passed to future generations, including the retroviral sequence. This retroviral sequence has no activator mechanism, and thus is harmless, but here is the point. Not only do man and chimpanzee have the same number of muscles, bones and teeth, our DNA has a correlation of nearly 99%. But in addition, an identical alien viral sequence can be found at the same locus point on both human and chimp DNA. A rational explanation is that the viral sequence became attached to the DNA of a common precursor. It has remained in the DNA, and has been copied in both man and chimp for millions of years. This additional confirming data for relatedness to an animal that already looks to be a close relative anyway, makes a strong case for a brachiating forbear on our family tree. The theory that the highest primates, including man, are all divergent twigs off a common branch has strong supporting evidence. Whether we like it or not, gorillas, chimps, and man do not appear to be separately created entities." (Fischer, D., "The Origins Solution: An Answer in the Creation-Evolution Debate," Fairway Press: Lima OH, 1996, p.65. Emphasis mine)

Or "Syndactyly in Australian marsupials" [http://members.iinet.net.au/~sejones/cmnctsry.html#syndctyly]:

"Aside from the dasyuroids [small-to-medium-sized insectivores, carnivores, and omnivores], all other adequately known Australian marsupials share a specialization of the rear foot in which digits 2 and 3 are greatly reduced and incorporated in a single sheath of tissue, a configuration termed syndactyly (Figure 19- 21). These specialized digits are used in grooming. Genera with syndactyly include two very distinct groups, the Perameloidea, or bandicoots, and the Diprotodontoidea, a much more diverse assemblage.. ... The diprotodonts include three superfamilies, the Vombatoidea (including the wombats of the modern fauna and a variety of extinct groups), the Phascolarctoidea (koalas), and the Phalangeroidea, which encompasses the modern phalangerids, kangaroos, and gliding and pygmy possums. The diprotodonts are united by the derived condition of the lower incisors, which are reduced to two procumbent teeth. The group consists of primarily herbivorous forms." (Carroll, R.L., "Vertebrate Paleontology and Evolution," W.H. Freeman & Co: New York NY, 1988, p.436)

"When marsupials first appeared in the fossil record of Australia in the late Oligocene, they were already very diverse and the interrelationships of the various lineages have not been satisfactorily established. The dasyuroids appear to form an ancestral stock that is comparable to the didelphoids in the New World. The carnivorous Tasmanian wolf and Tasmanian devil converge closely on the pattern of the South American borhyaenoids. All other Australian marsupials are specialized in having digits 2 and 3 greatly reduced and incorporated in a single sheath of tissue. This condition is termed syndactyly." (Carroll, R.L., "Vertebrate Paleontology and Evolution," W.H. Freeman & Co: New York NY, 1988, p.440)

See also new tagline quote.

BTW, this syndactly argument for common ancestry is my own discovery. I found it while doing a major assignment on Australian Marsupials in an unit in my biology degree called "Australian Animals". It is particularly strong because it is easy to understand (compared to pseudogenes and retroviral sequences) in the sense you can go to a zoo or museum and see it in the rear feet of Australian kangaroos, koalas, possums (not opossums) and wombats, for yourself, if the zoo or museum has those marsupials.

ON>However the more general argument from homologies is mitigated by the ubiquity of convergence. See the previous article by Conway Morris I cited. Of course Conway Morris doesn't interpret it that. I imagine he would see convergence as merely as difficulty not a major problem. The same could be argued for the conflicting phylogenetic trees.

Same answer. It is fallacious to point to the problems of a position (e.g. common ancestry), and then explicitly or implicitly accept the alternative (separate creations) when the problems of that alternative position is not even considered.

What *are* the alternative separate creations explanations for: 1) "Vitamin C pseudogene", i.e.the loss in all primates in the order Anthropoidea (monkeys, apes and man) of the ability to synthesise vitamin C which is traceable to an *identical* pseudogene (non-functional gene) in the vitamin C metabolic pathway in *all* of them? The separate creations alternative must presumably be that God separately created monkeys, apes and man basic kinds with either: a) the identical non-functional gene; or b) these three basic kinds were originally separately created but an identical gene mutation occurred in the last common ancestor of each?

2) "Common chimp-human DNA endogenous retroviral (ERV) sequences", i.e. humans and chimps (and apes and monkeys and monkeys and humans), having identical stretches of DNA evidently caused by an RNA retrovirus infection that started and stopped at exactly the same loci in homologous chromosomes? Again, on the separate creations explanation, either a) God would have separately created each basic kind with the same stretch of RNA retrovirus infection, or b) each basic kind's common ancestor had an identical infection at the same loci?

3) "Syndactyly in Australian marsupials", i.e. the suborder Diprotodontia (see tagline), all have the same "specialization of the rear foot in which digits 2 and 3 are greatly reduced and incorporated in a single sheath of tissue". So again, on the separate creations explanation, either a) God would have separately created each basic kind with the same "specialization of the rear foot in which digits 2 and 3 are greatly reduced and incorporated in a single sheath of tissue"; or b) each kangaroo, possum, koala, wombat, and marsupial lion (to name only some), which are so morphologically different they would be presumably have to be each a basic kind, had an identical mutation which modified their rear foot only?

Which of the above: 1) a) or b); 2) a) or b); or 3) a) or b)? is it, so we can compare the problems of the common ancestry hypothesis in parallel with the problems of the separate creation hypothesis?

OR>In other words when does a "difficulty" become a major problem? I don't have a fully developed argument for either separate creation or common descent. Just questions.

Quite frankly I find it hard to believe that someone who is motivated enough to make comments to a C/E list or blog about "argument for either separate creation or common descent" (or any major C/E topic), is neutral. There was someone on my CED list who claimed he was "Just [asking] questions", but it seemed to me and at least on other member that it was just a debating ploy, and he really was on the evolutionist side. In your case, I assume as a starting point that your position at present is separate creations (although I do not rule out that you may be open to considering the evidence for common descent).

But the bottom line is I have been through this *many* times with both YECs and OEC separate creationists in the 10+ years I have debated on C/E lists, and experience has taught me that it is a waste of time discussing the problems of common ancestry, without discussing in parallel the *even greater* problems of separate creations.

OR>orion

Steve

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"Diprotodontia is a large taxon of about 120 marsupial mammals including the kangaroos, wallabies, possums, Koala, wombats, and many others. Extinct members include the giant Diprotodon family, and Thylacoleo, the so-called "marsupial lion". Diprotodonts are almost all herbivorous: there are a few insectivores and omnivores, but these seem to be relatively recent adaptations from the mainstream herbivorous mould. Diprotodonts are restricted to Australasia. … There are two key anatomical features that, in combination, identify the diprotodonts. The first of these is that they are diprotodont: they have a pair of large, procumbent incisors on the lower jaw. This is a common feature of many early groups of mammals and mammaliforms. The diprotodont jaw is short, usually with 3 pairs of upper incisors (wombats, like rodents have only one pair), and no lower canines. Secondly, diprotodonts exhibit syndactyly: they have the second and third digits of the foot fused together up to the base of the claws, leaving the claws themselves separate." ("Diprotodontia," Wikipedia, http://en.wikipedia.org/wiki/Diprotodontia)
Stephen E. Jones, BSc (Biol)
http://members.iinet.net.au/~sejones
http://creationevolutiondesign.blogspot.com/
http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
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Anonymous said...

And what about "Common chimp-human DNA endogenous retroviral (ERV) sequences

Fuz Rana makes a case for common design based on the discovery that the "endogenous retroviruses" have an immunological function against the retrovirus. For more details see "Are retroviruses evidence for common ancestry with apes?"[http://www.reasons.org/resources/multimedia/rtbradio/cu_archives/protected/200407-12archives.shtml]

Remember that Morris is talking about "conflicting" phylogenies that are far deeper than ape-human common ancestry (which is what separate creationists are most concerned about). There are no major problems (that I am aware of) with "the [phylogenetic] evidence" for common ancestry at that comparatively low level, which is just within a family, Hominidae (humans and apes).

Therein lies one of the problems that I have, the extrapolation of low level common ancestry to an all inclusive common ancestry from a single common ancestor.

Quite frankly I find it hard to believe that someone who is motivated enough to make comments to a C/E list or blog about "argument for either separate creation or common descent" (or any major C/E topic), is neutral.

It's a biblical principal that people are innocent until proven guilty. All inclusive common ancestry may or may not be true. Either answer is interesting. Neither answer is determinative of my faith.

Orion

John A. davison said...

Virtually nothing is known for certainty concerning the question of a common ancestry. There are many difficulties associated with the monophyletic view of the neoDarwinian camp. Leo Berg, whom I regard as one of the greatest evolutionists of all time, presented the following summary at the end of Nomogenesis.

"Organisms have developed from tens of thousands of primary forms, i.e, polyphyletically."
page 406

Who is prepared to prove he is wrong? The many body plans presented in the Burgess Shale would suggest that he is most probably correct at the Phylum level simply because it is virtually inconceivable to imagine transitional forms at least for this investigator. On the other hand at the Family (subOrder) level one can account for a common origin on chromosomal structural grounds as is so evident in the comparative karyology of the genera Homo, Pan, Pongo and Gorilla. So in retrospect, Berg's estimate of tens of thousands of separate creations my be in the ball park of what can be considered reasonable at least to this investigator.

In any event, the origin of life certainly qualifies as a miracle and miracles by definition need not be limited as to frequency.

In any event, there is absolutely no reason to suspect that Homo sapiens and his present closest relatives are not exactly that. To deny a past evolution is unthinkable. It is only the mechanism that remians undisclosed and that for not much longer. One thing is for certain. Chance had no role in phylogeny just as it has no role at present in ontogeny.

"Neither in the one nor in the other is there room for chance."
Nomogenesis, page 134

Stephen E. Jones said...

Orion

>SJ>And what about "Common chimp-human DNA endogenous retroviral (ERV) sequences

OR>Fuz Rana makes a case for common design based on the discovery that the "endogenous retroviruses" have an immunological function against the retrovirus. For more details see "Are retroviruses evidence for common ancestry with apes?" [http://www.reasons.org/resources/multimedia/rtbradio/cu_archives/protected/200407-12archives.shtml]

Thanks. But that ERVs "have an immunological function" is an explanation of why they have *persisted* relatively unchanged in the chimp and human (and other) genomes, but it is not an explanation of why a retrovirus would start at exactly the same homologous loci in humans and chimps and then continue for exactly the same length.

>SJ>Remember that Morris is talking about "conflicting" phylogenies that are far deeper than ape-human common ancestry (which is what separate creationists are most concerned about). There are no major problems (that I am aware of) with "the [phylogenetic] evidence" for common ancestry at that comparatively low level, which is just within a family, Hominidae (humans and apes).

OR>Therein lies one of the problems that I have, the extrapolation of low level common ancestry to an all inclusive common ancestry from a single common ancestor.

Well, that's not *only* what I do. It is the common genetic code and biochemistry of *all* life that convinces me of "common ancestry from a single common ancestor".

My point was that the issue of human-ape common ancestry is what drives the opposition to common ancestry as a whole.

But again what I want to see on the table for criticism is your separate creations alternative. Otherwise there is no point me wasting my time discussing the issue.

>SJ>Quite frankly I find it hard to believe that someone who is motivated enough to make comments to a C/E list or blog about "argument for either separate creation or common descent" (or any major C/E topic), is neutral.

OR>It's a biblical principal that people are innocent until proven guilty.

That is impossible in Internet lists and blogs because it is the rule rather than the exception that participants are not completely upfront about who they are, what they believe, and why, so I have no choice but to make my own judgments, based on the evidence of their posts.

I assume as a starting that if someone claims they are neutral, but criticises a position, their real position is the opposite of the position they are criticising.

OR>All inclusive common ancestry may or may not be true. Either answer is interesting. Neither answer is determinative of my faith.

OK. But having once argued on Internet discussion lists that "common ancestry" is not true, and then being forced by the evidence to admit that my opponents were right:

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http://members.iinet.net.au/~sejones/cmnctsry.html
Stephen E. Jones
Why I (a Creationist) Accept Common Ancestry […]
2. My original position
My original position on common ancestry was that I did not accept it, and argued vigorously against it on the Internet for about a year, until in 1995 I was convinced by the evidence and a series of `coincidences' that common ancestry was true. … See my post to the Calvin Reflector, "Clarification of my Progressive Creationist position," 28 June 1995. [http://www.asa3.org/archive/evolution/199505-10/0391.html]
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and then passing through a Kuhnian paradigm shift, after which everything looked different on the other side, I now have no doubt that universal common ancestry *is* true.

OR>Orion

Steve

PS: In my debates on Internet lists, I realized early on that the debates themselves were ephemeral and that the quotes I usually posted could form a permanent public database, accessible to search engines like Google (although when I started neither Google, nor even the Web, existed). Those quotes, starting at [http://members.iinet.net.au/~sejones/cequotes.html] now `weigh' over 5 megabytes! If there was no relevant quote to be made in the body of my post, I would often scan and post a new one on my tagline. I will start doing that again (see tagline).

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"Some of Darwin's staunchest supporters disagreed with him on key points. For example, the British biologist T H. Huxley earned the name `Darwin's Bulldog' for his spirited and unrelenting efforts to convince scientists and members of the lay public alike of the truth of evolution. Huxley wrote one article after another about evolution and sent them to the leading periodicals of the day. He defended Darwin against criticisms, and replied to unfavorable reviews of Darwin's book. Yet Huxley's views differed from Darwin's in several different respects. For example, Darwin attributed evolution to the action of natural selection. Huxley wasn't so sure about this. He believed that other factors might play a role. He spoke of evolution in `predetermined' directions, an idea that appeared nowhere in Darwin's writings. And he expressed the opinion that evolution was not always so gradual a process as Darwin conceived it to be. Huxley was not the only evolutionist who disagreed with Darwin. The botanist Joseph Hooker, another strong supporter of evolutionary ideas, also took issue with Darwin about the specifics of the theory. So did the naturalist Alfred Russel Wallace, who had discovered the idea of natural selection independently. All these men argued with Darwin privately in letters and sometimes in print." (Morris R., "The Evolutionists: The Struggle for Darwin's Soul," W.H. Freeman and Co: New York NY, 2001, pp.viii.-ix)
Stephen E. Jones, BSc (Biol).
http://members.iinet.net.au/~sejones
http://creationevolutiondesign.blogspot.com/
http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
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John A. Davison said...

The problem with a monophyletic evolution is the conversion of fundamentally different body plans. I don't see how it can be done. It is interesting that Berg never really explained his "tens of thousands of primary forms," although in the text of Nomogenesis he presents plenty of examples of polyphyleticism. His grasp of both plant and animal taxonomy and anatomy is mindboggling. I regard Nomogenesis as the single most significant volume ever published dealing with evolution. He was able to do this, it seems to me, because he was largely insulated from the influence of Western science and the enormous influence Darwin's book had in an era which unfortunately came to be known as the Age of Enlightenment. The publication of the Origin issued in a new Dark Age which to this day denies a purpose for the universe and man's role in it.

Stephen E. Jones said...

John

JD>John A. Davison said...

Thanks for your comment.

JD>The problem with a monophyletic evolution is the conversion of fundamentally different body plans.

I am not arguing for "monophyletic *evolution*". I am arguing for "monophyletic" *creation* (i.e. progressive mediate creation). I regard "common ancestry", or "common descent", or "descent with modification [Darwin's original term] from a common ancestor"), or just "descent", as neutral, non-question-begging terms, that are "equally compatible" with either creation or evolution:

"It is true that both genuine homologous resemblance, that is, where phenomenon has a clear genetic and embryological basis (which as we have seen above is far less common than is often presumed), and the hierarchic patterns of class relationships are suggestive of some kind of theory of descent. But neither tell us anything about how the descent or evolution might have occurred, as to whether the process was gradual or sudden, or as to whether the causal mechanism was Darwinian, Lamarckian, vitalistic or even creationist. Such a theory of descent is therefore devoid of any significant meaning and equally compatible with almost any philosophy of nature." (Denton M.J., "Evolution: A Theory in Crisis," Burnett Books: London, 1985, pp.154-155)

and so they are the terms I will use (as was my policy on my list CED). I will be quite pedantic on this, because to concede tacitly that it *was* "evolution", is to concede the main point at issue, and lose the debate before it has even begun.

If the "problem with a monophyletic" descent from a single ancestor "is the conversion of fundamentally different body plans", then the even *greater* problem (IMHO) of the alternative *polyphyletic* descent from multiple ancestors, is in explaining the underlying *unity* (at the molecular, biochemical and genetic levels) of those "fundamentally different body plans".

When I did a major assignment on the Cambrian Explosion I found a nice diagram in de Rosa R, et al.:

"Understanding the early evolution of animal body plans requires knowledge both of metazoan phylogeny and of the genetic and developmental changes involved in the emergence of particular forms. Recent 18S ribosomal RNA phylogenies suggest a three-branched tree for the Bilateria comprising the deuterostomes and two great protostome clades, the lophotrochozoans and ecdysozoans. Here, we show that the complement of Hox genes in critical protostome phyla reflects these phylogenetic relationships and reveals the early evolution of developmental regulatory potential in bilaterians. We have identified Hox genes that are shared by subsets of protostome phyla. These include a diverged pair of posterior (Abdominal-B-like) genes in both a brachiopod and a polychaete annelid, which supports the lophotrochozoan assemblage, and a distinct posterior Hox gene shared by a priapulid, a nematode and the arthropods, which supports the ecdysozoan clade. The ancestors of each of these two major protostome lineages had a minimum of eight to ten Hox genes. The major period of Hox gene expansion and diversification thus occurred before the radiation of each of the three great bilaterian clades." (de Rosa R, et al., "Hox genes in brachiopods and priapulids and protostome evolution," Nature, 399, June 24, 772-776. http://www.nature.com/nature/journal/v399/n6738/abs/399772a0_fs.html)

showing how the protostome and deuterostome animal phyla are related to a common bilaterian common ancestor at the Hox gene level. Unfortunately the diagram does not seem freely available on the Web (i.e. one would have to pay NATURE for it, or get it from a source that has a paid NATURE licence, e.g. a university, where I got mine).

JD>I don't see how it can be done.

What I wrote in my assignment, about "set aside cells" being "less restricted by larval development constraints and their ability to migrate around the body and in conjunction with homeotic genes could build a wide variety of larger size adult body forms", seems a reasonable explanation:

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The Cambrian Evolution of Animal Body Plans
Stephen E. Jones, 1 November 2004 [...]

Set aside cells
A complementary proposed trigger for the Cambrian explosion was the emergence of “set aside” cells that are held in reserve during larval development, but later are activated to build the adult body form (Davidson, Peterson & Cameron, 1995; Hecht, 1995). The theory is that until set aside cells evolved, animals would be confined to a larval stage (Hecht, 1995; Davidson, Peterson & Cameron, 1995). After set aside cells emerged, they would be less restricted by larval development constraints and their ability to migrate around the body and in conjunction with homeotic genes could build a wide variety of larger size adult body forms (Davidson, Peterson & Cameron, 1995; Hecht, 1995). [...]
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BTW, in case someone accuses me of hypocrisy in calling my assignent "The Cambrian *Evolution* of Animal Body Plans", its title was compulsory (i.e. if I wanted to write on the Cambrian Explosion - there were about 30 alternative topics but none that interested me as much - that is the title I had to use).

JD>It is interesting that Berg never really explained his "tens of thousands of primary forms," although in the text of Nomogenesis he presents plenty of examples of polyphyleticism. His grasp of both plant and animal taxonomy and anatomy is mindboggling. I regard Nomogenesis as the single most significant volume ever published dealing with evolution.

Thanks for this. I have added Berg's "Nomogenesis" (MIT Press, 1969) to my book wants list.

JD>He was able to do this, it seems to me, because he was largely insulated from the influence of Western science and the enormous influence Darwin's book had in an era which unfortunately came to be known as the Age of Enlightenment. The publication of the Origin issued in a new Dark Age which to this day denies a purpose for the universe and man's role in it.

I don't see it as part of my brief to defend Darwin, or his Origin of Species, but I personally regard him as a great (albeit flawed) genius, who deserves a place in biology's hall of fame for his "special theory" (of microevolution) which "is relatively conservative and restricted in scope and merely proposes that new races and species arise in nature by the agency of natural selection" (see tagline). It is Darwin's *extrapolation* of his "special theory" into his "general theory" (of macroevolution), "that the same simple natural processes which had brought about the diversity of the Galapagos finches had ultimately brought forth all the diversity of life on earth and all the adaptive design of living things" where I consider that Darwin went wrong.

Steve

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"In his book Darwin is actually presenting two related but quite distinct theories. The first, which has sometimes been called the `special theory', is relatively conservative and restricted in scope and merely proposes that new races and species arise in nature by the agency of natural selection, thus the complete title of his book: The Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. The second theory, which is often called the `general theory', is far more radical. It makes the claim that the `special theory' applies universally and hence that the appearance of all the manifold diversity of life on Earth can be explained by a simple extrapolation of the processes which bring about relatively trivial changes such as those seen on the Galapagos Islands. This `general theory' is what most people think of when they refer to evolution theory. ... If the Origin had dealt only with the evolution of new species it would never have had its revolutionary impact. It was only because he went much further to argue the general thesis that the same simple natural processes which had brought about the diversity of the Galapagos finches had ultimately brought forth all the diversity of life on earth and all the adaptive design of living things that the book proved such a watershed in western thought. ... It is clear, then, that Darwin's special theory was largely correct. Natural selection has been directly observed and there can be no question now that new species do originate in nature ... The validation of Darwin's special theory, which has been one of the major achievements of twentieth-century biology, has inevitably had the effect of enormously enhancing the credibility of his general theory of evolution. ... Yet, despite the success of his special theory, despite the reality of microevolution, not all biologists have shared Darwin's confidence and accepted that the major divisions in nature could have been crossed by the same simple sorts of processes. ... However attractive the extrapolation, it does not necessarily follow that, because a certain degree of evolution has been shown to occur therefore any degree of evolution is possible. There is obviously an enormous difference between the evolution of a colour change in a moth's wing and the evolution of an organ like the human brain, and the differences among the fruit flies of Hawaii, for example, are utterly trivial compared with the differences between a mouse and an elephant, or an octopus and a bee. ... Whatever the merits of the extrapolation may be in biology, there are certainly many instances outside biology where such an extrapolation is clearly invalid, where large scale `macro' changes can only be accounted for by invoking radically different sorts of processes from those responsible for more limited `micro' types of change. ... The technique of problem solving by trial and error, for example, a mechanism which is strictly analogous to evolution by natural selection, is often successful in solving relatively simple problems, but it would obviously be wrong to conclude that it is capable, at least in finite time, of solving more involved complex sorts of problems. ... The same rule applies in the case of most other sorts of complex systems where function arises from the integrated activity of a number of coadapted components. Take the case of a watch, where only very trivial changes in the structure and function of the cogwheel system can be achieved gradually through a succession of minor modifications. Any major functional innovation, such as the addition of a new cogwheel or an increase in the diameter of an existing cogwheel, necessarily involves simultaneous highly specific correlated changes throughout the entire cogwheel system. Like a sentence, the function of a watch cannot be gradually converted through an innumerable series of transitional forms into a quite different sort of watch. ... There is no doubt that the success of the Darwinian model in explaining microevolution invites the hope that it might be applicable also to macroevolutionary phenomena. Perhaps in the end this might prove to be the case; but, on the other hand, there is the depressing precedent, as the history of science testifies, that over and over again theories which were thought to be generally valid at the time proved eventually to be valid only in a restricted sphere." (Denton M.J., "Evolution: A Theory in Crisis," Burnett Books: London, 1985, pp.44-46, 85-92)
Stephen E. Jones, BSc (Biol).
http://members.iinet.net.au/~sejones
http://creationevolutiondesign.blogspot.com/
http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
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John A. Davison said...

I really don't expect anyone to agree with me any more as I intend to say "I told you so" when Darwinian doomsday finally comes which is very soon now. Here are my convictions, many of which were anticipated by others as I have cited in my papers.

Sexual reporduction is quite unable to support speciation or any of the higher categories. The production of gametes from diploid precursor cells takes place in two steps, trhe first of which takes the cell from tetraploid back to diploid and is a normal form of diploid reproduction as has been experimentally verified. I have proposed that this first step WAS the mechanism by which new life forms were instantly produced. It is called the Semi-meiotic Hypothesis. I proposed it in 1984 and it has yet to be tested with appropriate material, something I was unable to achieve prior to my retirement which coincided with the loss of my laboratory.

Not only is sexual reproduction incompatible with creative evolution, it is basically anti-evolutionary as it can only recombine minor variants (point mutations) which do not trancend the species barrier as defined by Dobzhansky, that is hybrid infertility. His attempts to speciate Drosophila experimentally failed and it is to his credit that he admitted as much. I know of no further serious attempts to verify the very heart of the Darwinian hypothesis.

Furthermore, Natural Selection, the cornerstone of the Darwinian scheme, never had anything to do with evolution either. Quite the contrary, like sexual reproduction which is the device for the expression of the variants, Natural Selection also is entirely conservative, serving only to maintain the standard exactly as Leo Berg and Reginald C. Punnett understood early in the 20th century. Mivart too knew this in Darwin's own day.

In short, there is absolutely NOTHING in the neoDarwinian paradigm that EVER had any role in creative evolution. Exactly as the information for a unique individual organism is contained in the fertlized egg from which it develops, so, I am now convinced, was the necessary information encapsulated somehow in the originally created organisms from which those geneologies developed. There is good reason to believe that there were several such original forms, with the exact number still unknown. The universal genetic code in no way militates against separate origins. The triplicate code is simply the simplest one that can code for the twenty odd amino acids as was anticipated by George Gamov long before it was established experimentally. It is quite reasonable that a universal metabolism is the ONLY way that life can proceed. Besides it really isn't that universal anyway with many basic differences between the various kingdoms. The fundamental diferences between the cytochrome respiratory enzymes and the enzymes for photosynthesis involve the substitution of the magnesium atom for iron. Perhaps that is the only way to convert respiration to its reverse, photosynthesis.

Considerations such as these are what prompted me, in 1984, to publish the Semi-meiotic Hypothesis for organic evolution and twenty-one years later, in 2005, to propose the Prescribed Evolutionary Hypothesis. The two are intimately related and neither has as yet been subjected to rigorous experimental investigation. Since the Darwinians no longer test their own hypothesis, it does not surprise me that they might hesitate to test one that with a single well controlled experiment could destroy the Darwinian model once and for all. Even should such an experiment fail, everything we are now learning from both chromosome structure and function as well as the great antiquity of several gene families pleads in favor of the prescribed scenario in which the environment played, at best, the trivial role of releasing latent, endogenous creative potentials exactly as ontogeny proceeds today. There is absolutely no need to postulate an intervening element in a phenomenon which is no longer occurring anyway.

I understand why some might not be interested in the Prescribed Evolutionary Hypothesis but I am quite unable to present my evaluation of organic evolution without presenting it as the only remaining explanation for the great mystery of evolution.

Thanks for listening.

John A. Davison said...

I do not agree that new species are now being generated. The Darwinians keep saying thisyet have not been able to simulate the process under laboratory conditions. As an experimentalist I will accept experimental evolution through selection and allelic mutation only when that has been demonstrated under controlled conditions.
Two forms are considered separate species when their hybrid is partially or completely sterile. This definition, proposed by Dobzhansky a Darwinian, is sound as a dollar and has yet to be verified. I have also repeatedly offered the following challenge. Name any two extant species for which it can be proved that one is ancestral to the other. No responses to date.

We observe a past evolution, not evolution in action as the Darwinians continue to assert.
Evolution has involved a progressive loss of potentiality until today we see little more than the substitution of alleles. Once again I will defer to a great zoologist.

"Thqe period of great fecundity is over: present biological evolution appears as a weakened process, declining or nearing its end. Aren't we witnessing the remains of an immense phenomenon close to extinction? Aren't the samll variations which are being recorded everywhere the tail end,the last oscillations of the evolutionary movement? Aren't our plants, our animals lacking some mechanisms which were present in the early flora and fauna?
Pierre Grasse, Evolution of Living Animals, page 71

I do not hesitate to answer Grasse's three questions with a resounding yes. Also Grasse has done what Darwinians rarely do. He has asked questions which is what science is all about.

I further propose that the mechanisms now missing may prove to be those proposed in the form of the Semi-meiotic hypothesis which I introduced in 1984, an hypothesis which to this day remains unacknowledged and untested.