Sunday, April 01, 2007

Dino demise no trigger for rise of mammals

Dino demise no trigger for rise of mammals, ABC, March 29, 2007, Anna Salleh ...

[Left: Mammal family tree, Science Daily. See full mammal family tree (1.6Mb pdf), BBC]

The death of the dinosaurs was not the catalyst for modern mammalian evolution that many people think, a new study shows. According to an international team of researchers, mammals evolved much slower than people believe. And it was not until 10 million years after the dinosaurs went extinct that there was a rise in the rate of new mammal species. ... evolutionary biologist, Dr Marcel Cardillo, part of team that publishes its results today in the journal Nature. Dr Cardillo ... and colleagues constructed the largest, most complete family tree of modern mammals. This involved mapping the relationship between 99 per cent of the roughly 4,500 mammalian species that exist today. "It's the first time anyone has put together an essentially complete evolutionary tree for mammals," Dr Cardillo said. The phylogenetic 'supertree' reveals an evolutionary pattern that contradicts conclusions based on the fossil record. The fossil record suggests there was one big burst in mammal evolution immediately after the dinosaurs died out, Dr Cardillo says. But the new supertree shows that mammals diversified into major groups such as primates, rodents and carnivores, 100 to 85 million years ago, during the age of the dinosaurs. The tree also shows the rate of evolution of mammals remained fairly constant after the dinosaurs died out 65 million years ago. And it was not until 10 million years later that the rate of mammalian evolution started to pick up again. By 35 million years ago, most of the modern day families of mammals, such as the dog and cat families, had evolved ... To create their phylogenetic supertree, Dr Cardillo and colleagues combined data from 2,500 different family trees, based on fossil, molecular and morphological data. Molecular studies compare similarities in the DNA of living species to find evolutionary relationships between them. ... The researchers used a large computer to analyse the data and to determine the branches of the tree. For each section of the tree they calculated the length of the branches, which represent the time elapsed between divergent groups, using a known rate of DNA mutations. They then used fossil data to peg absolute dates on the tree. The research challenges the short-fuse 'burst' model of mammalian evolution, which assumes mammals rapidly diversified into the number of species we see today. ... See also: BBC, CBS, CNews, CNN, EurekAlert!, Livescience, National Geographic, New Scientist, New York Times, ScienceDaily, ScienceNOW & The Independent.

Assuming this holds up (e.g. the molecular clock is accurate), this would then be evidence for major genotypic changes occurring hidden deep within genomes, millions of years before they are expressed as phenotypic changes, which then can appear in the fossil record.

This would then be consistent with my General Theory of Progressive Mediate Creation, in which God supernaturally imparts new genetic information:

"OLD-AGE or PROGRESSIVE CREATION: God guided the process of development, injecting information at key stages in the development of the universe and life to design new forms of organization." (Pearcey N., "We're Not in Kansas Anymore," Christianity Today, May 22, 2000, Vol. 44, No. 6, p.42)

at strategic points in life's history:

"Progressive creationism accepts much of the scientific picture of the development of the universe, assuming that for the most part it developed according to natural laws. However, especially with regard to life on earth, PCs hold that God intervened supernaturally at strategic points along the way. On their view, Creation was not a single six-day event but occurred in stages over millions of years. ... The PC view tends to overlap with other views, particularly with old-earth creationism." (Pennock, R.T., "Tower of Babel: The Evidence Against the New Creationism," MIT Press: Cambridge MA, 1999, Fourth Printing, pp.26-27).

But it would then be inconsistent with Darwinian evolution because natural selection can only `see' the phenotype (body), not the genotype (genes), i.e. "natural selection. ... simply cannot see genes ... [it] views bodies":

"No matter how much power Dawkins wishes to assign to genes, there is one thing that he cannot give them-direct visibility to natural selection. Selection simply cannot see genes and pick among them directly. It must use bodies as an intermediary. A gene is a bit of DNA hidden within a cell. Selection views bodies. It favors some bodies because they are stronger, better insulated, earlier in their sexual maturation, fiercer in combat, or more beautiful to behold. If, in favoring a stronger body, selection acted directly upon a gene for strength, then Dawkins might be vindicated. If bodies were unambiguous maps of their genes, then battling bits of DNA would display their colors externally and selection might act upon them directly. But bodies are no such thing. ... Bodies cannot be atomized into parts, each constructed by an individual gene. Hundreds of genes contribute to the building of most body parts and their action is channeled through a kaleidoscopic series of environmental influences: embryonic and postnatal, internal and external. Parts are not translated genes, and selection doesn't even work directly on parts. It accepts or rejects entire organisms because suites of parts, interacting in complex ways, confer advantages. The image of individual genes, plotting the course of their own survival, bears little relationship to developmental genetics as we understand it. Dawkins will need another metaphor: genes caucusing, forming alliances, showing deference for a chance to join a pact, gauging probable environments. But when you amalgamate so many genes and tie them together in hierarchical chains of action mediated by environments, we call the resultant object a body. Moreover, Dawkins's vision requires that genes have an influence upon bodies. Selection cannot see them unless they translate to bits of morphology, physiology, or behavior that make a difference to the success of an organism." (Gould S.J., "Caring Groups and Selfish Genes," in "The Panda's Thumb: More Reflections in Natural History," [1980], Penguin: London, Reprinted, 1990, pp.77-78).

Of course, such hidden genotypic changes, when they do eventually become expressed phenotypically, "must justify their existence before the tribunal of natural selection" (i.e. they must at least survive), but as the late Neo-Darwinist mathematician-geneticist J.B.S. Haldane (1892-1964), pointed out, "that is a very different matter" from "aris[ing], as Darwin thought, by natural selection (my emphasis):

"But if we come to the conclusion that natural selection is probably the main cause of change in a population, we certainly need not go back completely to Darwin's point of view. In the first place, we have every reason to believe that new species may arise quite suddenly, sometimes by hybridisation, sometimes perhaps by other means. Such species do not arise, as Darwin thought, by natural selection. When they have arisen they must justify their existence before the tribunal of natural selection, but that is a very different matter." (Haldane, J.B.S., "The Causes of Evolution," [1932], Princeton University Press: Princeton NJ, 1993, Second Printing, p.75)

Whatever, it sounds like yet another one among "nearly all ... evolutionary stories" that "have now been `debunked'" (my emphasis)!:

"It must be significant that nearly all the evolutionary stories I learned as a student, from Trueman's Ostrea/Gryphaea to Carruthers' Zaphrentis delanouei, have now been `debunked'. Similarly, my own experience of more than twenty years looking for evolutionary lineages among the Mesozoic Brachiopoda has proved them equally elusive." (Ager, D.V., 'The nature of the fossil record," Presidential Address delivered 5 March 1976, Proceedings of the Geologists' Association, Vol. 87, No. 2, 1976, p.131-135, p.132)

Stephen E. Jones, BSc. (Biology).


Exodus 11:1-10. 1Now the LORD had said to Moses, "I will bring one more plague on Pharaoh and on Egypt. After that, he will let you go from here, and when he does, he will drive you out completely. 2Tell the people that men and women alike are to ask their neighbors for articles of silver and gold." 3(The LORD made the Egyptians favorably disposed toward the people, and Moses himself was highly regarded in Egypt by Pharaoh's officials and by the people.) 4So Moses said, "This is what the LORD says: 'About midnight I will go throughout Egypt. 5Every firstborn son in Egypt will die, from the firstborn son of Pharaoh, who sits on the throne, to the firstborn son of the slave girl, who is at her hand mill, and all the firstborn of the cattle as well. 6There will be loud wailing throughout Egypt-worse than there has ever been or ever will be again. 7But among the Israelites not a dog will bark at any man or animal.' Then you will know that the LORD makes a distinction between Egypt and Israel. 8All these officials of yours will come to me, bowing down before me and saying, 'Go, you and all the people who follow you!' After that I will leave." Then Moses, hot with anger, left Pharaoh. 9The LORD had said to Moses, "Pharaoh will refuse to listen to you-so that my wonders may be multiplied in Egypt." 10Moses and Aaron performed all these wonders before Pharaoh, but the LORD hardened Pharaoh's heart, and he would not let the Israelites go out of his country.

2 comments:

Unguided said...

You say that this is evidence for PMC but this seems contrary to PMC to me. If God wanted to make changes by "secondary" means, why would he make changes that take 10-35M years to kick in? Wouldn't it be much simpler, more efficient and "better designed" for them to take effect immediately? What reason could a designer have to build in such a lag? If you were a designer and were happy to allow some lag for the joy of seeing your creation evolve, why make a change at a later date that takes 10-35M years when you could have just built it in at the start? Unless of course you are an incompetent designer and are tinkering with it as you go.

Also, I don't see how this new material is inconsistent with random mutation and natural selection. From my very rudimentary understanding, I thought the idea was that there can be a build up of mutations which may eventually result in a change to the phenotype. To that end there could also be changes to the phenotype as a result of random mutation which do not affect natural selection. For example, my understanding is that your DNA can have more in common with a person who has a major phenotype difference (eg skin colour) than one who may have your skin colour. As random mutation does not have to "see bodies" these changes can happen without the influence of "secondary" means. It is only if you mistakenly state that evolution is only natural selection that I could see the problem you are suggesting arising.

And yes the beauty of science is that explanations do change and improve over time, regardless of, but often impeded by, religion. Not just in biology but many areas of science. This is one of science's strengths not a weakness. It would be a weakness if science kept insisting the earth was flat, despite substantial evidence to the contrary.

Stephen E. Jones said...

Unguided

>You say that this is evidence for PMC but this seems contrary to PMC to me. If God wanted to make changes by "secondary" means, why would he make changes that take 10-35M years to kick in? Wouldn't it be much simpler, more efficient and "better designed" for them to take effect immediately?

This is an example of the atheist/agnostic "I would not do it that way, therefore God would not do it that way" argument.

First, that "changes .. to take effect immediately" would be "simpler" to us limited (in time, space and intellect) humans, it does not follow that they would be "simpler" (or if they were that that has any advantage) to an unlimited (in time, space and intellect) God.

Second, "more efficient" and "better designed" are not synonyms. I remember from my days of building a set of hi-fi speakers that the best designed speakers were those which had the lowest "efficiency"!

Third, what is "better designed" depends on what the designer's goals are. For example, if God's design goals assign a high value to what the physicist Freeman Dyson calls "The principle of maximum diversity":

"Why do we suffer? Why is the world so unjust? What is the purpose of pain and tragedy? I would like to have answers to these questions, answers which are valid at our childish level of understanding even if they do not penetrate far into the mind of God. My answers are based on a hypothesis which is an extension both of the Anthropic Principle and of the argument from design. The hypothesis is that the universe is constructed according to a principle of maximum diversity. The principle of maximum diversity operates both at the physical and at the mental level. It says that the laws of nature and the initial conditions are such as to make the universe as interesting as possible. As a result, life is possible but not too easy. Always when things are dull, something new turns up to challenge us and to stop us from settling into a rut. Examples of things which make life difficult are all around us: comet impacts, ice ages, weapons, plagues, nuclear fission, computers, sex, sin and death. Not all challenges can be overcome, and so we have tragedy. Maximum diversity often leads to maximum stress. In the end we survive, but only by the skin of our teeth." (Dyson F.J., "Infinite In All Directions," [1988], Harper & Row: New York NY, Reprinted, 1989, p.298)

then a Designer may well decide to "make changes by secondary means" which could "take 10-35M years to kick in".

>What reason could a designer have to build in such a lag? If you were a designer and were happy to allow some lag for the joy of seeing your creation evolve, why make a change at a later date that takes 10-35M years when you could have just built it in at the start? Unless of course you are an incompetent designer and are tinkering with it as you go.

See above.

One reason that God might have created in such that He could be dismissed as "an incompetent designer" by those who wanted there to be no God, was given by the French mathematican and Christian apologist Blaise Pascal (1623-1662). That is, God designed nature with: 1) enough evidence for the believer in Him to have rational grounds for his belief; but 2) not enough evidence to force those who don't want to believe in Him to believe unwillingly; and yet, 3) enough evidence that those who choose not to believe in Him to have no excuse for their unbelief on the Day of Judgment:

"There is sufficient clearness to enlighten the elect, and sufficient obscurity to humble them. There is sufficient obscurity to blind the reprobate, and sufficient clearness to condemn them and make them inexcusable." (Pascal B., "Pensées," 578, [1660], W.F. Trotter, Trans).

I agree with Pascal on this.

>Also, I don't see how this new material is inconsistent with random mutation and natural selection.

Nothing is "inconsistent with random mutation and natural selection" in an absolute sense. As Dawkins pointed out, between any "X" and "Y", "it is always possible to conceive of a series of infinitesimally graded intermediates between them":

"To 'tame' chance means to break down the very improbable into less improbable small components arranged in series. No matter how improbable it is that an X could have arisen from a Y in a single step, it is always possible to conceive of a series of infinitesimally graded intermediates between them. However improbable a large-scale change may be, smaller changes are less improbable. And provided we postulate a sufficiently large series of sufficiently finely graded intermediates, we shall be able to derive anything from anything else, without invoking astronomical improbabilities." (Dawkins, R., "The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design," W.W. Norton & Co: New York NY, 1986, pp.317-318)

irrespective of whether it actually happened that way.

So if you want an all-purpose, Swiss-Army knife, mechanism that can be imposed over the top of any "X [that] could have arisen from a Y" irrespective (and even despite) the evidence, then Darwinian "random mutation and natural selection" is for you.

>From my very rudimentary understanding, I thought the idea was that there can be a build up of mutations which may eventually result in a change to the phenotype.

A "very rudimentary understanding" is an advantage for believing in Darwinian "random mutation and natural selection! See above.

>To that end there could also be changes to the phenotype as a result of random mutation which do not affect natural selection.

Indeed. Darwin had to admit there were "numerous other cases" of "modifications of structure, which are considered ... to be generally of a highly important nature" but which "cannot have been influenced by natural selection" and "would not have been accumulated and augmented through natural selection":

"In numerous other cases we find modifications of structure, which are considered by botanists to be generally of a highly important nature, affecting only some of the flowers on the same plant, or occurring on distinct plants, which grow close together under the same conditions. As these variations seem of no special use to the plants, they cannot have been influenced by natural selection. ...We thus see that with plants many morphological changes may be attributed to the laws of growth and the inter-action of parts, independently of natural selection. ... From the fact of the above characters being unimportant for the welfare of the species, any slight variations which occurred in them would not have been accumulated and augmented through natural selection. ... Thus, as I am inclined to believe, morphological differences, which we consider as important ... first appeared in many cases as fluctuating variations, which sooner or later became constant through the nature of the organism and of the surrounding conditions, as well as through the intercrossing of distinct individuals, but not through natural selection; for as these morphological characters do not affect the welfare of the species, any slight deviations in them could not have been governed or accumulated through this latter agency. " (Darwin, C.R., "The Origin of Species By Means of Natural Selection," [1859], John Murray: London, Sixth Edition, 1872, Reprinted, 1882, pp.174-176)

But then that just shows that natural selection is not the "Master Breeder infinitely wise and patient ... a Being ... little less than God Himself" that Darwin originally conceived it to be:

"… Darwin asked his imaginary reader to suppose the existence of: `a Being with penetration sufficient to perceive differences in the outer and innermost organization quite imperceptible to man, and with forethought extending over future centuries to watch with unerring care and select for any object the offspring of an organism produced under the foregoing circumstances, I can see no conceivable reason why he could not form a new race (or several were he to separate the stock of the original organism and work on several islands) adapted to new ends. As we assume his discrimination, and his forethought, and his steadiness of object, to be incomparably greater than those qualities in man, so we may suppose the beauty and complications of the adaptations of the new races and their differences from the original stock to be greater than in the domestic races produced by man's agency.... With time enough, such a Being might rationally (without some unknown law opposed him) aim at almost any result....Seeing what blind capricious man has actually effected by selection during the few last years, and what in a ruder state he has probably effected without any systematic plan during the last few thousand years, he will be a bold person who will positively put limits to what the supposed Being could effect during whole geological periods' [Darwin, F., ed. "The Foundations of the Origin of Species, Two Essays Written in 1842 and 1844, by Charles Darwin," Cambridge UK, 1909, pp.85-87]. A striking conception, this idea of a Master Breeder infinitely wise and patient, with infinite time at his disposal, who, carefully selecting from among the variations in nature those which suited his purposes, molded organic nature to his own wise ends. Such a Being could be little less than God Himself." (Greene J.C., "The Death of Adam: Evolution and its Impact on Western Thought," [1959], Mentor: New York NY, 1961, reprint, pp.261-262).

>For example, my understanding is that your DNA can have more in common with a person who has a major phenotype difference (eg skin colour) than one who may have your skin colour.

I (and I expect that most biologists) would not regard "skin colour" as "a major phenotype difference".

>As random mutation does not have to "see bodies" these changes can happen without the influence of "secondary" means.

You are getting "random mutation" mixed up with natural selection. It is natural selection that `sees' bodies, not "random mutation."

But if mutations can make major changes `below the radar' of natural selection, then, that would relegate natural selection to a minor role. As Gould put it, "genetic variation ... must be undirected" otherwise if there is "heritable, adaptive variation, then creativity lies in the process of variation, and selection only eliminates the unfit":

"Darwin's contemporaries understood that natural selection hinged on the argument for creativity. Natural selection can only eliminate the unfit, his opponents proclaimed; something else must create the fit. Thus, the American Neo-Lamarckian E. D. Cope wrote a book with the sardonic title The Origin of the Fittest, and Charles Lyell complained to Darwin that he could understand how selection might operate like two members of the `Hindoo triad'-Vishnu the preserver and Siva the destroyer-but not like Brahma the creator ... The claim for creativity has important consequences and prerequisites that also become part of the Darwinian corpus. Most prominently, three constraints are imposed on the nature of genetic variation (or at least the evolutionarily significant portion of it). (i) It must be copious since selection makes nothing directly and requires a large pool of raw material. (ii) It must be small in scope. If new species characteristically arise all at once, then the fit are formed by the process of variation itself, and natural selection only plays the negative role of executioner for the unfit. True saltationist theories have always been considered anti-Darwinian on this basis. (iii) It must be undirected. If new environments can elicit heritable, adaptive variation, then creativity lies in the process of variation, and selection only eliminates the unfit. Lamarckism is an anti-Darwinian theory because it advocates directed variation; organisms perceive felt needs, adapt their bodies accordingly, and pass these modifications directly to offspring." (Gould, S.J., "Darwinism and the Expansion of Evolutionary Theory," Science, Vol. 216, 23 April 1982, pp.380-387, p.381).

Of course if an Intelligent Designer/God directed mutations at strategic points in life's history (which is what my PMC theory maintains), then both random mutation and natural selection would be relegated to a comparatively minor role.

>It is only if you mistakenly state that evolution is only natural selection that I could see the problem you are suggesting arising.

I don't "state that evolution is only natural selection." But Darwinism does state that "natural selection" is the only creator of biological design, particularly "the 'Paley's watch', or 'Organs of extreme Perfection and complication', kind of adaptation that seems to demand a shaping agent at least as powerful as a deity":

"The theory of species selection, growing out of that of punctuated equilibria, is a stimulating idea which may well explain some single dimensions of quantitative change in macroevolution. I would be very surprised if it could be used to explain the sort of complex multidimensional adaptation that I find interesting, the 'Paley's watch', or 'Organs of extreme Perfection and complication', kind of adaptation that seems to demand a shaping agent at least as powerful as a deity." (Dawkins, R., "The Extended Phenotype: The Long Reach of the Gene," [1982], Oxford University Press: Oxford UK, 1983, p.108)

>And yes the beauty of science is that explanations do change and improve over time, regardless of, but often impeded by, religion.

There is no such thing as "religion". Just religions. And far from being impeding science, the Christian religion gave birth to science, i.e. "it is the Christian world which finally gave birth ... to the experimental method of science itself ...science ... owes its origins to an act of faith that the universe can be rationally interpreted, and that science today-is sustained by that assumption.":

"Although we may … deplore the unconscionable persecution of thought which is one of the less appetizing aspects of medieval history, we must also observe that in one of those strange permutations of which history yields occasional rare examples, it is the Christian world which finally gave birth in a clear articulate fashion to the experimental method of science itself. Many things undoubtedly went into that amalgam: Greek logic and philosophy, the experimental methods of craftsmen in the arts as opposed to the aristocratic thinker-all these things have been debated. But perhaps the most curious element of them all is the factor dwelt upon by Whiteheadthe sheer act of faith that the universe possessed order and could be interpreted by rational minds [Whitehead, A.N., "Science and the Modern World," Mentor, 1948, pp.4-15]. For, as Whitehead rightly observes, [Ibid., p.17] the philosophy of experimental science was not impressive. It began its discoveries and made use of its method in the faith, not the knowledge, that it was dealing with a rational universe controlled by a Creator who did not act upon whim nor interfere with the forces He had set in operation. The experimental method succeeded beyond men's wildest dreams but the faith that brought it into being owes something-to the Christian conception of the nature of God [Ibid., p. 14]. It is surely one of the curious paradoxes of history that science which professionally has little to do with faith, owes its origins to an act of faith that the universe can be rationally interpreted, and that science today-is sustained by that assumption." (Eiseley, L.C., "Darwin's Century: Evolution and the Men Who Discovered It," [1958], Anchor Books: Doubleday & Co: Garden City NY, Reprinted, 1961, p.62)

And you have made science your "religion" if you believe that its "explanations" all "change and improve over time."

Even those "explanations" that scientists find most uncongenial (like if the origin of the Universe with its fine-tuned initial conditions, constants and laws; the origin of life; the origin of life's major groups and the origin of man; was due not to a `blind watchmaker', but to an Intelligent Designer, who is also the God of the Bible, to whom scientists like all humans are accountable).

The fact is that because science is run by humans (who like all humans are also guilty sinners) it will never "change and improve over time" to accept that, even if it is true, but will continue to dismiss it as "religion".

Like you do.

>Not just in biology but many areas of science. This is one of science's strengths not a weakness. It would be a weakness if science kept insisting the earth was flat, despite substantial evidence to the contrary.

See above on "science" being your "religion" and, if Christianity is true (which it is) a false one at that!

Stephen E. Jones