een fysicus over de kosmos, de aarde en het leven

Presentatie over: "een fysicus over de kosmos, de aarde en het leven"— Transcript van de presentatie:

1 een fysicus over de kosmos, de aarde en het leven
Dr. Ard Louis Department of Physics University of Oxford

2 Botsende culturen? Woorden Gewoonten Tradities Gedrag Geloof Waarden
Christelijke subculturen Wetenschapelijke subculteren cultuur ligt vaak onder de oppervlakte Woorden Gewoonten Tradities Gedrag Geloof Waarden Aanamen Mijn argument: Much of the tension between “evolution” and “faith” is due to unrecognized “cultural assumptions” Gebed: Heer, dit is een moeilijk onderwerp waarover veel van Uw kinderen sterke gevoelens hebben. Help mij om niet meer of niet minder te zeggen dan U zou willen. Laat mijn woorden to opbouw en niet tot afbreken zijn. mijn achtergrond met HG classic evangelical -- high view of scripture as the inerrant inspired word of God Indian student and Holy Spirit joke about Englishman, German, Frenchman, Italian quite good ( quite good v.s. really quite good suspenders and braces lots of stories ... I come from a particular scientific culture, but my work is interdisciplinary, and so I often have to cross cultures PhD in theoretical physics, but last 8 years in chemistry department, now working a lot on biologically inspired problems Broad-brush approach -- choose good examples to illustrate (a la Nicky Gumbel) -- hopefully better than my HS talk Finally, I am a critical realist -- critical because from a reformed background: our minds are easily fooled -- realist because I think there is a real world out there -- not postmodern, although I appreciate that our knowledge is always mediated etc..

3 Beginnen met de Bijbel Bijbel aan de grondslag van mijn leven
Ik ben classiek evangelisch/charismatisch in mijn Bijbel interpretatie en praxis Wetenschap heeft een dienende relatie, geen gezag – kan b.v. helpen met interpretatie Henri Blocher “In the Beginning” IVP (1984) p 25 Nooit ons wereldbeeld boven de Bijbel B.v. Copernicus/Galileo en Aristoteles

4 Culturele verschillen:
Metaphoren zijn belangrijk Toeval etc… Antropomorphisatie (survival of the fittest) Waarom een groot verschil tussen Christelijke profesioneele wetenschappers en leken? Wetenschappelijk “bewijs” met tapijt argumenten

5 Biologische self-assembly
Keiichi Namba, Kyoto about 10 times as many bacteria in your gut as cells in your body 1014 v.s 1013 Keiichi Namba, Osaka Biologische systemen self-assemble (ze vormen zichzelf) Kunnen we dat begrijpen? Kunnen we het nabootsen? (Nanotechnologie)

6 Virus self-assembly viruses T=1 T=3 4/4/2017 6

7 Self-assembly van “computer virusen”
Monte-Carlo simulaties: stochastische optimalisatie 7

8 Self-assembly met lego?
I pinch myself that I am paid to do this ... 8

9 Eiwitten en het Paradox van Levinthal
C.M. Dobson, Nature 426, 884 (2003) Levinthal Paradox: 150 amino acids ~10 angles between them ~10150 different states. How does protein find its folded native structure? CULTUUR VERSCHIL: Physici/Chemici/Ingenieurs vinden dit belangrijk; Biologen niet zo belangrijk The self-assembly stories I just told you are closely related to a different and very famous problem, namely that of how a protein folds to find its native state. Proteins, the molecular workhorses of the cell, are long molecules made up of a string of individual amino-acids, or residues. They fold up into a compact structure, not unlike a piece of string bunching up into a small ball. What is amazing, is that many proteins fold into essentially the same three-dimensional structure each time, and that their biological function is closely linked to this shape. How do proteins find (or self-assemble) into this shape each time? Naively, this would seem almost impossible, as illustrated by the following famous argument first put forward by Cyrus Levinthal : The average protein is about 300 residues long – if you wish think of it as a string of 300 beads. Now assume for simplicity that each residue (or bead) can rotate around it’s neighbour at 10 different angles (this is an underestimate). Then the number of different states of the protein is on the order of 10300, a number so enormous that even the adjective astronomical is insufficient. If you assume that a protein can sample a new configuration very quickly, say every femtosecond (10-15s), it would still take 1010 (10 Billion) times the age of the universe for a protein to sample all its configurations. Nevertheless proteins do fold in finite time, often in fractions of a second. So the Levinthal paradox raises the question: How does the protein achieve this feat of finding the same state, this needle in the haystack, each time? What is guiding this process of self-assembly? What now think that proteins search for their ground states in a free-energy landscape that looks more like a funnel. As you can see on the slide, many different starting configurations lead to the same low free-energy folded state. So a functioning protein has encoded in it not only its final structure, but also the topology of its search-space. Our understanding of how this search process works has benefited from many thousands of researchers working on this problem. In fact, we used some of the concepts form the protein folding literature to design our “self-assembling computer viruses”. we used same design principles to make viruses self-assemble

10 Biologicsche self-assembly
Als we het niet zouden zien zouden argumenten er tegen sterk lijken(Levinthal) “onmogenlijkheids argumenten” hebben weinig success in de biologie Now I want to also make this point: If somehow proteins came to us fully formed, and we never observed them folding, then a theoretical argument like Levinthal’s paradox might seem quite compelling. The fact that it doesn’t work at all, is a good example of why purely deductive mathematical arguments are often treated with some suspicion in biology. There is a lot that we still don’t understand. So the main point of this section was to introduce to you the amazingly beautiful concept of self-assembly, but also to describe the Levinthal paradox, which on the surface may seem like a real paradox, but is in fact, in a rather subtle way, based on the false premise of an unstructured search space.

11 Hoe interpreteren we de natuur?: Natuur Theologie:
Paley – Newman – Barth ….. The fundamental thesis of the book is that if nature is to disclose the transcendent, it must be "seen" or "read" in certain specific ways -- ways that are not themselves necessarily mandated by nature itself. It is argued that Christian theology provides a schema or interpretative framework by which nature may be "seen" in a way that enables and authorizes it to connect with the transcendent. --- A. McGrath p x about "the Open Secret"

12 Wonderlijke toepasselijkheid van de taal van de wiskunde
Quantum Mechanics + Relativity = Antimatter Schrödinger equation (Quantum Mechanics) + Paul Dirac Energy-Momentum (Special Relativity) = Dirac Equation (1928) Electrons Positrons (antimatter) discovered 1932 See also: “The applicability of mathematics as a philosophical problem”, Mark Steiner HUP (1998); E. Wigner "The Unreasonable Effectiveness of Mathematics in the Natural Sciences," in Communications in Pure and Applied Mathematics, vol. 13, No. I (February 1960) See also the work of Polkinghorne, e.g. “Beyond Science” CUP or Canto In many ways the “design” here elicits wonder, similar to that experienced when viewing mountains, or the stars etc Thus science helps us to better appreciate the wonders of creation, it extends our ability to view spatial design -- from the smallest atoms, to the mysterious creatures of the ocean depths, to the distant galaxies -- as well as temporal design -- think of the amazing age of the universe, and our own very brief sojourn, “a few seconds before midnight”. Zie ook: “The applicability of mathematics as a philosophical problem”, Mark Steiner HUP (1998); "The Unreasonable Effectiveness of Mathematics in the Natural Sciences," in Communications in Pure and Applied Mathematics, vol. 13, No. I (February 1960), Eugene Wigner

13 Wij zijn gemaakt van sterrenstof: He C via een resonancie
“A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics .. and biology” His atheism was “deeply shaken” This quote comes from the November 1981 issue of the Cal Tech alumni magazine, where Hoyle wrote: “Would you not say to yourself, "Some supercalculating intellect must have designed the properties of the carbon atom, otherwise the chance of my finding such an atom through the blind forces of nature would be utterly minuscule." Of course you would.... A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.” (Hoyle F., "The Universe: Past and Present Reflections", in Engineering and Science, November 1981, p12). See also (O. Gingerich, "Dare a Scientist Believe in Design", in J.M. Templeton ed., Evidence of Purpose: Scientists Discover the Creator, Continuum: New York, 1994, pp24-25) Hoyle( ) is also know for his advocacy of the “Steady State” model of the universe, a position he defended in part because he was unhappy with the way the Big Bang theory points to a beginning, and therefore suggests a “beginner”. Sir Fred Hoyle, Cambridge U

14 Tapijt argumenten Wetenschap als een “tapijt”
--de kracht ligt niet aan één enkele draad maar aan het geheel en hoe ze zijn zamengewoven. Je kunt aan een paar draadtjes trekken, maar daardoor breek je het tapijt niet. Oma I was a PhD student at Cornell, working with David Mermin’s great text book collaborator Neil Ashcroft, when Collins and Pinch wrote their book -- Pinch was on the floor just above us. Mermin is one of my heroes -- he writes beautifully, I recommend for example his book “Boojums all the way through” The Golemization of Relativity, David Mermin, Physics Today 49, p11 April 1996 . Ik geloof net zo in het christendom als dat ik geloof dat de zon is opgegaan – niet alleen omdat ik hem zie, maar omdat dit mij in staat stelt om al het andere te zien C.S. Lewis, “Theology as Poetry” in The Weight of Glory,

15 Natuurgeschiedenis Grootheid van God het universum:
100 miljard stellenstelsels, met elk 100 miljard sterren De hemel verhaalt van Gods majesteit - Psalm 19 Wat is de mens? Psalm 8 In our galaxy there are 100,000 million stars, like our sun. our galaxy is one of 100,000 million galaxies. In a throwaway line in Genesis, the writer tells us, "he also made the stars" .. Gen 1:16 Such is his power To put this into perspective, animals didn’t appear until the last 2 hours -- dinosaurs went extinct in the the last 20 minutes -- anatomically modern humans -- the last one or two seconds .... recorded history, about last 0.1s -- your lifespan, the last millisecond Earth's history can be divided into five major time units called eras. The first two eras (the archean and the proterozoic) will be grouped together and called the: Precambrian. The next three eras are the Paleozoic, Mesozoic, and Cenozoic. These three eras are further divided into units called periods. For example, the Mesozoic era contains the Triassic, Jurassic, and Cretaceous periods. or the Paleozoic ends with the Permian period Many of the geological time periods end with mass extinction. The Permian-Triassic extinction event wipes out about 90% of all animal species; this fourth extinction event is the most severe mass extinction known. Cretaceous-Tertiary extinction event in 65 wipes out 50-80% of all species If it were one 24 hour day, then last 2 seconds humans appear..... Psalm 8: 3 When I consider your heavens, the work of your fingers, the moon and the stars, which you have set in place, 4 what is man that you are mindful of him, the son of man that you care for him? In our galaxy there are 100,000 million stars, like our sun. our galaxy is one of 100,000 million galaxies. In a throwaway line in Genesis, the writer tells us, "he also made the stars" .. Gen 1:16

16 Natuurgeschiedenis Grootheid van God Analoog aan het universum:
Ruimte   tijd 24 uurige aarde – je leven = 1 milliseconde De hemel verhaalt van Gods majesteit - Psalm 19 Wat is de mens? Psalm 8 In our galaxy there are 100,000 million stars, like our sun. our galaxy is one of 100,000 million galaxies. In a throwaway line in Genesis, the writer tells us, "he also made the stars" .. Gen 1:16 Such is his power To put this into perspective, animals didn’t appear until the last 2 hours -- dinosaurs went extinct in the the last 20 minutes -- anatomically modern humans -- the last one or two seconds .... recorded history, about last 0.1s -- your lifespan, the last millisecond Earth's history can be divided into five major time units called eras. The first two eras (the archean and the proterozoic) will be grouped together and called the: Precambrian. The next three eras are the Paleozoic, Mesozoic, and Cenozoic. These three eras are further divided into units called periods. For example, the Mesozoic era contains the Triassic, Jurassic, and Cretaceous periods. or the Paleozoic ends with the Permian period Many of the geological time periods end with mass extinction. The Permian-Triassic extinction event wipes out about 90% of all animal species; this fourth extinction event is the most severe mass extinction known. Cretaceous-Tertiary extinction event in 65 wipes out 50-80% of all species If it were one 24 hour day, then last 2 seconds humans appear..... Psalm 8: 3 When I consider your heavens, the work of your fingers, the moon and the stars, which you have set in place, 4 what is man that you are mindful of him, the son of man that you care for him?

17 Natuurgeschiedenis EMOTIONEEL DEBAT ? Determineert waar we vandaan komen wie we zijn en hoe we zouden moeten leven?

18 Intermezzo: het vertroebelend woord Evolutie
1) Evolutie as Natuurgeschiedenis De aarde is oud(+/- 4.5 Billion years) Complexere levensvormen volgen op simplere levensvormen 2) Evolutie as a mechanisme voor biologische complexiteit Mutaties en natuurlijke selectie (note: Christenen zijn het er over eens dat God dit geschapen heeft) micorevolutie, immuunsysteem etc… 3) Evolutie als wereldbeeld (evolutionisme) George Gaylord Simpson: "De mens is het resultaat van een doelloos en natuurlijk proces dat hem niet heeft bedoeld. Hij is niet gepland. of Richard Dawkins: "Darwin maakt het mogelijk om intellectueel vervulde atheist te zijn.” Zie ook Bas Haring, Midas Dekkers, etc.. If you want to go “gloves off” then surely it is the scientism of the “big picture” that you should attack? 18

19 Tapijt argumenten: case study 1: een oude aarde ?
Science is a tapestry -- you can pick at a few strings, but that doesn’t break the whole cloth Radiometric dating (many overlapping isotopes) ice cores: up to 8000 years -- volcanoes like Vesuvius up to 740,000 years Milankovitch cycles Tree rings All these methods (when used properly) agree. There is no scientific controversy Radiometric Dating A Christian Perspective Dr. Roger C. Wiens

20 Tapijt argument: een oude aarde ?
Milankovitch Cycles: here seen in 420,000 years of ice core data from Vostok, Antarctica research station.

21 Common descent in biology?
So, having established that there are difference in cultures between the way that physicists and biologists weave together tapestry arguments in their respective subfields, let me give you an example of the kinds of tapestry arguments evolutionary biologists use to weave together evidence for the hypothesis of common descent, the idea that we share common ancestors with other species -- here on this slide you see the first picture we know of in Darwin’s notebooks of this idea, dating from 1836. Page from Darwin's notebooks ~ circa1837 showing his first known sketch of an evolutionary tree depicting common descent.

22 Case study 2: evolution of horses
Can sound like weak inductive reasoning to many physical scientists And in this slide we see a reconstruction of what biologists think is the story of common descent for horses -- I’ve recently seen a biologist use this to prove to his audience that evolution is true. The story emphasises things like a sustained decrease in the size of the extra bones in the forefoot as fossils become more recent. Biologists tend to think this is very convincing, but to some physical scientists, this stringing together of fossil pictures seems like a pretty weak strand of evidence. Part of the reason for this difference in assessment is that the biologists are implicitly thinking of this story as one of a great multitude of strings in a tapestry of evolutionary common descent, but that they don’t make these assumptions explicit.

23 Case study 3: common descent of human & chimp?
Let me give you another, perhaps more controversial example, relating the common descent of apes and humans. Here you see the sequence: New world monkeys -> old world monkeys -> gibbons -> orang-utans -> gorillas -> chimpanzees -> humans Divergence of the chimpanzee and human lineages occurred about 6 million years ago; the times of lineage divergence are not to scale News & Views: The chimpanzee and us, Wen-Hsiung Li and Matthew A. Saunders, Nature 437, (1September 2005) .

24 tapestry arguments in biology: chromosomal banding:
Humans have 46 (2 X 23) chromosomes Apes have 48 (2 X 24) chromosomes chromosomal banding comes from staining, and gives a rough coarse-grained indication structure of the DNA. Note how similar the human DNA is to that of other primates (H=Human, C=Chimp, G=Gorilla, U=Urang-Utan) chromosome 2: Human, Chimp, Gorilla, Orang-utan The origin of man: a chromosomal pictorial legacy. J.J Yunis and O. Prakash, Science 215, 1525 (1982)

25 tapestry arguments in biology: fusion of chromosome 2?
chromosomal banding comes from staining, and gives a rough coarse-grained indication structure of the DNA. Note how similar the human DNA is to that of other primates (H=Human, C=Chimp, G=Gorilla, U=Urang-Utan) chromosome 2: Human, Chimp, Gorilla, Orang-utan

26 tapestry arguments in biology: evidence from the human genome
Chromosome 2 is unique to the human lineage of evolution, having emerged as a result of head-to-head fusion of two acrocentric chromosomes that remained separate in other primates. The precise fusion site has been located in 2q13−2q14.1 (ref. 2; hg16:114,455,823−114,455,838), where our analysis confirmed the presence of multiple subtelomeric duplications to chromosomes 1, 5, 8, 9, 10, 12, 19, 21 and 22 (Fig. 3; Supplementary Fig. 3a, region A). During the formation of human chromosome 2, one of the two centromeres became inactivated (2q21, which corresponds to the centromere from chimp chromosome 13) and the centromeric structure quickly deterioriated [42]. Now this would have some consequences – for example, we know that chromosomes have special sequences at their ends called telomeres, and a special sequence in the middle called a centromere that they use to make sure that when a cell divides, one copy goes to one cell and the other goes to the other. If two chromosomes fuse, then we would expect to see extra telomere and centromere remnants. So it was very satisfying when, in 2005, the exact fusion site was found, with a remnant of the telomeres from base-pairs from 114,455,823−114,455, I think that’s pretty amazing. Generation and annotation of the DNA sequences of human chromosomes 2 and 4, L.W. Hillier et al., Nature 434, 724 (2005).

27 endogenous retroviruses
HERV-K insertions There is further genomic evidence for common descent. For example retroviruses can sometimes insert their DNA into our germ cells, and when we look at these viral insertions, and when they came in, it again correlates nicely with the expected evolutionary tree. There are other similar threads of evidence related to mobile genetic elements and pseudo-genes, all of which correlate well with common descent. In humans endogenous retrovirus sequences make up about 1% of the genome. Lebedev, Y. B., et al. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247:

28 tapestry arguments in biology: more threads of evidence
Genetic threads SINEs (Alu ) LINEs Retroviral insertions pseudo genes (e.g. olefaction) chromosomal inversions Phenotypal similarities Fossils

29 Tapestry arguments in biology
The tapestry for: do humans and chimpanzees share a common ancestor? seems to most biologists to be unbreakably strong For some physicists, mathematicians and engineers -- these arguments may still seem foreign and vague; It doesn’t “smell” like the scientific method they are familiar with -- for example: where is the repeatability? What is the predictive power of these arguments? Where are the numbers? So, the tapestry for: humans and chimpanzees share a common ancestor seems to most biologists and to me to be almost unbreakably strong Now these slides are ones I sometimes use to try and convince my audience that the threads for common descent can be woven together tightly. But in spite of my best efforts, I often meet scepticism, particularly by those trained in the physical sciences. They find these types of arguments less than convincing – the kinds of criticisms I often hear are: Isn’t this a “just so story?” Where is the predictability? Can you repeat this in the lab? Their scepticism comes, I believe, from different cultures of science that are clashing here. These difference are especially pronounced when we look at a historical science like evolution, where the logic is closer to that of a court of law trying to piece together “who done it”, rather than what we all know and love as repeatable lab-based science.

30 TERUGBLIK: Tapijt argumenten Vaak moeilijk voor een leek om goed in te schatten Verschillen van discipline tot discipline Biologen (ook Christelijke) geloven in de evolutie (type 1 & 2) omdat tapijt argumenten daarvoor sterk zijn. Er blijven uiteraard nog veel vragen over details. VOLGENDE VRAAG: Hoe zit het dan met de Bijbel en Genesis 1&2

31 Newton en de planeten De planeet banen zijn onstabiel: God “hervormd” ze Sir Isaac Newton This quote is from Principia Mathematica Isaac Newton wrote extensively on theology, especially about prophecy, much of it rather heterodox. For example, later in life he began to doubt the trinitarian nature of God. Nevertheless, he was, I believe, deeply motivated by Christian belief. The best biography on Newton is probably “Never at Rest : A Biography of Isaac Newton” by Richard S. Westfall (Cambridge University Press, 1983), see also the shorter The Life of Isaac Newton by the same author (CUP, 1994). For a recent discussion of his faith, see the web page John Hedly Brooke, Science and Religion , CUP 1991, p147 For, as Leibniz objected, if God had to remedy the defects of his creation, this was surely to demean his craftmanship

32 Leibnitz werpt tegen “als God de gebreken van zijn schepping moest herstellen, dit zeker afbreuk zou doen aan zijn ambachtelijke vaardigheid” John Hedley Brooke, Science and Religion, CUP 1991, p147 Newton thought that God might have to occasionally intervene to stabilise the solar system. John Hedly Brooke, Science and Religion , CUP 1991, p147 For, as Leibniz objected, if God had to remedy the defects of his creation, this was surely to demean his craftmanship

33 Leibnitz werpt tegen “En ik houd vol dat God, als hij wonderen verricht, dat niet doet om in de behoeften van de natuur te voorzien, maar in die van de genade. En wie anders denkt moet noodzakelijk een lage dunk hebben van de wijsheid en macht van God” -- geen God van de gaten! Newton thought that God might have to occasionally intervene to stabilise the solar system. John Hedly Brooke, Science and Religion , CUP 1991, p147 For, as Leibniz objected, if God had to remedy the defects of his creation, this was surely to demean his craftmanship And I hold, that when God works miracles, he does not do it in order to supply the wants of nature, but those of grace. Whoever thinks otherwise, must needs have a very mean notion of the wisdom and power of God (cited in Colin Brown “Miracles and the Critical Mind”) And I hold, that when God works miracles, he does not do it in order to supply the wants of nature, but those of grace. Whoever thinks otherwise, must needs have a very mean notion of the wisdom and power of God Leibniz -- Clarkson letters (cited in Colin Brown “Miracles and the Critical Mind”)

34 God van de gaten? “God of the Gaps” was coined by Charles Coulson in his book Christianity in an Age of Science, 25th Riddell Memorial Lecture Series, (Oxford University Press, 1953 ). Coulson was one of the great theoretical chemists of the past century, famous for his development of valence theory. He was also an active Methodist minister, as is Norman March, who was his successor at Oxford. I often hear Christians say: “Isn’t X amazing -- scientists don’t understand ...”, Similarly, I hear people saying -- now we do understand Y, therefore we no longer need God. At the popular level, the perception that “Design” by God mainly relates to things that appear to be miraculous is very common. Cardinal Newman in “The Idea of a Christian University” critiques Archdeacon Paley’s Natural Theology We begrijpen iets niet --> God in het gat van onze kennis “When we come to the scientifically unknown, our correct policy is not to rejoice because we have found God; it is to become better scientists” Prof. Charles Coulson, Oxford U 34

35 Meer Intermezzo’s? Bijbelse taal
“jaagt God voor de Leeuwen? (Job 38, Ps 104)? Secondaire en Primaire oorzaken Natuurwetten beschrijven het “gewone handelen” van God? Denkpatronen over wetenschap en geloof Nietsandersdanisme Mechanisme en betekenis Wetenschapisme God van de gaten

36 Dawkins en atheisme van de gaten?
"The individual organism ... is not fundamental to life, but something that emerges when genes, which at the beginning of evolution were separate, warring entities, gang together in co-operative groups as "selfish co-operators". The individual organism is not exactly an illusion. It is too concrete for that. But it is a secondary, derived phenomenon, cobbled together as a consequence of the actions of fundamentally separate, even warring agents. From Richard Dawkins, Unweaving the Rainbow, (Penguin, London, 1998) p 308. The Frontiers of Scientific Vision, Ed. J Cornwell. Oxford University Press, Oxford, 1995, . (pp. 123, 131). Prof. Richard Dawkins (Oxford)

37 Gene language [Genes] are trapped in huge colonies, locked inside highly intelligent beings, moulded by the outside world, communicating with it by complex processes, through which, blindly, as if by magic, function emerges. They are in you and me; we are the system that allows their code to be read; and their preservation is totally dependent on the joy that we experience in reproducing ourselves. We are the ultimate rationale for their existence. [Genes] swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. Here, even the “is” is contested … Denis Noble -- The Music of Life: Biology Beyond the Genome (OUP 2006) Richard Dawkins -- The Selfish Gene (1976)

38 Natuurgeschiedenis EMOTIONEEL DEBAT ? Determineert waar we vandaan komen wie we zijn en hoe we zouden moeten leven?

39 Intermezzo: het woord Evolutie
1) Evolutie as Natuurgeschiedenis De aarde is oud(+/- 4.5 Billion years) Complexere levensvormen volgen op simplere levensvormen 2) Evolutie as a mechanisme voor biologische complexiteit Mutaties en natuurlijke selectie (note: Christenen zijn het er over eens dat God dit geschapen heeft) micorevolutie, immuunsysteem etc… 3) Evolutie als wereldbeeld (evolutionisme) George Gaylord Simpson: "De mens is het resultaat van een doelloos en natuurlijk proces dat hem niet heeft bedoeld. Hij is niet gepland. of Richard Dawkins: "Darwin maakt het mogelijk om intellectueel vervulde atheist te zijn.” Zie ook Bas Haring, Midas Dekkers, etc.. If you want to go “gloves off” then surely it is the scientism of the “big picture” that you should attack? 39

40 Metaforen: Toeval of Stochastisch?
Random mutations and natural selection... Stochastic (Monte Carlo) optimisation e.g. used to price your stock portfolio ..... 40

41 Lego blocks or clay? Evo-Devo Lego Blocks: pax6 sonic-hedgehog
shaven-baby tinman Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom. S.B. Carroll (Blackwell Science 2005) 41

42 Why so few genes? Mycoplasma genitalium (483) E.coli (5416)
(300 minimum?) E.coli (5416) S. cerevisiae (5800) Mycoplasma genitalium, a procaryote, has the smallest genome of an independent organism -- it can cause Escherichia coli, the most popular model procaryote Saccharomyces cerevisiae is the most popular simple model eucaryote; it is a a species of budding yeast (Baker’s yeast) Drosophila Melanogaster is one of the most popular models for genetics The roundworm Caenorhabditis elegans, is very important for laboratory studies in development -- Pristionchus. pacificus (Sommer et al) is very similar to C. elegans (but lives in beetles) -- has many more genes. Why? The roundworm Caenorhabditis elegans, the staple of laboratory studies in development, contains only 959 cells, looks like a tiny formless squib with virtually no complex anatomy beyond its genitalia, and possesses just over 19,000 genes. The general estimate for Homo sapiens - sufficiently large to account for the vastly greater complexity of humans under conventional views - had stood at well over 100,000, with a more precise figure of 142,634 widely advertised and considered well within the range of reasonable expectation. Homo sapiens possesses between 30,000 and 40,000 genes, with the final tally almost sure to lie nearer the lower figure. In other words, our bodies develop under the directing influence of only half again as many genes as the tiny roundworm needs to manufacture its utter, if elegant, outward simplicity. Drosophila Melanogaster (13,500) C. elegans (19,500) & P. pacificus (29,000) H. sapiens (23,000) 42

43 Why so few genes? We share 15% of our genes with E. coli
“ “ % “ “ “ “ yeast “ “ % “ “ “ “ flies “ “ % “ “ “ “ frogs “ “ % “ “ “ “ chimps what makes us different? 43

44 Gene language Why are there so few genes?
complexity comes from the interactions gene networks systems biology transcriptional network for yeast: Saccharomyces cerevisiae 44

45 Gene language [Genes] are trapped in huge colonies, locked inside highly intelligent beings, moulded by the outside world, communicating with it by complex processes, through which, blindly, as if by magic, function emerges. They are in you and me; we are the system that allows their code to be read; and their preservation is totally dependent on the joy that we experience in reproducing ourselves. We are the ultimate rationale for their existence. Denis Noble -- The Music of Life: Biology Beyond the Genome (OUP 2006) [Genes] swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. Richard Dawkins -- The Selfish Gene (1976) 45

46 Contingency v.s.``deep structures’’: Re-run the tape of evolution?
“Wind back the tape of life to the early days of the Burgess Shale; let it play again from an identical starting point, and the chance becomes vanishingly small that anything like human intelligence would grace the replay.” In evolution, there is no direction, no progression. Humanity is dethroned from its exalted view of its own importance S.J. Gould: “Wonderful Life”; (W.W. Norton 1989) When you examine the tapestry of evolution you see the same patterns emerging over and over again. Gould's idea of rerunning the tape of life is not hypothetical; it's happening all around us. And the result is well known to biologists — evolutionary convergence. When convergence is the rule, you can rerun the tape of life as often as you like and the outcome will be much the same. Convergence means that life is not only predictable at a basic level; it also has a direction. Simon Conway Morris “Life's Solution: Inevitable Humans in a Lonely Universe”; (CUP, 2003) 46

47 Convergent Evolution? "For the harmony of the world is made manifest in Form and Number, and the heart and soul and all poetry of Natural Philosophy are embodied in the concept of mathematical beauty." (On Growth and Form, 1917.) D'Arcy Wentworth Thompson (May 2, 1860–June 21, 1948) was a biologist and mathematician and the author of the 1917 book, On Growth and Form, an influential work of striking originality. Nobel laureate P. Medawar called On Growth and Form "the finest work of literature in all the annals of science that have been recorded in the English tongue"[1]. Born in Edinburgh, Scotland, Thompson has been called "the first biomathematician" by Simon Singh[2] He died in St. Andrews, Scotland. On Growth and Form The central thesis of On Growth and Form is that biologists of his day overemphasized the role of evolution, and underemphasized the roles of physical laws and mechanics, as determinants of the form and structure of living organisms. Transformations on crocodilian skulls Enlarge Thompson pointed out example after example of correlations between biological forms and mechanical phenomena. He showed the similarity in the forms of jellyfish and the forms of drops of liquid falling into viscous fluid, and between the internal supporting structures in the hollow bones of birds and well-known engineering truss designs. His observations of phyllotaxis (numerical relationships between spiral structures in plants) and the Fibonacci sequence has become a textbook staple. Thompson's illustration of the transformation of Argyropelecus Olfersi into Sternoptyx diaphana by applying a 70° shear Utterly sui generis, the book never quite fit into the mainstream of biological thought. It does not really present any single central discovery, nor, in many cases, does it attempt to establish a causal relationship between the forms emerging from physics with the comparable forms seen in biology. It is a work in the "descriptive" tradition; Thompson did not articulate his insights in the form of experimental hypotheses that can be tested. Thompson was aware of this, saying that "This book of mine has little need of preface, for indeed it is 'all preface' from beginning to end." The huge (1116 pages in an edition currently in print), well-written, and extensively illustrated tome has enchanted and stimulated generations of biologists, architects, artists, and mathematicians, and, of course, those working on the boundaries of disciplines. Perhaps the most famous part of the work is Chapter XVII, "The Comparison of Related Forms." He explored the degree to which differences in the forms of related animals could be described by means of relatively simple mathematical transformations. Convergent evolution in mechanical design of lamnid sharks and tunas Jeanine M. Donley, et al. Nature 429, (6 May 2004) 47

48 Convergent Evolution North America: Placental Sabre-toothed cat
South America” Marsupial Sabre-toothed cat 48

49 Convergent Evolution compound eye camera eye 49

50 Convergent Evolution? Each of these mammals has a long, sticky, worm-like tongue, no teeth to speak of and scimitar claws. Each has bulging salivary glands, a stomach as rugged as a cement mixer and an absurd, extenuated, hairless snout that looks like a cross between a hot dog and a swizzle stick. Despite their many resemblances, the three creatures are unrelated to one another; the spiny anteater, in fact, lays eggs and is a close cousin of the duck-billed platypus. What has yoked them into morphological similitude is a powerful and boundlessly enticing process called evolutionary convergence. By the tenet of convergence, there really is a best approach and an ideal set of tools for grappling with life's most demanding jobs. The spiny anteater, pangolin and giant anteater all subsist on a diet of ants and termites, and myrmecophagy, it turns out, is a taxing, specialized trade. As a result, the predecessors of today's various ant hunters gradually, and quite independently, converged on the body plan most suited to exploit a food resource that violently resists exploitation. Enormous number of examples ... from proteins to vision up to societies to intelligence. Are rational conscious beings an inevitable outcome? “ The principal aim of this book has been to show that the constraints of evolution and the ubiquity of convergence make the emergence of something like ourselves a near-inevitability. SCM, “Life’s Solution”, (CUP 2005) pp328 50

51 TERUGBLIK: Metaforen zijn belangrijk “toeval –v.s. kansprocess” “genen taal etc.. Er is nog veel te ondekken Atheisme van de gaten? VOLGENDE VRAAG: Waarom de sterke consensus onder biologen dat de evolutie waar is?

52 Tapijt argumenten Wetenschap als een “tapijt”
--de kracht ligt niet aan één enkele draad maar aan het geheel en hoe ze zijn zamengewoven. Je kunt aan een paar draadtjes trekken, maar daardoor breek je het tapijt niet. Oma I was a PhD student at Cornell, working with David Mermin’s great text book collaborator Neil Ashcroft, when Collins and Pinch wrote their book -- Pinch was on the floor just above us. Mermin is one of my heroes -- he writes beautifully, I recommend for example his book “Boojums all the way through” The Golemization of Relativity, David Mermin, Physics Today 49, p11 April 1996 .

53 Wonderlijke toepasselijkheid van de taal van de wiskunde
Quantum Mechanics + Relativity = Antimatter Schrödinger equation (Quantum Mechanics) + Energy-Momentum (Special Relativity) = Dirac Equation (1928) Electrons Positrons (antimatter) discovered 1932 See also: “The applicability of mathematics as a philosophical problem”, Mark Steiner HUP (1998); E. Wigner "The Unreasonable Effectiveness of Mathematics in the Natural Sciences," in Communications in Pure and Applied Mathematics, vol. 13, No. I (February 1960) See also the work of Polkinghorne, e.g. “Beyond Science” CUP or Canto In many ways the “design” here elicits wonder, similar to that experienced when viewing mountains, or the stars etc Thus science helps us to better appreciate the wonders of creation, it extends our ability to view spatial design -- from the smallest atoms, to the mysterious creatures of the ocean depths, to the distant galaxies -- as well as temporal design -- think of the amazing age of the universe, and our own very brief sojourn, “a few seconds before midnight”. See also: “The applicability of mathematics as a philosophical problem”, Mark Steiner HUP (1998); "The Unreasonable Effectiveness of Mathematics in the Natural Sciences," in Communications in Pure and Applied Mathematics, vol. 13, No. I (February 1960), Eugene Wigner

54 Wetenschap en Schoonheid
A Scientist does not study nature because it is useful; he studies it because he delights in it, and he delights in it because it is beautiful. If nature were not beautiful, it would not be worth knowing, and if nature were not worth knowing, life would not be worth living. Henri Poincaré 1854 – 1912 54

55 Tapijt argument: een oude aarde ?
Science is a tapestry -- you can pick at a few strings, but that doesn’t break the whole cloth Radiometric dating (many overlapping isotopes) ice cores: up to 8000 years -- volcanoes like Vesuvius up to 740,000 years Milankovitch cycles Tree rings All these methods (when used properly) agree. There is no scientific controversy Radiometric Dating A Christian Perspective Dr. Roger C. Wiens

56 Tapijt argument: een oude aarde ?
Milankovitch Cycles: here seen in 420,000 years of ice core data from Vostok, Antarctica research station.

57 Tapijt argument: gezamelijke afstamming Mens en Chimpanzee?
Here I will try to show an example of a tapestry argument in biology, Tapestries was what the biologist Theodosius Dobzhansky meant when he wrote his famous essay: Nothing in Biology Makes Sense Except in the Light of Evolution. see e.g. Dobzhansky was apparently a Russian Orthodox Christian Divergence of the chimpanzee and human lineages occurred about 6 million years ago; the times of lineage divergence are not to scale News & Views: The chimpanzee and us, Wen-Hsiung Li and Matthew A. Saunders, Nature 437, (1September 2005) .

58 tapestry arguments in biology: chromosomal banding:
Humans have 46 (2 X 23) chromosomes Apes have 48 (2 X 24) chromosomes chromosomal banding comes from staining, and gives a rough coarse-grained indication structure of the DNA. Note how similar the human DNA is to that of other primates (H=Human, C=Chimp, G=Gorilla, U=Urang-Utan) chromosome 2: Human, Chimp, Gorilla, Orang-utan The origin of man: a chromosomal pictorial legacy. J.J Yunis and O. Prakash, Science 215, 1525 (1982)

59 tapestry arguments in biology: fusion of chromosome 2?
chromosomal banding comes from staining, and gives a rough coarse-grained indication structure of the DNA. Note how similar the human DNA is to that of other primates (H=Human, C=Chimp, G=Gorilla, U=Urang-Utan) chromosome 2: Human, Chimp, Gorilla, Orang-utan

60 tapestry arguments in biology: evidence from the human genome
Chromosome 2 is unique to the human lineage of evolution, having emerged as a result of head-to-head fusion of two acrocentric chromosomes that remained separate in other primates. The precise fusion site has been located in 2q13−2q14.1 (ref. 2; hg16: − ), where our analysis confirmed the presence of multiple subtelomeric duplications to chromosomes 1, 5, 8, 9, 10, 12, 19, 21 and 22 (Fig. 3; Supplementary Fig. 3a, region A). During the formation of human chromosome 2, one of the two centromeres became inactivated (2q21, which corresponds to the centromere from chimp chromosome 13) and the centromeric structure quickly deterioriated [42]. Note that even this evidence is not entirely conclusive about the existence of the telomere remnants (see the paper for a fuller discussion) Generation and annotation of the DNA sequences of human chromosomes 2 and 4, L.W. Hillier et al., Nature 434, 724 (2005).

61 endogenous retroviruses
HERV-K insertions In humans endogenous retrovirus sequences make up about 1% of the genome. Lebedev, Y. B., et al. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247:

62 tapestry arguments in biology: more threads of evidence
Genetic threads SINEs (Alu ) LINEs Retroviral insertions pseudo genes (e.g. olefaction) chromosomal inversions Phenotypal similarities Fossils The tapestry for: do humans and chimpanzees share a common ancestor? seems to most biologists almost unbreakably strong We have 1,000 “olfactory receptor” genes that encode proteins needed for our sense of smell. About 600 of these can no longer make functional proteins, and many are defunct also in chimps, gorillas, and orangutans—and have the same inactivating mutations in each species. Such mutations occurred in an ancestor of all the species that currently own (by inheritance) the common mutation. 7 Similarly, humans and chimps have 33 genes that make proteins used to sense bitter taste. Some of these genes are derelicts (with the same inactivating mutations) in both humans and chimps, scrambled in a common ancestor. Y. Gilad, O. Man, S. Paabo, and D. Lancet, “Human Specific Loss of Olfactory Receptor Genes,” Proceedings of the National Academy of Science of the USA 100 (2003): 3324; Y. Gilad, V. Wiebe, M. Przeworski, et al., “Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates,” PLoS Biol 2 (2004): 120. We and other primates have emergency patches on our DNA, marking sites where radiation once caused DNA breaks. Many patches are common to chimps and humans. Our DNA has the scars of radiation damage that occurred in reproductive cells of long-extinct ancestors. 13a Finlay et al, PSCF 9, 236 (2006) There are many other independent strands of evidence suggesting common ancestry between humans and chimps -- together they make a very strong tapestry that is hard to break. Take a break here: Speak to audience for whom might be a difficult story --- for many people “where we come from determines who we are and how we should then live” -- John Stott on “Homos Divinus?” recommend “Can we believe Genesis Today”, by Ernest Lucas Thank you very much, Melvyn. Good evening; it's a huge honor to be here. I'm only here because I intercepted an invitation for Mark Ridley. Just to be clear, the excellent book about Richard is edited by Alan Grafen and Mark, not by me, although I do have a chapter in it, just to confuse people. We have, Mark and I have had our Y chromosomes analyzed by Brian Sykes and we have the same Y chromosomes haplotypes, so he'd say the same thing as I'm going to say anyway. After all, we are supposed to believe in genetic determinism. What I want to talk about tonight is a throwaway remark in The Selfish Gene, which I think was not only prophetic but in a sense made the book much more literal than it otherwise is. At the time, in the early 1970s, it had just been discovered that genomes have a lot more DNA in them than is necessary for coding for proteins. And this was a big puzzle. Richard suggested a solution to this, which turned out to be mostly true, and was completely original. The remark is found on page 47 of the first edition of The Selfish Gene, and it goes: Biologists are wracking their brains trying to think what useful tasks this apparently surplus DNA in the genome is doing. But for the point of view of the selfish genes themselves there is no paradox. The true purpose of DNA is to survive, no more no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger hitching a ride in the survival machines created by other DNA. And as a classic of the argument in The Selfish Gene, what he's doing is saying cui bono, who benefits. Is it possible that perhaps this stuff is there not for the good of the species, but for the good — not even for the good of the whole genome, but for the good of the bits of DNA itself. He's turning the world upside down. Just to recount the history of why this is an interesting question, by 1971 the phrase the C-value paradox had been coined for this problem, that nuclear genomes vary enormously in size, up to 300,000-fold, but the number of proteins made from them doesn't vary nearly as much. Some species have enormous genomes and produce no more proteins than others. The idea was beginning to be abroad in the late '60s, early '70s, that this might just be junk — that an awful lot of the DNA in the genome might stand for nothing; it might have no purpose. And in a lecture at MIT in 1972 Crick said, What is all this DNA for? Is it junk or is it an evolutionary reserve? Still thinking, though, in terms of what's it for in terms of the organism. And in 1978 Tom Cavalier-Smith suggested that perhaps it's there to support the rest of the DNA, to place the genes in the right parts of the nucleus, to spread the genes out, and things like that. And that's an idea that I'll come back to in a minute, because it has a second history. But it's in 1980 that the idea of selfish DNA is coined in two papers in Nature by Doolittle and Sapienza and Orgel and Crick, arguing that perhaps most of, or some of this DNA is simply selfish DNA, that it's there because it's good at getting itself there. It's good at replicating itself, it's good at copying itself. They were quite explicit, they said this idea is not new, it's sketched briefly but clearly by Dawkins in his book The Selfish Gene. There's no question that this originated as an idea with Richard. By the way, — in 1982 the first computer virus was created, the Elk Cloner virus — and that of course has an interesting parallel with the argument that I'm talking about. Just to illustrate what we're talking about — genome size bears very little relation to the complexity of an organism; two creatures like a puffer fish and a zebra fish have very different size genomes, even though they look very similar. From this end of the telescope, human beings look like they have quite a big genome, but if you turn the telescope around and look from another direction, the human genome looks rather a small one, compared with that of grasshoppers, which is at least three times as large, or deep-sea shrimps, which have ten times as much DNA as us. Salamanders get even bigger, and the king of the genomes in the animal kingdom at least, is the marbled lung fish. Some people say amoebae have larger genomes at 500 gigabases, but they're almost certainly polyploid, as are lilies, which also have very big genomes. This is a perfectly ordinary diploid genome in the marbled lungfish, and it has as much digital information in it as about ten British Museum reading rooms. So what's it all for? Well, it does appear that Richard was partly wrong. It does appear that the genome size is under selection, and that it's linked to the size of the cell. The bigger the nucleus the bigger the cell, it's a pretty good rule. And there's all sorts of evidence to suggest that animals are optimizing the size of their genomes, so parasites often minimize the amount of junk in their genomes in order to shrink themselves. Malaria parasites have very little junk in their genomes, and very small cells. At the other extreme, ciliates have very large cells, and they achieve this with small genomes by making a huge macronucleus in which they put sort of working copies of all their genes in multiple numbers. They are an exception that proves the rules; they have a small genome but a large cell but only because they make a special sort of working nucleus that's a whole lot bigger. And high-metabolism animals, like bats, and birds, have got rid of quite a lot of the junk in their genome, in order to be able, it appears, to have small blood cells with larger surface areas. A lesser horseshoe bat like this has a genome less than two gigabases, compared with three gigabases for us. Why the lungfish, the marble lungfish, has such a gigantic genome is not clear, but it does look like it may be something to do with having very big cells, in order to be able to store glycogen when it estivates during a drought, when it disappears into the mud and lives there for six months off its glycogen reserves. That's a possibility. But one of the strongest pieces of evidence that genome size is not — that it's not possible simply to expand your genome at length by letting parasites run riot is the ALU sequence, which is one of the commonest sequences in our genomes, which has appeared in the last 30 or 40 million years. Mice don't have it, but our genome is not bigger than mice. In other words it's come at the expense of another sequence, rather than added to it. Just in passing, it does seem that big genomes go with small brains. This is particularly true in amphibia, where — in frogs and salamanders, the larger the genome the smaller the brain. A frog has about five gigabytes and a comparably large brain; a salamander has about 30 gigabytes and a smaller brain, and a mudpuppy has an 85- gigabase — sorry, I keep saying byte, I mean base — gigabase genome, and has an extremely small brain. Human beings luckily have larger brains than frogs. There are two reasons for this: the bigger your genome the slower you are at duplicating yourselves, so the harder it is to grow a big brain by multiplying cells. And also it's harder to fit the same number of neurons in your head if neuron bodies are bigger. How much of the human genome might be selfish DNA? Well, what we think of the genomes consisting of is genes; well, there is the proportion of our genome that actually consists of real protein-coating genes, sequences that direct the manufacture of proteins themselves. One and a half percent. Add in another three and a half percent for all the control sequences, all the functional DNA that seems to be under very strong purifying selection. That's where all the promoters and enhancers and switches that control the expression of the genes is. We've only got to five percent and we've got all that we need to build and run a human body. Eight percent consists of retro-viruses. 450,000 copies of the retroviruses, complete or incomplete, in our genomes. They're there because they're good at being there; they're simply left over from infections in the past, with viruses that are good at stitching copies of themselves back into our genes. There's three percent transposons — these are just cut-and- paste sequences that are good at moving around the genome. Many more of them in plants and fruit flies, but fewer in us. But the really interesting ones are the LINEs: long interspersed nuclear elements. Or autonomous retroposons. These are sequences that are several thousand base pairs long, they're transcribed, two proteins are made from them, the proteins bind to the messenger RNA and take it straight back into the nucleus, make a DNA copy, and stitch it back into the genes. That's all they ever do. They are as clear a definition as you can get of a selfish gene, they are simply copying themselves and spreading themselves around the nucleus. The SINEs are very similar, there's 13 percent of our genomes consist of them. The ALU that I mentioned is one of these. The only difference is that they parasitize the LINEs. They don't make their own machinery for copying themselves, they use the LINE machinery. These are lesser fleas on greater fleas. All that gets you to about half the human genome. What's left? Well, there's introns — gaps inside genes — there's simple sequence repeats, the bits we use for DNA finger printing and things like that, segmental duplications, and a whole bunch of other stuff. Broadly speaking, the green stuff I think is true junk DNA. In other words it doesn't matter what its sequence is. The blue stuff is the functional DNA that builds and runs our bodies. And the red stuff is there because it's good at being there. It's things that have spread at the expense of other sequences, it's selfish DNA. Just to clarify the LINEs and SINEs, at any given time in the last 60,000,000 years there's been one different LINE that's been dominant, that's been most dominant in the human lineage, there's been 16 overall that have been rampaging through our genomes. The one that's currently doing so is called LINE 1, it's at the moment taking up about 17 and a half percent of your genome as you sit here today. Likewise the ALU sequences have gone berserk, their activity peaked about 40,000,000 years ago in the primate lineage, it's a 280-base per sequence, and it's repeated over a million times. Now interestingly the LINEs are found in the AT-rich regions. These are where there's fewest genes — which is what you'd expect if the organism was saying, we don't like these parasites, we want to keep them out of the way of genes. But the older SINEs are actually found in the CG-rich regions, the areas where most genes are. In other words the longer a SINE has been hanging around, the more it's been recruited to areas where there are genes, so it looks like the organism has somehow co-opted some of these sequences to actually affect the expression of genes, which is an interesting case of a selfish gene being, if you like, tamed. Just worth reminding ourselves that junk DNA has spawned a bigger industry than coding DNA already — I'm referred to DNA finger-printing — and the two people of course who made DNA a household word are, Monica Lewinsky and O.J. Simpson, if you think about it. Ladies and gentlemen, my conclusion is that it looks like about 45 percent of the human genome is made up of what you might literally call selfish genes — sequences that copy themselves very efficiently. And that Richard's suggestion was right. However, selfish DNA can, it seems, spread at the expense of neutral junk, but doesn't seem to be able to actually expand the genome. We're not in danger of suddenly have our genomes grow bigger and bigger and bigger. And these selfish elements range from unwanted parasites to co-opted symbionts, and most of them are somewhere in between the two. Richard was absolutely right, in a very literal sense, and the genome would actually be inexplicable without the notion of the selfish gene. Thank you. for physicists, mathematicians and engineers -- these arguments may still seem foreign and vague; where is the “proof”?, how do you know? -- so communities talk past each other

63 tapestry arguments in biology
“But others [biologists], I soon came to realize, regarded logical arguments as suspect. To them, experimental evidence, fallible as it might be, provided a far surer avenue to truth than did mathematical reasoning Their implicit assumption seemed to be: How could one know one’s assumptions were correct? Where, in a purely deductive argument, was there room for the surprises that nature might offer, for mechanisms that might depart altogether from those imagined in our initial assumptions? Indeed for some biologists, the gap between empirical and logical necessity loomed so large as to make the latter seem effectively irrelevant. Evelyn Fox Keller, in “Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines, HUP, (2002) Biologists have a long-standing distrust of theoretical or purely mathematical argumentation, in part for the reason Fox Keller point out, and in part because, in all honesty, there hasn’t been a great track record of success either. That is not to say that physical thinking has not been very helpful, think of Crick, Delbruck, Gilbert, and many others who were initially trained as physicists, or think of the influence of “What is Life” by Schroedinger, etc.. but pure mathematically oriented logical thinking, which has been so successful in physics (e.g. the Dirac prediction of anti-matter), has not had the same track record in biology. I experience this distrust all the time when interacting with biological colleagues, witness the tirade by a biologist at a conf I co-organised on protein-protein interactions. Example of my work on the Nuclear Pore complex and interactions with people like MS -- he’s always telling me I should spend some time in his lab, to go over to the dark side, to see what it is all really like. I think that by and large they are right, but that I do sometimes have a role to play and that moreover, as biology enters the “omic” age, people with my training will be more and more needed to understand all the data. example of .. ‘s advice on our new course in biological physics isolation of mathematical biology Fox Keller and the Isaac Newton Statistical Mechanics and Biology programme You can’t ask those kinds of questions!!!! (Biologist to AAL at “Protein-Protein Interaction Conf”, June 2004) “Where are the equations” -- a physicist might ask

64 Tapestry arguments Basic scientific principles are shared across fields But what is considered “necessary” or “sufficient” for a (self-organised) tapestry varies from field to field (often unwritten) cultural iceberg, above and below waterline evidence: grant or paper review demarkation problems mathematics->physics->chemistry->biology->medicine->engineering Differences --in spite of apparent epistemic laxity ... it still works! Christian evaluation needs communities of scholars Different “Inferences to the best explanation” (Gilbert Harman) As a trained physicist and chemist, I am sometimes surprised by the crude noisy data that biologists will consider to be a sufficient “proof”. But despite this apparent epistemic laxity, biology progresses happily, even spectacularly. One of the most difficult things I have had to learn as I entered biological research was how to assess the strength and reliability of biological arguments. For that reason it is critical to constantly interact with biologists who are themselves involved in the experiments. Of course there is a sense in which this is socialised, but it is continually being tested by experiment, and making a careful evaluation of a biological argument is a craft that -- your skill is revealed by how well your judgements hold up over time. My guess is that the reason so many anti-evolutionists (both YECS and ID) are physical scientists or engineers, is related in part to differences in how their fields approach tapestry arguments. They first come across the tapestry arguments that biologists use, and find them too fuzzy. That is to a large extent because they fail to appreciate how biologists think. On the one hand, the arguments within any field are not sacred, and should be open to critical discussion. On the other hand, it is important to first understand well their craft and expertise before claiming that biologists are completely wrong abou fundamental issues in their field. Perhaps I can explain it this way: if I were to tell a heart surgeon that he is not performing his procedures correctly, but I haven’t actually bothered to study medicine properly, nor have I bothered to master his skills, he/she may react in a way that appears arrogant and dismissive. In the same way biologists often

65 TERUGBLIK: Tapijt argumenten Vaak moeilijk voor een leek om goed in te schatten Verschillen van discipline tot discipline Biologen (ook Christelijke) geloven in de evolutie (type 1 & 2) omdat tapijt argumenten daarvoor sterk zijn. Er blijven uiteraard nog veel vragen over details. VOLGENDE VRAAG: Hoe zit het dan met de Bijbel en Genesis 1&2

66 Bijbels of cultureel? Wise men at birth -- wrong
Three wise men? No evidence Angels with wings -- no evidence Did the angels sing? No evidence -- they were praising God In a stable? -- no evidence, only inferred through the manger Snow? Probably not in winter

67 Wat is de genre? Genesis 1-2:3 Phrases that occur 10 times:
10 times “God said” (3 for mankind, 7 for other creatures) 10 times creative commands (3 x “let there be” for heavenly creatures, 7 x “let” for world below) 10 x To make 10 x According to their kind Phrases that occur 7 times (heptads) “and it was so” “and God saw that it was good” Genesis 1:2-3 Phrases that occur 3 times God blessed God created God created men and women Other numerical patterns: Intro 1:1-2 contains 21 words (3 x 7) and conclusion (2: 1-3) contains 35 words (5 X 7) Earth is mentioned 21 times and “God” 35 times -- see e.g. H. Blocher “In the Beginning”, p 33 or E. Lucas “Can We Believe Genesis Today” , p 97

68 Wat is de genre? FRAMEWORK VIEW Day 7:
SHAPED Day 1 The separation of light and darkness Day 2 The separation of the waters to form the sky and the sea Day 3 The separation of the sea from dry land and creation of plants INHABITED Day 4 The creation of the lights to rule the day and the night Day 5 The creation of the birds and fish to fill the sky and sea Day 6 The creation of the animals and humans to fill the land and eat the plants Bara only used in v 1, 21 and is for sea monsters Genesis 1 The Beginning 1 In the beginning God created the heavens and the earth. 2 Now the earth was [a] formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters. 3 And God said, "Let there be light," and there was light. 4 God saw that the light was good, and He separated the light from the darkness. 5 God called the light "day," and the darkness he called "night." And there was evening, and there was morning—the first day. 6 And God said, "Let there be an expanse between the waters to separate water from water." 7 So God made the expanse and separated the water under the expanse from the water above it. And it was so. 8 God called the expanse "sky." And there was evening, and there was morning—the second day. 9 And God said, "Let the water under the sky be gathered to one place, and let dry ground appear." And it was so. 10 God called the dry ground "land," and the gathered waters he called "seas." And God saw that it was good. 11 Then God said, "Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds." And it was so. 12 The land produced vegetation: plants bearing seed according to their kinds and trees bearing fruit with seed in it according to their kinds. And God saw that it was good. 13 And there was evening, and there was morning—the third day. 14 And God said, "Let there be lights in the expanse of the sky to separate the day from the night, and let them serve as signs to mark seasons and days and years, 15 and let them be lights in the expanse of the sky to give light on the earth." And it was so. 16 God made two great lights—the greater light to govern the day and the lesser light to govern the night. He also made the stars. 17 God set them in the expanse of the sky to give light on the earth, 18 to govern the day and the night, and to separate light from darkness. And God saw that it was good. 19 And there was evening, and there was morning—the fourth day. 20 And God said, "Let the water teem with living creatures, and let birds fly above the earth across the expanse of the sky." 21 So God created the great creatures of the sea and every living and moving thing with which the water teems, according to their kinds, and every winged bird according to its kind. And God saw that it was good. 22 God blessed them and said, "Be fruitful and increase in number and fill the water in the seas, and let the birds increase on the earth." 23 And there was evening, and there was morning—the fifth day. 24 And God said, "Let the land produce living creatures according to their kinds: livestock, creatures that move along the ground, and wild animals, each according to its kind." And it was so. 25 God made the wild animals according to their kinds, the livestock according to their kinds, and all the creatures that move along the ground according to their kinds. And God saw that it was good. 26 Then God said, "Let us make man in our image, in our likeness, and let them rule over the fish of the sea and the birds of the air, over the livestock, over all the earth, [b] and over all the creatures that move along the ground." 27 So God created man in his own image, in the image of God he created him; male and female he created them. 28 God blessed them and said to them, "Be fruitful and increase in number; fill the earth and subdue it. Rule over the fish of the sea and the birds of the air and over every living creature that moves on the ground." 29 Then God said, "I give you every seed-bearing plant on the face of the whole earth and every tree that has fruit with seed in it. They will be yours for food. 30 And to all the beasts of the earth and all the birds of the air and all the creatures that move on the ground—everything that has the breath of life in it—I give every green plant for food." And it was so. 31 God saw all that he had made, and it was very good. And there was evening, and there was morning—the sixth day. Day 7: The heavens and earth were finished and God rested 68

69 Wat is de genre? A completely different emphasis!
Gen2: more patterns: These are the generations of the heavens and the earth when they were created in the day that the Lord God made the earth and the heavens. Chiastic structure (C. John Collins, Genesis 1-4 P&R (2006)) When no bush of the field was yet in the land and no small plant of the field had yet sprung up—for the Lord God had not caused it to rain on the land, and there was no man to work the ground, and a mist was going up from the land and was watering the whole face of the ground— then the Lord God formed the man of dust from the ground and breathed into his nostrils the breath of life, and the man became a living creature. A completely different emphasis!

70 Wat is de genre? More like Revelation than like Luke
But very clear in its teaching e.g. God created the world Creation is good I Tim 4: 1The Spirit clearly says that in later times some will abandon the faith and follow deceiving spirits and things taught by demons. 2 Such teachings come through hypocritical liars, whose consciences have been seared as with a hot iron. 3 They forbid people to marry and order them to abstain from certain foods, which God created to be received with thanksgiving by those who believe and who know the truth. 4 For everything God created is good, and nothing is to be rejected if it is received with thanksgiving, 5 because it is consecrated by the word of God and prayer.

71 Wat is de genre? More like Revelation than like Luke?
But very clear in its teaching e.g. God created the world Creation is good Man is made in God’s image Mankind (adam) has fallen into sin A promise of redemption (seed of woman) MANY! More things No problems with perspecuity on doctrine

72 Wat is de genre? Is it chronological?
"Now what man of intelligence will believe that the first and the second and the third day … existed without the sun and moon and stars?” Origen : First Principles, 4.3 “On this subject there are three main views. According to the first, some wish to understand paradise only in a material way. According to the second, others wish to take it only in a spiritual way. According to the third, others understand it both ways, taking some things materially and others spiritually. If I may briefly mention my own opinion, I prefer the third” Augustine of Hippo ( ) De Gen. ad litt VIII, 1. (on the literal interpretation of Genesis)

73 Jewish Commentators “…the sages agree that the creation of this earth and sky was a single divine event and not a series of distinct occurrences spread out over six or seven days N.M. Samuelson, “Judaism and the Doctrine of Creation”, CUP (1994) p115 “The text does not point to the order of the [acts] of creation … the text does not by any means teach which things were created first and which later [it only] wants to teach us what was the condition of things at the time when heaven and earth were created, namely, that the earth was without form and a confused mass” Rashi ( ), “Commentary on Genesis” Many more examples, e.g. Maimonides ( ) etc…

74 Wat is de genre? Strong internal hints at “elevated prose”, more like Revelation than like Luke Two separate narratives (tablets) Numerical patterns Thematic patterns A common understanding of church fathers, early Jewish commentators and early Evangelical leaders. Main theological teachings are crystal clear (perspicuity) Physical interpretation less so -- there science can take a “servant role” and help you decide. We must be very careful not to import our own cultural biases into interpretation Word bara v 1 v 21 sea creatures and v sn over literal interpretation misses key points

75 Bijbel en Wetenschap De wetenschap: een knechtenrol voor Bijbel interpretatie “The Bible must not be placed under any other authority! …no authority, even one at the apex of the scientific world, may impose his authority on the Bible in order to dictate how it is to be understood, even with the best intentions.” “Instead of an authority, however, a ministerial, servant-role apears possible. ….. The knowledge derived from the observation of reality (`science’) would help us to understand the language of the Bible better.” Henri Blocher “In the Beginning” IVP (1984) p 25

76 Aside:Emergence of Humans?
e.g. at what age is a child spiritually responsible to God? John Stott on “Homos Divinus” Advice from C.S. Lewis When the author of Genesis says that God made man in His own image, he may have pictured a vaguely corporeal God making man as a child makes a figure out of plasticine. A modern Christian philosopher may think of the process lasting from the first creation of matter to the final appearance on this planet for an organism fit to receive spiritual as well as biological life. Both mean essentially the same thing. Both are denying the same thing -- the doctrine that matter by some blind power inherent in itself has produced spirituality. (C.S. Lewis, God in the Dock Eerdmans (1970), p 46) Because some people will feel worried -- particularly those exposed to populist Christian teaching .... Lewis on same page: Does this mean that Christians on different levels of general education conceal radically different beliefs under an identical form of worlds? Certainly not. For waht they agree on is the substance, and what they differ about is the shadow. When one imagines his God seated in a local heaven above a flat earth, where another sees God and creation in terms of Professor [Albert North] Whitehead’s philosoph [loosely, process theology], this difference touches precisely what does not matter.

77 Advice from Billy Graham
"I don't think that there's any conflict at all between science today and the Scriptures. I think that we have misinterpreted the Scriptures many times and we've tried to make the Scriptures say things they weren't meant to say, I think that we have made a mistake by thinking the Bible is a scientific book. The Bible is not a book of science. The Bible is a book of Redemption, and of course I accept the Creation story. I believe that God did create the universe. I believe that God created man, and whether it came by an evolutionary process and at a certain point He took this person or being and made him a living soul or not, does not change the fact that God did create man. ... whichever way God did it makes no difference as to what man is and man's relationship to God.” - Billy Graham quoted by David Frost Source: Book - Billy Graham: Personal Thoughts of a Public Man (1997, p ) quote taken from

78 Samenvatting Complexe materie! Evolutie als Natuurgeschiedenis
Mechanisme om biologische complexiteit te maken Wereldbeeld (evolutionisme) Metaforen zijn belangrijk Mechanismen van evolutie kunnen mooi zijn Tapijt argumenten en de consensus onder wetenschappers omtrent Evolutie 1&2 Bijbel interpretatie – belangrijk om goed naar genre te kijken.

79 Writers of “the Fundamentals”
One of the original “Fundamentalists” There is not a word in the Bible to indicate that in its view death entered the animal world as a consequence of the Sin of man. When you say there is the “six days” and the question whether those days are meant to be measured by the twenty-four hours of the sun’s revolution around the earth -- I speak of these things popularly. It is difficult to see how they should be so measured when the sun that is to measure them is not introduced until the fourth day. Do not think that this larger reading of the days is a new speculation. You find Augustine in early times declaring that it is hard or altogether impossible to say what fashion these days are, and Thomas Aquinas, in the middle ages, leaving the matter an open question. The Christian View of God and the World (Edinburgh, Andrew Elliot 1904, p 197) quote 2 -- from Hugh Ross “A matter of days”, p 30 James Orr

80 The Bible and Science The lesson of Galileo, …, should remind us that careful observation of the natural world can cause us to go back to Scripture and reexamine whether Scripture actually teaches what we think it teaches. Sometimes, on closer examination of the text, we may find that our previous interpretations were incorrect. Wayne Grudem, “Systematic Theology” IVP (1994) p 273 Wayne Grudem

81 The Bible is not a science textbook
The whole point of scripture is to bring us to a knowledge of Christ --- and having come to know him (and all that this implies), we should come to a halt and not expect to learn more. Scripture provides us with spectacles through which we may view the world as God’s creation and self-expression; it does not, and was never intended, to provide us with an infallible repository of astronomical and medical information. Cited in Alister E. McGrath, The foundations of Dialogue in Science and Religion (Oxford, UK ,Blackwell 1998) p 124 John Calvin

82 Advice from Schaefer Francis Schaefer
We must take ample time, and sometimes this will mean a long time, to consider whether the apparent clash between science and revelation means that the theory set forth by science is wrong or whether we must reconsider what we thought the Bible says. Francis Schaefer Francis Schaefer Francis Schaeffer, No Final Conflict (Downers Grove: InterVarsity Press, 1975), 24.

83 Warfield on evolution B.B. Warfield 1851-1921
B. B. Warfield ( ). A biblical inerrantist as evolutionist. Livingstone DN, Noll MA, 1: Isis Jun;91(2): The theological doctrine of biblical inerrancy is the intellectual basis for modern creation science. Yet Benjamin Breckinridge Warfield of Princeton Theological Seminary, the theologian who more than any other defined modern biblical inerrancy, was throughout his life open to the possibility of evolution and at some points an advocate of the theory. Throughout a long career Warfield published a number of major papers on these subjects, including studies of Darwin's religious life, on the theological importance of the age of humanity (none) and the unity of the human species (much), and on Calvin's understanding of creation as proto-evolutionary. He also was an engaged reviewer of many of his era's important books by scientists, theologians, and historians who wrote on scientific research in relation to traditional Christianity. Exploration of Warfield's writing on science generally and evolution in particular retrieves for historical consideration an important defender of mediating positions in the supposed war between science and religion. B.B. Warfield

84

85 God openbaart zich door de natuur
Psalm 19: De hemel verhaalt van Gods majesteit, Het uitspansel roemt het werk van zijn handen Melkweg: 100 miljard sterren Universum: 100 miljard sterrensteden Milky way is a spiral galaxy Our solar system revolves around the galactic center with an orbital period of about 240 million years. The spiral arms are also rotating, in the same direction but more slowly. Therefore, the solar system catches up to and moves through the spiral arms. In our galaxy there are 100,000 million stars, like our sun. our galaxy is one of 100,000 million galaxies. In a throwaway line in Genesis, the writer tells us, "he also made the stars" .. Gen 1:16 Such is his power ”God maakte … ook de sterren" .. Gen 1:16

86 Intelligent Design (capitalised)
heterogeneous movement -- will focus on ID centred at Discovery Institute some key publications and people The Mystery of Life’s Origin (1984) Charles B. Thaxton, Walter L. Bradley, Roger L. Olsen Evolution, a Theory in Crisis (1986) Michael Denton Darwin on Trial (1991) Philip Johnson Darwin’s Black Box (1996) Michael Behe (CT book of the year) Icons of evolution (2000) Jonathan Wells No Free Lunch (2001) William Dembski

87 What is ID Intelligent agency, as an aspect of scientific theory making, has more explanatory power in accounting for the specified, and sometimes irreducible complexity of some physical systems, including biological entities, and/or the existence of the universe as a whole, than the blind forces of. . . matter.’[1] That is, intelligent design is a better explanation for entities exhibiting complex specified information (CSI) than are appeals to the inherent capacities of nature (i.e. chance and/or physical necessity). ID suggests that the world contains objects that exhaust the explanatory resources of undirected natural causes, and can only be adequately explained by recourse to intelligent causation. (definition from Peter S. Williams) taken from Intelligent Design Theory – An Overview Peter S. Williams (MA, MPhil) [1] Beckwith, Francis J, Law, Darwinism, and Public Education: The Establishment Clause and the Challenge of Intelligent Design, (New York: Rowman & Littlefield, 2003), p. xiii.

88 Irreducible Complexity
Michael Behe (1996) Bacterial flagellum, immune system, etc... are too complex to have evolved This result is so unambiguous and so significant that it must be ranked as one of the greatest achievements in the history of science ... The discovery [of intelligent design] rivals those of Newton and Einstein, Lavoisier and Schroedinger, Pasteur and Darwin.”

89 Complex Specified Information
William Dembski CSI -- information that could not have come there by chance alone? e.g. when we see a statue v.s. weathered rock “Law of the conservation of information”

90 Intelligent Design Philosophical issues: Theological issues:
Definition of science (demarcation) ? Problems, but why not follow the evidence? Theological issues: when/why does God intervene? miracles? Newman/Barth critique

91 ID and Christians Major issues is -- why these miracles?
Miracles occur to serve God’s redemptive purpose Origin, Augustine, Aquinas, Luther, Calvin etc... “And I hold, that when God works miracles, he does not do it in order to supply the wants of nature, but those of grace. Whoever thinks otherwise, must needs have a very mean notion of the wisdom and power of God” Leibnitz e.g. what is the Biblical rationale for supernatural action aiding the creation of the flagellum?

92 Intelligent Design (capitalised)
GOOD Looking at complex questions in science/philosophy counteracting evolutionism middle road, broad church? LESS GOOD Detached from scripture doesn’t solve some pressing questions (like death before fall) very political William Dembski, Michael Behe, Stephen Meyer, Paul Nelson

93 Calvin on using science
As far as I am aware, there is no evidence that Galileo had any direct knowledge of Calvin's writings. Nevertheless his understanding of the nature of the language used by the Bible when referring to the natural world is the same as Calvin's as the following quotations from the Letter to the Grand Duchess Christina show. B1. These propositions set down by the Holy Ghost were set down in that manner by the sacred scribes in order to accommodate them to the capacities of the common people, who are rude and unlearned. (p. 181) B2. It is necessary for the Bible, in order to be accommodated to the understanding of every man, to speak many things which appear to differ from the absolute truth so far as the bare meaning of the words is concerned. (p. 182) B3. For that reason it appears that nothing physical which sense-experience sets before our eyes, or which necessary demonstrations prove to us, ought to be called in question (much less condemned) upon the testimony of biblical passages which may have some different meaning beneath their words. (p. 182f) B having arrived at any certainties in physics, we ought to utilize these as the most appropriate aids in the true exposition of the Bible and in the investigation of those meanings which are necessarily contained therein, for these must be concordant with demonstrated truths. (p. 183) The first two quotations express the same 'accommodation' understanding of biblical language as Calvin adopted. The third recognises that, as a result of this, the literal sense of the biblical text may sometimes be at variance with the scientific understanding of the natural phenomenon described. In the final quotation Galileo makes the point made by Prof. McKay that one reason why biblical interpreters should take scientific knowledge into account is that it will help them to recognise when the biblical writers are using the language of appearance or cultural idioms, and so help them avoid the kind of misinterpretation made by those who condemned Galileo. lehttp://