Evolution and Intelligent Design

Evolution and Intelligent Design

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1. Introduction


Intelligent Design is a successor to creationism, but more subtle and more acceptable of the evolution theory. It arose from biochemist Michael Behe’s book Darwin’s Black Box,1 and was seconded, mainly on statistical grounds, by William Dembski.2 They claim that certain complex systems, like the immune system, bloodclotting, visual mechanism and bacterial flagella, cannot have arisen from a darwinian sequence of mutation-selection steps, but must be the result of ‘Intelligent Design’ (ID). Behe calls them ‘irreducibly complex systems’, defined as systems consisting of several closely fitting and interacting components that cease to function when a single component is removed. This implies to him that they cannot have been formed by an evolutionary process. He does not explain the mechanism of ID, and scrupulously avoids the use of the term ‘God’. This is presumably because the purpose of Behe and his adherents is to obtain a place for ID in biology textbooks for public schools in the United States in order to pull evolution down a peg.3

A well-funded institute, the Discovery Institute, Seattle, Washington, was set up to lobby state legislatures and school boards on the textbook issue. This i nstitute also sponsors Intelligent Design and Evolution Awareness (IDEA) clubs on US college campuses, of which there are now twenty.4 ID falls on a fertile ground in the USA as shown by a poll taken by the Pew Forum on Religion and Public Life in July 2005:5 Strict creationist views are held by 42% of the respondents, 48% believe in human evolution, but only 26% by natural selection and 18% by a supreme being. Of the respondents 64% favor teaching both creationism and evolution; 38% would replace evolution by creationism.

There are now 70 controversies over the teaching of ID pending in 26 states.5 In Pennsylvania a court case has been brought by eleven parents against the York County school district for requiring teaching of ID next to evolution. The hearings have been completed, and the judge will give his verdict in January 2006. Meanwhile in a new election all members of the Schoolboard have been voted out of office, and the new board has decided against including ID in the teaching of evolution. On the other hand, the Kansas state legilature passed a law that requires teaching of ID.

Dubious tactics by the ID movement are not always avoided, as shown by a news item in Science,6 mentioning that the ID New Mexico Network had announced that in a poll among 16,000 scientists of the Los Alamos and Sandia Laboratories 79% were in favor of teaching ID in schools. Inquiries by Science led to statements by the president of Sandia L aboratory and of the American Insitute of Physics that there had not been such a poll.

The ID message has also reached Europe. In the Netherlands ID is promoted in a translation of a creationist book, originally published in the United States,7 and some reputable academic scientists (without much knowledge of the American background) appear to be impressed with ID.8 Whence this enchantment with ID even for scientists? Because, Michael Ruse says, for many evolutionary biologists, ” evolution was their profession …evolutionism their obsession “.9 These scientists reject Christianity, only to replace it with evolutionism. To this some believing scientists react by embracing ID. Both groups forget that evolution theory – like any scientific theory – can neither prove nor disprove God’s creative action in the world. I shall treat here the evolution theory as nothing more than a scientific explanation of the mechanism by which new species arose from preceding ones.


2. Analyzing the problem

In itself it is a valid scientific question to ask whether complex systems like the ones cited by Behe can arise through a mutation-selection process or not. Unfortunately, neither the proponents nor the opponents in their numerous publications cite significant scientific evidence for their positions. However, in sections 3 and 4 I shall show that our rapidly increasing insight in molecular genetics can provide answers to this question, even in the face of the obvious lack of fossil evidence for the development of complex systems.

Another problem is that ID – notwithstanding the repeated claim of its adherents – is not a scientific, but a metaphysical concept, which by its nature cannot be proven right or wrong by scientific observations or experiments. Science can very nicely elucidate the cause-effect steps occurring in evolution, but it cannot explain a First Cause, such as the operation of God or of ID in biological evolution. That is the province of theology, which I shall apply to the ID hypothesis in section 5..

Before proceeding, I shall briefly review the arguments presented in support of the ID hypothesis by Behe and Dembski. Behe basically says no more than that complex systems, such as the visual mechanism, bloodclotting system, immune system, and bacterial flagellum, cannot have arisen from a mere sequence of mutation-selection steps, because this would take much longer than the history of evolution permits. Moreover, he calls these systems irreducibly complex, meaning that removal of one component makes them lose function. And this, he says, implies that they could not have developed through an evolutionary process. But in sections 3 and 4 I shall show that these are dubious claims.

Dembski claims that design can be detected objectively by means of his ‘design-detection filter’. There are, he says, only three possibilities for the appearance of a complex system: chance (random evolution), necessity (operation of natural laws), and design .10 For ‘chance’ he takes the example of the bacterial flagellum, which is made up of a base consisting of 10 proteins and anchored in the cell membrane and a tail consisting of 20 proteins. Assuming that the 30 proteins are composed of 300 aminoacids each, and knowing that there are 20 different natural aminoacids, he obtains a probability of 20 -300 for each protein. He concedes that the proteins need not get the exact aminoacid sequence right in order to be functional, so he cuts the odds to 20 -30 = 10 -39 . For 30 proteins the probabilities must be multiplied, giving an overall probability of 10 -1170 . This, he says, clearly rules out formation of the flagellum by chance. [However, in section 4 I shall explain that the flagellum has not arisen in a single ‘chance’ operation, so Dembski’s probability calculation and thus his conclusion are not correct.] ‘Necessity’ he rules out because it would make the system inflexible. [Here he disregards the fact that so-called non-linear systems (to which all living organisms belong) are according to natural law subject to chaos events. In other words, a process governed by natural law doesn’t necessarily lead to inflexibility.] Having ruled out (he thinks) ‘chance’ and ‘necessity’, he concludes that complex systems must be the result of ‘design’.

Some obvious questions are not answered by the ID proponents: What is the mechanism of ID? How frequently does design occur? What percentage of organisms exhibit ID? Do we find design to be more prevalent in some lines of descent than others? Are human pathogens such as AIDS, cholera, and malaria intelligently designed?11 The latter question points to the observation that there are in nature many examples of what might be called ‘unintelligent’ design.12 Of all species that have arisen more than 99% have died out. While rabbits have a large and functional appendix, humans have only a vestigial, non-functional appendix that makes us prone to appendicitis. The recurrent laryngeal nerve in mammals does not go directly from cranium to larynx, but extends down the neck to the chest, loops around a lung ligament and then runs back up the neck to the larynx. This means that in a giraffe this nerve has a length of 20 ft., where one foot would have done. In the cephalopod (e.g., squid) eye the photoreceptor cells are turned towards the incoming light, which seems a good design, but in the mammalian eye they are pointing in the opposite direction, which would be poor design.


3. Recent insights from molecular genetics

The major reason for Behe to adopt the ID hypothesis is that the evolutionary development of complex systems would take too long. However, gene play , as I like to call the interaction and regulation of genes, is now known to be much more complex and flexible than was thought.

For example, the biosynthesis of a flower pigment may involve a dozen or more steps, each controlled by a different enzyme, and thus by a different gene.13 Both synthesis and activity of these enzymes are controlled by regulator proteins, for which additional genes are needed. These regulator proteins also affect the time and place where the pigment is produced. Still other proteins control stability and subcellular localization of the pigment. Genes coding for the latter proteins are in turn regulated by another set of proteins, ‘transcription factors’, each encoded by a different gene. When a single gene seems to control a trait, it is because the enzyme encoded by that gene acts as the rate-limiting factor, not because this gene is the only one involved.

Species-specific genes are rare: in the mouse only 1% of its 30,000 genes are specific for the mouse, while it shares 77% of its genes with all other mammals.14 The phenotype (what makes a mouse a mouse) must be determined to a large extent by other factors than the genome. Of 1300 coding genes in the coral Acropora millepora 450 are found in humans, but 50 of these are missing in fruitfly Drosophila melanogaster and nematode worm Caenorhabditis elegans .15

Gene doubling , the phenomenon that many genes occur in doubles (in yeast 25% of its genes)16 offers better protection against harmful mutations, and also accelerates evolution by having one gene maintain the function, while its double is free to evolve a new function. In mice such doubles are involved in important functions, like reproduction, immunity, detoxification and smell.

Hox genes are genes that direct embryonic development.17 An example is the pac-6 gene that controls the development of all three eye types, the facet eye of insects, the cephalopod eye (visual cells turned towards the lens) and the vertebrate eye (visual cells turned away from the lens).18 When the mouse pac-6 gene is inserted in the fruitfly Drosophila , many facet eyes (not mouse eyes!) develop on its wings and legs. This gene must have arisen in a mutual ancestor that emerged from the Cambrian explosion, 540 million years ago. The hox genes hox-10 and hox-11 control skeletal development in all vertebrates.19 The hox gene twist plays a crucial role in the dorsal-ventral orientation, an important early step in embryonic development. This gene is activated by the protein b-catenin , which is released by embryonic cells when they are compressed during transition from the blastula to the gastrula stage.20

Transcription factors are proteins that can switch genes on and off.21 Each cell has many of these factors, which regulate transcription. They form a complex network, because one factor can bind to several genes and vice versa. Yeast has 141 transcription factors of which 106 bind to 2300 locations in the genome, humans even have 1700 transcription factors.

Junk DNA (up to 98% of all DNA), until recently thought to be useless because it does not code for any protein, now appears to have a function after all.22 By interaction with neighboring genes, it appears to regulate the activity of these genes and thereby increase the ability of the organism to evolve. ‘Junk DNA’ thus acts as a reservoir of ready-to-use segments for nature’s evolutionary experiments. Mammalian junk DNA sequences are strongly conserved, remaining largely unchanged for as long as 300 million years, and are therefore now called ‘conserved non-genic sequences’ (CNGs).23 Junk DNA affects inheritance, development and disease, and may be responsible for what makes one person different from the next.24 It forms RNA transcripts that control other genes by destroying their messenger RNAs. This process, called RNA interference , serves to silence genes in differentiated cells.25 It has probably emerged a billion years ago to protect some common ancestor to plants, animals and fungi against viruses and ‘hopping genes’. When not defending against attack, the system apparently serves to silence normal genes during differentiation.

The environment plays an important role in the development of complex traits. From studies of single-egg human twins it is known that ‘nature’ (genes) and ‘nurture’ (environment, education, etc.) have about an equal effect.26 This has been confirmed in a long-term study of the titmouse ( Parus major ), of which there are two types: active and timid birds.27 When males and females of the same type were mated in captivity for many generations, the active line showed increased activity, the timid line increased timidity. Rearing mixed nests by foster parents gave an estimate of the genetic component of behavior: 54% in captivity, 30-40% in the field. This was confirmed by analysis of blood samples. The smaller genetic effect in the field is ascribed to the more varying conditions as compared to captivity.

The flexibility and complexity of gene play may make possible relatively rapid evolutionary changes. E.g., whereas the 5-mm-size shrimp Xenoleberis has not evolved in 425 million yr, the cichlid fish in Lake Victoria developed 500 species in only 12,000 yrs. Another example is the case of the titmouse described in the preceding paragraph. There is also the case of the stickleback, where the marine form has 35 body plates and three pelvic spines.28 Upon transfer to a fresh-water lake it loses within a few generations the plates and pelvic spines and also undergoes changes in jaw and gill-protecting bones. The gene responsible is Pitx-1 , a hox gene that also plays a role in hindlimb formation in mice. Breeding the fresh-water form in seawater reverses the changes in two generations. It appears that the Pitx-1gene is active in sea water and inactive in fresh water. Not the mutation of a gene, but its activation or inactivation is responsible for this large phenotypical change.

None of these findings are mentioned in the publications of Behe and his associates.


4. ‘Irreducibly’ complex is not quite that

Here I shall show that none of the four prime examples of irreducibly complex systems mentioned by Behe is quite ‘irreducible’.

Rhodopsin, the light-sensitive component of the visual system, consists of a protein called opsin, to which is bound retinaldehyde (oxidized form of vitamin A). Rhodopsin is found in all three eye types (insect, cephalopod, vertebrate), but also in bacteria, where it serves as the light-sensitive element of a proton pump. It may, therefore, be some 600 million years old and flexible enough to serve two quite different functions and operate in three widely different eye types. Recently, 782 rhodopsin homologs (varying in the aminoacid composition of the opsin) were detected in samples of microbial populations collected from the Sargasso Sea.29 These findings indicate that rhodopsin is not irreducibly complex and suggest a gene-based evolution of the many different types of rhodopsin

The bloodclotting system in humans consists of twelve factors that work together in a cascade to produce bloodclotting. The dolphin misses one of these factors, the Hagemann factor (Factor XII), yet it has normal bloodclotting, while humans missing this factor are hemophiliacs.30 A primitive clotting system was already present in the jawless vertebrates hagfish and lamprey that diverged over 450 million years ago.31 The system consists of three factors, tissue factor, prothrombin and fibrinogen, all part of the present mammalian blood clotting system. This suggests that the blood clotting system has evolved over a period of at least 450 million years, and cannot be called ‘irreducibly complex’.

The immune system is a complex system with several components. A crucial component is the protein immunoglobulin G (IgG) that is responsible for the production of antibodies against harmful intruders. In humans the IgG is made up of four protein chains, two heavy and two light ones. Each of these consists of an invariable and a variable part, which permits the production of millions of different antibodies. The IgG of camels has no light chains,32 which means that it can produce only a few thousands of antibodies. Yet, the camel lives happily with this restricted system. Presumably, the simple system of the camel evolved to the more complex and more potent system in humans. Recently, it was found that the Drosophila fruit fly has a gene Dscam that can encode up to 38,000 slightly different proteins which function as primitive antibodies.33 It appears to be an early step in the evolution of the immunoglobulins. Again not ‘irreducibly complex’.

The bacterial flagellum , the crown jewel of the ID movement, is composed of a base made up of 10 proteins and located in the cell membrane to which is attached a tail made up of 20 proteins. The same 10 proteins of the base form the type III secretion system (TTSS) by which gram-negative bacteria insert their toxins into the cells of the host.34 Here we have an example of ‘evolutionary convergence’,35 the return of an earlier developed structure in a later, more advanced species, like the fin of the ichthyosaurus returning in the dolphin, and rhodopsin first appearing in the protonpump of bacteria and then returning in a different function in the three eye types. So the flagellum does not fit Behe’s definition of an irreducibly complex system.

Not mentioned in the ID literature is the case of the Myxococcus xanthus bacteria. Normally these bacteria move collectively over a solid nutrient medium by means of pili (digital extrusions). When the gene for pili formation is destroyed, the bacteria develop within 32 generations a novel motility system consisting of an extracellular matrix of protein fibrils, which allows them to move even more rapidly.36 Would we have to believe that the Designer was looking over the shoulders of the microbiologists and then designed on the spot a new motility system for the manipulated bacteria?

All the above indicates that none of the systems described by Behe as examples of irreducibly complex systems, nor the motility system of the Myxococcus bacteria, fits his definition of ‘irreducible complexity’. There are, moreover, clear indications for evolutionary development in all these cases.


5. Theological aspects

Behe, Dembski and all other ID adherents vigorously claim that ‘intelligent design’ is a scientific hypothesis to explain what they consider the inability of the commonly accepted evolution theory to explain the origin of complex systems in living organisms. However, they fail to explain the concept of ‘intelligent design’ in scientific terms and to give the merest scientific explanation of its operation. This makes it a scientifically untestable hypothesis. Behe doesn’t make any attempt to prove the hypothesis. Dembski uses his ‘design-detection filter’ to show that complex systems cannot have arisien by ‘chance’ or ‘necessity’ and thus must be the result of design, but this is unconvincing, to say the least (section 2)..

This means that ‘Intelligent Design’ is not a scientific but a metaphysical concept. Inasmuch as design requires a designer, ID implies an ‘Intelligent Designer’, a creator god. This makes ID a theological concept. The fact that Behe, Dembski and their adherents deny this,37 can be ascribed to their desire to have the ID hypothesis included in biology textbooks of the American public schools.3

Its theological nature then makes the ID hypothesis a form of ‘God in the gap’ theology, in which a specific act of God is proposed for a natural phenomenon that cannot (yet) be explained scientifically. However, the rapid advances in molecular genetics, described in sections 3 and 4, appear to be filling up the gap more and more. This leaves God at the mercy of scientific advances, which is theologically unacceptable.. Moreover, the examples of ‘unintelligent’ design, described in section 2, appear to make God a ‘bumbling hobbyist’ rather than a ‘superior engineer’.

It seems to me more reasonable, theologically as well as scientifically, to assume that the design of the entire creation, including complex systems, was laid down in the beginning in the form of the physical laws and fundamental constants, which have governed cosmic and biological evolution.ever since. Its capricious and often ‘unintelligent’ course suggests that God permits biological evolution to proceed in a trial-and-error process to explore all possibilities. This allows the process to achieve the optimal endresult, unlikely to be reached by imposing ad hoc designs for every complex system in nature. However, I suggest that God retains the possibility to keep this free process on the rails by incidentally influencing a chaos event.38

The basic fallacy of the ID proponents is that they fail to distinguish between the questions that can and should be answered by science (how-questions) and by theology (why-questions). If scientists would have to conclude that certain complex systems cannot have originated by a traditional evolutionary scenario, then it is up to them to find out how they did originate without appealing to a transcendent cause. Theologians must ask themselves why the Creator made these systems develop, regardless of the exact mechanism by which they arose. In a dialogue between scientists and theologians it will then be possible to reach a deeper and comprehensive understanding of their respective findings.39


6. Conclusions

(1) ‘Gene play’, the operation and interaction of genes, turns out to be much more complex and flexible than a simple darwinian sequence of mutation/selection steps. This suggests that major evolutionary steps can occur much faster than has been thought.


(2) All four of Behe’s examples of ‘irreducibly complex systems’ and the motility system of the Myxococcus bacteria are not ‘irreducibly’ complex, and show signs of evolutionary development.


(3) This means that there is no solid scientific basis for the ID hypothesis, and that in time to come it may well become superfluous.


(4) The theological weakness of the ID hypothesis is that it is basically a form of ‘God in the gap’ theology, with the gap being rapidly narrowed by advances in molecular genetics.


(5) The basic fallacy of the ID proponents is that they fail to distinguish between the questions that can and should be answered by science (how-questions) and by theology (why-questions).


(6) More reasonable, theologically as well as scientifically, is to assume that the design of the entire creation, including complex biological systems, was laid down in the beginning in the physical laws and fundamental constants, which have governed cosmic and biological evolution ever since, and that God allows evolution to proceed in a trial-and-error process exploring all possibilities and providing the optimal endresult. The examples of ‘unintelligent’ design in nature support this.assumption.


(7) God keeps creation on the rails by influencing a chaos event in crisis situations.


Notes and References

1. Michael J.Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution , Touchstone, New York, 1996.

2. William Dembski, Intelligent Design: The Bridge between Science and Theology, Intervarsity Press, Downers Grove, Ill, 1999.

3. An opposite argument for inclusion of ID in biology textbooks is taken by constitutional lawyer John H. Calvert (published online by Discovery Institute, Sept.25, 2004). He argues that the e volution theory is methodological naturalism, which is an ideology, a non-theistic belief system. The same is true for ID. Since the Supreme Court has ruled that religion also includes nontheistic belief systems (Elk Grove Unified School District et al v. Newdow et al., Supreme Court, June 14, 2004), a school that teaches evolution theory, must also permit teaching of ID in Calvert’s view, as the First Amendment requires governments (incl. schoolboards) to observe neutrality between religions.

4. Geoff Brumfield, Who has designs on your students’ minds?, Nature 434 , 1062-1065, 2005 Apr.28. Six Gallup polls between 1982 and 2001 showed that between 44 and 47% of Americans are creationists and between 35 and 40% believe in evolution guided by God, the ID position. Only 9 to 12% believe in evolution without divine guidance.

5. Laurie Goodstein, Teaching of Creationism Is Endorsed in New Survey, New York Times , Aug.31, 2005.

6. Scientists Irate Over Creationist Poll, Science 301 , 1043, 2003.

7. Ariel A. Roth, Origins, linking science and scripture , Review and Herald, Hagerstown, MD, 1998.

8. Cees Dekker et al., eds., Schitterend Ongeluk of Sporen van Ontwerp? [Brilliant Mishap or Traces of Design], Ten Have, Kampen, 2005.

9. Michael Ruse, The Evolution–Creation Struggle , Harvard University Press: 2005.

10. William Dembski, No Free Lunch , Rowman&Littlefield, Lanham, MD,

2002, p.301.

11. Gregory R. Peterson, The intelligent-design movement: science or ideology? Zygon , 37 (1): 07-23, March 2002.

12. Jim Holt, Unintelligent Design, New York Times , Feb.20, 2005.

13. H.F. Nijhout, The Importance of Context in Genetics, American Scientist 91

(no.5), 416-423, 2003 Sept./Oct.

14. Ken Howard, Key to exploring genomes is more genomes, Scientific American 287 (no.5), 13, 2002 Nov.

15. R.D. Kortschak et al, EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Current Biology , 13, 2190-2195, (2003).

16. Zhenglong Gu et al, Role of duplicate genes, Nature 421 , 63-66, 2003.

17. Elizabeth Pennisi and Wade Roush, Developing a New View of Evolution,

Science, 277 :34-37, 1997; J.H. Schwartz, Sudden Origins: Fossils, Genes, Emergence of Species , Wiley, New York, 1999.

18. Charles S. Zuker, On the Evolution of Eyes, Science 265 :742-743, 1994. Two additional eye regulator genes, ey and dac, have been found in Drosophila , which suggests the existence of a hierarchy of such genes (Wade Roush, Science, 275 :618-619, 1997).

19. D.M. Wellik and M.R. Capecchi, Hox 10 and Hox 11 Genes Are Required to Globally Pattern the Mammalian Skeleton, Science 301 , 363-367, 2003.

20. Ian C. Scott and Didier Y.R. Stainier, Twisting the body into shape, Nature 425 , 461-462, 2003.

21. Scientists Produce the Script for Life, ASBMB Today , Dec. 2002, pp.14-15.

22. W. Makalowski, Not Junk After All, Science 300 , 1246-1247, 2003;

23. M. Johnston and G.D. Stormo, Heirlooms in the Attic, Science 302 , 997-999, 2003.

24. W.W. Gibbs, The Unseen Genome: Gems among the Junk, Scient. Amer. 289 (5), 26-33, 2003; W.W. Gibbs, The Unseen Genome: Beyond DNA, Scient. Amer. 289 (6), 78-85, 2003.

25. Nelson C. Lau and David P. Bartel, Censors of the Genome, Scient. Amer. 289 (2), 26-33, 2003. See also a series of five articles on RNA interference in Nature 431 , 343-378 (16 September 2004).

26. Thomas J. Bouchard, Genes, Environment, and Personality, Science, 264 , 1700-1701, 1994.

27. Pieter J. Drent et al., Realised heritability of personalities in the great tit ( Parus major ). Proc.Roy.Soc. London B 270 (no.1510), 45- 52, 2003.

28. Elizabeth Pennisi, Changing a Fish’s Bony Armour In the Wink of a Gene, Science 304 , 1736-1739, 2004 June 18.

29. J. Craig Venter et al., Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science 304 , 66-74, 2004 Apr.2.

30. A.J. Robinson et al, Hagemann Factor (Factor XII) Deficiency in Marine Mammals. Science 166 : 1420-1422, 1969.

31. C.J. Davidson et al , 450 million years of hemostasis, Journal of Thrombosis and Heamostasis 1 , 1487-1494, 2003.

32. V.K. Nguyen et al, Heavy-chain only antibodies derived from dromedary are secreted and displayed by mouse B cells, Immunology 109 (1):93-101, 2003 May.

33. Elizabeth Pennisi, Versatile Development Gene Aids Insect Immune Response, Science 309 , 1166-1167, 2005 Aug.19.

34. S.-I. Aizawa, Bacterial flagella and type III secretion systems, FEMS Microbiology Letters 202 , 157-164, 2001.

35. Simon Conway Morris, We were meant to be…, New Scientist , 26-29, 2002; Ibid., Life’s Solution, Cambridge University Press, Cambridge , 2003.

36. Gregory J. Velicer and Yuen-tsu N. Yu, Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus , Nature 425 , 75-78, 2003.

37. Actually, in the trial of the case of 11 parents against the Dover schoolboard, Michael Behe as a witness for the defense admitted on cross-examination that to him the designer is God. In his verdict Judge John E. Jones concludes that ID is not science and that, therefore, “it is unconstitutional to teach ID as an alternative to evolution in a public school science classroom.” He speaks about “the breathtaking inanity of the Board’s decision.”

38. joerd L. Bonting, <em