Mathematics vs. Darwinism

A Mathematician's View of Evolution

Granville Sewell July 23, 2015 3:59 AM |

 Editor's note: Chapter 2 in Dr. Sewell's new book In the Beginning and Other Essays on Intelligent Design (2nd edition) originated as an Opinion piece published in 2000 in The Mathematical Intelligencer, Volume 22, number 4, pp. 5-7 (used with permission from Springer). We present the accepted manuscript below; the final publication is available here.

In 1996, Lehigh University biochemist Michael Behe published a book entitledDarwin's Black Box (Free Press), whose central theme is that every living cell is loaded with features and biochemical processes that are "irreducibly complex" -- that is, they require the existence of numerous complex components, each essential for function. These features and processes cannot be explained by gradual Darwinian improvements, because until all the components are in place, the assemblages are completely useless, and thus provide no selective advantage.

Behe spends over a hundred pages describing some of these irreducibly complex biochemical systems in detail, then summarizes the results of an exhaustive search of the biochemical literature for Darwinian explanations. He concludes that while biochemistry texts often pay lip-service to the idea that natural selection of random mutations can explain everything in the cell, such claims are pure "bluster," because "there is no publication in the scientific literature that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred."

When Dr. Behe was at the University of Texas El Paso in May of 1997 to give an invited talk, I told him that I thought he would find more support for his ideas in mathematics, physics, and computer science departments than in his own field. I know a good many mathematicians, physicists, and computer scientists who, like me, are appalled that Darwin's explanation for the development of life is so widely accepted in the life sciences. Few of them ever speak out or write on this issue, though -- perhaps because they feel the question is simply out of their domain. However, I believe there are two central arguments against Darwinism, and both seem to be most readily appreciated by those in the more mathematical sciences.

Little by Little

First, the cornerstone of Darwinism is the idea that major (complex) improvements can be built up through many minor improvements; that the new organs and new systems of organs which gave rise to new orders, classes, and phyla developed gradually, through many very minor improvements.

We should note that the fossil record does not support this idea. For example, Harvard paleontologist George Gaylord Simpson ("The History of Life," in Volume I of Evolution after Darwin, University of Chicago, 1960) writes:

It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution...This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes, and phyla are systematic and almost always large. These peculiarities of the record pose one of the most important theoretical problems in the whole history of life: Is the sudden appearance of higher categories a phenomenon of evolution or of the record only, due to sampling bias and other inadequacies?

An April 1982 article in Life Magazine, excerpted from Francis Hitching's book, The Neck of the Giraffe: Where Darwin Went Wrong, contains the following report:

When you look for links between major groups of animals, they simply aren't there..."Instead of finding the gradual unfolding of life," writes David M. Raup, a curator of Chicago's Field Museum of Natural History, "what geologists of Darwin's time and geologists of the present day actually find is a highly uneven or jerky record; that is, species appear in the fossil sequence very suddenly, show little or no change during their existence, then abruptly disappear." These are not negligible gaps. They are periods, in all the major evolutionary transitions, when immense physiological changes had to take place.

Even among biologists, the idea that new organs, and thus higher categories, could develop gradually through tiny improvements has often been challenged.¹ How could the "survival of the fittest" guide the development of new organs through their initial useless stages, during which they obviously present no selective advantage? (This is often referred to as the "problem of novelties".) Or guide the development of entire new systems, such as nervous, circulatory, digestive, respiratory, and reproductive systems, which would require the simultaneous development of several new interdependent organs, none of which is useful, or provides any selective advantage, by itself?

French biologist Jean Rostand, for example, wrote (A Biologist's View, Wm. Heinemann Ltd., 1956):

It does not seem strictly impossible that mutations should have introduced into the animal kingdom the differences which exist between one species and the next...hence it is very tempting to lay also at their door the differences between classes, families and orders, and, in short, the whole of evolution. But it is obvious that such an extrapolation involves the gratuitous attribution to the mutations of the past of a magnitude and power of innovation much greater than is shown by those of today.

Behe's book is primarily a challenge to this cornerstone of Darwinism at the microscopic level. Although we may not be familiar with the complex biochemical systems discussed in this book, I believe mathematicians are well qualified to appreciate the general ideas involved. And although an analogy is only an analogy, perhaps the best way to understand Behe's argument is by comparing the development of the genetic code of life with the development of a computer program.

Suppose an engineer attempts to design a structural analysis computer program, writing it in a machine language that is totally unknown to him. He simply types out random characters at his keyboard, and periodically runs tests on the program to recognize and select out chance improvements when they occur. The improvements are permanently incorporated into the program while the other changes are discarded. If our engineer continues this process of random changes and testing for a long enough time, could he eventually develop a sophisticated structural analysis program? (Of course, when intelligent humans decide what constitutes an "improvement," this is really artificial selection, so the analogy is far too generous.)

If a billion engineers were to type at the rate of one random character per second, there is virtually no chance that any one of them would, given the 4.5 billion year age of the Earth to work on it, accidentally duplicate a given 20-character improvement. Thus our engineer cannot count on making any major improvements through chance alone. But could he not perhaps make progress through the accumulation of very small improvements?

The Darwinist would presumably say yes, but to anyone who has had minimal programming experience this idea is equally implausible. Major improvements to a computer program often require the addition or modification of hundreds of interdependent lines, no one of which makes any sense, or results in any improvement, when added by itself. Even the smallest improvements usually require adding several new lines. It is conceivable that a programmer unable to look ahead more than five or six characters at a time might be able to make some very slight improvements to a computer program, but it is inconceivable that he could design anything sophisticated without the ability to plan far ahead and to guide his changes toward that plan.

If archeologists of some future society were to unearth the many versions of my PDE solver, PDE2D, which I have produced over the last 20 years, they would certainly note a steady increase in complexity over time, and they would see many obvious similarities between each new version and the previous one. In the beginning it was only able to solve a single linear, steady-state, 2D equation in a polygonal region. Since then, PDE2D has developed many new abilities: it now solves nonlinear problems, time-dependent, and eigenvalue problems, systems of simultaneous equations, and it now handles general curved 2D regions. Over the years, many new types of graphical output capabilities have evolved, and in 1991 it developed an interactive preprocessor, and more recently PDE2D has adapted to 3D and 1D problems.

An archeologist attempting to explain the evolution of this computer program in terms of many tiny improvements might be puzzled to find that each of these major advances (new classes or phyla?) appeared suddenly in new versions; for example, the ability to solve 3D problems first appeared in version 4.0. Less major improvements (new families or orders?) appeared suddenly in new subversions, for example, the ability to solve 3D problems with periodic boundary conditions first appeared in version 5.6. In fact, the record of PDE2D's development would be similar to the fossil record, with large gaps where major new features appeared, and smaller gaps where minor ones appeared.²

That is because the multitude of intermediate programs between versions or subversions which the archeologist might expect to find never existed, because -- for example -- none of the changes I made for edition 4.0 made any sense, or provided PDE2D any advantage whatever in solving 3D problems (or anything else) until hundreds of lines had been added.

Whether at the microscopic or macroscopic level, major, complex, evolutionary advances, involving new features (as opposed to minor, quantitative changes such as an increase in the length of the giraffe's neck, or the darkening of the wings of a moth, which clearly could occur gradually) also involve the addition of many interrelated and interdependent pieces. These complex advances, like those made to computer programs, are not always "irreducibly complex" -- sometimes there are intermediate useful stages. But just as major improvements to a computer program cannot be made five or six characters at a time, certainly no major evolutionary advance is reducible to a chain of tiny improvements, each small enough to be bridged by a single random mutation.

Just Add Sunshine?

The second point is very simple, but also seems to be appreciated only by more mathematically oriented people. It is that to attribute the development of life on Earth to natural selection is to assign to it -- and to it alone, of all known natural "forces" -- the ability to violate the second law of thermodynamics and to cause order to arise from disorder. It is often argued that since the Earth is not a closed system -- it receives energy from the Sun, for example -- the second law is not applicable in this case. It is true that order can increase locally, if the local increase is compensated by a decrease elsewhere, i.e., an open system can be taken to a less probable state by importing order from outside.

For example, we could transport a truckload of encyclopedias and computers to the moon, thereby increasing the order on the moon, without violating the second law. But the second law of thermodynamics -- at least the underlying principle behind this law -- simply says that natural forces do not cause extremely improbable things to happen,³ and it is absurd to argue that because the Earth receives energy from the Sun, this principle was not violated here when the original rearrangement of atoms into encyclopedias and computers occurred.

The biologist studies the details of natural history, and when he looks at the similarities between two species of butterflies, he is understandably reluctant to attribute the small differences to the supernatural. But the mathematician or physicist is likely to take the broader view. I imagine visiting the Earth when it was young and returning now to find highways with automobiles on them, airports with jet airplanes, and tall buildings full of complicated equipment, such as televisions, telephones, and computers. Then I imagine the construction of a gigantic computer model which starts with the initial conditions on Earth 4 billion years ago and tries to simulate the effects that the four known forces of physics (the gravitational, electromagnetic and strong and weak nuclear forces) would have on every atom and every subatomic particle on our planet (perhaps using random number generators to model quantum uncertainties!).

If we ran such a simulation out to the present day, would it predict that the basic forces of Nature would reorganize the basic particles of Nature into libraries full of encyclopedias, science texts, and novels, nuclear power plants, aircraft carriers with supersonic jets parked on deck, and computers connected to laser printers, CRTs, and keyboards? If we graphically displayed the positions of the atoms at the end of the simulation, would we find that cars and trucks had formed, or that supercomputers had arisen? Certainly we would not, and I do not believe that adding sunlight to the model would help much. Clearly something extremely improbable has happened here on our planet, with the origin and development of life, and especially with the development of human consciousness and creativity.

References:

(1) See this New York Times article, for example.

(2) See this ENV article for more on the similiarities between the evolution of life and the evolution of human technology.

(3) An unfortunate choice of words. I should have said, the underlying principle behind the second law is that natural forces do not domacroscopically describable things that are extremely improbable from themicroscopic point of view. See "Entropy and Evolution," Granville Sewell, Bio-Complexity, 2013, for a more complete treatment of this point. 

Hebrews1-7New Jerusalem Bible

1)1 At many moments in the past and by many means, God spoke to our ancestors through the prophets; but

2 in our time, the final days, he has spoken to us in the person of his Son, whom he appointed heir of all things and through whom he made the ages.

3 He is the reflection of God's glory and bears the impress of God's own being, sustaining all things by his powerful command; and now that he has purged sins away, he has taken his seat at the right hand of the divine Majesty on high.

4 So he is now as far above the angels as the title which he has inherited is higher than their own name.

5 To which of the angels, then, has God ever said: You are my Son, today I have fathered you, or: I shall be a father to him and he a son to me?

6 Again, when he brings the First-born into the world, he says: Let all the angels of God pay him homage.

7 To the angels, he says: appointing the winds his messengers and flames of fire his servants,

8 but to the Son he says: Your throne, God, is for ever and ever; and: the sceptre of his kingdom is a sceptre of justice;

9 you love uprightness and detest evil. This is why God, your God, has anointed you with the oil of gladness, as none of your rivals.

10 And again: Long ago, Lord, you laid earth's foundations, the heavens are the work of your hands.

11 They pass away but you remain, they all wear out like a garment.

12 Like a cloak you will roll them up, like a garment, and they will be changed. But you never alter and your years are unending.

13 To which of the angels has God ever said: Take your seat at my right hand till I have made your enemies your footstool?

14 Are they not all ministering spirits, sent to serve for the sake of those who are to inherit salvation?

2)1 We ought, then, to turn our minds more attentively than before to what we have been taught, so that we do not drift away.

2 If a message that was spoken through angels proved to be so reliable that every infringement and disobedience brought its own proper punishment,

3 then we shall certainly not go unpunished if we neglect such a great salvation. It was first announced by the Lord himself, and is guaranteed to us by those who heard him;

4 God himself confirmed their witness with signs and marvels and miracles of all kinds, and by distributing the gifts of the Holy Spirit in the various ways he wills.

5 It was not under angels that he put the world to come, about which we are speaking.

6 Someone witnesses to this somewhere with the words: What are human beings that you spare a thought for them, a child of Adam that you care for him?

7 For a short while you have made him less than the angels; you have crowned him with glory and honour,

8 put all things under his feet. For in putting all things under him he made no exceptions. At present, it is true, we are not able to see that all things are under him,

9 but we do see Jesus, who was for a short while made less than the angels, now crowned with glory and honour because he submitted to death; so that by God's grace his experience of death should benefit all humanity.

10 It was fitting that God, for whom and through whom everything exists, should, in bringing many sons to glory, make perfect through suffering the leader of their salvation.

11 For consecrator and consecrated are all of the same stock; that is why he is not ashamed to call them brothers

12 in the text: I shall proclaim your name to my brothers, praise you in full assembly; or in the text:

13 I shall put my hope in him; followed by Look, I and the children whom God has given me.

14 Since all the children share the same human nature, he too shared equally in it, so that by his death he could set aside him who held the power of death, namely the devil,

15 and set free all those who had been held in slavery all their lives by the fear of death.

16 For it was not the angels that he took to himself; he took to himself the line of Abraham.

17 It was essential that he should in this way be made completely like his brothers so that he could become a compassionate and trustworthy high priest for their relationship to God, able to expiate the sins of the people.

18 For the suffering he himself passed through while being put to the test enables him to help others when they are being put to the test.

3) 1 That is why all you who are holy brothers and share the same heavenly call should turn your minds to Jesus, the apostle and the high priest of our profession of faith.

2 He was trustworthy to the one who appointed him, just like Moses, who remained trustworthy in all his household;

3 but he deserves a greater glory than Moses, just as the builder of a house is more honoured than the house itself.

4 Every house is built by someone, of course; but God built everything that exists.

5 It is true that Moses was trustworthy in the household of God, as a servant is, acting as witness to the things which were yet to be revealed,

6 but Christ is trustworthy as a son is, over his household. And we are his household, as long as we fearlessly maintain the hope in which we glory.

7 That is why, as the Holy Spirit says: If only you would listen to him today!

8 Do not harden your hearts, as at the rebellion, as at the time of testing in the desert,

9 when your ancestors challenged me, and put me to the test, and saw what I could do

10 for forty years. That was why that generation sickened me and I said, 'Always fickle hearts, that cannot grasp my ways!'

11 And then in my anger I swore that they would never enter my place of rest.

12 Take care, brothers, that none of you ever has a wicked heart, so unbelieving as to turn away from the living God.

13 Every day, as long as this today lasts, keep encouraging one another so that none of you is hardened by the lure of sin,

14 because we have been granted a share with Christ only if we keep the grasp of our first confidence firm to the end.

15 In this saying: If only you would listen to him today; do not harden your hearts, as at the Rebellion,

16 who was it who listened and then rebelled? Surely all those whom Moses led out of Egypt.

17 And with whom was he angry for forty years? Surely with those who sinned and whose dead bodies fell in the desert.

18 To whom did he swear they would never enter his place of rest? Surely those who would not believe.

19 So we see that it was their refusal to believe which prevented them from entering.

4)1 Let us beware, then: since the promise never lapses, none of you must think that he has come too late for the promise of entering his place of rest.

2 We received the gospel exactly as they did; but hearing the message did them no good because they did not share the faith of those who did listen.

3 We, however, who have faith, are entering a place of rest, as in the text: And then in my anger I swore that they would never enter my place of rest. Now God's work was all finished at the beginning of the world;

4 as one text says, referring to the seventh day: And God rested on the seventh day after all the work he had been doing.

5 And, again, the passage above says: They will never reach my place of rest.

6 It remains the case, then, that there would be some people who would reach it, and since those who first heard the good news were prevented from entering by their refusal to believe,

7 God fixed another day, a Today, when he said through David in the text already quoted: If only you would listen to him today; do not harden your hearts.

8 If Joshua had led them into this place of rest, God would not later have spoken of another day.

9 There must still be, therefore, a seventh-day rest reserved for God's people,

10 since to enter the place of rest is to rest after your work, as God did after his.

11 Let us, then, press forward to enter this place of rest, or some of you might copy this example of refusal to believe and be lost.

12 The word of God is something alive and active: it cuts more incisively than any two-edged sword: it can seek out the place where soul is divided from spirit, or joints from marrow; it can pass judgement on secret emotions and thoughts.

13 No created thing is hidden from him; everything is uncovered and stretched fully open to the eyes of the one to whom we must give account of ourselves.

14 Since in Jesus, the Son of God, we have the supreme high priest who has gone through to the highest heaven, we must hold firm to our profession of faith.

15 For the high priest we have is not incapable of feeling our weaknesses with us, but has been put to the test in exactly the same way as ourselves, apart from sin.

16 Let us, then, have no fear in approaching the throne of grace to receive mercy and to find grace when we are in need of help.

5)1 Every high priest is taken from among human beings and is appointed to act on their behalf in relationships with God, to offer gifts and sacrifices for sins;

2 he can sympathise with those who are ignorant or who have gone astray, because he too is subject to the limitations of weakness.

3 That is why he has to make sin offerings for himself as well as for the people.

4 No one takes this honour on himself; it needs a call from God, as in Aaron's case.

5 And so it was not Christ who gave himself the glory of becoming high priest, but the one who said to him: You are my Son, today I have fathered you,

6 and in another text: You are a priest for ever, of the order of Melchizedek.

7 During his life on earth, he offered up prayer and entreaty, with loud cries and with tears, to the one who had the power to save him from death, and, winning a hearing by his reverence,

8 he learnt obedience, Son though he was, through his sufferings;

9 when he had been perfected, he became for all who obey him the source of eternal salvation

10 and was acclaimed by God with the title of high priest of the order of Melchizedek.

11 On this subject we have many things to say, and they are difficult to explain because you have grown so slow at understanding.

12 Indeed, when you should by this time have become masters, you need someone to teach you all over again the elements of the principles of God's sayings; you have gone back to needing milk, and not solid food.

13 Truly, no one who is still living on milk can digest the doctrine of saving justice, being still a baby.

14 Solid food is for adults with minds trained by practice to distinguish between good and bad.
6)1 Let us leave behind us then all the elementary teaching about Christ and go on to its completion, without going over the fundamental doctrines again: the turning away from dead actions, faith in God,

2 the teaching about baptisms and the laying -- on of hands, about the resurrection of the dead and eternal judgement.

3 This, God willing, is what we propose to do.

4 As for those people who were once brought into the light, and tasted the gift from heaven, and received a share of the Holy Spirit,

5 and tasted the goodness of God's message and the powers of the world to come

6 and yet in spite of this have fallen away -- it is impossible for them to be brought to the freshness of repentance a second time, since they are crucifying the Son of God again for themselves, and making a public exhibition of him.

7 A field that drinks up the rain that has fallen frequently on it, and yields the crops that are wanted by the owners who grew them, receives God's blessing;

8 but one that grows brambles and thistles is worthless, and near to being cursed. It will end by being burnt.

9 But you, my dear friends -- in spite of what we have just said, we are sure you are in a better state and on the way to salvation.

10 God would not be so unjust as to forget all you have done, the love that you have for his name or the services you have done, and are still doing, for the holy people of God.

11 Our desire is that every one of you should go on showing the same enthusiasm till the ultimate fulfilment of your hope,

12 never growing careless, but taking as your model those who by their faith and perseverance are heirs of the promises.

13 When God made the promise to Abraham, he swore by his own self, since there was no one greater he could swear by:

14 I will shower blessings on you and give you many descendants.

15 Because of that, Abraham persevered and received fulfilment of the promise.

16 Human beings, of course, swear an oath by something greater than themselves, and between them, confirmation by an oath puts an end to all dispute.

17 In the same way, when God wanted to show the heirs of the promise even more clearly how unalterable his plan was, he conveyed it by an oath

18 so that through two unalterable factors in which God could not be lying, we who have fled to him might have a vigorous encouragement to grasp the hope held out to us.

19 This is the anchor our souls have, reaching right through inside the curtain

20 where Jesus has entered as a forerunner on our behalf, having become a high priest for ever, of the order of Melchizedek.

7)1 Melchizedek, king of Salem, a priest of God Most High, came to meet Abraham when he returned from defeating the kings, and blessed him;

2 and Abraham gave him a tenth of everything. By the interpretation of his name, he is, first, 'king of saving justice' and also king of Salem, that is, 'king of peace';

3 he has no father, mother or ancestry, and his life has no beginning or ending; he is like the Son of God. He remains a priest for ever.

4 Now think how great this man must have been, if the patriarch Abraham gave him a tenth of the finest plunder.

5 We know that any of the descendants of Levi who are admitted to the priesthood are obliged by the Law to take tithes from the people, that is, from their own brothers although they too are descended from Abraham.

6 But this man, who was not of the same descent, took his tithe from Abraham, and he gave his blessing to the holder of the promises.

7 Now it is indisputable that a blessing is given by a superior to an inferior.

8 Further, in the normal case it is ordinary mortal men who receive the tithes, whereas in that case it was one who is attested as being alive.

9 It could be said that Levi himself, who receives tithes, actually paid tithes, in the person of Abraham,

10 because he was still in the loins of his ancestor when Melchizedek came to meet him.

11 Now if perfection had been reached through the levitical priesthood -- and this was the basis of the Law given to the people -- why was it necessary for a different kind of priest to arise, spoken of as being of the order of Melchizedek rather than of the order of Aaron?

12 Any change in the priesthood must mean a change in the Law as well.

13 So our Lord, of whom these things were said, belonged to a different tribe, the members of which have never done service at the altar;

14 everyone knows he came from Judah, a tribe which Moses did not mention at all when dealing with priests.

15 This becomes even more clearly evident if another priest, of the type of Melchizedek, arises who is a priest

16 not in virtue of a law of physical descent, but in virtue of the power of an indestructible life.

17 For he is attested by the prophecy: You are a priest for ever of the order of Melchizedek.

18 The earlier commandment is thus abolished, because of its weakness and ineffectiveness

19 since the Law could not make anything perfect; but now this commandment is replaced by something better-the hope that brings us close to God.

20 Now the former priests became priests without any oath being sworn,

21 but this one with the swearing of an oath by him who said to him, The Lord has sworn an oath he will never retract: you are a priest for ever;

22 the very fact that it occurred with the swearing of an oath makes the covenant of which Jesus is the guarantee all the greater.

23 Further, the former priests were many in number, because death put an end to each one of them;

24 but this one, because he remains for ever, has a perpetual priesthood.

25 It follows, then, that his power to save those who come to God through him is absolute, since he lives for ever to intercede for them.

26 Such is the high priest that met our need, holy, innocent and uncontaminated, set apart from sinners, and raised up above the heavens;

27 he has no need to offer sacrifices every day, as the high priests do, first for their own sins and only then for those of the people; this he did once and for all by offering himself.

28 The Law appoints high priests who are men subject to weakness; but the promise on oath, which came after the Law, appointed the Son who is made perfect for ever

Darwinian argumentation is not evolving

Flagellar Diversity Challenges Darwinian Evolution, Not Intelligent Design
Casey Luskin July 22, 2015 3:56 AM |

Over the past week I've been writing about the latest iteration of the Darwinian response to Michael Behe's argument for intelligent design based on what Dr. Behe calls irreducible complexity. I use the word "iteration" not in the sense of our seeing something new, but in the sense that it's another round of the same unworkable objections that we've seen before.

Behe's case for ID goes back nearly twenty years now, yet the objections to it have not evolved much in that time. I have been looking specifically at an article written by biophysicist Matt Baker for the Australian Broadcasting Corporation, "The bacterial flagellar motor: brilliant evolution or intelligent design?," arguing that the flagellum is not irreducibly complex. In the first part of my response I showed how he misunderstands how we test irreducible complexity, and in the second part I showed why the Type III Secretory System cannot serve as an evolutionary precursor to the flagellum.

But Dr. Baker has one other argument up his sleeve to try to show that the flagellum evolved. In his view, God wouldn't have done it that way. Essentially, Baker has imbibed Nick Matzke and Mark Pallen's fallacious theological argument that because there is diversity among flagella, the structure must not have been designed. He writes:

In the aftermath of the first legal challenges to curriculum requirements to teach intelligent design, evolutionary biologists Mark Pallen and Nicholas Matzke wrote "either there were thousands or millions of individual creation events ... or one has to accept that the highly diverse contemporary flagellar systems have evolved from a common ancestor".

Now maybe some (or even most) flagella are indeed related to one another, but there's no reason why a designer couldn't design diverse flagella. After all, in our experience with technological systems devised by human beings, we see incredible diversity! Look at all of the different ways that people have designed cell phones, trucks, or even something as simple as a key. These devices come in all kinds of myriad forms. Diversity doesn't negate design.

Thus, Baker is proffering a theological argument that is simply irrelevant to the scientific case for intelligent design. In reality, flagella are distributed in a polyphyletic manner that doesn't fit what we'd expect from common ancestry:

tim_flag_phyl_500.jpg

Reprinted from Figure 2, Trends in Microbiology, Vol 17, LAS Snyder, NJ Loman, K. Fuetterer, and MJ Pallen, "Bacterial flagellar diversity and evolution: seek simplicity and distrust it?," pp. 1-5, Copyright 2009, with permission from Elsevier.

What you see in the figure above are various major groups of bacteria, represented by triangles (or in some cases written text). They are arranged here according to a standard phylogeny of bacteria. The purple groups have flagella throughout the clade, and the groups with question marks have only a minority of species with flagella within that clade. The white triangles show groups not thought to have flagella.

What's the problem? The groups with flagella are scattered all about the tree and do not form a single monophyletic group. In other words, the diversity of flagella cannot be easily explained by common ancestry. Writing in Trends in Microbiology, the authors of the figure reprinted above explain the problem:

When we attempted to map the known distribution of flagellar genes on to a recently published 'tree of life', instead of a single monophyletic grouping of flagella-bearing phyla, we found multiple apparent points of origin for flagellar systems on the phylogenetic tree (Figure 2). This highlights a fundamental problem with any simple model of flagellar divergence: although there is some agreement as to the existence of bacterial phyla, there is no consensus on the order of their divergence.

The problem here is that flagella do not fit into the nice, neat nested hierarchy that you'd expect from common ancestry. Quite the opposite -- their diversity conflicts with what you would expect from a Darwinian origin of the flagellum. Indeed, the caption for the figure above from the paper states, "Arrows indicate apparent points of origins for flagellar lineages." Common descent predicts there should be just one arrow, but as you can see on the diagram there are five arrows, because there are no fewer than five clades -- widely separated on the tree -- that have flagella. This is not what common descent predicts. Common design, on the other hand would predict that complex features like flagella might be re-used in a manner that doesn't match a nested hierarchy, which is exactly what we see here. Ironically, the nature of bacterial flagellar diversity -- far from being a problem for intelligent design -- is actually a significant problem for Darwinian evolution.

Baker's argument here is ironic. We constantly see evolutionists arguing that homology (i.e., sequence similarity) between proteins is evidence that they evolved. In particular, we see this argument made regarding the flagellum. In fact, in a striking comment that appears after his article, Baker himself states that he feels no obligation to provide anything like a stepwise explanation for the evolution of the flagellum precisely because "commonality" between proteins is sufficient to demonstrate flagellar evolution:

I don't think we need to actually directly show an injectisome can be step by step evolved into a flagellum, the field of experimental evolution is very young! We can look, with greater and greater ease, at the historical genetic record, and look for commonality. This is the basis of most evolutionary genetics. By phylogenetics and common ancestors, we can show that systems share elements, and we do.

Yet in his article he affirmatively quotes Pallen and Matzke saying that the "highly diverse" nature of flagellar proteins also demonstrates their evolution. So now apparently both similarity between proteins and differences between proteins demonstrates evolution. No matter what you find, it demonstrates evolution!

What a sweet deal it must be to be a Darwinian evolutionist. You don't have to provide any evidence that your theory is true (i.e., offer some semblance of a stepwise evolutionary explanation), and no matter what evidence you do find, it is guaranteed to show that your theory is true!

Indeed, Pallen and Matzke's paper presents other related contradictions. They repeatedly denigrate "typological" thinking, stating:

As the great evolutionist Ernst Mayr noted, one of Darwin's greatest achievements was to abolish typological or essentialist thinking from biology; instead, the emphasis in biology is on variation and individuality3. Therefore, when discussing flagellar evolution it is important to appreciate that there is no such thing as 'the' bacterial flagellum. Instead, there are myriad different bacterial flagella, showing extensive variation in form and function.

Since their article is an explicit attack on ID, I suppose their point is that they're trying to tag ID as a form of typological thinking, wrongly suggesting that ID can't accommodate the diversity among flagella. Ironically, however, Pallen and Matkze later admit that "all (bacterial) flagella share a conserved core set of proteins," numbering around 20 proteins, and they further concede that there is a common core of subsystems found in known bacterial flagella:

Three modular molecular devices are at the heart of the bacterial flagellum: the rotor-stator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum.

There you have it: despite all the apparent "diversity" of flagella, and the evolutionists' distaste for "typological thinking," they admit that all bacterial flagella share a conserved core of about 20 proteins, and a common core (what I would call an irreducible core) of subsystems: a motor, a chemotaxis mechanism, and a secretion apparatus. It seems like the many diverse types of flagella are variations on a common thematic archetype.

And how do we know this core is irreducibly complex? Because the experimental data shows it is. Scott Minnich's genetic knockout experiments on the E. coli flagellum have shown that it fails to assemble or function properly if any one of its approximately 35 structural parts are missing.

Baker discloses none of this, but simply asserts that the irreducible complexity of the flagellum has been refuted:

Typically, intelligent design proponents persevere despite this evidence. They simply adjust their goal posts by selecting other systems to act as poster boys for irreducible complexity. It is difficult to respond to these movable challenges. But as we learn more about the origins of these and other complex systems, we can at least reduce the number of available candidates used to prop up the theory of intelligent design.

Actually ID proponents haven't abandoned arguing for the irreducible complexity of the flagellum because, as we've seen, it was never refuted in the first place. Rather than moving goal posts, we're building a formidable team, as ID advocates have expanded their arguments far beyond irreducible complexity. But I suspect that Dr. Baker doesn't pay any much attention to any of that.

Thus, he closes with a typically inaccurate rant about the dangers of intelligent design:

While all this may seem relatively harmless, the intelligent design movement is well funded, slickly presented, and actively challenges educational curricula in many countries. It is a dangerously well-articulated distraction from the large body of evidence supporting evolutionary theory.

Actually our funding is nothing compared to the wealth of support available to upholders of Darwinian evolution. Setting that aside, consider Baker's claim that ID distracts from the "large body of evidence supporting evolutionary theory." In fact, as we've seen, both evidence and logic contradict Baker's arguments. In fact, he openly refuses to demonstrate what Darwinian evolution requires: a stepwise evolutionary explanation of the flagellum! He apparently wants to blame ID for his failure to make a convincing case.

The world is very different from the one that many Darwin advocates believe they live in. Despite their protests to the contrary, this debate is far from ov

Malachi1-4ASV

1  The burden of the word of Jehovah to Israel by Malachi.

2 I have loved you, saith Jehovah. Yet ye say, Wherein hast thou loved us? Was not Esau Jacob's brother, saith Jehovah: yet I loved Jacob;

3 but Esau I hated, and made his mountains a desolation, and gave his heritage to the jackals of the wilderness.

4 Whereas Edom saith, We are beaten down, but we will return and build the waste places; thus saith Jehovah of hosts, They shall build, but I will throw down; and men shall call them The border of wickedness, and The people against whom Jehovah hath indignation for ever.

5 And your eyes shall see, and ye shall say, Jehovah be magnified beyond the border of Israel.

6 A son honoreth his father, and a servant his master: if then I am a father, where is mine honor? and if I am a master, where is my fear? saith Jehovah of hosts unto you, O priests, that despise my name. And ye say, Wherein have we despised thy name?

7 Ye offer polluted bread upon mine altar. And ye say, Wherein have we polluted thee? In that ye say, The table of Jehovah is contemptible.

8 And when ye offer the blind for sacrifice, it is no evil! and when ye offer the lame and sick, it is no evil! Present it now unto thy governor; will he be pleased with thee? or will he accept thy person? saith Jehovah of hosts.

9 And now, I pray you, entreat the favor of God, that he may be gracious unto us: this hath been by your means: will he accept any of your persons? saith Jehovah of hosts.

10 Oh that there were one among you that would shut the doors, that ye might not kindle fire on mine altar in vain! I have no pleasure in you, saith Jehovah of hosts, neither will I accept an offering at your hand.

11 For from the rising of the sun even unto the going down of the same my name shall be great among the Gentiles; and in every place incense shall be offered unto my name, and a pure offering: for my name shall be great among the Gentiles, saith Jehovah of hosts.

12 But ye profane it, in that ye say, The table of Jehovah is polluted, and the fruit thereof, even its food, is contemptible.

13 Ye say also, Behold, what a weariness is it! and ye have snuffed at it, saith Jehovah of hosts; and ye have brought that which was taken by violence, and the lame, and the sick; thus ye bring the offering: should I accept this at your hand? saith Jehovah.

14 But cursed be the deceiver, who hath in his flock a male, and voweth, and sacrificeth unto the Lord a blemished thing; for I am a great King, saith Jehovah of hosts, and my name is terrible among the Gentiles.

American Standard Version (ASV)

2  And now, O ye priests, this commandment is for you.

2 If ye will not hear, and if ye will not lay it to heart, to give glory unto my name, saith Jehovah of hosts, then will I send the curse upon you, and I will curse your blessings; yea, I have cursed them already, because ye do not lay it to heart.

3 Behold, I will rebuke your seed, and will spread dung upon your faces, even the dung of your feasts; and ye shall be taken away with it.

4 And ye shall know that I have sent this commandment unto you, that my covenant may be with Levi, saith Jehovah of hosts.

5 My covenant was with him of life and peace; and I gave them to him that he might fear; and he feared me, and stood in awe of my name.

6 The law of truth was in his mouth, and unrighteousness was not found in his lips: he walked with me in peace and uprightness, and turned many away from iniquity.

7 For the priest's lips should keep knowledge, and they should seek the law at his mouth; for he is the messenger of Jehovah of hosts.

8 But ye are turned aside out of the way; ye have caused many to stumble in the law; ye have corrupted the covenant of Levi, saith Jehovah of hosts.

9 Therefore have I also made you contemptible and base before all the people, according as ye have not kept my ways, but have had respect of persons in the law.

10 Have we not all one father? hath not one God created us? why do we deal treacherously every man against his brother, profaning the covenant of our fathers?

11 Judah hath dealt treacherously, and an abomination is committed in Israel and in Jerusalem; for Judah hath profaned the holiness of Jehovah which he loveth, and hath married the daughter of a foreign god.

12 Jehovah will cut off, to the man that doeth this, him that waketh and him that answereth, out of the tents of Jacob, and him that offereth an offering unto Jehovah of hosts.

13 And this again ye do: ye cover the altar of Jehovah with tears, with weeping, and with sighing, insomuch that he regardeth not the offering any more, neither receiveth it with good will at your hand.

14 Yet ye say, Wherefore? Because Jehovah hath been witness between thee and the wife of thy youth, against whom thou hast dealt treacherously, though she is thy companion, and the wife of thy covenant.

15 And did he not make one, although he had the residue of the Spirit? And wherefore one? He sought a godly seed. Therefore take heed to your spirit, and let none deal treacherously against the wife of his youth.

16 For I hate putting away, saith Jehovah, the God of Israel, and him that covereth his garment with violence, saith Jehovah of hosts: therefore take heed to your spirit, that ye deal not treacherously.

17 Ye have wearied Jehovah with your words. Yet ye say, Wherein have we wearied him? In that ye say, Every one that doeth evil is good in the sight of Jehovah, and he delighteth in them; or where is the God of justice?

American Standard Version (ASV)

3  Behold, I send my messenger, and he shall prepare the way before me: and the Lord, whom ye seek, will suddenly come to his temple; and the messenger of the covenant, whom ye desire, behold, he cometh, saith Jehovah of hosts.

2 But who can abide the day of his coming? and who shall stand when he appeareth? for he is like a refiner's fire, and like fuller's soap:

3 and he will sit as a refiner and purifier of silver, and he will purify the sons of Levi, and refine them as gold and silver; and they shall offer unto Jehovah offerings in righteousness.

4 Then shall the offering of Judah and Jerusalem be pleasant unto Jehovah, as in the days of old, and as in ancient years.

5 And I will come near to you to judgment; and I will be a swift witness against the sorcerers, and against the adulterers, and against the false swearers, and against those that oppress the hireling in his wages, the widow, and the fatherless, and that turn aside the sojourner from his right, and fear not me, saith Jehovah of hosts.

6 For I, Jehovah, change not; therefore ye, O sons of Jacob, are not consumed.

7 From the days of your fathers ye have turned aside from mine ordinances, and have not kept them. Return unto me, and I will return unto you, saith Jehovah of hosts. But ye say, Wherein shall we return?

8 Will a man rob God? yet ye rob me. But ye say, Wherein have we robbed thee? In tithes and offerings.

9 Ye are cursed with the curse; for ye rob me, even this whole nation.

10 Bring ye the whole tithe into the store-house, that there may be food in my house, and prove me now herewith, saith Jehovah of hosts, if I will not open you the windows of heaven, and pour you out a blessing, that there shall not be room enough to receive it.

11 And I will rebuke the devourer for your sakes, and he shall not destroy the fruits of your ground; neither shall your vine cast its fruit before the time in the field, saith Jehovah of hosts.

12 And all nations shall call you happy; for ye shall be a delightsome land, saith Jehovah of hosts.

13 Your words have been stout against me, saith Jehovah. Yet ye say, What have we spoken against thee?

14 Ye have said, It is vain to serve God; and what profit is it that we have kept his charge, and that we have walked mournfully before Jehovah of hosts?

15 And now we call the proud happy; yea, they that work wickedness are built up; yea, they tempt God, and escape.

16 Then they that feared Jehovah spake one with another; and Jehovah hearkened, and heard, and a book of remembrance was written before him, for them that feared Jehovah, and that thought upon his name.

17 And they shall be mine, saith Jehovah of hosts, even mine own possession, in the day that I make; and I will spare them, as a man spareth his own son that serveth him.

18 Then shall ye return and discern between the righteous and the wicked, between him that serveth God and him that serveth him not.

American Standard Version (ASV)

4  For, behold, the day cometh, it burneth as a furnace; and all the proud, and all that work wickedness, shall be stubble; and the day that cometh shall burn them up, saith Jehovah of hosts, that it shall leave them neither root nor branch.

2 But unto you that fear my name shall the sun of righteousness arise with healing in its wings; and ye shall go forth, and gambol as calves of the stall.

3 And ye shall tread down the wicked; for they shall be ashes under the soles of your feet in the day that I make, saith Jehovah of hosts.

4 Remember ye the law of Moses my servant, which I commanded unto him in Horeb for all Israel, even statutes and ordinances.

5 Behold, I will send you Elijah the prophet before the great and terrible day of Jehovah come.

6 And he shall turn the heart of the fathers to the children, and the heart of the children to their fathers; lest I come and smite the earth with a curse.

American Standard Version (ASV)