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Wednesday, 13 January 2016

The minority report:Nothing in Darwinism makes sense apart from biology.

Why Do We Invoke Darwin?:
Darwin's theory of evolution offers a sweeping explanation of the history of life, from the earliest microscopic organisms billions of years ago to all the plants and animals around us today.


By Philip Skell

Darwin's theory of evolution offers a sweeping explanation of the history of life, from the earliest microscopic organisms billions of years ago to all the plants and animals around us today. Much of the evidence that might have established the theory on an unshakable empirical foundation, however, remains lost in the distant past. For instance, Darwin hoped we would discover transitional precursors to the animal forms that appear abruptly in the Cambrian strata. Since then we have found many ancient fossils – even exquisitely preserved soft-bodied creatures – but none are credible ancestors to the Cambrian animals.

Despite this and other difficulties, the modern form of Darwin's theory has been raised to its present high status because it's said to be the cornerstone of modern experimental biology. But is that correct? "While the great majority of biologists would probably agree with Theodosius Dobzhansky's dictum that 'nothing in biology makes sense except in the light of evolution,' most can conduct their work quite happily without particular reference to evolutionary ideas," A.S. Wilkins, editor of the journal BioEssays, wrote in 2000.1 "Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one."

I would tend to agree. Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.

I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.

In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.

When I recently suggested this disconnect publicly, I was vigorously challenged. One person recalled my use of Wilkins and charged me with quote mining. The proof, supposedly, was in Wilkins's subsequent paragraph:

"Yet, the marginality of evolutionary biology may be changing. More and more issues in biology, from diverse questions about human nature to the vulnerability of ecosystems, are increasingly seen as reflecting evolutionary events. A spate of popular books on evolution testifies to the development. If we are to fully understand these matters, however, we need to understand the processes of evolution that, ultimately, underlie them."


In reality, however, this passage illustrates my point. The efforts mentioned there are not experimental biology; they are attempts to explain already authenticated phenomena in Darwinian terms, things like human nature. Further, Darwinian explanations for such things are often too supple: Natural selection makes humans self-centered and aggressive – except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed – except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery.Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology. This becomes especially clear when we compare it with a heuristic framework such as the atomic model, which opens up structural chemistry and leads to advances in the synthesis of a multitude of new molecules of practical benefit. None of this demonstrates that Darwinism is false. It does, however, mean that the claim that it is the cornerstone of modern experimental biology will be met with quiet skepticism from a growing number of scientists in fields where theories actually do serve as cornerstones for tangible breakthroughs.

Philip S. Skell tvk@psu.edu is Emeritus Evan Pugh Professor at Pennsylvania State University, and a member of the National Academy of Sciences. His research has included work on reactive intermediates in chemistry, free-atom reactions, and reactions of free carbonium ions.

He can be contacted at tvk@psu.edu.

The epistle of James New Jerusalem Bible

1)1 From James, servant of God and of the Lord Jesus Christ. Greetings to the twelve tribes of the Dispersion.

2 My brothers, consider it a great joy when trials of many kinds come upon you,

3 for you well know that the testing of your faith produces perseverance, and

4 perseverance must complete its work so that you will become fully developed, complete, not deficient in any way.

5 Any of you who lacks wisdom must ask God, who gives to all generously and without scolding; it will be given.

6 But the prayer must be made with faith, and no trace of doubt, because a person who has doubts is like the waves thrown up in the sea by the buffeting of the wind.

7 That sort of person, in two minds,

8 inconsistent in every activity, must not expect to receive anything from the Lord.

9 It is right that the brother in humble circumstances should glory in being lifted up,

10 and the rich in being brought low. For the rich will last no longer than the wild flower;

11 the scorching sun comes up, and the grass withers, its flower falls, its beauty is lost. It is the same with the rich: in the middle of a busy life, the rich will wither.

12 Blessed is anyone who perseveres when trials come. Such a person is of proven worth and will win the prize of life, the crown that the Lord has promised to those who love him.

13 Never, when you are being put to the test, say, 'God is tempting me'; God cannot be tempted by evil, and he does not put anybody to the test .

14 Everyone is put to the test by being attracted and seduced by that person's own wrong desire.

15 Then the desire conceives and gives birth to sin, and when sin reaches full growth, it gives birth to death.

16 Make no mistake about this, my dear brothers:

17 all that is good, all that is perfect, is given us from above; it comes down from the Father of all light; with him there is no such thing as alteration, no shadow caused by change.

18 By his own choice he gave birth to us by the message of the truth so that we should be a sort of first-fruits of all his creation.

19 Remember this, my dear brothers: everyone should be quick to listen but slow to speak and slow to human anger;

20 God's saving justice is never served by human anger;

21 so do away with all impurities and remnants of evil. Humbly welcome the Word which has been planted in you and can save your souls.

22 But you must do what the Word tells you and not just listen to it and deceive yourselves.

23 Anyone who listens to the Word and takes no action is like someone who looks at his own features in a mirror and,

24 once he has seen what he looks like, goes off and immediately forgets it.

25 But anyone who looks steadily at the perfect law of freedom and keeps to it -- not listening and forgetting, but putting it into practice -- will be blessed in every undertaking.

26 Nobody who fails to keep a tight rein on the tongue can claim to be religious; this is mere self-deception; that person's religion is worthless.

27 Pure, unspoilt religion, in the eyes of God our Father, is this: coming to the help of orphans and widows in their hardships, and keeping oneself uncontaminated by the world.

2)1 My brothers, do not let class distinction enter into your faith in Jesus Christ, our glorified Lord.

2 Now suppose a man comes into your synagogue, well-dressed and with a gold ring on, and at the same time a poor man comes in, in shabby clothes,

3 and you take notice of the well-dressed man, and say, 'Come this way to the best seats'; then you tell the poor man, 'Stand over there' or 'You can sit on the floor by my foot-rest.'

4 In making this distinction among yourselves have you not used a corrupt standard?

5 Listen, my dear brothers: it was those who were poor according to the world that God chose, to be rich in faith and to be the heirs to the kingdom which he promised to those who love him.

6 You, on the other hand, have dishonoured the poor. Is it not the rich who lord it over you?

7 Are not they the ones who drag you into court, who insult the honourable name which has been pronounced over you?

8 Well, the right thing to do is to keep the supreme Law of scripture: you will love your neighbour as yourself;

9 but as soon as you make class distinctions, you are committing sin and under condemnation for breaking the Law.

10 You see, anyone who keeps the whole of the Law but trips up on a single point, is still guilty of breaking it all.

11 He who said, 'You must not commit adultery' said also, 'You must not kill.' Now if you commit murder, you need not commit adultery as well to become a breaker of the Law.

12 Talk and behave like people who are going to be judged by the law of freedom.

13 Whoever acts without mercy will be judged without mercy but mercy can afford to laugh at judgement.

14 How does it help, my brothers, when someone who has never done a single good act claims to have faith? Will that faith bring salvation?

15 If one of the brothers or one of the sisters is in need of clothes and has not enough food to live on,

16 and one of you says to them, 'I wish you well; keep yourself warm and eat plenty,' without giving them these bare necessities of life, then what good is that?

17 In the same way faith, if good deeds do not go with it, is quite dead.

18 But someone may say: So you have faith and I have good deeds? Show me this faith of yours without deeds, then! It is by my deeds that I will show you my faith.

19 You believe in the one God -- that is creditable enough, but even the demons have the same belief, and they tremble with fear.

20 Fool! Would you not like to know that faith without deeds is useless?

21 Was not Abraham our father justified by his deed, because he offered his son Isaac on the altar?

22 So you can see that his faith was working together with his deeds; his faith became perfect by what he did.

23 In this way the scripture was fulfilled: Abraham put his faith in God, and this was considered as making him upright; and he received the name 'friend of God'.

24 You see now that it is by deeds, and not only by believing, that someone is justified.

25 There is another example of the same kind: Rahab the prostitute, was she not justified by her deeds because she welcomed the messengers and showed them a different way to leave?

26 As a body without a spirit is dead, so is faith without deeds.

3)1 Only a few of you, my brothers, should be teachers, bearing in mind that we shall receive a stricter judgement.

2 For we all trip up in many ways. Someone who does not trip up in speech has reached perfection and is able to keep the whole body on a tight rein.

3 Once we put a bit in the horse's mouth, to make it do what we want, we have the whole animal under our control.

4 Or think of ships: no matter how big they are, even if a gale is driving them, they are directed by a tiny rudder wherever the whim of the helmsman decides.

5 So the tongue is only a tiny part of the body, but its boasts are great. Think how small a flame can set fire to a huge forest;

6 The tongue is a flame too. Among all the parts of the body, the tongue is a whole wicked world: it infects the whole body; catching fire itself from hell, it sets fire to the whole wheel of creation.

7 Wild animals and birds, reptiles and fish of every kind can all be tamed, and have been tamed, by humans;

8 but nobody can tame the tongue -- it is a pest that will not keep still, full of deadly poison.

9 We use it to bless the Lord and Father, but we also use it to curse people who are made in God's image:

10 the blessing and curse come out of the same mouth. My brothers, this must be wrong-

11 does any water supply give a flow of fresh water and salt water out of the same pipe?

12 Can a fig tree yield olives, my brothers, or a vine yield figs? No more can sea water yield fresh water.

13 Anyone who is wise or understanding among you should from a good life give evidence of deeds done in the gentleness of wisdom.

14 But if at heart you have the bitterness of jealousy, or selfish ambition, do not be boastful or hide the truth with lies;

15 this is not the wisdom that comes from above, but earthly, human and devilish.

16 Wherever there are jealousy and ambition, there are also disharmony and wickedness of every kind;

17 whereas the wisdom that comes down from above is essentially something pure; it is also peaceable, kindly and considerate; it is full of mercy and shows itself by doing good; nor is there any trace of partiality or hypocrisy in it.

18 The peace sown by peacemakers brings a harvest of justice.

4)1 Where do these wars and battles between yourselves first start? Is it not precisely in the desires fighting inside your own selves?

2 You want something and you lack it; so you kill. You have an ambition that you cannot satisfy; so you fight to get your way by force. It is because you do not pray that you do not receive;

3 when you do pray and do not receive, it is because you prayed wrongly, wanting to indulge your passions.

4 Adulterers! Do you not realise that love for the world is hatred for God? Anyone who chooses the world for a friend is constituted an enemy of God.

5 Can you not see the point of the saying in scripture, 'The longing of the spirit he sent to dwell in us is a jealous longing.'?

6 But he has given us an even greater grace, as scripture says: God opposes the proud but he accords his favour to the humble.

7 Give in to God, then; resist the devil, and he will run away from you.

8 The nearer you go to God, the nearer God will come to you. Clean your hands, you sinners, and clear your minds, you waverers.

9 Appreciate your wretchedness, and weep for it in misery. Your laughter must be turned to grief, your happiness to gloom.

10 Humble yourselves before the Lord and he will lift you up.

11 Brothers, do not slander one another. Anyone who slanders a brother, or condemns one, is speaking against the Law and condemning the Law. But if you condemn the Law, you have ceased to be subject to it and become a judge over it.

12 There is only one lawgiver and he is the only judge and has the power to save or to destroy. Who are you to give a verdict on your neighbour?

13 Well now, you who say, 'Today or tomorrow, we are off to this or that town; we are going to spend a year there, trading, and make some money.'

14 You never know what will happen tomorrow: you are no more than a mist that appears for a little while and then disappears.

15 Instead of this, you should say, 'If it is the Lord's will, we shall still be alive to do this or that.'

16 But as it is, how boastful and loud -- mouthed you are! Boasting of this kind is always wrong.

17 Everyone who knows what is the right thing to do and does not do it commits a sin.

5)1 Well now, you rich! Lament, weep for the miseries that are coming to you.

2 Your wealth is rotting, your clothes are all moth-eaten.

3 All your gold and your silver are corroding away, and the same corrosion will be a witness against you and eat into your body. It is like a fire which you have stored up for the final days.

4 Can you hear crying out against you the wages which you kept back from the labourers mowing your fields? The cries of the reapers have reached the ears of the Lord Sabaoth.

5 On earth you have had a life of comfort and luxury; in the time of slaughter you went on eating to your heart's content.

6 It was you who condemned the upright and killed them; they offered you no resistance.

7 Now be patient, brothers, until the Lord's coming. Think of a farmer: how patiently he waits for the precious fruit of the ground until it has had the autumn rains and the spring rains!

8 You too must be patient; do not lose heart, because the Lord's coming will be soon.

9 Do not make complaints against one another, brothers, so as not to be brought to judgement yourselves; the Judge is already to be seen waiting at the gates.

10 For your example, brothers, in patiently putting up with persecution, take the prophets who spoke in the Lord's name;

11 remember it is those who had perseverance that we say are the blessed ones. You have heard of the perseverance of Job and understood the Lord's purpose, realising that the Lord is kind and compassionate.

12 Above all, my brothers, do not swear by heaven or by the earth or use any oaths at all. If you mean 'yes', you must say 'yes'; if you mean 'no', say 'no'. Otherwise you make yourselves liable to judgement.

13 Any one of you who is in trouble should pray; anyone in good spirits should sing a psalm.

14 Any one of you who is ill should send for the elders of the church, and they must anoint the sick person with oil in the name of the Lord and pray over him.

15 The prayer of faith will save the sick person and the Lord will raise him up again; and if he has committed any sins, he will be forgiven.

16 So confess your sins to one another, and pray for one another to be cured; the heartfelt prayer of someone upright works very powerfully.

17 Elijah was a human being as frail as ourselves -- he prayed earnestly for it not to rain, and no rain fell for three and a half years;

18 then he prayed again and the sky gave rain and the earth gave crops.

19 My brothers, if one of you strays away from the truth, and another brings him back to it,

20 he may be sure that anyone who can bring back a sinner from his erring ways will be saving his soul from death and covering over many a sin.

One of these things is not like the others (with apologies to sesame street)

What's the Difference Between a Buckyball and a BMC?
Evolution News & Views January 13, 2016 4:47 AM

We've all seen geodesic domes that were intelligently designed by humans. The inventor, the great designer Buckminster Fuller, might have been quite surprised to learn that nature got there first. Two years after his death in 1983, a new form of carbon was discovered: C60, a geodesic-dome shaped molecule that was named buckminsterfullerene in his honor. Since then, numerous other "fullerenes" have been discovered, comprising shapes of spheres, ellipsoids, and rods. The carbon nanotubes we hear about in electronics are rod-shaped members of the fullerene family. Spherical ones are the most common. Because they look like miniature soccer balls they are often called "buckyballs" for short. The smallest has 20 carbons, but others have hundreds.

Fullerenes can be synthesized in the lab, but some are produced naturally. One can only imagine Dr. Fuller's surprise if he were to learn, while constructing one of his famous domes, that similar structures could be found in his car's tailpipe soot! Natural fullerenes can be produced by lightning, and have been detected in some high-carbon minerals and even in interstellar dust. But now, here's a design-detection puzzle to consider: some geodesic domes are also found in living cells. Is there a difference?

A buckyball's shape is called a truncated icosahedron. Similar icosahedral shapes are widespread in bacteria, where they are called bacterial microcompartments, or BMCs. Some viruses also have icosahedral shapes called capsids. Let's focus on BMCs for now. BMCs are organelles entirely made of protein. They provide a protective shell for various enzymes, and function like membranes, in that they selectively let substances in or out. Interestingly, viral capsid proteins do not appear to have any sequence similarity to BMCs.

Now that we know what BMCs are, how are they formed? Perhaps you expect that we're going to say that they are genetically encoded and constructed by enzymes, so they meet the criteria for intelligent design. Let's not get ahead of ourselves, though. There is some self-assembly involved. A news item from the Lawrence Berkeley National Laboratory says:

Scientists have for the first time viewed how bacterial proteins self-assemble into thin sheets and begin to form the walls of the outer shell for nano-sized polyhedral compartments that function as specialized factories. [Emphasis added.]

The research team spoke of this as "nature's masonry" and "natural origami." They're interested in BMCs because they'd like to imitate them. They'd like to manufacture 3-D "nanoreactors" that can "selectively suck in toxins or churn out desired products." To do that, they first have to understand how bacteria make them. Here's an interesting paragraph:

"We usually only get to see these structures after they form, but in this case we're watching them assemble and answering some questions about how they form," Kerfeld said. "This is the first time anyone has visualized the self-assembly of the facets, or sides, of the microcompartments. It's like seeing walls, made up of hexagonally shaped tiles, being built by unseen hands."

Whoa; that's cool. Sounds like design so far. But we mustn't rush our design inference. What about those buckyballs? Don't unseen hands make them, too? We have to be careful not to personify nature. ID proponents do not conceive of "unseen hands" doing the work of biological design any more than a chemist proposes unseen hands assembling a buckyball.

The building blocks of BMCs are hexagonal proteins. Inside the bacterium, the hexagons assemble into thin sheets like a honeycomb. Because the proteins are convex on one side, and concave on the other, they assemble into spheres. The researchers watched this happen outside the cell:

Liverpool's atomic-force microscope, BioAFM, showed that individual hexagon-shaped protein pieces naturally join to form ever-larger protein sheets in a liquid solution. The hexagons only assembled with each other if they had the same orientation -- convex with convex or concave with concave.

"Somehow they selectively make sure they end up facing the same way," Kerfeld added.

The study also found that individual hexagon-shaped pieces of the protein sheet can dislodge and move from one protein sheet to another. Such dynamics may allow fully formed compartments to repair individual sides.

If we're going to make a design inference, we have to take account of the fact that some natural self-assembly is involved. We need to distinguish between the assembly processes of BMCs and buckyballs to be able to argue that the former are designed and the latter are not. A few months ago we asked, "Are hexagons natural?" Now here's another interesting facet, if you'll pardon the pun: BMCs and buckyballs both have pentagons, too!

Fully-formed 3-D microcompartments have a soccer-ball-like geometry that incorporates pentagon-shaped protein structures known as pentamers, for example, that were not included in the latest study.

"The holy grail is to see the structure and dynamics of an intact shell, composed of several different types of hexagonal proteins and with the pentagons that cap its corners," Kerfeld said.

It's possible that simply adding these pentamers to the protein sheets from the latest experiment could stimulate the growth of a complete 3-D structure, but Kerfeld added, "I wouldn't be surprised if there's more to the story."

You now have the data on BMCs and buckyballs. Could you prove to a skeptic that BMCs give evidence of intelligent design, whereas buckyballs can be explained by natural law? Turn your head away for a minute and think it through before continuing.

We have two similar structures that self-assemble into spherical shapes with facets made of hexagons and pentagons. Why would we infer design for the BMC and not the buckyball? Consider what differentiates the two.

Carbon atoms are all the same (allowing for isotopes). Proteins are not.

The carbons form the vertices of the buckyballs, whereas proteins make up the facets of BMCs.

The proteins in BMCs are made up of amino acids that do not naturally link up into hexagons and pentagons, particularly ones that are convex on one side.

All the amino acids in the proteins are left-handed. There is no known way outside of life to get 100 percent pure homochiral chains of amino acids.

All proteins derive from complex specified information encoded in genes.

The genes for BMC proteins must be translated from one genetic language (DNA) into another (proteins) by means of a symbolic logic system.

The proteins must be folded into their proper orientation upon translation.

The bacterium has to "know" how to get an enzyme inside the BMC, and know which enzyme goes in which organelle.

The resulting BMC is selectively permeable.

Buckyballs don't "do" anything. BMCs have a function that is ensured by assembly instructions, maintenance, and repair systems.

You may be able to add to this list. The point is, you can explain a buckyball by laws of physics and the chemistry of the carbon atom. You cannot explain a BMC from its building blocks. Some amino acids can form naturally, but not homochiral polypeptide chains that perform a function. For that, you need complex specified information and irreducibly complex systems to translate it into functional structures: that is, you need intelligent design.

Those interested in following up on the Lawrence Livermore research can read the open-access paper in Nano Letters. It says very little about Darwinian evolution. Actually, nothing.


Incidentally, the carbon atom is quite interesting, requiring a finely tuned resonance in stars that made Sir Fred Hoyle wonder if someone had monkeyed with physics. But that's another story.