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.

Sharks Vs. Darwin

Shark Knows with Its Nose Where It Goes in the Dark
Evolution News & Views January 12, 2016 3:26 AM 

As Illustra Media showed in Living Waters by taking viewers inside the nose of a salmon, the olfactory (smell) organs of fishes are stupefyingly complex. A mainframe computer network could hardly surpass the computing power packed into the tiny space of a fish nostril. Similar complexity has been demonstrated recently in cartilaginous fish such as sharks, which would only be distantly related to bony fish in the evolutionary scheme.

"The ability of sharks to navigate the vast and seemingly featureless ocean has been a mystery," Traci Watson writes for National Geographic. Michael Casey agrees at Fox News, "One of the great mysteries with sharks has been how they manage to navigate a straight path between distant locations in the ocean." They're commenting on a "tantalizing clue" that emerged from recent experiments with sharks by the Scripps Institution of Oceanography. A news item from PLOS ONE explains what the scientists did:

Little is understood about how sharks navigate straight paths between distant sites in the ocean. The authors of this study used shoreward navigation by leopard sharks to test whether olfaction contributes to ocean navigation. About 25 leopard sharks were captured alongshore. About half had their sense of smell temporarily impaired, and then they were transported 9 km offshore, released, and acoustically tracked for approximately four hours each. [Emphasis added.]

The sharks with unhindered noses came back like the proverbial cat, 62.7 percent closer to shore than the nose-plugged sharks (37.2 percent). Significantly, the impaired sharks took more tortuous paths. Live Science quotes one of the researchers:

"We basically kidnapped these sharks from their home and confused them for an hour on the way out," said study lead researcher Andrew Nosal, a postdoctoral researcher at the Scripps Institution of Oceanography and the Birch Aquarium in California. "Yet, within 30 minutes of being released in the middle of the ocean -- a place that they had probably never been -- they [those without nose plugs] knew exactly where shore was, which was really neat."

Now that we see the overall result, how does the shark do it? What equipment is required? The open-access paper in PLOS ONE doesn't say. But it does describe how olfactory expertise is widespread in the animal kingdom:

Relatively little consideration has been given to chemical cues guiding animals through the pelagic environment, even though this dynamic three-dimensional medium in many ways resembles the dynamic three-dimensional atmosphere, where chemosensory modalities are widely accepted to participate in bird and insect navigation. Evidence for olfaction-mediated homing and navigation in fishes had heretofore been limited to salmonid fishes, rockfishes, and fish larvae, operating mostly in nearshore environments. Even the most recent work, which demonstrated olfaction-mediated homing in juvenile sharks, was conducted wholly within a shallow bay. Although olfaction has also been hypothesized to contribute to pelagic navigation in sharks, this had never been tested until now.

None of the five articles says anything about evolution, either. How could they? The scientists or reporters are faced with two major Darwinian dilemmas.

First, they would have to explain the irreducible complexity of olfaction. As shown in Living Waters, olfaction is composed of numerous systems that must work together as a unit. The cilia on the olfactory sensory neurons need receptors for odorants that fit like a glove. Each neuron must respond to an odorant with a complex cascade of signals, including gene-expression feedback loops and electrical currents that travel down the axons of the cell. The signals need to know where to go: to particular points on the olfactory bulb.

The olfactory bulb (shown in the animation) is a fantastic sorting device, that takes the incoming signals from millions of neurons, measures their strength, number and time delays, and reduces all that information into a combinatorial code. That information must then target specific parts of the fish's brain, where the information must be understood and recognized by the animal. The information will only be useful, though, if the fish has a way to incorporate it into a map sense, so it knows where it is and where it needs to go. Finally, the fish needs to have software to know what to do with the information: change direction, hunt prey, flee a predator, or perform whatever other action is appropriate. That software, in turn, must tie into muscles and nerves that can produce the appropriate behavior rapidly.

Second, the evolutionist would have to explain how this amazing ability evolved in insects, birds, and two groups of fish (bony fish and cartilaginous fish). "Convergent evolution" is not an answer. It's a phrase hiding the lack of an answer. If by some miracle you could imagine one animal arriving at olfaction and the ability to navigate with it, it strains credibility to expect it to evolve independently multiple times.

Adding to the challenge for Darwinian processes to explain this is the fact that sharks (like salmon and the other animals), can supplement olfaction with other senses that are just as complex: hearing, vision, and sensing the Earth's magnetic field.

Another interesting observation was that shortly after crossing back over the continental shelf, some sharks, even after swimming for hours at relatively constant depths, suddenly and deliberately dove to the benthos, as if they were confident a bottom of suitable depth was there (S3 Fig). Surely the sharks could not see the bottom from 50 m above it, but the 'soundscape' may be fundamentally different over the shallow shelf compared to deeper offshore areas. Lastly, geomagnetic cues are strongly suspected to play a role in shark navigation and these may very well contribute to shoreward navigation by leopard sharks. In short, olfaction plays a role in pelagic navigation, but is apparently supplemented by other sensory modalities, warranting further work to elucidate how these are integrated and organized hierarchically for navigation.

If an alien intelligence visited Earth and found only sharks with abilities like these, it would be justified in inferring an intelligent cause for them. How much more when thousands of other examples in the plant and animal worlds, to say nothing of the human body, are abundantly on display? The navigation of a monarch butterfly for 3,000 miles to the exact tree its grandparents knew (Metamorphosis), the flight of the Arctic tern from pole to pole (Flight: The Genius of Birds), and fish navigation are just a taste of what's out there to study.

All one has to do is look at any creature, even a single cell, in detail. As Paul Nelson says at the conclusion of Living Waters,

I want to understand the world. I want knowledge. I want to know what's true about the world; and the assumption that living things are not random assemblages but that there's a rational logic underlying them -- that assumption is enormously fruitful for gaining knowledge. And if it's knowledge that you want, that's the direction you should go. All you need is an open heart, open eyes, and an open mind, and that signal of design that's there in nature it will be clear to you. Unmistakably. It's everywhere."


What we have is a super-abundance of evidence for intelligent design. These systems rule out blind, unguided processes of natural selection. The authors of these articles did not need Darwinian theory to add to our understanding of animal navigation, or they would have mentioned it.

Another failed Darwinian prediction III

The DNA code is not unique:
Shortly after the discovery of the DNA code, which is used in cells to construct proteins, evolutionists began theorizing how it evolved. The same code was found in very different species which means that the same code was present in their distant, common ancestor. So the DNA code arose early in evolutionary history and remained essentially unchanged thereafter. And since it arose so early in evolutionary history, in the first primitive cell, the code must not be unique or special. For how could such a code have evolved so early in the history of life? As Nobel Laureate Francis Crick wrote in 1968, “There is no reason to believe, however, that the present code is the best possible, and it could have easily reached its present form by a sequence of happy accidents.” (Crick) Or as one widely used undergraduate molecular biology text later put it, “The code seems to have been selected arbitrarily (subject to some constraints, perhaps).” (Alberts et. al., 9) And an evolution textbook further explained, “The code is then what Crick called a ‘frozen accident.’ The original choice of a code was an accident; but once it had evolved, it would be strongly maintained.” (Ridley, 48)

In other words, somehow the DNA code evolved into place but it has little or no special or particular properties. But we now know that the code’s arrangement uniquely reduces the effects of mutations and reading errors. As one research study concluded, the DNA code is “one in a million” in terms of efficiency in minimizing these effects. (Freeland) Several other studies have confirmed these findings and have discovered more unique and special properties of the code. One found that the DNA code is a very rare code, even when compared to other codes which already have the error correcting capability. (Itzkovitz) Another found that the code does not optimize merely one function, but rather optimizes “a combination of several different functions simultaneously.” (Bollenbach) As one paper concluded, the code’s properties were “unexpected and still cry out for explanation.” (Vetsigian)

References

Alberts, Bruce., D. Bray, J. Lewis, M. Raff, K. Roberts, J. Watson. 1994. Molecular Biology of the Cell. 3d ed. New York: Garland Publishing.

Bollenbach, T., K. Vetsigian, R. Kishony. 2007. “Evolution and multilevel optimization of the genetic code.” Genome Research 17:401-404.

Crick, Francis. 1968. “The origin of the genetic code.” J. Molecular Biology 38:367-379.

Freeland, S., L. Hurst. 1998. “The genetic code is one in a million.” J. Molecular Evolution 47:238-248.

Itzkovitz, S., U. Alon. 2007. “The genetic code is nearly optimal for allowing additional information within protein-coding sequences.” Genome Research 17:405-412.

Ridley, Mark. 1993. Evolution. Boston: Blackwell Scientific.

Vetsigian, K., C. Woese, N. Goldenfeld. 2006. “Collective evolution and the genetic code.” Proceedings of the National Academy of Sciences 103:10696-10701.

Why the real world continues to be the elephant in the room re:darwinism.

Common Sense Design Principles and the Real World:
Ann Gauger January 11, 2016 3:00 AM

A recent paper in PLOS Genetics considers the origins of new "genes" in humans and chimps. By comparing RNA sequences, researchers identified over 600 transcriptionally active "genes" that appear to be present only in humans and not in chimps or the other mammal species tested. They claimed that these "genes" were the product of evolution from previously non-coding, untranscribed DNA. They argued that some of the "genes" are made into proteins and perhaps may be subject to selection, meaning that they are evolving.

I put genes in quote because this is not what the term gene typically means. It used to be that a gene was a stretch of DNA that coded for a protein, meaning it was a stretch of DNA that was copied into RNA (transcribed), and then translated into protein.

These researchers are using "gene" to signify any stretch of DNA that is copied (transcribed) into RNA and that meets certain criteria (size, the frequency with which they found it, etc.). They do not require that the RNA be turned into protein. In fact most of the time it probably isn't. But still they call them genes. Only in some cases do they find evidence that these genes actually make protein, protein that may be evolving new functions, they say.

Something to bear in mind -- all these conclusions are based only on the comparison of DNA sequences among species. They are conclusions based on the assumption that the differences reflect some sort of genetic history based on common descent -- the conclusions are not based on any experiments or observations of real events happening in real time.

As to their claims: I believe them when they say there are more than 600 regions of the genome that are transcribed in a manner unique to humans. After all, humans are different from chimps and can reasonably be expected to have genetic differences. Second, they may even be genes, if they produce a functional RNA, which is possible. I suspect they will be functional as RNAs. Third, these genes are in parts of the genome that used to be thought of as junk. Well, that's no surprise either. ID proponents have always expected most DNA to have a function and not be junk.

What I doubt is the claim that these genes evolved from untranscribed random sequences that somehow acquired promoter sequences, became transcribed, and even further, sometimes became translated and then became functional. The reason I doubt this? Douglas Axe's and my work on the evolution of enzymes, and a dose of common sense.

First of all, it is no trivial thing to "acquire" the promoter sequences that turn on a gene's transcription, and the signals that say when to stop. That one little undemonstrated word hides a multitude of requirements, and probably signifies a designer's action. Second, the words "became translated" hide all sorts of complex signals and activities, and likely require a designer as well. But the biggest problem of all is the business of taking non-functional protein and turning it into functional protein.

This scenario is what we tested in our most recent paper in BIO-Complexity. First, how hard is it to take a piece of junk protein and turn it into a brand new functional enzyme -- without a designer -- even if the junk protein already has a small amount of the new function to start? The answer -- it's not possible. We tested it in silico (using a computer program called Stylus, available online), and in the lab with a real protein. We were unable to improve the "junk" protein's function much at all, even after multiple rounds of mutation and selection.

Second, it's not possible to take a weakly functional, but already structured enzyme and change it to a new function at wild-type levels, even when the protein's not junk to start, and already has a small amount of the new function. If it has the wrong shape, the function can't be improved much at all -- nowhere near the levels normal wild-type enzymes have.

Third, if you are only a few selectable mutations away from a new function, it is possible to get there -- as long as each step is an improvement. That means in order for evolution to be able to make a wild-type enzyme, it has to begin with something that is most of the way there -- it's already pretty much the enzyme that's needed. New proteins have to be essentially of the right design in order to be improved to wild-type function.

Why bother with these experiments on proteins in the first place, you may ask. The answer is this -- what is true in the microscopic world about evolution is also true in the macroscopic world. What works (or doesn't work) with enzyme evolution demonstrates what evolution can or can't accomplish on a large scale.

If it's not possible to evolve new proteins from any starting point, evolving buttercups or cows won't work either. That is, unless the buttercups and cows pretty much already are buttercups and cows.

Evolution can't build something new from scratch. And it can't reconfigure something that already exists into something different. That's why I doubt the story of evolving new human genes from random non-coding sequences. I don't doubt that the genes are there -- they are. It's just that I think they were designed, not evolved.

Now for the dose of common sense. Let's turn the microscopic to macroscopic analogy on its head and use what we already know of design in the macroscopic world.

We all know you can't take a pile of scrap metal and turn it into a washing machine. You'd have to start from scratch, even though they are both made mostly of metal. What about turning a washing machine into a dishwasher? There's more similarity there -- after all, they both wash things. Still, neither process will happen without a designer or without considerable refashioning. Now what if a washing machine was merely broken? What if it had a few loose bolts and a torn gasket on the door? A blindfolded repairman might be able to fix that. That would be harder but not impossible. But even this analogy breaks down because the repairman is intelligent.

These are not perfect comparisons to biological processes -- the examples used all require intelligence and are man-made. But these things are simpler than enzymes, so perhaps our design intuitions do transfer to the biological realm.


Don't just take my word for it, though. For the real experimental data, read the paper and see for yourself. Check out the experiments that demonstrate in real time what really can and can't be accomplished.

Biology and Maths make a second try at a closer relationship

Biology and Mathematics
Evolution News & Views May 24, 2011 6:00 AM

Perhaps mathematics can explain certain biological phenomenon.

While the chemistry and physics students suffered through semester after semester of mathematics, the biology students finished their calculus sequence and moved on. The idea was that biology does not lend itself to mathematical application in the same way chemistry and physics does, so students didn't need very much math. However, that may be old news. According to an article in New Statesman by Ian Stewart, biology may be undergoing another revolution and the result will be "biomathematics":
Maths has played a leading role in the physical sciences for centuries, but in the life sciences it was little more than a bit player, a routine tool for analysing data. However, it is moving towards centre stage, providing new understanding of the complex processes of life.
Stewart mentions at the beginning of the article that biology has undergone five great revolutions:
• Invention of the microscope
• Classification
• Evolution
• Discovery of the Gene
• Discovery of the structure of DNA
He contends that mathematics may be the new, sixth revolution in biology. If we are talking about scientific revolutions in the sense that Thomas Kuhn describes them in The Structure of Scientific Revolutions, then the important point here is while the prior revolutions may have provided a greater understanding of biology they did not account for certain other observations. The next revolution provides a different framework by which that field of science operates, and opens the door for asking different kinds of questions.

What drives the research questions is the framework through which you are asking the questions. Stewart indicates that mathematics provides an apt framework for looking at the complexity of biological systems and for bringing up new research questions. He provides three interesting examples of research that was guided by questions that came out of mathematical theory. This post will look at one of them, animal markings. This particular theory had to do with work based on Alan Turing's equations and Mendelbrot's fractals.

Two scientists from Japan wanted to study the striking stripe pattern on a particular type of tropical angelfish (Pomacanthus imperator). They applied Turing's mathematical models to the patterns on the angelfish, but came up with odd results. The Turing model predicted that the angelfish's stripes move along its body. So the scientists decided to test this theory. From the article:

It seemed wildly unlikely, but when Kondo and Asai photographed specimens of the angelfish over periods of several months, they found that the stripes slowly migrated across its surface. Moreover, defects in the pattern of otherwise regular stripes, known as dislocations, broke up and re-formed exactly as Turing's equations predicted. They did this because the pigment proteins leaked from cell to cell, drifting from the fish's tail towards its head. (In animals whose stripes are fixed, this does not happen; but once the size of the animal and other factors are known, the maths can predict whether its markings will move.)
Most likely these scientists would not have considered the possibly of the angelfish's markings migrating across its body had they not used the mathematical models which pointed towards this research.

As scientists delve deeper into biological systems, they find more and more layers of complexity. Mathematics can help scientists understand the mechanisms behind the function.

Stewart mentions how DNA had changed the way we do biology. DNA, and genetics in general, turned biology into a micro-scale endeavor. Biochemistry emerged as a prominent discipline. Stewart points out that while we are able to identify the DNA sequence, we still do not understand how the genes work together:
A creature's genome is fundamental to its form and behaviour, but the information in the genome no more tells us everything about the creature than a list of components tells us how to build furniture from a flat-pack. What matters is how those components are used, the processes that they undergo in a living creature. And the best tool we possess for finding out what processes do is mathematics.
Stephen Meyer discusses how mathematics, particularly information theory, can help our understanding of DNA in chapter 4 of his book, Signature in the Cell. One of the important features to applying information theory to DNA is that DNA is mathematically similar to text (he compares it to English text) because it is not only non-compressible information, but is capable of carrying information. But it doesn't just carry information, it also conveys functional information. This leads to new research questions, particularly in origin of life research.


From a philosophical standpoint, what does it mean that these biological systems can be explained by mathematical theories (DNA and information theory, animal markings and fractals, viruses and geometry, plankton and chaos theory)? The mathematical predictability certainly implies non-randomness. It also seems to imply layers of complexity and layers of information. These layers of complexity seem to indicate something more than unguided or random processes. It seems to indicate either a front-loading of information or at least some kind of mechanism that has the end goal in mind.

Chimera: coming soon to a lab near you.

Scientists Make Part-Human Animals -- Good Idea?
Wesley J. Smith January 8, 2016 12:13 PM

Public money is being used to pay for research that create animals that are part human. From the MIT Technology Review story:

Braving a funding ban put in place by America's top health agency, some U.S. research centers are moving ahead with attempts to grow human tissue inside pigs and sheep with the goal of creating hearts, livers, or other organs needed for transplants.

The effort to incubate organs in farm animals is ethically charged because it involves adding human cells to animal embryos in ways that could blur the line between species.

This begins to cross into Dr. Moreau territory. Even the often compliant NIH is alarmed:

The agency, in a statement, said it was worried about the chance that animals' "cognitive state" could be altered if they ended up with human brain cells. The NIH action was triggered after it learned that scientists had begun such experiments with support from other funding sources, including from California's state stem-cell agency.

The human-animal mixtures are being created by injecting human stem cells into days-old animal embryos, then gestating these in female livestock. Based on interviews with three teams, two in California and one in Minnesota, MIT Technology Review estimates that about 20 pregnancies of pig-human or sheep-human chimeras have been established during the last 12 months in the U.S., though so far no scientific paper describing the work has been published, and none of the animals were brought to term.

Birthing these animals will be the next step. And who knows what health problems they could have? This is an animal welfare issue as well as bearing obviously on human exceptionalism.

Creating such chimeric beings isn't the same thing as, say, genetically altering an animal so their organs can be used for transplant, or inserting a human gene to make transgenic animals that produce a specific hormone in their milk for medicinal uses.

Hard regulatory lines need to be drawn -- which won't be easy -- and all public money limited to research that is both ethical and respectful of proper boundaries between humans and all other species.


Scientists clearly cannot be trusted to govern themselves on this matter. It is time to set well-defined limits.

Ps. Of course it's far too late to put this genie back in the bottle the lure of potential profits and fear of losing out to the competition is going to trump any appeal to virtue.

A clash of titans IV

On the uniting of the United Kingdom

Some assembly required?

Can You Build WALL-E from Repeating Legos?
Evolution News & Views January 8, 2016 3:31 AM

"A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain." Thus begins a new paper on sequence space for proteins, a concept that has been key to work by leading ID theorists Douglas Axe, Stephen Meyer, and William Dembski. This is the question: Out of the vast space of possible amino acid sequences, how many can fold into functional proteins? ID argues that functional space is such a small subset of sequence space, the probability that a blind search will find any is vanishingly small.

Nine researchers led by some of our Seattle neighbors over at the University of Washington, publishing in Nature, decided to investigate how much of the sequence space nature has sampled. It's obviously far too big a space to search, so they limited it to just "repeat proteins" -- those that use certain structural motifs over and over.

To our knowledge, all designed repeat protein structures to date have been based on naturally occurring families. These families may cover all stable repeat protein structures that can be built from the 20 amino acids or, alternatively, natural evolution may only have sampled a subset of what is possible.

By applying experimental protein design, they show that you can get many more potential proteins by simply repeating certain "building blocks" over and over, something like assembling Lego pieces blindly. They manufactured some Lego-like protein kits by generating scads of "a simple helix-loop-helix-loop building block" and putting them together using an automated process. Out of 83 they built, 44 showed a stable fold. But is this experiment about evolution or intelligent design?

We have shown that a wide range of novel repeat proteins can be generated by tandem repeating a simple helix-loop-helix-loop building block. As illustrated by the comparison of 15 design models to the corresponding crystal structures (Fig. 4), our approach allows precise control over structural details throughout a broad range of geometries and curvatures. The design models and sequences are very different from each other and from naturally occurring repeat proteins, without any significant sequence or structural homology to known proteins (Extended Data Fig. 8). This work achieves key milestones in computational protein design: the design protocol is completely automatic, the folds are unlike those in nature, more than half of the experimentally tested designs have the correct overall structure as assessed by SAXS, and the crystal structures demonstrate precise control over backbone conformation for proteins over 200 amino acids. The observed level of control over the repeating helix-loop-helix-loop architecture shows that computational protein design has matured to the point of providing alternatives to naturally occurring scaffolds, including graded and tunable variation difficult to achieve starting from existing proteins. We anticipate that the 44 successful designs described in this work (Extended Data Fig. 9), and sets generated using similar protocols for other repeat units, will be widely useful starting points for the design of new protein functions and assemblies.

Note that word "function" at the end. A search of the paper shows nothing about whether any one of the design models actually does anything. Yet they seem to have one ear open to the possible whisper of Darwin speaking in the background:

Naturally occurring repeat protein families, such as ankyrins, leucine-rich repeats, TAL effectors and many others, have central roles in biological systems and in current molecular engineering efforts. Our results suggest that these families are only the tip of the iceberg of what is possible for polypeptide chains: there are clearly large regions of repeat protein space that are not sampled by currently known repeat protein structures. Repeat protein structures similar to our designs may not have been characterized yet, or perhaps may simply not exist in nature.

The authors only mention evolution twice. It's not really a focus in this paper. The word "design," however, appears a whopping 74 times, even before the Methods section. They did interesting and important work. But lest anyone think their conclusion weakens the arguments of Axe, Meyer, and Dembski by expanding the potential functional space accessible to random search within sequence space, let's apply a heavy dose of realism.

They sampled only part of the "repeat protein" portion of sequence space.

They began with "building block" motifs that already fold (helices and loops).

They used only left-handed (homochiral) amino acids.

They did not test to see if any of the stable structures perform a function.

They did not test to see if any of their structures could interact with other proteins or structures (for this problem, see this earlier article on this subject).

Their work was highly dependent on intelligent design (i.e., their own).

You could liken their results to a robot programmed to assemble Legos according to a rule: "fasten, twist, repeat." If the Lego pieces are already designed, the algorithm can say nothing about where the pieces came from. As all kids know, the holes in Lego pieces have to be spaced properly to fit together. Similarly, amino acids need to be properly sequenced to fold into a helix or loop. If that's a given, it's not surprising that you could generate quite a few unique structures by the algorithm "fasten, twist, repeat." Even WALL-E the robot could do that without thinking. Whether anything worthwhile would result is dubious.

Actually, you can assemble a WALL-E robot using Lego pieces now. The Lego company offers that and many other elaborate, complex kits that go well beyond the simple building-block sets from decades ago. A kid could put the WALL-E pieces together and show off his pride and joy in a matter of hours or maybe even minutes. But could nature pull that off by blind search? Think of the programming that would be required to get WALL-E to assemble his likeness out of Lego pieces! It's intelligent design all the way down.


Here's the take-home: Despite a hint of "protein evolution" in this paper, the experimental evidence has again vindicated ID. Without a mind directing assembly of amino acids according to a design goal, nothing interesting will happen by chance or repetition by an aimless process. Sequence space is too vast and functional space too vanishingly small to expect success by blind search.