For Darwinism:Danger from the dark.

The Dark Proteome and Dark Evolution
Evolution Did It

A new PNAS paper published last week on the dark proteome has some interesting implications for the theory of evolution. The paper presents a survey of protein sequences, focusing on the many sequences for which the corresponding three dimensional protein structure is not known, and cannot be inferred from any remotely similar sequence. Why is this so-called “dark proteome” is so large? The survey finds that the various hypotheses to explain this—that the dark proteins are intrinsically disordered, or their sequences are compositionally biased, or they are transmembrane proteins, all reasons that can confound structure determination—don’t work very well. The paper concludes that “a surprisingly large fraction of dark proteins … cannot be easily accounted for by these conventional explanations.” And not surprisingly, these dark proteins are less common across the species. So where did all these dark protein sequences come from? Well evolution did it. As the paper explains, “dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches.”

We might call this dark evolution. Once again, the pattern is not one of common descent, but of unique structures.

The results also have implications for the so-called orphans, open reading frames found only in a particular species. Such genetic sequences contradict evolution and when they were first discovered evolutionists predicted they would be found in other species as more genomes were decoded. Instead the number of orphans just continued to grow.

Evolutionists next predicted that orphan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That has not been found to be true, and this new survey provides further evidence for this. As the authors conclude, “Thus, our results suggest that many of the uncharacterized orphan sequences … are indeed real proteins.”

Protein science, however, is clear that blind mutations cannot form real proteins this fast from scratch (or at all for that matter). Hence we must believe that built-in cellular processes must have created these proteins—processes that are complex and require, among other things, proteins.

Real ones.

Posted by Cornelius Hunter at Monday, November 23, 2015 

Ezekiel1-7 New Jerusalem Bible

1)1 In the thirtieth year, on the fifth day of the fourth month, as I was among the exiles by the River Chebar, heaven opened and I saw visions from God.

2 On the fifth of the month -- it was the fifth year of exile for King Jehoiachin-

3 the word of Yahweh was addressed to the priest Ezekiel son of Buzi, in Chaldaea by the River Chebar. There the hand of Yahweh came on him.

4 I looked; a stormy wind blew from the north, a great cloud with flashing fire and brilliant light round it, and in the middle, in the heart of the fire, a brilliance like that of amber,

5 and in the middle what seemed to be four living creatures. They looked like this: They were of human form.

6 Each had four faces, each had four wings.

7 Their legs were straight; they had hooves like calves, glittering like polished brass.

8 Below their wings, they had human hands on all four sides corresponding to their four faces and four wings.

9 They touched one another with their wings; they did not turn as they moved; each one moved straight forward.

10 As to the appearance of their faces, all four had a human face, and a lion's face to the right, and all four had a bull's face to the left, and all four had an eagle's face.

11 Their wings were spread upwards, each had one pair touching its neighbour's, and the other pair covering its body.

12 And each one moved straight forward; they went where the spirit urged them, they did not turn as they moved.

13 Between these living creatures were what looked like blazing coals, like torches, darting backwards and forwards between the living creatures; the fire gave a brilliant light, and lightning flashed from the fire,

14 and the living creatures kept disappearing and reappearing like flashes of lightning.

15 Now, as I looked at the living creatures, I saw a wheel touching the ground beside each of the four-faced living creatures.

16 The appearance and structure of the wheels were like glittering chrysolite. All four looked alike, and their appearance and structure were such that each wheel seemed to have another wheel inside it.

17 In whichever of the four directions they moved, they did not need to turn as they moved.

18 Their circumference was of awe-inspiring size, and the rims of all four sparkled all the way round.

19 When the living creatures moved, the wheels moved beside them; and when the living creatures left the ground, the wheels too left the ground.

20 They moved in whichever direction the spirit chose to go, and the wheels rose with them, since the wheels shared the spirit of the animals.

21 When the living creatures moved on, they moved on; when the former halted, the latter halted; when the former left the ground, the wheels too left the ground, since the wheels shared the spirit of the animals.

22 Over the heads of the living creatures was what looked like a solid surface glittering like crystal, spread out over their heads, above them,

23 and under the solid surface, their wings were spread out straight, touching one another, and each had a pair covering its body.

24 I also heard the noise of their wings; when they moved, it was like the noise of flood-waters, like the voice of Shaddai, like the noise of a storm, like the noise of an armed camp; and when they halted, they lowered their wings;

25 there was a noise too.

26 Beyond the solid surface above their heads, there was what seemed like a sapphire, in the form of a throne. High above on the form of a throne was a form with the appearance of a human being.

27 I saw a brilliance like amber, like fire, radiating from what appeared to be the waist upwards; and from what appeared to be the waist downwards, I saw what looked like fire, giving a brilliant light all round.

28 The radiance of the encircling light was like the radiance of the bow in the clouds on rainy days. The sight was like the glory of Yahweh. I looked and fell to the ground, and I heard the voice of someone speaking to me.
2)1 He said, 'Son of man, get to your feet; I will speak to you.'

2 As he said these words the spirit came into me and put me on my feet, and I heard him speaking to me.

3 He said, 'Son of man, I am sending you to the Israelites, to the rebels who have rebelled against me. They and their ancestors have been in revolt against me up to the present day.

4 Because they are stubborn and obstinate children, I am sending you to them, to say, "Lord Yahweh says this."

5 Whether they listen or not, this tribe of rebels will know there is a prophet among them.

6 And you, son of man, do not be afraid of them or of what they say, though you find yourself surrounded with brambles and sitting on scorpions. Do not be afraid of their words or alarmed by their looks, for they are a tribe of rebels.

7 You are to deliver my words to them whether they listen or not, for they are a tribe of rebels.

8 But you, son of man, are to listen to what I say to you; do not be a rebel like that rebellious tribe. Open your mouth and eat what I am about to give you.'

9 When I looked, there was a hand stretch- ing out to me, holding a scroll.

10 He un- rolled it in front of me; it was written on, front and back; on it was written 'Lamentations, dirges and cries of grief '.
3)1 He then said, 'Son of man, eat what you see; eat this scroll, then go and speak to the House of Israel.'

2 I opened my mouth; he gave me the scroll to eat

3 and then said, 'Son of man, feed on this scroll which I am giving you and eat your fill.' So I ate it, and it tasted sweet as honey.

4 He then said, 'Son of man, go to the House of Israel and tell them what I have said.

5 You are not being sent to a nation that speaks a difficult foreign language; you are being sent to the House of Israel.

6 Not to big nations that speak difficult foreign languages, and whose words you would not understand -- if I sent you to them, they would listen to you;

7 but the House of Israel will not listen to you because it will not listen to me. The whole House of Israel is defiant and obstinate.

8 But now, I am making you as defiant as they are, and as obstinate as they are;

9 I am making your resolution as hard as a diamond, harder than flint. So do not be afraid of them, do not be overawed by them, for they are a tribe of rebels.'

10 Then he said, 'Son of man, take to heart everything I say to you, listen carefully,

11 then go to your exiled countrymen and talk to them. Say to them, "Lord Yahweh says this," whether they listen or not.'

12 The spirit lifted me up, and behind me I heard a great vibrating sound, 'Blessed be the glory of Yahweh in his dwelling-place!'

13 This was the sound of the living creatures' wings beating against each other, and the sound of the wheels beside them: a great vibrating sound.

14 The spirit lifted me up and took me, and I went, bitter and angry, and the hand of Yahweh lay heavy on me.

15 I came to Tel Abib, to the exiles beside the River Chebar where they were living, and there I stayed with them in a stupor for seven days.

16 After seven days the word of Yahweh was addressed to me as follows,

17 'Son of man, I have appointed you as watchman for the House of Israel. When you hear a word from my mouth, warn them from me.

18 If I say to someone wicked, "You will die," and you do not warn this person; if you do not speak to warn someone wicked to renounce evil and so save his life, it is the wicked person who will die for the guilt, but I shall hold you responsible for that death.

19 If, however, you do warn someone wicked who then fails to renounce wickedness and evil ways, the wicked person will die for the guilt, but you yourself will have saved your life.

20 When someone upright renounces uprightness to do evil and I set a trap for him, it is he who will die; since you failed to warn him, he will die for his guilt, and the uprightness he practised will no longer be remembered; but I shall hold you responsible for his death.

21 If, however, you warn someone upright not to sin and this person does not sin, such a one will live, thanks to your warning, and you too will have saved your life.'

22 While I was there the hand of Yahweh came on me; he said, 'Get up, go out into the valley, and there I shall speak to you.'

23 I got up and went out into the valley; the glory of Yahweh was resting there, like the glory I had seen by the River Chebar, and I fell to the ground.

24 The spirit of Yahweh then entered me and put me on my feet and spoke to me. He said, 'Go and shut yourself in your house.

25 Son of man, you are about to be tied and bound, and unable to mix with other people.

26 I am going to make your tongue stick to the roof of your mouth; you will be dumb, and no longer able to reprove them, for they are a tribe of rebels.

27 When I speak to you, however, I shall open your mouth and then you will say to them, "Lord Yahweh says this: Let anyone prepared to listen, listen; let anyone who refuses, refuse!"-for they are a tribe of rebels.'
4)1 'For your part, son of man, take a brick and lay it in front of you; on it scratch a city, Jerusalem.

2 You are then to besiege it, trench round it, build earthworks, pitch camps and bring up battering-rams all round.

3 Then take an iron pan and place it as though it were an iron wall between you and the city. Then fix your gaze on it; it is being besieged and you are besieging it. This is a sign for the House of Israel.

4 'Lie down on your left side and take the guilt of the House of Israel on yourself. You will bear their guilt for as many days as you lie on that side.

5 Allowing one day for every year of their guilt, I ordain that you bear it for three hundred and ninety days; this is how you will bear the House of Israel's guilt.

6 And when you have finished doing this, you are to lie down again, on your right side, and bear the guilt of the House of Judah for forty days. I have set the length for you as one day for one year.

7 Then fix your gaze on the siege of Jerusalem, raise your bared arm and prophesy against her.

8 Look, I am going to tie you up and you will not be able to turn over from one side to the other until the period of your seclusion is over.

9 'Now take wheat, barley, beans, lentils, millet and spelt; put them all in the same pot and make them into bread for yourself. You are to eat it for as many days as you are lying on your side -- three hundred and ninety days.

10 Of this food, you are to weigh out a daily portion of twenty shekels and eat it a little piece at a time.

11 And you are to ration the water you drink -- a sixth of a hin -- drinking that a little at a time.

12 You are to eat this in the form of a barley cake baked where they can see you, on human dung.'

13 And Yahweh said, 'This is how the Israelites will have to eat their defiled food, wherever I disperse them among the nations.'

14 I then said, 'Lord Yahweh, my soul is not defiled. From my childhood until now, I have never eaten an animal that has died a natural death or been savaged; no tainted meat has ever entered my mouth.'

15 'Very well,' he said, 'I grant you cow-dung instead of human dung; you are to bake your bread on that.'

16 He then said, 'Son of man, I am going to cut off Jerusalem's food supply; in their extremity, the food they eat will be weighed out; to their horror, the water they drink will be rationed,

17 until there is no food or water left, and they fall into a stupor and waste away because of their guilt.'
5)1 'Son of man, take a sharp sword, use it like a barber's razor and run it over your head and beard. Then take scales and divide the hair you have cut off.

2 Burn one-third inside the city, while the days of the siege are working themselves out. Then take another third and chop it up with the sword all round the city. The last third you are to scatter to the wind, while I unsheathe the sword behind them.

3 Also take a few hairs and tie them up in the folds of your cloak;

4 and of these again take a few, and throw them on the fire and burn them. From them fire will come on the whole House of Israel.

5 'The Lord Yahweh says this, "This is Jerusalem, which I have placed in the middle of the nations, surrounded with foreign countries.

6 She has rebelled more perversely against my observances than the nations have, and against my laws than the surrounding countries have; for they have rejected my observances and not kept my laws."

7 'Therefore, the Lord Yahweh says this, "Because your disorders are worse than those of the nations round you, since you do not keep my laws or respect my observances, and since you do not respect even the observances of the surrounding nations,

8 very well, the Lord Yahweh says this: I, too, am against you and shall execute my judgements on you for the nations to see.

9 Because of all your loathsome practices I shall do such things as I have never done before, nor shall ever do again.

10 Those of you who are parents will eat their children, and children will eat their parents. I shall execute judgement on you and disperse what remains of you to the winds.

11 For, as I live -- declares Lord Yahweh -- as sure as you have defiled my sanctuary with all your horrors and all your loathsome practices, so I too shall reject you without a glance of pity, I shall not spare you.

12 A third of your citizens will die of plague or starve to death inside you; a third will fall by the sword round you; and a third I shall scatter to the winds, unsheathing the sword behind them.

13 I shall sate my anger and bring my fury to rest on them until I am avenged; and when I have sated my fury on them, then they will know that I, Yahweh, spoke out of jealousy for you.

14 Yes, I shall reduce you to a ruin, an object of derision to the surrounding nations, in the eyes of all who pass by.

15 You will be an object of derision and insults, an example, an object of amazement to the surrounding nations, when I execute judgement on you in furious anger and furious punishments. I, Yahweh, have spoken.

16 On them I shall send the deadly arrows of famine, which will destroy you -- for I shall send them to destroy you; then I shall make the famine worse and cut off your food supply.

17 I shall send famine and wild animals on you to rob you of your children; plague and bloodshed will sweep through you, and I shall bring the sword down on you. I, Yahweh, have spoken." '
6)1 The word of Yahweh was addressed to me as follows,

2 'Son of man, turn towards the mountains of Israel and prophesy against them.

3 Say, "Mountains of Israel, hear the word of the Lord Yahweh. The Lord Yahweh says this to mountains and hills and ravines and valleys: Look, I am going to summon the sword against you and destroy your high places.

4 Your altars will be wrecked, and your incense burners smashed; I shall fling your butchered inhabitants down in front of your foul idols;

5 I shall lay the corpses of the Israelites in front of their foul idols and scatter their bones all round your altars.

6 Wherever you live, the towns will be destroyed and the high places wrecked, to the ruin and wrecking of your altars, the shattering and abolition of your foul idols, the smashing of your incense burners and the utter destruction of all your works.

7 As the butchered fall about you, you will know that I am Yahweh.

8 "But I shall spare some of you to escape the sword among the nations, when you have been dispersed in their lands;

9 and your survivors will remember me among the nations where they are held captive, since I shall have broken their adulterous hearts for having deserted me, and destroyed their eyes for having turned adulterously towards their foul idols. They will loathe themselves for all the wrong they have caused by their loathsome practices.

10 Then they will know that I am Yahweh and that I was not talking lightly when I said that I would inflict these disasters on them."

11 'The Lord Yahweh says this, "Clap your hands, stamp your feet, and say: Alas for all the loathsome sins of the House of Israel, which is about to fall by sword, famine and plague!

12 Far off, they will die by plague; near at hand they will fall by the sword; and any who survive or are spared will die of famine. This is how I shall sate my fury on them.

13 Then you will know that I am Yahweh, when their butchered corpses lie among their foul idols, all round their altars, on every high hill, on every mountain top, under every green tree, under every leafy oak, wherever they offer a smell pleasing to all their idols.

14 I shall point my finger at them and reduce the country to an empty wasteland from the desert to Riblah, everywhere they live, and they will know that I am Yahweh." '
7) The word of Yahweh was addressed to me as follows,

2 'Son of man, say, "Lord Yahweh says this to the land of Israel: Finished! The end is coming for the four corners of the country.

3 This is the end for you; I shall unleash my anger on you, and judge you as your conduct deserves and call you to account for all your loathsome practices.

4 I shall show you no pity, I shall not spare you; I shall repay you for your conduct and for the loathsome practices in which you persist. Then you will know that I am Yahweh.

5 "The Lord Yahweh says this: Disaster, a unique disaster, is coming.

6 The end is coming, the end is coming, it is on the move towards you, it is coming now.

7 Now it is your turn, you who dwell in this country. Doom is coming, the day is near; no joy now, only tumult, on the mountains.

8 Now I shall soon vent my fury on you and sate my anger on you: I shall judge you as your conduct deserves and repay you for all your loathsome practices.

9 I shall show neither pity nor mercy, but shall repay you for your conduct and the loathsome practices in which you persist. Then you will know that I am Yahweh and that I strike.

10 "Now is the day, your turn has come, it has come, it appears, the sceptre has blossomed, pride is at its peak.

11 Violence has risen to become the scourge of wickedness . . .

12 Doom is coming, the day is near. Neither should buyer rejoice, nor seller regret, for the fury rests on everyone alike.

13 The seller will not be able to go back on his bargain; each persists in his sins; they take no defensive measures.

14 The trumpet sounds, all is ready, but no one goes into battle, since my fury rests on all alike.

15 "Outside, the sword; inside, plague and famine. Whoever is living in the countryside will die by the sword; whoever is living in the city will be devoured by famine and plague.

16 And those who escape will escape to the mountains and there, like doves of the valleys, I shall slaughter them all, each one for his sin.

17 Every hand will grow limp, every knee turn to water.

18 They will put on sackcloth, each one trembling. Every face will be ashamed and every head be shaved.

19 They will throw their silver away in the streets and their gold they will regard as a pollution; neither their silver nor their gold will be able to save them on the day of Yahweh's fury. Never again will they have enough to eat, never again will they fill their bellies, since that was the occasion for their guilt.

20 They used to pride themselves on the beauty of their jewellery, out of which they made their loathsome images, their horrors; so now I have made it pollute them.

21 I shall hand it over as plunder to foreigners, as loot to the most evil people on earth. They will profane it.

22 I shall turn my face away from them, while my treasure-house is profaned and robbers will force their way in and profane it.

23 "Forge yourself a chain; for the country is full of bloody executions and the city full of deeds of violence,

24 so I shall bring the cruellest of the nations to seize their houses. I shall put an end to the pride of their e'lite, and their sanctuary will be profaned.

25 Terror is on the way: they will look for peace and there will be none.

26 Disaster will follow on disaster, rumour on rumour; they will pester the prophet for a vision; the priest will be at a loss over the law and the elders on how to advise.

27 The king will go into mourning, the prince be plunged in grief, the hands of the country people tremble. I shall treat them as their conduct deserves, and judge them as their own verdicts merit. Then they will know that I am Yahweh!" '

Civil War III

Has The Skeptical Zone Finally Earned its Name
November 23, 2015 Posted by Barry Arrington under Intelligent Design

Perhaps.  Its founder is preaching materialist heresy.

In a post over at The Skeptical Zone Elizabeth Liddle joins the ranks of our opponents who are finally admiting that biological design inferences are not invalid in principle.  She writes:

Has Barry finally realised that those of us who oppose the ideas of Intelligent Design proponents do not dispute that it is possible, in principle, to make a reasonable inference of design?  That rather our opposition is based on the evidence and argument advanced, not on some principled (or unprincipled!) objection to the entire project?

EL, welcome to the ranks of biological design theorists, by which I mean that group of people willing to follow the evidence for (or against) design in biology wherever it leads.

There is more good news.  EL quoted me when I set forth the following objection ID proponents often get:  “All scientific claims must employ methodological naturalism, and you violate the principle of methodological naturalism when you make a design inference in biology.”

EL writes:

Yes, indeed, Barry.  It is not a valid objection . . . There is nothing wrong with making a design inference in principle. We do it all the time, as IDists like to point out.  And there’s nothing wrong with making it in biology, at least in principle.  There is certainly nothing that violates the “principle of methodological naturalism when you make a design inference in biology”

There is even more good news.  EL rejects the idea that one most know who the designer is before one can infer design:

The objection to ID by people like me . . .  is not that it is impossible that terrestrial life was designed by an intelligent agent, nor that it would be necessarily impossible to discover that it was, nor even, I suggest, impossible to infer a designer even if we had no clue as to who the designer might be (although that might make it trickier).

She even agrees that biological design inferences can be made without invoking any supernatural agent:

If Barry means that we can only infer natural, not supernatural, design, he is absolutely correct

I have been saying biological ID infers merely “design” and not supernatural design for several years.  I am glad it has finally sunk it.

More good news.  EL quotes me again:  “You agree with us that it is the EVIDENCE that is important, and objections thrown up for the purpose of ruling that evidence out of court before it is even considered are invalid.”

And she agrees:

Yes, it is the EVIDENCE that is important,

Then she runs of the rails:

Of course, by the same token, nobody can claim that ID is false – it may well be true that life was designed by a supernatural designer

EL writes this sentence as if biological ID theory posits a supernatural designer.  Sigh.  Every prominent ID theorist has always (when speaking qua ID) said that it is a project to detect design, not supernatural design.

Then back to good news:

EL says she does not object to the broader ID project

. . . as stated in the UD FAQ:  In a broader sense, Intelligent Design is simply the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose. Design detection is used in a number of scientific fields, including anthropology, forensic sciences that seek to explain the cause of events such as a death or fire, cryptanalysis and the search for extraterrestrial intelligence (SETI). An inference that certain biological information may be the product of an intelligent cause can be tested or evaluated in the same manner as scientists daily test for design in other sciences.

Wow.  Yes, that is EL folks.  Don’t believe me, follow the link and check it out yourself.

As I write this her post has gotten over 750 comments, some of which are very interesting.

The first one is EL’s own:

And that’s my point, really – that it’s perfectly possible to test ID hypotheses (small case id I guess) because you can test specific predictions arising from specific hypothesised scenarios.

ID opponent Glen Davidson joins the bandwagon and even adds an area of biological design that has received too little attention:

It is done in biology in fact as well as in principle. Genetic engineering can often be detected, and certainly would be searched for in the case of any biologic warfare. I wouldn’t particularly disagree with Allan Miller so long as there is no context, but, within known context, we can find telltale evidence of genetic tampering or of domestication.

Our William J. Murray jumps in with this zinger:

REC and Moran say they can detect convincing indications of design by intelligence …. what are their definitions and methodology? I mean, isn’t that what you guys always ask ID advocates?

A heaping helping of hypocrisy anyone?  :-)

Our old foe Kantian Naturalist agrees with EL!

I concur with the general sentiments expressed here.

EL even comes up with a not-half-bad definition of “intelligence” for the “I” in ID.

an entity with a human-like type capacity to invent things

EL then writes:

I absolutely agree that inferring design does not require a supernatural hypothesis. That was one of the points I was making in the OP.

I am not quite sure how she squares that with what she wrote before (which seemed to imply that she believes the “D” in ID is always posited to be supernatural agent even though all ID proponents say otherwise):

Of course, by the same token, nobody can claim that ID is false – it may well be true that life was designed by a supernatural designer

KN makes an astute observation:


I also think, quite frankly, that Dembski and Behe are also methodological naturalists (on my suggestion of what that concept means), and this comes out in their refusal to identify the putative designer(s) with any deity or deities. ID is consistent with methodological naturalism — as well as consistent with metaphysical naturalism.

Curtains for Darwinism? II

Why Darwinism is failing II:
November 21, 2015 Posted by News under Culture, Darwinism, News


In “Why Darwinism is failing,” I noted that genome mapping changed the way we look at evolution: We are now much closer to the world of mechanism, not theory—closer to Popular Mechanics than to Philosophical Quarterly. The “single greatest idea anyone ever had” gives way to descriptions of mechanisms few expected or predicted—each of which might account for some evolution, though most of the picture is still missing.

Darwin’s defenders, apart from endless terminology quibbles, respond by insisting that natural selection acting on random mutation (Darwinism) can find room for all of it somehow. They seem not to have noticed that all useful theories are bounded. A theory that explains everything explains nothing.

By contrast, no one claims that horizontal gene transfer is so vast as to include epigenetics, genome doubling, and endosymbiosis. Each is a distinct, demonstrable mechanism in its own right.

But there is something else: Evolution has become a history. Histories are specific, and resilient in the long run to grand theories of the sort that produce accolades like ”most influential academic book” ever.

As noted here:

The more we learn about the history of life on earth, the less evolution is theory and the more it is history. It is less like Epicureanism and more like World War II. That cannot be good for Darwinian thinking, which fills in large gaps in history by the exercise of theory. Things that “must have” happened if the theory is correct are assumed to have happened.

But history is not like that. Consider, for example, Pearl Harbor, when the Japanese crippled the U.S. Pacific fleet in a surprise attack, though the United States was not at war with Japan. Assume that the account broke off there. Maybe a theory can fill in the blanks for us and tell us what “had to” happen.

But then, what if we later discover more and more evidence for what actually happened? It will be bad news Tuesday for some theories developed in the absence of evidence — maybe for quite a few theories. More.

After a while, gerrymandering a grand theory to “account for” unexpected evidence seems like a waste of time to anyone but true believers.

Darwinism is not, of course, failing in the popular imagination, or at least, not yet. Bimbette’s vast TV audience still believes, as does the “breath of fresh air” theology prof, and Zack Kopplin. But increasingly, the impetus comes less and less from keen minds like Collins and Venter, more and more from celebs, zealots, and lobbyists.


The history of life just cannot sustain the weight of so grand a theory.

Curtains for Darwinism?

Why Darwinism is failing:
November 20, 2015 Posted by News under Culture, Darwinism, News, Philosophy




Further to Barry Arrington’s post, “Zachriel goes into insane denial mode,” which has garnered so far 170 comments, and doubtless counting:

The biggest problem for Darwin’s supporters (paleo, neo, extended, whatever) today has nothing to do with Uncommon Descent or with any design hypothesis.

The problem is genome mapping. Blame people like Francis Collins and Craig Venter.

Darwinian evolution was always a theory, by which Darwinism (natural selection acting on random mutation generates huge levels of information, not noise) .

It was the single greatest idea anyone ever had, and could be believed without evidence because “Darwinism is the only known theory that is in principle capable of explaining certain aspects of life.” (p. 287, Blind Watchmaker, 1986)

And it has been believed without evidence. Darwin’s On the Origin of Species is considered by a broad swathe of lay people to be the most influential academic book they know, with very little evidence backing it.

It is a theory that is in constant search for evidence, which results in masses of Darwinian fairy-tales about everything from why stressed mares miscarry through why insects kill their moms, or how people vote and why they tip at restaurants.

One need only map some circumstance in life onto the theory, chop off the inconvenient bits, and there we are: More “science” at work.

Loud crash is heard, some time around 2000.

Today, we know much more than we used to about how life forms change over time. Evolution has become a history, not a theory. Like all histories, it is messy. It only indifferently supports a theory.

Mechanism differs from theory in that it answers Behe’s question, “How, exactly?”: For example, one mechanism of the evolution of some life forms is simply absorbing genes from another organism (horizontal gene transfer):

Bacteria that grow on crustaceans can absorb fragments containing more than 40 genes, using a small “spear.” Researcher Melanie Blokesch describes that number as “an enormous amount of new genetic information.” That may explain why antibiotic resistance sets in so quickly. More.

Jut think of all the Darwinian fairy tales that could have been, and maybe were, told about how natural selection acting on random mutation caused the antibiotic resistance, when they were, for practical purposes of explanation, caused by bacterium equipped with a small spear.

We are now much closer to the world of Popular Mechanics than the world of Philosophical Quarterly.

Mechanism doesn’t answer the kinds of questions “science vs. religion” types or “God-and-science” types explore. But it does answer questions about how evolution happens.

It happens in a variety of ways.  Sometimes it doesn’t happen (stasis). Sometimes it reverses (devolution). Sometimes there are patterns. Other times, that’s unclear.

It has become a history.

Nowhere is there any reason to believe that Darwin’s claimed mechanism, that massive increases in information somehow happen just because the “fittest” at any given time survive and reproduce, explains anything in particular. And the claimed random creation of high levels of information just does not fit with what we know about the universe we live in.

Darwin’s faithful are thus reduced to endless terminological squabbles about what “stasis” or “primitive” mean.

It keeps us on our toes, and keeps up our site numbers.

Note: Francis Collins has had to walk back his earlier enthusiasm for junk DNA, to support some kind of Christian Darwinism, and Craig Venter doesn’t even put much faith in common descent.


And these guys still have jobs! Goodness! Darwin’s lobby must start calling on Top People for support more often, not?

JEHOVAH'S suboptimal beats man's optimal

Engineering a Bionic Eye
David Klinghoffer August 31, 2012 5:22 AM

Richard Dawkins is fond of citing the German phyisologist Hermann von Helmholtz (1821-1894) who complained of the eye that if a human engineer designed such an organ -- with its counterintuitive wiring and virtually unnoticeable blind spot -- he'd have sent the engineer away, disgusted with the incompetence of the plan.

With 40 million blind people in the world today, it would be a wonderful thing if some modern bioengineer were to come up with a design for a bionic eye capable of restoring vision and replacing, as needed, our own natural organ of sight. Yet as a bioengineering problem, developing a bionic eye has proved to be frustratingly difficult, as I noted here earlier.

In this context a headline out of Australia this week -- "'World-first' bionic eye implanted in human patient" (Agençe France-Presse) -- catches your attention. It sounds like scientists have finally solved the problem of designing a working visual prosthesis. Great! How exciting, right? Um, not so fast. Unfortunately as you read the article the impressiveness of the achievement, and the hope it holds out to the blind, have to be adjusted sharply downward with almost every paragraph.

The lucky recipient of the bionic eye is Dianne Ashworth, who suffers from degenerative retinitis pigmentosa. The article first calls it the "'world-first' bionic eye prototype." In the next paragraph it's demoted to an "early prototype." We then learn that what's called an "incredible experience" for Ms. Ashworth was no more than perceiving some flashing lights.

"I didn't know what to expect, but all of a sudden, I could see a little flash -- it was amazing," she said in a statement.
"Every time there was stimulation there was a different shape that appeared in front of my eye."

You read on and find that even this can be done for her only in a lab, so outside the lab Ms. Ashworth is back to being blind.
The team with government-funded Bionic Vision Australia hopes to improve on the current model, which employs 24 electrodes. They are

working towards a "wide-view" 98-electrode device that will provide users with the ability to perceive large objects such as buildings and cars, and a "high-acuity" 1,024-electrode device.
Patients with the high-acuity device are expected to be able to recognise faces and read large print, and BVA said it would be suitable for people with retinitis pigmentosa and age-related macular degeneration.

So anything remotely like achieving normal vision lies far in the future. The article concludes by quoting researcher David Penington who says the device so far has "fulfilled our best expectations, giving us confidence that with further development we can achieve useful vision." Meaning that Ms. Ashworth, when she can swing by the lab, currently enjoys vision that is not "useful" to her.

That is strange since Hermann von Helmholtz, going back more than a century and a half, talked like he could have done a better job in designing an eye than nature or nature's designer actually did. Despite Dawkins's admiration, maybe the guy was just an arrogant ass, after all.

Reductionism takes another hit

A Philosopher Chastises Reductionist Myopia
Evolution News & Views August 29, 2012 5:14 PM

"Through their thorough arguments, the essays in Processes of Life challenge widely held assumptions about biology and evolution. Dupré provides a view of life grounded in recent research and current understanding. His perspective also reminds us how much we do not know."

This is how Christian Julian Villabona-Arenas ends his review in Science of John Dupré's new collection of essays, Processes of Life: Essays in the Philosophy of Biology (Oxford University Press, 2012). We've mentioned Dupré before here, here and here. He's a philosopher of biology who describes himself as a philosophical naturalist, but is critical of reductionism. Based on Villabona-Arenas's review, the book offers more criticisms of Darwinism than supports for it.

As philosophers are wont to be, Dupré is a gadfly raising doubts about all the things scientists take for granted: What is life? What is a species? What is an organism? What is a gene?

One fundamental argument Dupré offers against reductionism is that biology works with concepts that depend not only on their constituents but also on the larger systems of which they are part. Debates over the nature of species have generated a substantial fraction of the evolutionary biology literature; less attention has been placed on the definition of genes. In addition to the concerns around such issues, there is the central question of what constitutes the individual organism. (Emphasis added.)
Inherent in these questions are questions about evolution. At several points in his review, Villabona-Arenas, a molecular evolutionist at the University of São Paulo, indicates that Dupré is critical of standard evolutionary theory to the point of chastising evolutionists for their pretensions. But at no point in the review does the reviewer show the author granting neo-Darwinism evidentiary support, even though he is clearly an evolutionist himself.
For instance, the title of his review, "Ending Microbial Myopia," alludes to Dupré's contention that microbes are far more significant than "macrobes" (anything not a microbe) as units of evolution. For most of earth history, they were it:

Although their scientific importance remains generally unappreciated, microbes surpass macrobes (a term Dupré advocates for those organisms that are not bacteria, archaea, or protists) in their contribution to evolutionary history: the first three billion years of life on Earth were overwhelmingly microbial. Even today, they include most living things, exhibit a greater metabolic diversity, and inhabit a wider range of environments (including extremely harsh ones); their collaborative enterprise is so extensive that at the heart of every interface between multicellular eukaryotes and the external environment lies a complex multispecies microbial community. In three essays, Dupré and coauthor Maureen A. O'Malley (University of Sydney) present a strong case for ending the myopia that leads us to undervalue microbes.
That being said, does Dupré show how they came to be? On the contrary, in describing the complexity and variety of microbes, and their interactions, he leaves the door wide open for reassessment of basic evolutionary concepts:
As Dupré and O'Malley note, paying proper attention to microbes has already yielded observations that may force us to rethink fundamental ideas about evolution. In light of the extent of lateral gene transfer, the "tree of life" seems better considered as a net. Studies of cooperation, development, competition, and communication among unicellular organisms have revealed that they can possess many of the characteristics used to define multicellularity. Given that the entities that form lineages are not always the same as those that form metabolic wholes, collaboration may be the central characteristic of living matter. Traditional organisms cannot be seen as "'the' biological individuals on which selection operates." Abandoning some theoretical commitments will open the way for further understanding nature.
Looking at a few finch beaks, in other words, puts the focus on irrelevant details but misses the big picture. It's myopic, Dupré is saying, to see an individual bird or moth as a unit of selection when the living world is a complex, interacting, cooperative, dynamic whole. We might even treat our own microbial travelers (that comprise 90% of the cells we carry with us) as one big "single composite entity." Dupré's view of the biosphere recalls a kind of Heraclitan flux that defies simplistic evolutionary principles. Villabona-Arenas writes,
A living world where none of the entities that constitute an organism are static implies an interactive flux subtly different in every iteration but similar enough to be a distinctive process. Because biological concepts are static abstractions from life processes and different abstractions provide different perspectives on these processes, we face considerable difficulties in reconciling satisfactory general concepts.
So far, they've taken away Darwin's tree and replaced it with a net. They've questioned the unit of selection. They've elevated microbes to collaborative, communicating entities on par with multicellular organisms. They've undermined the ability to describe satisfactory general concepts of evolution. Will they provide something to rescue Darwin from obsolescence? No. They turn on the heat with epigenetics, undermining the Central Dogma:
The author's reasons for recognizing the importance of the environment accentuate the relevance of epigenetics and developmental systems theory, areas that for a long time attracted little interest but have now become very active. Beyond doubt, Dupré emphasizes, the perpetuation of life from one generation to the next requires much more than simply the passage of DNA. He concludes that genomes do not merely store information. Because of their constant dynamic interaction with other constituents of the cell, their capacities depend not only on their sequence of base pairs. More important, those capacities are determined by the systems of which the DNA molecules are only part.
That's not all. Dupré continues by chastising evolutionary psychology, claiming that "evolution has had ample time since the Stone Age to shift our behavior" and "the complexity of the developmental interactions between a wide variety of internal and external factors" (such as epigenetics) discounts the evo-psych claim that we are as we are because we were as we were: e.g., we are obese because our hunter-gatherer ancestors had to store fat for periods of famine. "He applies similar reasoning in rejecting claims of genes for race, highlighting the mistake made in thinking of strings of DNA as having specific functions defined only in terms of phenotypic outcomes. For such reasons, he rejects genetic determinism."
Readers are undoubtedly finding implicit support in all these statements for intelligent design theory, while neo-Darwinism is getting a whipping. Don't look for a last-minute rescue. In his last paragraph, Villabona-Arenas ends the review with one last rebuke:


Through their thorough arguments, the essays in Processes of Life challenge widely held assumptions about biology and evolution. Dupré provides a view of life grounded in recent research and current understanding. His perspective also reminds us how much we do not know.

A line in the sand XXV

Paris attacks: UN backs 'all necessary measures' against IS:

The UN Security Council has unanimously adopted a resolution to "redouble" action against Islamic State, following last week's deadly attacks in Paris.
The French-drafted document urges UN members to "take all necessary measures" in the fight against IS.
IS said it carried out the Paris attacks, in which 130 people died.
It also claimed deadly bombings in Lebanon this month, while an IS-linked group said it downed a Russian passenger plane in October.

The UN resolution 2249 also condemns recent attacks in Sousse, Tunisia, and Ankara, Turkey.

Aristotle on body and soul

Aristotle's Theory of Soul:

Aristotle's theory, as it is presented primarily in the De Anima (for a complete account, see Aristotle's Psychology), comes very close to providing a comprehensive, fully developed account of the soul in all its aspects and functions, an account that articulates the ways in which all of the vital functions of all animate organisms are related to the soul. In doing so, the theory comes very close to offering a comprehensive answer to a question that arises from the ordinary Greek notion of soul, namely how precisely it is that the soul, which is agreed to be in some way or other responsible for a variety of things living creatures (especially humans) do and experience, also is the distinguishing mark of the animate. According to Aristotle's theory, a soul is a particular kind of nature, a principle that accounts for change and rest in the particular case of living bodies, i.e. plants, nonhuman animals and human beings. The relation between soul and body, on Aristotle's view, is also an instance of the more general relation between form and matter: thus an ensouled, living body is a particular kind of in-formed matter. Slightly simplifying things by limiting ourselves to the sublunary world (cf. De Anima 2.2, 413a32; 2.3, 415a9), we can describe the theory as furnishing a unified explanatory framework within which all vital functions alike, from metabolism to reasoning, are treated as functions performed by natural organisms of suitable structure and complexity. The soul of an animate organism, in this framework, is nothing other than its system of active abilities to perform the vital functions that organisms of its kind naturally perform, so that when an organism engages in the relevant activities (e.g., nutrition, movement or thought) it does so in virtue of the system of abilities that is its soul.

Given that the soul is, according to Aristotle's theory, a system of abilities possessed and manifested by animate bodies of suitable structure, it is clear that the soul is, according to Aristotle, not itself a body or a corporeal thing. Thus Aristotle agrees with the Phaedo's claim that souls are very different from bodies. Moreover, Aristotle seems to think that all the abilities that are constitutive of the souls of plants, beasts and humans are such that their exercise involves and requires bodily parts and organs. This is obviously so with, for instance, the abilities for movement in respect of place (e.g., by walking or flying), and for sense-perception, which requires sense-organs. Aristotle does not, however, think that there is an organ of thought, and so he also does not think that the exercise of the ability to think involves the use of a bodily part or organ that exists specifically for this use. Nevertheless, he does seem to take the view that the activity of the human intellect always involves some activity of the perceptual apparatus, and hence requires the presence, and proper arrangement, of suitable bodily parts and organs; for he seems to think that sensory impressions [phantasmata] are somehow involved in every occurrent act of thought, at least as far as human beings are concerned (De Anima 3.7, 431a14-7; 3.8, 432a7-10; cf. De Memoria 1, 449b31ff.). If so, Aristotle in fact seems to be committed to the view that, contrary to the Platonic position, even human souls are not capable of existence and (perhaps as importantly) activity apart from the body (cf. De Anima 1.1, 403a3-25, esp. 5-16).

It is noteworthy that Aristotle's theory does not mark off those vital functions that are mental by relating them to the soul in some special way that differs from and goes beyond the way in which vital functions in general are so related. It is certainly not part of Aristotle's theory that the soul is specially and directly responsible for mental functions by performing them on its own, whereas it is less directly responsible for the performance by the living organism of other vital functions such as growth. As this aspect of his theory suggests, Aristotle is confident that once one has a proper understanding of how to explain natural phenomena in general, there is no reason to suppose that mental functions like perception, desire and at least some forms of thinking cannot be explained simply by appealing to the principles in terms of which natural phenomena in general are properly understood and explained (cf. Frede 1992, 97).


It might be thought that since Aristotle's theory treats mental functions and other vital functions exactly alike, it obscures a crucial distinction. This worry, however, turns out to be unjustified. The theory treats mental and other vital functions alike only in that it views both kinds of functions as performed by natural organisms of the right kind of structure and complexity. Viewing mental and other vital functions in this way is perfectly compatible with introducing a distinction between mental and other functions if concerns of some kind or other call for such a distinction. Aristotle is perfectly capable, for instance, of setting aside non-mental vital functions as irrelevant for the purposes of practical philosophy (NE 1.13, 1102b11-12).

Animal navigation turns mount improbable into an inaccessible plateau for Darwinism.

Animal Magnetism Comes to Light
Evolution News & Views November 20, 2015 11:44 AM

Perhaps you saw them in Living Waters: sea turtles navigating alone for thousands of miles in the open sea, then returning to the exact beach where they had hatched; salmon swimming from Canada halfway to Japan, then finding their way back to the mouth of their natal stream.

The only global force available to make long-distance migration possible for sea creatures is the Earth's magnetic field -- something humans cannot sense. A compass can point a hiker north, but it cannot tell her the intensity of the field at any given point. A map can tell her companion where he is, but cannot tell him which bearing to take. Both tools are necessary, and both are available to many animals with input from the magnetic field.

At long last, Chinese investigators recently reported in Nature Materials the putative discovery of the physical basis of the magnetic sense in animals: "A Magnetic Protein Biocompass." If their findings are correct, the capability resides in a rod-shaped complex of iron-rich proteins inside particular cells. The abstract explains:

Here, we report a putative magnetic receptor (Drosophila CG8198, here named MagR) and a multimeric magnetosensing rod-like protein complex, identified by theoretical postulation and genome-wide screening, and validated with cellular, biochemical, structural and biophysical methods. The magnetosensing complex consists of the identified putative magnetoreceptor and known magnetoreception-related photoreceptor cryptochromes (Cry), has the attributes of both Cry- and iron-based systems, and exhibits spontaneous alignment in magnetic fields, including that of the Earth. Such a protein complex may form the basis of magnetoreception in animals, and may lead to applications across multiple fields. [Emphasis added.]

"It's an extraordinary paper," one biochemist remarked in Nature News. It may settle long-standing debates about the source of this incredibly accurate sense. David Cyranoski describes the system as "a biological compass needle: a rod-shaped complex of proteins that can align with Earth's weak magnetic field." The Nature News piece includes a diagram of the proposed magnetic receptor (MagR), looking like a rod of ring-shaped proteins rich in iron surrounded by cryptochromes. The Chinese researchers watched these rods orient themselves to magnetic fields. New Scientist takes us into the lab:

The researchers then identified and isolated this protein complex from pigeons and monarch butterflies.

In the lab, the proteins snapped into alignment in response to a magnetic field. They were so strongly magnetic that they flew up and stuck to the researchers' tools, which contained iron. So the team had to use custom tools made of plastic.

The solution looks intriguing, but Cyranoski writes that other scientists remain skeptical. Controversies have gone on for years about the roles of cryptochromes v. particles of magnetite. New Scientist reviews the history of the debate:

There used to be two competing theories about magnetic sense: some thought it came from iron-binding molecules, others thought it came from a protein called cryptochrome, which senses light and has been linked to magnetic sense in birds.

Xie's group was the first to guess these two were part of the same system, and has now figured out how they fit together.

Some skeptics are not convinced that such small amounts of iron in MagR can respond to magnetic fields. Some want to see the magnets work in vivo. Others doubt that the team's research was free of contamination. At best, this may represent "a major step forward towards unravelling the molecular basis of magnetoreception."

What the articles fail to address is the bigger picture of stimulus and programmed response. A compass is useless without eyes to read it and a brain to interpret it. If MagR is a compass needle, how does the animal sense its orientation and respond appropriately? The response mechanism must be able to discern not only the direction of the needle, but the angle of inclination of the field line at a given point as well as its intensity. Even with all this equipment, the animal must have a map inherited at birth to tell it where to go. Magnetosensation is networked with other senses, such as olfaction, proprioception and biological clocks. Without doubt, years of additional work will be required to put all the pieces together.

It immediately becomes apparent that we have here an astonishing example of convergence:

The biocompass -- whose constituent proteins exist in related forms in other species, including humans -- could explain a long-standing puzzle: how animals such as birds and insects sense magnetism....

Many organisms -- ranging from whales to butterflies, and termites to pigeons -- use Earth's magnetic field to navigate or orient themselves in space.

Animals known to have magnetoreception skills range from worms to mammals, insects to fish, bacteria to reptiles. Cows have been observed to prefer to stand in a north-south direction. Even humans appear to possess these protein complexes, suggesting we could develop the skill to a degree. Don't some people have a keener sense of direction than others?

There is an astonishing range of magnetosensing creatures that are unrelated according to Darwinian theory. Maybe that's why none of the articles tried to explain how this ability evolved. Will they say all these lineages hit upon the same systems independently? Or will they claim that bacterial ancestors developed it, but some descendent lineages lost it? Either answer seems dubious.


Intelligent design, on the other hand, predicts that organisms will be equipped with complex systems that can take advantage of environmental cues and respond with precision. That's exactly what we observe. We see similar equipment in our own remote sensing machines like spacecraft and weather instruments, so we are not surprised to find it in living creatures.