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Tuesday 24 November 2015

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!" '