Shaking the foundation of Darwinism

 The Other Unsolved Problem of Evolution

Granville Sewell

It is generally accepted that the main problem with Darwin’s explanation for evolution is the existence of many apparently “irreducibly complex” features in living things, and especially in their cells. How could these features evolve gradually through apparently useless intermediate stages? In a 2020 Evolution News post I offered one spectacular example: the aquatic bladderworts, whose carnivorous traps have

trigger hairs attached to a valve-like door which normally keeps the trap tightly closed. The sides of the trap are compressed under tension, but when a small form of animal life touches one of the trigger hairs the valve opens, the bladder suddenly expands, and the animal is sucked into the trap.

Wolf-Ekkehard Lӧnnig and Heinz-Albert Becker, in their article on carnivorous plants that is quoted in the post, write that 

it appears to be hard even to imagine clearcut selective advantages for all the thousands of postulated intermediate steps in a gradual scenario…for the origin of the complex carnivorous plant structures examined above.

A More Fundamental Difficulty

How plants could gradually evolve water-tight traps with valve-like doors and trigger hairs is a very difficult problem. But a recent article of mine, “Human-Engineered Self-Replicating Machines,” focuses on a more fundamental problem: we really have no idea how living things are able to pass their current complex structures on to their descendants generation after generation, without significant degradation — much less how they evolve even more complex structures.

The new peer-reviewed article in the journal BioCosmos explains why human engineers are not close to building self-replicating machines and argues that “we are unlikely to be successful in explaining how the self-replicating machines we see everywhere in the living world could have arisen through entirely natural causes, when we still do not know how such machines could be designed.”

The Problem of Self-Replicating Machines

A few paragraphs from the new article:

With all our advanced technology, we are not close to producing human-engineered self-replicating machines. This is significant because it is widely believed that the first self-replicators on Earth must have arisen through chance chemical processes — it being impossible to appeal to natural selection of replication errors before anything could self-replicate. 

To better appreciate the enormous difficulties in designing such machines, and thus the difficulties in understanding how the first living things arose on Earth, let’s think about what would be required to build, say, a self-replicating “Model T” car.

We know how to build a simple Model T. Now let’s build a factory inside this car, so that it can produce Model T cars automatically, and call the new car, with the Model T factory inside, a “Model U.” A car with an entire automobile factory inside, which never requires any human intervention, is far beyond our current technology, but it doesn’t seem impossible that future generations might be able to build a Model U.

Of course, the Model U cars are not self-replicators, because they can only construct simple Model T’s. So let’s add more technology to this car so that it can build Model U’s, that is, Model T’s with car-building factories inside. This new “Model V” car, with a fully automated factory inside capable of producing Model U’s (which are themselves far beyond our current technology) would be unthinkably complex. But is this new Model V now a self-replicator? No, because it only builds the much simpler Model U. The Model V species will become extinct after two generations, because their children will be Model U’s, and their grandchildren will be infertile Model T’s. So back to work, and each time we add technology to this car, to move it closer to the goal of reproduction, we only move the goalposts, because now we have a more complicated car to reproduce. It seems that the new models would grow exponentially in complexity. And even if we were able to engineer self-replicating cars, it is hard to imagine that without any human maintenance these cars could keep reproducing themselves for more than a few generations before errors accumulate to the point that all replication halts.

And here we have ignored the very difficult question of where these cars get the raw materials they need to supply their factories. 

Some will object here that the first living things may have been much simpler than self-replicating cars. It is widely believed that you only need to explain how very simple self-replicators could have arisen though chance chemical processes, because then natural selection of the resulting duplication errors could take over and explain how self-replicators far more complex than cars could have arisen. But even if we could explain the appearance of simple self-replicators, imagining trying to design self-replicating cars may help us appreciate the enormity of the difficulties facing any scientific explanation (let alone one which relies on replication errors) for the unimaginably complex self-replicators that we see everywhere in the living world. 

Against nincsnevem X

 The tenth installment in my responses to Mr.nevem.

 "The fact that Jesus "only" wanted to "prove" that he is not "invisible spirit creature perhaps a demon" and "not such a conjuring", etc. only your vision into in the text,"

This unhinged rant is based on Mr.Nevem's attempted use of 

Luke ch.2:36-39NIV" they were talking about these things, Jesus himself stood among them, and said to them, “Peace to you!”irit 37But they were startled and frightened and thought they saw a spirit. 38And he said to them, “Why are you troubled, and why do doubts arise in your hearts? 39See my hands and my feet, that it is I myself. Touch me, and see. For a spirit does not have flesh and bones as you see that I have."

To prove that the resurrected Jesus was human and not superhuman.i

  I simply pointed out that if this spirit was visible then what is being refer to is not a spirit being as these tend to be unseen. The account further shows they were afraid of the sight, so obviously they thought they were seeing an apparition of some sort perhaps conjured by a demon which would explain the apprehension

 We know that spirit beings can take on fleshly bodies indistinguishable from humans see Luke ch.24:4-6. so Jesus' demonstrating that he was not an apparition would prove nothing about whether he had become a spirit being or not

  In support of the claim that Jesus was made a spirit being with corresponding spirit body upon his resurrection

1Corinthians ch.15:45KJV"And so it is written, The first man Adam was made a living soul; the last Adam was made a quickening spirit."

1Corinthians ch.15:47,48KJV"The first man is of the earth, earthy: the second man is the Lord from heaven. 48As is the earthy, such are they also that are earthy: and as is the heavenly, such are they also that are heavenly. 

The first Adam is made of dust the second Adam(since his resurrection) is not made of dust i.e no longer human but super human

2Corinthians ch.5:1KJV"For we know that if our earthly house of this tabernacle were dissolved, we have a building of God, an house not made with hands, eternal in the heavens."

 Let us take careful note of the sequence of events there is no remodeling of the earthly house it is DISSOLVED and replaced by a heavenly house not of human origin.

Galatians ch.1:1NIV"Paul, an apostle—sent not from men nor by a man, but by Jesus Christ and God the Father, who raised him from the dead—"

suggesting that Paul did not consider the risen Christ to be human but superhuman.

Against Nincsnevem IX

 The ninth installment of my responses to mr.nevem

"The "spiritual body" ("sōma pneumatikos", 1 Cor 15:44) is not the opposite of the real human body, but is contrasted with the corruptible, mortal, sinful human body, as we have seen, Jesus' "spiritual body"had flesh and bones Luke 24:39

Jesus mortal body had no sin so the contrast could have nothing to do with sin if his body had sin it could not serve as a sin offering the contrast is not between what is sinful and what is sinless but what is mortal and what is immortal 

Luke ch.24:36-39NIV"While they were still talking about this, Jesus himself stood among them and said to them, “Peace be with you.”

37They were startled and frightened, thinking they saw a ghost. 38He said to them, “Why are you troubled, and why do doubts rise in your minds? 39Look at my hands and my feet. It is I myself! Touch me and see; a ghost does not have flesh and bones, as you see I have

 Spirit creatures are invisible so spirit is being used here in the sense of a phantasm that such an invisible spirit creature perhaps a demon might conjure, thus Jesus allowed them to touch his incarnated superhuman form to prove that he was not such a conjuring. So this passage in no way proves your contention the fact that Jesus could not take his sinless flesh and blood into heaven proves that sin is not the issue only the superhuman can enter spirit realm.

There are also legal considerations all sin offerings must be completely consumed for instance whatever was left of the Passover had to be burned 

Exodus ch.12:9:10NIV"Do not eat the meat raw or boiled in water, but roast it over a fire—with the head, legs and internal organs. 10Do not leave any of it till morning; if some is left till morning, you must burn it. "

Thus to conform to this pattern Jesus cannot legally retrieve his human body as that would cancel the atonement.

The wages of sin is eternal death not temporary disembodiment for his atonement to have truly substitutionary value the loss of his human perfection to death must be permanent

One more thing you are not scoring any points with me with your half-truths and distortions against the brothers. You see contrary to your lies I am fully aware of our past I am also aware of the bloodstained and corrupted past and present of your church  and not for all the money in the world would I exchange pasts with that cabal of murdering thugs called the Catholic church.

Revelation ch.18:24KJV"And in her was found the blood of prophets, and of saints, and of all that were slain upon the earth.

Against NincsNevem VIII

 The eight in my responses to Mr.nevem

Nincsnevem:"JEHOVAH Cannot foreknow a thing if it is not foredetermined."

This is a very poor "solution" for the problem of how free will and divine predestination relate to each other. The way WTS theology handles this issue, and the end result they got out of it (a God who is not inherently omniscient, therefore existing in the flow of time) clearly shows how absurd the biblicist approach is.

AservantofJEHOVAH: The CONCLUSION that infallible foreknowledge is only possible where there is an unalterable predetermination combined with a knowledge of this predetermination is not a Solution to any problem. It is a logical deduction we live in a cause and effect reality thus every effect must have a preceding and effective cause JEHOVAH is the first Cause(and in an important sense the only one that matters). But there are no effects without preceding causes.

 If  the eternal future is unalterably predetermined then logically there is a causal chain

 Responsible and if JEHOVAH is the first cause then the buck stops

With him.

Nincsnevem:But okay, let's say that inherent omniscience implies that there is no free will (as Calvinism - according to many - follows). Well, then there is no free will, because the believer does not absolutize the truths concerning man against those concerning God, but vice versa.

Don't like the end result? Chapter 9 of the Epistle to the Romans is the answer for you.

The bible declares that JEHOVAH is the epitomy of Justice if this word is to be more than an academic matter it certainly ought to mean that he deals with is intelligent creation in a fair minded way i.e the opposite of asking us to accomplish what he fully knows is impossible and then charging his failure to render us capable of compliance to us as wrongdoing on our part 

And then not content with this punish us with eternal suffering for what is plainly his fault.

Some wonder why there are so many atheist, I marvel that there are so few with the mainline churches promoting this nonsense as divine revelation

Daniel ch.4:37NIV"Now I, Nebuchadnezzar, praise and exalt and glorify the King of heaven, because everything he does is right and all his ways are just. And those who walk in pride he is able to humble."

Nincsnevem:In church history, the following solutions were basically created:

1. Pelagianism

2. Semipelagianism

3. Molinism

4. Thomism

5. Calvinism

I have given the order not in the order of the development of the given theology, but in the extent to which human free will is absolutized at the expense of divine order. In this regard, WTS is Pelagian.

AservantofJEHOVAH:Mr.nevem speaks as if liberty is some kind of human invention and not the creation of a truly omnipotent God who is free to communicate his own genuine liberty to his offspring it is an inability to produce such a genuine liberty

Which would be a necessary(though not sufficient ground,) for any true morality that injures the divine majesty.

 Any affection mechanistically predetermined from eternity is affection in name only, as would be any other "virtue" so predetermined be a mockery of said virtue. If JEHOVAH Cannot the deliver the liberty that makes true virtue possible then a huge question mark is put over his deity

Fortunately for all concerned the JEHOVAH of scripture is incomparably superior to the "jehovah" of Christendom.

And has promised to deliver GENUINE liberty in abundance to all the faithful

Romans ch.8:21NIV"For the creation waits in eager expectation for the children of God to be revealed. 20For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope 21that h the creation itself will be liberated from its bondage to decay and brought into the freedom and glory of the children of God."

Nincsnevem :Does God's foreknowledge influence our free actions? In theory, we must answer no, otherwise we cannot talk about free will. However, how this foresight is compatible with freedom is answered by different theories – as we have seen – the Thomists and Molinists have different views. Before the Thomist-Molinist debate, answers were usually given that viewed divine knowledge separately from divine will.

They said that if we contemplate God's foreknowledge in itself, it cannot influence people's actions. Jerome writes, "Something will not happen in the future because God knows it will happen in advance; but God knows it in advance because it will happen" 

AservantofJEHOVAH :missing the point as usual ,if it is accurately foreknown from eternity then it was unalterably predetermined from eternity ,the causal chain starts with JEHOVAH exclusively so the buck stops with him for every eternally predetermined outcome.

                Isaiah ch.46:10NIV"I make known the end from the beginning, from ancient times, what is still to come. I say, ‘My PURPOSE will stand, and I will DO all that I please.’"ose

So JEHOVAH is not a mere passive of observer of a future that has determined itself he is the architect and builder of the future. He goes about this project with the liberty of his intelligent creation in mind.

Nincsnevem:(Dial adv Pel 3 6). Similar statements are made by Origen, Eusebius, Epiphanius, Chrysostom, Augustine, etc.). Modern analogy: I look at my watch and find that a train will arrive at the railway station in half an hour; it does not arrive because I know it, but I know it because it will arrive. Augustine says that just as our reminiscences do not alter or influence past events, so God's foreknowledge does not influence future events (Lib arb III 4 4; cf. Civ V 10).

No thought ,just mindless parroting of dead men. I'm sorry but it's difficult to take anyone who thinks JEHOVAH'S foreknowledge is comparable to man's seriously .JEHOVAH is the first cause ,ALL of the information and energy in the universe came out of him he has established by his omnipotence what is determined and what is undetermined. He can create genuine liberty because he is invincible ,no creature can interfere in his purpose regardless of the choices they make or don't make hence he is utterly fearless.

It seems like the source much of the ideology undergirding predestination is a desire to project human type insecurity and presumption of scarcity on JEHOVAH. JEHOVAH Possesses absolute logistical supremacy . He has the ultimate high ground unlimited firepower and an unblinking all-seeing eye on the entirety of the theatre he has no need to plan. He does not need certainty as to the future decision(s)

 of any creature to be guaranteed of absolute success. Thus He has no apprehension about conferring Genuine liberty upon his intelligent creation.

Nincsnevem: However, this solution holds only as long as we are solely considering divine knowledge, disregarding divine will. In reality, God does not merely observe future things; they do not have an existence independent of His will that would determine divine understanding.

God does not weigh our actions after the fact, their motives, and the responsibility for them. He foresaw all this, and everything happened as he saw. In His knowledge, things and actions appear with their full causality, hierarchy of values, and interaction.

AservantofJEHOVAH: the "it's God's will" argument invariably makes things worse because it means that without violating any objective standard He could have willed otherwise and arbitrarily chose to will the eternal suffering for the vast majority of humanity and a sizable plurality of his angelic hosts. Truly a doctrine of devils. See 1Timothy4:1 surely it would have been better to create no intelligent being at all

        Job ch.3:11NIV"“Why did I not perish at birth,

and die as I came from the womb?"

Nincsnevem: why God's foreknowledge does not influence us? The full answer depends on answering another question: in what does God foresee our free acts of will? There are three  answers to the latter question: either the Thomists', the Molinists', or the one that it is an unfathomable mystery for us.

aservantofJEHOVAH : Talk about a round about way of saying I don't know. One more time JEHOVAH is the first cause free moral agency is not some human contrivance it is a divine gift if the gift is phony which would be the case if eternal determinism is true then the giver is to blame not receiver

Nincsnevem:"either so if evil is eternally predetermined then logically JEHOVAH Alone is to blame."

This is also a very poor solution to the theodicy problem. With this much power, God is to blame because he kept the murderer alive, even though if he hadn't kept him alive, he would have fallen back into the primordial chaos.

AservantofJEHOVAH: or God could have chosen to not create the killer at all having known from eternity that he had no choice but to kill because murder is a value term that only applies to those with genuine free moral agency we don't speak of random falling objects objects as murdering those they may fatally strike.

So if determinism is true there is no crime only divinely predetermined misfortune. 

The fall of eastern Rome

 

Against Nincsnevem. VII

 "This is really easy to answer: according to his human nature, Jesus is a Messianic King, according to his human nature he is the heir to David's throne, and of course Jesus' humanity is not God, not YHWH. Jesus' human and divine natures are distinct but inseparable.,"

Here is the thing Mr.nevem the verse makes no mention of a nature but of a person so if this person( not nature) is equal to his Father is not the most high or he is his own Father stop putting words in the prophet's mouth 

Also there is a small matter of the Holy Spirit who is not the Father of Jesus according to the Nicene creed and not incarnated if he is equal to the Father then obviously the Father of Jesus is not the most high.

So your fudge fails the person (not the nature) of the Father is greater than the person of the Son and if the spirit is a person greater than the person of the spirit.

Luke ch.1:32NIV"He will be great and will be called the Son of the Most High. And the Lord God will give to him the throne of his father David, "

A similar problem exists with Matthew ch.24:36

Matthew ch.24:36KJV"But of that day and hour knoweth no man, no, not the angels of heaven, but my FATHER ONLY. "

Why would the unincarnated Spirit not know the day or hour

And if you could just put the smug away for a minute(because it is clearly impeding your judgment) you will see that the question was mainly about the identity of the most high because, by definition the most high can have no equals so who is this unequalled Father of Jesus.

So it really doesn't matter whether the human Jesus was less than his father if there is a divine Jesus that is equal to his Father his Father is not the MOST HIGH as per the dictionary definition of that term

Against nincsnevem VI

 The sixth of my responses to Mr.Nevem

"obviously only for God. Predestination tries to emphasize the viewpoint according to God, which doesn't deny, just relativizes the human viewpoint."

Actually it relativizes away the human viewpoint

Where obedience is impossible a charge of wrongdoing is simply not permissible according to natural Justice and of course where determinism is the case, any obedience to any command at variance to what has been predetermined from eternity would by definition be impossible.

  

 Romans ch.4:15NIV"because the law brings wrath. And where there is no law there is no transgression."

Where compliance is impossible a Just accusation of wrongdoing cannot be made.

It's still paved with the best intentions

 

Against nincsnevem V

 The fifth installment in my responses to Mr.Nevem

"But of this, the formula Jehovah / God = the Father is only logical for the Watchtower Society. The divine name Yahweh or Jehovah does not denote only one person,"

Well how about this then

 Luke ch.1:32NIV"He will be great and will be called the Son of the Most High. And the LORD God will give to him the throne of his father David, "

Most high =Father of Jesus

JEHOVAH = Most High Psalm ch.83:18

JEHOVAH =Father of Jesus

 

Of course if the Father of Jesus is truly the MOST HIGH as per the dictionary no other can be his equal or even his approximate.

On the most high God and his son

 The God and Father of Jesus Christ is the most high God (human councils notwithstanding)

Psalms ch.83:18KJV"That they may know that thou alone, whose name is JEHOVAH, Art the Most High over all the earth."

Thus no one not numerically identical to JEHOVAH can be the God of Israel or the most high God

If the claim is that the triune God is JEHOVAH Then it logically follows that no one other than this triune God can be called JEHOVAH in as much as Jesus nor the Father are triune according Trinitarian orthodoxy then neither Jesus nor the father can be called the most high or the God of Israel

it is also claimed that no member of the trinity is a God there are not three gods but three persons.

So the fact that the father is called the God and one God is a problem because it means that the father is A God in his own right also the Father is the God of the son

Revelation ch.3:12 KJV" that overcometh, I will make him a pillar in the temple of my God, and he shall go out thence no more: and I will write upon him the name of my God, and the name of the city of my God, the new Jerusalem, which cometh down out of heaven from my God, and mine own new name. "

There fore the Son is definitely not the most high

Acts ch.3:13NIV"The God of Abraham, and of Isaac, and of Jacob, the God of our fathers, hath glorified his Servant Jesus; whom ye delivered up, and denied before the face of Pilate, when he had determined to release him. "

Luke ch.1:32NIV"He will be great and will be called the Son of the Most High. The LORD God will give him the throne of his father David,"

So the God and Father of Jesus is the Most High God I.e JEHOVAH

Against nincsnevem IV

 My fourth installment on my responses to Mr.Nevem

Edgar Foster's blog

"God would undergo change by incarnation if he were to become human in such a way as to cease to remain God; "

God would also under go change if he became a creature the categories of Creator and creature are mutually exclusive.

Hosea ch.11:9ESV"I will not execute my burning anger;

I will not again destroy Ephraim;

for I am God and not a man,

the Holy One in your midst,

and I will not come in wrath.c"

Unless this is not meant to be understood as a permanent and unchangeable in carries no force.

1Kings ch.18:27KJV"27And it came to pass at noon, that Elijah mocked them, and said, Cry aloud: for he is a god; either he is talking, or he is pursuing, or he is in a journey, or peradventure he sleepeth, and must be awaked."

The notion that JEHOVAH Can ever be subject to human frailties is nothing but grist for mockery

Sophistry masquerading as sophistication.

Against nincsnevem III

 The third installment of my responses to Mr.Nevem

Edgar Foster's blog

"The Catholic doctrine does not claim that the Son was Changed by the incarnation" well ,before the incarnation he had one nature and afterward he simultaneously possessed two mutually exclusive natures

Romans ch.1:22,23ESV"Claiming to be wise, they became fools, 23and exchanged the glory of the immortal God for images resembling mortal man and birds and animals and creeping things." Paul is saying that is foolish to even suppose that JEHOVAH Would outwardly resemble a mortal man.

How much more so then to claim that he is literally a mortal man.

Against nincsnevem II

 My responses to mr.nevem continued

Edgar Foster's blog

Next Jesus dares to judge:

You claimed"Jesus, on the other hand, pronounced a clear judgment on Satan (Jn 16:11; cf. Jn 5:22, 27; 1 Jn 3:8; Col 2:15)."

John ch.16:7-11NIV"But very truly I tell you, it is for your good that I am going away. Unless I go away, the Advocate will not come to you; but if I go, I will send him to you. 8When he comes, he will prove the world to be in the wrong about sin and righteousness and judgment: 9about sin, because people do not believe in me; 10about righteousness, because I am going to the Father, where you can see me no longer; 11and about judgment, because the prince of this world now stands condemned."

So it is the advocate from the Father in effect the Father himself who has condemned Satan. So like Michael Jesus defers to his God when it comes to Judging the great enemy

Jude 9 NASB"But Michael the archangel, when he disputed with the devil and argued about the body of Moses, did not dare pronounce against him an abusive judgment, but said, “The LORD rebuke you!”

So it was Michael's fear of JEHOVAH Not any imaginary subordination to the prince of darkness that restrained him

Colossians ch.2:14,15NASB"having canceled the certificate of debt consisting of decrees against us, which was hostile to us; and He has taken it out of the way, having nailed it to the cross. 15When He had [n]disarmed the rulers and authorities, He Made a public display of them, having triumphed over them through [o]Him."

So nothing to do with condemning Satan but rather with his fulfilling of the Law . Which disarmed the religious leaders the victory was not in his own strength but through his God JEHOVAH.

Colossians ch.2:12 NASB"Having been buried with Him in baptism, in which you were also raised with Him through faith in the working of God, who raised Him from the dead. "

1John ch.3:7,8NASB"Little children, make sure no one deceives you; the one who practices righteousness is righteous, just as He is righteous; 8the one who practices sin is of the devil; for the devil [c]has been sinning from the beginning. The Son of God appeared for this purpose, to destroy the works of the devil. "

Christ was sent by his God and Father to liberate us from sin. So again the pronouncing of the Father Judgment which is what Michael did btw

Against nincsnevem

 A response to an interlocutor at Edgar Foster's blog 

Timestamp 6:27 A.M

@nincsnevem Next:our hope

You claimed"Ephesians 4:4 easily disproves the two-class salvation invented by Rutherford in 1935, since there is only "one hope".

Ephesians ch.4:4-6ESV"There is one body and one Spirit—just as you were called to the one hope that belongs to your call— 5one Lord, one faith, one baptism, 6one God and Father of all, who is over all and through all and in all. "

Of course there is nothing in this verse that proves or disproves an earthly paradise for the vast majority of humanity. It's not the location or the surroundings that make a paradise it's the company joyful fellowship with JEHOVAH and his saints.

After all sin began in heaven

Paul says that those he was writing were CALLED to a single hope by whom by the one Lord i.e the Risen Christ those who live and died prior to Christ ascension certainly can't respond to this call because they are incapable of hearing.

Those who passed on without a witness can't hear this call

Romans ch.10:14NIV"How, then, can they call on the one they have not believed in? And how can they believe in the one of whom they have not heard? And how can they hear without someone preaching to them?"

Of course if there was some kind of post mortem evangel to departed spirits none of this would be an issue. Spirit beings would not need faith they would see these spiritual realities first hand.

But Paul's urgency suggest that if the living aren't reached in this life with the gospel and if they don't put faith in it. They have no share in these promises i.e heaven.

Paul says that those he was writing were CALLED to a single hope by whom by the one Lord i.e the Risen Christ those who live and died prior to Christ ascension certainly can't respond to this call because they are incapable of hearing.

Those who passed on without a witness can't hear this call

Romans ch.10:14NIV"How, then, can they call on the one they have not believed in? And how can they believe in the one of whom they have not heard? And how can they hear without someone preaching to them?"

Of course if there was some kind of post mortem evangel to departed spirits none of this would be an issue. Spirit beings would not need faith they would see these spiritual realities first hand.

But Paul's urgency suggest that if the living aren't reached in this life with the gospel and if they don't put faith in it. They have no share in these promises i.e heaven.

John ch.3:5 NIV "Jesus answered, “Very truly I tell you, no one can enter the kingdom of God UNLESS they are born of water(Baptism) and the Spirit."

That would appear to rule out the dead.

Luke ch.16:16NIV"“The Law and the Prophets were proclaimed until John. Since that time, the good news of the kingdom of God is being preached(Not to spirit beings), and everyone is forcing their way into it."

Matthew ch.11:11NIV"Truly I tell you, among those born of women there has not risen anyone greater than John the Baptist; yet whoever is least in the kingdom of heaven is greater than he. "

This is clearly not refering to anyone's present status but their prospects Jesus himself was not at that time literally in the kingdom

The ancient worthies represented by John had no prospect of a place in the heavenly paradise.

Hebrews ch.11:39,40NIV"These were all commended for their faith, yet none of them received what had been promised, since God had planned something BETTER for us so that only together with us would they be made perfect."So by JEHOVAH'S design the vast majority of mankind have no prospect for entry into the heavenly kingdom. This is only a conundrum for those emotionally invested in the false heaven/eternal conscious torment binary. The bible does not recognise any such binary.

Let's go back to the begining

Genesis ch.2:8,9ASV"And JEHOVAH God planted a garden eastward, in Eden; and there he put the man whom he had formed. 9And out of the ground made JEHOVAH God to grow every tree that is pleasant to the sight, and good for food; the TREE OF LIFE also in the midst of the garden, and the tree of the knowledge of good and evil."

Note there was no tree of death in this garden so death and the death dealing were not part of JEHOVAH'S purpose for man.

The tree of life was a symbol of the permanent physical perfection man was meant to enjoy.

Genesis ch.3:22,23ASV"And JEHOVAH God said, Behold, the man is become as one of us, to know good and evil; and now, lest he put forth his hand, and take also of the tree of life, and eat, and live for ever-therefore JEHOVAH God sent him forth from the garden of Eden, to till the ground from whence he was taken. "

The restoration of the earthly paradise i.e the human perfection epitomised both Adams has always been a key component JEHOVAH'S agenda

Acts ch.3:21NIV"Heaven must receive him until the time comes for God to RESTORE everything, as he promised long ago through his holy prophets."

To be continued.

Primeval tech not letting up vs. Darwinism

 Irreducibly Complex, Bacterial Cell Wall Manufacture Is an Evolutionary Enigma

Jonathan McLatchie

One of the most incredible features of cellular life is the capability of self-replication. Bacterial cells divide by a process known as binary fission — an amazing feat of engineering, requiring a myriad of different proteins. Several features of bacterial cell division exhibit irreducible complexity. This represents a fundamental challenge to evolutionary explanations of its origins, since a precondition of natural selection is differential survival, and self-replication is itself required for differential survival. Thus, one cannot plausibly appeal to natural selection to explain the origins of bacterial cell division without assuming the existence of the very thing one is attempting to explain. Here, I will focus only on the severing and re-synthesis of the bacterial cell wall.

The Breaking and Manufacture of the Cell Wall

The peptidoglycan cell wall is a rigid structure that surrounds and protects the bacterium, conferring upon the cell structural integrity and shape. As a bacterial cell divides, its cell wall must grow as the cell elongates in preparation for division. In rod-shaped bacteria, this takes place at multiple locations along the cell, whereas in coccus-shaped bacteria, the cell wall grows outward from the FtsZ ring in opposite directions.1 Cell wall growth requires the controlled cleavage of the existing peptidoglycan layer. The β-1,4 glycosidic bonds that link N-acetylglucosamine and N-acetylmuramic acid are hydrolyzed by enzymes called autolysins, which have to be very carefully regulated because they can result in programmed cell death.2,3 Specific regulatory mechanisms guide the localization of autolysins to the site of cell division.4,5,6 These regulatory mechanisms ensure that autolysins are targeted only to the appropriate region of the cell. Autolysins bind to the peptidoglycan at the site of cell division, and catalyze the hydrolysis of the peptide cross-links within the cell wall. This cleavage weakens the peptidoglycan at the division site, allowing the cell wall to undergo controlled breakage. The gaps are then filled in with additional cell wall material.

          The first stage of re-synthesis of the cell wall is the formation of the peptidoglycan precursors.7 A chain of five amino acids (a pentapeptide) is added to N-acetylmuramic acid.8 N-acetylglucosamine is subsequently attached to the end of the N-acetylmuramic acid. The result is a peptidoglycan precursor. An extremely hydrophobic molecule, called bactoprenol, is embedded in the inner cytoplasmic membrane.9,10 Bactoprenol shuttles the hydrophilic peptidoglycan precursors from the inner side of the membrane, where they are synthesized, to the outer side of the membrane where they are needed for the assembly of the cell wall. This hydrophobic protein is essential because the hydrophilic precursors cannot easily traverse the hydrophobic membrane on their own.

Once bactoprenol reaches the periplasmic space (in gram-negative bacteria) or the cell exterior (in gram-positive bacteria), it transfers the peptidoglycan precursors to the peptidoglycan assembly site. There, glycosyltransferases and penicillin-binding proteins (also called transpeptidases) utilize these precursors to build the glycan chains and cross-link them to provide the cell wall with stability and strength.11,12 The penicillin-binding proteins are responsible for catalyzing the cross-linking of the peptide side chains between diaminopimelic acid and D-alanine on adjacent peptides. In gram-positive bacteria, cross-links typically occur from an L-lysine to a D-alanine of adjacent peptides. At the end of the peptidoglycan precursor, there exist initially two D-alanine residues, but one is removed during the reaction leaving one in the final molecule. In E. coli a specialized penicillin-binding protein called FtsI is the key player in transpeptidation at the septum.13 Localization of FtsI to the septum itself requires an intact N-terminal membrane anchor in addition to the division proteins FtsZ, FtsA, FtsQ, FtsW, and FtsL.14,15

An Evolutionary Enigma

What about this process is a challenge to evolution? Absolutely critical to cell division in virtually all bacteria is the ability to re-synthesize peptidoglycan. How do we know it is so crucial? The mechanism of action of beta-lactam antibiotics (including penicillin, cephalosporins, and monobactams) is to interfere with the peptidoglycan cross-linking.16,17 As their name implies, penicillin-binding proteins are the target of penicillin, which causes them to lose their enzymatic activity. The activity of the autolysins weakens the cell wall to such an extent that the cell lyses (bursts open). Some other, non beta-lactam, antibiotics (e.g., lactivicins) have a similar mechanism of action.18,19 Antibiotics may also target cell wall precursors. For instance, the antibiotic nisin associates with cell wall precursor lipid II and locks it in a stable complex, thereby effectively inhibiting the peptidoglycan synthesis cycle.20,21

Consider the following two observations: 

Critical to the elongation process is the severing of the peptidoglycan cell wall by the autolysins. 

Critical to cell viability is the re-synthesis of the peptidoglycan cell wall. 

These processes have to be highly coordinated. If the mechanism for severing the cell wall arose without simultaneously having a mechanism in hand to rebuild the cell wall, the cell would not survive the division process. Both mechanisms must arise together. One might object that a mechanism for repairing breaks in the cell wall could have arisen first, before being coopted into the cell division machinery. But without being able to sever the cell wall, there could be no division and thus no differential survival, and by extension no natural selection.

This process of severing and rebuilding the cell wall is critical to cell division in almost all bacteria. A notable exception is species belonging to the genus Mycoplasma, which lack a cell wall. But this has little relevance to accounting for the origins of the mechanisms of severing and rebuilding the peptidoglycan in those species that dopossess a cell wall. As soon as the cell wall — which is a rigid outer layer that provides structural support to the cell — arose, there would need to be a mechanism for re-modelling and splitting it to allow the bacterium to divide into two daughter cells. Moreover, Mycoplasma species are obligate parasites, dwelling in osmotically protected habitats. Furthermore, in place of a cell wall they typically have sterols in their cytoplasmic membrane, which imparts to them greater rigidity and strength.

Foresight Is Required, Pointing to Intelligent Design

In summary, cell wall remodeling and splitting, essential to the cell division process in bacteria, is irreducibly complex, requiring both the mechanism for severing the peptidoglycan and the resynthesis process to arise simultaneously. Without being able to rebuild the cell wall, the cell will burst due to the osmotic pressure. But without being able to sever the peptidoglycan, the cell cannot divide. Evolutionary processes cannot select for some future utility that is only realized after passing through a maladaptive intermediate. This phenomenon therefore requires foresight, and is thus much more probable on the hypothesis of design than it is on mindless chance and necessity.

Notes

Margolin W. Sculpting the bacterial cell. Curr Biol. 2009 Sep 15;19(17):R812-22.

Zoll S, Pätzold B, Schlag M, Götz F, Kalbacher H, Stehle T. Structural basis of cell wall cleavage by a staphylococcal autolysin. PLoS Pathog. 2010 Mar 12;6(3):e1000807.

Mitchell SJ, Verma D, Griswold KE, Bailey-Kellogg C. Building blocks and blueprints for bacterial autolysins. PLoS Comput Biol. 2021 Apr 1;17(4):e1008889.

Zielińska A, Billini M, Möll A, Kremer K, Briegel A, Izquierdo Martinez A, Jensen GJ, Thanbichler M. LytM factors affect the recruitment of autolysins to the cell division site in Caulobacter crescentus. Mol Microbiol. 2017 Nov;106(3):419-438.

Mueller EA, Iken AG, Ali Öztürk M, Winkle M, Schmitz M, Vollmer W, Di Ventura B, Levin PA. The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment. Mol Microbiol. 2021 Jul;116(1):311-328.

Schlag M, Biswas R, Krismer B, Kohler T, Zoll S, Yu W, Schwarz H, Peschel A, Götz F. Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl. Mol Microbiol. 2010 Feb;75(4):864-73.

        Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus. 2021 Jan;9(2).

Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. 1972 Dec;36(4):407-77.

Thorne KJ, Kodicek E. The structure of bactoprenol, a lipid formed by lactobacilli from mevalonic acid. Biochem J. 1966 Apr;99(1):123-7.

Barker DC, Thorne KJ. Spheroplasts of Lactobacillus casei and the cellular distribution of bactoprenol. J Cell Sci. 1970 Nov;7(3):755-85.

Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev. 2008 Mar;32(2):234-58. doi: 10.1111/j.1574-6976.2008.00105.x. Epub 2008 Feb 11. Erratum in: FEMS Microbiol Rev. 2008 May;32(3):556.

Sauvage E, Terrak M. Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials. Antibiotics (Basel). 2016 Feb 17;5(1):12

       Wissel MC, Weiss DS. Genetic analysis of the cell division protein FtsI (PBP3): amino acid substitutions that impair septal localization of FtsI and recruitment of FtsN. J Bacteriol. 2004 Jan;186(2):490-502.

Mercer KL, Weiss DS. The Escherichia coli cell division protein FtsW is required to recruit its cognate transpeptidase, FtsI (PBP3), to the division site. J Bacteriol. 2002 Feb;184(4):904-12.

Weiss DS, Chen JC, Ghigo JM, Boyd D, Beckwith J. Localization of FtsI (PBP3) to the septal ring requires its membrane anchor, the Z ring, FtsA, FtsQ, and FtsL. J Bacteriol. 1999 Jan;181(2):508-20.

Beadle BM, Nicholas RA, Shoichet BK. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation. Protein Sci. 2001 Jun;10(6):1254-9.

Mora-Ochomogo M, Lohans CT. β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates. RSC Med Chem. 2021 Aug 4;12(10):1623-1639.

Nozaki Y, Katayama N, Harada S, Ono H, Okazaki H. Lactivicin, a naturally occurring non-beta-lactam antibiotic having beta-lactam-like action: biological activities and mode of action. J Antibiot (Tokyo). 1989 Jan;42(1):84-93.

             Brown T Jr, Charlier P, Herman R, Schofield CJ, Sauvage E. Structural basis for the interaction of lactivicins with serine beta-lactamases. J Med Chem. 2010 Aug 12;53(15):5890-4.

Müller A, Ulm H, Reder-Christ K, Sahl HG, Schneider T. Interaction of type A lantibiotics with undecaprenol-bound cell envelope precursors. Microb Drug Resist. 2012 Jun;18(3):261-70.

Münch D, Müller A, Schneider T, Kohl B, Wenzel M, Bandow JE, Maffioli S, Sosio M, Donadio S, Wimmer R, Sahl HG. The lantibiotic NAI-107 binds to bactoprenol-bound cell wall precursors and impairs membrane functions. J Biol Chem. 2014 Apr 25;289(17):12063-12076.

Design on the wing.

 Appreciating Bird Mimicry and the Other Exceptional, Designed Talents

David Coppedge

From the hummingbird with its nectar-trap tongue, to starlings in formation flight, to Arctic terns in long-distance migration, it would take a book of Evolution News articles even to begin to do justice to the many diverse kinds of birds that warrant our admiration. From time to time we can, though, point out particular cases that have come to light in scientific research.

Image Stabilization

Lovebirds; aren’t they sweet. We’re not talking about newlyweds, but small parrots that inhabit Africa and Madagascar (which do, by the way, show affectionate behavior). A zoologist incorporated the help of mechanical engineers to study something Olympic about them: they can turn their heads “super-fast” in flight (pictured above). In a paper in PLOS ONE, the team measured the head turn rate. Although the birds flick their heads back and forth, the rotational motion measured by a high-speed camera is exceptionally fast: 2700 degrees per second. 

High-speed flight recordings revealed that rapidly turning lovebirds perform a remarkable stereotypical gaze behavior with peak saccadic head turns up to 2700 degrees per second, as fast as insects, enabled by fast neck muscles. In between saccades, gaze orientation is held constant. By comparing saccade and wingbeat phase, we find that these super-fast saccades are coordinated with the downstroke when the lateral visual field is occluded by the wings. Lovebirds thus maximize visual perception by overlying behaviors that impair vision, which helps coordinate maneuvers…. Our observations show that rapidly maneuvering birds use precisely timed stereotypic gaze behaviors consisting of rapid head turns and frontal feature stabilization, which facilitates optical flow based flight control.

The strategy resembles the way early combat aircraft could fire machine-gun rounds without blowing off the propellers. The bird turns the head just in time to minimize the time the wing is in the way of seeing. A summary of the findings at Phys.org gives another reason why this research is interesting. “The authors also hope that the accuracy and speed of these visually guided flight-maneuvers may inspire camera rotation design in drones to improve imaging.” 

Lest you feel any sense of inferiority at this little bird’s design, notice what the authors write in the Abstract: “Similar gaze behaviors have been reported for visually navigating humans.” This paper in Current Biology about “microsaccades” (tiny eye movements), which unwittingly sample our visual field during focused attention, also bears reading (see the summary at Medical Xpress).

Smell Navigation

The ability to navigate by the sense of smell or by the Earth’s magnetic field is widespread in many types of animals. Here’s a case in point: seabirds. An article at Live Science reports on work by zoologists in the UK who found that “Seabirds smell their way home.” Flying over large expanses of open water, birds like Cory’s shearwaters manage to find their nesting sites and feeding grounds without error. How do they do it? There aren’t many cues available. The authors ruled out some senses, like sound.

Observing how the birds explore an area in detail then move a distance and repeat (a search strategy called a Lévy flight pattern), the researchers found that models based on the sense of smell gave the best fit. It’s not easy, though. For smell navigation to work, not only must the sense of smell be incredibly acute, but the birds have to be able to integrate olfactory data with other forces in the environment.

Birds may associate smells, such as those from phytoplankton, with wind directions, the researchers noted. For instance, the seabirds may know to fly westward when they smell one odor and to fly eastward when they smell another. Or, a combination of both smells may prompt them to fly northeast, the researchers said.

However, smells aren’t always detectible because of atmospheric turbulence, so birds will reorient and change direction until they find another recognizable smell, the researchers found.

In addition, the birds must have an “odor map” written in the brain that associates the odor cues with memory. In effect, the cues tell the bird, “This combination of odors means you are here, and you need to head that way.” As the feeding ground approaches, the birds can rely on additional cues, like “landmarks, flights of other birds and ‘colony odors’.” Some fish, including salmon, have a similar capability: a nasal switchboard that guides them through a maze of tributaries to its natal stream.

Vocal Imitation

Who hasn’t had fun listening to parrots imitate human speech? It takes a special kind of brain to do this. Parrots, parakeets (budgerigars), cockatiels, keas, and our affectionate friends the lovebirds are good at it. Neurologists at Duke University were curious to know what structures in the brain seem to be responsible. They found particular regions they dubbed “shells” around core speech centers that are found in all these species. One researcher’s reaction has some bearing on Kuhnian science:

“The first thing that surprised me when Mukta and I were looking at the new results is, ‘Wow, how did I miss this all these years? How did everybody else miss this all these years?’” said Jarvis, who is also member of the Duke Institute for Brain Sciences. “The surprise to me was more about human psychology and what we look for and how biased we are in what we look for. Once you see it, it’s obvious. I have these brain sections from 15 years ago, and now I can see it.” 

The news release seems obsessed with how this brain region evolved, stating that whatever mutation led to it happened 29 million years ago, based on assumed evolutionary lineages. That doesn’t come close to explaining it:

The new results support the group’s hypothesis that in humans and other song-learning animals, the ability to imitate arose by brain pathway duplication. How such a copy-and-paste job could have happened is still unknown.

It’s not clear how duplicating a gene or pathway can cause a new complex ability like voice imitation: “It takes significant brain power to process auditory information and produce the movements necessary for mimicking sounds of another species,” one of the researchers said. The article does not speculate on what kind of mutational event led to the exceptional abilities of unrelated birds, like the mockingbird or lyrebird.

Let the reader enjoy the 350+ word vocabulary of Clover, alleged to be the best talking parrot in the world. 

But of what evolutionary survival value is this ability? Clover seems to be enjoying her intricate brain and vocal apparatus. If we don’t think human impressionists evolved their repertoire by mistake, perhaps we should give intelligent design, not Darwinian evolution, the credit for bird mimicry and the other exceptional talents.

Still continuing to rethink the unrethinkable.

 

Cocaine shark?

 

Science as servant vs. science as master.

 Science for Insight or Science for Power?

Peter Biles

“Should machines replace mathematicians?” That’s the headline of a new post by science writer John Horgan, who comments on the current state of mathematics and the growing potential of AI and computers to do all the “heavy lifting” in the mathematical enterprise. Horgan notes that mathematicians were the ones to develop computers in the first place, but now, with the advent of advanced computing and artificial intelligence, the role of human-driven mathematics is getting to be less certain. However, maybe math is not only about input and output but a “way of being human.” For Horgan, data and computation don’t get to the heart of scientific and mathematical endeavors. It needs to mean something more than an impersonal process geared towards calculable ends. 

Science’s Core Purpose

Horgan not only talks about math in his article. He also relates the discussion to the core purpose of science. Science, in one definition, means gaining insights into nature. However, in today’s utilitarian society, science is less about contemplating the beauty of nature and more about securing power over nature for the sake of our ease, convenience, and control. He writes, 

We value science for its applications, too. Sentimental science writing, including mine, implies that science’s purpose is insight into nature. In the modern era, however, science’s primary goal is power. Science helps us manipulate nature for various ends: to extend our lives, to enrich and entertain us, to boost the economy, to defeat our enemies. Modern physics, to most of us, is unintelligible, but who cares when physics gives us smartphones and hydrogen bombs?

JOHN HORGAN, SHOULD MACHINES REPLACE MATHEMATICIANS? — JOHN HORGAN (THE SCIENCE WRITER)

Science and Magic

The comment reminds me of a famous observation by C. S. Lewis, who wrote in The Abolition of Man:

There is something which unites magic and applied science while separating both from the wisdom of earlier ages. For the wise men of old the cardinal problem had been how to conform the soul to reality, and the solution had been knowledge, self-discipline, and virtue. For magic and applied science alike the problem is how to subdue reality to the wishes of men.

It sounds strange to equate “applied science” (i.e., technology) with magic, but doing so reveals the potential of using scientific knowledge merely as a means to power instead of as a source of “insight,” as Horgan writes.

No intelligence allowed?

 

On the relevance of God.

 

The Iranian revolution: an exploration.

 

The West's destiny : not so manifest after all?

 

On making a killing doing those dirty jobs that need doing.

 

On Korea's Poland syndrome?

 

Machiavelli: a brief history.

 

How to not get taken for a ride re:your next car deal.

 

Trinitarian theology : gateway drug to Unitarian Christianity?

 

Nuking the carbon issue?

 

Primeval tech trolling Darwinism continued.

 Cell Vesicles Wear Sophisticated Coats, Defying Unguided Evolutionary Explanations

 David Coppedge

Envision a day when self-driving cars make driving obsolete. Now, imagine a far-future day when you don’t even have to get in the car. Instead, as you walk out the front door, a car assembles around you, lifts off the ground, floats you to your destination, then disassembles in anticipation of picking up the next passenger. Something like this actually happens in living cells. According to news from the European Molecular Biology Laboratory (EMBL):

Researchers at EMBL Heidelberg have produced detailed images of the intricate protein-coats that surround trafficking vesicles — the “transport pods” that move material around within biological cells. The study, published today in Science, provides a new understanding of the complex machines that make up the cells’ logistics network.

Vesicles are responsible for transporting molecules between the different compartments within a cell and also for bringing material into cells from outside. There are several types of vesicle: each has a specific type of coat which is made up of different proteins and assembles onto a membrane surrounding the vesicle.

There are three models of “transport pods” that molecular biologists know about, each with its own specific coat proteins: Coat Protein 1 (COPI), Coat Protein 2 (COPII), and clathrin-coated vesicle (CCV). Each coat has its own proteins, adaptors, and functions. The paper in Science looks in detail at COPI; but first, let’s mention COPII. This type of vesicle takes proteins from the endoplasmic reticulum (ER), where they were assembled, to the Golgi apparatus where they will be packaged for delivery. This is called anterograde (forward) transport.

COPI is the reverse; it takes proteins from the Golgi back to the ER, or to different compartments of the Golgi. This is called retrograde (backward) transport. Surprisingly, the coat proteins on these vesicles are very different. COPII coats are made of four proteins that assemble with four-fold symmetry in a sequential manner, using separate adaptor proteins. COPI is more complicated. It has seven discrete proteins that come together simultaneously, forming complexes with triangular symmetry that include the adaptor function (i.e., allowing the complex to attach to the vesicle membrane).

Pushing the Envelope

The EMBL researchers pushed the envelope of cryoelectron microscopy to determine the nature of the “triads” called coatomers that make up the coat. They found that the seven proteins form two complexes that overlap into a layer 14 nanometers (nm) thick — a substantial fraction of the typical 100-nm-diameter vesicle. A Perspective article in the same issue of Science says there’s still a lot to learn about these coats: “it remains to be determined what specific roles these conformations play in the respective coat functions,” Noble and Stagg write. What is known is that the coatomer triads make contact with up to four neighboring triads. This gives them structural flexibility that is distinct from the other coated vesicle types. The authors of the paper speculate about the reasons for this:

In existing models for clathrin and COPII vesicle coats, multiple identical subunits each make the same set of interactions with the same number of neighbors. Structural flexibility allows formation of vesicles from different total numbers of subunits. Based on these principles, both clathrin-like and COPII-like models have been proposed for the assembled COPI coat. We found instead that assembled coatomer can adopt different conformations to interact with different numbers of neighbors. By regulating the relative frequencies of different triad patterns in the COPI coat during assembly — for example, by stabilizing particular coatomer conformations — the cell would have a mechanism to adapt vesicle size and shape to cargoes of different sizes. 

The paper includes color models and two motion animations of how the proteins fit together, protecting the cargo as it rides to its destination from organelle to organelle.

Clathrin Coats

A better-understood protein coat is made of clathrin. The name comes from a Latin word for lattice. Individual clathrin molecules, made of three heavy chains and three light chains, look like a three-spoked pinwheel called a triskelion. They fit together beautifully around the vesicle into a cage-like structure that resembles a geodesic dome. A beautiful Animation from Harvard Medical School shows how numerous other proteins work with clathrin to form the vesicle coat and disassemble it after use, so the triskelia can be recycled. The vesicles can import and export molecules to the exterior of the cell or transport them within the cytoplasm. Clathrin proteins are also implicated in cell division, where they assist in arranging chromosomes on the spindle.

In Need of an Update

The animation will require an update, though, because something new was reported about clathrin-coated vesicles (CCV) and the pits (CCP) that form when the membrane invaginates to bring cargo in from outside. Another EMBL team, also reporting in Science, found that clathrin is more gymnastic than previously recognized. 

Unlike as shown in the animation, the clathrin lattice forms flat on the inner membrane surface before invagination begins. Then, as the membrane folds inward, the lattice stretches and reconfigures itself, maintaining the same surface area but following the shape of the vesicle as it elongates. With its cargo safely inside, the vesicle pinches off and forms a sphere. The news from EMBL expresses surprise at the shape changes:

John Briggs, senior scientist at EMBL Heidelberg, said: “Our results were surprising, because the proteins have to undergo some complicated geometric transformationsto go from a flat to a curved shape, which is why the second model was favoured by scientists for such a long time.”

(The “second model”, now falsified, refers to the idea that “clathrin assembles directly, assuming the shape of the membrane as it is drawn inwards.”) The paper describes how the growing cage must change its geodesic structure as the vesicle forms: 

In order to bend, flat lattices composed primarily of hexagons must acquire pentagons requiring extensive molecular rearrangements and removal of triskelia.

Why would the cell perform this more difficult gymnastic routine? The final paragraph offers some possible reasons:

Recruitment of clathrin before membrane bending provides a flat, dynamic array as a platform for cargo recruitment. This implies that the membrane to be internalized and the size of the future vesicle are not determined by clathrin geometry during assembly into a curved cage but rather are selected before invagination during cargo recruitment. Rapid clathrin exchange is consistent with a dynamically unstable lattice — dynamic instability is a common property within networks of low-affinity protein interactions. It would allow for stochastic abortion of sites that initiate but fail to cross a growth- or cargo-mediated checkpoint before investing energy in membrane bending. During invagination, further exchange would allow clathrin reorganization and bending of the lattice into a defined cage that requires active disassembly.

One thing not mentioned in the articles is the rapidity of vesicle formation and disassembly. Suffice it to say that clathrin-coated endocytosis and exocytosis occur at the tips of nerve cells, where electrical signals must cross synapses. The vesicles form at one nerve, cross the synapse carrying the cargo, and are taken in by the next nerve cell in line. How long does it take your brain to feel pain from a stubbed toe? A lot of CCVs formed, crossed synapses, and disassembled in that very quick response!

Evolution or Design?

As usual, the articles and papers say very little about evolution. If mentioned at all, it was about the lack of evolution: e.g., “The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human.” Only the Perspective piece by Noble and Stagg ventures further: 

Individual proteins in the three different coat protein complexes share similar folds and are proposed to be distant evolutionary relatives. Despite these similarities, the coats have evolved different functional mechanisms….

One possibility is that the proto-COPI coat evolved the four different linkages to expand the repertoire of geometries that the coat can accommodate and thus adapt to the secretory needs of the cell.

These suggestions amount to little more than after-the-fact assertions of evolutionary belief. One cannot invoke a blind, unguided process to say that it “evolved to” meet the needs of the cell. Darwinian natural selection has no foresight.

The complexity of these coats, and the accessory proteins that build them, attach them to vesicles, and disassemble them, defy unguided evolutionary explanations. They exhibit irreducible complexity; they don’t work unless all the protein parts are present simultaneously. They exhibit beauty in the way they organize into geometric shapes. The shapes, in turn, are dictated by digital codes in the genome that produce sequences that fold into building blocks. These building blocks, like the triskelion of clathrin, have no knowledge of the elegant geodesic domes that they will be fitted into. The triskelia are also blind to their attachment points that will be used by two other proteins that will disassemble the vesicle. 

We see only glimpses of structures we don’t yet fully understand. Why are separate coats needed for the three types of transport? What types of vesicles need the different coats? What specific advantages do the different coats provide for transport in one direction and not the other? What molecules need coated vesicles as opposed to uncoated vesicles? What function does each protein in the coat provide? 

Further research at higher resolution will undoubtedly yield more knowledge about vesicular transport. One thing is clear so far; the elegance of these systems, their ability to reshape their geometry as they grow, their adaptability to cargoes of many sizes, the rapidity of their action, and their conservation from yeast to humans all proclaim, “Intelligent design!”