"The stones will cry out" II

File under 'Well said' XI

Happiness is when what you think, what you say, and what you do are in harmony.
Mahatma Gandhi

Psalms22-28 JPS Tanakh.

22)1.(For the Leader; upon Aijeleth ha-Shahar. A Psalm of David.)
2My God, my God, why hast Thou forsaken me,
And art far from my help at the words of my cry?
3O my God, I call by day, but Thou answerest not;
And at night, and there is no surcease for me.
4Yet Thou art holy,
O Thou that art enthroned upon the praises of Israel.
5In Thee did our fathers trust;
They trusted, and Thou didst deliver them.
6Unto Thee they cried, and escaped;
In Thee did they trust, and were not ashamed.
7But I am a worm, and no man;
A reproach of men, and despised of the people.
8All they that see me laugh me to scorn;
They shoot out the lip, they shake the head:
9‘Let him commit himself unto the LORD! let Him rescue him;
Let Him deliver him, seeing He delighteth in him.’
10For Thou art He that took me out of the womb;
Thou madest me trust when I was upon my mother’s breasts.
11Upon Thee I have been cast from my birth;
Thou art my God from my mother’s womb.
12Be not far from me; for trouble is near;
For there is none to help.
13Many bulls have encompassed me;
Strong bulls of Bashan have beset me round.
14They open wide their mouth against me,
As a ravening and a roaring lion.
15I am poured out like water,
And all my bones are out of joint;
My heart is become like wax;
It is melted in mine inmost parts.
16My strength is dried up like a potsherd;
And my tongue cleaveth to my throat;
And Thou layest me in the dust of death.
17For dogs have encompassed me;
A company of evil-doers have inclosed me;
Like a lion, they are at my hands and my feet.
18I may count all my bones;
They look and gloat over me.
19They part my garments among them,
And for my vesture do they cast lots.
20But Thou, O LORD, be not far off;
O Thou my strength, hasten to help me.
21Deliver my soul from the sword;
Mine only one from the power of the dog.
22Save me from the lion’s mouth;
Yea, from the horns of the wild-oxen do Thou answer me.
23I will declare Thy name unto my brethren;
In the midst of the congregation will I praise Thee.
24‘Ye that fear the LORD, praise Him;
All ye the seed of Jacob, glorify Him;
And stand in awe of Him, all ye the seed of Israel.
25For He hath not despised nor abhorred the lowliness of the poor;
Neither hath He hid His face from him;
But when he cried unto Him, He heard.’
26From Thee cometh my praise in the great congregation;
I will pay my vows before them that fear Him.
27Let the humble eat and be satisfied;
Let them praise the LORD that seek after Him; May your heart be quickened for ever!
28All the ends of the earth shall remember and turn unto the LORD;
And all the kindreds of the nations shall worship before Thee.
29For the kingdom is the LORD’S;
And He is the ruler over the nations.
30All the fat ones of the earth shall eat and worship;
All they that go down to the dust shall kneel before Him,
Even he that cannot keep his soul alive.
31A seed shall serve him;
It shall be told of the Lord unto the next generation.
32They shall come and shall declare His righteousness
Unto a people that shall be born, that He hath done it.
THE HOLY SCRIPTURES
ACCORDING TO THE MASORETIC TEXT
A NEW TRANSLATION
Jewish Publication Society
1917
23)1.The LORD is my shepherd; I shall not want.
2He maketh me to lie down in green pastures;
He leadeth me beside the still waters.
3He restoreth my soul;
He guideth me in straight paths for His name’s sake.
4Yea, though I walk through the valley of the shadow of death,
I will fear no evil, for Thou art with me;
Thy rod and Thy staff, they comfort me.
5Thou preparest a table before me in the presence of mine enemies;
Thou hast anointed my head with oil; my cup runneth over.
6Surely goodness and mercy shall follow me all the days of my life;
And I shall dwell in the house of the LORD for ever.
24)1.The earth is the LORD’S, and the fulness thereof;
The world, and they that dwell therein.
2For He hath founded it upon the seas,
And established it upon the floods.
3Who shall ascend into the mountain of the LORD?
And who shall stand in His holy place?
4He that hath clean hands, and a pure heart;
Who hath not taken My name in vain,
And hath not sworn deceitfully.
5He shall receive a blessing from the LORD,
And righteousness from the God of his salvation.
6Such is the generation of them that seek after Him,
That seek Thy face, even Jacob.
Selah
7Lift up your heads, O ye gates,
And be ye lifted up, ye everlasting doors; That the King of glory may come in.
8‘Who is the King of glory?’
‘The LORD strong and mighty,
The LORD mighty in battle.’
9Lift up your heads, O ye gates,
Yea, lift them up, ye everlasting doors;
That the King of glory may come in.
10‘Who then is the King of glory?’
‘The LORD of hosts;
He is the King of glory.’
(Selah)
25)1.א

Unto Thee, O LORD, do I lift up my soul.
ב

2O my God, in Thee have I trusted, let me not be ashamed;
Let not mine enemies triumph over me.
ג

3Yea, none that wait for Thee shall be ashamed;
They shall be ashamed that deal treacherously without cause.
ד

4Show me Thy ways, O LORD;
teach me Thy paths.
הו

5Guide me in Thy truth, and teach me;
For Thou art the God of my salvation; For Thee do I wait all the day.
ז

6Remember, O LORD, Thy compassions and Thy mercies;
For they have been from of old.
ח

7Remember not the sins of my youth, nor my transgressions;
According to Thy mercy remember Thou me, For Thy goodness’ sake, O LORD.
ט

8Good and upright is the LORD;
Therefore doth He instruct sinners in the way.
י

9He guideth The humble in justice;
And He teacheth the humble His way.
כ

10All the paths of the LORD are mercy and truth
Unto such as keep His covenant and His testimonies.
ל

11For Thy name’s sake, O LORD,
Pardon mine iniquity, for it is great.
מ

12What man is he that feareth the LORD?
Him will He instruct in the way that He should choose.
נ

13His soul shall abide in prosperity;
And his seed shall inherit the land.
ס

14The counsel of the LORD is with them that fear Him;
And His covenant, to make them know it.
ע

15Mine eyes are ever toward the LORD;
For He will bring forth my feet out of the net.
פ

16Turn Thee unto me, and be gracious unto me;
For I am solitary and afflicted.
צ

17The troubles of my heart are enlarged;
O bring Thou me out of my distresses.
ר

18See mine affliction and my travail;
And forgive all my sins.
19Consider how many are mine enemies,
And the cruel hatred wherewith they hate me.
ש

20O keep my soul, and deliver me;
Let me not be ashamed, for I have taken refuge in Thee.
ת

21Let integrity and uprightness preserve me,
Because I wait for Thee.
22Redeem Israel, O God, out of all his troubles.
THE HOLY SCRIPTURES
ACCORDING TO THE MASORETIC TEXT
A NEW TRANSLATION
Jewish Publication Society
1917
26)1.Judge me, O LORD, for I have walked in mine integrity,
And I have trusted in the LORD without wavering.
2Examine me, O LORD, and try me;
Test my reins and my heart.
3For Thy mercy is before mine eyes;
And I have walked in Thy truth.
4I have not sat with men of falsehood;
Neither will I go in with dissemblers.
5I hate the gathering of evil doers,
And will not sit with the wicked.
6I will wash my hands in innocency;
So will I compass Thine altar, O LORD,
7That I may make the voice of thanksgiving to be heard,
And tell of all Thy wondrous works.
8LORD, I love the habitation of Thy house,
And the place where Thy glory dwelleth.
9Gather not my soul with sinners,
Nor my life with men of blood;
10In whose hands is craftiness,
And their right hand is full of bribes.
11But as for me, I will walk in mine integrity;
Redeem me, and be gracious unto me.
12My foot standeth in an even place;
In the congregations will I bless the LORD.
27)1.The LORD is my light and my salvation; whom shall I fear?
The LORD is the stronghold of my life; of whom shall I be afraid?
2When evil-doers came upon me to eat up my flesh,
Even mine adversaries and my foes, they stumbled and fell.
3Though a host should encamp against me,
My heart shall not fear;
Though war should rise up against me,
Even then will I be confident.
4One thing have I asked of the LORD, that will I seek after:
That I may dwell in the house of the LORD all the days of my life,
To behold the graciousness of the LORD, and to visit early in His temple.
5For He concealeth me in His pavilion in the day of evil;
He hideth me in the covert of His tent;
He lifteth me up upon a rock.
6And now shall my head be lifted up above mine enemies round about me;
And I will offer in His tabernacle sacrifices with trumpet-sound;
I will sing, yea, I will sing praises unto the LORD.
7Hear, O LORD, when I call with my voice,
And be gracious unto me, and answer me.
8In Thy behalf my heart hath said: ‘Seek ye My face’;
Thy face, LORD, will I seek.
9Hide not Thy face far from me;
Put not Thy servant away in anger;
Thou hast been my help;
Cast me not off, neither forsake me, O God of my salvation.
10For though my father and my mother have forsaken me,
The LORD will take me up.
11Teach me Thy way, O LORD;
And lead me in an even path,
Because of them that lie in wait for me.
12Deliver me not over unto the will of mine adversaries;
For false witnesses are risen up against me, and such as breathe out violence.
13If I had not believed to look upon the goodness of the LORD
In the land of the living!—
14Wait on the LORD;
Be strong, and let thy heart take courage;
Yea, wait thou for the LORD.
THE HOLY SCRIPTURES
ACCORDING TO THE MASORETIC TEXT
A NEW TRANSLATION
Jewish Publication Society
1917
28)1.Unto thee, O LORD, do I call;
My Rock, be not Thou deaf unto me;
Lest, if Thou be silent unto me,
I become like them that go down into the pit.
2Hear the voice of my supplications, when I cry unto Thee,
When I lift up my hands toward Thy holy Sanctuary.
3Draw me not away with the wicked,
And with the workers of iniquity;
Who speak peace with their neighbours,
But evil is in their hearts.
4Give them according to their deeds, and according to the evil of their endeavours;
Give them after the work of their hands;
Render to them their desert.
5Because they give no heed to the works of the LORD,
Nor to the operation of His hands;
He will break them down and not build them up.
6Blessed be the LORD,
Because He hath heard the voice of my supplications.
7The LORD is my strength and my shield,
In Him hath my heart trusted, And I am helped;
Therefore my heart greatly rejoiceth,
And with my song will I praise Him.
8The LORD is a strength unto them;
And He is a stronghold of salvation to His anointed.
9Save Thy people, and bless Thine inheritance;
And tend them, and carry them for ever.
THE HOLY SCRIPTURES
ACCORDING TO THE MASORETIC TEXT
A NEW TRANSLATION
Jewish Publication Society

1917

Why Darwinism remains an ill-fitted Cornerstone

Why Do We Invoke Darwin?
Darwin's theory of evolution offers a sweeping explanation of the history of life, from the earliest microscopic organisms billions of years ago to all the plants and animals around us today.
 By Philip Skell | August 29, 2005


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

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

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

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

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

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

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

In reality, however, this passage illustrates my point. The efforts mentioned there are not experimental biology; they are attempts to explain already authenticated phenomena in Darwinian terms, things like human nature. Further, Darwinian explanations for such things are often too supple: Natural selection makes humans self-centered and aggressive – except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed – except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery.


Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology. This becomes especially clear when we compare it with a heuristic framework such as the atomic model, which opens up structural chemistry and leads to advances in the synthesis of a multitude of new molecules of practical benefit. None of this demonstrates that Darwinism is false. It does, however, mean that the claim that it is the cornerstone of modern experimental biology will be met with quiet skepticism from a growing number of scientists in fields where theories actually do serve as cornerstones for tangible breakthroughs.

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


He can be contacted at tvk@psu.edu.

A Darwinian apparatchik rallies the faithful.

Latest Cambrian Explosion "Explanation" Qualifies as Propaganda

Evolution News & Views October 9, 2015 10:37 AM

Many of us remember Pravda and Izvestia, the official propaganda organs of the former USSR. Having silenced the free press long ago, these "newspapers" were free to dole out the party line without opposition, giving the impression to unwary readers that there was no opposition. Well, another major science journal has followed this strategy. Fortunately, social media provides a "black market" for samizdat publishing.

To celebrate its 25th anniversary, Current Biology offers a special issue on "The History of Life on Earth." The 16 open-access articles amount to a treasure trove of evolutionary thinking on a wide variety of subjects: RNA World, insect evolution, bird evolution, and more -- all presented by big-name Darwinian proponents who ignore alternative views. A case in point is the primer on "The Cambrian Explosion" by Derek E. G. Briggs. Any mention of Stephen Meyer? No. Or critiques of the Darwinian explanation? Nope. Intelligent design? Are you kidding?

One might think that the editors would find it strategic to allay the fears of readers worried about the challenge to Darwinism raised by Meyer's best seller Darwin's Doubt by answering it. Instead, they chose to ignore it. That seems a risky strategy, considering that Meyer and others cogently responded to their critics' best objections in the follow-up book released this summer, Debating Darwin's Doubt. It's hard to imagine Briggs or the editors being unaware of these books. Apparently they think that enough of their readers don't know of the controversy, or they don't wish to give Meyer publicity. To illustrate our love for freedom of the press, we'll encourage you to hear both sides.

It's interesting to see what Briggs admits about the Cambrian explosion (emphasis added):

1. It's real: "We now know that the sudden appearance of fossils in the Cambrian (541-485 million years ago) is real and not an artefact of an imperfect fossil record," he says.
2. It saw diverse body plans: "In effect, the major body plans or phyla were established during the Cambrian explosion," but how? (Keep reading.)
3. Hard parts were not required: "Exceptionally preservedCambrian fossil deposits, such as the famous Burgess Shale, yield examples of 14 of the 19 soft-bodied phyla" of the ~33 animal phyla recognized today.
4. Not oddballs: "The affinities of some of the Cambrian creatures that were dubbed 'weird wonders' are still debated but phylogenetic analyses have shown that most of them are much less weird than first thought -- they do not represent extinct higher taxa, but are early offshoots of the lineages leading to modern groups."
5. Complex parts: "Various arthropods from the Cambrian of China have recently been shown to preserve evidence of the brain and nervous system, which were fossilized in rapidly precipitating minerals," Briggs says.
6. No answers: "The drivers behind the Cambrian explosion were varied and complex, and there is no simple explanation of either the timing or ecological mechanisminvolved." All he can do is offer possibilities.
7. Bottom line: Briggs still is looking for clues about how "all the major animal groups evolved in a relatively short timeduring the Cambrian explosion."

We see that Briggs doesn't dispute the observable facts. He knows that all the major animal body plans appeared quickly. So what is his explanation?

1. He stretches out the explosion, giving it the largest possible range of 56 million years. 10 million years is more widely accepted, but no matter how many years are granted, the problems of missing ancestors and abrupt appearances remain.
2. He considers the Ediacaran period ancestral to the Cambrian, asserting that this resolves "Darwin's dilemma" about the missing Precambrian fossils. "Darwin's dilemmaregarding the absence of Precambrian fossils was not resolved until the 1940s when a diversity of large animals of Ediacaran age (635-541 million years ago) was discovered in South Australia, providing spectacular evidence of life prior to the appearance of the first shells." This is very misleading, as most biologists do not consider the Ediacaran organisms ancestral to the Cambrian animals.
3. He makes the most of early arrivals: "However, a number ofEdiacaran fossils are interpreted with reasonable certainty as early offshoots (stem taxa) of lineages leading to modern groups -- including sponges (Palaeophragmodictya),cnidarians, and bilaterians such as molluscs (Kimberella) and possibly arthropods." This misdirects attention from the complexity of these phyla, and fails to account for at least 15 more new body plans that exploded onto the scene in the early Cambrian.
4. He puts a lot of trust in molecular inferences: "Molecular clock dates indicate that the ancestors of most modern marine phyla had evolved by the Ediacaran, but identifying their representatives, even among the remarkable range of Ediacaran forms, is not straightforward." His conclusion is more confident: "Phylogenies calibrated by fossil occurrences allow molecular clocks to estimate the timing of branching even where fossil evidence is wanting."
5. He uses the power of suggestion: "The rise of oxygen levels in the earth's atmosphere and oceans has often been implicated in initiating rapid diversification." We responded to this hypothesis before. Another suggestion: "The rise of zooplankton allowed particles to sink to the sea floor as fecal material which significantly augmented the nutrient supply," he speculates. "Such increases in environmental complexity during the Cambrian may well have resulted in a proliferation of diverse ecological strategies that were not present earlier." Should we call this the crap theory?
6. He offers promissory notes: "And in due course, experiments on the role of control genes in the development of animals from embryo to adult may provide clues to how all the major animal groups evolved in a relatively short time during the Cambrian explosion."

Here's another key passage expressing hope for an answer:

Although the fossil record is silent on mechanisms to explainhow morphology could have evolved so rapidly, developmental biology investigates how genetic mechanisms affect body plans. Evolutionary developmental biology (evo-devo) may provide clues to how such a remarkable range of morphology evolved so quickly, at least in organisms amenable to experimental manipulation.

There's really nothing new here. All these hypotheses have been answered in Darwin's Doubt and Debating Darwin's Doubt. Our job is to get the information past the censors, so that the organs of propaganda are defeated by free and open inquiry.

Today's supernatural is tomorrow's scientific revolution.

Science and Credulity

David Klinghoffer January 31, 2013 5:15 AM

The Center for Science & Culture's John West did an interesting interview with the Australian-based commentary/news site Mercator, commenting on the recent Discovery Institute Press book The Magician's Twin: C. S. Lewis on Science, Scientism, and Society ("Exposing scientism"). The interviewer asked about a seeming paradox in Lewis's thought:

MercatorNet: C.S. Lewis claimed that science has made us more gullible. But how can this happen if science is based on empirical facts?

West: Lewis observed that many non-scientists simply checked their critical faculties at the door when they heard claims made in the name of science. People who didn't think we could know anything with confidence about historical figures like Julius Caesar or Napoleon because they lived such a long time ago had no problem accepting the most outlandish claims made about "pre-historic" man, because the latter claims were dressed up as science. Lewis was concerned that this kind of blind deference to scientific authority opened the door to tyranny. That's one of the reasons it's so concerning today when people are routinely attacked as "anti-science" just for raising thoughtful questions about claims made in the name of science. If we want to avoid the abuse of science, we need to encourage that kind of questioning, not suppress it.

This reminded me of a comment I came across by Harvard geneticist George Church, about whom, on reflection, I think I was probably too harsh and quick to judgment the other day when he was in the news on the subject of cloning Neanderthals (see here, here, and here). For which, if so, I apologize. Church has done a lot of important work that we've highlighted at ENV -- in fact, we do so in our current cover story ("Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA").

Church has tangled honorably and creditably with Jerry Coyne -- see his response to Coyne's criticism at the end of this post from Why Evolution Is True. Among other things he remarks on the different ways that a "considerable amount of faith drives everyday science."

Incidentally, a noteworthy aspect of Coyne v. Church is that George Church has said things that make Coyne wonder if he's "somewhat of a creationist, or at least sympathetic to intelligent design." Coyne demands from his more distinguished colleague, yes, a statement of faith in Darwinian evolution: "If he's not [an ID sympathizer], and firmly adheres to the naturalistic theory of evolution, let him state that."

Church's reply is intriguing:

I like the theory of evolution -- I even harness it industrially to make practical materials. Perhaps, another less-than-ideal dichotomy here is between "naturalistic" and "supernaturalistic." "Natural" is what is known to science at the moment. If we discover next year quantum computing and/or aliens capable of transferring bits of information to minds or DNA, then we might reconsider past "naturalism." I like a simple Occam's razor, but not if it gets in the way of a revolution.

He "likes" evolution -- microevolution, he means, since that's the only kind you'll ever have a chance of observing at work.

As I say, that's very interesting, coming form a Harvard geneticist. Note the smart deconstruction of "natural" v. "supernatural." This line is a keeper: "'Natural' is what is known to science at the moment." So for science to continue insisting on "naturalistic" explanations of everything guarantees that knowledge can't advance further than it already has done. True.

Yet more iconoclasm II

Lee Spetner on Darwin’s iconic finches

Published on October 9th, 2015

Written by: News

Further to What’s happened since Icons of Evolution (2002)? Well, for one thing, Darwin’s textbook finches took a beating (no speciation)

From The Evolution Revolution by physicist Lee Spetner:

The proximate biochemical signal evoking the change in beak shape [of Galapagos finches] has been discovered to be a protein growth factor Bmp4. The more Bmp4 that is made, the broader and deeper is the bird’s beak. This protein acts as a signal to the development of the craniofacial bones which determines the beak’s shape. If my suggestion is correct that the hormones triggered by environmental inputs affect embryonic development, then those hormones induce these growth factors to form the finch beak….The built-in mechanism of the NREH [Non Random Evolutionary Hypothesis] enables the bird population to adapt to a new environment quickly and efficiently without having to call upon the slow and wasteful neo-Darwinian process of random mutation and natural selection. p. 76

Note from reader:

Spetner’s Non Random Evolutionary Hypothesis proposes that certain genetic traits lie dormant within the genomes of various living things until environmental cues turn them on and they appear in the next generation. In other words, living things are front loaded with a host of options which allow for rapid and specified adaptations for various enviroments. There is neither chance nor selection in this process. Moreover, it also accounts for the rapid return of smaller finch beaks when the drought ceases. It points towards exquisite design and accounts for the variability of Darwin’s finches without invoking the confusions of natural selection. If mutations are random, why is it that thicker, larger beaks appear reliably with every drought on the Galapagos Islands? Why don’t longer tail feathers or unusual colors appear? If natural selection works slowly and imperfectly, why are the changes in beak size so rapid? If the mutations are embedded in the genomes of the birds, why do they disappear so quickly when conditions change?

Here for more on Spetner’s The Evolution Revolution.

It's design all the way down V

Gate-Crashing the Nuclear Pore Complex

Evolution News & Views October 8, 2015 10:14 AM

ho would have thought a hundred years ago that a simple fungus contains high-tech security gates guarded by agents that authenticate cargo before letting it through? That's what advances in imaging are allowing scientists to observe. We must be among the most privileged in history to witness the foundations of biological life coming into focus in all their glory!

You got a simplified glimpse of this gate 13 years ago in the filmUnlocking the Mystery of Life. It's that circular portal that allows the messenger RNA out into the cytoplasm. We've learned a lot since then. We know now that the nuclear pore complex (NPC) is one of the largest and most complex molecular machines in the cell. Each eukaryotic nucleus is studded with NPCs. They resemble portholes with nets, like basketball hoops, but much more sophisticated. They are the gateways for traffic in and out of the nucleus, but not just any molecule can pass through. Each macromolecule needs a ticket and an escort, represented by tags and accessory proteins that first authenticate the cargo then accompany it in or out.

New details of the NPC architecture came to light in a couple of papers in Science this month. Regarding these papers, Katharine S. Ullman and Maureen A. Powers state:

Nuclear pore complexes (NPCs), first observed by electron microscopy 65 years ago, mediate selective transport of macromolecules between the nucleus and cytoplasm of eukaryotic cells. Although the exact size and protein composition of NPCs can vary between species, these massive and complex machines are highly conserved in their overall organization, which consists of multiple copies of ∼30 nuclear pore proteins, or nucleoporins (Nups), in asymmetrical eightfold radial arrangement. Deciphering the structure of this immense complex has required ongoing multifaceted approaches. On page 106 and 56 in this issue, Chug et al. and Stuwe et al., respectively, have employed parallel approaches in very distant species and arrived at remarkably similar and informative structures of an essential subcomplex of the NPC.

What were the "very distant species" with conserved structures? The Chug team used a frog; the Stuwe team studied a thermophilic (heat-loving) fungus. Both teams looked at one element of the eight-fold radial structure at the central inner ring of the pore. They found that this domain has coils of protein that extend out into the pore and make contact with coils from the opposite side. These coils form a net that blocks entry unless the cargo has the right password, consisting of an "usher" of sorts called a nuclear transport receptor (NTR).

What's emerging is a different model from the previously-held vision of pores that dilate and constrict to allow passage. "Instead they suggest arigid pore in which flexible domains called FG repeats fill the channel and form a barrier that can be traversed by receptors that carry cargos across," Valda Vinson explains in a brief summary of the papers inScience. FG repeats are so named for the phenylalanine-glycine amino acid patterns. "Interactions between NTRs and FG repeats are essential for facilitated translocation," Chug's team says.

NPCs grant free passage to small molecules but becomeincreasingly restrictive as the size of the diffusing species approaches or exceeds a limit of ≈30 kD in mass or 5 nm in diameter. This property is critical for keeping nuclear and cytoplasmic contents separate. NTRs, however, are not bound by this size limit. They mediate facilitated NPC passage and ferry cargoes up to the size of newly assembled ribosomal subunits (≈25 nm in diameter) between the two compartments.

For size comparison, consider that the inner ring complex is 425 kilodaltons (kD) compared to the 30kD mass limit of unescorted cargo (one Dalton = one atomic mass unit). The specific order of amino acids in each Nup protein is critical to its structure and function. Nup62, for instance, requires "kinks" that fold it into the pore-traversing domain.

"The kink is stabilized by a network of highly conserved hydrophobic and hydrophilic contacts," the researchers say. Indeed, many of the residues show "extreme evolutionary conservation" in animals as diverse as amoebas, fungi, and higher animals. That's the only context in which Chug et al. mention evolution -- the lack of it.

Stuwe's team also mentioned evolution only in the context of conservation, except for a nonspecific comment in the opening paragraph:

One of the hallmarks of eukaryotic evolution is the enclosure of genetic information in the nucleus. The spatial segregationof replication and transcription in the nucleus from translation in the cytoplasm imposes the requirement of transporting thousands of macromolecules between these two compartments. Nuclear pore complexes (NPCs) aremassive transport channels that allow bidirectional macromolecular exchange across the nuclear envelope (NE) and thus function as key regulators of the flow of genetic information from DNA to RNA to protein.

You can find the word conserved or conservation 16 times in the paper. In one case, structural conservation was found despite low sequence conservation. Mutation experiments, however, usually broke the function or reduced it dramatically; some cases were lethal.

The nuclear pore complex, therefore, is a highly selective filter for macromolecules. Why does that matter? Chug et al. explain:

For transport selectivity, preventing the passage of unwanted material is as important as allowing NTR•cargo species to pass. This is straightforward to explain by an adaptive barrier that seals around a translocating species, particularly because cohesive FG domains readily assemble such self-sealing barriers in the form of FG hydrogels.

But if anything and everything can attach NTRs to let it pass through, selectivity is also lost. "A 'general gate' would therefore stand open at all times and consequently fail as a barrier," they realize. How do the NTRs know which cargo is legitimate? This point is not clear from the papers and probably will require more analysis. It appears that multiple interactions with other nucleoporins (Nups) take part in discrimination against unwanted molecules. But the mechanism is general enough to allow the FG domains to rapidly facilitate passage of a wide range of cargo sizes.

In a news item from Rockefeller University, Professor Michael P. Rout sheds some light on the tradeoff between selectivity and speed:

"Usually, binding between traditionally folded proteins is a time consuming, cumbersome process, but because the FG Nups are unfolded, they are moving very quickly, very much like small molecules. This means their interaction is very quick," explains Rout.

The disordered structure of the FG regions is critical to the speed of transport, allowing for quick loading and unloading of cargo-carrying transport factors. At the same time, because transport factors have multiple binding sites for FG Nups, they are the only proteins that can specifically interactwith them -- making transport both fast and specific.

So in this case, "fuzzy" interactions are an asset. Rout thinks that this is "the first case where the 'fuzzy' property of an interaction is a key part of its actual biological function."

How fast are the NPCs? Chug et al. provide some details about the diffusion rate of large molecules through the pore:

Facilitated translocation is usually completed within 10ms[milliseconds].. NPCs can conduct ≈1000 facilitated translocation events or a mass flow of ≈100 MD [megadaltons] per pore per second, which further implies that NPCs can translocate numerous species in parallel.

With some 2,000 NPCs in a typical vertebrate cell (Wikipedia), that provides a huge capacity for facilitated, authenticated transport.

Not sufficiently impressed yet? Consider that the entire nuclear envelope breaks down at cell division, all the parts are duplicated (including all the genetic information, which is also error-checked), and the entire nucleus, NPCs and all, is reassembled in both daughter cells, ready to go sometimes in just minutes. That's intelligent design!