Saturday 20 May 2023
Micah 5:2 and the true origin of Israel's messiah
Micah5:1 JPS"But thou, Beth-lehem Ephrathah, Which art little to be among the thousands of Judah,
Out of thee shall one come forth unto Me that is to be ruler in Israel;
Whose goings forth(mozaah) are from of old, from ancient days.(Olam)"
Strong's:Feminine of mowtsa'; a family descent; also a sewer (marg.; compare tsow'ah) -- draught house; going forth.
Common theme going forth from the belly.
Compare:
Hebrews ch.1:10-12NIV"He also says,
"In the beginning, Lord, you laid the foundations of the earth,
and the heavens are the work of your hands.
11They will perish, but you remain;
they will all wear out like a garment.
12You will roll them up like a robe;
lie a garment they will be changed.
But you remain the same,
and your years will never end.”
Here our brother Paul quotes psalms102:25,26 and applies them to Jesus ,earlier on at verse 2 he had made the point that the Son was the one through whom JEHOVAH made the ages. Thus both JEHOVAH and his agent could be credited with the production of the physical world. Also both JEHOVAH and his subordinate would need to proceed physical world to logically be made responsible for its existence
Hebrews ch.1:2NIV"but in these last days he has spoken to us by his Son, whom he appointed heir of all things, and through whom also he made the universe. "
Thus the verse could apply to both the ultimate source of the power and wisdom manifest in the creation and the primary instrument of that source.
Note please that the creation in question is perishable ,thus we are not discussing anything spiritual, likely the ages in question refer to humanity or human civilization,
Compare:
Genesis ch.1:26JPS"And God said: ‘Let US make(Hebrew asah) man in OUR image, after OUR likeness; and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth.’"
Thus here is the living intelligent instrument through which JEHOVAH accomplished his work that is the only way this instrument could be said to bear God's image an expression that must always pertain to either a human or superhuman Son of God.
Compare:
Hebrews ch.1:3"The Son is the radiance of God’s glory and the exact representation of his being, sustaining all things by his powerful word. After he had provided purification for sins, he sat down at the right hand of the Majesty in heaven. "
Compare:
Proverbs ch.8:30JB" I was by his side, a master craftsman, delighting him day after day, ever at play in his presence,"
Compare:
Colossians ch.1:15-17"The Son is the IMAGE of the invisible God, the firstborn over all creation. 16For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. 17He is before all things, and in him all things hold together. "
John tried to tell Israel the true origins of the one walking among them
John ch.1:30NIV"This is the one I meant when I said, ‘A man who comes after me has surpassed me because he was before me.’ "
Of course from an earthly standpoint Jesus does not precede John in any sense.And it does no good to make this preceding abstract because John would also have existed abstractly in JEHOVAH'S mind prior to his birth,and is also the product of a divine miracle. John's ministry also precedes Jesus'
John continues:
John ch.1:31NIV"The one who comes from above is above all; the one who is from the earth belongs to the earth, and speaks as one from the earth. The one who comes from heaven is above all."
Thus John showed why Jesus is greater than himself.
Jesus tried to tell Israel his true origin
John ch.6:62NIV"Then what if you see the Son of Man ascend to where he was before! 63The Spirit gives life; the flesh counts for nothing. The words I have spoken to you—they are full of the Spirit e and life."
If heaven refers to his being born again why would he need to return there ,heaven of course refers to no particular vector but the superhuman state he surrendered in order to become a sacrifice for our sins
Hebrews ch.2:9NIV"But we do see Jesus, who was made lower than the angels for a little while, now crowned with glory and honor because he suffered death, so that by the grace of God he might taste death for everyone."
One cannot return to where one has never been and one need not return to where one has never left ,the glory and honor then is a restoration of a previous superhuman glory.
John ch.17:5"And now, Father, glorify me in your presence with the glory I HAD with you before the world began."
Here our Lord prays for the restoration of his forfeited superhuman glory which forfeiture was necessary to meet the legal requirements of the atonement.
Hebrews ch 2:14NIV"Since the children have flesh and blood, he too shared in their humanity so that by his death he might break the power of him who holds the power of death—that is, the devil"
Hebrews ch.2:16NIV"For surely it is not angels (spirit beings)he helps, but Abraham’s descendants."
This cannot refer to the new creation because he never forfeited his place in the new creation thus there would be no need to plea for any such restoration.
John ch.3:13NIV"No one has ever gone into heaven except the one who came from heaven—the Son of Man. "
Jesus is saying that he is unique among all men who ever lived for this reason , obviously Jesus never ceased being part of the new creation,thus this is a strike against the idea that"heaven" pertains to the new creation in this verse , once Jesus became part of JEHOVAH'S new creation he could not exit same without disqualifying himself as Savior.
As stated before heaven refers to his previous superhuman glory. He laid it aside to legally qualify as Savior and upon being born again he reclaimed it hence his prayer at John ch.17:5
John ch.8:23NIV"But he continued, “You are from below; I am from above. You are of this world; I am not of this world. 24I told you that you would die in your sins; if you do not believe that I am he, you will indeed die in your sins.”"
Sin began in heaven, so the pall that was cast over JEHOVAH'S workmanship would extend into heaven ,thus it is fitting that the one that JEHOVAH would rate his first and foremost work in heaven and earth be tested so as to vindicate JEHOVAH'S Workmanship this vindication of JEHOVAH'S Godhood is the primary issue that must be settled.
Our brother Paul against E.C.T
Romans ch.7:1NKJV"Or do you not know, brethren (for I speak to those who know the law), that the law [a]has dominion over a man as long as he lives?"
Of course if the real man never dies this would be a moot point,
Once a man is dead justice can make no further demands upon him. The presupposition then is that death is real,and that the real man does in fact die.
Romans ch.7:6NKJV"But now we have been delivered from the law, having died to what we were held by, so that we should serve in the newness of the Spirit and not in the oldness of the letter."
Thus if Christ did not actually die ,which would be the case if we take reductive spiritualism as our premise because the physical body would then have nothing to do with ones identity,there is no atonement,also if his death did not completely satisfy divine justice ,which would be the case if we take E.C.T as our premise, there would be no atonement. So much for eternal conscious torment.
Friday 19 May 2023
Substitutionary atonement v. The God-man hypothesis.
1Corinthians ch.15:21KJV"For since by man came death, by man came also the resurrection of the dead."
It was a perfect man's (not a God-man's) rebellion that condemned us therefore it is a perfect man's (not God-man's) obedience that reconciles us to JEHOVAH
1Timothy1:17NIV"Now to the King eternal, immortal, invisible, the only God, be honor and glory for ever and ever. Amen."
Matthew ch.20:28NIV"just as the Son of Man did not come to be served, but to serve, and to give(not lend) his life(Soul) as a ransom for many.”"
Leviticus ch.17:11NIV"For the life(soul,Hebrew.nefesh) of a creature is in the blood, and I have given it to you to make atonement for yourselves on the altar; it is the blood that makes atonement for one’s life(soul). c"
Only flesh and blood necessary for the sustaining of the SOUL of the victim can be offered acceptably on JEHOVAH'S altar for the expiation of sin.
Thus to make our Lord the God-man is to cancel the legal basis of the substitutionary atonement.
As the God- man his blood would possess no atoning value as it would be unnecessary for sustaining his soul. That is why he had to completely surrender his superhuman glory to qualify as a substitute.
Hebrews ch.2:17NIV"For this reason he had to be made like them, k fully human in EVERY way, in order that he might become a merciful and faithful high priest in service to God, and that he might make atonement for the sins of the people. "
he were the God-man he would be INFINITELY unlike any man who has ever existed and thus would not qualify as a substitute for us.
Origin of Life science needs an intervention?
ASCB Addresses Problem of False Science
The American Society for Cell Biology (ASCB) task force on reproducibility in life science research has issued an undated white paper on scientific rigor. The problem is, as we discussed here and here, life science research has been found to lack reproducibility. John Ioannidis is a bit more blunt as he explains that “most published research findings are false,” and that “claimed research findings may often be simply accurate measures of the prevailing bias.” The ASCB white paper is no doubt a step in the right direction. It offers 13 recommendations to encourage more rigor in training, publishing, and standards. But the most important recommendation of all continues to be ignored.
Daniel Sarewitz has noted not only the problem of bias in scientific research but also the causes. Note his final thought in this quote:
All involved benefit from positive results, and from the appearance of progress. Scientists are rewarded both intellectually and professionally, science administrators are empowered and the public desire for a better world is answered. The lack of incentives to report negative results, replicate experiments or recognize inconsistencies, ambiguities and uncertainties is widely appreciated — but the necessary cultural change is incredibly difficult to achieve.
And so it is that science’s much touted self-correcting, feedback loop which ensures science converges on the truth (after all, that’s what Mr. Wells told us in seventh grade science class) is sometimes a little slow to act.
And if the ASCB is still needing to remind scientists to clean their beakers and use checklists, imagine the difficulty in achieving more fundamental change?
This brings us to the recommendation that ASCB did not make—the most important of all. And that is for science to free itself of the excessive metaphysics. Unfortunately, progress on that front is glacial. As Sarewitz notes, one reason bias persists, and is so harmful, is that in the moment it is not perceived as bias. Asking an evolutionist to stop with the metaphysics goes nowhere because it isn’t recognized as metaphysics. Deep philosophy is a part of their “science” as much as red meat is a part of hamburgers.
Even if the ASCB task force members wanted to address this fundamental problem, they wouldn’t for the backlash would be overwhelming and their professional reputations would be ruined.
So while the pipettes will be sterilized and results double checked to the third decimal point, ASCB will continue to publish junk science driven by the Epicurean mandate that the world must have arisen spontaneously. Unfortunately, the ASCB task force has missed the most important recommendation of all.
The fossil record's flying reptiles may have eaten Darwinist's homework
Fossil Friday: The Explosive Origin of Flying Reptiles in the Mid Triassic
This Fossil Friday features the gliding reptile Sharovipteryx mirabilis from the Mid Triassic of Central Asia.
Within only two million years of the Mid-Triassic era (about 230-228 million years ago) there was a sudden appearance of a large diversity of gliding and flying reptiles, such as Sharovipteryx with wings on the legs, Mecistotrachelos and the unrelated Kuehneosauridae with a gliding membrane across lateral rib-like projections, Longisquama with long feather-like scales on the back, and the earliest pterosaurs such as Preondactylus with bat-like wings supported by a single enlarged finger.
Considerable Re-Engineering
All these very different solutions for gliding and active flight required considerable re-engineering of the tetrapod body plan, and such biological novelty arguably required new and highly specific genetic code. Such specified information cannot be produced by blind mechanisms and certainly not in such a short window of time of only two million years, which corresponds to just about half the average longevity of a vertebrate species.
Personally, I am quite sympathetic to the dissenting view of my paleontologist colleague Simon Conway Morris, who suggested that evolution does not work through a blind and random mechanism, but rather like a search engine that searches for pre-existing platonic forms in a constrained hyperspace of biological possibilities. However, this would no longer be Darwinian evolution but a highly teleological process and thus a kind of intelligent design combined with platonist idealism as metaphysics.
Whatever the mechanism of design may have been, the abrupt origin of flying reptiles is just one example within a kind of carpet bombing of biological explosions during the Triassic era, when many new orders and families of metazoan animals suddenly appeared after the end-Permian mass extinction event. This has been called the Early Triassic Metazoan Radiation, and includes marine invertebrates (e.g., bivalves and ceratite cephalopods), insects (e.g., coleopterans and dipterans), 15 different families and body plans of marine reptiles (Bechly 2023), as well as the first representatives of modern terrestrial tetrapod taxa that appeared suddenly within a short window of time between 251-240 million years ago (Ezcurra 2010). The latter include the first dinosaurs (Nyasasaurus), the first lizard-relatives (Lepidosauromorpha such as Paliguana), the first croc-relatives (Crurotarsi such as Ctenodiscosaurus), the first mammal-like animals (Mammaliaformes such as Haramiyida), and allegedly the first turtles (Pappochelys) even though this is more dubious (Bechly 2022).
Goal-Directed and Intelligent
The well-known paleontologist Peter Ward, who is an ardent Darwinist and a strong opponent of intelligent design theory, explicitly acknowledged that “the diversity of Triassic animal plans is analogous to the diversity of marine body plans that resulted from the Cambrian Explosion. It also occurred for nearly the same reasons and, as will be shown, was as important for animal life on land as the Cambrian Explosion was for marine animal life” (Ward 2006:160). I totally agree that all these explosions occurred for the same reasons and by the same causes, which must have been goal-directed and intelligent.
References
Bechly G 2022. Fossil Friday: Turtles All the Way Down. Evolution News July 1, 2022. https://evolutionnews.org/2022/07/fossil-friday-turtles-all-the-way-down/
Bechly G 2023. Fossil Friday: The Triassic Explosion of Marine Reptiles. Evolution News March 31, 2023. https://evolutionnews.org/2023/03/fossil-friday-the-triassic-explosion-of-marine-reptiles/
Ezcurra MD 2010. Biogeography of Triassic tetrapods: evidence for provincialism and driven sympatric cladogenesis in the early evolution of modern tetrapod lineages. Proceedings of the Royal Society B 277(1693), 2547–2552. DOI: https://doi.org/10.1098/rspb.2010.0508
Ward PD 2006. Out of Thin Air. Joseph Henry Press, Washington (DC), 296 pp. https://books.google.at/books?id=baJVAgAAQBAJ
The main event?
Origin of Life: James Tour and Dave Farina Will Debate at Rice University on Friday; Watch Here
Everyone’s favorite fake professor, Dave Farina, has devoted many hours on his YouTube Channel, “Professor Dave Explains,” to spewing venom at skeptics of materialist doctrine on biological origins. Perhaps you thought, “Gee, wouldn’t it be interesting if Dave agreed to an in-person debate with, let’s say, Rice University chemist James Tour on the origin of life?”
Dr. Tour is highly skeptical that theorists have got it all figured out about how life arose from non-life on a barren early Earth through known material processes alone. Farina attacked him and his “idiot followers” repeatedly for that. Yeah, Farina is a real mensch, as you may know. Tour, considering that Farina has a YouTube subscriber base of 2.48 million, and thus is reaching a lot of vulnerable people who have no idea how uniformed he is, responded accordingly. In videos of his own, Dr. Tour even offered to fly Farina out to Rice to debate him — put him up at Tour’s home, give him dinner, etc.
<iframe width="460" height="259" src="https://www.youtube.com/embed/qOopv-0BmzY" title="Dr James Tour and Dave Farina Debate Announcement" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
I thought, “Dream on, Professor Tour. ‘Professor Dave’ is never going to take you up on that. At some level he knows what he is.” Guess what? I was wrong. Tomorrow at 7 pm Central (5 pm Pacific), Dave Farina will indeed be debating James Tour at Rice. The topic: “Are We Clueless About the Origin of Life?” That’s Friday, May 19. I trust that Mr. Farina will enjoy his homecooked meal courtesy of the Tour household. What will it be? Meatloaf? Salmon steaks? Don’t forget the first course, a nice bowl of primordial soup fresh from the kitchen. It takes a world-renowned chemist to get that recipe right.
<iframe width="460" height="259" src="https://www.youtube.com/embed/pxEWXGSIpAI" title="Dr. James Tour vs Dave Farina | Are we clueless about the origin of life? #abiogenesis" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
The Western schism: a brief history.
The western schism
Western Schism, also called Great Schism or Great Western Schism, in the history of the Roman Catholic Church, the period from 1378 to 1417, when there were two, and later three, rival popes, each with his own following, his own Sacred College of Cardinals, and his own administrative offices.Shortly after the return of the papal residence to Rome following almost 70 years of the Avignon papacy, the archbishop of Bari was elected pope as Urban VI amid demands by the Roman populace for “a Roman or at least an Italian.” Urban VI proved to be so hostile to the cardinals, who had assumed great powers during the years at Avignon, that a group of cardinals retired to Anagni and elected one of themselves, Robert of Geneva, as Clement VII, claiming the election of Urban VI had been invalid because it was made under fear. Clement VII then took up residence at Avignon. Although Roman Catholic church historians generally agree that Urban VI and his successors were the legitimate popes, there has never been an official pronouncement to this effect.The double election had disastrous effects upon the church. The followers of the two popes were divided chiefly along national lines, and thus the dual papacy fostered the political antagonisms of the time. The spectacle of rival popes denouncing each other produced great confusion and resulted in a tremendous loss of prestige for the papacy.
Various proposals for ending the schism were made, especially by the University of Paris, which suggested either mutual resignation or a decision by an independent tribunal or a general council. This last proposal was in line with the growing conciliar movement, according to which a general council has greater authority than a pope. Both lines of popes refused to submit. Eventually cardinals from both obediences, seeking to end the schism, arranged the Council of Pisa, which met in 1409 and elected a third pope, Alexander V, who was succeeded shortly thereafter by Baldassare Cossa, who took the name John XXIII. Under pressure from the emperor Sigismund, John convoked, in 1414, the Council of Constance, which deposed him, received the resignation of the Roman pope, Gregory XII, and dismissed the claims of the Avignon pope, Benedict XIII. That series of events opened the way to the election of Martin V in November 1417, whereby the schism was ended.
Thursday 18 May 2023
Matthew Henry's Commentary on Daniel ch12:1.
On Michael the great prince
Jesus Christ shall appear his church's patron and protector: At that time, when the persecution is at the hottest, Michael shall stand up, v. 1. The angel had told Daniel what a firm friend Michael was to the church, ch. 10:21. He all along showed this friendship in the upper world; the angels knew it; but now Michael shall stand up in his providence, and work deliverance for the Jews, when he sees that their power is gone, Deu. 32:3. 6. Christ is that great prince, for he is the prince of the kings of the earth, Rev. 1:5. And, if he stand up for his church, who can be against it? But this is not all: At that time (that is, soon after) Michael shall stand up for the working out of our eternal salvation; the Son of God shall be incarnate, shall be manifested to destroy the works of the devil. Christ stood for the children of our people when he was made sin and a curse for them, stood in their stead as a sacrifice, bore the cure for them, to bear it from them. He stands for them in the intercession he ever lives to make within the veil, stands up for them, and stands their friend. And after the destruction of antichrist, of whom Antiochus was a type, Christ shall stand at the latter day upon the earth, shall appear for the complete redemption of all his.
The miracle of a nice day.
Intelligent Design in Weather — The “Perfect Day” Conspiracy
Yesterday where I live was one of those rare days in spring that might prompt the comment, “What a perfect day!” The air was fresh, the sky was blue, the temperature rose to about 75 degrees Fahrenheit, and a gentle breeze was blowing. While we all know that weather conditions can change drastically and become harsh, seasons come when most people can enjoy being outside.
Whether we feel thankful for the weather, or just ignore it, it may be of interest to ponder some things that go into providing our weather conditions on Earth. The cast of characters that play a behind-the-scenes role in our weather each have the potential to wreak havoc with the livability of our climate. Seeing how they usually all conspire together for our benefit could be called the perfect day conspiracy.
The Investigation Begins
Our undercover investigation of this conspiracy first takes us a long way from home, on a dive into the very core of our Sun. Conditions there are far from idyllic — for humans, but they’re just right for a sustained thermonuclear fusion reaction that converts hydrogen into helium. At a temperature of 15 million degrees Celsius, and a crushing density of 14 times the density of lead, this solar furnace annihilates four million tons of matter each second to produce what we blithely refer to as “sunshine.” To further add to the exotic origin of our sunlight, about 3.8 percent of the energy from each fusion reaction in the solar core comes from matter-antimatter annihilations between positrons and normal electrons, in a scenario as sci-fi sounding as the iconic warp drive in Star Trek.
The total power output from the Sun’s nuclear furnace is a steady 4×1026 Watts, radiating uniformly into all directions of space. Since the Earth revolves around the Sun in a nearly circular orbit, the heat and light intercepted by the Earth stay constant to within a few percent throughout the year. Due to the large distance from the Sun to the Earth, out of all the power emitted by the Sun, the entire Earth only intercepts the tiniest fraction — less than one part per billion. Yet that fraction (0.45×10-9 out of all the Sun’s power) is just right to give us seasons when the temperature outdoors is just right.
The Marvel of Rain
But what about those rainy days? Today, just a couple of days after I started writing this article, the skies are grey with clouds and rain is predicted for the next 24 hours. In the Midwest, rainy days and thunderstorms roll through frequently enough that the farm country across several states can predictably grow crops during the summer months without resorting to artificial irrigation. The marvel of regular rainfall hits home if you’ve ever lived in a drier region. When I lived in Southern California, the entire summer often lacked any measurable precipitation.
We all know that rain clouds consist of condensed water vapor that evaporated primarily from ocean water, although surface water on land also contributes. With 71 percent of our planet covered by oceans, and an average planetary temperature of about 59 degrees Fahrenheit (15 degrees Celsius), plenty of evaporation occurs. The resultant clouds need to hold their water, however, for a journey of hundreds to thousands of miles to fall as rain on the interior of continents. Prevailing winds, powered by the Sun’s energy and the Earth’s rotation, are major factors in bringing rain clouds to regions far removed from any ocean. The water cycle is far more complex than can be described in a few sentences, but it’s all part of giving us a perfect day.
Explaining a Blue Sky
“Why is the sky blue?” is a familiar question, but the answer to how this atmospheric color contributes to our perfect day conspiracy may not be well known. Sunlight is composed of all colors, so when the Sun shines on the atmosphere on a clear day, why does the sky predominantly appear blue? It has to do with sunlight being composed of oscillating electric and magnetic fields that interact with the molecules of air (primarily N2 and O2). The electrons in the air molecules are set into oscillating motion by the light and this causes them to reradiate at the same frequency. However, and here’s the blue-sky secret, high frequency light (blue-violet) is reradiated almost ten times more strongly than low frequency visible light (red). When we look at the sky in any direction away from the Sun, we’re only seeing scattered or reradiated light, which favors the high-frequency blue color.
This pleasant phenomenon of blue-light scattering also depends on the relative size of the air molecules being much smaller than the wavelength of light. When the atmosphere contains clouds or fog composed of water droplets much larger than the wavelength of light, sunlight is scattered without preference for color, causing clouds and fog banks to look white or gray.
A Rosy Glow
At the end of a perfect day, when the Sun is setting, the beams of light we see slant through the atmosphere nearly parallel (tangent) to the Earth’s surface. The light therefore journeys further through the air, so most of the bluish colors are scattered away by the time it reaches our eyes, and guess what? This also provides us with the gorgeous reddish-orange sunset colors that highlight and provide a rosy glow on any clouds lingering near the horizon.
So much beauty from an obscure electromagnetic phenomenon that nobody understood until about 150 years ago! From nuclear fusion in the Sun to Earth’s orbital radius, to atmospheric conditions and the interaction of light with molecules, to the properties of water, and many more details that I had to leave out, it seems like a line-up of more than “the usual suspects” conspired together to bring us a perfect day.
Begotten not made?
John ch.1:18LSB"No one has seen God at any time; the only begotten God who is in the bosom of the Father, He has explained Him."
John ch.1:18NWT Study Edition"No man has seen God at any time;+ the only-begotten god+ who is at the Father’s side+ is the one who has explained Him.+"
John ch.6:57LSB"As the living Father sent Me, and I live because of the Father, so he who eats Me, he also will live because of Me."
If the first cause argument is to retain coherence the most high God MUST be unbegotten/self-sustaining. As to what is meant by JEHOVAH'S Begetting of his unique son ,Jesus helps us by using his resurrection of those who faithfully follow him up to their deaths as an analog. Thus JEHOVAH does not merely sustain his Logos he caused his origin.
Birth language as applied to JEHOVAH in scripture always refers to creation/recreation
Psalm ch.90:1,2LSB"Lord, You have been our dwelling place from generation to generation.
2Before the mountains were bor
Or You brought forth the earth and the world
Even from everlasting to everlasting, You are God.",
Note the birth language used to describe JEHOVAH'S very temporal Creating of the planet.
What about the Begetting of the unique Son of the God.
Acts ch.13:33LSB"that God has fulfilled this promise to our children in that He raised up Jesus, as it is also written in the second Psalm, ‘You are My Son; today I have begotten You.’"
Thus the very temporal resurrection of the son is called a Begetting of him, and to be clear the resurrection is a creative act by JEHOVAH.
Psalm ch.104:29,30LSB"You hide Your face, they are dismayed;
You take away their spirit, they breathe their last
And return to their dust.
You send forth Your Spirit, they are created;
And You renew the face of the ground."
If our Lord's Begetting in time via re-creation does not invalidate his sonship the neither should his Begetting in time via creation.
Colossians ch.1:15KJV"Who is the image of the invisible God, the firstborn of every creature: "
Wednesday 17 May 2023
That crash in the distance is sound of the fall of Darwin's tree of life?
The Dawkins Test Returns an Answer: Intelligent Design
In 2009 atheist biologist Richard Dawkins offered a scientific test to decide between Darwinian evolution and intelligent design (ID). The results are in, and as guest Casey Luskin explains on a new episode of ID the Future, the evidence has broken strongly in favor of intelligent design. At the time Dawkins presented the test, he was confident that comparative DNA evidence supported Darwin’s tree of life and its idea of universal common ancestry. He made the point in his 2009 book The Greatest Show on Earth and in two interviews. As he Put it, “The single most convincing fact or observation you could point to” in favor of Darwinian evolution over against ID “would be the pattern of resemblances that you see when you compare the genes … of any pair of animals you like … and then plot out the resemblances and they form a perfect hierarchy, a perfect family tree. And the only alternative to it being a family tree is that the intelligent designer deliberately set out to deceive us in the most underhanded and devious manner.”
But 14 years later the picture looks very different. Dr. Luskin details the various ways that the rapidly developing field of phylogenomics is uncovering data that powerfully fits the ID model of life’s history and strongly undermines the idea of universal common ancestry via mindless evolution. As Luskin says in a recent Evolution News Article, “Now, years later, scientists have sequenced a great number of whole genomes. And as a consequence, they know that Dawkins was wrong. Every gene does not deliver ‘approximately the same tree of life.’… On its own terms, the Dawkins test for evolution has come up for ID.”
So why haven’t evolutionary biologists given up on universal common ancestry? Luskin says that some have, while others reflexively invoke auxiliary hypotheses and employ question-begging computer models to generate tree-like ancestries in the face of contrary data. Luskin compares the behavior to astronomers who protected the dying geocentric model of the solar system by invoking “epicycles” to explain away contrary astronomical data. Better to let the Dawkins Test speak for itself, Luskin says. Download the podcast or listen to it here.
Why no simple middle either.
Jonathan McLatchie on Classic Examples of Irreducibly Complex Systems
On a new episode of ID the Future, Dr. Jonathan McLatchie talks with with host Tom Gilson about the key features of irreducibly complex biological systems. McLatchie is a Fellow with Discovery Institute’s Center for Science and Culture. He holds advanced degrees in evolutionary biology and molecular bioscience. He is also an assistant professor of biology at Sattler College in Boston and speaks and interviews regularly on science topics. Here, McLatchie offers a close examination of two classic examples of irreducibly complex systems — the bacterial flagellar motor and the process of DNA replication in cell division. He explains the intricacies of each process and shows why each stands up to scrutiny as a true instance of irreducible complexity. Along the way, he explains why the RNA world scenario isn’t likely to be the answer to irreducible complexity that materialists are looking for. And near the end, be sure to listen to McLatchie explain the “likelihood ratio” of the evidence for irreducible complexity, a top-heavy ratio he says strongly supports a design hypothesis. Download the podcast or listen to it here.
Tuesday 16 May 2023
If you are loosing on every sale no amount of market share will help you.
Natural Selection Subtracts, It Doesn’t Add — And That Matters
In my previous post (“A New Look at Natural Selection”), I said that “natural selection” was Charles Darwin’s crowning intellectual achievement, for it created what appeared to be a naturalistic and mechanistic explanation for how organisms evolved. I also noted that evolution itself was already considered to have been well demonstrated in the fossil record by Lamarck and others some fifty years before Darwin.
In the 20th century, natural selection has been almost uniformly adopted by biologists as the explanatory agency for evolution. What appeals to naturalists is that it provides an explanation for the appearance of design in organisms, without an actual designer. Moreover, Darwin had invoked the presence of heritable changes between generations that provided the variety among organisms upon which natural selection could operate. Half a century later, genetics came into focus, seeming to provide the biochemical foundation for Darwin’s intuition as to the cause of heritable variance among species.
Real but Not as Envisioned
Natural selection, we saw, is indeed quite real, but by no means in the way that Darwin envisioned. There can be no doubt that the natural environment establishes severe constraints and requirements upon organisms. In the wild, all organisms must live within their niche. There are no wild polar bears in Arizona, and no iguanas in Alaska. To be sure, the single most incredible fact of the biosphere is the fastidiously precise formation of creatures whose physiology so exquisitely fits their environment. The wonder of this goes far beyond the fact that cetaceans do not breathe through their mouths. Their very existence depends on echolocation, but the funny thing is, it is difficult to hear underwater. Difficult, that is, unless you have a middle ear unique to cetaceans among mammals, making their underwater existence and communication possible. And it’s not just that penguins, who are birds, have bones of greater density than elephants, quite unlike their hollow-boned flying ancestors. They need those iron-dense bones in order to be able to dive for fish, because the rest of their body is composed of fat and feathers, both lighter than water, yet necessary for insulation.
I have further pointed out that the natural environment, which does passively exert selection on living creatures in all of the varying environments, was consciously designed, making the reality of the ecological niche possible.
In Keeping with the Times
History teaches that ideas and inventions comport with the times. Petroleum until 1900 was only used for kerosene, while gasoline was discarded. Now it is the reverse. We do not see any steam engine locomotives in operation anymore. We are actually on the precipice of eliminating internal combustion even for cars. In the same way, ideas from 150 years ago may have been suitable for their time, but very few scientific ideas last forever. When Darwin thought of natural selection, it seemed to make sense in an incredibly oversimplified version of how life actually operates. We are at least fifty years beyond that now. The examples I gave above about exquisite adaptability to unique environments for whales and penguins are utterly trivial compared to the intracellular and inter-organ physiology and biochemistry of every living thing. There really is no reasonable way to believe that all of those trillions and trillions of modifications occurred randomly and without a designer.
It has been said many times before but it is certainly worth repeating: Natural selection creates nothing. It only subtracts. The big question is, how does the uniqueness of form and function among organisms actually originate? That will be the subject of upcoming posts.
Why the search for Darwinism's simple beginning keeps getting more complex.
Could Blind Forces Build a Self-Replicating Molecule?
Photo: Greater blind mole rat, by GalinaGouz, CC BY-SA 4.0 , via Wikimedia Commons.
On a new episode of ID the Future, scientist and Stairway to life co-author Rob Stadler and host Eric Anderson examine a recent PNAS paper on the origin of life, “An RNA Polymerase Ribozyme that Synthesizes Its Own Ancestor.” A superficial look at the paper — and its title in particular — might give the impression that the laboratory findings here render the blind evolution of the first self-replicating biological system appreciably more plausible. Not so fast, says Stadler. He and Anderson highlight various ways the laboratory work in question is wildly unrealistic. Download the podcast or listen to it here.
File under "well said" XCII
"The true soldier fights not because he hates what is in front of him, but because he loves what is behind him."
G.K Chesterton.
Let's be grateful that Richard Dawkins et al did not design the human eye.
Is the Human Eye Really Evidence Against Intelligent Design?
Editor’s note: To celebrate the new course from DiscoveryU with biologist Jonathan Wells, equipping you to think critically about life’s origins, we are delighted to present some of our favorite past posts by Dr. Wells.
Some people argue that the human eye is flawed, proving that it was not intelligently designed but evolved by unguided processes.
Both vertebrates (animals with backbones, such as humans) and cephalopods (molluscs with tentacles growing from their heads, such as squids and octopuses) have camera eyes, which are roughly spherical organs with lenses that focus images on light-sensitive retinas. In vertebrate eyes, the light-sensing cells (c and f in the drawing below) point towards the back of the retina, and the nerve cells that transmit signals to the brain (b in the drawing) are between the light-sensing cells and the incoming light. By contrast, in cephalopod eyes the light-sensing cells point toward the incoming light and the nerve cells are at the back.
In 1986, Richard Dawkins published The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. In it, Dawkins used the vertebrate eye as evidence against design:
Any engineer would naturally assume that the photocells would point towards the light, with their wires leading backwards towards the brain. He would laugh at any suggestion that the photocells might point away from the light, with their wires departing on the side nearest the light. Yet this is exactly what happens in all vertebrate retinas. Each photocell is, in effect, wired in backwards, with its wire sticking out on the side nearest the light. The wire has to travel over the surface of the retina, to a point where it dives through a hole in the retina (the so-called “blind spot”) to join the optic nerve.
An Offense to Tidy-Mindedness?
Vertebrate eyes work reasonably well, Dawkins conceded, but “it is the principle of the thing that would offend any tidy-minded engineer!”1
Six years later, evolutionary biologist George Williams wrote, “There would be no blind spot if the vertebrate eye were really intelligently designed. In fact it is stupidly designed,” while “the retina of a squid is right side up.”2
In 1994, biology professor Kenneth R. Miller argued similarly that the human eye — “that supposed paragon of intelligent design” — is badly designed. “Quite naturally,” he wrote, “you (and any other designer) would choose the orientation that produces the highest degree of visual quality. No one, for example, would suggest that the neural wiring connections should be placed on the side that faces the light, rather than on the side away from it. Incredibly, this is exactly how the human retina is constructed.” By contrast, a cephalopod retina is “wired right-side-out.”3
In 2005, Douglas Futuyma published a textbook about evolution claiming that “no intelligent engineer would be expected to design” the “functionally nonsensical arrangement” of cells in the human retina.4 The same year, geneticist Jerry Coyne wrote that the human eye is “certainly not the sort of eye an engineer would create from scratch.” Instead, “the whole system is like a car in which all the wires to the dashboard hang inside the driver’s compartment instead of being tucked safely out of sight.” Like Dawkins, Williams, Miller, and Futuyma, Coyne attributed this to unguided evolution, which “yields fitter types that often have flaws. These flaws violate reasonable principles of intelligent design.”5
A 2014 biology textbook by Kenneth Mason, Jonathan Losos, and Susan Singer informs students, “an excellent example of imperfect design is the eye of vertebrate animals, in which the photoreceptors face backward, toward the wall of the eye.” By contrast, the eyes of cephalopods “are more optimally designed.”6
Molecular biologist Nathan Lents wrote in 2015, “The photoreceptor cells of the retina appear to be placed backward, with the wiring facing the light and the photoreceptor facing inward…. This is not an optimal design for obvious reasons. The photons of light must travel around the bulk of the photoreceptor cell in order to hit the receiver tucked in the back. It’s as if you were speaking into the wrong end of a microphone.” According to Lents, “there are no working hypotheses about why the vertebrate retina is wired in backwards. It seems to have been a random development that then ‘stuck’ because a correction of that magnitude would be very difficult to pull off with random mutations…. During the evolution of the cephalopod eye, the retina took shape in a more logical way, with the photoreceptors facing outward toward the light. Vertebrates were not so lucky.”7
Evidence for Intelligent Design
So from the perspective of evolutionary theory, the human eye is evidence for unguided evolution and against intelligent design. But is the human eye really evidence against design?
The light-sensing cells in a vertebrate retina require lots of nutrients and vast amounts of energy. In mammals, they have the highest metabolic rate of any tissue in the body.8 About three-quarters of the blood supply to the eye flows through a dense network of capillaries called the “choriocapillaris,” which is situated behind the retina (e in the drawing).9,10 Oxygen and nutrients are transported from the choriocapillaris to the light-sensing cells by an intermediate layer of cells called the “retinal pigment epithelium” (RPE, d in the drawing).11
In addition to transporting oxygen and nutrients to the light-sensing cells, the RPE performs two other essential functions. First, the dark pigment in it absorbs scattered light, improving the optical quality of the eye. Second, it removes toxic chemicals that are generated in the process of detecting light. The light-sensing cells contain stacks of discs, and in 1967 Richard Young showed experimentally that a photoreceptor cell continually renews itself by shedding discs at the end closest to the RPE and replacing them with newly synthesized discs at the other end.12 The RPE then engulfs the shed discs and neutralizes the toxins.13
Blood is almost opaque, and the RPE absorbs light. If the light-sensing cells were to face the incoming light, the blood-filled choriocapillaris and the RPE would have to be in front of the retina, where they would block most or all of the light. By contrast, nerve cells (b in the drawing) are comparatively transparent, and they block very little of the incoming light. Because of the high metabolic requirements of the light-sensing cells and their need to regenerate themselves, the inverted retina is actually much better than the “tidy-minded” design imagined by evolutionary biologists.
Not a Serious Problem
The blind spot (a in the drawing) is not a serious problem, because the blind spot produced by the left eye is not in the same place as the blind spot produced by the right eye. This means that in humans with two good eyes, the field of vision of one eye covers for the blind spot of the other eye, and vice versa.
What about the claim that cephalopod eyes are better than vertebrate eyes? In 1984, a team of Italian biologists pointed out that cephalopod eyes are physiologically inferior to vertebrate eyes. In vertebrate eyes, the initial processing of visual images occurs in the retina, by nerve cells right next to the photoreceptor cells. In cephalopod eyes, nerve impulses from the photoreceptor cells must travel all the way to the brain to be processed. So a cephalopod eye “is just a ‘passive’ retina which is able to transmit only information, dot by dot, coded in a far less sophisticated fashion than in vertebrates.” The result is slower processing and fuzzier signals.14
All of the research cited above about the choriocapillaris and RPE, and the superiority of vertebrate eyes to cephalopod eyes, was published before Dawkins published The Blind Watchmaker. But Dawkins and the other critics of intelligent design didn’t bother to check the scientific literature. They simply assumed that evolution is true and that they knew how an eye should be designed. Then they concluded that the human eye is badly designed, claimed it as evidence for evolution, and ignored the contrary evidence.
Good empirical science searches for explanations that fit the evidence. But another kind of “science” is committed to telling materialistic stories about unguided evolution, even when those stories don’t fit the evidence. The stories are empirically dead, but they keep coming anyway, like zombies. I recently published a book about such stories titled Zombie Science.15
Richard Dawkins, The Blind Watchmaker (New York: W.W. Norton, 1986), 93.
George C. Williams, Natural Selection: Domains, Levels, and Challenges (New York: Oxford University Press, 1992), 73.
Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97 (February-March, 1994): 24-32.
Douglas J. Futuyma, Evolution (Sunderland, MA: Sinauer Associates, 2005), 49.
Jerry A. Coyne, “The faith that dare not speak its name: The case against intelligent design,” The New Republic (August 22 & 29, 2005): 21-33.
Kenneth A. Mason, Jonathan B. Losos, and Susan R. Singer, Raven and Johnson’s Biology, 10th ed. (New York: McGraw-Hill, 2014), 428-429.
Nathan H. Lents, “The poor design of the human eye,” Human Evolution Blog (January 12, 2015).
Sidney Futterman, “Metabolism and photochemistry in the retina,” pp. 406-419 in Adler’s Physiology of the Eye, ed. Robert A. Moses, 6th ed. (St. Louis: C. V. Mosby, 1975), 406.
Albert Alm and Anders Bill, “Ocular and optic nerve blood flow at normal and increased intraocular pressures in monkeys (Macaca irus): A study with radioactively labeled microspheres including flow determinations in brain and some other tissues,” Experimental Eye Research 15 (1973): 15-29.
Paul Henkind, Richard I. Hansen, and Jeanne Szalay, “Ocular circulation,” pp. 98-155 in Physiology of the Human Eye and the Visual System, ed. Raymond E. Records (Hagerstown, MD: Harper & Row, 1979), 139-140.
Roy H. Steinberg, “Interactions between the retinal pigment epithelium and the neural retina,” Documenta Ophthalmologica 60 (1985).
Richard W. Young, “The renewal of photoreceptor cell outer segments,” Journal of Cell Biology 33 (1967): 61-72.
Richard W. Young and Dean Bok, “Participation of the retinal pigment epithelium in the rod outer segment renewal process,” Journal of Cell Biology 42 (1969).
Alberto Wirth, Giuliano Cavallacci, and Frederic Genovesi-Ebert, “The advantages of an inverted retina,” Developments in Ophthalmology 9 (1984): 20-28.
Jonathan Wells, Zombie Science (Seattle: Discovery Institute Press, 2017).
Monday 15 May 2023
ID and the Darwin delusion.
Intelligent Design Passes the Dawkins Test
Richard Dawkins is famed as an evolutionary biologist and as an aggressive advocate for atheism. He has made some strong statements about the nonexistence of a designer behind life, including in his bestselling book The God Delusion. In light of his position, here is a question someone ought to put to him. Scientists often work by making predictions. As evidence comes in, the prediction can be shown to be true or false. This may have serious consequences. For his part, Dawkins has repeatedly described a test that at the time he thought proved evolution. Now, however, taking into account accumulating scientific evidence, the same test demands a conclusion of intelligent design (ID). Will he accept that conclusion and come out as an ID proponent?
The test that Dawkins has formulated goes this way: He says that if Darwinian evolution is correct, every gene in a group of organisms will give “approximately the same tree of life.” If ID is correct, on the other hand, the designer could have “picked and chosen” the “best proteins for the job” in each organism. In that case, he says, genes would not all give the same tree of genetic resemblances.
Dawkins offered this test in his 2009 book, The Greatest Show on Earth: The Evidence for Evolution. He described it as “extremely powerful evidence for evolution.” At the time, he apparently believed that each gene really did give approximately the same tree. He wrote:
Comparative DNA (or protein) evidence can be used to decide — on the evolutionary assumption — which pairs of animals are closer cousins than which others. What turns this into extremely powerful evidence for evolution is that you can construct a tree of genetic resemblances separately for each gene in turn. And the important result is that every gene delivers approximately the same tree of life. Once again, this is exactly what you would expect if you were dealing with a true family tree. It is not what you would expect if a designer had surveyed the whole animal kingdom and picked and chosen — or “borrowed” — the best proteins for the job, wherever in the animal kingdom they might be found.
He’s Said It Other Times
That’s not the only time Dawkins has made this prediction. He said it in an Interview given in 2009:
The single most convincing fact or observation you could point to would be the pattern of resemblances that you see when you compare the genes … of any pair of animals you like … and then plot out the resemblances and they form a perfect hierarchy, a perfect family tree. And the only alternative to it being a family tree is that the intelligent designer deliberately set out to deceive us in the most underhanded and devious manner.
He said it again in a 2010 Interview:
The single most convincing fact or observation you could point to would be the pattern of resemblances that you see when you compare the genes … of any pair of animals you like … and then plot out the resemblances and they form a perfect hierarchy, a perfect family tree. And the only alternative to it being a family tree is that the intelligent designer deliberately set out to deceive us in the most underhanded and devious manner.
It’s a simple test. Dawkins sets up two competing predictions: one for evolution and one for intelligent design. He claims that evolution predicts “perfect” congruency among different representations of the tree of life — evidence that is so “powerful” he believes it “proves that evolution is true.” On the other hand, he gives incongruency or conflicts among different gene-based trees as a prediction of the “alternative” to evolution, namely intelligent design.
What Do the Data Show?
Now, years later, scientists have sequenced a great number of whole genomes. And as a consequence, they know that Dawkins was wrong. Every gene does not deliver “approximately the same tree of life.”
This is an issue that I and others have written about before (see Here, for example), but I thought of it again recently when I watched the inaugural lecture of a professor of evolutionary genomics at Queen Mary University of London. The lecture is intriguingly titled “Trees of life : Do They Exist?”
The professor, Dr. Richard Buggs, mentions that scientists doing phylogenetic studies normally assume the existence of the Darwinian tree of life. It is quite rare in the literature to find someone actually seeking to prove its existence. He points to Dawkins’s statements in The Greatest Show on Earth as one of these rare examples, along with a Nature paper published in 1982 that Dawkins references. In the lecture, Buggs quotes Dawkins, who says “every gene delivers approximately the same tree of life.” Buggs then comments:
Many of you who work, like me, with sequence data every day, probably winced a little bit when you heard me read that out because, you know, it is actually not the case.
Indeed, Buggs’s own research led to a paper he co-authored in Nature Ecology & Evolution — “Convergent molecular evolution among ash species resistant to the emerald ash borer” — where different genes led to widely different gene trees among closely related species of ash trees. In his lecture he notes that yes, the paper produced a “consensus” tree, but that doesn’t mean the genes gave the same tree. Instead, it was “the best tree that we could get out of all the very, very divergent gene trees.”
That example might be dismissed by Dawkins because it is looking only at species within a genus, and the species might still be capable of crossing with each other. But Buggs points out that different genes are found to give different trees even when the species being studied are very different. He gives the example of a paper that studied the relationships of eudicots (a group of flowering plants that have two seed leaves). This is penetrating deep into the tree of life. He shows a diagram from the paper revealing the “discordance” of various gene-based trees:
Dr. Buggs then comments:
So according to Richard Dawkins’s test of the Darwinian Tree of Life, we don’t have much support for it, do we? It looks more like the hypothesis that he set up for an intelligent designer.
On its own terms, the Dawkins test for evolution has come up for ID.
So where does Richard Dawkins now stand on this issue? Does he still think that this is a powerful test for ID versus Darwinian evolution? Will he abandon the test, or is he now persuaded by ID? Or has he now changed his mind about how evolution works?
Many Other Recent Papers
It isn’t just Dr. Buggs who is saying this. There are many other examples from other recently published papers showing incongruence among trees of life (all emphases added):
Dominik Schrempf and Gergely Szöllősi (2020). The Sources of Phylogenetic Conflicts. In Scornavacca, C., Delsuc, F., and Galtier, N., editors, Phylogenetics in the Genomic Era, chapter No. 3.1, pp. 3.1:103.1:23 (2021).
This paper finds that a “conflicting phylogenetic signal between genes is commonplace.”
Richard H. Adams, Todd A. Castoe, and Michael DeGiorgio, “PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments,” Bioinformatics, 37(13), 1923–1925 (2021).
Says this paper: “An immediate challenge is to address the pervasive phylogenetic conflict observed in whole genome data.”
Caroline Parins-Fukuchia, Gregory W. Stull, and Stephen A. Smith, “Phylogenomic conflict coincides with rapid morphological innovation,” Proceedings of the National Academy of Sciences (PNAS), 118, No. 19: e2023058118 (2021).
This paper notes that, “Phylogenomic conflict, where gene trees disagree about species tree resolution, is common across genomes and throughout the Tree of Life.”
Gonzalo Giribet, “Genomics and the animal tree of life: conflicts and future prospects,” Zoologica Scripta, 45: s1, pp 14-21 (2016).
Similarly, this paper states: “A ‘new kid on the block’, phylogenomics, is adding another type of controversy never seen before in molecular phylogenetics: highly supported contradictory results.”
Nosenko et al., “Deep metazoan phylogeny: When different genes tell different stories,” Molecular Phylogenetics and Evolution, 67: 223-233 (2013).
This paper reviews studies examining the relationships of animals and finds many examples of conflicts:
To unravel the causes for the patterns of extreme inconsistencies at the base of the metazoan tree of life, we constructed a novel supermatrix containing 122 genes, enriched with non-bilaterian taxa. … Different gene matrices tell different stories … The lack of resolution for the deep nodes in this tree reflects major conflicts between the previously published metazoan phylogenies … the best-fitting model left the relative positions of the Bilateria, Coelenterata, and Placozoa–Porifera clades unresolved. … The multiple conflicting metazoan phylogenies presented here and in previous publications have one feature in common: they have long terminal and short internal branches. … To summarize, this study generated three incongruent, yet strongly supported tree topologies…
Reddy et al., “Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling,” Systematic Biology, 66(4): 857-879 (2017).
This paper also notes that scientists hoped that by sampling large amounts of data, they would resolve conflicts among trees. But the hope was dashed, especially within the class of birds:
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflict in estimates of phylogeny. … [P]hylogenomics seemed poised to fulfill this promise to resolve the tree of life. However, analyses of large data matrices have sometimes yielded incongruent topologies, emphasizing that data collection alone is not sufficient to reach this goal.
Cédric Blais and John M. Archibald, “The past, present and future of the tree of life,” Current Biology, 31: R311-R329 (2021).
This review of the debate between proponents and critics of the “tree of life” hypothesis acknowledges how frequently gene-based trees can conflict, though it postulates that some vertical signal of descent is still present even if it is obscured by processes such as horizontal gene transfer:
Some twenty years ago, the foundations of the tree of life were shaken by the realization that prokaryotic genomes are comprised of genes with different evolutionary histories. … The subsequent explosion of whole-genome sequencing in the late 1990s and the rise of comparative genomics was expected to validate and solidify Woese’s tree. These hopes were short-lived. Phylogenetics soon showed that different genes within the same genome could yield very different tree topologies, and even closely related organisms were found to differ substantially in gene content. A new evolutionary force was invoked: lateral gene transfer, the exchange of genetic material between different species. …
[…]
Resolving a statistical tree of life that unites all extant species may still be possible, contrary to the expectation that only localized tree patterns would survive pervasive lateral gene transfer. But it no longer corresponds to a complete, all-encompassing representation of the genetic history of organisms, as it does not follow any single gene’s history. If the tree of life still stands, it does so in a qualified sense. …The continued use of the tree of life for classification is thus as much a reflection of its practical convenience and historical and cultural inertia as it is a commitment to natural classification.
Extracting phylogenetic signal from genomic data can be difficult, and much of the evidence for ancient relationships is inconclusive at best. Phylogenetic methods designed to build a tree will do so whether it is the best fit with the underlying data or not. Networks, on the other hand, capture incongruences in genomic data without imposing an interpretation.
Juli Berwald, “Why evolution is not a tree of life but a fuzzy network,” Aeon (2022).
This article quotes geneticist Rasmus Nielsen of UC Berkeley: “That whole abstraction of evolution as being a tree, we always knew was a little inadequate … But now we know it’s really inadequate.”
Nielsen continued: “‘I think that process of splitting up and merging back together again, and getting a bit of DNA from here to there, that’s happening all the time, in all of the tree of life,’ Nielsen said. ‘And it’s really changing how we’re thinking about it, that it really is a network of life, not a tree of life.’”
The article thus describes the history of life as a reticulated pattern rather than a tree: “The hypothesis of reticulate evolution is that species are not as isolated from each other as Haeckel’s branching trees propose. Instead, species both diverge and merge together. The tree of life doesn’t look like a tree so much as the reticulated pattern of a python’s skin.”
This phenomenon of genes appearing in locations not expected by traditional vertical common descent is found very frequently, for “Roving genes have been found in every branch of the tree of life where geneticists have looked.” The article asks “If species don’t rest neatly on the ends of tree branches, what does that mean for Haeckel’s model of the evolutionary tree? Should we throw it out?”
A paper examined studies of fish relationships and found: “For a long time, geneticists studying this large group puzzled over its evolutionary history, with different studies finding different relationships that seemed to conflict with each other.”
The article closes by explaining that nice, neat evolutionary trees are not accurate: “I imagine having the chance to speak to my students again. I would place Haeckel’s tree on the screen and tell them that it is an anachronism.”
Testing the Test
I can’t conclude before remarking on the validity of Dawkins’s test of intelligent design. In some ways it is dubious, but in other ways it makes some sense. He’s probably right that “perfect” congruency among trees is not best explained by intelligent design. But ID as a scientific theory does not claim that everything must be the result of design. After all, the most that perfect phylogenetic congruency would demonstrate is common ancestry — an idea that’s accepted by some proponents of intelligent design because the original design could have been located in the common ancestor!
Also, Dawkins would be wrong to claim that any degree of treelike distribution of genes refutes intelligent design. This is because designed structures are loaded with functions, and functional components often depend upon and interact with other functional components in logical, functionally necessary ways. This can lead to non-random correlations and hierarchical distributions of traits — i.e., design can give you some treelike structure in a dataset!
For example, when you find buttons on a shirt, you’re also going to find buttonholes. When you find a wheel on a vehicle, you’re almost always going to find an axle, too. These correlations can lead to a treelike distribution of traits. Physicist Brian Miller explains this concept in a recent Volume, Science and Faith in Dialogue:
Design architectures often fall into a hierarchical pattern. All transportation vehicles have certain common features such as allocated space for cargo and or passengers, propulsion system and steering. Cars possess all these features plus such components as wheels, breaks, coolants, lubricants and axles. Toyota Camry models possess all these features plus additional specialised components. The similarities in transportation vehicles would likely fit into a constructed tree at least as well as different groups of species.
There are undoubtedly many analogous correlations between biological traits —which lead to some treelike structure to a dataset. For example, genes for noses in mammals will probably also be found with genes for nose hairs. And genes for toes in terrestrial tetrapods often correlate with genes for toenails! But intelligent agents are not compelled to distribute traits as a rule according to a nested hierarchy. Thus, as Dr. Miller explains, finding some treelike structure but also lots of non-treelike distribution of traits is a reasonable expectation of design:
While many features in human products fit into a hierarchical tree-like pattern, many break that pattern. A police car and an airplane both have two-way radios while two-way radios are absent in most other cars. In addition, the same circuitry is implemented in a wide variety of vehicles to meet similar goals. This pattern reflects how engineers often create modules that can be used in diverse contexts. The modules must be designed with the explicit intent of operating in different products, and the products that use the modules must be designed to properly incorporate them into their operations. The same pattern and constraints are observed in life.
A further note: In the 2009 interview, Dawkins’s refers to “genes that are no longer functional,” aka so-called pseudogenes. He argues that this refutes intelligent design because no designer would put identical non-functional genes in the same locations of the genomes of different species. But this is a weak argument given that so many pseudogenes are now known to have function. Shared pseudogenes that truly are nonfunctional are probably better explained by common ancestry than by common design. That said, even if they are nonfunctional today, it’s possible that such pseudogenes were originally designed to be functional but their functions degraded over time so that they are “no longer functional.”
This is again where design and common ancestry could intersect: shared pseudogenes — if truly nonfunctional — may have been originally designed as functional, but they would most likely have been designed in the common ancestor rather than designed in species separately. Dawkins’s point about pseudogenes is not a test of design on the grand scale but only a test of separate yet common design as compared with common ancestry (which could still potentially involve design).
What Will Richard Dawkins Say Now?
In any case, it’s true that the papers and articles I cited above were not written to support intelligent design. However, they affirm that there are frequent conflicts between phylogenetic trees, and they affirm non-treelike data among different genes and different species. This conclusion doesn’t come only from old papers or papers studying the tips of the tree of life, but from recent studies looking at key aspects of that tree, such as fundamental animal or plant or microorganismal relationships. And this frequent incongruity and discordance between phylogenetic trees is exactly what Dawkins says is predicted by intelligent design.
Dawkins has set up a test for Darwinian evolution versus intelligent design. He needs to live with his own repeated statements. Will he admit that his prediction has failed for evolution but succeeded for intelligent design?
Subscribe to:
Posts (Atom)