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Saturday 14 May 2022

The selfish gene dethroned?

Biologist Michael Denton: Paradigm Shifts

Evolution News
 
On a classic episode of ID the Future, biologist Michael Denton reflects on paradigm shifts in science he’s witnessed in his lifetime and how his own thinking has changed. He also looks at how these shifts challenge Darwinian evolution in new ways. Denton is the author of the new book The Miracle of Man: The Fine Tuning of Nature for Human Existence. Download the podcast or listen to it here.

 

Beware the ides of march?

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The new Rome?


Why OOL science remains the key issue in the design debate.

 How does one select the key issue in the design debate. I would say that it is the one most likely to force the opposition to play defense. From that standpoint OOL science, in my humble opinion, is hard to beat. Darwinism is the opposition's opening salvo against the notion of actual design being a necessary explanation for the technology evident in nature. The claim is that some combination of chance and necessity is a better explanation for this technology and thus any perception of intelligent design was illusory,a kind of pareidolia. Well if you say so mr. materialist, but in as much as science is about objectively testing truth claims how are we to test this particular claim. Well,if Darwinian evolution is the source of the (apparent) design in biology we should surely be able to observe some co-relation between the amount of Darwinian evolution and the amount of Design in the history of life. Hence the need for a simple beginning to life.

It simply will not do for there to exist any of the design that Darwinism is supposed to have successfully explained away prior to any Darwinian processes. So how's that search for a simple lifeform going?

Yes,the technology is real.

Natural Machinery Operates Without Intervention; But How?

David Coppedge
 
 

In Francis Bacon’s day, it was easy to oversimplify nature. Elizabethan scientists began to conceive of a world that ran like a machine. Robert Boyle was a strong proponent of the mechanical philosophy. Soon, Isaac Newton’s clockwork heavens reinforced the notion that all the Creator had to do was wind it up, and let it run all by itself. From Boyle to Babbage, the Newtonian revolution showed the way for scientific progress: just uncover the natural laws that make the universe run. 

By the late 18th century and into Victorian times, mechanical philosophy was sufficient unto itself. An original Designer could be conceived of, perhaps, but as science progressed, the Prime Mover had less and less to do. Some argued that it was an insult to the Watchmaker to suggest he needed to intervene and fix the watch.

Then molecular biology arrived, and we found out the clocks are real. Literal machines made of molecules make life run. Simultaneously, the computer age dawned and we learned a bit about programming. Now, robotics is here. We’re going to need a new philosophy: one that can handle realities the Elizabethans and Victorians could never have imagined.

It’s important to note that we’re not speaking of mechanistic or reductionist philosophy. See Jay Richards’s clarification. We seek an explanation for how natural machinery can operate without continuous intervention.

Real Clocks

Paley’s “watch on a heath” was only an analogy in 1805. Now, we can see real biological clocks of amazing design and precision in the cells of life. Current Biology talks about “unexpected biochemical cogs” in a cyanobacterium, freely using the word “clock” as well as “oscillator,” “regulator,” and “switch.” The circadian clock runs on a much slower schedule than most cellular reactions. It’s calibrated to the 24-hour day-night cycle, and keeps constant time even when the temperature changes. It would have been astonishing to Paley or Bacon to learn that a three-protein oscillating machine is found in such a tiny organism. In higher vertebrates, biological clocks are even more elaborate.

Real Engines

Is this the little engine that could? Penn State News finds that “little engines” of kinesin (see our animation) can do more than thought on their microtubule tracks. These little walking robots, one ten-thousandth the diameter of a human hair, not only walk the tracks but help them grow. When kinesin-5 pauses at the end of a microtubule, it “generates pushing forces, which slide the microtubules apart and essentially allow the motor to grow the microtubules.” [Emphasis added.]

Real Solar Panels, Quality Control, and Recycling

The Salk Institute calls chloroplasts “solar panels” and reveals how the cell monitors them with a “quality control check” that can “recycle” the parts of damaged chloroplasts. Notice the mechanical word: they uncovered “how plants thrive using a natural mechanism to recycle chloroplasts.” 

Real Stress Management

Another “fundamental biological mechanism” is described by bioscientists at the University of Heidelberg. In a common lab plant, they found that proteins are “further adapted” after they are manufactured “for their specific jobs.” In one case they studied, chemical tags regulate the stress response to drought by closing the stomata and lengthening the primary root.

Real Coordinated Timing and Assembly

Scientists at Virginia Tech found that, during development, “timing is indeed everything.” They use music as an analogy:

Everyone who has played in a band or orchestra knows that playing in time creates music, while playing out of time creates cacophony. In an orchestra, each player may be out of tune when warming up, but eventually, all players must reach the same pitch, rhythm, and timing to produce a viable piece of music.

They found something similar in dividing cells. Just as live musicians can compensate for other players’ changes in tempo, “cells modulate the exact timing of when crucial cellular eventshappen, slowing down or speeding everything up to make sure everything is playing its proper part at the right time.” They were “astonished to see how greatly the starting conditions for each cell could differ and still lead to the same outcome,” the article says.

Is it just an analogy to call a ribosome a “protein-making factory“? Ask the researchers at Rockefeller University, who think “factory” is an appropriate description:

Ribosomes, the molecular factories that produce all the proteins a cell needs to grow and function, are themselves made up of many different proteins and four RNAs. And just as an assembly line must be built before it can manufacture cars, these tiny factoriesmust be constructed before they can put proteins together.

Real Mobile Factories

Rockefeller is not alone in using the word factory — only the one they found escaped detection till now. “Salk Scientists Discover Protein Factories Hidden in Human Jumping Genes,” a news item from Salk Institute says. Researchers found a third Open Reading Frame (ORF0) in certain jumping genes known as LINE-1 elements. 

“Jumping genes with ORF0 are basically protein factories with wheels,” they said. The fact that they consider “evolution” to be the driver of the bus does not negate the fact that they are real machines that must function properly, otherwise it could cause disease. And there are 3,500 of these “factories with wheels” in the human genome.

Real Repair Stations

The nuclear membrane gained new respect from scientists at the University of Southern California when they found that it’s a lot more than “just a protective bubble” around the nuclear material. A team at USC has documented “how broken strands of a portion of DNA known as heterochromatin are dragged to the nuclear membrane for repair.” At the inner wall of the nuclear membrane, “a trio of proteins mends the break in a safe environment, where it cannot accidentally get tangled up with incorrect chromosomes.” (The discovery was made in fruit flies.)

As for heterochromatin, this “mysterious part of the genome” composed of repetitive elements has been promoted from “junk DNA” to superhero (watch the word “mechanism”):

The reason why we don’t experience thousands of cancers every day in our body is because we have incredibly efficient molecular mechanisms that repair the frequent damages occurring in our DNA. But those that work in heterochromatin are quite extraordinary.

Real Repair Machines

We see “mechanism” also used to describe a “new class of DNA repair enzyme” found by researchers at Vanderbilt University. This adds to the same work that earned a Nobel Prize earlier this year. This enzyme has some “remarkable properties,” they said, such as the ability to find damage indirectly without actually contacting the lesion, and the ability to fix bulkier lesions than other repair mechanisms can. 

“Our discovery shows that we still have a lot to learn about DNA repair, and that there may be alternative repair pathways yet to be discovered. It certainly shows us that a much broader range of DNA damage can be removed in ways that we didn’t think were possible,” said Eichman. “Bacteria are using this to their advantage to protect themselves against the antibacterial agents they produce. Humans may even have DNA-repair enzymes that operate in a similar fashion to remove complex types of DNA damage.

Real Shaping Machinery

Nonsense-mediated mRNA decay (NMD) is described in Nature Reviews: Molecular Cell Biology as “an intricate machinery that shapes transcriptomes.” The abstract mentions “intricate steps” in this process, “cellular quality control,” and the ability of NMD to “dynamically adjust their transcriptomes and their proteomes to varying physiological conditions.”

Real Packaging

grad student at MIT is studying how cells pack two meters’ worth of DNA into a cell nucleus. It’s like “trying to fit 24 miles of string into a tennis ball,” Abe Weintraub says. He’s intrigued by the fact that “DNA gets packed tightly in organized loops, rather than being haphazardly crammed into cell nuclei.” The specific 3-D organization appears to affect its functionality, because mistakes cause cancer and other diseases.

Philosophical Implications

Those are a few recent examples of the “machine talk” pouring out of labs around the world. This is not just metaphorical language for “nature” like the Victorians used. It’s observation and description of realities the early mechanical philosophers could not have imagined. And it’s everywhere. Machine talk is driving an explosion of discovery in science. 

The old mechanical philosophy is hopelessly inadequate for these realities. The reason? We know from our experience that unguided natural law does not produce machinery, factories, and quality control. Something else is required: information.

The Santa Fe Institute identifies this critical part of the new 21st-century philosophy. A working group met to discuss the question, “What physical principles predict life?” They put the question into stark perspective:

We are immersed in life here on Earth, but life isn’t found on the Moon. Nor has it arisen, so far as we know, anywhere else in the solar system. Why do some physical environments precipitate life, and why don’t others?

It’s not enough to say that the moon has no water:

If the Earth really does use sunlight to convert a disorderly lump of mass and energy into organized living things, why can’t the Moon, Earth’s nearest neighbor, do something similar using different mechanisms?

This implies that “natural laws” alone are insufficient to account for the difference. David Wolpert was on hand to share an important suggestion:

One part of the answer, Wolpert says, might lie in information theory. In addition to being central to modern biologists’ understanding of evolution, information theory overlaps heavily with thermodynamics, the area of physics concerned with how the different kinds of internal energy of a system (such as heat and stored chemical energy) might be affected by the outside world.

In a video clip Wolpert elaborates on this theme. Apparently many others in the working group felt it was a promising avenue of thought.

“In many talks and discussions, the nature of information flow between different scales of organization emerged as an important theme and open question,” says O’Dwyer. “We look forward to future collaboration on each of these ideas.”

Willaim Dembski’s book Being as Communion would serve as a fine discussion starter. Wolpert comes so close, but is still so far from explaining what he set out to explain: why the moon differs from the earth. He talks about information flow through the system, but the moon gets exactly the same sunlight the earth does. And he never defines what information is, or where it comes from. Here is where intelligent design can offer real, substantive insight.

Information is the key to a “mechanical” philosophy for the 21st century. We know, because we have a great deal of experience producing information and imposing it on matter. We build computers. We make robots. We make clocks and trucks and factories. Indeed, we can even make machines that make other machines, and robots that increasingly look and act like us. 

Our machines can run like clockwork, not because we shined sunlight on a “disorderly lump” and waited for natural laws to take their unguided course, but because we infused the lumps with information. And since we know that intelligence was the true cause that resulted in those lumps of raw material becoming Steinway pianos, Toyota robotic assembly lines, and New Horizons spacecraft, it’s a fair inference that intelligence is the true cause behind atoms that become kinesins, ribosomes, and circadian clock proteins.

This article was originally published in 2015.

 

Trying to school JEHOVAH again?

Is the Human Shoulder Badly Designed?

Jonathan Wells
 
 

A few months ago, I fell and dislocated my left shoulder. My upper arm bone was put back in its socket the same day, but then I spent months in physical therapy to regain full function. In the process, I have learned a lot about an amazing joint that I previously took for granted.

The drawing below shows only part of the human shoulder’s anatomy. Not shown is the large deltoid muscle, which overlies the shoulder joint and connects the upper arm bone (humerus) to the collarbone (clavicle) and the shoulder blade (scapula). Also not shown is the trapezius muscle across the back, which connects the left and right scapulas. Both the deltoid and the trapezius play important roles in stabilizing the joint. 

Image source: National Institute Of Arthritis And Musculoskeletal And Skin Diseases (NIAMS); SVG version by Angelito7, Public domain, via Wikimedia Commons.

Anatomy of the Shoulder Joint

In the drawing, yellow indicates bone, red indicates muscle, blue indicates tendon, and purple indicates bursa (a fluid-filled cushion). The dashed black lines indicate the hidden ball-and-socket joint between the humerus and the scapula. Unlike the hip joint, in which the ball is deeper in the socket, the shoulder joint is more open. This means the shoulder joint is less stable than the hip joint, but it is also much more flexible. In fact, it is the most flexible joint in the human body. 

The biceps muscle at the lower left gets its name from the fact that it has two heads. One attaches, through a tendon and a small bursa, near the top of the humerus. The other head attaches to the coracoid process, an extension of the scapula. The lower end of the biceps muscle is attached to the forearm. Although it is primarily involved in moving the forearm, its divided head helps to stabilize the shoulder joint.

Both the flexibility and stability of the shoulder joint are due primarily to the muscles of the “rotator cuff,” listed on the left side of the drawing. All four of the listed muscles stretch across the scapula and attach to the top of the humerus. For a 10-minute tutorial on the rotator cuff, see here. For a longer (20-minute) tutorial on the movements, bones, and muscles of the shoulder, see here.

The more I have learned about the shoulder joint, the more I have been impressed by its specified complexity, which points to intelligent design. Imagine my surprise when I came across a six-and-a-half-minute video claiming that the human shoulder is a “design disaster.” The video was made by Cheddar News, which describes itself as “the only news network focused on the next generation of innovators and decision-makers[.] Cheddar News is where forward thinkers go to learn about the people, ideas and innovations that are driving change and creating what’s next.”

 

I am confident that a rigorous argument can be made for the intelligent design of the human shoulder. But that is not what I present here. In what follows, I examine the claims against design that are made in the Cheddar News video.

Proof that the Human Shoulder Is a Design Disaster?

The video’s producer is Natalia Ryzak, who has a master’s degree in journalism from Columbia University. At the beginning, Ryzak explains that “human shoulder blades tilt down and outwards, whereas chimps tilt up. Small variations like this are the reason humans have awful shoulders. And chimps, with whom we share nearly 99% of our DNA, don’t.” For that, Ryzak continues, “we can thank evolution — or more specifically, how we are outpacing it.”

But the tilt difference does not explain why the human shoulder is “awful.” If we spent most of our time swinging from tree branches, it might; but we don’t. And the claimed 99% similarity between human and chimp DNA has no bearing on the issue.

Ryzak goes on (from 0:47 to 0:59) to say:

Side effects of a human shoulder may include dislocation, separation, rotator cuff tears, bursitis, tendonitis, tendonosis, impingement syndrome, instability, arthritis, adhesive capsulitis (frozen shoulder), and fracture.

But these are not “side effects,” any more than getting a flat tire is a “side effect” of making an automobile. Or having a roof torn off by a tornado is a “side effect” of building a house. And these problems are not unique to humans: Chimps can also suffer from arthritis and fractures, among other things.

Enter Nathan Lents, professor of biology at the John Jay College of Criminal Justice in New York City. In 2015, Lents argued on his blog that the human eye is badly designed, primarily because “the vertebrate retina is wired in backwards.” Like Richard Dawkins and others before him, Lents based his claim on the fact that the light-sensing cells face away from the incoming light. But evidence published from the 1960s onward — and reported in standard textbooks — shows that this arrangement is far better than the one Lents favors.

Back to the video on “Why the Human Shoulder is a Design Disaster.” Lents says (at 1:30) that the shoulder is “more of a floating joint than any other joint in the body.” Ryzak explains that the outer layer of muscles (consisting of the deltoid and trapezius) is stronger than the inner layer (the rotator cuff). Then Lents continues (from 1:59), “Having such an overlapping meshwork of muscles, what you’re inviting is pinching, and tearing, as the orientation can shift.” Lents compares the shoulder joint to the hip joint, in which “the relationship of the hip to the leg is fairly fixed in place.”

So far, the video has summarized the structure of the shoulder and its difference from the hip. The shoulder is more flexible than the hip. Good thing, too, or we wouldn’t be able to perform many of the actions we do. Just watch an acrobat performing on the parallel bars. Or a baseball player pitching a fastball. Or an athlete swimming the butterfly.

But journalist Ryzak confidently concludes ex cathedra (starting at 2:19) that “we’ve proven to you just how cr*ppy our shoulders are.” How so? Ryzak doesn’t say. Instead she simply suggests going “back into the evolution part.”

Does Evolution Explain It All?

According to Lents (starting at 2:28), “In our quadrupedal ancestors, in our deep past, really we had four legs, they weren’t really arms, to speak of. When you think of a dog and a cat, they don’t have arms, they have legs. But they still have a shoulder joint, as we can think of it.”

Then Ryzak says, “Our shoulders evolved for a life in the trees, swinging and hanging out. Then we left the trees behind and began to stand upright. This freed our arms up for other purposes, like hunting and gathering.” So from four-legged animals that walked and ran on the ground, we get animals that spend some of their time on the ground but mostly swing from branches to branches in the trees. Then those animals “evolved” into animals that stood upright and used their arms for other purposes. This is the standard Darwinian narrative. But how, exactly, did four-legged animals on the ground evolve into two-armed animals that swung on tree branches, which then evolved into two-armed animals that stood upright on the ground? The video offers no explanation; only an imaginative story.

Lents continues (starting at 2:54), “We are partially adapted for throwing, which is… no other animal in our group of animals throws anything.” This is not true: Chimps can throw, though not as far or as accurately as humans. Indeed, they are infamous for flinging feces at visitors to zoos.

But that’s a minor detail. Lents goes on to say, “So we believe that throwing was a very strong evolutionary pressure as we began to hunt — throwing spears, thrusting as well, so thrusting and throwing are very specific kinds of motion. And that required that floating nature to our shoulder.” But “evolutionary pressure” just means that throwing favored the survival of early humans. It does not account for the origin of the human shoulder. As Darwinian biologists wrote in 1996, adaptations “concern the survival of the fittest, not the arrival of the fittest.”

So the claim that “we left the trees behind and began to stand upright” does not explain the remarkable anatomy of the human shoulder. After all, chimps leave the trees on a regular basis (though they don’t stand upright). Yet their shoulder anatomy has not changed.

The Problem and Its Solution

According to Lents (at 3:57), “Part of the problem in present-day humans is not so much a bad shoulder design but a mismatch between what our shoulder is designed to do and how we use it on a daily basis.” Of course, Lents doesn’t think the shoulder was intelligently designed. As a Darwinist, he believes that the shoulder evolved through accidental variations and survival of the fittest. And in our immediate ancestors, the shoulder was adapted (“designed”) to swing through trees.

Most of our modern activities are very different. Ryzak adds (starting at 4:16), 

It might surprise you, but simply sitting at your desk is a major contributor to shoulder problems. When we hunch forward for days, hours, months, years on end, we end up causing unnecessary pulls and strains on our rotator cuff muscles. That can lead to injuries.

Lents explains (starting at 5:20) that you can minimize shoulder problems by “changing the way you eat, changing the ways you use your body.” And, Ryzak adds (from 5:34 to 5:52), “pay attention to basic posture.” So after all the talk about bad design and evolutionary mismatch, the solution to our “design disaster” is for us to pay attention to dietexercise, and posture

I think I could have figured that out without all the anti-design rhetoric and Darwinian storytelling. Oh, and I would add: Be careful not to fall in such a way as to dislocate your shoulder.

The sanctity of life: The Bible's view.

The question of the sanctity of human life(specifically at what point should human life be regarded as "sacred") has returned to the public square in big way recently. Much of the discussion has been about what the sciences of medicine and biology have to say as to when any human offspring should be considered a person.

Some maintain that as long as the infant is biologically attached to its mother it ought not to be considered a person and its life ought not to be accorded the same value as a person. This post is addressed primarily to those who are interested in what the bible has to say about the matter,there are individuals on both sides of the issue who are citing scriptures as an authority. I would like to lay out what scriptures and reasonings thereon inform the position of my brothers and me.

Genesis1:27KJV"So God created man in his own image, in the image of God created he him; male and female created he them. "

All life is the property of God Almighty, human life has a peculiarly sacred quality because Man is a living representation of the supreme divinity. Therefore the destruction of any human life apart from due process is sure to incur divine wrath.

Genesis9:5,6ASV"And surely your blood, the blood of your lives, will I require; At the hand of every beast will I require it. And at the hand of man, even at the hand of every man's brother, will I require the life of man.

6Whoso sheddeth man's blood, by man shall his blood be shed: For in the image of God made he man."

Does this include life in the womb? Consider.

Psalms139:15KJV"My frame was not hidden from thee, When I was made in secret, And curiously wrought in the lowest parts of the earth.

16Thine eyes did see mine unformed substance; And in thy book they were all written, Even the days that were ordained for me , When as yet there was none of them."

The Psalmist was certain that the Lord JEHOVAH loved him from the very beginning,because He knew that there was latent potential to reflect His glory in a unique way in this nascent being. Thus even before this potential was known to any other it was being keenly and sympathetically observed by its source.

Liluke1:42KJV"And she spake out with a loud voice, and said, Blessed art thou among women, and blessed is the fruit of thy womb. 43And whence is this to me, that the mother of my Lord should come to me? " No dedicated servant of JEHOVAH worthy of that designation could ever say "my body my choice". when we made our dedication we handed over all that we are and possess to their rightful owner i.e the God and Father of Jesus Christ. For all of JEHOVAH'S servants the fruit of the womb is JEHOVAH'S we are merely custodians of what is our Lord's the above quoted text further confirms his interest in the potential in the impregnated womb.

1Corinthians6:20NIV"you were bought at a price. Therefore honor God with your bodies."