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A “Mechanical” Philosophy for the 21st Century

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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 events happen, 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 factories must 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

A 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 latest 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.

Image: From The Workhorse of the Cell: Kinesin.