Yet more on the undeniability of the role of information in biology.

As Undeniable Debuts in Paperback, Frontiers in Biology Demonstrate Axe’s “Functional Coherence”
Evolution News | @DiscoveryCSC

Three brand new avenues of scientific discovery appear to need nothing from Darwinism. Instead they display in life what protein chemist Douglas Axe calls “functional coherence.” As Dr. Axe writes in his book Undeniable: How Biology Confirms Our Intuition That Life Is Designed — now out in paperback! — this quality represents “the hierarchical arrangement of parts needed for anything to produce a high-level function — each part contributing in a coordinated way to the whole.”

He writes there:

No high-level function is ever accomplished without someone thinking up a special arrangement of things and circumstances for that very purpose and then putting those thoughts into action. The hallmark of all these special arrangements is high-level functional coherence, which we now know comes only by insight — never by coincidence.

This is just what we see at the leading edges of biology.

What Is Circular DNA?

Writing in the journal Science, Elizabeth Pennisi quips, “Circular DNA throws biologists for a loop.” There’s something old and new about these closed loops of DNA that range in length from 300 to 16,000 base pairs. As she explains:

Are geneticists ready for the circulome? For decades biologists have known of mysterious rings of DNA in the nuclei of some human cells, interspersed among the linear chromosomes. Now, what were once curiosities are increasingly looking like key players in health and disease. The circulome, a term introduced at the Biology of Genomes meeting here, may turn out to be a new frontier in genetics. 

Not to be confused with bacterial chromosomes, which are often circular, nor with circular RNA transcripts, these circular DNA loops, formally called “extrachromosomal circular DNA” or eccDNA, are just now coming to the attention of molecular biologists. “That they exist in normal cells with such huge complexity is amazing,” one said. Another commented, “It basically opens a new field and a new way of thinking about DNA and about how dynamic the genome is.” The approach proposed by Axe and other design proponents, approaching a problem with the assumption that parts of a working system must be playing important roles, seems best suited to find out what eccDNA is doing.

How Can We Crack the Sugar Code?

The DNA code was the first to be elucidated. The protein code, with its more complex alphabet, is still being deciphered. But coming up in the challenge of biological forensics is the sugar code. In Nature, Esther Landhuis looks ahead to “sweet success” with new tools for making progress in glycobiology, or glycoscience.

What makes this area in molecular biology so challenging is the “crazy complexity” in the glycome. Proteins and genes, for all their complexities, can be boiled down to linear sequences of building blocks. Sugars, by contrast, branch out in all kinds of directions. Landhuis explains why cracking this code is so hard:

Researchers generally study biomolecules such as DNA and peptides by synthesizing them in the lab and then probing how they react to different circumstances. But DNA and peptides are linear molecules with no branches, and tools for analysing them took off in the 1970s and 1980s. Sugars, however, have numerous branching points and each of those linkages can exhibit left- or right-handed asymmetrical forms depending on the orientation of the attached molecule. They also have exponentially more potential configurations than do DNA or proteins, and that makes them much harder to synthesize in the lab, says Peter Seeberger, a biochemist at the Max Planck Institute of Colloids and Interfaces in Munich, Germany. DNA is made up of four nucleotides (G, A, T and C), so there are theoretically 4,096 possible ways to build a string of six elements, or a 6-mer. Proteins have more building blocks (20 amino acids) and can potentially assemble into 64 million different 6-mers. But 6-mer carbohydrates can adopt 193 billion possible configurations. As a result, tools for synthesizing sugars are about 35 years behind those for DNA and peptides, Seeberger says.

Despite these challenges, Landhuis says that new tools are becoming available to analyze and classify sugars and detect their roles in cells. One new technique allows researchers to detect which “glycans” (sugars that stud the surfaces of cell membranes) bind to proteins. This can accelerate functional studies, cutting through years of difficult work. With an eye out for functional coherence, the sky is the limit for discovering roles of sugars in biology.

How Does a Cell Become an Organism?

Ever since John Sulston began to map the fate of every cell in the lab roundworm Caenorhabditis elegans, a dream of biologists has been to follow the pathways of cells in complex organisms, including human beings, from zygote to adult. In Nature, Ewen Callaway calls this project “The trickiest family tree in biology.”

The effort is attracting not just developmental biologists, but also geneticists and technology developers, who are convinced that understanding a cell’s history — where it came from and even what has happened to it — is one of biology’s next great frontiers. The results so far serve up some tantalizing clues to how humans are put together. Individual cells from an organ such as the brain could be related more closely to cells in other organs than to their surrounding tissue, for example. And unlike the undeviating developmental dance of C. elegans, more-complex organisms invoke quite a bit of improvisation and chance, which will undoubtedly complicate efforts to unpick the choreography.

Sulston and two colleagues went on to receive the Nobel Prize in Physiology or Medicine in 2002 for their work on the humble roundworm. In a video from Discovery Institute, “How to Build a Worm,” Paul Nelson explains the implications for intelligent design. Each cell division begins a descent down a decision tree, he shows, leading to specializations and irreversible fates as different genes get switched on or off, and organs develop.

Sulston set the “gold standard” with his work. Following the development of more complex animals, like mammals or birds, will be extraordinarily more challenging. “But even incomplete cellular ancestries could be informative,” Callaway says hopefully. With new tools like CRISPR-Cas9 and recombinases, some of the problems are becoming tractable. Here’s one brief look into this frontier:

The trees they produced show that a small number of early-forming embryonic lineages give rise to the majority of cells in a given organ. More than 98% of one fish’s blood cells, for instance, came from just 5 of the more than 1,000 cell lineages that the team traced. And although these five contributed to other tissues, they did so in much lower proportions. They were almost entirely absent from the muscle cells in the heart, for example, which was mostly built from its own small number of precursors. “It was profoundly surprising to me,” says Shendure. His colleague Schier says he is still trying to make sense of the data.

Many questions arise in this field: Is there more than one way to build a heart? How comparable are the developmental stages in different individuals? Callaway ends with images of the great voyages of discovery:

It is that vast unknown that could make such work transformative, says Elowitz: “It would change the kinds of questions you could ask.” Sulston’s map led biologists into uncharted territory, says Schier, and this could do the same. “We can’t tell you what exactly we’re going to find, but there is a sense that we’re going to find some new continents out there.”

Opportunities for Design Science

These three frontiers show how much work remains in biology. The shallow science of Darwinism seems ill-prepared for it; indeed, none of the three articles talks about evolution at all. When poised at the dock of a great voyage of discovery, the time may be ripe for new heads and new ideas.

The recent failings of Darwinism with ENCODE, junk DNA and other fallen predictions are fresh in scientists’ minds. Books we published in 2016 and 2017 by  Michael Denton, Tom Bethell, and Jonathan Wells  document Darwinism’s theory in crisis, a tottering house of cards, reliant on zombie icons that only serve to delay the inevitable. They make the negative case against Darwin compellingly.

But the frontiers described above are just a few that help open up a fresh, new, positive case. They offer the opportunity to prove the value of the integrated “systems biology” approach that Steve Laufmann talked about in a recent pair of ID the Future podcasts (see here and here ). He described how biologists with an engineer’s perspective are able to detect patterns of function, making sense of the welter of data, showing that “this makes sense because” it fits into the big picture.

Doug Axe’s concept of “functional coherence” can be a guiding light in the unknown waters of these voyages of discovery. Needless to say, the potential benefits of successful design-theoretic biology at the cutting edge are enormous: new approaches to cancer treatment, improvements to agriculture, or insights into biomimetic applications. This is our chance to redeem science from a veritable dark age of materialistic reductionism — stepping boldly forward into a new era where the design everyone admits is intuitive becomes design that is transformative.