In the field of biomimetics, scientists study biological systems in the hopes of using what they learn to help improve human civilization. For example, a recent study of ants’ foraging behavior opened up an opportunity to enhance solutions to dynamic problems such as the closure of an airport, road, or manufacturing plant. This kind of research also carries implications for the debate between creation and evolution. 

Two roads diverged in a wood, and I—I took the one less traveled by,And that has made all the difference.

— Robert Frost, “The Road Not Taken”

Though popular in graduation speeches, these lines from Robert Frost’s famous poem likely would lack appeal among ants, even the literate ones. Rugged individualism just isn’t a virtue in the ant world. Ants rely on their colony to find the quickest routes between food sources and the nest; this is a phenomenon known as “swarm intelligence.”

Swarm intelligence represents decentralized computing by the ant colony. It relies on individual ants to find the most efficient paths to and from a food source. Scout ants lay a trail of pheromones to the food source, which routes foragers to these paths. As the foragers travel these paths, they lay more pheromones, amplifying the signal. This is an example of adaptive network design where, over time, the fastest routes tend to become more popular, while longer routes die away. For ants, adaptive network design works because the pheromone they deposit is volatile (meaning it evaporates). Thus, less efficient paths sit idle longer and eventually lose all trace of pheromones, while shorter paths are traversed more frequently and, thus, continuously reinforced with scent.

Ant-Inspired Algorithms

Ants’ foraging strategy for finding the shortest path to and from a food source inspired scientists to create the ant colony optimization (ACO) algorithm. An optimization algorithm is a set of instructions for finding the best solution to a problem. For example, an algorithm for finding the cleanest spoon might be as follows: (1) Compare spoon 1 and spoon 2. Keep the cleanest. (2) Compare cleanest spoon from previous round to spoon 3. (3) Repeat previous steps until you have compared nth spoon. Finding the cleanest spoon is pretty easy with this algorithm until you have more spoons than particles in the known universe, but even then it isn’t impossible.

ACO falls into a class of algorithms used to solve some of the most difficult computational problems, NP-hard problems. NP (nondeterministic polynomial time) problems yield numerical solutions (meaning you cannot find an equation to describe the solution); NP-hard problems yield numerical solutions that can take more than the lifetime of the universe to compute. (And you thought dial-up was slow!) How a protein folds into a three-dimensional shape and the famous traveling salesman problem (TSP) are both examples of NP-hard problems.

ACO has been used to solve various NP-hard problems. Studying actual ant colonies may lead to new principles for solving optimization problems and inspire enhanced ACO algorithms. In recent years, a group of researchers set out to observe how ants respond to dynamic mazes in order to find the shortest path between the nest and the food source.¹ By mapping the graphical solutions to an NP-hard problem known as the Tower of Hanoi (a mathematical game or puzzle), the researchers constructed a maze that could test the ants’ ability to find the shortest route. Even though the maze represented a relatively “simple” problem, there were over 30, 000 different possible paths from end to end of the maze.

Amazingly, the ant colonies were indeed able to find the shortest path through the maze from nest to food source. Additionally, the ants responded to blocks in the minimal path by finding a new alternative minimal path. How quickly the maze was solved could be mapped to two key parameters: colony size and exploration pheromones. Larger colonies found solutions more quickly than smaller colonies. Exploration pheromones mark the paths traveled by ants as they forage the maze. Not surprisingly, when pre-exploration was allowed, a new colony could reconstruct a minimal path more rapidly.

Observing how ants respond to changing mazes may inspire programmers to develop algorithms that offer efficient solutions to dynamic problems, like the closure of an airport, road, or manufacturing plant. Ants, as well as bees and slime molds, offer researchers in the fields of biomimetics and computer sciences the opportunity to reverse-engineer (or crack the secrets of) highly efficient optimization algorithms utilized in nature to benefit an advanced society. Yet, lurking in this quest are some important assumptions that bear on our philosophical understanding of nature.

Philosophical Implications

In looking to biological systems to inspire better designs, scientists are signaling that they expect to find that biological systems are regulated by rational rules and structures. Scientists are, in fact, trying to uncover the rules and structures. They do not expect to discover a hackneyed system with limited applicability; what they hope to find are universal guiding principles encoded into natural biological systems that can be applied to human problems.

While these assumptions and examples do not preclude an evolutionary explanation, they do not fit neatly into the popularized models of evolutionary theory. Instead, biomimetics compels us to ask the question, why would we expect to find intricate, sophisticated designs in nature unless they emanate from a rational source? How can it be that the solutions in nature are not just better adapted, but inherently structured as (or even more) elegantly than the best algorithms yet invented by humans?

Christians should not be surprised to find the natural world is rationally ordered, knowable, and useful because, as Scripture affirms, the Creator of the natural world is a rational being. For example, John 1 describes Christ as “the Word” (logos, which can also be translated as “reason”). Neither should the Christian be surprised to find that God has embedded special knowledge within creation. In Job 12, for example, the Bible implores, “Ask the animals and they will teach you.” The concordance we see between natural biological systems and the biblical description of the Creator add weight to the body of evidence for the Bible’s validity. The study of nature is just one of many disciplines that continue to point to Christ as logos, Savior, and Lord. (RTB,G)

Romans 1:20

Growing up in the Midwest instilled in me a fascination with thunder and lightning. Summer storms would light up the sky with brilliant flashes, filling the air with deafening thunderclaps. While others would seek refuge, I would search for the best vantage point to witness the spectacular show. One time, lightning struck a tree about 40 feet away from where I stood (in full disclosure, I was inside the house and not in danger of being struck)!

Lightning, as fleeting as it may be, shapes the land around us. Although many processes weather the landscape, a recent paper published in the journalGeomorphology demonstrates that rock formations of a particular shape and signature were thought to result dominantly from cold temperatures. However, studies of such rock formations in Lesotho, South Africa show that lightning strikes also play a major role.

The magnetic fields contained in the rocks distinguish the role of lightning in rock formation compared to that of cold weather. When rocks cool, they record the magnetic field of Earth in the location where they formed. However, lightning can reorient this field because of the high temperatures reached during a strike. Scientists found the magnetic signature expected from a lightning strike in rock formations usually attributed to cold weather processes.¹

This research confirms my intuition that we should pay attention to lightning whenever possible. Not only does it produce dramatic displays across the sky, it also significantly affects how quickly mountains change. (RTB)

*** Will Myers

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1. Matthew 6:25
   Therefore I say unto you, Take no thought for your life, what ye shall eat, or what ye shall drink; nor yet for your body, what ye shall put on. Is not the life more than meat, and the body than raiment?

   
   

2. Matthew 7:14
   Because strait is the gate, and narrow is the way, which leadeth unto life, and few there be that find it.

   
   

3. Matthew 10:39
   He that findeth his life shall lose it: and he that loseth his life for my sake shall find it.

   
   

4. Matthew 16:25
   For whosoever will save his life shall lose it: and whosoever will lose his life for my sake shall find it.

****Middle school is often a difficult time for students. I remember being one of five boys in a classroom with tables that sat four. Sitting at the table with three other kids, I noticed the fifth boy sitting at a table all by himself. As I moved over to his table so that everyone would have company, he seized the opportunity and moved into the seat I had vacated. Despite my desire to include everyone, I ended up alone. Planets also face difficult challenges due to interactions with other planets and stars—and the latest research indicates they often end up alone, floating through space.

Using a survey primarily sensitive to young, small stars, astronomers recently found an object dubbed PSO J318.5-22. Detailed analysis of this object led the researchers to conclude that it has a mass 6.5 times the mass of Jupiter and a surface temperature of 1160K (1628°F). Coupled with the spectral features of the object’s light (most notably, the lack of methane signatures) and its likely membership in the β Pic moving group of stars, PSO has an age near 12 million years.¹

While PSO J318.5-22 moves through space like a star, it exhibits all the characteristics of a planet. In fact, when astronomers compare the light signatures from PSO J318.5-22 with the light from planets in the HR 8799 system, they find great similarity. This result implies two things. First, PSO J318.5-22 appears to be a planet, not a star. Second, since planets form around stars, some process dislodged PSO J318.5-22 from its host star.

Because PSO now wanders around space unattached to a star, astronomers have the opportunity to study its light in much more detail than normally possible. For planets like those around HR 8799, the light from the star overpowers the light from the planet, making such observations difficult. Without this obstacle to overcome, telescopes can collect detailed information about the planet that will help determine how it formed and understand its future development.

The direct observation of a planet freely floating through space also buttresses the idea that planets in young systems encounter circumstances that drastically alter the planetary system configuration. For example, some scientists argue that our solar system started with five gas giants (Jupiter, Saturn, Neptune, Uranus, and one more). However, dynamics in the early solar system ejected the fifth planet, changed the orbits of the other four, and cleaned out the comet and asteroid debris leftover from the formation of the system.

Given that these dynamic changes resulted in changes to the planetary system, it’s reasonable to infer that the changes usually bring damage and destruction. Yet in the solar system, they brought benefits, namely the increased the capacity of Earth to support life—almost like they happened by design.

*** Will Myers

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1. 1 Corinthians 1:7
   So that ye come behind in no gift; waiting for the coming of our Lord Jesus Christ:

   
   

2. 1 Thessalonians 2:19
   For what is our hope, or joy, or crown of rejoicing? Are not even ye in the presence of our Lord Jesus Christ at his coming?

   
   

3. 1 Thessalonians 3:13
   To the end he may stablish your hearts unblameable in holiness before God, even our Father, at the coming of ourLord Jesus Christ with all his saints.

   
   

4. 1 Thessalonians 4:15
   For this we say unto you by the word of the Lord, that we which are alive and remain unto the coming of the Lord shall not prevent them which are asleep.

   
   

5. 1 Thessalonians 5:23
   And the very God of peace sanctify you wholly; and I pray God your whole spirit and soul and body be preserved blameless unto the coming of our Lord Jesus Christ.

****

In September 2012, the ENCODE Project Consortium announced the results of the second phase of research designed to identify and catalog all the functional elements in the human genome.¹ I reported on this announcement in the September 6, 2012 episode of RTB’s Science News Flash podcast, and suggested that the ENCODE results may well be one of the most important scientific achievements in my lifetime, or at least in my time as a professional biochemist.

Since the initial sequencing of the human genome, many skeptics and evolutionary biologists have asserted that the most compelling evidence for human evolution—and the most potent challenge against intelligent design/creationism—is the vast amount of junk DNA in the human genome. And yet, with the results of the ENCODE Project, these arguments evaporate. We can no longer consider the human genome a vast wasteland of junk, but an elegant system that displays sophistication in its architecture and operation, far beyond what most evolutionary biologists ever imagined.

When announced, the ENCODE results generated quite a bit of Internet chatter. Many skeptics asserted that the media and design proponents overhyped and misconstrued the project’s discoveries. Shortly thereafter, several papers appeared in the scientific literature highlighting ENCODE’s “flaws.”² Many evolutionary biologists hope these critiques will undermine the project’s conclusion that 80 percent of the human genome, at minimum, contains functional DNA elements.

Yet, very good reasons exist for thinking that the ENCODE Project’s results are still valid. In fact, I have written several articles that provide a detailed response to each criticism. I conclude that the charges against ENCODE lack technical merit and appear to be motivated by philosophical considerations more than anything else. To read my response to these criticisms click on the below links:

• “Responding to ENCODE Skeptics”
• “Do ENCODE Skeptics Protest Too Much?” (part 1, part 2, and part 3)

It is interesting to note that not everyone in the scientific community agrees with the ENCODE skeptics. Molecular geneticist John Mattick, executive director of the Garvan Institute of Medical Research in Australia, believes in ENCODE’s validity.³ In a recent article, Mattick and his coauthor, Marcel Dinger, argue, like me, that the criticisms of ENCODE are unwarranted technically and are motivated by non-scientific considerations.

One of the chief criticisms leveled at ENCODE relates to its use of a causal definition of function to determine functionality within the human genome. That is, a sequence element in the genome possesses function if it performs an observationally or experimentally identified role. ENCODE skeptics argue that this definition is faulty; instead, the project should have relied on sequence conservation (the so-called selected effect definition) as a way to measure function.

According to the selected effect definition, sequences in genomes can be deemed functional only if they evolved under evolutionary processes to perform a particular function. Once these sequences are evolved, the effects of natural selection make them resistant to change because, at this point, any further alteration would compromise the function of the sequence and, consequently, be deleterious. Reduced survivability and reproductive success would then eliminate organisms possessing deleterious sequence variations from the population. Hence, functional sequences are those under the effects of selection. And based on a selected effect definition of function, only 10 percent (not 80) of the human genome could be considered functional.

Mattick and Dinger decry the weakness of the selected effect definition. They argue that the genome’s regulatory regions are much more malleable than the selected effect idea suggests, retaining function in the face of mutational changes. Thus, sequence conservation (one way to detect selection at work) cannot be a valid marker of function. Mattick and Dinger propose and defend differential transcription, an alternative measure of function. They note that during the course of development, the vast majority of the human genome (and the genome of other mammals) is “differentially transcribed in precise cell-specific patterns” to generate RNA molecules with a regulatory role. It is interesting to note that this is a causal definition of function, meaning it relies on cause-and-effect relationships.

In response to Mattick and Dinger’s definition of function, ENCODE skeptics claim that transcription of the genome is noisy (random, and arbitrary). As such, transcription cannot be viewed as an indicator of function. In a previous article, I offer a response to this challenge. So, too, do Mattick and Dinger. They state:

Assertions that the observed transcription represents random noise…is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells…⁴

ENCODE skeptics also complain that the results of the project don’t make sense in light of the C-value paradox. This paradox states that most of an organism’s genome consists of DNA that doesn’t code for proteins or regulate gene expression. Researchers have long held that the non-coding DNA serves no real purpose—they view it as useless junk, vestiges of evolutionary processes.

The concern among ENCODE skeptics is that if the project’s conclusion is valid, then most, if not all, of the human genome contains functional DNA. Thus, the human genome contains very little junk DNA, which would constitute an absurdity in light of the C-value paradox. Therefore, the project’s results cannot be correct according to ENCODE skeptics.

The C-value paradox also explains why organisms less sophisticated than humans have larger genomes. That is, genome size is due to junk DNA and has no relationship to an organism’s complexity. Again, if the ENCODE results are correct, then this phenomenon has no explanation.

But as Mattick and Dinger point out, the large genome sizes of relatively simple organisms appear to stem from duplications of extensive genome regions (a phenomenon referred to aspolyploidy). To put it differently, the ENCODE conclusions are fully compatible with the C-value paradox.

Also, Mattick and Dinger rightly point out that the ENCODE skeptics appear to be motivated by non-scientific factors.

There may also be another factor motivating the Graur et al. and related articles (van Bakel et al. 2010; Scanlan 2012), which is suggested by the sources and selection of quotations used at the beginning of the article, as well as in the use of the phrase “evolution-free gospel” in its title (Graur et al. 2013): the argument of a largely non-functional genome is invoked by some evolutionary theorists in the debate against the proposition of intelligent design of life on earth, particularly with respect to the origin of humanity. In essence, the argument posits that the presence of non-protein coding or so-called ‘junk DNA’ that comprises > 90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins 2006). This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells2011).⁵

In other words, there are many in the scientific community who are concerned that the results of the ENCODE Project play right into the hands of creationists and intelligent design proponents—and that’s a reason for dismissing the ENCODE conclusions.

It is safe to say there are scientists who accept the ENCODE project even though the results undermine what many consider to be the most compelling argument for biological evolution—while at the same time highlighting the elegant design of the human genome, a system befitting the work of the Creator. (RTB)

*** Will Myers