Today’s New Reason To Believe

Fazale ‘Fuz’ Rana, Ph.D.

Rational Design of Novel Enzyme Highlights Biochemical Design

In 1978, three scientists (Hamilton Smith, Werner Arber, and Daniel Nathans) were awarded the Nobel Prize in Physiology or Medicine for the discovery of restriction enzymes and their applications. These proteins make genetic engineering possible. They have also contributed to the wave of advances that led to the sequencing of the human genome and to the emergence of other biotechnologies.

Restriction enzymes (or endonucleases) are important for another reason. They represent an interesting example of a chicken-and-egg biochemical system and comprise part of the collection of evidence that indicates life must stem from a Creator. Recent work on these proteins highlights this point.

Endonucleases are a family of proteins. This class of biomolecules cleaves DNA. Restriction endonucleases cut both strands of DNA at specific nucleotide sequences, called restriction sites. Specifically, restriction endonucleases protect the cell from foreign DNA, like viruses, by cutting the invading DNA into fragments.

These vital biomolecules occur in conjunction with proteins (called DNA methylases) that attach methyl groups to the same DNA sequences that would normally be cleaved by restriction endonucleases. When these sequences are methylated, restriction endonucleases cannot cut them. Restriction sites of the bacterial DNA are methylated to completely protect the bacterial DNA from being chopped up by its own restriction endonulceases. Foreign DNA, however, is not afforded this same protection.

DNA methylases and restriction endonucleases form a chicken-and-egg pair. Restriction endonucleases would destroy bacterial DNA without DNA methylases. On the other hand, if bacteria did not utilize restriction endonucleases there would be no need for DNA methylases. These two proteins are interdependent and must come into existence simultaneously.

New research by scientists from the Indian Institute of Science (Bangalore, India) helps demonstrate why biochemical systems like restriction endonucleases require the work of an intelligent Agent. These researchers performed experiments to understand the origin of restriction endonucleases from an evolutionary perspective. They also wanted to develop a strategy for engineering novel, nonnatural restriction endonucleases.

Evolutionary biologists think restriction endonucleases evolved from non-specific endonucleases through point mutations in the gene region that codes the DNA binding site on the protein surface. According to this model, once specificity was established recombination and genetic shuffling of the DNA sequences that encode the DNA recognition sites would have generated new restriction endonucleases with different specificities.

To explore this possibility the research team attempted to engineer a highly specific restriction endonuclease from one (R. KpnI) that promiscuously binds to DNA. To accomplish this goal, the scientists employed a rational design strategy to determine which amino acids in the R. KpnI structure to change. These workers had to make use of the detailed understanding of this protein’s structure and functional properties in order to develop the redesign strategy.

They successfully achieved their intended goal by replacing an aspartic acid residue with an isoleucine moiety at amino acid position 163 in the R. KpnI protein chain.

This research illustrates how carefully-thought-through single amino acid substitutions can alter the specificity of restriction endonucleases. This is important work that paves the way to engineer novel, nonnatural restriction enzymes that can expand the arsenal of tools available to molecular biologists and biochemists.

The researchers involved in this study also interpreted their success as support for the evolutionary origin of restriction enzymes with point mutations ushering in the first stage in the molecular evolution of these proteins. At first glance, this interpretation seems warranted.

Still, it’s important to keep in mind that the production of the highly specific restriction endonuclease from the original promiscuous protein required intelligent input from a team of highly trained biochemists who relied on the past work of other highly accomplished scientists. In a sense, this study empirically demonstrates that protein “evolution” requires the work of an intelligent Agent.

It’s also important to note that the researchers didn’t design the companion methylase protein. This protein isn’t necessary for most biotechnology applications. But without the methylase cohort, the reengineered restriction endonuclease would wreck havoc in vivo, destroying DNA that comprises the bacterial genome.

It’s very unlikely that a restriction endonulcease and its partner methylase would simultaneously appear in an evolutionary scenario. These coordinated events would require that changes in the restriction endonuclease would take place at exactly the same time as corresponding changes in the methylase. The only way for coordinated changes like this to happen is under the auspices of an intelligent Agent.

As I point out in my new book The Cell’s Design, human engineers frequently encounter chicken-and-egg problems when designing systems and processes. Everyday experience teaches that chicken-and-egg systems can come to fruition only through intentional planning and implementation. Chicken-and-egg systems, therefore, serve as a potent indicator of intelligent design.

I describe several other examples of chicken-and-egg systems in The Cell’s Design.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Invention of a New Type of Microscope Delineates the Difference between ID and Science

The debate over including intelligent design (ID) in public school science curricula remains a hot topic. The pivotal question of this controversy is whether ID is or isn’t science.

Many in the scientific community answer, “ID is not science.” There are two primary reasons for their rejection of ID: the appeal to a supernatural agent to explain the universe and life; and the absence of a scientific theory of intelligent design.

Last week, I discussed the first concern. This week, I will address why we, at RTB, agree with the scientific community’s second criticism of ID.

The production of a new type of miniaturized microscope helps illustrates why we don’t think ID, as currently conceived by the ID movement, is science.

Lensless High-Resolution Microscope on a Chip

Microscopy is one of the most important techniques in the life sciences. Remarkably, the fundamental design used to construct microscopes today is the same as when these devices were invented in the early 1600s.

The endurance of this design stems from the fact that it performs well. Yet there are problems. One is the expense. The optics and cameras used in contemporary microscopes are costly to manufacture. Additionally, the design is extremely difficult to miniaturize.

Miniaturization represents an important way to reduce costs and improve work efficiency in the biosciences and biomedicine. Because of this need, one of the goals of bioengineering is to develop a cost-effective, miniaturized microscope.

Recently a team of engineers from the California Institute of Technology invented a lensless microscope that could be placed on a CMOS chip. (To hear an interview with the senior investigator of this research team go here.) This design radically departs from the blueprint of a conventional microscope. And it’s amazingly simple, essentially consisting of a thin film of metal coating a grid of CMOS chips. A linear sequence of regularly spaced small holes is punched into the metal film.

The sample is imaged by suspending it in water and passing it over the pinholes. Ambient light illuminates the chip and makes its way through each pinhole to the sensor below. As the sample moves over each hole it prevents sunlight from impinging on the sensor. This creates an image of that object. By orienting the line of holes at an angle with respect to the direction of the flow, the image at each pinhole overlaps with images of adjacent openings. This overlap allows a two-dimensional image of the sample to be constructed. The resolution of the microscope is not limited by the wavelength of light, but instead by hole size with a magnification that is comparable to a conventional light microscope.

The cost of this new microscope, which is about the size of George Washington’s nose on a US quarter, is about $10.

The applications for this microscope are limitless. Its low cost and portability make it particularly suited for field work and biomedical applications in the Third World. It can also be used to develop high-throughput devices that can examine large numbers of samples simultaneously.

Is it Science?

As important as microscopy is to the life sciences and medicine, the design of improved (or, in this case, miniaturized) microscopes is not science. It’s an activity that enables science. As such, these types of endeavors are associated with the scientific enterprise, but they are not in the strictest sense science. Scientists and engineers who build new instruments or devise new methods and techniques may even employ the scientific method to develop workable designs and optimize methods, but still these activities are not science. They are the creation of tools that allow scientists to answer questions that are part of the scientific construct.

At its very essence, science centers on advancing and evaluating hypotheses, theories, and models. Science is more than a collection of facts and observations about nature. Instead it’s an enterprise that seeks to explain the natural world. In order to accomplish this goal, scientists propose hypotheses, theories, and models as descriptions of how natural phenomena behave. For an explanation to be “scientific,” it must be testable. It must make predictions about scientific discoveries. These predictions serve as a way to validate and falsify the hypotheses, theory, or model. If the model successfully predicts scientific discoveries, then it has validity. If not, then the theory must be scrapped, or revised. Good scientific theories also provide a framework to organize and make sense of observations and guide scientific investigations.

Tools like microscopes help scientists evaluate their theories. Looking into a microscope and seeing cells is not science. Looking into a microscope and observing cells in order to form a theory about cell biology or evaluate an existing cell model is science.

Currently the ID movement has no theory or model. ID holds no positions on critical ideas like the age of the Earth, the history of life on Earth, and common descent. ID makes no attempt to identify the designer. Because of these self-imposed limitations, this movement offers no explanation of the natural world. The design detection methods developed by the ID community represent powerful tools to evaluate ID models—if they are ever developed—but do not serve as a science.

The new lensless microscope is not an alternative to cell theory. It’s a tool that could be used to advance an alternative to cell theory, but it’s not a scientific construct. In the same vein, ID is not an alternative (at least in the way it’s been presented to the scientific and educational communities) to the theory of biological evolution. It’s a developing collection of tools that can be used to support an alternative to the evolutionary paradigm.

Can Intelligent Design become Part of Science?

This criticism does not mean that we don’t think that ID can’t be science. It can be. All that is required is a model that explains life’s origin, history, and diversity. In fact, at RTB we have proposed an ID model, of sorts, in direct response to the concern raised by many scientists that creation and ID is not science, since it cannot be falsified. (For a summary of RTB’s creation model see Hugh Ross’ book Creation as Science.)

The RTB creation model finds its basis in the descriptions of God’s creative work found in Scripture. The process of building the creation model starts by collating the biblical data from the major creation accounts and individual scriptural passages that describe God’s creative actions. Once interpreted, the biblical data are recast in scientific terms rendering the biblical creation account testable.

Biblical statements about God’s creative activity are subjected to experimental validation. They also lead to predictions regarding future scientific discoveries. This approach makes creation a scientific endeavor. Creation becomes testable. Creation falls within the domain of science. The models’ predictions delineate the features we would expect to see in the record of nature—God’s fingerprints—if the creation model has validity.

Scriptural text inspires the creation models’ tenets and constrains the overall model. However, within these constraints, the model finds considerable freedom for adjustments and fine-tuning as scientists and theologians make new discoveries.

With the advent of the creation model approach, creation (and ID) falls squarely within the domain of science. The tools developed by Behe and Dembski to detect design in nature (and the approach I propose in my book The Cell’s Design) can be used as tools to evaluate key prediction of our model and enable science.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Invention of a New Type of Microscope Delineates the Difference between ID and Science

Is it science or isn’t it? This question lies at the heart of the controversy about intelligent design (ID) and whether it should be included in high school science curricula.

Many in the scientific community reject ID because they claim it isn’t science. There are two primary reasons for their rejection: the appeal to a supernatural agent to explain the universe and life; and the absence of a scientific theory of intelligent design.

RTB’s position on intelligent design has surprised some and has raised the ire of others. We agree with some of the scientific community’s criticisms of ID, namely that ID isn’t science. (For a good discussion about ID and science, see RTB apologist Richard Deem’s article

Interestingly, the invention of a new type of miniaturized microscope helps clarify RTB’s position on ID and illustrates why we don’t think it qualifies as science, at least as currently conceived by the ID movement.

Our complaints about ID don’t mean that we think the work done by the ID community lacks value. We largely agree with their criticisms of methodological naturalism as the sole philosophy guiding science. We are on board with many of the scientific challenges they have raised against biological evolution. (For example, see my books Origins of Life and Who Was Adam?.)We also concur with much of the arguments and evidence ID scholars cite in favor of intelligent design. (As a case in point, see my book The Cell’s Design.)

Can Science Detect the Work of an Intelligent Agent?

Additionally, we agree with ID proponents that ID shouldn’t be excluded from the scientific enterprise simply because it appeals to the work of an intelligent agent. Even though many scientists would claim otherwise, science has the capacity to adopt explanations for the universe and life that rely on the work of a Creator.

Science routinely deals with directly unobservable phenomena, such as forces, fields, and subatomic particles. Scientists infer the properties and monitor the effects of unobservables indirectly by examining observable macroscopic phenomena that directly affect our senses. It should be possible to do the same for a Creator’s activity.

Within a Christian framework, ID naturally integrates with science. Christians believe that God reveals himself through nature. If this is true, then scientists should be able to ascertain God’s fingerprints in nature if he has intervened to bring about life’s origin, for example. Though scientists may not be able to directly detect the Supernatural Being, they can examine the material realm looking for telltale signs of God’s work.

Science also possesses the capacity to investigate intelligent causation. Criminal investigators who utilize the principles of forensic science routinely detect and characterize intelligent activity at crime scenes. Archeologists study artifacts produced by humans, and anthropologists, who study the hominid fossil record, discriminate between stones intelligently shaped into tools and those artificially resembling tools but formed by the forces of nature. The search for extraterrestrial intelligence (SETI) is a search for signatures in the cosmos that reflect the existence of aliens living in another star system. Finally, Francis Crick and Leslie Orgel’s model of directed panspermia appeals to intelligent activity to explain life’s first appearance on Earth?an idea they demonstrate to be testable. By extension, life’s appearance on Earth by a supernatural, extra-universal Intelligence should, too, be detectable and testable.

Is Intelligent Design Science?

It’s true that the case for ID rests in large measure on the scientific evidence for design and the scientific challenges to biological evolution. Still, this doesn’t make ID a scientific enterprise. Rather, it is a program that draws philosophical and theological implications from the scientific data—at least as it currently operates.

ID proponents point out that their scholars have developed techniques and methods to detect the work of an intelligent designer, and that this design detection represents a scientific endeavor. This would include Michael Behe’s use of irreducible complexity to detect design and William Dembski’s explanatory filter and concept of specified complexity.

Unfortunately, most in the scientific community would disagree with this point. In fact, we at RTB would also disagree with it. Next week I describe how the invention of a new type of microscope helps illustrate why.