The Cell's Design--final section

Toward the end of his book, The Cell's Design, Dr. Rana completes his discussion of many startling molecular features inside the cell and focuses on a common challenge leveled against arguments for intelligent design -- imperfections found in nature. Critics say odd arrangements and funny solutions are proof of evolution because a sensible God would never put things together that way.

Rana admits there are some designs that are less than perfect. But he says these designs merely reflect the unavoidable consequences of the laws of nature instituted by the creator. As an example, he points to the second law of thermodynamics (entropy). Living systems which experience this law tend toward disorder. For example, chemical and physical damage to DNA inevitably cause abnormalities. Over time, the accumulation of these damaging mutations can transform an optimally design biochemical system into one that is substandard. He also says complex, human-engineered systems often involve trade-offs . When confronted with these trade-offs, the engineer carefully manages them in such a way to achieve the best overall performance of the system itself. As an example, think of today's automobile. Each car is a balanced system that attempts to deal with issues regarding safety, performance, and gas economy.

Dr. Rana spends time discussing systems that at one time were seen to be imperfect but have recently been discovered to serve a vital purpose. He looks at glycolysis, bilirubin production, uric acid metabolism, junk DNA, and genetic redundancy as examples. His explanations made my head spin, so I'm not going to try to discuss all of them here. But over and over again, he shows how something that originally appeared badly designed has recently been shown to have a highly useful design. Here's one example -- uric acid metabolism. Many people develop kidney stones due to what appears to be poor design in their cells. However, uric acid helps prevent cancer and may contribute to long human life spans since it is a potent antioxidant. Then, of course, there's junk DNA, which appears to be a portion of DNA that has no purpose. Much to the surprise of scientists, junk DNA has function.

Rana concludes his book by criticizing evolutionary solutions attempting to explain life's chemical picture. Origin-of-life researchers maintain that information-rich biomolecules, like DNA and proteins, emerged under the influence of chemical selection. Evolutionary biologists also claim that irreducibly complex systems did not have to rise all at once but could emerge in a stepwise fashion. He says these naturalistic scenarios proposed to account for the origin of these incredibly complex systems are highly speculative and lack any type of detailed mechanistic undergirding. The formation of biochemical information systems is a probability problem. It appears astronomically improbable for the essential gene set to emerge through natural means alone. In other words, there does not appear to be enough time for evolutionary processes to stumble upon the universal genetic code. Another problem has occurred in the last decade or so when scientists have discovered that a number of life's molecules and processes, though virtually identical, appear to have originated independently, multiple times.

At the very end of his book he summarizes features of life's chemical systems that seem to argue for intelligent design. Here is a list of just some of the ones he mentions – irreducible complexity, chicken-and-egg systems, fine-tuning, biochemical information systems, structure of biochemical information, biochemical codes, quality control, molecular motors, and cell membranes. Take a look sometime at his complete list (pp. 279-282).

Dr. Fuzale Rana (The Cell’s Design) and Dr. Stephen Meyer (Signature of the Cell) have created two books which make significant, serious contributions to scientific literature pointing to intelligent design. Don't be scared off either of these books because of their technical discussions. Skip anything you don't understand; you'll still be impressed with the overall points being made. I recommend both of these books highly.

The Cell's Design--part 4

Let’s pick up where I left off last time as I summarize the findings of Dr. Fuz Rana, in his book The Cell’s Design. This is an important book that explores the biochemical reasons to believe there is a designer behind the creation of life.

Dr. Rana continues where he left off talking about the genetic code inside the cells. He says recent discoveries have unwittingly stumbled across the most profound evidence yet for intelligent activity -- a type of fine-tuning in code rules. These rules create a surprising capacity to minimize errors and communicate critical information with high fidelity. There is a redundancy to the code which is not haphazard. Deliberate rules were set up to protect the cell from the harmful effects of substitution mutations. The conclusion is that any genetic code assembled through random biochemical events could not possess such ideal error-minimization properties. Nobel laureate Francis Crick argued in 1968 that the genetic code cannot undergo significant evolution because any change would result in a large number of defective proteins. What is really amazing is that the genetic code originated at the time when life first appeared on earth. The complexity of the code makes it virtually impossible that natural selection could have stumbled upon it by accident in such a short period , according to Dr. Rana’s book.

A later chapter talks about biochemical quality control systems which are in place to identify and rectify any production errors. Biochemists have discovered that, like any manufacturing operation designed by human engineers, key cellular processes incorporate a number of quality control checks. Checkpoints occur at several critical junctions during protein manufacture, including mRNA production, export from the nucleus, and translation at ribosomes. One of the most remarkable features is the ability to discriminate between misfolded proteins and partially folded proteins that appear misfolded but are well on the way to adopting their intended three-dimensional architectures.

Next, Dr. Rana asks a key question. If life results solely from evolutionary processes, then shouldn't scientists expect to see very few cases in which evolution has repeated itself? Random processes shouldn’t repeat over the history of the earth. That makes sense to me. He goes on to say, however, if life is the product of an intelligent creator, then the same designs should repeatedly appear in biochemical systems. He gives one hundred recently discovered examples of repeated biochemical designs (see pages 207-214). The explosion in the number of these examples is odd if life results from historical sequences of chance evolutionary events. However, if there is a creator, it's reasonable to expect he would use the same designs repeatedly.

There is one more chapter devoted to recent discoveries that seem to require a supernatural agent. Dr. Rana takes a look at cell membranes. Forty years ago they were seen as little more than haphazard, disorganized systems. However, since then advances have dramatically changed how scientists think about these membranes. Biochemists have discovered the cells’ boundaries are highly structured, highly organized systems. They require fine-tuning of their composition to be as stable as they are. These membranes not only form a key boundary layer, but they also play a critical role in regulating the activity of proteins associated with the membrane. Some biochemists go further, suggesting that cell membranes harbor information.

The last part of his book responds to one of the most common challenges leveled against arguments for intelligent design -- imperfections found in nature. I'll save that for one last blog on The Cell’s Design.

The Cell's Design--part 3

The next section of Dr. Fuzale Rana’s book, The Cell's Design, covers biochemical fine-tuning which conveys a sense of the remarkable exactness of biochemical systems. Aquaporins form channels in cell membranes where they transport water across the membrane. Amino acids have to be brought into an exact alignment to form a useful three-dimensional architecture. In addition, collagens, the most abundant proteins in the animal kingdom, also contained an exact, fine-tuned amino acid composition.

Exact fine-tuning is not limited to the structure of the biomolecules. The rate of chemical processes is also carefully refined. For example, the cell's machinery copies mRNA from DNA only when the cell needs the protein encoded by a particular gene housed in the DNA. When that protein is not needed, the cell shuts down production. Biochemists have also discovered that the breakdown of mRNA molecules is not random but precisely orchestrated. Proteins are constantly made and destroyed by the cell. Those that take part in highly specialized activities within the cell are manufactured with great timing -- only when they are needed. Once the proteins are no longer useful, the cell breaks them down into the amino acids of which they are made up. This also is an exacting, delicately balanced process.

Rana then spends some time on the precise arrangement of elements in the cell. Amino acids link together in a head-to-tale fashion to form chains of proteins. These sequences appear to be highly optimal. Their exact positioning makes proteins better able to withstand mutations to DNA that result in a change to the amino acid sequence. Their structures also appear perfect to withstand damage caused by oxygen in the cell. The molecules that make up the backbone of DNA and RNA appear to be in a highly specific arrangement. Their chemical properties produce a stable helical structure capable of storing the information needed for the cell’s operation.

The Cell’s Design continues by highlighting the information found in the cell. Proteins and DNA are information-rich molecules. Just as letters form words in our language, amino acids are strung together to produce useful information. The chief function of DNA is to store information; it houses the directions necessary to make change-like molecules (polypeptides). DNA compares to the reference section of the library where books can be read but not removed. The material stored in these books has to be copied before it can be taken from the library -- exactly the same thing happens in the cell. The language of DNA and RNA is translated at the ribosome into the amino acid language of proteins. DNA can store an enormous amount of information -- theoretically one gram of DNA can house as much information as nearly one trillion CDs. To summarize, it's not the mere presence of information that argues for a designer. It's the structure of the information housed in proteins and DNA. There is a direct analogy between the architecture of human language and the makeup of biochemical systems. This information is handled exactly like a computer would do. For example, computer scientist Leonard Adleman recognized that the proteins responsible for DNA replication, repair, and transcription operated as Turing machines, which gave rise at a fundamental level for all computer operations. I don't have the space here to develop this, but check pages 163-168 in Rana’s book.

I need a couple more blogs to finish reporting on Rana's book. The detail in it blew me away with its careful analysis of the cell's abilities. Hope you feel the same.

The Cell's Design--part 2

In the last blog, I introduced you to Dr. Fuzale Rana's book, The Cell’s Design. His claim is that today's biochemists have uncovered amazing molecular features inside the cell that lead to one reasonable conclusion -- a supernatural agent must be responsible for life. Let's move on to further chapters in the book which offer more reasons why he believes this is the case.

In Chapter 4, he introduces molecular motors. He starts with a famous example, which has been brought up in previous books -- the bacterial flagellum. Made up of over 40 different kinds of proteins, this is essentially a molecular-sized electrical motor which rotates a propeller, allowing the bacterial cell to navigate through its environment. But the rest of the chapter has many more examples of these molecular motors. Some are rotary in nature, including parts such as turbines, rotors, cams, and stators. Some motors spin, and some swivel. One amazing molecular motor, dynein, carries cargo throughout the cell along microtubule tracks. This motor literally shifts gears in response to the load that it is carrying. You can see a terrific video put out by Harvard showing dynein in operation--Google "The world inside the cell" then "cell--inner life." His conclusion? Eexperience teaches us that machines and motors don't just happen.

He sees these motors as an update of the watchmaker argument (just as watches which display design are the product of a watchmaker, so organisms which also display design are the product of a creator ). The discovery of these biomolecular motors and machines inside the cell revealed a diversity of form and function that mirrors the diversity of designs produced by human engineers. In addition, researchers working with nanotechnology reinforce the idea that molecular motors in the cell are literal motors in every sense. The contrast between synthetic molecular motors designed by some of the finest organic chemists in the world and the elegance and complexity of molecular motors found in cells is striking. Actually, the cell's machinery is vastly superior to anything that the best human designers can conceive or accomplish. For example, bacterial flagella operate near 100% efficiency while man-made electric motors only function at 65% efficiency ,and the best combustion engines only attain a 30% efficiency.

Dr. Rana’s next chapter deals with a chicken-and-egg problem. DNA houses the information the cell needs to make proteins, which play such a vital role in almost every cell function. Biochemists call DNA a self-replicating molecule. However, DNA cannot replicate on its own. Instead, it requires a variety of proteins. So here's the problem -- proteins cannot be produced without DNA, and DNA cannot be produced without proteins. Many proteins, in addition, need the assistance of other proteins to fold into the proper three-dimensional shape after they've been produced at the ribosome. Once again, you need proteins to help fold proteins. You can't have one without the other. Biochemical chicken-and-egg systems represent a special type of irreducible complexity where you need all the parts to function properly. He raises questions about the ability of evolutionary processes to produce these systems.

I need more space to explore further chapters in Dr. Rana's book, but the information is pretty dense. I'll keep these blogs short enough for you to digest the ideas--more to come next time.

A tiny world of precision and engineering

Back in November, I got to meet Dr. Fazale Rana, a biochemist and author of several books. He gave a presentation on the complexities inside the cell, which he used as an indication of the existence of God. This represents a continuation of the design argument, which says God is the ultimate engineer who designed everything in the universe. I recently finished reading Dr. Rana’s new book called The Cell’s Design. It makes an important contribution to the argument of design by explaining recent scientific discoveries that seemed to indicate complexity far beyond anything that random processes can create. For the next couple of blogs, I'd like to explore his key points in this book.

He starts by mentioning another famous book, Darwin's Black Box by Michael Behe. This earlier book presented a case for intelligent design from the biochemical perspective. Behe had argued that biochemical systems, by their very nature, are irreducibly complex. He argued for intelligent design by emphasizing the inability of natural selection to generate such complex systems through a gradual evolutionary process. Critics, however, said that this book rested on a lack of understanding, so they rejected his argument. As result of this, Dr. Rana wanted to write a book that went beyond irreducible complexity to communicate a vast range of amazing properties that characterize life's chemistry. These indicators of design seen inside the cell make a case for a creator based on what scientists know, not on what we don't understand.

Before Dr. Rana starts on his proof, he describes and justifies the approach used to argue for intelligent design in biochemical systems. He says when people distinguish between the work of an intelligent agent and the outworking of natural processes, they don't use intuition. Instead, they use pattern recognition. If biochemical systems are indeed the product of a creator who made man in his image, then the defining characteristics of those systems should be very close to the hallmark characteristics of humanly crafted systems. The rest of his book makes use of pattern recognition to build a positive case for biochemical intelligent design.

His first chapter which presents his argument talks about the minimum number of genes and essential biochemical systems necessary for life. It appears as if a lower bound of several hundred genes exist, below which life cannot be pushed and still be recognized as life. If left up to an evolutionary process, not enough resources or time exists throughout the universe’s history to get life even in the simplest form. Scientists used to see bacteria as simple bags of assorted molecules haphazardly arranged inside the cell. But actually these bacteria, as simple as they are, display an incredible degree of internal organization and exquisite composition of biochemical activity. Origin-of-life researcher David Deamer remarked, " . . . one is struck by the complexity of even the simplest form of life." So even these tiny bacteria speak of intelligent design.

Some surprising science stories of 2009

I recently received the 2009 annual report from Access Research Network,an organization that exists to provide "accessible information on science, technology and society issues from an intelligent design perspective." The part that intrigued me was its review of some of the key news stories this past year that came from mainstream, nontheological sources. There were two main findings -- more articles are coming out critical of evolution, and scientists keep finding patterns in nature that could not happen by chance or law. Here are some of the science stories that back up this assertion. Again, keep in mind that these are written by those with no interest in helping the intelligent design community. This blog covers some of their findings; the rest will follow in the next blog.

Several articles point out the disappearance of what was known as the modern synthesis. In the 1930s and 40s, scientists gathered evidence from natural selection, population genetics, cytology, systematics, botany, morphology, ecology, and paleontology to wrap it into one modern theory of neo-Darwinian evolution. But the modern synthesis has fallen apart because of revolutions in the molecular, microbiological, and genomic areas. What's interesting is that articles are now appearing in the peer-reviewed scientific literature declaring the modern synthesis theory needs to be abandoned because it no longer fits the new data.

There has also been more research done and reports on cellular motors. Scientists are now finding that some of these incrediby small but complex machines work together in groups. In other words, molecular motors are actually coordinating their efforts. This contradicts earlier models that pictured these motors competing with each other in some sort of tug-of-war.

Then there was the hoopla surrounding the Ida fossil lemur. People soon realized how much hype was involved. There is no doubt that the scientists behind it were hoping to capitalize on the Darwin bicentennial by creating a sensational "missing link" media blitz. Critical articles have since come out to show that it may simply be a typical lemur.

One amazing story came out in the middle of the year dealing with white blood cells. These soldiers of our immune system get to the site of infection or injury by crawling swiftly along the lining of the blood vessel. They grip it tightly to avoid being swept away in the blood flow, all the while searching for temporary road signs made of specialized molecules that let them know where to cross the blood vessel barrier so they can get to the damaged tissue. You can see an animation of this at Harvard BioVisions. Click on the media file labeled "Extravasation." The legs on these blood cells don't just walk; they act as probes as they press into the tissue lining the vessels so they can locate the damaged tissue and make their way to it. These tiny legs are used for gripping, moving, and sensing distress signals from the damaged tissue.

These are just some articles that came out last year critical of evolution and indicating design in nature. More to follow in the next blog.

The final segment on Serious Times

Serious Times, by James Emery White, is a book that deserves more than one reading. It can change our lives if we are willing. Here's the final section of the book.

Next, the author talks about the importance of turning our vocation into a form of worship. He says all secular life should be made into a vocation aimed at God. Whatever we choose to do with our lives, we need to do that with a higher meaning and purpose. He tells a powerful story of William Borden, a student of Yale University who decided to become a missionary. He was a millionaire because he was part of the Borden dairy estate, but he gave it all up to prepare for the mission field. After making this decision, he wrote in his Bible: "No Reserves." He finished his education at Yale with purpose and determination, having established Bible studies and an organization to reach the poor in the surrounding community. When he graduated, he was offered high-paying jobs, but he turned them down to pursue his dream of becoming a missionary. Again, he wrote down two more words in his Bible: "No Retreats." On his way to the mission field, he stopped in Egypt to study Arabic, but after contracting meningitis there, he was dead within a month. Before his death, he had written two more words in his Bible: "No Regrets." Toward the end of the chapter, White has a powerful statement from Thomas Kelly that sums up his point: "The times are too tragic, God’s sorrow is too great, man's night is too dark, the Cross is too glorious for us to live as we have lived, in anything short of holy obedience."

Finally, White says we must become part of the church. Its mandate is to engage in "countersecularization." Through the church we are to reach out to those who are relationally divorced from Christ and turn them into fully-devoted followers. The church is not optional for a follower of Jesus Christ. He lists things that have been entrusted to the church for the sake of the Christian: the very proclamation of the gospel, corporate worship, the sacraments, the new community in Christ, the use of and benefit from spiritual gifts, spiritual care and protection through pastors. We will need to make the church effective, so we must scrutinize "tired methods, inane traditions, and outmoded approaches to outreach." We need to translate the gospel into our generation’s unique cultural context. We began by taking our place in the church as a member. We cannot truly followed Christ apart from community, as indicated in so many verses (Gal. 5:13, 1 Thess. 5:11, Rom. 15:7, Col. 3:13). Jesus believed that the church, demonstrating a community of love and witness, would capture the attention of the world and affirm his message of salvation. In addition, we need a place to develop corporate worship, which helps us encounter and experience God in a way unlike any other. We should also see ourselves as ministers, personally gifted and called by God. Besides this, each of us needs to serve as a missionary; we can see this in Paul’s declaration, "We are therefore Christ’s ambassadors, as though God were making his appeal through us" (2 Cor. 5:20).

White’s concluding chapter attempts to motivate us. Our culture is getting thin, stripped of so much spiritual depth and weight, but we do little except stand around and wring our hands. In the ancient world Christians stopped infanticide, ended slavery, liberated women, and created hospitals, orphanages and schools. During the medieval era, Christianity kept classical cultural alive through copying manuscripts, building libraries, and creating colleges and universities. Over the last several hundred years, Christians have led the development of science, contributed greatly to political and economic freedom, and provided a tremendous source of inspiration for art, literature and music. But the danger today is the absence of a sense of personal responsibility. We don't think that anything we do will really matter. We become spectators of the world. But White challenges us: "When we live like salt and light, with lives infused by Christ, it affects the world around us in disproportionate measure." Since we live in serious times, we need to undertake a serious life. We know what to do, but the question is whether we will attempt it. I highly recommend everyone to get this book—it’s easy to read, it’s short, and, most of all, it can make a real difference in how we live.

Serious Times--the second half

In my last blog I mentioned a challenging book called Serious Times. It started by giving a history of worldviews, beginning with the Middle Ages and continuing to modern times. The author, James Emery White, talked about the results of the current worldview, one which has been shaped by moral relativism, autonomous individualism, narcissistic hedonism, and reductive naturalism. What does our world look like now? It is one with a crisis in values, a lack of vision, an abundance of empty souls, and the feeling of an inadequate human experience. White uses the second half of his book to suggest what our response as Christians should be to this world. There’s a lot to this part, and I don’t want to rush it, so I will go over part of it here and the rest in one additional blog. Please slow down, read, and think about his challenge to us today.

First, he believes we should deepen our souls. We need to seek God and live like Jesus. How do we do this? We start by reading our Bibles and meditating on what we have read. We develop a better prayer life. We seek a time of silence and solitude. We develop a spiritual direction from reading or talking to people. He stresses the need to set up our own spiritual disciplines much like Christians have done since the time of St. Benedict. There are a lot of books and articles to help in this area. But we must do this slowly at first so that we don't feel overwhelmed. It was this area that challenged me greatly since I seem to be in a hurry throughout my day with little time for meditation, prayer, or solitude. This is where I need a lot of work.

Secondly, White says we must develop our minds. We badly need a Christian worldview that helps us understand and react to the world as it is. We need to be able to answer key questions of life -- Who am I? What's wrong with the human race? What's the remedy? We must read good books and reflect on what we read. Now, for me this part comes much easier. I read a lot and use some of my blog space to share my findings. For other people, this section may be more of a challenge. If this is your situation, feel free to e-mail me, and I can send you a list of good resources to develop a Christian mind (radio stations, Internet sites, books, etc.). I also have started an apologetics class at our church, Emmanuel Faith, where we meet to explore rational defenses of the Christian faith in a skeptical age--this both strengthens Christians and helps them interact with those who don't believe. The church also has worldview classes that look at various worldviews and why the Christian one is superior. Ask me for further info on any of these (zachs@cox.net).