“There was a footpath leading across the fields to New Southgate, and I used to go there alone to watch the sunset and contemplate suicide. I did not, however, commit suicide, because I wished to know more about mathematics.”
-Bertrand Russell, Nobel Laureate and Mathematician

It is mystical when you step outside on a snowy morning. Snowflakes are swirling around the vast sky and falling and blanketing the ground. If a snowflake lands on you, it is like a winter angel. There are no flowers around, for they cannot survive the cold; yet what lies before your eyes is an incredible beauty. And it’s remarkable, you come to realize, that no two snowflakes are alike. It is as if the uniqueness of a snowflake is controlled by a divine force. The individuality of a snowflake’s structure draws a parallel to human life. Like snowflakes, everyone has a unique story to tell.

I am not the only one who ponders about snowflakes; many mathematicians do the same. Actually, they think about the characteristics of snowflakes because they are particularly important for three basic mathematical principles: pattern, symmetry, and symmetry breaking.

A little-known scientist, Wilson Bentley, a.k.a. “the Snowflake Man” took pictures of snowflakes almost every day and observed them until he died. You can buy his book about his work on Amazon. If you wish to know why he did it, read about it at snowflakebentley.com.

“Under the microscope, I found that snowflakes were miracles of nature; and it seemed a shame that this beauty should not be seen and appreciated by others. Every crystal was a masterpiece of design and no one design was ever repeated. When a snowflake melted, that design was forever lost. That beauty was gone, without leaving any record behind.”
-Wilson Bentley

When I checked the Oxford dictionary, there were 3 definitions for the word “pattern.” Two of these definitions [listed below] are important for this article.

Pattern: 1. A repeated decorative design; 2. An example for others to follow.

When we check the pictures and delve deeper into each snowflake, we will see that the structures of the snowflakes are totally different. However, they have something in common: symmetry and a hexagonal structure.

These perfect ice crystals are genuine, even though it is hard to believe they are not fake.

When I take a close look at a snowflake, the beauty of the combination of ice molecules fascinates me every time; each flake is unique. However, uniqueness is not the point here. The things that make snowflakes important objects for mathematicians are their symmetry and their hexagonal structure. Math-loving people have a lot of interest in transformations. They love moving objects. And, surprisingly, if an object is symmetric, transformations are not even noticed by many.

To be more precise, when you have a hexagonal symmetric snowflake, or any other symmetrical object, when you rotate it in any direction, 60°, 120°, 180°, 240°, 300°, or 360°, people watching you wouldn’t realize it. If you check the images below, you will see rotated shapes but no difference. It appears to be the same shape in exactly the same place.

1- Counterclockwise rotation by 120°

2- Reflection through a vertical axis

3- Reflection axes of a snowflake[1]

Snowflakes also possess reflectional symmetry. If we stand in front of a mirror, our reflection looks exactly the same. Hence, if we put a mirror in the middle of a snowflake, there will be a reflection. For a snowflake, we can put a mirror 6 different ways. Thus, we can say that a snowflake has 12 symmetries: 6 from reflections, and 6 from rotations.[2]

Now we can define symmetry as a transformation that leaves things unchanged. We can also claim that a combination of any of the transformations will give us exactly the same shape. For instance, we can rotate our snowflake 60° two or three times in a row and flip it over, and it will remain unchanged.

At this point, you might ask the question: “You have all these fancy symmetries for this particular snowflake. But, does every snowflake possess the same symmetries?”

Snow is a molecular structure of an ice crystal. And ice is a structured substance. It is a different form of water. When the water cools down, the molecules move more slowly, and this begins to impact how the molecules line up. Hydrogen atoms of one water molecule bond with two oxygen atoms. As the water freezes, the molecules arrange into hexagonal patterns. They prefer to stay as far away from each other as possible, and that makes them take up more space. The large space affects density. The density of ice becomes less dense than water. This is why ice floats. Almost all other liquids have a higher density when they freeze.

When we examine an ice crystal carefully under normal conditions, we always see a combination of molecules with six-fold symmetry. Snowflake molecules make a honeycomb structure. This results in an inordinate amount of hexagonal symmetry in these molecular three-dimensional structures.

Okay, we saw the structure of a snowflake under normal conditions. But, what if we changed those conditions? Johannes Kepler answered this question after his experiments and wrote a book about snowflakes, particularly The Six-Cornered Snowflake.

There are two key elements which affect the structure of a snowflake: temperature and moisture. Each time the temperature or the amount of moisture change, the structure of a snowflake changes. If you check the snow crystal morphology diagram below, you will see that when the temperature nears 0° and humidity is high, the structure of a snowflake will be flowery. Flowery structures are called dendrites. When you make it a little bit colder, the structure will be fancy hexagonal plates. We can apply many combinations and get varying structures.

The Snow Crystal Morphology Diagram. Source: Snow Crystals – http://www.snowcrystals.com/science/science.html

Professor of physics Kenneth G. Libbrecht is the owner of the diagram below. In a PBS interview, he said, “It’s a mystery as to why snowflake shapes go from plates to columns to plates to columns as the temperature lowers. That’s one of the things I’ve been trying to understand. It has been a mystery for about 75 years, and it’s still unsolved.”[3]

The Shapes of Snowflakes | Source

In the end, although the structure of (almost) all snowflakes are the same, some of them are not completely hexagonal. For instance, there are some snowflakes that have tree structures. Some snowflakes have branches, and each branch has tiny branches.

But, why is the structure of some snowflakes not hexagonal?

So far, we have talked about pictures which were taken at a particular instant. We have seen the pictures of the motion of the snowflakes for the smallest amount of time that can be measured. However, a snowflake never stops spinning in the air. They tend to oscillate. That means the shape of the snowflake is changing all the time. But how? When you see a snowflake in the air, it changes its place after a second because it would be whirled about, and it will be under different conditions at that time. This process will occur up until the snowflake lands on the ground. We know from the diagram that the temperature and amount of moisture always affect the shape of a snowflake. While small-scale conditions are almost the same, on a larger-time scale, conditions will differ. And these differences will change every corner of a hexagonal snowflake, resulting in a different structure. This is the main reason behind the variety of snowflake structures and uniqueness.

In conclusion, we can say that a snowflake can preserve its six-fold symmetry at all times. I think we have another reason to love mathematics! I want to finish my piece with Hermann Hankel’s words:

“In most sciences one generation tears down what another has built, and what one has established another undoes. In mathematics alone, each generation adds a new story to the old structure.”

The first is the preservation of characteristic, long term data imprints that describes the development of an organism in the stable DNA sequences.

Second is the storage of medium term epigenetically featured data that is carried a couple of generations further down the cellular level. Epigenetic information is not stored within nucleotide sequences but in the chemical modifications of these sequences (like the methylation of repeated strings of GC dinucleotide).

Third is the storage of data generated as a result of dynamic interactions between proteins, RNA and DNA in order to adapt to the events and changes during cellular life cycle in the form of nucleoprotein or DNA-protein complexes.

The data generation and storage capacity of DNA in three different hierarchical levels and time periods demonstrates that genome plays a plethora of roles in cellular activities and heredity. Formatting of genome for its generation and storage of data is carried out via DNA sequences of various features. Genomic system is composed of repeating DNA sequences. DNA sequences (satellite) function as a marker as they repeat numerous times in various frequencies. Genome includes genomic folders similar to that of computer systems. These genomic folders, also known as the epigenetic index of genomes, are responsible for the remodeling of chromatin and the coordinated control of genomic functions. Repeating DNA sequences play a critical role in replication of genome (making a copy of DNA), dispersal of copied DNA into daughter cells and construction of support systems that enable organization of chromatins.

It is possible to better understand genomic functions in relation to examples such as memory sticks and hard drives that are used in electronic information systems. The difference between a genome as a basic data-information storage medium from a hard disc is that it can be replicated as required by its nature and these replicas can be transferred to daughter cells. Following examples could be given to illustrate that a genome gains function only when it interacts with various data processing modules in the cell.

1. A copy of genome is produced by cellular DNA replication system
2. Correct localization of each genome copy towards daughter cells is only possible when chromosome segregation system works (the centrosomes and microtubules)
3. The central transcription system is responsible for the copy of data from DNA to RNA. Different gene expression patterns are developed via regulation of transcription time and level with the help of transcription factors and a web of cell signalization.

Very intricately organized genomic system structures are designed through the successive combination of protein encoding sequences, signals distributed in various places and repeating DNA sequences. Formatting of genome resembles formatting of computer programs. Various repeated serial commands of computer software are used to allocate addresses to files independent of the original data contained; different computer systems use different signals and structures to manage programs. In a similar fashion, diverse living species often utilize repeating DNA sequences and chromosomal structures to organize the encoded information and to format their genomes.

Diversity and variation of repeating DNA sequences are building blocks that are constructed into different genomic system structures. Genomes of different organisms bear characteristic system morphology just like computers with various operating systems and hardware. For instance, animal cells are created as a good model to take and incorporate foreign DNA into their genomes. Genetic data transfer among organisms of the same kind is referred to as “vertical gene transfer” whereas transfers between different species, genuses and classes are called “horizontal gene transfer.” Mobile DNA sequences like transposons are very effective horizontal gene transfer agents.

Cellular differentiation and morphogenesis (formation of tissue and organ from cell) is not programmed completely in the primary structure of the DNA sequence. Components of modular programs are encoded in a flexible way and a continuous renewed and recombined arrangement is enabled when needed.

The reason behind creation of different organisms from a single genome is this utilization of such genomic structure. Metamorphosis, that is the development of different organisms like invertebrates such as a caterpillar and a butterfly, is a good example of this feature.

Two organisms from the perspective of the same genomic protein and RNA codes can be considered as two different species. Different genomic structures and repetition of sequences among different organisms are distinctive criteria for the identification of species since these features can lead to mismatch of reproductive cells, different expression patterns of genetic code sequences, and may cause ecological diversity as well. That is why repeated DNA sequences are very important in studying parental relationships. Today, microsatellite DNA as repeated DNA sequences are used to configure biological relations among individuals in forensic sciences. Plant species vary in respect to the repeated sequences in centromeres in their chromosomes; these variations are used for identification of species. Main determinants of genomic system structure are diversity, frequency, and genomic localization of repeated DNA sequences. To explain this with examples, we could say that successively repeated sequences at centromeres, telomere repetitions and transcription, packing of chromatin, repeated sequences that are spread throughout genome in charge of cellular functions like nucleus localization are the main elements of the genome system structure. Genome is a single integrated system that is controlled closely and remotely via communication webs that use repeated sequences.

While explaining the Qur’anic concept of the Manifest Record (36:12) Bediuzzaman Said Nursi, the great renovator of Islamic thought in Turkey in the twentieth century, wrote that the Manifest Record expresses one aspect of Divine knowledge that is related “more to the past and future than to the present. It is a book of Divine Destiny that contains the origins, roots, and seeds of things, rather than their flourishing forms in their visible existence” (30th Word, Second Aim).

Inspired from this view, a seed can be considered as a tiny adorned form of Divinely creative command as programs and indexes and as a determinant for those programs and indexes in the organization of an entire tree. Since the Manifest Record book, as a title of Divine knowledge and command, observes the past and the future rather than the present, the genome of a grain or a seed acts like a library and an archive in which the future and past of an organism is written.

Sequences encoding different information in DNA

Different information types corresponding with various DNA sequences exist in the genome. These DNA sequences that were considered junk for a long time because they were not coding proteins, have in fact been found to be responsible for an amazing array of functions in genomic structure. Some of these sequences include:

1. Group determining sequences that enable coordinated or successive expression of genes,
2. Sequences acting as a marker in charge of initiation and termination during transcription of DNA to RNA ,
3. Signal sequences responsible for conversion of primary immature RNA, sequences into smaller functional RNA molecules,
4. Transcription control sequences that determine the expression frequency of genes,
5. Sequences that identify and mark the initiation regions for intensification and remodeling of chromatins,
6. Sequences that make binding regions which affect the relocation of genome in nucleus or nucleolus,
7. Sequences that target regions where covalent DNA modification (methylation) with functional groups like methyl takes place,
8. Sequences that control and identify the regions responsible for initiation of DNA replication,
9. Sequences that make the structures which enable completion of replication at terminal ends,
10. Sequences at the segregation points that enable equal distribution of copied DNA molecules into daughter cells and centromere sequences,
11. Sequences responsible for guidance during repair of DNA bound errors and damages,
12. Start point sequences used for repackaging of genomes,

Recurring sequences exist in the genomes of many organisms and shows great structural diversity. Recurring elements function as an initiator or terminator for heterochromatin regions. Furthermore they form an important scaffold and binding spots for folding of DNA structure. As if they carry out the job of an architectural mold in specific shaping of genome to be packed into a very limited area. The ratio of repeating sequences in genome (60-90%) is much more than sequences that are encoding proteins and RNA (10-40%). To explain it with an example, chromosomes in human genome are made up of packages of protein-DNA such as heterochromatin and euchromatin. Heterochromatin regions usually make up the regions with no transcription whereas euchromatin regions feature DNA transcription.

The ratio of protein encoding sequences to the entire human DNA is approximately 1.2%. Around 43% of euchromatin regions are composed of recurring and mobile DNA elements. 18% of heterochromatin region is also made of satellite (dense repeating sequences) and mobile DNA elements. Therefore almost 50% of human genomic DNA is composed of these repeating DNA sequences. In bacteria however, these only make up around 5-10% of the genome. These sequences were described as parasitic and junk individual DNA structures up until today and still continues to be described thus by many researchers and scientist. Nevertheless, even today, mobile DNA elements and repeating sequences are accepted as genomic parasites. Recent advances in the last ten years that have demonstrated this is not true, have instead revealed the vital importance of repeating sequences in genomic functions.

Repeating DNA sequences affect chromatin (dense pack of DNA and protein) structure in two ways. Irregular repeating DNA sequence copies contain binding regions for proteins that organize DNA. Heterochromatin (darker since it is densely packed chromatin) inhibits transcription and recombination, delays replication, and generally blocks the reading of information in DNA sequences that contain genetic coding. Heterochromatin regions are distributed throughout the chromosome. Because of this, presence of regions with coupled successive repeated sequences triggers heterochromatin formation.

In fruit flies, placement of protein encoding loci required for eye pigmentation near the heterochromatin blocks in centromeres (phenomenon of position effect) is provided via organization of chromosomes and thus, formation of phenotypic characters are inhibited. The “phenomenon of position effect” is convincing evidence that genome is a major system which is integrated with composition of partially repeating DNA sequences. When heterochromatin amount is increased in XYY male fruit flies, reorganized pigmentation of eye expression decreases. In XO males, when heterochromatin amount decreases, inhibition becomes severe. Changes in levels of protein which binds to special heterochromatin specific DNA regions generate opposite effects. Decrease in these proteins reduces or suppresses “phenomenon of position effect.” Surplus synthesis of these proteins also enriches this effect.

Repeating DNA sequences play an important role in the transfer of genome into daughter cells. For instance, they function in formation of the centromeres as chromosomal binding regions for microtubules, during gamete formation as linear terminals of chromosomes are replicated, and during chromosomal matching. Distribution of repeating sequences plays a major role in configuration of genomic functions. Each genome has genomic system structure that is shaped dependent on the amount of repeating DNA sequences to a major extent.

Going back to Nursi’s explanation of the Manifest Record, we can draw a parallelism between the book of the universe and the book of revelation, the first of which shows us that certain sequences in the genome are repeated for significance and necessity, just as many verses are repeated frequently in the Qur’an with nuances to refer to different meanings, benefits, and purposes, opening a wider space for many interpretations.

A genome is not only a book that contains protein and RNA codes, but also has a complex system structure with many functions for cellular vitality. The most needed sequences are those that are repeated more frequently. They are not pieces of junk DNA as predicted, they are jewels Divinely constructed.

References

• Shapiro J. A. 2001. “Genome Formatting for Computation and Function :Genome Organization and Reorganization in Evolution: Formatting for Computation and Function.” Presented at a symposium on “Contextualizing the Genome,” Ghent University, Belgium, November 25 – 28, 2001 (Ann. N.Y. Acad. Sci., in press)
• Shapiro, J.A. 2005. “A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering.” Gene 345, pp: 91–100.
• Shapiro J. A. and Sternberg R. V. 2005. “Why repetitive DNA is essential to genome function.” Biol. Rev., 80, pp. 1–24. Cambridge Philosophical Society.

Gómez-Valdés et al. Lack of Support for the Association between Facial Shape and Aggression: A Reappraisal Based on a Worldwide Population Genetics Perspective. PLoS ONE, 2013; 8 (1)

It is a common misconception that some people are profiled to be angry or aggressive because of their physical appearances, particularly their craniofacial shapes. In addition, there have been some studies suggesting that men with certain facial traits (round-shaped faces) are more likely to develop aggressive and unethical behavior. A new study using a sample of around 5000 individuals from 94 different countries has found no correlation between facial shape and aggressive/criminal behaviors. Researchers analyzed fWHRs (facial width-to-height ratio) and 2D/3D craniofacial landmark coordinates to estimate any possible correlation between skull shape and aggressive behaviors in men. First, they utilized the famous skull collection in Hallstatt/Austria to investigate any potential correlation between skull features and life history parameters of individuals, such as their overall fitness. Second, they analyzed the male prisoners convicted of crimes like inter-personal aggression (homicide, robbery etc.) from Mexico City Federal Penitentiary to see whether there is any relation between skull shape traits and aggressive crimes. Analyses of both databases have found no significant correlation between skull shape traits either with the fitness of males or with their aggressiveness. This study has very important social and political implications in today’s societies, as we unfortunately see many ethnical, racial and even physical prejudices. This comprehensive study has undoubtedly showed once more that physical traits cannot be a reliable predictor of complex human behaviors, which are mostly shaped by external factors such as education and socio-cultural practices.

Biggest Structure in the Universe Discovered

Clowe et al. A structure in the early Universe at z ∼ 1.3 that exceeds the homogeneity scale of the R-W concordance cosmology. Monthly Notices of the Royal Astronomical Society, January 11, 2013

Throughout history, mankind has been trying to answer the questions of “how big” or “how far,” when looking into the vast expanse of the universe. As new technologies are developed, bigger discoveries and consequently bigger numbers are brought to light. An international team of astronomers recently discovered a collection of 73 quasars which form a single structure; the largest structure ever observed in the entire universe. A quasar, short for quasi-stellar object, is the luminous center of a galaxy that surrounds a super massive black hole. The distance of these newly large quasar groups to the earth is about 9 billion light years (1 light year is approximately 9.5 trillion kilometers). The size of these structures is simply mind-blowing. Even if we have a spacecraft that travels at the speed of light, it would still take about 4 billion years to cross. If we put this overwhelming size into perspective, the Milky Way—earth’s home galaxy—is only about 100,000 light-years wide and our neighbor galaxy Andromeda is only 2.5 million light-years away from the Milky Way. So these quasars are 1600 times larger than the distance from the Milky Way to Andromeda. This discovery seriously challenges the size calculations based on the widely accepted Cosmological Principle which assumes that the universe is essentially homogeneous when viewed at a sufficiently large scale. Cosmological Principle predicts that there should not be any structure in the universe larger than 1.2 billion light-years. A four billion light-years wide structure would obviously be an outlier when compared to other structures in the universe and it might contradict with the homogeneity of the universe. However, scientists think that such contradiction would not necessarily falsify the Cosmological Principle originally established by Albert Einstein. It might only change the assumptions of the theory that define at which scale the universe can sufficiently be viewed.

More Twists on Double Helix

Biffi et al. Quantitative visualization of DNA G-quadruplex structures in human cells. Nature Chemistry, 20 January 2013.

About 60 years ago, on April 25th 1953, James Watson and Francis Crick published a one-page paper where they described the “double helix” structure of the DNA, the molecule that carries genetic information from parent to offspring. This discovery not only revolutionized the biological sciences and medicine but also dramatically changed the way we perceive life, nature and most importantly ourselves. Yet, new findings on DNA structure keep surprising us. Scientists from Cambridge University discovered the first quadruple helix—a four-stranded DNA structure in human cells which they named “G-quadruplex.” These structures were previously observed in test tubes but they were never found in cells. The building blocks of DNA molecules consist of four different bases: Adenine (A), Guanine (G), Cytosine (C) and Thymine (T). G-quadruplexes (G stands for Guanine) are formed by four guanine bases that forms a square DNA helix. Researchers found that these structures are enriched in rapidly-dividing cancer cells, specifically at the ends of chromosomes called telomeres. When researchers targeted and trapped these quadruple DNA structures with synthetic molecules, they found that DNA replication slows down and cell division is blocked. Researchers suspect that these quadruple DNA structures in telomeres of cancer cells could explain why cancer cells rapidly proliferate and divide. It is still not clear whether G-quadruplexes exist in healthy cells but targeting these structures in cancerous cells with pharmacology seems to be a promising method to stop the spread of cancer.

Shadowing effect: the game of who is taller

When sunlight falls on Earth, some shadowy areas do not receive it due to an elevated structure nearby. This causes the shadowy areas to have a different set of plants, which are usually shorter and smaller than the plants in the sunny areas. In brief, the shadowing effect is the input (here sunlight) reception behavior caused by height differences across a surface. The game here is that the taller ones grab more input than the shorter ones. In systems where the input is some kind of material falling on the surface, the most important outcome of the shadowing effect is slowly-rising columnar structures. The ultimate surface morphology depends heavily on the strength of the shadowing effect. Hills of snow following a heavy snow fall and forests with trees of various heights are examples of the shadowing effect.

Reemission effect: the game of reflections

When things bounce, they follow certain physical rules. When you throw something, it may stick or bounce depending on several factors. For instance, when the light falls onto a surface, some of it penetrates the surface and gets absorbed while the rest gets reflected. Reemission is another name for bouncing or reflection in physics, though the idea is not just equivalent angle reflection or equivalent reaction force bouncing.

Figure 1 illustrates the shadowing and reemission effects on a sample surface with hills. Falling particles will most often hit the hills first due to the shadowing effect. If the hill cannot grab the particle on the first hit, then the particle reemits, and it becomes possible for the particle to fall into a valley. In order for a particle to settle in a valley (e.g., particle B in Figure 1), it will have to go through a sequence of reemissions. Let’s say that a particle’s reemission probability (i.e., residual of the sticking coefficient) is p during a hit onto the surface. By simple math, if k reemissions are needed in order for a particle to settle in a valley point, then the probability of this valley point grabbing a particle is while it is for a hilltop under no shadow. In this very approximate model, k will be larger for a deeper valley point, thereby further reducing the grab probability. To get a quick sense of it, for p=0.5, the grab probability is 50% for a hilltop and 25%, 12.5%, and 6.25% for valley points with k=1, 2, and 3 respectively. Similarly, the parameter p represents the importance the of reemission effect in the growth of the surface. Higher p means more reemissions and a larger grab probability for valley points. That is, for p=0.9 (which means the material reemits 90% of the time), the grab probability is 10% for a hilltop; and 9%, 8.1%, and 7.3% for k=1, 2, and 3 respectively.

Intuitively, when the shadowing effect is dominant, the hills will grow larger and maybe merge with each other while sites at the valleys will remain short. The final surface will not be smooth but rough. Figure 2 shows this phenomenon on the macro scale for Tibetan forest growth under the shadowing effect, and Figure 3 shows it on the nano scale (1 nanometer corresponds to 1 billionth of a meter or about hundred thousand times smaller than the diameter of a human hair) for growth of nanostructures like nanorods (i.e., sticks at nanometer lengths). When the reemission effect is dominant, one can expect that the hills will get eliminated as the valleys will quickly grab the reemitted particles. In this case, the final surface will be smooth with evenly distributed growth.

Scientists have been using these effects to control the growth of the surface, especially recently for nanostructure growth. By changing the material characteristics (which affects the reemission probability) or the angle at which the atoms arrive at the surface (which affects shadowing), the scientist can control the dominance of the shadowing or reemission effects [3]. The final outcome of the nanostructures depends on other factors as well, such as (i) temperature of the substrate surface, (ii) energy of the particles, (iii) movement of the underlying substrate, and (iv) the initial pattern of the substrate as in Figure 3(b). By using a combination of these techniques, designers have been able to grow interesting structures such as nanosprings as shown in Fig. 3(b), or nanoballs as in Fig. 3(c). These nanostructures attracted the interest of researchers for various applications such as biosensors [4], engineering of light propagation [5], and microchip production [6].

A social perspective

It is not hard to see the role of shadowing and reemission effects on people and social growth as well. One typical tendency is that well-connected and well-known people or institutions are more likely to grab attention of newcomers to a society or a network. This phenomenon has been regularly observed in the growth of online social networks (e.g., Facebook) [3]. Similarly, wealthier people are more likely to receive a larger share of the aggregate social revenue, which yields a highly skewed wealth distribution. These social trends exist for valuable goods (i.e., “attention” in the former example and “money” in the latter) which have a high “sticking coefficient” and less reemission probability. A well-known phrase to describe this is “the rich get richer,” which Figure 3(a) clearly reveals, showing nanorod growth with a highly sticky material, silicon.

“Equal sharing” in societies is certainly achievable through a more dominant reemission effect. An analogy between reemissions and charity (or helping others) is plausible. Again, the social tendency has been to equally share (or reemit) items that are mostly commodity. Water, electricity, education, and health are examples of such commodities that people “reemit” in many societies, though even the water is not reemitted in some societies.

Conclusions

The interesting observation we would like the reader to recognize here is that shadowing and reemission effects take place at nano as well as at macro levels, and both play important roles in shaping formations or structures. Though these effects are mainly studied in physical structures, they certainly exist in unphysical structures such as societies. Sharing both physical wealth and knowledge is strongly advised for a strong community that lives in harmony. This is similar to the reemission effect during the growth of materials on the nano scale, in which reemission leads to smoother and denser films with structural integrity. On the other hand, when reemission is poor and the shadowing effect is dominant, it leads to isolated structures that look nicer but are structurally fragile (See Figure 3).

Dr. M. Yuksel is an Assistant Professor at the Computer Science and Engineering Department of the University of Nevada, Reno. Dr. T. Karabacak is an Assistant Professor at the Applied Science Department of the University of Arkansas at Litte Rock. Dr. H. Guclu is an Assistant Professor at the Biostatistics Department of the University of Pittsburgh.

References

1. T. Karabacak, H. Guclu, and M. Yuksel, “Network Behavior in Thin Film Growth Dynamics,” Physical Review B, 79(19), May 2009.
2. D. Winkler, “Patterns of forest distribution and the impact of fire and pastoralism in the forest region of Tibet,” In: G. Miehe and Y. L. Zhang, Editors, Environmental Changes in High Asia. Selbstverlag der Marburger Geographischen Gesellschaft, Marburg 135, pp. 201–227, 2000.
3. T. Karabacak, G.-C. Wang, and T.-M. Lu, “Physical self-assembly and the nucleation of 3D nanostructures by oblique angle deposition,” J. Vac. Sci. Technol. A 22, pp. 1778, 2004.
4. J.-X. Fu, A. Collins, and Y.-P. Zhao, “The optical properties and biosensor application of ultra thin Silver films prepared by oblique angle deposition,” J. Phys. Chem. C 112, pp. 16784–1679, 2008.
5. D.-X. Ye, Z.-P. Yang, A.S.P. Cang, J.Bur, S.Y. Lin, T.-M. Lu, R.Z. Wang, S. John, “Experimental realization of a well-controlled 3D silicon spiral photonic crystal,” J. Phys. D: Appl. Phys., 40, pp. 1, 2007.
6. P.-I. Wang, S. H. Lee, T. C. Parker, M. D. Frey, T. Karabacak, J.-Q. Lu, and T.-M. Lu, “Low temperature wafer bonding by copper nanorod array,”, Electrochem. and Solid State Lett., 12, pp. H138-H141, 2009.
7. R. Kumar, J. Novak, and A. Tomkins, “Structure and evolution of online social networks,” Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 611-617, Philadelphia, PA, August 2006.

For the sake of simplicity, the very complex – yet flawless – organization of a single cell can be portrayed as a city. Even in a very small city that has a relatively low population there are different establishments of various sizes and capabilities that work in concert. Likewise, in order to keep the cell alive the intracellular organelles and proteins of a cell complement each other’s functions. Even though the majority of cities may have the resources to supply themselves, they also need to import and export goods. In addition, some cities may have greater industrial, residential, or agricultural strengths, making it necessary for it to communicate and trade with neighboring towns to eliminate shortages. In a similar way, cells have to communicate with neighboring cells, and bring in new sustenance and get rid of waste at different stages in their life cycles. In this article we will focus on one of the key elements of the import mechanism that is used by living cells, endocytosis.

Endocytosis is the process by which cells take in substances from outside. Since living cells are surrounded by a membrane, the cargo molecules, which are too large to penetrate through the membrane, have to be internalized by different means; this can be classified as Cell eating (i.e. phagocytosis: the endocytosis of large solid materials), cell drinking (i.e. pinocytosis: the endocytosis of liquids in large amounts) and receptor mediated endocytosis (the internalization of molecules that have specific receptors on the cell membrane) (Figure 1). During the course of these events, the portion of the cell membrane that surrounds the cargo is also internalized. However, at the present time, very little is known about the mechanisms that cause the cell membrane to invaginate and eventually be pinched off during the onset of endocytosis. Here we will concentrate on receptor mediated endocytosis, which has been intriguing biologists for more than three decades now.

Receptor molecules, which are located on the outer surface of living cells, function like receiving docks for cells. These are sites where the membrane-encountering molecule is first engaged. The cargo molecules, which arrive at the receiving docks, are often known as ligands (Latin ligare = to bind). Ligand molecules are either secreted from a neighboring cell or come directly from the bloodstream and can bind to the specific receptor molecules on the cell surface. In most cases the ligand is either a signaling molecule, which transmits information to the cell from the extracellular milieu, or a nutritious substance that needs to be internalized via endocytosis.

Unlike other forms of endocytosis, receptor mediated endocytosis occurs in a very controlled way. First of all, the ligand determines whether endocytosis will occur or not. Basically, a ligand molecule that does not have a corresponding receptor on the cell membrane cannot interact with the cell and, as a result, will not be internalized. For instance, a certain virus, which can cause severe lesions in the mouths of horses, cannot infect human cells, as our cells do not have the receptors that link the virus to the cell membrane. Secondly, the ligand cell determines how much intake will take place. That is, cells can control the amount of receptors on their membranes and thus how much the ligands that are recognized by these receptors will be internalized. By acting in this way, cells can adapt to different conditions by controlling the rate of endocytosis through the receptor molecules. The third way of control is concerned with the size of the molecules that are to be internalized. As we will discuss below, receptor mediated endocytosis is performed via some scaffold proteins that form cages (i.e. coats) around the membrane. These cages are fairly small in size, and molecules that are larger than 100 nanometers (100 nanometer is one-thousandth of the thickness of a human hair) cannot fit into them nor enter the cells along this pathway.

The conformation of the plasma membrane changes substantially during endocytosis. Given that the cell membrane has a fluidic nature, it must be accompanied by a firmer construction in order to perform these structural modifications. In the case of receptor mediated endocytosis, this function is carried out by clathrin cages (or clathrin coats), which are formed adjacent to the membrane. The clathrin protein is a three-legged molecule which can freely diffuse inside the cell. However, when a ligand molecule binds to a receptor on the membrane then multiple clathrins aggregate into that region and polymerize into cages composed of pentagons and hexagons (Figure 2a). These cages surround the cell membrane, compelling it to engulf the cargo (ligand) by invagination. When the cargo is entirely enclosed by the membrane a scission protein seals off the enclosed cargo from the plasma membrane (Figure 2b). The completely internalized membrane pouch rapidly casts away its clathrin coat with a quick uncoating reaction. After this point, the membrane pouch, including the cargo, can be transported to the inner compartments of the cell. In living cells, this process takes a little less than a minute. Even though the lifetimes of the clathrin coats are not very long, scientists have found ways of ascertaining the detailed organization of these molecules.

One of the most intriguing findings about the clathrin scaffold (or coat) is its breathtaking geometry. X-ray crystallography studies showed that the cages formed by the polymerization of multiple clathrin proteins are composed of pentagons and hexagons (Figure 3a). It has been also shown that in the majority of the cases the three dimensional structures of the cages are very similar to a soccer ball, where 12 pentagons are accompanied by 20 hexagons in order to create a curve (Figure 3b). However this is not the only geometry that clathrin coats can have. Electron microscopy images taken on frozen cells reveal that clathrins can also form some large flat arrays on the membrane which look exactly like honeycombs. In this configuration the pentagons are missing and all the clathrins align in the hexagon geometry to preserve a flat surface (Figure 3c).

The function of the honeycomb-shaped flat clathrin arrays is still a mystery. All we know is that they are more durable than the cages. In other words, although they do not have definite sizes like cages, they last much longer. Some scientists believe that these structures might be functional in the internalization of huge cargo molecules, such as bacteria, however, these claims still need to be proved. More research is needed if scientists are to be able to better understand clathrin-based endocytosis. Nevertheless, the fact that a simple geometrical modification at the molecular level can alter the entire mechanism of a biological process is on its own a very fascinating discovery.

Hamdi Sener is a biophysicist living in Boston. He can be contacted at hamdisener@gmail.com.

Note

1. Even though bacteria are the smallest cells known, compared to the regular cargo molecules they are gigantic structures.

Figure 1. Taken from Wikipedia.org

Figure 2. A) A clathrin coat (or cage) formed by the polymerization of multiple three-legged clathrin molecules. A single clathrin molecule is shown died with cyan. Adapted from RCSB protein data bank website (http://www.rcsb.org/pdb). B) The different stages of receptor-mediated endocytosis. The entire process takes a little less than a minute.

Figure 3. Taken from Wikipedia.org

The surfaces of soap bubbles have a very important feature. These surfaces which have minimum surface-tension potential energy also have minimum areas. That is, soap bubbles or clusters have a natural tendency to minimize area for the volumes they enclose. Two different frames and the areas formed are shown in Figure 1. For a given closed frame, at least one such minimal area can be formed; however, mathematicians have had to strive to prove it.

The famous mathematician Richard Courant (1888–1972), together with his students, did soap bubble experiments with various frames.

Minimal areas can also be formed by using more than one closed frames. Figure 2 shows the minimal surfaces obtained by holding two circular frames parallel. If the frames are kept too far from each other, no surface will form. If they are kept sufficiently near to each other, surfaces similar to those shown in Figures 2a and 2b will be obtained. If they are kept close enough to each other, then three minimal surfaces adjacent to each other as shown in Figure 2c can form.

The minimum energy principle is commonly observed not only in living organisms, but also in lifeless matter. A chain will take the shape which produces the least potential energy of attraction when it is fastened at two points onto a rod as shown in Figure 3. This form (function) is called “catenary” in mathematics.

The areas which are formed as a result of rotating the catenary curve around an axis A are called catenoids. Two different types of catenoids are shown in Figures 4a and 4b. As presumed, catenoids are minimal areas and can be obtained by the use of soap bubbles. If such formations were selected and used in everyday utensils, such as glasses, dishes and so forth, ideal shapes which cause the least loss of heat could be designed.

If the katenoid shown in Figure 5a is cut from its edge as shown in Figure 5b and turned by being slightly extended, a helical form or a helicoid will be obtained as shown in Figure 5f. This helicoid also is a minimal surface. Architects have widely used this form in spiral-shaped staircase structures. See Fig. 6.

Fig. 1-Closed frames and soap film surfaces formed1 Fig. 2a&b–Single foam film surfaces over two parallel circular frames1 Plus, the perpetual screw system which is widely in use in technology is also in a form similar to this geometry.

If a cylinder of the smallest volume that can house a helicoid is drawn (Fig.7a) and the lines on which the surface and the cylinder intersect are marked, then a double helix structure (Fig. 7b) is obtained; this is used in modeling DNA molecules which are the genetic codes of living species.

There are two elementary principles related to soap bubbles. The first principle says that if a bubble touches a surface that supports it, it unites with that surface in a way to make 90° angles. The soap bubble on that plain surface forms into a semi-spherical shape and the angle between the bubble surface and the supporting surface will be 90° at every point of contact. The second principle says that if three soap bubble surfaces come together, they form 120° angles along a line. If soap films come together within a tetrahedron frame as in figure 8, then the angles between the lines will be 109° 28′ 16″.

The Steiner problem which is an elementary problem in mathematics can be solved by the application of the 90° and 120° principles. The Steiner problem investigates how n points over a surface can be united in the shortest way by a web. Two transparent surfaces are connected with thin and parallel pins of equal lengths and then dipped into a soapy solution. When it is taken out, soap films will form. These films have a 90° angle with the supporting transparent surfaces and when three soap films come together, they connect at 120° angles with one another.

When observed from above, the intersecting lines between the soap film and one of the surfaces give the shortest web which unites the points in n numbers. How four points are united is shown in Figure 9a and how five points are united is shown in Figure 9b. Someone seems to have equipped lifeless objects such as soap bubbles with the ability to solve complex problems like a math genius.

Periodically repeated minimal areas have been observed on walls separating organic and inorganic substances in the skeletons of certain sea animals like the sea urchin and the starfish. Figure 10 shows the micro structure of a sea urchin’s skeleton. It has calculated that the geometry of its skeleton has perfectly been shaped in such a way as to prevent the extension of possible cracks.

Experiments with soap bubbles have been a source of inspiration also for architects. Such experiments have yielded inspiration for roof and tent designs. The German architect Frei Otto is one of the most eminent names in this regard. Figure 11 shows the minimal areas which Frei Otto managed to obtain by dipping hair-thin threads in soapy water.

In order for such a soap bubble model to be converted into an architectural structure, it is carefully photographed and precisely measured. Later, solid models are made and tested in wind tunnels. The tensile pressures likely to form under loads of wind and snow are measured by special precision instruments. In real structures, thin steel cables having high tensile strengths replace the hairy threads, and transparent plastic and synthetic materials replace the soap bubble film.

Figure 12 shows roof of the Munich Olympic Stadium, Figure13 shows the roof of the Munich Olympic Athletic Arena and Figure 14 shows the roof of the Olympic Swimming Arena in the same city. All these roofs have been designed and erected using the minimal surfaces obtained from soap bubble experiments.

Children love playing with soap bubbles very much; they usually blow a round circle after dipping a wand into soapy water and then watch the bubbles flying out of it. However, it is not only children who play with soap bubbles and soap films. Scientists have, for hundreds of years, been doing experiments with soap bubbles, developing mathematical theories, obtaining various surfaces and transferring the compiled data into technology.

Experiments with soap bubbles have been a source of inspiration also for architects. Such experiments have yielded inspiration for roof and tent designs.

2) These roofs can easily be erected, dismantled and transported to elsewhere, whereas traditional buildings cannot easily be re-located.

3) These structures which are designed according to tensile strengths are very sturdy all over, whereas the tensile pressures of classical buildings are so high that extremely heavy materials such as concrete and brick are used in order to balance the pressure.

The structures of light and strong materials granted to living things are splendid. The lightness and endurance of our skeleton system, the perfect endurance in the stems of slender plants such as wheat and barley, the extremely thin and elastic structure of a fly’s wing, and thousands of similar examples can be given.2 The word of German architect Frei Otto in this subject are expressive: “Biology has become indispensable for architecture.” Witnessing similar perfections also in inanimate structures such as soap bubbles proves that laws in nature originate from the same hand.

Obtaining minimal surfaces has become much easier as a result of immense increases in computer capabilities. Extremely complicated minimal surfaces which can be obtained through computer-aided-designs and calculations have become easily available as alternatives to soap bubble experimentations. If we, as human beings, are aiming to realize developments in science and technology, we should look,more carefully and meditatively, at events which are seemingly simple and unimportant around us and we should also discover the beauties and perfections that God has granted us and put them into service of humanity. The more our designs are compatible with the laws of nature, the higher our chances of success will be.

References

• S. Hilderbrandt, A. Tromba, The Parsimonious Universe, Springer-Verlag, New York, 1996.
• M. S. Polatöz, Tabiatta Mühendislik (Engineering In Nature), Kaynak Publications, Izmir, 2003.
• A. B. Smith, The stereom microstructure of the echinoid test. Special Papers in Palaeontology, 25, 1–85, 1981.

Scientists were working on ways of obtaining complex micro or nano (a billionth of a meter) structures by using simple inorganic substances like silicon. Producing a micro-scale device such as a transistor required difficult and expensive processes such as cutting a silicon layer neatly. A species of sponge (tethya aurantia) has proved to be a model for a possible solution.

Like every other creature, sea sponges are given the ability to use chemical substances in the exact proportions they need to carry out their vital functions like an expert chemist. A sea sponge obtains siliceous acid from the water around it a few hundred meters under the sea. By a mechanism where chemical energy is used at high efficiency and silicatein enzyme functions as a catalyzer, this acid is transformed into silicon dioxide or silica, and perfect three-dimensional structures are built from it.

The most noteworthy aspect of this process is that there is no need for the poisonous chemicals or high temperatures scientists use to obtain complex inorganic structures. Sea sponges are granted the ability to build these complex structures far more effectively than the engineers who try to produce semi-conductive materials. When the outer tissue of a sponge is removed, the 2mm-long skeletal structure, which is thinner than human hair and which takes the form of glass needles, becomes visible.

Sponges fall into three categories with respect to the abundance of their cavities and the intricacy of the channels between them. Those with the maximum proportion of cavities and channels are the most desired ones. We can better understand how wonderful are the nano-scale structures within sponges by observing the relation between a sponge and water. When we dip a hand-size sponge in water and take it out, we see that it holds water equivalent to thousands of times more than its own weight. This is caused by the countless nano-cavities invisible to the naked eye within the body of the sponge. In these minute capillary distances, the adhesion and surface tension forces are given a dominant role between water and the substance of the sponge by the divine will. Sponges, which are classified as simple structured animals by some biologists, are granted some specialties to inspire us in making high technology products such as computer microchips and solar cells.

Daniel Morse and two of his colleagues from the University of California are working on some semi-conductive materials with amazing electronic features like turning daylight into electricity. The most important application field of this new technique will be more efficient photovoltaic solar cells. Presently, solar cells are produced under high temperatures and low pressure, which requires too much energy. However, the method taught to sea sponges is highly efficient and does not require high energy. Scientists have managed to produce simpler and cheaper solar cells by imitating sea sponges and using zinc oxide instead of silicon. This way the billion-dollar facilities where the semi conductive materials are produced can possibly be replaced by smaller units of production. The world of living beings has always opened doors to new horizons. Things we take for granted and to which we do not give much thought are waiting to be reflected upon and seen through the eye of wisdom.

References

• Paul Marks, Sea sponge leads way to cheaper solar cells, New Scientist, 24 March 2007, p. 32.

The innovations implemented in nature have the potential to improve the way we do everything, from desalinating water, gluing things together, to streamlining cars. Where there is a design problem, there is a solution for it in nature created by nature’s Designer. We can distinguish the levels in biology that technology can be modeled after as i) mimicking the natural methods in the manufacture of chemical compounds to create new ones, and ii) imitating mechanisms found in nature. There are a few examples of biomimetic materials that are already part of our daily lives. Velcro, for instance, is a brand name of a fabric that consists of hook and loop fasteners used to connect objects. It was invented by Georges de Mestral, a Swiss engineer/inventor. The idea came to him after he took a close look at the Burdock seeds which stuck to his clothes and his dog’s fur on their daily walk in the Alps. He closely examined the hook-and-loop system that the seeds used under a microscope, and realized that the same approach could be used to join other things together. Velcro is commonly used in many different areas, such as in the automotive industry, clothing, shoe making, and for bringing rigid or soft surfaces together. The lotus, which possesses tiny wax crystals on the surface of its leaves, remains pristine and white, even in the midst of swampy, contaminant-rich conditions. For some, the lotus plant is even a symbol of cleanliness.

The lotus effect in material science is defined as the observable self-cleaning property found in the lotus plant. The characteristics of the lotus brought about a new application of biomimetics to the self-purification of surfaces, such as paints and roof tiles that maintain a clean surface like the lotus, by creating a surface that is similar to that of the lotus plants.1 The figure shows that dirt particles are unable to adhere to the paint and simply flow away with the rain. Everybody knows about the vivid colors of butterflies. But where does this color come from? One would naturally think that butterflies must use pigments, as in the paint industry. Actually, there are two fundamental mechanisms by which color is produced on butterfly wings. One leads to what we call ordinary color, and the second leads to the spectacular iridescent color. The ordinary color is due to the presence of chemical pigments, which absorb certain wavelengths and transmit or reflect others. The iridescent color is produced not by pigmentation, but by the interference of light due to multiple reflections within the physical structure of the material. The parts of a butterfly wing are shown in the Figure 3 in the following order, from left to right: Wing > Scales > Veins > Ridges. The size and periodicity of arrangement of the features on the wings causes interference with the visible light, creating color. Using this concept, structures and physical mechanisms that produce a shining color, like that found on the wings of butterflies, have been reproduced in carbon by an international team based at Allied Signal in Morristown, N.J. These highly periodically patterned novel carbon materials possess unique and potentially useful properties. 2 Another striking example that inspires design principles is the box-fish. These are rigid-bodied marine fish that live predominantly in shallow-watered, highly energetic, tropical reef environments. They are remarkably stable and agile swimmers.

They are able to maintain smooth swimming trajectories with minimal pitching, rolling, or yawing, even in highly turbulent waters. Moreover, they are capable of swimming rapidly (> 6 body lengths s-1), can spin around with a minimal turning radius, and can maintain precise control of their position and orientation.3 What applications could these types of properties be used for? In fact, one of the leading car manufacturers produced a bionic concept car that is based on the contours of the boxfish carapace and takes advantage of its drag reduction benefits. Not only the shape, but also the organizational composition of living organisms is highly advanced.

Therefore, great efforts are made to study and understand the formation of the hierarchical structures of these creatures. The shell of the abalone, for instance, is known for being exceptionally strong. It is made of microscopic calcium carbonate tiles that are stacked like bricks. Between the layers of tiles is a sticky protein substance. Even though calcium carbonate is one of the softest materials in nature, when the abalone shell is struck, the tiles slide, instead of shattering and the protein stretches to absorb the energy of the blow. Material scientists at the University of California, San Diego are studying the tiled structure for insight into stronger ceramic products, such as body armor. Researchers at Princeton, working on a grant from NASA, are analyzing the remarkable strength of abalone shells to help make impact-resistant coatings for thermal tiles. There are numerous groups that are working towards a better understanding of the structure and the governing mechanisms involved in the assembly of natural composite systems that have amazing mechanical properties. In synthetic composite structures, the hardness of the material is proportional to the inorganic/mineral content. However, there are striking examples of design in nature in which almost negligible amounts of minerals are used in a specially tailored environment, and very high levels of hardness, comparable to human dentine, can be achieved. An interesting example is sea-worms. Although mainly consisting of soft tissue, these worms have very hard jaws that have an exceptionally low amount of inorganic consistency. The jaw material is of particular interest because of its hard, lightweight and abrasive-resistant properties due to some gradient elements. The chemical surrounds and forms of these elements are not clear enough to be able to identify or mimic the arrangement/structure. These jaws, in addition to their extraordinary mechanical properties, are very good examples of natural gradient materials that have a perfect interface between the hard and soft tissues. Although many high-tech analysis techniques have been devised to understand how such a composite could be formed, particularly in highly unfavorable salty sea or ocean water, and how they have such great mechanical strength, the findings are still incomplete.

The information gathered is like the scattered pieces of a puzzle; to finish the puzzle, the missing pieces must be found with new advancements in analytical tools. What about mussels then? “If we have Batman and Spider-Man, why don’t we have any mussel super heroes?” asks Professor Herbert Waite of the University of California, Santa Barbara. Mussels may not be the biggest or the flashiest creatures in the sea, but they do one thing exceedingly well. They make a glue that lets them anchor themselves firmly to a rock and remain there-drenched by water, buffeted by the ocean’s waves. “I don’t know any other adhesive that can do that,” says Waite.6 Not only the glue, but the threads they make to attach themselves to the rocks are very significant in terms of both their composition and complexity, according to Niels Holten, who is conducting research on these systems at the University of California, Santa Barbara. These threads can elongate and relax with extraordinary mechanical flexibility under great impacts from ocean waves. The Waite group research on these thread cuticles reveals a very important aspect of material science, the significance of which has only very recently been understood: interface engineering. These threads have a very low amount, ca. 1-2 wt%, of metal ions in a polymeric matrix holding together large polymeric chains, which is possibly what gives the structure its flexibility and extensibility. Man-made structures cannot compete with the mechanical performance of these threads, especially at such a low volume of metal ion ingredients.

The ultimate goal of ongoing research is to understand the formation principles of these features so that similar structures can be made, using the same set of principles in laboratory conditions. In fact, the perfections of designs that are implemented in nature turn out to be an enormous fountain of ideas. Jewel beetles, which lay their eggs in freshly charred trees, can detect fires from miles away; the defense industry is studying these beetles for clues to design new low-cost, military-grade infrared detectors. Meanwhile, one of the leading car manufacturers is tapping the locusts’ famed ability to fly in dense swarms without colliding for a possible key to anti-collision devices in cars. And the Defense Advanced Research Projects Agency is funding development of a robot that can climb vertical surfaces, using the same principle that geckos use to walk up walls and saunter upside down across ceilings. There are several examples that could be given on this matter, but, due to limited space, we can only briefly summarize some of them. However, our understanding of the mechanism in nature is very limited, and it is expected that better insight will be gained with the advancement of available analytical tools. The great diversity of product designs in nature is produced from only a few common components, whereas we use a great number of materials and components to achieve new designs. Such high control and hierarchy in design in nature can only be attributed to an artist or designer who hides the perfection of his creation in the details. It is up to us to find out, see, and appreciate these perfections. Material scientists, of course, have the duty of transferring the findings from nature for the service of humankind by turning them into applicable forms in our daily lives.

Notes

1. Lotusan Paints. (2002). Retrieved 12 Nov, 2003, from http://www.lotusan.de Translated by http:// www.google.com.
2. Anvar A. Zakhidov et. al., Science, 282, 897 (1998).
3. URL: http://www.gharib.caltech.edu/bioinspired_ design/index.html
4. http://www.daimlerchrysler.com/dccom/0-5-7154-1-503504-1-0-0-503518-0-0-135-7145-0-0- 0-0-0-0-1.html
5. http://en.wikipedia.org/wiki/Abalone#_note-0
6. Anne Underwood, “Nature’s Design Workshop,” Newsweek, U.S. Edition, September 26 (2005).

Even if the defenders of the theory admit it to be just a theory, it is still being presented to the masses as if it were a scientific fact. In fact, there is a great deal of evidence against the theory, and this accumulates, day by day. Recently, the claims of great genetic similarity between apes and human beings have been refuted. The article entitled, “Chimpanzee Chromosome Surprised,” published in Nature reveals that the genes of humans and chimpanzees are far more different than they were thought to be.

An interview was held with Dr Michael J. Behe, a leading American biochemist. Dr Behe, famous for his work criticizing the theory of evolution, has made important contributions to shedding light on the question of the true origin of life:

Dr Behe, could you tell us about your opinions concerning the scientific data given in the article published in Nature that proves the genes of humans and chimpanzees to be very different in reality?

A group of researchers from the University of Tokyo have compared all the letters on the alphabets of the 21st and 22nd chromosomes. The conclusion they arrived at is very remarkable, for it has turned out that there was a far greater difference between the two species, as opposed to what was formerly accepted. Darwin’s theory really gets into trouble here. As a matter of fact, the more we learn about biology, the more trouble Darwinism gets into. If we have a superficial knowledge of living beings, we think them to be simple and we can accept Darwinism, which tries to explain seemingly simple systems through small accidental changes. Within the last thirty years however, we have learned that life is incredibly complex, beyond our imagination. For instance, bacteria, seen by evolutionist taxonomy to be the simplest creatures, have minute but very complicated and perfect biochemical motors that enable them to move. The only way to explain how bacteria can have such a complex mechanism is to accept the existence of a supernatural creation.

Then what does the similarity between the different proteins, genes, and organs of different creatures signify?

Can they be considered as evidence supporting Darwinist claims?

No, similarities between different creatures first of all fail to answer the basic question of biology. That is, how did organs and systems so peculiar and complicated come to exist? Darwinism can give no answer to that.

On the other hand, there are surprising similarities even between the species that are thought to be very different from each other. Between humans and bacteria for instance. . . The question is: “Do these similarities constitute a picture compatible with Darwin’s theory?” In fact, they don’t, because the species which are supposed to be close relatives according to Darwinist claims sometimes turn up to be genetically different. Or some living beings that are supposed to be totally irrelevant to each other have very similar organs or genes. For example, the human eye and the eye of the octopus are almost the same. But of course this does not mean that we are relatives of octopuses. It is more logical to accept that these two eye structures do not come from a “common ancestor,” but from a design that emanates from “the knowledge of a single Creator.”

In my opinion, this concept of “design” is based on the theory of “intelligent design,” which you also support. Do you think this theory explains the similarities between living things better?

Yes, you can explain these similarities through design. We know that many designers or inventors use similar parts in different systems. For instance bolts, nuts, or cables are used in different devices. They are the best pieces to be used in the relevant mechanical systems. Of course, we cannot say that one device with a cable evolved from another. They were designed separately. The intelligent design theory is very consistent in its accounting for such similarities.

The intelligent design theory is sometimes severely criticized by defenders of Darwinism and they have tried to refute it. There is an inclination to present Darwinism as if it were an undeniable part of biology. What do you think is the reason behind this?

The reason is not scientific, but rather there is a philosophical and ideological aspect. Some scientists believe that we must explain the universe and life by natural factors alone. The basis for their belief is presumption that accepts the universe as a product of natural forces alone. But what if this is not so? Even when we see a pair of eyeglasses, we know that it is not a product of natural forces; we can infer that it was made by an intelligent and skilled optician. And life is thousands of times more complex than that. Therefore, we conclude that life must have been created as well. Here, the important point is evaluating scientific evidence without prejudice, as much as possible. Darwinists claim that science cannot accept a supernatural power. But until the mid-19th century, a great majority of scientists accepted the existence of a creative power, namely, God. The claim that science should be materialistic became widespread after Darwin. However, this claim increasingly conflicts with scientific evidence. Science should not try to give a materialistic explanation for life but rather to produce a correct explanation for life. Evidence should be analyzed, even if some people’s philosophical assumptions are disturbed.

Your book “Darwin’s Black Box” has been chosen as one of the most important 100 books of the 20th century by National Review magazine. In your opinion, what was it that made this book so important?

As a matter of fact, the reason for this was not the new and original information found in the book. I only showed the reader that in molecular levels of life there are very sensitive and complex systems and all these constitute evidence for a conscious planning and organization. When most people take a superficial look, when they consider plants, animals, birds, or fish, they can feel that there is some plan and program. But Darwin’s theory of evolution, which is taught in schools, tells us that this order and system in nature can be explained without a Creator. I think the greatest influence of my theory was to show that the Darwinist explanation was too superficial and misleading.

What do you think is the greatest challenge Darwinism faces?

The greatest problem for Darwinism is explaining how new biological structures, how new creatures, come into existence. Darwinism can shed light on how already existing biological structures may undergo small changes. For example, it can offer you an explanation about how the small differences in the beaks of finches in the Galapagos Islands appeared. But how did birds come to exist in the beginning? How did complex structures like the feathers or wings of a bird form? How did all the sensitive organs and systems like the brain, the eyes, the clotting of blood, all of which require several parts to work in perfect harmony, come to be? It is impossible for Darwinism to explain these, for each of these is a very complex structure that can function only when complete. The most consistent way to account for their origin is to accept the interference of a Conscious and Omnipotent Power, a supernatural Creator.

Do you have any expectations about the future of Darwinism? Do you think Darwinism will survive?

I believe that Darwinism is leaving the stage. It will be seen that explaining life through this theory is not possible and the theory will be abandoned. The process leading to this end has already begun. The reason for this is not what I and scientists like me are doing. The more we learn about life, the better we understand how complex it is. Scientists are beginning to realize that such complex structures cannot be attributed to purposeless and random mechanisms.

As we know, the supporters of Darwinism usually say that they think within scientific grounds, and those who oppose them base their ideas only on religious belief. The picture you are giving seems to be refuting this claim. Do you agree?

Yes, exactly. In the past people used to reject Darwinism on a religious basis. And the defenders of the theory so far have always claimed science to be on their side. But the surprising findings obtained since the last quarter of the 20th century have reversed the picture. Today, our rejection of Darwinism is not based on what we do not know; rather it is based on what we know. Now the followers of dogmatic thought are Darwinists themselves. We present them scientific evidence demonstrating that living beings are created in a planned and programmed fashion, whereas they reject this only due to their philosophical and ideological worldviews.

There are insistent narrow-minded defenders of old theories that occurred before scientific revolutions. But then science is victorious against false theories. I think this is what will happen to Darwinism soon.

Who is Michael Behe?

Dr Michael Behe, still teaching biochemistry at Lehigh University, shook the scientific world with his book Darwin’s Black Box: The Biochemical Challenge to Evolution in 1997. The National Review magazine defined his work as “one of the most influential books of the 20th century.” In his book, Dr Behe has put forward a new theory called “the intelligent design” in order to explain the origin of life. Today, there are hundreds of scientists, several institutions and scientific foundations that support the intelligent design theory. As a result of these organizations, the Darwinist claims in the school books in Georgia, Ohio, and New Mexico states have been taken out. The debates concerning this in other states are still going on. The organization Discovery Institute, which leads the intelligent design movement, is presided by Bruce Chapman, one of the consultants of Ronald Reagan.

Human and Chimpanzee Genes Have Proven to Be Very Different

The latest scientific research for comparing the genetic structures of humans and chimpanzees has revealed there to be a far greater difference between the two species than was thought to be. In the research carried out by a group of scientists presided by Dr Todd Taylor in Riken Genome Science Institute in Yokohama Japan, human and chimpanzee genes were compared one by one for the first time. The conclusion surprised the scientists, who had expected to find a great similarity. Dr Taylor et al. published the result of their research in their article in the famous science magazine, Nature. In the article entitled “Chimpanzee Chromosome Surprised” the first detailed comparisonhas revealed that human and chimpanzee genes are unexpectedly different.

Formerly, it was claimed that there was a 98% similarity between human and chimpanzee genes as a result of some limited comparison, and this proof was often repeated in support of evolutionist claims. Dr Fujiyama et al. for the first time made a detailed research on the subject. The scientists who meticulously compared the 22nd chromosome of chimps and the 21st chromosome of humans, which are claimed to be similar, found that 68,000 DNA units in total were different. The researchers have stated that in the 231 genes they studied, they determined a great deal of difference, approaching 83%, and that 23% percent of the genes they studied were completely irrelevant.

Sydney Morning Herald newspaper commented on this result, saying “chimps are not as close to us as they were thought to be.” Dr Jean Weissenbach, the leader of Genoscope, a genetic research institute in France, agreed and pointed to the fact that chimpanzees have thousands of genes that are different from us.

Smart structures can sense changes in their environment and respond accordingly. These adaptive structures can autonomously modify their shapes to perform the desired task regardless of the particular environmental disturbance.

“It’s difficult to bet on technology-you cannot always pick the winners, but it looks like smart materials would be the next step in engineering design,” says Craig A. Rogers, director of Virginia Tech’s Center for Intelligent Systems and Structures.

By using smart materials instead of adding mass, engineers can endow structures with built-in responses to a myriad of contingencies. In their various forms, these materials can perform as actuators, which can adapt to their environments by changing such characteristics as shape and stiffness, or as sensors, which provide actuators with information about structural and environmental changes.

Smart structures have numerous applications, among them the following:

SPACE STRUCTURES

Large space structures are subject to a variety of dynamic perturbations produced by the crew, the docking of other spacecraft, transient thermal states during the orbit, micrometeorities, and so on. The vibration amplitude of the perturbations has to be dampened in time to avoid further nonstability in the space structure.

In addition to that, the dampening of the flexible models is a necessary ingredient in achieving robust attitude control of the spacecraft.

AIRPLANES

Smart wings. Airplanes that have smart wings will control surfaces that can reshape themselves on the fly. Airplane wings will flex themselves like fish tails. With the help of smart structures, airfoil will be shaped and the aircraft’s lift will be improved. This improved lift will help to get a single-engine fighter off the deck of an aircraft carrier without a catapult.

Replacing current (and heavy) hydraulic control systems with light-weight, high-performance smart materials could increase aircraft payloads by as much as 30 percent and flight range by 50 percent.

Adaptive surfaces would replace stiff structures designed as a compromise among ideal wing shapes for various maneuvers. Eventually vertical tails, ailerons, and stiff structures could be eliminated.

HELICOPTERS

Active helicopter blades that adjust shape continuously to respond to vibration-engendering pressure changes in the air. These fluctuations knock the machinery out of alignment and cause a lot of down time. A helicopter’s maintenance schedule is approximately 15 percent of its time. In the helicopter project, piezoelectric patches on blade surfaces function both as sensors and as actuators, or as generators of counter-force.

Flutter suppression is a particularly important problem. Recent experiments in NASA wing tunnels with unoptimized smart structure designs have shown a 70 percent decrease in displacement and a 20 percent increase in blade speed by utilizing active vibration control concepts.

Active noise suspension for helicopter cabins promise greatly decreased acoustic noise/vibration intensities. This reduces stress upon crew members involved in increasingly longer duration missions.

SUBMARINES

Stealth submarines using smart skins. Smart materials technology may result in stealth submarines. Their acoustically hypersensitive smart skins would detect the pressure of an incoming sonar wave, and then automatically generate an equal but opposite counter-pressure to cancel out the ping. With nothing reflected back to enemy boat, the submarine would be invisible.

CARS

The automotive industry also is eager to incorporate intelligent materials technology. Some of the areas where smart material will be used are:

Smart car seats. Researchers are working on an industry-sponsored project to develop smart car seats that can identify primary occupants and adapt to their preferences for height, leg room, back support, and so forth.

Maintenance information. The technology exists to enable cars to tell owners how much air pressure tires have, when oil changes are needed, and other maintenance information.

Suspension and transmission. Smart materials that can change their viscosity (inherent thickness or resistance to flow) when exposed to electric or magnetic fields. This kind of smart material will lead to new kinds of auto suspensions and transmissions.

SKIS

A revolutionary piezo control module, developed by Active Control eXperts, Inc. (ACX), serves as “the brain inside the ski.”

The ACX “brain” is a small, thin, rectangular card containing piezoelectric smart materials and control circuits, which are embedded while the skis are being made. These materials detect unwanted vibrations in the skis and convert them into useful electrical energy. The control circuitry then uses the energy to smooth out the vibrations, putting the skis back on the snow. The result is a smoother ride, more responsive turning, and “solid stability.”

SOUND

Ultra-high-fidelity stereo speakers. Using piezoelectric actuators, such speakers can expand and contract in thousandths of a second in response to applied voltage. Speaker speakers in their homes and cars to achieve maximum musical effects. Their cars and houses will offer built-in surround-sound.

BUILDINGS

New bridge systems using fiber-optic lines and other sensors as strain indicators. Embedded in building materials, these devices would generate telltale optical or electrical signals when the system is stressed. Eventually, earthquake-resistant structures could be made using materials that would alter their stiffness in response to the ground’s motion, much as horseback riders flex their legs while riding.

Earthquake resistant structures. Smart structures will shake the building to cancel the effect of the earthquake.

Early warning. Smart structures will help determine possible structural damages due to the onset of structural degradation.