Research

Everyone agrees that life is full of systems and structures that have an appearance of intelligent design. The big question is whether or not that appearance is misleading. Although scientists disagree on the answer to this, they ought to agree that careful science is the best way to resolve scientific disputes. And as with any dispute, ‘careful’ implies ‘fair-minded’—allowing the competing alternatives to be properly developed and presented.

The scientists of Biologic Institute are developing and presenting the scientific case for intelligent design in biology. We think life looks designed because it was designed, and we think that careful science is backing this up—not just in one field, but in many.

Biologic brings together experts in molecular biology, biophysics and biochemistry, bioinformatics and genomics, astrobiology, and engineering and information science in order to examine the question of design from all angles, the aim being to build a comprehensive and coherent picture.

Orion Nebula, photographed by Guillermo Gonzalez. The image was captured with an 8-inch f/4 Schmidt- Newtonian telescope.

Core Ideas

A few key ideas run through all of our work. One is the idea that information is as real and fundamental as physical quantities, like mass or energy. As a measurable substance with real-world effects subject to law-like constraints, information is undeniably the stuff of science. It is also the stuff of technology… which is the stuff of design. Interestingly, the only places in the universe where we see information stored, processed and transmitted in digital code are the complex systems of human design and the even more complex design-like systems of life.

Another key idea is that highly complex functional systems cannot be understood properly just by examining their elementary constituents. The behavior of whole systems might be explained in terms of the behavior of their constituents, but it won’t be understood that way. To grasp the whole picture you have to look at the whole picture.

Both of these ideas suggest a broader principle that we have adopted. As designers, we humans know something about design. So if we really want to know whether the design-like systems in biology were designed, we ought to draw on that knowledge. To take this principle seriously, we need to promote a serious exchange of ideas between biology and the engineering disciplines.

Areas of Research

The origin and role of information in biology.

All organisms depend on large amounts of genetic information. We understand how this information is used to specify protein sequences, but what else is it doing? What is it capable of doing and what is it incapable of doing? How much functional information do genomes hold, and where did it come from? Do cells use any non-genetic means of storing and transmitting information? Are there fundamental laws governing the origin of information?

To address these questions, we are measuring the functional information in proteins by examining their ability to withstand sequence alterations. We are teaming up with mathematicians, like William Dembski, to examine the issue of fundamental constraints on search-based acquisition of information. And we are building and testing computational models that mimic the role of genetic information in specifying functions by means of structure-forming sequences.

The difficulty of interconverting the functions of structurally similar enzymes (Kbl and BioF) has been assessed experimentally by Ann Gauger and Douglas Axe.

Functional constraints and design constraints.

We are examining both what it takes for life to be possible, and what it would take for life in its various extant forms to be probable. The first question requires an examination of the physical context needed for life. What kind of planet does it take to support complex life? How many such planets might there be? Where on such a planet might life originate spontaneously? What conditions would be needed, and how likely might those conditions be?

The second question is being addressed by examining what it takes for cells to work the way they do. What would be needed for a working genetic code to originate? What would the simplest possible metabolic system for a free-living organism look like? What would the simplest force transducing molecular machine look like? How would new protein folds appear in working form?

These are difficult problems, but they can all be addressed. The key is to couple what we know about complex systems in general with what we can observe for specific biological systems.

To get answers, at least provisional ones, we are examining the properties of stars that make Earth-like planets possible. We are looking at the nature of information and codes, and probing molecular machines and enzyme folds. We are modifying, analyzing, and modeling genes and genomes, and building model systems to see how they evolve.

Model proteins based on analogy between the structure—function relationship in written Chinese and in proteins (see Perspectives article).

Design patterns and hallmarks.

The way that humans go about designing complex things is open to scientific investigation. Are there universal principles of complex design? What are they? What stamp, if any, do they leave on things manufactured according to a complex design specification? Are any of these stamps present in living systems? Are there consistent aesthetic aspects of design—aspects of designed things that are neither functional nor logical necessities, but which are reliably present in human designs? Are any of these present in life?

Questions of this kind are amenable to scientific exploration. They also happen to be particularly interesting, which is why we are addressing them.

Selected Publications

D’Andrea-Winslow L, Novitski AK (2008) Active bleb formation is abated inLytechinus variegatus red spherule coelomocytes after disruption of acto-myosin contractility. Integrative Zoology 3: 106-113. doi:10.1111/j.1749-4877.2008.00086.x

Axe DD, Dixon BW, Lu P (2008) Stylus: A system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints. PLoS ONE 3: e2246. doi:10.1371/journal.pone.0002246

Sternberg RV (2008) DNA codes and information: Formal structures and relational causes. Acta Biotheoretica doi:10.1007/s10441-008-9049-6. PMID: 18465197

Gonzalez G (2008) Parent stars of extrasolar planets - IX. Lithium abundances. Monthly Notices of the Royal Astronomical Society, Online Early Articlesdoi:10.1111/j.1365-2966.2008.13067.x

Duren RW, Marks II RJ, Reynolds PD, Trumbo ML (2007) Real-time neural network inversion on the SRC-6e reconfigurable computer. IEEE Transactions on Neural Networks 18: 889-901. PMID: 17526353

Gonzalez G, Laws C (2007) Parent stars of extrasolar planets VIII. Chemical abundances for 18 elements in 31 stars. Monthly Notices of the Royal Astronomical Society 378: 1141-1152. doi:10.1111/j.1365-2966.2007.11867.x

Gravagne IA, Marks II RJ (2007) Emergent behaviors of protector, refugee and aggressor swarms. IEEE Transactions on Systems, Man and Cybernetics, Part B: Cybernetics 37: 471- 476. PMID: 17416173

Weinschenk JJ, Combs WE, Marks II RJ (2007) On the avoidance of rule explosion in fuzzy inference engines. International Journal of Information Technology and Intelligent Computing 1, #4.

Gonzalez G (2006) Condensation temperatures trends among stars with planets. Monthly Notices of the Royal Astronomical Society: Letters 367: L37-L41.doi:10.1111/j.1745-3933.2005.00136.x

Gonzalez G (2006) The sun’s interior metallicity constrained by neutrinos. Monthly Notices of the Royal Astronomical Society: Letters 370 : L90–L93.
doi:10.1111/j.1745-3933.2006.00197.x

Gonzalez G (2006) The chemical compositions of stars with planets: A review.
Publications of the Astronomical Society of the Pacific 118: 1494-1505 (invited review paper). doi:10.1086/509792

Gonzalez G (2005) Habitable zones in the universe. Origins of Life and Evolution of Biospheres 35: 555-606. doi:10.1007/s11084-005-5010-8

Keller D, Brozik JA (2005) Framework model for DNA polymerases. Biochemistry 44: 6877-6888. PMID: 15865433

Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential to genome function. Biological Reviews 80: 227-250. Review. PMID: 15921050

von Sternberg R, Shapiro JA (2005) How repeated retroelements format genome function. Cytogenetic and Genome Research 110: 108-116. PMID: 16093662

Axe DD (2004) Estimating the prevalence of protein sequences adopting functional enzyme folds. Journal of Molecular Biology 341: 1295-1315. PMID: 15321723

Lu H, Macosko J, Habel-Rodriguez D, Keller RW, Brozik JA, Keller D (2004) Closing of the fingers domain generates motor forces in the HIV reverse transcriptase. Journal of Biological Chemistry 279: 54529-54532. PMID: 15385563

Keller D, Swigon D, Bustamante C (2003) Relating single-molecule measurements to thermodynamics. Biophysical Journal 84: 733-738. PMID: 12547757

von Sternberg R, Cumberlidge N (2003) Autapomorphies of the endophragmal system in trichodactylid freshwater crabs (Crustacea: Decapoda: Eubrachyura). Journal of Morphology 256: 23-28. PMID: 12616572

Bustamante C, Keller D, Oster G (2001) The physics of molecular motors. Accounts of Chemical Research 34: 412-420. PMID: 11412078

D’Andrea-Winslow L, Strohmeier G, Rossi B, and Hofman P (2001) Identification of a Na/K/2Cl cotransporter (NKCC) in sea urchin coelomocytes: microfilament dependent surface expression mediated by hypotonic shock and cAMP. Journal of Experimental Biology 204: 147-156. PMID: 11104718

Gonzalez G, Brownlee D, Ward P (2001) The Galactic Habitable Zone: Galactic chemical evolution. Icarus 152: 185-200. doi:10.1006/icar.2001.6617

Axe DD (2000) Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors. Journal of Molecular Biology 301: 585-595. PMID: 10966772

von Sternberg R (2000) Genomes and form. The case for teleomorphic recursivity.
Annals of the New York Academy of Sciences 901: 224-236. PMID: 10818573

Wuite GJ, Smith SB, Young M, Keller D, Bustamante C (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404: 103-106. PMID: 10716452

Axe DD, Foster NW, Fersht AR (1998) A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease. Biochemistry 37: 7157-7166. PMID: 9585527

Axe DD, Foster NW, Fersht AR (1996) Active barnase variants with completely random hydrophobic cores. Proceedings of the National Academy of Sciences USA. 93: 5590-5594. PMID: 8643620

Gauger AK, Goldstein LS (1993) The Drosophila kinesin light chain. Primary structure and interaction with kinesin heavy chain. Journal of Biological Chemistry 268: 13657-13666. PMID: 8514798