Design in Biology Which One is Designed?

1. Design in Biology Which One is Designed?

2. The Appearance of Design “Biology is the study of complicated thingsthat give the appearance of having been designed for a purpose.” (Dawkins, The Blind Watchmaker)“Biologists must constantly keep in mind that what they see was not designed, but rather evolved.” (Crick, What Mad Pursuit)They believe that random mutation and natural selection is a design substitute.Question: Is there a design substitute, or is the design from an intelligent source?

3. Beware of Definitions for Life’s Development A. Evolution--Change over time; or a heritable change in the characteristics within a population from one generation to the next. B. Darwinian Evolution--The common descent of all organisms from single celled organisms by the mechanism of variation operated on by natural selection. C. Neo-Darwinian Evolution--Darwinian Evolution with random genetic mutation as the variation mechanism. D. Micro-Evolution--Small changes in organisms due to random mutations, genetic variability, and natural selection. E. Macro-Evolution--Darwinian or Neo-Darwinian evolution. F. Chemical Evolution--Chemicals forming the molecules of life then organizing to form the first cells by random, natural processes. A or D being true do not imply that B, C, E, or F are true.

4. Life’s Building Blocks Atoms--the building blocks of matter (hydrogen, oxygen, carbon, and others) Molecules--combination of atoms bound together by electrical forces (water, sugar, salt, amino acids, and many others) Amino Acids--molecules that are the building blocks of proteins Proteins--folded chains of amino acids that form the structural building blocks and machinery in cells DNA--a long, ladder-like molecule, found in a cell’s nucleus, that stores the information (code or directions) for building and regulating proteins (deoxyribonucleic acid) Mutation--an error in the DNA code Cells--the building blocks of living organisms

5. Design in the Cell

6. Cells are the Basic Building Blocks of Living Organisms 1839, Schleiden & Schwann proposed that cells are the smallest, most fundamental unit of life. Until the late 19th century, cells were thought to be simple bags of protoplasm. In the late 19th century, scientists started discovering that cells contain compounds which undergo complex chemical reactions. Today, we see a staggering complexity that suggests design.

7. The Cell Has Design Characteristics Separate compartments with unique chemical environments and controlled access passages between compartments A molecular transportation network to supply raw materials and distribute finished products Microprocessor regulation of gene expression, growth, repair, and response to environmental conditions Molecular protein machines that do cell work Cargo haulers Cables, ropes, pulleys Propulsion Switches Energy conversion Manufacturing Unzipping, reading, and duplicating DNA A library containing information that specifies all the above (DNA) From Unlocking the Mystery of Life See M. Behe, Darwin’s Black Box, pg 4-5.

8. Design in Proteins Molecular Machines

9. A Protein is a String of Amino Acids Amino acids are molecules. There are 20 different amino acids used in proteins. There are hundreds to thousands of amino acids in a protein string. Amino acids in a string, from Darwin’s Black Box

10. A Protein (Amino Acid String) Folds into a Precise Three Dimensional Shape. Proteins form the structure and machinery of a cell. Shape and charges on the protein’s surface determine interaction with other proteins and molecules. Many proteins have the characteristics of a microprocessor combined with a functional machine. They are sometimes called enzymes. DNA Polymerase From David Keller

11. Molecular Machines--The Ribosome The ribosome is a molecular machine made of 50 proteins that uses mRNA as a template to assemble amino acids, brought to it by tRNA, into proteins.

12. Molecular Machines--F1F0 ATP Synthase This machine is imbedded in the wall of a mitochondria. H+ powers a protein motor that drives a turbine that attaches PO4 to ADP to make ATP for cell energy. Or it works in reverse to pump H+.

13. Molecular Machines--Bacterial Flagellum From Behe; Darwin’s Black Box, p 71. Originally fromVoet and Voet

14. Design in DNA

15. DNA is a Molecule that Folds and Twists Into a Chromosome Chromosome Chromosome pairs (One from Mother, one from Father) humans 23 apes 24 dogs 39 flowering plants >100 Our 46 chromosomes are made of 3 billion base pairs. base pair molecules DNA sugar & phosphate molecules Harris; DDD-V; September 2004

16. DNA Has a Ladder-like Structure Sugar and phosphate molecules form the sides. Base molecules form the rungs. Phosphate Base A Base T Sugar C G G C T A There are 4 types of base molecules: Adenine--Thiamine Cytosine--Guanine A & T always go together. C & G always go together.

17. DNA Base Pairs 2% of DNA Consists of Base-Pair Sequences That Are Codes for Building Proteins Instead of a sequence of letters that form words and ideas, DNA uses a sequence of molecules (bases) as a code that gives directions for protein assembly and regulation. Three bases in a row (a codon) specifies an amino acid. Sequences of codons specify the sequence of amino acids to be used in assembling a protein. GCT = Alanine AAA= Lysine TCT = Serine TTT = Phenylalanine (The other 98% of DNA is highly organized software that regulates cell and protein functions.)

18. How the DNA-Protein Process Works 1(Greatly Simplified) A protein machine, RNA polymerase, reads the bases in a DNA gene. It copies the base sequence to make a messenger RNA (mRNA) Molecule. The structure of RNA has a single strand, sugar-phosphate backbone with bases attached. The bases are the same as for DNA except uracil is substituted for thiamine. RNA Polymerase mRNA From Unlocking the Mystery of Life

19. How the DNA-Protein Process Works 2(Greatly Simplified) The mRNA is transported out of the nucleus to a protein manufacturing machine called a ribosome. Amino acids are brought to the ribosome by transfer RNA (tRNA). The ribosome uses the mRNA as a template to assemble amino acids into a string. The string of amino acids folds, with help from another machine, into a functioning protein. Robosome Protein assembly From Unlocking the Mystery of Life

20. Journey Inside the Cell Video

21. DNA is a Code The entire DNA code contains roughly the same quantity of information as 300 encyclopedia volumes. The information in DNA is highly organized with efficient data retrieval, cross references, and a sophisticated hierarchical structure. All known codes have an intelligent cause: Computer codes Written language Morse code Numbers Construction plans

22. Both Proteins and DNA are Required for Reproduction The information from DNA is read by molecular reading machines and transferred to molecular manufacturing machines. Molecular manufacturing machines use the information from DNA to assemble amino acids into proteins. Proteins form the molecular machines that replicate DNA during cell reproduction. Evolution requires reproduction. Reproduction requires the interdependent system of DNA and molecular machines. This interdependent system is evidence for design. Unzipping from Unlocking the Mystery of Life Video

23. Can Chemical Evolution Design the First Cell?

24. Water Hydrogen Methane Carbon monoxide Carbon dioxide Ammonia Nitrogen No Oxygen Fatty acids Amino Acids Sugars Purines Pyrimidines Membranes Proteins RNA & DNA Protocells Cells All in about 170 M Years The Chemical Evolution Hypothesis 1. Chemicals in the early Earth atmosphere formed the basic molecules necessary for life, which settled into oceans and ponds; 2. The basic molecules assembled into proteins and DNA; 3. Proteins, DNA, and other molecules assembled into the first living cells; and 4. All of the above were done by natural, chemical processes.

25. Life’s Basic Molecules Have Been Formed, But Chemical Evolution Stops There The Miller-Urey experiment in 1953 (and others) synthesized amino acids (the building blocks of proteins), and heterocyclic bases (the building blocks of DNA) from the gases assumed to compose the “early atmosphere.” But there are serious problems: 1. Oxygen in the early atmosphere. 2. Contaminants. 3. Chirality: left and right “handedness.” 4. The building blocks have never been seen to assemble naturally into proteins and DNA outside the cell. Thaxton, Bradley, Olsen; The Mystery of Life’s Origin; Philosophical Library, NY, 1984. Wells; Icons of Evolution; Regnery, 2000.

26. Assembling a Protein from Amino Acids Without Design is Extremely Improbable A reproducing cell requires at least 100 proteins with a median length of 400 amino acids. If a “right handed” amino acid is included in the amino acid chain, the chain cannot function as a protein. Randomly synthesizing a chain of 400 left-handed amino acids with 1080 tries (number of atoms in the universe) every micro-second since the beginning of time is less likely than 1 in 10 billion. There are not enough atoms and time in the universe to randomly assemble 400 exclusively left-handed amino acids into a chain. In addition, the right type of bond between amino acids is required. Even with proper bonds and chirality, very few amino acid strings will fold into functioning proteins. And, there is no known natural means of assembling amino acids into strings outside the cell.

27. Crick (co-discovered DNA structure in 1953), Life Itself, 1988: “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.”

28. Can Neo-Darwinian Evolution be a Design Substitute?

29. Random Mutation and Natural Selection are the Basis for Neo-Darwinian Theory Charles Darwin believed that observed small changes in organisms (micro-evolution) were due to variation acted upon by natural selection. Micro Evolution He reasoned that if small changes occur over a short time, change in basic form (macro-evolution), due to accumulated small steps are possible over a long time. Macro Evolution

30. Can Random Mutation and Natural Selection Explain Innovations? Evolution From a Single Cell to Modern Organisms Requires Thousands of Innovations: Sight Nervous systems Respiratory systems Circulatory systems Skeletal systems Immune systems Molecular machines These innovations require thousands of new proteins and new inter-protein interactions. Proteins work in multi-protein complexes, usually 6 or more.

31. The Bacterial Flagellum is an Innovation Requiring Interaction Among 40 Proteins For a simple bacterium to develop a flagellum would require roughly 40 new interacting proteins produced by mutations. The flagellum, like other innovations, is irreducibly complex, which means the flagellum is useless unless all proteins are present.* Useless protein interactions and associated mutations do not spread in a population because of their energy cost. All 40 interacting proteins would have to be present at the same time to give an advantage. *combination lock analogy

32. Interactions Among More than Three Proteins are Out of Reach for Neo-Darwinian Processes According to Michael Behe: No new “advantageous” inter-protein interactions have been seen in 1020 malaria, 1020 HIV, and 1013 E. Coli cells. We would not expect to see two coordinated interactions among three proteins in 1040 cells.* Only 1040 bacterial cells have lived since life began; therefore, interactions among more than three proteins are out of reach. Intelligent design, with a goal in mind, is a much better explanation than a neo-Darwinian process. *combination lock analogy Michael Behe; The Edge of Evolution; Free Press, 2007.

33. What About The Fossil Record? • The fossil record shows a progression from single celled organisms to complex multi-celled organisms over time. • OrganismAsserted Age • Blue-green algae and bacteria 3.5 billion • Single celled animals 1 billion • Cambrian Explosion 550 million • Higher plants on land 425-400 million • Fish, amphibians, forests, insects 400-345 million • Reptiles 345-280 million • Dinosaurs, flowering plants 225-65 million • Mammals, birds 65 million • Man 1 million? • It also shows major animal classes and phyla appearing abruptly, fully formed, and living unchanged for millions of years. During the Cambrian Explosion, most phyla (main groups) appeared without intermediate forms over a few million years.

34. Famous “Intermediates” The fossil record contains few if any intermediate links, and all are controversial. Are they intermediate or independent with intermediate characteristics? Archaeopteryx— “Paleontologists now agree that Archaeopteryx is not the ancestor of modern birds1.” Whales—A 2001 National Geographic article cited evidence that Hippos are the closest land dwelling relatives of whales. A 2007 Nature article cited evidence that Indohyus, a small, deerlike animal is the whale’s closest land relative. Tiktaalik—A 2006 article in Nature calls this fish with limb-like front fins the intermediate between fish and amphibians. A 2010 Nature article tells of finding tetrapod footprints, with toes, dated at 20 million years before Tiktaalik. 1. Wells, Icons of Evolution Picture from Icons of Evolution

35. Problems With Neo-Darwinian Evolution Organization and Information Content of DNA—The information in DNA is highly organized with efficient data retrieval, cross references, and a sophisticated hierarchical structure.* It does not fit a random mutation scenario. Necessity of New Protein Interactions—Random mutation and natural selection cannot explain the new proteins and inter-protein interactions necessary for biological innovations. Common Descent—New body plans appearing suddenly and questionable intermediates make common descent doubtful. Epigenetic information and body plans—DNA (and mutation) may have little to do with body plan. New research is showing that something in the egg besides DNA determines body plan*. Common Descent by the mechanism of random mutation and natural selection is not a credible design substitute. *See the Epilogue of Stephen Myer’s Signature in the Cell.

36. According to the Evidence, They are Both Designed.

37. How Can We Explain Design In Biology? Genesis 1: In the beginning, God created the heavens and the earth and every living thing according to its kind. John 1: In the beginning was the Word, and the Word was with God, and the Word was God. Through Him all things were made. Rom 1:20 For since the creation of the world, God's invisible qualities-his eternal power and divine nature-have been clearly seen, being understood from what has been made, so that men are without excuse.

38. Reading The Mystery of Life’s Origin; Thaxton, Bradley, Olson, 1984 Evolution: A Theory in Crisis; Michael Denton, 1986 Darwin on Trial; Phillip Johnson, 1993 Darwin’s Black Box; Michael Behe, 1996 Nature’s Destiny; Michael Denton, 1998 Intelligent Design; William Dembski, 1999 Icons of Evolution; Jonathan Wells, 2000 The Edge of Evolution; Michael Behe, 2007 Signature in the Cell; Stephen C. Meyer, 2009 The Myth of Junk DNA; Jonathan Wells; 2011 Internet Discovery.org IntelligentDesignNetwork.org NMIDnet.org ARN.org

39. Probability of Randomly Assembling a Protein Consider an average protein that is 400 amino acids long. 19 of 20 amino acids are naturally produced in both left and right handed molecules Assume amino acids are randomly attached into a string (polymer). The probability of getting a polymer made of all “left handed” amino acids is 1/2380 = 4 x 10-115. Assume that we get 1080 tries (very generous) at building this protein every micro-second since the beginning of time (very generous). 1080 is roughly the number of atoms in the universe. The number of micro-seconds since the beginning of time is: 15x109 yr x 8760 hr/yr x 3600 sec/hr x 106 micro-sec/sec = 4.7 x 1023 micro-seconds We get 1080 x 4.7 x 1023 = 4.7 x 10103 tries.

40. Probability of Randomly Assembling a Protein The probability of getting one success over all these tries is, 4.7 x 10103x 4 x 10-115 = 1.9 x 10-11 which is less than 1 in 10 billion. This is almost impossible odds, and we have been very generous. A reproducing cell requires at least 100 proteins. The probability of getting the right bond is ½ for each amino acid. Other kinds of amino acids will poison the process. Very few left-handed amino acid polymers will fold into functional proteins. An estimate is 1 in 1074 for 150 amino acids. There is no known natural mechanism for assembling amino acids into polymers outside the cell.