Problems with Neo-Darwinian Evolution

1. Problems with Neo-Darwinian Evolution Can chemical evolution create the first living cell? Can Neo-Darwinian evolution explain all the organisms we see today?

2. Biological Origins:The Controversy “It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid, or insane (or wicked, but I’d rather not consider that).” Richard Dawkins (Professor of Zoology at Oxford University), New York Times, 1989.

3. Review of Biochemistry 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 Cells--the building blocks of living organisms DNA--a long, ladder-like molecule, found in a cell’s nucleus, that stores the information (code or directions) for building proteins, cells, and organisms (deoxyribonucleic acid) Mutation--an error in the DNA code

4. Basic Molecules Fatty acids Amino Acids Sugars Purines Pyrimidines Chemicals Water Hydrogen Methane Carbon monoxide Carbon dioxide Ammonia Nitrogen No Oxygen Membranes Proteins RNA & DNA Living Cells Protocells The Chemical Evolution Hypothesis

5. 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 Darwinian Evolution Starts With a Living Organism

6. Beware of Definitions for Evolution 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.

7. How Does Neo-Darwinian Evolution Work? 1. Chemicals combine to form DNA, proteins, and the first living, reproducing cell. 2. Genes in DNA duplicate, making them free to mutate without destroying original function. 3. Random mutation creates new genes, and new genes code for new proteins. 7. The fossil record shows intermediate body plans and common descent. 6. Accumulated innovations produce new body plans. 5. Advantageous innovations spread throughout a population by natural selection. 4. New proteins and interactions among new proteins provide innovations.

8. Can Chemical Evolution Create the First Living Cell?

9. 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: both left and right “handed” amino acids are formed. 4. Amino acids and bases have never assembled 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.

10. Proteins are 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. Proteins use only “left handed” amino acids. In 19 of the 20 amino acids, both “left and right handed” are “naturally” formed in equal numbers. From Darwin’s Black Box

11. Randomly Assembling a Protein 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 (15 billion years) is less likely than 1 in 10 billion. There are not enough atoms and time in the universe to randomly assemble 400 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.

12. Grasping at Straws: The RNA World Since the assembly of DNA and proteins are both highly improbable, perhaps life started with a self-replicating RNA molecule. Some RNA molecules (ribozymes) have catalytic capabilities like proteins and store information like DNA. Response: Their catalytic properties are insufficient for the integrated, coordinated function required for reproduction. To date, no sugar, phosphate, and base molecules have self-assembled under natural conditions outside the cell. RNA has the same chirality problem as proteins. Without reproduction, RNAs cannot advance to a reproductive system.

13. 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.”

14. How Does Neo-Darwinian Evolution Work? X 1. Chemicals combine to form DNA, proteins, and the first living, reproducing cell. 2. Genes in DNA duplicate, making them free to mutate without destroying original function. 3. Random mutation creates new genes, and new genes code for new proteins. 7. The fossil record shows intermediate body plans and common descent. 6. Accumulated innovations produce new body plans. 5. Advantageous innovations spread throughout a population by natural selection. 4. New proteins and interactions among new proteins provide innovations.

15. Can Genes Duplicate in DNA?

16. The Evidence for Gene Duplication is Declining There is some evidence for gene duplication: Polyploids (extra chromosomes) in some plants, Pseudogenes thought to be damaged duplicates. Gene duplication was thought to be the source of “junk” DNA, 97-98% of human DNA. The ENCODE project is showing that at least 90% of “junk” DNA is not junk. Current research is showing at least some pseudogenes have function. If there are no “junk” DNA or pseudogenes, there is no “duplicated” DNA to support neo-Darwinian evolution.

17. How Does Neo-Darwinian Evolution Work? X X 1. Chemicals combine to form DNA, proteins, and the first living, reproducing cell. 2. Genes in DNA duplicate, making them free to mutate without destroying original function. 3. Random mutation creates new genes, and new genes code for new proteins. 7. The fossil record shows intermediate body plans and common descent. 6. Accumulated innovations produce new body plans. 5. Advantageous innovations spread throughout a population by natural selection. 4. New proteins and interactions among new proteins provide innovations.

18. Can Neo-Darwinian Evolution Design Innovations?

19. Point Mutation A Mutation is a Copy Error in the DNA Base Pair Sequence A point mutation gets a single base pair wrong. There are also deletions, insertions, transpositions, and etc. Mutations are infrequent but real. Most mutations destroy protein function and are detrimental. Some mutations are neutral. A very few may be beneficial to the organism under some conditions and spread throughout a population in future generations. Human sickle-cell anemia--resistance to malaria. Antibiotic resistance of bacteria. A new variety of bacteria that eats oil or plastic.

20. 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 Bacterial Flagellum Innovations require new proteins with binding sites (shapes and charges) that allow new inter-protein interactions. Proteins work in multi-protein complexes, usually 6 or more.

21. The Bacterial Flagellum is an Innovation Requiring 40 Interacting Proteins For a simple bacterium to develop a flagellum, roughly 40 new proteins that fit together must be 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, and even die out because of their energy cost. All 40 interacting proteins would have to be present at the same time to give an advantage, which is improbable. *combination lock analogy

22. New Binding Sites For More than Three Proteins are Out of Reach for Neo-Darwinian Processes According to Michael Behe: No new “advantageous” inter-protein binding sites have been seen in 1020 malaria, 1020 HIV, and 1013 E. Coli cells. Generously, assume that one new binding site between two proteins is possible in 1020 cells. We might expect to see two coordinated binding sites 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. *combination lock analogy Michael Behe; The Edge of Evolution; Free Press, 2007.

23. Evolutionists Argue: There is a stepwise evolutionary path to every innovation where each step, requiring new proteins and binding sites, is beneficial--significantly increasing innovation probability. (combination lock analogy) Response: Since the bacterial flagellum needs all 40 proteins, each protein had to serve some other beneficial function until all were present. If so, we would expect to find each protein used in another beneficial function in the cell, but we don’t. We would also expect to find proteins for assembly, repair, regulation, and control that came together, but we don’t. Such a pathway has never been demonstrated for any innovation. And, each step may be implausible.

24. Can a Functional Protein Develop a New Function Through Mutation? Doug Axe & Ann Gauger experimented with proteins that have the most similar structures but have different functions. They found that at least 7, and probably more coordinated mutations are required to change the function from one to the other. Using a population-genetics model, they found that such a change would require far longer than 15 billion years. The Neo-Darwinian mechanism (mutation & natural selection) for developing new functions is not plausible. Gauger & Axe; The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway

25. Orphan Genes Orphan genes code for proteins that have a unique sequence and structure. All organisms have a significant number of orphan genes. They are so different from other genes that they are unexplainable by a neo-Darwinian process of random mutation and natural selection.

26. How Does Neo-Darwinian Evolution Work? X X 1. Chemicals combine to form DNA, proteins, and the first living, reproducing cell. 2. Genes in DNA duplicate, making them free to mutate without destroying original function. X 3. Random mutation creates new genes, and new genes code for new proteins. 7. The fossil record shows intermediate body plans and common descent. 6. Accumulated innovations produce new body plans. X 5. Advantageous innovations spread throughout a population by natural selection. 4. New proteins and interactions among new proteins provide innovations.

27. Can Neo-Darwinian Evolution Design New Body Plans?

28. DNA Does Not Determine Body Plans; Thus, Mutations Cannot Lead to New Body Plans Recent research indicates that DNA does not determine an organism’s architecture (body plan)1,2. Something in the egg besides DNA (centrosomes and membrane patterns) is involved with determining architecture. This is called epigenetic information. Embryos develop according to the egg species’ plan (until death) when its DNA is replaced by that from another species.3 1. See the Epilogue of Stephen Myer’s Signature in the Cell. 2. See Chapter 14 of Myer’s Darwin’s Doubt. 3. Jonathan Wells; lecture given in Albuquerque, NM on January 20th, 2009; “DNA Does Not Control Embryo Development.”

29. How Does Neo-Darwinian Evolution Work? X X 1. Chemicals combine to form DNA, proteins, and the first living, reproducing cell. 2. Genes in DNA duplicate, making them free to mutate without destroying original function. X X 3. Random mutation creates new genes, and new genes code for new proteins. 7. The fossil record shows intermediate body plans and common descent. 6. Accumulated innovations produce new body plans. X 5. Advantageous innovations spread throughout a population by natural selection. 4. New proteins and interactions among new proteins provide innovations.

30. What About Common Descent?

31. Does The Fossil Record Show Common Descent? • The fossil record shows a progression from single celled organisms to complex multi-celled organisms over time. • OrganismAsserted Age • Blue-green algae in the oceans 3.5 to 1 billion • Blue-green algae and bacteria on land 1.2 billion to 800 million • Single celled animals 1 billion • Complex, multi-celled animals* 530-520 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.

32. Cambrian Explosion Video

33. 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

34. Are We Related to Chimpanzees? mtDNA estimates a chimpanzee-human common ancestor about 10 Mypb, but this is based on assumptions: common descent, mutation rates are known, and all differences in DNA are due to mutations. Base pair sequences of protein coding genes for chimps and man may be 98-99% the same, but total DNA may be only 70-76%* the same. Humans and chimpanzees have the same “broken copy” of a vitamin C gene that may indicate a common ancestor. Similar “pseudo-genes” are found to have an important function, implying that common descent may not be the only explanation. *Richard Buggs as quoted by Casey Luskin; Critically Analyzing the Argument from Human/Chimpanzee Genetic Similarity; evolutionnews.org, 9/2011.

35. Is there an Evolutionary Tree? Contradictory trees are derived from different protein and gene sequence comparisons. Contradictory trees are derived from embryonic development patterns. These imply that the tree model is wrong. See Myer’s; Chapter 6, Darwin’s Doubt.

36. How Does Neo-Darwinian Evolution Work? X X 1. Chemicals combine to form DNA, proteins, and the first living, reproducing cell. 2. Genes in DNA duplicate, making them free to mutate without destroying original function. X X 3. Random mutation creates new genes, and new genes code for new proteins. 7. The fossil record shows intermediate body plans and common descent. 6. Accumulated innovations produce new body plans. X 5. Advantageous innovations spread throughout a population by natural selection. 4. New proteins and interactions among new proteins provide innovations.

37. Conclusion The Neo-Darwinian mechanism of mutation and natural selection is a theory in crisis. Evidence for common descent is declining. Genesis 1: In the beginning, God created the heavens and the earth and every living thing according to its kind.

38. How Do The Darwinists Respond? All critiques of Darwinian evolution are religiously motivated. Intelligent Design Creationism is creationism in disguise, not science. Darwinian evolution is a fact and is the best supported of all scientific theories. Nearly all biologists believe in Darwinian evolution. People who doubt Darwinian Evolution just don’t understand. Imperfections in biological designs demonstrate that the designs were not created by an intelligent cause. Substantive responses are infrequent.

39. 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 Darwin’s Doubt; Stephen Meyer, 2013 Internet Discovery.org IntelligentDesignNetwork.org NMIDnet.org ARN.org

40. Probability of Randomly Assembling a Protein-1 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.

41. Probability of Randomly Assembling a Protein-2 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 1077 for 150 amino acids. There is no known natural mechanism for assembling amino acids into polymers outside the cell.