The Cell's Design
p 18 Pays tribute to Behe and "Darwin's Black Box".
p 19-20 Outlines the intent of the book and plan to start with Behe and present a range of different phenomena and ideas to reinforce the idea of design. Cautions against "God of the Gaps" type thinking. He particularly points to the origin of the genetic code (Ch 9) and the emergence of cell membranes(Ch 12) as areas that imply design.
Ch. 1 Masterpiece or Forgery?
p 25 Makes use of Dembski's work in "The Design Inference".
p 31 Defends reasoning by analogy and gives a set of guidelines
p 32 Deals with "God of the gaps"
Ch. 2. Mapping the Territory
p 36 The nature of the cell. 5 to 40 microns in size, human hair 20 to 180 microns.
p 37 Detailed cell diagram
p 42 Proteins. "These 'workhorse' molecules of life take part in essentially every cellular and extracellular structure and activity. "
p 43 good detailed section on types and functions of proteins
p 44 Diagrams of protein structure
p 45 Cell membrane details.
p 46 Diagram of phospholipid structure
p 46 Diagrams of phospholipid bilayer and some details of cell membrane with integral proteins.
p 48 diagram of fluid mosaic model.
p 48 DNA discussion
p 49 DNA structure diagram
p 50 Central dogma of molecular biology
p 51 Excellent perspective of DNA macrostructure leading to chromosome.
p 52 Diagram for central dogma, transcription and translation.
Ch. 3 The Bare Essentials
p53 Talks about the minimimum of essential content for something to be called "life"
p55 Pelagibacter unique as most streamlined genome, 1354 gene products for bacteria that makes up 25% of microbial cells in the open ocean.
p59 Estimates of essential genome size.
p61 Summary of essential steps required for life, leading one to conclude with David Deamer "one is struck by the complexity of even the simplest form of life."
p66 After comments on some of the essential steps, comments on on the coordinated system of processes which must be in place for life.
Ch. 4 Such a Clean Machine
p70 Discusses molecular machines starting with the bacterial flagellum
p71-78 discusses a gallery of rotary motors at molecular level, including more detail on the bacterial flagellum
p81 Dynein as the molecular motor in eukaryotic flagella and an agent in the transfer of cargo along microtubules in the cell.
p85 Discussion of Paley's Watchmaker argument, the "analogy" criticisms of Hume and Johnson, and then makes the case that the existence of molecular machines with specific purposes strengthens the argument by analogy.
p88 Paley's Biochemical Watch, box
p91 Brownian ratchets and the generation of translational motion.
p93 Kinesin as molecular motor that transports cargo along microtubules
p95 Argument from molecular motors to design
Ch. 5 Which Came First?
p98 Deals with "chicken and egg" dilemmas
p98 DNA information necessary to make proteins, but DNA needs multiple proteins to do it, and proteins necessary to make DNA
p107 "chemical systems in the cell that ..consist of components strictly interdependent upon one another" In human design experience such "chicken and egg" problems "can be resolved only by the strategic and simultaneous implementation of interdependent components"
Ch. 6 Inordinate Attention to Detail
p110 Arguing for design by the meticulous exactness of some complex cellular machinery - perhaps you could see this as an extension of the idea of irreducible complexity based on the exactness of processes which fulfill an essential purpose.
p119 regulation of production
Ch. 7 The Proper Arrangement of Elements
p125 Deals with a number of cellular systems which extend the idea of fine-tuning to the cellular level.
p126 optimized proteins
p129 Just-right DNA
p135 Regulation of gene expression
p 137 Glycolysis - link to ATP as currency, glucose to 2 ATP plus 2 NADH
p 138 Discussion of the rate of glycolysis and the role of ATP.
Ch. 8 The Artist's Handwriting
p 143 The central dogma
p 144 biochemical linguistics, 684 rules of natural antibiotics
p 146 par 4 carbohydrate role
p 147 information in oligosaccharides
p 148 gene organization - operons, alternate splicing and overlapping genes.
p 149 Lac operon in E Coli, lactose response
p 151 exons, introns and spliceosome
p 152 "Alternate splicing allows the cell to produce several different proteins from the same mRNA."
p 154 "one gene one protein" rule violated by overlapping genes, different reading frames.
p 155 64 codons from genetic code - shifting codons can encode for different peptides. With codons, 3 possible read frames.
p 156 frameshift mutations
p 158 DNA parity code, at least 16 other bases could have been used, but AGCT make possible a parity code
p 159 Parity code box emphasis
p 160 AGTC base pairing rules.
p 163 DNA computing
p 164 1 gram of DNA equiv to a trillion CDs
p 165 DNA barcodes
Ch. 9 Cellular Symbolism
p 170 Genetic code, 171 Error minimizatioin, Code nearly universal in living organisms
p 172 Discussion of 5' and 3' ends - check for hp use.
p 173Start GUG
p 173Error minimization, last par substitution errors
p 175 The genetic code better than all but about 0.02% of randomly generated codes, but improved to 1 part in million when the nature of AGCT examined, Out of 1018 codes.
p 176 Error minimization diagram, Crick - hard to evolve the code since a change affects every polypeptide in the cell. "Nearly any conceivable change to the genetic code would be lethal to the cell."
p 177 Some alternate genetic codes, but very close to the universal code. Can argue that they can evolve, but observed cases were in small genomes and seldom expressed .
p 177 Yockey - code is one of about 1070, not time to establish it by chance. The genetic code's origin may coincide with life's origin at about 3.8 Gy.
p 178 Most proteins require all 20 amino acids, ferridoxins only 13.
p 178 The histone code, 5 different histones
p 179 Histone structure
p 180 histone positioning code
p 180 Histone detainls, 2 1/2 turns to include 150 nucleotides. formation of nucleosomes -- beaded necklace image, solenoid
p 180 par 4 Wrap around histone, blocks transcription, initiation sites in linker positions between nucleosomes
Ch. 10 Total Quality
p 186 Denton if there are significant errors in protein production, the cell self-destructs. Since proteins make proteins, you enter a destructive spiral.
p 186 mRNA, tRNA and ribosome discussion
p 187 tRNA details, diagram on p 188
p 189 ribosome details
p 190 Translation diagram, 3 to 5 amino acids per second, so the smallest proteins of some 100-200 amino acids can be made in less than a minute.
p 191 Error checking the tRNA and rRNA, which must be very stable.
p 193 mRNA checking process
p 195 par 1, Interesting error checking process. Proteins attach to mRNA, but if not correct, they don't release, so mRNA strand cannot get out through the pore.
p 195 tRNA checking 1 error in 3000
p 196 Further error checking via the elongation factor - error correction in the finely tuned strength of binding - too strong or too weak eliminated.
p 197 1 in 10,000 error rate minimum for life but gives acceptable production rate, whereas higher accuracy would make the process too slow.
p 198 endoplasmic reticulum role
p 199 oligosaccharides info used in ER for protein-folding monitors.
Ch. 11 A Style All His Own
p 205 Gould in "Wonderful Life" "No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel."
p 205 Gould's metaphor of "replaying life's tape".
p 205 molecular convergence
p 207 100 examples of molecular convergence
p 216 details on DNA replication
p 221 proteins for DNA replication
Ch. 12 An Elaborate Mosaic
A discussion of the fluid mosaic model of the cell membrane and then details about the complex constituents and functions of the cell membrane.
Ch. 13 Coloring Outside the Lines
p 245 Tackles the problem of imperfections in the way life is formes - sometimes called the theodicy problem. "apparent defects and faulty designs of some biochemical systems".
p 246 good statement of general evolutionary biologists' objections to design - cites Gould and The Panda's Thumb.
p 246 quote For Gould, "odd arrangements and funny solutions are the proof of evolution - paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce." In other words, even though biochemical systems are replete with elegant design features, the assortment of imperfections in life's chemistry undermines the case for biochemical intelligent design. From an evolutionist viewpoint, an all-powerful, all-knowing Designer would never scribble so haphazardly.
p 247 Does cite 2nd Law of Thermodynamics and allows for contingency in mutations. But backs away from contingency in development by citing 2nd law degradation of optimal designs.
p 248 Optimal designs involve tradeoffs so that some aspects of a process may appear suboptimal in order to achieve optimization of the process as a whole.
p 249-51 Glycolysis - An excellent section citing the marvel of the glycolytic pathway but the "futile cycle" of the back-conversion to fructose 6-phosphate. Likens it to a toddler quickly undoing a mother's hard clean-up work. Then proceeding to discuss how this apparently futile loop creates a situation where there can be a quick and sensitive response to an increased energy need. An additional perspective is that the so-called "futile cycle" can be used to warm the body.
p 251 Bilirubin - part of an "inelegant" process of breaking down hemoglobin. It has seemingly unnecessary steps, consumes energy, and produces bilirubin as a toxic end product. He argues that there is a broader picture of potent antioxidant properties of bilirubin that contribute positively to the protection of cells.
p 254 Uric acid - kidney stones affect 1 in 10 and account for 10 of 1000 hospital admissions. They are formed because part of the adenine and guanine in the life process is excreted by first forming uric acid. Only primates don't further process the uric acid to soluble form. This is seen as an imperfection since it produces kidney stones and gout. Rana again points to an anti-oxidant function of uric acid, leading to cancer resistance and longer life.
p 255 Junk DNA. Identical segments of "junk" DNA appear in a wide range of related organisms. Most widely recognized are pseudogenes, endogenous retroviruses, SINEs and LINEs.
p 256 pseudogenes - diagram on p257, unitary and duplicated
p 258 endogenous retroviruses - retrovirus produces DNA which can be incorporated in the genome as non-functional segments.
p 258 These elements jump around genome, direct making of additional copies, maybe with the use of RNA and reverse transcriptase.
p 259 Argues that junk DNA has function
p 261 Protein synthesis with 30% defect rate, but a fraction of the protein fragments keeps cells primed to respond to viral infection.
p 262 Rubisco - carbon fixation during photosynthesis. Protein rubisco is catalyst for carbon adding and as such is the most abundant protein in nature. Inefficient, but appears optimum when whole process is considered.
p 265 Dynein and kinesin transport cellular cargo along microtubules in opposite directions.
Ch. 14 The Masterpiece Authenticated
p 270 Life, a Magnificent Masterpiece
p 270 Can evolution explain it
p 271 Evolutions stepping stones - argument that complex systems developed by co-opting elements that evolved for other purposes.
p 273 What are the odds, Yockey revisited
p 278 Paley and Hume, analogical analysis
p 279 Summary of types of evidence
p 281 Extra elements in the argument
p 286 The elements of the RTB model of creation.