Evolution Before Our Eyes: Complex Mutations in Microbes Giving New Functions

OUTLINE

( 1 ) Barry Hall’s lac Bug

( 2 ) Lenski’s Long Term E. Coli Evolution Experiment

         Lenski’s E. coli Evolve Ability to Metabolize Citrate under Aerobic Conditions

( 3 ) Bacteriophage Lambda Evolves a New Protein Binding Site Using Four Mutations

( 4 ) The Significance of These Complex Mutations

         Plate Tectonics: An Example of Evidences

         Diverse Evidence for Evolution

( 5 ) The Core Issue in Rejecting Evolution

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

( 1 ) Barry Hall’s lac Bug

Lactose is a sugar that bacteria can use as a food. In order to do this, they first have to cut lactose in half, releasing two simple sugars (glucose and galactose) that the metabolism of the cell can use for energy. In E. coli, the ability to metabolize lactose depends on having (1) a gene that produces the protein (the enzyme beta-galactosidase) that cuts the lactose, (2) an appropriate regulatory region which turns on this gene when lactose is present but turns it off (to conserve metabolic energy) when lactose is absent, and (3) another protein, called a permease, which imports lactose through the otherwise-impermeable cell membrane. These three functions are normally co-located on a stretch of DNA called the lac operon.

Structure of lactose and the products of its cleavage. Source: https://en.wikipedia.org/wiki/Lac_operon

In 1982, Professor Barry Hall at the University of Rochester initiated a set of experiments using some E. coli in which he deleted the gene for the beta-galactosidase from this lac operon. The loss of this gene knocked out the operation of the three-part system, which made it impossible for the bacteria to metabolize the sugar lactose. He then let the bacteria reproduce in a nutrient mixture which contained galactose. The bacteria would only thrive if they managed to evolve a new metabolic pathway to digest galactose. The bacteria needed to evolve both (1) a gene which would produce the enzyme beta-galactosidase, and also (2) the appropriate controlling region of DNA. The growth medium contained the chemical IPTG, which promoted the cellular production of permease from the original lac genetic region, since that function had been disabled by Hall’s gene knock-out. Having the permease present in this way allowed the experimenters to detect any new mutants which had evolved the ability to cleave galactose.

As it happened, in the course of many generations, the bacterium did exactly that. Two mutations in a distant gene converted it into an effective gene for making beta-galactosidase enzyme, and further mutation in the DNA which controls the expression of this new gene gave it the needed galactose sensitivity. Neither part was greatly effective without the other. So, this is an example of a new multi-part genetic system, with a function which was new to this hacked bacterial strain, which was produced by mutation coupled with natural selection.

In further series of mutation and natural selection experiments, Hall found a new set of bacteria which had a new enzyme which was able to switch on the production of the lac permease, in addition to having the new regulated beta-galactosidase gene.

Intelligent Design proponent Michael Behe has attempted to minimize the significance of these observations. His main objection seems to be that this evolution of a new function took place by various alterations to existing genetic material. But that is exactly how evolution normally proceeds! Evolutionary biologists do not claim that fully functional, whole new genes suddenly appear in the genome ex nihilo. That seems to be what Behe is demanding. Rather, evolution is typically a matter of step by step modifications in the DNA which is already there.

Ken Miller rebuts all of Behe’s objections, and concludes:

Does Barry Hall’s ebg system fit the definition of irreducible complexity? Absolutely. The three parts of the evolved system are:

(1) A lactose-sensitive ebg repressor protein that controls expression of the galactosidase enzyme
(2) The ebg galactosidase enzyme
(3) The enzyme reaction that induces the lac permease

Unless all three are in place, the system does not function, which is, of course, the key element of an irreducibly complex system.

( 2 ) Lenski’s Long Term E. Coli Evolution Experiment

Richard Lenski’s group at Michigan State University has been running a long-term evolution experiment on asexual E. coli bacteria since 1988. Six populations (Ara-1 through Ara-6) were started from a one strain, and six further populations (Ara+1 through Ara+6) from a nearly identical strain. Each population is kept in a flask at 37 C with 10 ml of a growth medium which contains only enough glucose to support about 5 x 10+8 cells per culture. Each day, 0.1 ml of the previous day’s culture is transferred into 9.9 ml of fresh growth medium, and the cells reproduce up to the limit of the nutrients. The result is about 6.64 generations per day, or 2400 generations per year. Samples of each population are cryo-preserved every 500 generations. These preserved cells can be revived and further studied as needed.  Fitness is periodically assayed by measuring growth rates versus an ancestral strain. A photo of the twelve population flasks is shown below.

Long Term Expt 12 Flasks

The 12 E. coli LTEE populations on June 25, 2008. Source: Wikipedia article “E. coli long-term evolution experiment”, originally from: Brian Baer and Neerja Hajela – http://myxo.css.msu.edu/ecoli/citrateflasksphotos.html

Over the first 10,000 generations, each of the twelve populations demonstrated significant increases in fitness.  The figure below shows the increases in average cell size as each population accumulates mutations to make them better adapted to their environment. Since then, fitness has continued to improve, but at ever-slower rates.

Growth in cell size of bacteria in the Lenski experiment over the first 10,000 generations of Lenski’s long-term evolution experiment. From https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment

Clearly, these bacteria are accumulating multiple, step-by-step beneficial mutations, which improve their fitness in their environment. This is evolution in action.

The plots below show the numbers of mutations retained in each population, through about 50,000 generations. Six of the populations have evolved hypermutator strains, where point mutations appear much faster than usual. These populations show in Plot (a) as having 800-2500 mutations after 50,000 generations. Plot (b) is rescaled to show more clearly the trajectories in the six non-hypermutable populations, which have accumulated 60-110 mutations apiece. Across all the cells and all generations in a given flask (population), over a billion mutations have occurred; it is likely that every possible point mutation in the bacterial genome has been sampled many times over. However, most of these mutations did not spread and become fixed in the population as a whole. See STAN3–From Micro-Evolution to Macro-Evolution: Beneficial Mutations, the Pace of Evolution, and Increasing Genome Complexity     for more details on numbers and patterns of the mutations in this experiment.

Numbers of accumulated mutations in the twelve populations of the long-term E. coli experiment. Source: Olivier Tenaillon, et al., Nature 536, 165–170 (2016)
http://www.nature.com/nature/journal/v536/n7615/full/nature18959.html

 

It is worth noting that “beneficial” or “fitness” is always defined relative to a particular environment, typically the environment currently occupied by the organism. A strain of E. coli in “the wild” needs to cope with a variety of temperatures, acidities, availability of different nutrients, etc. A typical microbe therefore has versatile metabolic mechanisms to respond to variations in conditions. However, the bacteria in the Lenski experiment experience the same conditions, day after day, year after year, for thousands of generations. This particular environment is characterized by a limited amount of nutrient, primarily glucose. Thus, Lenski’s bugs have evolved to be greedy specialists in consuming glucose at a constant temperature of 37 C. To maintain other functions (e.g. the ability to metabolize the sugar ribose) in this situation is a waste of metabolic energy, and so it has been advantageous for these bacteria to accumulate mutations which disable some of these functions.

Lenski’s E. coli Evolve Ability to Metabolize Citrate under Aerobic Conditions

One of the most interesting features of this experiment is that after about 33,000 generations, one of the populations (“Ara-3”) evolved the ability to make use of the large amount of citrate which happened to be present in the growth medium. The photo below shows a close-up view of experiment flasks, where the middle (Ara-3) population is clearly more turbid (cloudy) than the others, due to the enormous bacterial cell mass in that flask.

The population designated Ara-3 (center) is more turbid because that population evolved to use the citrate present in the growth medium. Figure from Wikipedia article “E. coli long-term evolution experiment” ; original source: Brian Baer and Neerja Hajela – http://myxo.css.msu.edu/ecoli/citrateflasksphotos.html

Normally E. coli is unable to make use of citrate under the aerobic (presence of oxygen) conditions used in this experiment. The metabolic machinery for utilizing citrate exists in E. coli, and it can ferment citrate under anaerobic conditions in the presence of a reducing substrate, but it cannot transport citrate under oxic conditions.

In an effort to probe how this one population evolved this ability, the researchers resurrected (thawed) cells from previous generations in that population and let them evolve, to see whether these parallel lines would also develop the ability to metabolize citrate. A few of the lines restarted from generation 20,000 evolved the ability to utilize citrate, whereas none of the lines restarted from generation 15,000 could.

Apparently some key but essentially neutral mutation (which has not yet been identified) occurred between generation 15,000 and 20,000. This potentiating mutation (or complex of mutations) had no distinctive effect on citrate metabolizing, but it enabled some further mutation to produce a weakly effective Cit+ (citrate-metabolizing) variant by generation 31,500. This variant constituted about 0.5% of the cells in the population at generation 31,500, and rose to 15% and 19% at generations 32,000 and 32,500. At generation 33,000, the dominance of the Cit+ variant plummeted to 1.1%, presumably because the Cit- subpopulation produced a beneficial mutation which allowed it to out-compete the emerging Cit+ subpopulation. However, after a few hundred more generations the optical turbidity of the population took a step change to a higher level, indicating some further mutation at that point had increased the viability of the Cit+ subpopulation to a very high level. Thus, this set of mutations gave to the cells an important function (ability to digest citrate in the presence of air) which they did not have before. [1]

Young earth creationists and Intelligent Design proponents have tried to downplay the import of this evolutionary gain of function. Their usual rhetorical tactic is to characterize this as a minor tweak to the regulatory region of the existing citrate gene, as merely “turning on an existing switch in the genetic machinery” which did not involve evolution of any new information or added functionality. The graduate student chiefly responsible for this research, Zachary Blount, has stated that this description of the changes in the cells is simply “a lie”:

“….No, the ability to grow on citrate is not a matter of simply flipping a pre-existing regulatory switch.  Continuing the electrical metaphor, the evolved Cit+ function is instead about rewiring.  My dear little Cit+ cells gained their ability to partake of the previously forbidden citrate by a genetic duplication involving a gene, called citT, which encodes a transporter protein that is used during anaerobic growth on citrate.

“This duplication did something very special.  You see, one of the major aspects of gene regulation is that genes have associated regulatory DNA sequences, including what are called promoters that control when genes are expressed.  The citT gene is normally controlled by a promoter that tells the cell to turn it on only when there is no oxygen present.  As shown in the Figure below, the gene duplication put one copy of citT next to, and under the control of, a promoter that normally controls another gene called rnk.  The rnk gene is normally turned on when oxygen is present.  The new association between citT and the rnk promoter – what we call the rnk-citT regulatory module – turns citT on when oxygen is present, and allows Cit+ cells to use citrate under the conditions of the LTEE.  (To really feast on the citrate involved additional evolutionary changes, both before and after this rewiring, but I’ll leave that point aside for this post.)

“…True, the duplication responsible for Cit+ did rearrange components that were already there, but that rearrangement generated a new association between components that did not previously exist, and it produced a new function that also did not previously exist.  To argue that rearrangements cannot produce innovation is akin to arguing that a novelist has done nothing creative in writing her novels because she only used words that already existed.”  [emphasis in the original]

 Here is the figure to which Blount referred, showing schematically the tandem duplication in the population that evolved the new ability to grow on citrate. This duplication produced the new rnk-citT regulatory module by placing the second copy (“Tandem Copy 2”) of the citT gene adjacent to the rnk promoter region.

Tandem amplification in Cit+ genomes, showing altered spatial and regulatory relationships generated by the amplification. The figure comes from Blount, et al., Genomic analysis of a key innovation in an experimental Escherichia coli population, Nature 489, 513–518. http://www.nature.com/nature/journal/v489/n7417/full/nature11514.html?foxtrotcallback=true

This tandem duplication is the key mutation which enabled uptake of citrate, but by itself it only gave only weak performance. A further mutation just after generation 33,000 in a different spot in the bacteria’s genome greatly enhanced the cell’s growth in the presence of citrate. This second mutation involves the regulation of the dctA gene, enabling the reuptake of succinate or other C4-dicarboxylates that are exported in exchange for citrate import by the CitT system, thus completing a cycle that permits sustained citrate transport and utilization without an unbalanced loss of intracellular C4-dicarboxylate substrates. [2] It is the cells with this second mutation that grow so fast that they show high turbidity.

To summarize, at least three separate mutations were involved here: (1) a potentiating mutation(s) around generation 15,000-20,000 which of itself had no noticeable effect on citrate uptake; (2) a duplication of a stretch of DNA around generation 31,500, which created a new gene function by pairing a copy of the citrate uptake gene with a different promoter; and (3) another mutation around generation 33,000 which balanced out the cell’s C4-dicarboxylates in the presence of citrate uptake. This multistep, complex modification of the genome provided the cell with a new function (the ability to robustly take up citrate under aerobic conditions), with no loss in other functions. So again, this is clearly a “gain-of-function” set of mutations. Opponents of evolution try to downplay the significance of this complex mutational change, but the facts speak for themselves.

( 3 ) Bacteriophage Lambda Evolves a New Protein Binding Site Using Four Mutations

A bacteriophage is a virus that infects and replicates within bacteria cells. The Lenski lab published a study [3] in 2012 involving a bacteriophage (“ lambda phage”) which infects E. coli. The phage normally works by using its protein called “J” to bind to a protein on the surface of the E. coli called “LamB”. To test the ability of the phage to evolve the capability of binding to a different protein, the researchers cultured lambda phage with a population of E. coli which had mutated such that only a few of the bacteria had the LamB protein present. The phage population could subsist at a low level on this tiny minority of the bacteria, but would only thrive if they evolved the ability to infect the rest of the bacterial population which lacked the LamB protein on its surface.

In an initial experiment, such a phage was found to evolve in one out of six flasks. Analysis showed that the phage had developed the capability of binding to a different E. coli protein, OmpF, while retaining its original ability to bind to LamB. Despite the efforts of Intelligent Design advocates to spin it otherwise, this again is a “gain-of-function”, pure and simple.

Lenski’s team then repeated the experiment on a larger scale, using 96 more bacteria/phage communities. In 24 of these 96 communities, the phage developed the capability to thrive by binding to the OmpF protein. This protein has a similar 3-dimensional structure as the original LamB, but differs considerably in amino acid sequence.

The researchers did genome sequencing to identify the mutations responsible for the new function in the phage. Figure 3 of their paper illustrates their findings. A portion of that figure is reproduced below. The labels across the top denote the point mutations at specific nucleotide positions along the phage genome. The top 24 rows show some of mutations observed in the 24 phage strains whose expressed J protein was able to bind to the E. coli OmpF. For comparison, a few rows from the lower half of the figure are shown to illustrate the mutations at these genome positions for some of the phage populations which did not evolve that capability.

Taken from Figure 3 of Meyer, et al., Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda. Science 27 Jan 2012: Vol. 335, Issue 6067, pp. 428-432.
Caption of original Figure: “Mutations affecting the J protein in phage isolates from 48 independent populations of the large-scale experiment. Isolates are shown in rows (with alternate labels offset for readability) and mutations in columns; gray fill indicates an isolate has the mutation. The top 24 rows show phage isolates that can target the new OmpF receptor; the bottom 24 rows show phage that remain dependent on LamB.” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306806/

All of the top 24 rows (i.e. the strains able to bind to the different OmpF protein) shared four changes: mutations from A-to-G at nucleotide position 3034, G-to-A at 3319, a mutation at either position 3320 or 3321 (affecting the same codon as the mutation at 3319), and at least one mutation between positions 2969 and 2999). We have labeled these four changes “A” to “D” as they appear from left to right in the figure above.

It is likely that these four canonical mutations, alone or in various combinations, improve the binding to the original LamB protein target in the E. coli, and that this selectively drove their initial appearance in various strains of the phage. However, all four of these mutational changes together are needed in order for the phage to robustly bind to the different OmpF protein.

In The Edge of Evolution Michael Behe had claimed that the appearance of a new protein binding site which required more than two mutations was, for all practical purposes, impossible – – beyond the “edge of evolution”. As noted by Dennis Venema, the evolution of this new protein binding capability in Lenski’s phage, requiring four distinct mutations, accomplished what Behe said was impossible.

 The Significance of These Complex Mutations

Behe published a literature review in 2010 [4] which sought to minimize the significance of these sorts of experiments on bacteria and viruses in flasks. He states that in these experiments, what is observed is the “breaking and blunting” of genetic functionality, rather than an increase in functionality. In response, Paul Braterman [5] noted that Behe had to engage in numerous rhetorical contortions to press his case, and Jerry Coyne [6] pointed out that Behe had limited his review to situations which where are the least likely to yield new functional mutations. For instance, bacteria under normal circumstances can undergo substantial beneficial genetic changes by importing sizeable chunks of DNA from other microbes. However, in many of the laboratory experiments discussed by Behe, there was only one species of bacteria in the flask, so there was no possibility of such DNA exchange.

The reality is that in all three cases discussed above, a new (new to the starting organism) functionality arose via multiple mutations, which gave a significant improvement to fitness in the environment currently occupied by the organism. Moreover, in each of these cases the gain of the new function did not come about by “breaking or blunting” other important functions. This is indeed “evolution before our eyes.” [7]

That said, these changes fall far short of producing a new organelle or a whole new species. Is this all merely “micro-evolution”, with no relevance to the changes involved in, say, the divergence of modern humans from other primates?

Plate Tectonics: An Example of Evidences

An analogy may help in putting these mutation results in perspective. As Ron Miksha    pointed out in The Mountain Mystery , prior to the 1960’s geologists had no clear idea as to how most mountain ranges were formed. Today nearly everyone accepts the notion that giant crustal plates move around and crumple into mountain ranges in zones where these plates are forced together. But the notion of “continental drift” on such a gigantic scale seemed so bizarre when it was suggested by Alfred Wagener in 1912 that it was rejected by most scientists  : “Without detailed evidence and a force sufficient to drive the movement, the theory was not generally accepted: the Earth might have a solid crust and mantle and a liquid core, but there seemed to be no way that portions of the crust could move around”.

Nowadays we can use GPS measurements to directly measure the movements of the continents. For instance, we find that Africa is moving away from South America at a rate of about an inch (2.5 cm) per year. That is about as fast as your fingernails grow. If that were the only evidence we had of continental drift, perhaps severe skepticism would be warranted. In your entire lifetime, only about 7 feet (~2 meters) of relative motion will occur. Can this slow creeping really account for the tearing apart of whole continents, and the formation of a 3000 mile wide ocean?

Well, of course it can, if this process continues on and on, for many millions of years. However, if plate tectonics is real, there should be some other, corroborating evidence. And there is.  The coastlines (or more precisely, the continental shelves) of Africa and South America, and (less obviously) of North American and Europe can be fit together like puzzle pieces. Moreover, distinctive geological formations can be found in matching locations on the coasts on either side of the Atlantic Ocean.

Dramatic confirmation of the spreading of the seafloor came with measurements showing symmetric magnetic striping in the oceanic crust on either side of the mid-Atlantic Ridge. This is clearly explained by basalt magma welling up all along this ridge, taking on the prevailing direction of the earth’s magnetic field as it cools and hardens, and then moving away from the ridge in either direction. The earth’s magnetic field is known to reverse its orientation at irregular intervals during geologic history, typically several hundred thousand years apart. Other evidences supporting plate tectonics include the radioactive dates of the rocks of the seafloor, the geographical patterns of fossils of various ages, and the location of belts of volcanos and earthquakes at the edges of the crustal plates.

Seafloor magnetic reversals, giving rise to seafloor magnetic striping. Source: Wikipedia article “Vine–Matthews–Morley hypothesis” https://en.wikipedia.org/wiki/Vine%E2%80%93Matthews%E2%80%93Morley_hypothesis

 

Diverse Evidence for Evolution

With evolution, there is an analogous array of diverse evidence. If mutational changes have indeed been going on and on and on for billions of years, with accompanying evolution of today’s biota from much simpler ancestors, there should be some sort of progression visible in the fossil record, and there should be signs of common ancestry in today’s genomes.

If there has been no large-scale evolution, and thus modern plants and animals have always existed, we would expect to find modern plants and animals at all levels of the fossil record, possibly commingled with other, now-extinct creatures. But that is not what we find. What we actually find is a clear progression of initial appearances of various life-forms from the lowest (oldest) rock layers to the younger layers and on to the present, which cannot be explained away as the result of the hydraulics of Noah’s Flood [8].

In the lowest rock layers we find single-celled bacteria; after many hundreds of million years, simple multi-celled organisms like sponges and jellyfish appear. Millions of years later, in yet higher rock layers, we start to find fossils of soft-bodied animals known as Ediacaran fauna. Then in the rock layers from the Cambrian period (542 to 485 million years before the present), there is a rapid progression from mainly worms and slugs to an array of fauna which represent many of phyla which have persisted to the present [9].

The actual specimens within these phyla present in the Cambrian fossils, however, are typically quite unlike any modern species – – no modern fish or reptiles or mammals or flowering plants appear in the Cambrian. Trilobites (early arthropods which are distant cousins to today’s insects and crustaceans) always appear in sedimentary layers below any rocks containing dinosaurs, never above. Fossils of modern mammals are always found in layers above those of dinosaurs. Moreover, fossils of modern marine animals like clams can be found in rock layers above fossils of large, active land animals like dinosaurs, so these sequences cannot be attributed to a world-wide Flood first burying marine creatures whilst land dwellers were climbing to higher ground.

In the vertebrate lineage, worm-like swimmers with a primitive notochord (no spine, no jaws yet) first appear in the Cambrian, followed in higher (younger) rock layers by jawed fish (fossils first seen 400-450 million years ago) , then tetrapod amphibians, then the first reptiles around 300 Mya, dinosaurs in yet higher rock layers, and finally modern mammals make their appearance. (The earlier types of animals often persist in the presence of the newer arrivals – – sponges, jellyfish, fish, amphibians, and reptiles persist in the fossil record and into the present, but the specific species of fossilized fish, amphibians and reptiles change over geological time.)

It is known that the fossil record is not complete, and the basic arithmetic of population genetics shows that transitional species will mainly occur in small, isolated populations which are unlikely to leave a fossil trace. Nevertheless, a steady stream of discoveries since Darwin’s time has filled in many of the major transitions in the animal family. For instance, a number of fossils with part fish/part amphibian characteristics, and with part reptile/part mammal characteristics, are found at about the times expected for these transitions. (See Realistic Expectations for Transitional Fossils ). Donald Prothero  states [10], “We now have abundant evidence for how all the major groups of animals are related, much of it in the form of excellent transitional fossils”, and he supplies examples which include dinosaurs and modern mammals.

With the sequencing of genomes in the past twenty years, a whole new realm of evidence supporting evolution has become available. For instance, the patterns of “endogenous retroviruses” (ERVs) in the human and chimpanzee genomes are clear evidence that humans and chimps descended from a common ancestor.   There are many other lines of genetic evidence for evolution, which are summarized by Douglas Theobald in “29+ Evidences for Macroevolution” .

The physical changes that appear from species to species to the next species in the fossil record are largely the result of ongoing mutational changes. Opponents of evolution claim that there is a some limit to mutational changes, that would prevent evolutionary changes going beyond some threshold (such as one “kind” developing into a different “kind”), but they have no actual evidence of such a limit [10]. Theobald explains:

If the general observation of geneticists was that of genomic stasis and recalcitrance to significant genetic change, it would be weighty evidence against the probability of macroevolution. For instance, it is possible that whenever we introduce mutations into an organism’s genome, the DNA could back-mutate to its former state. However, the opposite is the case—the genome is incredibly plastic, and genetic change is heritable and essentially irreversible…. Extremely extensive genetic change has been observed, both in the lab and in the wild. We have seen genomes irreversibly and heritably altered by numerous phenomena, including gene flow, random genetic drift, natural selection, and mutation. Observed mutations have occurred by mobile introns, gene duplications, recombination, transpositions, retroviral insertions (horizontal gene transfer), base substitutions, base deletions, base insertions, and chromosomal rearrangements. Chromosomal rearrangements include genome duplication (e.g. polyploidy), unequal crossing over, inversions, translocations, fissions, fusions, chromosome duplications and chromosome deletions.

It is thus reasonable to infer that the same sorts of mutations observable today have been going on and on and on for geological history, and that these accumulated rearrangements of DNA over millions and millions and millions of years have led to large changes in physical features, including new organs, etc. [12]  Indeed, the rates of genetic mutation and physical changes inferred from the fossil record match reasonably well with currently observed mutational rates and physical changes.

However, the evidence from the fossil record indicates that evolutionary changes typically proceed very, very slowly. For instance, it took something like 50 million years to evolve today’s large horses from different and much smaller ancestors. It is estimated that there are seven successive genera in the branchy lineage from Hyracotherium or Eohippus (size of a small fox, teeth for nibbling tips of branches, 3-4 toes per foot) to the present-day Equus horse (one toe per foot, large teeth for grinding up grass) [13]. This gives an average phyletic taxonomic rate of 0.13 genus per million years, or 7.5 million years per genus. Triassic and earlier ammonites evolved at a rate of 0.05 genus per million years. The last common ancestor of hominids and chimpanzees is considered to have lived around 6 million years ago. These transitions did not involve significant whole new organs, yet they still spread over millions of years.

The reptile to mammal transition was a more significant transition, including many changes to the jaws and the reproductive system and elsewhere, although these were both still tetrapods. In the fossil record, this transition is spread over some 100 million years. This all indicates that it is unrealistic for us to expect to see a major change in bodily function evolve in a hundred years or even a hundred thousand years.

We simply don’t have enough information to track each of the thousands of mutations that would be involved in the transformation of one species in the fossil record to another. We have many fossils of hard body parts, but have recovered little DNA from fossils older than a few million year. For instance, we have no clearly sequenceable DNA from any dinosaur fossils. We can tabulate all the differences between the human and the chimp genomes, but we don’t know the genome of our common ancestor some six million years back; and even if we did, it would not be possible to reconstruct the exact sequence of mutations that led from that common ancestor to the two current species.

There are some cases, however, where there is enough information to reconstruct the mutations to a particular gene which gave rise to some significant new function. Long et al. [14] describe the mechanisms of gene duplication and exon shuffling, and note 22 genes in various species whose history has been reconstructed in some level of detail, using mutational steps of the types which are routinely observed today. For instance, the Antarctic notothenoid fishes have an unusual “antifreeze” glycoprotein (AFGP) which inhibits the formation of ice crystals in their bodies in the sub-freezing (-1.9 C) Antarctic waters. The AFGP is a polymer of a Thr-Ala-Ala glycopeptide monomer. It appears that in an ancestral copy of a trypsinogen protease gene the Thr-Ala-Ala region was expanded through multiple internal duplications. The exons coding for the protease sequences were lost, to yield the present form of the AFGP gene. Thus, a gene with an entirely different function was evolved, by means of mutations which are observable today (duplications, deletions, etc.). See details here.

Young earth creationists commonly complain about what has not yet been discovered – – for instance, we don’t possess fossils of every transitional form, and we do not know all the step by step mutations that produced the genomes of today’s organisms. But if we look at the evidence that HAS been found, instead of complaining or speculating about what has not yet been found, that evidence is overwhelmingly supportive of common descent driven by evolution.

The slow accumulation of mutations and the modest production of new functions that are observable in controlled laboratory experiments over the course of a few years or a few decades is analogous to the slow creep of the continents. In both cases, slow processes operating over many millions of years can produce enormous changes.

For both plate tectonics and macroevolution, there is abundant circumstantial evidence to complement the modest changes that we are able to observe in our day. To dismiss the evidence for evolution because we cannot observe a whole new organ develop within the span of historical human observation is as senseless as rejecting plate tectonics because we cannot personally see a whole continent torn apart to form a new ocean before our eyes.

( 5 ) The Core Issue in Rejecting Evolution

Having spent this much time addressing the physical evidence, I’ll briefly mention a factor which is actually more important for many people. The folks (in North America, at least) who reject evolution come largely from a conservative religious background. They have been told that evolution contradicts the Bible, and that “Darwinism” leads to a debased view of humans. Thus, they are predisposed to believe the proponents of Intelligent Design and of young earth creationism who publish a steady stream of articles that allegedly disprove evolution. (See  A Creationist Speaker Comes to Town for my experience with a young earth creationist coming to give a workshop in my area ).

In order to become open to really hearing the evidence in favor of genuine science, these people need to realize that evolution is not a threat to their core values. The sneering and jeering of atheist biologists like Richard Dawkins, Jerry Coyne, and P.Z. Myers towards people of faith is counterproductive in this regard. Rather, it should be made known that many devout Christians, from Billy Graham to the Pope , find that “evolutionary creation” is fully compatible with their faith. Christian geneticist Francis Collins, director of the National Institutes of Health, former head of the Human Genome Project and author of The Language of God, established the Biologos Foundation which works to share this message. This entails applying a non-literal interpretation to some creation passages in the Bible, just as the church eventually let go of a literal interpretation of the verses which speak of a stationary earth.

The core problem is that young earth creationists misrepresent what the Bible is really about. In II Timothy 3:15-17 Paul states the purpose and function of the Scriptures: they make us “wise for salvation through faith which is in Christ Jesus”, and are “profitable for doctrine, for reproof, for correction, for instruction in righteousness”, so that we are “equipped for every good work.” This is all theology and morals. There is nothing here about authoritatively teaching geology or biology.

Likewise, Jesus said that the function of the Old Testament was to testify about him and his saving work (John 5:40; Luke 24:44), and Peter (I Pet 1: 10-12) wrote that prophets spoke of the sufferings and glory of Christ. This is “special revelation” of divine purposes which could not be inferred from the “general revelation” of nature. This is a biblical view of the Bible’s intent, which differs from some evangelical statements about inerrancy which mistakenly over-extend the Bible’s sphere of authority into general science or history.

If there really were clear evidence (e.g. rock layers from a recent worldwide Flood) of miraculous intervention on a geologic scale, or clear evidence of the un-natural origin of the human species, that would constitute a widely-accessible supernatural “sign” for unbelievers. However, Jesus flatly declared that no such sign would be given. Young earth creationism is thus founded on premises which run counter to what Christ himself taught (see Jesus on Seeing God in Nature: No Signs, No Justice, No Fear ). For a more general treatment of Bible passages dealing with creation issues, see Evolution and Faith: My Story, Part 2.

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

ENDNOTES

[1] The story of this flask gets even more interesting after the evolution of the robust Cit+ strain. That strain mushroomed in numbers each generation as it fed on the abundant citrate in the growth medium. In the process of metabolizing the citrate, this strain released the dicarboxylic acids succinate, fumarate, and malate into the medium. A strain of Cit- cells then evolved to make use of those dicarboxylic acids produced by the Cit+ bacteria. These two strains co-existed in the overall flask population. “Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades.” – – from “Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli”, by Caroline B. Turner, Zachary D. Blount, Daniel H. Mitchell, Richard E. Lenski , http://www.biorxiv.org/content/early/2015/06/17/020958 .   (The timeline in the Wikipedia article indicates that this Cit- strain later disappeared from this Ara-3 population).

[2] For details on this second mutation see:    Quandt, et al, Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli, PNAS February 11, 2014, vol. 111 no. 6, 2217-2222     http://www.pnas.org/content/111/6/2217.abstract

[3] Justin R. Meyer, Devin T. Dobias, Joshua S. Weitz, Jeffrey E. Barrick, Ryan T. Quick, Richard E. Lenski, Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda. Science 27 Jan 2012: Vol. 335, Issue 6067, pp. 428-432. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306806/

[4] Behe M.J., Quarterly Review of Biology 85(4), 2010, 419-415.

[5] Paul Braterman https://pandasthumb.org/archives/2010/12/behes-review-in.html pointed out the rhetorical maneuvers employed by Behe in his 2010 review:

Behe constructs an elaborate apparatus for classifying mutations as “gain”, “modification”, or “loss” of what he calls a Functional Coded Element (FCT). The definition is skewed to make “gain” as difficult to prove as possible. The process needs to be understood at the molecular level, rather than simply in terms of phenotype expression. This enables him to dismiss as of unproven relevance the Lenski group’s famous demonstration of E.Coli acquiring the ability to metabolise citrate under anaerobic conditions. Moreover, advantageous removal of inhibition is treated as “loss”, but advantageous disruption of a function by IS duplication and insertion is classified as “modification”, rather than “gain”. Using these restrictive and asymmetric criteria, Behe classifies most sufficiently well-understood mutations in laboratory-bred bacteria as loss or modification, although he does recognise a few gains…..

But there are numerous well-known counterexamples, many of them discussed in this review.

The next stage is rhetorical dismissal of such counterexamples. Here the strategies include limiting the search (ignoring the massive creative role of gene duplication and polyploidy in eukaryotes, and of horizontal transfer followed by selection in bacteria themselves), narrowing the criteria (new functions don’t count unless they can be demonstrated to arise from additions, rather than any other kinds of alterations, to the molecular machinery), and inventing additional constraints (creation of a new category, the FCT, classifying the process as a loss if either material or function is lost at any stage in the change being discussed, dismissing changes in function as mere transformations, rather than novelties). This stage switches the emphasis from what is possible in principle, to the demand that each case be demonstrated in practice, and fully analysed in detail, at the molecular level.

Finally, any counterexamples still surviving this moving of the goalposts and restricting and tilting of the playing field are dismissed as untypical, and therefore unimportant.

[6]   Jerry Coyne [ https://whyevolutionistrue.wordpress.com/2010/12/12/behes-new-paper/ ] noted that Behe limited his survey to precisely the sorts of experiments which are heavily biased towards NOT observing a dramatic increase in functional complexity:

Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these—Rich Lenski’s study— extends over several decades). But his conclusions may be misleading when you extend them to bacterial or viral evolution in nature, and are certainly misleading if you extend them to eukaryotes (organisms with complex cells), for several reasons:

  1. In virtually none of the experiments summarized by Behe was there the possibility of adapting the way that many bacteria and viruses actually adapt in nature: by the uptake of DNA from other microbes. Lenski’s studies of E. coli, for instance, and Bull’s work on phage evolution, deliberately preclude the presence of other species that could serve as vectors of DNA, and thus of new FCTs (Functional Coded elemenTs).   This is not an idle objection, since we know that adaptation in natural populations of microbes often arises by incorporating new FCTs from other species. Pathogenicity and antibiotic resistance in bacteria, for example, arise in this way…
  2. In relatively short-term lab experiments there has simply not been enough time to observe the accumulation of complex FCTs, which take time to build or acquire from a rare horizontal transmission event. Finding adaptation via point mutations or loss of function is much more likely…
  3. Finally, Behe does not mention—and I think he should have—the extensive and very strong evidence for adaptation via gain-of-FCT mutations in eukaryotes. While that group may occasionally acquire genes or genetic elements by horizontal transfer, we know that they acquire new genes by the mechanism of gene duplication and divergence: new genes arise by duplication of old ones, and then the functions of these once-identical genes diverge as they acquire new mutations.   Or, new genes can arise by unequal crossing-over between different genes, so that new genes arise by mixing bits of old ones.

[Emphases added]

[7] Some readers may wonder why the “nylon-eating bacteria” was not included in these list of complex mutations which give rise to new functions. It was found in 1975 that this bacterium in a pond in Japan had developed the novel ability to digest the waste products from nylon manufacture. In 1984 Susumu Ohno proposed that a key gene for this ability had arisen as a result of a “frameshift” mutation. Most types of mutations keep most of the protein products of a gene intact, while making a change in some portion of it. Thus, the expressed protein after the mutation is largely similar to the protein before the mutation. A frameshift mutation, on the other hand, can alter a gene such that an entirely new sequence of amino acids is produced, with little similarity to the original protein. https://en.wikipedia.org/wiki/Frameshift_mutation

For some years, this “nylon bug” was cited as an example of how a more or less random recoding of an entire gene product could produce a completely new and beneficial enzyme. However, papers published by Seiji Negoro since 2006 indicate that in fact no frameshift mutation was involved in the evolution of the 6-aminohexanoic acid hydrolase. Rather, it seems that the new enzyme came about by changes to two amino acids from a pre-existing gene. This is still a nice example of a new function arising from multiple mutations, but it is not as dramatic as a total remake stemming from a frameshift. See   https://en.wikipedia.org/wiki/Nylon-eating_bacteria  .

[8] Some direct rebuttals of the notion that the order of fossils in the rocks can be explained by a global Flood are given here:  https://rationalwiki.org/wiki/Fossil_sorting_by_the_global_flood

and here:  http://debunkingcreationism.blogspot.com/2012/11/real-geology-vs-flood-geology-via.html

Index fossils provide further evidence that life-forms have evolved over millions of years. Fossils which have a wide (sometimes global) geographic distribution but a relatively short time of appearance in the rocks are called “index fossils”, since they are useful in determining the relative ages of the rocks in which they occur:

These index fossils were all sea creatures, so it is not that the Pecten gibbus scallops all got buried in higher rock layers because they ran faster to higher ground as the Flood-waters rose whilst all the sluggish Paradoxides trilobites were left behind. At all levels there are fossils of animals that are big and small, skinny and fat, so this sequence is not a result of hydrodynamic sorting during one big Flood. Rather, the order of their world-wide appearance in the rock layers reflects their temporal appearance, then disappearance, across the times of deposition in the sedimentary rocks in which they are found.  There are sound reasons to believe that that these deposition times extended over millions of years.   The reality of this world-wide “faunal succession” in the sedimentary rock layers was recognized by geologists well before Darwin proposed a mechanism for how new species could arise.

[9] Contrary to the claims of anti-evolutionists, this “Cambrian explosion” of new life-forms is readily explicable within conventional evolutionary science. See Cambrian Contention: Disputing “Darwin’s Doubt”

[10]  Donald Prothero, What Missing Link? NewScientist, 1 March 2008, 35-41 http://www.donaldprothero.com/files/92313517.pdf

[11] Michael Behe argued for such a limit to evolution in The Edge of Evolution, but his arguments fail, as shown by the examples here. This is further discussed in STAN 4: Assessing Limits to Evolution and to Natural Selection:   Reviews of Michael Behe’s “Edge of Evolution” and John Sanford’s “Genetic Entropy”

[12] Michael Behe claimed that some biological systems are “irreducibly complex”, such that all the parts must be in place for the system to work – and hence these systems cannot be built up from step by step mutations. However, some of the examples described here directly disprove this thesis, and it has been addressed multiple times by the scientific community. https://en.wikipedia.org/wiki/Irreducible_complexity

[13] Motoo Kimura, The Neutral Theory of Molecular Evolution, (Cambridge: Cambridge University, 1983 Press) p. 63. Equus itself is excluded from the count of genera because its span is incomplete.

[14] Manyuan Long, Esther Betrán, Kevin Thornton & Wen Wang, “The origin of new genes: glimpses from the young and old,” Nature Reviews Genetics 4, 865-875 (November 2003)  http://faculty.washington.edu/wjs18/Newgenes.pdf

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Historicity of Jesus: Class Notes

Some time ago I was asked to teach a short, informal class on “The Historicity of Jesus”. Was Jesus a real person who did and taught the things we read about in the New Testament, or did wishful believers just make all that stuff up many years after the deaths of the people who actually knew him?

I made up a handout to serve as notes for that class.  Four classes of documents are examined: Paul’s letters, the Gospels, the writings of other early Christians, and the works of non-Christian historians. I have edited that handout, and added some lengthy footnotes (endnotes) and an Appendix to deal with ancillary topics. It ended up being too long to work well as a regular blog post, so I posted it along with longer essays up at the top of this blog page. It is visible there, or you can just click to it from here: ” Historicity of Jesus

The contents are:

( 1 ) The World of Jesus and His Followers

( 2 ) Authenticity of the New Testament Text

( 2.1 ) Many ancient physical copies of New Testament have been found

(2.2) Quotes from New Testament books appear in other early Christian writings

( 3 ) Paul’s Writings: The Earliest Documents About Jesus

( 3.1) Galatians 1-2 : Paul visits other apostles just a few years after the Resurrection

( 3.2) I Corinthians 15 : Paul receives teaching about Jesus’ death and resurrection from other apostles

(3.3) Paul’s Portrait of Jesus

(3.4) The Significance of Paul’s testimony

( 4 ) The Testimony of the Gospels

( 5 ) Luke the Meticulous Historian

( 6 ) John the Accurate Geographer  

( 7 ) Differences Among the Gospels

( 8 ) Significance of Textual Variants

( 9 ) Settling of the New Testament Canon

( 10 ) Mention of Jesus Christ in Extrabiblical Literature

Josephus, Pliny, and Tacitus

Endnotes

APPENDIX: Historical Accuracy in the Gospel of Luke

 

 

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Total Solar Eclipse Visible Across the U.S. on August 21

The Moon’s orbit around the Earth is inclined by about 5 degrees from the plane of the Earth’s orbit around the Sun, so only occasionally does the Moon come between the Earth and the Sun so as to cause a solar eclipse. The diameter of the Moon as viewed from the Earth is about the same as the apparent diameter of the Sun, so the Moon can just barely cover the whole disk of the Sun. Because the Moon’s orbit around the Earth is elliptical, most of the time when there is a solar eclipse, is only partial. It is only when the Moon is closest to the Earth that the Moon can completely block out the Sun and cause complete darkness for a few minutes of totality

As the diagram below indicates, the zone of total eclipse, where the Sun is completely blocked, is very small. Only about one in a thousand people ever witness a total eclipse.

You could become one of those fortunate total eclipse viewers, if you can get to a narrow swathe across the U.S. on August 21, 2017. Around noon that day, the path of totality will run from coast to coast. A map is shown below. The next total eclipses after this will be 2019 and 2020 in Chile and Argentina, 2021 in Antarctica, 2024 in Mexico/central U.S./ eastern Canada, 2026 through Iceland and Spain, and 2027 across North Africa. The next solar eclipse with totality passing over much of Europe occurs in 2081.

 

All of the contiguous 48 states, as well as parts of Canada and Mexico will be exposed to a partial eclipse on August 21. Faint orange lines on the map show the limits of 90%, 75%, and 50% solar occlusion. The path of totality is only about 70 miles (117 km) wide. Below is a zoomed-in section of this map.

This site has links to this interactive map by NASA and another map from Google, and also tables of eclipse times for cities in some states. New York City, Philadelphia, Houston and San Francisco, Los Angeles, and Toronto will max out at about 70%-75% occlusion of the sun. That will be interesting to observe through eclipse glasses if the sky is not cloudy, but may otherwise be fairly unimpressive.

Totality is supposed to be a whole different experience. “Daylight is replaced by a mysterious dusk, and bright planets and stars become visible. Plants and animals act as though it were nightfall as flowers close up and birds return to roost. There’s a chill in the air because the temperature drops a dozen degrees or more. The brilliant Sun is replaced by a black orb surrounded by a ghostly halo. The colors of sunset ring the horizon…”. [1] “…When the shrinking visible part of the photosphere becomes very small, Baily’s beads will occur. These are caused by the sunlight still being able to reach the Earth through lunar valleys. Totality then begins with the diamond ring effect, the last bright flash of sunlight”. [2]

Here is a 1999 photo of the Sun being almost entirely blocked by the Moon. Solar prominences (in red) can be seen along the edge, as well as the extensive fainter filaments of the corona.

For this 2017 eclipse, totality will last about 2.5 minutes, but only near the center of the path of totality. Thus, it may be worth a little extra travel to move toward the central 40 mile wide strip. One should anticipate that many other people will be crowding into the same patch, especially if it is near a major highway, and therefore plan for traffic jams coming and going. It would also make sense to check the weather forecast a day or two before, and aim for locales expected to be less cloudy.

The safe and convenient way to look at the sun during the eclipse is with specially designed glasses.

 

These can be purchased for about a dollar apiece in some stores and on-line at Amazon or speciality sites   . Experts warn against looking at the sun through home-made filters.

A good science project for classroom or family is to make some sort of pinhole projector, which will project an image of the Sun’s disk and which will show it being occluded. This can be as simple as a piece of cardboard with pinhole held high above a sheet of white paper on the ground, or a more elaborate box affair. Here is how to make a largish box projector into which you put your head:

 

This  links to a short video showing how to build a small pinhole projector into a shoebox. I helped my daughter’s elementary school class make these many years ago for a partial solar eclipse. They turned out well, although the size of the projected image with this short box is pretty small. It is also possible to project a larger, clearer image of the sun using binoculars and a tripod.

 

[1] “Get Eclipsed” pamphlet, by Pat and Fred Espenak

[2] https://en.wikipedia.org/wiki/Solar_eclipse#Viewing

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Listing of Articles on Science, Faith and Other

Here is a listing of some of the more popular articles on this blog, grouped by topic:

Geology/Fossils

Grand Canyon Geology

Realistic Expectations for Transitional Fossils

“Unconformities” Showed Geologists By 1800 That The Earth Was Very Old

Soft Tissue in Dinosaur Fossils: Evidence for a Young Earth?

 The Cambrian Explosion (Reviews of “Darwin’s Doubt”)

 Assessment of Evidences for a Young Earth

        Some Simple Evidences for an Old Earth

.       “Big Daddy” Chick Tract: The Most Widely-Distributed Anti-Evolution Publication     (Shows intermediate fossils between apes and modern humans)

 Genetics

Endogenous Retroviruses in Your Genome Show Common Ancestry with Primates

Gorilla, Orangutan, Chimp and Human Genomes: Population Genetics and Intelligent Design

 Junk DNA, the ENCODE Project, and Intelligent Design: Facts, Hype, and Spin

       From Micro-Evolution to Macro-Evolution: Beneficial Mutations, the Pace of Evolution, and Increasing Genome Complexity   (“STAN 3”)

Assessing Limits to Evolution and to Natural Selection:   Reviews of Michael Behe’s “Edge of Evolution” and John Sanford’s “Genetic Entropy” (“STAN 4”)

        Link to “Science Meets Religion” site by David H. Bailey; tackles many evolution/ID issues, including genetics/information issues like irreducible complexity and generating novel genetic features

.      Evolution Before Our Eyes: Complex Mutations in Microbes Giving New Functions

Theology/Bible Interpretation

Adam, the Fall, and Evolution

A Survey of Biblical Natural Theology

Jesus on Seeing God in Nature: No Signs, No Justice, No Fear

Early Church Fathers: Excerpts From Christian Writings, 100-200 A.D. (including observations on the natural world)

Was the “Expanse” Overhead in Genesis 1 a Solid Dome?

Evolution and Faith: My Story, Part 2   (summarizes ways to interpret Genesis in the light of evolution)

 An Answer to the Intellectual Problem of Evil

        “The World’s Last Night”: C. S. Lewis on the Second Coming

.      Billy Graham on Evolution

.      The Historicity of Jesus

History and Cultural Context of Creationism

Exposing the Roots of Young Earth Creationism (traces the origin of Young Earth “Flood geology” to nineteenth-century Adventist cult prophetess Ellen White)

University of Washington Biology Professor Brags About Bullying Religious Students

Whatever Happened to Intelligent Design Theorist William Dembski?

A Creationist Speaker Comes to Town (I attend and assess a talk by Jonathan Sarfati)

       The Great Debate of 2014: Creationist Ken Ham versus Bill Nye the Science Guy

.      Was Darwin An Atheist?

Remarkable Healings

Engineer’s Wife Healed of Multiple Sclerosis

Healing of Nearly-Deaf Boy on YouTube

Healing Miracles in Mozambique: Medical Journal

  

Applied Technology/Economics

Folding and Electric Scooters and Bikes for Commuting the Last Mile

Comparison of Composting Toilets: Towards a Global Commode

       Fun Things to Ride: Stepper Bikes, Carving Scooters, Electric Unicycles, etc.

Fun Things to Fly: Powered Parachutes, Trikes, and Gyroplanes

Simple, Featherweight Alcohol Stoves for Camping

Overview of the U. S. Monetary System (What is money and how it is created; interactions of the Treasury, the Federal Reserve, and commercial banks; government and trade deficits)

High-Yield Investments

 

Work of the American Scientific Affiliation or Its Members

Some Highlights of American Scientific Affiliation 2015 Meeting

Brain, Mind, Faith: 2016 American Scientific Affiliation Meeting

A New Resource for Creationism: “The Grand Canyon, Monument to an Ancient Earth”

      How Science Can Inspire and Inform Worship: NASA’s Jennifer Wiseman

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N.T. Wright: If Creation Is Through Christ, We Should Expect Something Like Evolution

N.T. Wright is a leading biblical scholar, former Bishop of Durham in the Church of England, and current Research Professor of New Testament and Early Christianity at the University of St. Andrews. He holds a Doctor of Divinity from Oxford University and has written over fifty books. He was a keynote speaker at the Biologos Christ and Creation conference last month in Houston, TX .

Here is a link to a Biologos post which includes a 4-minute clip of his “Christ and Creation: Exploring the Paradox” talk, and a link to the full speech. A theme of this talk is that if creation is through Christ, we should (based on what the Gospels teach of the progress of the kingdom of God) expect something like evolution:

If creation comes through the kingdom bringing Jesus, we ought to expect it be like a seed growing secretly. That it would involve seed being sown in a prodigal fashion in which a lot went to waste, apparently, but other seed producing a great crop. We ought to expect that it be like a strange, slow process which might suddenly reach some kind of harvest. We ought to expect that it would involve some kind of overcoming of chaos.

…We ought to have anticipated that the Deists’ models of creation, conceived on the analogies of the early industrial successes, in the 17th and 18th centuries, might in fact be misleading. And that they would need correcting in the light of either of a better picture of the one through whom creation was accomplished—the Deists were keen to getting Jesus out of the picture—or in the light of fresh scientific research. No one in the late 18th or early 19th centuries was doing the kind of fresh work on Jesus and the gospels that would lead to this picture. But various scientists (not least the Darwin family a century before Charles Darwin), motivated by quite a different worldview—namely, Epicureanism—nonetheless come up with a picture of Origins that looks remarkably like Jesus’ parables of the Kingdom: some seeds go to waste, others bear remarkable fruit; some projects start tiny and take forever, but ultimately produce a great crop; some false starts are wonderfully rescued, others are forgotten. Chaos is astonishingly overcome.

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Though the Market Is a Winner, Most Stocks Are Losers

The U.S. “stock market” is represented by various collections of stocks, such as the Dow Jones Industrial Average (30 stocks), the NASDAQ Composite (securities listed on the NASDAQ; weighted towards information technology), and the Standard and Poors 500 Index. The S&P 500 is an index of the largest 500 companies listed on the New York Stock Exchange and the NASDAQ, weighted by capitalization. The version of the S&P usually cited just takes into account stock prices. History shows that, over a reasonably long time frame, the U.S. stock market rises. Here is a chart, using a logarithmic axis, of the S&P from January, 1950 to February, 2016. It shows a rise in value by a factor of about 65 between 1950 and 2016.

S&P 500 daily closing values from January 3, 1950 to February 19, 2016
Source: https://en.wikipedia.org/wiki/S%26P_500_Index

Another way to view market returns is to include the effects of dividends and of inflation. The long-term returns are still positive:

 

A lab technician I knew in my company in the 1990s took every bit of savings he had (about $50,000) and plowed it all into the stock of America Online (AOL). This was when the internet was just taking off, and AOL was a leading company in that field. My friend held on while his investment doubled, then had the conviction to hang on until it doubled again. He then cashed out with around $200,000, quit his job, got an MBA in finance, and ended up managing money on Wall Street.

With these sorts of success stories, and the (so far) reliable performance of the stock market, how hard can it be for the average small investor to pick a winning basket of stocks? Surprisingly hard, it turns out.

A study of the returns of U.S. stocks from 1926 to 2015 has been published by Hendrik Bessembinder, a business professor at Arizona State University. A draft copy is here . He works with total returns (stock price plus dividends).

He found that the rise of the S&P is entirely due to huge gains by a tiny subset of stocks. The average stock actually loses money over both short and long time periods. In statistical terms, this is an extremely skewed data set; the mean return is greater than the median. There is a sort of Darwinian selection that occurs in a market index like the S&P 500. The companies that are doing well tend to get more represented in the index as their stock prices rises relative to other companies, while the relative weighting of losers automatically diminishes.

This asymmetry between winners and losers is partly a result of the following math: If you invest $1000 in a company that then tanks, the most you can lose is $1000. But if that company is one of the rare firms that really takes off, you could make many times your initial investment. If you had put $1000 into Microsoft (MSFT) in 1986, your shares would now be worth nearly $700,000.

Half of the U.S. stock market wealth creation has come from a mere 0.33% of the listed companies. The top five companies (ExxonMobil, Apple, GE, Microsoft, and IBM) accounted for a full 10% of the market gain. Each of these companies has created half a trillion dollars or more for their shareholders.

Out of some 26,000 listed companies, 86 of them (0.33%) provided 50% of the aggregate wealth creation, and the top 983 companies (4%) accounted for the full 100%. That means the other 25,000 companies netted out to zero return. Some gave positive returns, while most were net losers.

The average stock which you might pick by throwing darts at the Wall Street Journal listings lost money 52% of the time in any given month, and 51% of the time over the life of the company. The lifetime of the average company was only seven years, with only 10% of companies lasting more than 27 years.

This helps explain why actively managed stock funds, where diligent experts analyze and select some subset of stocks in an attempt to beat the market, typically underperform the broad market indices. This also explains why about half the small-cap stocks I have bought over the years in my little recreational brokerage account have lost money. I had thought I was particularly inept at stock-picking. Turns out I was just about average.

The takeaway for small investors is that they will likely do better putting most of their money in a broad index fund like the low-fee Vanguard S&P500 ETF (VOO), than into individual stocks or specialized funds. That has become my baseline approach.

Two side comments here. First, there are some securities whose return does not depend so much on their price going up, but rather on their paying out a steady high yield of dividends. I find this attractive, since I suspect that the returns on stocks as a whole will be lower in the future than they have been in the past. With a slowdown in population and productivity growth rates, the growth rate of GDP (at least in developed countries like the U.S.) will be slower than in the past century. Corporate earnings generally don’t rise much faster than GDP for an extended period. A big part of the rise in stock prices since 1980 has been the steady decline in interest rates, which rationally drives an increase in the price/earnings ratio. However, it looks like this secular decline in interest rates has run its course; it’s tough to go much below zero percent interest.

For instance, “business development companies” (BDCs) typically make short term, high-interest loans to small, growing companies that regular banks would not lend to. One of the largest, most-stable BDCs is Aries Capital (ARCC) which currently yields 8.6%. I have described several other classes of high yield investments in Adventures in High-Yield Investing, such as real estate investment trusts (REITs) and closed end funds (e.g. ETV, yielding 8.8%) which sell options on stocks or which take advantage of the spread between short term and long term interest rates. FOF is a fund which holds a basket of these closed end funds and which currently yields 8.3% .

The prices of these securities can bounce around a lot, so it can be worth waiting to buy till they come down from their 52-week high, but on the whole I have found them to be worthwhile as a diversification from the main stock market. They might also be attractive as an alternative to, say, European or Japanese stock markets whose price gains do not seem to match those in U.S. stocks.

Second, if you are interested in broader topics like what is money and how it is created in our financial system, the relation between government deficits and trade deficits, how investment creates savings (not the other way around), etc., etc. – – – this article deals with all that stuff: Monetary System .

 

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Whatever Happened to Intelligent Design Theorist William Dembski?

Summary: Young earth creationists have knocked out of action one of the most effective advocates for Intelligent Design. This is symptomatic of the rift between these two anti-evolution movements which are both mainly composed of Bible-believing Christians.

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

Among Christians who take the Bible seriously as revelation, there are three main schools of thought regarding human evolution and the age of the earth. Evolutionary creationists, also known as theistic evolutionists, acknowledge the physical evidence for common ancestry between humans and other primates (e.g. Endogenous Retroviruses in Your Genome Show Common Ancestry with Primates ). They understand that the Bible, including the Genesis creation narrative, was given to teach spiritual truths (II Timothy 3:15-17), not physical history.

There is abundant and clear evidence that the earth is far older than the 6000 years dictated by a literal reading of Biblical genealogies. For instance, we can drill down into glaciers in central Greenland and Antarctica, and observe over 100,000 years of alternating summer/winter ice layers, with no trace of a global Flood. “Old earth” creationists accept the reality of this evidence, but typically reject the notion that humans evolved from other primates.

Young earth (YE) creationists reject both evolution and the notion of an old earth. They propose an alternate reality, in which the earth and the universe are only 6000 years old, and most sedimentary rock layers were laid down in a year-long global Flood. This Flood geology was developed in the early twentieth century by George McCready Price in obedience to the visions of Adventist prophetess Ellen White. John Whitcomb and Henry Morris appropriated Price’s geology while covering up its cultic origin , and published it in 1961 in The Genesis Flood. Weighing in with some 500 pages of dense, footnoted text and figures, The Genesis Flood seemed to offer scientific support for a literal six-day creation.  This evidence was all bogus, but that did not matter. The book became wildly popular among fundamentalists, going through 29 printings. For the century prior to 1961, almost no Christians, fundamentalist or not, held that a young earth and a six 24-hour day creation was justified either biblically or scientifically. By 1970, however, The Genesis Flood had established YE creationism as the standard position among conservative evangelicals in America, with growing numbers of adherents in Australia and the U.K.

The 1991 publication of Phillip Johnson’s Darwin on Trial sparked the Intelligent Design (ID) movement. ID advocates generally fall in the old earth camp. While recognizing the great antiquity of the universe, they attempt to find gaps in our current understanding of the history and mechanisms of evolution. They then use these gaps to claim that the intervention of an Intelligent Agent is necessary to explain today’s biota.

YE creationists are typically quite forthright in stating the religious foundation of their worldview. Their starting point is their particular interpretation of the Bible, and they fit all the physical evidence around that. The earth must be young and thus any evidence that it is old must be flawed. That accounts for their resolute denial of the facts (such as the annual layers in glacier ice) that are conclusive for everyone else.

ID advocates, on the other hand, are more coy about their motivations. They typically purport to be objective scientists who happen to discover evidence for design in the biological world, and who simply wish to broaden the education of schoolchildren by exposing them to “the controversy” over the adequacy of evolutionary theory.

The epicenter of the ID movement is the Discovery Institute in Seattle. A number of pedigreed PhD’s are on staff there, producing books and articles which are intended to withstand the scrutiny of the greater academic world. They are careful to not specify the identity of the Intelligent Designer who must have intervened somehow to produce new batches of plants and animals through the eons of geologic time.

However, outsiders are not fooled. Only God (or some super-intelligent, powerful and long-lived alien civilization) would be capable of making the sorts of repeated genetic interventions over millions of years needed to bridge the alleged gaps in natural evolution. Most of the founders and principals of the Discovery Institute are conservative Christians, and the leaked 1998 manifesto of the Institute, the “Wedge Document”  clearly articulated a religious goal: to “reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.”

Relations were initially warm between YE creationists and ID theorists. The large, established YE creationist base helped provide venues for ID speakers, and the academic credentials of the ID scholars lent credibility to the anti-evolution plank of the YE platform. The ID folks minimized mention of their views on the earth’s age, and the YE crowd did not press them on it. In recent years, however, YE creationists have taken to vehemently denouncing old earth creationists as “compromisers”.

Some ID advocates write mainly about observable aspects of the physical world, such as fossils and mutations in DNA. It is straightforward to do basic fact-checking and to show that the conclusions asserted by those ID proponents are insupportable (see e.g. here  on Stephen Meyers’ treatment of the Cambrian explosion, and here  on Jonathan Wells’ “Icons of Evolution”).

The writings of William Dembski, on the other hand, deal with more intangible concepts like information theory. Dembski became a key figure in the ID movement in the 1990’s and beyond. His breakout book was The Design Inference: Eliminating Chance through Small Probabilities (1998), which became something of a best-seller. In this and his other works, Dembski claimed to have demonstrated that the sort of increases in genetic information content required by unguided evolution were mathematically impossible. There is “no free lunch”; only the intervention of an Intelligent Agent can explain the observed “specified complexity” in the biological world.

Critics have published numerous articles denouncing Dembski’s work. They claimed to find inconsistencies and outright errors in his writings. However, due to the nature of the subject, both Dembski’s writings and those of his opponents are somewhat hard for nonspecialists to follow. Thus, his writings were often considered by anti-evolutionists to be unrefuted, and to be the final nail in the coffin of Darwinism.

Opponents of evolution were, of course, delighted to have such a smart and articulate guy confidently proclaiming the demise of Darwinism. For many years he was a golden boy of ID. Books and articles flowed from Dembski’s keyboard, and he was invited to speak in many venues. His face adorned the cover of WORLD magazine. He was a long-time fellow at the Discovery Institute. However, he is no longer is very active in the field. What happened?

He and some ID colleagues set up an ID think tank at Baylor University in 1999. That was soon quashed after an outcry by the other faculty members. In 2006, Dembski took up a faculty position at Southwestern Baptist Theological Seminary (SWBTS) in Fort Worth, Texas, and continued highly visible activities promoting Intelligent Design. Dembski was clear with the seminary that he was an old-earth, not a young-earth creationist.

In 2009 he published The End of Christianity. In that book he attempted to reconcile the evidence from the fossil record that animal suffering and death occurred for millions of years before humans appeared, with the traditional theological notion that this suffering and death is collateral damage from man’s Fall. Western Christianity, following Augustine, has often held that the original peaceable, vegan animal world was plunged into carnivory as a outworking of man’s Fall and the subsequent curse on humans and their world. Dembski accepted this basic premise, and speculated that the effects of man’s sin may have (since God dwells outside of the linear time to which we are constrained) propagated backwards as well as forward in time. Thus, the carnage in the animal world during the eons before humans appeared was indirectly a result of the actions of those later humans. Towards the end of the book, as a sort of afterthought, Dembski mentioned the possibility that Noah’s Flood was actually a local flood in the Middle East, rather than a global deluge.

That, alas, proved to be his undoing. Hard-core YE creationists such as Ken Ham were incensed that Dembski would question the reality of a global Flood. They denounced him coast to coast and orchestrated letter-writing campaigns to his employer, demanding his ouster. Dembski was hauled before an inquisition at Southwestern Baptist Theological Seminary. It was made clear that if he did not satisfy them on the global extent of Noah’s Flood, he would be immediately fired as a heretic.

This put Dembski in an agonizing personal dilemma. If he had been financially solvent, he would have simply resigned right away. However, he had a severely autistic son plus two other children to support, and had no other way to pay the medical bills. He therefore “finessed” it, issuing a statement with sufficient ambiguity to keep him his job, while allowing him to later clarify his actual convictions. He did seek, and find, alternative employment as quickly as possible, first at another seminary, and then (2013-2014) back at the Discovery Institute as a full-time research fellow. Here is how Dembski described this experience at Southwestern :

At the meeting with president, provost, dean, and senior professor, the president made it clear to me from the start that my job was on the line. “Job on the line” in this context does not mean finishing out the academic year and giving me a chance to find another academic job. My questioning the universality of Noah’s flood meant I was a heretic, or at least not suitable for teaching at Southern Baptist seminaries, and thus I’d need to be clearing my desk immediately—unless my theological soundness could be quickly reestablished.

With a severely autistic son, debts, and a family still upset about my experience at Baylor, I wasn’t about to bare my soul and tell this second star chamber (my first being Baylor’s External Review Committee) what I really thought. I therefore finessed it. You can read the statement I wrote for yourself, especially paragraph three, where I said just enough to keep my job, and just enough to give me room to recant, as I’m doing here.

If I had been feeling less vulnerable, if I had independent financial means, I would have said goodbye to Southwestern Baptist Theological Seminary right then and there. This is one of the things I find most destructive about fundamentalism, the constant threat that at any moment one can run afoul of the orthodoxy du jour, and be thrown under the bus because that’s the proper place for heretics.

This is a deeply unhealthy situation for theological education, leading to a slavish mentality among faculty, who must constantly monitor and censor themselves if they are to stay in the good graces of the fundamentalist power structures.

He remarks further:

Christian orthodoxy is one thing. A “canst thou be more conservative than I?” mentality is another. And this is what I saw emerging.

What’s behind this is a sense of beleaguerment by the wider culture and a desire for simple, neat, pat solutions. Life is messy and the Bible is not a book of systematic theology, but to the fundamentalist mentality, this is unacceptable. …Fundamentalism, as I’m using it, is not concerned with any doctrinal position, however conservative or traditional. What’s at stake is a harsh, wooden-headed attitude that not only involves knowing one is right, but refuses to listen to, learn from, or understand other Christians, to say nothing of outsiders to the faith. Fundamentalism in this sense is a brain-dead, soul-stifling attitude. I see it as a huge danger for evangelicals.

Dembski notes elsewhere that the young earth creationists

…were friendly to ID in the early 2000s, until they realized that ID was not going to serve as a stalking horse for their literalistic interpretation of Genesis. After that, the young-earth community largely turned away from ID, if not overtly, then by essentially downplaying ID in favor of anything that supported a young earth.

The Noah’s Ark theme park in Kentucky is a case in point. What an embarrassment and waste of money. I’ve recently addressed the fundamentalism that I hold responsible for this sorry state of affairs.

For Dembski, “…this entire incident left so bad a taste in my mouth that I resolved to leave teaching, leave the academy, and get into a business for myself, in which my income would not depend on political correctness or, for that matter, theological correctness.”

Thus, in 2014 he retired from active research and teaching in intelligent design, to focus on issues of education, human freedom, and technology. Dembski still believes that ID is correct, and will someday triumph over standard evolution. But his interests have largely “moved on”. In 2016 he resigned his formal associations with the ID community, including his Discovery Institute fellowship of 20 years. He currently supports his family by building educational software and websites.

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