DARWIN'S GIFT TO SCIENCE AND RELIGION

THE BOOK BY FRANCISCO J. AYALA

DARWIN'S GIFT to Science and Religion was published in 2007 by John Henry Press in Washington, D.C.  The 237 pages are easy reading.  The shock to me was its content did a remarkable job of covering some of the main points I made in my unpublished Evolution Insights a few years later.

The Scientific Method

I particularly liked his comment on page 186 about the scientific method, saying.

 "The most interesting and fruitful scientific hypotheses are not simple generalizations.  Instead scientific hypotheses are creations of the mind, imaginative suggestions as to what might be true."

His accompanying discussion is well worth reading if you want to be a scientist.

The Molecular Clock

He does a good job of discussing the conventional view without indicating his expertise and publications which place him among the national leaders.  On page 135 at the end of the four pages on the topic, he says.

"As the length of time increases, periods of rapid and slow evolution in any lineage are likely to cancel one another out."

The faulty opinion of canceling out was included over half a century ago in the first major publication of the science of molecular clocks by Zuckerkandl and Pauling (1965).  The opinion has plagued attempts to use molecular clocks in determining the higher level evolutionary relationships of organisms ever since.  My post on May 31, 2013 was part of my attempt to alert professional biologists to the problem.  Other posts on the deep sea and pogonophorans are important aides to understanding a solution to the problem.

About Ayala

His experience in biology and early exposure to more philosophical subjects  make him well suited to write the book he did.  His youthful picture on the dust-jacket of his book must have been taken in mid-life between his birth in 1934 and his book's 2007 publication.  He is a credit to both science and religion.  I am about six years older than he is and have far less to show for it professionally.

On page 3 in his introduction he says-

"Evolution, I learned in my theology classes, had provided theologians with the "missing link" in the explanation of evil in the world . . . . .".  Maybe you will find his explanation more intelligible on the topic than my post of March 22, 2016.

I was unaware of his book before today (April 25, 2016) but the above was the outcome from a two-hour visit to the library, with perhaps less than an hour spent on the book.  His book is of special interest if you are interested in the unnecessary conflict between science and religion. 

Joseph G. Engemann    Kalamazoo, Michigan    April 25, 2016

EVOLUTION: MOLECULAR CLOCKS

MOLECULAR CLOCKS AND EVOLUTION

Here are a few copied and pasted annotated references, from a file of references on the computer I currently use, that may help show the validity of my 6^th post – Science Screw-up No. 1 – posted May 31, 2013.  I shudder when I think how many others were lost in various ways from the overwhelming amount of literature on the topics that interested me enough to make index cards, entries on earlier computers, and stacks of journals and clippings still unpacked from moves.  Some were cited in the post noted above, but lacked the annotations and/or quotes from the articles.

Because structure and functions of organisms are the direct targets of natural selection they can be a better clue to branching pattern of the tree of life until the generation time of organisms is properly incorporated in the process of tree construction.  Many of my posts rely on this concept for interpreting relationships as well as the views of natural history oriented biologists.

MOLECULAR CLOCK VARIABLES

Ayala, Francisco J.  1997.  Vagaries of the molecular clock.  Proc. Natl. Acad. Sci. USA, 94:7776-7783.  Found as much as a ten-fold difference between divergence times estimated by two different Drosophila genes (GPDH and SOD, or, glycerol-3-phosphate dehydrogenase and super oxide dismutase).  Generation times were identical in this study so did not affect the rate variation determined.

Bleiweiss, Robert.  1998.  Slow rate of molecular evolution in high-elevation hummingbirds.  Proc. Natl. Acad. Sci. USA, 95:612-616.  “A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context.” The effect remained “significant even after taking into account a significant negative association between body mass and molecular rate.”

Britten, Roy J.  1986.  Rates of DNA sequence evolution differ between taxonomic groups.  Science, 231:1393-1398.  “Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5.  The slowest rates are observed for some higher primates and..”
 

Buckley, Thomas R., Chris Simon, and Geoffrey K. Chambers.  2001.  Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support.  Syst. Biol., 50(1):67-86.  variation in variability across data sets changes estimates, under different model assumptions, of nodal support and branch length   

Campbell, J. H.  1987.  The New Gene and Its Evolution.  Pp. 283-309 in Campbell, K. S. W., and M. F. Day (Eds.).  Rates of Evolution.  Allen and Unwin, London.  314 pp.  Rates of evolution pp 303- “To the extent that biological mechanisms participate in evolutionary change they allow its rate to be programmed internally as an attribute of the species.”

 Clegg, Michael T., Michael P. Cummings, and Mary L. Durbin.  1997.  The evolution of plant nuclear genes.  Proc. Natl. Acad. Sci. USA, 94:7791-7798.  “Analyses of synonymous nucleotide substitution rates for Adh genes in monocots reject a linear relationship with clock time.”  New genes that encode the enzymes ribulose-1,5-biphosphate carboxylase and alcohol dehydrogenases occurred at ten times the rate of new genes for alcohol dehydrogenases.    

Denver, Dee R., Krystalynne Morris, Michael Lynch, Larissa L. Vassilieva, W. Kelley Thomas.  2000.  High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.  Science, 289:2342-2344.  generation time of 4 days, used 74 lines of single worms, analyzed base pairs for mutations; 9.7 x 10 to the minus 8 per site per generation or 8.9 per site per million years.  “ . . . revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates,”

Field, Katharine G., Gary J. Olsen, David J. Lane, Stephen J. Giovannoni, Michael T. Ghiselin, Elizabeth C. Raff, Norman R. Pace, and Rudolf A. Raff.  1988.  Molecular phylogeny of the animal kingdom.  Science, 239:748-753.  “Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.”  “The use of cellular RNA for these studies guarantees that sequences will represent commonly transcribed RNA genes, not minor or inactive genes.  The method provides sequences in the most conservative portions of the 18S rRNA molecule, which are the most useful for broad phylogenetic comparisons.” see following sentence page 748 also [“For distantly related organisms, it is not possible to establish homology between nucleotides in the rapidly evolving portions of the molecule; thus, even if the entire 18s rRNA sequence is known, only some parts of it can be used for phylogenetic inference.”].  Study was based on 18S ribosomal RNA sequences. Pogonophoran used was a thermal-vent species, annelids were a polychaete and an earthworm, chordates were a tunicate, amphioxus, a frog, and a human.

Fitch, Walter M., Robin M. Bush, Catherine A. Bender, and Nancy J. Cox.  1997.  Long term trends in the evolution of H(3) HA1 human influenza type A.  Proc. Natl. Acad. Sci. USA, 94:7712-7718.  Variation of replacement substitution rate of codons as much 7.2 times greater in a hypervariable one.  Rate lowest in trunk codons, intermediate in twigs, and greatest in tip branches.  [thought added 2/6/03 – might be an expression of selection against deleterious substitutions eliminated more effectively due to time as one goes to older twigs and trunk. (jge) I had just been thinking of that while trying to improve on method of calibrating molecular clocks with generation time corrections for both calibration species (if not from lines studied) and generation time difference of branch species (A correction of up to 199.999% of uncorrected bifurcation value is needed if generation time of shortest lived species was used; whereas estimate could need reduction of up to 99.999% if based on longest lived species); therefore two separate generations time corrections must be considered if calibration species is a third species; no correction for generation time is needed if all three have same generation time.]

Gillooly, James F., Andrew P. Allen, Geoffrey B. West, and James H. Brown.  2005.  The rate of DNA evolution: effects of body size and temperature on the molecular clock.  Proc. Natl. Acad. Sci. USA, 102:140-145.  support a single molecular clock, “but that it “ticks” at a constant substitution rate per unit of mass-specific metabolic energy rather than per unit of time.”

Keightley, Peter D., and Adam Eyre-Walker.  2000.  Deleterious mutations and the evolution of sex.  Science, 290:331-333.  [13 Oct 2000]  Deleterious mutations were eliminated more rapidly in short generation time species.  The study did not support (MD) “mutational deterministic” hypothesis for obligate sexuality.

Kimura, Motoo, and Tomoko Ohta.  1971. On the rate of molecular evolution.  J. Molec. Evolution, 1:1-17. citing various sources for a rate of about one centipauling for histones to four paulings for Fibrinopeptide A.  (1 pauling = “rate of substitution of 10 [to minus 9] per amino acid site per year.)

Kuman, Sudhir, and S. Blair Hedges.  1998.  A molecular timescale for vertebrate evolution.  Nature, 392:917-920.  [30 Apr 1998]  In estimates of divergence times using different genes, a standard error of about 10% was found using ten genes, but the standard error was only 5% if 50 genes were used and 3% with use of 100 genes.  Their study used 658 genes distributed among 207 species of vertebrates (mostly mammals).  [note added 11/25, 2014 -  this shows the ability of statistical analysis to give a more precise wrong answer, if a uniform rate premise is wrong – a point of my May 31, 2013 post; see Maley and Marshall, 1998 below also]

Laird, Charles D., Betty L. McConaughy, and Brian J. McCarthy.  1969.  Rate of fixation of nucleotide substitutions in evolution.  Nature, 224:149-154. a ten-fold higher rate of nucleotide sequence variation for rodents compared to artiodactyls is found when time estimates are in years  “This difference diminishes if generations, rather than years, represent the appropriate interval of evolutionary divergence.”

Maley, Laura E., and Charles R. Marshall.  1998.  The coming of age of molecular systematics.  Science, 279:505-506.  “Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought.” . . .  “In extreme cases the inferred relationships between groups may change when different representative species are used.” . . “as the amount of data analyzed increases, so does the apparent statistical support for an incorrect phylogenetic tree.”

Mishmar, Dan, Eduardo Ruiz-Pesini, Pawel Golik, Vincent Macaulay, Andrew G. Clark, Seyed Hosseini, Martin Brandon, Kirk Easley, Estella Chen, Michael D. Brown, Rem I. Sukernik, Antonel Olckers, and Douglas C. Wallace.  2003.  Natural selection shaped regional mtDNA variation in humans.  Proc. Nat. Acad. Sci. USA, 100(1):171-176.  p. 171-“multiple amino acid changes found in ATP6, cytochrome b, and cytochrome oxidase I appeared to be functionally significant.  From these analyses we conclude that selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate.”  P. 176 –“If selection has played an important role in the human mtDNA lineages, then the rate of mtDNA molecular clock may not have been constant throughout human history.  If this is the case, then conjectures about the timing of human migrations may need to be reassessed.” 

Miyamoto, Michael M., Jerry L. Slightom, and Morris Goodman.  1987.  Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region.  Science, 238:369-373.  “. . the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans.” 

Mooers, Arne Ø., and Edward C. Holmes.  2000.  The evolution of base composition and phylogenetic inference.  Trends in Ecology and Evolution (TREE), 15(9):365-369. “. . , in the early 1990s, phylogeneticists discovered that the variation in GC content among organisms could wreak havoc on attempts to reconstruct evolutionary history.  This was because the tree-building techniques then in use often grouped together unrelated species with similar GC content.” 

Nichols, Richard.  2001.  Gene trees and species trees are not the same.  Trends in Ecology and Evolution (TREE), 16(7):358-364.  different genes may evolve at different points in time in the same lineage giving different times of separation if only one is considered to calculate divergence time

Shaw, Kerry L.  2002.  Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.  Proc. Natl. Acad. Sci. USA, 99:16122-16127.  “The discrepancy between mtDNA and nDNA phylogenies reveals that speciation histories based on mtDNA alone can be extensively misleading.”

Simmonds, P., and D. B. Smith.  1999.  Structural constraints on RNA virus evolution.  Journal of Virology, 73(7):5787-5794.  Evidence of rate of mutations variation with nucleotide location in relation to secondary structure of GB virus C.  In this case, molecular clock assumptions are incorrect.  

Joseph Engemann    Kalamazoo, Michigan   November 25, 2014

EVOLUTION: NUCLEOTIDE MUTATION RATES

Evolution: Nucleotide Mutation Rates

MOLECULAR CLOCKS

If nucleotide mutation rates were the same for all organism and all parts of the genome, they would be the basis for a perfect molecular clock to determine relationships for constructing evolutionary trees.  But they are neither the same for all organisms nor even for various portions of the genome for the same organism.

For those wishing a more comprehensive view of the variables, they may be found by searching for nucleotide mutation rates in Wikipedia, or elsewhere, on the internet.  To the best of my knowledge, my peers have neither found nor embraced the evidence I have presented in other posts on this blog showing the major errors in the current published articles on the relationships of phyla and the importance of the Pogonophora in demonstrating those relationships.

MUTATON RATE VARIABLES

Some variables are known but not considered in several major studies, thus producing major errors in proposed schemes of animal evolution.  A variation produced by different generation times is the major factor affecting rates of origin of phyla when extremely low evolutionary rates occur - as noted elsewhere in this blog for pogonophorans and perhaps nematodes.  Most variables would have a proportional affect within the variation caused by generation time.  Fortunately, the affect of generation time diminishes to near zero as one approaches the species level.

Variables

There are many documented studies showing different rates for different groups of species.

1. Viruses with RNA genomes mutate at a much faster rate than organisms with DNA genomes.

2. Mitochondrial DNA has a faster mutation rate than nuclear DNA.

3. Methylated DNA is more resistant to mutation than DNA that is not methylated, as in sperm which have higher mutation rates than eggs.  This is perhaps tied in with the fact that sperm genes may be expressed in the individual produced more than is expressed by genes from the egg.  Methylated DNA from the egg may also be a reason that dosage affect on gene expression has less impact than one might expect from comparison with instances where three of a particular chromosome are present.  The methylation effect is not total; that is shown by Medel's pea experiments where the flower pigment expressed is dosage dependent, and in humans where the sickle cell gene is less debilitating in the heterozygous condition.

4. Mutations are more likely to occur near sites where chromosomal deletion or insertions have occurred than in more distant locations from those mutated sites on the chromosome.

5. Genetic factors may affect rates; perhaps through variations in function of chromosomal damage repair functions.  Rates may be subject to natural selection balancing the value of introducing change versus the stability desired in successful genes.

6. Environmental factors such as variation in background radiation and/or the extremes of deep sea pressure  may also affect rates.

7. Generation time is the current source of error in relating major groupings of phyla.  This error is also a factor in proposals of a time of origin of humans relative to monkeys and great apes.  But it is not a factor in most studies of animals sharing the same species, genus, or family.  However it may be more of a factor as one compares orders and classes of animals.

A botanist colleague maintains generation time is not a factor in evolution of flowering plants, although I think that has yet to be proven.

Generation time versus age affects?

The question might be of interest in human evolution because older individuals may be more likely to have experienced mutations in germ cells, especially sperm, whereas eggs may be spared much of the generation time effect by all being produced before birth as well as by having methylated DNA.

I have not given much thought to this as a general factor because it does not seem apparent for animals in the deep sea that were critical in providing the clue of the annelid ancestry of chordates.  If long generation time corresponds with more mutations per individual, it would seem to cancel out to some extent the generation time effect in evolutionary rates.  The extreme difference of generation time of abyssal animals critical in the early origin of phyla makes cancellation of this type of little importance when considering overall evolutionary trees of the major groups of animals.

Natural selection

The rate of mutations may not have as much to do with evolution as does natural selection.  Beneficial mutations, although they are much rarer than other mutations, tend to be incorporated in the species gene pool via natural selection or survival and reproduction of the individuals having them.  Whereas deleterious mutations tend to be eliminated.  In mammalian species much of the genome is thought to be non-coding and in the regions of the chromosome between the genes or coding regions.  Mutations in the non-coding regions are thought to be of little consequence as long as they maintain the chromosomal integrity.

Although rates are not necessarily of major impact on the direction of evolution, they are essential to consider in establishing the branching pattern of evolutionary trees, especially as regard major group relationships.


Joseph G. Engemann    Emeritus professor of Biological Sciences, Western Michigan University  October 1, 2014