MOLECULAR AND HUMAN EVOLUTION

Why today's comments?

I happened across an old personal journal entry from October 13, 2006 with the follow (slightly edited).

Kimura and Ohto 1961 on Molecular evolution is good for general principles, but the final page in particular need rebuttal about- 

assumption that verbal arguments based on evolutionary principles will become useless as computer approaches improve; and- 

presumption that neutral mutations are increasing at the same rate in “living fossils” as they are in others changing more rapidly. 

Aspects of human evolution thought about this morning (may be in the literature but) included: bipedal human ancestors were favored in surviving drying conditions at forest edge by ability to reach fruit on small branches better than others living in trees or as quadrupeds on ground.  Ancestors were also favored by being able to see other tree clumps across neighboring grasslands, and ability to see over grass to avoid predators or even frighten them by their erect posture providing an imposing frontal profile. Of course, views of Hamilton (Life’s Color Code) need to be included in discussion of human evolution.

The two rebuttal needing assumptions of the 1961 article cited were in error because (1) verbal arguments may be able to bridge a linear impasse a computer approach is incapable of evaluating.  And (2) neutral mutation rates would seldom increase at the same rate in "living fossils" as they are in other organisms.  (1) is shown by the failure of molecular phylogeny programs to compensate for generation time.  (2) is dramatically shown by the appearance of pogonophorans via "long-branch attraction" within computer generated trees of other groups.

Hamilton's book provides good evidence of how observation and reason can provide insightful understanding of human evolution. 

Numerous other posts of this blog provide support for the above rebuttals.  Although evolution may be used in labels with topics other than evolution, it is almost always used in labels for relevant evolution posts.  

Joseph G. Engemann      Kalamazoo, Michigan     February 20, 2015

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

SCIENCE PEER REVIEWS

The Peer Review Problem and a Proposed Solution

Peer review

The peer review process is not as flawed as many think.  It is needed to keep professional journals and granting agencies functioning at a high level.  When working as intended, it is a benefit to scientists, saving time from having to sort through useless material that should never have been published, and making research money go to those most likely to do productive research.

The feared failures such as reviews that are uninformed, biased, eliminating work from competitors or other lapses are minimal according to some research on the topic done years ago.  Peer reviewers may be overworked and usually unpaid volunteers.  They usually are active publishers in the field they review.  But complaints arise.

I have thought about the problem.  The following overlong suggestion for a solution was formulated about seven years ago.  It was after about ten years of retirement, keeping up my interest in biological sciences, and it occurred to me that I could have been part of the solution.  It is too late for me now, but it might provoke someone to do something about it.

Joe Engemann      June 7, 2013

December 14, 2005

I just finished lunch as I looked a bit at the AARP Bulletin.  A brief train of thought brought me to a solution to the editorial and peer review problem facing top journals.  The solution seemed to be an equivalent organization to the Good Housekeeping Seal of Approval or Consumers Union/Consumers Reports.  Perhaps NSF would fund startup or AARP could help advance such a project.

The problem

Editors of scientific journals do not have the time and/or the competence to properly consider and evaluate all submissions.  Reviewers face similar problems.  Peer reviewers are seldom true peers of workers in all aspects of a discipline.  Errors that creep in to a discipline are unlikely to be seen by either those that let the error in or by those they taught. 

The goal

Establish a core of retired volunteer reviewers in various specialties to establish an independent journal review program.  Panels of three or more should produce evaluations of Science, Nature, and the top (one to three) specialty journals in each major subdiscipline.  The evaluations would reflect standards of the area, with some input from outsiders to the discipline.  A sampling process could be used unless sufficient reviewers or panels are available to evaluate all papers and editorial content. 

The review program could be a clearing house for individuals to submit complaints and/or for journals to refer complaints regarding their perception of failings of particular published materials.  Emphasis on the complaint generated review process could reduce unnecessary reviews of journals that have an effective high quality program or output.  A method of evaluating complaints would be desirable, particularly if excess numbers were generated.  Perhaps a quantitative score could be developed to prioritize review choices to those getting the highest relative score (relative to readership and available reviewers or better criteria).

Choice of reviewers

Retirees that normally read the journal

Over 65 or retired over 5 years

Over ten years since editorial board or other service for a journal or related entity

Degree and/or employment, publication, or other credentials in the discipline

Tenure of reviewers

One year renewable for five years upon unanimous agreement of other panel members

A second five year term could ensue if no replacements are available

Removable by petition of one or more panel members if validated by the majority of each of two of the three most closely related panels

Oversight board

One member elected from each panel to serve on a roster from which a six member board to be selected by lot – three from the panels making up the third having most review activity, two from the next third, and one from the remaining third having least activity

Remaining elected members to serve as alternates (by request of board chair or member needing replacement) and/or replacements (next on alphabetical list of those elected)

Function of board to be administration or administrative oversight and development of rules or by-laws as necessary

Funding

Volunteers could cover their own expenses as a public service

Reviewers should not be paid, except for expenses if available, to maintain independence and avoid conflicts of interest

Foundations might provide support either long term or to get started

The Western Michigan University Evaluation Center might provide advice or funding

Possible funding from the National Science Foundation for secretarial and office expenses in start-up phase

Possible funding from membership fees from journals if mechanism avoiding conflict of interest is possible

Possible funding from newsletter reporting evaluations available by subscription; perhaps libraries might find use in evaluating acquisitions

Independent results might be of use to granting agencies (NSF, NIH, Foundations, etc) to evaluate grants made for factors producing quality publications (grant support of publications could be in database of reviews).  The public might find it a valuable way to evaluate giving to non-profit organizations sponsoring research.

Submission for AARP (bulletin or journal)

Is peer review failing?

Retired members of scientific societies, do you still read your journals?  If you do, your input is desired.  Do you think you could provide independent review of the validity of research published in your specialty?

A disgruntled emeritus biology professor maintains two leading general scientific journals have been publishing research articles based on research violating both valid principles of research and basic research published in specialty journals.  The professor wants AARP to survey members to see if journals they read also show such a failing of peer review.

The professor thinks the independent input of retired scientists could help correct some of the deficiencies of the peer review process based on the following reasoning.  The information explosion along with specialization required to produce research in molecular biology has resulted in most publications being produced by those lacking the broad background prevalent in most researchers of two generations ago.  The peer review process is great to preserve quality, but it also preserves errors that become ingrained in those winning a competitive race to publish.  They are slow, unwilling, or incapable of seeing views in conflict with their own work.  They have learned some of the errors as accepted principles of their discipline.

The best example is the error of calculating relationships of animals in an evolutionary tree of life based on faulty molecular clock studies.  Life cycle duration was a possible variable noted in a major publication starting molecular clock studies.  It was ignored because it was unknown how to deal with it, it had little effect on closely related groups, and the oversight became institutionalized in the field.  The error was further compounded by using single chemical compounds (variability in speed of change in different groups was widely documented), too small a sample size (less than the minimum number shown to be needed), and data selection.

It seemed a horrendous error to replace the results of studies developed through a century of work using comparative anatomical, embryological, and biochemical, as well as paleontological and other studies, on the basis of an oversimplified molecular clock study.

Is the professor a kook?  Or do you agree something needs to be done and/or would be willing to participate in reviewing one or more journals in your field?  Send your response to the AARP, Peer review survey, - - - - - .

6/7/2013   The above was not sent.  But, is anybody out there ready to do something about it?