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

CREATIVITY: FRAME OF MIND

Preparation for creativity

A dilemma is presented by the broad and deep background that is desirable for creativity - it can be an impediment to an unbiased view and preoccupy us with thinking that has not produced a solution. "A fresh approach is then more difficult than it would be for an intelligent, ignorant neophyte."

If you come up with a good idea without having studied the subject intensively, you won't know whether it has been done before or if some evidence exists showing it is impractical.  A second approach can be useful to both expert and neophyte, the development of a questioning attitude.

Questioning attitude

"A questioning attitude must be balanced with a confidence in the existence of solutions, answers, and causality.  Rather than let knowledge of an uncertainty principle escape its bound of valid application and erode our confidence in areas it has no application, we should focus on the universal relationship of cause and effect.  For every question, there is an answer, if only that the question is nonsense.  A questioning attitude can dampen the free flow of ideas.  Negative expressions are wisely excluded from group brainstorming sessions in the initial proposal developing stage.  Realistic evaluation comes later."

So, a questioning attitude, keep it reasonable.  The following cartoon may apply.

The caption says "Have you noticed how he never seems to agree when you say 'nice day'"

"Our minds can become channelized by factors other than the knowledge of literature and accomplishments in the subject.  Just as we use repetition to learn and fix things in our mind, repetition will make the implausible seem axiomatic.  This is a special danger to those ignorant of the the subject and in the favorable position of viewing it freshly.  The first idea, unless readily disproved, has the greatest chance of being repeated.  Succeeding ones have progressively less chance of taking the favored position.  Perhaps some people cherish their own idea because it is their only one."

The cartoon below speaks to the subject.

The caption says "Tell me it's not cancer doc, I've been worried ever since I got this persistent pain in my posterior."

"It is worth attempting a little self analysis to determine our personal quirks so we can compensate for them.  Do we reject the new?  Do we overvalue and revere the new experience just because it is new?  Is the old outmoded?  Is the old the proven best?  Do we delight in complexity, or simplicity?  Can we answer always to any of the preceding? If so we may have a built in bias toward or away from some ideas.  The hypochondriac, those with special fears, and those with special love do.  Don't we all?"

Honesty

"Honesty is essential to the maintenance of creativity.  Honesty with others will reduce self-deception.  Honesty does not mean that everything known must be used or told."

The cartoon for this subject follows.

 The caption says "I wish what went in Pat's ear went out the other ear instead of the mouth!"


Quotes and cartoons are from Chapter 4 of my unpublished 1974 manuscript, "The Two Way Street: One Approach to Creativity"

Joseph G. Engemann    Kalamazoo, Michigan     November 19, 2014

GOD: WOMEN PRIESTS?

CBS 60 MINUTES, November 16, 2014

A young reporter became a little more penetrating in her questions of Cardinal Sean O'Malley, Archbishop of Boston and presumably an adviser of Pope Francis, after some comfortable questions about progress in dealing with Vatican problems.  She did not seem satisfied with his assertion of a greater role for women and an existing high position of esteem for women in the church.

There may be practical reasons for not having women priests at this time, but the role of women and their relationship to Jesus was more extensive than seems consistent with the operation of society at that time.  Having only men among the twelve apostles closest to him was simpler than fighting societal norms of the time.  So the notion of Pope Benedict that relativism should be rejected, in favor of objective truth in moral and/or ethical decisions or their rules or guidance, could apply to favor women priests.  In the United States and many other countries women are taking their rightful place in society.  Unfortunately, not all countries offer them that role.

The church has enough problems with many celibate clergy having difficulty handling their role gracefully.  Add women to the mix - would that solve or exacerbate the problems?  I one time thought it would be a good idea to direct homosexual males into the priesthood; in my mind they had a reputation of being gentler, more social, and almost devoid of macho tendencies.  I think the past problems of pedophiles in the priesthood may be a separate problem of heterosexuals perpetuating the behavior they were victimized by as children.

The reporter said or implied that women were being discriminated against and denied a right.  But it is not anybodies right to be a priest.  I thought priests were special when I was a child.  I still think so, but now I know they are human and probably as prone to failure as anyone.  I was upset in early high school when a classmate informed me that a priest in a nearby country parish had a drinking problem.  It was later confirmed by reliable sources and may have helped me get a better sense of reality.  But people still expect more of the clergy and rightly so.

The church gets enough bad press without having to deal with unplanned pregnancies of clergy, remodeling rectories when the next pastor is a different sex, and the minds and actions of members unable to accept change.

Change can be good or bad.  It is good to challenge the status quo.  But change for change's sake is more likely to be a mistake in a well tuned system.  That is the principle we can get from evolution by means of natural selection.  But it also indicates changes that fine tune the system can be worthwhile.  I don't think voting on it is necessarily wise.  I hope the Pope is in a better position to wisely make that decision.  But now can 60 Minutes find out the chances of the next Dali Lama being a woman?

About twenty years ago I sent a long letter to Pope John Paul listing all the scriptural and other reasons I thought ordaining women was appropriate.  I doubt if the letter every reached him, but I had enough postage on it.  About ten years ago I wrote another letter to a pope about the compatibility of evolution and religion when some catholic publications were printing anti-evolutionary views, but I never mailed it.  Now it is evident the pope does not need it [see post of October 31].

Joseph Engemann       November 17, 2014

EVOLUTION AND MARINE SEDIMENTS

MISH-MASH

Mish-mash is a title to accommodate comments with varied connections to the four main pages of this blog.   As may be evident from earlier posts, I am not as reluctant as I should be to talk about things I am not particularly well qualified to talk about.

Evolution, Invertebrates, And The Deep Sea 

Prior to the early 1980's it occurred to me that the conditions of much of the ocean bottom were so stable that a record of unusual disturbances is preserved for a long time in many locations.  Major disturbances show as unconformaties in rocks between periods of greater stability of deposition rates.  A study of deposition as it happens today makes interpretation of fossil deposition easier.  The gradual change in features of microfossils seems to be the rule when sediments are added without major disturbances such as those that characterize gaps separating major geologic times.  Disturbances were frequent enough during the sediment accumulation process that there is often a gap where transitional forms are not present; the concept of punctuated equilibrium is probably an artifact of those missing transitional sediments.  The opposite effect can be produced by action of bottom dwelling organisms or wave action mixing sediment above and below a gap and blurring the estimate of time of existence of a group.

Forams

A particularly useful group for dating sediments and seeing changes is the protozoan group known as the foraminiferans.  Microfossils of the planktonic ones are particularly useful because their skeletons can be carried by ocean currents to coat the sea bottom of an ocean.  The mixture of types can be a unique identifier of sediments that can span great distances on the ocean floor or continental rocks formed in past oceans.  Even climates of the past can be determined from isotope studies of their skeletons.

An introduction to some of the literature about bottom communities in the ocean can be found in the final few pages of the text I was working on at the time [Engemann, Joseph G., and Robert W. Hegner.  1981.  Invertebrate Zoology, 3^rd ed.  Macmillan Publishing Co., New York.  746 pp.].  The references at the end of the chapter include some such as Grassle (1977, Slow recolonization of deep-sea sediment.  Nature 265:618-619); and others about sedimentation rates and other topics pertinent to the topic.

An environmental consideration

The content of the last chapter made me aware the long term effects of ocean pollution could be much more severe and persistent than localized damage to communities.  The chapter was a step along the way to understanding the extreme age potential in the abyssal region organisms.  Marine sediment communities could have a sequence of animals recolonizing them that might yield an estimate of the time of major sediment disturbances.  Such actions might blur the clarity of community lines in the fossil record.  Are we in the process of leaving a major unconformity in sediments by our actions?  The widespread dispersal of chlorinated carbon pesticides shows the potential hazard of unlimited ocean dumping of wastes, either intentionally or by contaminated rivers and atmosphere.
  
Pogonophorans

Pogonophorans living in tubes in abyssal sediments are thought to have their tubes vertically oriented in the sediments.  One line of evidence is the lack of the posterior segmented region in most dredged specimens.  Such orientation indicates they could be getting nutrition from deeper sediments that are much older; that would make carbon dating of their age a near impossibility if fossil food in the sediments is a major source of their nutrients.

The complex of ideas involved in the topic were part of the preparation enabling me to make the pogonophoran connection of protostomes and deuterostomes.  Seeing that made understanding the tree of life correctly and the error needing correction in molecular proposals of Ecdysozoa and Lophotrochozoa possible.  That eureka moment began with my reading the paper of Gans and Northcutt, 1983, as described in earlier posts on evolution and creativity.

Joseph G. Engemann     November 6, 2014 (some editing on 10/18/2015)