NATURE & SCIENCE MISS THE MARK
I was thinking about my previous post and it seemed to me the obvious answer to determining animal phylogeny stared me in the face. The data I had cited from Francis S. Collin's book, The Language of God, seemed to provide proof of the point I have been trying to make in many evolutioninsights.blogspot.com posts. On page 127 his Table 5.1 compares the liklihood of finding comparable DNA sequences of humans in other organisms. It makes the comparison, first of protein coding genes from humans with six other species, then randomly selected DNA from between genes of those species.
Human compared Protein coding Random DNA
with DNA between genes
Chimp 100% 98%
Dog 99% 52%
Mouse 99% 40%
Chicken 75% 4%
Fruit fly 60% -0%
Roundworm 35% -0%
Your first thought might be that the protein coding genes make more sense to use for determining relationships. That is probably the rationale the two flawed studies proposing Ecdysozoa (in Nature, 1997) and Lophotrochozoa (in Science, 1995) used in selecting 18S ribosomal DNA. But there would be stringent selection to keep that DNA from changing, with a proportionality to its functional importance.
The random DNA from non-coding regions would lack selection and thus could change proportional to the number of generations between the two being compared. Thus if liklihood percentages are apportioned inversely to generation time in constructing the branch lengths from common ancestors, an ancestral tree could be determined better than by any other available method. Of course, pairwise comparisons would need to be made for each other possible combination of species considered.
Looking at the data in the table, because mice have shorter generation time they would accumulate more changes since our common ancestry and may thus actually be closer in common ancestry to us than the dog, even though there has been greater change in their between genes DNA. The big jump between the chicken and the mammals is due to the much greater antiquity of the separate lines from early ancestral reptiles. With very low liklihood of DNA relationship the accuracy of relationship determination is greatly reduced and fossils and anatomical analysis may be more useful.
I would send this as letters to the editors of Nature & Science, but I doubt they would be any more likely to publish them than my previous submissions many years ago. Too bad, it might have prevented the Ecdysozoa error which put the roundworm and fruit fly in relatively close relationship. The same method used for the Lophotrochozoa is consequently almost equally erroneous.
Science and Nature are two excellent science journals. I am puzzled by the fact that the error has not been corrected. Perhaps others read it much as I have in the past when reading things I am not very familiar with, assuming the research finding are accurate. I did so despite the fact that long ago I realized not everything in print, or on internet, must be correct.
Joseph G. Engemann Emeritus Professor of Biological Science, Western Michigan University, Kalamazoo, MI March 7, 2015
Friday, March 6, 2015
EVOLUTION: QUIET PRE-CAMBRIAN GENES
THE PRE-CAMBRIAN ENVIRONMENT AND ANIMALS
Genes of the Pre-Cambrian can be inferred from common genes and biochemical pathways shared by extant species. But there is reason for saying that genes that have not left echoes of their voice had an important role in evolution as well. Those quiet genes, sometimes important for their silence, can also be inferred from analysis of how some characteristics developed, especially the annelid theory of chordate origin that, I maintain, is the best explanation of origin of chordates via pogonophorans and hemichordates.
Introns and exons
Natural selection is effective in eliminating useless features because there will be no selective force maintaining them, other than the chromosomal duplication process. The portion of the genome active in protein coding is thought to be about 1.5 percent. The 98.5 percent of the DNA not active in production of RNA needed to produce structural and functional proteins and control substances may have some value in other ways that are less dependent upon their exact nucleotide sequence. In comparison to human DNA Collins (2006) shows the sequence for protein codes is 100% the same as in a chimpanzee, 75% the same in a chicken, and 35 % in a roundworm; whereas random segments of DNA between the genes only corresponded at rates that were 98% for a chimpanzee, 4 % for a chicken, and -0 % for a roundworm. Human to human DNA comparisons show about 99.9% identical DNA.
What happened to the fossils?
Very little fossil record exists for times before the Cambrian. Because fossils of numerous phyla show up in Cambrian rocks, it is apparent that many important evolutionary events occurred earlier. I will omit discussion of sponge spicules, and tubes that may well have been made by pogonophorans, to go directly to presumed jellyfish fossils. Pre-Cambrian jellyfish fossils were in the form of doughnut-shaped fossils thought to be casts of sand filled cavities of the bells of jellyfish.
It is not surprising that more ancient fossils are not found because extinction-causing events were more frequent as our orbit was more frequently hit by intrusion into our orbit of asteroids. Localized destruction was probably much more frequent than the era-ending type giving worldwide unconformity of rock layers. Even dating of intermediate layers produced by those major events may be difficult due to destruction of potential fossils. Large areas may have been wiped clear by the event, so dating of sediments above and below an unconformity my show very different times of deposition. A blended layer might be deposited in such locations and provide an intermediate date of origin.
Surviving extinction
Jellyfish deprived of food have the ability to survive and use their own substance as they "grow" smaller. In the process they are found to first absorb reproductive organs completely as they shrink in size. When food becomes reavailable the organs are eventually regenerated. The finding that corals preceded jellyfish (described in an earlier post) provides support for the polyp-medusa-planarian sequence suggested.
The illustration above indicates how the polyp released from a starving coral could drift free to survive burial by sediments. Adaptations aiding survival eventually result in the medusa shown in side view above and top view below where a later series of extinction events, depleting planktonic food, selected forms descending to sediments with nutrition enabling them to eventually take on the planarian shape that enabled better bottom feeding.
The jellyfish would naturally invert from the polyp orientation because the ring of tentacles would have a higher density due to concentration of protoplasmic structures and the potential buoyancy of the bell having trapped air bubbles.
The above enabled survival of jellyfish because their sexual generation could provide widely dispersed larvae capable of colonizing new post-extinction locations in shallow waters they required. On the other hand pogonophorans survived because the abyssal region they inhabit is so extensive that remnants of habitat survived and the sediments themselves were the source of nutrition capable of bridging a long period of no nutrient input. Also the extinction event may have given a temporary boost to dying and sedimenting food organisms replenishing abyssal food deposits.
Remember the quiet genes
Pogonophorans apparently adapted to the very low food supply by reduction of unneeded structure. They have been shown to be able to take up amino acids from sediment water at naturally occurring concentrations. Even though selection is not maintaining the code needed for gut formation, its slow rate of deterioration shown by the percentage comparisons in the second paragraph, enough remained to provide a basis for selection of a new gut much more efficiently than totally new selection would have required. Most of the segment formation of annelids was lost by pogonophorans as well. But enough of the process code survived to make the repeated structures - ribs, vertebrae, muscles, blood vessels, nerves - of chordate systems exist.
If every gene were always expressed, it would be difficult to have the diversity of cells making up our bodies. There must be a very sensitive mechanism capable of turning gene activity on and off. The process must also be varied in slight ways and sensitive to internal and/or external environmental cues to make well-adapted organisms.
Reference: Collins, Francis S. 2006. The Language of God. Free Press (Simon & Schuster), New York, NY. 295 pp.
Joseph G. Engemann, Emeritus Professor of Biological Science, Western Michigan University, Kalamazoo, Michigan March 6, 2015
Genes of the Pre-Cambrian can be inferred from common genes and biochemical pathways shared by extant species. But there is reason for saying that genes that have not left echoes of their voice had an important role in evolution as well. Those quiet genes, sometimes important for their silence, can also be inferred from analysis of how some characteristics developed, especially the annelid theory of chordate origin that, I maintain, is the best explanation of origin of chordates via pogonophorans and hemichordates.
Introns and exons
Natural selection is effective in eliminating useless features because there will be no selective force maintaining them, other than the chromosomal duplication process. The portion of the genome active in protein coding is thought to be about 1.5 percent. The 98.5 percent of the DNA not active in production of RNA needed to produce structural and functional proteins and control substances may have some value in other ways that are less dependent upon their exact nucleotide sequence. In comparison to human DNA Collins (2006) shows the sequence for protein codes is 100% the same as in a chimpanzee, 75% the same in a chicken, and 35 % in a roundworm; whereas random segments of DNA between the genes only corresponded at rates that were 98% for a chimpanzee, 4 % for a chicken, and -0 % for a roundworm. Human to human DNA comparisons show about 99.9% identical DNA.
What happened to the fossils?
Very little fossil record exists for times before the Cambrian. Because fossils of numerous phyla show up in Cambrian rocks, it is apparent that many important evolutionary events occurred earlier. I will omit discussion of sponge spicules, and tubes that may well have been made by pogonophorans, to go directly to presumed jellyfish fossils. Pre-Cambrian jellyfish fossils were in the form of doughnut-shaped fossils thought to be casts of sand filled cavities of the bells of jellyfish.
It is not surprising that more ancient fossils are not found because extinction-causing events were more frequent as our orbit was more frequently hit by intrusion into our orbit of asteroids. Localized destruction was probably much more frequent than the era-ending type giving worldwide unconformity of rock layers. Even dating of intermediate layers produced by those major events may be difficult due to destruction of potential fossils. Large areas may have been wiped clear by the event, so dating of sediments above and below an unconformity my show very different times of deposition. A blended layer might be deposited in such locations and provide an intermediate date of origin.
Surviving extinction
Jellyfish deprived of food have the ability to survive and use their own substance as they "grow" smaller. In the process they are found to first absorb reproductive organs completely as they shrink in size. When food becomes reavailable the organs are eventually regenerated. The finding that corals preceded jellyfish (described in an earlier post) provides support for the polyp-medusa-planarian sequence suggested.
The jellyfish would naturally invert from the polyp orientation because the ring of tentacles would have a higher density due to concentration of protoplasmic structures and the potential buoyancy of the bell having trapped air bubbles.
The above enabled survival of jellyfish because their sexual generation could provide widely dispersed larvae capable of colonizing new post-extinction locations in shallow waters they required. On the other hand pogonophorans survived because the abyssal region they inhabit is so extensive that remnants of habitat survived and the sediments themselves were the source of nutrition capable of bridging a long period of no nutrient input. Also the extinction event may have given a temporary boost to dying and sedimenting food organisms replenishing abyssal food deposits.
Remember the quiet genes
Pogonophorans apparently adapted to the very low food supply by reduction of unneeded structure. They have been shown to be able to take up amino acids from sediment water at naturally occurring concentrations. Even though selection is not maintaining the code needed for gut formation, its slow rate of deterioration shown by the percentage comparisons in the second paragraph, enough remained to provide a basis for selection of a new gut much more efficiently than totally new selection would have required. Most of the segment formation of annelids was lost by pogonophorans as well. But enough of the process code survived to make the repeated structures - ribs, vertebrae, muscles, blood vessels, nerves - of chordate systems exist.
If every gene were always expressed, it would be difficult to have the diversity of cells making up our bodies. There must be a very sensitive mechanism capable of turning gene activity on and off. The process must also be varied in slight ways and sensitive to internal and/or external environmental cues to make well-adapted organisms.
Reference: Collins, Francis S. 2006. The Language of God. Free Press (Simon & Schuster), New York, NY. 295 pp.
Joseph G. Engemann, Emeritus Professor of Biological Science, Western Michigan University, Kalamazoo, Michigan March 6, 2015
Monday, March 2, 2015
ABANDONED THEORIES and LIBBIE HYMAN
THE ANNELID THEORY
A major focus of my posts is clarifying why the abandoned annelid theory of chordate origin should be reinstated. People don't abandon theories without reason. But reasons for abandoning a theory may have a validity that doesn't extend to all instances where they are applied.
A theory discredited before publication
An undergraduate research project by a former student, studying the protozoan Stentor, provided new observations for us that got us quite excited. The protozoan is one of the larger protozoans that can be seen, although poorly, with the naked eye. They are usually attached to solid surfaces in their aquatic environment. Like many other ciliates, they have a macronucleus with many (sets of?)chromosomes, and a micronucleus with one set. In the photo below you can see the trumpet like shape they have when attached and the beaded macronucleus inside. They use cilia to circulate water to the large oral end and filter out food particles.
Figure above. Two Stentor protozoans. The macronucleus is elongate and enclosed within a membrane that is constricted to make the macronucleus appear beaded.
The observation that excited us was the presence of many free-swimming Stentor's taking on the shape typical of the mobile state. There was a concentrated population and many had a large central enclosure, like the picture below shows in the upper Stentor, that encloses another Stentor.
Figure above. Free-swimming Stentor with an enclosed Stentor.
Some ciliates are known to reproduce by producing internal buds. But it had never been reported for this protozoan. So he was excited when he told me about it. He had even dissected one to release the internal bud and when released it swam away.
Observing the process for a day or so we finally came to the awareness that it was not a bud. It was another Stentor that had been swallowed whole. Apparently, cannibalism occurs when food supply decreases in crowded populations.
The annelid theory
The annelid theory was popular a hundred years ago. It may never have been universally accepted. But it was as good as any competing theory of chordate ancestry at the time. The clincher responsible for its rejection was the observation that developmental stages often are a great clue to relationships that are not evident in adult organisms.
The annelid theory had support for the correspondence of relationships of systems of annelids and inverted chordates, or vice versa.
Two Figures above. Annelid/Vertebrate systems as illustrated in early 20th Century texts, the upper in Romer and the lower in Lull, with one inverted so you don't have to turn your monitor upside down.
The drastic change in embryology of annelids versus chordates was used to discredit the theory. But the evidence I present of the probable role of pogonophorans in expediting the shift should be sufficient to reconsider the annelid theory. Gould* presented a good assessment of why it should be reconsidered due to a better understanding of the limitations of the "biogenetic law".
In reviewing volume five of Hyman's The Invertebrates (1959, McGraw-Hill, New York), I found on page 224 the beginning statement on relationhips of pogonophorans read "It is not open to doubt that the Pogonophora belong to the Deuterostomia." Later she says "the Pogonophora appear most closely related to the Hemichordata." Earlier, on page 201, she said about the hemichordate-chordates, "Such identity is inconceivable except on the basis of a common ancestry. Hence a phylogenetic relationship between hemichordates and chordates is not open to question."
Those comments were made before the evidence of relationship of pogonophorans to earlier polychaete annelids was discovered.
A bit about Libbie Henrietta Hyman
Libbie Henrietta Hyman was perhaps the most outstanding zoologist of the last century. She produced a comparative anatomy manual used by many of the pre-med students of her era. Then, in her position at the American Museum of Natural History in New York, she produced a multi-volume treatise on invertebrates that remains a remarkable resource.
In the final chapter of volume five discussing new developments of topics in earlier volumes she uses colorful language to express definite opinions. For example on page 750 - "The author hoped that the enterocoel theory was dead and buried, as it deserves, but . . .". Then "The author regards the enterocoel theory as fantastic nonsence, for which there does not exist a single scrap of genuine evidence."
She criticizes views putting Proterospongia in line with the origin of sponges. She provides arguments that the anthozoans cannot be the earliest cnidarians. Both of those views are contradicted in earlier posts of this blog.
She had command of a vast amount of biology of organisms so her opinions have had considerable influence. She proposed putting several phyla in a natural grouping she named Aschelminthes. It had some acceptance until some experts in some of the groups disagreed, perhaps they thought it minimized the importance of the groups they researched. So she later abandoned the view although I think it was correct in the inclusion of most of the groups it included.
A lesson learned
The short life of many ideas and theories, changed because of varying emphasis on major or minor features, gives me pause when I think about my evolutionary ideas. I have learned from the evidence to support the coalescence of the annelid theory as correct in the connection suggested, that gross features can be important. They can also mislead, as the importance of radial versus bilateral symmetry did in forming major clusters of phyla; the transition either way among the two symmetries is eventually selected by the habit of being attached to a substrate versus having active movement over a surface. So it is difficult to state unequivocally that some parameter is the ultimate measure of the direction of relationships.
*Gould, Stephen Jay. 2002. The Structure of Evolutionary Theory. The Belknap Press ofHarvard University Cambridge , Massachusetts
Joseph G. Engemann March 2, 2015
Emeritus Professor of Biology, Western Michigan University
A major focus of my posts is clarifying why the abandoned annelid theory of chordate origin should be reinstated. People don't abandon theories without reason. But reasons for abandoning a theory may have a validity that doesn't extend to all instances where they are applied.
A theory discredited before publication
An undergraduate research project by a former student, studying the protozoan Stentor, provided new observations for us that got us quite excited. The protozoan is one of the larger protozoans that can be seen, although poorly, with the naked eye. They are usually attached to solid surfaces in their aquatic environment. Like many other ciliates, they have a macronucleus with many (sets of?)chromosomes, and a micronucleus with one set. In the photo below you can see the trumpet like shape they have when attached and the beaded macronucleus inside. They use cilia to circulate water to the large oral end and filter out food particles.
Figure above. Two Stentor protozoans. The macronucleus is elongate and enclosed within a membrane that is constricted to make the macronucleus appear beaded.
The observation that excited us was the presence of many free-swimming Stentor's taking on the shape typical of the mobile state. There was a concentrated population and many had a large central enclosure, like the picture below shows in the upper Stentor, that encloses another Stentor.
Figure above. Free-swimming Stentor with an enclosed Stentor.
Some ciliates are known to reproduce by producing internal buds. But it had never been reported for this protozoan. So he was excited when he told me about it. He had even dissected one to release the internal bud and when released it swam away.
Observing the process for a day or so we finally came to the awareness that it was not a bud. It was another Stentor that had been swallowed whole. Apparently, cannibalism occurs when food supply decreases in crowded populations.
The annelid theory
The annelid theory was popular a hundred years ago. It may never have been universally accepted. But it was as good as any competing theory of chordate ancestry at the time. The clincher responsible for its rejection was the observation that developmental stages often are a great clue to relationships that are not evident in adult organisms.
The annelid theory had support for the correspondence of relationships of systems of annelids and inverted chordates, or vice versa.
Two Figures above. Annelid/Vertebrate systems as illustrated in early 20th Century texts, the upper in Romer and the lower in Lull, with one inverted so you don't have to turn your monitor upside down.
The drastic change in embryology of annelids versus chordates was used to discredit the theory. But the evidence I present of the probable role of pogonophorans in expediting the shift should be sufficient to reconsider the annelid theory. Gould* presented a good assessment of why it should be reconsidered due to a better understanding of the limitations of the "biogenetic law".
In reviewing volume five of Hyman's The Invertebrates (1959, McGraw-Hill, New York), I found on page 224 the beginning statement on relationhips of pogonophorans read "It is not open to doubt that the Pogonophora belong to the Deuterostomia." Later she says "the Pogonophora appear most closely related to the Hemichordata." Earlier, on page 201, she said about the hemichordate-chordates, "Such identity is inconceivable except on the basis of a common ancestry. Hence a phylogenetic relationship between hemichordates and chordates is not open to question."
Those comments were made before the evidence of relationship of pogonophorans to earlier polychaete annelids was discovered.
A bit about Libbie Henrietta Hyman
Libbie Henrietta Hyman was perhaps the most outstanding zoologist of the last century. She produced a comparative anatomy manual used by many of the pre-med students of her era. Then, in her position at the American Museum of Natural History in New York, she produced a multi-volume treatise on invertebrates that remains a remarkable resource.
In the final chapter of volume five discussing new developments of topics in earlier volumes she uses colorful language to express definite opinions. For example on page 750 - "The author hoped that the enterocoel theory was dead and buried, as it deserves, but . . .". Then "The author regards the enterocoel theory as fantastic nonsence, for which there does not exist a single scrap of genuine evidence."
She criticizes views putting Proterospongia in line with the origin of sponges. She provides arguments that the anthozoans cannot be the earliest cnidarians. Both of those views are contradicted in earlier posts of this blog.
She had command of a vast amount of biology of organisms so her opinions have had considerable influence. She proposed putting several phyla in a natural grouping she named Aschelminthes. It had some acceptance until some experts in some of the groups disagreed, perhaps they thought it minimized the importance of the groups they researched. So she later abandoned the view although I think it was correct in the inclusion of most of the groups it included.
A lesson learned
The short life of many ideas and theories, changed because of varying emphasis on major or minor features, gives me pause when I think about my evolutionary ideas. I have learned from the evidence to support the coalescence of the annelid theory as correct in the connection suggested, that gross features can be important. They can also mislead, as the importance of radial versus bilateral symmetry did in forming major clusters of phyla; the transition either way among the two symmetries is eventually selected by the habit of being attached to a substrate versus having active movement over a surface. So it is difficult to state unequivocally that some parameter is the ultimate measure of the direction of relationships.
*Gould, Stephen Jay. 2002. The Structure of Evolutionary Theory. The Belknap Press of
Joseph G. Engemann March 2, 2015
Emeritus Professor of Biology, Western Michigan University
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