Part 6 Cons: Hollow Trees, Twigs Without Trunks

[jordanriver]

SO, is everyboy on board the Nested Hierarchy (or hierarchies)? It appears to have achieved ubiquitous approval, from YEC to OEC to RM/NS (that means 'random-mutation/natural-selection, in case anybody is new to this)
It has 'SCIENCE' status.

The Smithsonian says 'scientists' design it:
The Tree of Life is an ever-evolving depiction of life’s common ancestry. Scientists design the Tree of Life from careful observations and comparisons of living things. The tree shows that all organisms are related through their descent (the branches) from a common ancestor (the root).
The more structural and genetic similarities that organisms share, the more closely related they are and the closer they are on the Tree of Life.

http://www.mnh.si.edu/exhibits/darwin/treeoflife.html

and Talk Origins provides its falsifiability:

Prediction 1.2: A nested hierarchy of species
Potential Falsification:
It would be very problematic if many species were found that combined characteristics of different nested groupings. Proceeding with the previous example, some nonvascular plants could have seeds or flowers, like vascular plants, but they do not. Gymnosperms (e.g. conifers or pines) occasionally could be found with flowers, but they never are. Non-seed plants, like ferns, could be found with woody stems; however, only some angiosperms have woody stems. Conceivably, some birds could have mammary glands or hair; some mammals could have feathers (they are an excellent means of insulation). Certain fish or amphibians could have differentiated or cusped teeth, but these are only characteristics of mammals. A mix and match of characters like this would make it extremely difficult to objectively organize species into nested hierarchies.

http://www.talkorigins.org/faqs/comd...sted_hierarchy

...and then guess what happened...

Some PROKARYOTE phenomena from the 1950s splashed into the purview of laymen for the first time, HORIZONTAL GENE TRANSFER (HGT) ...AKA lateral gene transfer (LGT), with a sensationalism that only annoyed evolutionists who were already aware of that genetic mechanism.

First, in 2002

THE SCIENTIST, September 16, 2002
'Uprooting the Tree of Life' By Brendan Maher
"Comparative physiology and fossil records can take one only so far, so many researchers are trying to reach the tree of life's roots with tools of a genetic nature. Yet, the more they dig, the more convoluted those roots appear to be. Lateral gene transfer, the square peg in cellular evolution's round hole, casts doubt on the verity of the Darwinian tree with its single point of origin and straight branching. This uprooting leaves room for numerous speculations about life's origins..."
"...Horizontal gene transfer just uproots the tree of life," says Eugene V. Koonin, senior investigator, National Center for Biotechnology Information. Gene transfer has affected nearly every gene family, Koonin says, but he finds that single-gene phylogenetic construction is useful--to a point. "It will tell you the story of a gene family--the story of a gene for short--but it will not necessarily tell you the story of the organism...."
"...Put 10 theorists in a room, and 12 differing opinions will likely emerge. With ideas ranging from an endosymbiotic origin for eukaryotes to a tree depicting such complex cells as the most ancient, the kingpin of much of this discussion is (Carl)Woese, who, for the past 30-plus years, has stirred the primordial pot to bring forth evocative concepts, challenging Darwin's single-trunk tree of life and making friends and enemies along the way..."

http://www.the-scientist.com/?articl...-Tree-of-Life/

ok, so what. That was just PROKARYOTES,

as Lynn Margulis said in the same article, "It's an enormous extrapolation to say it's in the tree of life when what it is, is the tree of cytochrome oxidase or it's the tree of 16S ribosomal RNA,"

(the late Lynn Margulis--BIG NAME PLAYER, her 'Symbiotic Theory of Eukaryotic Origins' is a Biology textbook page, on p 349 of my old Ken Miller/J. Levine 1991 Biology text, a full page in the 2000 David Krogh Biology textbook, p 312 in the 2004 Campbell-Reece-Simon Essential Biology textbook, among others)

...BUT THEN guess what happened (again)
January 2009, NEW SCIENTIST spashed a big "Darwin Was Wrong" COVER STORY (with a big green tree)

NEW SCIENTIST Jan 24-30, 2009
'Why Darwin was wrong about the tree of life' 21 January 2009 by Graham Lawton
p 34
'Uprooting Darwin's Tree'
"...Darwin argued successfully that the tree of life was a fact of nature, plain for all to see though in need of explanation.The explanation he came up with was evolution by natural selection.
Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top – these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life.For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded..."
and on p 38
"...As ever more multicellular genomes are sequenced, ever more incongruous bits of DNA are turning up. Last year, for example, a team at the University of Texas at Arlington found a peculiar chunk of DNA in the genomes of eight animals – the mouse, rat, bushbaby, little brown bat, tenrec, opossum, anole lizard and African clawed frog – but not in 25 others, including humans, elephants, chickens and fish. This patchy distribution suggests that the sequence must have entered each genome independently by horizontal transfer..."

http://www.newscientist.com/issue/2692

ok, now ITS NOT JUST PROKARYOTES, now we're talking MAMMALS and REPTILES.
and just in case there were still people who didn't see that New Scientist 'Darwin Was Wrong' Cover, The Guardian UK published a sort of 'Heads-Up':

The Guardian UK Wednesday 21 January 2009
'Evolution: Charles Darwin was wrong about the tree of life'
'Evolutionary biologists say crossbreeding between species is far more common than previously thought, making a nonsense of the idea of discrete evolutionary branches'
By Ian Sample, science correspondent
"We have no evidence at all that the tree of life is a reality," Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, told New Scientist magazine"
"....The findings mean that to link species by Darwin's evolutionary branches is an oversimplification. "The tree of life is being politely buried," said Michael Rose, an evolutionary biologist at the University of California, Irvine. "What's less accepted is that our whole fundamental view of biology needs to change."

http://www.guardian.co.uk/science/20...cies-tree-life

and, just to be sure, in case some Creationists (usually politically Conservative) still missed it, the Free Republic also posted another heads-up:

'Charles Darwin's tree of life is 'wrong and misleading', claim scientists'

http://www.freerepublic.com/focus/f-news/2169993/posts

reaction?
Boyhowdie, the anti-creationists?
THEY WERE REALLY MAD.
Prof Jerry Coyne U. of Chicago even wanted a boycott of NEW SCIENTIST.
http://old.richarddawkins.net/articl...ientists-again

and not just Chicago U. prof Jerry Coyne, better yet PZ Myers U. of Minnesota-Morris Prof was unhinged (good, because he is a mocker, and good because he gave me a hard time when I didn't know any of this stuff during my first attempts blogging Talk Origins on usenet back in the 1990s) you can youtube Jerry and PZ defending 'why evolution is true'.
and immediately,

the 'Texas Citizens For Science' issued a statement:
'News of the Death of the Tree of Life Has Been Greatly Exaggerated'
(because)
"On 2009 January 22, Texas State Board of Education member Barbara Cargill told the audience in the Travis Building hearing room in Austin that there have been recent "significant challenges" to evolution that rejected Darwin's "Tree of Life."

and included the protest letter to New Scientist from the usual suspects, "four prominent evolutionary scientists and writers, Daniel Dennett, Jerry Coyne, Richard Dawkins, and PZ Myers."
http://www.texscience.org/reports/sb...e-2009feb7.htm

but the New Scientist article was not one-sided:

p 37
"In an ambitious study, a team led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, examined 191 sequenced genomes from all three domains of life – bacteria, archaea and eukaryotes (complex organisms with their genetic material packaged in a nucleus) –and identified 31 genes that all the species possessed and which showed no signs of ever having been horizontally transferred. They then generated a tree by comparing the sequences of these “core” genes in everything from E. coli to elephants. The result was the closest thing yet to the perfect tree, Bork claimed..."

(citing Science 3 March 2006: Vol. 311 no. 5765 pp. 1283-1287, 'Toward Automatic Reconstruction of a Highly Resolved Tree of Life' )
http://www.sciencemag.org/content/31.../1283.abstract

as well as the counter to the Peer Bork paper:

p 37 (still New Scientist article)
Other researchers begged to differ. Amongthem were Tal Dagan and William Martin atthe Heinrich Heine University in Düsseldorf,Germany, who pointed out that in numerical terms a core of 31 genes is almost insignificant, representing just 1 per cent of a typical bacterial genome and more like 0.1 per cent of an animal’s. That hardly constitutes a mighty oak or even a feeble sapling – more like a tiny twig completely buried by a giant web. Dagan dubbed Bork’s result “the tree of 1 per cent” and argued that the study inadvertently provided some of the best evidence yet that the tree-of-life concept was redundant (citing Genome Biology, vol 7, p 118, 'The Tree of One Percent, Dagan and Martin)

http://genomebiology.com/2006/7/10/118
AND, the New Scientist cited plenty of papers, for example, the Univ of Texas-Arlington finding was cited from PNAS
(Proceedings of the National Academy of Sciences, vol 105, p 17023 'Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods'
which reported evidence for the Horizontal Introduction of SPIN Elements (SPIN, a family of DNA transposons, called SPACE INVADERS or SPIN)
http://www.pnas.org/content/105/44/17023.full

AND not just HGT, but the article was also about natural hybridisation,

p 38 (still the New Scientist article)
“If there is a tree of life, it’s a small anomalous structure growing out of the web of life,” says John Dupré, a philosopher of biology at the University of Exeter, UK. More fundamentally, recent research suggests that the evolution of animals and plants isn’t exactly tree-like either. “There are problems even in that little corner,” says Dupré. Having uprooted the tree of unicellular life, biologists are now taking their axes to the remaining branches. For example, hybridisation clearly plays an important role in the evolution of plants. According to Loren Rieseberg, a botanist at theUniversity of British Columbia in Vancouver,Canada, around 14 per cent of living plant species are the product of the fusion of two separate lineages.

(and an insert of the article 'NATURAL CHIMERAS' cites Journal of Theoretical Biology,vol 112, p 333)

p 38
The idea that microbes regularlyswap portions of genetic code with individuals from another species doesn’t seem so far-fetched (see main story). But could the same process also have shaped the evolution of multicellular animals? In 1985, biologist Michael Syvanen of the University of California,Davis, predicted that it did.

Journal of Theoretical Biology,vol 112, p 333, 'Cross-species Gene Transfer; Implications for a New Theory of Evolution' by MICHAEL SYVANEN
"Singh, Purdom & Jones (1980) have found that a middle repetitive sequence from reptiles—a sequence that they suspect is a transposable element—cross hybridizes with sequences from fruit flies and mice."

http://www.dcn.davis.ca.us/vme/hgt/J...-343yr1985.PDF

**now it's important not to take anything in this article out of context,

as the editorial on p 5 warns, "...None of this should give succour to creationists, whose blinkered universe is doubtless with the news that "New Scientist has announced Darwin was wrong". Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not"

so, How prevalent is HGT?

MICROCOSM: E. coli AND THE NEW SCIENCE OF LIFE 2008 Carl Zimmer ISBN 9780375424304
p 112
Horizontal gene transfer not only spreads resistance genes around but also speeds up their evolution. Once a gene evolves some resistance to antibiotics, it can benefit not just its original host but other bacteria that take it up. And once in its new host, the gene can continue to undergo natural selection and become even more effective. Microbes can assemble arsenals to defend themselves against antibiotics, gathering weapons from the community of bacteria rather than just inheriting them from their ancestors.

Biologists were slow to recognize just how important the Shigella outbreak in Japan was. Horizontal gene transfer was helping to create a medical disaster, one that is continuing to unfold. At first biologists did not see much evidence of horizontal gene transfer beyond resistance to antibiotics. In the 1990s, scientists began to compare the entire genome of E. coli with that of other bacteria and make a careful search for traded genes. And when they did, our understanding of the history of life changed for good. Horizontal gene transfer, we now know, is no minor trickle of DNA. Its a flood. And it played a big part in making E. coli what it is today.
p 117
Viruses are quickly losing their reputation as insignificant parasites. They are the most abundant form of life on Earth, with a population now estimated at 1030--a billion billion trillion. Most of the diversity of life's genetic information may reside in their genomes. Within the human gut alone there are about a thousand species of viruses. As viruses pick up host genes and insert them in other hosts, they create an evolutionary matrix through which DNA can shuttle from species to species. According to one estimate, viruses in the ocean transfer genes to new hosts 2 quadrillion times every second.
p 131
...Horizontal gene transfer is common, the scientists found, but the genes usually don't survive very long in their hosts. Many of them become disabled by mutations, turning into pseudogenes. Eventually, other mutations slice the genes out of their genomes completely, and the bacteria suffers no ill effects from the loss...

(emphasis mine on how HGT also transfers pseudogenes, so that phenomena is not just vertically inherited)
AND, Not to take Carl Zimmer too much out of context, he notes that HGT is rare in humans and other animals, and that many scientists have decided that 'The Tree' still stands.

And it wasn't just New Scientist and the papers they cited in their article:
HGT apparently transfers from bacteria to animals
....remember Eugene V. Koonin from the earlier 2002 The Scientist article above, he with colleagues published another paper in 2006:

Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation
Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes.
Conclusion
The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1630690/

so how do you falsify that?

Remember the Gould citation from Part 5 'Pros':

THE STRUCTURE OF EVOLUTIONARY THEORY Stephen Jay Gould 2002 ISBN 0674006135
p 682
This fully nested hierarchy operates with Linnaean logic in requiring that lower units amalgamate completely, and under strict genealogical constraint--so that no lower unit can belong to more than one higher unit, while no higher unit can "forage" outside its hereditary line to incorporate the lower units of other distinct evolutionary branches at the same level. Just as a genus can't belong to two families, a species of flies cannot incorporate some onychophores and a few myriapods to construct a more versatile species-individual.

so one of those little nematode wormies squirts some pseudogene into two critter twigs from 'distinct evolutionary branches' and Creationists say "AH-HA! looks like there's been some "foraging" outside heriditary lines", the RM/NS advocate can just say, "ah no, that was just some HGT, just more proof of evolution"
and that Koonin paper tells us the HGT goes in both directions, how can you now tell if there was a common ancestor and you have a synapomorphic set, or if there was just an HGT event?
or that Univ of Texas-Arlington paper that reported 'SPACE INVADERS (or SPIN)' transposons in reptiles and mammals, usually inferring an ancient common ancestor, except that it was missing in 19 other mammals, violating Talk Origins falsifiability test "It would be very problematic if many species were found that combined characteristics of different nested groupings...", except for the horizontal transfer.
AND an ancient ancestor would have been inferred also (in a paper recommended by Jerry Coyne);
http://whyevolutionistrue.wordpress....gene-transfer/
a "nice five-page primer on horizontal gene transfer by Olga Zhaxybayeva and W. Ford Doolittle":

CURRENT BIOLOGY Volume 21, Issue 7, 12 April 2011, Pages R242–R246
'Lateral gene transfer' Olga Zhaxybayeva, W. Ford Doolittle
Of all known animals, only two closely-related aphid species have certain genes for carotenoid biosynthesis, genes that are otherwise common among bacteria, archaea, plants and fungi. Explaining this by differential loss would require that the last common ancestor of all animals carried these genes and that there have since been scores of independent gene losses in lineages branching off below the two aphid species. LGT would be by far the favored explanation.

http://www.sciencedirect.com/science...60982211001011

(LGT - lateral gene transfer, another name for HGT)
and in that recommendation from Jerry Coyne, from his blog 'Why Evolution is True' (named after his book cited in the Part 5 post here) Jerry makes lemonaide out of the lemon of HGT/LGT , in a post titled:

'How important is lateral gene transfer?'
This doesn’t really overturn modern evolutionary theory, since lateral gene transfer (“LGT;” also called “horizontal” gene transfer) simply introduces into a species new genetic variation from a different species; that genetic variation still must be subject to the well known processes of natural selection and genetic drift.
(and then Jerry goes on to dismiss the importance of it anyway):
Does LGT invalidate the tree of life? Since the phenomenon is far more common in bacteria than in eukaryotes, we face more serious problems in reconstructing evolutionary “histories” in the former groups. LGT makes the evolutionary history of species diverge somewhat from the evolutionary histories of their genes.

http://whyevolutionistrue.wordpress....gene-transfer/

It does get interesting though, because Michael Syvanen, cited above in the New Scientist article, (and quoted in the 'NATURAL BORN CHIMERAS' insert from the New Scientist article as concluding;
“We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”) rebuts Jerry's blog in a reply, concluding in his reply
from

Jerry Coyne's 'Why Evolution is True' blog, reply post by Michael Syvanen (Posted April 13, 2011 at 3:18 pm):
"The problem that is being revealed in this debate happens to be an insistence of the modern rules of taxonomy to force categories to obey pure tree like patterns of descent. Horizontal gene transfer is the new fact of life that makes those rules obsolete."

and HGT transfers ERVs between mammals and the Trematoda class of parasites, both in the 'Amimalia' kingdom.

Horizontal and vertical transfer of mouse endogenous retroviral DNA sequences in schistosomes.
Imase A, Kobayashi K, Ohmae H, Irie Y, Iwamura Y.
Abstract
The in situ polymerase chain reaction (PCR) results revealed that mouse type A and type C retroviral sequences were transmitted horizontally from the host to schistosomes. The signals to these retroviral sequences were observed in the nuclei of the mesenchymal and reproductive cells of 8-week Schistosoma japonicum. These signals were also detected in the nuclei of the mesenchymal and reproductive cells and in the cytoplasm of the tegumental tubercles of 24-week S. mansoni. Furthermore, mouse type A retroviral sequence was detected in the DNA extracted from the cercariae of both species. However, mouse type C retroviral sequence and mouse type 2 Alu sequence (B2) were difficult to detect in the cercarial DNA of either species. These findings may indicate that some host sequences are propagated in the schistosome progeny, that is to say, not only horizontal but also vertical transfer of the host gene may occur in schistosomes.

http://www.ncbi.nlm.nih.gov/pubmed/11085235

Look, S. japonicum infects 31 species of mammals, including HUMANS.
AND that S. mansoni infects 87 million HUMANS worldwide:

Disease Control Priorities in Developing Countries 2nd ED 2006, Dean T. Jamison, Joel G. Breman, Anthony R. Measham, George Alleyne, Mariam Claeson, David B. Evans, Prabhat Jha, Anne Mills, Philip Musgrove ISBN 0821361791
S. mansoni - 87 million - Sub-Saharan Africa, Americas
S. japonicum - 1 million - China and East Asia

http://books.google.com/books?id=ENFAAQAAIAAJ&q=mansoni

so how do you falsify shared ERVs?

Talk Origins
Prediction 4.5: Molecular evidence - Endogenous retroviruses
Potential Falsification:
It would make no sense, macroevolutionarily, if certain other mammals (e.g. dogs, cows, platypi, etc.), had these same retrogenes in the exact same chromosomal locations. For instance, it would be incredibly unlikely for dogs to also carry the three HERV-K insertions that are unique to humans, as shown in the upper right of Figure 4.4.1, since none of the other primates have these retroviral sequences.

http://www.talkorigins.org/faqs/comd...l#retroviruses

NATURE
'The Schistosoma japonicum genome reveals features of host–parasite interplay'
Three principal species can infect humans: Schistosoma japonicum, Schistosoma mansoni and Schistosoma haematobium. The first of these is prevalent in the Philippines and parts of Indonesia, and is a major disease risk for 66 million people living in southern China. It remains a major public health concern in China despite over 50 years of concerted campaigns for its control. Approximately one million people in China, and more than 1.7 million bovines and other mammals, are currently infected

http://www.nature.com/nature/journal...ture08140.html
AND the PTERV1 skipping from branch to branch like monkeys

Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans
Chris T Yohn, Zhaoshi Jiang, Sean D McGrath, Karen E Hayden, Philipp Khaitovich, Matthew E Johnson, Marla Y Eichler, John D McPherson, Shaying Zhao, Svante Pääbo, Evan E Eichler
"Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes...."
"...We designed two probes to the gag and env portions of PTERV1 and assessed the distribution of PTERV1 among apes and Old World monkeys by Southern analysis. More than 100 copies of the endogenous retrovirus were detected in each African ape and Old World monkey species. Comparison between DNA digested with methylation-sensitive and -resistant restriction enzymes indicated that most copies were extensively methylated in these species. In contrast, analysis of multiple Asian apes (siamang, gibbon, and orangutan) and a panel of human DNAs showed no hybridization signal. These findings were consistent with early DNA hybrid melting experiments and DNA hybrid electron microscopic studies that indicated that DNA from the African great apes harbored sequences homologous to both colobus monkey and baboon exogenous retroviruses while the genomes of man and Asian apes did not. These data were sometimes used as supporting evidence for an Asian origin of modern humans..."
"...The absence of PTERV1 among Asian apes and humans is shown in contrast to a generally accepted catarrhine species phylogeny."

http://www.plosbiology.org/article/i...l.pbio.0030110

IOW, according to the Nested Hierarchy, if Old World monkeys diverged from Hominoidea (African apes, Asian apes, and us humans) long before the superfamily Hominoidea began to diverge, and PTERV1 is in both Hominoidea groups and Old World monkeys, then the common ancestor of both groups must have carried the PTERV1, but somehow it missed some of its descendants in the Hominoidea group, the Asian apes and us Humans.

But that does not mean falsification, nope, it just assumes HGT.
so you find 'shared' ERVs in humans and some non-primate mammal, but not in another primate which would have a more recent common ancestor with humans than with bovines ...so what?
And the 'glue' of the 'Tree', synapomorphies aren't all that consistant, not all of the descendants of the 'last ancestor' will carry the synapomorphic trait:

Cladistics: The Theory and Practice of Parsimony Analysis 2nd ED 1998 Ian J. Kitching ISBN 0198501382
p 62-64
'Underlying synapomorphy'
p 62-64
Perhaps the most idiosyncratic model of character change is that of underlying synapomorphy. Championed by Ole Saether, underlying synapomorphy is defined as 'close parallelism as a result of common inherited genetic factors causing incomplete synapomorphy' of 'the inherited potential to develop parallel similarities', although this potential may not be realized in all descendants. (emphasis mine jordanriver) Consequently, it refers to the occurence of synapomorphies in only some members of a putative monophyletic group. Consider a highly simplified cladogram of the Bilateria. Haemoglobin is known to occur in only three of the many lineages: Tubifex worms, some chironomid midges and vertebrates. The application of standard optimization methods would lead us to conclude that haemoglobin had been independently derived three times. However, the amino-acid sequences in the three groups are all very similar and it would seem most unlikely that such a complex molecule could have arisen de novo on three separate occasions. Underlying synapomorphy would assert that we are mistaken when we code the other taxa as lacking haemoglobin. These taxa all possess the relevant gene, but the genes are switched off because it is simply not selectively advantageous for them to be active. It is this unexpressed capacity to develop a feature that is the underlying synapomorphy. Thus, in this example, the potential 'capacity' (expressed or not) to manufacture haemoglobin can be used to unite all the taxa in Fig. 3.12 (Tubifex, other annelids, other insects, Chironomidae, Vertebrata) into a monophyletic group.
Saether argued that the use of underlying synapomorphies had been advocated by Hennig (1966), who called them homoiologies. However, Hennig considered homoiology to be equivalent to convergence, which he specifically rejected as a valid tool for estimating cladistic relationships. It may indeed be true that the haemoglobin gene occurs in all taxa in Fig. 3.12. However, the monopoly of the Bilateria cannot be supported by only scattered occurences of an expressed gene, for this is using the absence of information (observations, characters) as evidence for groups. By invoking ad hoc hypothesis to explain away conflict in the data as 'unexpressed', underlying synapomorphies provide a licence to group in any way whatsoever. While it is perfectly acceptable to use the occurence of haemoglobin in Tubifex worms, chironomid midges and vertebrates as evidence of the monopoly of each group separately, the distribution of this character does not provide evidential support for the monopoly of the Bilateria as a whole. It may eventually be possible to detect an unexpressed gene directly using nucleotide sequencing or another molecular technique. But if we found such an inactive gene, then it would be coded as present and would no longer be an underlying synapomorphy.

so how do you know if your synapomorphic trait (shared derived trait) is not actually an autapomorphy (derived trait, not shared). if you don't have access to the 'common ancestor'.

is it still in Karl Popper's science category?

*disclaimer* this does not invalidate Nested Hierarchies, but in the adherence of Biblical Hermeneutics, avoiding interpretation contrary to scientific or historical truth, the idea that the observation of Nested Hierarchies and ERVs are classic tests for evolution, needs no longer be taken into consideration....

[oxmixmudd]

SO, is everyboy on board the Nested Hierarchy (or hierarchies)? It appears to have achieved ubiquitous approval, from YEC to OEC to RM/NS (that means 'random-mutation/natural-selection, in case anybody is new to this)
It has 'SCIENCE' status.

http://www.mnh.si.edu/exhibits/darwin/treeoflife.html

and Talk Origins provides its falsifiability:

http://www.talkorigins.org/faqs/comd...sted_hierarchy

...and then guess what happened...

Some PROKARYOTE phenomena from the 1950s splashed into the purview of laymen for the first time, HORIZONTAL GENE TRANSFER (HGT) ...AKA lateral gene transfer (LGT), with a sensationalism that only annoyed evolutionists who were already aware of that genetic mechanism.

First, in 2002

http://www.the-scientist.com/?articl...-Tree-of-Life/

ok, so what. That was just PROKARYOTES, (the late Lynn Margulis--BIG NAME PLAYER, her 'Symbiotic Theory of Eukaryotic Origins' is a Biology textbook page, on p 349 of my old Ken Miller/J. Levine 1991 Biology text, a full page in the 2000 David Krogh Biology textbook, p 312 in the 2004 Campbell-Reece-Simon Essential Biology textbook, among others)

...BUT THEN guess what happened (again)
January 2009, NEW SCIENTIST spashed a big "Darwin Was Wrong" COVER STORY (with a big green tree)

http://www.newscientist.com/issue/2692

ok, now ITS NOT JUST PROKARYOTES, now we're talking MAMMALS and REPTILES.
and just in case there were still people who didn't see that New Scientist 'Darwin Was Wrong' Cover, The Guardian UK published a sort of 'Heads-Up':

http://www.guardian.co.uk/science/20...cies-tree-life

and, just to be sure, in case some Creationists (usually politically Conservative) still missed it, the Free Republic also posted another heads-up:

http://www.freerepublic.com/focus/f-news/2169993/posts

reaction?
Boyhowdie, the anti-creationists?
THEY WERE REALLY MAD.
Prof Jerry Coyne U. of Chicago even wanted a boycott of NEW SCIENTIST.
http://old.richarddawkins.net/articl...ientists-again

and not just Chicago U. prof Jerry Coyne, better yet PZ Myers U. of Minnesota-Morris Prof was unhinged (good, because he is a mocker, and good because he gave me a hard time when I didn't know any of this stuff during my first attempts blogging Talk Origins on usenet back in the 1990s) you can youtube Jerry and PZ defending 'why evolution is true'.
and immediately,
and included the protest letter to New Scientist from the usual suspects, "four prominent evolutionary scientists and writers, Daniel Dennett, Jerry Coyne, Richard Dawkins, and PZ Myers."
http://www.texscience.org/reports/sb...e-2009feb7.htm

but the New Scientist article was not one-sided:
(citing Science 3 March 2006: Vol. 311 no. 5765 pp. 1283-1287, 'Toward Automatic Reconstruction of a Highly Resolved Tree of Life' )
http://www.sciencemag.org/content/31.../1283.abstract

as well as the counter to the Peer Bork paper:

http://genomebiology.com/2006/7/10/118
AND, the New Scientist cited plenty of papers, for example, the Univ of Texas-Arlington finding was cited from PNAS
(Proceedings of the National Academy of Sciences, vol 105, p 17023 'Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods'
which reported evidence for the Horizontal Introduction of SPIN Elements (SPIN, a family of DNA transposons, called SPACE INVADERS or SPIN)
http://www.pnas.org/content/105/44/17023.full

AND not just HGT, but the article was also about natural hybridisation,

(and an insert of the article 'NATURAL CHIMERAS' cites Journal of Theoretical Biology,vol 112, p 333)


http://www.dcn.davis.ca.us/vme/hgt/J...-343yr1985.PDF

**now it's important not to take anything in this article out of context,

so, How prevalent is HGT?

(emphasis mine on how HGT also transfers pseudogenes, so that phenomena is not just vertically inherited)
AND, Not to take Carl Zimmer too much out of context, he notes that HGT is rare in humans and other animals, and that many scientists have decided that 'The Tree' still stands.

And it wasn't just New Scientist and the papers they cited in their article:
HGT apparently transfers from bacteria to animals
....remember Eugene V. Koonin from the earlier 2002 The Scientist article above, he with colleagues published another paper in 2006:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1630690/

so how do you falsify that?

Remember the Gould citation from Part 5 'Pros':

so one of those little nematode wormies squirts some pseudogene into two critter twigs from 'distinct evolutionary branches' and Creationists say "AH-HA! looks like there's been some "foraging" outside heriditary lines", the RM/NS advocate can just say, "ah no, that was just some HGT, just more proof of evolution"
and that Koonin paper tells us the HGT goes in both directions, how can you now tell if there was a common ancestor and you have a synapomorphic set, or if there was just an HGT event?
or that Univ of Texas-Arlington paper that reported 'SPACE INVADERS (or SPIN)' transposons in reptiles and mammals, usually inferring an ancient common ancestor, except that it was missing in 19 other mammals, violating Talk Origins falsifiability test "It would be very problematic if many species were found that combined characteristics of different nested groupings...", except for the horizontal transfer.
AND an ancient ancestor would have been inferred also (in a paper recommended by Jerry Coyne);
http://whyevolutionistrue.wordpress....gene-transfer/
a "nice five-page primer on horizontal gene transfer by Olga Zhaxybayeva and W. Ford Doolittle":

http://www.sciencedirect.com/science...60982211001011

(LGT - lateral gene transfer, another name for HGT)
and in that recommendation from Jerry Coyne, from his blog 'Why Evolution is True' (named after his book cited in the Part 5 post here) Jerry makes lemonaide out of the lemon of HGT/LGT , in a post titled:

http://whyevolutionistrue.wordpress....gene-transfer/

It does get interesting though, because Michael Syvanen, cited above in the New Scientist article, (and quoted in the 'NATURAL BORN CHIMERAS' insert from the New Scientist article as concluding;
“We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”) rebuts Jerry's blog in a reply, concluding in his reply
from
and HGT transfers ERVs between mammals and the Trematoda class of parasites, both in the 'Amimalia' kingdom.

http://www.ncbi.nlm.nih.gov/pubmed/11085235

Look, S. japonicum infects 31 species of mammals, including HUMANS.
AND that S. mansoni infects 87 million HUMANS worldwide:

http://books.google.com/books?id=ENFAAQAAIAAJ&q=mansoni

so how do you falsify shared ERVs?

http://www.talkorigins.org/faqs/comd...l#retroviruses


http://www.nature.com/nature/journal...ture08140.html
AND the PTERV1 skipping from branch to branch like monkeys

http://www.plosbiology.org/article/i...l.pbio.0030110

IOW, according to the Nested Hierarchy, if Old World monkeys diverged from Hominoidea (African apes, Asian apes, and us humans) long before the superfamily Hominoidea began to diverge, and PTERV1 is in both Hominoidea groups and Old World monkeys, then the common ancestor of both groups must have carried the PTERV1, but somehow it missed some of its descendants in the Hominoidea group, the Asian apes and us Humans.

But that does not mean falsification, nope, it just assumes HGT.
so you find 'shared' ERVs in humans and some non-primate mammal, but not in another primate which would have a more recent common ancestor with humans than with bovines ...so what?
And the 'glue' of the 'Tree', synapomorphies aren't all that consistant, not all of the descendants of the 'last ancestor' will carry the synapomorphic trait:



so how do you know if your synapomorphic trait (shared derived trait) is not actually an autapomorphy (derived trait, not shared). if you don't have access to the 'common ancestor'.

is it still in Karl Popper's science category?

*disclaimer* this does not invalidate Nested Hierarchies, but in the adherence of Biblical Hermeneutics, avoiding interpretation contrary to scientific or historical truth, the idea that the observation of Nested Hierarchies and ERVs are classic tests for evolution, needs no longer be taken into consideration....

Nice post, very interesting - at least the information itself. I would tend to think that as relates to the 'tree of life' in 'higher' species, HGT represents noise that would prevent resolution below a certain level, much like graininess in a photograph. I would think it a stretch to say it 'undoes' the concept of a 'tree of life', if one might be motivated to say such a thing, because the majority of the genetic information in these higher species does form a very robust nested hierarchy. And even these retro-viral insertions tend to be nested, in spite of the anomalies here mentioned. It could be a 'problem' for the tree of life concept IF large blurring of the lines of descent were discovered. So far, the very fact this kind of thing has not resulted in large anomalous deviations when comparisons of theoretically related genomes (e.g. chimpanzee and human) have be done would support the hypothesis it is more in the noise than the signal.


Jim

[jordanriver]

Nice post, very interesting - at least the information itself.

Jim

Thank you, Oxmix.
(And Thank you TWEB for providing a forum to post this information I found)
My motivation is to try to do my share, providing information to creationists as they provide information to me. I want more informed creationists.

I hope I was able to provide both sides of arguments, before offering my own opinion. Others can read both sides and decide for themselves which pile of evidence is more compelling. If I left out anything in the 'pro's', sides, ...well, this is TWEB, somebody will post it.

jr

[Debbaux]

SO, is everyboy on board the Nested Hierarchy (or hierarchies)? It appears to have achieved ubiquitous approval, from YEC to OEC to RM/NS (that means 'random-mutation/natural-selection, in case anybody is new to this)
It has 'SCIENCE' status.

http://www.mnh.si.edu/exhibits/darwin/treeoflife.html

and Talk Origins provides its falsifiability:

http://www.talkorigins.org/faqs/comd...sted_hierarchy

...and then guess what happened...

Some PROKARYOTE phenomena from the 1950s splashed into the purview of laymen for the first time, HORIZONTAL GENE TRANSFER (HGT) ...AKA lateral gene transfer (LGT), with a sensationalism that only annoyed evolutionists who were already aware of that genetic mechanism.

First, in 2002

http://www.the-scientist.com/?articl...-Tree-of-Life/

ok, so what. That was just PROKARYOTES, (the late Lynn Margulis--BIG NAME PLAYER, her 'Symbiotic Theory of Eukaryotic Origins' is a Biology textbook page, on p 349 of my old Ken Miller/J. Levine 1991 Biology text, a full page in the 2000 David Krogh Biology textbook, p 312 in the 2004 Campbell-Reece-Simon Essential Biology textbook, among others)

...BUT THEN guess what happened (again)
January 2009, NEW SCIENTIST spashed a big "Darwin Was Wrong" COVER STORY (with a big green tree)

http://www.newscientist.com/issue/2692

ok, now ITS NOT JUST PROKARYOTES, now we're talking MAMMALS and REPTILES.
and just in case there were still people who didn't see that New Scientist 'Darwin Was Wrong' Cover, The Guardian UK published a sort of 'Heads-Up':

http://www.guardian.co.uk/science/20...cies-tree-life

and, just to be sure, in case some Creationists (usually politically Conservative) still missed it, the Free Republic also posted another heads-up:

http://www.freerepublic.com/focus/f-news/2169993/posts

reaction?
Boyhowdie, the anti-creationists?
THEY WERE REALLY MAD.
Prof Jerry Coyne U. of Chicago even wanted a boycott of NEW SCIENTIST.
http://old.richarddawkins.net/articl...ientists-again

and not just Chicago U. prof Jerry Coyne, better yet PZ Myers U. of Minnesota-Morris Prof was unhinged (good, because he is a mocker, and good because he gave me a hard time when I didn't know any of this stuff during my first attempts blogging Talk Origins on usenet back in the 1990s) you can youtube Jerry and PZ defending 'why evolution is true'.
and immediately,
and included the protest letter to New Scientist from the usual suspects, "four prominent evolutionary scientists and writers, Daniel Dennett, Jerry Coyne, Richard Dawkins, and PZ Myers."
http://www.texscience.org/reports/sb...e-2009feb7.htm

but the New Scientist article was not one-sided:
(citing Science 3 March 2006: Vol. 311 no. 5765 pp. 1283-1287, 'Toward Automatic Reconstruction of a Highly Resolved Tree of Life' )
http://www.sciencemag.org/content/31.../1283.abstract

as well as the counter to the Peer Bork paper:

http://genomebiology.com/2006/7/10/118
AND, the New Scientist cited plenty of papers, for example, the Univ of Texas-Arlington finding was cited from PNAS
(Proceedings of the National Academy of Sciences, vol 105, p 17023 'Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods'
which reported evidence for the Horizontal Introduction of SPIN Elements (SPIN, a family of DNA transposons, called SPACE INVADERS or SPIN)
http://www.pnas.org/content/105/44/17023.full

AND not just HGT, but the article was also about natural hybridisation,

(and an insert of the article 'NATURAL CHIMERAS' cites Journal of Theoretical Biology,vol 112, p 333)


http://www.dcn.davis.ca.us/vme/hgt/J...-343yr1985.PDF

**now it's important not to take anything in this article out of context,

so, How prevalent is HGT?

(emphasis mine on how HGT also transfers pseudogenes, so that phenomena is not just vertically inherited)
AND, Not to take Carl Zimmer too much out of context, he notes that HGT is rare in humans and other animals, and that many scientists have decided that 'The Tree' still stands.

And it wasn't just New Scientist and the papers they cited in their article:
HGT apparently transfers from bacteria to animals
....remember Eugene V. Koonin from the earlier 2002 The Scientist article above, he with colleagues published another paper in 2006:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1630690/

so how do you falsify that?

Remember the Gould citation from Part 5 'Pros':

so one of those little nematode wormies squirts some pseudogene into two critter twigs from 'distinct evolutionary branches' and Creationists say "AH-HA! looks like there's been some "foraging" outside heriditary lines", the RM/NS advocate can just say, "ah no, that was just some HGT, just more proof of evolution"
and that Koonin paper tells us the HGT goes in both directions, how can you now tell if there was a common ancestor and you have a synapomorphic set, or if there was just an HGT event?
or that Univ of Texas-Arlington paper that reported 'SPACE INVADERS (or SPIN)' transposons in reptiles and mammals, usually inferring an ancient common ancestor, except that it was missing in 19 other mammals, violating Talk Origins falsifiability test "It would be very problematic if many species were found that combined characteristics of different nested groupings...", except for the horizontal transfer.
AND an ancient ancestor would have been inferred also (in a paper recommended by Jerry Coyne);
http://whyevolutionistrue.wordpress....gene-transfer/
a "nice five-page primer on horizontal gene transfer by Olga Zhaxybayeva and W. Ford Doolittle":

http://www.sciencedirect.com/science...60982211001011

(LGT - lateral gene transfer, another name for HGT)
and in that recommendation from Jerry Coyne, from his blog 'Why Evolution is True' (named after his book cited in the Part 5 post here) Jerry makes lemonaide out of the lemon of HGT/LGT , in a post titled:

http://whyevolutionistrue.wordpress....gene-transfer/

It does get interesting though, because Michael Syvanen, cited above in the New Scientist article, (and quoted in the 'NATURAL BORN CHIMERAS' insert from the New Scientist article as concluding;
“We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”) rebuts Jerry's blog in a reply, concluding in his reply
from
and HGT transfers ERVs between mammals and the Trematoda class of parasites, both in the 'Amimalia' kingdom.

http://www.ncbi.nlm.nih.gov/pubmed/11085235

Look, S. japonicum infects 31 species of mammals, including HUMANS.
AND that S. mansoni infects 87 million HUMANS worldwide:

http://books.google.com/books?id=ENFAAQAAIAAJ&q=mansoni

so how do you falsify shared ERVs?

http://www.talkorigins.org/faqs/comd...l#retroviruses


http://www.nature.com/nature/journal...ture08140.html
AND the PTERV1 skipping from branch to branch like monkeys

http://www.plosbiology.org/article/i...l.pbio.0030110

IOW, according to the Nested Hierarchy, if Old World monkeys diverged from Hominoidea (African apes, Asian apes, and us humans) long before the superfamily Hominoidea began to diverge, and PTERV1 is in both Hominoidea groups and Old World monkeys, then the common ancestor of both groups must have carried the PTERV1, but somehow it missed some of its descendants in the Hominoidea group, the Asian apes and us Humans.

But that does not mean falsification, nope, it just assumes HGT.
so you find 'shared' ERVs in humans and some non-primate mammal, but not in another primate which would have a more recent common ancestor with humans than with bovines ...so what?
And the 'glue' of the 'Tree', synapomorphies aren't all that consistant, not all of the descendants of the 'last ancestor' will carry the synapomorphic trait:



so how do you know if your synapomorphic trait (shared derived trait) is not actually an autapomorphy (derived trait, not shared). if you don't have access to the 'common ancestor'.

is it still in Karl Popper's science category?

*disclaimer* this does not invalidate Nested Hierarchies, but in the adherence of Biblical Hermeneutics, avoiding interpretation contrary to scientific or historical truth, the idea that the observation of Nested Hierarchies and ERVs are classic tests for evolution, needs no longer be taken into consideration....

It would take me months to read through and digest all of this. Do you have an 'Executive Sumary'?

[jordanriver]

It would take me months to read through and digest all of this. Do you have an 'Executive Sumary'?

I guess the summary would be my words without the citations. My words don't amount to much more than a page, just little comments about what the citations say.
And as far as that goes, if you think the citations are big, you should have seen the books they came from. Compared to the sources, with what little I took from them, I'm practically quote-mining

Its really a pretty condensed version of a decades long story.

jr