Saša Knežević: ENDOGENI RETROVIRUSI – DOKAZ MAKROEVOLUCIJE? Ок. пост

[Zoran Đurović]

 

 

 

 

Saša Knežević: ENDOGENI RETROVIRUSI – DOKAZ MAKROEVOLUCIJE?

 

 

 

Šta su endogeni virusi i kakav su oni dokaz za evoluciju je tema o kojoj ćemo u ovom postu raspravljati.

Na netu još uvek se mogu naći tekstovi o endogenim »virusima« koji dokazuju makroevoluciju. Osnovna ideja je da su jednom u prošlosti »virusi« napali određenu vrstu, preko polnih ćelija se fiksirali u gene i (sada kao marker koji dokazuje makroevoluciju) preneli se na novu vrstu zajedno sa ostlim genomom, radi čega mi možemo da iskonstruišemo »genetsko stablo« i dokažemo koja se vrsta razvila od koje. Tako hipoteza, tako teorija.

Kako ta logika zvuči, sledi:

Npr: ... In humans, endogenous retroviruses occupy about 1% of the genome, in total constituting ~30,000 different retroviruses embedded in each person's genomic DNA (Sverdlov 2000). There are at least seven different known instances of common retrogene insertions between chimps and humans, and this number is sure to grow as both these organism's genomes are sequenced (Bonner et al. 1982; Dangel et al. 1995; Svensson et al. 1995; Kjellman et al. 1999; Lebedev et al. 2000; Sverdlov 2000). Figure 4.4.1 shows a phylogenetic tree of several primates, including humans, from a recent study which identified numerous shared endogenous retroviruses in the genomes of these primates (Lebedev et al. 2000). The arrows designate the relative insertion times of the viral DNA into the host genome. All branches after the insertion point (to the right) carry that retroviral DNA - a reflection of the fact that once a retrovirus has inserted into the germ-line DNA of a given organism, it will be

 

 

http://www.talkorigins.org/faqs/comdesc/section4.html

Da ovu priču iliti dokaz o makroevoluciji završimo, bilo bi u stvari dovoljno da shvatimo šta nam wikipedija kaže o tim »virusima«. Jer samo wikipedija potvrđuje/priznaje gore izložena logika nije o.k. prvenstveno zbog činjenice da su jedno virusi a drugo transpozabilni retroelementi ...

 

 

Na Wikipediji čitamo šta su ENDOGENI VIRUSI:

Endogenous retroviruses (ERVs) are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome (lower estimates of ~1%).[1][2] ERVs are a subclass of a type of gene called a transposon, which can be packaged and moved within the genome to serve a vital role in gene expression and in regulation.[3][4] They are distinguished as retrotransposons, which are Class I elements.[5] Researchers have suggested that retroviruses evolved from a type of transposable gene called a retrotransposon, which includes ERVs; these genes can mutate and instead of moving to another location in the genome they can become exogenous or pathogenic. This means that not all ERVs may have originated as an insertion by a retrovirus but that some may have been the source for the genetic information in the retroviruses they resemble.[6] When integration of viral DNA occurs in the germ-line, it can give rise to an ERV, which can later become fixed in the gene pool of the host population.[1][7]

https://en.wikipedia.org/wiki/Endogenous_retrovirus

 

 

Verujem da je ovo mnogima nejasno i da je potrebno objašnjenje.

Ovde, kod ove makroevolucionističke hipoteze (nekada je to bila KRUNSKI DOKAZ MAKROEVOLUCIJE), su bitne tri stvari – 1.) reč je o virusima, 2.) oni se endogeniziraju i 3.) dokazuju makroevoluciju pošto je prosto statistički nemoguće da su se ti »virusi« preko napada endogenizirali na istom (orthologous) mestu u genomu dvaju vrsta ...

Međutim, sve tri tvrdnje su vremenom pobijene. Krenimo redom.

Virusi – kad ćujemo tu reč – pomislimo na nešto loše. Najmanje što možemo da se nadamo je da ćemo, ako se zarazimo sa nekim virusom, biti zdravi. Ali ovi »virusi« u DNK bez obzira što podsećaju na viruse, ne samo što nas neće »oboriti sa nogu«, već bez njih ni jedna vrsta neće moće da opstane. Oni imaju jako važnu funkciju u razvoju bića i nisu »smeće« ili deo »junk DNK« koji se nakupio kroz evoluciju. Oni su jako bitan deo našeg genoma. Oni imaju jaku bitnu arhitektonsku ulogu u genomu. Ako bi ih uklonili iz genoma jednog bića, to biće bilo bi osuđeno na mučeničku smrt. Zato je pravilnije ove viruse zvati »retroelementi«.

Navedimo nekoliko izvora. U članku  R. von Sternberg,a J.A. Shapiro: Retrotransposable Elements, Retrotransposition and Genome Evolution...

 

http://shapiro.bsd.uchicago.edu/Sternberg&Shapiro2005.pdf

navode se funkcije tih elemenata, kao:

-providing promoter and enhancer activity to modulating transcript elongation,

- targeting mRNA to specific tissues,

- stimulating mRNA translation,

- providing replication origin recognition sequences,

- contributing to pericentromeric heterochromatin,

- serving as telomere caps, nucleating heterochromatin in chromosome arms,

- supplying chromatin boundary signals,

- providing S/MAR attachment sites.

 

 

U svakoj vrsti, tvrde autori, ovi elementi odgovorni su sa »organizaciju« genoma: Taxonomically-specific genome system architecture... genome is a hierarchically organized data storage system formatted by repetitive DNA sequence elements. This implies that each organism has a genome system architecture, in the same way that each computer has a characteristic architecture. In the computer example, architecture depends upon the operating system and hardware that are used, not upon the content of each data file. Macintosh, Windows and Unix machines can all display the same images and text files, even though the data retrieval paths are operationally quite distinct. Similarly, many protein and RNA sequences (data files) are conserved through evolution, but different taxa organize and format their genomes in quite different ways for replication, transmission and expression. An overall system architecture is required since these processes must be coordinated to operate without mutual interference. DNA segments must be in the right place at the right time for function. In other words, the genome must be organized in space and time for operation ... (str. 4)

Retroelements are important components of the cellular apparatus for chromosome replication and distribution (e.g. origins, centromeres and telomeres). Accordingly, we predict that significant changes in the retroelements that format genome maintenance and transmission can lead to reproductive isolation, thereby setting the stage for subsequent clade-restricted changes in phenotype. In other words, we suggest that key adaptive events can initiate within the retroelement portion of the genome. (str. 7)

 

 

 Retroelements and other DNA repeats provide the physical basis within the genome for functional integration. Dispersed regulatory sites of the kind provided by retrotransposons connect unlinked coding sequences into coordinately controlled subsystems. Similarly, replication and genome transmission processes are organized by elements carrying generic signals for origins, telomeres, centromeres and other structures essential to genome maintenance ... (str. 7)

A kao zaključak, autori čak najavljuju kraj koncepta »junk DNA«, koji će potvrditi ENCODE program 7 godina kasnije – naime da gotovo ni jedan nukleotid u arhitekturi našeg genoma nije tamo slučajno, jer ima svoju funkciju – a to znači da je praktički nemoguće da bi neki »strani« element tamo zalutao:

... As we increasingly apply computational metaphors to cellular function, we expect that a deeper understanding of retroelements and other repeats, the integrative fraction of cellular DNA, will lead to increased understanding of the logical architecture inherent to genome organization. In the era of biocomputing and systems biology, the study of cellular information processing promises to revolutionize not only the life sciences but also the information sciences. We anticipate learning powerful new computational paradigms as we come to understand how cells use myriad molecular components to regulate millions of biochemical events that occur every minute of every cell cycle. Our expectation is that, one day, we will think of what used to be called “junk DNA” as a critical component of truly “expert” cellular control regimes.

 

 

 

Dalje vredi poslušati autora tog članka : Richard Sternberg - Endogenous Retroviruses Debunk - https://www.youtube.com/watch?v=SrEOe2E0Euc&list=WL&index=55

 

 

... Utvrđeno je, da su ti elementi jako bitni kot razvoja placente kao i u embrionalnom razvoju zametka ili ploda. Ako ove »viruse« blokiramo, razvoj bića (embriogeneza) staje na stadiju 4 ćelije!

Zato je prosto nemoguće tvrditi da su ti elementi virusi, a još gore da su došli sa spolja, jer bi onda ovo biće moralo najpre da SE ZARAZI da bi uopšte moglo da se rodi ... što je veliki non-sense.

2.) Da li su oni endogeni ili eksogeni, to jest da li su ti elementi došli sa vana ili obratno o tom rasuđuje sledeći članak: The Natural History of Retroviruses https://answersingenesis.org/genetics/the-natural-history-of-retroviruses/ (I sama definicija na wikipediji to tvrdi – ti elementi se eksogeniziraju, a ne endogeniziraju)

A kod tačke 3.) moraćemo malo duže da se zadržimo.

Da, tačno je. Utvrđeno je da nekoliko identičnih elemenata HERV-K nalazimo na istim pozicijama kod šimpanza i čoveka. Uzećemo podatak sa Talks origin – 7 od 30.000!

Ovde treba najpre reći da je jedno stvar »common ancestor« i druga »common design«. Jedna štala u Donjim Pofalićima imaće vrata i prozore, ali to ne znaći da je Hotel Hayat kod Baščaršije, koji takođe ima vrata i prostore, nastao od štale. Ne, to samo znaći da ove dve zgrade imaju u određenom delu zajednički dizajn. Još je manje to moguće tvrditi kad utvrdimo da su materijal (npr. cigla, malter, kreč), arhitektura, stil gradnje, vreme, vlastnik itd. dve različite stvari – U našem slučaju se time bavi komparativna genetika.

Prva stvar koju nas može kod gornjeg podatka zbuniti je neverovatan disbalans. Ako imaju čovek i šimpanz zajedničkih 99% genoma – to je mit star nekoliko decenija – novija istraživanja potvrđuju samo 92% sličnost ....

http://www.evolutionnews.org/2017/01/fake_science_ab103399.html

ili http://www.discovery.org/multimedia/audio/2016/11/how-chimps-and-humans-are-different-pt-1-the-genome/

 

 

– jer taj genom »se razvijao« kroz »milione godina« (kako tvrde evolucionisti), bilo bi logično da i dele i 92% tih elemenata, a ne samo 0,0023%!

Drugo. Ako ta logika važi – to jest da su ljudi postali od šimpanza a ovaj od gorile – zašto onda gorila i šimpanz imaju jedan zajednički HERV-K, a čovek nema?

A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans. https://www.ncbi.nlm.nih.gov/pubmed/11378389

We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus...

 

 

Ono što bi moralo potvrditi zajedničkog pretka, sada ga odbacuje. A to je u neku ruku FORENZIČKA EKSPERTIZA. Jer jedno je kada Megan Foks tvrdi da sam ja otac njene troje dece i tuži me za neplaćanje alimentacije, a drugo je kada sudska medicina utvrdi ko je istinski otac ... (Uostalom, ja se ne bih branio Megan Fox)

Taj disbalans mogli bi objasniti i drugačije. Ovih 7 virusa je zajedničkih, a ostalih 29.993 je »napalo« vrstu čoveka posle razilaženja (divergencije) šimpanza i čoveka pre 5 mio godina.

A ovo je još gore. Jer ispada da se svaki takav napad virusa dešavao u proseku na 160 godina.

Ako uzmemo (evolucionističku) pretpostavku da članova ljudske populacije nikada (po evolucionističkim modelima) nije bilo manje od 10.000, da su oni živeli u nekom zatvorenom sistemu gde je svaka jedinka imala otprilike istu verovatnoću da prenese svoje gene na potomstvo, za fiksaciju jednog ovog virusa – uzmimo algoritam Motto Kimura i Tomoko Ohta – trebalo bi nam 40.000 generacija ili otprilike 800.000 godina (generacija je na 20 godina) … Iliti za 29.993 virusa to iznosi  23.994.400.000 godina (ili 24 milijarde godina …

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1212239/pdf/763.pdf

(Još da kažemo da ni jedna ni druga ni treća pretpostavka nisu realne. Jer kao prvo »virus« verovatno ne donosi »selektivnu prednost«, već obratno –  drugo, populacija vrsta koje nemaju nemaju negativnog korektiva (to jest nalaze se na vrhu »prehrambenog lanca«) nikad nisu kontantne, jer se one množe eksponencijalno dok ne iscpre resurse i kolapsiraju (ovo nam otprilike i obećava zadnja knjiga Svetog Pisma – Apokalipsis), i treće, ljudi se ne sparuju svak sa svakim ili »na lutriji« (ili slučajno), npr. Srbi se ne mešaju sa Albancima, jevreji sa muslimanima ...)

Iz svega toga proizlazi da je fiksacija bilo koje promene genoma ili »mutacije« u jednog vrsti kao čovek tehnički/matematički neizračunljiva, a sa ograničenim pretpostavkama čak suluda.

Npr. ako koristite MENDELJEV KALKULATOR http://mendelsaccount.sourceforge.net/ možete sami da proverite i računate koliko je realno potrebno vremena za bilo koju fiksaciju.

Na primer za samo jednu pozitivnu mutaciju od promene dva nukleotida i fiksaciju trebalo 84 mio godina, a za promenu 5 nukleotida 2 milijarde godina!

Biologically realistic numerical simulations revealed that a population of this type required inordinately long waiting times to establish even the shortest nucleotide strings. To establish a string of two nucleotides required on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. We found that waiting times were reduced by higher mutation rates, stronger fitness benefits, and larger population sizes. However, even using the most generous feasible parameters settings, the waiting time required to establish any specific nucleotide string within this type of population was consistently prohibitive ...

John Sanford, Wesley Brewer, Franzine Smith and John Baumgardner: THE WAITING TIME PROBLEM IN A MODEL HOMININ POPULATION http://tbiomed.biomedcentral.com/articles/10.1186/s12976-015-0016-z

 

 

Došli smo do čuvenog »GENEALOŠKOG STABLA«. Na gornjem prikazu iscrtano je jedno ovakvo drvo, skonstruisano na osnovu evolucionističe pretpostavke o endogenim »virusima« - o kojima smo upravo rekli da nisu ni virusi, a još manje da su se endogenizirali. Samo zbog te činjenice je taj crtež falsifikat, jer pretpostavlja da su retroelementi endogenizirali virusi – a znamo da nisu. (A i matematički ova priča ne drži vodu).

 

 

No, pretpostavimo da je ovo stablo tačno. Radi eksperimenta. Ako je tačno, to bi trebalo da potvrde i drugi »nalazi/analize«.

U članku koji se bavi ovim problemom Problem 6: Molecular Biology Has Failed to Yield a Grand "Tree of Life" http://www.evolutionnews.org/2015/02/problem_6_molec091151.html čitamo:

...When fossils failed to demonstrate that animals evolved from a common ancestor, evolutionary scientists turned to another type of evidence -- DNA sequence data -- to demonstrate a tree of life. In the 1960s, around the time the genetic code was first understood, biochemists Cmile Zuckerkandl and Linus Pauling hypothesized that if DNA sequences could be used to produce evolutionary trees -- trees that matched those based upon morphological or anatomical characteristics -- this would furnish "the best available single proof of the reality of macro-evolution."99 Thus began a decades-long effort to sequence the genes of many organisms and construct "molecular" based evolutionary ("phylogenetic") trees. The ultimate goal has been to construct a grand "tree of life," showing how all living organisms are related through universal common ancestry.

 

 

The Main Assumption

 

The basic logic behind building molecular trees is relatively simple. First, investigators choose a gene, or a suite of genes, found across multiple organisms. Next, those genes are analyzed to determine their nucleotide sequences, so the gene sequences of various organisms can then be compared. Finally, an evolutionary tree is constructed based upon the principle that the more similar the nucleotide sequence, the more closely related the species. A paper in the journal Biological Theory puts it this way:

[M]olecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness.100

This assumption is essentially an articulation of a major feature of the theory - the idea of universal common ancestry. Nonetheless, it's important to realize that it is a mere assumption to claim that genetic similarities between different species necessarily result from common ancestry.

Operating strictly within a Darwinian paradigm, these assumptions flow naturally. As the aforementioned Biological Theory paper explains, the main assumption underlying molecular trees "derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change."101 So the theory is assumed to be true to construct a tree. But also, if Darwinian evolution is true, construction of trees using different sequences should reveal a reasonably consistent pattern across different genes or sequences.

This makes it all the more significant that efforts to build a grand "tree of life" using DNA or other biological sequence data have not conformed to expectations. The basic problem is that one gene gives one version of the tree of life, while another gene gives a highly different, and conflicting, version of the tree. For example, as we'll discuss further below, the standard mammalian tree places humans more closely related to rodents than to elephants. But studies of a certain type of DNA called microRNA genes have suggested the opposite -- that humans were closer to elephants than rodents. Such conflicts between gene-based trees are extremely common.

The genetic data is thus not painting a consistent picture of common ancestry, showing the assumptions behind tree-building commonly fail. This leads to justifiable questions about whether universal common ancestry is correct.

 

 

Conflicts in the Base of the Tree of Life

 

Problems first arose when molecular biologists sequenced genes from the three basic domains of life -- bacteria, archaea, and eukarya -- but those genes did not allow these basic groups of life to be resolved into a treelike pattern. In 2009, the journal New Scientist published a cover story titled, "Why Darwin was wrong about the tree of life" which explained these quandaries:

The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.102

This sort of data led biochemist W. Ford Doolittle to explain that "Molecular phylogenists will have failed to find the 'true tree,' not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree."103 New Scientist put it this way: "For a long time the holy grail was to build a tree of life ... But today the project lies in tatters, torn to pieces by an onslaught of negative evidence."104

Many evolutionists sometimes reply that these problems arise only when studying microorganisms like bacteria -- organisms which can swap genes through a process called "horizontal gene transfer," thereby muddying the signal of evolutionary relationships. But this objection isn't quite true, since the tree of life is challenged even among higher organisms where such gene-swapping is not prevalent. Carl Woese, a pioneer of evolutionary molecular systematics, explains:

Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.105

Likewise, the New Scientist article notes that "research suggests that the evolution of animals and plants isn't exactly tree-like either."106 The article explains what happened when microbiologist Michael Syvanen tried to create a tree showing evolutionary relationships using 2000 genes from a diverse group of animals:

He failed. The problem was that different genes told contradictory evolutionary stories. ... the genes were sending mixed signals. ... Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another.107

The data were so difficult to resolve into a tree that Syvanen lamented, "We've just annihilated the tree of life."108 Many other papers in the technical literature recognize similar problems.

 

 

Conflicts Between Higher Branches

 

A 2009 paper in Trends in Ecology and Evolution notes that, "A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome."109 Similarly, a paper in Genome Research studied the DNA sequences in various animal groups and found that "different proteins generate different phylogenetic tree."110 A June, 2012 article in Nature reported that short strands of RNA called microRNAs "are tearing apart traditional ideas about the animal family tree." Dartmouth biologist Kevin Peterson who studies microRNAs lamented, "I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree." According to the article, microRNAs yielded "a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents." Peterson put it bluntly: "The microRNAs are totally unambiguous ... they give a totally different tree from what everyone else wants."111

 

 

Conflicts Between Molecules and Morphology

 

Not all phylogenetic trees are constructed by comparing molecules like DNA from different species. Many trees are based upon comparing the form, structure, and body plan of different organisms -- also called "morphology." But conflicts between molecule-based trees and morphology-based trees are also common. A 2012 paper studying bat relationships made this clear, stating: "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."112 This is hardly the only study to encounter conflicts between DNA-based trees and trees based upon anatomical or morphological characteristics. Textbooks often claim common descent is supported using the example of a tree of animals based upon the enzyme cytochrome c which matches the traditional evolutionary tree based upon morphology.113 However, textbooks rarely mention that the tree based upon a different enzyme, cytochrome b, sharply conflicts with the standard evolutionary tree. As one article in Trends in Ecology and Evolution observed:

[T]he mitochondrial cytochrome b gene implied . . . an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.114

Strikingly, a different article in Trends in Ecology and Evolution concluded, "the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent [evolutionary relationship] probably being the grouping of elephants and sea cows."115 Because of such conflicts, a major review article in Nature reported, "disparities between molecular and morphological trees" lead to "evolution wars" because "[e]volutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."116

Finally, a study published in Science in 2005 tried to use genes to reconstruct the relationships of the animal phyla, but concluded that "[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved." The following year, the same authors published a scientific paper titled, "Bushes in the Tree of Life," which offered striking conclusions. The authors acknowledge that "a large fraction of single genes produce phylogenies of poor quality," observing that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom." The paper suggests that "certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available." The paper even contends that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics."117

Unfortunately, one assumption that these evolutionary biologists aren't willing to re-evaluate is the assumption that universal common ancestry is correct. They appeal to a myriad of ad hoc arguments -- horizontal gene transfer, long branch attraction, rapid evolution, different rates of evolution, coalescent theory, incomplete sampling, flawed methodology, and convergent evolution -- to explain away inconvenient data which doesn't fit the coveted treelike pattern. As a 2012 paper stated, "phylogenetic conflict is common, and frequently the norm rather than the exception."118 At the end of the day, the dream that DNA sequence data would fit into a nice-neat tree of life has failed, and with it a key prediction of neo-Darwinian theory.

Ili ovaj članak: James H. Degnan and Noah A. Rosenberg: Gene tree discordance, phylogenetic inference and the multispecies coalescent.

 

 

 

Kraći rezime: ...

 

 

The problem of gene tree discordance - Until recently, the state of the art for molecular phylogenetic studies typically involved (i) sequencing a gene in individual representatives of a collection of species; (ii) inferring a ‘gene tree’ (see Glossary) for the sequences; and (iii) declaring the gene tree to be the estimate of the tree of species relationships. With the increasing abundance of molecular data and the recognition that evolutionary trees from different genes often have conflicting branching patterns [1–8], it is becoming increasingly feasible to implement multilocus approaches to phylogenetic inference. Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids [9–11], pines [12], cichlids [13], finches [14], grasshoppers [15] and fruit flies [16] have all detected genealogical discordance so widespread that no single tree topology predominates. These examples highlight the issue of ‘incomplete lineage sorting’ and the need to account for gene tree discordance in phylogenomic studies.

 

 

... The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome.

 

https://web.stanford.edu/group/rosenberglab/papers/DegnanRosenberg2009-TREE.pdf

 

 

Dakle, M. Syvanen, Carl Woese, W.F. Doolittle, Zuckerkandeln – ako pomenemo samo neke, zaključuju:

- Ne postoji evolutivno stablo. Jer svaki marker, svaki gen konstruiše svoje stablo i to uslovno, jer često puta ne možemo da iskonstruišemo ništa jače od grma.

- Više podataka i otkrića nije rešilo ovaj problem, već ga uvećalo!

- Postoje ozbiljne inkongruence. Svaki gen govori »svoju« evolutivnu priču.

- To važi kako za »niže« tako i za »više« organizme.

- Dok Kevin Peterson (svi su oni evolucionisti), analizom mikroRNA sve okreće na glavu! Ako je pre važilo da je slon postao od miša i bio bliži čoveku, evolucija mikroRNA crta stablo gde su miš i čovek bliski rođaci, a slon daleki predak ...

 

 

TE tvrdi da se sve razvilo iz JEDNOG bića koje je bilo jako prosto i moglo je da se reprodukuje. Pošto je sve postalo iz JEDNOG bića (evolucionisti ga nazivaju LUCA), logično je da postoji ovo drvo, a ono mora da ima jedan koren!

Ako zaboravimo »sitni detaljić« da TE nikako ne može da pojasni odakle to prvo biće (LUCA) – to jest ono je već u startu toliko kompleksno da pravazilazi i najjaču maštu kako je ovo biće naturalističkim slučajem moralo da nastane, a ono je moralo da nastane jer je evolucija dokazana (cirkularni argument);– proučavanje encima topoisomeraze utvrđeno je da ne možemo čak ni da tvrdimo da je to prvo LUCA biće bilo u početku JEDNO, SAMO.

Topoisomereze su enicimi koji se nalaze u sve jednoj ćeliji svejednog bića, jer su toliko bitni za ćeliju kao i DNK. Bez njih ni jedna ćelija ne može da živi, jer bi se DNK zapetljala i ne bi mogla da se prepisuje.

I umesto očekivane slike (drveta) koje predviđa teorija za tri osnovne grupe bića (bakterije, arhaje i evkarije):

 

https://www.nsf.gov/mobile/news/news_images.jsp?cntn_id=124386&org=ERE

dobijemo ovo: 

https://www.researchgate.net/figure/23999064_fig4_Hypothetical-scenario-in-which-cellular-topoisomerases-originated-from-an-ancestral-pool

 

 

Ne samo što ne možemo da iskonstruišemo drvo, nego ne možemo da definišemo JEDAN KOREN, jedan početak …

U zavisnosti od gena ili markera nauka ne može ništa kongruentno da iskonstruiše. Ta inkongruentnost pokušava se pak objašnjavati npr. »horizontalnim transferom« gena. Npr. krokodil ima četriprekatno srce, isto kao čovek, svinja ima sličnije zube nama nego majmun, a kokoš ima najsličniji sadržaj aminokiselina.

Ali preduslov za horizontalni transfer gena – je da ta bića mogu međusobno da se razmožavaju! A ako mogu međusobno da se razmnožavaju onda ne možemo da ih smatramo za RAZLIČITE vrste.

Horizontalni transfer gena bi se desio kada bi npr. prasac oprašio kokoš, a petao krokodila koji bi se onda spanđao sa čovekom.

A još gore po evoluciju dolazi saznanje da svako biće koje je očito moguće »sklopiti« samo genetskim inžinjeringom, ima od 10-20%, kod nekih vrsta i do 80%, gena u genomu koji nemaju svog analoga ni u jednoj drugoj vrsti, koji nemaju svojih evolucionističkih predaka, geni koji su za svaku od nekoliko miliona vrsta specifični. Oni se zovu siroti gene, geni bez roditelja – ili orphan genes. (https://en.wikipedia.org/wiki/Orphan_gene).

Realno je malo ljudi koji bi mogli, ako je TE tačna, tu teoriju da razumeju. Jer ispada, npr. da se je ptica nastala tako što se jedna vrsta dinozavra koja je imala npr. kljun, parila sa vrstom dinosaura koja je imala šuplje kosti, a ova se vrstom koja je imala perje ... i onda je taj mutant, himera (koji je morao ex nihilo da stvori još 10-20% svog genoma – da napiše kroz puki slučaj sam svoj SOFTVER) počeo da leti ...

Zato i ne čudi što je vodeći svetski molekularni biolog, jedan od 10 na svetu, koji je napisao i objavio oko 500 peer-review naučnih članaka i patentovao 36 izuma, Tour James, iskreno priznao: There’s no scientist alive today who understands macroevolution.

 

http://www.uncommondescent.com/intelligent-design/a-world-famous-chemist-tells-the-truth-theres-no-scientist-alive-today-who-understands-macroevolution/

 

 

 

 

Ostali smo dužni još jednu stvar. Razjasniti u kakvom su odnosu čovek i primati, saglasno sa slikom zajedničkog pretka na početku ove rasprave.

Ingo Ebersberger, Petra Galgoczy et. Mapping Human Genetic Ancestry

https://academic.oup.com/mbe/article/24/10/2266/1072057/Mapping-Human-Genetic-Ancestry

 

 

Isečci:

The human genome is a mosaic with respect to its evolutionary history. Based on a phylogenetic analysis of 23,210 DNA sequence alignments from human, chimpanzee, gorilla, orangutan, and rhesus, we present a map of human genetic ancestry. For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. ...

 

Ili

However, with both amount of data and number of studies increasing, the crux of the matter emerges. Regardless of the type of phylogenetically informative data chosen for analysis, the evolutionary history of humans is reconstructed differently with different sets of data (summarized in Ebersberger 2004).

 

 

... In here, these variants persist until they join in their most recent common ancestor (MRCA). Some genetic lineages, however, do not coalesce in the progenitor exclusively shared by humans and chimpanzees. They enter, together with the lineage descending from the gorilla, the ancestral population of all 3 species, where any 2 of the 3 lineages can merge first. Thus, in two-thirds of the cases, a genealogy results in which humans and chimpanzees are not each other's closest genetic relatives. The corresponding genealogies are incongruent with the species tree. In concordance with the experimental evidences, this implies that there is no such thing as a unique evolutionary history of the human genome. Rather, it resembles a patchwork of individual regions following their own genealogy.

 

FIG. 1.—

 

 

Dakle, filogenetskom analizom slučajnih 20.000 + sekvenci DNK čoveka, šimpanza i gorile utvrđeno je da postoje geni koje imaju šimpanz i čovek a nema gorila, geni koje ima šimpanz i gorila a nema čovek i geni koje imaju zajedno gorila i čovek, a nema šimpanz!

To je fakat! I to je veliki problem. Kako to objasniti? Ako je makroevolucija tačna, nemamo puno opcija – moralo je doći do »horizontalnog trasfera« između linije 1 i linije 2 (crvena i zelena linija na prikazu).

Linija 1 je »proizvela« svoje gene, linija 2 »svoje«. Svo to vreme – nekoliko miliona godina - ove linije, iako slične, nisu smele da se »množe« međusobno, već isključivo unutar svoje populacije, kako bi se fiksirale genetske promene u celoj svojoj populaciji. Tek kad je to uspešno urađeno, »ukinuti su rasni zakoni« i jedna linija (vrsta) naših predaka je počela da se meša sa drugom … (pri tom avtori ne objašnjavaju za koliko % genetskog materijala se jedna linija razlikovala od druge. Šimpanz i gorila su »linije« koje ne mogu da se pare.).

Zato mi ljudi, kažu evolucionisti, nemamo JEDNOG već DVA ZAJEDNIČKA PRETKA!

A pošto svako biće ima sličan problem, jer su njegovi geni MOZAIK (slon i morska krava imaju određen broj gena istih), svako biće je nastalo kao himera – spajanjem brojnih LINIJA …

Istina, horizontalni transfer gena između različitih vrsta nije nemoguć. Npr. naučnici su gene morskog psa usadili u paradajz. Problem je u tome što se taj »genetski inžinjering« ne dešava u prirodi (ne govorimo o bakterijama), već u visokotehnološkim laboratorijumima uz jako specifične uslove – i samo u određenom obimu.

A uz to da se ne zaboravi, da su sami od sebe posle ukrštavanja različitih vrsta (tada su to bile još »linije«) morali da se DE NOVO pojave i »siroti geni«, koji su za svaku vrstu specifični, i nemaju svojih analoga u »bratskim« linijama.

Stvarno, uz svo poštovanje za trud koji ulažu pripadnici TE da bi pojasnili ove anomalije – a njih je sa novim podacima i otkrićima sve više - Andrersenove bajke izgledaju realnije... Mislim da i ćete i sami sada sve više da shvaćate James Toura.

 

 

 

 

ZAKLJUČAK

»Endogeni virusi« trebalo je da potvrde evolucionisitčku hipotezu o zajedničkom pretku. Nekad u prošlosti, ovi elementi su ušli u genom polnih ćelija i fiksirali se. Ako ih pronađemo na istom mestu kod drugih vrsta, logično je da su se te vrste razvile jedna od druge budući da je statistički nemoguće da bi se neki virus slučajno endogenizirano na istom mestu kod dvaju vrsta.

 

Istraživanja su pokazala da ti »virusi« nisu baš virusi već retroelementi, jako bitni za arhitekturu živih bića. Bez njih biće ne bi moglo da funkcionište (da živi, da se razvije), zato ti elementi organizmu nisu strani, već jako bitan deo genetskog materijala. Niko normalan verovatno neće da tvrdi da bi jedno biće moralo najpre da se zarazi jednim takvim virusom, da bi moglo uopšte da se razvije.

Po istoj logici – praćenjem određenih markera – evolucionisti su u skladu sa teorijom pokušali da iskonstruišu »genealoško stablo«. Budući da svi – kako oni tvrde – imamo zajedničkog pretka, to ne bi trebalo da je problem. Potrebno je samo da forenzički pogledamo u »gene«.

Ali analize su utvrdile bolne činjenice. Svaki gen priča svoju evolutivnu priču, radi čega je svako biće u stvari MOZAIK, HIMERA koje je moralo da nastane iz VIŠE zajedničkih predaka uz horizontalni transfer gena.

A što je još gore – nije samo poteškoća to da ne možemo iskostruisati »geneološko drvo«, već ne možemo više ni da tvrdimo da to drvo ima JEDAN KOREN (LUCA), to je da je cela evolucija krenula iz JEDNOG bića iz kog se sve moralo da razvije.

Da li ove sitne »anamalije« obaraju TE ili je ipak u pravu Mojsije, presudite sami.