Molecular Phylogeny Proves Evolution is False.

In 1837, Charles Darwin sketched out for the first time a tree of life that he thought might visualize the idea of descent of

Darwin's notebook and his tree of life.

Darwin’s notebook and his tree of life.

animal lineages with modifications which would help to explain the origin of species.  Though the tree of life idea had been used to visualize taxonomy by Carl Linneaus, it became foundational as a tool for the development of Darwin’s evolutionary hypothesis.  Lines connecting groups of organism branched off to more specific and supposedly related forms.  Darwin saw that the connections made to groups and the position of species within a group were the result of shared similarities through ancestral descent.  His theory was one attempt at explaining how those relationships might have come to exist.  Ancestry was presumed to give rise to multiple lineages that diverged to create new life forms.  Natural selection was the driving force for the divergence of species from a common ancestor.  Natural variation within a type of organism was the generator of novel traits.  Together, variation and selection would prove life evolved to its current time in existence.

What happened to descent with modification?

What happened to descent with modification?

For a century and a half evolutionary biologists have been trying to prove that this tree is real rather than just a mental concept or a taxonomic tool for naming things.  The discovery of DNA was thought to be the answer to validating the hereditary associations of different species.  By sequencing the genetic material of living things it was predicted that the relationships of animals could be shown to be real; ultimately supporting the idea that similar beings share ancestry. Gene sequences were thought to enable an unbiased proof of evolution through the construction of molecular phylogenetic trees.  It was hoped that random modification in the DNA code would allow scientists to literally visualize the history of evolutionary change.  However, what actually has happened is that an entirely new genetic branch of life was discovered; totally unrelated to the bacteria or multicellular organisms.  The discovery

Molecular phylogeny discovers an entire new branch of life form - the archaebacteria.

Molecular phylogeny discovers an entire new branch of life form – the archaebacteria.

of the archaeal bacteria established an entirely new branch of biology.  And now there is more unrelated organism to deal with than related organisms. Molecular phylogeny created new problems for evolution and has not answered any problems save the revelation of a failed theory.  I repeat, the development of a tree of related species has proven to be false.  Gene sequence alignments create “networks” of connections of completely different, obviously unrelated types of beings.  DNA did not and will not conform to descent with modification.

For example, 2000 gene sequences common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes were compared.(1)  Theoretically, the results should have constructed a tree that revealed evolutionary relationships.  However, different genes aligned in different sequence among the 6 types of life forms. No  tree is possible in such an analysis.   Ultimately, there appears to be no consistent relationship among these animals.  Evolution is undone.

Typical sequence alignment.

Typical sequence alignment.

Molecular phylogeny represented as a tree, though widely published as a viable tool for deducing ancestry, has not supported evolutionary suppositions.  Though similar life forms that share a fundamental body plan (the mammals, the apes within the mammals) do share many of the same protein genes, they do not share the programming for the use of those genes. For instance, chimpanzees have been said to have only a 3 to 6% difference from humans and yet the chimp genome is some 10% larger to begin with.  This means we are at least 10% different because of the larger chimp genome.  Currently the assessment of the difference between the two genomes is 70%.  Seventy percent different!  Not similar.

This method of aligning sequences was hoped to reveal not only the relatedness of living organism but also the point in time when speciation or divergence from a common ancestor occurred.  Each attempt at creating such a genetic or molecular clock has failed or when it does align different species the rate of the molecular clock is either too consistent for different gene sequences or never consistent enough for similar sequences.  Evolutionary scientists pick and choose which gene they want to use in order to support the dogma of biological relatedness of species.  This is neither scientific nor objective.  It

Pick and choose.

Pick and choose.

is very much like churches that choose to accept some biblical passages but ignore others in an effort to support the teachings of their founder.  People, whether religionists or evolutionists, are prejudice.  They believe what they want and never let the facts get in the way.

Instead of accepting the evidence (or lack thereof) of molecular alignment, which speaks loudly against common ancestry, evolutionists have decided that other mechanisms are at play in the development of different life forms.  Instead of a linear descent of genetic information from one species into another species, genes must have moved horizontally from one form to another.

This transfer of intact genes does occur among some bacterial forms and in the lab has been shown to occur between completely unrelated bacterial species.  Virus particles also have been used to move chunks of DNA between bacteria as well as mammalian cell types.

The network of "same genes" found by molecular analysis of genes.  Horizontal gene transfer?  Homoplasty?

The network of “same chunks of DNA” found by molecular analysis. Horizontal gene transfer? Homoplasty?

Viral transfers of DNA are highly cell specific. However, no virus has been caught transferring DNA between higher life forms.  One group of bacteria, the agrobacteria, can infect wounded plants and transfer its DNA into plant tissues.  This transfer is a complex and highly controlled process that requires an elaborate and specialized genetic apparatus and well-defined genetic elements that direct the specific bacterial DNA into the wounded plant cells.  Once cells are infected with this DNA the genes code for the over-production of plant hormones and a few unique amino acids.  The plant tissue grows uncontrollably into a gall or tumor that encompasses the bacteria.  The gall produces amino acids that only the bacteria can metabolize.  It is truly a unique way to infect, colonize and parasitize plant tissue.  This kind of invasion of foreign DNA into plant biology is not known to pass any genes onto the sex cells of the plant; a requirement of horizontal gene transfer to be useful to the propagation of novel traits in the next generation of the plant.

Cartoon of Agrobacteria transfer of genes into wounded plant cell.

Cartoon of Agrobacteria transfer of genes into wounded plant cell.

Also, all viral infections are specifically about the transfer of genetic material into a host cell. The cold and flu virus’, HIV, hepatitis, cytomegalovirus and herpes virus’ in humans and bacterial phage particles in bacteria are examples of infectious particles that transfer the entire genome of the virus into the host cell.  There it may integrate into the genome of the host for some time or the viral particles may replicate to extend the infection to other

Virus' infection a bacterium.

Virus’ infecting a bacterium.

host cells.  Not all cell types are susceptible to such viral infection and, keep in mind, to be useful to any sort of evolutionary propagation such infection would have to occur in the gonadal (sex) tissues.  There are no known virus’ that infect the ovary or testis of any animal or plant for that matter.

I guess what makes matters even more embarrassing for the materialistic scientists is their dependence on unproven and purely speculative hypothesis of just how such gene transfers have occurred in the past.  The endosymbiotic theory of mitochondrial and chloroplastic development from the invasion of bacterial cells into the eukaryotic cellular machinery is an unsubstantiated claim now accepted as though a proven fact.  It has been proposed that sometime in the distant past a bacterium was engulfed by a eukaryotic cell.  This fusion of cell types complemented the pair of cell types and over the eons symbiosis between the self replicating pair resulted in a permanent adaptation.  The bacteria gave up independent life to specialize as a respiratory package for the larger cell.  Genes somehow transferred to the large cell type so that without the genome of both life forms, respiration cannot occur. A similar story is told about how the photosynthetic chloroplast came to be found in plant cells.  Far more

The endosymbiote theory: is all of evolutionary biology purely speculative? (yes)

The endosymbiote theory: is all of evolutionary biology purely speculative? (yes)

voluminous to discuss than in this post is the extensive comparative analysis of mitochondrial function and structure to a bacterial cell.  It is like comparing your fingernail to the entire human body in terms of function and structure.  Yet, the minor similarities between the size and structure of the respiratory organelle called the mitochondrion and a bacterial cell warrant sufficient evidence for those dedicated to materialism to accept the endosymbiotic theory as reality.

There are also rare transfers of genes from bacteria to yeast cells and from here speculations go wild, becoming forensic in nature, requiring interpretation of existing genetic oddities to potential sources of such gene transfer.  None of them are convincing to the skeptic of scientism.  Each evidence is shrouded in mystery and begs for some explanation. The only explanation materialists are able to come up with are not based on knowledge or experiment but supposed unseen and untestable events in the distant past; events for which no known mechanism is available.

The tree of life does not exist.  Horizontal gene transfer is more of an excuse than an answer as to how the many forms of life share so many identical sequences and why so many genes do not align with their expected ancestral precursors.  Among prokaryotic (bacterial) genes, nearly 80% are considered to have been exchanged by transfer to create new species, rather then to have evolve by Darwinian mechanisms.  HGT is the rule not the exception.  Descent with modification is foiled.

And not to be undone, multicellular life is now claimed to engage in cross species

Animal hybridization explains the genetic variability among species!

Animal hybridization explains the genetic variability among species!  Meet the Donkey (dog/monkey).

hybridization to create new life forms.  Does this make sense?  If Neanderthal was one species and Homo erectus man another, hybridization cannot take place!  The very definition of a species is a population of organisms that is reproductively isolated, i.e., reproduction only takes place within a specie not between species.  Hybridization is only between varieties or strains within the species.  But the need for evolutionists to explain the failure of DNA to support biological evolution opens up the careless and flippant use of terms until those words become conveniently meaningless.  If the public would study the information for themselves they would discover that Neanderthal was far more advanced than modern people are today.  They had religion, made and used musical instruments, enjoyed art, and made their own clothing, tools, weapons, thread, needles and so on.  Neither Neanderthal nor Homo erectus have any statistically significant morphological differences from modern man.  Both fall into traits typical of the human population.  Hybridization is a farce not a feature of evolution.

Chunks of DNA that have been found common to a wide diversity of animals from frog to bat to opossum and are being accounted for by HGT.  A chunk of DNA peculiar to snakes was found in cow.  Did the cow give it to the snake or the snake to the cow?  “The number of horizontal transfers in animals is not as high as in microbes but it can be evolutionarilly significant”, one scientist, says.(1)  The vertical descent of Darwinian evolution has been shown to be meaningless by DNA sequence analysis.  Yet evolutionist continue to claim that Darwin’s vision has triumphed when it is apparent in every way

The god of evolution

The god of evolution

that it has failed.  “It does not mean evolution is wrong- just that evolution is not as tidy as we would like…”(1).  Why continue to support a failed theory?  It is because no other materialistic explanation can be thought up.  It does not matter that the mechanisms of such gene transfer in higher species does not exist.  Anything goes in an attempt to hold materialism as creator god.

One scientists came close to admitting the failure’s of Darwin’s bad idea, “Our standard model of evolution is under enormous pressure.  We’re clearly going to see evolution as much more about mergers and collaborations than change within isolated lineages.”  Another scientist said of the tree of life, “It helped us to understand that evolution was real. But now we know more about evolution, it’s time to move on.” This is delusional and evasive thinking.  If the tree is proven useless then it taught nothing about truth or science or evolution.  We know more about evolution than we did before this genetic research.  We now know evolution is false, failed, and fruitless.

Evolution gets a Darwin award.

Evolution gets a Darwin award.

The evidence in molecular biology damns the descent with modification hypothesis.  New evidence does not just blur the edges of this incredibly poor hypothesis but it erases its hold on biological science altogether.  My prediction is that with increased understanding of the totality of many genomes we will discover that evolution is pure nonsense.  However, science will not let evolution go.  Newer and stranger ideas will come into vogue.  Fusion of whole animal types will be acceptable as events in the distant past and inter-species reproduction will be taught as the means of creating new life forms.  Butterfly metamorphosis will be explained by teaching that a moth ate a worm and their genomes fused to produce two life forms that we currently know as the butterfly. This has already been put forth for the dimorphic forms of coelomates (corals, jellyfish) No evidence will be given. It will be assumed as fact just as Mary was assumed into heaven (The Catholic church call this the “Assumption”).

Meanwhile other molecular events are being imagined to explain those genetic sequences that simply do not conform to the presumption of molecular evolution.  Homoplasty is one such means used to explain away the data. Homoplasty describes the independent development of genes in different groups of organisms that have arrived at the same or very similar sequence.  It is a form of convergent evolution and the probability of such events occurring are beyond astronomical.  Nevertheless, anything goes in order to preserve evolution, as we have seen.  Homoplasty is a real problem for evolutionists yet listen to Richard Dawkins take on the problems of the tree of life:

“… there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened. It exists. It is in principle knowable. We don’t know it all yet. By 2050 we should – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.” R. Dawkins  (2).

Dawkins is prepared for the failure of the molecular revolution to support evolution.  So even if it is defeated, he will claim it is only at the terminal twigs.  What this means is that only the organisms that exist will interfere with our analysis since these are the organisms that are found at the terminal twigs of the tree… everything else is non existent and theoretical.  So, when facts get in the way, toss them out for the sake of the god of evolution.

Will Dawkins ever choose knowledge over speculation?

Will Dawkins ever choose knowledge over speculation?

A recent publication announced genes as a source of public goods; meaning genes are randomly passed from organism to organism… the phylogeny is unknown. The evolutionary biologists published that the tree of life is, “…becoming increasingly implausible.” and “…given our knowledge of the data, it seems that the elastic limit of the original hypothesis (descent with modification) has been passed.”  and “It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet.”  (3)  Other researchers are speaking of the tree of life made from molecular phylogeny as a knowledge tool, a heuristic tool for discovery and these comments with respect to tossing the tree of life completely out the window.(4)  The new Darwinian theory based on genetic information has proven unequivocally that Darwin was wrong.  Evolution is neither by descent nor by lateral gene transfer.  The evidence is that biological evolution is a failed hypothesis.  The only other alternative is creation by design.  Blueprints are specific for each kind of living being.

It is apparent that molecular phylogeny does not support evolution.   The first protein sequence used to develop molecular phylogeny was cytochrome C.  It was published with

Evolution versus Facts: Square peg versus round hole.

Evolution versus Facts: Square peg versus round hole.

much acclaim but in fact further scrutiny revealed that trees conflict repeatedly. Each conflict is explained away and the theory leads the data rather than the data dictating the theory.  Journal articles spend as much time explaining away problems as they do force fitting the data to support evolution.  Rather than articles admitting that molecular phylogenetic attempts dispel evolution, the titles always say that molecular sequence alignments are “rewriting evolution”.

This, my dear friends is shear, unadulterated madness.  Square pegs do not fit in round holes.



Lawton, G. 2009. Why Darwin Was Wrong About the Tree of LifeNew Scientist. 2692: 34-39.

2.  Dawkins R (2003) A devil’s chaplain. New York: Houghton Mifflin.

3.  Biology Direct 2011, 6:41

4.  Biology Direct 2011, 6:32


23 Responses to “Molecular Phylogeny Proves Evolution is False.”

  1. jksea5

    Article does good job of illustrating difference between speculation and observation

  2. Koelsch

    Excellent article! I think molecular biology should be a ‘general education’ course in universities, very revealing. I couldn’t help but be dismayed when a new program on the Animal Planet channel this weekend again stated that we share 97% of our genome with chimps, implying they may as well be our cousins!

  3. Mody Nader

    Great , allow me to add that DNA does not provide any template for forms nor any causal power for
    Describing behavior .

  4. Sariel Shade

    Wow, what an excellent article. Wish that Dawkin’s would read this. Seems that he too tries to force pieces that do not fit into the evolutionary “puzzle” and makes a lot of money doing it.

  5. Charles

    I am writing an essay called Evolution: A modern myth, soon i will post it on the internet. EVOLUTION IS WRONG!

  6. Chris

    Hi I was wondering if you would be so kind as to give me the title of the study you referred to below;
    “For example, 2000 gene sequences common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes were compared.(1) Theoretically, the results should have constructed a tree that revealed evolutionary relationships.”

    Reference (1) is for a popular article in New Scientist, which is behind a paywall


    • Dr. Daniel Moran, Ph.D.

      I can get you some of the abstracts…
      Published cladistic reconstructions of galagonid phylogeny based on morphological, behavioral, and genetic data have had few elements in common. A recent molecular study indicated that 2 of the 3 generic groupings derived from morphological data were not consistent with tree topologies constructed from the analysis of mitochondrial DNA sequences. In this study, we compiled and analyzed a data set based on craniodental morphology in 13 galagonid and 8 outgroup taxa, comprising 3 dwarf-lemur and 5 loris species, and subjected it to cladistic analysis. Our aim was not only to generate a new phylogenetic hypothesis based on these data, but also to investigate the conditions under which congruence could be achieved between these results and those obtained previously. The data set was found to be highly sensitive to the choice of outgroup, with the lorises showing high interspecific variability in cranial structure. Congruence between the craniodental and molecular trees could be achieved only if Arctocebus was used as the outgroup and two characters were preferentially weighted. Further progress in the reconstruction of galagonid phylogeny will require seeking consensus in a variety of other data sets, including postcranial morphology, behavior, and additional gene sequences. The effect of different outgroups on molecular analysis needs attention. Am J Phys Anthropol 117:79–93, 2002. © 2002 Wiley-Liss, Inc.

      Science. 2006 Mar 3;311(5765):1283-7.
      Toward automatic reconstruction of a highly resolved tree of life.
      Ciccarelli FD1, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P.
      Author information

      Erratum in
      Science. 2006 May 5;312(5774):697.
      We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.

      Acta Biotheor. 2007;55(3):269-81. Epub 2007 Jul 27.
      Congruence of morphological and molecular phylogenies.
      Pisani D1, Benton MJ, Wilkinson M.
      Author information

      When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.

      Mol Phylogenet Evol. 2009 May;51(2):190-200.
      Molecular phylogenetics reveals extreme morphological homoplasy in Brazilian worm lizards challenging current taxonomy.
      Mott T1, Vieites DR.
      Author information

      Amphisbaenians are fossorial squamate reptiles distributed mainly in South America and Africa. Brazilian worm lizards belong to the family Amphisbaenidae, which has far more recognized species than any of the other five amphisbaenian families. Morphological datasets recovered Amphisbaenidae as paraphyletic, while previous molecular phylogenetic studies did not include enough taxa to solve the generic-level relationships within this family. We present a molecular phylogenetic hypothesis based on a sample of 58 amphisbaenians, including representatives of six of the seven South American genera. Our molecular data include sequences from two mitochondrial genes (16S, ND2; 1,184 characters) and three nuclear genes (RAG-1, C-MOS, BDNF; 1,898 characters). Our phylogenetic hypothesis is not fully resolved, although it does not support the monophyly of most genera except Leposternon. Morphological characters currently used to diagnose genera of South American amphisbaenians are homoplastic, and the taxonomy based on them is not appropriate. We revise the taxonomy of this group and sink several South American genera of Amphisbaenidae (Cercolophia, Bronia, Aulura, Anops and Leposternon) into Amphisbaena.

      J Biomed Inform. 2006 Feb;39(1):86-102. Epub 2005 Sep 28.
      Tree disagreement: measuring and testing incongruence in phylogenies.
      Planet PJ.
      Author information

      The branching patterns of phylogenetic trees often disagree even when they have been constructed using different portions of the same data. This phylogenetic discord (incongruence) can be explained by real differences in evolutionary process or history, but also may be due simply to random chance or sampling error. Techniques for measuring and testing the significance of phylogenetic incongruence are used widely in systematic biology, and are necessary when considering genome-scale datasets composed of multiple genes that may or may not have different histories. They are also applicable wherever tree algorithms are used for ordering and interpreting data (e.g., DNA microarrays). Here, I review the different incongruence tests and use them to test the phylogenetic discord of a potentially mobile genetic element (the widespread colonization Island) in the gamma-proteobacteria. I then consider how incongruence tests may be used as a starting point for phylogenetic analysis that accounts for horizontal transfer and duplication events as explanations for homoplasy.

      Every science paper needs scrutinized for its inadequacies, not its excuses. Evolution will never be published outright as a failure but publications are revealing for those who understand what is actually missing in the evidence for a position.

      good luck.

      • Abdrew Herzman

        OK, so where’s your Nobel Prize for this? If this is true, you would change the world and the way we look at it. So why is this only on a website and not in every news headline?

        • Dr. Daniel Moran, Ph.D.

          Those are really good questions. Why is this not common knowledge?

  7. Robert Keller

    So I guess the idea of kinds diversifying as they left the ark is disproved then?

    • Dr. Daniel Moran, Ph.D.

      There is a distinction between change within a species and change beyond the level of a species. The first kind of change exists within kinds or types of organisms. The second requires new genetic information, not simply a rearrangement of information. These two distinctions are real within the science of biology and from known sequences must occur by different molecular mechanisms. The first is by independent assortment and cross over events that occur during gametogenesis. The second is assumed to have occurred since there is nothing living or dead that represent intermediate forms connecting the vast array of living beings on the planet. The last kind of change is supposed to be responsible for the process of evolution. It has not yet been observed in science and has is still in the hypothesis testing stage… unfortunately the evidence available indicates a failed hypothesis. The theoretical biologists will not let it go.

  8. Robert Keller

    From your first two sentences you define kind and species to be synonymous terms.

    Are the typical ring species presented in college texts books different species where they are unable to mate at the ends of the ring?

    Foxes and dogs have been presented as being the same kind by creationists and having been represented by a single kind on board the ark yet there are more differences in the DNA between foxes and dogs than exists between humans and chimpanzees.

    You mention new genetic information but we can measure new genetic information from one generation to the next with current technology. Something like 60 new genetic mutations occur that did not exist in the genome of either parent each time a child is born.

    Yet you state that the second is “assumed” to have occurred since there is nothing living or dead that represent intermediate forms.

    But that is exactly what we see with ring species is it not? We see the end species that are different species incapable of interbreeding and we find all the intermediate forms between them. The only difference is the variation takes place in a spatial rather than a time dimension.

    You state it has not been observed in science. Nylonase and corn come to mind and I have a list of many more.

    • Dr. Daniel Moran, Ph.D.

      Since species is not used in a defined sense in biology, I take the meaning of species to be a reproductively isolated group of interbreeding organisms. There are some sloppy uses of the term otherwise. Yes, ringed “species” like Rana pipiens show true genetic isolation at the extremes of their geographic isolation. If they cannot be mated to produce viable offspring then they would be, in my narrow definition of species, different species. Note that none of these ringed examples show macro evolutionary change, all of this is within the existing gene pool. You mentioned genetic mutations and new information in the same context as though these are interchangeable. I do not believe they are. Mutations so far have proven to be disadvantageous or neutral so far as known science is aware. Just because mutations are inherited does not make them informational. New information in a human being would be the genetics needed to produce feathers. Both the genes for the proteins and the genes for the developmental pathway as well as the needed regulatory genetic information would be required. This information would make something novel, and potentially fit the requirement for “a gain of function.” New mutations is not the same as information. So far as we actually know in science, mutations only corrupt information though it is too often presumed to have added information and made improvements.

      As to nylonase, this “new feature” involves multiple enzymes found existing on a plasmid. If you further your reading, nothing new was found. Here are a few articles written well after the announcement that the nylonase gene “evolved”.
      Yomo, T., Urabe, I. and Okada, H., “No stop codons in the antisense strands of the genes for nylon oligomer degradation,” Proceedings of the National Academy of Sciences USA 89:3780–3784, 1992. Back to text
      Negoro, S., et al., “Nylon-oligomer Degrading Enzyme/Substrate Complex: Catalytic Mechanism of 6-Aminohexanoate-dimer Hydrolase,” Journal of Molecular Biology, 370(1):142–156, 2007, ISSN 0022-2836, DOI: 10.1016/j.jmb.2007.04.043

      As to corn, you will have to be more specific as to what you are speaking of here.

      Good remarks. Thanks.

  9. JDS

    Your article misses the forest for the trees

    “It does not mean evolution is wrong- just that evolution is not as tidy as we would like…”(1). Why continue to support a failed theory? – See more at:

    Just like Newtonian physics was supplanted by Einsteinian, that did not *invalidate* the physics before it. i.e. Newtonian models still work perfectly well for most use cases. The Einsteinian models add nuance and explain the bits that Newton did not. Nor could Newton even have known that his model breaks down at certain scales, since there was no way for him to observe the universe at the speed of light or at the atomic level.

    The fleshing out of the “tree of life” into a much richer, more complex, “mangrove forest of life” or “bush of life”, does not invalidate the tree of life model, nor does it invalidate evolution itself.

    • Dr. Daniel Moran, Ph.D.

      You might have an argument if we knew that DNA can be “improved” upon. We don’t know that at all. There is no known gain of function to be found in all of the mutations we have catalogued since learning how to sequence the genome. Gain of function is the point of evolution. It must happen at the genetic level and yet, what we find are defects and some neutral mutations… nothing that adds a new function or improves survivability.

      Here is what one scientist says: Another scientist said of the tree of life, “It helped us to understand that evolution was real. But now we know more about evolution, it’s time to move on.” This is delusional and evasive thinking. If the tree is proven useless then it taught nothing about truth or science or evolution. We know more about evolution than we did before this genetic research. We now know evolution is false, failed, and fruitless.

      While it is seductive reasoning to find two different organism with similar genetics this in no way proves that are related. Whole tracts of DNA from the genome of a cow are found to be identical to snakes but no other species… This kind of phenomenon is not explained by random events. Meanwhile, we like to think the chimp is only 3 percent different in its genome than humans. But the chimps genome is 10-12% larger than our own. It is fraudulent to say we are 3 % different in genomes when the studies simply show we are 3% different in gene sequences which represent only 1% of the genome! Taking the whole of the genomes into consideration current calculations suggest we are approaching a 70% difference in whole genome identity. The “junk DNA” makes all the difference in regulation and development of body plans.

      Furthermore, though not touched on in this post, bioinformatics are designed only to find similarities. It is not an objective means of analysis. Something to consider when determining “affinities” between species.

      Finally, the tree of life was developed by Linnaeus for categorizing life forms. Bioinformatics as biased as its algorithms are, does not support Linnean trees as expected. There are more exceptions than rules. And after it is all said and done, we still have not witnessed a change in type. We remain with phyla quite completely unrelated to other phyla, completely distinct with no bridging. The present proves this and the fossil record confirms this. Evolution is not a working hypothesis.

      • JDS

        “[1]There is no known gain of function to be found in all of the mutations we have catalogued since learning how to sequence the genome. [2]Gain of function is the point of evolution.”

        [1] This is false. I know you are trying to say that mutation is always harmful, but that is simply false.

        [2] There is no point to evolution. Evolution is just the change in genome of populations over time. There’s no “point” to it at all.

        For someone who comes across as smart, you really don’t seem to understand the Theory of Evolution by Natural Selection.

        Ugh, I could go on, but unfortunately I’m tired atm. The simple fact of the matter is, evolution as a process is an observed fact, as well as or better observed as any other “fact” of the natural world. The Theory of Evolution by Natural Selection is a model to describe how evolution in fact works to produce new species. But the *fact* of evolution has been observed. The Theory is just a model to describe it. Models are by their very nature, imperfect, and as such the models change over time. But finding one ding in a very well vetted and evidenced model does not unravel and disprove the model.

        However, there are a number of things that *would* disprove the model. Falsifiable portions of the model. For example, finding fossil evidence out of order in the geological strata. Say, finding a rabbit skeleton in stratum to early to predcitably contain a rabbit skeleton.

        However, none of the falsifiable predictions made by the Theory of Evolution by Natural Selection have every been falsified. Ever. Period.

        The claim about percentages of DNA match between humans and chimps and strands of snake DNA in a cow’s genome are not at all in the realm of “falsifiable predictions”. They are, at best, indications that the model needs to be tuned. But thrown out? hardly.

        In fact, let’s take this analogy further and apply it to the christian bible. By your reasoning in this article, any flaw found in the bible should thus invalidate the entire bible.

        I’m honestly bewildered by the mental gymnastics people take to maintain beliefs that are obviously false. If you can present truly demonstrable evidence that a falsifiable claim made by the theory of evolution is false, you would win the adoration and adulation of the entire biological science community. You would win a Nobel Prize. You would make world news headlines. Fans would literally line up at your door to meet you. I realize this line of reasoning has no direct bearing on the truth or falseness of this article, but seriously, just think for a few minutes. Why has no creationist with claims that they’ve falsified evolution had this happen to them? Why is this not front page news?

        • Dr. Daniel Moran, Ph.D.

          You said “The simple fact of the matter is, evolution as a process is an observed fact, as well as or better observed as any other “fact” of the natural world.”

          Dawkins admits the same with one caveat. Evolution is an observed fact except, and here is the kicker, “its just that no one has observed it when it is happening.” I realize you have adopted against all reason the idea that evolution is a fact. But there is only one thing missing and that is evidence. Nothing in the fossil record is transitional. “Nothing”. Spiders have been found back to 450 million years and we know they are spiders because they are … spiders. Sharks forgot to evolve. So did fish, octopi, all mollusks, most vertebrates. Bats are found 50 million years ago. Nothing has changed. Why aren’t forest found with dinosaurs? Why isn’t any plant life found with dinosaurs for that matter? Odd! Why do digs actually stink like rottenness? How are organics preserved for 10s of millions of years. Why are actual bones found lying about in the Arctic and still called to be 50 million years old? How did T rex migrate to above the arctic circle and die there under flood conditions and fossilize? How is it that fossilized forests around the world are proof of a global flood occurring instantaneously and no one suggests this is a possibility?

          I think you know this already.

          No one will win a nobel prize by destroying evolution. You are a good example of people who adopt theories without evidence. Nothing transitional exists in the world today and nothing in the rocks is transitional. Organisms appear, remain and disappear. The sediments are marine in nature. And, even for those who understand that catastrophe is responsible for at least 5 major deposits, no one will admit that the fossils we find had to have been buried in water, by flooding on a massive scale. No one talks about these facts or it might sound like a flood scenario. Furthermore, embryology does not follow phylogeny.. this is a myth and cannot but proven scientifically to be true. Homologies are the only thing suggestive of relatedness between current existing life forms and genetics prove one thing, the architecture of the genomes determine the body plan. Similar plans, similar bodies. To suggest otherwise one must have evidence, not assumption or presumption. This kind of scientific thinking is faith based, no empirical evidence.

          Beyond the level of species diversification within kinds, which is wholly dependent on existing genetics and meiotic rearrangements, evolution on a macro scale is assumed and cannot be proven.

          And yes, gain of function is the important point in evolution. If you cannot prove in real time that new information arises to create new functions in an organism you have nothing for evolution to do. This was a major question asked of me during my defense. This has also been asked of Dawkins who was had nothing to say… stimied, dumbfounded.

          Furthermore, and you most likely will argue this point, the material start of life from abiotic processes is beyond reason. Chemistry as we know it, under any conditions but one, will never proceed to form living cellular life. The only exception is intelligence. Complexity and information science solidly prove that biological molecules do not, cannot and will not assemble themselves into living systems or for that matter an enzymatic cascade of any simple reaction. AND, Darwin proposed that this was part of his theory.

          As to flaws in the Bible, if it could be shown that God inspired men to contradict themselves on who he is and what he has revealed then I agree that such is evidence of a phony revelation. The only flaws I have found have to do with a few names and numbers which are attributable to copyists errors and are easily resolved because these are found in places where redundancy exists. We do not have the autographs or the world of Christians would worship the papyrus and not God.

          While I am sure you have nothing that will convince me that evolution has more than a chance of snow ball in hell to work, I will never convince you of the sensibility of reason. Having said this, I do thank you for your thoughts.

          • JDS

            It is unfortunate that only one thing in this entire response of yours is true, and it is this: “While I am sure you have nothing that will convince me that evolution has more than a chance of snow ball in hell to work, I will never convince you of the sensibility of reason”

            Literally nothing else you spouted out here is true, or even makes sense.

            I realize this is your blog, and you can see fit to post whatever you like. I am actually pretty appreciative of the fact that you didn’t censor my comments — I think that is quite admirable. However, if you truly believe that all that stuff you just said is true, then yes, I probably never will be able to convince you of the fact of evolution.

            I find it mind-boggling, though. That people would take the unproven word of men, written almost 2000 years ago, as the truth, when things discovered and actually demonstrably true are discounted because of that book. It seriously makes zero sense to me.

            Anyway, you dumped out too much at once to deal with coherently, so I’ll focus on one single paragraph, your first one, about how “nothing has changed” and there are no transitional forms. Quite the contrary, *every* fossil found, ever, is a “transitional form”. In fact, *every currently living species* is a “transitional form”. However, that’s obviously not going to convince you. But I’ll name two, very famous transitional forms in the fossil record: tiktaalik and archaopteryx.

            Also, to counter, just because some species have been around for 50 million years without obvious change does not mean “nothing changes”. It just means, those species haven’t changed as much. But even those have changed.

            If you start with “god did it” and try to work your way backward, then of course you will not be able to accept evolution. But if you start with “I don’t know how it happened” and then take the evidence that is presented, I find it vanishingly unlikely that you would come up with god as a hypothesis.

            Finally, saying “god did it” doesn’t even preclude the fact of evolution. There are plenty of christian and other world religions that accept evolution as fact, but inject god into the mechanism (in a way that I find ridiculous, but that’s beside the point). The point is, why don’t all christians agree about evolution? (effectively) All scientists do.

          • Dr. Daniel Moran, Ph.D.

            I am going to leave your reply as it stands as part of the post to show your unwillingness to think critically about your metaphysical belief in evolution. You have not offered evidence of living things being transitional forms. Nothing! And many if not most evolutionists are now convinced that evolution has stopped because of various reasons. Your other transitionals have no basis in fact. Tiktaalik is classed as a fish. Followup papers on the anatomy say so and fail to convince the authors that the fin is anything other than a fin; no structures which are needed to support weight are found in the fossil. Archaeopteryx is classed as a mosaic, not a link, since it show nothing transitional but rather a mosaic of features. Meanwhile, true birds have been found in sediments 60 million years earlier than the two fossils of this bird/reptile mosaic. Much like the platypus, this creature does not show what you have been said, and which apparently you have come to “believe” is a transitional fossil.
            evolutionist Lecomte du Mouy recognizes this. he writes:

            ‘… we are not even authorized to consider the exceptional case of Archaeopteryx as a true link. By link, we mean a necessary stage of transition between classes such as reptiles and birds, or between smaller groups. An animal displaying characters belonging to two different groups cannot be treated as a true link as long as the intermediary stages have not been found, and as long as the mechanism of transition remains unknown.’

            You will note that I have nowhere suggested that “God did it” as a foundational premise for any of my arguments. On the other hand I suspect you have started with the premise, “God does not exist”, in order to conclude that evolution is a working hypothesis. Such is the basis for Dawkins belief. I must wonder how anyone could put their faith in an unknowable and untestable solution which is falsified by chemistry, biochemistry, basic biology, physics, information science, statistics and reason.

            Evolution evolves things unless it doesn’t. It evolves organs separately but simultaneously across classes, orders; unless it doesn’t. It Creates design that only looks that way. It is observed to work except no one has observed it working when it works. It runs on sexual reproduction except when it doesn’t and it results in the survival of the fittest except no one knows what that means since the ones that survive are obviously the fittest; for some reason. It answers everything except when it doesn’t and as every evolutionist knows, it is a fact except no one agrees on the details.

            You have lost credibility when you fail to show why you believe what you believe. Your arguments about a position I have never taken (God did it) is a failed argument since that is not my premise. You cannot attribute to me things that are convenient for you to argue as those things are not my position. Rather, when science invents unworkable hypotheses, honest people need to admit it. The ramifications of a failed theory hold science back and is passed off as fairy tale, not facts.

            NO. Having studied science for 50 years and spent 13 years in formal education in science, with academic accomplishments in biology, microbiology, molecular and cellular biology and having spent 35 years in medical research, plant biotechnology and industrial fermentation, implementing the tools of gene engineering to create new strains of plants and bacteria I conclude that evolution is a farse. God might as well have done it. You have a snowball chance in hell of convincing me otherwise… I have done the homework and ask that you do the same.

          • JDS

            Truly amazing. While you haven’t specifically said “god did it” in this article, literally every pixel of this blog screams “god did it!”. You have a background image of the beginning of Genesis juxtaposed with double helices, for goodness’ sake!

            The fact of the matter is, I *have* done my homework. Just saying I haven’t is just smoke and mirrors. And likewise, stating you don’t believe something doesn’t make that something false.

            I haven’t started with the premise “god does not exist”, but I also will freely admit I don’t believe in god or gods or anything supernatural. I think those beliefs are silly and childish, no matter how old one is.

            Repeating the statements that there’s no evidence does not suddenly make there be no evidence. Frankly, you are doing the same thing you are accusing me of. For example, “many if not most evolutionists are now convinced that evolution has stopped because of various reasons” — who? which evolutionists? cite references

            (Incidentally, there’s no such thing as an “evolutionist” — people who understand evolutuon are called “biologists”)

            Lastly, this is not a debate. I am not trying to gain or lose credibility. I’m just trying to get you to use your brain and think critically.

            What do you believe about how humans came to exist? Why do you believe that?

      • Nathan M.

        “Furthermore, though not touched on in this post, bioinformatics are designed only to find similarities.”

        I see that you, like most of the creationist scientists I have encountered, have not actually used these programs, and probably only taken cursory genetics class and have very little practical experience with regards to these programs.

        First, “bioinformatics” are not designed to do anything – bioinformatics is a field. Perhaps you were referring to phylogenetics analysis programs? Not knowing the difference is a big red flag as to the extent of your relevant knowledge. Further, SOME phylogenetics programs are designed to find similarities, but not all. Many (most) employ models of nucleotide substitution and analyze the probabilities that pairs or groups of sequences will share apomorphies by chance alone (among other parameters).
        Your ‘model’ merely asserts that magic made, say, apes and humans share unique mutations or sequences. That is not even a working hypothesis, it is religious apologetics.

        And regarding the canard about the chimp genome being bigger than ours – odd that a molecular biologist does not seem to know about indels and such.

        • Dr. Daniel Moran, Ph.D.

          The article is for a general audience to understand. Bioinformatics even as you assert do indeed use assessments made from examining similarities only when it comes to phylogeny. “Perhaps you are referring to phylogenetic analysis programs.” This is the title of the article and the content of the argument. End of that discussion. As to the chimp genome being larger there are many more reasons for its size than indels but indels are sufficient to show that we are not an evolutionary branch of that genome. At least the argument is as sound as the assumptions otherwise accepted or in the case of indels ignored by religious evolutionists like yourself.

          Meanwhile, molecular biology has proven that the tree of life does not exist. It is a web that shows distantly “related” creatures sharing whole chunks of coding regions which should be proof that snakes are closely related to cows … hence Horizontal gene transfer. No credible scientist should be espousing such concepts as proof until the proof exists; a mistake quite typical of evolutionary biologists. No absurdity is to absurd to such religious fanatics in their effort to substantiate a failed hypothesis. The eye has evolved over a dozen times independently? There should be a law that governs such development yet evolution is bankrupt in this regards… it is only assumed; it is not science.

          Evolution is not observed to produce new forms of life. Not in the present day nor in the geological record. Anyone who knows anything of paleontology knows that the tree of life is not to be found there… there is not branching but what we make up in the mind, not in fact. Creatures are found in the rocks and exist in layers before they disappear and are replaced by other creatures in a new bed laid on top of the first like stacks of books. They leave no intermediates save for those characterized by a good cartoonist.


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