Genetic Phylogeny

Genetic Phylogeny

https://reasonandscience.catsboard.com/t1521-genetic-phylogeny



For many evolutionary biologists, the most significant single piece of evidence supporting the Darwinian theory of origins is the nested hierachical pattern that is formed when comparing various genetic sequences in different organisms.  The similarities and differences, it is argued, map out into a kind of "Tree of Life".  It is this consistent pattern created by numerous different genes and genetic sequences that appears to many to be extremely compelling evidence. 1

Richard Dawkins was asked, "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory?" (Link).  Dawkins' response is most interesting:
.
"I think to me perhaps the most compelling evidence is comparative evidence, from modern animals -- particularly biochemical comparative evidence, genetic, molecular evidence.
If you take any set of animals, and identify the same gene in different animals, and you really can do that, because the letters of the DNA code -- that is, the same code in all animals -- and you really can find a gene which is the same -- in, say, all mammals. For example, there's a gene called FOXP2, which is a couple of thousand letters long, and most of the letters are the same in any mammal, so you know it's the same gene. And then you go through, and you literally count the number of letters that are different.
So, in the case of FOXP2, if you count the number of letters that are different between humans and chimpanzees, it's only about 9. If you count the number of letters that are different in humans and mice, it's, I don't know, 30 or something like that. Actually, frogs have them as well, you find a couple of hundred that are different.
So, you can take any pair of animals you like -- kangaroo and lion, horse and cat, human and rat -- any pair of animals you like, and count the number of differences in the letters of a particular gene, and you plot it out, and you find that it forms a perfect branching hierarchy.
It's a tree, and what else could that tree be, but a family tree.

The problem with this claim is, of course, is that more and more inconsistent phylogenies are being discovered and more and more genes and genetic sequences are studied.  And, quite surprisingly for many scientists, many of the phylogenies based on these various genetic sequences are very inconsistent with each other and with standard Darwinian ideas based on morphologic classification models.

mollusks (scallops) are more closely related to deuterostomes (sea urchins) than arthropods (brine shrimp).  Of course, this is not too surprising.  Intuitively, a scallop seems more like a sea urchin than a shrimp.  So, the 82% correlation between the scallop and sea urchin is not surprising.  However, in this light it is surprising is that a tarantula (also an arthropod) has a 92% correlation with the scallop.  Here we have two different arthropods, a shrimp and an tarantula.  How can a scallop be much more related to one type of arthropod and much less related to the other type of arthropod? This troubling thought led the authors of the Science article to remark:

Different representative species, in this case brine shrimp or tarantula for the arthropods, yield wildly different inferred relationships among phyla. Both trees have strong bootstrap support (percentage at node). . .  The critical question is whether current models of 18S rRNA evolution are sufficiently accurate to successfully compensate for long branch attraction between the animal phyla. Without knowing the correct tree ahead of time, this question will be hard to answer. However, current models of DNA substitution usually fit the data poorly . . .

But when the data does not match to have the wished result, things are simply made up, proposing LGT ( lateral gene transfer )

A 1999 Science article by Stiller and Hall:
   "A precipitous acceptance of such widespread LGT places evolutionary biologists in the untenable position of adopting an unfalsifiable hypothesis, at least in terms of the techniques of comparative sequence analyses that currently dominate the field of molecular evolution. Any phylogenetic pattern inferred from any given gene can be fit to some suitable mix of conventional intraspecies gene transmission and interorganismal genetic promiscuity. Thus, unless more reliable evidence is uncovered, the scientific method requires that we invoke the idea of ubiquitous LGT only as a last resort." 2

Question : Why are the emergence of new body form, cell shape, organs and functions not analyzed in regard of FUNCTION and INTERDEPENDENCE, rather than just phylogeny? Cells of Multicellular organisms work in an INTERDEPENDENT fashion. A Merkel sensory cell bears only function when interconnected with the brain. A Bud taste cell only if connected to the nerve that goes to the right cortex in the brain to produce the sensation of taste. This leads with ease to the conclusion that back in the tree of life, there had to be a crucial point, where the development from unicellular to multicellular, and further branching producing new phyla and traits, required the emergence of new genes, instructing SYSTEM CHANGE, able to produce all at once new body members and organs that are interdependent. That would also mean the addition or mutation of multiple genes with multiple NEW instructions all at once through Darwin's natural selection. A hard sell..... But since Darwin's holy cow cannot be sacrificed, let's keep the practice of genetic phylogeny comparison. And when the evidence does not lead to the wished result of common ancestry, let's make up an assertion, like horizontal gene transfer, which will be swallowed by the audience as holy truth....

1. http://www.detectingdesign.com/geneticphylogeny.html
2. http://science.sciencemag.org/content/286/5444/1443

Genetic Phylogeny 

http://reasonandscience.heavenforum.org/t1521-genetic-phylogeny

One of the main flaws I see in evolutionary biology is the method of which evolution, is inferred. That is, to compare genome sequences and homologs. If two genes look similar, it means, they look similar. Nothing else. Jump from that observation to the conclusion that there was gene transition from one gene sequence to the other by evolutionary mechanisms is ad-hoc guesswork. 

Question : Why are the emergence of new body form, cell shape, organs and functions not analyzed in regard of FUNCTION and INTERDEPENDENCE, rather than just phylogeny ? Cells of Multicellular organisms work in an INTERDEPENDENT fashion.  A Merkel sensory cell bears only function when interconnected with the brain. A Bud taste cell only if connected to the nerve that goes to the right cortex in the brain to produce the sensation of taste. This leads with ease to the conclusion that back in the tree of life, there had to be a crucial point, where the development from unicellular to multicellular, and further branching producing new phyla and traits, required the emergence of new genes, instructing SYSTEM CHANGE, able to produce all at once new body members and organs that are interdependent. That would also mean the addition or mutation of multiple genes with multiple NEW instructions all at once through Darwin's natural selection. A hard sell..... But since Darwin's holy cow cannot be sacrificed, let's keep the practice of genetic phylogeny comparison. And when the evidence does not lead to the wished result of common ancestry, let's make up an assertion, like horizontal gene transfer, which will be swallowed by the audience as holy truth....

Why are biologists ignoring to ask other questions? As for example: How could the subunit or co-factor x of protein y have acquired its 3D shape to become FUNCTIONAL by genetic change, to fit like lock and key? How could the conformational change of proteins to get a specific enzymatic reaction have emerged slowly, by evolutionary mechanisms, if intermediate stages during the process do not confer function? Many proteins use prosthetic groups.

A prosthetic group is a tightly bound, specific non-polypeptide unit required for the biological function of some proteins. The prosthetic group may be organic (such as a vitamin, sugar, or lipid) or inorganic (such as a metal ion), but is not composed of amino acids. Prosthetic groups are bound tightly to proteins and may even be attached through a covalent bond
https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Prosthetic_Group

Why would natural selection select for components of a complex system that would be useful only in the completion of that much larger system ? Take FE/S clusters as example.

The supposed  Last Universal Common Ancestors (LUCA's) biochemistry was replete with FeS clusters and radical reaction mechanisms.  Proteins containing Fe–S clusters exist in all living organisms and play an essential role in diverse biological processes at the cellular level. It was thought for a long time that the assembly of Fe–S proteins occurred spontaneously since the process was easily replicated chemically in vitro and led to the view that these cofactors can assemble spontaneously in proteins. However, genetic, biochemical, molecular, and cell biology studies in the late 1990s provided ample evidence that demonstrated that the assembly of Fe–S clusters in vivo is a catalyzed process rather than a spontaneous one and that it requires a plethora of genes assisting in the maturation of Fe–S clusters and their insertion into the apoproteins. Therefore, the formation of intracellular Fe–S clusters does not occur spontaneously but requires a complex biosynthetic machinery.  Despite the relative simplicity of Fe–S clusters in terms of structure and composition, their synthesis, assembly, and transfer to apoproteins is a highly complex and coordinated process in living cells. Numerous Fe–S cluster synthesis components have been discovered that assist Fe–S protein maturation according to distinct biosynthetic principles in several model organisms

The recognition of the severity of the problem to explain the origin of FE/S clusters did lead to the proposal of the " Iron-Sulfur world hypothesis".

The iron-sulfur world hypothesis is a set of proposals for the origin of life and the early evolution of life advanced in a series of articles between 1988 and 1992 by Günter Wächtershäuser, a Munich patent lawyer with a degree in chemistry, who had been encouraged and supported by philosopher Karl R. Popper to publish his ideas. The hypothesis proposes that early life may have formed on the surface of iron sulfide minerals, hence the name
https://en.wikipedia.org/wiki/Iron%E2%80%93sulfur_world_hypothesis

These are all indeed patchworked explanations. The origin of prosthetic groups and protein subunits in general, and how they acquire their specific function and 3d shape is a very serious origin of life, and evolution problem.

An important consideration as well is the fact, that the basic building blocks must be obtained in the natural surrounding, imported into the cell, transformed into useful products, and integrated in the build-up - synthesis process. That requires a plethora of further molecular machines, which not rarely use the very own cofactors, of which the origin we try to explain. Catch22 says hello.

In my view, all this constitutes an unpenetrable barrier for the attempt to give naturalistic explanations.

Biosynthesis of Iron-sulfur clusters, basic building blocks for life  
http://reasonandscience.heavenforum.org/t2285-iron-sulfur-clusters-basic-building-blocks-for-life

functioning biological systems, like man-made machines, must make leaps per saltum rather than slow gradual steps. Biological systems tend to polarize and group, they don’t seem to like gradual transitions for certain major architectures or body plans. It’s not that the fossils can’t be found, they can’t exist even in principle.
https://uncommondescent.com/darwinism/taxonomic-nested-hierarchies-dont-support-darwinism/