Response to the Intelligent Design Critics On Biological Information

One of the most common criticisms in regards to intelligent design is the opposition that DNA is not information in a sense that originated from an intelligent based cause but rather under naturalistic laws, including that of biochemistry. The exclusion of an intelligent cause over the behavior of biochemistry as being the ultimate explanation for how DNA managed to be sequential and orderly based is a well synthesized argument made by the ID critics. By referring to examples such as sand dunes or to make things even more vividly, the formation of a snowflake, it is insisted that the same process must be true for DNA as well. In a nutshell, given that there are things in nature that appeared to be well orderly structured, it must be too that DNA is nothing more but the same by-product.

The argument pressed by the ID critics exclude that biological information is the result of some intelligent based cause over a purely biochemical cause. The idea of biochemistry or the laws of physics capable of creating such information, sequential order or structure is something that comes from what is known as self-organization. Self-organization is a process where some form of overall order arises out of the local interactions between smaller component parts of an initially disordered system.

So then has the infromation argument for intelligent design been refuted? Not so fast

Problems with the self-organization model:

 The main central problem with ID critics conflating DNA information to that of Sand Dunes or of that of a self-organized snowflake is really not that hard to grasp if one paid close attention to the distinct characteristics between that of DNA and those that are self-organized or structured in nature. Self-organizational theorists like to often point to simple geometric shapes or repetitive forms of order like the Sand Dunes arising from or being modified by purely physical or chemical processes. They suggest that such order provides a model for understanding the origin of biological information or body-plan morphogenesis. Self-organizational theorists like love to point out to even that of crystals, vortex, and even convection currents to illustrate the supposed power of physical processes to generate order for free. However, there are flaws with this type of reasoning.

The Flaws Behind Self-Organization:

The first point to consider here is that both DNA & self-organized structures like salt crystals are all chemistry based. They are all made up of atoms that can be expressed in a simple chemical formula. Salt crystals for example are based on the chemical formula as NaCl, that is Sodium Chloride while DNA can be expressed as A,T,C, & G. Now here is where it gets interesting.

If you look closely at not just the molecular structure of a self-organized system, but the behavior, you would notice an interesting observation: there is 1) order of repetitiveness or pattern & 2) geometric and translational symmetry. Salt crystals, for example, which were the first structures determined using X-ray techniques, have a highly repetitive molecular structure of sodium and chlorine atoms arranged in a three-dimensional grid, a pattern in which one type of atom always has six of the other types surrounding it. That is you would find a highly periodic molecular structure of nothing but NaCl, NaCl, NaCl, NaCl, NaCl. Not only does the salt crystal have a highly repetitive pattern, but it also has geometric and translational symmetry, that is the atoms are arranged in a symmetrical fashion on the three dimensional face and also look the same even when moved.

The point here is that it is a well established fact that the self-assembly of crystals and other self-organizing structures that are governed by the pure laws of chemistry are by rule, repetitive, pattern-based, and geometrically symmetrical. The same repetitive and symmetrical molecular structure as observed in salts crystals are as true as the molecular structure and atoms observed in snowflakes. This is well know among those that study the physics of crystallology and in the field of self-assembly chemistry. Here we can finally make an important distinction on what differentiates the information of DNA from natural geometric structures.

Unlike the self-assembly molecular structure of a snowflake, crystal, and other self-organizing systems which are strictly governed by the laws of chemistry, the molecular structure of DNA, more specifically the nucleotides or presence of amino acids of a given functional protein, are actually non-repetitive and sequence specific with respect to function without being based on some certain pattern, following rather an irregular and highly unusual behavior contrary to the ubiquitous laws of self-assembly chemistry. Following the rule that the self-assemblage of inorganic molecular structures formed in nature are periodic and geometrically symmetric, as observed in that of salt crystals and snowflakes, one would therefore expect the arrangement of nucleotides or amino acids from a protein to be highly repetitive and arranged into a similar 3rd dimensional molecular fashion as that of simple geometric shapes formed in nature. Yet, that is not what is observed in DNA, for reasons stated before.

In addition, there are distinguishing characteristics between the information of DNA and those that appeared to be naturally formed by nature. One of the unique things about DNA is that it contains specified complexity. Specified complexity, not to be confused with irreducible complexity, is basically meaningful information that results into a specific communicative effect or function conveyed by the precise or special arrangement of symbols or discrete units. Let’s look at an actual example of specified complexity.

“This message here is specifically complex.”

When it comes to specified complexity, there are unique characteristics involved that only intelligent minds can put into effect. 1) There is no pattern nor repetitiveness involved in determining the overall sentence structure and content of the message. In other words, the precise arrangement of the English alphabet letters that convey meaningful information cannot be predicted mathematically nor expressed by using some certain equation. Patterns by definition are repetitive, whether obvious or subtle, and are therefore predictable to a certain degree. In specified complexity; however, no matter how hard you try, you will not find a distinct regularity or some certain pathway that determines the precise arrangement of the characters or symbols and the words used. In specified complexity, the precise arrangement of characters or symbols, in this case the English alphabet letters, are not necessarily random like of that found in gibberish sentence structure, but rather directed. By contrast, simple geometric figures like salt crystals, snowflakes, spiral galaxies and so on can be determined and predicted mathematically as they are by nature repetitive and follow a certain pattern.

Geometric spirals, for example, formed by nature follow a golden ratio rule that can be expressed and predicted mathematically using the Fibonacci sequence. Even among the laws of physics, there is repetitiveness as the laws only describe repetitive or pattern based phenomena. The distinguishing differences between information produced by a mind are 1) non-repetitive or non-pattern based, 2) unpredictability & 3) special arrangement of characters or symbols that conveys meaningful information.

What does all this have to do with the ID skeptics claim of nature being capable of producing information? Simply this: the law-like, self-organizing processes that generate the kind of order present in a crystal or a vortex do not generate specified information, the kind of non-repetitive and highly sequence specific order present in the genetic code. Laws of nature by definition only involve order in the sense that can be described with differential equations or universal “if-then” statements.

The information bearing sequences in protein coding DNA and RNA molecules do not once again exhibit such repetitive pattern. As such, these sequences can be neither described nor explained by reference to a natural law or law-like self-organizational process. The kind of non-repetitive non-pattern based on display in DNA and RNA, a precise sequential order necessary to ensure function, is not the kind that laws of nature in principle generate or explain. Even among self-organization in biological organisms, they are all based on already pre-existing information, which does not help the case at when explaining the origin of biological information.   

So it seems that one of the problems ID critcs face in regards to the claim that information of DNA can be explained by purely chemical means under some self-organization or necessity is denied by the fact that the self-assembly of molecular structures and repetitive order or pattern of sand dunes, vortexes, spiral galaxies, created by nature do not really coincide so well with the biochemical structure and arrangement found in DNA, including the precise arrangement sequencing of nucleotides or amino acids in respect to function and its specific 3rd dimensional protein fold. There is actually no law outside the field of organic chemistry that is able to coincide with the non-repetitive and special arrangement that convey specified information & function as observed in living organisms.

Another point I would like to emphasize is that the laws of biochemistry themselves do not predetermine nor account for the precise arrangement of amino acids nor DNA information. This seems rather self-evident, as it is clear that the laws like gravity themselves are incapable of properly self-tuning into the appropriate conditions for life, without flattening anything on the face of the Earth or throwing them out to space. Until an actual mechanism is observed that coincides with the unique characteristics of DNA being non-repetitive and sequence-specific, there is no reason to presume a biochemical cause, as that has yet to be demonstrated. 

Something which the intelligent design skeptics never really bothered to explain in complete detail in regards to what exactly in biochemistry is predetermining or accounting for the specified information or at least the special arrangement in DNA.

Polypoidy: A “Dead-End” For Evolution

Here’s an interesting food for thought in regards to the origin & evolution of plants and how they became so diverse.
One of the common arguments evolutionists use to support the claim that evolution can create new novelty/new genetic information is polyploidy. Polyploidy, also known as genome doubling, is the process where a living organism acquires one or more additional set of chromosomes. 

Conceived from the early 1900s down to the present, polyploidy has been viewed as one of the major forces that contributed to the evolution of new species, new genera, etc. However, polyploidy is considered to be rare among animals in general, but very common among the plant kingdom. Due to the extreme rarity of polyploid from animals in general, evolutionists believe that the major diversification and macro-evolutionary changes of plants have been mostly associated with genomic doubling/chromosome duplication. 

As the pro-evolution site, Talk Origins, states in their +29 Evidences For Macroevolution:

Special paradiumerous plants, both angiosperms and ferns (such as hemp nettle, primrose, radish and cabbage, and various fern species) has been seen via hybridization and polyploidization since the early 20th century. 

Yet, one of the greatest and influential botanist and geneticist evolutionary figures, G. Ledyard Stebbins, has created harsh scientific criticism against the assumption that polyploidy is able to create novelty or large-scale morphological features, as required by the neo-Darwinian paradigm. Here are some of his arguments:

 The classical paradigm of Polyploidy:

Polyploids as “dead-ends”: Limited importance in diversification 

“Stebbins (1950 , 1971 ), as well as another highly influential plant biologist of the 1900s, W. “Herb” Wagner, argued that while polyploids were frequent in plants, they had limited long-term evolutionary potential. This traditional view that both strongly promoted maintained that polyploids were “evolutionary noise” ( Wagner, 1970 , p. 146) unimportant to the main processes of evolution (e.g., Stebbins, 1950 ; Wagner, 1970 ). For Stebbins and other students of polyploidy from that time period, the evolutionary action was at the diploid, not the polyploid, level. For example, Stebbins (1950 , p. 358) stated, “Polyploidy, therefore, may be looked upon as a process which is most effective as a means of enabling species groups which have reached a certain stage of depletion of their biotypes…to adapt themselves to new environmental conditions which arrive relatively suddenly. It is much less important in stable environments and in diploid species which are still widespread and rich in ecotypic differentiation.” Stebbins (1950 , p. 359) further noted, “The long-continued evolution needed to differentiate genera, families and orders, and phyla appears to have taken place chiefly on the diploid level…” Stebbins (1950 , p. 366) later states “… polyploidy has appeared as a complicating force producing innumerable variations on old themes but not originating any major new departures.”

To rephrase it seems that polyploidy, the doubling or duplication of chromosomes which is believed by evolutionists to be a major driving evolutionary force of novelty or new morphological features, has serious limitations. The most gravest problem with polyploidy according to Stebbins is that it is essentially an evolutionary dead-end, as it does not lead to the evolution of new genera, families, nor orders. The best polyploid can acheive is simply produce new species with innumerable variations of already pre-existing traits, but nevertheless lacks the ability to produce new major morphological innovation/macro-evolutionary changes. 

Furthermore, the creation of lower to higher taxa (i.e. from genera to orders/families) have been found to be present only at the diploid level, meaning that they were derived from species with normal chromosome counting obtained by their parents as opposed to the addition of new chromosomes.

In addition to the limitation: 

“Recent reanalyses of data for ferns and angiosperms revived the concept of polyploids as evolutionary dead-ends, indeed using this very word ( Mayrose et al., 2011 ; see also Arrigo and Barker, 2012 ). Mayrose et al. (2011) argued that polyploids have higher extinction rates than diploids and are therefore often “dead-ends” that do not leave a legacy.”

It seems that species that undergo polyploidy, the addition of new chromosomes, are often associated with higher mortality rates: including deadly genetic diseases, infertility, etc. Essentially, polyploidy is for evolution an evolutionary dead-end, as it leads to the route of extinction rather than survival.  

but wait, there’s more:

“A question of great interest is: Can populations of independent origin interbreed, or do they represent reproductively isolated lineages? Experimental demonstration of such interbreeding among polyploid lineages of separate origin is still rare. Recent work on Mimulus indicates that polyploid populations of separate origin are interfertile ( Sweigart et al., 2008 ). A mixture of results is apparent for populations of Tragopogon polyploids of separate origin; some populations appear to be interfertile, whereas some combinations are sterile”

According to Stebbins and thinkers like him, not only are polyploid speciation events associated with just evolutionary dead-ends, but they are also found to be so commonly infertile that successful reproduction would be considered a rarity among polyploid living organisms. 

Summing everything up: it seems that polyploidy can no longer can be conceived as a major evolutionary force for the creation of new genera, families, & orders. The addition of new chromosomes is rather a counter-productive route for the modern synthesis of evolution, as it leads to the route of extinction and infertility. This brings biologists back to square one, where do all the new biological novelties come from if polyploid is not the mechanism? 

Evolutionists to the rescue:

Despite the harsh criticism used against the neo-Darwinian model of polyploidy able to generate novelty or macro-evolutionary changes, some evolutionists wanted to put up a fight, something which they named the revolution and new paradigm of polyploidy. 

The paper, published in the American Journal of Botany:

The polyploidy revolution then…and now: Stebbins revisited” 

Here Soltis, an evolutionist in favor of the neo-Darwinian synthesis, has argued that polyploidy is not an evolutionary dead-end and that it is able to cause macro-evolutionary events. This was clearly going against what classics like Stebbins stated about polyploidy. 
What was his line of defense? 

The identification of ancient WGD events at many points in angiosperm phylogeny provides the opportunity to assess the correspondence between inferred genome duplication events and major diversifications—the role of polyploidy in “macrodiversification.” Many ancient WGDs are associated with key diversification events in angiosperm evolution, such as the origins of angiosperms, eudicots, and monocots. Examination of polyploidy events in Brassicaceae, Poaceae, and Solanaceae suggests that ancient WGD was followed by a burst in species richness, typically a few nodes after the WGD (Soltis et al., 2009). 

The reasoning behind the logic goes like this:

“We think we see an ancient polyploidy event in this genome, therefore its novel traits must be due to the polyploidy mechanism.”

To rephrase, 

“since we can’t find any evidence of novelty or macro-evolutionary changes occurring in present polyploids, we can go back looking to the past and point out that ancient polyploid/whole genome duplication events were the cause of such large-scale morphological and novel changes.”

So what evidence do they present to defend polyploidy? Ancient polyploidy/WGD events. Rather than demonstrating macro-evolution in the present and in action, they presumed that it must have been the case in ancient whole genome duplication events that occurred many million years ago. 

The problem with this logic though is that it commits the fallacy of Post hoc ergo propter hoc (after this, therefore because of this)

The logic relies on the presumption that ancient polyploidy/whole genome duplication events were the cause of such novel body-plans. However, that reasoning itself is insufficient and fallacious, given that correlation is not evidence for causality. 

Soltis matter is nothing more but mere speculation and wishful thinking. The idea that ancient polyploidy/whole genome duplication events have shaped the biodiversity observed in plants is also not free of problems. Quite the contrary, the whole ancient WGD hypothesis is brought with controversy in the scientific community rather than remain as a scientific consensus:

As stated in this 2014 paper:

The rainbow trout genome provides novel insights into evolution after whole genome duplication in vertebrates

Here researchers examined a recent whole gene duplication event named the salmonid-specific 4th WGD; otherwise abbreviated as Ss4R that has been dated 25 to 100 mya, Due to the recent Ss4R arrival, researchers had the opportunity to better understand the early steps of gene fractionation. They performed an analysis on the whole-genome sequence of the rainbow trout. 

By examining the Ss4R regions, they discovered that most of the duplicated regions have revealed a surprising discovery: they found that nearly all of the duplicated regions have remained highly conserved and hardly diverged for 100 million years after the Ss4R event. Furthermore, they found that despite 100 million years of evolution after the Ss4r whole genome duplication event, they found that the ancestral gene and gene copies of it have extreme stability, emphasizing that the duplicated regions have remained remarkably well conserved in sequence identity and gene order on chromosomes. Which demonstrates interesting crucial points against the whole genome duplication hypothesis. 
Problem with Ancient Whole Genome Duplication Hypothesis:

1) WGD does not involve many genomic rearrangements such as inversions or translocations that would otherwise modify the order of genes in the genome

2) It hardly involves deletions and neo-functionalizations
&
3) Pseudogenization is more common than producing functional genes. Even among pseudogenes caused by failed gene duplications, they remained highly strongly conserved across the entire genome  

This is quite contrary to what the scientists in the paper argued, that body-plan morphogensis can be explained by whole genome duplication given that they involve large-scale genomic rearrangements, deleterious mutations, and neo-functionalization.
Rather, what this study reveals is that the rate of deletion, rearrangments, inactivation etc. is extremely tiny. It is in fact so slow that even after 100 million years after the Ss4R WGD event, there hardly ever remains any evidence of significant divergence in the entire genome. Given that Whole Genome Duplication involves more failures rather than success, this brings Soltis claim that ancient polyploid/WGD events drive the evolution of new body-plans into question. 

As the researchers from the paper conclude:

“Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here CHALLENGES the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.”

It seems that even after a considerable amount of time for whole genome duplicaiton to occur, there still hardly remains any evidence of divergence in the genome. This says a lot, since it shows that novelty by genome duplication is extremely rare, even in a 100 million year time scale. 

Ironically, Soltis and his colleagues admit that:

Despite great progress in documenting the genomic and transcriptomic changes in polyploids relative to their diploid parents, we know little about the impact of WGD on the proteome (e.g., Albertin et al., 2006, 2007;Gancel et al., 2006; Carpentier et al., 2011;Hu et al., 2011, 2013; Kong et al., 2011;Koh et al., 2012; Ng et al., 2012). Given that the functional states of proteins in a proteome directly affect molecular and biochemical events in cells that determine phenotype, investigating how changes in gene expression profiles and AS events relate to protein-level changes is essential for understanding the molecular and evolutionary consequences of polyploidy, including molecular, biochemical, and physiological mechanisms that ultimately result in evolutionary change. Despite only a handful of proteomic studies of polyploids and their parents, some have revealed that the proteome of the polyploid does not always match the results predicted from the transcriptome alone; furthermore, novel proteins not found in either parent may be produced. 

 Judging by their overall conclusion, it seems like they admit that their understanding of what WGD events can achieve is very unclear, as they do not know for certain whether such can generate novel complexities. To them, there only remains the expression of hope and dreams that one day with enough research they will finally be able to find the smoking gun mechanism involving novel/macro-evolutionary changes. 

Perhaps the reason why biologists can’t find any such mechanism that leads to macro-evolutionary changes is because probably there was never such thing. Instead, all the biodiversity present could be explained that perhaps biological life was seeded rather than evolved from one form to the other.

They have yet to provide a feasible mechanism that can explain how life became so diversified from one different taxonomy to the other. 

Nevertheless, that has yet to be seen. 

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Problems With Dinosaur to Bird Evolution: The III Digits

One of the most widely held evolutionary claims in regards to the origin of species is the transition between Theropods and birds. Birds according to the evolutionary paradigm are considered to be the byproduct descendants from Theropod dinosaurs. The view that birds are the descendants from Theropods has been widely regarded as a scientific consensus. Just like how humans and their so-called closely related cousins the apes are asserted to have branch off from the last common ancestor, so too does the same concept apply for the transition between Theropods and early to modern day birds.

Proponents in favor of bird to dinosaur evolution have long relied in the fields of genetics, paleontology, comparative anatomy/embryology, to support this view. In addition, they hold these fields to be very strong evidence for their position in defense of dinosaur to bird evolution. In this article we are going to focus on one of the evidences that are claimed by these proponents to support this evolutionary view.

Evidence for Dinosaur to Bird Evolution: The III Fingered Digits

One of the evidence that is considered to be very strong evidence for dinosaur to bird evolution is the homology of the 3 fingered digits found between the hands of the advanced Triassic Theropods and in the forelimbs or wings that are found in the early and modern day birds. In the Triassic Theropod lineage, there were only 3 digits present in the theropod hands that were in the orders of Digits I, II, & III as demonstrated in the fossil record. Just like human hands, Digital I corresponded to the Thumb, Digit II for the index finger, and III for the middle finger. Because theropods in the Triassic period have lost Digits IV & V that were only present from their ancestors and birds are considered to have derived from the Theropod lineage that lost IV & V, it was predicted that the earlier to modern day birds should have the same evolutionary pathway of fingered digits. Theropods had Digits of I, II, & III and so the same homology should be true for birds if they truly derived from that lineage.

Studies in paleontology and comparative anatomy starting from the late 70s  investigating the developmental pathway of the fingers located in the bird wings/forelimbs have revealed that the fingered digits of the birds’ forelimbs do indeed follow the same pattern as dinosaurs. That is both the dinosaurs and birds follow Digits I, II, & III, exactly as predicted in the fossil record. Paleontologists have widely considered this as very strong evidence for dinosaur to bird evolution due to the strong homology present between them. This has been considered to be indisputable evidence that birds derived from the Triassic Theropod lineage. [1, 2, 3, 4]

The Conflict

Unfortunately, later studies in the field of embryology have challenged the common evolutionary view that the III digits present in birds provide very strong evidence for the dinosaur to bird transition. Contrary to the claims of paleontologists, embryologists have disputed the association of the I, II, & III digits homology as demonstrated in the fossil record and paleontological data. They claimed that the III digits in birds actually correspond to Digits II, III, & IV and not I, II, & III. The appearance of embryological data conflicting with that of paleontological have caused a great rage and controversy in regards to dinosaur to bird evolution. [5, 6, 7]

Although these two conflicting views were controversial, it was later confirmed by Alan in 2002 & Michael Richardson in 2003 using embryos that the development of bird forelimbs do indeed correspond to the digits of II, III, & IV unlike the Triassic Theropods of I, II, & III. By contrast, Digits I, II, & III that have been reported in the paleontology of birds were nothing more but the misleading result of convergent evolution. In other words, the III digits homology found between the dinosaurs and birds were due to different developmental pathways that converged independently to the same solution. Rather than those common characteristics being derived from common descent, birds acquired those digit similarities completely independent and distinct from the Triassic Theropod lineage. Thus, confirming the embryologists finding that the wing bird digits are II, III, & IV, not I, II, & III. [8, 9]

The Frameshift Mutation to the Rescue

Given the increasing evidence that the digit bird wings followed II, III, IV according to embryological papers and conflicted with the traditional I, II, III view predicted by the fossil record, the view that birds are dinosaurs was not dead yet. Some evolutionary biologists (despite others like Alan insisting that birds derived from an unknown lineage separate from Theropods) have insisted that such conflict between paleontology and embryology does not contradict the view of Theropods to birds transition. The reason, they claimed, is because of a frameshift that occurred during bird evolution. The Frameshift hypothesis predicts that the conflict of the birds possessing II, III, IV during embryogenesis can be best explained as the result of a frameshift mutation. This frameshift mutation is speculated to have occurred during bird evolution, where at that point the dinosaur digits of I, II, III have frameshifted into II, III, IV in the origin of bird evolution. Originally, on the onset action of bird evolution, the official digits were I, II, & III but since a frameshift has occurred, the birds digits shifted from I, II, III to II, III, & IV. A paper published in 1999 by J.P. & J.A. entitled, “A solution to the problem of the homology of the digits in the avian hand”.has been considered by some as a relief and savior to the conflicting view against dinosaur to bird evolution. [10]

Problems with the Frameshift Hypothesis

The frameshift hypothesis involves the introduction of complete homeosis, the transformation of one organ into another, arising from mutation in or misexpression of specific developmentally critical HOX genes. HOX genes are special protein-coding DNA segments that involve the protein synthesis of genetic switches. These proteins that act like on/off switches in the genome regulate the expression of other genes that play an important role in body-plan development by switching them on and off. HOX genes play a crucial in body-plan development, however, such body-plan structure is pre-determined by the cell long before the expression of HOX genes. Thus, any mutation in the HOX gene only affects the development of pre-determined body-plan structures. The Frameshift Hypothesis is considered as a resolution to the conflict between morphological and embryological data.

Molecular evidence in favor of the frameshift hypothesis by HOX gene expression is a 2004 paper published by Vargas & Fallon entitled, “Birds have dinosaur wings: the molecular evidence.” In this paper  Vargas & Fallon (2004) argue that the prospective digit 1 is characterized by the Hox d 13 expression alone while digits 2 to 5 have Hox d 13 and Hox d 12 expression. Since the anterior wing digit has only Hox d 13 gene expression, they argue it is digit 1 on the grounds of molecular homology, as quote unquote:

Our evidence contradicts the long standing argument that the development of the wing does not support the hypothesis that birds are living dinosaurs [11]

Unfortunately for these authors, their conclusion has been unconvincing as reported in the literature. A review paper published in the same year as Vargas & Fallon’s paper has criticized their claim that the solo presence of HOX D 13 expression only in the wing of birds has demonstrated unambiguously digits I, II & III. In their critique of Vargas & Fallon’s hypothesis Gallis (2005) argues convincingly that the molecular evidence cited is unconvincing as the mutants cited (eg talpid and Hox d deletion mutants) show only a weak correlation of Hox d 12/13 expression with digit identity. As quote unquote,

 

At the moment the data on mutant limbs does not present a challenge to the hypothesis that is based on developmental data; that is, the digits of bird wings are homologous to digits 2, 3, 4 in other amniotes. Other additional problems with the frameshift hypothesis are also highlighted in the same review paper as clearly demonstrated here.  [12,]

Although morphological data remain in conflict with that of embryological, not all embryological studies support the II, III, IV bird wing digit hypothesis. Fate mapping methodology based on Shh expression (Sonic Hedgehog Gene) and polarizing regions that relied on developmental/anatomical criteria have revealed that the digits of the birds are I, II, & III, exactly as predicted by the fossil record.

In Towers’ 2011 paper entitled, “Insights into bird wing evolution add digit specification from polarizing region fate maps” which the paper leads to the support of digits I, II, III & axis shift hypothesis, the authors have concluded that the three digits found in the forelimbs of neornithines developed from positions I, II & III. [13]

However, this view has remained inconsistent with the accepted early condensation patterns for digit progenitors, which show that the three hand digits of modern adult birds developed from the three middle positions. [14, 7, 9]. Furthermore, the assumption that a single frameshift mutation is capable of shifting Digits I, II III into II, III, IV has been shown to be unreliable given that such mutation reveals no adaptive advantage. Rather numerous frame shifts are required to even create an adaptive advantage, as demonstrated by Alan and other researchers. [15]

Another embryology paper that claims to support the Digits I, II, III view is a 2011 paper entitled, “Embryological Evidence Identifies Wing Digits in Birds as Digits I, II, and III. The methodology used was similar to Towers’ 2011 paper, and although they arrived to the same conclusion of Digits 1, 2, 3, it did not support the axis shift hypothesis.

However, just like Vargas & Fallon’s paper, this paper has been reviewed and criticized by a 2011 Nature paper entitled, “Comment on Embryological evidence identifies wing digits in birds as digits 1, 2, and 3.” Here, the authors critiquing the paper found the authors’ conclusions to be flawed and unconvincing due to incorrect methodology as highlighted here.

In summary, the peer-reviewed science literature shows no clear evidence that birds derived from Theropod dinosaurs. Studies in palenotology/comparitive anatomy criteria often tend to create contradictory results when compared to the data of embryology and positional criteria. The fact that these two fields don’t generally agree with each other has become rather a great difficulty for establishing dinosaur to bird evolution. In either case, both morphological and embryological analyses lead to the support that the bird digits are either I, II, III or II, III, IV. However, given the problems for the frameshift hypothesis, it has no longer been generally supported. Rather a new alternative hypothesis, known as the lateral shift, has been more supported in recent literature. However, lateral shift hypothesis unlike frameshift no longer predicts that the digits of the bird wings are I, II, III as predicted in the fossil record. The lateral shift hypothesis proposes that the digits of the wings are II, III, IV, showing no homology at all between the digits of Theropods and birds.

Given the contrary results, evolutionists can no longer claim using fingered digits homology as a back up. Rather than the literature demonstrating evidence of dinosaur to bird evolution, it has rather demonstrated quite the opposite.

References:

[1]   Gauthier, J. 1986. Saurischian monophyly and the origin of birds. Memoirs of the California Academy of Sciences, 8: 1-55.

[2] Ostrom, J. 1977. Archaeopteryx and the origin of birds. Biological Journal of the Linnean Society, 8: 91-182.

[3] Romer, A. S. 1966. Vertebrate Paleontology, University of Chicago Press, Chicago.

[4] Sereno, P.C. 1993. Shoulder girdles and forelimb of Herrerasaurus. Journal of Vertebrate Paleontology, 13: 425-450.

[5] Shubin, N. & Alberch, P. 1986. A morphogenetic approach to the origin and basic organisation of the tetrapod limb. Evolutionary Biology, 20: 319-387

[6] Muller, G.B.& Alberch, P. 1990. Ontogeny of the limb skeleton in Alligator mississipiensis: developmental invariance and change in the evolution of archosaur limbs. Journal of Morphology, 203:151-164.

[7] Burke, A. & Feduccia, A. 1997. Developmental patterns and the identification of the homologies in the avian hand. Science, 278: 666-669.

[8] Welten,.C.M., Verbeek, F.J., Meijer, A.H. & Richardson, M.K. 2005. Gene expression and digit homology in the chicken embryo wing. Evolution and Development, 7,18-28

[9] Nowicki, J. & Feduccia, A. 2002. The hand of birds revealed by early ostrich embryos. Naturwissenschaften, 89: 391-393.

[10] Wagner, G.P. & Gauthier, J.A. 1999. 1,2,3=2,3,4: a solution to the problem of the homology of the digits in the avian hand. Proceedings of the National Academy of Science USA, 96: 5111-5116.

[11] Vargas, A.O. & Fallon, J. 2004. Birds have dinosaur wings: the molecular evidence. Journal of Experimental Zoology (Molecular Development and Evolution), 304B, 85-89.

[12] Galis, F., Kundrat, M. & Metz, J. A. J. 2005. Hox genes, digit identities and the theropod/bird transition. Journal of Experimental Zoology (Molecular Development and Evolution), 304B: 198-205.

[13] Towers M, Signolet J, Sherman A, Sang H, Tickle C: Insights into bird wing evolution ad digit specification from polarizing region fate maps.

[14] “Embryological Evidence Identifies Wing Digits in Birds as Digits I, II, and III

The problem of phylogenetic inference as means to establish common descent

Despite how widely evolution is taught across academia and considered to be strongly supported by science, there is an apparent conflict that exists and lurks deep in the shadows behind phylogenetic inference in support of common descent. Despite the widely held claim that evolution has been strongly supported by the utilization of phylogenetic or phylogenomic  (i.e. data derived from genome rather than individual genes) data, in reality the utilization of comparitive  anatomy / genetic sequencing establish true evolutionary history has been conflicting, though not necessarily mentioned to the students of academia.

There are two types of methods used to infer evolutionary relationships: 1) morphological & 2) molecular.

Phylogenetic relationships derived from morphological data is mostly what is known as comparative anatomy. Comparative anatomy involves the utilization of anatomical structures and doing a compare and contrast analysis. If two or more different taxon groups share anatomical features that underlie common morphological, for example the case of forelimbs, the radius, the ulna, etc. they are considered homologous. Homology is not necessarily dependent on whether two or more separate anatomical features look similar, but rather is defined on the basis of individual anatomical interdependent parts, that is the radius, the ulna, etc.

The essential idea is, if two or more different taxon share homologous features, those features must have been derived from a common ancestor. Similarly, in the case of molecular homology, that is the finding of nucleotide or amino acid sequence similarity between two different group species, it is also derived from common descent.  However, the logic of constructing phylogenetic relationships based on homologous anatomical structures or genetics is actually something not necessarily consistent with the scientific literature.

The Incomplete Lineage Sorting: A Problem for Evolution

In Rokas 2005 paper, “Animal Evolution and the Molecular Signature of Radiations Compressed in Time”

Here researchers sought to determine the evolutionary history of the animal phyla by analyzing about 50 genes across 17 taxa. At the same time, he hoped that a single dominant phylogenetic tree would emerge. Rokas and his team reported that

“a 50-gene data matrix does not resolve relationships among most metazoan phyla………..Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved”

Their conclusion was unambiguous: instead of them establishing true evolutionary history, they constructed inconsistent molecular phylogenies that contradicted evolutionary history. What was the cause of such incongruent phylogeny? The answer to that was a mysterious rapid ancient event known as incomplete lineage sorting. It is where the species have diverged extremely rapidly as opposed to speciating slowly. Due to the rapid divergence, like the Cambrian Explosion, genetic markers in genes from species has become rather elusive and quite difficult. Thus, generating numerous conflicting evolutionary relationships from genetics. Scientists like Rokas realized just how difficult it is to get high-resolution relationships when the divergence between them is extremely short, like during the ‘Cambrian explosion’, as is being researched in the paper.

Both Rokas and Carroll tried to explain the many contradictory molecular trees by proposing that the animal phyla might have evolved too quickly for the genes to record some signal of phylogenetic relationships into the respective genomes. In their view, if the evolutionary process responsible for anatomical novelty works quickly enough, there would not be sufficient time for differences to accumulate in key molecular markers, in particular those used to infer evolutionary relationships in different animal phyla.

Therefore, when groups of organisms branch rapidly and then evolve separately for long periods of time, this can overwhelm the true historical signal, leading to the inability to determine true evolutionary history. So unfortunately for evolutionists the argument of using all genetics to determine true evolutionary history doesn’t work either since the rapid divergence of species has corrupted the genetic markers that scientists use to establish a high resolution evolutionary history signal.

Not even the highly respected scientific findings of “evolution” has been found to be conclusive when it comes to establishing evolutionary relationships.

In the peer-reviewed paper, “Insect Phylogenomics: results, problems and the impact of matrix composition”

Researchers in this paper tried to establish evolutionary history of insect lineages using phylogenomic (i.e. genome data) & matrix data. As the abstract reads:

In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense).

Yet, despite evolutionary expectations of establishing such phylogeny, reality has flipped that expectation upside down as they have found problems in their data as quoted below:

Even though molecular studies on the insect phylogeny are legion [1–9], a consensus on the relationships between the insect orders is not yet in sight. The difficulties in reaching a robust phylogenetic tree are most probably due to an ‘ancient rapid radiation’ phenomenon [10–12]: most of the modern lower neopteran orders appeared in a geologically relatively short time span in the Early Mesozoic [13], followed by a long period of intra-ordinal diversification. Thus, only traces of phylogenetic signal are left in the data. Molecular analyses based on ribosomal RNA (rRNA) genes, complete mitochondrial (mt) genomes, and few housekeeping protein-coding genes, are not only plagued by this loss of phylogenetic signal, but also hampered by lineage-specific substitution rates and base compositional biases potentially misleading tree inference. For example, genes of flies (Diptera) show highly accelerated substitution rates, whereas genes of roaches (Blattodea) evolve comparatively slowly [3,10,13].

Corruption of ribosomal RNA, mitochondrial genomes, and protein-coding genes blurred out by non-sensical noise/misleading phylogeny? What happened to the so-called claim that evolution has been strongly supported with mountains of evidence containing no problems whatsoever? Sounds more like evolution has many holes in its theory given the numerous conflicts that exist in the scientific literature.

Even though researchers have acknowledged this problem, they tried to use reasonable approaches by trying to eliminate signal from noise and more prestigous approaches:

Our approach provides the first phylogenomic support for the monophyletic origin of several lineages of Polyneoptera, and for a sistergroup relationship between webspinners and stick insects (i.e. Eukinolabia). Furthermore, our analyses suggest a sistergroup relationship between true bugs and cicadas, leaf hoppers, and their allies. Since our analyses did not include several polyneopteran orders and thrips, as well as only one family of plant hoppers and leaf hoppers, respectively, they must be seen as preliminary and as a first step towards a phylogenomic approach to the reconstruction of inter-ordinal relationships.

but despite their best to establish true evolutionary history, they have found conflicts that still exist in their phylogenomic analysis,

Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.

So it seems that rather these evolutionists establishing a single phylogenomic tree, they have rather generated numerous conflicted groupings where one group of insect is said to be related to this certain insect group while ironically the other says no it is that other group. Due to the ambiguity found in evolutionary relationships, the evolutionists in the paper have failed to justify true evolutionary relationships given the numerous conflicts that exist. Thus, giving the researchers the expression of hope that better methods will and once for all prove evolution to be true.

Yet, that has all yet to be proven true.