Lenski’s E-coli Citrate Experiment: New Genetic Information?

 

Lenski’s 15 year (E-coli generation = 31,500) E-coli experiment (along with nylonase) is perhaps one of the most famous argument used by evolutionists as an illustration of evolution creating irreducible-like systems or novelty in action. The Long Term Evolutionary Experiment (i.e. LTEE) involved a certain group of bacteria known as E-coli that were isolated under aerobic conditions and eventually had the new evolved the ability to metabolize citrate. Lenski’s E-coli experiment is a well known tactic used by evolutionists to refute creation/intelligent design arguments by implying evolution is capable of creating novel biological proteins for cellular functions that did not otherwise exist before. Is this position reasonable? A cross-examination between the arguments used by evolutionists and actual peer-reviewed literature revealed no based on numerous points:

Point # 1: Despite the evolutionary claim of E-coli’s ability to metabolize citrate as new genetic material, it is not at all completely new.

On first sight, it may seem that Lenski’s E-coli experiment does indeed seem to show evolution in action, considering the fact that E-coli orginally lacked the ability to utilize citrate. However, this is not at all completely true. Contrary to popular belief, the ability for E-coli to metabolize citrate is really nothing special.

As demonstrated in a July 1982 peer-reviewed paper published in the Journal of Bacteriology by Barry G. Hall:

“Chromosomal Mutation for Citrate Utilization by Escherichia coli K-12,”

“E. coli is not, however, totally inert toward citrate. It may utilize citrate anaerobically provided that a second substrate such as glucose or lactate is available to provide reducing power for the formation of succinate from oxaloacetate (13). The failure of E. coli to utilize citrate aerobically has been attributed to the absence of a citrate transport system (10), but the co-metabolism of citrate implies that E. coli does possess a citrate transport system that functions anaerobically (13).”- Barry G. Hall

Based on the paper, it seems that E-coli did indeed actually already had the ability to metabolize cirate in the first place although it was restricted. Originally, they are limited to utilizing citrate only under anaerobic conditions, meaning they were only capable of doing so under an environment that is absent of oxygen. So here’s a question to consider. Is citrate really something that is completely new? The true answer is no, as E-coli already possessed the genetic information to utilize citrate although restricted to the level where oxygen is absent.

Point # 2: E-coli’s ability to utilize citrate under oxic conditions is actually nothing more but a modification of an already existing system rather than a novel one.

By contrast, Lenski’s E-coli experiment involved isolation of the bacterial population with citrate under aeorboic conditions, i.e. environments with oxygen present. Due to the limitation stated above, they were unable to metabolize citrate. However, as Barry Hall has explained in his 1982 paper:

“(13). The failure of E. coli to utilize citrate aerobically has been attributed to the absence of a citrate transport system (10), but the co-metabolism of citrate implies that E. coli does possess a citrate transport system that functions anaerobically (13).”

To rephrase, the reason why E-coli lacked the ability to utilize citrate was due to the fact of E-coli lacking a ‘citrate transport system’ that although functional under the absence of oxygen, is non-functional under such conditions. Even Lenski himself has suggested this in his paper, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli,”

“A more likely possibility, in our view, is that an existing transporter has been coopted for citrate transport under oxic conditions. This transporter may previously have transported citrate under anoxic conditions (43) or, alternatively, it may have transported another substrate in the presence of oxygen. The evolved changes might involve gene regulation, protein structure, or both (61).” – Lenski

How did the citrare metabolism under aerobic conditions came about?

According to Barry G Hall in his 1982 paper, the ability for E-coli to metabolize citrate under oxygenated conditions was due to “genetic recombination” (the shuffling of pre-existing genetic information) that involved the activation of the so-called cryptic genes.

“The mutational activation of these genes suggests that they should be considered cryptic genes which have persisted in a silenced state since E. coli diverged from its Cit+ ancestor. That suggestion is supported by the observation that the kinetic parameters for citrate uptake in strain D2004 are of the same order as those for succinate uptake in E. coli (Km = 14 ,uM succi- nate; Vm,, = 20 ,umolImin per g [dry weight]) (11). It is unlikely that mutations conferring a specificity for citrate upon some already existing transport system would result in such a low Km for citrate. More detailed comparisons between the citrate transport system of strain D2004, the citrate transport systems specified by Cit+ plasmids in E. coli, and citrate transport systems of such citrate-utilizing organisms as Salmonella and Klebsiella should shed some light on the possibility that the citrate genes are cryptic in wild-type E. coli”

 Cryptic genes are silently phenotypic genes not normally expressed in the normal life cycle of organisms. They are silent genes and unexpressed, though giving the name cryptic. Interestingly though, cryptic genes are remotely activated and involved in helping organisms adapt to their environment whenever exposed to extreme environmental stress stimuli or selective pressure. They are activated by the cell rearranging its genome such as transposable genetic elements (genes that can copy-paste or cut-paste from one genome position to another or chromosome) Cryptic activation is believed to be a non-random and intelligent targeted response though this remains controversial.

It seems that E-coli rather obtained the ability to metabolize citrate via not by gene duplication but the mere activation of pre-existing cryptic genes. Despite what evolutionists claim that gene duplication created new genetic information of citrate in E-coli, it did not. Rather gene duplication was found to be more of an “amplifier” that helped them to metabolize citrate more effectively than they would without it. However, the modified pre-existing gene that gave them the capacity to utilize citrate under oxygen substrates had already existed long before gene duplication even took place.

How does this demonstrate that evolution is capable of creating brand new biological systems? Truth is it doesn’t. As  Hall has stated in his paper, the ability for E-coli to metabolize citrate was derived from an already existing complex biological system expressed from the activation of ‘cryptic genes.’ Rather than demonstrating the evolutionary origin of where biological systems actually come from, it only demonstrated a mere modification of an already existing system that adapted itself to function in oxygen conditions. Yet, no new component, no new novelty was actually generated in the evolution of citrate.

Point # 3: E-coli’s ability to use citrate is not new genetic information, not according to creationists but also to the 2016 peer-reviewed paper:

After doing a literature review, I came across an interesting 2016 peer-reviewed science paper entitled, “Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA,”

This paper, rather than supporting the neo-Darwinian synthesis of evolution, criticized the common evolutionary claim of Lenski’s experiment being great evidence for new genetic information. Despite such criticism over the evolutionary claim of new genetic information, somehow it managed to pass peer-review. As the researchers in the paper quote:

“We conclude that the rarity of the LTEE mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.”

No new genetic information? Well, there you have it folks. No new genetic information was actually generated in Lensi’s E-coli experiment.

Despite the fact that it took Lenski 15 years of experimentation for E-coli to metabolize citrate under aerobic conditions (i.e. 31,500 generations), the previously quoted study “Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA,” found E-coli already doing so in 12 to less than 100 generations.

and yet, contrary to the 2016 paper, the opposite was rather demonstrated:

“Importantly, potentiated and actualized E. coli Cit-strains were obtained in as few as 12 generations and refined phenotypes in fewer than 100 generations. Phenotypic and geneticanalyses of these E. coli Cit-strains provided insight into the mechanism for the adaptations and suggested why the LTEE took 33,000 generations to reach this phenotype. Also, this study provided a unique opportunity to compare the results of a direct selection with those of a long-term genetic screen. Finally, because this adaptation did not generate any new genetic information and required expanded expression of only two existing transporters (citT and dctA), generation of E. coli Cit-phenotypes in our estimation does not warrant consideration as a speciation event”

With just 12 to less than 100 generations, E-coli already had the ability to metabolize citrate under aerobic conditions. 12 to less than 100 is nothing compared to Lenksi’s 31,500 exact generations.

Also there was no significant difference between the E-coli in the 2016 paper to that of Lenski’s LTEE (Long Term Evolutionary Experiment) as they both had the same genetic material, making it a justifiable comparison. What was the reason why Lenski’s E-coli took more than 30,000 generations to develop citrate metabolism but only 12 to 100 in the 2016 paper? The reason was the difference in selection. The selection used in the 2016 paper was directive, as the E-coli were forced to try to metabolize citrate. Due to the extreme conditions, a certain population of E-coli was able to metabolize citrate quite rapidly in very few generations.

On the other hand, Lenski’s LTEE was not directive, as the E-coli were not forced only to citrate conditions. Rather the E-coli in Lenski’s experiment was free of selection, as they were exposed to other resources to obtain energy.

but regardless,  they were clearly criticizing Lenski’s finding:

In summary, E. coli can rapidly mutate to a Cit-phenotype in
a relatively short time if subjected to direct selection. This indi-
cates that the 33,000 generations to potentiate the evolutionary
resources for the Cit-phenotype do not reflect a direct requirement but merely experimental conditions. As such, Cit-mutants exemplify the adaptation capability of microorganisms but, as ofyet, the LTEE has not substantiated evolution in the broader senseby generation of new genetic information, i.e., a gene with a newfunction. Interestingly, our findings parallel the conclusions from bacterial starvation studies by Zinser and Kolter (44) in which E.coli adaptations were dominated by changes in the regulation ofpreexisting gene activities rather than by the generation of new gene activities, de novo. The LTEE isolation of Cit⁺ mutants has become a textbook example of the power of long-term evolution to generate new species. But, based on our results, E. coli arrives at the same solution to access citrate in days versus years, as originally shown by Hall (14). In either case, genes involved in the process maintain their same function but show expanded expression by deregulation. Because of this, we argue that this is not speciation any more than is the case with any other regulatory mutant of E. coli. A more accurate, albeit controversial, interpretation of the LTEE is that E. coli‘s capacity to evolve is more limited than currently assumed.

There you have it, no new genetic information was actually generated in the evolution of E-coli’s ability to metabolize citrate.

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. 

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.

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