Can fish make fishy fingers? & Did They ever actually walk? Or even learn to ride a bike?
An article on a popular science website discusses an interesting experiment relating to the Hox family of genes (that act like master switches during development and turn other gene sequences on or not). It is entitled: How the genetic blueprints for limbs came from fish.
[…] the transitional path between fin structural elements in fish and limbs in tetrapods remains elusive. Both fish and land animals possess clusters of Hoxa and Hoxd genes, which are necessary for both fin and limb formation during embryonic development. Scientists compared the structure and behavior of these gene clusters in embryos from mice and zebrafish. The researchers discovered similar 3-dimensional DNA organization of the fish and mouse clusters, which indicates that the main mechanism used to pattern tetrapod limbs was already present in fish. […]
Does this imply that digits are homologous to distal fin structures in fish? To answer this question, the geneticists inserted into mice embryos the genomic regions that regulate Hox gene expression in fish fins. ‘As another surprise, regulatory regions from fish triggered Hox gene expression predominantly in the arm and not in the digits. Altogether, this suggests that our digits evolved during the fin to limb transition by modernizing an already existing regulatory mechanism’, explains Denis Duboule.
[…] Fin radials are not homologous to tetrapod digits.
The researchers conclude that, although fish possess the Hox regulatory toolkit to produce digits, this potential is not utilized as it is in tetrapods. Therefore, they propose that fin radials, the bony elements of fins, are not homologous to tetrapod digits, although they rely in part on a shared regulatory strategy.
The key phrase in this article in my opinion is …fin radials, the bony elements of fins, are not homologous to tetrapod digits, “although they rely in part on a shared regulatory strategy”. The other important part of the above article, is that the fact that the fish Hox complex was not able to activate digits in the mouse, which we know the mouse has the materials to build such limbs, and therefore, the limitation may lie in the less sophisticated Hox complex of the fish as suggested in the above article. Furthermore, the skeleton architecture of even the most developed fish even today lack girdles and attachments for limbs that would support a large limb (ed) tetrapod’s body.
In combination, this is good supporting evidence for fish remaining fish as the fossil record does not present any convincing evidence for the transition between certain types of lobbed-finned fish and walking tetrapods as I will discuss below. And the fossil-fish record shows nothing but all varieties of fish up to our present day, including ones we thought were extinct and used to be candidates for this transition.
I will argue that Hox genes are the reason why fish cannot make fishy fingers, but other vertebrates with the same tool-kit can. For example, feet are no good to fish, but fins are very useful to vertebrates that live in water. But first I will review some of the conventional interpretation of the fossil record and recent studies addressing this so-called transition of fin to foot or what I call the Walking Fish hypothesis.
Below, for example, is a very recent article on the updated Hox gene study that I discussed above regarding the activation of digits in mice via Hox gene complex and the lack of activation of actual digits in fish employing the same genetic switch mechanism.
Deep conservation of wrist and digit enhancers in fish
There is no obvious morphological counterpart of the autopod (wrist/ankle and digits) in living fishes. Comparative molecular data may provide insight into understanding both the homology of elements and the evolutionary developmental mechanisms behind the fin to limb transition. In mouse limbs the autopod is built by a “late” phase of Hoxd and Hoxa gene expression, orchestrated by a set of enhancers located at the 5′ end of each cluster. Despite a detailed mechanistic understanding of mouse limb development, interpretation of Hox expression patterns and their regulation in fish has spawned multiple hypotheses as to the origin and function of “autopod” enhancers throughout evolution. Using phylogenetic footprinting, epigenetic profiling, and transgenic reporters, we have identified and functionally characterized hoxD and hoxA enhancers in the genomes of zebrafish and the spotted gar, Lepisosteus oculatus, a fish lacking the whole genome duplication of teleosts. Gar and zebrafish “autopod” enhancers drive expression in the distal portion of developing zebrafish pectoral fins, and respond to the same functional cues as their murine orthologs. Moreover, gar enhancers drive reporter gene expression in both the wrist and digits of mouse embryos in patterns that are nearly indistinguishable from their murine counterparts. These functional genomic data support the hypothesis that the distal radials of bony fish are homologous to the wrist and/or digits of tetrapods.
Yes, now they are saying that these are probably homologous – that is the fins and digits in these species. It does get confusing as the earlier study of mice and fish Hox gene activation did not develop anything resembling digits in the fish. However, the important part of the article is that they at least acknowledge the epigenetic processes involved in the Hox expression and the fact that they haven’t conclusively demonstrated anything and only tentatively hypothesize that distal radials and digits in tetrapods are homologous. I believe the link between fins and feet is still missing and that epigenetic processes and environmentally triggered activation of particular genes is the key to this rather quantum-like transition from water to land. I’ll return to this below.
Now some of you might think that we actually have the evidence in the fossil record for this fish that learned to walk and therefore the definitive proof for these homologous distal fins to fishy fingers. So let us look a little closer at the evidence. According to conventional thinking (walking fish hypothesis), it took almost 200 million years for this fishy-pod to evolve limbs that could walk and a whole breathing apparatus and many, other things that allow a fish to live in water rather than land. Yet we have no evidence of this great feat of biological engineering, at least not using our conventional understanding of this scenario.
“Our first four-legged land ancestor came out of the sea some 350 million years ago. Watching a lungfish, our closest living fish relative, crawl on its four pointed fins gives us an idea of what the first evolutionary steps on land probably looked like. However, the transitional path between fin structural elements in fish and limbs in tetrapods remains elusive. […]
Millions of dollars later and with much concerted effort in 2004, they found it: a real contender for the walking tetrapod was an early lobe-finned fish, which propped itself up in shallow fresh water known as tiktaalik. The only problem was the more recent discovery of fossilized tetrapod tracks, which are dated to some 18 million years before the tiktaalik fossil, and actually several million years before the time that lobe-finned fish were believed to be paddling about in muddy water trying to grow some walking limbs. The fossil record of the earliest tetrapods (vertebrates with limbs rather than paired fins) consists of body fossils and trackways.
The fossil record of the earliest tetrapods (vertebrates with limbs rather than paired fins) consists of body fossils and trackways. The earliest body fossils of tetrapods date to the Late Devonian period (…) and are preceded by transitional elpistostegids such as Panderichthys and Tiktaalik that still have paired fins. Claims of tetrapod trackways predating these body fossils have remained controversial with regard to both age and the identity of the track makers. Here we present well-preserved and securely dated tetrapod tracks from Polish marine tidal flat sediments of early Middle Devonian (Eifelian stage) age that are approximately 18 million years older than the earliest tetrapod body fossils and 10 million years earlier than the oldest elpistostegids. They force a radical reassessment of the timing, ecology and environmental setting of the fish–tetrapod transition, as well as the completeness of the body fossil record. (In Nature by Niedźwiedzki et al, 2010 Abstract)
Maybe we really do need another way of non-vertebrate tetrapods to become land-walkers. How about Leap-frog evolution? But first let us look at the other evidence for evolving fish that ended up remaining fish and not changing all that much over the 100s of millions of years of their existence.
In an article in Science Now, the title reads: “Living Fossil” Gets its genome sequenced (2013) and states the following:
“The coelacanth isn’t called a [“living fossil”] for nothing. The 2-meter-long, 90 kg fish was thought to have gone extinct 70 million years ago—until a fisherman caught one in 1938—and the animal looks a lot like its fossil ancestors dating back 300 million years. Now, the first analysis of the coelacanth’s genome reveals why the fish may have changed so little over the ages. It also may help explain how fish like it moved onto land long ago. […]
Then, the same article goes on to explain what they found after sequencing its genome:
“[…] they calculated the number of estimated changes that occurred in the genes over the time since the coelacanth branched off from other vertebrates on the animal family tree. Finally, they compared those data with the corresponding rates of genetic change in various mammals, lizards, birds, and fish. The coelacanth genes changed at a [“markedly”] slower rate than those from other animals, […] The genes of lizards and mammals evolved at least twice as quickly as those of the coelacanth, the team reports online today in Nature. That could explain, […], why the fish has changed so little in 300 million years. ”
Essentially, it seems that as fish are well-established even in the early Cambrian as fish and go from primitive forms from the outset of the Cambrian period to rapidly evolving fish throughout this period and into the next major epoch of time. This is all before anything colonized land, not even the plants or soils or the insects or first tetrapods. Therefore, it is only logical to look for potential code-carrying stem-chordates that haven’t become primitive fish even millions of years later in the Middle Cambrian period and seem to be still floating around in their primordial pond. The type of floating, pooping, filter-feeding body-form (as yet not defined, just like a larval/embryo stage of speciation) would appear to be a good candidate – the elegant one that hasn’t decided what it will become when it grows up. Interestingly, this is the only chordate type (I’m sure there were many more with different evolutionary histories and epigenetic coding hidden inside – but who would know what it would become), that is now extinct (apparently) in its current form. It makes you wonder, why this chordate turns up in the Middle Cambrian and is never seen again. Could it be that it metamorphosed into something else more interesting, but in the interim (almost 100 million years later) still quietly evolving?
Descent with modification via Hox genes:
In an EVO-DEVO paper by Gilbert S. F. in Developmental Biology (2000) entitled: Hox Genes: Descent with Modification, as the title implies, Gilbert views evolution as being driven in part by a commonly shared process/mechanism, a tool-kit, if you like, by which basic body-plans of organisms such as animals can be laid out (built modular-ly) according to a specific set of instructions as Gilbert states: “This means that the enormous variation of morphological form in the animal kingdom is underlain by a common set of instructions” http://www.ncbi.nlm.nih.gov/books/NBK9978/
Gilbert also outlines the evolution of the mechanism has itself evolved and in turn, evolved and adapted many life-forms, which is a rather rapid and large means of changing a species (macro-evolutionary change).
The number of Hox genes may play a role in permitting the evolution of complex structures. All invertebrates have a single Hox complex per haploid genome. In the most simple invertebrates—such as sponges—there appear to be only one or two Hox genes in this complex […] In the more complex invertebrates, such as insects, there are numerous Hox genes in this complex. […].
By the time the earliest vertebrates (agnathan fishes) evolved, there were at least four Hox complexes. The transition from amphioxus to early fish is believed to be one of the major leaps in complexity during evolution […]. This transition involved the evolution of the head, the neural crest, new cell types (such as osteoblasts and odontoblasts), the brain, and the spinal cord. […]
1. Commonly shared set of instructions – a toolkit of MASTER switches that turn genes on or off during development of an organism.
2. This underlying set of instructions is common to all animals and the number of switches or complexes corresponds to the fundamental complexity of the animal. E.g. invertebrates are much simpler animals than vertebrates.
3. This results in MACRO-EVOLUTIONARY VARIATION and LEAPS of COMPLEXITY.
4. The mechanism itself has EVOLVED, causing evolutionary complexity.
So where did the set of instructions come from? How does an evolving/developing organism know what sequence, when and where to switch genes on or not?
Hox genes – epigenetic switches and the common ancestral evolutionary toolkit
There can be a significant degree of species divergence depending upon when, where and why certain genes were expressed (in the evolutionary past) via genetic switches (the Hox complex) according to environmental conditions and species complexity. How genes were expressed in the past when the species itself was forming according to its adaptive needs, which is essentially epigenetic evolution in action. For instance, in an article relating to the NOVA channel documentary entitled: Ghosts in your genes
the following is stated:
[…]Gene switches such as Ubx make the initial decisions of which genes to turn on or off in different body regions and cell types. .. This highly evolved, highly orchestrated ability to make genes active or inactive—both genetically and epigenetically—is the key to the success of multicellular plants and animals, including the most complex and mysterious of all, us.
In a science paper entitled: Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium by
Soshnikova N1, Duboule D., they state the following in their abstract:
Temporal and spatial control of Hox gene expression is essential for correct patterning of many animals. In both Drosophila and vertebrates, Polycomb and Trithorax group complexes control the maintenance of Hox gene expression in appropriate domains. In vertebrates, dynamic changes in chromatin modifications are also observed during the sequential activation of Hox genes in the embryo, suggesting that progressive epigenetic modifications could regulate collinear gene activation.
Epigenetics. 2009 Nov 16;4(8):537-40. Epub 2009 Nov 21
Another science paper outlines the following:
The outcome is profoundly influenced by the role of epigenetics through transcriptional regulation of key developmental genes. Epigenetics refer to changes in gene expression that are inherited through mechanisms other than the underlying DNA sequence, which control cellular morphology and identity. It is currently well accepted that epigenetics play central roles in regulating mammalian development and cellular differentiation by dictating cell fate decisions via regulation of specific genes.
Among these genes are the Hox family members, which are master regulators of embryonic development and stem cell differentiation and their mis-regulation leads to human disease and cancer. The Hox gene discovery led to the establishment of a fundamental role for basic genetics in development. Hox genes encode for highly conserved transcription factors from flies to humans that organize the anterior-posterior body axis during embryogenesis. Hox gene expression during development is tightly regulated in a spatiotemporal manner, partly by chromatin structure and epigenetic modifications. Here, we review the impact of different epigenetic mechanisms in development and stem cell differentiation with a clear focus on the regulation of Hox genes.
Ann Anat. 2010 Sep 20;192(5):261-74. doi: 10.1016/j.aanat.2010.07.009. Epub 2010 Aug 6. http://www.ncbi.nlm.nih.gov/pubmed/20739155
There are many other science papers on the topic of the epigenetic regulation/control of genetic switches such as the Hox gene cluster that act as master switches for other genes and are fundamentally important during the earlier stages of development and therefore evolutionary development of a species and all it would take for a reptile to lose its legs and become a snake is for a set of genes not to be activated as documented in Gilbert’s paper quoted at the beginning of this blog and entitled: Hox Genes: Descent with Modification. Therefore, it should not stretch the imagination to see how fish might remain as water-living vertebrates not requiring legs, just fins, while, as-yet-undefined species of basal groups of chordata (proto-fish & proto-tetrapods) with as yet, unexpressed genetics, had the wear-withal to produce actual digits instead of just floppy fins – eventuality, when the time (environmental conditions) was just right.
Epigenetics activation of dormant gene potential will only occur when the time is right for a species to become all it can be. I call this the Goldie Locks evolutionary adaptation model and it is based upon Lamarck’s observations and common sense, that a spring flower does not bud in the middle of Autumn. Now another way of looking at all this is: that organisms go from the primitive form with a shared common ancestral condition and that some organisms simply don’t express their full potential as they adapt more rapidly to their environmental niche than others as indicated in the fossil record, within developmental studies (EVO-DEVO), epigenetic studies and historically demonstrated in terms of Lamarckian principles around the turn of the 20th century as discussed in my books on the subject, forthcoming and already published (See book section on this blog).
What I’m proposing, is not new. I didn’t sit down and invent it. No, I just studied deeply the past evolutionary ideas beyond the Neo-Darwinian doctrine and I assessed these in the light of our most recent molecular data. I found that this concept was not unlike what Lamarck and others had conceived, now being borne out in molecular studies, that evolution proceeds from the primitive and less defined to the more complex and specialized across all domains of life – from a common ancestral condition or, using a common ancestral tool-kit, rather than literal simplistic common descent from a fully speciated fish, even if it is supposed to be a fishypod creature with loppy fins. For instance, Dr. Butler is a Professor Emerita (retired) in the Molecular Neuroscience Department in the Krasnow Institute for Advanced Study states the following: in Evolution of Vertebrate Brains:
… reptiles did not give rise to mammals any more than mammals gave rise to reptiles. In regard to embryological development, it likewise generally proceeds from the general (common ancestral features) to the specific (specializations of the taxon) […]. What is clearly established is that all taxa have their own specializations. Each taxon has a mix of primitive features.
The conclusion in this brain vertebrate study clearly indicates that the simplistic common descent model may be flawed. Indeed, increasing evidence suggests that all complex animals have evolved from their essential primitive form, COMMON ANCESTRAL CONDITION towards increased specialisation within their ecological niche. For example, a fish doesn’t need feet because fins are more efficient for its watery niche. Back before Darwin’s evolutionary theory was published, for decades before this, many believed in analogous forms that were independently evolved via a shared common FUNCTION rather than direct common ANCESTRY (convergent evolution as it would be known today), a type of archetype (template) upon which nature developed many variations upon the same basic theme.
Indeed, one way of explaining why some proto-fish remained fish and never expressed digits can be seen in the scientific studies dealing with gene silencing within an organism when it has reached its fundamental level of complexity. In principle, this is very similar to how Lamarck, in a pre-genetic world, over 200 years ago, seen evolutionary development – Lamarck seen evolution of fundamental forms (going from the generalist to the specialist) until the organism reached its fundamental limit of evolution, driven by environmental factors and needs (adaptive needs) of the organism which we now know as epigenetic inheritance of acquired characteristics. Furthermore, an organism is particular adaptable when it is in its more primitive (less fixed) state as Lamarck had long ago proposed.
Again, these concepts are finding support via our most recent molecular studies. For instance, according to studies by Adrian P. Bird from the Institute of Cell and Molecular Biology, University of Edinburgh, the first main level of life’s complexity that we can detect is associated with prokaryote to eukaryote transition and the next great transition is between the animals which fall into two main types: invertebrates (less complex creatures with no backbone such as worms and jelly fish) and the vertebrates (more complex animals with a backbone such as fish and ourselves). Bird, shows that the timing of earlier evolution is not linear and as simple as you might think. For example, in his recent paper regarding the eukaryote and vertebrate evolution he states the following in an abstract regarding gene activity at these fundamental (macro-evolutionary) boundaries:
“Preliminary estimates suggest that gene number, and hence biological complexity, increased suddenly at two periods of macroevolutionary change (the origin of eukaryotes and the origin of vertebrates), but otherwise remained relatively constant. As the genome is in constant flux, what normally constrains the number of different genes that an organism can retain? Here, I suggest that an important limitation on gene number is the efficiency of mechanisms that reduce transcriptional background noise. The appearance of both eukaryotes and vertebrates coincided with novel mechanisms of noise reduction”.
An Alternative scenario to the Neo-Darwinian view would best be described as: convergent evolution according to environmental adaptation and genome silencing once an organism has efficiently adapted (macro-evolution) to its niche. E.g a fish is a fundamental species of vertebrate that can only live in water. If, as the record (fossil) shows, fish adapted more rapidly (became genomic-ally silenced perhaps) than more complex tetrapod generalists such as amphibians, part water-living vertebrates: part-land-walking vertebrates depending on their evolutionary maturity or stage. This is what I would call evolutionary metamorphosis – tadpole-like stage into tetrapod stage. Hybridization, HGT (horizontal gene transfer across distinct species boundaries and domains of life) along with WGD (whole gene doubling) are some of the ways diversity and novel genes can provide the genetic fuel for profound evolutionary leaps in complexity, and by which, environment (epigenetic regulation of gene expression) can shape and sculpt an organism towards increased specialization within its environmental niche – going from the generalist to the specialist.
If we see evolutionary development as akin on a much greater scale to embryonic development (See anything on Von Baer’s laws dating to before Darwin’s time), then we begin to get an insight into how organisms used a common ancestral mechanism to adapt and evolve without having had a direct common ancestor from which adaptation and change were only possible by directly inheriting their genes in mutation/selection terms as the Neo-Darwinists would have us believe.
This more recent understanding of the molecular basis of evolutionary development being broadly and in principle reflective of the development of the embryo itself (going from the general ancestral condition to more specialized and diversified forms) directly reflects older less literal common descent models such as Lamarckian principles of evolution in much looser larger classes of fundamental divisions rather than strict classifications of species – evolution going from the primitive (less perfected) forms to more perfected and specialized forms, within their fundamental domains of life.
This is perhaps the most profound aspect of attempting to find an over-arching principle that might reveal how evolution unfolded; an alternative to the Darwinian simplistic common descent model, which is not borne out in the fossil record, or by our deeper understanding of the hidden aspects of the genome or epigenome, or what is revealed within microbial or molecular studies.
Just some more thoughts on evolutionary alternatives that explain the fossil record much better, in my opinion, than our current model of evolutionary thought, which is after all, just an hypothesis that was proposed: it was never proved and should always be open to scrutiny, particularly as new data contradicting it emerges.