Whale of a Tale: Straining at Mutational Gnats While Swallowing Genetic Camels
Evolution News & Views
If there was ever a prime hunting ground for evolutionary evidence in the genes, it should be in the relationship between land mammals and marine mammals. Think of the obvious differences between a four-footed ancestor and a whale: the scope of the genetic changes necessary to transform one into the other in a relatively short time would be staggering.
According to Darwin's theory, furthermore, it happened three times! Cetaceans (dolphins and whales), pinnipeds (seals, sea lions and walruses), and sirens (manatees and dugongs) are believed to have evolved their seagoing lifestyles independently within the last 60 million years.
Three scientists from the University of Pittsburgh looked into the genes for insight into this "great transformation" undertaken by the three groups of marine mammals. In a paper in Molecular Biology and Evolution, they announce the discovery that "Hundreds of genes experienced convergent shifts in selective pressure in marine mammals" [emphasis added].
A look at the details, though, gives a critical reader cause to think celebrations might be a tad premature. Why? Well, for one thing, shouldn't there be thousands? In the film Living Waters, Richard Sternberg considers the number of adaptations required to be "unfathomably complicated" to allow a land animal to live entirely in an aquatic environment. The film lists just a few categories of adaptations for humpback whales:
Respiratory system
Locomotive structures
Musculoskeletal system
Dentition
Urinary system
Cardiopulmonary system
Thermoregulation
Sensory organs
Reproductive organs
You can imagine any of these outward changes requiring thousands of genetic changes. "Just think of all the parameters that would have to be modified," Sternberg says, "and then multiply that by, I don't know -- a thousandfold, or more than that. That's the scale of the problem that you're dealing with." In the Q&A feature of the film Icons of Evolution, David Berlinski tried to quantify the number of morphological changes necessary to turn a cow into a whale (like turning a car into a submarine), and stopped counting at 50,000.
It's hard, therefore, to get excited about "hundreds of genes" announced by the Pittsburgh crew. Do these genes deal with the major modifications in whales? You decide:
We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals.
Let's grant that adaptations to skin, muscles, lungs, and sensory systems are important. It's a little odd that they get excited about "loss of function" in taste and smell that "has been suggested to result from change in prey, swallowing food whole, and the masking of tastes by seawater." That sounds Lamarckian. You'd hope to hear about how Darwinian natural selection produced one of the real innovations, like the origin of dolphin sonar, the blowhole, the tail fluke, or the cooling system for the internalized male testes described in Living Waters. But score a few points for Darwin. Not quite 50,000, but four or five.
But wait! When you look into the details of the paper, you find reasons to doubt even the examples they offer as evidence of positive selection in the genes.
First of all, they didn't really witness genetic evolution as much as convergence in the "rate" of change in genes that they assume occurred by evolution. Isn't that circular? Don't you have to believe the animals evolved in the standard evolutionary timeline before accepting this as evidence?
While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment.
In other words, they looked at the endpoint differences and merely assumed natural selection brought them about. Design advocates would expect the differences were planned for the aquatic lifestyle of these mammals.
Second, cases of "positive selection" appear strained. They "observed strong evidence of positive selection and a marine-acceleration in a large number of skin-associated proteins." They claim further positive selection for some lung surfactant proteins. But those are only building-block changes; they say nothing about how hairy cowhide turned into tightly-knit, waterproof armor over blubber arranged into a long, sleek form suitable for gliding in water. They didn't say how the skin took form in fins and a powerful tail fluke. They couldn't even rule out that the rate increases were due to selective pressure from pathogens on the skin and lungs in seawater.
A third problem is that the genetic changes do not appear specific to marine mammals.
All of the marine-accelerated genes under positive selection also showed significant evidence of positive selection across the mammalian tree (Supplemental Table S1), so their positive selection is not specific to marine branches. However, they did nevertheless show increased evolutionary rates on marine branches, suggesting these genes experienced a greater pressure to adapt in the marine environment (Supplemental Table S3).
Anyone see a strong genetic case for cow-to-whale evolution? Fourthly, the researchers in many cases could not rule out neutral evolution. (Here's where the camel trots in.) It's hard to know whether to laugh or cry at the imploding story:
Convergent changes on marine branches could have resulted from neutral processes or alternatively due to positive selection for the same amino acid variant. For the latter case, we would expect there to be more convergent amino acid changes in these genes for marine species compared to negative control species. We tallied convergent changes within a control set of species not expected to show convergence and chosen to match the topology and branch lengths of the marine species (Supplemental Fig. S3C) (alpaca, camel and their ancestral branch, bushbaby, human, and aardvark). As an additional control, we tallied the convergent changes between the marine and control branches (Supplemental Fig. S3D). The marine branch dataset did not show an excess of convergent amino acid sites (mean proportion = 0.086) compared to the control datasets (0.088 and 0.052, for control branches and marine-versus control branches, respectively) (Supplemental Fig. S3). Furthermore, the proportion of convergent changes on marine branches is small compared to the amount of excess changes that led to the acceleration in relative rate (mean proportion = 0.549; Supplemental Fig. S3B). Overall, we found no evidence for adaptively driven site- and amino acid-specific convergence in marine-accelerated genes.
This is sad. There was far greater evidence for "relaxation of constraint" than for positive selection (that's the kind of evolution that turns cave fish blind). There was NO evidence for "adaptively driven" change to the genes they decided had "accelerated" their evolution. Here's where the gnat flies into the picture:
On the other hand, marine-accelerated genes participating in olfaction, gustation, and muscle function exhibited overwhelming evidence of relaxation of constraint. These observations included greatly accelerated rates consistent with neutral evolution and even obvious genetic lesions and pseudogenization (e.g. GNAT3).
Obviously, genetic lesions (deleterious mutations) and pseudogenization are not going to help a cow swim. In Living Waters, Sternberg showed mathematically that it would take longer to expect just two cooperative mutations to occur than the maximum time expected for the entire evolution of a whale (100 million years vs 9 million years).
If this is the best evidence for the story of a Darwinian transformation of a land animal into a successful full-time marine creature, they should watch Living Waters and consider the explanatory power of "Intelligent Design in the Oceans of the Earth." It's not enough to point to possible amino acid differences here or there (not specific to marine mammals, and not clearly tied to innovative complex structures like echolocation) and announce Q.E.D. by saying they might have evolved faster in whales than they did with camels.
A good scientific explanation needs to account for the whole animal, with all its parts. A designing intelligence knows how to integrate multiple complex systems for function. Unguided natural processes are incapable of that, as Granville Sewell illustrated here with tornadoes and iPhones recently.
Once the materialistic bias against intelligence is lifted from the causal toolkit, science is liberated from an unnecessary restriction against knowledge. Sternberg says in the film:
Darwinism provided an explanation for the appearance of design, and argued that there is no Designer -- or, if you will, the designer is natural selection. If that's out of the way -- if that just does not explain the evidence -- then the flip side of that is, well, things appear designed because they are designed.
Whales illustrate a "global architecture that only a mind can bring about," Paul Nelson adds.
The data from genetics and molecular biology and a host of other fields have proven impossible to reconcile with undirected material causes. And, if science is an open-ended search for the truth, regardless of where the evidence leads, then what difference should it make if it leads to an intelligent cause?
Straining at irrelevant details to support a predetermined narrative because of some arbitrary rule that disallows non-material causes blinds science to the obvious. It strains at gnats while swallowing camels.
Evolution News & Views
If there was ever a prime hunting ground for evolutionary evidence in the genes, it should be in the relationship between land mammals and marine mammals. Think of the obvious differences between a four-footed ancestor and a whale: the scope of the genetic changes necessary to transform one into the other in a relatively short time would be staggering.
According to Darwin's theory, furthermore, it happened three times! Cetaceans (dolphins and whales), pinnipeds (seals, sea lions and walruses), and sirens (manatees and dugongs) are believed to have evolved their seagoing lifestyles independently within the last 60 million years.
Three scientists from the University of Pittsburgh looked into the genes for insight into this "great transformation" undertaken by the three groups of marine mammals. In a paper in Molecular Biology and Evolution, they announce the discovery that "Hundreds of genes experienced convergent shifts in selective pressure in marine mammals" [emphasis added].
A look at the details, though, gives a critical reader cause to think celebrations might be a tad premature. Why? Well, for one thing, shouldn't there be thousands? In the film Living Waters, Richard Sternberg considers the number of adaptations required to be "unfathomably complicated" to allow a land animal to live entirely in an aquatic environment. The film lists just a few categories of adaptations for humpback whales:
Respiratory system
Locomotive structures
Musculoskeletal system
Dentition
Urinary system
Cardiopulmonary system
Thermoregulation
Sensory organs
Reproductive organs
You can imagine any of these outward changes requiring thousands of genetic changes. "Just think of all the parameters that would have to be modified," Sternberg says, "and then multiply that by, I don't know -- a thousandfold, or more than that. That's the scale of the problem that you're dealing with." In the Q&A feature of the film Icons of Evolution, David Berlinski tried to quantify the number of morphological changes necessary to turn a cow into a whale (like turning a car into a submarine), and stopped counting at 50,000.
It's hard, therefore, to get excited about "hundreds of genes" announced by the Pittsburgh crew. Do these genes deal with the major modifications in whales? You decide:
We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals.
Let's grant that adaptations to skin, muscles, lungs, and sensory systems are important. It's a little odd that they get excited about "loss of function" in taste and smell that "has been suggested to result from change in prey, swallowing food whole, and the masking of tastes by seawater." That sounds Lamarckian. You'd hope to hear about how Darwinian natural selection produced one of the real innovations, like the origin of dolphin sonar, the blowhole, the tail fluke, or the cooling system for the internalized male testes described in Living Waters. But score a few points for Darwin. Not quite 50,000, but four or five.
But wait! When you look into the details of the paper, you find reasons to doubt even the examples they offer as evidence of positive selection in the genes.
First of all, they didn't really witness genetic evolution as much as convergence in the "rate" of change in genes that they assume occurred by evolution. Isn't that circular? Don't you have to believe the animals evolved in the standard evolutionary timeline before accepting this as evidence?
While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment.
In other words, they looked at the endpoint differences and merely assumed natural selection brought them about. Design advocates would expect the differences were planned for the aquatic lifestyle of these mammals.
Second, cases of "positive selection" appear strained. They "observed strong evidence of positive selection and a marine-acceleration in a large number of skin-associated proteins." They claim further positive selection for some lung surfactant proteins. But those are only building-block changes; they say nothing about how hairy cowhide turned into tightly-knit, waterproof armor over blubber arranged into a long, sleek form suitable for gliding in water. They didn't say how the skin took form in fins and a powerful tail fluke. They couldn't even rule out that the rate increases were due to selective pressure from pathogens on the skin and lungs in seawater.
A third problem is that the genetic changes do not appear specific to marine mammals.
All of the marine-accelerated genes under positive selection also showed significant evidence of positive selection across the mammalian tree (Supplemental Table S1), so their positive selection is not specific to marine branches. However, they did nevertheless show increased evolutionary rates on marine branches, suggesting these genes experienced a greater pressure to adapt in the marine environment (Supplemental Table S3).
Anyone see a strong genetic case for cow-to-whale evolution? Fourthly, the researchers in many cases could not rule out neutral evolution. (Here's where the camel trots in.) It's hard to know whether to laugh or cry at the imploding story:
Convergent changes on marine branches could have resulted from neutral processes or alternatively due to positive selection for the same amino acid variant. For the latter case, we would expect there to be more convergent amino acid changes in these genes for marine species compared to negative control species. We tallied convergent changes within a control set of species not expected to show convergence and chosen to match the topology and branch lengths of the marine species (Supplemental Fig. S3C) (alpaca, camel and their ancestral branch, bushbaby, human, and aardvark). As an additional control, we tallied the convergent changes between the marine and control branches (Supplemental Fig. S3D). The marine branch dataset did not show an excess of convergent amino acid sites (mean proportion = 0.086) compared to the control datasets (0.088 and 0.052, for control branches and marine-versus control branches, respectively) (Supplemental Fig. S3). Furthermore, the proportion of convergent changes on marine branches is small compared to the amount of excess changes that led to the acceleration in relative rate (mean proportion = 0.549; Supplemental Fig. S3B). Overall, we found no evidence for adaptively driven site- and amino acid-specific convergence in marine-accelerated genes.
This is sad. There was far greater evidence for "relaxation of constraint" than for positive selection (that's the kind of evolution that turns cave fish blind). There was NO evidence for "adaptively driven" change to the genes they decided had "accelerated" their evolution. Here's where the gnat flies into the picture:
On the other hand, marine-accelerated genes participating in olfaction, gustation, and muscle function exhibited overwhelming evidence of relaxation of constraint. These observations included greatly accelerated rates consistent with neutral evolution and even obvious genetic lesions and pseudogenization (e.g. GNAT3).
Obviously, genetic lesions (deleterious mutations) and pseudogenization are not going to help a cow swim. In Living Waters, Sternberg showed mathematically that it would take longer to expect just two cooperative mutations to occur than the maximum time expected for the entire evolution of a whale (100 million years vs 9 million years).
If this is the best evidence for the story of a Darwinian transformation of a land animal into a successful full-time marine creature, they should watch Living Waters and consider the explanatory power of "Intelligent Design in the Oceans of the Earth." It's not enough to point to possible amino acid differences here or there (not specific to marine mammals, and not clearly tied to innovative complex structures like echolocation) and announce Q.E.D. by saying they might have evolved faster in whales than they did with camels.
A good scientific explanation needs to account for the whole animal, with all its parts. A designing intelligence knows how to integrate multiple complex systems for function. Unguided natural processes are incapable of that, as Granville Sewell illustrated here with tornadoes and iPhones recently.
Once the materialistic bias against intelligence is lifted from the causal toolkit, science is liberated from an unnecessary restriction against knowledge. Sternberg says in the film:
Darwinism provided an explanation for the appearance of design, and argued that there is no Designer -- or, if you will, the designer is natural selection. If that's out of the way -- if that just does not explain the evidence -- then the flip side of that is, well, things appear designed because they are designed.
Whales illustrate a "global architecture that only a mind can bring about," Paul Nelson adds.
The data from genetics and molecular biology and a host of other fields have proven impossible to reconcile with undirected material causes. And, if science is an open-ended search for the truth, regardless of where the evidence leads, then what difference should it make if it leads to an intelligent cause?
Straining at irrelevant details to support a predetermined narrative because of some arbitrary rule that disallows non-material causes blinds science to the obvious. It strains at gnats while swallowing camels.
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