Scientists now know a lot more about the genetic changes that helped give rise to mammoths, thanks to a recent study led by Vincent Lynch, PhD, assistant professor of human genetics at Penn State University, and published in Cell Reports on July 2. The study raises a fascinating question for Intelligent Design proponents who are interested in pinning down the “edge of evolution”: were woolly mammoths designed?
University of Chicago science reporter Kevin Jiang summarizes the methods used by Lynch and his team, in a Science Life article titled, The genes that make a woolly mammoth a woolly mammoth (July 2, 2015):
To thoroughly characterize mammoth-specific genes and their functions, Lynch and his colleagues deep sequenced the genomes of two woolly mammoths and three Asian elephants – the closest living relative of the mammoth. They then compared these genomes against each other and against the genome of African elephants, a slightly more distant evolutionary cousin to both mammoths and Asian elephants.
The team identified roughly 1.4 million genetic variants unique to woolly mammoths. These caused changes to the proteins produced by around 1,600 genes, including 26 that lost function and one that was duplicated. To infer the functional effects of these differences, they ran multiple computational analyses, including comparisons to massive databases of known gene functions and of mice in which genes are artificially deactivated.
Mammoths and Asian elephants are believed to have shared a common ancestor 5 million years ago, while Asian and African elephants are thought to have diverged somewhat earlier, about 7.6 million years ago.
The team’s findings about the genes that distinguished mammoths are described in a Live Science report by Tia Ghose titled, Woolly Mammoth Clones Closer Than Ever, Thanks to Genome Sequencing (July 2, 2015):
They found that several unique mammoth genes helped the cold-loving creatures survive. These included genes for their shaggy, curly, heat-trapping fur, as well as for their small ears and short tails, which lose less heat than the big ears and tails that keep elephants cool.
The pudgy ice-age pachyderms also had genetic differences from the Asian elephant in the way they stored fat and processed insulin, the hormone that regulates how the body uses blood sugar for energy, according to the study, which was published today (July 2) in the journal Cell Reports. Because fat is insulating, the animals’ chubby physiques helped them weather the Arctic tundra, which could routinely plunge to minus 58 degrees Fahrenheit (minus 50 degrees Celsius), according to the study.
Mammoths and elephants also had different temperature-sensing receptors in the body. In the mammoth, the receptors were essentially turned down, like a dimmer switch. That likely made the shaggy creatures less sensitive to both heat and cold, Lynch said.
For the benefit of those readers who are interested, here’s the summary from the abstract of the new study by Vincent Lynch et al., which is titled, “Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic” (Vincent Lynch et al., Cell Reports, July 2, 2015, DOI: http://dx.doi.org/10.1016/j.celrep.2015.06.027):
Woolly mammoths and living elephants are characterized by major phenotypic differences that have allowed them to live in very different environments. To identify the genetic changes that underlie the suite of woolly mammoth adaptations to extreme cold, we sequenced the nuclear genome from three Asian elephants and two woolly mammoths, and we identified and functionally annotated genetic changes unique to woolly mammoths. We found that genes with mammoth-specific amino acid changes are enriched in functions related to circadian biology, skin and hair development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. Finally, we resurrected and functionally tested the mammoth and ancestral elephant TRPV3 gene, which encodes a temperature-sensitive transient receptor potential (thermoTRP) channel involved in thermal sensation and hair growth, and we show that a single mammoth-specific amino acid substitution in an otherwise highly conserved region of the TRPV3 channel strongly affects its temperature sensitivity.
Finally, here are some highlights from the article itself:
Woolly mammoths (Mammuthus primigenius), perhaps the most charismatic of the extinct Pleistocene megafauna, have long fascinated humans and have become emblems of the last ice age. Unlike the extant elephantids, which live in warm tropical and subtropical habitats, woolly mammoths lived in the extreme cold of the dry steppe-tundra where average winter temperatures ranged from −30° to −50°C (MacDonald et al., 2012). Woolly mammoths evolved a suite of adaptations for arctic life, including morphological traits such as small ears and tails to minimize heat loss, a thick layer of subcutaneous fat, long thick fur, and numerous sebaceous glands for insulation (Repin et al., 2004), as well as a large brown-fat deposit behind the neck that may have functioned as a heat source and fat reservoir during winter (Boeskorov et al., 2007, Fisher et al., 2012). They also likely possessed molecular and physiological adaptations in circadian systems (Bloch et al., 2013, Lu et al., 2010) and adipose biology (Liu et al., 2014, Nelson et al., 2014), similar to other arctic-adapted species. Mammoths diverged from Asian elephants (Elephas sp.) ∼5 Ma (Rohland et al., 2007) and likely colonized the steppe-tundra 1–2 Ma (Debruyne et al., 2008), suggesting that their suite of cold-adapted traits evolved relatively recently (Figure 1).
Identifying the genetic changes that underlie morphological differences between species is daunting, particularly when reconstructing how the genotype-phenotype map diverged in non-model or, especially, extinct organisms. Thus, while the molecular bases of some phenotypic traits have been identified, these studies generally are limited to a few well-characterized genes and pathways with relatively simple and direct genotype-phenotype relationship… Most traits, however, have complex genotype-phenotype relationships with phenotypic divergence arising through the accumulation of numerous variants of small individual effects rather than one or a few mutations of large effect…
We identified ∼33 million putative single-nucleotide variants (SNVs) among the three elephantid species (see Experimental Procedures for details), including ∼1.4 million nucleotide variants fixed for the derived allele in the two mammoths, but for the ancestral allele in the African and Asian elephants. Among the variants were 2,020 fixed, mammoth-derived amino acid substitutions in 1,642 protein-coding genes and 26 protein-coding genes with premature stop codons (putative LOF [loss-of-function] substitutions)…
Woolly mammoths evolved a suite of morphological adaptations to life in the extreme cold, including small ears and tails, a long thick coat, and, unlike other elephants, numerous large sebaceous glands, which are thought to have helped repel water and improve insulation (Repin et al., 2004). Woolly mammoths also evolved a characteristic set of skeletal traits, including a high, domed skull with dorsally expanded parietals; an anterio-posteriorly compressed skull; and a sloping back. Consistent with mammoth-specific amino acid changes contributing to these traits, we found that genes with mammoth-specific substitutions were enriched in KO [mouse knockout] phenotypes such as abnormal tail morphology…, abnormal tail bud morphology…, small tail bud…, abnormal ear morphology…, cup-shaped ears…, and abnormal sebaceous gland morphology…, including substitutions in three genes leading to enlarged sebaceous glands. We also found numerous enriched KO phenotypes that affected the skeleton, including domed cranium…, abnormal parietal bone morphology…, and short snout….
Fixed, derived mammoth-specific amino acid substitutions occurred in eight genes associated with circadian biology, including those that play central roles in maintaining normal circadian rhythms and entraining the circadian clock to external stimuli such as temperature…
The enrichment of genes with derived amino acid (Figure 2) and LOF [loss-of-function] substitutions (Figure 3) in woolly mammoths that function in lipid metabolism, adipose development, and physiology suggests modifications of these processes may have played an important role in the evolution of woolly mammoths and adaptation to arctic life. We identified 54 genes with fixed, derived amino acid substitutions and KO [mouse knockout] phenotypes that affect adipose tissue, including phenotypes that alter both the location and abundance of white and brown fat deposits throughout the body… We also identified 39 genes with KO phenotypes that affect insulin signaling, and found that genes with mammoth-specific amino acid substitutions were enriched in several KO phenotypes related to insulin signaling, including abnormal circulating insulin level…, insulin resistance…, and impaired glucose tolerance…
The most intriguing mouse KO [knockout] phenotype enriched among genes with woolly mammoth-specific amino acid changes was abnormal thermal nociception (13 genes). For example, we identified woolly mammoth-specific amino acid changes in five temperature-sensitive transient receptor potential (thermoTRP) channels … that sense noxious cold (TRPM8)…, innocuous warmth (TRPV3 and TRPV4)…, or noxious cold or heat depending on species (TRPA1) … or that are heat sensitive but not known to be involved in temperature sensation (TRPM4) …
Our results suggest that changes in circadian systems, insulin signaling and adipose development, skin development, and temperature sensation may have played important roles in the adaptation of woolly mammoths to life in the high arctic. Our identification of a hypomorphic woolly mammoth amino acid substitution in TRPV3 is particularly noteworthy given its pleiotropic roles in temperature sensation, hair growth, and adipose biology, suggesting that this substitution may have contributed to cold tolerance.
So, were mammoths designed or weren’t they?
I don’t have any strong opinions on the question of whether woolly mammoths were intelligently designed or not. Instead, I’d like to briefly list the arguments for and against, and let readers draw their own conclusions.
Arguments in favor of mammoths having been specially designed
As I see it, the main argument in favor of the woolly mammoth’s having been intelligently designed is that a large suite of highly specific changes were required at the genetic level, to make elephantids (the taxonomic family which includes elephants and mammoths) adapted to life in a very cold climate. These changes took place over a relatively short period: a few million years at the outside.
A second argument that might be put forward is that the genetic differences between Asian elephants and woolly mammoths are roughly comparable in magnitude to those between humans and chimpanzees, if we go by molecular clock dating techniques (see here). If (as most Intelligent Design proponents would maintain) humans were intelligently designed, then by the same token, so were mammoths. On the other hand, molecular clock dating techniques don’t tell the whole story: humans are strikingly distinguished from chimps and all other vertebrates by 49 segments of the human genome known as human accelerated regions, which may well have been intelligently engineered. See also my online article, Who was Adam and when did he live? Twelve theses and a caveat for more on the genetic and neurological differences between human beings and chimpanzees.
Arguments against mammoths having been specially designed
There are several weighty arguments against mammoths having been intelligently designed.
First, as far as I am aware, no-one has yet identified any orphan genes in the lineage leading to mammoths.
Second, no-one has yet put forward a mathematical argument showing that the genetic mutations that would have been required in order to transform an ancestral elephantid population into mammoths were highly improbable. Without such an argument, it is difficult to make a case for the intelligent design of this lineage.
Third, even creationists seem to regard African and Asian elephants and mammoths as belonging to one big “elephant kind.” (See, for instance, Michael Oard’s article, The Elephant Kind in Answers in Genesis, October 1, 2004. As Oard points out, the creationist author Jonathan Sarfati believes that the order Proboscidea represents a single created kind — the elephant kind.)
Fourth, it is known that Asian and African elephants can interbreed successfully – which presumably means that mammoths and Asian elephants would have been able to do the same, as they diverged even more recently. If the differences between mammoths and their nearest relatives, Asian elephants, aren’t even enough to prevent them from interbreeding, then what good grounds do we have for ascribing these differences to intelligent design?
Finally, there is absolutely no reason to believe that the suite of genetic changes required to make elephantids adapted to life in the Arctic occurred simultaneously. If the changes occurred sequentially, over a period of millions of years, then we would have to suppose that literally scores of separate interventions must have occurred, if these changes were the product of intelligent engineering. I have to say that sounds messy to me. It also seems to violate Occam’s razor: as far as I can tell, there is nothing about these changes which places them beyond the reach of unguided processes, such as natural selection and/or random genetic drift.
I’d now like to throw the discussion open to readers. What do you think? Were mammoths intelligently designed or not?