Science Literature

Although there are currently 3,524 species of mosquito (Family Culicidae), there are relatively few examples of fossil species. The most recently published discovery has increased the total number to 26 species, with the earliest coming from Cretaceous amber (much to the delight of Jurassic Park enthusiasts - as these mosquitos could have sucked the blood of dinosaurs). The new fossils are from the Eocene Epoch and have been named Culiseta kishenehn and Culiseta lemniscata. They were unearthed from the Kishenehn Basin, northwestern Montana, USA. They are not in amber, but are compression fossils - the first to be identified from the genus Culiseta.

Ancient mosquito species, Culiseta kishenehn, is very similar to a species living today that spreads a deadly virus affecting horses. (Source here)

As is so often the case, the fossils can be assigned to modern-day families and genera. Speciation within genera with time means that fossils are less frequently linked with extant species. However, in this example, similarities are apparent:

"they look very similar to some living species of the same genus Culiseta", Harbach explains, "Culiseta kishenehn bears close resemblance to the living North American Culiseta melanura, which is a vector of Eastern and Western equine encephalitis viruses (EEE and WEE)".

The modern mosquito carries viruses that infect the brains of horses, causing paralysis and very often death. However, there were no horses in North America during the Eocene Epoch, so this raises questions about what blood these mosquitos drank. It appears that many living species of Culiseta feed on birds. So, says Harbach, "these ancient mosquitoes probably fed on birds too. [. . .] mosquitoes are basically opportunistic and will feed on other types of animals if their preferred hosts are unavailable."

Inevitably, discoverers of new fossils seek to locate their finds within an evolutionary context. If Culiseta shows stasis, which it does, how does this relate to other fossil mosquitos? The researchers suggest that Culiseta is "primitive" and can be interpreted as a stem group which diversified. Whilst the diversification story may be viable, we do need to be careful about the terms "primitive" and "stem group", because the Culiseta are still alive and well today!

"Extant species of Culiseta exhibit generalized features that indicate the genus is a primitive lineage of subfamily Culicinae. Culiseta may be what paleontologists refer to as a "stem group", a paraphyletic or polyphyletic assemblage of species that share features of extinct taxa."

No doubt some readers want to have more on whether mosquitos fed on dinosaur blood. This is the parting comment in the news story from the Natural History Museum:

"Since some of today's mosquitoes also feed on reptiles, could the more ancient mosquitoes have sucked from a dinosaur? Harbach says it's possible. Evidence suggests mosquitoes evolved in the Jurassic Period [. . .]. Harbach concludes, "If the early ancestral mosquitoes had already evolved to feed on blood, it is conceivable that they may have fed on dinosaurs"."

Two Eocene species of Culiseta (Diptera: Culicidae) from the Kishenehn Formation in Montana
Ralph E. Harbach & Dale Greenwalt
Zootaxa, 3530: 25-34 (2012)

Culiseta kishenehn, sp. n. and Cs. lemniscata, sp. n. (Diptera: Culicidae: Culisetini) are described from compression fossils from the 46 million year old Kishenehn shale deposits in Montana, USA. The new species appear to share features with extant species of subgenera Climacura and Culicella, respectively. The antiquity of Culiseta is examined and previously described Eocene fossil species are discussed. Eoaedes gen. n. and Aetheapnomyia gen. n. are established for Aedes damzeni PodÄ—nas and Ae. hoffeinsorum Szadziewski, two Eocene fossil species in Baltic amber.

See also:

New ancient mosquitoes, could there be blood? Natural History Museum News (19 November 2012)

For more on stasis in the fossil record of insects: harvestmen, splay-footed cricket, lacewing, stick grasshopper, Leaf insect.

Blog Alert

In 1988, Richard Lenski (of the University of Michigan) and colleagues founded 12 populations of the bacteria Escherichia coli from the same clone. Since then, the bacterial populations have been studied over thousands of generations to provide data relating to real-time experimental evolution. In 2008, Blount, Borland, and Lenski reported significant developments in the ability of E. Coli to metabolise citrate (see here). This was widely perceived as an evolutionary innovation because normal E. coli is unable to digest citrate in the presence of oxygen (although the bacterium can metabolize citrate in the absence of oxygen). In the intervening years, Blount and the research group have analyzed 29 genomes from different generations to find the mutational events that were involved in the observed changes. The research paper has now been published in the journal Nature, and the Editor's summary is as follows:

"It has been suggested that small evolutionary steps pave the way for more major evolutionary leaps - in a combination of Darwinian gradualism and saltationism - but mechanistic details have been hard to determine from natural history. Rich Lenski and colleagues have now combined full-genome sequencing and 'evolutionary replay' experiments to dissect the multi-step origin of one key innovation - the evolution of aerobic citrate-utilization in an experimental bacterial population - over more than 30,000 generations and two decades. The three-step process they unveil, in which potentiation makes a trait possible, actualization makes it manifest and refinement makes it effective, is likely to be typical of other biological revolutions such as the colonization of land by proto-tetrapods."

Zachary Blount, postdoctoral researcher in MSU's BEACON Center for the Study of Evolution in Action, led a team of researchers in documenting the step-by-step process in which organisms evolve new functions. (Credit: Courtesy of Brian Baer, source here)

The Press Release accompanying the paper suggests that it provides the key to understanding evolutionary innovation: "How Organisms Evolve New Functions: Evolution is as Complicated as 1-2-3". There are three steps, which are described as follows:

"The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events. The second step, actualization, is when the bacteria first began eating citrate, but only just barely nibbling at it. The final stage, refinement, involved mutations that greatly improved the initially weak function. This allowed the citrate eaters to wolf down their new food source and to become dominant in the population.
"We were particularly excited about the actualization stage," Blount said. "The actual mutation involved is quite complex. It re-arranged part of the bacteria's DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. That is a new trick for E. coli." " (Source here)

Probably few readers of these reports are aware that experimental evolution has provided evidence that fails to map well on to neodarwinian theory. Instead of mutations creating novel genes, they are typically degradative and sometimes essentially neutral. This was pointed out by Behe in an academic paper an in a recent blog:

"In a manuscript published a few years ago in the Quarterly Review of Biology (Behe 2010), I discussed laboratory evolution results from the past four decades up to that point, including Lenski's. His laboratory had shown clearly that random mutation and selection improved the bacterium with time, as measured by the number of progeny it could produce in a given time. He demonstrated without doubt that beneficial mutations exist and can spread quickly in a population of organisms. However, once Lenski's lab eventually identified the mutations at the DNA level (a difficult task), many of the beneficial mutations turned out to be, surprisingly, degradative ones. In other words, breaking or deleting some pre-existing genes or genetic regulatory elements so that they no longer worked actually helped the organism under the conditions in which it was grown. Other beneficial mutations altered pre-existing genes or regulatory elements somewhat."

It is of interest, consequently, to know whether a similar situation applies to the citrate-consuming E. coli. In Behe's blog, the reported mutations are considered in the light of his 2010 paper. Here is the comment on Actualisation:

"They divide the mutations conceptually into three categories: 1) potentiation; 2) actualization; and 3) refinement. "Actualization" is the name they give to the mutation that first confers a weak ability to transport citrate into the laboratory E. coli. (It turns out that the bacterium is lacking only a protein to transport citrate into the cell in the presence of oxygen; all other enzymes needed to further metabolize citrate are already present.) The gene for the citrate transporter, citT, that works in the absence of oxygen is directly upstream from the genes for two other proteins that have promoters that are active in the presence of oxygen. A duplication of a segment of this region serendipitously placed the citT gene next to one of these promoters, so the citT gene could then be expressed in the presence of oxygen. Gene duplication is a type of mutation that is known to be fairly common, so this result, although requiring a great deal of careful research to pin down, is unsurprising." "

So, in this case, the gene for citrate transportation and all other enzymes needed to metabolize citrate pre-exist. What is new is the mutation that puts the citT gene next to a suitable promoter. This was achieved via a gene duplication mutation. No new information was created, but the mutation was sufficient to activate this key gene. Blount et al. use the term "amplification mutation" to describe what happened: "Amplification mutations can alter the spatial relationship between structural genes and regulatory elements, potentially causing altered regulation and novel traits." Behe comments also refinement stage as follows:

"Further work showed this was due to multiple duplications of the mutant gene region, up to 3-9 copies. Again, gene duplication is a fairly common process, so again it is unsurprising. In another experiment Lenski and co-workers showed that increasing the concentration of the citrate transporter gene was sufficient in itself to account for the greater ability of E. coli to grow on citrate."

Analysis of the potentiation stage is different. Behe finds that degradation is the most likely mechanism for this:

"It turns out that the original E. coli they began with decades ago could not benefit from the gene duplication that brought together a citT gene with an oxygen-tolerant promoter. Before it could benefit, a preliminary mutation had to occur in the bacterium somewhere other than the region containing the citrate-metabolism genes. Exactly what that mutation was, Lenski and coworkers were not able to determine. However, they examined the bacterium for mutations that may contribute to potentiation, and speculated that "A mutation in arcB, which encodes a histidine kinase, is noteworthy because disabling that gene upregulates the tricarboxylic acid cycle." (They tried, but were unable to test this hypothesis.) In other words, the "potentiation" may involve degradation of an unrelated gene."

So, a the whole scenario involves the combination of an initial degradation mutation, making it possible for a gene duplication mutation to position the citrate transporter gene next to a promotor, followed by other gene duplication events to enhance the ability to metabolise citrate. These mechanisms do not go beyond the findings of Behe's 2010 paper - which suggests that whilst mutations can tinker with genetic systems, they cannot build them. There are no grounds here for the claim, made by the Editor of Nature, that the three-stage process documented by Blount et al. "is likely to be typical of other biological revolutions such as the colonization of land by proto-tetrapods". There is a great gulf between genetic tinkering and the engineering of complex functional systems. Neodarwinists (such as Hendrickson & Rainey, referenced below) would do well to reflect on Behe's Edge of Evolution concept and the concluding comment of his blog:

"In retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski's work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient - that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism."

Genomic analysis of a key innovation in an experimental Escherichia coli population
Zachary D. Blount, Jeffrey E. Barrick, Carla J. Davidson & Richard E. Lenski
Nature, 27 September 2012, 489, 513-518 | doi: 10.1038/nature11514 (pdf here)

Abstract: Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit+), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations before its emergence. The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population's history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

How the unicorn got its horn
Heather Hendrickson & Paul B. Rainey
Nature, 489, 504-505 (27 September 2012) | doi:10.1038/nature11487

An experiment studying bacterial populations over thousands of generations shows that a novel trait can evolve through rearrangement and amplification of a few pre-existing genes.

Rose-Colored Glasses: Lenski, Citrate, and BioLogos
Michael Behe
Evolution News & Views (13 November 2012)

See also:

How Organisms Evolve New Functions: Evolution is as Complicated as 1-2-3, ScienceDaily (Sep. 19, 2012)

The Latest From Lenski's Lab, Uncommon Descent (8 October 2012)

Innovation or Renovation? by Ann Gauger, Biologic Institute (24 September 2012)

The Central Dogma has had an enormous impact on the way genetics research has developed over the past 50 years. Basically, the dogma states that DNA genes encode mRNA, and mRNA allows proteins to be constructed, and proteins do all the work needed for cells to function. There is a linear logic here that fits into a view of the genome that is static throughout its life and provides a blueprint for life. This is how Franklin and Vondriska introduce their paper:

"Arguably the greatest postmodern coup for reductionism in biology was the articulation of the central dogma. Not since "humors" were discarded from medical practice and logic and experiment instituted as the cornerstones of physiology (which they remain today) had such a revolutionary idea transformed biology and enabled scientific inquiry. Because of its simplicity, the central dogma has the tantalizing allure of deduction: If one accepts the premises (that DNA encodes mRNA, and mRNA, protein), it seems one cannot deny the conclusions (that genes are the blueprint for life). As a result, the central dogma has guided research into causes of disease and phenotype, as well as constituted the basis for the tools used in the laboratory to interrogate these causes for the past half century."

The classic view of the central dogma of biology (source here)

In their review of these issues, Franklin and Vondriska present a systems biology perspective which makes it clear that the central dogma is deficient in numerous ways and that our understanding of living things needs extensive revision. This is an imperative drawn from scientific research and should not be regarded as just another 'point of view'.

"The past decade, however, has witnessed a rapid accumulation of evidence that challenges the linear logic of the central dogma. Four previously unassailable beliefs about the genome - that it is static throughout the life of the organism; that it is invariant between cell type and individual; that changes occurring in somatic cells cannot be inherited (also known as Lamarckian evolution); and that necessary and sufficient information for cellular function is contained in the gene sequence - have all been called into question in the last few years."

Undoubtedly, the trigger for change has been the discovery of extraordinary complexity in cellular processes as revealed by systems biology research. It is now necessary to refer to networks of interactions when explaining any aspect of cellular function. And the very existence of these networks defies the central dogma:

"However, these studies have yet to reveal an invariant relationship between structure and function. There is no code that can account for how the hierarchical structure of DNA and proteins establishes the complex genomic regulatory programs that exist in distinct differentiated cells, as there is to explain, for example, how DNA encodes RNA and RNA, protein."

Systems biology has stimulated thought about the complexity of interacting entities and processes. There is an enormous difference between a DNA gene coding for a protein, and the formation and orchestration of the infrastructure of the whole cell. Those who grasp the nettle by posing questions about cellular processes realise that we do not have the answers. Some form of organising principle must be invoked - transcending the genetic code for making proteins. The central dogma is not central enough - for the really important questions are never asked by its advocates!

"The presence of such properties suggests emergent control in the formation of the network in addition to emergent control of its function once formed. How can this emergence be measured rather than just observed? An enigma in biology is how a cell with (at least) thousands of proteins can reproducibly form and behave in the same manner without central control."

Research findings that point to the inadequacies of the central dogma are summarised in a Table and discussed in the text. It is not the purpose of this blog to precis this part of the paper, but the key issues for consideration are evident in these words by the authors:

"[W]e identify 5 ways in which "-omics" technologies are changing basic and clinical research and contributing to a revisiting of the central dogma: First, by deemphasizing the unidirectional flow of information (i.e, DNA to RNA to protein); second, by placing an emphasis on modules of genes/proteins/molecules rather than individual factors; third, by enabling the discovery and quantification of emergent properties present at different scales of information; fourth, by revealing the role of networks in biological function; and fifth, by allowing for new dimensionality in the analysis of all biological molecules."

The key point being made here is that a change in thinking about molecular biology is urgently needed. There is a tendency for people to say that the central dogma is still valid, but it needs supplementing and enhancing. This would be a mistake. The consequence of treating this as incremental learning is that fundamental questions are neglected and science suffers. Arguably, science is already suffering. The meagre results emerging from medical genetics appears to be a consequence of researchers adopting the central dogma paradigm; and there are serious concerns about the whole of GM food research because the science shows no signs of being informed by any systems thinking. Incremental learning and tweaking of the central dogma can be ruled out because the five observations discussed in the review paper demonstrate outcomes that are not predicted by the central dogma, and in some cases actually falsify the central dogma.

This conclusion has important implications for the debate about design in nature. What can be said about the organising principles within the cell? Should intelligence be invoked, or is causation naturalistic? The authors refer to an "unknown process" - which at very least implies that there is a scientific debate to be had. However, note this concluding paragraph of the paper:

"The greatest present challenge for biology is the limit of reductionism. The term systems biology itself underscores our linguistic circumscription of this problem. A system, no matter how complex, is a defined entity; it is a human creation. We conceptualize an evolvable central information unit that describes (and orchestrates) the piecewise assembly of the machine that is a cell. We conceptualize watches, even if we shun the watchmaker."

The authors are saying that by using a systems biology approach, we need to invoke the concept of a central information unit that orchestrates cellular processes. In other words, the cell looks designed and there are analogies with human creations. But they also suggest that we may choose to shun the designer. Some of us want to see the day when shunning the designer of cells is perceived to be as incoherent and as irrational as shunning the designer of a watch.

Genomes, Proteomes, and the Central Dogma
Sarah Franklin and Thomas M. Vondriska
Circulation: Cardiovascular Genetics, October 2011; 4: 576 | DOI: 10.1161/CIRCGENETICS.110.957795

Abstract: Systems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology. Rather than studying individual molecules or even single reactions, a systems approach allows integration of orthogonal data sets from distinct tiers of biological data, including gene, RNA, protein, metabolite, and other component networks. Together these networks give rise to emergent properties of cellular function, and it is their reprogramming that causes disease. We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the role of modules of molecules as opposed to individual proteins acting in isolation; (3) it enables discovery of novel emergent properties; (4) it demonstrates the importance of networks in biology; and (5) it adds new dimensionality to the study of biological systems.

See also:

Tyler, D. Beyond Genes and the Central Dogma, ARN Literature Blog (14 September 2007).

Words convey meaning, and the word pseudogene conveys the sense of a gene that is a sham, that is spurious, that is phoney. It is a word that is widely used in the literature on genetics, where pseudogenes are regarded as defunct relatives of functional genes. The dominant reason for studying them is because they "provide a record of how the genomic DNA has been changed without [. . .] evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome" (Source here). Recent research has challenged this assessment of these genetic elements and the textbooks need to be revised comprehensively. Nearly everything that has been widely accepted about pseudogenes has been proven false.

"Pseudogenes were long considered as junk genomic DNA: present in the genome but non-coding and without function. However, discoveries in the ancient protist T. brucei, as well as in some metazoan, indicate that pseudogene regulation is widespread in eukaryotes. Accordingly, the moniker "pseudogene" has been challenged. Interestingly, in addition to eukaryotes, pseudogenes have also been reported from bacteria, although their function remains unknown. [. . .] Once pseudogene functions are shown to occur in all sorts of organisms, including eukaryotes and prokaryotes, the concept of pseudogene will need to be substantially modified." (p.30-31)

Comparing genomes of related organisms has been likened to reading alternative history novels, but there really is no reason why there should not also be consideration of alternative design scenarios. (source here)

In an informative review paper, Wen et al. (2012) document recent findings that warrant a radical revision of the pseudogene concept. The first line of evidence concerns conservation. We should note first that "pseudogenes are pervasive, and usually abundant, in all eukaryotic organisms." (p.27) We are not addressing a trivial aspect of genetics! Conserved pseudogenes do not fit the above claim that they "provide a record of how the genomic DNA has been changed without [. . .] evolutionary pressure."

"[C]omparative analysis of processed pseudogenes in the mouse and human genomes has surprisingly demonstrated that 60% of the processed pseudogenes are conserved in both mammalian species. The high abundance and conservation of the pseudogenes in a variety of species indicate that selective pressures preserve these genetic elements, and suggest that they may indeed perform important biological functions." (p.27)

The second line of evidence is that many examples of functionality have been documented.

"Evidence of expression of pseudogenes has been demonstrated not only in animals but also in plants, such as Arabidopsis (2-5%) and rice (2-3%). The issue arises, if pseudogenes are dysfunctional, why are they so highly expressed? Two possibilities may explain it. One possible explanation is that these pseudogenes are only incidental by-products in the transcription events of other genes, because they are under the effect of the same promoters. An alternative explanation, which we are more inclined to accept, is that the pseudogene transcripts are in fact functional but not random products. More and more accumulating examples support this alternative explanation." (p.28)

Three distinct types of functionality have been documented. These are: natural antisense suppression, RNA interference and gene competitors. Antisense suppression was first proposed in 1986 and first documented in 1992. The regulatory potential of the pseudogene was established. More cases followed, demonstrating that it was not an isolated instance. "These results suggested that antisense binding is an important pseudogene modulation pathway." (p.28.

The RNA interference (RNAi) pathway has been found in many eukaryotes, the first being reported in 2008. The pseudogene is involved in the production of small interference RNAs or microRNAs. The authors write:

"Recently, we established a library of small RNAs (<30 nt) from the bloodstream forms of Trypanosoma brucei by high through-put sequencing, and identified a large fraction of small RNAs derived from the pseudogenes by pairing with complementary transcripts. Ensuing experimental results proved that these pseudogene-derived siRNAs suppressed the expression of their homological protein-coding genes by RNAi. This discovery in an ancient protist, as well as similar discoveries in mouse and plants, indicates that pseudogene-RNAi regulation must have evolved early and thus be widely spread among eukaryotes." (p.28)

Regarding gene competitors, the authors explain that pseudogenes have been shown to act as endogenous competitive RNAs to their cognate genes. "Pseudogenes can perform not only as decoys of stabling/decaying factors but also as small inhibitors." (p.28) An example is cited that has a bearing on our understanding of some cancers.

There is also a fourth category of pseudogene activity: they actually do code for an active product, but researchers have difficulty detecting this using conventional methodologies. This is because the coding only takes place in special circumstances (such as within a cancerous cell).

"Results from the [proteomic mass spectrometry] analysis in mouse has disclosed nine processed pseudogenes that display unique peptide sequences suggesting that they are translated into proteins. Altogether, these results indicate that the discovery of pseudogene functions depends on the skills and methodologies used. Many expressed pseudogenes remain to be annotated. We believe that more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future." (p.31)

This review paper explains that we are just beginning to understand the role pseudogenes play in cells. It seems utterly foolish for people to carry on writing about pseudogenes as though none of this research has taken place. With hindsight it appears obvious that we ought to have presumed functionality and not allowed ourselves to be led by a blind dogma that assigns a "junk" status based on a presumed evolutionary history. Those people who persist in using pseudogenes as an argument against design in living things are only showing their ignorance of contemporary research and betraying the fundamental principles of science.

Pseudogenes are not pseudo any more
Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J Ayala and Zhao-Rong Lun
RNA Biology, Volume 9, Issue 1, January 2012, Pages 27 - 32.
http://dx.doi.org/10.4161/rna.9.1.18277

Abstract: Recent significant progress toward understanding the function of pseudogenes in protozoa (Trypanosoma brucei), metazoa (mouse) and plants, make it pertinent to provide a brief overview on what has been learned about this fascinating subject. We discuss the regulatory mechanisms of pseudogenes at the post-transcriptional level and advance new ideas toward understanding the evolution of these, sometimes called "garbage genes" or "junk DNA", seeking to stimulate the interest of scientists and additional research on the subject. We hope this point-of-view can be helpful to scientists working or seeking to work on these and related issues.