Jonathan McLatchie

The mechanisms and processes of cellular information storage, processing and retrieval have always been a focus of ID argumentation and research. Indeed, it was the complexity and elegance of these systems which first captured my attention as a junior undergraduate as I became interested in the implications of information-rich systems in biology and the possible explicative powers of intelligent causation.

In recent years, there has been a dramatic surge in our appreciation of genomics and the processes of information flow in the cell. Papers continue to flood in, reporting on a plethora of recent discoveries which take genomic complexity to a whole new level, leading many academics to tentatively re-evaluate the causal sufficiency of Darwinian mechanisms, the dual forces of chance and necessity.

One recent paper, published in the journal, Nature, documents the discovery that human cells have the largescale capacity to copy, not only DNA, but also RNA molecules. According to the paper’s Abstract,

Small (<200 nucleotide) RNA (sRNA) profiling of human cells using various technologies demonstrates unexpected complexity of sRNAs with hundreds of thousands of sRNA species present. Genetic and in vitro studies show that these RNAs are not merely degradation products of longer transcripts but could indeed have a function. Furthermore, profiling of RNAs, including the sRNAs, can reveal not only novel transcripts, but also make clear predictions about the existence and properties of novel biochemical pathways operating in a cell. For example, sRNA profiling in human cells indicated the existence of an unknown capping mechanism operating on cleaved RNA, a biochemical component of which was later identified. Here we show that human cells contain a novel type of sRNA that has non-genomically encoded 5′ poly(U) tails. The presence of these RNAs at the termini of genes, specifically at the very 3′ ends of known mRNAs, strongly argues for the presence of a yet uncharacterized endogenous biochemical pathway in cells that can copy RNA. We show that this pathway can operate on multiple genes, with specific enrichment towards transcript-encoding components of the translational machinery. Finally, we show that genes are also flanked by sense, 3′ polyadenylated sRNAs that are likely to be capped.

An article appeared in The New York Times last week written by the popular geneticist, Sean B. Carroll, who is probably best known for his professional and popular work on the emerging science of evo devo. Carroll’s article attempts to refute the challenges posed by the Cambrian fossil record to evolutionary thought. Carroll writes,

The difficulty posed by the Cambrian Explosion was that in Darwin’s day (and for many years after), no fossils were known in the enormous, older rock formations below those of the Cambrian. This was an extremely unsettling fact for his theory of evolution because complex animals should have been preceded in the fossil record by simpler forms.
In “On the Origin of Species,” Darwin posited that “during these vast, yet quite unknown, periods of time, the world swarmed with living creatures.” But he admitted candidly, “To the question why we do not find records of these vast primordial periods, I can give no satisfactory answer.”

Advocates of intelligent design have long been skeptical of the claim that the majority of our genome is nonfunctional gibberish, a mere relic of our evolutionary past. Many of the key arguments for common ancestry are based around the supposition that certain loci of our genome are functionless. But the gaps in our knowledge of the genome (in which such supposition resides) are continually shrinking.

A recent paper published in Science by Kondo et al. reported on the discovery that some of the supposed “non-coding” regions of the RNA transcript actually actively encode for short peptides that regulate genes involved in Drosophila development.

According to the Abstract,

A substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a repressor to an activator. Our results demonstrate that during Drosophila embryogenesis, Pri sORF peptides provide a strict temporal control to the transcriptional program of epidermal morphogenesis.

Recently, Nick Lane, a biochemist and Provost’s Venture Research Fellow in the Department of Genetics, Evolution and Environment at University College London, published a new book, Life Ascending: The Ten Great Inventions of Evolution.

Nick Lane lays out ten biological phenomena for which he seeks to propose plausible evolutionary explanations. Among the phenomena discussed by Lane are the origin of life, DNA, photosynthesis, the complex cell, sex, movement, sight, hot blood, consciousness, and death. But does Darwinism have the goods? Or does Nick Lane offer us only a series of wishful speculations?

New Scientist offered the following praise for Lane’s work:

What makes this such a great read is that Lane, a biochemist by training, does not simply rehash the standard evolutionary tales – unlike many books published recently. Instead, he is familiar with all the latest research and has made up his own mind about who is right. The result is an original and awe-inspiring account. The first two chapters are the most coherent and convincing summaries of the dawn of life and of DNA that I have ever read.

The literature continues to flood in demonstrating that so-called ‘junk’ regions of the genome are not junk after all, but serve significant and important functions. One such recent paper reports evidence that retrotransposons may play significant roles in the cell. According to the abstract,

Retrotransposons including endogenous retroviruses and their solitary long terminal repeats (LTRs) compose >40% of the human genome. Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host functions is not known. Here we show that an LTR retrotransposon of ERV-9 human endogenous retrovirus located 40–70 kb upstream of the human fetal γ- and adult β-globin genes serves a long-range, host function. The ERV-9 LTR contains multiple CCAAT and GATA motifs and competitively recruits a high concentration of NF-Y and GATA-2 present in low abundance in adult erythroid cells to assemble an LTR/RNA polymerase II complex. The LTR complex transcribes intergenic RNAs unidirectionally through the intervening DNA to loop with and modulate transcription factor occupancies at the far downstream globin promoters, thereby modulating globin gene switching by a competitive mechanism.

Retrotransposons include the long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), endogenous retroviruses (ERVs), and the solitary long terminal repeats (LTRs) of ERVs, and compose over 40% of the human genome. Retrotransposons possess enhancers and promoters which promote the expression of downstream polycistronic gene sequences. The cited paper seeks to determine whether the retrotransposons which are located in the intergenic (regions which intersperse genes, also known as ‘introns’) of the genome – which are often several hundred kilobases removed from the promoters – serve any beneficial function.

A few weeks ago, PZ Myers commented on so-called ‘Junk DNA’. Under the headline, ‘Junk DNA is still junk’, Myers wrote:

The ENCODE project made a big splash a couple of years ago — it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn’t junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is a noisy place, and coupled with the observations that the transcripts were not evolutionarily conserved, it suggested that these were non-functional transcripts.

What we know about the complexity of the cellular information storage, processing and retrieval mechanisms continues to increase exponentially, and at an unprecedented rate. Almost on a daily basis, new papers are published revealing the ingenuity of the elaborate mechanisms by which the cell processes information — processes and mechanisms that bespeak design and continue to elude explanation by Darwinian means. For how exactly could such a system – apparently, an irreducibly complex one – be accounted for in terms of traditional Darwinian selective pressure?

A new paper has just been published in Molecular Cell, in which the researchers, Karginov et al. reported their discovery that messenger RNA (mRNA) can be targeted for destruction by several different molecules.

According to the paper’s summary,

The life span of a mammalian mRNA is determined, in part, by the binding of regulatory proteins and small RNA-guided complexes. The conserved endonuclease activity of Argonaute2 requires extensive complementarity between a small RNA and its target and is not used by animal microRNAs, which pair with their targets imperfectly. Here we investigate the endonucleolytic function of Ago2 and other nucleases by transcriptome-wide profiling of mRNA cleavage products retaining 5′ phosphate groups in mouse embryonic stem cells (mESCs). We detect a prominent signature of Ago2-dependent cleavage events and validate several such targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in site-specific mRNA cleavage. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events that functionally regulate mRNA levels in mESCs, including one in the Dgcr8 mRNA. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.

Translated into English, the paper makes the following points:

• RNA interference (RNAi) refers to a cellular pathway that helps to regulate the activity of genes within the cell. Fundamental to the process of RNA interference are small interfering RNAs (siRNA) and microRNAs (MiRNA).
• Small RNAs can prevent the translation of a target messenger RNA into protein, thereby reducing the activity of the RNAs to which it binds.
• MicroRNAs also act as regulators, binding to their complementary sequences on a target messenger RNA to result in gene silencing. MiRNAs also serve as guides to a family of proteins called Artonautes. When a miRNA-Artonaute complex binds to its complementary mRNA target, it triggers its destruction.
• The researchers surveyed a population of cleaved mRNAs in mammalian embryonic stem cells, discovering that mRNAs had been sliced or cleaved by the enzyme Ago2 and other enzymes.
• It was previously thought that the destruction was due to the destabilization of mRNA by initiation of cellular pathways. In contrast, Karginov et al. have discovered a host of ways that mRNA may be destroyed by enzymatic cleavage.

Casey Luskin recently posted two blogs showing that textbooks still misuse Haeckel’s long-discredited embryo drawings when attempting to provide evidence for Darwinian evolution (see here and here). Luskin provided ample documentation to demonstrate that these drawings are still printed in some recent textbooks.

Over at The Panda’s Thumb blog, apologists for Darwinian theory have defended (see here and here) Ernst Haeckel from the charge of fraud and have argued, albeit unconvincingly, that, in principle, the concept of recapitulation is a valid one.
According to Nick Matzke:

Haeckel didn’t ignore the differences in embryos in the earliest period just after fertilization (differences which are visually significant but mostly fairly trivial, due to the different amounts of yolk in different vertebrate eggs).

Scott F. Gilbert’s “Developmental Biology” (eighth edition) provides a stunning overview of the elegant biochemical mechanisms controlling the development of organismal form during ontogeny. The final section of the book, chapter 23 (“Developmental Mechanisms Of Evolutionary Change”) is devoted to a discussion of the new evolutionary synthesis, encompassing the new science of ‘evo devo’ (short hand for ‘evolutionary developmental biology’). The book even contains a short rebuttal directed at proponents of intelligent design and, in particular, Michael Behe.

A paper has just been published in Nature which uncovers a host of new coding-independent functions for pseudogene mRNAs, including a role in tumor regulation. More exciting is that Poliseno et al. describe an entirely new regulatory function of RNA. This stands in contrast to conventional wisdom which maintains that the only function of mRNAs is encoding for proteins. According to the abstract, The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs could possess a regulatory role that relies on their ability to compete for microRNA binding, independently of their protein-coding function. As a model for the protein-coding-independent role of RNAs, Read More ›