Robert Deyes

Put intuition aside for a moment and imagine a scenario where E.coli knockout strains that have been deleted for conditionally essential genes are rescued by proteins taken from a protein library composed of >10⁶ de novo designed sequences.  The prevailing assumption- that functional proteins are constrained to a very small subset of possible sequences- would lead us to infer that finding them by a random search through sequence space would be tantamount to impossible.  But a PLOS One paper published in early 2011 appears on the surface to have given us much room for thought.  Scientists from Princeton’s Department of Chemistry and Molecular Biology used a combinatorial library of 102-residue long proteins to rescue non-viable E.coli knockouts.   The functional losses in the knockout strains affected serine, glutamate and isoleucine biosynthesis and disabled the cells’ natural capacity for iron acquisition in iron-limited environments. Read More ›

In his 1987 seminal work entitled Impossibility In Medicine  the American psychiatrist Jean Goodwin presented to the world the following acutely insightful vista of the brain: “Despite many assertions to the contrary, the brain is not “like a computer.” Yes, the brain has many electrical connections, just like a computer. But at each point in a computer only a binary decision can be made—yes or no, on or off, 0 or 1. Each point in the brain, each brain cell, contains all the genetic information necessary to reproduce the entire organism. A brain cell is not a switch. It has a memory; it can be subtle. Each brain cell is like a computer. The brain is like a hundred billion computers Read More ›

Not for the faint-hearted….a fascinating clip on the work of Dutch kinetic sculptor Theo Jansen who has created his own brand of beach creatures.  With over twenty years of arduous work under his belt, Jansen started by pulling his ‘offspring creatures’ up into the wind, then gave them propellers and wings/sails to increase their running power.  The commentator on this clip notes that: “through hours of experimenting and trial and error, Theo’s designs are becoming more and more independent”. Jansen’s own conclusion? “What I have found about this experience of making new forms of life is that you discover all the problems that the real creator must have had creating this world” And these are not even thinking, autonomous beings!  Read More ›

Three months ago Princeton evolutionary biologist Andrea Graham became the talk of the ecoimmunology town through her summarization of the apparent connection between immunity and fertility (1). From trials carried out on 1476 individuals of wild Soay sheep from the St Kilda island archipelago in northern Scotland, Graham et al painted a complex picture of competing trade-offs the strengths of which were intimately dependent on the prevalence of environmental extremes. They found that higher immunity amongst animals, while promoting better survival, negatively affected reproductive prowess (1,2). More specifically sheep with increased immune readiness against ‘parasite infested winters’ were less likely to sire offspring, which Graham et al attributed to the concomitantly higher levels of auto-reactive antibodies (1,2).

Low immune-response animals fared better in low ‘parasite prevalence’ environments perhaps because energy for reproduction was not frivoled away on energy-costly antibody manufacture (1,2). The conclusion drawn was that the selective advantage of low immune-and high-immune response animals in low parasite prevalence and high parasite prevalence environments respectively explains why evolution has in effect “failed to eliminate alleles that confer susceptibility to infection or promote autoimmunity”(2).

So can we pack our bags and head home content with yet another open-and-shut case in which natural selection has been incontrovertibly authenticated? Not quite. Read More ›

Buried in the most recent scientific literature there is a story of love, sex, and intrigue that has all the makings of a hearty Mills & Boon novel.  The central characters of this plot are not lovers wrapped in each others arms but fruit flies that choose their sexual partners according to the microbiota that line their guts (1,2).  Lactobacillus plantarum is the ‘cupid gut bug’ that seems to have greatest influence on sexual preferences (1,2)  And it appears to do so by influencing the release of a class of Drosophila pherormones known as cuticular hydrocarbons (1,2).  For evolutionists this finding is cited as one possible avenue through which speciation might take place in Drosophila (1,2).  For those of us who are critical of such work however there exists one small but important catch.  That is that the sexual preferences observed are easily eradicated by simply treating fruit flies that had been raised on different diets, with antibiotics (1,2).  In other words no genetic changes that would ensure irreversible reproductive isolation, and hence speciation, have taken place.   Read More ›

Shattered assumptions, broken rules and overturned beliefs.  The science media seems eager these days to emphasize science’s capacity to shift paradigms.  And it was such a handful of descriptives that was used to convey the implications of a new study that redefines our view of genome architecture (1).  At the heart of such excitement lay a tunicate organism called Oikopleura dioica that carries in its genetic armory “several peculiarities” (1).  Weighing in with its 70 million base pairs of DNA Oikopleura is today venerated as the animal with the smallest known genome (1).  But what stands out for biologists who have dedicated years to unpacking Oikopleura’s treasure box genome is the ‘odd ball’ physical location of many of its genes (1).  The Scientist’s Megan Scudellari remarked that “Oikopleura’s genes appear to have been shuffled like a deck of cards” (1).

At the apex of this presumed shuffling is that all-elusive but much loved patch-all process called evolution.  “UV rays and other mutagens” that bombard Oikopleura as it ekes out its existence just below the ocean surface are the suggested deck dealers of this particular shuffle (1).  But apart from this rather misty association between cause and effect, there is precious little in the evolutionary inferences of this study to satisfy an appetite for robust scientific argumentation. Read More ›

Unlike Darwin’s bicentennial, here is one anniversary that is certainly worth celebrating.   Unlike Darwin’s rock pile, here is one example of how the science of today is building on the solidity of yesteryear’s durable substructure.  Anti-evolutionists are not anti-science.  But they are opposed to the beligerence of those who contumaciously refuse to accept the broader implications of science’s beautiful procession towards the truth.

Written by Felipe Aizpún Viñes,  OIACDI; 2010, ISBN 10-1452800790; Review by Carlos Javier Alonso, University of Navarra, Spain (see original review in Spanish at OIACDI); Translation by Robert Deyes

Evolucionismo y conocimiento racional (Evolution and rational thought) presents a thoroughly comprehensive analysis of both the arguments in favor and against evolution and demonstrates the author’s  deep understanding of  scientific literature published over the last few decades on the subjects of life’s origins and the evolution of man.  This timely volume deals with the subject matter in extraordinary depth through its coverage of both classical and contemporary viewpoints from the various schools of evolutionary thought.  The 622-page text of Evolucionismo y conocimiento racional is divided up into 21 chapters that systematically unpack the following topics: Darwinism, Evolution: fact or theory, materialist prejudices, creationism, fundamentalism, rational thought, science and philosophy, routes of reason, shortcomings of the scientific method, the ‘new biology’, intelligent design, evolution and creation and the philosophy of life.

Evolucionismo y conocimiento racional stands out as a resource that brings together the core elements of the topics it covers and thus provides an avenue for readers to assess the current state of debate.  In this regard Evolucionismo y conocimiento racional can be seen as the ‘evolution bible’.  Rather than giving the impression of a rapidly assembled collection of facts put together for the sole purpose of disseminating information, the book bears all the hallmarks of a well thought out literary masterpiece.  Most notable is the rich collection of arguments through which each of the evolutionary hypotheses are expounded and systematically considered.  And yet Evolucionismo y conocimiento racional is not exclusively directed towards specialist readers.  On the contrary.  In my assessment, it is easily accessible to those who have a basic training in philosophy and science and a firm grasp of the multi-faceted problems surrounding evolutionary reasoning. Read More ›

During the 1990s I had untold opportunities to witness the full exuberance of nature’s rich offerings. My parents’ house on the southwestern edge of Ecuador’s capital Quito was set in a prime location for observing all manner of wildlife. And most memorable of all were the hummingbirds that frequented our garden attracted as they were to the blooming plants that had been strategically potted next to the outside walls of our living room. These veritable masters of flight, the smallest of warm blooded creatures on our planet, arrived with the sole purpose of extracting sweet nectar from the flowers we had laid before them. Their hovering maneuverability was their most striking attribute. Read More ›

Review Of Programming of Life By Donald Johnson, ISBN-10: 0982355467

There are some science writers that quite simply have a knack for combining the detail of their subject of expertise with a talent for exposition that a wide audience can easily understand. Donald Johnson is one of them. After carefully defining the various types of information- functional, prescriptive and Shannon- that information theorists have set out in their realm of study, Johnson takes the reader on a tour of cellular gene expression by focusing on the digital code of DNA. Shannon information, which provides a mathematical measure of improbability without regard to functionality does not help us in the description of life since the digital code of DNA is rich in what Johnson terms “functional prescriptive information”. Read More ›

“Keep walking back with your kite.  There you go.  Now stop where you are.  The distance between you and me right now is equivalent to about half the height of California redwoods—the tallest trees on earth.  Can you imagine that?” This was my stab at an illustration of how tall trees can really get.  But my eight year old son was having none of it.  “Wind all that string around the reel Dad, and let’s go home!”  Disappointed as I was with his response to my efforts, it was plainly obvious that he had to see something a lot more well-grounded than an unwound length of string tied onto a diamond-shaped piece of flyable canvas. Read More ›

(The following piece makes reference to the late philosopher of science David Hull’s ‘God Of the Galapagos’.  Hull died peacefully earlier this week at the age of 75)

Much has been said about how in The Origin of Species, the problem of suffering in nature tinted Darwin’s view and convinced him of a world that bore none of the expected hallmarks of a loving God (Ref 1). Indeed in a letter to a friend Darwin reflected on the “misery in the world” and expressed his aversion towards the female digger wasp that, ghastly as its feeding habits were, could not have been the product of a,”beneficent and omnipotent God” (Ref 1, p.12). So it is that we begin to understand biophysicist Cornelius Hunter’s assertion that much of Darwin’s own theory was based not on scientific premises but instead on a personal expectation of what God’s creation should look like (Ref 1, p.13). Darwin was disenchanted with Christianity and he wrote as much in the autobiographical account of his younger years (Ref 2, p.57). But he was also deeply affected by the ugliness of nature and what this meant for the existence of a benevolent God. As he wrote:

“A being so powerful and so full of knowledge as a God who could create the universe, is to our finite minds omnipotent and omniscient, and it revolts our understanding to suppose that his benevolence is not unbounded, for what advantage can there be in the sufferings of millions of the lower animals throughout almost endless time? Read More ›

A Review of Peter Forbes’ The Gecko’s Foot: Bio-inspiration: Engineering New Materials from Nature

ISBN-13:978-0-393-06223-6

Bio-inspiration is a relatively new field of science that is trying to replicate the phenomena and designs of nature in ways that are of benefit to man. The manner in which a gecko’s foot allows it to climb glass, the way in which the wings of a butterfly sparkle in the sunlight and the complex methods of flight used by insects have all inspired technologists to emulate nature. More recently the cellular world with its molecular machines has provided a source of ideas for nano-technological design. This ‘nanorealm’ that is the cell has become the last frontier of natural exploration. Bioinspiration has likewise brought together disparate disciplines of science to tackle some of the major challenges of engineering and medicine – proteins that stick onto silica chips, for example, that may one day help in finding a cure for cancer. Read More ›