Literature

An Editorial in Nature deflects legitimate concerns about the ethics of a specific research project by interpreting these concerns as a luddite attack on science by vitalists who think the research is "an affront on God". The offence has been caused by the Venter Institute which is applying for worldwide patents on what they refer to as Mycoplasma laboratorium. This novel bacterium is claimed to have been made with synthetic DNA in the laboratory.
The attack comes from the ETC Group, which is known as an environmental pressure group. They are not associated with a religious agenda. Although one of the employees is quoted as saying "For the first time, God has competition", this reference to God is the only instance I can find on the ETC site. The person went on to say: "Venter and his colleagues have breached a societal boundary, and the public hasn't even had a chance to debate the far-reaching social, ethical and environmental implications of synthetic life".
The concerns of the ETC Group are as follows: synthetic life takes us into previously unexplored areas, raising questions about the ethics of research and the need for a public debate. Specifically: "How could their accidental release into the environment be prevented or the effects of their intentional release be evaluated? Who will control them, and how? How will research be regulated?" These concerns are heightened by the knowledge that large corporations are financing this research and looking for ways to commercialise the findings. Previous experience reveals a story of ethical concerns and public debate being trampled underfoot in the zeal for financial benefits.
The ETC Group seems to have commendable concerns. However, instead of encouraging a debate on the ethics of research, the Editorial goes on the offensive against those raising accusations against "scientists". Furthermore, it takes the opportunity to attack "chronic vitalism" which is apparently any perception "of a need for a qualitative difference between inert and living matter". The editorial adds: "It would be a service to more than synthetic biology if we might now be permitted to dismiss the idea that life is a precise scientific concept." It goes on: "Synthetic biology's view of life as a molecular process lacking moral thresholds at the level of the cell is a powerful one. And it can and perhaps should be invoked to challenge characterizations of life that are sometimes used to defend religious dogma about the embryo."
The Editorial fails to reveal any ethical framework apart from scientific autonomy. It is as though scientists operate outside any regulative framework, and any discussion of ethics is deemed religious or ideological interference with the legitimate process of science. This is really worrying and it should raise concerns in society at large about how scientists have come to accept spokespersons like this.
From an ID perspective, this situation can be understood in terms of the philosophical materialism that has captured the minds of the scientific intelligentsia. There is no possibility of developing ethics within naturalistic science, and there is a resolute refusal to accept the authority of any ethical claims that are not developed by using the scientific method.
Do ID scientists say that "life is a precise scientific concept"? Yes, we do. We say life has complex specified information and this differentiates life clearly from non-life. We do not deny that life can be made in the lab, but we do predict that it will not be made using natural processes. It will only ever be possible with intelligent design.

Meanings of 'life' (Editorial).
Nature 447, 1031-1032 (28 June 2007) | doi:10.1038/4471031b

Abstract: Synthetic biology provides a welcome antidote to chronic vitalism.

See also:

Patenting Pandora's Bug: Goodbye, Dolly...Hello, Synthia!
J. Craig Venter Institute Seeks Monopoly Patents on the World's First-Ever Human-Made Life Form
ETC Group Will Challenge Patents on "Synthia" - Original Syn Organism Created in Laboratory

First paragraph: Ten years after Dolly the cloned sheep made her stunning debut, the J. Craig Venter Institute is applying for a patent on a new biological bombshell - the world's first-ever human-made species. The novel bacterium is made entirely with synthetic DNA in the laboratory.

Ball, P. Genome transplant makes species switch, news@nature.com: 28 June 2007; | doi:10.1038/news070625-9

Natural proteins are remarkable materials, and immense efforts have been devoted to engineering proteins for use in biotechnology applications. Two methodologies have been used: Darwinian blind searches (inspired by evolutionary theory) and rational design (requiring an understanding of the principles of protein structure and function). In their review paper, Leisola and Turunen point out that "some impressive practical achievements have been done using directed evolution methodologies". The analogy here is not with natural selection, but with the artificial selection of desired traits. It should be noted that "the starting point is always a functional protein". These are not engineered from scratch, but promising materials are chosen in order to improve existing properties. The authors raise questions about this approach. "In view of the very substantial challenges remaining and the considerable effort expended thus far, we should pause to ask what things are most impeding our progress." They identify three significant obstacles: lack of a theory for structure design, lack of a general approach for sequence design, and over-reliance on the Darwinian methodology. The problem is that the directed evolution methodology does not focus on understanding the way proteins work. "Thus, we are still missing general theories that would help us to design novel enzymes without a need to use methods that are based on a random search in the local sequence space." "In spite of the progress, we still do not have a general theory on how a sequence produces a specific structure and how a structure determines a function. Therefore, a blind Darwinian search within a known protein scaffold is often used to modify proteins. Unfortunately, blind searches have hard resource limits whereas insight has not. Therefore, in the long run, blind searches are of limited value in compensating our present ignorance."
This is a very interesting conclusion. It illustrates the central theme of Michael Behe's new book: that there are limits to what Darwinian processes can do. Tweaking existing materials is feasible, but if you want to go further than that, you need a rational design methodology. Darwinian mechanisms can be used to explain the adaptation of proteins, but it is unwarranted extrapolation to think that the same mechanisms explain the origins of those proteins.

Protein engineering: opportunities and challenges
Matti Leisola and Ossi Turunen
Applied Microbiology and Biotechnology, 75(6), July 2007, 1225-1232.

Abstract: The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

According to Eugene Koonin, the central problem facing origin of life researchers concerns the emergence of biological evolution (that transitional phase before the time when Darwinian mechanisms were able to operate). The origin(s) of replication and translation (OORT) "is qualitatively different from all other problems in evolutionary biology and might be viewed as the hardest problem in all of biology". The distinction comes about because Darwinists think they have natural mechanisms to account for the origin of complexity, but these only work when replication and translation processes are in place. "The crucial question, then, is how was the minimal complexity attained that is required to achieve the threshold replication fidelity."
Koonin identifies the first paradox of OORT in this way: although we talk about a "minimal" system for enabling Darwinian mechanisms to operate, even this system is a "highly evolved one"! The hurdle that must be jumped is very high indeed. "How such a system could evolve, is a puzzle that defeats conventional evolutionary thinking."
The second paradox of OORT "pertains to the origin of the translation system from within the RNA world via a Darwinian evolutionary process: until the translation system produces functional proteins, there is no obvious selective advantage to the evolution of any parts of this elaborate (even in its most primitive form) molecular machine." Current thinking about the RNA world faces "formidable difficulties".
Basically, Koonin offers no resolution of these paradoxes from within conventional evolutionary thinking. His way out of the impasse is to reposition the debate to take into account recent developments in cosmology. This means adopting the multiverse hypothesis: "The model of eternal inflation implies that all macroscopic histories permitted by the laws of physics are repeated an infinite number of times in the infinite multiverse." This model radically alters our perspectives, such that the "emergence of highly complex systems by chance is inevitable." This is claimed to be the answer to the OORT paradoxes. The multiverse "model not only permits but guarantees that, somewhere in the infinite multiverse [. . .] such a system would emerge." Thus, given the multiverse, chance and the weak anthropic principle are sufficient explanations for the appearance of life as we know it.
This paper is worthy of our attention on several counts: (a) it presents a realistic assessment of the problems of OORT; (b) it explains why the multiverse concept is needed in biology as well as cosmology in order to avoid the need to make design inferences; (c) it provides an appendix on the probabilities of the emergence, by chance, of getting through the OORT impasse (less than 10 to the power -1018).
The paper is accompanied by referees comments and author responses, which enhance its' value. However, two additional critical comments need to be made. The first concerns the author's appeal to the "infinite". Granted that probabilities deemed impossible become possible when multiplied by infinity, it is worth saying that "infinity" is not a concept that belongs to science. It is to be found in pure maths and in philosophy. Koonin does not clearly differentiate science from philosophy here and this detracts from what he has to say. The second critical comment relates to his attitude to the "weak anthropic principle" and the "strong anthropic principle". The latter idea, Koonin asserts, "does not belong in the scientific domain." It must be pointed out that whilst science does not have access to teleology, this does not mean that there is no purpose or goal in the Cosmos. To develop a science that is overtly opposed to the idea of teleology is actually to force-fit science into scientism. Science should never be in the position of declaring what the natural world should be like; its role is to explore what it is like. For more on this interesting paper, go here.

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
Eugene V Koonin
Biology Direct 2007, 2:15 doi:10.1186/1745-6150-2-15 [open access]

Background: Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.
Hypothesis: Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse).
Conclusion: The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.

According to Poole and Penny, there has been far too much speculation about the origin of eukaryotes. "The conflicting hypotheses currently on offer show a curious disregard for mechanism." Up until the mid-1990s, the 'archezoa hypothesis' was dominant. "This maintained that a protoeukaryote (with nucleus) engulfed the mitochondrial ancestor". Support for the theory came from archezoa: anaerobic eukaryotes with no mitochondria, suggesting that "eukaryotes began diversifying before mitochondria entered the picture". The authors point out that this hypothesis has two independent components: "(a) that a protoeukaryote host (PEH) engulfed the mitochondrial ancestor, and (b) that modern archezoa are 'missing links' that never possessed mitochondria."
Hypothesis (b) "is now universally rejected" and the evidence is that the archezoa are derived, not missing links. The authors continue: "Hypothesis (a) was also rejected, and because eukaryotes and archaea share a number of similar genes, the deposed PEH was replaced with archaea. Consequently, incorporation of the mitochondrion - not the origin of the nucleus - was hailed as the defining event in eukaryotic origins. This opened the floodgates of speculation, and numerous new hypotheses emerged. None is supoported by observation: no archaea reside within bacteria, viruses have preposterously few similarities to the nucleus, and no RNA cells exist." The authors go on to develop their critique of these newer hypotheses and to defend the PEH theory. They argue that a nucleus-bearing protoeukaryote was the direct ancestor of modern eukaryotes.
The comments about "floodgates of speculation" in the name of science are undoubtedly correct. They apply generally to the Darwinian story-telling tradition, in which scientists propose speculative scenarios rather than document the real problems that should constrain thinking. Poole and Penny have provided us with a welcome caution about the way science should be done, but have they really gone further than acknowledging the problems? Their ancestral host is a protoeukaryote, not something else! This is the problem of irreducible complexity (noted previously here and here) and it is not going to go away!

Engulfed by speculation
Anthony Poole & David Penny
Nature 447, 913 (21 June 2007) | doi:10.1038/447913a

Abstract: The notion that eukaryotes evolved via a merger of cells from the other two domains - archaea and bacteria - overlooks known processes.

The Human Genome Project was anticipated to have provided us with a blueprint of what makes us human. Very quickly, it became apparent that the published genome was not a blueprint: we had raw data but no information. Although a watershed, it was but a first step in understanding the genetics of human beings.
The follow-on ENCODE Project Consortium focused on a selected 1% of the human genome "to map a variety of sequence elements including genes, promoters, enhancers, repressor or silencer sequences, exons, replication origin and termination sites, transcription factor binding sites, methylation sites, DNase I hypersensitive sites, chromatin modifications, conserved sequences, and RNA transcripts, to name only those considered in the pilot project." One of the major conclusions concerns the organisation of functional elements in the genome. In some cases, this confirmed current models but, the authors of the Nature paper write, "we also uncovered some surprises that challenge the current dogma on biological mechanisms." The surprises all involve unexpected complexity in the genome; complexity that necessitates a revision of the way we think about transcription and genes.
Furthermore, the ENCODE findings should lead to the final demise of the term "Junk DNA". "The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active." The majority of the genome now appears to have functionality. It must be regarded as a "complex, interwoven network" with genes being just one of many functional elements.
It is worth reminding ourselves that the "long-standing view" of the human genome has been used to argue against Intelligent Design. Evolutionary biologists have regarded the existence of Junk DNA as evidence supporting their Darwinian perspective (having a pool of non-functional genetic material with the potential to mutate into something biologically meaningful). Not only has the supposed reservoir of variability evaporated (by the discovery of functionality for most of the genome), the organisational structure of the functional elements has been found to be breathtakingly complex. No wonder the evolutionary biologists find it difficult to avoid using the word "surprise"! ID biologists, on the other hand, have received the findings with enthusiasm, because the discovery of functionality and extraordinary complexity fits the expectation of design-oriented thinking.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium
Nature, 447, (14 June 2007), 799-816 | doi:10.1038/nature05874 [Open Access]

Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

See also:

National Human Genome Research Institute (Press Release), New Findings Challenge Established Views on Human Genome, June 13 2007.

Weinstock, G.M., ENCODE: More genomic empowerment, Genome Research, 2007 17: 667-668. [Open Access]

In the minds of large swathes of the intellectual community, there is a line between facts and values, between the objective findings of science and the subjective beliefs of individuals. This line goes back a long way in history and many regard it as the only way to bring harmony to science and faith questions.
In a recent issue of the New York Times, Senator Brownback explained his reservations about the way the theory of evolution is used in contemporary discourse. In particular, he wrote: "It does not strike me as anti-science or anti-reason to question the philosophical presuppositions behind theories offered by scientists who, in excluding the possibility of design or purpose, venture far beyond their realm of empirical science."
This comment, and several others in his article, has stirred strong reactions from the Editor of the journal Nature. "But there are lines that should not be crossed, and in a recent defence of his beliefs and disbeliefs in the matter of evolution, US Senator Sam Brownback (Republican, Kansas) crosses at least one." The particular point at issue concerns the human mind, and the Editorial insists that the conceptual framework for understanding humanity is evolutionary theory. Thinking based upon human minds being "the product of evolution is not atheistic theology. It is unassailable fact." Furthermore, the Editorial goes on, "our feelings, intuitions, the ways in which we love and loathe, are the product of experience, evolution and culture alone." The Editorial concludes: "Scientific theories of human nature may be discomforting or unsatisfying, but they are not illegitimate. And serious attempts to frame them will reflect the origins of the human mind in biological and cultural evolution, without reference to a divine creation." The abstract of the Editorial reads: "With all deference to the sensibilities of religious people, the idea that man was created in the image of God can surely be put aside."
The real problem is a belief that there is a line between facts and values. Senator Brownback pointed to this when he wrote about "philosophical presuppositions behind theories", but the implications of this have eluded the writer of the Editorial. We do not have empirical evidence that the human mind is the product of evolution: the "unassailable fact" is actually a deduction imposed by the a priori adoption of evolutionary premises (that everything about the human mind can be understood in terms of natural causes: "the product of experience, evolution and culture alone"). In denying the reservations of Senator Brownback, the Editorial has to cross the line in the other direction! Apparently, "science" requires Christians to put aside the idea that man was created in the image of God, and evolutionary psychology requires Christians to abandon the idea that feelings, intuitions and emotions are related to the relationship people have with God. The assertion that "science" has these theological implications should surely make us realise that the fact/value demarcation is inappropriate and that it is time to revisit these issues. The "science" of the Editorial is naturalistic and it is inherently impoverished. We need ID inputs to this debate to reclaim science from the tyranny of naturalism.

Evolution and the brain (Editorial)
Nature 447, 753 (14 June 2007) | doi:10.1038/447753a

Abstract: With all deference to the sensibilities of religious people, the idea that man was created in the image of God can surely be put aside.

See also:
Brownback, S. What I Think About Evolution, New York Times, May 31, 2007.

IN our sound-bite political culture, it is unrealistic to expect that every complicated issue will be addressed with the nuance or subtlety it deserves. So I suppose I should not have been surprised earlier this month when, during the first Republican presidential debate, the candidates on stage were asked to raise their hands if they did not "believe" in evolution. As one of those who raised his hand, I think it would be helpful to discuss the issue in a bit more detail and with the seriousness it demands. [snip]

Michael Behe's sequel to Darwin's Black Box appeared this week and the occasion was marked by a scathing review in the journal Science, authored by Sean Carroll. The reviewer starts by saying that his experience of reading the book reminded him of Thomas Huxley's words during his 1860 debate with Samuel Wilberforce: "The Lord hath delivered him into mine hands." He expands on this with this comment: "Behe makes a new set of explicit claims about the limits of Darwinian evolution, claims that are so poorly conceived and readily dispatched that he has unwittingly done his critics a great favor in stating them."
Unfortunately for Carroll, the words attributed to Huxley were unknown for at least 30 years after the event. They were probably a retrospective invention to further the aims of those trying to represent any questioning of Darwinism as anti-science. Sad to say, Carroll continues to affirm the warfare thesis in this review, painting Behe as writing for "various flavors of creationists", drawing attention to legal decisions declaring ID to be a religious concept, and more.
Readers of Carroll will learn very little about what actually is to be found in Behe's book. This excerpt comprises most of what he has to say: "Behe also explores some examples of Darwinian evolution at the molecular level, including an extensive treatment of the evolutionary "trench warfare" fought between humans and malarial parasites over the millennia - all in the context of what Darwinian evolution "can do." So what's the problem? The problem is what Behe asserts Darwinian evolution can't do: produce more "complex" changes than those that have enabled humans to battle malaria or allowed malarial parasites to evade the drugs we throw at them. Behe's main argument rests on the assertion that two or more simultaneous mutations are required for increases in biochemical complexity and that such changes are, except in rare circumstances, beyond the limit of evolution. He concludes that "most mutations that built the great structures of life must have been nonrandom." In short, God is a genetic engineer, somehow designing changes in DNA to make biochemical machines and higher taxa."
Although Behe's book is packed with arguments from evidence, Carroll has only broad brush rejections of his thesis. He declares "an immense body of experimental data directly refutes this claim". Also, that Behe has "again gone "public" with assertions without the benefit (or wisdom) of first testing their strength before qualified experts." This type of reasoning has often been heard before. Instead of engaging with ID scholarship, there is an appeal to mountains of contrary evidence and to qualified experts who know best.
What Carroll does not acknowledge is that Behe's thesis is recognised as significant among many professional biologists: they have been talking for years about what Darwinism can and can not do! Carroll's selection of literature should not be read as a fait accompli, but as a rear-guard defence of the Darwinian paradigm. There should be an academic debate about the significance of these data.
The real issue is: will a debate within science be allowed? If Behe is not allowed the right of reply, this review should be treated as an exercise in polemics, designed to protect the world of science from ever having to face up to evidences of ID. If there is the opportunity to reply, readers will enjoy a genuine scientific debate. This review must backfire, because science has shown that there are limits to Darwinism and it is perfectly legitimate to ask what Darwinism can and cannot do.

God as Genetic Engineer
Sean B. Carroll
Science 316, 8 June 2007, 1427 – 1428 | DOI: 10.1126/science.1145104

Review of The Edge of Evolution: The Search for the Limits of Darwinism by Michael J. Behe, Free Press, New York, 2007. 331 pp. ISBN 9780743296205.

"The Lord hath delivered him into mine hands."
Those are the words that Thomas Huxley, Darwin's confidant and staunchest ally, purportedly murmured to a colleague as he rose to turn Bishop Samuel Wilberforce's own words to his advantage and rebut the bishop's critique of Darwin's theory at their legendary 1860 Oxford debate. They are also the first words that popped into my head as I read Michael J. Behe's The Edge of Evolution: The Search for the Limits of Darwinism. In it, Behe makes a new set of explicit claims about the limits of Darwinian evolution, claims that are so poorly conceived and readily dispatched that he has unwittingly done his critics a great favor in stating them. [snip]

See also:
John Hedley Brooke, The Wilberforce-Huxley Debate: Why Did It Happen? Science & Christian Belief, (2001), 13(2), 127-141
Excerpt: "Far from any lasting significance, the event almost completely disappeared from public awareness until it was resurrected in the 1890s as an appropriate tribute to a recently deceased hero of scientific education. That delicious remark, "the Lord hath delivered him into mine hands", was probably a retrospective invention of that decade. There is, to my knowledge, no reference to it in the few contemporary reports."(p.129)

Behe, M. Response to Critics, Part 2: Sean Carroll,
AmazonConnect Blog, June 26, 2007

Luskin, C. Sean Carroll Fails to Scale The Edge of Evolution (Part IV): Mistaking Protein Sequence Similarity for Natural Selection
Evolution News & Views, July 2, 2007 [This essay has links to the other three parts of this response to Carroll]

In a major review paper, Jacquelyn Thomas and Fazale Rana argue the critical importance of cell membranes: "Few would question if life, or at least life as we know it today, could exist without boundaries. Should the cell membrane be compromised, key processes of the cell are disrupted. Membrane formation is an essential step in the emergence of life."
Research has tended deliver "proof-of-principle" results designed to show that feasibility of membranes forming by natural processes, but there have been two omissions. The first is an integrated approach, because there are many steps involved in forming a workable membrane. The second concerns the "exacting relationship between environmental conditions and amphiphile composition and phase behaviour": "we have discovered that virtually every step in the process of membrane origins and evolution appears to be crucially influenced by environmental conditions, and lipid composition and polymorphic phase behavior. While researchers have noted the influence of these factors on the emergence of cell membranes, their pervasiveness has largely gone unrecognized."
When an overview of the research is assembled in this way, the landscape can only be described as totally fragmented: "It is almost like having 50 pieces to a puzzle and finding no two pieces fit together because they are from 50 different puzzles." When environmental factors are brought into the analysis, it is found that factors permitting some outcomes prevent others: "Proof-of-principle experiments indicate that physicochemical processes could conceivably lead to the origin and birth of cell membranes, but environmental and lipid compositional fluctuations on early Earth could hinder the emergence of cell membrane systems and the transition to contemporary cell membranes."
The conclusion of the paper is that the focus needs to be shifted towards understanding the role of environmental conditions.
Elsewhere, Rana has this to say about the research outcomes to date: "The exacting conditions needed to self-assemble and maintain biological membranes make the conclusion that these structures could emerge by natural processes improbable. At the same time, the fine-tuning and singularity of conditions needed for cell membrane structure and function stand as hallmark characteristics of Intelligent Design - reasonable expectations if God is responsible for life."

The influence of environmental conditions, lipid composition, and phase behavior on the origin of cell membranes
Jacquelyn A. Thomas and F. R. Rana
Origins of Life and Evolution of Biospheres, 2007 Jun, 37(3), 267-85 | doi 10.1007/s11084-007-9065-6

At some point in life's development, membranes formed, providing barriers between the environment and the interior of the 'cell.' This paper evaluates the research to date on the prebiotic origin of cell membranes and highlights possible areas of continuing study. A careful review of the literature uncovered unexpected factors that influence membrane evolution. The major stages in primitive membrane formation and the transition to contemporary cell membranes appear to require an exacting relationship between environmental conditions and amphiphile composition and phase behavior. Also, environmental and compositional requirements for individual stages are in some instances incompatible with one another, potentially stultifying the pathway to contemporary membranes. Previous studies in membrane evolution have noted the effects composition and environment have on membrane formation but the crucial dependence and interdependence on these two factors has not been emphasized. This review makes clear the need to focus future investigations away from proof-of-principle studies towards developing a better understanding of the roles that environmental factors and lipid composition and polymorphic phase behavior played in the origin and evolution of cell membranes.

From the conclusion: While precise membrane composition and environmental factors may be regulated in individual steps, major difficulties arise when trying to integrate the conditions essential for each step into a cohesive stepwise evolution. It is almost like having 50 pieces to a puzzle and finding no two pieces fit together because they are from 50 different puzzles. Likewise, the conditions necessary for each step of the transition from free saturated fatty acids to modern cell membranes does not "fit" together to form the completed puzzle. [snip] Proof-of-principle experiments indicate that physicochemical processes could conceivably lead to the origin and birth of cell membranes, but environmental and lipid compositional fluctuations on early Earth could hinder the emergence of cell membrane systems and the transition to contemporary cell membranes. Future investigations need to concentrate on developing a better understanding of the role that environmental conditions, and lipid composition and phase structure play in membrane origins.

We've had the "Junk DNA" debacle; now it is the turn of the brain to be analysed as endowed with "anachronistic junk". According to David Linden, the brain is a product of the tinkering blind watchmaker espoused by Darwinist biologists. Unfortunately, few readers will realise that this "central thesis" is a deduction from dogma and not empirical evidence. The data that is discussed is perfectly capable of being understood within a design perspective, including the tendency for our minds to distort reality and to act foolishly.
The reviewer, although sympathetic, baulks at the crassness of the thesis: "More difficult to show is that the use of pre-existing parts imposes functional constraints or 'bad design'." Also: "Linden is right to stress that brains evolved, but hasty to conclude that they are flawed in their design. We still know too little about the brain's inner workings to judge how well it does its job. What we do know, and what The Accidental Mind helps us to realize, is that the human brain is not designed as many have imagined."
Some of us look at the biology of the brain and find exquisite design, not an organ full of flaws. It is true to say that the science of understanding the brain is in its infancy: without hesitation, a prediction can be offered that, as research develops, exquisite design will replace "an imperfect amalgam of shoddy components" in the minds of researchers. This book tells us more about the ideology of its writer than it does about the human mind.
Books like this, and reviews like this, demonstrate yet again how unlevel the playing field is in contemporary science journals. Contributions that deny design, meaning and intelligent agency are given space, whereas proponents of design, meaning and intelligent agency are excluded (and told they have abandoned the scientific method). This is a good example of the tendency for "our minds to distort reality and to act foolishly"!

Brain botch
Georg Striedter
Nature 447, 640 (7 June 2007) | doi:10.1038/447640a

A review of The Accidental Mind: How Brain Evolution Has Given Us Love, Memory, Dreams, and God by David Linden, Harvard University Press: 2007. 288pp.

The human brain, and hence the human mind, is not an optimal, designed-from-scratch apparatus. Rather, it is an imperfect amalgam of shoddy components. That is the central thesis of David Linden's new book The Accidental Mind. Neurons are slow, leaky, and unreliable - hardly ideal computing elements. The whole brain, too, is not designed to the plan of some omnipotent engineer. Instead, evolution has endowed it with plenty of 'anachronistic junk': Which is why, according to Linden, our minds often distort reality and can lead us to act foolishly. [snip]

See also:
http://accidentalmind.org

UK researchers have contributed a fascinating study of assisted bipedalism in orangutans. These animals can keep their legs straight as they move through trees with support provided by the arms. This mode of locomotion occurs when the animals are feeding from small, flexible branches or moving between trees. "Our results are consistent with the prediction that bipedalism allows orangutans to move along multiple supports that are more slender, and hence more deformable, than does quadrupedalism or even orthograde suspension." This confirms the hypothesis that hand-assisted bipedalism confers selective advantages on arboreal apes.
However, the empirical research is not the reason why this paper was the cover story in Science. The authors use their study to argue that bipedalism is a trait that evolved in an arboreal context. One media story describes the significance thus: "The new theory marks a U-turn in scientific thinking. Previously it was assumed humans only began to stand upright after moving out of the forests on to the wide open savannahs of East Africa." The authors claim: "Hand-assisted locomotor bipedality, adopted under these strong selective pressures, seems the most likely evolutionary precursor of straight-limbed human walking."
Although the paper has created a stir, what has been totally lacking is a design perspective. This, I think, is to the detriment of the scientific debate. In particular, the differences between "hand-assisted locomotor bipedality" and the bipedality evidenced by humans are not explored. Yet a fundamental aspect of design thinking is that a whole raft of characters must be in place to enable humans to balance and move on two feet! These include: arched feet, strong big toes, long legs, upright knee joints, angled femur bones, upright hip joints, straight back, upright skull, flat face and a very fine sense of balance. To develop a coherent account of the origin of bipedalism from a "hypothetical common ancestor of the great apes", observations of orangutans moving through trees with straight legs must be supplemented by an extensive analysis of other relevant information. In this analysis, design perspectives have a significant contribution to make.
Another conclusion of interest is that knuckle-walking is inferred to be a derived (rather than a primitive) feature. They suggest that early bipedalism was retained, not gained, in humans but lost by apes and chimps. One is tempted to observe that many widely-held scenarios about human evolution have had to be abandoned like this. Adopting a cautionary stance does seem the wisest long-term strategy.
One last point: the debate over bipedality has artificially restricted boundaries. The participants are all presuming that there is a "hypothetical common ancestor of the great apes". There is no hypothesis that there may not be such an ancestor. This is because the evolutionary framework is accepted as a 'given', deemed to have been proved long ago and not worth revisiting. Consequently, this whole exercise is an example of Kuhnian 'normal' science. The researchers are working within a closed paradigm and trying to put the jigsaw together. Some of us want to change the boundaries of the debate, to revisit the claims of evolutionary theory and to test hypotheses that others are not testing. This, we think, should be deemed essential for the health of science.

Origin of Human Bipedalism As an Adaptation for Locomotion on Flexible Branches
S. K. S. Thorpe, R. L. Holder, and R. H. Crompton
Science, 316, 1 June 2007: 1328-1331.

Abstract: Human bipedalism is commonly thought to have evolved from a quadrupedal terrestrial precursor, yet some recent paleontological evidence suggests that adaptations for bipedalism arose in an arboreal context. However, the adaptive benefit of arboreal bipedalism has been unknown. Here we show that it allows the most arboreal great ape, the orangutan, to access supports too flexible to be negotiated otherwise. Orangutans react to branch flexibility like humans running on springy tracks, by increasing knee and hip extension, whereas all other primates do the reverse. Human bipedalism is thus less an innovation than an exploitation of a locomotor behavior retained from the common great ape ancestor.

See also:

O'Higgins, P. and Elton, S., Walking on Trees, Science, 316, 1 June 2007: 1292-1294.

Gibbons, A., Walk Like an Orangutan, ScienceNOW Daily News, 31 May 2007.

Breitbart.com, May 31 2007, Humans 'learned to walk in trees'