Science Literature

Although geographically widespread, the genus Pelecanus has only 7 or 8 species extant (depending on the classification system used). A similar number of fossil species have been identified, although the morphological differences are quite small. Until recently, the earliest fossil form was dated as Early Miocene. Newly published work pushed the first appearance back to the Early Oligocene, considered to be about 30 million years old. The point of interest for us is that the fossil, and specifically the beak, is said to be "morphologically identical to modern pelicans".

"All these characteristics of the fossil are identical to those of the species in Pelecanus, the single extant genus in the family. [. . .] Therefore, [the specimen] can be considered a morphologically modern pelican of the genus Pelecanus, but it is not closer to any particular extant species."

"It is so similar to modern pelicans, despite its 30 million years" (image: A. Louchart, source here)

The beak is of particular interest, because it is "highly derived" and unique when compared with all other birds. Since the component parts are both unusual and inter-dependent, convergent evolution is not perceived as a viable hypothesis.

"Thus, the evolution of this advanced feeding apparatus, one of the most distinctive arrangements among birds, had already been achieved by the early Oligocene and its morphology is found unchanged in extant pelicans after ca. 30 million years, which can be considered a stasis of long duration."

The authors set out some thoughts to explain this stasis. The first hypothesis is that the beak is functionally optimal over 30 million years, and there has been no selection for change. The whole family can be considered to occupy an adaptive peak on their sector of the adaptive landscape. Another hypothesis is that flying ability is a constraint on morphological adaptation. However, neither of these options are found satisfying and the authors indicate their preference for keeping an open mind:

"The remarkable stasis in the beak of pelicans remains intriguing, and is probably in need of new explanations."

They are undoubtedly right: the stasis is intriguing and new explanations are needed. What we are seeing here is a particular type of stasis, and it concerns complexity. Much diversification has little or no effect on complexity and examples of diversification therefore have little or no bearing on the origin of complexity. The pelican beak, however, is not just a big beak! There are numerous coordinated elements that have to be present for the beak to function at all. The fossil find is important because the earliest fossil of a pelican exhibits the full functionality of the modern birds. As far as the known fossil record is concerned, complexity was present - before the radiation of the Pelecanidae. Yes, this makes stasis in the pelican beak intriguing and it means that Darwinism has nothing to offer by way of an explanation. New explanations should include the options opened up by intelligent design.

The earliest known pelican reveals 30 million years of evolutionary stasis in beak morphology
Antoine Louchart, Nicolas Tourment and Julie Carrier
Journal of Ornithology, advanced publication June 2010 | DOI: 10.1007/s10336-010-0537-5

Abstract: The feeding apparatus of Paleogene birds is rarely well-preserved. Here, we describe the earliest known pelican (early Oligocene, Luberon, southeastern France), with its almost complete beak. Morphologically identical to modern pelicans, the new fossil already shows several advanced features unique to extant species of the genus Pelecanus. It probably belongs to the lineage ancestral to all or some of these pelican species. This fossil reveals a remarkable evolutionary stasis in the morphology of such an advanced avian feeding apparatus through ca. 30 million years. Several hypotheses are proposed to suggest explanations for such examples of long stases in volant homeothermic vertebrates.

See also:

Hecht, J. Pelican fossil poses evolutionary puzzle, New Scientist (22 June 2010)

Today, there seem to be many vested interests in scientific consensus. Universities and science associations often make use of the concept when explaining the importance of science in society and in making pronouncements on issues of public significance. Consensus is relevant to funding agencies, who focus their awards on science that appears to be building on an existing knowledge base. It is a factor in peer review, for it is much harder to get unorthodox ideas past the journal review processes. It influences the media: who is regarded as an 'expert' and who should not get exposure because of their unorthodox ideas. How refreshing, then, to find the Royal Institute of Philosophy offering some cautionary words in an editorial:

"One of the most striking aspects of Karl Popper's philosophy of science is his insistence that scientific consensus is sleep inducing, intellectually speaking. He did not actually put it quite like that. What he pointed out was that the most successful scientific theory ever devised turned out to be false, even though it had been treated as scientifically practically unquestionable for nigh on two centuries. Popper was thinking of Newton's theory, whose refutation (as Popper saw it) in 1917 was a key moment in his own intellectual life."

Popper "called for a clear demarcation between good science, in which theories are constantly challenged, and what he called "pseudo sciences" which couldn't be tested. His debunking of such ideologies led some to describe him as the "murderer of Freud and Marx". [Some of us think the name of Darwin should be added to this list]." (Source here)

Even more welcome are the two examples selected of modern-day scientific consensus: "critics of the theory of evolution and of the reality of climate change". Although the public has been assured time after time that the "science is settled" on these issues, the guardians of these consensus positions will not be pleased by these cautionary words, nor by the judgment offered that the critiques "are not all or entirely without weight".

"Popper's lesson is little heeded to-day. Critics of the theory of evolution and of the reality of climate change are not so much argued with as vilified, excluded and marginalised in polite scientific and even political circles. It is what one might expect from a very powerful institution, like the medieval Church, but not perhaps from one ostensibly committed to critical rationality and the pursuit of falsification. The criticisms which are made of the theory of evolution and of climate change, as these things are currently and consensually understood, are not all or entirely without weight."

It appears to me that the philosophers are not making a judgment on the science, but on the quality of the debate. There are real issues to discuss - the philosophers can recognise that. Furthermore, they are not impressed by the way the defenders of scientific consensus are treating the critiques: ad hominem arguments, straw man arguments, much handwaving, smokescreens and even a refusal to engage with the real issues. Even saying there should be a proper debate can be dangerous:

"We hope that saying that will not bring a heap of opprobrium on our heads. But even if the criticisms were off the wall, those who take Popper seriously may still occasionally catch a whiff of the falsifying rat behind the painted and perfumed consensus."

A recent example of the lack of real debate can be found in the reception of What Darwin Got Wrong by Jerry Fodor and Massimo Piattelli-Palmarini. Here is Douglas Futuyma in Science (7 May 2010) in a review entitled: "Two critics without a clue".

"Fodor and Piattelli-Palmarini show little familiarity with the vast literature on genetic variation, experimental analyses of natural selection, or other topics on which they philosophically expound. They are blithely agnostic about the causes of evolution and apparently uninterested in fostering any program of research. Because they are prominent in their own fields, some readers may suppose that they are authorities on evolution who have written a profound and important book. They aren't, and it isn't."

Another example is the ID prediction of functionality for Junk DNA, and the establishment Darwinists defence of Junk. An interesting report on some recent exchanges is by Jonathan Wells. This concludes:

"If one overlooks the nastiness, it is clear that there are some interesting issues in this debate. Conceptually, what does it mean to say that a segment of DNA has function? Empirically, what does the evidence show? One might think that professors Matheson, Hunt and Moran would address the conceptual issue calmly, rationally, and collegially. But they don't; instead, they stoop to misrepresentation and ridicule. And one might think that they would address the empirical issue by citing published scientific evidence. But they don't; instead, they simply proclaim themselves the only authorities on the subject."

What we are seeing is a warped science. Instead of championing empiricism and testing of hypotheses, the consensus scientists end up appealing to authority and treating the evidence lightly. They are making the same mistake as the Medieval Church.

Scientific Consensus
Editorial
Philosophy, April 2010, 85(2), 181 | doi: 10.1017/S0031819110000161

[Much of the text of this editorial is cited above]

See also this review by another philosopher:

Midgley, M. What Darwin Got Wrong by Jerry Fodor and Massimo Piattelli Palmarini, The Guardian, 6 February 2010.

It took 20 skilled people working for a decade, and an estimated $40 million of funding, but the outcome is spectacular. It is described as "a defining moment in the history of biology and biotechnology" by Mark Bedau, editor of the journal Artificial Life. The BBC News headline was succinct: 'Artificial life' breakthrough announced by scientists. The Economist declared: "Artificial life, the stuff of dreams and nightmares, has arrived". The research paper claims to have made a synthetic cell, and uses the word "creation" in the title.

"We refer to such a cell controlled by a genome assembled from chemically synthesized pieces of DNA as a "synthetic cell", even though the cytoplasm of the recipient cell is not synthetic. Phenotypic effects of the recipient cytoplasm are diluted with protein turnover and as cells carrying only the transplanted genome replicate. Following transplantation and replication on a plate to form a colony (>30 divisions or >10^9 fold dilution), progeny will not contain any protein molecules that were present in the original recipient cell."

"Interesting creatures will be bubbling out of the Venter Institute's labs" (image source here)

It seems obvious that the research team should be congratulated, but we do need to ask - what exactly is it that they are being congratulated for? In a news article in Science, Pennisi wisely puts the word "synthetic" in quotation marks when referring to the whole organism, but is happy with "synthetic genome" in her title. So let's look at the genome and clarify what was done. The exercise was based on the bacterium with the smallest genome: Mycoplasma mycoides. In the past, the team has published a series of papers on constructing building blocks and assembling them. They have learned how to make changes to the code so they could trace progress. Pennisi summarises as follows:

"The researchers started building their synthetic chromosome by going DNA shopping. They bought from a company more than 1000 1080-base sequences that covered the whole M. mycoides genome; to facilitate their assembly in the correct order, the ends of each sequence had 80 bases that overlapped with its neighbors. So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations. Using yeast to assemble the synthetic DNA in stages, the researchers first stitched together 10,000-base sequences, then 100,000-base sequences, and finally the complete genome."

In view of the complexities experienced, the successful assembly was a magnificent achievement. The researchers then embedded their new genome in the cytoplasm of a recipient cell - the related bacterium Mycoplasma capricolum. Unfortunately, the cell died. It took three months to find the problem. The team systematically replaced stretches of the assembled genome with the natural genome until they identified the cause: a single-base mistake in the synthetic code. The research moved on to check the functioning of the replicating bacterium.

"They sequenced the DNA in this colony, confirming that the bacteria had the synthetic genome, and checked that the microbes were indeed making proteins characteristic of M. mycoides rather than M. capricolum. The colony grew like a typical M. mycoides as well. "We clearly transformed one cell into another," says Venter."

The research has long-term practical goals. Will it be possible to design bacteria that have novel functionalities? Clearly, many are working towards that goal. According to one expert, "One thing is sure, interesting creatures will be bubbling out of the Venter Institute's labs". The authors write:

"This work provides a proof of principle for producing cells based upon genome sequences designed in the computer. DNA sequencing of a cellular genome allows storage of the genetic instructions for life as a digital file. The synthetic genome described in this paper has only limited modifications from the naturally occurring M. mycoides genome. However, the approach we have developed should be applicable to the synthesis and transplantation of more novel genomes as genome design progresses."

One of the greatest concerns we should all have is the idea that because we can copy the processes found in living things, we can engineer those processes. The reality continues to be that we are ignorant of so much that is going on in the cell. The incident with the single-base mistake in the coding is just the tip of the iceberg! The information content of cells is such that we are continually out of our depth in understanding even the most basic functions. A specific concern is the way the research team describe the role of the recipient cell: a vessel that can be reprogrammed by the novel genome. This may be feasible with close relatives, but the danger is that information embedded in the recipient cell may be overlooked. The comments of Mae-Wan Ho are pertinent:

"Clearly the scientists have not created life or the bacterial cell. There is a yawning chasm in the physics and chemistry of the living state that the team hasn't even begun to address, let alone bridge. They did not create the genome that was used to transform the bacteria cell, only copied it from another species of the genus, adding a "water mark" for identification, and no doubt, for staking their claim to the synthetic genome. This synthetic genome was not even made from scratch, but cobbled together from pieces found in a catalogue, and then 'transplanted' into cells of the recipient bacterium species (a close relative of the donor) using an antibiotic to select for cells that have accepted the artificial chromosome and allow them to grow."

In his Muse column, Philip Ball also discusses reasons for caution. If we are going to research life, we must not reduce it to engineering the genome, where "the membranes, the cytoplasm - everything except the genes - are mere peripherals to the hard drive of life, whose algorithmic instructions need only be rejigged to produce new organisms."

"Attempts to make a genuinely 'designed' genome, rather than one based on a naturally evolved bacterium, will remind us how sketchy our understanding is of the rules that govern the crucial interactions among genes and with other elements of living cells. In the post-genomics era, our ideas of where the real business of life resides are shifting again. We are moving away from a linear 'code' and towards something altogether more abstract, emergent and entangled. So in marking yet another deepening appreciation of how life operates, the latest 'synthesis of life' seems likely to repeat the historical template."

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Daniel G. Gibson, John I. Glass, Carole Lartigue, Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison III, Hamilton O. Smith & J. Craig Venter.
Science Express (May 20, 2010), doi 10.1126/science.1190719

Abstract: We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

See also:

Ball, P. A synthetic creation story, Nature online 24 May 2010 | doi:10.1038/news.2010.261

Ho, M-W., Synthetic Life? Not By a Long Shot, ISIS Report 24/05/10

Life after the synthetic cell, Nature, 465, 422-424, (27 May 2010) |doi:10.1038/465422a

Pennisi, E. Synthetic Genome Brings New Life to Bacterium, Science 328, 21 May 2010, 958-959.

Wells, J. Has Craig Venter Produced Artificial Life? Evolution News & Views (May 24, 2010)

Kaebnick, G., Is the "Synthetic Cell" about Life? The Scientist, 24(7), July 2010, 27. [need to register for access]