Science Literature

Robert Deyes

Switches, rheostats, electrical circuits and complex feedback loops that regulate household devices as well as national power grids are things that we have become so accustomed to in our own lives that we generally take them for granted. That is, until they break down. We saw this on a massive scale in the summer of 2003 when New York and other US and Canadian cities were brought to a stand still as power blackouts swept the east coast. A New Scientist report at the time claimed a total of 50 million people were affected (Ref 1). Needless to say, it took several days to bring things back to normal. The economic impact of the catastrophe cost the American and Canadian governments billions of dollars (Ref 1).

Switches turn genes on and off in the cell

Incredibly, regulated circuits and switches also exist inside the microscopic world turning genes on at the precise moments that their products are required and shutting them off when those same products become unnecessary, superfluous or even detrimental. In a fascinating study headed by a group at the Wistar Institute in Philadelphia it has now become clear that histones - proteins that are involved in packing DNA into individual chromosomes - play a fundamental role in regulating which genes are turned on and off in the cell (Ref 2). It appears that small molecular groups attached onto these histone proteins can serve as on/off switches that modulate which genes are on or off at any given moment. These molecular groups become attached to the histones as a result of multi-component machines that turn on genes. Karl Henry's group at the Wistar has revealed the functionality of one of these multi-component machines called the SAGA complex that attaches a molecular group called ubiquitin onto one of the Histones (Ref 2). What is surprising about the SAGA complex is that the removal of the ubiquitin molecular group from the Histones does not turn genes off. Rather it seems that both the addition and subsequent removal of ubiquitin, both by the SAGA complex, provide an essential sequence for turning genes on (Ref 2). This finding places an extra level of complexity to the previously held view that genes could be turned on or off through simple on/off switches. Now it appears that such switches operate through a specified order of molecular changes. In the case of SAGA, the correct order is absolutely critical if genes are going to be turned on correctly.

So it is that we learn that the 'conversion' of the genetic instruction into protein through the initial step of transcription involves more than polymerases - the reading molecules that chug along the DNA and generate RNA. It is a carefully planned, well-orchestrated series of events involving molecular switches. We see a complexity that intuitively does not seem to be accessible to unguided assembly. As mathematician David Berlinski quipped, "wherever the biologist looks, there is complexity beyond complexity, the entanglement of things ramifying downward from the organism to the cell" (Ref 3).

What caused the east coast electricity blackout? According to the New Scientist report there were two crucial pieces of software that failed on that frightful day (Ref 1). As alarm systems failed, more lines shut down and voltages fluctuated, the entire network spun out of control with the inevitable consequence of a massive power shut down. America suffered its worst power cut in recent memory because the correct order of processes and procedures so essential for the smooth running of an electricity grid had not been met. What happened on that horrific day during the heat of the summer sun was due to operator failure and could have been easily prevented. The New Scientist report mentions, for example, that one engineer left for lunch when a critical maneuver needed to be carried out (Ref 2). It is profoundly ironic that one of America's worst power failures should occur at precisely the moment that intelligent agency left the scene. As with man-made designs, evidence points to an intelligence behind the precision functioning of the cellular world.

References

1. Celeste Biever (2003) 'Preventable' failures caused US power blackout, New Scientist, 20th November, 2003

2. Karl W. Henry, Anastasia Wyce, Wan-Sheng Lo, Laura J. Duggan, N.C.Tolga Emre, Cheng-Fu Kao, Lorraine Pillus, Ali Shilatifard, Mary Ann Osley, Shelley L. Berger (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation mediated by SAGA-associated Ubp8, Genes & Development Vol 17 pp2648-2663

3. David Berlinski (1996), The Deniable Darwin, http://www.discovery.org (see 'Articles by Center Fellows')

The "Age of Fishes" was in the Devonian Period of Earth history, when placoderm fishes became the dominant group of vertebrates. Largely on the basis of their place low down in the Tree of Life, placoderms have been regarded as "early primitive fish" which were slow and dull. We now need to question the validity of this perspective and whether it owes more to evolutionary presuppositions than to evidence.

Masterpricis attenboroughi is revealed as viviparous

The great majority of modern fish indulge in spawning: females lay large numbers of eggs and males fertilise those eggs after they have left the mothers' bodies. The process appears inefficient because few of the eggs grow to mature adults. However, in the absence of predators (such as after an environmental crisis), it is a great way for populations to expand rapidly.

Some fish, like sharks and rays, fertilise internally. Some are ovoviviparous, whereby the eggs remain in the body cavity of the female for protection, but the mother does not provide the embryos with nutrients. The rest are viviparous, giving both food and protection before they are born. Palaeontologists had "suspected that some placoderms fertilised internally". This is because "The males of a sub-group of placoderms , called ptyctodontids, have clasper-like appendages dangling from their pelvic fins - these are reminiscent of the claspers of modern sharks that are used to inseminate females." How far were these placoderms like the sharks and rays? The new fossil finds show that at least some placoderms were viviparous.

"With the discovery of the embryos we can now be sure that at least some placoderms gave birth to live young" says Per Ahlberg at Uppsala University in Sweden.
[. . .]
"Our ongoing investigations suggest that viviparity is more widespread than previously thought in early placoderms," says Long [at Museum Victoria in Melbourne, Australia].

From an evolutionary perspective, these placoderms "had a remarkably advanced reproductive biology". The reproductive system for internal fertilisation and viviparity is far more complex that the system for spawning. Yet the complex system appears in the placoderms, which represent the first flowering of vertebrate life in the fossil record.

For a long time, trilobite eyes served as an icon of complexity in the Cambrian. As time passes, this has been supplemented by many evidences of advanced morphologies (for examples, go here and here). Analysis of the genomes of so-called "primitive" organisms has revealed genes that are also found in more sophisticated animals. This new research reveals viviparity in some placoderm fish. How much more evidence do we need to show that Darwinian gradualism is in tension with the data?

Looking for patterns of oviparous, ovoviviparous and viviparous animals allows some generalisations. Mammals (with the exception of monotremes) are viviparous and there are a few cases of vivipary in reptiles, fish and insects. But when the focus changes to look at the details, and when the interpretive framework is the Tree of Life, then there are many difficulties. In a comment on the Nature news item, David Bump draws attention to the problems the authors have identified:

"...the complex behavioural, morphological, and physiological mechanisms required for successful copulation and internal fertilisation in chondrichthyans (Hamlett & Koob 1999) must have evolved independently and non-reversibly 12 times in teleosts..." It also claims that "Live bearing evolved from egg laying independently in all classes of vertebrates except birds, and also in many invertebrate clades." That's a lot of independent, sudden appearances of a complex reproductive strategy. It must take a lot of faith to believe in all that being the result of purely natural evolutionary processes, which haven't yet been shown to be capable of producing such changes.

This is a fair comment. We need a different paradigm - one that is not embarrassed by the riches of biological information found in supposedly primitive life-forms.

Live birth in the Devonian period
John A. Long, Kate Trinajstic, Gavin C. Young & Tim Senden
Nature 453, 650-652 (29 May 2008) | doi:10.1038/nature06966

The extinct placoderm fishes were the dominant group of vertebrates throughout the Middle Palaeozoic era1, yet controversy about their relationships within the gnathostomes (jawed vertebrates) is partly due to different interpretations of their reproductive biology. Here we document the oldest record of a live-bearing vertebrate in a new ptyctodontid placoderm, Materpiscis attenboroughi gen. et sp. nov., from the Late Devonian Gogo Formation of Australia (approximately 380 million years ago). The new specimen, remarkably preserved in three dimensions, contains a single, intra-uterine embryo connected by a permineralized umbilical cord. An amorphous crystalline mass near the umbilical cord possibly represents the recrystallized yolk sac. Another ptyctodont from the Gogo Formation, Austroptyctodus gardineri, also shows three small embryos inside it in the same position. Ptyctodontids have already provided the oldest definite evidence for vertebrate copulation, and the new specimens confirm that some placoderms had a remarkably advanced reproductive biology, comparable to that of some modern sharks and rays. The new discovery points to internal fertilization and viviparity in vertebrates as originating earliest within placoderms.

See also:

Dennis, C., The oldest pregnant mum, Nature 453, 575 (28 May 2008) | doi:10.1038/453575a

Morelle, R. Fossil reveals oldest live birth, BBC News, 28 May 2008

Mother fish, Museum Victoria News, 29 May, 2008 (with two video clips)