The Aquatic Ape Hypothesis of Elaine Morgan is a classic "just-so" story that attempts to explain the evolution of modern humans by claiming that our ancestors once lived in water. It's a typical adaptationist perspective on biology since it begins with the assumption that every phenotype of humans must have been due to natural selection. [Hat Tip: John Hawks]
Posted yesterday on Evolution News & Views: European scientists working in conjunction with Biologic Institute.The anti-ID crowd has an old canard about there being no serious scientists who doubt Darwin, let alone any that support intelligent design. And they like to say that there is no science being done by ID scientists. Both ideas are not just false, but absurdly so. Note this announcement of new scientific arrivals at Biologic Institute. Professor Matti Leisola, the Dean of Chemistry and Materials Science at Helsinki University of Technology in Finland; Colin Reeves, Professor of Operational Research in the School of Mathematical and Information Sciences at Coventry University; and Professor Stuart Burgess, Head of the Department of Mechanical Engineering at the University of Bristol.Three "serious scientists", eh? And not a biologist in the bunch. That's what we've come to expect in an institute that's supposed to be studying
1. I steal a lot of John's ideas but let's not tell him, OK? It gives him a swelled head.
4) a person who is unaware that they have said or done something foolish, childlike, noobish, lame, or inconvenient.and ...
A whining fool shouting loudly for liberty but not willing to pay the bill."After most American workers saw more money in their paycheck due to the lower tax rate, the teabaggers at Fox News railed against high taxes, but did not discuss how much Jesus hated hypocrisy."
Carl Zimmer has an article in Science with a provocative title: On the Origin of Eukaryotes. This is well-timed since it appears just when I've returned from a meeting on this very topic. [Go here if you can't see the article on the Science website.]
Whatever the exact series of events turns out to be, eukaryotes triggered a biological revolution. Prokaryotes can generate energy only by pumping charged atoms across their membranes. That constraint helps limit their size. As prokaryotes grow in size, their volume increases much faster than their surface area. They end up with too little energy to power their cells. Eukaryotes, on the other hand, can pack hundreds of energy-generating mitochondria into a single cell. And so they could get big, evolving into an entirely new ecological niche.This is a widely believed explanation for the adaptive value of mitochondria and internal membranes. But many species of bacteria have internal membranes and, in the case of photosynthetic species, those internal membranes are packed full of energy-producing proteins.
Day One, Day Two
After a short break we returned to hear a presentation by William (Bill) Martin of Heinrich-Heine-Universität in Düsseldorf (Germany). His presentation was Endosymbiosis and gene transfers from endosymbionts, the most glaring insult to the tree. As the title implies, the key point is that a large percentage of nuclear genes in eukaryotes is derived from mitochondrial genes (proteobacteria) or from chloroplast genomes (cyanobacteria).
Andrew Roger is a former student of Ford Doolittle. He is now a professor in the Department of Biochemistry and Molecular Biology at Dalhousie University in Halifax, Nova Scotia (Canada). The title of his talk is a challenge to his former mentor: Deconstructing deconstructions of the tree of life: why a tree of microbes might be realizable, meaningful and useful.
)[Photo Credit: These photos are from Christina Behme. The bottom one is of me having dinner on the first evening with Ford Doolittle (left), John Dupré (standing), and Andrew Roger (right).]
Sometime around midday you could write the exact time and date as 12:34:56 07/08/09 and if you were up early you could have witnessed 04:05:06 07/08/09.
At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.
One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?THESE days most people think it unscientific to believe in "miracles", and irreligious not to believe in them. But would the occurrence of miracles really violate the principles of science? And would their non-occurrence really undermine religion? David Hume and Richard Dawkins have attempted to answer these questions in their different ways, but I am not convinced by their arguments, and for me they remain open questions.So, it's an open question whether miracles are compatible with science, eh? I wish Hugh McLachlan had given us some examples of miracles that he thinks would be compatible with science.
The title of the press release on Biology News Net caught my eye: UNC researchers decode structure of an entire HIV genome. I clicked the link on my aggregator and read the first two paragraphs.The structure of an entire HIV genome has been decoded for the first time by researchers at the University of North Carolina at Chapel Hill. The results have widespread implications for understanding the strategies that viruses, like the one that causes AIDS, use to infect humans.By the time I finished the article I thought I had a pretty good idea of what they were talking about but, just to be sure, I visited the Nature website to read the actual scientific paper.
The study, the cover story in the Aug. 6, 2009, issue of the journal Nature, also opens the door for further research which could accelerate the development of antiviral drugs.
Watts, J.M., Dang, K.K., Gorelick, R.J., Leonard, C.W., Bess Jr., J.W., Swanstrom, R., Burch, C.L. and Weeks, K.M. (2009) Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460:705-710 [doi: 10.1038/nature08237]The authors determined the two- and in some cases the three-dimensional structure of the HIV RNA genome. In other words, they figured out the way RNA folds to form regions of secondary structure (double-stranded RNA). This RNA molecule functions as a complex messenger RNA and the secondary structure plays a role in regulating how the molecule is translated.
Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.
Our discovery that the peptide loops that link independently folded protein domains are encoded by highly structured RNA indicates that these and probably other mRNAs encode protein structure at a second level beyond specifying the amino acid sequence. In this view, higher-order RNA structure directly encodes protein structure, especially at domain junctions. The extraordinary density of information encoded in the structure of large RNA molecules (Figs 1, 2 and 4d) represents another level of the genetic code, one which we understand the least at present. This work makes clear that there is much to be discovered by broad structural analyses of RNA genomes and intact mRNAs.I'm not sure this language is helpful.
It might not be super high-res, but researchers at the University of North Carolina at Chapel Hill have described the first full structure of the HIV-1 genome.
The paper, published online today in Nature, maps out the virus' genome down to a one-nucleotide resolution with the help of a technique call SHAPE—selective 2'-hydroxyl acylation analyzed by primer extension—to paint the full, previously unknown picture of the virus (Scientific American is part of Nature Publishing Group).
This is a very famous molecular complex. You need to identify this complex by naming all the major components. You will not win if you skip this part. (Don't forget the red bit.)1. Because immunology isn't biochemistry and possibly not even a real science.
The figure is from Reinherz et al. (1999).
Reinherz, E.L., Tan, K., Tang, L., Kern, P., Liu, J., Xiong, Y., Hussey, R.E., Smolyar, A., Hare, B., Zhang, R., Joachimiak, A., Chang, H.C., Wagner, G., and Wang, J. (1999) Science 286:1913-1921. [PubMed] [doi: 10.1126/science.286.5446.1913]
Mark Buchanan believes that physics has entered a new era where it has gone beyond the fundamental forces into the realm of "collective phenomena". He claims that biology is about to do the same as he explains in an article that was just published in Nature Physics: "Collectivist Revolution in Evolution."It now seems clear that biology may also have a second act linked to the widespread importance of collective phenomena. The explosion of genetic and genomic data, of course, has ushered in the era of systems biology, as biologists have come to recognize the need to gain a more holistic understanding of the functioning of organisms. But this may not be the most radical transformation in store for biological science. A coming revolution in biology, some suggest, may go so far as to unseat Darwinian evolution (ran in its modern form) from its position as the key explanatory process in biology, and may just bring back some form of Lamarckian evolution—that old idea of the inheritance of acquired characteristics.No, it's not epigenetics, it's lateral gene transfer (LGT) that's going to unseat Darwinian evolution and bring back Lamarck.
The conjecture is that horizontal gene transfer was indeed required for the present genetic code to take the form it has, and that the emergence of life most likely went through a series of stages, with the early stage more Lamarckian in character, and only the latter stages becoming more Darwinian.This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it.1
Exploring that point in greater detail will be a task for a new kind of biology, one that breaks with many of the presuppositions of traditional evolutionary thinking, and explores the potential for rich and surprising dynamics in a collective setting. It will almost surely benefit from the ideas and experience of physics, which has already experienced its own collectivist revolution.
1. I wonder if Nature Genetics publishes opinion pieces by evolutionary biologists on the overthrow of quantum mechanics?
I wish that Obama had picked someone else as his nominee for Director of NIH. I'm not opposed to Collins simply because he is religious. I'm opposed to him because he has taken a very public and vocal position on the roles of science and religion. Here's how I've expressed my viewpoint in comments on my own blog and elsewhere.I'm not opposed to Collins just because he is an evangelical Christian. And I would not be opposed to someone from another faith, nor to an atheist.This seems to be a difficult position for most people to grasp. PZ Myers shares my perspective on the appointment [Is it really that hard to understand?] but no matter how many times he tries to explain it, there's always someone who tries to turn it into an attack on all Christians. The latest is Matt Springer.
But when a person becomes an outspoken advocate of a particular religious belief and establishes a foundation and a website to promote that belief (e.g. BioLogos) then that's a different story.
The banner on the BioLogos site reads, "We believe that faith and science both lead to truth about God and creation." Collins has gone beyond merely holding a belief that may or may not be compatible with science. He is now actively identified with a particular position; namely, that science and evangelical Christianity are compatible.
Not only that, Collins is on record favoring the use of his office to promote his personal religious beliefs [Mixing Science, Religion, and Politics].
It would be far better to appoint someone who could maintain a decent separation between religion and science. The Director of a major government funding agency should not be openly advocating a religious perspective on science.
It would be just as unwise to appoint a vocal atheist or a vocal Muslim.
