Monday, 30 July 2007

Science for the people

During my wanderings I have found the original manifesto Towards A Science For The People by Bill Zimmerman, Len Radinsky, Mel Rothenberg and Bart Meyers written in 1972. The text is full of ideological lingo, for a person who grew under communist rule reminiscent of the Party slogans and directives. It is so highly critical of the `ruling class', `military-industrial complex' and inequality in science that if such criticism was written under the communist rule, the authors would end up in prison. The worst that has happened to the authors in the US was the refusal of publication in Science.

While the text is, in its political fervour, almost crazy, the ideological blindness that makes it funny lies in small details. The predictions and accusations that almost all were falsified by the passage of time. Two sinful monopolies were mentioned: ATT (that soon was broken down by the very `capitalist government') and IBM (that is now far from a monopoly). An example of inequality of access to science was provided by computers and - that are far removed from ordinary people (just a couple of years before PC was invented). Lasers and other advances in telecommunications were supposed to benefit only the telco company. Who could envision ubiquitous mobile phones...

One thing for certain, a lesson for today: when we are blinded by our own ideas, our own goals it is so easy to miss the reality of the world. When we think about the environment protection, nuclear energy or empowerment of the people it is worth to spend a minute analyzing the fate of the predictions from 1972. Read it, whether you are conservatist or leftist.

PS. In the current Science for the People WEB site many of the problems have changed. Obviously. Some were solved, some - never appeared. But the language has remained truly revolutionary. Point for Dawkins and his meme concept.

Sunday, 22 July 2007

Quantum Mechanics again: point for experimentalists

Understanding the basic principles of QM is really difficult. The philosophical and theoretical discussions, even those coupled with a lot of more or less developed mathematics are only adding to the confusion. Of course - they are needed - because thanks to such theoretical musings as EPR's or Bell's the path may be opened for experimental evidence. And such evidence, very often, is more surprising than we could expect.

A fine example is provided by
Jacques, V.; Wu, E.; Grosshans, F.; Treussart, F.; Grangier, P.; Aspect, A. & Roch, J. Experimental realization of Wheeler's delayed-choice gedanken experiment. Science, 2007, 315, 966-968

Let me just quote here the conclusions of the paper:
Our realization of Wheeler’s delayed choice Gedanken Experiment demonstrates beyond any doubt that the behavior of the photon in the interferometer depends on the choice of the observable which is measured, even when that choice is made at a position and a time such that it is separated from the entrance of the photon in the interferometer by a space-like interval. In Wheeler’s words, since no signal traveling at a velocity less than that of light can connect these two events, “we have a strange inversion of the normal order of time. We, now, by moving the mirror in or out have an unavoidable effect on what we have a right to say about the already past history of that photon”. Once more, we find that Nature behaves in agreement with the predictions of Quantum Mechanics even in surprising situations where a tension with Relativity seems to. appear

I wonder if this result will hold on repetitions. If yes, then this would reaffirm that we have a lot to understand yet. Especially about time in Quantum Mechanics.

Friday, 20 July 2007

Beyond DNA and RNA

One of the basic messages of current biology, one of its paradigms is the circular flow of information and selection, in which DNA (in some cases RNA) carries the information, which directs development and some aspects of operation of organisms. These organisms then compete, cooperate, coexist; and as result of selective events, pass (or fail to pass) their DNA to their descendants. The flow of information from nucleic acids to the main building blocks of organisms --- proteins, is unidirectional. Of course when we look at the processes more carefully we see that proteins themselves are not only products of the genetic code translation, but heavily influence the process. They make the process possible, may speed it, slow it down, influence what gets translated.
But in general this cycle: `DNA -> RNA -> proteins (complete organism) -> survival and reproduction' is seen as basic and universally true rule.

The discovery of prions (and the subsequent fame of this discovery related to the `mad cow' disease and its relation to Creutzfeldt–Jakob disease in humans has shown that there might be very interesting exceptions. For me it has been exactly this sort of an exception that makes it necessary to have a deeper look at the rule itself.

I have found a short, but very readable article summarizing this subject,
by A. E. Bussard, A scientific revolution?
The prion anomaly may challenge the central dogma of molecular biology
, European Molecular Biology Organization Reports, 2005, 6, 691-694
The prion anomaly may challenge the central dogma of molecular biology. The main line of reasoning is not the existence of prions, but the fact that in some cases, relevant information may be stored and transmitted between generations not via DNA or RNA, but via proteins:

Recent discovery of prions as genetic elements that store and transmit information in various organisms, mainly yeast, the fungi Podospora and the sea hare Aplysia.

How is it possible? How does it work? The first evidence came from studying yeast, where evidences of non-mendelian transmission of phenotypic traits were found in late 1960's. As Bussard describes the situation:

Much of this evidence relies on Lindquist’s work on yeast prions. Not only did she show that prion domains in some proteins act as molecular switches that activate or deactivate the protein, she also showed that prions are non-mendelian genetic elements that have an important volutionary role by producing new phenotypes, which are often beneficial. Her work on sup35 revealed that the protein switches to its prion state [PS1+] when the environmental conditions for yeast deteriorate, which decreases translation fidelity and causes the ribosome to read beyond nonsense codons. This in turn enables the expression of formerly silent genes and gene variants, and creates new phenotypes. [PS1+] is passed on to daughter cells in which it self-replicates by imposing its conformation on normal sup35 proteins, until a new phenotype eventually emerges that is better adapted to the new environment. In another elegant experiment, Li and Lindquist showed the generality of this mechanism for controlling protein activity by fusing a yeast prion domain to a rat protein.

For more detailed informations see, for example,
True, H. L. & Lindquist, S. L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature, 2000, 407, 477-483
Lindquist, S.; Krobitsch, S.; Li, L. & Sondheimer, N. Investigating protein conformation-based inheritance and disease in yeast. Philos Trans R Soc Lond B Biol Sci, 2001, 356, 169-176

When we start to think how really complex the molecular biology of life is, when we take into account the myriad of interactions and influences, then we may begin to believe in wonderful nature of life --- and, at least for me, in the wonderful nature of the study of life, of discovering the links and relationships, between various elements.

There is a very significant message that Bussard emphasizes:

Biologists need to get used to the idea that there is no end in sight when it comes to new insights and scientific breakthroughs; this idea has long been abandoned by physicists who are subject to regular scientific revolutions. I wonder if knowledge is, like the Universe, basically endless and in constant expansion, just as the complexity of life itself is also expanding infinitely.

And this is exactly what I believe myself.

Saturday, 14 July 2007

Astrophysics directions

Recent years have been very fruitful for astrophysics. Sometimes even to the point of overeagerness in accepting new paradigms. For example I am somewhat surprised with the speed of acceptance of the Dark Energy (73%) / Dark Matter(22%) / Normal components (5%) model of the Universe.
Yes, I am impressed with the explaining powers of this model, especially with respect to the increasing speed of expansion, but the question is: how did it come about that the scientific community has accepted so fast the Dark Energy explanation (and the Dark Matter as well), without any inklings as to what this Dark Energy is?

More - with the 120 orders of magnitude difference between our possible explanations and the observed value! Yet so many astrophysicists behave in a way as if the problem does not exist.

When the ApPEC and ASPERA, which are consortia of national agencies that pay for astroparticle physics research in Europe, published the report on Status and Perspective of Astroparticle Physics in Europe the collaborators have identified six `basic questions that need to be addressed by the astroparticle community over the next decade:

1. What is the Universe made of?
2. Do protons have a finite life time?
3. What are the properties of neutrinos? What is their role in cosmic evolution?
4. What do neutrinos tell us about the interior of the Sun and the Earth, and about Supernova explosions?
5. What is the origin of cosmic rays ? What is the view of the sky at extreme energies ?
6. Can we detect gravitational waves ? What will they tell us about violent cosmic processes and about the nature of gravity?

As for the question 1, the particular focus is on Dark Matter, which is described as
`Dark Matter turns out to be the majority
component of cosmic matter. It holds the Universe together through the gravitational force but neither emits nor absorbs light. Dark Matter (including a small admixture of massive neutrinos) has likely played a central role in the formation of large scale structures in the Universe. Its exact nature has yet to be determined. The discovery of new types of particles which may comprise the dark matter would confirm a key element of the Universe as we understand it today.

But for the Dark Energy, the report states only that `The nature of dark energy remains a mystery, probably intimately connected with the fundamental question of the cosmological constant problem.'

The plans are - one should notice - made by astroparticle
rather than astrophysics organizations. So, perhaps it is not too surprising that in the list of planned and supported experiments the authors state:
`It is this part of the search for Dark Matter that we assign to the field of astroparticle physics. Dark Energy has a similar density to dark matter; unveiling of its nature would have profound impact on astroparticle physics. On the other hand, current projects exclusively rely on tools of astronomy; therefore we express strong support for dark energy projects but leave detailed recommendations to the strategic planning of astronomy roadmaps.'

Despite these remarks (perhaps written slightly tongue-in-cheek), the report is very clear and can be a good initial review on the current state of knowledge. Recommended reading!

Saturday, 7 July 2007

Network of genes, network of patents

I was away on a business trip for a few days, and in a hotel lobby I have chanced upon an International Herald Tribune (July 4th, 2007). And there I found a longish article in the economy section (!): Biotech industry rocked as theories change. The change of theories is described as:
"challenging the traditional view of our genetic blueprint as a tidy collection of independent genes, pointing instead to a complex network in which genes, along with regulatory elements and other types of DNA sequences that do not code for proteins, interact in overlapping ways not yet fully understood."
While this may be interesting scientific result, the IHT article aptly points that the one gene-one effect (one protein) stance led the way to gene patents: patents based on the assumption that industrial gene (made by splicing techniques) would have defined, owned, tracked and uniform effect, moreover with ability to sell and retract. But when the genes really work in a complex network how can we be sure which effects is due to what? Biologically. And legally too: if one patented gene depends on other natural or patented ones? Especially in ways we do not understand? How to pay royalties? How to split an eventual responsibility for damages? How to ensure that effects are uniform and as promised?

Well, there is much more to the subject. I was never in favour of granting patents on genes, but the US law has allowed the companies to do it. Without, as it turns out, proper understanding of the separability of the "inventions". And because we lack real understanding of the most of the genome (the original paper that has prompted the IHT article speaks about 1% of the genome) we are blundering blindly -- and this is never a good thing.

For more information see:
The ENCODE Project Consortium, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 447
Mark B. Gerstein at al. What is a gene, post-ENCODE? History and updated definition, Genome Res. 2007 17: 669-681
Thomas R. Gingeras Origin of phenotypes: Genes and transcripts Genome Res. 2007 17: 682-690