A TWENTY-FIRST CENTURY SCIENCE:

Nature magazine has recently published an interesting essay under the 'Connections' column(Nature:445:Feb 2,2007, p489) The title is as above, and the essay describes how "network math" may help the social sciences in making predictions that can be tested in a scientific way. The author makes a case that internet communications can provide a field wherein the ambiguities of ordinary sociological analysis are reduced so that precise predictions can be made and tested. The author admits that the results derived from internet research are "limited" . The author also, unfortunately, calls for a loosening of the privacy protections on internet communications so that research can be conducted on these matters. NOW, Molly has little doubt that a "science of society" can be constructed that supersedes political ideologies such as Marxism, conservatism, liberalism(or crude anarchism with whatever neologisms it may devise). Time marches on after all. Part of the book that I am trying to review, "A Beautiful Math', refers to such system mathematics. But still...my first objection here is as an individual concerned about their own privacy, and whether the benefit is worth the cost. In a class society such research will be framed in terms of how it can benefit the managerial controllers of the society. I assume that such research can yield testable predictions which I don't assume for most leftoid rhetoric. What I will say plain and simply is that the doomed effort to put chains on scientific inquiry is much more applicable to this case than it is in any other case of simple inquiry. These results will come to view, and leftists are obliged to come to terms with them no matter how much they might like to hide behind rhetoric.

Molly personally is not a leftist in the sense of believing in the underlying ("lying" is an appropriate word) philosophical beliefs of leftism (which includes the so-called "post leftists"). But she is still a "leftist" in terms of believing that the ultimate goals of "the left" are both valuable and achievable. What "the left" has to do is face reality such as that presented in papers such as this and use it for their own purposes.

Molly

A REVIEW OF A REVIEW:
Molly has recently read 'One Good Deed' (Nature: vol 444/7, December 7, 2006), a review of the book 'The Altruism Equation:Seven Scientists Search for the Origins of Goodness'. The book, of course, is another item in the continuing exposition of the rise of sociobiology and evolutionary psychology, fields that were called into being by the necessity to explain "altruism" in a Darwinian fashion. I haven't read the book, but I can immediately detect some matters of "unfairness" in the review by Oliver Curry, apparently a philosopher rather than a practicing scientist. The first is a confusion in regards to the "level of selection". Curry assumes that the proposition that "genes" are the unit of selection is a fundamental paradigm shift that somehow demands that explanations be directed in a totally different manner. In actual fact the "unit of selection" is irrelevant for the explanation of altruism. The mathematics remain the same whether the unit be the gene, the organism, the group, the species or the clade. See 'The Structure of Evolutionary Theory' by the late Stephan J. Gould for a further exposition of this matter, even though I disagree with Gould in that I believe that the individual organism is the primary object of selection.
The author of the review in Nature gives little indication of what exactly the authors of the compilation said. He whines and complains that "kin selection", the most obvious manner in which altruism evolved, and the source of a majority of empirical research to this day, is given an excessive play. Well...it is also the most successful in terms of predictions verified in the real world. Put that in your pipe! He also devotes an excess of complaining to the level of "biographical detail" of the Kropotkin versus Huxley debates and -strangely enough given his first complaint- that W.C. Allee's theories of altruism as divorced from kinship is given excessive play. Had the author of the review been a little more knowledgeable he would have realized that the Russian Darwinists, of whom Kropotkin was one, had posed this question long before Allee did.
It seems to Molly like a bad review of a good book, and I hope to read in in the future.
Molly

CARE FOR THE COMMUNITY: *
I've just read an interesting article in the journal Nature on the evolution of the adaptive immune system (1). Adaptive immunity differs from innate immunity in that the response of the immune system to encounters with foreign organisms or antigens depends on previous encounters. Adaptive immunity, in other words, "remembers" while innate immunity does not.
The article, 'Care for the Community' by Margaret McFall-Ngai claims that all vertebrates have an adaptive immune system along with the innate one while invertebrates rely entirely on the innate immune system (2). The presence of both immunological arms, according to the author,
"...has been thought to promote heightened resistance to microbial pathogens. But this assumption presents a conundrum-invertebrates are no less challenged by the microbial world, nor are they less able to remain healthy."
Why ? One answer is that invertebrates are small, short-lived and have many young at once ie they follow a "R-reproductive strategy" (3) to a greater extent than vertebrates do. In other words they have no need for the "long haul" system of adaptive immunity. The game will be long over before the first inning has barely begun. McFall-Nagai notes, however, that there are many invertebrates that are indeed long-lived, large and have only a limited number of offspring per year. She proposes a different explanation,
"...that adaptive immunity has evolved in part to recognize and manage complex communities of beneficial microbes living on or in vertebrates."
Complex microbial communities associated with vertebrates seem to be a shared feature of the subphylum while invertebrates have far fewer co-evolved partners (4). For instance there have been over 2,000 bacterial species found to exist as either commensal or mutualist partners of humans while fewer than 100 species of human pathogenic bacteria have been identified.
Invertebrates in contrast have far fewer "resident" bacteria. Their guts, for instance, have been shown to contain fewer than 8 residents to date. Most of the bacteria present are "tourists" from the outside world. Their innate immune system has evolved to limit the range of interactions to all but a few "welcome guests".
Three mechanisms have been suggested for how invertebrates "recognize and manage their resident microbial partners". One is intracellular maintenance where the bacteria are housed, hidden from the immune system, within cells. Another is a physical barrier such as the chitin layer of the hindguts of termites and their relatives. Thirdly, the ability of the innate immune system to recognize larger numbers of antigens than previously suspected has recently been demonstrated (5). The author concludes,
"The absence of these three strategies among vertebrates is consistent with the idea that the adaptive immune system has provided them with a different, more versatile, microbial-management strategy."
She suggests the following lines of inquiry to test her hypothesis:
a)Further research on comparative gut microbiota to test whether all vertebrates do indeed have a co-evolved microbial population while invertebrates rarely do.
b)Comparative physiology to see if these co-evolved populations do indeed always provide selective advantages to their hosts.
c)Finally, the price to be paid for this advantage. As she says,
"Is autoimmunity a collateral consequence of the bargain we have cut with microbes(6)."
Many other questions pop up in Molly's tiny feline mind. Like many other aspects of evolutionary biology, from the origins of organelles such as mitochondria and chloroplasts to the achievements of human societies, this is an example of the mutualist mechanism of evolution. Cooperation as opposed to competition will get you everywhere, even to multicellularity. How are interspecific partnerships first established ? What can be said to be evolving in these partnerships ? The vertebrate or the microbes ? It seems plain that the "unit of selection" is not just an animal but the animal along with its associated microflora. It gives a different twist to the idea of "individuality".
MOLLY NOTES:
*'Care for the Community' by Margaret McFall-Ngai, Nature, Vol. 445, 11 January 2007, p153.
1)For an interesting contrast between the innate and adaptive immune systems see Innate Vs Adaptive Immunity.
2)This is not entirely proven, as the author admits later in her article. A search can discover many hints of adaptive immunity in invertebrates. The argument backward from theory is from a lack of the molecular precursors of adaptive immunity in invertebrates. Their is no reason, however, that adaptive immunity couldn't evolve via separate pathways. Simple convergent evolution actually. Look up how many times eyes have evolved independently, with wholly different mechanisms, to see an example of such convergence. Also there is also some dispute about the immune system of "jawless fish".
3) For a brief description of r versus k reproductive strategies see Reproductive Strategies.
4)Once more this waits to be proven. Humans and domestic animals have, for obvious reasons, been the subject of greatest inquiry. To a large extent invertebrates are an unexplored continent.
5)Molly wonders if this isn't, in fact, a dawning realization that there may be an adaptive immune system in invertebrates albeit of a different type and with different mechanisms. It seems I repeat myself here.
6)And perhaps the mechanisms of cancer as well ? Not that invertebrates never develop cancer, but the rate may be significantly lower than amongst vertebrates. Why ?

Transmissible tumours:
The September 7th edition of Nature Magazine has an article under the News and Views section entitled 'Infectious Tumour Cells' (Vol 443, pp35-36). This article discusses the two types of cancer that are directly transferable from individual to individual under normal conditions. These are the canine transmissible venereal tumour (CTVT) and the devil facial tumour disease (DFTD) of Tasmanian Devils. I have read articles on the latter, but, like most veterinarians, I have been familiar with CTVT for much longer. So my memory lapse can perhaps be forgiven when I quoted to a client recently that CTVT was the only cancer known to be directly infectious "as a cancer". My stock of Tasmanian devil faces in memory is exactly zero, so the second fact easily slips my mind.
In any case the article presents the evidence that these tumours are in fact infectious clones of original tumour cells that arose in animals other than those infected rather than being malignant transformations of the cells of the present host animal. The evidence is much stronger in the case of CTVT. Murgis et al (Cell 126 ,477-487-2006) show that the tumours from dogs across 5 continents are closely related genetically and distinct from the genome of the host dog. They use a combination of techniques [dog leukocyte antigens (dla similar to the human hla), haplotyping (chromosome analysis), microsatellite DNA and mitochondrial DNA sequencing]. The various tumours, "had less genetic variability than that observed within even the most inbred breed of dog".
The evidence for the facial tumours of Tasmanian Devils is less robust. It consists merely of consistent patterns of chromosome abnormalities.
The authors of this review (David Dingli and Martin A. Novak) go on to discuss the limited ways in which tumours are transmitted directly in humans. These include mother to fetus transfer, interfetal transfer in multiple pregnancies and transmission via organ donation. Mercifully such events are quite rare. In the case of organ transplants the rate is 0.04% of solid organ transplants and 0.06% of haematopoietic stem cell transfers.
The reason why cancer generally is not transferable is graft rejection due to the MHC antigens that distinguish self from non-self. CTVT cells reduce their expression of MHCs (the DLA previously mentioned) and thereby avoid graft rejection on the part of killer T cells. They do not, however, totally inhibit the expression of such antigens as this would stimulate attack by the NK (natural killer cells), a less specific form of the cellular immune defenses.
The authors go on to say that this phenomenon is evidence of the theory that the MHC evolved mainly as a defense against tumours.

"Horniness in a Perfume Bottle"
I can remember the days when a perfume was marketed that "claimed" to have androgenic pheromones in its odour. It sort of worked on one occasion when I was a "roadie" for a band and found one woman crawling all over me in public claiming that she "liked the smell of construction workers". Never seemed to work so visibly on any other occasion. That men's' cologne has been off the market for years, probably because it never worked in almost all situations. I suspect that the "secret ingredient" was boiled down tomcat piss or something similar.
In the august 3rd, 2006 edition of 'Nature Magazine' there is an article in the news section entitled 'Mouse Data Hint At Human Pheromones'. The article basically describes research (described further in this issue of Nature) that says that there are genetically encoded odour receptors in mice that respond to mouse pheromones that have human analogues.
This field has been very fertile for the grant grabbers over the years in both veterinary and human research, and the general consensus is that the jury is still out in both cases. The article describes some of the previous findings, but it conspicuously omits "negative results". So hold on if the next "wonder cologne" promises too much at too high a price.

"Genetic Horoscopes"
From the "made in the USA Department":
The August 3, 2006 edition of Nature Magazine contains a news article on a new scam now being offered in the USA. The scam is basically that a company advertises over the Internet that it can do "DNA analysis" and report back on the risk of future ailments. Affiliated companies- of course- then offer nutritional supplements that purport to reduce the risk of the diseases discovered by these "tests". The supplements are nothing but multivitamins dispensed with a hefty dose of quack medicine theories.
The US Government Accountability Office (GAO) conducted an investigation using the DNA of only two people in their submissions, a 48 year old man and a nine month old girl. The "results" from 4 companies surveyed were "contradictory and warned of various conditions". The study posed as 14 different individuals and the "results" for the 14 "individuals" differed even if the DNA was the same.
Littler better than your horoscope in the newspaper. Perhaps worse, but, once more, never trust anything with the adjective "natural" attached to it.

Frontiers of Chemistry:
A recent issue of Nature Magazine (August 3,2006) has an article on the "relevance of chemistry". This comes at a time when chemistry is increasingly seen as less exciting than physics, biology, astronomy,etc.. Other disciples are seen as "nibbling away at the edges of chemistry", and because chemistry is so important to industry, "the scientific enterprise that fuels industry" according to the article, it may be that chemistry is only "a form of engineering- a quest for particular solutions to particular problems".
The article above tries to set forth some of the big problems that working chemists see as important. Hence its title, 'What Chemists want To Know'. One of the core problems is, of course, the chemistry of life. As the article states,
"...many of the gaps in scientific understanding of the fundamental processes of molecular biology, such as protein folding, genetic encoding of biomolecular function, and highly selective molecular recognition, are fundamentally chemical problems."
The article go on to say that despite the misconceptions of many (most ?) molecular biologists that,
"Scientific understanding is still not good enough to provide a rational and predictive basis for the kind of molecular scale interventions needed in biomedicine and drug development."
The article goes on to mention that processes such as signal transduction are making chemistry part of information science. This leads via the study of self assembly to the information science of self organization in general.
Another of the frontiers is the design of "chemical learning systems" that can be "trained". This merges into neurobiology at its edges. There is also the unresolved problem of the interface between structure and function, and this is "...often possible only for relatively simple, small molecules-and even then there are many details of the problem that have yet to be clarified."
The article further goes on to state that "the dynamic behavior of molecules can play as big a role in their reactivity as their molecular structure.", and that, "the interactions between biomolecules aren't simply a matter of fitting a key into a lock".
As an aside I can see this as something that used to bother me a a chemist/biochemist. No matter the "perfect fit" of things such as an enzyme and substrate what are the stochastic probabilities of a proper conformational "fit" in the environment of a cell ?
It may be that the newer view of reactions as, "how the molecule's peptide chain negotiates a trajectory across this energy landscape so that it ends up in a 'valley' corresponding to the correct conformation" may contain many parts of the solution to this problem. In other words, the dynamics are key.
Some chemical reactions, but only the simpler ones, are now susceptible to guidance across an energy landscape by methods such as lasers. This comes back to the eternal problem of chemical synthesis- how to "assemble atoms into new molecules in a predictable and effective way". To be cynical about it- how to avoid the sludge that is only 1% desired product.
The estimate is that the number of possible molecules that could be made of the size of a typical drug is about 10 to the 40th power. The number of known natural chemical compounds and artificial ones doesn't even come close to 1% of that number.
The article ends with an aesthetic justification of the small problem approach of most chemistry today because,
"...in chemistry, as in any science, the biggest breakthroughs often come from unexpected directions"