Tuesday, May 29, 2007

Evolutia... pragmatica

"...suntem datori, conform teoriei evolutiei mecanice, pentru toate clipele fericite pe care le-a cunoscut vreodata organismul nostru, pentru toate formele care gandirea noastra isi construieste un ideal, datori legilor ce asigura redistribuirea materiei si miscarii. Dar propria lor fatalitate condamna aceste legi la destramarea a ceea ce au facut, la distrugerea a tot ce isi va implini, cu ajutorul lor, evolutia!" (William James-Pragmatismul)

Saturday, May 26, 2007

Antidot la superstitie

"Intre o explicatie stiintifica si o explicatie mistica, indiferent de subiect, prima este intotdeauna mai superficiala si mai deceptionanta" (Cioran)

Diferenta dintre stiinta si astrologie este ca in stiinta poti urmari pas cu pas, din aproape in aproape, legile cauzale (->) care duc la aparitia unui fenomen (A,B,C,D,E,F,G,H), in timp ce in astrologie acest lucru nu este posibil.

A->B->C->D->E->F->G->H stiinta

A->H astrologia

Fiindca astrologia se bazeaza in general pe influenta evenimentelor cosmice asupra destinului unor persoane, haideti sa luam ca exemplu influenta apropierii Soarelui de Pamant asupra relatiei amoroase dintre, sa zicem, X si Y.

Din perspectiva stiintei, lucrurile au loc cam in felul urmator:

A. Pamantul se afla pe traiectoria cea mai apropiata de Soare.

B. Are loc o eruptie solara

C. Plasma, constand in particule de electroni si protoni, traverseaza distanta dintre Soare si Pamant

D. Ajungand in apropierea Pamantului, produce perturbarea campului magnetic al acestuia

E. Perturbarea campului megnetic atrage dupa sine perturbarea functionarii satelitului de comunicatie

F. Satelitul de comunicatie era tocmai folosit de catre telefonul lui X pentru a clarifica situatia cu Y, cu care se certase acum cateva zile

G. Datorita incapacitatii satelitului, convorbirea dintre cei 2 se intrerupe brusc, nemaidand ocazia celor doi sa se impace

H. Relatia amoroasa dintre X si Y este iremediabil compromisa

Din perspectiva astrologiei, lucrurile stau in felul urmator:

A. Pamantul se afla pe traiectoria cea mai apropiata de Soare.

H. Relatia amoroasa dintre X si Y va fi iremediabil compromisa

In timp ce prima explicatie este logica, a doua nici macar nu este o explicatie, ci doar o afirmatie fara nici un fundament.

Tuesday, May 15, 2007

Aparitie editoriala

Editura Aquila 93 a scos de curand pe piata o carte de exceptie. Este vorba despre Istoria completa a evolutiei umane, de Chris Stringer si Peter Andrews. Cartea apare sub o prezentare remarcabila, cu coperti tari si avand 240 de pagini bogat ilustrate alb-negru si color. Cartea face o sinteză a ultimelor descoperiri cu privire la apariţia si evolutia noastră ca specie.

Unul dintre autori, Chris Stringer, ocupa pozitia de Merit Researcher Human Origins al departamentului de Paleontologie, sectia Vertebrate si Antropologie, din cadrul Muzeului de Istoria Naturala din Londra. Am avut curiozitatea sa-l contactez personal prin Email pe autor, si am avut placuta surpriza sa raspunda foarte prompt abordarii mele.

Sunday, May 13, 2007

James Watson: The double helix and today's DNA mysteries

Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his partner, Francis Crick, discovered the structure of DNA. The tale is full of colorful details: How Watson had planned to be an ornithologist until Schroedinger's book What Is Life? transformed him into a geneticist. The painful rejections he suffered along the way, first from Caltech and then from a certain girl. And finally, how the basic DNA model ultimately came together in just a few hours. Watson finishes with one of the topics currently making him tick: the search for genetic bases for major illnesses.

James Watson has led a long, remarkable life, starting at age 12, when he was one of radio's high-IQ Quiz Kids. By age 15, he had enrolled in the University of Chicago, and by 25, working with Francis Crick (and drawing, controversially, on the research of Maurice Wilkins and Rosalind Franklin), he had made the discovery that would eventually win the three men the Nobel Prize.
Watson and Crick's 1953 discovery of DNA's double-helix structure paved the way for the astounding breakthroughs in genetics and medicine that marked the second half of the 20th century. And Watson's classic 1968 memoir of the discovery, The Double Helix, changed the way the public perceives scientists, thanks to its candid account of the personality conflicts on the project.
Since 1968, he's presided over the Cold Spring Harbor Laboratory, first as Director, later as President and now as Chancellor. From 1988 to 1994, he ran the Human Genome Project. His current passion is the quest to identify genetic bases for major illnesses.

Evolutionary "tree" or evolutionary "net"? / "arbore" filogenetic sau "retea" filogenetica?

Since the time of Darwin, the evolutionary relationships between organisms have been represented as a tree, with the common ancestors at the base of the trunk and the most recently evolved species at the tips of the branches. Microbiologists have argued that this representation doesn’t really hold true for microbes, which often exchange genes among different species. Their claim has been that the evolution of these organisms is better represented by a net, rather like that of a tree.
Initially these speculations were based on discoveries made in medical microbiology; namely that genes for resistance to antibiotics were found to move from one bacterial pathogen to another, but recent analysis of DNA sequences suggests that horizontal gene transfer has also occurred within eukaryotes.
Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved. Most thinking in genetics has focused on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon.
Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene. The original metaphor of a tree no longer fits the data. For example, given two distantly related bacteria that have exchanged a gene, a phylogenetic tree including those species will show them to be closely related because that gene is the same, even though most other genes have substantially diverged. For this reason, it is often ideal to include as wide a range of genes for phylogenetic analysis as possible.

Inca de pe timpul lui Darwin, relatiile filogenetice dintre organisme au fost reprezentate sub forma unui arbore, avand la baza trunchiului stramosul comun, iar speciile mai recent aparute spre varful ramurilor. Microbiologii sustin ca acest tip de reprezentare nu este valabila si pentru speciile de microbi, care schimba frecvent gene intre ele. Ei pretind ca procesul evolutiv al acestor organisme este reprezentat mai fidel sub forma unei retele, decat sub forma unui arbore.
Initial, aceste speculatii s-au bazat pe descoperirile facute in domeniul microbiologiei medicale, si anume pe observatia ca genele raspunzatoare de rezistenta la antibiotice se transfera de la un microorganism patogen la altul, de la o specia la alta. Insa cercetari mai recente au scos la iveala faptul ca acest transfer are loc si in cazul organismelor Eucariote, nu numai Procariote.
Transferul orizontal al genelor (TOG), sau transferul lateral al genelor (TLG), este orice proces prin care un organism transfera material genetic unei alte celule care nu este descendent direct al organismului respectiv. Prin opozitie, transferul vertical are loc cand un organism primeste material genetic de la parintele sau direct sau de la o specie din care a evoluat. Majoritatea cercetatilor de pana acum s-au bazat in mod preferential pe transferul vertical, insa se pune din ce in ce mai mult accent pe transferul orizontal.
Transferul orizontal al genelor este un factor problematic in alcatuirea de arbori filogenetici pe baza analizelor genetice. Vechea metafora a arborelui nu mai corespunde datelor. De exemplu, fiind date doua specii de bacterii inrudite de departe, dar care au schimbat intre ele o gena pe cale orizontala, un arbore filogenetic incluzand cele doua specii le va arata ca fiind inrudite de aproape, deoarece au in comun gena respectiva, asta in ciuda faptului ca restul genelor lor sunt diferite. Din acest motiv, este indicat sa se includa in analizele filogenetice cat mai multe gene posibile, nu numai una singura, si a miscora astfel probabilitatea de a gresi.

Wednesday, May 09, 2007

"Minimum separabile" and the MEMETIC CODE / "Minimum separabile" si CODUL MEMETIC

I have been following the memetic debate on Internet for more than a year now, when I realized that something is missing. I also think that the debate has been going on for too long at the abstract level and it is time to make the shift to the concrete. The reason there are so many unbelievers is that we do not have any reference to the MEMETIC CODE and a mechanistic model of the structure of the meme. We also do not have a proper definition regarding the ENCODING MEDIUM of the memetic code. But, in the process of correcting this, we forget that prior to the gene was the proteine and prior to the codon was the amino-acid. We already knew a lot about the amino-acids and the proteins long before we knew anything about the gene itself. We have been following the wrong path all along all along trying to find out the structure of the meme first. It is like trying to broke the nutshell from inside out. It is known that the gene is built up from sub-units we call codons and we define this in reference to the amino-acids. If the gene have such sub-units, I wonder why shouldn't the meme have too? In the following I hope to prove, indirectly, the existence of these memetic sub-units as real, physical entities by demonstrating the existence of an anatomical structure similar to the amino-acid, which functions as encoding medium for the memetic code. In the same way the codons code for amino-acids, the memetic sub-units also code for something I will temporarily call "minimum separabile". Hold that idea! The term "minimum separabile" belongs to Lorenz, who studied the phylogenetic development of voluntary movements through the animal kingdom (the term was originally used to explain the separation power of the retina).

I've been reading these days this book on ethology, in Romanian, when I stumbled on this passage:

"As I emphasized earlier, there is a basic physiological difference between two types of instinctive motion: one type which refuses to comply to the learning process, and another type which, on the contrary, possess a high tendency to associate with diverse conditioning stimuli during the learning process. This basic physiological difference between the behaviours unsuited for the learning process and those suited, relies on the fact that the former are activated by a single unitary and extremely specific motivation, while the later are not activated by such a single unitary motivation. The later can be incorporated in more than one behaviour, each with different motivations. For this reason they are called instrumental activities. When the environment and life conditions of a species demands a sudden and total adaptability of the motions of that species, which cannot be provided by the existing complexes of ereditary motions, than the phylogenetic adaptation is realized by fragmentation in many small elements (units), each of these remaining just as rigid as any centrally coordinated motion; each of these, because of their limited size and because of their permanent availability, are suitable to be used as separate pieces in the process of learning new motions, with practically infinite complexity. Metaphoricaly speaking, the ereditary coordinated motions does not alter like an elastic ribbon, moulding itself on the demands of the environment, but rather like A CHAIN CONSISTING OF MANY SMALL RINGS WHICH CAN INTERCHANGE. This becomes very obvious if we compare the locomotion of a few related species, but species living in different environments. The more homogenous the environment is, the narrower the adaptability it demands. In the case of Ungulates the locomotion (walk, trot, gallop) is globally coordinated. In this case the soil, being relatively homogeneous, provides each step with the same support. But, being confronted suddenly with obstacles unforeseen, these Ungulates, which live on open steppe, stumble almost always, because they lack the proper coordination. A more precise coordination of motion is possible only when the smallest autonomous unit of motion - "minimum separabile" or voluntary motion, as Lorenz calls it - is as limited as possible. Indeed, for the animal to be able to target a particular point, like the surface of a small stone on a mountain side, and successfully pass through it, he must coordinate its each step as precisely as possible. So, in order to coordinate its motions, it is vital that this smallest unit to be available independently from other similar units. This capacity to fragment the global ereditary coordination in small, isolated units, which makes them available to be organized, through learning, in a succession of voluntary motions, is a phylogenetic adaptation more obvious in the case of mammals which lives at high altitudes, with rough terrain, like Capra ibex, Capra pyrenaica etc. The environment which demands the largest flexibility of the coordination of locomotion, and the greatest possibility to combine these isolated units in complex, learned motions is the tree canopy. The fragmentation is more obvious in Primates because they can use their prehensile hands, legs and tail to grasp deliberately a certain branch. K. Lorenz concludes that the process by means of which small elements of motion are extracted from the whole, in order to gain a relative autonomy - which allows them to be used to the construction of new, learned behaviours - leads to the apparition of the so called voluntary motions."

So, I conclude that these "minimum separabile" are in fact the _encoding medium_ for the memetic code. They are anatomical structures used to create a variety of complex motions, in the same way the amino-acids are uses to create a large variety of complex proteins. Each amino-acid in the protein has its corresponding codon within the structure of the gene, and each
"minimum separabile" has its corresponding sub-unit within the structure of the meme. One involves the other. In fact, all that a learning system needs is a code (genetic or memetic) and an encoding medium, a set of recombinable elements that we call amino-acids or, in the case of memetic code, these "minimum separabile". All we have to do now is to delimit anatomically these "minimum separabile".

P. Weiss postulated 6 levels of inclusiveness for motion:

Level 1. Basic unit of contraction (muscle fiber)

Level 2. All the muscle fibers which belong to the same muscle

Level 3. The synergistic activity of all the muscles which move the same joint

Level 4. The co-ordinated motion of one leg, hand etc

Level 5. The co-ordinated motion of more organs

Level 6. The motion of the whole body

Considering that we cannot voluntarily move a single muscle fiber (Level 1) or even a single muscle (Level 2), the best match for our above description of "minimum separabile" seems to be Level 3. It is the smallest irreducible voluntary motion. I will remind you that most animal joints have one, two, or three degrees of freedom. Most joints have _at least_ two muscles for each degree of freedom (two "minimum separabile"), because each muscle is paired with a muscle of the opposite effect. If we take the human ankle, for instance, we can see that it has two degrees of freedom, because it can exhibit flexion and extension, as well as inversion and eversion. We can conclude that, in the case of the human ankle, there are at least four "minimum separabile" (four "amino-acids") which forms the basic elements to a large variety of motions that the human ankle can perform through learning. Just think at the amazing performance of a ballet dancer. If we consider the human jaw, we can see that it has three degrees of freedom: it can move right and left, up and down, back and forth. Of course, through the combination of these six (six "minimum separabile"), the jaw can perform a large variety of other, more complex, motions (many of them involved in speech). In this case there are not one, but two joints involved (but this is not relevant). Another example is the human eyelid. It can perform only two basic motions: up and down. But through the combination of these two, it may result very complex and subtle motions (just remember the way your girl-friend looks at you sometimes). All this is true for the vocal apparatus, too: the tongue and the larynx. One might object that the tongue makes an exception because it doesn't have a bony skeleton, so it doesn't have joints. But this is not true because the tongue's body does have a fibrous skeleton which serves as insertion points for the tongue's muscles.

Everybody knows that each amino-acid has its corresponding codon within the genetic code. If we accept all that I said above, we must also accept that each "synergistic activity of all the muscles which move the same joint", each "minimum separabile", has its corresponding "codon" within the MEMETIC CODE. In respect with the term "codon", I will name it "MEMON".

Published on the "Journal of Memetics - Evolutionary Models of Information Transmission" on Feb. 2003

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Saturday, May 05, 2007

Tinerete fara batranete? / Life without death?

Recent, revista Nature a publicat un studiu al cercetatorului Martin Holzenberg, de la institutul Insern din Paris, care sustine ca a descoperit gena tineretii fara batranete. Studiul se refera la corelatia care ar exista intre regimul de hrana si expresia unei anumite gene reglatoare responzabile de longevitate, si care ar avea ca efect o durata de viata mai scurta sau mai lunga. Studiul a fost efectuat pe soareci (sau pe viermi?), cu care omul are in comun gena respectiva. (Ca o paranteza, precizez ca in presa romaneasca informatia a aparut in 2 publicatii, Evenimentul Zilei si Gardianul, insa, ca de atatea ori, informatiile sunt contradictorii. In timp ce una din surse sustine ca experimentele au fost efectuate pe soareci, cealalta sustine ca au fost efectuate pe viermi, probabil Nematozi).

Dincolo de conotatiile subiectiv-afective (cine nu vrea sa traiasca cat mai mult?), se pune intrebarea oare care este functia adaptativa a mortii? Ca orice alta insusire a sistemelor biologice, si moartea (pornind de la premiza ca nu este un accident sau un produs secundar) trebuie sa fi evoluat prin selectie naturala… Problema rezida in faptul ca moartea (sau durata limitata de viata a unui individ) pare sa constituie o exceptie de la regula, deoarece este un dezavantaj pentru individ. Ori se stie ca, prin definitie, selectia naturala tocmai ca favorizeaza orice insusire care confera individului cel mai mic avantaj pe scena evolutiei. Cu alte cuvinte, moartea nu putea sa apara prin selectie naturala, deoarece nu confera nici un avantaj individului, din contra. Deci moartea sfideaza Darwinismul. Contradictia este insa doar aparenta. In realitate moartea este o piese importanta in teoria selectiei naturale, si o cerinta obligatorie pentru evolutie. Un organism ipotetic care ar trai vesnic, nu ar putea evolua. El ar ramane vesnic cu aceeasi combinatie de gene cu care s-a nascut. In realitate selectia naturala are nevoie in permanenta de cat mai multe combinatii de gene pentru a le testa si a le selecta pe cele mai adaptate, fapt in care rezida functia adaptativa a mortii. Nu mai vorbim de faptul ca o populatie formata din indivizi cu durata de viata nelimitata si-ar epuiza in scurt timp resursele vitale si ar disparea.