Dmitry Kobak (kobak) wrote,
Dmitry Kobak
kobak

The Logic of Chance

Прочел полдюжины обзорных статей человека и парохода (H≈140) eugene_koonin, а сейчас, для закрепления материала, дочитываю его свежую книжку «The Logic of Chance: The Nature and Origin of Biological Evolution». Основной лейтмотив — изучение эволюции в последние лет 20 радикально изменилось: раньше о многом приходилось лишь догадываться, а теперь можно напустить статистические алгоритмы на гигантские генетические базы, и многие вопросы прояснить непосредственно. Захватывающая область, от которой у меня ощущение чуть ли не чуда. Примерно как от большого адронного коллайдера: удается заглянуть куда-то туда, куда, казалось бы, заглянуть невозможно — в тераэлектронвольты или в миллиарды лет назад. И, кстати, любопытно, что в обоих случаях, чтобы хоть что-то «увидеть», нужна компьютерная обработка гигантских объемов информации.

Ниже — ссылки и выписки (много); почти все статьи лежат в открытом доступе. Книжка (ее нетрудно скачать самизнаетегде) во многом представляет собой все эти обзоры, собранные вместе.


Koonin, Darwinian evolution in the light of genomics
http://nar.oxfordjournals.org/content/37/4/1011.full.pdf

Длинный и подробный обзор; в сущности -- краткая версия книги. Если читать одну статью, то эту. В начале полезный список разных важных эволюционных идей, высказанных после Modern Synthesis. Выводы:
The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin. [...] By contrast, the insistence on adaptation being the primary mode of evolution that is apparent in the Origin, but especially in the Modern Synthesis, became deeply suspicious if not outright obsolete [...].


Koonin and Wolf, Is evolution Darwinian or/and Lamarckian?
http://www.biology-direct.com/content/pdf/1745-6150-4-42.pdf

Очень интересный обзор, хорошее краткое введение про идеи Ламарка.
Stress-induced mutagenesis is a rule among bacteria rather than an exception [...]
...
Adaptive evolution resulting from stress-induced mutagenesis is not exactly Lamarckian because the stress does not cause mutations directly and specifically in genes conferring stress resistance.
...
Highly sophisticated mechanisms are required for this bona fide Lamarckian scenario to work, and in two remarkable cases, the CASS and the piRNA system, such mechanisms have been discovered.

Indeed, evolution is a continuum of processes, from genuinely random to those that are exquisitely orchestrated to ensure a specific response to a particular challenge. The critical realization suggested by many recent advances referred to in this article is that genomic variation is a far more complex phenomenon than previously imagined and is regulated at multiple levels to provide adaptive reactions to changes in the environment. The distinction between Lamarckian and Darwinian mechanisms of evolution potentially could be considered as one of only historical, semantic or philosophical interest.


O'Malley and Koonin, How stands the Tree of Life a century and a half after The Origin?
http://www.biology-direct.com/content/pdf/1745-6150-6-32.pdf

Обзор о том, как быть с Tree of Life в свете горизонтального переноса генов. Текст с сильным философским уклоном (Tree of Life -- это эвристика или гипотеза?) и эпиграфом из Джона Донна. Любопытная дискуссия в комментариях.
However, somewhat paradoxically, the very process of building phylogenies with molecules revealed the extent of horizontal gene transfer (HGT), and thereby threatened the TOL concept in regard to its core ideas of a unique ever-bifurcating branching pattern.


Puigbo et al., Search for a 'Tree of Life' in the thicket of the phylogenetic forest
http://www.biomedcentral.com/content/pdf/jbiol159.pdf

Отличная статья с очень красивыми картинками о том, что эволюционные деревья генов, которые есть почти во всех организмах, топологически очень близки друг к другу в "лесу" из 7000 деревьев для разных генов. Узнал слово thicket -- чаща!
We analyzed the structure of the forest of life by embedding the 3,789 COG trees into a 669-dimensional space [и так далее]
...
The most straightforward interpretation of the detected central trend in the forest of life is that it represents vertical inheritance permeating the entire history of archaea and bacteria. A contribution from ‘highways’ of HGT (that is, preferential HGT between certain groups of archaea and bacteria) that could mimic vertical evolution [15] cannot be ruled out.


Koonin, A Non-Adaptationist Perspective on Evolution of Genomic Complexity or the Continued Dethroning of Man
http://www.landesbioscience.com/journals/cc/kooninCC3-3.pdf

Краткое и очень понятное резюме идеи Линча и Конери (Continued Dethroning of Man! название отличное). Идея заключается в том, что сложные многоклеточные организмы возникли не в результате естественного отбора (бактерии гораздо лучше приспособлены к окружающей среде), а в результате ослабленного стабилизирующего отбора из-за малых размеров популяции. Иными словами, мы с вами (и все остальные многоклеточные) -- не венец творения, а чудовищные мутанты, которых отбор не вычистил только потому, что нас очень мало.
[...] comes a major puzzle. Along with the (at least potentially) ‘useful’ complex features, genomes of multi-cellular eukaryotes have accumulated numerous ‘selfish’ elements, which have no function in the ‘host’ organism.3-5 Questions of paramount importance and interest are why are selfish elements so abundant in the genomes of complex organisms but not in those of simpler ones, and what is the connection (if any) between the propagation of selfish elements and emergence of ‘useful’ aspects of complexity. A recently published theory suggests an astonishingly simple, general, and plausible solution.
...
Although the actual fraction of eukaryotic DNA that is subject to selection is intensely debated, the amount of DNA that is indisputable junk is huge.
...
Purifying selection is intense in large populations, essentially precluding fixation of significantly deleterious mutations. In contrast, in small populations, even mutations with a substantial deleterious effect can be and often are fixed by random drift.
...
This means that, simply by the power of the Okkam razor, we must accept this nonadaptationist explanation as the current null hypothesis on the origin of biological complexity.
...
To put it succinctly once again, the null hypothesis on evolution of biological complexity is that complexity is but a by-product of entropy increase which, in turn, is a ‘genomic syndrome’ caused by reduced population size.
...
The entropic theory of complexity evolution makes a qualitatively new step by establishing a direct connection between environmental catastrophes, which result in an abrupt drop of population size of many species, and genome evolution.


Lynch and Conery, The origins of genome complexity
http://www.sciencemag.org/content/302/5649/1401.short

Исходная статья Линча и Конери в Science 2003.
We argue here that the transitions from prokaryotes to unicellular eukaryotes to multicellular eukaryotes are associated with orders-of-magnitude reductions in population size; by magnifying the power of random genetic drift, reduced population size provides a permissive environment for the proliferation of various genomic features that would otherwise be eliminated by purifying selection.


Lynch, The frailty of adaptive hypotheses for the origins of organismal complexity
http://www.pnas.org/content/104/suppl.1/8597.full

Агитка Линча в PNAS.
The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory.
...
It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated [...]
...
Most biologists are so convinced that all aspects of biodiversity arise from adaptive processes that virtually no attention is given to the null hypothesis of neutral evolution, despite the availability of methods to do so.
...
The field of population genetics is technically demanding, and it is well known that most biologists abhor all things mathematical.


Gray et al, Irremediable Complexity?
http://www.sciencemag.org/content/330/6006/920.full

Еще один коротенький обзорчик на ту же тему, из Science. Тут в одном абзаце сведены две идеи: идея Линча и идея храповика и собачки (люблю храповик и собачку, особенно после Фейнмановских лекций): нейтральная мутация может закрепиться по каким-нибудь случайным причинам.
As an alternative to such adaptationist thinking, Lynch invoked fixation of neutral or slightly deleterious features as a general and unavoidable source of complexity in taxa with small populations (3, 7). Such nonselective processes could account for the origins and spread of transposons (mobile DNA elements), introns, and other contributors to the high DNA content of many eukaryotes, which typically have small populations relative to prokaryotes. Neutrally fixed complexity could be neutrally “unfixed” (through random reversion), but ratchet-like (one-directional) tendencies might prevent this. For example, a genome once infected with an active but harmless transposon will not likely regain its simpler, pristine condition without selection for reduced element number. At the organismal level, Maynard Smith and Szathmary proposed that a ratchet mechanism called contingent irreversibility might render previously independent evolutionary units interdependent for “accidental reasons [...]”


Gould and Lewontin, The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist program
http://rspb.royalsocietypublishing.org/content/205/1161/581.short

Ну и заодно -- классика жанра! Критика оголтелого адапционизма от великого Гульда, 1979 год. Пазухи сводов (?) Сан Марко и проч.
[...] male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain *why* they got so small [...]
...
Since Darwin has attained sainthood (if not divinity) among evolutionary biologists, and since all sides invoke God's allegiance, Darwin has often been depicted as a radical selectionist at heart who invoked other mechanisms only in retreat, and only as a result of his age's own lamented ignorance about the mechanisms of heredity. This view is false.


Stoltzfus, Mutationism and the dual causation of evolutionary change
http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2006.00101.x/abstract

Довольно путаный исторический обзор автора статьи о "constructive neutral evolution", но со множеством цитат. Мне помог несколько прояснить суть дебатов раздел о генном пуле с точки зрения modern synthesis. Modern synthesis утверждает, что мутации не играют никакой роли, потому что в генном пуле и так уже есть вся возможная изменчивость; поэтому курс эволюции (якобы) определяется только естественным отбором, а мутации ни на что не влияют. Странноватая точка зрения, по-моему, но автор приводит соответствующие цитаты из Майра, Докинза и др. На всякий случай: Штольтцфус (?) утверждает, что это досадное заблуждение.
Thus, “evolution is not primarily a genetic event. Mutation merely supplies the gene pool with genetic variation; it is selection that induces evolutionary change” (Mayr 1963, p. 613).
...
Mutations are rarely if ever the direct source of variation upon which evolutionary change is based. Instead, they replenish the supply of variability in the gene pool which is constantly being reduced by selective elimination of unfavorable variants … Consequently, we should not expect to find any relationship between rate of mutation and rate of evolution. (Stebbins 1966, p. 29)
...
For simplicity we speak of mutation as the first stage in the Darwinian process, natural selection as the second stage. But this is misleading if it suggests that natural selection hangs about waiting for a mutation which is then either rejected or snapped up and the waiting begins again. It could have been like that: natural selection of that kind would probably work, and maybe does work somewhere in the universe. But as a matter of fact on this planet it usually isn't like that. (Dawkins 1996, p. 87)


Stoltzfus, On the possibility of constructive neutral evolution
http://www.springerlink.com/content/4pjtur064qhq2wl6/

А вот и исходная статья. Первую половину я не читал, посмотрел только discussion.
Constructive neutral evolution, then, would differ from the classical model of adaptive refinement in three respects. Directionality or the recurrence of similar steps is due not to a common adaptive benefit to which the steps accrue, but to a common bias in the production of variants. A novel attribute is not immediately beneficial but, instead, by a subsequent change at an interacting site that renders loss of the attribute deleterious.


Koonin, Are there laws of genome evolution?
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002173

Возвращаясь к Кунину -- обзор на другую тему: как недавно было обнаружено, в геномах наблюдается несколько очень простых статистических закономерностей вроде гауссиан и power laws. Кунин с соавторами опубликовали работу, в который очень простая модель без всякого естественного отбора воспроизводит эту статистику. Это любопытно, но мне кажется, что глубокие выводы из этого нужно делать с очень большой осторожностью: power law возникают где попало.
So should evolutionary biologists strive to turn their science into physics or should they collect the colorful stamps of unique adaptations? Certainly both! Adaptations are incredibly interesting and beautiful but to understand their nature and origins, as opposed to concocting “just so stories” [39], the description of the underlying evolutionary background with models akin to those used in statistical physics is crucial.


Vogan and Higgs, The advantages and disadvantages of horizontal gene transfer and the emergence of the first species
http://www.biology-direct.com/content/pdf/1745-6150-6-1.pdf

Очень любопытная статья и такая свежая (2011), что не упоминается и не обсуждается в книжке Кунина (хотя он на нее написал очень положительную рецензию). Авторы предлагают очень простую модель с двумя параметрами: скорость горизонтального переноса генов и надежность "вертикальной" репликации. Оказывается, что оптимальная скорость горизонтального обмена тем выше, чем ниже надежность репликации. Если скорость горизонтального обмена сделать свойством организма и дать ей эволюционировать, то она приблизится примерно к оптимуму. Наконец, и это самое важное, если дать обеим переменным эволюционировать, то они обе будут убывать к нулю, т.е. происходит возникновение видов ("darwinian threshold").
Although there is the potential to gain useful new genes by HGT, there is also the possibility of acquiring useless or harmful genes. HGT is a risky evolutionary strategy, whereas vertical inheritance is safe because the genes have been tried and tested in the parent.
...
Woese has argued that HGT was particularly important in the early stages of life on Earth [7]. In his view, separate lineages of species did not exist, but rather the entire community of organisms co-developed and evolved as one interconnected network. When individuals attained a certain degree of complexity, the likelihood of a gene gained by HGT being beneficial would decrease, and the net HGT rate would decrease. At this point, the population would cross what Woese coined, the “Darwinian Threshold”.
...
We study a model for genome evolution that incorporates both beneficial and detrimental effects of HGT. We show that if rate of gene loss during genome replication is high, as was probably the case in the earliest genomes before the time of the last universal common ancestor, then a high rate of HGT is favourable. HGT leads to the rapid spread of new genes and allows the build-up of larger, fitter genomes than could be achieved by purely vertical inheritance. In contrast, if the gene loss rate is lower, as in modern prokaryotes, then HGT is, on average, unfavourable. [...] In the model, natural selection leads to gradual improvement of the replication accuracy and gradual decrease in the optimal rate of HGT. By clustering genomes based on gene content, we show that there are no separate lineages of organisms when the rate of HGT is high; however, as the rate of HGT decreases, a tree-like structure emerges with well-defined lineages. The model therefore passes through a Darwinian Threshold.
В рецензии Кунин сожалеет о выборе названия "Darwinian threshold" и остроумно замечает:
The problem, however, is that (short version of) Darwin’s title is extremely misleading - indeed, given the unprecedented importance of the book, this might be the most misleading book title in history. In his book, Darwin does not explain the mechanism of speciation in any satisfactory manner.


Напоследок из книжки приведу только две цитаты.
In essence, even if not in actual history, these discoveries [Watson & Crick] seem to supersede Darwin, in the sense that the entire Darwinian scheme of evolution is a straightforward and necessary corollary of the replication mechanism.
...
The consolidation of Modern Synthesis in the 1950s was a somewhat strange process that included remarkable “hardening” (Gould’s word) of the principal ideas of Darwin (Gould, 2002). [...] This “hardening” shaped Modern Synthesis as a relatively narrow, in some ways dogmatic conceptual framework.


Heggarty et al., Splits or waves? Trees or webs? How divergence measures and network analysis can unravel language histories
http://rstb.royalsocietypublishing.org/content/365/1559/3829.short

Ну и на закуску: увидел эту статью в ссылках где-то в обсуждении Tree of Life. Тут обсуждается вопрос о том, можно ли строить эволюционные деревья языков (на примере германской ветви индоевропейских языков), или лучше строить графы более общего вида. Статья несколько путаная, но картинки очень красивые, рекомендую. Кроме известного дерева Грея и Аткинсона, тут масса сетей германских языков, построенных по фонетике (!). Красота!

Более того, фонетические базы Paul Heggarty выкладывает онлайн: http://www.languagesandpeoples.com/Germanic.htm. Вряд ли до сюда кто-нибудь дочитает, но вообще это кладезь, посмотрите. Славянская база уже частично выложена на отдельном сайте, романская готовится. Похоже, эти исследования только начинаются, будет интересно посмотреть на новые графы.
Subscribe
  • Post a new comment

    Error

    default userpic

    Your IP address will be recorded 

    When you submit the form an invisible reCAPTCHA check will be performed.
    You must follow the Privacy Policy and Google Terms of use.
  • 20 comments