Неполноценность генома бактерий объяснили помощью соседей

Биологи из Мичиганского Университета и Университета Теннесси объяснили потерю жизненно важных генов цианобактериями рода Prochlorococcus помощью со стороны соседей и предположили, что подобный механизм редукции генома может лежать в основе образования взаимозависимых бактериальных сообществ. Работа опубликована в журнале BMC Evolution.
Исследователи сравнили геномы Prochlorococcus с родственными микроорганизмами и определили, что все представители рода потеряли в ходе эволюции гены, помогающие разлагать перекись водорода. Поскольку известно, что эти гены свободно обмениваются между разными бактериями, и Prochlorococcus не потеряли возможности их приобрести, авторы решили, что их отсутствие выгодно для бактерий.

С другой стороны, в своей предыдущей работе исследователи установили, что в стерилизованной океанической воде под воздействием солнца происходит образование перекиси в концентрациях, которые являются смертельными для цианобактерий. Prochlorococcus выживают потому, что перекись удаляется из среды другими бактериями сообщества, которые таким образом выполняют “чужую работу” и несут связанные с этим издержки. Поскольку перекись свободно циркулирует между всеми клетками и водной средой, то ее концентрация фактически является общей для всех. Те организмы, которые избавляются от защитных генов, приобретают эволюционное преимущество за счет экономии ресурсов.

Подобное эгоистичное поведение известно для сообществ бактерий, состоящих из одного вида. Оно носит название “проблемы безбилетников”. Многие бактерии выработали механизмы борьбы с таким оппортунистическим поведением, так как большое их число может наносить вред сообществу в целом. В данном случае впервые было показано образование “безбилетников” за счет другого вида. Авторы исследования особо отмечают, что бактерии, экономящие ресурсы за счет соседей, не обязательно им вредят, как это всегда бывает во внутривидовом случае. Дело в том, что разные виды в сообществе конкурируют за разные ресурсы, и здесь скорее наблюдается процесс образования взаимовыгодного сотрудничества, ведь цианобактерии являются основным продуцентом биомассы, которая, в свою очередь, тоже становится ресурсом.

Планктонные цианобактерии Prochlorococcus живут в океане и являются одними из самых распространенных микроорганизмов на Земле. В некоторых частях океана они составляют до половины массы всех цианобактерий.

http://lenta.ru/news/2012/03/27/cheaters/

Сообразим на троих

Версия для печати | PDA/КПК

Слизевик Metatrichia vesparia. Фото с сайта uwlax.edu

Ученые обнаружили на Земле коллективный разум

Несколько дней назад новостные издания сообщили, что японцы создали робота, который двигается точь-в-точь как слизевик. Многие кликали на странное сообщение хотя бы для того, чтобы узнать, что же это за зверь такой - слизевик. Ученых эти непонятные существа - не то грибы, не то амебы, у которых нет мозга и органов чувств - интересуют по многим причинам: например, они умеют находить выход из лабиринтов, решать головоломки, обучаться и даже обманывать друг друга. Уникальные свойства слизевиков даже подвигли некоторых исследователей заняться созданием робота на их основе.

Колонии

Слизевики, или, как их еще называют, миксомицеты, были впервые детально описаны американским биологом Джоном Тайлером Боннером (John Tyler Bonner). Ученый подробно исследовал слизевика Dictyostelium discoides и даже использовал его как простую модель человеческого эмбриона. На первый взгляд, идея проводить параллели между микроскопическим комочком неясного вещества и Homo sapiens кажется странной, однако при более внимательном рассмотрении выясняется, что миксомицеты - это, действительно, весьма сложно организованные системы.

Большую часть своей жизни слизевики существуют не как отдельные организмы, а в виде колонии клеток, объединившихся вместе и действующих сообща - например, слизевики умеют ползать, стремясь добраться до подходящей пищи или избежать воздействия раздражителя. Двигаются миксомицеты не очень быстро - в среднем за минуту они преодолевают от 0,1 до 0,4 миллиметра, но если вспомнить, что размер каждой отдельной клетки не превышает нескольких десятков микрометров (микрометр - это одна миллионная часть метра, или одна тысячная миллиметра), то впечатление о медлительности слизевиков оказывается обманчивым.

Прекрасные фотографии необычных слизевиков можно посмотреть, например, здесь и здесь.

"Коллективный разум" миксомицетов не только решает, куда ползти. Когда вокруг слизевика заканчивается еда, он "принимает решение" размножаться. Чтобы выполнить эту важную функцию, слизевик заползает на пенек или другое место повыше и там с ним происходят удивительные метаморфозы. Амебовидное тело вдруг превращается в самый настоящий гриб со шляпкой и длинной ножкой. Благодаря внешнему сходству готовящихся размножаться слизевиков с грибами их долгое время причисляли именно к этому царству - и в старых учебниках еще можно увидеть статьи о миксомицетах в соответствующих разделах.

Ни то, ни се

Однако слизевики только притворяются грибами - по целому ряду признаков они никак не вписываются в эту группу. Начать с того, что "нормальные" грибы не двигаются: они захватывают пространство, дорастая до него (эту тактику слизевики тоже используют). Любовь к путешествиям - не единственная "неправильная" особенность миксомицетов: с точки зрения грибов, они совершенно непотребным образом питаются. Вместо того чтобы при помощи специальных ферментов расщеплять пищу до простых составляющих и спокойно всасывать их, слизевики заглатывают и переваривают еду, как какие-нибудь амебы. Наконец, в клеточных стенках грибов обязательно есть хитин – специфический углевод, который укрепляет тела грибов и членистоногих. В клетках слизевиков хитина нет.

Учитывая все эти странности, ученые после долгих споров причисли слизевиков к царству Protista (простейших). Другими словами, их признали родственниками известных всем со школы амеб, инфузорий-туфелек и эвглен зеленых. Но в отличие от туфелек и прочих малярийных плазмодиев, ведущих одиночный образ жизни, клетки слизевиков, как уже упоминалось выше, предпочитают объединяться в сложные сообщества, причем нередко одинаковые с виду клетки начинают выполнять совершенно разные функции. Например, шляпка псевдогриба, в который аморфный миксомицет превращается перед размножением, содержит огромное количество спор, начало которым положили клетки, волею случая оказавшиеся в верхней части слизевика. Их более невезучим собратьям достается роль ножки, которая выносит споры максимально высоко над землей. После того, как зачатки будущих слизевиков распространятся вокруг "гриба", ножка погибает.

Недавно ученые выяснили, что такой порядок дел не устраивает некоторые клетки слизевика. Оказалось, что они намеренно стремятся пролезть в ту часть тела миксомицета, которая впоследствии сформирует шляпку. Специалисты пришли к выводу, что способность жульничать заложена в клетках генетически - так как у обманщиков больше шансов выжить, она передается потомкам, и в популяциях сохраняется определенное количество "нечестных" клеток. Как и в человеческом обществе, такая стратегия работает только тогда, когда вокруг есть "честные" особи: если собрать слизевиков, несущих "гены обмана" вместе, то в неблагоприятных условиях часть из них вынуждена будет принести себя в жертву.

Сложный способ взаимодействия клеток и умение образовывать псевдомногоклеточные структуры ("тела" некоторых видов слизевиков вообще представляют собой одну гигантскую - до нескольких десятков сантиметров - клетку со множеством ядер) сформировались за очень долгую эволюционную историю слизевиков. Псевдомногоклеточность дала слизевикам существенные преимущества - относительно крупные по сравнению с отдельными клетками тела перемещались гораздо быстрее и разбрасывали споры куда дальше, чем любой одноклеточный организм.

Генетический анализ показал, что эти существа появились на планете как минимум 600 миллионов лет назад, а общий предок всех миксомицетов и вовсе мог бы отметить свой миллиардный день рождения. То есть слизевики вместе с другими простейшими и бактериями были первыми существами, осваивавшими сушу и создававшими почву, на которой потом смогли прижиться растения.

Море талантов

Здесь можно послушать "написанную" слизевиками музыку: ученые в течение нескольких дней записывали электрическую активность миксомицетов, а затем перекодировали ее в ноты и "впихнули" в 1,5 минуты.

Необычные существа заинтересовали ученых, и они научились выращивать их искусственно - оказалось, что миксомицеты с готовностью селятся на том же агаре, на котором во всех лабораториях мира разводят бактерий, и с большим удовольствием едят овсяные хлопья. Наблюдая за миксомицетами, исследователи обнаружили у них массу удивительных талантов. Например, слизевики умеют находить кратчайшее расстояние между двумя точками: если поместить слизевика на карту, скажем, Португалии, и разместить кусочки его любимой пищи в крупнейших городах, то очень быстро миксомицет при помощи своих отростков доберется до еды, причем выберет кратчайший из возможных маршрутов. В 2010 году ученые из Новой Англии провели ровно такой опыт, и оказалось, что маршруты, проложенные слизевиком, практически полностью повторяют существующую дорожную сеть.

Японские исследователи использовали необычные способности слизевиков для того, чтобы составить оптимальную схему транспортного сообщения в Токио. Они провели такой же опыт, как описано выше, только еду разместили в главных железнодорожных узлах столицы. Будут ли токийские власти использовать найденное слизевиком решение - неизвестно: пока труд миксомицетов и работающих с ними ученых оценил только комитет Шнобелевской премии. Слизевики приносят исследователям альтернативную Нобелевку уже второй раз - первый приз тот же коллектив специалистов получил в 2008 году за доказательство того, что их подопечные умеют решать головоломки.

Стремясь добраться до пищи, миксомицеты умеют не только прокладывать новые дороги, но и находить выходы из лабиринтов. Здесь можно увидеть, как слизевик пророс сквозь все коридоры до заветной горстки хлопьев в центре лабиринта.

Еще более замечательным оказалось то, что слизевики, у которых нет ни мозга, ни нервной системы, способны обучаться. Ученые заметили, что в более сухой атмосфере миксомицеты ползают медленнее, чем когда воздух влажный. Они стали подвергать "подопытных" периодическому воздействию сухого воздуха и выяснили, что через некоторое время слизевики начинают замедляться еще до того, как влажность воздуха упадет. Если ученые прекращали мучить миксомицета, он забывал, что нужно снижать скорость, но при повторном воздействии вновь научался реагировать на него.

Слизевик Lycogala conicum. Фото с сайта uark.edu

Наконец, ученые показали, что в сложных ситуациях выбора слизевики ведут себя точно как люди - то есть ориентируются не на абсолютную, а на сравнительную ценность объектов. Исследователи предлагали миксомицетам выбор: кусочки несъедобного агара с хлопьями, лежащие на свету и в темноте. Слизевики не любят свет и поэтому при прочих равных предпочитали ползти к еде, лежащей в тени. Когда в освещенных кусочках агара было 5 процентов хлопьев, а в затененных - три, слизевики с примерно одинаковой частотой выбирали оба варианта. Но когда ученые уменьшили содержание агара в "темных" кусочках до одного процента, 80 процентов слизевиков стали стремиться именно к этой приманке: при таком раскладе разница между опасным и безопасным вариантом стала куда более очевидной.

В другой серии сходных опытов, дополненных неблагоприятными воздействиями, ученые показали, что в первой ситуации слизевики принимают решение быстрее: в некомфортных условиях разница в содержании хлопьев в освещенных и неосвещенных кусочках становилась непринципиальной, и микосмицеты быстрее определялись с выбором (то есть рисковали).

Выдающиеся способности слизевиков настолько впечатлили исследователей из университета Западной Англии, что они решили создать на их основе робота - авторы назвали его плазмоботом. По задумке ученых, машина будет способна определять тип встретившихся ей объектов, находить кратчайшую дорогу от одного объекта до другого, а также переносить небольшие предметы по заданному маршруту. Впрочем, пока сообщений о прогрессе в создании плазмобота нет.

Все описанные выше удивительные таланты ученые обнаружили, работая, в основном с двумя наиболее изученными видами слизевиков. В ходе глобального исследования Global Eumycetozoan Project биологи удвоили известное количество видов миксомицетов: они обнаружили, что слизевики обитают даже на листьях домашних растений. Так что существа, которых смело можно использовать для написания фантастических романов, на самом деле живут на Земле повсюду. Причем они могут называть себя исконными землянами с куда большим правом, чем люди.

Ирина Якутенко

LENTA.RU

Почему мы не следуем собственным нравственным правилам (inopressa.ru)

февраль 18, 2012, 12:33
Майкл Маршалл | New Scientist

Человек устроен так, что имеет "две параллельных нравственных системы, и они не всегда согласуются", - так интерпретирует The New Scientist исследование по этике, опубликованное в Evolution and Human Behavior.

Размышляя о природе нравственных запретов, многие психологи приходят к выводу, что они являются разновидностью так называемого родственного отбора у животных, суть которого в том, что самопожертвование одной особи повышает шансы на выживание генома данного вида в целом. Однако Роберт Курцбан из Пенсильванского Университета (Филадельфия) полагает, что существует комплекс нравственных правил, развившихся независимо от родственного отбора.

К такому выводу он пришел, слегка изменив условия известного мысленного эксперимента с трамваем, состоящего из двух частей: "Проблема вагонетки" и "Толстый человек". В первой части человеку предлагается решить, переводить ли стрелку, чтобы отвести вагонетку с пути, на котором лежат пять человек, на другую ветку, где к рельсам привязан один. Вторая часть в классическом варианте представляет собой дилемму: столкнуть ли на пути одного человека, который может остановить вагонетку, чтобы спасти пятерых? На первый вопрос большинство отвечает утвердительно, а на второй - отрицательно, и это, как пишет The New Scientist, показывает, что у большинства из нас есть "строгий [внутренний] запрет на неопосредованное убийство людей, пусть и во имя высшего блага".

Дополнение Курцбана - просьба к испытуемым оценить свои действия во второй части эксперимента с нравственной точки зрения. Несмотря на негативную оценку подобных действий, столкнуть незнакомца ради сохранения жизни пятерым другим незнакомцам согласились 28% респондентов, а когда речь шла о шести братьях испытуемого, готовность пожертвовать одним ради пятерых выразили 47%, говорится в статье.

Источник: New Scientist

Tags:архаика, наука, отношение с контекстом, психология, эволюция мозга

On The Inadequacy Of The Empiricist Tradition In Western Philosophy

by Stuart Kauffman


I find myself beginning to realize that the philosophy that I studied, from Descartes to Hume to Kant to Russell to logical positivism and the early Wittgenstein, and perhaps the late Wittgenstein of the Investigations, is seriously inadequate.

It starts with Descartes who conceived of his task to be a lone mind who would doubt all that could be doubted to find that which could not be doubted about what that single mind can know about the world. The emphasis is on "knowing."

Then we come to Hume of the Scottish Enlightenment, essaying to understand "Human Understanding." How can we know the world? By sense impressions, welded together in "bundles," in which the "self," or "I," itself disappears as just a bundle of perceptions: roughly, "all I am aware of is a jumble of sequential awareness," I am aware of no 'I'."

Kant seeks the conditions of knowing in the inner conditions of the mind, categories of perception such as space and time. He considers the phenomenal world we can know and behind it the noumenal world we can never know.

Russell brings us sense data such as "red here" and the tone, "A flat now," then sense data statements, "For Kauffman, 'red here' is true," and hopes that his recently developed predicate calculus working on sense data statements will allow philosophers to build a maximally reliable way of knowing the world, constructed out of sense data statements linked by logic, including quantifiers such as "there exists" and "for all."

To early Wittgenstein's famous "Tractatus": "The world is the collection of true facts" about that world.

On to logical positivism: "Only those statements (about the world) are meaningful which are empirically verifiable," which, ironically drove Western philosophy, yet whose founding statement just noted is not itself empirically verifiable.

The "empiricist tradition" sought and seeks to elucidate how we know the world.

What is wrong?

In the beginning, 5 billion years ago, no life existed on the forming planet. Either life started here or arrived from elsewhere. Let's assume the former. As a concrete working hypothesis let's take collectively autocatalytic sets of polymers like peptide sets, RNA sets, or DNA sets, all realized experimentally, in some bounding membrane like a liposome. For example Gonen Ashkenazi has a 9 peptide (small protein) collectively autocatalytic set reproducing happily in his Ben Gurion University lab.

So what?

So existing as a self reproducing system in a universe that is non-ergodic, (not repeating) above the level of atoms, where most complex things will never exist, is the first condition of life. "Knowing" is not yet a condition.

But that protocell typically lived in an environment with toxic and food molecules. By hook or crook, say by semipermiable membranes, the protocell "discriminated" poison from food and admitted only the latter, thanks to natural selection on evolving protocells.

We now have the rudiments of agency and knowing. The protocell evolved to do something, i.e., discriminate and admit food and block poison. This discrimination required rudimentary "knowing" and hence "semantics", without invoking consciousness.

What the empiricist tradition entirely misses is living existence and agency. Without the existence of the protocell, there is no evolutionary point in knowing. Without agency there is no use in knowing. Suppose, per contra, that the protocell could discriminate poison from food, but could not selectively block the first and admit the second. It would fail natural selection's harsh sieve.

Without being and doing, no knowing could have emerged in evolution. The empiricist tradition misses this central issue, thus is deeply inadequate.

In summary of this first point: Without being and agency, knowing is both pointless and would not arise in evolution.

Not only do we not know what will happen, we often do not even know what can happen.

But the empiricist tradition runs into a still deeper problem. In past posts I have discussed Darwinian preadaptations, where we cannot prestate their emergence in evolution. This has led my colleagues, senior mathematician, Giuseppe Longo, his post doctoral fellow, Mael Montevil, both of the Ecole Polytechnique, Paris, and myself to submit a paper also posted on ArXiv, entitled, "No entailing laws, but enablement in the evolution of the biosphere."

This article is radical. It claims that no law entails the evolution of the biosophere. The grounds for this include the fact that we cannot prestate the ever newly emerging relevant variables in evolution that selection reveals, therefore the very phase space of evolution changes in ways we cannot know beforehand, so we can write no laws of motion for the evolving biosphere, nor, lacking knowledge of the boundary conditions, could we integrate those laws of motion even were to to have them.

These deep issues mean that often not only do we not know what will happen, as when we flip a fair coin 10,000 times and do not know how many heads will come up, but here know all the possible outcomes, so can construct a probability measure. In evolution we do not even know what can emerge in the Adjacent Possible of the becoming of evolution, so can construct no probability measure for we do not know the sample space of all the possibilities, thus not only do we not know what will happen, we do not even know what can happen.

The empiricist tradition is ignorant of this profound limitation to knowledge "beforehand" as the biosphere "becomes."

Even pragmatism, which seeks to unify knowing and doing, falls prey to this last issue: We often do not even know what can happen. Pragmatism takes no account of this feature of our living world.

Hume famously argued that one cannot deduce "ought" from "is." This is the naturalistic fallacy. But Hume is thinking only of a knowing subject, firmly in the empiricist tradition started by Descartes. Hume ignores agency.

I wrote an entire book, Investigations, attempting to define agency. My try: "A molecular autonomous agent is a self-reproducing system able to do at least one work cycle."

A bacterium swimming up a glucose gradient for food is an agent, reproduces and the rotating flagella is just one of the work cycles the bacterium does. All living cells fulfill the above definition.

But once there is agency, ought enters the universe. If the bacterium is to successfully get food, it "ought" to e.g., swim up the sugar gradient. Without attributing consciousness, one cannot have "actings" without "doing them wisely or poorly," hence ought.

In short, the empiricist tradition, in ignoring agency, wishes to block us from "ought," when we cannot have doing without "ought." The root of the issue is "doing" versus merely "happening," a topic in a near future post.

We need to rethink many problems in philosophy to take account of the issues above.


13.7: Cosmos And Culture : NPR

Comments



Vlad Piaskovskiy (0nothing1) wrote:

1

Stuart wrote:

"Without attributing consciousness, one cannot have "actings" without "doing them wisely or poorly," hence ought."

It seems to me that this phrase is very doubtful. Permissible to say - and I like it! - That living systems possess the innate knowing what for them is good and bad; but this is not consciousness yet. Consciousness - is something more; consciousness involves conflict.

vendredi 3 février 2012 12:40:52


Recommend (0)


Report abuse





Vlad Piaskovskiy (0nothing1) wrote:

2

And this conflict seems to be something more than just a competition between two (or more) concurrent stimuli: in this case, at first glance, there is no need for a particularly complex organization. I think it is the conflict between the immediate response to stimulus (what Stuart called knowing) and the reaction that takes into account the developments in the long run - long run adaptation ("in the long run," of course, is relative, if we're talking about the first, primitive consciousness). Ie the basis of the second trend is the ability to forecast and modeling of the world (note also that consciousness is not reducible to win of the second trend, but to their parity).

But it does mean that the long term prognosis can supress immediate response to a stimulus that Stuart called knowing - ie, this trend is against life itself (as the embodiment of creativity and diversity)!

vendredi 3 février 2012 12:40:20


Recommend (0)


Report abuse





Vlad Piaskovskiy (0nothing1) wrote:

3.

Life without death would destroy itself - if the death is sudden to disappear, it would be a disaster, and we ourselves would have to be urgently re-invent it! Stuart, you say yourself that the world exists because everything has its constraints, then what constrains your creativity and diversity?

Stuart wrote:

"If our religions from the Axial Age 2500 years ago or so, were sufficient, then what say we to the fact that in WWI, German and British soldiers in trenches 150 meters apart prayed to the SAME GOD OF LOVE. 2000 years after Christ taught us to love, we kill."

Stuart, do not you think that this is a sign that your theory does not account for something, and except for of creativity and diversity god includes the force that constrains them (negates)?

vendredi 3 février 2012 12:39:33


Recommend (0)




Vlad Piaskovskiy (0nothing1) wrote:

1

I want to dwell on what might mean knowing, which, according to Stuart, is an inherent property of all living things. Here was an excellent article:
http://www.npr.org/blogs/13.7/2010/03/the_evolution_of_symbolic_lang.html

In a nutshell the essence:
"Most organisms communicate, but humans are unique in communicating via symbolic language. This entails relationships between signifiers (e.g. words) and what's signified (e.g. objects or ideas), where what's special is the construction of a system of relationships among the signifiers themselves, generating a seemingly unlimited web of associations, organized by semantic regularities and constraints, retrieved in narrative form, and enabled by complex memory systems.
Humans are thus a symbolic species: symbols have literally changed the kind of biological organism we are."

there was another article on this topic:
http://www.npr.org/blogs/13.7/2010/03/the_iself_and_our_symbolic_spe.html


samedi 4 février 2012 11:45:02


Recommend (0)


Report abuse





Vlad Piaskovskiy (0nothing1) wrote:

2

So, this view seems to be not true. And Homo sapiens is just the only one capable through awareness (understanding) to de-symbolize perception of the world. Another thing, thanks to the development of speech, only humans have symbols that got autonomy to such an extent that separated from the objects which signify and have themselves become objects.

Think about it: how a primitive organism can know what he should eat? It apparently does not see plants, as we see them, it sees food. All its perception consists of such features: food, a partner for mating, the danger, and so on. It is sort of mosaic pattern, and the more perfect the nervous system, the more completely the perception - mosaic is becoming finer, and the picture of the world becomes more adequate.


samedi 4 février 2012 11:43:41


Recommend (0)


Report abuse





Vlad Piaskovskiy (0nothing1) wrote:

3

The thinking by symbols is typical for some psychiatric patients, and such a condition means a return to a more primitive, archaic form of perception. Interestingly, on the one hand, understanding means the destruction of old infantile features: instead of "grass" we begin to distinguish between different types of plants, and eventually realize that every single plant is unique. On the other hand, we are also creating new, "scientific" features, which more accurately reflect the reality (eg, species, etc.) and these new features have the property that the theory destroying facts - Newton's laws are a good example. I want to say that from this point of view understanding does not imply any new information, but just we have the kind of information transformation.


samedi 4 février 2012 11:42:57


Recommend (0)


Report abuse





Vlad Piaskovskiy (0nothing1) wrote:

4

It is also interesting that symbols, according to Jung, is the content of our collective unconscious, then what in this case means "collective"? If this is, in particular, the same as Alva has in mind when he says:
"Mind is not inside us; it is rather, the dynamic activity of the whole, embodied, environmentally situated human being."

than "the redness of red" is really all the same for all of us. On the other hand, if we assume that individual thinking is our internal speech, it arose as a result of communication. I do not know what that means, it's just my speculation ...


samedi 4 février 2012 11:42:21


Recommend (0)

WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION? - Richard Dawkins

Evolutionary Biologist; Emeritus Professor of the Public Understanding of Science,...

Redundancy Reduction and Pattern Recognition

Deep, elegant, beautiful? Part of what makes a theory elegant is its power to explain much while assuming little. Here, Darwin's natural selection wins hands down. The ratio of the huge amount that it explains (everything about life: its complexity, diversity and illusion of crafted design) divided by the little that it needs to postulate (non-random survival of randomly varying genes through geological time) is gigantic. Never in the field of human comprehension were so many facts explained by assuming so few. Elegant then, and deep—its depths hidden from everybody until as late as the nineteenth century. On the other hand, for some tastes natural selection is too destructive, too wasteful, too cruel to count as beautiful. In any case, coming late to the party as ever, I can count on somebody else choosing Darwin. I'll take his great grandson instead, and come back to Darwin at the end.

Horace Barlow FRS is the youngest grandchild of Sir Horace Darwin, Charles Darwin's youngest child. Now a very active ninety, Barlow is a member of a distinguished lineage of Cambridge neurobiologists. I want to talk about an idea that he published in two papers in 1961, on redundancy reduction and pattern recognition. It is an idea whose ramifications and significance have inspired me throughout my career.

The folklore of neurobiology includes a mythical 'grandmother neurone', which fires only when a very particular image, the face of Jerry Lettvin's grandmother, falls on the retina (Lettvin was a distinguished American neurobiologist who, like Barlow, worked on the frog retina). The point is that Lettvin's grandmother is only one of countless images that a brain is capable of recognising. If there were a specific neurone for everything we can recognise—not just Lettvin's grandmother but lots of other faces, objects, letters of the alphabet, flowers, each one seen from many angles and distances, we would have a combinatorial explosion. If sensory recognition worked on the 'grandmother principle', the number of specific recognition neurones for all possible combinations of nerve impulses would exceed the number of atoms in the universe. Independently, the American psychologist Fred Attneave had calculated that the volume of the brain would have to be measured in cubic light years. Barlow and Attneave independently proposed redundancy reduction as the answer.

Claude Shannon, inventor of Information Theory, coined 'redundancy' as a kind of inverse of information. In English, 'q' is always followed by 'u', so the 'u' can be omitted without loss of information. It is redundant. Wherever redundancy occurs in a message (which is wherever there is nonrandomness), the message can be more economically recoded without loss of information (although with some loss in capacity to correct errors). Barlow suggested that, at every stage in sensory pathways, there are mechanisms tuned to eliminate massive redundancy.

The world at time t is not greatly different from the world at time t-1. Therefore it is not necessary for sensory systems continuously to report the state of the world. They need only signal changes, leaving the brain to assume that everything not reported remains the same. Sensory adaptation is a well-known feature of sensory systems, which does precisely as Barlow prescribed. If a neurone is signalling temperature, for example, the rate of firing is not, as one might naively suppose, proportional to the temperature. Instead, firing rate increases only when there is a change in temperature. It then dies away to a low resting frequency. The same is true of neurones signalling brightness, loudness, pressure and so on. Sensory adaptation achieves huge economies by exploiting the non-randomness in temporal sequence of states of the world.

What sensory adaptation achieves in the temporal domain, the well-established phenomenon of lateral inhibition does in the spatial domain. If a scene in the world falls on a pixellated screen, such as the back of a digital camera or the retina of an eye, most pixels see the same as their immediate neighbours. The exceptions are those pixels which lie on edges, boundaries. If every retinal cell faithfully reported its light value to the brain, the brain would be bombarded with a massively redundant message. Huge economies can be achieved if most of the impulses reaching the brain come from pixel cells lying along edges in the scene. The brain then assumes uniformity in the spaces between edges.

As Barlow pointed out, this is exactly what lateral inhibition achieves. In the frog retina, for example, every ganglion cell sends signals to the brain, reporting on the light intensity in its particular location on the surface of the retina. But it simultaneously sends inhibitory signals to its immediate neighbours. This means that the only ganglion cells to send strong signals to the brain are those that lie on an edge. Ganglion cells lying in uniform fields of colour (the majority) send few if any impulses to the brain because they, unlike cells on edges, are inhibited by all their neighbours. The spatial redundancy in the signal is eliminated.

The Barlow analysis can be extended to most of what is now known about sensory neurobiology, including Hubel and Wiesel's famous horizontal and vertical line detector neurones in cats (straight lines are redundant, reconstructable from their ends), and in the movement ('bug') detectors in the frog retina, discovered by the same Jerry Lettvin and his colleagues. Movement represents a non-redundant change in the frog's world. But even movement is redundant if it persists in the same direction at the same speed. Sure enough, Lettvin and colleagues discovered a 'strangeness' neurone in their frogs, which fires only when a moving object does something unexpected, such as speeding up, slowing down, or changing direction. The strangeness neurone is tuned to filter out redundancy of a very high order.

Barlow pointed out that a survey of the sensory filters of a given animal could, in theory, give us a read-out of the redundancies present in the animal's world. They would constitute a kind of description of the statistical properties of that world. Which reminds me, I said I'd return to Darwin. In Unweaving the Rainbow, I suggested that the gene pool of a species is a 'Genetic Book of the Dead', a coded description of the ancestral worlds in which the genes of the species have survived through geological time. Natural selection is an averaging computer, detecting redundancies—repeat patterns—in successive worlds (successive through millions of generations) in which the species has survived (averaged over all members of the sexually reproducing species). Could we take what Barlow did for neurones in sensory systems, and do a parallel analysis for genes in naturally selected gene pools? Now that would be deep, elegant and beautiful.

http://www.edge.org/response-detail/2825/what-is-your-favorite-deep-elegant-or-beautiful-explanation

Конспекты

Оригинал взят у в Конспекты

Выложил слайды и конспекты лекций, прочтенных первокурсникам совместного бакалавриата ВШЭ и РЭШ. Здесь, по идее, нужны многословные оправдания: это полуфабрикат; редактировать времени нет; привести эти материалы в божеский вид - дело будущего; это не всегда точно соответствует тому, что реально было на лекциях; многие вещи вообще не отражены в тексте - в особенности это относится к темам, которые я был уверен, что внятно расскажу без шпаргалки; некоторые пространные куски, скопированные из-каких-то других моих книжек, статей и лекций, добавлялись в конспекты на всякий случай и в действительности не были оглашены. Несколько слайдов взято из лекций А.С.Кондрашова с его разрешения. Пара слайдов - из доклада А.Ю.Журавлева, любезно предоставившего свою презентацию. Львиная доля картинок взята из интернета с характерным для меня наплевательским отношением к копирайтам (плохо представляю, как еще можно сделать слайды для такого обзорного курса). Многое преднамеренно упрощено, даже примитивизировано, что для данного курса, по-моему, было правильно и необходимо - и уж чего мне совсем не хотелось, так это морочить студентам головы рассказами "о бессилии науки перед тайною Бермуд", поэтому некоторые гипотетические вещи поданы без достаточно пространных оговорок об их гипотетичности. Можно еще долго продолжать, но неохота. При всем при том надеюсь, что кому-то этот материал может пригодиться - для самообразования или при подготовке собственных курсов.
Слайды и конспекты курса "Введение в науки о жизни"

Lynn Margulis 1938-2011 "Gaia Is A Tough Bitch"

http://edge.org/conversation/lynn-margulis1938-2011

Jerry Coyne
Professor, Department of Ecology and Evolution, University of Chicago; author, Why Evolution is True

Lynn Margulis did indeed have a clever—and correct—idea that revolutionized our view of how life evolved, but later became a victim of the Big Idea Syndrome, thinking that because she was right about organelles, she was right about everything else. That led her to make repeated and completely unfounded attacks on evolutionary biology in the last decade, embarrassing herself with her pronouncements. Her legacy is a good one, but not unmixed.

Rereading her chapter "Gaia is a Tough Bitch" only reinforces my opinion about her misguided criticisms of neo-Darwinian evolution and her unwarranted antipathy toward population genetics. Not only did she fail to comprehend how population genetics has advanced our understanding of nature—the effects of inbreeding and of genetic drift are two such advances—but her views on speciation, a field in which I've worked for three decades, are simply wrong.

Margulis's idea that new species originate from symbiosis has no empirical support. When we try to understand the genetic underpinnings of new species, we find that, with the exception of polyploidy in plants, it always maps to changes in the DNA. That is, the splitting of lineages, like evolution within a lineage itself, is almost always the result of gradual, gene-by-gene change. We have no evidence that symbiosis has been responsible for even a single case of speciation.

All of us should honor Margulis's real contributions to biology: her recognition and working out of earlier suggestions that some cellular organelles were acquired by symbiosis, and that the ancestors of these organelles were bacteria. This was a tremendous advance, achieved in the teeth of substantial doubt. Sadly, Margulis's success in the face of such criticism seems to have made her stubborn and dogmatic about her other biological views. And, even sadder, those theories were often wrong. She strongly denied, for example, that AIDS was caused by the HIV virus, or that the HIV virus even existed. AIDS, she maintained, was simply syphilis, with the spirochete rendered undetectable because it formed a symbiosis with human cells. How does one balance her positive contributions against such a deadly form of denialism?

We should always honor those scientists who have advanced our understanding of nature in ways as profound as Margulis. But let us also remember that being right about one big matter does not render us immune to error in other matters, and that scientific fame does not give us a free pass for all of our ideas.


--------------------------------------------------------------------------------

LYNN MARGULIS was Distinguished University Professor in the Department of Geology at the University of Massachusetts, Amherst. She was the author of Symbiotic Planet, The Origin of Eukaryotic Cells, Early Life, and Symbiosis in Cell Evolution. She was also the coauthor, with Karlene V. Schwartz, of Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth and with Dorion Sagan of Acquiring Genomes, Microcosmos, Origins Of Sex, and Mystery Dance.


--------------------------------------------------------------------------------

Lynn Margulis 1938-2011

"Gaia Is A Tough Bitch"

From The Third Culture: Beyond the Scientific Revolution
Edge Online Edition
Amazon | B&N


Richard Dawkins: I greatly admire Lynn Margulis's sheer courage and stamina in sticking by the endosymbiosis theory, and carrying it through from being an unorthodoxy to an orthodoxy. I'm referring to the theory that the eukaryotic cell is a symbiotic union of primitive prokaryotic cells. This is one of the great achievements of twentieth-century evolutionary biology, and I greatly admire her for it.


[LYNN MARGULIS]: At any fine museum of natural history — say, in New York, Cleveland, or Paris — the visitor will find a hall of ancient life, a display of evolution that begins with the trilobite fossils and passes by giant nautiloids, dinosaurs, cave bears, and other extinct animals fascinating to children. Evolutionists have been preoccupied with the history of animal life in the last five hundred million years. But we now know that life itself evolved much earlier than that. The fossil record begins nearly four thousand million years ago! Until the 1960s, scientists ignored fossil evidence for the evolution of life, because it was uninterpretable.

I work in evolutionary biology, but with cells and microorganisms. Richard Dawkins, John Maynard Smith, George Williams, Richard Lewontin, Niles Eldredge, and Stephen Jay Gould all come out of the zoological tradition, which suggests to me that, in the words of our colleague Simon Robson, they deal with a data set some three billion years out of date. Eldredge and Gould and their many colleagues tend to codify an incredible ignorance of where the real action is in evolution, as they limit the domain of interest to animals — including, of course, people. All very interesting, but animals are very tardy on the evolutionary scene, and they give us little real insight into the major sources of evolution's creativity. It's as if you wrote a four-volume tome supposedly on world history but beginning in the year 1800 at Fort Dearborn and the founding of Chicago. You might be entirely correct about the nineteenth-century transformation of Fort Dearborn into a thriving lakeside metropolis, but it would hardly be world history.

"codifying ignorance" I refer in part to the fact that they miss four out of the five kingdoms of life. Animals are only one of these kingdoms. They miss bacteria, protoctista, fungi, and plants. They take a small and interesting chapter in the book of evolution and extrapolate it into the entire encyclopedia of life. Skewed and limited in their perspective, they are not wrong so much as grossly uninformed.
Of what are they ignorant? Chemistry, primarily, because the language of evolutionary biology is the language of chemistry, and most of them ignore chemistry. I don't want to lump them all together, because, first of all, Gould and Eldredge have found out very clearly that gradual evolutionary changes through time, expected by Darwin to be documented in the fossil record, are not the way it happened. Fossil morphologies persist for long periods of time, and after stasis, discontinuities are observed. I don't think these observations are even debatable. John Maynard Smith, an engineer by training, knows much of his biology secondhand. He seldom deals with live organisms. He computes and he reads. I suspect that it's very hard for him to have insight into any group of organisms when he does not deal with them directly. Biologists, especially, need direct sensory communication with the live beings they study and about which they write.
Reconstructing evolutionary history through fossils — paleontology — is a valid approach, in my opinion, but paleontologists must work simultaneously with modern-counterpart organisms and with "neontologists" — that is, biologists. Gould, Eldredge, and Lewontin have made very valuable contributions. But the Dawkins-Williams-Maynard Smith tradition emerges from a history that I doubt they see in its Anglophone social context. Darwin claimed that populations of organisms change gradually through time as their members are weeded out,...

"codifying ignorance" I refer in part to the fact that they miss four out of the five kingdoms of life. Animals are only one of these kingdoms. They miss bacteria, protoctista, fungi, and plants. They take a small and interesting chapter in the book of evolution and extrapolate it into the entire encyclopedia of life. Skewed and limited in their perspective, they are not wrong so much as grossly uninformed.

Of what are they ignorant? Chemistry, primarily, because the language of evolutionary biology is the language of chemistry, and most of them ignore chemistry. I don't want to lump them all together, because, first of all, Gould and Eldredge have found out very clearly that gradual evolutionary changes through time, expected by Darwin to be documented in the fossil record, are not the way it happened. Fossil morphologies persist for long periods of time, and after stasis, discontinuities are observed. I don't think these observations are even debatable. John Maynard Smith, an engineer by training, knows much of his biology secondhand. He seldom deals with live organisms. He computes and he reads. I suspect that it's very hard for him to have insight into any group of organisms when he does not deal with them directly. Biologists, especially, need direct sensory communication with the live beings they study and about which they write.

Reconstructing evolutionary history through fossils — paleontology — is a valid approach, in my opinion, but paleontologists must work simultaneously with modern-counterpart organisms and with "neontologists" — that is, biologists. Gould, Eldredge, and Lewontin have made very valuable contributions. But the Dawkins-Williams-Maynard Smith tradition emerges from a history that I doubt they see in its Anglophone social context. Darwin claimed that populations of organisms change gradually through time as their members are weeded out, which is his basic idea of evolution through natural selection. Mendel, who developed the rules for genetic traits passing from one generation to another, made it very clear that while those traits reassort, they don't change over time. A white flower mated to a red flower has pink offspring, and if that pink flower is crossed with another pink flower the offspring that result are just as red or just as white or just as pink as the original parent or grandparent. Species of organisms, Mendel insisted, don't change through time. The mixture or blending that produced the pink is superficial. The genes are simply shuffled around to come out in different combinations, but those same combinations generate exactly the same types. Mendel's observations are incontrovertible.

So J.B.S. Haldane, without a doubt a brilliant person, and R.A. Fisher, a mathematician, generated an entire school of English-speaking evolutionists, as they developed the neo- Darwinist population-genetic analysis to reconcile two unreconcilable views: Darwin's evolutionary view with Mendel's pragmatic, anti-evolutionary concept. They invented a language of population genetics in the 1920s to 1950s called neo-Darwinism, to rationalize these two fields. They mathematized their work and began to believe in it, spreading the word widely in Great Britain, the United States, and beyond. France and other countries resisted neo-Darwinism, but some Japanese and other investigators joined in the "explanation" activity.

Both Dawkins and Lewontin, who consider themselves far apart from each other in many respects, belong to this tradition. Lewontin visited an economics class at the University of Massachusetts a few years ago to talk to the students. In a kind of neo-Darwinian jockeying, he said that evolutionary changes are due to the Fisher-Haldane mechanisms: mutation, emigration, immigration, and the like. At the end of the hour, he said that none of the consequences of the details of his analysis had been shown empirically. His elaborate cost-benefit mathematical treatment was devoid of chemistry and biology. I asked him why, if none of it could be shown experimentally or in the field, he was so wedded to presenting a cost-benefit explanation derived from phony human social-economic "theory." Why, when he himself was pointing to serious flaws related to the fundamental assumptions, did he want to teach this nonsense? His response was that there were two reasons: the first was "P.E." "P.E.?," I asked. "What is P.E.? Population explosion? Punctuated equilibrium? Physical education?" "No," he replied, "P.E. is `physics envy,'" which is a syndrome in which scientists in other disciplines yearn for the mathematically explicit models of physics. His second reason was even more insidious: if he didn't couch his studies in the neo- Darwinist thought style (archaic and totally inappropriate language, in my opinion), he wouldn't be able to obtain grant money that was set up to support this kind of work.

The neo-Darwinist population-genetics tradition is reminiscent of phrenology, I think, and is a kind of science that can expect exactly the same fate. It will look ridiculous in retrospect, because it is ridiculous. I've always felt that way, even as a more-than-adequate student of population genetics with a superb teacher — James F. Crow, at the University of Wisconsin, Madison. At the very end of the semester, the last week was spent on discussing the actual observational and experimental studies related to the models, but none of the outcomes of the experiments matched the theory.

I've been critical of mathematical neo-Darwinism for years; it never made much sense to me. We were all told that random mutations — most of which are known to be deleterious — are the main cause of evolutionary change. I remember waking up one day with an epiphanous revelation: I am not a neo-Darwinist! It recalled an earlier experience, when I realized that I wasn't a humanistic Jew.

Although I greatly admire Darwin's contributions and agree with most of his theoretical analysis and I am a Darwinist, I am not a neo-Darwinist. One of Darwin's major insights is the recognition that all organisms are related by common ancestry. Today direct evidence for common ancestry — genetic, chemical, and otherwise — is overwhelming. Populations of organisms grow and reproduce at rates that are not sustainable in the real world, and therefore many more die or fail to reproduce than actually complete their life histories. The fact that all the organisms that are born or hatched or budded off do not and cannot possibly survive is natural selection. Observable inherited variation appears in all organisms that are hatched, born, budded off, or produced by division, and some variants do outgrow and outreproduce others. These are the tenets of Darwinian evolution and natural selection. All thinking scientists are in complete agreement with these basic ideas, since they're supported by vast amounts of evidence.

Neo-Darwinism is an attempt to reconcile Mendelian genetics, which says that organisms do not change with time, with Darwinism, which claims they do. It's a rationalization that fuses two somewhat flawed traditions in a mathematical way, and that is the beginning of the end. Neo Darwinist formality uses an arithmetic and an algebra that is inappropriate for biology. The language of life is not ordinary arithmetic and algebra; the language of life is chemistry. The practicing neo-Darwinists lack relevant knowledge in, for example, microbiology, cell biology, biochemistry, molecular biology, and cytoplasmic genetics. They avoid biochemical cytology and microbial ecology. This is comparable to attempting a critical analysis of Shakespeare's Elizabethan phraseology and idiomatic expression in Chinese, while ignoring the relevance of the English language!

The neo-Darwinists say that variation originates from random mutation, defining mutation as any genetic change. By randomness they mean that characters appear randomly in offspring with respect to selection: if an animal needs a tail, it doesn't develop this tail because it needs it; rather, the animal randomly develops all sorts of changes and those with tails survive to produce more offspring. H.J. Muller, in the 1920s, discovered that not only do X rays increase the fruit-fly mutation rate, but even if fruit flies are isolated completely from X rays, solar radiation, and other environmental perturbation, a spontaneous mutation rate can be measured. Inherited variants do appear spontaneously; they have nothing to do with whether or not they're good for the organism in which they appear. Mutation was then touted as the source of variation- -that upon which natural selection acted — and the neo-Darwinian theory was declared complete. The science remaining required filling in the gaps in a "theory" with very few holes.

From many experiments, it is known that if mutagens like X rays or certain chemicals are presented to fruit flies, sick and dead flies result. No new species of fly appears — that is the real rub. Everyone agrees that such mutagens produce inherited variation. Everyone agrees that natural selection acts on this variation. The question is, From where comes the useful variation upon which selection acts? This problem has not yet been solved. But I claim that most significant inherited variation comes from mergers — from what the Russians, especially Konstantin S. Mereschkovsky, called symbiogenesis and the American Ivan Emanuel Wallin called symbionticism. Wallin meant by the term the incorporation of microbial genetic systems into progenitors of animal or plant cells. The new genetic system — a merger between microbe and animal cell or microbe and plant cell — is really different from the ancestral cell that lacks the microbe. Analogous to improvements in computer technology, instead of starting from scratch to make all new modules again, the symbiosis idea is an interfacing of preexisting modules. Mergers result in the emergence of new and more complex beings. I doubt new species form just from random mutation.

Symbiosis is a physical association between organisms, the living together of organisms of different species in the same place at the same time. My work in symbiosis comes out of cytoplasmic genetic systems. We were all taught that the genes were in the nucleus and that the nucleus is the central control of the cell. Early in my study of genetics, I became aware that other genetic systems with different inheritance patterns exist. From the beginning, I was curious about these unruly genes that weren't in the nucleus. The most famous of them was a cytoplasmic gene called "killer," which, in the protist Paramecium aurelia, followed certain rules of inheritance. The killer gene, after twenty years of intense work and shifting paradigmatic ideas, turns out to be in a virus inside a symbiotic bacterium. Nearly all extranuclear genes are derived from bacteria or other sorts of microbes. In the search for what genes outside the nucleus really are, I became more and more aware that they're cohabiting entities, live beings. Live small cells reside inside the larger cells. Understanding that led me and others to study modern symbioses.

Symbiosis has nothing to do with cost or benefit. The benefit/cost people have perverted the science with invidious economic analogies. The contention is not over modern symbioses, simply the living together of unlike organisms, but over whether "symbiogenesis" — long-term symbioses that lead to new forms of life — has occurred and is still occurring. The importance of symbiogenesis as a major source of evolutionary change is what is debated. I contend that symbiogenesis is the result of long-term living together — staying together, especially involving microbes- -and that it's the major evolutionary innovator in all lineages of larger nonbacterial organisms.

In 1966, I wrote a paper on symbiogenesis called "The Origin of Mitosing [Eukaryotic] Cells," dealing with the origin of all cells except bacteria. (The origin of bacterial cells is the origin of life itself.) The paper was rejected by about fifteen scientific journals, because it was flawed; also, it was too new and nobody could evaluate it. Finally, James F. Danielli, the editor of The Journal of Theoretical Biology, accepted it and encouraged me. At the time, I was an absolute nobody, and, what was unheard of, this paper received eight hundred reprint requests. Later, at Boston University, it won an award for the year's best faculty publication. I was only an instructor at the time, so my Biology Department colleagues reacted to the commotion and threw a party. But it was more of "Isn't this cute," or "It's so abstruse that I don't understand it, but others think it worthy of attention." Even today most scientists still don't take symbiosis seriously as an evolutionary mechanism. If they were to take symbiogenesis seriously, they'd have to change their behavior. The only way behavior changes in science is that certain people die and differently behaving people take their places.

Next, expanding the journal article, after ten years of research and six weeks of intense writing, I produced a book called The Origin of Eukaryotic Cells. Even under contract, it was rejected by Academic Press. Finally, in 1970, the revised and improved work was published by Yale University Press. Now called Symbiosis in Cell Evolution, the most recent version of the statement is in a second — really a third — edition. Published by W.H. Freeman in 1993, that book is my life's work. It details the role of symbiosis in the evolution of cells, which leads directly to the origin of mitotic cell division and meiotic sexuality. My major thrust is how different bacteria form consortia that, under ecological pressures, associate and undergo metabolic and genetic change such that their tightly integrated communities result in individuality at a more complex level of organization. The case in point is the origin of nucleated (protoctist, animal, fungal, and plant) cells from bacteria.

While Gould and the others tend to believe that species only diverge from one another, I claim that — more important in generation of variation — species form new composite entities by fusion and merger. Symbiogenesis is an extremely important mechanism of evolution. Symbiogenesis analysis impacts on developmental biology, on taxonomy and systematics, and on cell biology; it hits some thirty subfields of biology, and even geology. Symbiogenesis has many implications, which is part of the reason it is controversial. Most people don't like to hear that what they have been doing all these years is barking up the wrong tree.

My argument is radical only to the extent that it inspires scientists to change their status quo about many issues. To take seriously our Five Kingdoms concept (the book by Karlene V. Schwartz and me is based on work by Robert H. Whittaker and Herbert F. Copeland) a school or a publisher would have to change its catalog. A supplier has to relabel all its drawers and cabinets. Departments must reorganize their budget items, and NASA, the National Science Foundation, and various museums have to change staff titles and program-planning committees. The change from "plants versus animals" to the five kingdoms (bacteria, protoctista, animals, fungi, and plants) has such a profound implication for every aspect of biology as a social activity that resistance to accept it abounds. Scientists and those who pay them have to dismiss or ignore this potential reorganization because accepting the shifting boundaries and new alliances is strange and costly. It is far easier to stay with obsolete intellectual categories.

For more than a billion years, the only life on this planet consisted of bacterial cells, which, lacking nuclei, are called prokaryotes, or prokaryotic cells. They looked very much alike, and from the human-centered vantage point seem boring. However, bacteria are the source of reproduction, photosynthesis, movement — indeed, all interesting features of life except perhaps speech! They're still with us in large diversity and numbers. They still rule Earth. At some point, a new more complex kind of cell appeared on the scene, the eukaryotic cell, of which plant and animal bodies are composed. These cells contain certain organelles, including nuclei. Eukaryotic cells with an individuated nucleus are the building blocks of all familiar large forms of life. How did that evolution revolution occur? How did the eukaryotic cell appear? Probably it was an invasion of predators, at the outset. It may have started when one sort of squirming bacterium invaded another — seeking food, of course. But certain invasions evolved into truces; associations once ferocious became benign. When swimming bacterial would-be invaders took up residence inside their sluggish hosts, this joining of forces created a new whole that was, in effect, far greater than the sum of its parts: faster swimmers capable of moving large numbers of genes evolved. Some of these newcomers were uniquely competent in the evolutionary struggle. Further bacterial associations were added on, as the modern cell evolved.

One kind of evidence in favor of symbiogenesis in cell origins is mitochondria, the organelles inside most eukaryotic cells, which have their own separate DNA. In addition to the nuclear DNA, which is the human genome, each of us also has mitochondrial DNA. Our mitochondria, a completely different lineage, are inherited only from our mothers. None of our mitochondrial DNA comes from our fathers. Thus, in every fungus, animal, or plant (and in most protoctists), at least two distinct genealogies exist side by side. That, in itself, is a clue that at some point these organelles were distinct microorganisms that joined forces.

David Luck and John Hall, research geneticists at Rockefeller University, recently made an astounding discovery that I more or less predicted twenty-five years ago. They demonstrated by well-developed techniques something they were not even seeking: a peculiar DNA — outside the nucleus of the cell, outside the chloroplast, and outside the mitochondria. This extranuclear DNA, these genes outside the nucleus, can be interpreted as remnants of ancient, invasive, squirming bacteria whose aggressive association presaged the merger.

If their discovery is correct — and at least three teams of researchers have disputed it — then the nonnuclear genetic system Hall and Luck revealed in green algae may represent the stripped-down remnants of bacteria inside all of us. The growth, reproduction, and communication of these moving, alliance-forming bacteria become isomorphic with our thought, with our happiness, our sensitivities and stimulations. If mine is a correct view, it organizes a great deal of knowledge. There are unambiguous ways of testing the main points. The implication is that we are literally inhabited by highly motile remnants of an ancient bacterial type that have become, in every sense, a part of ourselves. These thriving partial beings represent the physical basis of anima: soul, life, locomotion; an advocation of materialism in the crassest sense of the word. Put it this way: a purified chemical is prepared from brain and added to another purified chemical. These two chemicals — two different kinds of motile proteins — together crawl away, they locomote. They move all by themselves. Biochemists and cell biologists can show us the minimal common denominator of movement, locomotion. Anima. Soul. These moving proteins I interpret as the remains of the swimming bacteria incorporated by beings who became our ancestors as they became us.

The minimal-movement system is so physically and chemically characterizable that complete consensus exists that "motility proteins" are composed of typical carbon-hydrogen bonds, and so forth. All the details are agreed upon by cell biologists and biochemists. But I think an understanding of the extent to which the evolutionary origin involved symbiogenesis must be acknowledged. Such acknowledgment will lead to new awareness of the physical basis of thought. Thought and behavior in people are rendered far less mysterious when we realize that choice and sensitivity are already exquisitely developed in the microbial cells that became our ancestors. Even philosophers will be inspired to learn about motility proteins. Scientists and nonscientists will be motivated to learn enough chemistry, microbiology, evolutionary biology, and paleontology to understand the relevance of these fields to the deep questions they pose.

My primary work has always been in cell evolution, yet for a long time I've been associated with James Lovelock and his Gaia hypothesis. In the early seventies, I was trying to align bacteria by their metabolic pathways. I noticed that all kinds of bacteria produced gases. Oxygen, hydrogen sulfide, carbon dioxide, nitrogen, ammonia — more than thirty different gases are given off by the bacteria whose evolutionary history I was keen to reconstruct. Why did every scientist I asked believe that atmospheric oxygen was a biological product but the other atmospheric gases — nitrogen, methane, sulfur, and so on — were not? "Go talk to Lovelock," at least four different scientists suggested. Lovelock believed that the gases in the atmosphere were biological. He had, by this time, a very good idea of which live organisms were probably "breathing out" the gases in question. These gases were far too abundant in the atmosphere to be formed by chemical and physical processes alone. He argued that the atmosphere was a physiological and not just a chemical system.

The Gaia hypothesis states that the temperature of the planet, the oxidation state and other chemistry of all of the gases of the lower atmosphere (except helium, argon, and other nonreactive ones) are produced and maintained by the sum of life. We explored how this could be. How could the temperature of the planet be regulated by living beings? How could the atmospheric gas composition — the 20-percent oxygen and the one to two parts per million methane, for example — be actively maintained by living matter?

It took me days of conversation even to begin to understand Lovelock's thinking. My first response, just like that of the neo-Darwinists, was "business as usual." I would say, "Oh, you mean that organisms adapt to their environment." He would respond, very sweetly, "No, I don't mean that." Lovelock kept telling me what he really meant, and it was hard for me to listen. Since his was a new idea, he hadn't yet developed an appropriate vocabulary. Perhaps I helped him work out his explanations, but I did very little else.

The Gaia hypothesis is a biological idea, but it's not human-centered. Those who want Gaia to be an Earth goddess for a cuddly, furry human environment find no solace in it. They tend to be critical or to misunderstand. They can buy into the theory only by misinterpreting it. Some critics are worried that the Gaia hypothesis says the environment will respond to any insults done to it and the natural systems will take care of the problems. This, they maintain, gives industries a license to pollute. Yes, Gaia will take care of itself; yes, environmental excesses will be ameliorated, but it's likely that such restoration of the environment will occur in a world devoid of people.

Lovelock would say that Earth is an organism. I disagree with this phraseology. No organism eats its own waste. I prefer to say that Earth is an ecosystem, one continuous enormous ecosystem composed of many component ecosystems. Lovelock's position is to let the people believe that Earth is an organism, because if they think it is just a pile of rocks they kick it, ignore it, and mistreat it. If they think Earth is an organism, they'll tend to treat it with respect. To me, this is a helpful cop-out, not science. Yet I do agree with Lovelock when he claims that most of the things scientists do are not science either. And I realize that by taking the stance he does he is more effective than I am in communicating Gaian ideas.

If science doesn't fit in with the cultural milieu, people dismiss science, they never reject their cultural milieu! If we are involved in science of which some aspects are not commensurate with the cultural milieu, then we are told that our science is flawed. I suspect that all people have cultural concepts into which science must fit. Although I try to recognize these biases in myself, I'm sure I cannot entirely avoid them. I try to focus on the direct observational aspects of science.

Gaia is a tough bitch — a system that has worked for over three billion years without people. This planet's surface and its atmosphere and environment will continue to evolve long after people and prejudice are gone.