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Facilitated variation - Wikipedia
The theory of facilitated variation demonstrates how seemingly complex biological systems can arise through a limited number of regulatory genetic changes, through the differential re-use of pre-existing developmental components.[1][2] The theory was presented in 2005 by Marc W. Kirschner (a professor and chair at the Department of Systems Biology, Harvard Medical School) and John C. Gerhart (a professor at the Graduate School, University of California, Berkeley).

The theory of facilitated variation addresses the nature and function of phenotypic variation in evolution. Recent advances in cellular and evolutionary developmental biology shed light on a number of mechanisms for generating novelty. Most anatomical and physiological traits that have evolved since the Cambrian are, according to Kirschner and Gerhart, the result of regulatory changes in the usage of various conserved core components that function in development and physiology.[2] Novel traits arise as novel packages of modular core components, which requires modest genetic change in regulatory elements.
evolution 
18 hours ago by zryb
James A. Shapiro: Evolution: a view from the twenty-first century | SpringerLink
In the second part “the genome as read-write storage system” he reviews ways in which DNA is modified. In my opinion this is the nicest part of the book and touches on biological processes which are least well known outside biology. He emphasises the larger scale modification, through e.g. transposons which make up the largest part of the DNA of higher eukaryotes like us. He describes the somatic recombination and editing which is employed in the immune system (in his words “to anticipate on future challenges”), and the recently discovered CRISPR system as ’immune’ system in bacteria, where parts of viruses are incorporated in the genome, and therewith helps to fight these viruses. Continuing to emphasis the capability of cells to modify DNA, he describes the startling reconstruction of the so called macro-nucleus from the micro-nucleus in Ciliates which involves extensive and precise DNA cutting and pasting and is guided by RNA’s. Finally, he explains the so called ’epigenetic’ modification of DNA e.g by methylation which renders parts inaccessible, not only on the short term but also over several generations. This again is sound and interesting biology. He concludes his overview of DNA modification as follows: “one of the most profound lessons from the past 6 decades of molecular cell biology that all aspects of cell functioning and cell biochemistry are subject to regulation. We have no scientific basis for postulating that genome functioning is different in this regard. In other words we have every reason to expect that natural genetic engineering is also subject to regulation and do not operate in an uncontrolled way…” and continues to list a number of cases where e.g. starvation, antibiotics or DNA damage trigger various forms of DNA modification or transposon activation. He stresses that he thinks that the known regulatory processes are only the tip of the iceberg, and that much remains to be discovered.
evolution 
18 hours ago by zryb
Washington Monthly | Jordan Peterson’s Crackpot Sex Theories Are Pure Reagonomics
The Toronto attack spurred a bizarre discussion about the validity of incels’ grievances. According to a certain school of thought, and many incels themselves, the root of the problem is women’s sexual liberation. Once sex and marriage were decoupled in the West, the commodity of sex became subject to the forces of the free market. As a result, a small handful of elite men hoard all the mates, while less desirable men end up alone and angry. Some guys have all the luck.
evolution  Sex  Marriage  culture  WashingtonMonthly 
yesterday by HispanicPundit
Introducing Git protocol version 2 | Google Open Source Blog
An interesting case study in how to evolve existing software. How to safely signal new servers that you want the new protocol version, in a way old servers will ignore.

The Git project has tried on a number of occasions over the years to either limit the initial ref advertisement or move to a new protocol altogether but continued to run into two problems: (1) the initial request is rigid and does not include a field that could be used to request that new servers modify their response without breaking compatibility with existing servers and (2) error handling is not well enough defined to allow safely using a new protocol that existing servers do not understand with a quick fallback to the old protocol. To migrate to a new protocol version, we needed to find a side channel which existing servers would ignore but could be used to safely communicate with newer servers.
git  programming  dvcs  refactoring  evolution  software 
yesterday by jefframnani
The structure of the protein universe and genome evolution
Despite the practically unlimited number of possible protein sequences, the number of basic shapes in which proteins fold seems not only to be finite, but also to be relatively small, with probably no more than 10,000 folds in existence. Moreover, the distribution of proteins among these folds is highly non-homogeneous — some folds and superfamilies are extremely abundant, but most are rare. Protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties, which also extend to the number of connections between domains in multidomain proteins. All these distributions follow asymptotic power laws, such as have been identified in a wide variety of biological and physical systems, and which are typically associated with scale-free networks. These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle.
protein  molecular-evolution  evolution  eugene-koonin  to-read  reviews 
3 days ago by WMTrenfield
The genotype-phenotype map of an evolving digital organism
To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.
charles-ofria  andreas-wagner  evolution  evolutionary-computation  evolutionary-biology  artificial-life 
3 days ago by WMTrenfield
The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities
Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of evolution is an algorithmic process that transcends the substrate in which it occurs. Indeed, many researchers in the field of digital evolution can provide examples of how their evolving algorithms and organisms have creatively subverted their expectations or intentions, exposed unrecognized bugs in their code, produced unexpectedly adaptations, or engaged in behaviors and outcomes uncannily convergent with ones found in nature. Such stories routinely reveal surprise and creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. Bugs are fixed, experiments are refocused, and one-off surprises are collapsed into a single data point. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This paper is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems.
evolution  artificial-life  evolutionary-computation  to-read 
3 days ago by WMTrenfield
Интересный пример эволюции когнитивных способностей?: macroevolution
1. Во многих работах показано, что евреи-ашкеназы (но не другие группы евреев) имеют более высокие средние показатели IQ, чем другие человеческие популяции. Напр., если у североевропейцев средний IQ=100, то у живущих там же евреев в разных исследованиях получается где-то 107 - 116 (примерно на одно стандартное отклонение больше). В статье много ссылок на конкретные исследования, кому это интересно - посмотрите там. Вроде бы в самых недавних исследованиях разрыв получается меньше (?результат размывания репродуктивного барьера?) Причем преимущество у ашкеназов наблюдается не по всем типам задач в тестах на IQ, а только по вербальным и математическим (по пространственно-визуальным задачам у евреев результаты не лучше, чем у среднего европейца). У евреев испанского происхождения (сефардов) и восточных евреев (мизрахим) IQ такие же, как у окружающих народов (так что дело не в традициях грамотности и не в штудировании торы).

2. Наследуемость IQ высока, где-то в районе 0,7 - 0,8 для взрослых (у детей наследуемость IQ меньше - это обычная картина для количественных мультигенных признаков: пока организм растет, на него сильно может влиять среда, обучение, а с возрастом, увы, всё подравнивается под гены). Напомню, что наследуемость - это, говоря упрощенно, доля изменчивости по признаку, определяемая генами, а не средой. Речь идет только об изменчивости (будь у всех людей одинаковый IQ, сама постановка вопроса о наследуемости этого признака была бы бессмысленной).

3. При такой высокой наследуемости признак (т.е. в данном случае IQ) должен быть весьма чувствителен к отбору. Т.е. если в течение нескольких поколений обладатели более высокого IQ будут оставлять чуть больше потомков, чем представители той же популяции с более низким IQ, то среднепопуляционное IQ должно заметно вырасти. Поднять среднепопуляционное IQ на 10-15 пунктов за 800 лет - вполне реально, единственное, что для этого нужно, это репродуктивное преимущество особей с высоким IQ.
4. Репродуктивное преимущество особей с высоким IQ, по мнению авторов, имело место у евреев-ашкенази в Средние века (точнее, примерно с 9 века до 18-го), потому что, судя по историческим источникам, в это время ашкенази занимали уникальную социальную нишу: это единственная известная человеческая популяция, в которой большинство трудоспособного населения занималось делами, требующими высокого IQ

7. Хорошо известно, что у ашкенази имеется целый букет т.н. "еврейских болезней" - наследственных заболеваний, в основном рецессивных, частота которых резко повышена именно в этой популяции. Обычно это связывают с бутылочными горлышками численности и генетическим дрейфом. Но удивительно, что эти вредные мутации не рассеяны по геному абы как (что было бы логично ожидать, если бы дело было в дрейфе), а четко сгруппированы по функциональным кластерам (что очень трудно объяснить дрейфом). Например, есть кластер еврейских болезней, связанных с нарушением обмена сфинголипидов (болезнь Гоше, Ниманна-Пика, Тея-Сакса и др.). Это вещества, играющие важную роль в работе нейронов. Некоторые из них стимулируют рост аксонов и дендритов (что м. б. связано с обучаемостью). При перечисленных болезнях эти вещества накапливаются в клетках в слишком больших количествах.
biology  jews  evolution  talks  intellect  study 
4 days ago by some_hren
Roger Bennett from Men in Blazers on Slate’s Hang Up and Listen podcast
"I grew up in England around the time the Premier League started in 1992. back then the Italian Serie A--which is hard to believe b/c its become somewhat of a backwater--that was the place, that was the dream, that was the Hollywood of football: in Italy. and English football was a backwater. And to begin with the Premier League, the players that came to it were--the Premier League was seen as the elephant's graveyard--it was Italian stars at the end of their careers, they would do a year or 2 at Chelsea or Manchester United. There was, I remember an Italian player called Ravanelli, grey-haired gentleman, came over signed from Middlesborough and I remember speaking to an Italian journalist at the time who said "when Ravanelli, my hero, signed for the English Premier League, I felt sorry for him that he had to stoop so low." And you need to understand, we need to understand about MLS, it's only just over 20. The world's leagues are not a hierarchy which is cemented, they are absolutely fluid, the techtonic plates that underlie them are constantly shifting. Leagues grow, rise in the fervor, others collapse, some implode. And what happened in England to begin with we brought over the dinosaurs and then slowly we started to take some punts on new fresh talent: your Bergkamp who failed in Italy and thrived unbelievably in England, Theirry Henry who'd done the same. and the balance of power shifts at a certain point. And MLS right now has a fascinating, intoxicating young breed of South and Central american players, 19-20-21, who are outstanding. They're on the radar of European clubs."
-Roger Bennett
roger-bennett  slate  hang-up-and-listen  podcasts  soccer  sports  evolution 
4 days ago by actualitems

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