A programme for ageing research with worms

Luyten W, and 19 other authors including AML. 2016. Ageing with elegans: a research proposal to map healthspan pathways. Biogerontology  7: 71–782

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Posted in ageing, metabolism, peer-reviewed articles, Uncategorized

Diversity in Argentinian killifishes

Helmstetter AJ, Papadopulos AST, Igea J, Van Dooren TJM,  Leroi AM. Savolainen V. 2016. Viviparity stimulates diversification in an order of fish.  Nature Communications 7: 11271

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Posted in general evolution, peer-reviewed articles, Uncategorized

Mutational metabolomics

Davies SK, Leroi AM, Burt A, Bundy JG, Baer CF. 2016. The mutational structure of metabolism in Caenorhabditis elegans.  Evolution 70: 1558-564

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Posted in general evolution, metabolism, mutants & variants, peer-reviewed articles, Uncategorized

Pop data science – tv programme

The Secret Science of Pop. 2017.AMLGDO5

BBC4  (writer / presenter)

Director: Thomas Hewitson

1 x 60

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Posted in evolution of culture, general evolution, tv & radio, Uncategorized

Is it a hit you’re looking for?

Weekend Financial Times. Openings. 25.11.15

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Posted in evolution of culture, general evolution, journalism, Uncategorized

Waiting for the MOOCs

Weekend Financial Times. Openings. 18.09.15

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London Review of Books

by Adrienne Mayor 10.02.15

Great thinkers who pondered the mysteries of nature used to be known as ‘natural philosophers’. For centuries there wasn’t a separate term for those few individuals who practised science (Latin scientia, ‘knowledge’) in the physical sense of carrying out field work, devising experiments and testable explanations and predictions in order to understand experienced reality. In 1833 William Whewell, professor of mineralogy, created the term ‘scientist’ at a meeting of the new British Association for the Advancement of Science (founded 1831), by analogy with ‘artist’, to identify empirical thinkers who used all their senses and actually got their hands dirty to comprehend nature. ‘Science’ soon came to mean a methodology, a disciplined, systematic way of observing, studying and explaining the world. In fact, the ‘scientific method’ was first practised by Aristotle, the hero of Armand Marie Leroi’s new book.

The desire to ‘give an account of nature’ certainly existed before Aristotle, Leroi notes in his historical and personal account of Aristotle’s grand treatise on comparative zoology, the History of Animals, and other works on natural history. Aristotle is most famous for his Physics and Politics, but his most voluminous writings were biological. Leroi celebrates Aristotle as the first truly scientific thinker, in a modern sense, as the first to observe, describe and attempt to classify biology systematically, in all its ‘grandeur’ and myriad forms.

After Plato died in 348 BC, Aristotle left Athens for western Anatolia and took to the field, subsequently grounding biological studies in deductions based on observation. In the Physics, Aristotle maintained that the principles of change were teleological, that all things in nature moved towards achieving perfection of their potentials. In the History of Animals and other biological writings, the teleological process ‘directed towards a final goal’ still held sway. But Aristotle introduced a new empirical approach based on data obtained from many sources: from his own observations and dissections to the reports of previous writers and information relayed by informants including farmers, fishermen, sailors, hunters and travellers. Despite his interest in the principles of change and his awareness of transformations, deformities and mutation (lysis), his acceptance of the ‘fixity of species’ meant that ‘Aristotle never took the evolutionary leap.’

That Aristotelian blind spot was severely magnified by European Christians in the Middle Ages, effectively delaying enlightened zoological advances by millennia. The medieval insistence on divine creation and unchanging species eclipsed Aristotle’s innovative biological methodology, leading modern scientists to reject or misunderstand Aristotle’s important contributions to science. Today’s students of the animal and plant kingdoms, enriched by the wealth of ever-accumulating fossil evidence around the globe and informed by scientific theories of extinction and evolution, study the origins of life and seek to know how each animal and plant species flourished and either vanished forever or evolved over eons to become what they are in their present time and place. Leroi shows how Aristotle may have come close to expressing a principle of evolution in his ‘dynamic language’ about quadrupeds in Parts of Animals and his radical ‘version of natural selection’. But the rocks and earth that held the history of extinct, evolving life forms were bypassed as inanimate objects in Aristotle’s biology of living beings.

In Athens, Aristotle would eventually found the Peripatetic School of Philosophy, in which walking and thinking – meditating while meandering – were intimately entwined. But before that, most of Aristotle’s wandering took place around Kolpos Kalloni, a large inland lagoon connected to the Aegean Sea on the verdant island of Lesbos. Armand Leroi, an evolutionary biologist and ardent admirer of Aristotle, was drawn to retrace Aristotle’s path from Athens to Assos on the Turkish coast. From Assos, Leroi crossed the narrow strait to Lesbos: the nutrient-rich, calm lagoon harboured an abundance of salt and freshwater fish, eels, shellfish and other sea creatures, its marshy shores home to a chorus of birds, frogs and insects. All this life flourishing in the sheltered pool was a boon to Aristotle’s decision to favour observation over Plato’s abstract speculation, and inspired his grand endeavour to meticulously catalogue, describe and explain the biological world as he found it.

It’s easy to imagine that the Lesbian lagoon – and Plato’s charming image for Greeks clustered around the Aegean Sea ‘like frogs or ants around a pond’ – were not far from mind when Aristotle applied his powers of classification, taxonomy and explication to human beings, the most political of animals. ‘Inescapably,’ Leroi writes, ‘Aristotle’s Politics was political science written by a biologist’ and Aristotelian concepts of advantageous, teleological social behaviour anticipate modern sociobiology. In his discussion of the origin of the state, laws and servitude in the Politics, Leroi asks some provocative questions about Aristotle’s disturbing theory of ‘natural slavery’. Here Leroi draws on his own experience of growing up in ‘Apartheid South Africa, a state founded on the notion that Africans, were, by nature, incapable’ – in other words, that they were ‘natural slaves’ as described by Aristotle. As Leroi points out, the origins of social inequalities and doctrines of inherent incompetence are complex and remain unresolved since antiquity. ‘Political ironies haunt’ Aristotle’s Politics, Leroi concludes.

Ironies also hover over portions of The Lagoon. One example is Leroi’s description of Aristotle’s Athens. In a book that cites so many up-to-the-minute social scientists and current biological advances, it is jarring to hear Leroi echo 18th and 19th century anti-democratic sentiments: ‘The Athenian way of government [and] public life in fourth century Athens was squalid,’ Leroi writes. ‘Every citizen could go up to the Pnyx and vote on the legislation of the day.’ The result, he maintains, was ‘endemic corruption’ and ‘mob rule’ by ‘rabble’ and demagogues. This antiquated picture of what today’s historians and political scientists generally consider Athens’ golden age of democratic prosperity and political egalitarianism has gathered two-centuries’ worth of dust. Inexplicably, Leroi’s sole source is an 1872 history of Greece by Jacob Burckhardt, a fierce Swiss contrarian who detested Athenian democracy and glorified aristocracies (and Sparta).

Another irony is the missed opportunity to illuminate a lost chapter in the history of science. Some of the first inklings of the ‘scientific’ impulse can be traced to ancient Greek discoveries and interpretations of the remarkable petrified remains of long-extinct creatures that once populated the ancient Mediterranean world. This underappreciated body of evidence does not constitute formal science, of course, but the numerous ancient accounts of remarkable plant and animal fossils do demonstrate careful observation, measurement and rational attempts to explain evidence over time – crucial ingredients of scientific inquiry. For pre-Darwinian people, the easiest paleontological puzzle to solve was the presence of fossilised seashells and fish skeletons on mountains and deserts far from the sea. Because these marine fossils resembled known, living species, the explanations did not require supernatural or divine forces or the difficult concepts of extinction or evolution. All that was needed was a vision of land once submerged under the ocean to explain how marine creatures came to be stranded so long ago that they turned to stone. The natural philosopher Xenophanes in sixth century bc was the first to articulate the idea that impressions of seashells, fish and seaweed observed in rocks in Italy, Malta and on the Aegean island of Paros had been trapped in mud that hardened in the remote past. Xanthos of Lydia (fifth century bc) arrived at the same conclusion to explain myriad scallop and other shells found far inland, in Asia Minor, Armenia and Iran. This accurate understanding of shells and fish marooned by receding seas had become general knowledge by the time of Herodotus.

Aristotle knew the writings of Xenophanes, Xanthos and Herodotus, and he had examined and dissected countless fish and marine creatures. Like Plato, Aristotle envisioned the ongoing cycle of sea transgressions and emerging land formations over eons. Fossil shells embedded in stone appear everywhere in the Greek world; they were typically seen in quarries. Many Greek buildings were constructed of highly fossiliferous ‘shelly limestone’ blocks dense with recognisable brachiopods, crinoids, Moreover, fish fossils are common on Lesbos where Aristotle studied fish. But Aristotle never discussed marine fossils. It would be interesting to know how Leroi, who analyses in detail many other erroneous paths taken by Aristotle, would account for this lapse.

The mystery deepens. Leroi remarks that Aristotle ‘never mentions a single fossil in his works, or anything that can be construed as one’. (What might be faint gesture at fossilisation appears in the Parts of Animals, where Aristotle alludes to petrifaction from drying exhalations of the earth. But he seems to relegate the natural process to the realm of myth. After an animal’s death, Aristotle writes, ‘nothing remains except the configuration, like the animals in folktales that are turned to stone.’) So, not only did Aristotle overlook fossil fish but he also ignored fossilised plants, trees, and the femurs, scapulae, ribs, skulls, vertebrae, tusks and teeth of long extinct ancestral elephants, rhinos and other huge mammals of the Miocene through Pleistocene epochs. These remarkable fossils continually came to light throughout the Mediterranean region, in Greece, Italy and North Africa, on many Aegean islands, and in western Asia Minor. We know this because about a hundred accounts by more than thirty ancient Greek and Latin authors tell how extraordinary petrified remains of unknown creatures were revealed by erosion, storms, floods, earthquakes and human digging. Great excitement surrounded the discoveries, as people journeyed to view the bones, estimated their dimensions, and measured the skull capacities of beasts never seen alive.

Speculating on their appearance when living, the cause of their death en masse, people identified the creatures as giants, monsters or heroes from long ago times described in myth and legend. Greek sources say the fossils were displayed in temples or in situ all around the Mediterranean. According to Euagon, a fifth century BC historian of Samos, for example, one could view the bones of titanic creatures called Neades on the island; the monsters had been destroyed long ago and trapped under rock by earthquakes. Notably, Aristotle did cite Euagon on the tremendous Neades but did not mention their physical remains on Samos.

Leroi’s discussion of Aristotle’s sources is a fascinating survey of ancient biological writings available in the fourth century bc. We learn that Aristotle drew on his own experiences and the expertise of fellow scholars, often disputing their reasoning. Unlike Thucydides and Plato, however, Aristotle also valued folk knowledge. He combed through myths and local lore, gathered oral traditions, and solicited material from ordinary people, seeking nuggets of truth. This makes Aristotle’s omission of conspicuous evidence of extremely large mammalian fossils buried in the earth and petrified shells far from the sea all the more startling for such a curious, thorough biologist whose investigations embraced all manner of life forms and resources. Why was the pervasive, conspicuous fossil evidence that excited so much speculation and interest totally absent from his writings? ‘It is implausible that he knew nothing about them,’ Leroi concedes. But

Leroi’s excuse – ‘he did not know that in bygone ages the earth pullulated with creatures now extinct’ – seems weak. All around the Mediterranean, ordinary folk and other writers were interpreting remarkable fossil remains as proof that in bygone ages the earth did pullulate with giant creatures that no longer existed.

Leroi acknowledges the intriguing question of Aristotle’s omission of fossils in a brief section. But like other modern historians of paleontology, he underestimates Aristotle’s opportunities to hear about, see and touch stone bones of gigantic size – tangible evidence that Greek lands were once populated by giant beings that had died out long ago and were buried in the earth. The widespread fossil deposits of extinct species of stupendous size described in ancient Greek literature receive cursory attention from Leroi. Minimising the megafaunal remains he viewed in a small museum on Lesbos as ‘modest’, mentioning only giraffes, ‘dwarf elephants’, and large tortoises, he seems unaware of the immense size of the many species of mastodons and mammoths, whose tusks, thighbones and shoulder blades towered over the Greeks who found them.

In about 560 BC, for example, the Spartans excavated a colossal skeleton from a blacksmith’s well dug in Tegea. Herodotus recorded the dimensions, which match those of a mastodon or mammoth, common fossils in that region. The bones were hailed as the remains of Orestes and transported to Sparta with great fanfare. Kimon made an expedition to Skyros to retrieve the huge bones of the legendary Athenian king Theseus; these were placed in a shrine in Athens. Other cities sought out similarly impressive fossils to honour as their founding heroes. Meanwhile, in the temple of Tegea, Greeks could view a great, curved tusk of a woolly mammoth, said to belong to the giant ‘Calydonian Boar’ of myth, and in Olympia, they could marvel at the shoulder blade of the local hero Pelops, three times the size of a human scapula. At least two extensive fossil deposits in Greece, in Megalopolis and Chalkidiki, were so dense with jumbled, disarticulated limb bones of Ice Age megafauna that they were said to be battlefields where the gods had destroyed multitudes of giants and monsters. Modern paleontological and archaeological evidence confirms ancient fossil finds. In 1988, for example, German archaeologists discovered a very large fossil femur among the sixth-century bc dedications at the altar in the Temple of Hera on Samos. American archaeologists recovered a similarly sized fossil femur of an Ice Age woolly rhinoceros from the ancient acropolis at Nichoria in southern Greece; it had been brought there from the Megalopolis beds. A mammoth tooth was recovered from the ruins of Hippocrates’ medical school on Kos. A Greek vase from sixth-century bc depicts a monstrous skull emerging from a sea cliff near Troy. Aristotle had travelled to Assos in the Troad: the region’s megafaunal remains were rich.

The point is that Aristotle could not help but hear of these widespread discoveries and the popular understanding that gigantic beings once lived and then vanished. Lesbos boasted fossil traces of saber tooth cats, giraffes, rhinos, mastodons and mammoths weathering out of sandy clay soil a few miles south of Aristotle’s lagoon. But as Leroi points out, even more astonishing was Aristotle’s failure to take notice of plant fossils abounding on Lesbos. ‘How did he miss the vast petrified forest that litters the island?’ In the hills a few miles west of the lagoon, Leroi notes, is a petrified Miocene forest. There are huge palm trunks and sequoia trees, many still upright, with pinecones and roots.

In his informative discussion of Aristotle’s friend and successor, the botanist Theophrastus (ca 372-287 bc), Leroi suggests a credible reason for Aristotle’s silence on plant fossils. A native of Lesbos, Theophrastus had grown up in the midst of the island’s petrified forest. Theophrastus wrote On Plants and On Stones; some of his works survive but others are fragmentary. In his writings, Theophrastus described mottled fossil ivory tusks dug up from the earth, petrified reeds from India, the mineralisation of organic objects, and fish embedded in rocks near the Black Sea. Could the answer lie in missing texts? Did Aristotle set aside fossils because his friend Theophrastus had covered both plant and animal fossils in work that has not survived? For this hunch, Leroi cites Diogenes Laertius, a biographer in early third century ad. But much stronger support for this intriguing notion can be found earlier, in the first century ad. According to Pliny, Theophrastus wrote about ‘stones shaped like bones that are found in the earth’ in a two-volume treatise titled On Petrifactions, which was lost after Pliny’s day.

‘To continue the excuses’ for why Aristotle chose ‘to ignore the reports or even the evidence of his own eyes’, Leroi concludes that Aristotle’s belief in the eternal immutability of organic life forms led him to dismiss fields of stone bones and forests of stone trees. But the question deserves deeper examination, especially by a modern historian of evolutionary biology and mutant life forms. What was it about fossilised organic remains of unfamiliar creatures of outrageous stature that denied them a place in Aristotle’s world view and led him to pass over them without comment? Aristotle’s system was based on current living species, with no provision for anomalies, ‘mistakes in nature’, no-longer extant forms, or creatures that resisted categorisation, such as bizarre sea monster types observed by fishermen and sailors. Aristotle labelled such rarities as monstrous and irrelevant to his investigations because they violated principles of ‘order and purpose’. Aristotle was not the only natural philosopher blind to the ‘folk science’ of fossils. Even though popular interpretations of stone bones arose from observation and produced coherent concepts that anticipated modern theories of deep time, geomorphology and extinctions by catastrophe, the insights were often expressed in mythological terms, which natural philosophers tended to shun.

The last modern scientist to recognise the significance of the long-forgotten fossil discoveries of classical antiquity was the French father of paleontology, Georges Cuvier (1769-1832). Cuvier studied these accounts in developing his path-breaking theories of evolution and extinctions. Since Cuvier, however, the treasury of empirical folk knowledge of fossils preserved in classical literature has been rejected as superstitious trivia. A similar fate beset the grand scientific achievements of Aristotle. Leroi’s account is compelling and ameliorative. Blinded by the brilliance of the Enlightenment, modern scientists and historians pounced on inconsistencies and errors to condemn Aristotle’s biology and hold him responsible for medieval Christian over-interpretations of his ideas that held back science for 2000 years. In a note, Leroi promises to address these claims in depth elsewhere.

Leroi’s goal in The Lagoon is to restore his hero’s place in the scientific firmament. Leroi criticises the scientific revolutionaries from the 17th century to the present for turning a blind eye to Aristotle. So it is unexpected and ironic that Leroi himself turns so quickly away from the question of why Aristotle ignored the fossil record. One excuse for our modern ignorance of ancient discoveries and interpretations of fossils has been that Aristotle never discussed fossils. It is typically assumed that if fossils eluded the gaze of the great Aristotle with his insatiable curiosity about the natural world, his sweeping biological knowledge of everything under the Mediterranean sun, then fossils were unknown in his day. But in fact the bones of immense unknown animals were a prominent feature of the Mediterranean natural and cultural landscape and Aristotle’s silence remains a mystery.

These omissions do not detract from the magnificence of Leroi’s paean to Aristotle and the profound significance of his endeavour. Aristotle’s predecessors, notes Leroi, ‘viewed the world as if from Olympus . . . speculation filled in what they could not see’. But Aristotle went down to the shore. He devised a robust ‘research programme’ in which ‘he observed, applied his causes to his observations and wove them together in the books that make up his Great Course in Zoology’. The Lagoon is part personal memoir/travelogue, part long-overdue Festschrift for a cherished mentor, part idiosyncratic love letter to Aristotle, ‘a tribute to the power of his mind’. Leroi’s own curiosity and passion for nature evokes our awe for the infinite diversity of the natural world. We marvel along with him at Aristotle’s sheer energy and intelligence.

Aristotle, comments Leroi, ‘could not have conceived just how vast the science that he founded would become’. But in comparing ‘the elaborate tapestry of his science’ to our own, Leroi maintains that we can only now ‘see his intentions and accomplishments more clearly than any previous age has seen them’ and that is perhaps because we have finally ‘caught up’ with Aristotle, the man who ‘invented science from scratch’. One of the fascinating features of The Lagoon is the author’s ability to unpack Aristotle’s wildest misconceptions, so that we can understand exactly how and why the methodical, commonsensical scientist got some things so very wrong. With Leroi, we end up feeling that, had he time and world enough, Aristotle himself could have corrected his own mistakes

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Artefact — book

Leroi, AM. 2020.  Artefact:  the science of making things

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Aristotle on animals – book

Lennox, J., Falcon, A., Gotthelf, A., Connell, S. and Leroi, AM. (eds). 2017. Aristotle On Animals

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Journal of Hellenic Studies

Review by Sophia Connell 2015

This is an extraordinary book. Bringing to our awareness a fecund lagoon on the island of Lesbos, Armand Leroi attempts to uncover numerous aspects of Aristotle’s biological investigations there. The volume tries to be many things at once – a smart coffee table book, an accessible introduction to Aristotle’s biology for a general audience, a contribution to scholarship in the field of the history of zoology and a personal account of a deeply felt intellectual connection. This is what makes the book so singular but what also leads to some of its difficulties. Like the Elephant’s nose, although fantastically versatile, there is a limit to how many functions it can serve.

The book is divided into sixteen boldly headed chapters; there are also 114 sub-sections, most of which are brief. Although there are many quotations, no references are made. Instead, each sub-section has a corresponding ‘footnote’ where citations and any scholarly debate are starkly outlined. Most chapters begin with a tale from modern Greek life or zoological observations. You will find throughout almost every well-known (and not so well-known) reference to, association with and quotation about Aristotle on animals. As with most of the quotations taken directly from Aristotle’s texts, these are generally not analysed. In this way, then, the book is useful as an introduction to key themes from literary, historical and philosophical points of view. However, this is not its stated goal, which is rather to show that Aristotle is a scientist in the modern sense (7, 378). This is a contentious position: the term wasn’t coined until the 19th century and does not obviously exclude many of Aristotle’s predecessors. For Leroi a scientist is variously someone who feels wonder at the beauty of nature, someone who is a careful observer, someone who has a system, someone who wants to unify, someone who has a vision of the whole. As he himself admits in the closing sections, even now, there are different ways to do science (366). The fact that we have here no clear criteria for what counts as a ‘scientist’ is perhaps unsurprising given the fact that Leroi wishes to write as a scientist rather than as a philosopher. The scientist has access to special insights (10, 259) – a bold claim, which is not much substantiated.

As for the idea that Aristotle is a scientist, the term’s ambiguity is problematic. If this means that Aristotle investigates the natural world with some patterns in mind, and others that will develop only when he has accumulated enough data, that he tries to understand and explain his observations and makes connections between different parts of the natural world, then the claim is uncontroversial. But Leroi also assumes that Aristotle was engaged in ‘a pure and disinterested search for the causes of things’, just like he himself is now and that Aristotle ‘invented the science of biology’ (7). But Aristotle is not studying living things due to disinterested curiosity and separating it off from other interests. He is driven, instead, by philosophical questions such as ‘why are we here?’ and ‘how should we live?’, questions that seldom feature in the working lives of modern scientists, where life and its emergence are treated as brute facts of no relevance to human affairs. We have broken the links that the ancients had between our concerns and the make-up of the rest of the world – perhaps to our great detriment. (I cannot help but feel that more comment on how challenged the natural environment is now compared to in Aristotle’s time would have been apt at many points.)

The narrower ways in which Aristotle could be like a modern biological scientist are very hard to show. This seems to be why the author feels the need to continually apologise for Aristotle’s ‘mistakes’, for if he were a modern biologist, he would not have made them, e.g. in his anatomies (60, 66), his failure to experiment (364) and his acceptance of spontaneous generation (225-36). This is also why, after dismissing sections of de Anima as ‘irritatingly abstract’ (159), Leroi is intent on mechanising the soul (151-202). In order to be acceptably modern, Aristotle cannot be a vitalist (161). But this hardly proves that he wasn’t. The author also labours hard over why Aristotle didn’t recognise evolution (203-221, 269-378). Leroi ‘like[s] to think’ that ‘upon reflection, [Aristotle] would even have granted that species evolve’ (299). In attempting to appeal to the modern mind, this goes too far. There is no doubt that Aristotle’s biology has been wrongly neglected but this problem cannot be solved by showing that he was just like us – he is worthy of our attention even though (or maybe because) he wasn’t.

Some smaller problems include the frustrating anecdotal structure which can lead to occasional sensationalism. Two examples are the comment that ‘Aristotle has much to say about penises’ (184) and his rare remarks on female pleasure being presented as entire section entitled ‘the female orgasm’ (LXIV). Some of the footnotes are biased or incomplete and Appendix II is surely incorrect.

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The long-term benefits of zapping worm gonads

Weekend Financial Times. Openings. 21.08.15

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The eventual horizon

Weekend Financial Times. Openings. 17.07.2015

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ggplot2

library(ggplot2)
library(scales)

Scatterplot with points and a line
plot1<-ggplot()+
layer(data=d, mapping=aes(x=v1, y=v2), geom=”point”, colour=”black”, size=3)+
layer(data=d, mapping=aes(x=v1, y=v2), geom=”line”, colour=”black”, size=1)+
ylab(“LABEL”)+
xlab(“LABEL”)+
coord_cartesian(xlim = c(xvaluelow, xvalue2high), ylim = c(yvaluelow, yvaluehigh))+
#scale_y_continuous(breaks=pretty_breaks(n=x))+
theme_classic(base_size = 12, base_family = “”)
plot1

Colour code points with a third factor variable
 layer(data=d, mapping=aes(x=v1, y=v2, colour = factor(v3, labels = c(“NS”,
“<=0.05″, “<=0.01″))), geom=”point”,size=3)+
scale_colour_manual(values = c(“darkgoldenrod4″, “brown1″,”brown3″,”brown4″))+

Colour code points with a third factor variable and remove legend
layer(data=d, mapping=aes(x=halfyearfirstentry, y=selcoeff_PC3, colour = factor(P_PC3_sig)), geom=”point”,size=3)+
scale_colour_manual(values = c(“darkgoldenrod4″, “brown1″,”brown3″,”brown4″),guide = “none”)+

Add a polynomial smoother
layer(data=d, mapping=aes(x=v1, y=v2), geom=”smooth”, method=”lm”, formula = y ~ poly (x, 10), size=1, colour=”black”)+

Add a horizontal line
geom_hline(aes(yintercept=0),size=1)+

Volcano plot
volplot<-ggplot()+
layer(data=d, mapping=aes(x=v1, y=log(Pvalues), colour = factor(Pvaluesdiscreet, labels = c(“NS”, “<=0.05″, “<=0.01″))), geom=”point”,size=3)+
scale_colour_manual(values = c(“black”, “brown1″,”brown3″,”brown4″))+
ylab(“log(P value)”)+
xlab(“selection coefficient PC1″)+
coord_cartesian(xlim = c(-0.3,0.3))+
theme_classic(base_size = 12, base_family = “”)
volplot

2d density plot with contours and points
# Note: if one variable is a time chunks and chunks have uneven sample sizes,
# then take a random sample of each time chunk.
densplot<-ggplot()+
densplot stat_density2d(data=df, aes(x=v1, y=v2, fill = ..density..), geom=”tile”, contour = FALSE, n = 100)+
scale_alpha_continuous(limits = c(0, 1),breaks=seq(0,1,by=0.1))+
scale_fill_gradient(low=”white”, high=”black”, guide = “none”)+
geom_density2d(data=df, aes(x=v1, y=v2), colour=”grey”)+
geom_point(data=df, aes(x=v1, y=v2), colour=”darkgoldenrod4″,alpha=0.08,size=2)+
ylab(“LABEL”)+
xlab(“LABEL”)+
coord_cartesian(xlim = c(xvaluelow, xvaluehigh), ylim = c(yvaluelow, yvaluehigh))+
scale_y_continuous(breaks=pretty_breaks(n=10))+
theme_classic(base_size = 12, base_family = “”)
densplot

Set quartz size
quartz( width=14, height=14)

Arrange multiple plots
library(grid)
library(gridExtra)
grid.arrange(
plot1,
plot2,
plot3,
plot4,
nrow =2, main = “PLOTLABEL”)

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dataframe manipulations

merge two dataframes
df3<-merge(df1, df2, by.x=”v1″, by.y=”v1″)

get a random subset of rows from each group in a df with many groups
#Here the grouping variable is “groupv” and we want 70 rows
samp {
df[sample(1:dim(df)[1], size=70, replace=FALSE),]
}
subsampleddata<- ddply (df, .(groupv),  samp)

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plyr

library(plyr)
 Use ddply to summarize several vectors by some statistic
 summdf <- ddply(df, .(summv), summarise,
 mean   = mean(v1),
 N   = length(v1),
 SD  = sd(v1))
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date and time

Divide years into fractions
#first get year of first entry
d$yearfirstentry<-as.numeric(format(d$datefirstentry, “%Y”))
#then, using ifelse, chunk into half-years: syntax: condition, condition if true, condition if false
d$halfyearfirstentry<-ifelse((d$daterealfirstentry-g$yearfirstentry) > 0.5, 2, 1)
d$halfyearfirstentry<-as.numeric(paste(d$yearfirstentry, d$halfyearfirstentry,sep = “.”))

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The gifts of eternal Greece

New York Times Op Ed 03.07.2015

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Evolution of pop music


Dynamics and selection forces shaping the evolution of popular music 1960‐2010.pop

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Posted in current projects

Tom Stoppard’s The Hard Problem

Programme Notes for Tom Stoppard’s play, The Hard Problem, 01.01.15–extended version
Hard_Problem_poster_notitle

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Pop music revolutions

popMauch M, MacCullum RM, Levy M, Leroi AM. 2015. The evolution of popular music: USA 1960–2010  R. Soc. open sci. 2: 150081.

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Posted in evolution of culture, general evolution, peer-reviewed articles

New York Times

Sunday Review by Rebecca Newberger Goldstein. 31.10.2014.

Armand Marie Leroi is a scientist, and Aristotle is his hero. This conjunction is interesting because, in the official telling of modern science’s origins, Aristotle is hardly regarded as heroic. Instead he’s portrayed as the obstacle over which the early heroes of the scientific revolution–Copernicus, Kepler, Galileo–had to leap in order to impose a genuinely explanatory methodology over the often deceptive input of sense perception. After all, what could be clearer to the senses than that the Earth is stationary and the heavens revolve around it? If there was any ancient whom these pioneers of modern science esteemed it was Plato. He, too, had emphasized the deceptiveness of appearances. What’s more he had suggested, however obliquely, most especially in his “Timaeus,” that mathematics reveals the true structure of the cosmos, offering us the means by which we can distinguish between reliable and unreliable appearances. So, at least, did men like Galileo read the “Timaeus,” finding insights there to topple the formidable edifice of a Church-fortified Aristotelianism. The new scientists discarded at least two of the four Aristotelian causes, the formal and the final, the latter having injected a pernicious teleology into all physical explanations. (Flames leap and rocks fall because their constituent elements are striving to get to their right places.) In place of Aristotle’s qualitative categories, the new scientists put quantitative descriptions of matter in motion. What Aristotle had sundered, the celestial and the terrestrial, were united under one mechanics. And the rest, as they say, is history.

But this is the history of science as told from the vantage point of physics and cosmology. Leroi is a biologist, and he tells the story of science differently. He cannot mention Plato without hissing, often characterizing him as anti-scientific or, at the very best, a poor scientist: “Plato’s science is barely distinguishable from theology.” Instead Leroi’s heart belongs to Aristotle, who not only was, like him, an enthusiastic student of biology, particularly of zoology, but who also, unlike Plato, was besotted by the world of appearances. Aristotle, as Leroi makes wonderfully clear, exemplifies one kind of scientific aptitude. He was an enthralled observer of the natural world, bedazzled by data, seeking causal explanations not in abstract numbers but in concrete details acquired through avid sense perception.

The lagoon of Leroi’s title is on the Aegean island of Lesbos. Assos, on the coast of what is now Turkey, faced Lesbos, and it was in Assos that Aristotle lived between his two Athenian residencies, the first as a student and then teacher at Plato’s Academy, the second as head of his own school, the Lyceum. Leroi accepts the conclusion of the biologist D’Arcy Wentworth Thompson, who, in 1910, published a translation of Aristotle’s “Historia Animalium,” that it was primarily beside the life-teeming lagoon of Lesbos where Aristotle slaked his thirst for biological observations. This is why so many of the animals of Aristotle’s prose live in or near the sea. Given Leroi’s own impassioned empiricism, he must see it all with his own eyes, and so this book, partly a travelogue, treats us to vivid descriptions of fauna and flora, a lyricism arising from the density of the details and the delight taken in them. Leroi says that Aristotle’s writing is a “naturalist’s joy”; the same can be said for Leroi’s.

Plato and Aristotle: What an accident of history that two such contrasting orientations toward the physical world, animated by two such different aesthetic sensibilities, should have been pedagogically entangled with each other. One espies beauty in the elegance of the mathematical proportions he is certain rules the cosmos, the other in the richness of sensed particularities he is certain can be functionally explained. Both orientations would find application in the developed sciences to come, though neither Plato nor Aristotle was a “finished” scientist. Something methodologically original occurred during the observing, theorizing, experimenting activity of the scientific revolution. (Neither Plato nor Aristotle had mastered the concept of experiment.) To read some semblance of our science into these ancients requires charitably imaginative interpretations that clarify their obscurities with insights toward which they were themselves, perhaps, groping. Some of us are prepared to extend such interpretations toward Plato. Leroi extends them toward Aris­totle, so much so that he would vehemently reject my statement that Aristotle, like Plato, was not the finished scientific article. “As I contemplate the elaborate tapestry of his science, and compare it to ours, I conclude that we can now see his intentions and accomplishment more clearly than any previous age has seen them and that, if this is so, it is because we have caught up with him.”

This seems an extravagant claim, and, to justify it, Leroi energetically exhumes those moldering Aristotelian categories that the scientific revolution had supposedly buried and breathes the advances of modern biology into them. He performs the resuscitation with dexterity, though he’s not the first. The great evolutionary biologist Ernst Mayr, for example, urged, in his “Toward a New Philosophy of ­Biology: Observations of an Evolutionist,” that it is “quite legitimate to employ modern terms like ‘genetic program’ for ‘eidos’ where this helps to elucidate Aristotle’s thoughts.” (Mayr acknowledged, however, that Aristotle’s notion of fixed species is inconsistent with biology’s most important advance, the theory of evolution.)

Leroi follows closely in the footsteps of such generous elucidators. The modern understanding of genetically encoded information is applied not only to Aristotle’s formal cause, his “eidos,” and to his notion that all change is potentiality actualized, but also to his notion of the soul. “Aristotle’s belief that we should attend less to the matter than to the informational structure of living things makes him seem like a molecular geneticist avant la lettre.” And as far as that pernicious teleology of which Aristotle stands accused, Leroi asserts that it provides the very justification for proclaiming Aristotle the inventor of science. “He’s a comparative biologist; his real interest is specific teleology; he wants to know not only why this animal has that feature, but also why others haven’t. To answer this question, and the countless others like it, prompted by all the parts of all the animals in all the world, he devised a system of teleological principles and precepts. It’s the core of a system that has been used ever since.”

Leroi holds off admitting until late in the book that the charge he had leveled against Plato — that his science seems inseparable from theology — holds for Aristotle, too. “I have kept Aristotle’s theos in the shadows. It may even be that I have done so deliberately; that I have been reluctant to reveal the degree to which my hero’s scientific system is riddled with religion. Yet it is.” I admire Leroi for striving to naturalize Aristotle’s system in the light of modern biology. He certainly convinced me that Aristotle has gotten a raw deal in the official scientific story. And I admire Leroi, too, for fessing up, finally, that Aristotle can’t be entirely naturalized. On the whole, I admire this entertaining, insightful and felicitously written book. Just don’t trust anything he says about Plato. There is a diversity of talents and passions that contribute to the advance of science, and it isn’t necessary, in doing justice to some subset of these, to denigrate the others.

 

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Exemplary cultural analytics papers

A global study based on the birth and death locations of more than 150,000 notable individuals.

Schich, M. et al. 2014.  A network framework of cultural history. Science 345: 558-562.

A study based on 112,485 British trial records.

Klingenstein, S. et al. 2014. The civilizing process in London’s Old Bailey PNAS, USA 111: 9419–9424

A study based on 954,618 pages of digitized scores from the Western art music repertoire

Rodriguez Zivica PH, et al. 2013. Perceptual basis of evolving Western musical styles. PNAS, USA. 2013;110:10034–10038.

A study based on 7,733 literary works in the Project Gutenburg corpus.

Hughes, J. M et al. 2012. Quantitative patterns of stylistic influence in the evolution of literature.  PNAS, USA 109:7682–7686

A study based on millions of books scanned by Google.  

Michel, J,-P. et al. 2011. Quantitative Analysis of Culture Using Millions of Digitized Books. Science 331: 176-182 — an analysis of ngrams from millions of Google-scanned books.

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One Republic of Learning

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New York Times, Op Ed, 13.02.2015–extended version. 

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Posted in evolution of culture, general evolution, journalism

Biographile

On the Lagoon: How Aristotle Invented Science by Susan H. Gordon. 25.09.14

Twenty-three-hundred years ago, Greek know-it-all Aristotle wrote books about everything. Works like MetaphysicsSleepPlants, and Marvellous Things Heard are among the many Aristotelian works that have been shaping western thought for centuries, but passed down to us are also nine titles on animal anatomy, an Aristotelian passion largely forgotten in modern times. In a bookshop in old Athens, “next to a shop that sells canaries and quails from cages strung from the façade,” writer and evolutionary developmental biologist Armand Marie Leroi has his first encounter with Aristotle’s greatest achievement: Historia animalium, written in 350 BCE, is Aristotle’s biology compendium packed with fauna details both exterior and interior, with a special feature that weaves together those facts. Not only did Aristotle invent biology, says Leroi, he invented the scientific method itself.

Clever, acerbic Aristotle, said to adorn himself with flowing robes and multiple rings, exists in modern imagination as a philosopher. But his more lasting legacy, one especially pertinent to our twenty-first century love of scientific tales, comes from his entanglement with the living world. When Leroi opens that animal guide, what’s inside — shells categorically described by traits like smooth, rough, or ribbed textures and then, with even greater rigor (“The stomach follows closely upon the mouth and, by the way this organ in the snail resembles a bird’s crop. Underneath come two white formations, mastoid or papillary in form.”), anatomical portrayals of the shell-building creatures who live inside them — gives him the jolt of sudden peace that comes with stumbling upon an unexpected home: “He had evidently walked down to the shore, picked up a snail, asked ‘what’s inside?’; had looked, and had found what I found when, twenty-three centuries later, I repeated the exercise. . . . This was too wonderful to be ignored.”

And so Leroi sets off to see if Aristotle is a fellow biologist. His subject did much of his work in Kolpos Kalloni, cataloguing the life of that lagoon-like inland sea area off the island of Lesbos which is counted among the richest bodies of water in the eastern parts of the Aegean sea. Surrounded by oak, sweet chestnut, Turkish pine, terrapins, eels, storks, Aristotle wandered among the wildly diverse natural offerings of the European and Asian continental landmasses, which the lagoon divides — with elements like eelgrass beds filled with bream, bass, and paddle-legged crabs, and muddy slopes set upon ancient oyster reefs. Leroi naturally heads to the lagoon, too. It’s a tricky journey his books follows: an adventure set among the fish, sponges, birds, and great snails in the orange-pink and electric blue shoals of Aristotle’s hangout and within the alternately exhilarating and frustrating readings of his predecessor’s sometimes messy, contradictory, and just plain wrong facts and conclusions. Leroi’s glee is apparent the entire time: “This is the world Aristotle gave us: the vividly perceptible world of living things, whole and at home; the world that he enjoins us to love and understand.”

Aristotle dissected, he watched, he read the words of others who had described animals in the centuries before him, using all of this as data with which to answer his endless stream of questions: Why do fish have gills and not lungs? Why do human, uniquely, walk upright? What is the purpose of testicles and menstruation? How do living things stay alive? Why do they reproduce? Why do they die? He got a lot of things wrong and Leroi lists those dead ends along with the scientific truths he saw straight to. But even within the disorder, two things stand out: Aristotle’s intimate knowledge of the most minute parts of nature, and the potent organizing system with which he linked those gathered facts, one that stood as a condition of their inclusion in Historia animalium in the first place. Only Darwin, centuries later, would be worthy of a conversation with Aristotle. The two men had much in common — a powerfully logical mind, a physician father, an obsession with facts, and a tendency to make too much of some of the things they saw — but the scientific foundation upon which Darwin built his theory of evolution was one that Aristotle had invented first. Aristotle’s scientific method, his “demonstration,” was a technical achievement — in two parts: inferential logic (“A is necessary and sufficient to ensure B”) backed by empirical evidence of universals (all octopuses) and never particulars (this octopus) — that granted first him and then his best-known intellectual descendant the ability to make sense of the data they amassed.

And so, in 2014, Aristotle joins the ranks of his fellow biologists. “Intimacy with the natural world shines from his works,” writes Leroi, a communion that allowed Aristotle to “sieve the ocean of natural history folklore and travelogue for grains of truth from which to build a new science.” Following his new scientific inquiry, Aristotle arrived at a final why: Why does any of this happen at all? It would take centuries before Darwin could find a scientifically plausible answer, and in ancient Greece Aristotle looked again to the practical for his own: Biological systems are true so that we might exist. And to exist is simply better than to not exist.

 

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Daily Beast

Why Aristotle Deserves A Posthumous Nobel by Nick Romero 10.18.14 

Shortly before his death in 1882, Charles Darwin received a letter from a physician and classicist named William Ogle. It contained Ogle’s recent translation of Aristotle’s The Parts of Animals and a brief letter in which he confessed to feeling “some self-importance in thus being a kind of formal introducer of the father of naturalists to his great modern successor.”

Aristotle is not typically remembered as the father of naturalists, but Darwin acknowledged a line of intellectual descent. “I had not the most remote notion of what a wonderful man he was,” Darwin wrote of Aristotle in his reply to Ogle. “Linnaeus and Cuvier have been my two gods, though in very different ways, but they were mere school-boys to old Aristotle.”

A fascinating new book by the evolutionary biologist and science writer Armand Marie Leroi claims that Aristotle fully deserves Darwin’s high praise. In The Lagoon: How Aristotle Invented Science, Leroi argues that Aristotle developed many of the empirical and analytical methods that still define scientific inquiry.

An immediate problem for anyone trying to present Aristotle as a scientist is that he holds beliefs like this: too much sex causes sunken eyes because semen drains matter from the human brain. Or this: the right-hand side of the body is more honorable and therefore hotter than the left. There is also his conviction that the human heart processes and integrates sensations from the external world. The brain, beyond storing the matter that becomes semen, was just a cooling device for when the heart’s fires blazed too hot.

Some of his observations about animals appear equally bizarre. He reports that the European bison fires caustic dung when pursued and that the trunk of an elephant is in fact a snorkeling device that allows it to swim. He even claims that hen partridges conceive just by smelling the scent of males.

Mingled with all the bizarre zoology, however, are many impressively accurate and detailed descriptions. His accounts of the hyena’s genitals, the parental behavior of male catfish, and the limited sensory capacities of sea sponges are just a few of the many things about which he was essentially correct. 

Aristotle’s biological works mention roughly 500 different kinds of animals, and he gives such precise descriptions of internal anatomy that he probably dissected at least 35 of these. Lists of the errors and accuracies in his treatises can be multiplied nearly indefinitely, but a meaningful assessment demands more than a simple tallying of what he got right and wrong. Aristotle’s methods of analysis are the ultimate basis of Leroi’s claim that he invented science, and even when those methods generated results that are fanciful, eccentric, and simply wrong, their power is undeniable.

A fundamental technique of his scientific process was the collection of vast amounts of data. He interviewed hunters, travelers, fishermen, and farmers to get detailed information about the habits, structures, and environments of hundreds of animals. Some scholars think he may have even dissected an elephant that his former student Alexander the Great sent to Greece from India while he was off conquering the world. Today, collecting data is taken for granted as a necessary part of scientific inquiry. But Aristotle’s empirical emphasis was revolutionary for the fourth century BCE. He was a student of Plato, a thinker more interested in the abstractions of mathematics and metaphysics than the myriad details of the perceptible world. The cause of flatulence in elephants, for instance, was just not the type of question Plato pursued.

Aristotle, however, had an insatiable appetite for data on the vast variety of features, behaviors, and structures of biological life. He learned that near the Black Sea rams don’t have horns, while in Libya there’s a sheep with long horns. He notes that on Naxos sheep have very large gallbladders, but on Euboea they do not. 

While other authors in antiquity would simply repeat the myths and legends travelers brought back from distant regions (Herodotus on flying serpents comes to mind), Aristotle sought to verify reports whenever possible by observing phenomena for himself, dissecting animals, and interviewing people whose daily work brought them into close contact with the creatures he was studying. He even examined an aborted human fetus. Not only did he recognize the importance of gathering large sets of data, he also tried to monitor its quality.

But he was more than an encyclopedist. He collected such comprehensive data in order to analyze and interpret it. His theories and interpretations are often astonishingly insightful. One 20th-century Nobel laureate suggested that Aristotle deserved to receive the prize posthumously for his realization that the information that dictates and replicates an organism’s structure is stored in its semen. In some sense he was anticipating the discovery of DNA. His theory of inheritance can also account for recessive traits that skip generations, the contributions of both parents to the features of a child, and unexpected variations in traits that do not derive from either parent.

Many of his observations are readily recognizable to a reader of Darwin. He notes that an elephant’s size confers protection from predators and that fish with high rates of infant mortality produce a larger number of offspring to compensate for the likelihood that most of the progeny will perish. He showed a nuanced understanding of how the forms and features of animals are adapted to their environments. Darwin even mentions Aristotle as a forerunner who anticipates the theory of natural selection in the preface to the third edition of On the Origin of Species.

Aristotle perceived some of the universal associations between longevity, period of gestation, adult body size, and degree of embryonic development that biologists still study today. He noticed the correlations among these features, but he was sensitive to the distinction between correlation and causation and sought to eliminate confounding variables. Then he integrated his findings into broader theories with deep explanatory power.

Take his claim that “what nature takes from one party gives to another.” Essentially he is arguing that there are functional trade-offs in developmental biology. Growth in one body part often affects size and structure of other body parts. Darwin called the same phenomenon the “correlation of growth” and geneticist today study what they call “pleiotropic effects.” But the ideas are all fundamentally related.

Taxonomy was another major area in which Aristotle influenced the history of science. He considered the difficulties of placing certain animals—like the ostrich—within rigid classification schemes, and he recognized the subtle and blurred gradations that often separate different kinds of animals. But he ultimately arrived at the same principle of nested hierarchies that defined Linnaeus’ methodology. The genus-species distinction that we still use is a legacy of Aristotle.

Leroi is a brilliant guide to the history of science. He traces the history of ideas with skill and care, and he avoids the smug certainty of many contemporary science writers. This makes a certain sense given his deep knowledge of the theories of previous scientists. Studying the history of science is a necessarily humbling process; the countless blunders, dead-ends, and mistakes of earlier scientists are an invitation to reflect on how woefully flawed many aspects of our contemporary theories will appear after a few hundred or thousand years.

This is not to say that progress is impossible and each generation only makes different types of errors equidistant from the truth. Aristotle did make progress beyond earlier philosophers, just as Darwin advanced beyond Linnaeus and Cuvier. A careful reading of Leroi’s footnotes suggests that Aristotle may still have contributions to make. The Historia animalium contains around 9000 empirical claims; many are true, many are false, but some have yet to be tested. 

It was only fairly recently that two of Aristotle’s seemingly bizarre claims were actually confirmed. Marine biologists have found that that while dolphins may not snore, they do vocalize in their sleep. And elephants do occasionally use their trunks as snorkels while swimming. Mercifully, studies have yet to confirm that semen comes from the brain.

 

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Wall Street Journal

Why Aristotle Was Wrong by Stephen Budansky 18.10.2014

Aristotle, the world’s first polymath, was born in 384 B.C., studied at Plato’s Academy in Athens, and wrote with insatiable curiosity and dazzling originality—interspersed with breathtaking lapses in logic, facts and common sense—on everything from poetry to the movement of the planets to the nature of human happiness.

As Armand Leroi observes at the outset of his long, meandering tour through Aristotle’s scientific writings, the study of Aristotle has been the property of philosophers and classicists. “But the subject he loved most was biology,” suggests Mr. Leroi. He sets out to stake a claim for the proposition that a modern biologist such as himself (besides being a host of science shows on British television, Mr. Leroi is a professor of biology at Imperial College, London) “may just occasionally see in Aristotle’s writings something that the philologists and philosophers have missed.”

The author’s excitement at recognizing a scientific kindred spirit in an ancient Greek who lived two millennia before the founders of modern biology animates his account. Aristotle may have lacked a microscope or a knowledge of DNA or evolutionary theory, but he “speaks directly to any biologist’s heart” in wanting above all to know why: Why do fish have gills instead of lungs? Why do humans walk upright? Why do eagles lay so few eggs? Why do animals grow old and die?

Mr. Leroi is frequently able to make good on his ambition to pick up on points that philosophers and historians have missed. He uses Aristotle’s at times remarkably acute biological insights as a springboard for some beautifully clear explanations of some very difficult concepts in modern biology. Aristotle seems to have noticed, for instance, the interlocking reproductive adaptations that permit egg-laying fish to compensate for the high mortality of embryos: in such species, the females are larger than the males, they produce vast numbers of small eggs and the fertilized embryos grow rapidly to minimize their exposure to predators.

The author’s enthusiasm carries him away, however. He admits at the outset that Aristotle was often spectacularly and even ridiculously wrong about a lot of things. Mr. Leroi sticks, nonetheless, to pressing a sweeping claim: that (as his subtitle puts it) “Aristotle invented science” and that, whether we know it or not, modern science “absorbed the very structure of his thought. . . . His ideas flow like a subterranean river through the history of our science.”

There are two problems with this. One is that it is awfully hard to make a convincing case for the existence of a subconscious influence. A modern physicist uses in everything he does the laws of motion described by Newton 400 years ago; an engineer uses the precise mathematical tools brilliantly conceived by the inventors of calculus, Newton and Leibniz; in biology, the systematic approach to classification of Linnaeus and the evolutionary theories of Darwin are the very cornerstones of everything that has happened since. Try as he might, Mr. Leroi can offer no more than a vague symbolic or spiritual link between the research of a 21st-century scientist such as himself and the writings of Aristotle.

The other problem is that Aristotle has a lot to answer for. His ideas about physics and astronomy (which Mr. Leroi mostly, and conveniently, ignores) were wrong in every important respect. Aristotle thought celestial bodies moved in perfect circles, failed to recognize inertia, asserted that velocity—not acceleration— was proportional to applied force, rejected atoms, and argued that the Earth and the heavens were made of totally different substances. As Bertrand Russell observed: “Throughout modern times, practically every advance in science, in logic, or in philosophy has had to be made in the teeth of opposition from Aristotle’s disciples.”

Mr. Leroi’s determination to defend Aristotle against such charges leads him to increasingly strained excuses for his hero’s lapses. The author acknowledges that Aristotle’s ideas about the development of the embryo are “quite strange.” Among other things, Aristotle thought that eggs arose from the congealing of semen and menstrual fluids and that semen is hyper-refined blood, which only males are able to generate because they are “warmer” than females. But still, Mr. Leroi lamely concludes, “you have to admire the sheer audacity of his system.”

Aristotle indiscriminately mixed direct observations of animals with the most ludicrous mythical tales (lizards crawl into the noses of donkeys and stop them from eating). Mr. Leroi excuses this by suggesting, with no evidence whatsoever, that Aristotle at the same time must have “silently suppressed vast amounts of dubious data.” He pusillanimously sidesteps Aristotle’s unpleasant views about the subservience of women to men and the natural morality of slavery by suggesting that all Aristotle is saying is that some people are better suited than others to be managers, a view that he implies is really no different from modern corporate hiring practices. And while he indignantly rejects the contention that the legacy of Aristotle’s ideas held back scientific progress for centuries, even he is finally forced to admit that Aristotle’s theories of spontaneous generation “had a baleful effect on early modern science.”

The author’s decision to structure the book in part as a personal memoir would have worked better if the autobiographical anecdotes were not so humorlessly self-regarding and the bits of Aegean travelogue less clichéd (there are a lot of picturesque villagers sitting in cafes, invariably “sipping ouzo”). But I also could not help feeling that the book might have been better without its central character in places. Mr. Leroi is at his best explaining the ideas of modern developmental and evolutionary biology. Aristotle often seemed to keep getting in the way, forever diverting any attempts at sane discussion with his wild philosophizing, like some cranky uncle at the Thanksgiving dinner table. It was in fact Aristotle’s disdain for what we now recognize as the true invention of modern science—the experimental method—that makes him such a maddening figure, so brilliant, so precociously right at times, so avoidably muddle-headed at others.

 AML responds: Do read some of the comments by classical philosophers, among others, to this remarkably biased view of Aristotle’s accomplishments.

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Guardian

Review by Henry Gee, 02.10.2014

nightingale (Luscinia megarhynchos), sitting on a branch, singing, Greece, LesbosConsider the story of a famous natural scientist. A young man with a keen eye and an inquiring mind, the son of a doctor, was sent away to study in a city of culture. He took his studies with him on a voyage to islands overseas, whose wealth of animal and plant life immensely enriched his thought. A scholarly jackdaw, he took the lore of fishermen, stockmen and animal breeders, combining it with his own insight to produce a body of work whose influence resounds to this day. It can fairly be said that natural history, science as a whole, would be immeasurably the poorer without it.

Not Darwin, but Aristotle – whose life and work are reappraised by Armand Leroi in this magnificent book. Not surprisingly, we know so much less about his life than we do about Darwin’s. He was born in 384BC in Stagira, a town not far from modern Thessaloniki. His father, Nicomachus, was physician at the court of Amyntas III of Macedon, then a barbaric and backwoods nation (for all that Amyntas’ grandson, Alexander, would become Aristotle’s most famous pupil).

At 17, Aristotle was sent away for his education – to Athens, and the Academy of Plato. He stayed for 20 years, and became part of the Academic furniture. This makes his sudden flight from Athens in 348 or 347BC all the more mysterious. It could have been because he had fallen out with Plato (a tendency towards empiricism, perhaps, which irked the strictly anti-empirical stance of his ageing mentor). That Aristotle was passed over for the headship when Plato died might have been, in Aristotelian terms, the proximate cause. His association with Macedon had also put him at risk, given that Philip II, son of Amyntas III, had razed Olynthus, an ally of Athens, selling its citizens into slavery, along with a garrison of Athenian soldiers. With Demosthenes rousing Athenians to frothing xenophobia, Aristotle packed his bags.

His first port of call was Assos, in Asia Minor, where the tyrant Hermias had invited him and several other Academicians to adorn his court. Aristotle married there, but he and his new wife had to flee in 345BC when Assos was conquered by the Persians. They made landfall in nearby Lesbos, which is where Aristotle gathered the material for his zoological works. That he made his home in Lesbos might be solely due to the fact that one of his junior colleagues, the botanist Theophrastus, was a native and could show him around. The location was inspirational: Lesbos was to Aristotle what the Galápagos were to Darwin. The island is dominated by an enormous lagoon – hence Leroi’s title.

The Greeks are famous, perhaps notorious, for casting their science whole, from first principles, without troubling to examine the natural world it sought to explain. But Aristotle changed everything, providing lengthy accounts of fish and fowl, their lives, courtships, kinds, anatomies, functions, distribution and habits. They were often erroneous, but what sets Aristotle apart is his workmanlike attitude. One gets the impression of a practical man, given to neither the remote and crystalline idealism of his predecessors, nor the flights of fancy of later natural historians such as Pliny the Elder, described by one commentator as a “voluminous, industrious, unphilosophical, gullible, unsystematic old gossip”, for all that he gave his life to science by dying while studying the eruption of Vesuvius in 79AD (the one that did for Pompeii).

He does not seek absolutes; things aren’t absolutely true or absolutely false, but true or false “for the most part”. This is the first sign in the history of human inquiry that biology is a messy business that treasures its exceptions. In order to find any kind of order in the profusion of exceptions that forms the natural world, we have to take a pragmatic approach. We cannot simply impose our prearranged schemes on to the world. In our search for perfection, we must, at first, eschew it.

Everything Aristotle wrote, whether about natural history or poetry or politics, formed part of a grand, interlocking, philosophical scheme. Much of it seems ridiculous by modern standards. He held that matter was continuous, that life was a balance of four elements; that the heavens revolved around the Earth in ethereal spheres; and that plants, animals and humans did things for a reason, in order that the whole scheme could remain eternally in balance. Creatures were animated by souls of greater or lesser degree – that, and a magical entity calledpneuma.

Leroi treats this with great sympathy, and is right to do so, for to judge Aristotle “by modern standards” is by definition anachronistic. In science, there is no shame in being wrong. Scientists are wrong all the time. Aristotle was a pioneer in that he started not with a prior scheme, but sought, as dispassionately as he could, to explain what he saw.

His reputation as a proto-scientist took a hit when his philosophy was bowdlerised, repackaged and made altogether unintelligible by the schoolmen of the middle ages, so that by the time the Renaissance came along, he was seen as less an inspiration than a dead hand, something to be thrown off by the new era of experimentation. Later scientists, from Francis Bacon to the founders of the Royal Society, to Peter Medwar held him in scorn. Experimental scientists, who look very deeply at narrow areas of science, with all the appropriate caveats and controls, will have no time for Aristotelian musings. But natural historians, who survey large swathes of diversity in one synoptic glance, and are prepared to make mistakes along the way, are Aristotelian by nature. The pendulum is swinging his way, as experiments on tiny parts of nature in the form of genes and their activities, divorced from the creatures in which they are normally found, are giving way to genomics, in which scientists try to grasp the interplay of thousands of genes at once, with explicit reference to the questions Aristotle was interested in – how animals grow from eggs; why some animals live longer than others; and, ultimately, why we all grow old and die.

Darwin knew almost nothing of Aristotle until 1882, when William Ogle, physician and classicist, sent him a copy of The Parts of Animals he’d just translated. In his note of thanks, Darwin wrote: “From quotations which I had seen I had a high notion of Aristotle’s merits, but I had not the most remote notion of what a wonderful man he was. Linnaeus and Cuvier have been my two gods, though in very different ways, but they were mere schoolboys to old Aristotle.”

This book is powerful, graceful and charming. Leroi’s prose is as blue-white bright as an Aegean sky reflected from a whitewashed wall. Buy the hardback if you can – it is beautifully designed and deftly illustrated. Having airy theories is all very well, but if you really want to know the world, to discover what makes it tick, you have to observe it, catalogue it, and take it to pieces.

 

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Independent

Nature Books, by Max Liu, 12.09.14

Twenty-three centuries after his death, you might be familiar with Aristotle’s ideas about poetics and politics but, in The Lagoon (Bloomsbury Circus, £25), Armand Marie Leroi argues that the Greek philosopher’s studies in biology “flow like a subterranean river through the history of our science”. Leroi examines the zoological theories that Aristotle formulated while studying wildlife on Lesbos in 345 BC. Aristotle’s findings were ingenious even when they were inaccurate and Leroi celebrates the belief that every living creature reveals “something natural and something beautiful”. Whether Aristotle is exploring the meaning of existence, the structure of the human heart or the souls of cuttlefish, Leroi is an enthralling and irreverent guide to “the first scientist”.

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Open Letters Monthly

Book review: The Lagoon, by Steve Donoghue, 21.09.14

We typically refer to Aristotle as the first systematic philosopher in the West, (Dante, for instance, often referred to him simply as “The Philosopher”) and that forms a neat continuity with his mentor Plato and Plato’s mentor Socrates. But we only have a third of the books Aristotle wrote in a long lifetime full of writing, and what we know about what we don’t have leads to the central opening assertion of Armand Marie Leroi’s uproariously enjoyable new book The Lagoon: How Aristotle Invented Science: “To be sure, some philosophers and physicians had dabbled in biology before him, but Aristotle gave much of his life to it,” Leroi writes. “He was the first to do so. He mapped the territory. He invented the science. You could argue that he invented science itself.”

Of course, even as a scientist, Aristotle has his critics – including the smartest man in the Renaissance. Francis Bacon takes the ancient master to task for “undertaking not only to frame new words of science at his pleasure, but to confound and extinguish all ancient wisdom, insomuch as he never nameth or mentioneth an ancient author or opinion, but to confute and reprove …”

Leroi instantly rides to the rescue:

That Aristotle is generous with criticism and parsimonious with praise towards his predecessors is undeniable. But so what? It’s a scientist’s job to disagree. Besides, the remarkable thing is precisely how each of his books begins with a round-up of what his predecessors thought before moving on to his own solutions. Aristotle’s treatises have the structure that academics have used ever since. As Bertrand Russell said, Aristotle was the first man to write like a professor.

The Lagoon doesn’t unfold gradually and gracefully; it lunges and explodes all over with wit, erudition, and enthusiasm. Leroi goes to the island of Lesbos and its surroundings, walks around, pokes in the same tidal pools that Aristotle himself must have prowled as part of his inspiration for the many science books he wrote when he wasn’t yarning on about philosophy. Leroi is a big fan of those books; they set his imagination working:

The books that we have are a naturalist’s joy. Many of the creatures that he writes about live in or near the sea. He describes the anatomies of sea urchins, ascidians and snails. He looks at marsh birds and considers their bills, legs and feet. Dolphins fascinate him for they breathe air and suckle their young yet look like fish. He mentions more than a hundred different kinds of fish – and tells of what they look like, what they eat, how they breed, the sounds they make and the patterns of their migrations. His favourite animal was that weirdly intelligent invertebrate, the cuttlefish. The dandy must have plundered fish markets and hung around wharves talking to fishermen.

This is a very entertaining author, one who layers an arch wryness over almost everything he writes about (mentioning the first century AD polymath Pliny the Elder, for instance, he says, “He said that he valued first-hand reports, but didn’t mean it”), very much including his contrary hero, whom he lauds very perceptively for his groundbreaking physiological explorations but nevertheless resists the urge to make warm and cuddly:

Aristotle says that tortoises hiss, copulate and have shells. They also have large lungs, small spleens, simple stomachs and a bladder; male tortoises have internal testes and seminal ducts that converge in an ‘organ’. So he evidently dissected one. At least one tortoise came under his knife while still alive for he also says that if you cut out a tortoise’s heart and then put its shell back on it will keep wriggling its legs. Aristotle doesn’t have pets; he has specimens.

Leroi takes his readers through the whole gamut of the natural world as it’s addressed by Aristotle, from animals to embryology (“following Aristotle’s precepts if you want to father a daughter first take a long, cold shower, try your best and reflect that it beats ligating a testicle”) to earth science to cosmology, and before Leroi has gone on very long, he’s certainly made his case that we ought to regard Aristotle’s science-writing on at least a par with his philosophizing. And we quickly realize that Leroi, a professor of evolutionary biology at Imperial College London, is no slouch himself at writing science for the general reader. Take for instance the elementary question of why old age exists at all. “Aristotle sidesteps the question,” Leroi tells us. “He says that it is just the ‘nature’ of living things on earth to age and die. All that remains to be discussed is how and when. Darwin sidestepped it too. He said even less. The omission was glaring.” The current thinking on the subject is then adroitly illuminated:

Modern evolutionary biologists demur. They point out that ‘good of the species’ arguments are weak and at best a last resort. They argue instead that ageing is the result of the absence of natural selection. Most animals and plants have a constant risk of death from external causes such as accident and disease and since the dead cannot reproduce old age is invisible to natural selection. This invisibility means that bodies are designed to work when young but fall apart when old. When, therefore, we ask what ageing is for we must give the peculiar answer that it isn’t foranything; it is, instead, the evolved consequence of there being no reason to stay alive.

Wonderfully, The Lagoon ends with a series of appendices in which Leroi presents “some of Aristotle’s data and models as he might were he writing now: in tables and diagrams.” This is a fantastic, eye-opening innovation, a perfect capstone for a book that does so much to level the playing field for Aristotle the scientist (even the first scientist). Leroi assumes that the scientists looking at some of his simulations “will only wonder how Aristotle got as far as he did using mere words.” To which Leroi supplies, “I would ask them to remember that although he was smart, he did live a long time ago.” Anybody reading The Lagoon will come away feeling he didn’t live nearly as long ago as they used to think.

 

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New Scientist

Was Aristotle the inventor of science? by Nicolas Rasmussen, 22.09.14

The ancient Greek philosopher deserves our homage, and Armand Marie Leroi delivers it in his edifying and excellent book

EVERY generation of biologist must rediscover Aristotle for itself, to paraphrase Armand Leroi in a BBC documentary, Aristotle’s Lagoon.

Four years on, Leroi, a biologist at Imperial College London, has written a book with nearly the same name. The full fruits of the author’s decade of immersion in Aristotle, it represents both Leroi’s personal discovery of the ancient Greek and a quest to recover his science for biologists today.

Once a highway, this path has been trodden by only a few life scientists in four generations. And in taking it, the author retraces Aristotle’s footsteps to Kalloni lagoon on the island of Lesbos, where the philosopher studied nature, providing charming vignettes from his visits there.

There is a serious purpose, too. Aware that scientists tend to distort past thinkers by imposing present conceptions and values on them, Leroi argues that today’s biologists can think like Aristotle because he forged their basic concepts, and because nature shows us the same phenomena. But to best understand Aristotle, a biologist must see what he saw in Lesbos.

The Lagoon is an intellectual homage – an admiring, deeply researched and considered reconstruction of Aristotle’s thinking about living things. The effort to get inside his head seems driven by a heartfelt sympathy, a sense of wonder about life on Earth shared across 2300 years, and by the modern scientist’s urge to give credit where credit is due.

And for Leroi, Aristotle deserves credit for nothing less than inventing biology – perhaps even science. Earlier philosophers, like his teacher Plato, deduced stories about the fundamental causes of natural phenomena from first principles. But physicians in the empirical tradition, to which Aristotle was exposed by his physician father, learned how to predict the course of disease from observation. Aristotle was arguably the first to attempt an evidence-based natural philosophy (or “science”), melding empiricism with logic.

The book is structured with major sections corresponding to topic areas in Aristotle’s work, such as taxonomy, nutrition, or cosmology, each broken into half a dozen short chapters, often containing Leroi’s Lesbos experiences to make the natural phenomena accessible and intriguing. For example, we learn about the vigorous argument he observed among taverna patrons over whether sardelles and papalinas are really the same fish (they look similar but taste different, and live in different waters). This example of the classification problem nicely introduces Leroi’s discussion of Aristotle’s taxonomic system.

The prose is so lively, the thinking so lucid, and the use of such devices so artful, one might not notice it all adds up to a 500-page systematic analysis of a massive, dry, sometime jumbled philosophical corpus from a profoundly alien society. That many readers will come away entertained, and with even a slightly better understanding of Aristotle would be a major literary feat even if the book did not offer significant original contributions.

But it does. Take Leroi’s account of Aristotle’s concept of soul, psyche. It is well thought through, closely argued on textual evidence, and innovative. As my wonderful teacher, classicist Arthur Adkins, said, psyche was “for Greeks only the difference between a dead rabbit and a live rabbit”. In other words, to explain psyche is to explain life.

Leroi shows that Aristotle was no vitalist, in the sense that he required nothing more than ordinary matter and its properties to explain life. He understands that for Aristotle the soul was its form (eidos, which can also mean species), the order of a creature’s material – a pattern of activity constituting its life.

Organisation as life is a view remarkably close to modern biology: for Leroi, biology is all about mapping the body’s regular material transformations. I am sympathetic to his effort to credit Aristotle with something very like modern biological insights, and indeed, I find Leroi’s arguments that Aristotle invented the concepts of metabolic networks and feedback control plausible.

Leroi offers another innovation in finding a “dual-inheritance” theory in Aristotle’s writing, resolving the conundrum of form (eidos again) coming only from the father and the undeniable phenomenon that children resemble both parents. Thus, for Aristotle the movements of the generative fluids of female and male can, without major self-contradiction, transmit details of form (like Socrates’s snub nose) less significant than those defining the species, imparted by the father.

Elsewhere in Leroi’s discussion of reproduction, we read: “What is the immediate source of the design that we see in living things? It is the information that they inherit from their parents.” Or, to paraphrase the BBC documentary again, Aristotle taught that material self-assembles into organisms only with the help of information.

Here Leroi goes too far. Despite acknowledging the danger of anachronism, he is actually likening the Aristotelian concept of eidos to modern biology’s notion of genetic information. Biology’s concept of information is less than a century old, deriving from computer science. Psyche, the realisation of a creature’s eidos, was an activity, more like an oscillation than a formula or code.

 Furthermore, the Greeks did not have the problem vitalism and materialism both answer. Our premise that ordinary matter must be utterly passive stems from Reformation Christianity. Without this expectation, the difference between dead and alive is not as radical as we perceive. For ancient Greeks, all matter was dynamic, living matter only more so.

From this perspective we can see why Aristotle accepted spontaneous generation without anxiety: putrefying matter, already seething with change, could accidentally fall into self-perpetuating patterns of activity and thus spin off organisms –maggots in corpses or oysters in mud. Insufficiently attuned to the animism (or more accurately, hylozoism) of the Greeks, Leroi unfairly scolds Aristotle for inconsistency with his own metaphysics and his mature theory of reproduction.

Such quibbles are not meant to detract from this marvellous book. Leroi’s Aristotle is a fit hero for the biological century, and The Lagoon is a work as important to a historian and philosopher of science as it is informative to a biologist and entertaining to the general reader. As compelling as Stephen Jay Gould’s best work, it will long outlast most nature writing of recent years.

 

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Financial Times

Aristotle’s biological studies on Lesbos and their intriguing echoes in modern science by Sarah Bakewell, 29.08.14

Twenty-three centuries ago, Aristotle of Stagirus laid out a landscape of logic, physics, metaphysics, aesthetics, poetics, politics, psychology and natural science that would dominate western intellectual history for an astonishingly long time.
Only a minority of his 200-odd treatises survived, yet they made Aristotle the giant whom everyone had to acknowledge or battle against. Bertrand Russell observed that almost every major intellectual advance in history had begun with an attack on some Aristotelian doctrine. Aristotle seemed big enough to absorb it all but perhaps now he really is exhausted at last. Few still read him at length, and scientists are unlikely to cite him. Famous though his name is, he is no longer a living presence.

Armand Marie Leroi, the developmental biologist and broadcaster best known for an outstanding book on mutants, now sets out to bring Aristotle back to life, at least for a few hundred pages, to see what he has to offer. In The Lagoon he wisely focuses on just one direction of Aristotle’s endeavour (biology), on one period of his life (a two-year interlude beginning in 345 BCE), and on one place. He thus roughly observes the three classical rules of dramatic unity, as laid down by – who else? – Aristotle.

The place is the super-fertile, super-salty Kalloni lagoon on the Greek island of Lesbos. Aristotle lived there for two years with his new wife Pythias and his botanist sidekick Theophrastus – who comes across as something of a long-suffering Madge Allsop to Aristotle’s Dame Edna. Theophrastus plodded along making notes of the greenery, while the flashier Aristotle, festooned with rings and given to fussing over his hairstyle, dissected cephalopods, vivisected chameleons and piled up the facts that would fill the nine books of his Historia animalium.

Facts! Aristotle loved them. Leroi reports that there are around 9,000 distinct empirical claims in the Historia animalium, and descriptions of some 500 species. Many of the latter come not from the lagoon but from reportage, reading and Aristotle’s own later explorations, but those two years of fieldwork were his starting point: his years of marvels. Leroi spends time around the same lagoon and the island’s seas. He dissects the same creatures (“We place our cuttlefish – flaccid, pale, glutinous – on the table”) and speaks to local fishermen, some of whom apparently share Aristotelian ideas about the spontaneous generation of eels.

Aristotle was interested in everything: hyena genitalia, snail stomachs, seals’ flippers, elephant flatulence. Moreover, he wanted to understand why things were as they were. The facts generated questions, “hundreds of them”, says Leroi: “Why do pigeons have a crop and elephants a trunk? Why do eagles lay so few eggs, fish so many, why are sparrows so salacious?”

Aristotle’s great innovation was his initial leap away from his teacher Plato, who thought natural observations were the very things we must ignore if we want to know transcendental truth. Aristotle rejected that. He started with phainomena or appearances, which he amassed in quantity and then sorted into whatever order looked meaningful. Out of these orderings came speculations about cause and purpose. For example, having observed that birds had beaks and gizzards, he guessed that the gizzards were there because of the beaks, which ground food less efficiently than teeth.

Leroi stresses that none of this should be confused with modern scientific method, still less with Darwinian evolutionary theory. The similarities with Darwin, our own biological colossus, fascinate him, and he notes that Darwin did read Aristotle – though late and probably not thoroughly.

But Aristotle cannot be seen as struggling towards Darwinism; his vision of variation and gradation between species was static, not evolutionary. He also did no experiments in the 17th-century sense. He observed “things as they are” but did not set up artificial situations to test hypotheses, a notion that required Aristotelian foundations plus many more years of rebellion and new thinking. Yet Aristotle can be considered the first true scientist by virtue of two great things: his attention to the world as it presents itself – to the phenomena – and his drive to understand causes.

The Lagoon is compelling, sometimes contentious, and always thought-provoking. It ends with an intriguing coda: recent researchers in fields such as genetic bio­logy may be reverting to Aristotelianism after all. Even 10 years ago, they took a strictly 17th-century experimental approach, knocking out or activating a single gene, then looking to see what resulted. But with new “Big Data” techniques, they often collect thousands of metabolites or proteins, arrange them in a way that seems promising, then seek a causal narrative that makes sense of them. This is precisely Aristotle’s way, and, as Leroi remarks, it is the method most appropriate when opening up a new world of investigation. This was the case for Aristotle on Lesbos, and it is the case again now.

Thus, The Lagoon turns into a reflection on the nature of science itself. It celebrates what is most admirable in the Aristotelian tradition: its appreciation of what is actually there. “Ask Aristotle: what, fundamentally, exists?” writes Leroi. “He would not say – as a modern biologist might – ‘go ask a physicist’; he’d point to a cuttlefish and say – that.” Plato had no idea what he was missing.

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Saturday Times

The cleverest man who ever lived by Peter Jones 23.08.14

“All men, by nature desire to know” said Aristotle, and Dante called him the ultimate know-it-all. The dining professors in the dialogues of the Deipnosphistae, from the 2nd century AD, exasperatedly agreed. “Where did Aristotle get all this stuff from? exclaims Cynulcus. “It s the sort of thing comic poets “Marvels for Morons”, and goes on to list reams of “rubbish that this “drug dealer” had gathered about the lifespan of bees, non-copulating periwinkles and the evil habits of pop-eyed men. Cynulcus, would have surely enjoyed the Renaissance taunt that Aristotle was a cuttlefish hiding behind his own ink.

Aristotle (384-322B) of whom his teacher Plato said “Here comes the Brain”, did not think that was anything to be ashamed of. “Everyone says something true about the nature of things but while they may contribute little or nothing individually, a great deal is amassed by bringing it all together.” Clearly mere information does not a scientist make, but when it is seen as data to be analysed and so contribute to understanding, it is a quite different kettle of periwinkles. Armand Leroi, professor of evolutionary developmental biology at Imperial College, argues that Aristotle was the fist scientist and this work in biology which makes up a bout a third of the surviving corpus, made the great breakthrough.

Aristotle dissected creatures observed them minutely, drew and collated physiological conclusions, identified emerging patterns and correlated all this information against the creature’s lifestyle to explain the cause and so the true nature of their structures. The result, says Leroi, was one of the most important advances in understanding our world: the first classification of animal life (he identified 495 species) into a “nested hierarchy.”

Aristotle expounded his famous “four causes”, for which Leroi rightly prefers “questions”, which he applied to his analysis of any creature: (i) what is its goal, and so how does it adapt, develop, reproduce and so on? what is it is formal cause, ie, the information it receives from its parents? (iii) what is it made of? (iv) what causes it to change and move? Modern biology, Leroi suggests, still thinks in terms of these four, expressed today in evolutionary biology, genetics, biochemistry / physiology and biology / neurophysiology.

Likewise, Aristotle saw that correlation did not automatically equal causation. There would always be unknowns, or the example that threw a spanner in the ointment. But if absolute certainty was impossible, he argued, the closest empirical approximations would suffice. It remains a valid principle.

He invented the principle of “conditional necessity”. If your goal is X, for which you need tool Y, then Y had better fulfil condition Z to meet your goal. He applied this argument to explain the elephant’s trunk: the animal needed to breathe (X); so it needed a nose (Y); but it was a heavy, slow moving, water-loving creature that lived in swamps, always running the risk of stumbling into deep water; so it needed a snorkel-like nose. Incidentally, this was an inspired guess: we now know that the elephant did, in fact, evolve from an aquatic mammal.

And so Leroi takes us through Aristotle’s work, finding hints of modern thinking everywhere, from the concept of nutritional economy and cybernetics (via Aristotle’s concept of “soul” as a sort of information system) to even a sniff of DNA. None of which, of course, prevented Aristotle from getting a great deal hopelessly wrong. “The eel,” he proclaimed “is neither male nor female and produces no offspring…eels do not come into being by copulation nor do they lay eggs.” Wrong on all four counts. Equally wrong is his claim that hedgehogs copulate face to face to avoid each other’s spines, bears adopt a missionary position and camels take all day over it; that snakes eat catfish, flies generate spontaneously from rotten meat (even Homer knew that flies bred worms in dead bodies) and women have fewer teeth than men. But it is the methodology and what he got so dramatically right that is important.

However, that methodology – amassing data, looking for patterns in it, and inferring firm, logical causal associations – is not unique to science. Historians do it all the time. Much more importantly, Leroi admits that science’s touchstone, is the testing of hypotheses by experiment (as Francis Bacon in the 17th century argued). Aristotle never did that. For example, he simply accepted Empedocles’ view that the cosmos consisted of four material principles: earth, air, fire and water. It still astonishes that the cleverest man who ever lived should have never thought to test so bizarre a hypothesis.

But this in no way diminishes the brilliance of Aristotle’s intellectual achievement in biology or any other topic he investigated: from political theory (in eight books), astronomy and Homeric problems (six books) to proverbs, the Nile, ethics, physics, metaphysics, mechanics, rhetoric (the art of persuasion), literary criticism and much more, let alone the rules of logic, which he actually invented – an unparalleled human achievement.

Nor indeed does it diminish the excellence of Leroi’s book. Divided into 114 brief, very readable sections, each clearly elucidates a step in the argument, often using lyrical descriptions of, and examples from, the very lagoon on Lesbos where Aristotle did so much of his work. The Lagoon bubbles with enthusiasm for its subject, making an absolutely gripping read out what might seemed the most unlikely materials.

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Observer

What the ancient Greek did for us by Adam Rutherford 24.08.14.

seal460x276We see further by standing on the shoulders of giants. When isasc Newton expressed this idea, he also exemplified it: he was effectively quoting the 12th century philsopher Bernard of Chartres. Who was probably making reference to the classical Greek myth of Orion, the temporarily blinded hunter who carried his diminutive servant, Kedalion, in order to see ahead. The notion that we are indebted to the knowledge of the past is a deeply revered cornerstone of our understanding of the universe, particularly in the sciences.

In this lush, epic and hugely enjoyable book, biologist Armand Marie Leroi explores the idea that it was another ancient Greek giant whose shoulders we may all stand upon. In his mid 30s, around 346 BCE, Aristotle exiled himself from Athens to islands in the Aegean, where he spent time thinking and writing about nature, possibly near a lagoon on Lesbos. We primarily know him as a philosopher, but here, Aristotle’s biological output was titanic: he dissected dozens of species and compiled the birst biology textbook, Historian Animalium. It is this body of work, Leroi argues, that continues to percolate through scientific thought today.

There’s a great temptation in analysing historical scholars to suggest that they were “anticipating” things to come. Leroi does a splendid job of avoiding hagiography of his hero. Aristotle’s contention that seals are mutated quadrupeds is true in a purely Darwinian sense: they are mammals, evolved from terrestrial four-legged mammals. but Leroi points out that that this is not Aristotle’s thinking. The idea that mutation from common ancestors was the cause of species is not present in any of Aristotle’s work. he was not predicting evolution, nor did he once consider the Darwinian truth.

Leroi happily highlights Aristotle’s many errors, some trivial – the position of the dolphin’s mouth, most of his analysis of eels – and some conceptually flawed. In 1871, Darwin considered the origin of life occuring in a “warm little pond”, if all the right ingredients were present and invigorated by a bolt from the blue. This became the foundation of the concept of “primordial soup” and that quotation is often held up yet again to show Darwin’s undoubted genius. Alas, primordial soup is a flawed concept for the origin of life and Darwin’s speculation was mere idle pondering. Aristotle’s big conceptual mistake was also about the origin of life. He suggested that new life in certain instances arose from non-life, a related idea called “spontaneous generation.” This remained the prevailing view until Louis Pasteur killed it dead in the 19th century with that quintessential scientist’s tool – the experiment.

Leroi is a beautiful writer and it’s been too long, a decade, since his last outstanding book, Mutants. The ease with which he transports the reader both to Aristotle’s world and the contemporary Aegean is enviable to the point of being alarming. Maybe The Lagoon is a new genre: classical scientific travel. There are so many lines of virtuouso prose that to single one out seems churlish. But this typical sentence touched and stayed with me for over 500 page. “The shell had sat in the sunlight of a bathroom windowsill, buried in sedimentary layers of my father’s shaving talc, seemingly forever.”

The richness of the words can be overwhelming at times. But this is a minor criticism – The Lagoon is grand, but not grandiose, and probably should be consumed at leisure, poring over the words and illustrations, in the evening sun, with wine.

I am perpetually wary about placing scientists on pedastals. For me, the only Titan is Darwin, and the others merely Olympians, and Darwin was scrupulous in his humble acknowledgements of this intellectual forebears. The concepts of giants’ shoulders summons some sort of linear of great men (and they are always men) standing above their peers, inheriting the brilliance of an intellectual ancestor. Even though we continue to hallow the Nobel prizes, this is an age in which we have tried largely to eschew the worship of these figureheads in the history of science.

This whiggish view of progress led by gentlemen scientists punctuating the intellectual doldrums is a simplistic clean narrative, but it’s just not how science works. The shoulders are broader than individuals: we build on the works of all who proceed. Does all science rest on Aristotle’s base? Well, no, and Leroi doesn’t argue that. But his influence echoes through history and his rediscovery for my generation of scientists is appreciated. Science is a modern term, but while Aristotle was a philosopher, he also smells like a scientist to me: his craving for data in all forms – anatomical, reproductive, taxonomic – his seemingly anachronistic empiricism about biology; these are classic symptoms of our disposition.

This big sumptuous book made me hungry. Intellectually, to learn about the classical world’s take on what we now call science. but it made me viscerally and literally hungry: for grilled fish, oysters, figs and meze and to sit on the shores of the Aegean idling at barnacles and cuttlefish copulating in the spume. Not bad for a science book.

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Sunday Times

Gifted Greek by James McConnachie 24.08.2014

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If you ever thought that Aristotle was a fact-stacking bore with a pedantic turn of prose and mind, then this brilliant book, perfumed with the smell of sardines frying on a Greek dock, will put you deliciously straight. It depicts Aristotle as the first true scientist, a man who got his hands dirty dissecting everything from eels to catfish (not to mention vivisecting a leg-wiggling tortoise) and came close to beating Darwin to a theory of evolution.

“The Philosopher”, as he was known to the Middle Ages, was born in 384BC, and studied under Plato in Athens before becoming Alexander the Great’s tutor, then returning to Athens to write copious lecture notes that profoundly influenced Arab and Western thought. This much is well known. His impact on biology, however, is relatively obscure.

Armand Marie Leroi is a professor of evolutionary developmental biology at Imperial College London, and this book is designed to reclaim Aristotle’s scientific reputation. There are two Aristotle he says: “The first sat under a tree in Piraeus picking holes in Plato’s theory of definition, the second on a quay in Lesbos prodding a pile a fish.”

Rejecting his teacher’s idealistic speculations, Aristotle turned his attention to the natural world – specifically, Lesbos’ Kolpos Kallonis. This remarkable sea, the lagoon of Leroi’s title, was the source of the master’s richest observations and deductions – on the genitals of sea urchins, the bills and legs of sea birds, the blowholes of dolphins. Just as Darwin had his Galapagos islands, Aristotle had his lagoon.

His knowledge of it is intimate. The dandified philosopher (Aristotle “dressed rather too well and fussed about with his hair”) must have also “plundered fish markets and hung around wharves talking to fishermen”. Leroi does the same. He scuba dives in the lagoon, chats with taverna owners and shepherds, and has his shoes pecked at on the docks by a one-legged pelican, Odysseus.

All this results in not just a charismatic book, but one that places Aristotle in a freshly Aegean context. Of course, Leroi also explores Aristotle’s though in the context of his own specialism: evolutionary biology. It was Aristotle, he argues, who first saw that a bird is not just a cabinet of parts, but a toolbox on the wing.” Rather brilliantly, he reinterprets Aristotle’s version of the soul not as a Christian style divine spark, but as a shaping inner force responsible for the regulation of the body’s processes and goals, including survival and reproduction.

Francis Bacon, and the Enlightenment philosopher-scientists who followed him tried to kill of Aristotle. They laughed at his wider tales, drawn from travel books or hearsay – such as the notion that Ethiopians produce black semen. [AML note – Aristotle dismissed this Herodotean tale.] They argued that his experiments were mere observations and his explanations absurdly awry. It is true that he gets some things spectacularly wrong – notably the idea that flies spontaneously generate from rotting meat and human testicles are mere counterweights equivalent to the weights that weavers use to keep the warps of their looms in place.

Leroi shows that he got a great deal right too. The diagrams that might have accompanied his works are all lost, but “if you ferret through his texts”, he says, you could draw a working model of the modern metabolic system. Aristotle even grouped animals into related families and worked out that they inherited their form from their parents, and were designed to flourish in particular environments.

He may not have made the final leap, to the idea of natural selection, but Leroi believes that Aristotle’s scientific style is only now coming of age. Bacon believed that Aristotle’s interest in “final causes” – the purpose of things – was unscientific. Yet this is now precisely what adaptational evolutionary biologists now study. Bacon thought little better of Aristotle’s interest in “formal causes” – the forces that make animals take the shapes that they do. Yet this is what preoccupies geneticists. Above all, Leroi shows, science today trawls through reams of data for patterns and explanations in precisely Aristotle’s manner. We can only recognize Aristotle’s achievements, he concludes, “because we have caught up with him.”

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The Diary: Armand Marie Leroi

Weekend Financial Times 23.08.2014

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Literary Review

Collecting Cuttlefish on Lesbos by Patricia Fara 08.2014

Aristotle and Plato – their names conjure up thoughts of stone busts showing serene elderly men with long curly beards. Perhaps these revered Greek philosophers really did look like that at some stage in their lives, but according to the evolutionary biologist Armand Marie Leroi, Plato was so irascible that he once threw his favourite dog down a well and his student Aristotle was an overdressed dandy who compensated for his small eyes and thin legs by sporting plenty of jewellery and an elaborate hairstyle. Leroi also sets out to challenge traditional impressions of their intellectual activities. He makes little mention of the usual philosophical sound bites – shadows on the walls of a cave or syllogistic puzzles about the mortality of men. Instead, in Leroi’s revisionist version of the Academy in Athens, Plato emerges as an anti-scientific mythmaker mindlessly obsessed with numbers, while Aristotle is cast as the world’s first scientist and the founding father of biology.

As the title of Leroi’s latest book, The Lagoon: How Aristotle Invented Science, suggests, Aristotle is Leroi’s scientific hero, the essential precursor of Georges Cuvier, Charles Darwin, Gregor Mendel and all the other great men of the life sciences (virtually the only reference to women occurs when the author exchanges conquest notes with a scientific colleague in a harbour café). Even when admitting that Aristotle got it wrong by modern standards, Leroi finds ingenious reasons to let his hero off the hook. Earlier speculative philosophers, he writes, had condescendingly viewed the world from the mists swirling around Mount Olympus, whereas Aristotle stepped down to investigate the realities of life on the shore.

Leroi clearly adores Greece and he uses his detailed local knowledge to splendid effect, evocatively re-creating the experiences of this peripatetic philosopher, who wandered to the far reaches of the empire and for a while was employed as tutor to the young Alexander the Great. Much of Aristotle’s zoological research was carried out on the island of Lesbos; Leroi adopts lavish tourist-brochure prose to depict not only the sun-baked scenery but also the coloured plumage of the birds, the iridescent insides of a cuttlefish and the spiral whorls of a nautilus shell. He regales his readers with the gastronomic delights that can be experienced only by eating fish freshly plucked from the sea (including esoteric parts of sea urchins), cleverly using what might otherwise seem culinary diversions in order to weave together accounts of modern classification, mythological creatures and Aristotle’s own approach to species distinctions. While Leroi would like to see Aristotle as a proto-Linnaean, some local fishermen explain to him that, for them, taxonomical categories are never absolute: how they label any individual fish depends not only on its appearance, but also on other factors affecting its taste – where it was caught, its age, its diet.

Aristotle was an exceptionally talented observer; he may have lacked a microscope, but he looked closely, dissected carefully, described clearly and was evidently familiar with non-European fauna. As if a chameleon were laid out in front of us, he makes us see that its body

“is rough, like a crocodile’s. The eyes, very large and round, are covered in skin like the rest of the body and located in a cavity: in the centre is a small hole through which it sees and which is never covered by skin … Its change in colour occurs when puffed up, when its colour is actually black, not unlike a crocodile, or green like a lizard with black spots like a leopard … Even after it has been cut open completely, the chameleon continues to breathe for a long time and a tiny motion remains around the heart.”

At times, however, Aristotle relied on facile assumptions or allowed mythical stories to creep in. Despite mastering the complexities of a cuttlefish’s abdominal tract (it defecates on its head) and the ambiguities of hyena genitals (don’t ask), he miscounted the number of vertebrae in a lion’s neck, declared that ostriches have hooves and maintained that asses are well known to wage war on lizards, which prevent them from eating by climbing up their nostrils.

The Lagoon is a book written by a scientist for other scientists – or rather, for anyone who shares Leroi’s blithe confidence that only science can yield true and useful knowledge about the world. Like those old films where the goodies and the baddies are distinguished by the colours of their hats, Leroi’s world is split into two camps. While Aristotle leads scientists on the route to progress, Plato – along with most other philosophers – is relegated to the side of the losers. Fortunately for Plato, Aristotle read his great dialogue about nature, Timaeus, and ‘transmuted its conceptual lead into the gold of scientific explanation’.

As Leroi observes, science is cumulative. The path towards the future is influenced by the roads already travelled – or, as John Maynard Keynes put it, we should think of Isaac Newton not as the first great scientist, but as the last man to view the world through the eyes of his predecessors. Leroi is absolutely right to say that even those sections of Aristotle’s work we no longer believe to be correct have affected the knowledge that we have today. Where Leroi goes wrong is to deny that the Bible or any other religious texts have been important for science. The Aristotelianism prevailing in Europe for many centuries was a Christianised version that Aristotle himself might well have rejected. Whatever the intentions of their original authors, accounts in Genesis and elsewhere have had a profound impact on science: it is no coincidence that the big-bang explanation of creation feels intuitively more comprehensible than any Aristotelian-style steady-state theory.

Leroi concludes with Aristotle’s famous pronouncement: ‘All men, by nature, desire to know.’ Interpreting this as a paean to the beauty and value of science, he makes his hero seem prescient by squeezing his concepts into modern formulations. Another way of reconciling the ancients with modernity is to recognise our own limitations and acknowledge that scientists today are no more successful than were the Greeks in answering the truly big questions: How was the universe created? How can life emerge from matter? How are mind and body related?

AML Replies

When Patricia Fara writes that I champion Aristotle’s science at the expense of Plato’s metaphysics, she is perfectly correct. She is also correct in supposing that this is a book written by a scientist for scientists. She is incorrect about much else.

She writes that Plato threw his dog down a well. No, he didn’t — his nephew, Speusippus, did (maybe). She says that Aristotle wandered to the far edges of Alexander’s empire. Really? I claim that he was never out of sight of the Aegean. Much more seriously, she attributes to me the view that Aristotle was a proto-Linnaean. But I argue that he wasn’t. 19th century taxonomists such as Cuvier certainly saw him as one but they were mistaken. As for her complaint that there are no women in the book, well, that’s because it’s about ancient Greek biology, and in ancient Greece there were no female biologists.

Most seriously of all, she accuses me of making my hero seem prescient by squeezing his concepts into modern formulations. But, again and again, I warn against reading him so. Rather, my aim is to understand what he is getting at — to penetrate the abundant obscurities of his vocabulary and reasoning. That requires an act of translation into modern vocabulary — a very different thing from “squeezing concepts”.

The hostility is naked. What’s behind it? Who is Patricia Fara? She’s a historian of science from Cambridge. To get a sense of what she’s about, read the late, great Norman Levitt’s review of her 2009 book, conveniently posted on Amazon. It seems that her review of my book is just another blow in her campaign against genius, science and men. Levitt noted how this hostility led her into carelessness; it has done so again.

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Publisher’s Weekly (Starred Review)

Leroi (Mutants) lovingly rescues the reputation of Aristotle’s alternately meticulous and bizarre studies of animal behavior from the ruins left in the wake of derision during the Scientific Revolution. Leroi brings a modern sensibility to, yet evokes an air of timelessness with, his gorgeous descriptions of the ecology of the fishing villages of Lesbos where Aristotle both carefully dissected fishes and gave credence to the most fantastic of animal folk stories. His Aristotle creates systems of categories in a determined search for the reasons behind the existence of living things in their myriad forms. Leroi smoothly drops readers into Aristotle’s world of concocting elements and vital heat, of formal causes and nutritive, sensitive, and rational souls. He muses on how close Aristotle came to the ideas of Linnaeus and Darwin, having collected so much of the kinds of data they would eventually need despite being constrained by core axioms that saw animal types as diverse but essentially static. Leroi credits Aristotle with the most basic tenet of empirical science—to understand the world, look first and then try to explain what you see—but resists crediting him with textually unsupported prescience, which highlights beautifully the fact that ideas can be self-consistent, elegant, yet entirely wrong. Illus. (Oct.)

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Nature

Roberto Lo Presti applauds a brilliant reappraisal of Aristotle as the father of observational biology. 21.08.2014

AristotleAristotle is considered by many to be the first scientist, although the term postdates him by more than two millennia. In Greece in the fourth century BC, he pioneered the techniques of logic, observation, inquiry and demonstration. These would shape Western philosophical and scientific culture through the Middle Ages and the early modern era, and would influence some aspects of the natural sciences even up to the eighteenth century. Armand Marie Leroi’s reappraisal of this colossus, The Lagoon, is one of the most inspired and inspiring I have read. It combines a serious, accessible overview of Aristotle’s methods, ideas, mistakes and influence with a contextualizing travelogue that also found expression in Leroi’s 2010 BBC television documentary Aristotle’s Lagoon. Leroi’s ambitious aim is to return Aristotle to the pantheon of biology’s greats, alongside Charles Darwin and Carl Linnaeus. He has achieved it.

Leroi, an evolutionary developmental biologist, visits the Greek island of Lesvos — where Aristotle made observations of natural phenomena and anatomical structures — and puts his own observations in dialogue with those of the philosopher. It was in the island’s lagoon of Kolpos Kalloni that Aristotle was struck by the anatomy of fish and molluscs, and started trying to account for the function of their parts. Leroi’s vivid descriptions of the elements that inspired Aristotle’s biological doctrines — places, colours, smells, marine landscapes and animals, and local lore — enjoin the reader to grasp them viscerally as well as intellectually. Aristotle’s time on Lesvos was only a chapter in a life of discoveries, and Leroi covers those signal achievements with breadth and depth. He details the theoretical and methodological principles governing the functional anatomy of species from pigeons to tortoises, discussed by Aristotle in On the Parts of Animals, as well as the descriptive zoology expounded in his History of Animals. For instance, Leroi explores Aristotle’s theory of causation, based on the distinction between material, efficient, formal and final causes. He looks at the philosopher’s views on the directedness of natural phenomena and the role played by necessity and hazard. He sketches out the theory of four elements (fire, air, water and earth) as the prime constituents of natural bodies. And he looks at the theory of soul and its relationship to the body — through which Aristotle accounted for aspects of physiology and psychology, from nutrition to rational thinking.

Fascinating chapters are devoted to Aristotle’s gradualist conception of the natural world and living things — perhaps best expressed in the saying natura non facit saltum, or ‘nature does not make jumps’. Also covered is his theory of sexual generation and transmission of hereditary traits, which he expounded in the masterful On the Generation of Animals. Despite a number of mistaken assumptions (such as the lack of a female ‘seed’), this theory encompasses a huge number of valuable observations and insights that laid the foundations of modern embryology. The Lagoon traces other ways in which Aristotelian thought has permeated Western science. Leroi charts its influence on Renaissance anatomists and physiologists. The English physician William Harvey’s discovery of blood circulation, for instance, was largely inspired by Aristotle’s biological ideas, especially the concept of the heart as the most important organ in the body, as well as by Aristotle’s empirical emphasis on investigation and demonstration. Leroi shows how masters of comparative anatomy including Georges Cuvier (1769–1832) took inspiration from Aristotle in describing and comparing the parts of animals in light of their function as well as of their shape. He compares Aristotle’s theories with the thinking of taxonomists such as Linnaeus, of Darwin on evolution, and of the twentieth-century fathers of systems theory and cybernetics such as Walter Cannon and Norbert Wiener.

Leroi is careful not to represent Aristotle as a precursor in crude terms, or to read him through inappropriate contemporary lenses. Instead, he highlights aspects of Aristotle’s doctrines that still ‘speak’ to contemporary scientists, and that have been illuminated by modern scientific understanding — for example, Aristotle’s emphasis on direct observation and dissection. The philosopher argued, Leroi explains, “that ‘knowing’ in the sense of ‘perceiving’ is the foundation of ‘knowing’ in the sense of ‘understanding’”. As Leroi acknowledges, decades of scholarly effort by philosophers and historians such as Allan Gotthelf and James Lennox have gone into the reassessment of Aristotelian biology and its effect on the history of Western science. In this respect, the book broaches no new questions, and brings no new perspective to the heated debates among Aristotelian scholars. But that is to miss its point. The Lagoon is a wonderful introduction to Aristotle’s biology, which specialists will also enjoy. Every page is a reminder of the great beauty that we can experience by seeing the world through Aristotelian eyes.

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Kirkus (Starred Review)

Leroi (Evolutionary Development Biology/Imperial Coll. London; Mutants: On the Form, Variety and Errors of the Human Body, 2003) calls on his expertise and his experience as a BBC science presenter to explain why Aristotle’s writings on science are still relevant today.

The author introduces readers to Aristotle’s work in the field of biology and shows where it accords with modern understanding and where it is wildly off-base. Although best known as a philosopher, Leroi explains that the major body of Aristotle’s work (much of which has been lost) dealt with natural science. In his search for the causes of change, the philosopher embarked on an ambitious project. “By the time he was done,” writes the author, “matter, form, purpose and change were no longer the playthings of speculative philosophy but a research programme.” Aristotle based his groundbreaking efforts to discover the workings of nature on a wide variety of sources, including his own observations. In addition to humans, a whole host of animals came under his purview and led him to classify different species, thus anticipating Carl Linnaeus in the 17th century. Leroi shows how Aristotle pondered the common features of all living creatures, as well as their divergence, and attempted to account for their functional differences. According to the author, Aristotle’s line of thinking led him to attempt to understand the operation of “five interlocked biological systems”—the nutritional system, thermo-regulation, perception and cognition, and inheritance—and indirectly influenced Darwin’s discovery of the theory of natural selection. He dismisses critics who fault Aristotle for being unscientific because he did not conduct experiments using controls. Many of his assumptions proved to be wrong, but this is to be expected in a new field. Leroi compares Aristotle’s effort to assemble a huge volume of data to the practices of current scientists in the “age of Big Data.”

A wide-ranging, delightful tour de force.

 

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The lagoon – book

Leroi AM. 2014. The Lagoon:  How Aristotle invented science

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Posted in books, history of science

State-of-the-art-metabolomics for worms

Geier FM, Fuchs S, Valbuena G, Leroi AMBundy JG. 2013. Profiling the metabolic signature of senescence. Methods in Molecular Biology 965:355-37

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Posted in ageing, metabolism, peer-reviewed articles

What is your favourite deep, elegant or beautiful explanation?

Edge 2012: annual question.

Posted in general evolution, history of science, journalism

Royal institution 2012: Darwin tunes

Talk with Bob MacCallum at the RI
Tuesday 11 September 2012

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British humanists association 2011: Darwin day

Talk on neo-eugenics (audio)

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Sage centre for the mind UCSB 2011: distinguished fellows lectures

lectures

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Googleplex 2010: sci foo

Discussion of neo-cantometrics.

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Serpentine gallery 2010: map marathon

Discussion with John Brockman, Lewis Wolpert and Hans Ulrich Obrist.

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DarwinTunes – radio programme

DarwinTunes. 2012.

BBC Radio 4 (writer / presenter)

Producer: Ania Lichtarowicz

1 x 30

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Posted in evolution of culture, tv & radio

Darwinian evolution of music

MacCallum RM, Mauch M, Burt A, Leroi, AM. 2012. Evolution of music by public choice, Proceedings of the National Academy of Sciences, USA 109:12081–12086

 

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Methods to age worms by

Davies SK, Leroi AM, Bundy JG. 2012. Fluorodeoxyuridine affects the identification of metabolic responses to daf-2 status in Caenorhabditis elegans. Mechanisms of Ageing and Development. 133: 46-49

 

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Posted in ageing, metabolism, peer-reviewed articles

How dog transmissible cancers stay alive

Rebbeck CA, Leroi AM, Burt A. 2011. Mitochondrial capture by a transmissible cancer. Science. 311:1095-9203

 

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A microfluidic worm-sorter

Casadevall i Solvas X, Geier FM, Leroi AM, Bundy JG, Edel JB, deMello, AJ 2011 High-throughput age synchronisation of Caenorhabditis elegans. Chem Comm DOI: 101039/c1cc14076k

 

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Metabolomic methods

Geier FM, Want EJ, Leroi AM, Bundy JG. 2011. Cross-Platform Comparison of Caenorhabditis elegans. Tissue Extraction Strategies for Comprehensive Metabolome Coverage. Anal Chem. 83:3730-3736

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Aristotle at Edge

Edge 2011: Who is the greatest biologist of all time?

 

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A map for the serpentine gallery

Edge 2010: Maps

Serpentine Gallery discussion with John Brockman, Lewis Wolpert and Hans Ulrich Obrist.

 

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Metabolomics of ageing in worms

Fuchs S, Bundy JG, Davies SK, Bundy J, Leroi AM. 2010. A metabolic signature of long life in Caenorhabditis elegans. BMC Biology 8: 2

 

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Planet Cameron

Swire J, Leroi AM. 2010. Return to Pandora. Trends in Ecology and Evolution  25: 432–433

 

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Posted in aliens, general evolution, journalism

Aristotle’s Lagoon – tv programme

Aristotle’s Lagoon. 2010.

BBC4  (Co-Writer, Presenter)

Director: Harry Killas

1 x 60

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Nick Dear’s Frankenstein

Leroi AM. 2009. Programme notes for Nick Dear’s Frankenstein, directed by Danny Boyle.

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Chromosome painting in transmissible cancers in dogs

Thomas R, Rebbeck C, Leroi AM, Burt, A. 2009. Extensive conservation of genomic imbalances incanine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis. Chromosome Research 17: 927-934

 

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Posted in general evolution, peer-reviewed articles

Royal institution 2009: Darwin anniversary

Discussion with E.O. Wilson (by video), Sandy Knapp and Peter Bowler on the future of Darwin.

 

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Origin of transmissible cancers in dogs

Rebbeck CA, Thomas R, Breen M, Leroi AM, Burt A. 2009. Origins and evolution of a transmissible cancer. Evolution 63: 2340-2349

 

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The balloon hypothesis

Swire J, Fuchs S, Bundy JG, Leroi AM. 2009. The cellular geometry of growth drives the amino acid economy of Caenorhabditis elegans. Proc Biol Sci B. 276:2747-54

 

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Aristotle on life-history

Leroi AM. 2009. Function and Constraint in Aristotle and Evolutionary Theory in S Föllinger and W Kullmann Aristotle’s Conception of Life, Bamberg

 

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Around the world with Darwin – tv programme

Darwin’s Lost Voyage. 2009.

National Geographic TV (Presenter)

Director: Geoff Luck

1 x 60

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What Darwin did not know – tv programme

What Darwin Did Not Know. 2009.

BBC4 / Discovery USA. (Writer, Presenter)

Director: Tim Lambert

1 x 90

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Scopes revived

Leroi, AM. 2008. Review of  Inherit the Wind,  Old Vic., directed by Trevor Nunn

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Neo-cantometrics

Leroi AM,  Swire J. 2007. The Recovery of the Past. World of Music 48 101-118

 

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Posted in evolution of culture, history of science, peer-reviewed articles

Diet regulates ploidy and growth in worms

Tain LS, Lozano E, Saez AG, Leroi AM. 2008. Dietary regulation of body size via hypodermal polyploidization in C elegans BMC Developmental Biology 8:28

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Posted in growth, peer-reviewed articles

David Sedley’s book

Leroi AM. 2008. Creationism and its critics in antiquity. Nature:452:153-154.

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In galapagos

Leroi, AM. 2008. The actual and the possible. Observer, London. 27.04. 08

 

 

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Q&A with current biology

Leroi AM. 2007. Q&A for Current Biology05.07

 

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Exhibition catalogue

Leroi AM. 2007. On the exquisite geometry of joins:  Catalogue for an art exhibition by Shelley Wilson

 

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Posted in journalism, mutants & variants

Neo-cantometrics: a talk with John Brockman

Edge: the song of songs

Posted in evolution of culture, journalism

Ploidy drives growth in worms

Lozano E, Saez AG, Flemming AJ, Cunha A, Leroi AM. 2006. Regulation of growth by ploidy in Caenorhabditis elegans. Current Biology 7:493-8

 

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Neo-eugenics

Leroi AM. 2006. The future of neo-eugenics. Now that many people approve the elimination of certain genetically defective fetuses, is society closer to screening all fetuses for all known mutations? EMBO Reports. 7:1184-7.

 

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Posted in journalism, mutants & variants

The chuas of Pakistan

Leroi, AM. 2006. What makes us human? Daily Telegraph, London 01.08.06.

 

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Posted in journalism, mutants & variants

What makes us human – tv series

What Makes Us Human. 2006.

TigerAspect for Channel 4 / Discovery USA (Presenter, Writer)

Director: Tim Lambert

2 x 60

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Evolution of cell lineages

Azevedo, RBR, R Lohaus, V Braun M Gumbel, M Umamasheshewar, V Braun, P Agapow, G Borgonie, HP Meinzer, and AM Leroi. 2005. The simplicity of Metazoan cell lineages. Nature 433: 152-156

 

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Antagonistic pleiotropy and ageing

Leroi AM et al. 2005. What is the evidence for the existence of individual genes with antagonistic pleiotropic effects? Mechanisms of Ageing and Development. 126:421-9

 

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On race-2

Leroi AM. 2005. On human diversity.  The Scientist 24.10.05.

Posted in history of science, journalism, mutants & variants

On race-1

Leroi AM. 2005. A Family Tree in Every Gene.  New York Times 14.03.05

 

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The first songs

Leroi AM. 2005. Searching for the Song of Songs. Sunday Times, London. 24.12.0

Edge at the Serpentine Gallery

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Geoffroy’s lobster

Leroi AM. 2005. Le homard de Geoffroy Saint-Hilaire. La Recherche. 01.12.05

 

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Summer reads

Leroi AM. 2005. Hot Reads. Guardian, London 18.06.05

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A bishop’s rectum

Leroi, AM. 2005. The New Hunterian Museum.  Times Higher Education Supplement 09.04.05

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Life: but not as we know it – tv series

Alien Worlds. 2005.

BigWave for Channel 4 / National Geographic USA (Presenter)

Director: Nick Stringer

2 x 60

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The Razib Khan interviews on GNXP

Ten Questions for Armand Marie Leroi

Posted in general evolution, journalism, mutants & variants

Mutants at Edge

Edge 2004: the nature of normal variety

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Review of Wallace Arthur’s book

Leroi AM. 2004. Gentle Biases. Review of Biased Embryos and Evolution by W. Arthur, Nature 430: 294

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We are all mutants-2

Leroi AM. 2004. Mutants, One and All. New Scientist 12.06.04

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We are all mutants-1

Leroi AM. 2004. Why everyone is such a freak.  Times, London 29.05.04

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The Ovitz family

AM. 2004. Tortured in the name of “science”.  Guardian, London 20.05.04

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On beauty

Leroi AM. 2004. The world’s most perfect mutant.  Daily Telegraph, London 19.05.04

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An anecephalic infant mummy from Egypt

Geoffroy’s mummy

Dasen V, Leroi AM. 2004. Homme ou bête? Le dieu caché de l’anencéphale d’Hermopolis in A Carol (ed) Le monstre humain : imaginaire et societe UP Paris

Posted in history of science, mutants & variants, peer-reviewed articles

Cancer selection

Leroi, A. M. V. Koufopanou, A. Burt. 2003.  Cancer Selection. Nature Reviews Cancer 3:226-31.

 

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On scientists

Leroi AM. 2004. Addicts to the shock of the new. Times, London 13.11.2004

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Review of Schlosser and Wagner’s book

Leroi AM. 2004. A mania for modules.  Review of Modularity in Development and Evolution by G. Schlosser and G.P. Wagner. Trends in Ecology and Evolution 19: 284-285.

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Human mutants – tv series

Human Mutants. 2003.

TigerAspect for Channel 4 / Discovery USA (Presenter, Writer)

Directors:  Philip Smith, Damon Thomas

3 x 60

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Posted in growth, history of science, mutants & variants, tv & radio

Mutants – book

Leroi AM. 2003. Mutants: on the form, variety and errors of the the human body

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Posted in ageing, books, general evolution, history of science, mutants & variants

Mutational constraints on growth

Azevedo RB, Keightley PD, Lauren-Maatta C, Vassilieva LL, Lynch M, Leroi AM. 2002. Spontaneous mutational variation for body size in Caenorhabditis elegans Genetics 162:755-65

 

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Gonads regulate growth

Patel, M, CG Knight, C Karageorghi, AM Leroi. 2002. Evolution of germline signals that control growth and ageing in nematodes. Proceedings of the National Academy of Sciences, USA 99: 769-74

 

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Collagens and regulation of growth in worms

Nystrom J, Shen ZZ, Aili M, Flemming AJ, Leroi AM, Tuck S. 2002. Increased or decreased levels of Caenorhabditis elegans lon-3, a gene encoding a collagen, cause reciprocal changes in body length. Genetics 161: 83-97

 

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Evo-devo surveyed

Leroi AM. 2002. Evolution of Development in M Pagel et al (eds) Encylopedia of Evolution, Oxford University Press

 

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Molecular regulation of ploidy in worms

Morita K, Flemming AJ, Sugihara Y, Mochii M, Suzuki Y, Yoshida S, Wood WB, Kohara Y, Leroi AM, Ueno N. 2002. A Caenorhabditis elegans TGF-beta, DBL-1, controls the expression of LON-1, a PR-related protein, that regulates polyploidization and body length. Embo J. 21:1063-73

 

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Why worms moult

Knight C, Patel MN, Azevedo RBR, Flemming A, Leroi AM. 2001. A novel mode of ecdysozoan growth in Caenorhabditis elegans. Evolution & Development 4:16-27

 

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Life-history trade-off QTLs in worms

Knight CG, Azevedo RBR, Leroi AM. 2001. Testing life-history pleiotropy in Caenorhabditis elegans. Evolution 55:1795-1804

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Patterns of cell number variability

Azevedo, RBR, Leroi AM. 2001. A power law for cells. Proceedings of the National Academy of Science USA 98:5699-5704

 

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Rethinking life-history trade-offs

Leroi, AM. 2001. Molecular signals v the loi de balancement. Trends in Ecology and Evolution 16:24-29

 

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Posted in ageing, general evolution, peer-reviewed articles

The virtues of being short

Leroi AM. 2001. Could the future be “survival of the shortest?” The Independent 03.04.01

Posted in growth, journalism

Micro v. macroevolution

Leroi AM. 2000. The scale independence of evolution. Evolution & Development 2: 67-77

 

 

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Ploidy and growth in worms

Flemming AJ, Shen ZZ, Cunha A, Emmons SW, Leroi AM. 2000. Somatic polyploidization and cellular proliferation drive body size evolution in nematodes. Proceedings of the National Academy of Sciences USA 97: 5285-5290

 

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Nematodes are not eutelic

Cunha A, RB Azevedo, Emmons S, Leroi AM. 1999. Variable cell numbers in nematodes. Nature 402:253

Azevedo, RBR, Cunha, A, Emmons, SW, Leroi AM. The demise of the Platonic worm. Nematology. 2. 71-79

 

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Review of Stephen Jay Gould’s book

Leroi AM. 1999. The Giraffe’s Neck. Review of Leonardo’s mountain of clams and the diet of worms by S. J. Gould. Times Literary Supplement 2.07.99

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Nematode physiology

Leroi AM and Jones J. 1998. Development of Nematodes in R Perry and D J Wright (eds) Physiology and Biochemistry of Free-Living and Plant-Parasitic Nematodes p. 155-175

 

Posted in general evolution, peer-reviewed articles

Review of W.G. Runciman + the Zahavi’s books

Leroi AM. 1998. Sing, prance, ruffle, bellow, bristle and ooze. Review of The Handicap Principle by A. Zahavi and A. Zahavi and The Social Animal by W.G. Runciman. London Review of Books 17.09.98

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Posted in evolution of culture, history of science, journalism

Review of Wallace Arthur + Gerhart & Kirschner’s books

Leroi AM. 1998. The burden of the bauplan. Review of The Origin of Animal Body Plans: A Study in Evolutionary Developmental Biology, by W. Arthur, and Cells, Embryos and Evolution, by J. Gerhart and M. Kirschner. Trends in Ecology and Evolution 13: 82-83

Posted in general evolution, journalism

Food, sex, life-history

Chippindale AK, Leroi AM, H Saing, Borash D and Rose MR. 1997. Phenotypic plasticity and selection in Drosophila life-history evolution. 2. Mating status, nutrition and the cost of reproduction. Journal of Evolutionary Biology 10:269-293

 

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Posted in ageing, peer-reviewed articles

Review of Jared Diamond’s book

Leroi AM. 1997. Why rhino-mounted Bantu never sacked Rome.  Review of Guns, Germs and Steel by J. Diamond. London Review of Books 04.09.97

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Posted in evolution of culture, history of science, journalism

Review of Harriet Ritvo’s book

Leroi AM. 1997. The name of the beast.  Review of Buffon by J. Roget and The Platypus, The Mermaid and Other Figments of the Classifying Imagination by H. Ritvo.  London Review of Books 11.12.97

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Posted in history of science, journalism

Review of Henry Gee’s book

Leroi AM. 1997. A Duck Folded in Half. Review of Before the Backbone by H. Gee. London Review of Books. 06.97

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Posted in history of science, journalism

Thermal adaptation

Leroi AM, Lenski RE and Bennett AF. 1995. Evolution of Thermal adaptation III Phenotypic acclimation and genetic adaptation of Escherichia coli to a temporally variable environment. Evolution 48:1222-1229

 

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Posted in general evolution, peer-reviewed articles

Phenotypic and genetic trade-offs

Leroi AM, Kim SB and Rose MR. 1994. The evolution of phenotypic life-history trade-offs: an experimental study using Drosophila melanogasterAmerican Naturalist 144:661–676

 

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Posted in ageing, general evolution, peer-reviewed articles

Evolutionary stability of life-history genetic correlations

Leroi AM, Chen WR and Rose MR. 1994. Long term laboratory evolution of a life-history trade-off in Drosophila melanogaster. 2. Stability of genetic correlations. Evolution 48:1258-1268

 

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Posted in ageing, general evolution, peer-reviewed articles

Evolutionary instability of life-history trade-offs

Leroi AM, Chippindale AK, and Rose MR. 1994. Long term laboratory evolution of a life-history trade-off in Drosophila melanogaster. 1. The role of genotype x environment interaction Evolution 48: 1244-1257

 

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Posted in ageing, peer-reviewed articles

The beneficial acclimation hypothesis

Leroi AM, Bennett AF, Lenski RE. 1994. Heat acclimation increases high temperature survival in Escherichia coli. Proceedings of the National Academy of Sciences, USA 91:1917-1921

 

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Posted in peer-reviewed articles

Critique of the comparative method

Leroi AM, Rose MR, Lauder GV. 1994. Can the comparative method reveal adaptation? American Naturalist 143:381-402

 

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Posted in general evolution, peer-reviewed articles

Adapation & history

Lauder GV, Leroi AM, Rose MR. 1993. Adaptation and History. Trends in Ecology & Evolution 8: 294-297

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Posted in general evolution, peer-reviewed articles

Dietary restriction in Drosophila

Chippindale AK, Leroi AM, Kim SB, Rose MR. 1993. Phenotypic plasticity and selection in Drosophila life-history evolution. 1. Nutrition and the cost of reproduction. Journal of Evolutionary Biology 6:17-93

 

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Posted in ageing, peer-reviewed articles

Microfluidic Tech

A device to sort worms for ageing studies.

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Posted in Uncategorized

Hybrid Genetics

Using South American killifish, Austrolebias, to study the evolutionary genetics of growth and ageing.

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Posted in current projects

Human mutation load

Estimating how mutant we are from full‐genome sequence data.

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Posted in Uncategorized