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The Rough Guide to Evolution



An eclectic blog on evolution & DarwinianaWritten by Mark Pallen. The book Rough Guide to Evolution, given to 6000 students via Great Read at Birmingham. My other blog: bacterial pathogenomicsAny opinions are mine, not my publisher's



Updated: 2016-09-07T21:22:13.841-07:00

 



Visit of Randal Keynes part two

2012-07-09T23:12:40.871-07:00

Following on from the previous post, Randal has now sent me the speech he gave while receiving his honorary doctorate. Here it is:Deputy Pro-Chancellor, Vice Chancellor, my fellow Graduates, Graduands and guests,My thanks first to Professor Raine for his citation tracing all my relations and explaining my interests in conservation and science heritage. Fellow Graduands, I’ve come here today to join you in this wonderful ceremony with a strong sense of the excitement of Birmingham Biosciences in 2012, your success in your courses, and what now lies ahead for you all in all the different fields in which you’ll be putting to use all the knowledge and understanding you’ve gained here through your studies. For myself, thinking of links with the past as I do so often in my work on science heritage, the Lunar Society of Birmingham comes first to mind. Among its members were Joseph Priestley, Matthew Boulton, Josiah Wedgwood and Erasmus Darwin, scientists, doctors, manufacturers and inventors, each with different interests and skills, and all glad to talk freely together about their many interests. There must now be many echoings of those discussions in the collaborations that take place between the many teams in the School of Biosciences as they work today across its wide range of interests. I guess the School is working so well now just as the Lunar Society did before partly because these open exchanges are good ways to do innovative, productive science. But why should young scientists like you today bother with science in history? Why do I and others go on about Darwin and the other historical figures? I can suggest many answers. I’ll give you one of them quickly now because for me it’s one of the strongest, it starts here in Birmingham, and numbers of you may perhaps recognize the point one day in some scientific investigation you carry out or hear about.So, there’s one meaning of science - its conclusions, the body of latest knowledge. There’s another meaning – the process, how the explanations are developed, tested and agreed.On the process, Joseph Priestley was living here in the 1770s and in his experiments on electricity and gases he always used equipment that was cheap and easy to obtain, and described his experiments clearly and simply so that anyone could repeat them or vary them as they wanted. He was hoping to find clear and simple explanations that anyone else could test so that they could carry on from there. And he felt that the more experiments could be done by more people, the better the conclusions would be. Also, the best explanations would often be the simplest ones because with simplicity often came greater explanatory power. The value and power of his classic experiments on both electricity and gases were linked with these features of his method. Now Charles Darwin, in his experimental work on plants and insects at his home in Kent some eighty years later, followed Priestley’s method exactly in all these respects, including simplicity for explanatory power. When we look at the two men’s achievements together now, we can see a valuable approach that was used with great effect in two outstanding contributions to science. Yes of course, science has come a long way since then, but I’d suggest that key elements of that approach may still have great value in many areas of science today. Deputy Pro-Chancellor, I’m deeply grateful for the honour you have conferred on me today, and for the special link it gives me now with Birmingham and its heritage of science. [...]



Visit of Randal Keynes to University of Birmingham

2012-07-07T05:57:13.420-07:00

On July 4th 2012, it was my pleasure to host a visit by honorary graduand Randal Keynes, with his wife Zelfa and mother Anne, to the University of Birmingham. Their day here included lunch with the Vice-Chancellor and others, a trip to the Special Colletions and Archives, along with Alice Roberts to see a first edition Origin of Species (thanks to Sue Worrall), and a visit to the Lapworth Museum of Geology (thanks to Ivan Sansom).Randal received an honorary doctorate at the School of Biosciences graduation ceremony and the day concluded with a photo shoot of Darwin-descendent Randal alongside Huxley-descendent Adam Tickell, plus strawberries and champagne in the VC's office.Here is a video record of selected snippets from the day:  allowfullscreen="" frameborder="0" height="315" src="http://www.youtube.com/embed/yA_AmKuZPps" width="560">Unfortunately I was not allowed to film the graduation ceremony, nor does the University seem to realise that "information wants to be free", so the only way to get footage of the ceremony is to fork out for a DVD!At the graduation ceremony, Randal gave a speech in which he highlighted the links between the Lunar Society of Birmingham, his ancestors (Erasmus and Charles Darwin), Joseph Priestley and the birth of the scientific method. Randal was introduced with a speech from University orator Professor John Raine, which John wrote with help from Randal and myself. A hypertext-linked version of the speech follows. Chancellor, Vice Chancellor, Graduates, Graduands and Guests, The concept of conservation is one that associates equally with the natural environment of plants and animals and with the human-created world of architecture and buildings. Most conservationists usually work in one arena or the other, but today before us stands an individual whose contribution spans both and who can therefore properly be described as a conservationist in the most comprehensive and generic of senses. Randal is from a renowned lineage of English families – notably the Keyneses, the Adrians, the Darwins and the Wedgwoods. Born on July 29th 1948, he is a great nephew of the eminent economist, John Maynard Keynes; and he is also the great-great-grandson of naturalist Charles Darwin. In 1839 Charles Darwin had married Emma Wedgwood, descendant of Josiah Wedgwood the 18th century founder of industrialised pottery manufacture, and who, along with his friend Erasmus Darwin and other prominent Midlands figures, were founding members of the Lunar Society of Birmingham which played such an important role in science for the Industrial Revolution. Randal’s father was the eminent Cambridge physiologist Professor Richard Darwin Keynes and his father, Sir Geoffrey Langdon Keynes, was a distinguished surgeon and scholar whose work in developing blood transfusion saved thousands of lives in the First World War. On the other side of his family, Randal’s mother, Mrs Anne Pinsent Keynes, whom we are delighted to welcome here in the Great Hall with us today, is also of very distinguished lineage. Her mother, Hester, was Lady Adrian, a renowned penal reformer, and her father, Lord Adrian, was a Nobel Prize-winner in 1932 for his discoveries about the workings of the nerve cell. And Anne’s grandmother was Birmingham’s own Dame Ellen Pinsent – who is 1911 was the first woman to be elected to the City of Birmingham Council, and a pioneer in the education of children with special needs. She, for one, would have been delighted that last year Ofsted found the special school named after her in South Birmingham – The Dame Ellen Pinsent School – to be ‘outstanding’. Dame Ellen was awarded an honorary MA by this University in 1919, while her husband – Anne’s grandfather - Hume Chancellor Pinsent – a solicitor in this city, was Treasurer of this University until his retirement in 1913. It is also a great pleasure today to welcome Randal’s wife Zelfa Hourani. Unfortunately their two offspring – Soumaya and Skandar – are otherwise enga[...]



Interesting video and paper from Nature

2012-03-29T08:34:02.207-07:00

From the Nature video feed:
width="560" height="315" src="http://www.youtube.com/embed/mZ6v5ilOqec" frameborder="0" allowfullscreen="">
A few million years ago, our ancestors stopped climbing trees and started walking upright, on two feet. To work out how and when this happened, researchers look for fossils -- and recently they found a surprising set of foot bones in Ethiopia. The foot is about 3.4 million years old, making it roughly the same age as 'Lucy' and her species, Australopithecus afarensis. But while Lucy's species had feet much like modern humans, the new foot has an opposable big toe, like a chimp. So do the foot bones represent a new species of hominin? Watch the video and decide.

Read the original research paper: www.nature.com/nature/journal/v483/n7391/full/nature10922.html



The ‘Annie Hypothesis’: Did the Death of His Daughter Cause Darwin to ‘Give up Christianity’?

2012-03-22T00:49:39.868-07:00

(image) The paper that I wrote with John van Wyhe on what we call "the Annie Hypothesis" is now out here:

Here is the abstract:
This article examines one of the most widely believed episodes in the life of Charles Darwin, that the death of his daughter Annie in 1851 caused the end of Darwin's belief in Christianity, and according to some versions, ended his attendance of church on Sundays. This hypothesis, it is argued, is commonly treated as a straightforward true account of Darwin's life, yet there is little or no supporting evidence. Furthermore, we argue, there is sufficient evidence that Darwin's loss of faith occurred before Annie's death.

During peer review, the paper was criticised for mixing history with historiography and for being overly positivist, but what can you expect of a scientist! We are all positivists!

Sadly, the paper is not open access: if anyone wants a copy but cannot access it, please email me (m.pallen@bham.ac.uk).

Allow me to thank John van Wyhe for beating the paper into shape and nursing it through to publication!

Other previous posts on this topic:




Rap Guide to Evolution: new "I'm a African" video

2012-02-18T00:14:19.027-08:00

Back in the run-up to the Darwin bicentenary year, I persuaded Canadian Lit-Hop artist Baba Brinkman (creator of the Rap Canterbury Tales) to "do for for Darwin what he had done for Chaucer". He rose to the challenge majestically to create the Rap Guide to Evolution and I was thrilled to experience his premier performances at small poetry workshop in Hinxton near Cambridge in early 2009. The video below provides a glimpse of this earliest version of the show. In the week that followed I arranged for Baba to tour England, with shows in Cambridge, London, Birmingham and Shrewsbury. width="420" height="315" src="http://www.youtube.com/embed/dW2-oidNZ58" frameborder="0" allowfullscreen="">Since then the various songs have undergone "descent with modification", with two versions of the album now out there (original and revised) and a sell-out live show which ran off Broadway for many months. Also, thanks to an encounter during the very first performance, Baba won financial support from the Wellcome Trust (and did a bit of his own crowd-funding) to create educational and entertaining videos to accompany each track. This has been a slow process, as he has to wait for the animators and actors to find time in their busy schedules to contribute, but the videos have been steadily appearing on YouTube and a dedicated website.When I first suggested that Baba create the Rap Guide to Evolution, I asked if he could do something to communicate and even celebrate the Out-of-Africa theory, i.e. the idea first proposed by Chris Stringer and others that all modern non-African humans are descended from a small band of humans who left Africa 60-70 thousand years ago (pace John Hawks and Svante Paabo who now emphasise that a few percent of the non-African human genomes originated from archaic hominins from outside Africa). To me this theory gelled nicely with the pan-Africanism that permeates both reggae (check out this Black Uhuru track) and some rap music. Baba did a great job on this, with his track "I'm a African".A few months back Baba visited Birmingham to perform the Rap Guide to Evolution for our students. During his visit he solicited my help in finding a multi-racial cast of volunteers to appear in the video for "I'm a African". From amongst students and colleagues, we managed to find two Indians, two Greeks, an Afghan, a Chinese, a number of Europeans (including me!), plus some people with African ancestry more recent than 70Kya, all willing to lip-sync along to the track against a green background, hastily assembled Blue-Peter-fashion from some card and sticky tape. Filming all this within our Centre for Systems Biology was a truly surreal experience!Well, yesterday, just as Nick Loman was stoking our other blog up to blistering heat with the news of Oxford Nanopore, I received a note from Baba saying that the video for "I'm a African" was now finished and available online. So, here it is! Enjoy! Mine is the ugly mug a few seconds in! width="560" height="315" src="http://www.youtube.com/embed/G6r6POHC8zg" frameborder="0" allowfullscreen="">A few notes on the video:1. It's "I'm a African" rather than "I'm an African" for good reason, as Baba explains here.2. The track is modelled on a track from Pan-Africanist Hip-Hop group Dead Prez. Listen to that track here if you want to compare and contrast.3. Be sure to wait right until the end of Baba's video to see the architect of the out-of-Africa theory, Chris Stringer, make a cameo appearance, thanks to some footage I captured when he visited the University of Birmingham!4. I suspect that the Dead Prez track was influenced by a speech "I'm an African" by Thabo Mbeki. Although later deeply flawed as a president, in 1996 Mbeki gives a great speech.5. A few years back, in similar vein, with a Jamaican colleague, I created "Light be Thrown", a celebration in reggae format of our recent African origins and Darwin's predictions about how light will be thrown on human origins.[...]



Evolutionary Chemistry: from Darwinism to drugs

2011-12-10T05:20:38.817-08:00

Most therapeutic drugs work by binding to proteins and interfering with their function. A key challenge for chemists working in the pharmaceutical industry is to discover new medicinal chemicals that fit important protein targets, rather like a key fits a lock. The traditional way to do this is to take a long hard look at the protein “lock” and then rationally design a chemical “key” that fits it. However, analogies with biological evolution have recently inspired an alternative approach: evolutionary chemistry.Instead of attempting rational drug design, the evolutionary chemist simply generates a massive pool of variable DNA-like starting molecules (analogous to the variation that underlies biological natural selection). When these are then introduced to the target protein, only a small fraction of the molecules bind (the selection step). However, various chemical tricks then allow the chemist to amplify this population of molecules (the reproduction step). The amplified molecules are then used as the starting point for a subsequent round of selection and amplification. After several rounds of selection, the molecular mixture is greatly enriched for aptamers, molecules that bind tightly and specifically to the chosen target. This evolutionary approach, called SELEX, has already led to the development of one useful drug, Pegaptanib (with the trade name Macugen), which has been licensed as a medicine to treat a common cause of blindness (age-related macular degeneration). But this is just the start: evolutionary chemistry is all set to deliver additional medically useful aptamers in the next few years that will target heart disease or cancer. For example, the US company Archemix has a developed lead aptamer, ARC1779, which acts as a potent, selective antagonist of von Willebrand Factor (vWF), with potential for use as an anticoagulant or antithrombotic agent (http://www.ncbi.nlm.nih.gov/pubmed/19479665). It is currently undergoing evaluation in clinical trials in patients diagnosed with acute coronary syndrome undergoing percutaneous coronary intervention. For an unusual attempt to communicate how SELEX works (albeit applied to discovering new diagnostics rather than drugs), take a look at this video of the winning entry in the Dance you PhD competition of 2010! width="560" height="315" src="http://www.youtube.com/embed/45m4y2vyuCU" frameborder="0" allowfullscreen="">[...]



Darwin's Pilgrims: The Video

2011-11-22T23:29:59.429-08:00

In February 2009, I hosted 'Darwin's Pilgrims": a visit to England by two Americans with links to the Dover Pennsylvania trial, Cynthia Sneath and Lauri Lebo, and Canadian Lit Hop artist Baba Brinkman to celebrate Darwin's 200th birthday. The trip involved a "pilgrimage" to Darwin-related sites and a series of performances in English cities, including the premiere of the Rap Guide to Evolution. Previous blog posts captured the spirit of the event
But this is the first time I have presented the complete video, covering trips to Malvern, Cambridge and London, even though I finished it a couple of years ago. I hope you enjoy the footage and the great music! For a bunch of non-believers, we spent a lot of time in churches!


width="420" height="315" src="http://www.youtube.com/embed/GCf3Kg3ekeY" frameborder="0" allowfullscreen="">
http://www.youtube.com/watch?v=GCf3Kg3ekeY



Don’t want to believe in evolution?

2011-11-21T23:11:18.355-08:00

Is it possible to be a rationalist (a believer in the laws of logic) but not believe in evolution? Just about! But only just!There are several philosophical show stoppers that bring rational argument to a halt.Perhaps requiring the least mental gymnastics is the "Omphalos hypothesis", so-named after an 1857 book by English naturalist (and local Worcester man) Philip Gosse. Gosse argued that even if creation occurred from nothing, the creator would necessarily leave traces of previous existence that had never actually occurred. Although Adam was never hooked up to a placenta, he required a navel ("omphalos" in Greek) because it made him a complete human being. Similarly, God must have created trees with rings that they never grew and rocks with a fossil record of life that never actually existed. This kind of thinking has drawn adverse responses from Catholic scientist Ken Miller and the "Zoo Rabbi" Natan Slifkin, who both reject it as depicting God as a dishonest charlatan. A secular response, Last Thursdayism, proposes, that by this logic, the world might just as easily have been created last Thursday, but with the appearance of age such as false memories and fictitious history books. There is even a parody religion, The Church of Last Thursday.The first real philosophical show stopper is metaphysical solipsism: the belief that you, the reader, is all there is and that this blog and this author, this world and the evolution of life in it, are all just figments of your imagination. However, it is scarcely possible to hold this belief in your mind for even a minute and, as English philosopher Bertrand Russell once pointed out, solipsism “is rejected in fact even by those who mean to accept it. I once received a letter from an eminent logician… saying that she was a solipsist, and was surprised that there were no others. Coming from a logician and a solipsist, her surprise surprised me.”One modern variant on solipsism is the brain-in-a-vat idea, taken seriously by, among others, Berkeley philosopher Barry Stroud. In this scenario, your brain has been removed from your body, placed in a vat of life-sustaining liquid and your neurons hooked up to a supercomputer that provides you with a virtual reality indistinguishable from any “real” reality. So, the argument goes, if you are in a vat, all your conclusions about evolution in the real world are false. And, as you have no way of knowing whether you are in a vat or not, this leaves you free to doubt the reality of evolution.But why suppose you ever had a body in the first place, why not suppose you are a disembodied brain created yesterday with false memories of a biological world built by evolution? Some cosmologists are seriously discussing the idea of Boltzmann brains, self-conscious entities that arise from random fluctuations in vacuum energy (named after Austrian physicist Ludwig Boltzmann, who suggested that the whole universe resulted from such a fluctuation). If the universe lasts long enough, such entities are inevitable, say the cosmologists. But why stop at a brain—viewing yourself as a Boltzmann-brain-in-a-vat breaks none of the laws of physics and also gets you off the hook of having to believe in evolution.A more general case of the brain-in-a-vat idea is the simulation hypothesis. According to this viewpoint, popularized by the Matrix films, we are all living in a simulated reality, run on a computer powerful enough to create a internally consistent simulation, so detailed that it could not be distinguished from “real” reality. Swedish philosopher Nick Bostrom argues that it is more likely than not that we are living in such a simulation. His argument rests on the assumption that any sufficiently advanced civilization capable of creating simulations that contained intelligent individuals would be unlikely to restrict itself to a single simulation, instead[...]



Bio380 Human Evolution Genes and Genomes Bioinformatics Practical

2011-11-20T10:26:21.393-08:00

I have a bioinformatics practical class tomorrow and rather than hide it away, I thought I might as well share it with the world via this blog. Happy to receive comments on any mistakes or suggestions for improvements or additional reading.Bio380 Human Evolution Bioinformatics Practical 2011Follow this link to the entry for the FOXP2 chimpanzee protein:http://www.uniprot.org/uniprot/Q8MJA0Take a minute to explore the information on the page.Q. What is the evidence that this gene is functional in the chimpanzee?Q. Why is this entry called FOXP2_PANTRQ. What does the Forkhead domain do?Scroll down to the sequence at the bottom of the pageQ. What is unusual about the first third of the protein sequence?Click on the pop-up Fasta view buttonQ. What is a FASTA sequence?Select the sequence that pops up and copy it to the clipboard. Then return to the previous window.Open in a new tab and go to http://www.ncbi.nlm.nih.gov/BLAST/Select “protein blast”Q. What is BLAST?Paste the FoxP2 FASTA sequence into the search box. Click on the algorithm parameters link, then tick the box indicating Filter low complexity regionsQ. What does this do?Start the Blast search. The Blast search may take some time, so open a fresh tab and go to http://www.uniprot.org/Search for “foxp2_human”Spend some time exploring the information therein, while you wait for the Blast search to finish.Return to the Blast search result. Scroll through the results. In the segment of the query spanning residues 241-698, how many differences does the chimp protein show from the following:Orang utan (Pongo pygmaeus) Gorilla (Gorilla gorilla)Lar gibbon (Hylobytes lar) Macaque (Macaca mulatta)Horse (Equus cabellus) Mouse (Mus musculus)Humans (Homo sapiens)PS: use the sequence with header "FoxP2_Human"Q. What differences do you find?Q. How conservative or radical are the changes in amino-acid properties?Go to http://www.nature.com/nature/journal/v418/n6900/full/nature01025.htmlThis paper suggests that the human sequence undergoes an additional post-translational modification compare to the chimp sequenceQ. What is this difference and how significant is likely to be?Go to http://www.ncbi.nlm.nih.gov/omimSearch for FoxP2, then click on the first entry and explore the information therein, particularly that under the Evolution heading.Q. Does this confirm or deny any of your previous conclusions?Follow the link to this recent paper:http://dx.doi.org/10.1016/j.jhevol.2007.07.006Speed-read the abstract and introductionQ. On the basis of this, would you expect Neandertals to be able to speak?Q. What would you expect their FoxP2 gene to look like?Follow this link to another recent paperhttp://www.cell.com/current-biology/abstract/S0960-9822(07)02065-9Q. What do you conclude?Now read these blog entrieshttp://itre.cis.upenn.edu/~myl/languagelog/archives/005038.htmlhttp://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/foxp2_krause_el_sidron_2007.htmlhttp://johnhawks.net/weblog/reviews/genetics/brain/foxp2-bushman-variant-2010.htmlhttp://johnhawks.net/weblog/reviews/denisova/foxp2-denisova-humanlike-2011.htmlhttp://blogs.discovermagazine.com/loom/2011/11/14/neanderthal-neuroscience/http://discovermagazine.com/2011/oct/08-the-brain-language-fossils-buried-in-your-cells/article_printQ. Do your conclusions change?Q. Are blogs are useful source of scientific information?The genome of James Watson, Nobel laureate and co-discoverer of the structure of DNA can be found here: http://jimwatsonsequence.cshl.edu/Follow these linkshttp://www.independent.co.uk/news/science/fury-at-dna-pioneers-theory-africans-are-less-intelligent-than-westerners-394898.htmlhttp://www.nytimes.com/2007/12/12/science/12watson.html?_r=1http://isteve.blogspot.com/2007/12/james-watson-and-passing.htmlhttp://johnhawks.net/weblog/topics/biotech/testing/watson_african_dna_2007.htmlThen evalu[...]



Darwin and Mendel: The Great What If?

2011-11-06T03:47:08.331-08:00

Charles Darwin and Gregor Mendel were contemporaries. One of the great “what ifs” in the history of science is “what if Darwin and Mendel had met to discuss each other’s work, or, at least, had exchanged notes?”The closest they came to meeting was in the summer of 1862, when Mendel visited England to attend the International Exhibition, a world fair held in South Kensington. Charles Darwin was less than twenty miles away, but their paths never crossed as the Darwins were stuck at home, nursing their son Leonard through scarlet fever. Mendel read a German translation of Darwin’s Origin before publishing his seminal paper in 1865, but he did not see any connection between his work and Darwin’s. It has been claimed that Mendel’s paper sat on a shelf at Down House, unread, but this is just a myth. Although Darwin possessed two books that briefly referred to Mendel’s work, there is no evidence that he read the relevant sections; in one of the books, the pages are clearly uncut. Darwin leant one of these two books to his friend George Romanes, who used it to write an encyclopedia entry, priming another myth: that Darwin wrote about Mendel in the Encyclopaedia Britannica. How close was Darwin to discovering Mendel’s laws of inheritance? As early as 1838, Darwin scribbled in his notes a question that, in retrospect, seems pregnant with potential: “Do races of peas become intermixed & gardener have hybrid seedlings?” In a letter written to Wallace in February 1866, Darwin recognizes that inheritance can be non-blending: “My dear Wallace… I do not think you understand what I mean by the non-blending of certain varieties… I crossed the Painted Lady and Purple sweetpeas, which are very differently coloured varieties, and got, even out of the same pod, both varieties perfect but not intermediate.” Furthermore, as Chinese plant scientist Yongsheng Liu has pointed out, Darwin describes experiments that are uncannily similar to Mendel’s, in his 1868 work Variation Under Domestication: “Now I crossed the peloric snapdragon… with pollen of the common form; and the later, reciprocally, with peloric pollen. I thus raised two great beds of seedlings, and not one was peloric. The crossed plants, which perfectly resembled the common snapdragon, were allowed to sow themselves, and out of a hundred and twenty-seven seedlings, eighty-eight proved to be common snapdragons, two were in an intermediate condition between the peloric and normal state, and thirty-seven were perfectly peloric, having reverted to the structure of their one grandparent…” The ratio, at 2.4 to 1, is close enough statistically to conform to an expectation of 3 to 1, so this might count as a glimpse by Darwin of Mendel’s first law. But given that Mendel himself did not recognize the universality of his own work, it is unfair to expect Darwin or anyone else to do so, particularly in the face of less easily interpreted results from crosses in other species of plants and animals. Instead, the modern synthesis of Darwin's and Mendel's work had to wait until the mid-Twentieth Century.BibliographyThe extent of Charles Darwin’s knowledge of Mendel by Andrew SclaterThe Monk in the Garden: The Lost and Found Genius of Gregor Mendel, the Father of Genetics by Robin Marantz Henig [...]



The Rough Guide to Darwin

2011-10-12T02:25:03.157-07:00

As part of my attempt to put all my talks, whether for teaching or research online, I have put these two talks I gave yesterday in Oxford on to YouTube.

The Rough Guide to Darwin
width="425" height="349" src="http://www.youtube.com/embed/4yHHoCivCT0?hl=en&fs=1" frameborder="0" allowfullscreen>
http://www.youtube.com/watch?v=4yHHoCivCT0
Talk given to doctoral students in Oxford 11th Oct 2011
Covers Darwin's early life, including wayward youth, before discussing his major work, impact and legacy

Warning: Explicit discussion of Darwin and sexuality. "Let's get Downe and dirty with Darwin!"
Ignore grey screen YouTube snafu at very beginning. Soon sorts itself out.

From Darwin to Drug Resistance
width="425" height="349" src="http://www.youtube.com/embed/4iVQK9sYr2M?hl=en&fs=1" frameborder="0" allowfullscreen>
http://www.youtube.com/watch?v=4iVQK9sYr2M
Talk given to doctoral students in Oxford 11th Oct 2011
Brief review of Darwin's legacy and evolutionary thinking in bacteriology.
Ignore grey screen YouTube snafu at very beginning. Soon sorts itself out.



Wallace: Darwin’s Rival or Ambassador?

2011-10-07T23:57:04.450-07:00

Alfred Russel Wallace (1823-1913) was born in Llanbadoc, near the Welsh town of Usk and grew up in Hertfordshire. He worked as an apprentice surveyor for the six years. During a brief spell as schoolmaster in Leicester, Wallace met entomologist Henry Bates and developed an interest in natural history. He worked for several more years as a surveyor/engineer. Then, inspired by Humboldt and Darwin, Wallace set off with Bates on an expedition to Brazil. In 1852, after four years collecting specimens and surveying the Rio Negro, Wallace set off back to England. At sea, a fire forced Wallace to abandon his specimen collection and, adrift, he spent ten days in a lifeboat, awaiting rescue.Back safe in England, an insurance payment supported him while he wrote papers and forged links with naturalists, including Darwin. In 1854, Wallace embarked on an expedition to the Malay Archipelago (present-day Malaysia and Indonesia). During this six-year excursion, Wallace collected over a 100,00 specimens, discovered the discontinuity between the kinds of plants and animals found in the northern part of the archipelago and those found in the south (now called the Wallace line), and, crucially, hit upon the idea of evolution by natural selection independently of Darwin. Wallace’s experiences were written up as a lively travelogue, The Malay Archipelago. During his middle years Wallace was beset with financial problems, which we largely alleviated in 1881 by a government pension that Darwin helped him obtain. In late life, Wallace extended his work on biogeography, became an early environmentalist and toured the US promoting evolution and natural selection. In old age, he settled in Broadstone, a suburb of Poole in Dorset. He is buried in Broadstone cemetery in a grave capped with a (rather phallic!?) fossil tree trunk and block of limestone.Although often cast as Darwin’s rival, Wallace remained a loyal and lifelong supporter of Darwin, accepted Darwin’s claim to priority, dedicated The Malay Archipelago to Darwin and even entitled his major book on evolution Darwinism. Wallace was an altogether more colourful character than Darwin, but also rather more flakey. Wallace adopted spiritualism and unlike Darwin, expounded a progressive, teleological view of evolution, with the universe working towards the birth of the human spirit. He rejected natural selection as an explanation of the human mind, instead favouring interventions from the “unseen world of spirit”. He became a socialist and an opponent of smallpox vaccination. He got tangled up in disputes as to whether the earth was flat (in the Bedford Level experiment, he showed it wasn’t) or whether there were canals on Mars (he argued there weren’t). It is clear that, had Darwin died in South America, “Wallaceism” would have turned out quite different from Darwinism!Further Online ReadingThe Alfred Russel Wallace web page: http://www.wku.edu/~smithch/index1.htmAlfred Russel Wallace page in WikipediaImage RightsWallace Grave George W. Beccaloni: Creative Commons Attribution 3.0 Unported[...]



Open Education and Bio380 lecture on Neanderthals

2011-10-01T02:45:08.122-07:00

This academic year I have set myself the goal of making all my lecture available for all, in the public domain, via YouTube and maybe also Slideshare. The technical side of doing this is fairly straightforward (capture a screen movie via QuickTime), but the major hassle is ensuring and documenting permissions for all images. In my first attempt, I quickly realised that putting this information on the same slides as the images led to cluttered chaos, so I have piled them all up at the end of the talk.

It is unclear to me what the rules are about using material from published papers, but cannot see how authors would not want students to know about their work. So, in general, I am proceeding along the course of it is easier to apologise afterwards rather than ask permission in advance. If anyone objects to anything I have done, let me know and I will remove the offending material from the public domain. Also, if anyone has tips on how to do all this as efficiently and fairly as possible, please let us know via the comments. Ditto if you want to send words of encouragement!

It will be interesting to see if anyone other than my own students look at this stuff, but here we go, the game's afoot! Information wants to be free!

Here is my first lecture for this year from the Bio380 course: Waking the Dead, on Neanderthals and their influence on the modern human gene pool. Enjoy!

Slidecast via YouTube

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Slides via Slideshare
Bio380 Human Evolution: Waking the dead src="http://www.slideshare.net/slideshow/embed_code/9483679" width="425" height="355" frameborder="0" marginwidth="0" marginheight="0" scrolling="no">
View more presentations from Mark Pallen



Great Read at Birmingham: Captain Kirkup and Chris Stringer

2011-10-01T02:26:36.503-07:00

AV material associated with this week's Great Read at Birmingham events.

Captain Kirkup on Evolution and Game Theory

Video of the talk and subsequent Q&A : http://www.youtube.com/watch?v=15gxMlQQ6AA
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Slides to go with this: http://www.youtube.com/watch?v=RTk9_DlOpcQ
(Open these in a separate window as they will need to be manually paused and progressed forward: sorry no synchronised slidecast available)

Chris Stringer on The Origin of Our Species
Podcast of the talk via YouTube (publicly available): http://www.youtube.com/watch?v=QryLIaRORlU
width="420" height="315" src="http://www.youtube.com/embed/QryLIaRORlU" frameborder="0" allowfullscreen>



Live tweets from Great Read at Birmingham opening event

2011-09-25T06:24:52.052-07:00

Here are the live tweets from Great Read at Birmingham opening event, sorted from earliest to latest66. mjpallen: @mjpallen @greatreadatbham @unibirmingham live tweet under #GRAB2011 hashtag65. mjpallen: #grab2011 ken miller up on stage; textbook author, daughter had to read his book at school; she gave up biology for history :-)64. mjpallen: #grab2011 Ken testified in George and Pennsylvania; pervasive problem in US education and local politics; evolution in Ohio local politics63. mjpallen: #grab2011 “vote for proevolution candidate you vote for sin“ 2 of republican presidential candidates creationist; creationist museums62. mjpallen: #grab2011 antievolution bills pop up all over; problem coming to UK and Germany; Uk scientists published letter defending evolution61. mjpallen: #grab2011 creationist conference in Malvern, UK; now describing Dover trial why lawsuit? 1st amendment http://t.co/VffLhax060. mjpallen: #grab2011 Ken lead witness in Dover trial Goals: show ID not science; show it is religion.59. mjpallen: #grab2011 Conservative judge, so ID people thought easy time coming58. mjpallen: #grab2011 > 9 hours cross examination: like PhD viva over and over again. Trial showed collapse of ID as credible theory; icons of ID trashed57. mjpallen: #grab2011 ID claim: evo cannot make irreducibly complex systems; Michael Behe; missing part makes it nonfunctional; mousetrap example56. mjpallen: #grab2011 flagellar components alone have no function say ID ppl. Only designer can make it. But even Darwin knew of change of function55. mjpallen: #grab2011 testable to see if flagellar components can do anything if not all together; take away all but 10 parts of flagellum; still works54. mjpallen: #grab2011 works as type III secretion system; counters irreducible complexity claim. ID is wrong! Cites Pallen and Matzke paper. testability53. mjpallen: #grab2011 ID textbook Pandas and People; textbook evolved from creationist book with "creation" changed to ID; Barbara Forest testimony52. mjpallen: #grab2011 1987 book changed because creationism deemed in law religious; Dover trail covered by BBC in War on Science; showing clip fr Nova51. mjpallen: #grab2011 "judgment day" overblown rhetoric in nova show; received award; back to Dover case; Dec 20 2005; verdict ID not science!50. mjpallen: #grab2011 struggle continues; "only a theory" book written to contain antirationalism antiscience; US lagging in science & math; Nature edop49. pathogenomenick: Ken miller shows this great antievolution poster #GRAB2011 http://t.co/ur6sP88h http://t.co/ur6sP88h48. mjpallen: #grab2011 whoisyourcreator.com nonsense on web; abundance of human fossils; Darwin's tree from Origin dead ringer for human evo tree!47. mjpallen: #grab2011 new findings all the time; e.g. A. sediba; Matzke study on hominin brain size; sustained increase in brain size; no gap in record46. mjpallen: #grab2011 chimp genome confirms predictions from elsewhere; chromosomes 46 in man; 48 in great apes; chr 2 is fusion of two chimp chromosome45. mjpallen: #grab2011 fused chromsome has telomere in middle; 2 centromeres; one inactive; DNA seqs are facts; no ID explanation for this44. mjpallen: #grab2011 evolution doesn't imply Dawkinsism acc to Miller. Dan Dennett says God/evo not compatible; Miller says yes; Dobzhansky was X-ian43. mjpallen: #grab2011 nothing in biology makes sense in light of evolution; Dobzh also supported compatabilitism; evo is process of creation he said42. mjpallen: #grab2011 pope says evolution God do mix! St Augustine wrote universe evolved; Miller says scientists question 5th C mystic; but Mendel monk41. mjpallen: #grab2011 Mendel did expts even tho r[...]



Darwin's Shrewsbury

2011-09-25T06:00:35.352-07:00

Brief tour of Darwin sights in Shrewsbury for speakers at Great Read at Birmingham initiative. Sights include Darwin shopping centre, stained glass window of Darwin in McDonalds, Unitarian chapel, Darwin's schools and his birthplace (The Mount).

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http://youtu.be/iI1a2qybmlU



Visiting Down House with Randal Keynes

2011-09-25T05:51:30.542-07:00

I have now received two VIP tours of Down House with Randal Keynes (Darwin's great-great-grandson) as tour guide. Randal's mellifluous voice, sharp intellect and wide-ranging knowledge of Darwin's life, science and family make these trips an unforgettable treat!

Last Friday I visited with three eminent American speakers at the Great Read at Birmingham initiative: Ken Miller, John Hawks and Captain Ben Kirkup. John Hawks has already blogged on the experience here: http://johnhawks.net/weblog/hawks/travel/down-house-visit-2011.html

Last February, I visited with Eugenie Scott from the NCSE.

Below are links to YouTube videos of both trips. Watch them and fall under Randal's spell as he guides us through Darwin's home and gardens, his life and family.


Tour of Down House with Randal Keynes for Great Read at Birmingham speakers

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Tour of Down House with Randal Keynes and Eugenie Scott

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http://youtu.be/1EsAttZon0A

Relevant links



Ken Miller at the opening Great Read at Birmingham event

2011-09-24T12:24:02.656-07:00

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The Evolution Wars: Why they continue, Why they matter, by Ken Miller

Ken Miller speaking at the opening event of the Great Read at Birmingham initiative, in the Barber Institute, University of Birmingham, England, 22nd September 2011


















Adam Tickell on Thomas Henry Huxley at Great Read at Birmingham event

2011-09-24T12:07:34.583-07:00

Professor Adam Tickell, PVC for Research and Knowledge Transfer, University of Birmingham, speaking at the launch of the Great Read at Birmingham initiative, September 22nd 2011 Video and text of the speech width="425" height="349" src="http://www.youtube.com/embed/3pyp3UomaWY?hl=en&fs=1" frameborder="0" allowfullscreen>Dear students,I am sure that you have enjoyed the two excellent talks from our external speakers. First let me introduce myself. My name is Adam Tickell and I am Pro-Vice-Chancellor for Research here at the University of Birmingham, which means it is my job to ensure that the academics that lecture you produce the very best research that they can, on top of their excellent teaching.Now, I know that Mark Pallen later in the term is going to tell you about Charles Darwin, who formulated the Theory of Evolution. But it is worth stressing that Darwin was a retiring person who left the defence of his theory in the rough and tumble of Victorian society to others.His most famous, and robust, advocate was a remarkable man called Thomas Henry Huxley, who was so vociferous in his defence of Darwin’s theory that he earned the nickname Darwin’s Bulldog.Many of you will have heard of Huxley’s famous encounter in 1860 with the Bishop of Oxford, with the famous gibe about whether Huxley was descended from an ape via his grandmother or grandfather. In fact, that gibe was probably never uttered and one of the things you should learn in your three years is the importance of going beyond what is written in textbooks and newspapers and even academic publications and evaluating the evidence for yourselves!But whatever the truth of that encounter, Huxley was a remarkable individual. Although he left school at the age of ten, he was a voracious reader and taught himself science, philosophy, history and German. An adventurer medic, who served as surgeon’s mate on the delightfully named HMS Rattlesnake, as it surveyed northern Australia and New Guinea. An expert on invertebrate comparative biology, authoring several papers that clarified some tricky taxonomy.In 1854 Huxley took up a Chair of Natural History at the Royal College of Mines (now part of Imperial College), where for over thirty years he made valuable contributions to science and education in Britain. Huxley’s numerous achievements include his prescient classification of birds with dinosaurs (only recently recognized as correct), a treatise on the physical geography of the Thames valley, a classic book on crayfish and a biography of the Scottish philosopher David Hume. Huxley helped secularize schools, opened up adult education and transformed the academic activities of universities, viewing them as factories of new knowledge rather than storehouses of old. He even coined the word “agnostic”.Huxley also left behind a treasure trove of aphorisms:“After all, it is as respectable to be modified ape as to be modified dirt”“Life is too short to occupy oneself with the slaying of the slain more than once”“Science is organized common sense”“The great tragedy of science is the slaying of a beautiful hypothesis by an ugly fact.”From his biographer Edward Clodd, comes the greatest tribute of all: “It was worth being born to have known Huxley”!But why, you may ask I am bigging it up so much for Huxley?First, he is important in the history of ideas. Great ideas, like the theory of evolution, need to be argued over and Victorian society was, by no means, receptive to an explanation of life on earth that didn’t rely on God. Huxley’s advocacy of Darwin’s theor[...]



Great Read at Birmingham

2011-09-08T23:26:58.963-07:00

This week, all the new undergraduates at the University of Birmingham (~6000 students) will receive a copy of the same book in their Welcome Packs and be asked to read it before arriving to encourage to engage with academic ideas and to create a shared experience for all new students. That book is The Rough Guide to Evolution!The University believes that attending an institution like @uniBirmingham is about grappling with complex, multi-faceted, and even controversial ideas. As an academic community, the University welcomes and enjoys debate and hopes that this choice of book will stimulate discussion.The idea behind the the Great Read at Birmingham initiative was proposed by the Vice-Chancellor, Professor David Eastwood, and is based on many successful similar programmes run in North America. But no British university has ever implemented a programme on this scale before!There will be University-wide activities around the book during Welcome Week and the first term. Schools and departments will also use the book in study skills modules or in other ways.Events kick off with Great Read at Birmingham Guest Talks in Welcome WeekThursday 22 September 2011 15:30-17:00As part of the Great Read at Birmingham initiative, "Rough Guide to Evolution" author Professor Mark Pallen welcomes two great speakers on evolution to our University, speaking back to back in Welcome Week in the Barber Institute Concert Hall.This is open only to students at @uniBirmingham. Limited spaces available. First come, first served!THE EVOLUTION WARS: WHY DO THEY CONTINUE AND WHY DO THEY MATTER?Professor Ken Miller is a biochemist, textbook author, a Christian and an articulate spokesman for evolution. He played a key role laying out the evidence for evolution in the landmark Dover trial in 2005 and brings the full power of his engaging oratory to our first year students in his talk.NATURAL SELECTION, NEANDERTHAL GENOMES AND THE MYSTERY OF DENISOVA CAVEProfessor John Hawks is an expert on human evolution and a keen blogger. He will bring us all up to date with evidence for and ramifications of interbreeding between humans, Neanderthals and the mysterious Denisovans with his fascinating talk.Web page: http://www.birmingham.ac.uk/welcome/grab.aspxFacebook: http://www.facebook.com/pages/Great-Read-at-Birmingham/245600152143735Twitter: http://twitter.com/#!/greatreadatbham[...]



Rough Guide to Evolution now available on Kindle and as eBook

2011-09-08T12:58:09.745-07:00

Great news! The Rough Guide to Evolution is now available to buy as a Kindle eBook here:
And as a Adobe eBook here:
So, go on, indulge yourself and buy a copy now!



The evolution of biblical manuscripts

2011-08-30T13:08:29.126-07:00

In an ironic twist of fate that might infuriate creationist fundamentalist Christians, evolutionary thinking dominates scholarly studies of biblical manuscripts, particularly attempts to reconstruct original texts of the New Testament in the face of copying errors!The New Testament of the King James Bible is a seventeenth-century English translation of the Textus Receptus, a Greek text prepared by Dutch theologian Erasmus in the sixteenth century from a few late-medieval manuscripts. In the late nineteenth century, Birmingham-born theologian Brook Westcott and his Dublin-born collaborator Fenton Hort tried to improve on the Textus Receptus, publishing The New Testament in The Original Greek (1881), which incorporated information from a wide range of manuscripts, including the oldest fragments known at the time. Crucially, they adopted a genealogical view of manuscript affiliation that directly parallels the tree-like branching descent with modification seen in Darwin’s theory of evolution. In their own words: “All trustworthy restoration of corrupted texts is founded on the study of their history, that is, of the relations of descent or affinity which connect the several documents.” However, Westcott and Hort also recognized the potential for horizontal transfer between lineages, viewing the Byzantine textual lineage as a fusion of the two earlier traditions (the western and Alexandrian). In the early twentieth century, British theologian Burnett Streeter proposed a theory of local texts, in which textual traditions diverged as a result of geographical separation – a parallel with allopatric speciation in evolutionary biology. From the 1950s onwards, American biblical scholar Ernest Colwell attempted to bring quantitative methods into the analysis of New Testament textual traditions. Cladistic approaches borrowed from evolutionary biology now sit at the cutting edge of studies of New Testament manuscripts: exponents include David Parker, a theologian at the University of Birmingham, Gerd Mink at the Institute for New Testament Textual Research, Münster, Germany and among American scholars, Stephen Carlson.So, in conclusion, evolutionary thinking even illuminates the origins of the text of the Bible! [...]



Some Darwinian poetry to make you smile

2011-08-24T12:37:33.113-07:00

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Charles Darwin's grandfather Eramus Darwin was a brilliant but seriously bonkers chap--a kind of 18th Century English Rasta. You can read all about his interests on the relevant Wikipedia page, but I cannot help sharing these few lines from the Temple of Nature in which he sees the fruits of past (sensual or sexual) pleasure in geological sediments? What was he smoking?

"HEAR, O ye Sons of Time! your final doom,
And read the characters, that mark your tomb:
The marble mountain, and the sparry steep,
Were built by myriad nations of the deep, --
Age after age, who form'd their spiral shells,
Their sea-fan gardens and their coral cells;
Till central fires with unextinguished sway
Raised the primeval islands into day; --
The sand-fill'd strata stretch'd from pole to pole;
Unmeasured beds of clay, and marl, and coal,
Black ore of manganese, the zinky stone,
And dusky steel on his magnetic throne,
In deep morass, or eminence superb,
Rose from the wrecks of animal or herb;
These from their elements by Life combined,
Form'd by digestion, and in glands refined,
Gave by their just excitement of the sense
The Bliss of Being to the vital Ens.

"Thus the tall mountains, that emboss the lands,
Huge isles of rock, and continents of sands,
Whose dim extent eludes the inquiring sight,
ARE MIGHTY MONUMENTS OF PAST DELIGHT;
Shout round the globe, how Reproduction strives
With vanquish'd Death, -- and Happiness survives;
How Life increasing peoples every clime,
And young renascent nature conquers Time;
And high in golden characters record
The immense munificence of NATURE'S LORD!
For a roots reggae reinterpretation of some of Ras D's anti-slavery poetry, have a listen at this rough and ready bit of whimsy I cooked up a few years ago with a Jamaican friend.



Mary Anning: Fossil hunter extraordinaire

2011-08-12T00:02:17.516-07:00

Anyone off to Lyme Regis for their holidays should spare a thought for Mary Anning (1799-1847), who hailed from this English coastal town. Geologist and historian of science Hugh Torrens describes her as “the greatest fossilist the world ever knew”.

(image) Left destitute by the death of their father in 1810, Mary and her brother Joseph turned to collecting fossils from the local coastline (now styled the Jurassic Coast: see recent Guardian pics) in the hope of selling them to amateur collectors. At the age of twelve, just a few months after her father's death, Mary made a spectacular find that brought her to the attention of the scientific community: the first complete skeleton of an ichthyosaur (a giant "fish lizard") ever found. Although Joseph had found the skull (shown here) a year before, Mary was responsible for locating the rest of the fossil.

(image) Her subsequent discoveries included the first plesiosaur (her own drawing shown here) in 1821 and a remarkable specimen of an extinct ray-finned fish, Dapedium politum, in 1828. Anning also described the first complete skeleton of a flying reptile, the pterosaur Dimorphodon macronyx.

Later in life, Anning’s fame secured her financial support from the British Association for the Advancement of Science and honorary membership of the Geological Society of London—the only woman in an exclusively male club.

The chief impact of Anning’s work was that her fossils established beyond doubt the concept of extinction, proving that some extinct animals looked nothing like anything alive today. Anning died from breast cancer in her forties and is buried with her brother at St Michael’s Church, Lyme Regis, where a stained-glass window is dedicated to her memory.



Galton or Weismann first to continuity of the germ-plasm?

2011-08-11T07:08:51.208-07:00

While researching the previous post, my curiosity was piqued over a comment by Frank Darwin about his relative Francis Galton (who BTW was apprenticed here in Birmingham). While researching The Rough Guide to Evolution, I soon realised that many quotations are misattributed (here is one telling example) or quoted out of context and so good scholarship requires that one actually dig out the source and confirm that it says what it is purported to say. In the last few years, and even more so since I wrote the book, this has become a whole lot easier, largely thanks to the Google books initiative. So, let's return to what Frank wrote: “But in science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs. Not the man who finds a grain of new and precious quality, but to him who sows it, reaps it, grinds it and feeds the world on it.” which I and others have cited in the context of his father's theory of evolution. But if you look at the whole paragraph, it is clear that Frank was talking about an article in the Macmillan's Magazine by Francis Galton and the fact that Galton got to the theory of germ-plasm and what is often called the Weismann barrier earlier than August Weismann (who got there in the 1890s and is generally credited with priority):"With regard to the machinery of reproduction the essay is remarkable for containing what is practically identical with Weismann’s continuity of the germ-cell, and Galton’s priority is acknowledged by that author. But in science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs. Not the man who finds a grain of new and precious quality, but to him who sows it, reaps it, grinds it and feeds the world on it. This is true of this very Macmillan’s Magazine article. Who would know of these admirable views on Hereditary Genius and Eugenics, if this were Galton’s only utterance? This is the grain which has increased and multiplied: and it is to-day familiar nutriment, and is now assiduously cultivated by the Eugenics Education Society. But if Natural Inheritance, and Hereditary Genius had not been written; if the papers on eugenics had not appeared, and especially if he had not convinced the world of his seriousness by creating a eugenic foundation at University College, where his friend Professor Karl Pearson carries on the Galtonian traditions—why then the paper in Macmillan would have counted for very little. But it was not quite unnoticed. By my father it is referred to in the Variation of Animals and Plants under Domestication. Galton was encouraged and reassured by Darwin’s appreciation of his work: his words in Hereditary Genius are, “I feel assured that, inasmuch as what I then wrote was sufficient to earn the acceptance of Mr. Darwin . . . the increased amount of evidence submitted in the present volume is not likely to be gainsaid.” He was characteristically generous in owning his debt to the author of the Origin of Species, and characteristically modest in the value he ascribed to my father’s words." So, does this mean the textbooks (and wikipedia) need re-writing? Should Weismann be demoted in the pantheon of the history of science? Well, a few moments with Google turns up the article that Frank was discussing and here is the relevant passage:"If we examine the question from the opposite side, a list of life-long [...]