Sunday, January 25, 2009

Darwin Tree of Life mug & T-Shirt





Buy from Natural History Museum

I've already got the Tree of Life T Shirt.

VIDEO: Evolution of Technology, From Dinosaur Robots to Modern Androids

This is an ad for a German electronics store: "The evolution of technology, beginning in the early stone age and evolving to the most powerfull technology of all times." Via Laughing Squid via http://thedispersalofdarwin.blogspot.com/


The Dispersal of Darwin


Great resource by Darwins 21st Century Bulldog.

Hey Charley (1992) by Suzi Quatro

source: http://thedispersalofdarwin.blogspot.com

Saturday, January 24, 2009

Why Darwin was wrong about the tree of life

Letter responding to the 'Darwin was wrong' cover.

Darwin was right


What on earth were you thinking when you produced a garish cover proclaiming that "Darwin was wrong" (24 January)?

First, it's false, and second, it's inflammatory. And, as you surely know, many readers will interpret the cover not as being about Darwin, the historical figure, but about evolution.

Nothing in the article showed that the concept of the tree of life is unsound; only that it is more complicated than was realised before the advent of molecular genetics. It is still true that all of life arose from "a few forms or... one", as Darwin concluded in The Origin of Species. It is still true that it diversified by descent with modification via natural selection and other factors.

Of course there's a tree; it's just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA.

The accompanying editorial makes it clear that you knew perfectly well that your cover was handing the creationists a golden opportunity to mislead school boards, students and the general public about the status of evolutionary biology. Indeed, within hours of publication members of the Texas State Board of Education were citing the article as evidence that teachers needed to teach creationist-inspired "weaknesses of evolution", claiming: "Darwin's tree of life is wrong".

You have made a lot of extra, unpleasant work for the scientists whose work you should be explaining to the general public. We all now have to try to correct all the misapprehensions your cover has engendered.

• Find a longer version of this letter online.


Read our related editorial: Uprooting Darwin's tree

IN JULY 1837, Charles Darwin had a flash of inspiration. In his study at his house in London, he turned to a new page in his red leather notebook and wrote, "I think". Then he drew a spindly sketch of a tree.

As far as we know, this was the first time Darwin toyed with the concept of a "tree of life" to explain the evolutionary relationships between different species. It was to prove a fruitful idea: by the time he published On The Origin of Species 22 years later, Darwin's spindly tree had grown into a mighty oak. The book contains numerous references to the tree and its only diagram is of a branching structure showing how one species can evolve into many.

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth...

The tree-of-life concept was absolutely central to Darwin's thinking, equal in importance to natural selection, according to biologist W. Ford Doolittle of Dalhousie University in Halifax, Nova Scotia, Canada. Without it the theory of evolution would never have happened. The tree also helped carry the day for evolution. Darwin argued successfully that the tree of life was a fact of nature, plain for all to see though in need of explanation.

The explanation he came up with was evolution by natural selection.

Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top - these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life.

...The green and budding twigs may represent existing species, and those produced during each former year may represent the long succession of extinct species

For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence.

Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

So what happened? In a nutshell, DNA.

The discovery of the structure of DNA in 1953 opened up new vistas for evolutionary biology. Here, at last, was the very stuff of inheritance into which was surely written the history of life, if only we knew how to decode it. Thus was born the field of molecular evolution, and as techniques became available to read DNA sequences and those of other biomolecules such as RNA and proteins, its pioneers came to believe that it would provide proof positive of Darwin's tree of life.

The basic idea was simple: the more closely related two species are (or the more recently their branches on the tree split), the more alike their DNA, RNA and protein sequences ought to be.

It started well. The first molecules to be sequenced were RNAs found in ribosomes, the cell's protein-making machines. In the 1970s, by comparing RNA sequences from various plants, animals and microorganisms, molecular biologists began to sketch the outlines of a tree.

This led to, among other successes, the unexpected discovery of a previously unknown major branch of the tree of life, the unicellular archaea, which were previously thought to be bacteria.
By the mid-1980s there was great optimism that molecular techniques would finally reveal the universal tree of life in all its glory. Ironically, the opposite happened.


The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.


Which was correct? Paradoxically, both - but only if the main premise underpinning Darwin's tree was incorrect.


Darwin assumed that descent was exclusively "vertical", with organisms passing traits down to their offspring. But what if species also routinely swapped genetic material with other species, or hybridised with them? Then that neat branching pattern would quickly degenerate into an impenetrable thicket of interrelatedness, with species being closely related in some respects but not others.

We now know that this is exactly what happens. As more and more genes were sequenced, it became clear that the patterns of relatedness could only be explained if bacteria and archaea were routinely swapping genetic material with other species - often across huge taxonomic distances - in a process called horizontal gene transfer (HGT). (wikipedia) - See image HGT - This is a image of the more or less current tree of life showing the 5 kingdoms and how genetic inheritance is now thought to be not exactly vertical but also includes horizontal gene inheritance via at least virus infection and maybe other routes such as the incorporation of mitochondria and plastids as symbiotic partners within Eukaryote cells.

At first HGT was assumed to be a minor player, transferring only "optional extra" functions such as antibiotic resistance. Core biological functions such as DNA replication and protein synthesis were still thought to be passed on vertically. For a while, this allowed evolutionary biologists to accept HGT without jeopardising their precious tree of life; HGT was merely noise blurring its edges. We now know that view is wrong. "There's promiscuous exchange of genetic information across diverse groups," says Michael Rose, an evolutionary biologist at the University of California, Irvine.

From tree to web

As it became clear that HGT was a major factor, biologists started to realise the implications for the tree concept. As early as 1993, some were proposing that for bacteria and archaea the tree of life was more like a web. In 1999, Doolittle made the provocative claim that "the history of life cannot properly be represented as a tree" (Science, vol 284, p 2124). "The tree of life is not something that exists in nature, it's a way that humans classify nature," he says.
Thus began the final battle over the tree. Many researchers stuck resolutely to their guns, creating ever more sophisticated computer programs to cut through the noise and recover the One True Tree. Others argued just as forcefully that the quest was quixotic and should be abandoned.
The battle came to a head in 2006. In an ambitious study, a team led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, examined 191 sequenced genomes from all three domains of life - bacteria, archaea and eukaryotes (complex organisms with their genetic material packaged in a nucleus) - and identified 31 genes that all the species possessed and which showed no signs of ever having been horizontally transferred. They then generated a tree by comparing the sequences of these "core" genes in everything from E. coli to elephants. The result was the closest thing yet to the perfect tree, Bork claimed (Science, vol 311, p 1283).
Other researchers begged to differ. Among them were Tal Dagan and William Martin at the Heinrich Heine University in Düsseldorf, Germany, who pointed out that in numerical terms a core of 31 genes is almost insignificant, representing just 1 per cent of a typical bacterial genome and more like 0.1 per cent of an animal's. That hardly constitutes a mighty oak or even a feeble sapling - more like a tiny twig completely buried by a giant web. Dagan dubbed Bork's result "the tree of 1 per cent" and argued that the study inadvertently provided some of the best evidence yet that the tree-of-life concept was redundant (Genome Biology, vol 7, p 118).
The debate remains polarised today. Bork's group continue to work on the tree of life and he continues to defend the concept. "Our point of view is that yes, there has been lots of HGT, but the majority of genes contain this tree signal," Bork says. The real problem is that our techniques are not yet good enough to tease that signal out, he says.
Meanwhile, those who would chop down the tree of life continue to make progress. The true extent of HGT in bacteria and archaea (collectively known as prokaryotes) has now been firmly established. Last year, Dagan and colleagues examined more than half a million genes from 181 prokaryotes and found that 80 per cent of them showed signs of horizontal transfer (Proceedings of the National Academy of Sciences, vol 105, p 10039).

Surprisingly, HGT also turns out to be the rule rather than the exception in the third great domain of life, the eukaryotes. For a start, it is increasingly accepted that the eukaryotes originated by the fusion of two prokaryotes, one bacterial and the other archaeal, forming this part of the tree into a ring rather than a branch (Nature, vol 41, p 152).

The neat picture of a branching tree is further blurred by a process called endosymbiosis. Early on in their evolution, eukaryotes are thought to have engulfed two free-living prokaryotes. One of these gave rise to the cellular power generators called mitochondria while the other was the precursor of the chloroplasts, in which photosynthesis takes place. These "endosymbionts" later transferred large chunks of their genomes into those of their eukaryote hosts, creating hybrid genomes. As if that weren't complicated enough, some early eukaryotic lineages apparently swallowed one another and amalgamated their genomes, creating yet another layer of horizontal transfer (Trends in Ecology and Evolution, vol, 23, p 268).
This genetic free-for-all continues to this day. The vast majority of eukaryote species are unicellular - amoebas, algae and the rest of what used to be known as "protists" (Journal of Systematics and Evolution, vol 46, p263). These microscopic beasties have lifestyles that resemble prokaryotes and, according to Jan Andersson of the University of Uppsala in Sweden, their rates of HGT are often comparable to those in bacteria. The more we learn about microbes, the clearer it becomes that the history of life cannot be adequately represented by a tree.
Hang on, you may be thinking. Microbes might be swapping genes left, right and centre, what does that matter? Surely the stuff we care about - animals and plants - can still be accurately represented by a tree, so what's the problem?
Well, for a start, biology is the science of life, and to a first approximation life is unicellular. Microbes have been living on Earth for at least 3.8 billion years; multicellular organisms didn't appear until about 630 million years ago. Even today bacteria, archaea and unicellular eukaryotes make up at least 90 per cent of all known species, and by sheer weight of numbers almost all of the living things on Earth are microbes. It would be perverse to claim that the evolution of life on Earth resembles a tree just because multicellular life evolved that way.

"If there is a tree of life, it's a small anomalous structure growing out of the web of life," says John Dupré, a philosopher of biology at the University of Exeter, UK.

More fundamentally, recent research suggests that the evolution of animals and plants isn't exactly tree-like either. "There are problems even in that little corner," says Dupré. Having uprooted the tree of unicellular life, biologists are now taking their axes to the remaining branches.

For example, hybridisation clearly plays an important role in the evolution of plants. According to Loren Rieseberg, a botanist at the University of British Columbia in Vancouver, Canada, around 14 per cent of living plant species are the product of the fusion of two separate lineages.

Hybrid humans

Some researchers are also convinced that hybridisation has been a major driving force in animal evolution (see "Natural born chimeras", and "Two into one"), and that the process is ongoing. "It is really common," says James Mallet, an evolutionary biologist at University College London. "Ten per cent of all animals regularly hybridise with other species." This is especially true in rapidly evolving lineages with lots of recently diverged species - including our own. There is evidence that early modern humans hybridised with our extinct relatives, such as Homo erectus and the Neanderthals (Philosophical Transactions of the Royal Society B, vol 363, p 2813).

Hybridisation isn't the only force undermining the multicellular tree: it is becoming increasingly apparent that HGT plays an unexpectedly big role in animals too. As ever more multicellular genomes are sequenced, ever more incongruous bits of DNA are turning up. Last year, for example, a team at the University of Texas at Arlington found a peculiar chunk of DNA in the genomes of eight animals - the mouse, rat, bushbaby, little brown bat, tenrec, opossum, anole lizard and African clawed frog - but not in 25 others, including humans, elephants, chickens and fish. This patchy distribution suggests that the sequence must have entered each genome independently by horizontal transfer (Proceedings of the National Academy of Sciences, vol 105, p 17023).

Other cases of HGT in multicellular organisms are coming in thick and fast.

HGT has been documented in insects, fish and plants, and a few years ago a piece of snake DNA was found in cows. The most likely agents of this genetic shuffling are viruses, which constantly cut and paste DNA from one genome into another, often across great taxonomic distances.


In fact, by some reckonings,

40 to 50 per cent of the human genome consists of DNA imported horizontally by viruses, some of which has taken on vital biological functions (New Scientist, 27 August 2008, p 38). The same is probably true of the genomes of other big animals.

"The number of horizontal transfers in animals is not as high as in microbes, but it can be evolutionarily significant," says Bapteste.

Nobody is arguing - yet - that the tree concept has outlived its usefulness in animals and plants. While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another - a tree of 51 per cent, maybe. In that respect, Darwin's vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him.
Even so, it is clear that the Darwinian tree is no longer an adequate description of how evolution in general works. "If you don't have a tree of life, what does it mean for evolutionary biology?" asks Bapteste. "At first it's very scary... but in the past couple of years people have begun to free their minds." Both he and Doolittle are at pains to stress that

downgrading the tree of life doesn't mean that the theory of evolution is wrong - just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not. "We should relax a bit on this," says Doolittle. "We understand evolution pretty well - it's just that it is more complex than Darwin imagined. The tree isn't the only pattern."

Others, however, don't think it is time to relax. Instead, they see the uprooting of the tree of life as the start of something bigger. "It's part of a revolutionary change in biology," says Dupré. "Our standard model of evolution is under enormous pressure.

We're clearly going to see evolution as much more about mergers and collaboration than change within isolated lineages."

Rose goes even further. "The tree of life is being politely buried, we all know that," he says. "What's less accepted is that our whole fundamental view of biology needs to change." Biology is vastly more complex than we thought, he says, and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.

If he is right, the tree concept could become biology's equivalent of Newtonian mechanics: revolutionary and hugely successful in its time, but ultimately too simplistic to deal with the messy real world. "The tree of life was useful," says Bapteste. "It helped us to understand that evolution was real. But now we know more about evolution, it's time to move on."

Read our related editorial: Uprooting Darwin's tree

Two species become one

It could be time to ditch the old idea that hybrids are sterile individuals that cannot possibly have played a role in shaping the history of life on Earth. Hybridisation is a significant force in animal evolution, according to retired marine biologist Donald Williamson, formerly of the University of Liverpool, UK. His conclusion comes from a lifetime studying marine animals such as starfish, sea urchins and molluscs, many of which lead a strange double life, starting out as larvae and metamorphosing into adult forms.
The conventional explanation for metamorphosis is that it evolved gradually, with the juvenile form becoming specialised for feeding and the adult for mating, until they barely resembled each other. Williamson thinks otherwise. He points out that marine larvae have five basic forms and can be organised into a family tree based on shared characteristics. Yet this tree bears no relationship to the family tree of adults: near-identical larvae often give rise to adults from different lineages, while some closely related adults have utterly unrelated larvae.
BIOLOGICAL MASH-UP
It's as if each species was randomly assigned one of the larval forms - which is exactly what Williamson argues happened. He believes metamorphosis arose repeatedly during evolution by the random fusion of two separate species, with one of the partners assuming the role of the larva and the other that of the adult.
If that sounds unlikely, Williamson points out that many marine species breed by casting their eggs and sperm into the sea and hoping for the best, giving ample opportunity for cross-species hybridisation. Normally nothing comes of this, he says, but "once in a million years it works: the sperm of one species fertilises another and two species become one". The most likely way for this biological mash-up to function is if the resulting chimera expresses its two genomes sequentially, producing a two-stage life history with metamorphosis in the middle.
This explains many anomalies in marine biology, says Williamson. His star witness is the starfish Luidia sarsi, which starts life as a small larva with a tiny starfish inside. As the larva grows, the starfish migrates to the outside and when the larva settles on the seabed, they separate. This is perfectly normal for starfish, but in Luidia something remarkable then happens. Instead of degenerating, the larva swims off and lives for several months as an independent animal. "I can't see how one animal with one genome could do that," says Williamson. "I think the larval genome and the adult genome are different."

Natural born chimeras

The idea that microbes regularly swap portions of genetic code with individuals from another species doesn't seem so far-fetched (see main story). But could the same process also have shaped the evolution of multicellular animals? In 1985, biologist Michael Syvanen of the University of California, Davis, predicted that it did (Journal of Theoretical Biology, vol 112, p 333). Back then there was no way to test that claim, but there is now.
Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals.
He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes.
Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says.
The most likely explanation for this, he argues, is that tunicates are chimeras, created by the fusion of an early chordate and an ancestor of the sea urchins around 600 million years ago.
"We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?"

Monday, January 19, 2009

MPs in call for new public holiday for Darwin Day

via http://www.humanism.org.uk/news/view/205

MPs are being urged to give their support to an Early Day Motion tabled in the House of Commons to make Charles Darwin’s birthday – 12th February – an annual public holiday.

The motion, tabled by Ashok Kumar MP, which has already received the support of ten other MPs says:

That this House notes the extraordinary achievements of Charles Darwin; notes that 2009 marks both the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of On the Origin of Species; welcomes proposals for the creation of a Darwin Day in recognition of the ground-breaking work of the British scientist responsible for the theory of evolution by natural selection; and calls for Darwin's birthday, 12 February, to be designated a public holiday in honour of one of the fathers of modern science and one of Britain's greatest, if not the greatest, scientific minds.

2009 is the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of ‘On the Origin of Species’ and campaigners are making use of these anniversaries to redouble their efforts to have the day marked officially. In 2003, over 40 distinguished academics, philosophers, scientists and writers called for a new public holiday, including philosopher Simon Blackburn, biologist Richard Dawkins, co-discoverer of DNA Francis Crick, author Philip Pullman and writer and broadcaster Claire Rayner. Members of the public are being urged to write to their own MP to request their support for the motion.

Andrew Copson, BHA Director of Education and Public Affairs said, ‘Charles Darwin is one of the greatest and most influential thinkers who ever lived and one of Britain’s greatest scientists. In the middle of February we could all do with an extra public holiday and recognition of this particular day would be a great way of celebrating Britain’s great contribution to science, reason and freethought.’

The British Humanist Association supports the campaign to have Darwin Day made a public holiday and is running its own series of events in 2009 to celebrate Darwin’s anniversary.

Notes

You can read the EDM (number 377) here

You can email your MP and urge him or her to sign EDM 377

For further comment, contact Andrew Copson by email or on 020 7079 3584 or 07534 248596

The British Humanist Association (BHA) is the national charity representing the interests of the large and growing population of ethically concerned non-religious people living in the UK. It exists to support and represent such people, who seek to live good lives without religious or superstitious beliefs.

Thursday, January 15, 2009

Darwin 200 by Focus Magazine, Richard Dawkins, PZ Myers, Carl Zimmer, Steve Jones

Charles Darwin effectively rewrote the history of not only Man, but every living thing on the planet. This special section looks at the legacy of the man whose ideas changed everything

(This "digimag" requires the Flash player)

click here to read digimag.


Mark Steel: The Mark Steel lectures - Charles Darwin (1/3)

1/3


2/3



3/3

Mark Steel: What creationists really hate is that we emerged by accident



If all species were designed, it was hardly by someone intelligent

Wednesday, 7 January 2009

An undated picture of Charles Darwin (1809-1882)

PA photo/The Natural History Museum.

An undated picture of Charles Darwin (1809-1882)

Charles Darwin would probably love the fact that the 200th anniversary of his birth is being celebrated with radio shows, documentaries and exhibitions, but he might not have enjoyed the way that furious Christians still despise his theories and try to prove the Bible is more reliable.

For example, the Discovery Institute has announced that: "We want students everywhere to speak out... for the right to debate the evidence against evolution and turn 'Darwin Day' into 'Academic Freedom Day'."

But they're lucky Darwin isn't forced on us the way religion has been, otherwise the national anthem would start: "Our Gracious Queen will be saved or not according to a series of factors that are sod-all to do with God," and once a week school assemblies would start with everyone singing: "All things biological/ All matter sweet or frightening/ Are Godless, real and logical/ See – where's the bleeding lightning?"

The creationists demand that biblical theories are taught alongside Darwin's theories of natural selection, which might sound reasonable except that creationism depends not on evidence but on faith. If all theories are given equal status, teachers could say: "Your essays on the cause of tornadoes were very good. Nathan's piece detailing the impact of warm moist air colliding with cool air, with original sources from the Colorado Weather Bureau, contained some splendid detail. But Samatha's piece that went "Because God is cross" was just as good so you all get a B+."

To improve their standing the anti-Darwin lobby have changed their tactics, so now instead of arguing for creationism they call their theory "intelligent design".

Mostly this consists of trying to illustrate how species are too complex to have been formed by nature. But then they can't help themselves, so you get articles such as the one by prominent advocate of intelligent design, David Berlinski, that starts: "Charles Darwin says, 'In the struggle for survival, the fittest win out at the expense of their rivals.' Another man, Adolf Hitler says 'Let us kill all the Jews of Europe.' Is there a connection? Yes is the obvious answer."

So there we are – study the differences between finches and you're half way to organising a holocaust.

The founders of intelligent design are nearly all creationists, and one of their books, Of Pandas and People, is identical to a book used by creationists. Except that, after a ruling in the US Supreme Court that creationism couldn't be taught in schools, the word "creationist" was deleted throughout, and replaced with "intelligent design".

The new theory, where it is new, states there are many species that can't have become the way they are through gradual evolution, because if you remove any one part of them the whole structure would collapse. So they must have been created whole, as they are now, without changing. But

this ignores the beauty of Darwin's discovery, which is that species change not because they're on a march towards perfection but by accident.

What may be ideal for survival one day is no good once the environment has changed. For example if it gets colder, or the colour of the surroundings changes, the individuals in a species best suited to the new conditions will be the ones to last, and the species becomes altered.

Survival of the fittest means those accidentally matching the requirements of a new situation, not the creatures most prone to winning a scrap.
Otherwise by now the only hamsters to survive would be those ones who could pick up the wheel and smash it over their mate's head, and the only surviving parrots would be the ones squawking: "Who wants some? Who wants some?"

And this dominance of the accidental is the most damning argument against intelligent design, because if all species were designed, it was hardly done by someone intelligent. If it was, how do you account for the parasitic wasp that lays eggs on its prey so they hatch and eat its victim while it's still alive?

More to the point, why are your most sensitive nerves at the end of your toe, where they're most likely to get walloped? Why are men's nuts in such a vulnerable location, ay? Bloody vindictive design that is. Why do dogs do the squashiest, most unpleasant turds that hide in the grass and spread themselves in the indentations on the bottom of your shoe, but don't start smelling until you get indoors and then render the place uninhabitable until you've left every window open for a month? Why, why, why?

Come on intelligent design people, the questions you have to answer have barely begun.

Darwin Day Cards

Print them off: http://flickr.com/photos/flashmaggie/sets/72157612489407485/detail/

Wednesday, January 14, 2009

Dara O'Briain and Frankie Boyle on religion and creationism

just how good is the evidence for evolution?

Not everyone accepts the theory of evolution. This month, as part of our Darwin forum, Paul Craze invites you to discuss the question "just how good is the evidence for evolution?"

Scientific theories stand or fall on their ability to account for the available evidence and to accurately predict the outcome of experiments designed to test them. That is all. No matter who came up with the theory, no matter how clever they are or were, no matter how elegant their ideas, no matter how many programs have been made about them by the BBC or years dedicated to honour their birthdays; if there is enough good, reliable evidence that the theory is wrong then it is wrong.

And so the question “Just how good is the evidence for evolution?” is of vital importance. In fact, we should probably recognise two questions here; firstly, “Just how good is the evidence for natural selection?” and then “Just how good is the evidence for the larger scale processes of evolution?”.

There is an enormous body of reliable evidence that natural selection is a real biological process capable of altering the characteristics of populations over time. Such classic examples as industrial melanism in the peppered moth are the tip of a very large iceberg of studies that confirm the reality of natural selection.

As a rule, the larger scale processes of evolution (those that have caused the diversification of a single, ancient, ancestral lineage into the full array of organisms we see today) cannot be seen directly and so are more difficult to test. Except in a few unusual cases they take far too long for us to have any hope of seeing them actually taking place.

The fact that they have occurred and continue to occur must be inferred from indirect observations, in much the same way as the guilt or innocence of someone tried for a murder is inferred from the evidence by the judge and jury, none of whom actually witnessed the crime.

We have essentially two lines of evidence: the snapshots we have of the process of evolution occurring in the past (the fossil record) and the organisms we see alive today (which have evolved and continue to evolve).

Increasingly the evidence from current organisms includes their DNA, which is being shown to contain many indications of past evolution. The critical role of this evidence means it has to be considered objectively and honestly with any assumptions and uncertainties clearly stated. It also means multiple lines of evidence have to be considered together in order to come up with a conclusion based on “the balance of probabilities”.

Again, the analogy of a criminal trial is useful here. Convictions are usually made based on conclusions that are “beyond reasonable doubt” rather than definite. The judge and jury must weigh up multiple lines of evidence some of which may be uncertain or even appear contradictory.

It works most of the time and in those cases where mistakes are made it is always because new evidence comes to light. The similarities to the process of science are very clear. And so in this theme there is the opportunity to present and examine the available evidence openly and honestly and subject the theory of evolution to yet another re-trial. Let us see if it emerges “beyond reasonable doubt” as the most likely explanation.

Content last updated: 27/11/2008

The Genius of Evolution - BBC

Darwinian selection explains seemingly ‘designed’ complexity - biology, economy, technology & the arts


Document The Natural Order Of Things

by Matt Ridley, Spectator

Reposted from:
http://www.spectator.co.uk/the-magazine/features/3213246/the-natural-order-of-things.thtml

Matt Ridley says that Darwinian selection explains the appearance of seemingly ‘designed’ complexity throughout the world — not just in biology but in the economy, technology and the arts

Charles Darwin, who was born 200 years ago next month, has spent the 150 years since he published The Origin of Species fighting for the idea of common descent. Though physically dead, he is still doing battle for the notion that chimps are your cousins and cauliflowers your kin. It is a sufficiently weird concept to keep Darwin relevant, revered and resented in equal measure.
But in some ways it is less radical and topical than his other, more philosophical legacy: that order can generate itself, that the living world is a ‘bottom-up’ place.
On the internet, Darwinian unordained order is now ubiquitous as never before.

Living beings are eddies in the stream of entropy. That is to say, while the universe gradually becomes more homogeneous and disordered, little parts of it can reverse the trend and become briefly more ordered and complex by capturing packets of energy. It happens each time a baby is conceived. Built by 20,000 genes that turn each other on and off in a symphony of great precision, and equipped with a brain of ten trillion synapses, each refined and remodelled by early and continuing experience, you are a thing of exquisite neatness, powered by glucose. Says Darwin, this came about by bottom-up emergence, not top-down dirigisme.
Faithful reproduction, occasional random variation and selective survival can be a surprisingly progressive and cumulative force: it can gradually build things of immense complexity.
Indeed, it can make something far more complex than a conscious, deliberate designer ever could: with apologies to William Paley and Richard Dawkins, it can make a watchmaker.

Ideas evolve by descent with modification, just as bodies do, and Darwin at least partly got this idea from economists, who got it from empirical philosophers.
Locke and Newton begat Hume and Voltaire who begat Hutcheson and Smith who begat Malthus and Ricardo who begat Darwin and Wallace.
Before Darwin, the supreme example of an undesigned system was Adam Smith’s economy, spontaneously self-ordered through the actions of individuals, rather than ordained by a monarch or a parliament.
Where Darwin defenestrated God, Smith had defenestrated government.
Neatly, this year also sees a Smith anniversary, the 250th birthday of his first book, The Theory of Moral Sentiments, a book that is very Darwinian in its insistence that sympathy is what we would today call innate, that people are naturally nice as well as naturally nasty.

Darwin’s debt to the political economists is considerable. In his last year at Cambridge in 1829, he reported in a letter, ‘My studies consist in Adam Smith and Locke’. At Maer, his uncle Josiah Wedgwood’s house in Staffordshire, he often met the lawyer and laissez-faire politician Sir James Mackintosh (whose daughter married Darwin’s brother-in-law and had an affair with his brother). On the Beagle, he read the naturalist Henri Milne-Edwards, who took Adam Smith’s notion of the division of labour and applied it to the organs of the body. Darwin promptly re-applied it to the division of labour among specialised species in an ecosystem: ‘The advantage of diversification in the inhabitants of the same region is, in fact, the same as that of the physiological division of labour in the organs of the same individual body — a subject so well elucidated by Milne-Edwards.’

Today, generally, Adam Smith is claimed by the Right, Darwin by the Left. In the American South and Midwest, where Smith’s individualist, libertarian, small-government philosophy is all the rage, Darwin is reviled for his contradiction of creation.
Yet if the market needs no central planner, why should life need an intelligent designer?
Conversely, in the average European biol- ogy laboratory you will find fervent believers in the individualist, emergent, decentralised properties of genomes who prefer dirigiste determinism to bring order to the economy.

So long is the shadow cast by the determinism of Karl Marx that it is often forgotten how radical the economic liberalism of the political economists seemed in the 1830s, the decade when Darwin’s thinking crystallised. This is well illustrated by the case of Harriet Martineau, who had a small but seminal influence on Darwin. The daughter of a Norwich cotton manufacturer ruined by a bank crash in the 1820s, Martineau lived by her pen. She was a radical, outspoken feminist, who toured America bravely inveighing against slavery and became so notorious that there were plans to lynch her in South Carolina. Yet before that, she had shot to fame with a series of short fictional books called Illustrations of Political Economy, which were intended to educate people in the free-trade, free-market ideas of Adam Smith (‘whose excellence is marvellous’, she said), David Ricardo and Robert Malthus, and in particular to persuade the working classes that their interests were congruent with those of their employers.

Martineau’s Illustrations were written while Darwin was on HMS Beagle. After she returned from America she became a very close friend of his elder brother Erasmus, who saw her almost daily in the late 1830s. Erasmus introduced Harriet to Charles, who was soon hanging on her every word. Had he not been ‘astonished to find how ugly she is’, Charles might have justified his father’s worry that one of his sons would marry her (as it was, cautious Charles preferred his god-fearing mouse of a cousin Emma Wedgwood to this free-thinking literary lioness). Undoubtedly they discussed slavery, which had horrified Darwin in Brazil. But since Martineau had been a close confidante of Malthus — despite his speech impediment and her deafness — there is little doubt that they also talked political economy.

Was it a coincidence that Darwin read Malthus, probably not for the first time, in October 1838, just as he was looking for a mechanism to explain evolution?

Malthus taught Darwin the bleak lesson that overbreeding must end in pestilence, famine or violence — and hence gave him the insight that in a struggle for existence, survival could be selective. But the notion that, with random variation, this selective survival could then generate complexity and sophistication where there had been none before, that it is a cumulative and creative force, is entirely his. It is also one that applies to more than the bodies of living beings.
Technology is a case in point. Although engineers are under the fond illusion that they design things, nearly all of what they do consists of nudging forward descent with modification.
Every technology has traceable ancestry; ‘to create is to recombine’ said the geneticist François Jacob.

The first motor car was once described by the historian L.T.C. Rolt as ‘sired by the bicycle out of the horse carriage’.
Just like living systems, technologies experience mutation (such as the invention of the spinning jenny), reproduction (the rapid mechanisation of the cotton industry as manufacturers copied each others’ machines), sex (Samuel Crompton’s combination of water frame and jenny to make a ‘mule’), competition (different designs competing in the early cotton mills), extinction (the spinning jenny was obsolete by 1800), and increasing complexity (modern cotton mills are electrified and computerised).

Technology also experiences progress and ‘arms races’ between competitors. Just as a modern horse could outrun a Mesohippus three-toed horse from 30 million years ago, so a car can outrun a horse-drawn carriage. Yet horses can only just go fast enough to escape today’s lions, and Land Rovers can only just perform well enough to maintain market share against Toyotas.
Such running to stay in the same (improving) place is known to biologists as a Red Queen process after the character in Lewis Carroll’s Through the Looking Glass.
Software inventors have learnt to recognise the power of trial and error rather than deliberate design. Beginning with ‘genetic algorithms’ in the 1980s, they designed programmes that would experiment with changes in their sequence till they solved the problem set for them. Then gradually the open-source software movement emerged by which users themselves altered programmes and shared their improvements with each other. Linux and Apache are operating systems designed by such democratic methods, but the practice has long spread beyond programmers.
Wikipedia is a bottom-up knowledge repository and, though far from flawless, is proving easily capable, even in its first flush of youth, of matching expert-written encyclopaedias for accuracy and reach. It grows by natural selection among edits.
The internet is an increasingly Darwinian place, where decentralised, self-organising sophistication holds sway: swarm intelligence is the fashionable term. Trey Ratcliff, founder of a computer games company in Texas, tells me he feels more like a victim than a designer of technology’s evolution: ‘saying Edison invented the phonograph is like saying a spider invented silk’.
The supreme example of bottom-up, rather than top-down, complexity is the market itself. As the economist Paul Seabright has written, the almost miraculous system by which he can go out and buy a cotton shirt on a whim — and expect the cotton grower, the weaver, the shirtmaker, the shipper and the retailer to have got it ready for him just when he enters the shop — is not planned or designed, it evolves. The top-down alternative does not have a great track record. Can you doubt that if the shirt industry was run by a National Shirt Service, there would now be queues, quotas and shortages?
Dirigisme has a place, of course, in the regulation and operation if not the design of institutions. A school cannot work without a teacher, a firm without a manager, or an army without a general — just as a body is directed by a brain in its everyday operations. But hubristic human beings tend to exaggerate the degree to which they are in charge of, rather than at the mercy of, organisations.

The dark side of bottom-up Darwinism is that cumulative complexity can come about only through selective death or selective celibacy. Wonderful life may result, but it is born red in tooth and claw. The social Darwinists of the 19th century and the eugenicists of the 20th were of the view that the strong should therefore be encouraged to succeed, the better to keep natural selection going. But this is to misread human society.
The human body may have come about through three billion years of natural selection among genes, but civilisation and prosperity came from 50,000 years of much more rapid natural selection among ideas.
It is easily possible to blunt genetic selection in the name of kindness, while allowing cultural selection to continue: the death of an idea need not be cruel.

There is, however, one more disturbing and topical parallel between biological and cultural evolution. Just as natural selection’s constructive capacity did not prevent mass extinctions, one of which, 251 million years ago, eradicated over 96 per cent of marine species, so the market’s ability to build order cannot prevent crashes. Even sophisticated, entropy-defying complex systems are subject to the weather-like vagaries of mathematical chaos — and there Darwin cannot help.

Tuesday, January 6, 2009

10 Lectures on Darwin's Legacy

by Stanford University

10 lectures of around two hours each on Darwin's Legacy from the Continuing Studies course (DAR 200) at Stanford University.


Introductory lecture. Professor Durham provides an overview of the course; Professor Robert Siegel touches upon "Darwin's Own Evolution;" Professor Durham returns for a talk on "Darwin's Data;" and the lecture concludes with a panel discussion moderated by Dr. Lynn Rothschild.


Lecture 2 by Eugenie Scott. Dr. Scott explores the evolution vs. creationism debate and provides an argument for evolution. The lecture is concluded with a panel discussion with Brent Sockness and Jeff Wine.


Lecture 3 by Janet Browne. Dr. Browne presents a biography on Charles Darwin and explores Darwin's Origin of Species. The lecture is concluded with a panel discussion with Craig Heller and Robert Proctor.


Lecture 4 by Daniel Dennett. Dr. Dennett presents the philosophical importance of Darwin's theory of evolution. The lecture is concluded with a panel discussion with Hank Greely and Chris Bobonich.


Lecture 5 by Peter and Rosemary Grant. The Grants discuss how and why species multiply. The lecture is concluded with a panel discussion with Carol Boggs and Rodolfo Dirzo.


Lecture 6 by Niles Eldredge. Dr. Eldredge discusses Darwin's life and work. The lecture is concluded with a panel discussion with Ward Watt and Liz Hadly.


Lecture 7 by Professor Melissa Brown. Professor Brown speaks about the history and consequences of social Darwinism, and offers insight into new ways of thinking about social evolution.


Lecture 8 by Paul Ewald. Dr. Ewald speaks about how several pathogenic viruses have evolved over time to break down the cell's barriers to several types of cancer. He suggests that further research will aid in the discovery of additional viruses linked to the causation of cancer. The lecture is concluded with a panel discussion with Gary Schoolnik and Stanley Falkow.


Lecture 9 by Russell Fernald. Dr. Fernald discusses how social behavior changes the brains of fish, animals, and humans to adapt to situations typically involving mating behaviors. The lecture is concluded with a panel discussion with Eric Knudsen and Charles Junkerman.


Lecture 10 by George Levine. Dr. Levine discusses through analysis of Darwin's literary works, ways of seeing and being enchanted by the world as well as the poetic eloquence of Darwin's prose. The lecture is concluded with a discussion between Dr. Levine and Rob Polhemus.

Stanford's channel on YouTube

Monday, January 5, 2009

The Genius of Evolution - BBC



David Attenborough, Andrew Marr, Armand Leroi and Melyvn Bragg are among the key names who will explore Darwin's extraordinary life and work.




Radio - Beyond Belief : Darwinism and religion

Beyond Belief

iPlayer

In each episode of the Sony Award winning series Beyond Belief, Ernie Rea is joined by three guests who discuss how their particular religious tradition affects their values and way of looking at the world, often revealing hidden and contradictory truths.

05 January 2009
Darwinism and religion

As part of the Darwin season on Radio 4, Beyond Belief examines religious reactions to Darwin's Origin of the Species - from the 19th century to the present day.

A Jew, a Christian and a Muslim share their perspectives on their Scriptures creation narratives before examining the reasons why some of their fellow believers are threatened by evolutionary theory.

Darwin: In Our Time: On the Origins of Charles Darwin by Melvyn Bragg


To celebrate the 200th anniversary of the birth of Charles Darwin in 2009 and the 150th anniversary of the publication of On the Origin of Species, Melvyn Bragg presents a series about Darwin's life and work.

Melvyn tells the story of Darwin's early life in Shropshire and discusses the significance of the three years he spent at Cambridge, where his interests shifted from religion to natural science.

Featuring contributions from Darwin biographer Jim Moore, geneticist at University College London Steve Jones, fellow of Christ's College Cambridge David Norman and assistant librarian at Christ's College Cambridge Colin Higgins.
Broadcast on:
BBC Radio 4, 9:00am Monday 5th January
Duration:
45 minutes
Available until:
9:47am Monday 12th January
Categories:

Craig Venter, one of the men who first successfully mapped the human genome, tells Darwin about his own experiences

Five leading scientists address letters to Charles Darwin, expressing their thoughts on his work and legacy.

Dr Craig Venter, one of the men who first successfully mapped the human genome,
tells Darwin
about his own experiences as a collector, medic and geneticist.
Broadcast on:
BBC Radio 4, 3:45pm Monday 5th January
Duration:
15 minutes
Available until:
4:02pm Monday 12th January
Categories:

Radio - Melvyn Bragg & 'The Darwinian Sistine Chapel'

Radio

From early January 2009

The BBC begins a series of programmes on Darwin. Melvyn Bragg kicks off the season with a four-part documentary asking why Darwin's writings remain so influential.

Art

Other offerings include 'The Darwinian Sistine Chapel', which charts artist Tania Kovats's project of decorating the Natural History Museum's ceiling based on Darwinian theories, in the manner of Michelangelo's vision of creation in the Vatican.

Darwin Events: Interactive at British Library

Interactive

British Library, London NW1, to 22 March 2009 (0870 444 1500; www.bl.uk)

This innovative exhibition offers insight into how Darwin developed his evolutionary idea by producing a replica of his "sand walk" – a route he trod every day with his terrier. On this, he observed nature and reflected on his experiments and travels on the 'Beagle'; piecing his theory together. This playful idea complements the rich collection of letters owned by the British Library and revealing the private Darwin – a humorous, emotional and charmingly modest man.

Darwin Events: Cambridge Festival

Festival

Cambridge University, 5–10 July 2009 (www.darwin2009.cam.ac.uk)

A predominantly academic event, with the programme including debates on Darwin's impact on human nature and belief, focus sessions on fields influenced by Darwin, such as science ('On the Origin of Species': speciation studies now) and the arts (Darwin in poetry, music and on stage). Other events involve tours of the University Botanic Gardens and fringe events (live music, street theatre and soapbox talks) by Cambridge Footlights.

Darwin Events: Poetry

The Royal Society of Literature, Royal Society and Somerset House Trust will present 'The Life in the Stone – Charles Darwin, The Geology, The Poetry', with Padel reading from her book 'Darwin – A Life in Poems', with a response by Richard Fortey, on 9 February 2009. Contact the Royal Society of Literature on 020-7845 4676.

'Darwin: My Ancestor', four programmes written and presented by Ruth Padel, will be broadcast on Radio 4 every Tuesday for four weeks from 27 January at 9.30am.

'Darwin – A Life in Poems' is published by Chatto and Windus on 12 February at £12.99

Saturday, January 3, 2009

"Darwin: A Philosophical Naturalist?" by Tim Lewens

The British Humanist Association Darwin Day Lecture 2008

"Darwin: A Philosophical Naturalist?" by Tim Lewens

Tim LewensThe BHA's annual Darwin Day Lecture is held each year on or around Darwin Day (12th February) in the Darwin Theatre at University College London.

In 2008 the Lecture was again chaired by Richard Dawkins.

The Lecture was given by Tim Lewens whose talk was entitled "Darwin: A Philosophical Naturalist?"

Audio files are available of Dawkins's introduction and Lewens's lecture as well as the Q&A session which followed.

Thursday, January 1, 2009

Evolution MegaLab - you can study the evolution of snails in your garden


Evolution MegaLab background

Scientists have been studying the banded snail for many years and have found that the darker shell types tend to be more common in woodland where the background colour is brown, while in grass the banded snails tend to be lighter-coloured, yellow and more stripy. This camouflage is an example of adaptation.

Birds eat banded snails

We want your help to find out whether this pattern can still be found, because there has been a big decrease in the numbers of song thrushes in some places over the last 30 years. If there are fewer song thrushes about, you would expect the different snails to be less faithful to their particular habitats than they used to be.

Climate change

There is also a geographical pattern in the colour of shells that we think may have changed in response to the warming of the climate over the last 30 years. Darker shells used to be more common in the north than in the south. We think this was because darker shells warm up more quickly in sunlight, enabling the animals to be more active than light-coloured snails in colder areas.

Help us find out whether lighter coloured shells are more common further north than they used to be, now that the climate has become warmer.

Evolution

We have collected together all the historical records of banded snail shell patterns that we can find. There are many thousands of them, mainly collected at least 30 years ago. Do a survey of your own and when you register and enter your data the website will automatically search our historical database and show you any changes that have occurred in your area. Visit the Instructions page to get started.

Darwin 2009 commemorations

The Complete Work of Charles Darwin Online

Darwin's complete publications are listed here.