Tag Archives: evolution

Why you have kneecaps

Why Evolution Is True

by Matthew Cobb

All tetrapods have kneecaps, although it appears that they evolved more than once. Even tuatara have kneecaps (it was long thought they did not). And here’s a kneet biomechanics demonstration of why they are so useful, and what you can and can’t do without them.

View original post

4 Comments

Filed under Reblogs

12 Days of Evolution #11: Are we still evolving?

Why Evolution Is True

By far the most frequent issue I’m asked about when giving public lectures on evolution is this: “Are humans still evolving? If so, how? Where are we going?” The short answer is “Yes, we’re still evolving, but not in ways that excite most people.” And what answer you give depends on whether you’re talking about whether we’re evolving right now, are referring to the recent past (about 10,000 years ago), or whether you’re talking about the species evolving as a unit or whether different populations are evolving in different directions.

Rather than reprise all the answers, I refer you to a few posts I’ve written about this question (here, herehere, here, and here.)  The answer is that most recent human evolution has involved different populations evolving in different directions (for example, lactose tolerance evolving in pastoral populations, light skin pigmentation evolving in populations farther from…

View original post 249 more words

Leave a comment

Filed under Reblogs

The genetic blueprint of an octopus reveals much about this amazing creature

The Conversation

Jan Strugnell, La Trobe University and Alvaro Roura, La Trobe University

Octopuses are among the most impressive of the invertebrates thanks to their ability to solve puzzles, camouflage perfectly with their surroundings, mimic other species, use tools and potentially predict world cup victories.

Now that scientists this month have published the first octopus genome we are a step closer to understanding how these feats are achieved in a lineage so divergent from our own.

The octopus genome was of the California two-spot (Octopus bimaculoides) and it may provide us with some leads on how the highly unusual octopod body plan evolved.

Interesting body plan

Octopods are contained within the group Cephalopoda, which literally means “head-footed”, as the foot (i.e. the octopus arms) are connected directly to the head.

One family of genes that is known to influence body plan in animals is called Hox. These genes usually occur together, clustered in groups, and the order of the genes directly corresponds to the order in which they are activated along the body during development.

In the octopus genome the scientists found the Hox genes are completely scattered, with no two of them occurring together. This scattered nature of the Hox genes across the genome may provide insights into octopod body plan development and why octopus have a much more unusual body plan than their cousins, such as snails and oysters.

Another big finding of this octopus genome project is actually something the authors did not find: whole genome duplication. That is, evidence that the entire genome was duplicated throughout history so that two copies of the genome were present.

It was previously believed that a whole genome duplication event in the octopus lineage may have driven the evolution of some of the remarkable characteristics present within octopus, such as complicated behaviours including the use of tools or vertebrate-like eyes.

The idea was that a whole genome duplication event frees up a set of genes, allowing these copies to take on new functions. But the lack of evidence for this suggests other mechanisms are at play.

Blended genome

One of these mechanisms appears to be the huge expansion in some gene families previously thought to be expanded only in vertebrates and not in other invertebrate lineages. One of these families is the protocadherins, which are cell adhesion molecules required to establish and maintain nervous system organisation.

The octopus genome boasts 168 protocadherin genes, which presumably play a crucial role in the highly modified octopus nervous system and complex brain. In contrast, these protocadherins are found in relatively small numbers (17 to 25) in organisms such as limpets and oysters, and are completely absent in several invertebrate model organisms including the fruit fly and nematodes.

The fact that protocadherin genes occur in large numbers in vertebrates and octopus but not in other animals, and that they are expressed in octopus neural and sensitive tissues (suckers and skin), suggests that they might play an important role in the evolution of cephalopod neural complexity.

Protocadherin diversity provides a mechanism to establish the synaptic connections needed to interpret the vast amount of stimuli, including touch and smell perceived through the suckers, and organise complex behavioural responses like camouflaging through the change in skin colour and texture/sculpture. It is interesting that the diversity in these genes has been generated by different mechanisms in octopus and vertebrates.

The genome also shows a lot of evidence for transposon activity. Transposons are DNA sequences that move locations around the genome (sometimes called “jumping genes”) and they can drive evolution.

In comparison to other genomes, the scientists note that the octopus genome looks like it has been “put into a blender and mixed”. They show that these transposons play an important role in driving this mixing of the genome.

They also found that transposons are highly expressed in neural tissues. They suggest that these may play an important role in memory and learning as shown in mammals and flies.

The ability of octopuses to learn and solve puzzles is something that is fascinating to us and so this will be a fruitful area for further research.

Why did it take so long?

It is more than 14 years since the human genome was published in Nature and Science, and numerous genomes have been published since then such as pandas, bees and recently 48 species of bird.

But this latest publication represents the first genome of any cephalopod and one of only a handful of molluscs, (the group containing cephalopods). Other molluscan genomes include the limpet (Lottia gigantea), oyster (Crassostrea gigas) and the sea hare (Aplysia californica).

This first octopus genome gives us great insight into the evolution and function of this fascinating group and will serve as a great catalyst for further research on cephalopod genetics.

Jan Strugnell is Associate professor at La Trobe University and Alvaro Roura is Postdoctoral fellow at La Trobe University

This article was originally published on The Conversation. (Reblogged by permission). Read the original article.

Leave a comment

Filed under Reblogs

Darwin’s finches highlight the unity of all life

The Conversation

Frank Nicholas, University of Sydney

When Charles Darwin visited the Galapagos Islands in October 1835, he and his ship-mates on board HMS Beagle collected specimens of birds, including finches and mockingbirds, from various islands of the archipelago.

At the time, Darwin took little interest in the quaint finches, making only a one-word mention of them in his diary. As painstakingly shown by Frank Sulloway and more recently by John Van Whye, it wasn’t until two years later that the finches sparked Darwin’s interest.

By then he had received feedback from the leading taxonomist of the time, John Gould, that the samples comprised 14 distinct species, none of which had been previously described! Gould also noted that their “principal peculiarity consisted in the bill [i.e. beak] presenting several distinct modifications of form”.

So intrigued was Darwin by this variation in size and shape of beaks that in the second (1845) edition of Journal of Researches he included illustrations of the distinctive variation between species in the size and shape of their beaks. He added a comment that:

Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.

The famously varied beak shapes of the Galapagos finches, as illustrated in the second edition of Darwin’s Journal of Researches.
Wikimedia

Unfortunately for Darwin, the closer he examined the available evidence on Galapagos finches, the more confusing the picture became. This was partly because the specimens available to him were not sufficiently labelled as to their island of collection.

Presumably, it was his doubt about the available evidence that resulted in Darwin making no mention of Galapagos finches in any edition of Origin of Species.

Why, then, do people now label them as “Darwin’s finches”, and why are these finches now regarded as a classical textbook example of his theory of evolution by natural selection?

Paragons of evolution

Despite not mentioning Galapagos finches, Darwin did make much use of evidence from other Galapagos species (especially mockingbirds) in Origin of Species.

As the influence of Origin of Species spread, so too did the evolutionary fame of the Galapagos Islands. Increasingly, other biologists were drawn into resolving the questions about finches that Darwin had left unanswered.

By the end of the 19th century, Galapagos finches were among the most studied of all birds. By the mid-20th century, there was abundant evidence that Galapagos finches had evolved to fill the range of ecological niches available in the archipelago – a classic example of evolution by adaptive radiation.

Beak size and shape were key attributes in determining adaptation to the different types of food available. In the second half of the 20th century, classic research by Princeton University’s Peter and Rosemary Grant provided evidence of quite strong natural selection on beak size and shape.

Under the hood

New light has also been shed on the evolution of Darwin’s finches in a paper recently published in Nature. In this latest research, the entire genomes of 120 individual birds from all Galapagos species plus two closely related species from other genera were sequenced.

The work was done by a team led by Swedish geneticist Leif Andersson, with major input from Peter and Rosemary Grant, who are still leading experts on the finches.

Comparison of sequence data enabled them to construct a comprehensive evolutionary tree based on variation across the entire finch genome. This has resulted in a revised taxonomy, increasing the number of species to 18.

The most striking feature of the genome-based tree is the evidence for matings between different populations, resulting in the occasional joining of two branches of the tree. This evidence of “horizontal” gene flow is consistent with field data on matings of finches gathered by the Grants.

A comparison of whole-genome sequence between two closely related groups of finches with contrasting beak shape (blunt versus pointed) identified at least 15 regions of chromosomes where the groups differ substantially in sequence.

Unity of life

The most striking difference between the two groups was observed in a chromosomal region containing a regulatory gene called ALX1. This gene encodes a polypeptide that switches other genes on and off by binding to their regulatory sequences.

Like other such genes, ALX1 is crucially involved in embryonic development. Indeed, mutations in ALX1 in humans and mice give rise to abnormal development of the head and face.

It is an extraordinary illustration of the underlying unity of all life on Earth that Leif Andersson and his colleagues have shown that the ALX1 gene also has a major effect on beak shape in finches, and that this gene has been subject to natural selection during the evolution of the Galapagos finches.

If Darwin were alive today, he would be astounded at the power of genomics tools such as those used in generating the results described in this paper. He would also be delighted to see such strong evidence not only in support of evolution but also in support of one of its major forces, natural selection.

The ConversationFrank Nicholas is Emeritus Professor of Animal Genetics at University of Sydney

This article was originally published on The Conversation. (Reblogged by permission). Read the original article.

 

Leave a comment

Filed under Reblogs

Darwin’s theory may be brilliant but it doesn’t explain everything

The Conversation

Lewis Dean, University of St Andrews and Kate Cross, University of St Andrews

As evolutionary scientists, we devote much of our working lives to exploring the behaviour of humans and other animals through an evolutionary lens. So it may come as a surprise that our show at this year’s Edinburgh Fringe is named Alas, Poor Darwin …?, borrowing from one of the most searing critiques of evolutionary psychology ever written. We’ve added a question mark, but still – it’s no simple tale of how our minds evolved.

Evolutionary theory is a bit like a chocolate ice cream in the hands of a two-year old: it’s going to get applied everywhere, but will anything useful be achieved in the process? The central tenets of Darwinian theory – variability, heredity and selection – are as beautiful as they are compelling. They completely revolutionised biology.

But applying these principles to the study of human behaviour has caused far more controversy. The evolutionary explanations for human behaviour that grab the headlines can often be neat; really neat – like tightly-plotted narratives in which everything works out perfectly in the end, usually with a guy getting a girl, where everything happens for a reason.

Real life rarely makes for such a neat story. We’ve all seen enough action movies to notice that the more satisfying the ending, the more plot holes you have to ignore as you walk out of the cinema. Neatness makes a good story, but it’s not enough for good science.

Ovulation meets evolution

One good example of this problem is the story of how women’s preferences for masculine male partners shift throughout the menstrual cycle in a strategic way. It goes like this: at the time of ovulation, when “good genes” are most important, women are attracted to more masculine men. For the rest of the menstrual cycle when faithfulness and cooperation are paramount, the opposite is true (we’re glossing over some subtleties that are explained here).

‘Don’t blame me’ Everett Historical

In a similar vein, there’s an elegant account of male violence. It says that men are more likely than women to behave aggressively everywhere in the world because in the Pleistocene epoch (between 10,000 and 1.7m years ago), humans had a polygynous mating system, meaning one man mating with several women. The men who succeeded in aggressive competition with other men had more partners, and therefore more children, and so more of their genes got passed on.

These stories prompt some awkward questions. For example does a change in women’s attraction have to be directly selected for? Could it be the by-product of some other evolutionary process? Can we be sure that the preferences reported in the lab by female undergraduates in 2015 are a good proxy for the real-life choices made by women 100,000 years ago? What evidence is there that our ancestors were polygynous? What selection pressures were acting on women while the men were all busy fighting? (Women’s genes also get passed on to their children, in case anyone had forgotten.)

You begin to find that very accomplished scientists who know an awful lot about evolution and human behaviour disagree. Vociferously. And there’s a good reason for this: they’re scientists. Destruction-testing of ideas is very much in the job spec.

The reality of scientific enquiry

In our own work we don’t generally find neat, satisfying stories that are easy to tell, hard to critique, and make everything fall into place. We tend to end up with tantalising hypotheses, really interesting ideas that might be true but we haven’t quite gathered the data to nail down beyond all doubt. We find theories that are dazzling in their elegance but multitudinous in their caveats.

We find that the mind steadfastly refuses to behave like a collection of perfectly adapted units, each with a single function that afforded a clear evolutionary advantage at some weirdly specific yet curiously under-specified time during human evolutionary history. Instead the human mind seems to be full of compromises and by-products, highly flexible, and intricately intertwined with this weird thing called “human culture”.

Yet having been drawn to evolutionary science for its extraordinary elegance and having found a thousand times more questions than satisfactory answers, we persist. Because if you expand your ideas about what “evolutionary” means – if you cease looking for the neat stories and embrace the fact that it’s going to get very, very messy, you can start to get somewhere really interesting.

Culture and evolution are not opposites. Evolved doesn’t have to mean adaptation. It might or might not mean “useful under some circumstances”. (It certainly doesn’t mean – and has never meant – good or right).

Refuting one evolutionary hypothesis about human behaviour doesn’t invalidate all of them. That would be like saying that evolutionary theory is felled by the old question, “But if we evolved from monkeys, why are there still monkeys?”

Arguing about the how, when and why isn’t a sign of science denialism, nor a reason to scrap the whole line of investigation – it’s healthy disagreement and we’d like to see more of it. Being an evolutionary scientist is a bit like being Dirk Gently: you might not get where you were hoping to go, but you’ll probably end up somewhere it’s worth being.

Kate and Lewis’s show, Alas Poor Darwin …?, part of the Cabaret of Dangerous Ideas, is taking place at the Edinburgh Fringe on August 16

The ConversationLewis Dean is Research Fellow at University of St Andrews and Kate Cross is Lecturer in Psychology at University of St Andrews

This article was originally published on The Conversation. (Reblogged by permission). Read the original article.

1 Comment

Filed under Reblogs

Charles Darwin – where he was right and wrong

by Tim Harding, B.Sc.

(An edited version of this essay was published in The Skeptic magazine, June 2015, Vol 35 No 2, under the title ‘Darwin’s Missing Link’.  The essay is based on a talk presented to the Mordi Skeptics on Tuesday 5 May 2015).

Charles Darwin (1809-1882) is best known for his major contributions to evolutionary theory. In 1859, Darwin published his theory of natural selection as the mechanism of evolution in his revolutionary book On the Origin of Species. This book provided compelling evidence overcoming the scientific rejection of earlier concepts of transmutation of species. The basic principles of his theory have been shown to be correct and are now widely accepted as the basis of mainstream zoology, botany and ecology.

On the other hand, in a later book Darwin got it wrong with the mechanisms of inheritance.  The empirical rules of genetics, based solely on observational results, were largely understood since Gregor Mendel’s ‘wrinkled pea’ experiments in the 1860s. The postulated units of inheritance were called genes, but in Charles Darwin’s time it was not understood where genes were located in the body or what they physically consisted of. Darwin knew that there must have been a physical mechanism for inheritance, but his speculations about it – called pangenesis – were incorrect. Fortunately for the credibility of his theory of evolution by natural selection, he published these speculations later in a separate 1868 book titled Variation of Animals and Plants Under Domestication.

Darwin’s early career

Charles Robert Darwin was born in Shrewsbury, England, on 12 February 1809 at his family home, The Mount. He was the fifth of six children of wealthy society doctor and financier Robert Darwin, and Susannah Darwin (née Wedgwood).

Darwin went to Edinburgh University in 1825 to study medicine. In his second year he neglected his medical studies for natural history and spent four months assisting Robert Grant’s research into marine invertebrates. Grant revealed his enthusiasm for the concept of transmutation of species (the altering of one species into another), but Darwin initially rejected this concept (probably for religious reasons).

Ideas about the transmutation of species were controversial as they conflicted with theological beliefs that species were unchanging parts of a designed hierarchy and that humans were unique, unrelated to other animals. The political and religious implications were intensely debated, but transmutation was not accepted by the scientific mainstream until Darwin’s theory.

In December 1831, Darwin had joined the Beagle ship voyage as a gentleman naturalist and geologist.  In South America, he discovered fossils resembling huge armadillos, and noted the geographical distribution of modern species in hope of finding their ‘centre of creation’.  As the Beagle neared England in 1836, he began to think that species might not be immutable after all.

In March 1837, ornithologist John Gould announced that mockingbirds collected on the Galápagos Islands represented three separate species each unique to a particular island, and that several distinct birds from those islands were all classified as finches. Darwin began speculating, in a series of notebooks, on the possibility that ‘one species does change into another’ to explain these findings, and around July of that year sketched a genealogical branching of a single evolutionary tree.  Unconventionally, Darwin asked questions of fancy pigeon and animal breeders as well as established scientists.

Charles Darwin

Charles Darwin in 1860, aged 51

In late September 1838, Darwin started reading Thomas Malthus’s An Essay on the Principle of Population with its statistical argument that human populations, if unrestrained, breed beyond their means and struggle to survive. Darwin related this to the struggle for existence among wildlife and plants, so that the survivors would pass on their form and abilities, and unfavourable variations would be destroyed.  By December 1838, he had noted a similarity between the act of breeders selecting traits and a Malthusian nature selecting among variants thrown up by chance.

Darwin now had the framework of his theory of natural selection, but he was fully occupied with his career as a geologist and held off writing a sketch of his theory until his book on The Structure and Distribution of Coral Reefs was completed in May 1842.

Evolution by natural selection

Darwin continued to research and extensively revise his theory of natural selection while focusing on his main work of publishing the scientific results of the Beagle voyage.  He tentatively wrote of his ideas to the famous Scottish geologist Charles Lyell in January 1842; then in June he roughed out a 35-page pencil sketch of his theory. Darwin began correspondence about his theorising with the botanist Joseph Dalton Hooker in January 1844, and by July had rounded out his sketch into a 230-page essay, to be expanded with his research results and published if he died prematurely.

His famous 1859 book On the Origin of Species was written for non-specialist readers and attracted widespread interest upon its publication. As Darwin was already an eminent scientist, his findings were taken seriously.  The evidence he presented generated scientific, philosophical, and religious discussion. The debate over the book contributed to the campaign by Thomas Huxley and his fellow members of the X Club to secularise science by promoting scientific naturalism. Within two decades there was widespread scientific agreement that evolution, with a branching pattern of common descent, had occurred, but scientists were slow to give the mechanism of natural selection the significance that it deserved.

species divergence

Diagram representing the divergence of species, from Darwin’s Origin of Species

Darwin’s theory of evolution is based on some key facts (based on wild populations without human interference), which biologist Ernst Mayr has summarised as follows:

  • Every species is fertile enough that if all offspring survived to reproduce the population would grow.
  • Despite periodic fluctuations, populations remain roughly the same size.
  • Resources such as food are limited and are relatively stable over time.
  • Individuals in a population vary significantly from one another.
  • Much of this variation is heritable.

From these key facts, the following important inferences may be made, once again summarised by Ernst May:

  • A struggle for survival ensues.
  • Individuals less suited to the environment are less likely to survive and less likely to reproduce.
  • Individuals more suited to the environment are more likely to survive and more likely to reproduce and leave their heritable traits to future generations, which produces the process of natural selection.
  • This slow process gradually results in populations changing to adapt to their environments, and ultimately, these variations accumulate over time to form new species.

Natural selection provided a mechanism for variation and eventual speciation, but it did not explain the inheritance of variation.  Without some way to explain the inheritance of characteristics acted on by natural selection, his theory would be incomplete.

Mechanisms of inheritance

Before the advent of genetics, Hippokratic theories attempted to explain inheritance in terms of a blending of fluids extracted from all parts of both male and female bodies during intercourse.  It was thought that the characteristics of the offspring are determined by the relative amounts and strength of fluids from each part of the body of each parent.

On the other hand, ‘preformationist’ theories held that the new mammalian offspring is already preformed in miniature, either within the egg of its mother or in the semen of its father.  Both of these types of theories incorporated ‘encasement’, which was the thesis that God created all future organisms in miniature, and that reproduction was just the growth and development of these miniatures.

Hippokratic theories were very good at explaining inheritance but very bad at explaining growth and development; whilst preformationist theories were the opposite – very good at explaining growth and development but very bad at explaining inheritance.  To give some examples, Hippokratic theories were unable to adequately explain phenomena such as the regeneration of freshwater polyps; while preformationist theories were unable to adequately explain how the mating of a mare with a donkey produces a mule.

Darwin came to his hypothesis of pangenesis, from a different direction – to fill a gap left in his theory of evolution.  Darwin’s breeding experiments on domestic animals (mainly pigeons) in the 1850s and 60s were part of his attempts to complete his evolution theory.  He was attempting in these experiments to show just how quickly varying characteristics can be amplified by domestic breeding, and therefore how natural selection can operate.

Darwin called his explanation of inheritance ‘the hypothesis of Pangenesis’, which he published in 1868.  However, he provides a more succinct description of this hypothesis in an earlier unpublished manuscript on pangenesis sent to Thomas Huxley in 1865:

“Furthermore, I am led to believe from analogies immediately to be given that protoplasm or formative matter which is throughout the whole organisation, is generated by each different tissue and cell or aggregate of similar cells; – that as each tissue or cell becomes developed, a superabundant atom or gemmule as may be called of the formative matter is thrown off; – that these almost infinitely numerous and infinitely minute gemmules unite together in due proportion to form the true germ; – that they have the power of self-increase or propagation; and that they here run through the same course of development, as that which the true germ, of which they are to constitute elements, has to run through, before they can be developed into their parent tissues or cells. This may be called the hypothesis of Pangenesis”.

pangenesis

The Laws of Inheritance & Pangenesis

Darwin further proposed that his hypothesis would not only account for inheritance, but also for development:

“The development of each being, including all the forms of metamorphosis and metagenesis, as well as the so-called growth of the higher animals, in which structure changes, though not in a striking manner, depends on the presence of gemmules thrown off at each period of life, and on their development, at a corresponding period, in union with the preceding cells”.

Through these mechanisms, Darwin proposed that inheritance and development were tied together – not only in the generation of offspring and early stages of embryonic life, but throughout the life of the organism.  By giving ‘gemmules’ the power to be modified throughout the life of an organism and then be transferred to the next generation, he argued that inheritance should be viewed as a form of growth.

By means of this single hypothesis, Darwin attempted to not only fill a gap in his theory of evolution, but whether he meant to or not, he created an apparent synthesis between the then competing paradigms relating to inheritance and development.

After reading Variation Under Domestication, Francis Galton (a cousin of Darwin’s) arranged for a series of experiments to be conducted on rabbits initially housed in the Zoological Gardens of London and later at his Kensington home.  His intention was to demonstrate the transmission of ‘gemmules’ to succeeding generations via blood injected from one rabbit to another, using coat colour as a marker.  Galton ultimately found that not a single instance of induced variation of coat colour occurred in a total of 88 offspring from blood transfused parents, and in 1871 published his results in Nature.

In later editions of Variation Under Domestication, Darwin admitted in a footnote that he would have expected to find ‘gemmules’ in the blood, although their presence was not absolutely necessary to his hypothesis.  Darwin’s response is unconvincing, as he provides no alternative explanation as to how the ‘gemmules’ are transmitted from the parents’ somatic cells to the germ cells.  He made no real attempt to modify his hypothesis in response to Galton’s falsification of it, indicating a possible abandonment of commitment to his hypothesis.

After the rediscovery of Mendel’s work in the 1890s, scientists tried to determine which molecules in the cell were responsible for inheritance.  In 1910, Thomas Hunt Morgan argued that genes are on chromosomes, based on observations of a sex-linked white eye mutation in fruit flies.  In 1913, his student Alfred Sturtevant used the phenomenon of genetic linkage to show that genes are arranged linearly on the chromosome.  It was soon discovered that chromosomes consisted of DNA and proteins, but DNA was not identified as the gene carrier until 1944. Watson and Crick’s breakthrough discovery of the chemical structure of DNA in 1953 finally revealed how genetic instructions are stored inside organisms and passed from generation to generation.

In view of the fact that it took another 85 years after Darwin’s book Variation Under Domestication before the molecular mechanisms of inheritance to be discovered, Darwin can hardly be blamed for getting it wrong way back in 1868.  This was before even chromosomes had been discovered, let alone DNA.

On the plus side, Darwin’s theory of evolution by natural selection, with its tree-like model of branching common descent, has become the unifying theory of the life sciences. The theory explains the diversity of living organisms and their adaptation to the environment. It makes sense of the geologic record, biogeography, parallels in embryonic development, biological homologies, vestigiality, cladistics, phylogenetics and other fields, with unrivalled explanatory power; it has also become essential to applied sciences such as medicine, agriculture, conservation and environmental sciences.

References

Darwin, Charles (1859) The Origin Of Species. 6th ed. 1873. London: John Murray.

Darwin, Charles (1875) The Variation of Animals and Plants Under Domestication, Vol II London: John Murray.

Mayr, Ernst (1982) The Growth of Biological Thought: Diversity, Evolution, and Inheritance Harvard University Press.

Copyright notice: © All rights reserved. Except for personal use or as permitted under the Australian Copyright Act, no part of this website may be reproduced, stored in a retrieval system, communicated or transmitted in any form or by any means without prior written permission. All inquiries should be made to the copyright owner, Tim Harding at tim.harding@yandoo.com, or as attributed on individual blog posts.

If you find the information on this blog useful, you might like to consider supporting us.

Make a Donation Button


Leave a comment

Filed under Essays and talks

Darwin: a great scientist

by Rosslyn Ives

 On 12 February, we remember Charles Darwin’s birthday. His remarkable contribution to human knowledge, On the Origin of Species (1859), sets down the evidence and arguments for evolution by natural selection. By taking a scientific approach, Darwin (1809–82) and many others have changed the way we understand our origin and place within the biosphere.

Humanists hold science in high regard. We are confident that scientific knowledge has a high degree of reliability and can be trusted. If people claim to have gained knowledge by other means, e.g. revelation, hearsay or intuition, Humanists will view sceptically such claims until they can independently be verified by scientific investigation. For science differs from such unverified claims by being evidence-based, collaborative, open-ended and self-correcting.

Doing science, in a basic suck-it-and-see way, has always been essential to human survival. Like all animals our forebears would have observed natural phenomena in their environment. From such observations came knowledge about survival in particular locations.

When our ancestors acquired language, they gained an effective way to pass information down the generations. Language probably also coincided with the propensity of humans to make up hypotheses and theories about how things come to be the way they are. Today we regard these earlier “imaginings” as the myths, folklore and religious beliefs of particular groups of people.

The revival of learning in the Renaissance period encouraged people to be more adventurous. It led to an expansion in trade, exploration and colonisation by Europeans, followed by the development of natural philosophy. Early practitioners were especially interested in the ancient Greek and Latin texts on astronomy, animals, mathematics and plants, practical manuals of how things worked.

However, conflict between traditional scholars and the early natural philosophers (later called scientists) meant that the latter worked outside the existing universities. These men, usually of independent means, were the founders of modern science. They made observations, did experi­ments, wrote papers and sent them to other natural philosophers in different parts of Europe. They also founded the first scientific journals and formed the early scientific associations such as Accademia del Cimento (Tuscany), the Royal Society of London and Académie des Sciences (Paris).

Darwin followed in the footsteps of those natural philosophers and naturalists, and we can learn a lot about the methods of science from the way he went about assembling evidence for species change by natural selection. As a young naturalist he had the extraordinary good luck to spend five years journeying around the world on HMS Beagle.

While going around the world he collected speci­mens and took detailed notes of what he observed. Shortly after his return to England he married and settled, in 1842, into a domestic haven in Downe, Kent, where he lived for the rest of his life. After that he rarely travelled far from home, spending much of his time as a practicing scientist, reading, corresponding, experimenting, thinking and writing.

While travelling on the Beagle, Darwin saw a vast number of different plant and animal species. The question of how they had come to be so varied presented itself. He was well aware that the suggestion that species were able to change, i.e. evolve into different forms, ran counter to the established under­standing of the fixity of species — a view which seemed common sense and was reinforced by the Bible — God had made all the plants and animals in the form in which we saw them.

When in the 1840s others had written about life forms evolving, even established scientists of Darwin’s day were sceptical. So when the idea of species change by natural selection occurred to Darwin, he delayed publishing an account on this matter for fear of ridicule from his peers. He was also not comfortable with the fact that atheists and freethinkers were among the first to promote the idea of evolution.

In 1858 Darwin was disturbed to receive a letter from another naturalist, Alfred Wallace, outlining natural selection. Although Darwin had confided his ideas about natural selection to a few science friends, he had published nothing on this controversial matter.

To alleviate Darwin’s worry about being denied recognition, his friends organised for him to present a short paper along with Wallace’s letter to the AGM of the Linnean Society in 1858. Neither man was present at that meeting.

Darwin then worked at length to assemble all his notes into a book, On the Origin of Species. His aim was to convince others, especially his scientific peers, of the evidence and validity of his theory of natural selection. His approach was to set out the evidence that he had garnered from his travels, reading and corres­pondence in an objective manner so that even a critical reader would be convinced of the validity of his interpretations.

Like any great scientist Darwin never considered he had written the last word on natural selection. Up until his death in 1882 he continued to modify and rewrite sections of his great book as it went through many editions.

It is for his contribution to human knowledge and his intelligent use of the open-ended methods of science that we celebrate Charles Darwin on 12 February.

From the Victorian Humanist (Melbourne), 54 (1), February 2015: [1] & 6. Newsletter of the Humanist Society of Victoria www.victorianhumanist.com

Leave a comment

Filed under Reblogs

Bird tree of life shows ‘explosive evolution’: studies

The Conversation

By Bryonie Scott, The Conversation and Tessa Evans, The Conversation

Today’s land birds, from ducks to eagles, shared a common ancestor after dinosaurs went extinct – just one finding from bird gene studies published in journals, including Science and GigaScience, today.

Genetic data of 48 bird species were sequenced in a massive international collaboration to create a new and detailed version of the avian tree of life.

“Birds have always been very good for this kind of work because we have a greater understanding about the world’s birds than we do about any of the other vertebrate groups,” Simon Griffith, Associate Professor of Avian Behavioural Ecology at Macquarie University, said.

“We are familiar with almost all the birds in the world – around 10,000 species – and we know how they differ, in important characteristics such as how long they live, how many offspring they have each year, how old they are when they breed.”

About 66 million years ago, a mass extinction event wiped out around 80% of Earth’s plant and animal population, but opened the door for the rapid expansion of birds.

Giant terror birds are similar to a common ancestor of all land birds. Marcelo Braga/Flickr, CC BY

Only a few bird lineages survived the mass extinction, and most modern land birds such as songbirds, owls and woodpeckers share a common apex predator ancestor.

This top-of-the-food-chain brute was similar to the giant terror birds which stalked the Americas between 27 million and 15,000 years ago.

“The main problem in resolving the relationships among birds is that they diversified very quickly,” Research Director and the Curator of the Australian National Wildlife Collection, CSIRO, Leo Joseph said.

Extreme adaptations

Birds are among the most widespread land animals and have experienced evolutionary adaptations to extreme environments. Penguins live in some of the harshest conditions on Earth, and DNA analysis, published in GigaScience, confirmed fossil evidence that penguins first appeared in Antarctica around 60 million years ago.

“If you have a complete genome, you can compare the variations between the chromosomes and get a picture of the population history” Sankar Subramanian, a research fellow at Griffith University and who worked on the project, said.

“By comparing the complete genome of penguins living today we can track when evolutionary changes occurred, up to 200,000 years ago.”

This aspect of the research, Emperor penguins were found to have a stable population, but Adélie penguins present a very different story, showing fluctuations in population matching extreme climactic periods.

In a warmer period 150,000 years ago there was a large population explosion, but in a more recent glacial period the population declined dramatically.

Adélie penguins struggle in glacial periods as they require ice-free land for nesting. Dominique Génin/Flickr, CC BY-NC-ND

Rather than being evolutionary in origin, Dr Subramanian explained the fluctuations depended on “how much ice-free land is available for nesting and breeding”.

Compared to other bird species, penguins had more genes for lipid metabolism, which is essential for forming layers of blubber to withstand the cold.

This subgroup of the project hopes to look at penguins which live in tropical and temperate waters such as the Galápagos Islands and New Zealand to see how more recent evolutionary adaptations have affected genes of modern penguins.

Now that these hallmark studies have been completed, and the bird tree of life established with some degree of authority, it provides a scaffold for further research.

“This new study helps tease apart the rapid diversification of birds, which has been a long-standing problem,” Dr Joseph said.

“We can now address really interesting questions,” Associate Professor Griffith said. “When did song learning evolve? When did birds evolve different patterns of parental care?”

These insights provide sought-after answers about how species can diversify so quickly to fill the ecological niches.


This articled was edited on Friday December 12, 2014, to clarify some quotes by Dr Leo Joseph.

The ConversationThis article was originally published on The Conversation. (Republished with permission). Read the original article.

Leave a comment

Filed under Reblogs

Dawkins on the human brain

Richard Dawkins, FRS, FRSL (born 26 March 1941) is an English ethologist, evolutionary biologist,and writer. He is an emeritus fellow of New College, Oxford, and was the University of Oxford’s Professor for Public Understanding of Science from 1995 until 2008.

The human brain, probably uniquely in the whole of evolutionary history, can see across the valley and can plot a course away from extinction and towards distant uplands. Long-term planning – and hence the very possibility of stewardship – is something utterly new on the planet, even alien. It exists only in human brains. The future is a new invention in evolution. It is precious. And fragile. We must use all our scientific artifice to protect it.” – Richard Dawkins

Leave a comment

Filed under Quotations

Theories of Generation

by Tim Harding

Does Darwin successfully combine the two explanatory paradigms of inheritance, and growth and development?  If he does, is this a problem for Kuhn’s view of scientific change?

In this essay, I intend to show how Darwin’s hypothesis of pangenesis created a synthesis between the then competing paradigms relating to inheritance and development.  I think that this synthesis does present a problem for Kuhn’s view of scientific change, and that Popper’s account may actually be more relevant than Kuhn’s to certain aspects of this particular case study.

Before discussing Darwin’s theories, it is necessary to briefly describe the two paradigms that attempted to explain inheritance (how characteristics are transferred to offspring from parents), and growth and development (how the growth of offspring is organised).  These two paradigms were characterised by competing Hippocratic theories and preformationist theories (Verdnik, 1998:126, 157).

Before the advent of genetics, Hippocratic theories attempted to explain inheritance in terms of a blending of fluids extracted from all parts of both male and female bodies during intercourse.  It was thought that the characteristics of the offspring are determined by the relative amounts and strength of fluids from each part of the body of each parent (Verdnik, 1998:126).

On the other hand, preformationist theories held that the new mammalian offspring is already preformed in miniature, either within the egg of its mother (ovist preformationism) or in the semen of its father (animalculist preformationism).  Both of these types of theories incorporated emboîtment (encasement), which was the thesis that God created all future organisms in miniature, and that reproduction was just the growth and development of these miniatures (Verdnik, 1998:128).

Hippocratic theories were very good at explaining inheritance but very bad at explaining growth and development; whilst preformationist theories were the opposite – very good at explaining growth and development but very bad at explaining inheritance (Verdnik, 1998:126).  To give some examples, Hippocratic theories were unable to adequately explain phenomena such as the regeneration of freshwater polyps as observed by Trembley (Trembley 1744: 148); while preformationist theories were unable to adequately explain how the mating of a mare with a donkey produces a mule (Maupertuis 1745: 172).

Darwin came to his hypothesis of pangenesis, from a different direction – to fill a gap left in his theory of evolution, as published in his 1859 book The Origin of Species (Darwin, 1859).  Natural selection provided a mechanism for variation and eventual speciation, but it did not explain the inheritance of variation.  Without some way to explain the inheritance of characteristics acted on by natural selection, his theory would be incomplete.  Darwin’s breeding experiments on domestic animals (mainly pigeons) in the 1850s and 60s[1] were part of his attempts to complete his evolution theory (Bartley, 1992: 308).  He was attempting in these experiments to show just how quickly varying characteristics can be amplified by domestic breeding, and therefore how natural selection can operate (Verdnik, 1998:156).

evolution_peas

The Laws Of Inheritance & Pangenesis

Darwin called his explanation of inheritance ‘the hypothesis of Pangenesis’, which he published in Part II of Chapter XXVII of Variation Under Domestication (Darwin, 1875: 374-404).  However, he provides a more succinct description of this hypothesis in an earlier unpublished manuscript on pangenesis sent to Huxley in 1865:

‘Furthermore, I am led to believe from analogies immediately to be given that protoplasm or formative matter which is throughout the whole organisation, is generated by each different tissue and cell or aggregate of similar cells; – that as each tissue or cell becomes developed, a superabundant atom or gemmule as may be called of the formative matter is thrown off; – that these almost infinitely numerous and infinitely minute gemmules unite together in due proportion to form the true germ; – that they have the power of self-increase or propagation; and that they here run through the same course of development, as that which the true germ, of which they are to constitute elements, has to run through, before they can be developed into their parent tissues or cells. This may be called the hypothesis of Pangenesis’ (Olby 1963: 259).

Darwin further proposed that his hypothesis would not only account for inheritance, but also for development:

‘The development of each being, including all the forms of metamorphosis and metagenesis, as well as the so-called growth of the higher animals, in which structure changes, though not in a striking manner, depends on the presence of gemmules thrown off at each period of life, and on their development, at a corresponding period, in union with the preceding cells ‘ (Darwin, 1875: 403-404).

Through these mechanisms, Darwin proposed that inheritance and development were tied together – not only in the generation of offspring and early stages of embryonic life, but throughout the life of the organism (Bartley, 1992: 310).  By giving ‘gemmules’ the power to be modified throughout the life of an organism and then be transferred to the next generation, he argued that inheritance should be viewed as a form of growth (Bartley, 1992: 331).

By means of this single hypothesis, Darwin not only filled a gap in his theory of evolution, but whether he meant to or not, he created a synthesis between the then competing paradigms relating to inheritance and development.

The preceding discussion raises some significant philosophical issues.  How does it compare with Kuhn’s view of scientific change; and in particular, is Darwin’s paradigm synthesis a problem for the Kuhnian account?

According to Kuhn, ‘normal science’ operates within scientific paradigms[2] that not only determine which scientific theories are acceptable, but define scientific communities and even the areas of research undertaken (Kuhn, 1962: 10-11).

Kuhn says that in so far as he is engaged in normal science, the researcher is a solver of puzzles, not a tester of paradigms.

Paradigm-testing occurs only after persistent failure to solve a noteworthy puzzle has given rise to crisis.  And even then it occurs only after the sense of crisis has evoked an alternative candidate for a paradigm.  In the sciences, the testing situation never consists, as puzzle-solving does, simply in the comparison of a single paradigm with nature.  Instead, testing occurs as part of the competition between two rival paradigms for the allegiance of the scientific community (Kuhn, 1962: 144-145).

Kuhn notes that the schools guided by different paradigms are ‘always slightly at cross-purposes’ and that they ‘fail to make complete contact with each other’s viewpoints’, a phenomenon which describes as ‘incommensurability’ (Kuhn, 1962: 112, 148-150).  The failure of the adherents of Hippocratic and preformationist theories to focus on the strengths and weaknesses of both paradigms, and to engage in the testing of both paradigms, tends to support Kuhn’s notion of incommensurability.  No crisis occurred within each paradigm, because their adherents failed to focus on how well each paradigm explained both inheritance and development.

The formulation of Darwin’s hypothesis does not accord with the Kuhnian account.  He did not conduct his breeding experiments on domestic animals to test either the Hippocratic or the preformationist paradigms, but to fill a gap in his quite separate theory of evolution.  Similarly, his synthesis between the then competing paradigms relating to inheritance and development, was not done to resolve any crisis in these paradigms, but for a separate purpose.  A further problem for the Kuhnian account is that the scientific method Darwin used to formulate his hypothesis was essentially inductive, although this may also be a problem for the Popperian account.

Another aspect of the Kuhnian account is that the failure of experimental results to conform to the prevailing paradigm is seen as an ‘anomaly’, rather than as an instance of Popperian falsification.[3]  If scientists are confronted by anomalies, they will often devise ad hoc modifications in order to eliminate any apparent conflict.  Anomalies do not cause the abandonment of paradigm or theory unless and until the level of anomalies builds to a crisis where the prevailing paradigm or theory is replaced by a new one (Kuhn, 1962: 77-78).

After reading Variation Under Domestication, Francis Galton (a cousin of Darwin’s) arranged for a series of experiments to be conducted on rabbits initially housed in the Zoological Gardens of London and later at his Kensington home.  His intention was to demonstrate the transmission of ‘gemmules’ to succeeding generations via blood injected from one rabbit to another, using coat colour as a marker.  Galton ultimately found that not a single instance of induced variation of coat colour occurred in a total of 88 offspring from blood transfused parents, and in 1871 published his results in Nature (Brown, 2002: 290-291).  Although intended to verify Darwin’s hypothesis, it seems that Galton’s experiments provided a Popperian falsification instance.  Whether the purpose was verification or falsification, Galton’s experiments do not accord with Kuhn’s account of paradigm-testing discussed above.

In later editions of Variation Under Domestication, Darwin admitted in a footnote that he would have expected to find ‘gemmules’ in the blood, although their presence was not absolutely necessary to his hypothesis (Brown, 2002: 292).  I find Darwin’s response unconvincing, as he provides no alternative explanation as to how the ‘gemmules’ are transmitted from the parents’ somatic cells to the germ cells.  He made no real attempt to modify his hypothesis in response to Galton’s falsification of it.

I therefore conclude that whilst the Hippocratic and preformationist paradigms accord with Kuhn’s notion of incommensurability, Darwin’s synthesis of these two paradigms does not accord with the Kuhnian account of science.  Furthermore, Darwin’s failure to make an ad hoc modification to his hypothesis after the discovery by Galton of an anomaly, as would be expected under the Kuhnian account, supports a Popperian rather than a Kuhnian account of the scientific process in this case.

References:

Bartley, M.M. (1992) Darwin and Domestication: Studies on Inheritance. Journal of the History of Biology, Vol 25, No. 2 pp.307-333.

Browne, J. (2002) Charles Darwin – The Power of Place, Volume II of a Biography. London: Pimlico.

Darwin, C. (1859) The Origin Of Species By Means Of Natural Selection, Or The Preservation Of Favoured Races In The Struggle For Life. 6th ed. 1873. London: John Murray.

Darwin, C. (1875) The Variation of Animals and Plants Under Domestication, Vol II London: John Murray.

Kuhn, T.S. (1962) The Structure of Scientific Revolutions 3rd ed. Chicago: University of Chicago Press.

Maupertuis, P. (1745) The Earthly Venus in Verdnik, D. (ed.) (1998) Thinking about Science. Study Guide and Readings. Churchill: Monash Distance Education Centre.

Olby, R.C. (1963) Charles Darwin’s Manuscript of Pangenesis, British Journal for Philosophy of Science 1: 251-263.

Popper, K. (1959) The Logic of Scientific Discovery. rev. ed. 1968, in Verdnik, D. (ed.) (1998) Thinking about Science. Study Guide and Readings. Churchill: Monash Distance Education Centre.

Trembley, A. (1744) Memoires pour server a l’histoire d’un genre de polypes d’eau douce in Verdnik, D. (ed.) (1998) Thinking about Science. Study Guide and Readings. Churchill: Monash Distance Education Centre.

Verdnik, D. (ed.) (1998) Thinking about Science. Study Guide and Readings. Churchill: Monash Distance Education Centre.

 Endnotes:

[1] Darwin reported the results of these experiments in both The Origin Of Species and The Variation of Animals and Plants Under Domestication.

[2] Kuhn does not provide a concise definition of a scientific paradigm, but the Merriam-Webster Online dictionary defines it as ‘a philosophical and theoretical framework of a scientific school or discipline within which theories, laws, and generalizations and the experiments performed in support of them are formulated; broadly: a philosophical or theoretical framework of any kind.’

[3] Popper proposes falsifiability as the criterion of demarcation between scientific and non-scientific statements.  In other words, a theory is scientific if it is falsifiable (Verdnik, 1998:76).

Copyright notice: © All rights reserved. Except for personal use or as permitted under the Australian Copyright Act, no part of this website may be reproduced, stored in a retrieval system, communicated or transmitted in any form or by any means without prior written permission. All inquiries should be made to the copyright owner, Tim Harding at tim.harding@yandoo.com, or as attributed on individual blog posts.

If you find the information on this blog useful, you might like to consider supporting us.

Make a Donation Button

Leave a comment

Filed under Essays and talks