Darwin re-visited

[Michaelangelica]

Wouldn't old Mr D love to be alive today.
I wish I was a biologist.
Can we crack cancer in 20 years?-- aging in 40?
This would leave him gob-smacked -as it does me.

The discovery of P elements

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Stuart Gilchrist describes the role played by fruit flies in the discovery of P elements. P elements are sections of DNA which have become a universal tool of molecular biology. They have provided the tool used to clone most animal genes during the last 15 years. The story is linked to the proliferation of human transport and trade.

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Robyn Williams: Charles Darwin of course hadn't heard of genetics or genes, which makes his intellectual feat all the more formidable, having to imagine what might be there in you and me and beetles and flies, making it all happen.

And when genetics did take off, bang, at the start of the 20th century, people quickly got most of it worked out. Or did they? How come there are still huge surprises in the post-Darwinian world? Stuart Gilchrist is at the University of Sydney.

Stuart Gilchrist: Despite global financial turmoil, it's still easier to pick winners in the stock market than to predict winners in science. It is almost impossible to know whether basic research will lead to great advances in the future or merely end up in the dustbin of history. Even the venerable Isaac Newton spent more time studying alchemy and magic than he did studying physics or calculus. One could argue that at least half of current university research will turn out to have been pretty much a waste of time. The trouble is we don't know which half.

The discovery of P elements - Science Show - 7 February 2009

I just started reading Mr. Darwin's Shooter. Beautifully written and that's where I am going now to read some more.

[Michaelangelica]

An intersting couple of comments I thought.

"All our microscopes are customised for life as we know it - so it's no surprise that we haven't found microbes with different biochemistry," said Professor Davies.
. . .
we must begin trawling the world's most inhospitable environments - deserts, salt lakes, and areas of high pressure, temperature or UV radiation.

"We could have a 'mission to Earth'. There's a big long list of places we could be looking," observed Professor Davies.

"For example, if we are looking for arsenic life, we could head for environments which are both arsenic rich and phosphorus poor - such as deep ocean vents.
. . .


"The accepted definition of life is a molecule capable of Darwinian evolution, so we are trying to put together molecules that are capable of doing it."

But he questioned whether our definition of "living" is perhaps too "Earth-centric".

"Remember - just because you are a chemical system which is self-sustaining and capable of Darwinian evolution, that doesn't mean that is the universal definition of life," he said.

http://news.bbc.co.uk/2/hi/science/nature/7893414.stm

[Symbology]

Originally Posted by Michaelangelica

Stuart Gilchrist: Despite global financial turmoil, it's still easier to pick winners in the stock market than to predict winners in science. It is almost impossible to know whether basic research will lead to great advances in the future or merely end up in the dustbin of history. Even the venerable Isaac Newton spent more time studying alchemy and magic than he did studying physics or calculus. One could argue that at least half of current university research will turn out to have been pretty much a waste of time. The trouble is we don't know which half.

I'm guessing that if scientists were held to the same scrutiny as a publicly traded company, and required to file full disclosure financial... er research sheets - that we would also be able to predict who the winners and losers would be with equal ability. But until scientists start getting funded like corporations and their accounting departments, then I'm afraid Mr. Gilchrist is correct

[Michaelangelica]

Is Darwinism past its 'sell-by' date?

Monday, 16 February 2009
By Michael Ruse

We rightly celebrate the English naturalist Charles Robert Darwin in this year, 2009, the 200th anniversary of his birth. He is the author of On the Origin of Species by Means of Natural Selection, published in 1859.

In that work, he argues
. . .
. . etc. .good summary
. . .
So much then for Darwin’s theory of 1859. It was a smashing triumph. For all of the arguments, with scientists and bishops squaring off in public, within a decade almost everyone - with notable exceptions like the American South - was an evolutionist. This applies even to church-goers, who were happy to accept the doctrine, so long as one gives space for immortal souls, not the subject of science anyway.

But now my question is: what about today? Does Darwin’s theory still have legs? Is it still something to which we should subscribe today? Or is it past its “sell-by” date? Is it something that we should admire in a museum, rather like the Ptolemaic system of astronomy that put the earth at the centre of the universe? Is it something we should no longer go on believing in and using as a directive for our researches? In trendy language: is Darwinism an exhausted paradigm?

The answer is, as so often in life, both yes and no. Not one piece of Darwin’s original argumentation stands untouched, unrefined. Thank goodness! This could only be had evolutionary research stood still for a century and a half. And yet, it is so obviously Darwin’s theory that is alive and well today. Today’s professional evolutionists are Darwinians. The pre-Socratic philosopher Heraclitus said that you cannot step into the same river twice. That is true. The pre-Socratic philosopher Parmenides said that nothing changes. That is also true.

Run quickly through evolutionary theorising today, starting with the fact that as with Darwin it is a consilience of inductions that structures and informs - the living world is explained by evolution through natural selection and conversely the world supports evolution through natural selection. Darwin knew nothing of genetics - at least, he knew nothing right of genetics! Today, starting with the double helix, we have the highly sophisticated theory of molecular biology. With this, evolutionists can peer beneath the surface finding things quite unknown to Darwin.

In the social insects, of which Darwin’s bees are a prime example, we can show the funny genetic relationships between females - queens and workers

Is Darwinism past its 'sell-by' date?(ScienceAlert)

[Michaelangelica]

Professor Trevor Marshall of Murdoch University, Western Australia, has explained how Homo sapiens must now be viewed as a superorganism in which a plethora of bacterial genomes – a metagenome – work in concert with our own. Marshall and team contend that the human genome can no longer be studied in isolation.

Hidden bacteria trigger illness(ScienceAlert)

[Michaelangelica]

The tree of life goes into the re-cycling bin

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
. . .
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

. . .
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.
. . .
"There's promiscuous exchange of genetic information across diverse groups," says Michael Rose, an evolutionary biologist at the University of California, Irvine.
. . .
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.
. . .
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).
. . .
"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).
. . .
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).
. . .
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."

Why Darwin was wrong about the tree of life - life - 21 January 2009 - New Scientist

Hamlet: There are more things in heaven and earth,Horatio, than are dreamt of in your philosophy.
. . .
A little more than kin but less than kind.

[Michaelangelica]

Saved By Junk DNA: Vital Role In The Evolution Of Human Genome
. . .
Unstable repeats

The international team of scientists found that stretches of tandem repeats influence the activity of neighboring genes. The repeats determine how tightly the local DNA is wrapped around specific proteins called 'nucleosomes', and this packaging structure dictates to what extent genes can be activated. Interestingly, tandem repeats are very unstable -- the number of repeats changes frequently when the DNA is copied. These changes affect the local DNA packaging, which in turn alters gene activity. In this way, unstable junk DNA allows fast shifts in gene activity, which may allow organisms to tune the activity of genes to match changing environments -- a vital principle for survival in the endless evolutionary race.

Evolution in test tubes

To further test their theory, the researchers conducted a complex experiment aimed at mimicking biological evolution, using yeast cells as Darwinian guinea pigs. Their results show that when a repeat is present near a gene, it is possible to select yeast mutants that show vastly increased activity of this gene. However, when the repeat region was removed, this fast evolution was impossible. "If this was the real world," the researchers say, "only cells with the repeats would be able to swiftly adapt to changes, thereby beating their repeat-less counterparts in the game of evolution. Their junk DNA saved their lives."

The research has been funded by Human Frontier Science Program, Fund for Scientific Research Flanders, NIH, K.U. Leuven and VIB (the Flanders Institute for Biotechnology).

Journal reference:

1. Marcelo D. Vinces, Matthieu Legendre, Marina Caldara, Masaki Hagihara, and Kevin J. Verstrepen. Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability. Science, 2009; 324 (5931): 1213 DOI: 10.1126/science.1170097

Adapted from materials provided by VIB (the Flanders Institute for Biotechnology), via EurekAlert!, a service of AAAS.

http://www.sciencedaily.com/releases...0528203730.htm

[HydrogenBond]

If repeat regions of DNA help with gene activity and evolutionary adaptation, and since repeat regions imply ordered patterns of genes, does that mean that cells which can create a level of order in the DNA, are the ones that can evolve the fastest? Does this also imply that random changes in the DNA are more likely to become evolutionary, if the cell creates genetic order first instead of later?

[freeztar]

Originally Posted by HydrogenBond

If repeat regions of DNA help with gene activity and evolutionary adaptation, and since repeat regions imply ordered patterns of genes, does that mean that cells which can create a level of order in the DNA, are the ones that can evolve the fastest? Does this also imply that random changes in the DNA are more likely to become evolutionary, if the cell creates genetic order first instead of later?

It certainly raises some interesting questions, but I think the take home point here is that the "junk DNA" allowed for quicker selection by mutants in this particular strain of yeast, in this experiment. I don't think they are suggesting that this phenomena occurs across the board. More experiments are needed, on different organisms, to better understand the relationship present in this particular experiment.

Of course, if someone knows something I don't know (other studies), please post it.

[Michaelangelica]

We are what we spray?

BACKGROUND: Persistent organic pollutants (POPs) may influence epigenetic mechanisms; therefore, they could affect chromosomal stability and gene expression. DNA methylation, an epigenetic mechanism, has been associated with cancer initiation and progression. Greenlandic Inuit have some of the highest reported POP levels worldwide.
. . .
CONCLUSIONS: This is the first study to investigate environmental exposure to POPs and DNA methylation levels in a human population.
Global methylation levels were inversely associated with blood plasma levels for several POPs and merit further investigation.

DNA Methylation Database


Epigenetics Society
It needs to be a bit simpler for me.