Darwin re-visited

[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/2009/05/090528203730.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]

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.

[Pyrotex]

I'm amused by the various "headlines" quoted in the posts on this page. "Is Darwinism Past its Sell-By Date?" -- "Tree of Life Goes in the Recycling Bin"...

 

They all sound like one-liners on a Creationism website.

 

And typically, in the body of the article, one discovers that, No, Darwinism is not past its SBD, and the TOL is alive a kicking, except for that "10%" of all animals -- which turns out to be bacteria.

 

Yes, hybridization and DNA swapping and methylization and pseudo-lamarckian transwhateverism are ALL taking place -- or occassionally take place -- or have probably taken place at some time -- in some branches of the TOL -- during certain phases of the Moon -- and these things are all definately important and need to be studied. But none of them invalidates Darwin's original perception and insight.

 

The Tree of Life is still an important visual tool for understanding evolution. The Sell-By Date keeps getting annual extensions. Lamarck's central theory is still wrong, no matter how ingeniously we snip off little pieces of it and generously slather on 'spin' and 'recontextualization'. Darwin's mistakes, though numerous, were all tiny, inconsequential in the light of his main theory, and generally derive from his understandable ignorance of genetics, and the scarcity of geological and biological data that we take for granted today.

 

In this, the 200th Anniversary of Charles Darwin's birth, let us not forget that had any of us been in his shoes in the mid-nineteenth century, wandering the planet in search of adventure and a meaning for our lives, we, too, may have amassed an enviable collection of fossils and bugs, and may have written entertaining travelogs, and may even have earned an honored place in 'polite society'.

 

I seriously doubt that ANY of us could have put it all together and so logically and persuasively revealed to the world the core principle of biological evolution and its mechanisms of operation as he did.

[Biochemist]

I seriously doubt that ANY of us could have put it all together and so logically and persuasively revealed to the world the core principle of biological evolution and its mechanisms of operation as he did.

Nice post, and nice perspective, Pyro.

 

I think it is worthwhile to summarize the core issues that (one could argue) remain open, while, at the same time, noting those that are closed.

 

On the closed front:

 

1) The tree of life (for higher phyla) is incontrovertible. Those of us who still had questions in the '80s (mostly due to the incomplete nature of the fossil record) have had the TOL confirmed by the proliferation of genetic maps of species.

 

2) Relatedly, common descent (at least back to the early eukaryotes) is a given

 

Still open:

 

1) the primary mechanism for speciation (any perhaps more importantly, phylogenation) is open. The uneven arrival of phyla, and their "peak" at 70 phyla about 500 million years ago, is not cleanly supportive of any sort of gradualism. Gradualism may be a primary factor, but the lack of new body plans in the last 500 million years is indeed troublesome.

 

2) The degree of "front loading"- The surprising degree of biochemical complexity (completely unknown to Darwin) continues to rise. If you couple the massive chaotic complexity in later phyla with the advent of lysosomes in the first eukaryotes (thus essentially "locking in" the intracytoplasmic machinery at the first eukaryote), it suggests that the "end game" was somewhat decided, or at least limited at the first eukaryote. It remains surprising that the early biochemical cytoplasmic machinery could support such a broad array of body plans, and that such a broad array of body plans could arise without significant change in the cytoplasmic machinery.

 

 

Film at 11.

[Pyrotex]

...

1) the primary mechanism for speciation (any perhaps more importantly, phylogenation) is open. The uneven arrival of phyla, and their "peak" at 70 phyla about 500 million years ago, is not cleanly supportive of any sort of gradualism. Gradualism may be a primary factor, but the lack of new body plans in the last 500 million years is indeed troublesome.

Gradualism means slowly, be small degrees, in an accumulated fashion. There are no tenets demanding that the change always be at the same rate, in the same direction, or accumulated in a certain way. Why "70 phyla"? Why not? It had to be some number! It turned out to be 70. That is NOT a problem. Had it been 40 or 140 or 1400 phyla, I suspect you would STILL be complaining that it, "is not cleanly supportive of any sort of gradualism".

 

The lack of new body plans in the last 0.5 Gyr is not troublesome at all. I wonder where you got that? A new body plan represents a major departure from predecessors. Would you not agree to that? To create a new body plan, one of two situations must occur:

1) the "mutation" can be relatively simple, but ONLY IF the animal itself is simple and generalized.

2) animal can be arbitrarily complicated and specialized, but THEN the mutation must be equally complicated in order to relocate organs, redefine skeleton, interface new organs/components in with existing specialized body systems -- and is therefore EXTREMELY UNLIKELY to succeed.

 

The more complex and specialized a lifeform is, the less any single mutation will affect its body plan. On the other hand, we know that among the simple segmented worms (very old critters), it only takes a single mutation to increase or decrease the number of segments, or to change a pair of legs into a pair of antennae.

 

2) The degree of "front loading"- ....

I got a meeting. Will tackle this point later.

[Biochemist]

Gradualism means slowly, be small degrees, in an accumulated fashion. There are no tenets demanding that the change always be at the same rate, in the same direction, or accumulated in a certain way. Why "70 phyla"? Why not? It had to be some number! It turned out to be 70. That is NOT a problem. Had it been 40 or 140 or 1400 phyla, I suspect you would STILL be complaining that it, "is not cleanly supportive of any sort of gradualism".

Hmmm. I didn't mean to be particularly contentious here. I was merely suggesting that if the number of phyla went form 3 to 70 to 30 in roughly equal LONG time periods (3 about a 750 million years ago, 70 about 500 million years ago and 30 now) this is not particularly consistent with gradualism.

 

The lack of new body plans in the last 0.5 Gyr is not troublesome at all. I wonder where you got that? A new body plan represents a major departure from predecessors. Would you not agree to that?

Yes.

To create a new body plan, one of two situations must occur:

1) the "mutation" can be relatively simple, but ONLY IF the animal itself is simple and generalized.

2) animal can be arbitrarily complicated and specialized, but THEN the mutation must be equally complicated in order to relocate organs, redefine skeleton, interface new organs/components in with existing specialized body systems -- and is therefore EXTREMELY UNLIKELY to succeed.

 

The more complex and specialized a life form is, the less any single mutation will affect its body plan.

All true, Pyro (thanks) but not really my point. No one was requiring that all new phyla only come from more complex species. There would be nothing stopping the existing lower forms (or, more succinctly, the lower forms 500 million years ago) from creating additional new primitive branches in the tree.

 

But they didn't. And I am just suggesting that this set of fact does not really support gradualism as a generalized mechanism for speciation. It certainly does not refute it, but it also certainly does not particularly support it.

[Pyrotex]

Hmmm. I didn't mean to be particularly contentious here. I was merely suggesting that if the number of phyla went form 3 to 70 to 30 in roughly equal LONG time periods (3 about a 750 million years ago, 70 about 500 million years ago and 30 now) this is not particularly consistent with gradualism.

Hmmm...63 phyla per 250 MYr = approx 1 new phyla every 4 MYr. That sure seems "gradual" to me, BC. Then a loss of 40 phyla per 250 MYr = approx -1 phyla for every 6 MYr. That still looks "gradual". So, I guess you're gonna hafta explain to me what you mean by "gradualism" cause I just don't get it yet.

...No one was requiring that all new phyla only come from more complex species. There would be nothing stopping the existing lower forms (or, more succinctly, the lower forms 500 million years ago) from creating additional new primitive branches in the tree. But they didn't...

Well, maybe they did but you weren't looking! :confused:

Seriously, you make a good point. If any new phyla were going to appear over the last 250 MYr, the odds are, they're going to branches off the more primitive lifeforms, like worms and sponges and algae.

 

But consider this--when a new body plan spun off 500 MYr ago, what was its environment? Any sophisticated crabs, sea urchins, fish, snakes, sharks around to gobble them up? Not likely. Things were a lot easier for new body plans back then. An extra pair of legs or an extra pair of eyes might be just the ticket. For a while.

 

But today (meaning the last 100 MYr or so), the competition is a lot rougher. The sea is chock full of mean teeth, jaws, spikes, poisons, pincers and stabbie-thingies. The chemical nature of the oceans themselves are different. The ecosystems are all different. Everything is different.

 

So maybe worms and spongiglumphs are still creating new body plans, but they have no chance to thrive in today's environment. Some of those OLD body plans thrived for many 100s of MYrs, before they suddenly went bye-bye. What changed? Their environment and the sophistication of their predators and the availability of their prey. So, in hind sight, this all makes perfect sense.

 

And besides, just how many body plans do you think a planet can support? Doesn't it make sense that there would be a "ceiling" on the number of body plans, and that that ceiling just might drop slowly as the sophistication of ecosystems, plants and animals kept driving upward?

[Biochemist]

Hmmm...63 phyla per 250 MYr = approx 1 new phyla every 4 MYr. That sure seems "gradual" to me, BC. Then a loss of 40 phyla per 250 MYr = approx -1 phyla for every 6 MYr. That still looks "gradual". So, I guess you're gonna hafta explain to me what you mean by "gradualism" cause I just don't get it yet.

Gradualism does not require (or even imply) species or phyla need to go extinct slowy. Only that they accrue slowly. And the slow growth should be "reasonably" consistent (e.g., generally logarithmic) over long time horizons.

Well, maybe they did but you weren't looking! :hihi:

I know you were joking on this, but it is true that new phyla actually may have shown up, and we missed them.

But today (meaning the last 100 MYr or so), the competition is a lot rougher. The sea is chock full of mean teeth, jaws, spikes, poisons, pincers and stabbie-thingies. The chemical nature of the oceans themselves are different. The ecosystems are all different. Everything is different.

This is a valid hypothesis, but it feels more like a postulate. It is a little tought to falsify. Further, we are accepting that speciation occured regularly over the last 500 million years, but no phylogenation. This alone seems to argue against the postulate that the "niches" were all "filled up". Besides, the niches that were vacated actually had "time" to be repopulated by similar phyla. We have had twice as much time since we lost them as it took to generate them.

 

Again, my only point is that this is not particularly consistent with gradualism.

And besides, just how many body plans do you think a planet can support? Doesn't it make sense that there would be a "ceiling" on the number of body plans, and that that ceiling just might drop slowly as the sophistication of ecosystems, plants and animals kept driving upward?

This seems completely at odds with the experimental data (such as we have it). There may well be a ceiling, but we would not expect the ceiling to fall. We might expect the phyla/species count to approach the ceiling asymptotically, but not to hit it and fall backwards.

 

Reiterating, I an not suggesting your suggestions are unreasonable. Just that they are not particularly consistent with gradualism.

[Pyrotex]

Okay, I'm cool.

Personally, I feel the problem is sufficiently complex, that we can't establish expectations of how phylogenation "should" or "should not" occur over 100s of MYrs. It's all one huge number of chaotic systems within chaotic systems within chaotic systems...

 

Or as the Buddha said, "it's turtles all the way down." :hihi:

 

My feeling is that certain body plans are much more adaptable (that is, they wound up that way) than others, and better able to speciate in order to fill suddenly vacated niches. Over the long haul, then, we would expect the number of beetles to explode in a bewildering variety of forms, and the number of centipedes to peak out and slower decline. Beetles can evolve new forms and fill niches faster than the 'pedes. On another planet, it could just as easily turn out the other way, with their "beetles" slowly dwindling in number and variety as they are edged out by "speedi-pedes". :naughty:

 

I am always cautious when the conversation turns to "how evolution is supposed to go" this way or that.

[Biochemist]

Okay, I'm cool.

Personally, I feel the problem is sufficiently complex, that we can't establish expectations of how phylogenation "should" or "should not" occur over 100s of MYrs. It's all one huge number of chaotic systems within chaotic systems within chaotic systems...

This is undeniably true.

My feeling is that certain body plans are much more adaptable (that is, they wound up that way) than others, and better able to speciate in order to fill suddenly vacated niches.

Very likely to be true. And your argument above that higher phyla are less likely to branch is a strong one as well.

I am always cautious when the conversation turns to "how evolution is supposed to go" this way or that.

Absolutely agree. But the core of the scientific method is prediction and falsifiability. If we posit gradualism based on serial incrementalism, we should either defend (or question) the predictions, modify the hypothesis, or throw it out.

 

I continue to think the argument for gradualism is weak. We have strong examples of genetic drift, but these seem to be cases of selection of recessive alleles. There is just so much assumption about how those recessive alleles got there.

[Michaelangelica]

More epigenetics, or something else going on?

This process must speed up genetic changes but should't there be more genetically damaged (or exceptional) people?

Jumping Genes Discovery Challenges Current Assumptions

ScienceDaily (June 13, 2009) — Jumping genes do most of their jumping, not during the development of sperm and egg cells, but during the development of the embryo itself.

The L1 family of retrotransposons comprises about 17 percent of the human genome. Eventually, continuous jumping by retrotransposons expands the size of the human genome and may cause shuffling of genome content.

For example, when retrotransposons jump, they may take portions of nearby gene sequences with them, inserting these where they land, and thereby allowing for the creation of new genes.

Even otherwise unremarkable insertions of L1 may cause significant effects on nearby genes, such as lowering their expression.

. . .

Jumping Genes Discovery Challenges Current Assumptions

[riper]

NB

This is not a thread for Darwin Denialists but it is for those who would like to discuss, explore their understanding of, or disagree with, or even add to, or expand on Darwin's theories-- but not as Darwin's ideas conflict with the literal interpretation of the Bible.

 

 

It is interesting to note that the most vulnerable to the next Bird Flu are those with the best immune systems

Those between 15-20+ age group

How does this gel with Darwin's survival of the fittest (for the given environment)?

 

when we talk about survival of the fitest we do not mean the strongest. if the bird flu affects those with strong immune system mostly then those with weaker ones are meant to survive it.

imaging this. the people who live in areas with more cleaner air, air free of CO2, in villages, are said to be more healthier than those living in town, breathing polluted air. but in the period of global warming it is possible that the amount of CO2 will be so much that people will start dying from it. the ones who where living in a more polluted environment will survive better. because their lungs are more adapted to breath in the CO2. so in this case the weaker ones will survive. it all depends on the conditions we are talking about.