A surprisingly silly interview.

LiveScience is continuing with their series on nature’s “Greatest Mysteries”. Today it’s “What drives evolution?“.

In the second paragraph, we find this intriguing question:

Natural selection is accepted by scientists as the main engine driving the array of organisms and their complex features. But is evolution via natural selection the only explanation for complex organisms?

No, it isn’t. Genetic drift also plays a major role. However, as Dawkins points out repeatedly, natural selection is the only known mechanism capable of resulting in complex adaptations. The legitimate debate is therefore about how much phenotypic (or genetic) change is adaptive and how much is a product of chance. I wouldn’t consider it a “great mystery” but a debate about the relative contributions of fairly well understood mechanisms. Dawkins sees adaptations as the only interesting things to explain. Lynch (2007) provides an equivalently extreme argument from the drift side of the aisle. But this can’t be what the author has in mind, as it is all very standard.

“I think one of the greatest mysteries in biology at the moment is whether natural selection is the only process capable of generating organismal complexity,” said Massimo Pigliucci of the Department of Ecology and Evolution at Stony Brook University in New York “or whether there are other properties of matter that also come into play. I suspect the latter will turn out to be true.”

So we see that, indeed, the discussion is not about whether processes besides selection can generate complexity (they can, though it may not be adaptive complexity). It’s about whether totally different processes are at play. Reading Pigliucci’s statement immediately brings to mind thoughts about self-organizing complexity as emphasized by Stuart Kaufman and others about 15 years ago. Interesting ideas, but they didn’t really lead anywhere. But this is not what is discussed, and it’s here that the story takes a turn for the bizarre.

“Over the past decade or two, scientists have begun to suspect that there are other properties of complex systems (such as living organisms) that may help, together with natural selection, explain how things such as eyes, bacterial flagella, wings and turtle shells evolve,” Pigliucci told LiveScience.

One idea is that organisms are equipped with the flexibility to change their physical or other features during development to accommodate environmental changes, a phenomenon called phenotypic plasticity.

Phenotypic plasticity is a “property of matter”?

The change typically doesn’t show up in the genes. For instance, in social bees, both the workers and guards have the same genomes but different genes get activated to give them distinct behaviors and appearances. Environmental factors, such as temperature and embryonic diet, prompt genetic activity that ends up casting one bee a worker and the other a guard.

The cells in my fingers typing these words are very different from the cells in my brain thinking them, but they contain the same genome. The exact details of gene regulation and cell differentiation are still being studied, but this hardly constitutes either a “great mystery” of evolution or a challenge to Darwinian mechanisms. Same goes for castes within a bee hive, which has been described as being like a superorganism.

And just to prove that this is all very standard:

If beneficial, this flexibility could be passed on to offspring and so can lead to the evolution of new features in a species. “This plasticity is heritable, and natural selection can favor different kinds of plasticity, depending on the range of environmental conditions the organism encounters,” Pigliucci said.

So, phenotypic plasticity is not a property of matter but a standard biological process, and it can be shaped by natural selection like other heritable characteristics. Nothing new here.

But then we do finally get back to evolutionary changes resulting from “properties of matter” such that the mechanisms are non-Darwinian.

Self-organization is another evolutionary force that some experts say whips up complex features or behaviors spontaneously in living and non-living matter, and these traits are passed on to offspring through the generations.

That a Lamarckian process of inheritance of acquired characters played an important role would be surprising indeed. Perhaps it is not so silly as that. Maybe the author is thinking of epigenetic changes that can be passed on. But that would still be only a minor variant of the standard Darwinian process — natural selection was conceived long before any specific rules about hereditary systems were identified. Genetic or epigenetic, if it is inherited and has effects on fitness, it can be subject to natural selection.

“A classic example outside of biology are hurricanes: These are not random air movements at all, but highly organized atmospheric structures that arise spontaneously given the appropriate environmental conditions,” Pigliucci said. “There is increasing evidence that living organisms generate some of their complexity during development in an analogous manner.”

A biological illustration of self-organization is protein-folding. A lengthy necklace of amino acids bends, twists and folds into a three-dimensional protein, whose shape determines the protein’s function. A protein made up of just 100 amino acids could take on an endless number (billions upon billions) of shapes. While this shape-shifting takes on the order of seconds to minutes in nature, the fastest computers don’t have the muscle yet to pull off the feat.

The mechanism that triggers the final form could be a chemical signal, for instance.

So are we relying purely on chance every single time a protein folds? Or is three dimensional structure consistent given a particular string of amino acids? If the latter (which it is, or we’d be dead), then this would imply that self-organizing that could go any which way is not the explanation. Rather, the string of amino acids and the conditions in which it folds (e.g., the chemistry of the cell) are heritable and have fitness consequences. Where might that “chemical signal” comes from, pray tell?

After this, there is more about phenotypic plasticity. There’s an example of butterflies with different colour patterns depending on season (so again, a question of how the environment affects gene expression during development — interesting and important to consider in evolutionary biology, but not a challenge to natural selection because the switch in colouration is adaptive).

The last example is of shorebirds called red knots which “can morph their phenotypes depending on their migration routes.”

When brought into captivity and placed in colder temperature environments, the shorebirds’ flight muscles and organs shrink to reduce heat loss. The birds pass on to offspring the capacity to make these changes.

Maybe this is an innocuous statement, like claiming “If people work out, they will get big muscles, and they pass on the capacity to get big muscles by working out to their offspring”. One could even say that some individuals’ offspring (say, Arnold Schwarzenegger’s) have a higher capacity to become muscular under conditions of heavy exercise than others’. But then, this wouldn’t be nearly as interesting as implying that soft inheritance is taking place.

Overall, this piece was really quite confused, mixing very different issues in a strange sequence, which is a shame in light of the good article they posted last week.

I still wonder what can be done to improve the accuracy of science reporting; “nothing” seems less and less like an acceptable answer.


Why are there transitional animals?

“Uh oh,” thought I upon seeing this headline from LiveScience: Greatest Mysteries: Why Are There Transitional Animals?

“This could go wrong in so many different ways,” I said to myself, “let’s see which one they went with”.

Much to my pleasant surprise, the story is actually pretty good. There’s a bit of the usual anthropomorphizing of natural selection (“it shows us how evolution could have tinkered with variation”), but overall it is a reasonable discussion of an interesting topic. I doubt the existence of so-called “transitional animals” counts as a “great mystery”, but this is made up for by an excellent quote from Jack Conrad of the AMNH in New York (where I spent a year as a post-doc).

“These early whales were basically playing the same game that crocodiles play: Wait for something to come get a drink and then pull it in the water for dinner,” Conrad said. “This is also the same game that early land vertebrates, early amphibians and early relatives of crocs and dinosaurs were playing. These animals weren’t necessarily ‘on their way’ to being anything; they were well suited to being exactly where they were.”

It is quite refreshing, after the dazed hype about human evolution over the past couple of weeks, to see a statement so on the mark.


Beneficial mutations.

A reader asked me to post about beneficial mutations as an antidote to the common creationist (mis)conception that all mutations are detrimental. I replied that this isn’t an anti-creationist blog per se (I feel that I have more interesting things to talk about, frankly), and that the issue has been covered by others (e.g., here and here). I will, however, note the following article published recently in Science:

Perfeito, L., L. Fernandes, C. Mota, and I. Gordo. 2007. Adaptive mutations in bacteria: high rate and small effects. Science 317: 813-815.

Abstract: Evolution by natural selection is driven by the continuous generation of adaptive mutations. We measured the genomic mutation rate that generates beneficial mutations and their effects on fitness in Escherichia coli under conditions in which the effect of competition between lineages carrying different beneficial mutations is minimized. We found a rate on the order of 10–5 per genome per generation, which is 1000 times as high as previous estimates, and a mean selective advantage of 1%. Such a high rate of adaptive evolution has implications for the evolution of antibiotic resistance and pathogenicity.

As they note at the end of the paper,

Given the estimates for the overall mutation rate in E. coli and its genomic deleterious mutation rate, our estimate of Ua implies that 1 in 150 newly arising mutations is beneficial and that 1 in 10 fitness-affecting mutations increases the fitness of the individual carrying it. Hence, an enterobacterium has an enormous potential for adaptation and may help explain how antibiotic resistance and virulence evolve so quickly.

It is important to be clear that this is not a matter of mutations occurring in response to need, nor of whole populations of individuals changing to become resistant simultaneously. It is the normal Darwinian process of “random” mutation (with respect to fitness, but not such that all mutations are equally likely to occur) leading to increased or decreased reproductive output of individuals that happen to carry the mutation, with the proportion of genic variants changing over many generations. The main insight is that the pool of mutations on which this blind process of natural selection acts is larger and less biased toward deleterious changes than assumed. In this case, the study not only hits a common creationist misconception head on, it also shows how understanding evolution often has considerable medical importance.


Funny faces.

As noted in an earlier post, it is quite useful to have blogs, science news, and journal index searches all delivered to a single reader. Today I noticed an interesting juxtaposition of two news stories while skimming through my aggregated list of feeds. These two headlines were given in immediate succession (and from the same source):

Handsome By Chance: Why Humans Look Different From Neanderthals
Chance, not natural selection, best explains why the modern human skull looks so different from that of its Neanderthal relative.

Facial Attraction: Choice Of Sexual Partner Shaped The Human Face
Facial attractiveness played a major role in shaping human evolution, as studies on our fossil ancestors have shown our choice of sexual partner has shaped the human face.

These two studies aren’t mutually exclusive, of course. Neanderthals may have evolved their features by chance whereas human features evolved in response to sexual selection, but it’s amusing that such diametrically opposed explanations for facial features within the genus Homo — random genetic drift versus non-random mate choice — are given right next to each other in the news feed.


____________

The news stories are based on these articles:

Weaver, T.D., C.C. Roseman, and C.B. Stringer. 2007. Were Neandertal and modern human cranial differences produced by natural selection or genetic drift? Journal of Human Evolution 53: 135-145.

Weston, E.M., A.E. Friday, and P. Liò. 2007. Biometric evidence that sexual selection has shaped the hominin face. PLoS One 2(8): e710.


Acceptance of evolution in Canada, again.

As an update to the previous post about the acceptance of evolution in Canada vs. the USA, here are some highlights from a recently published (July 3) poll by Canadian Press-Decima Research. This is useful because it breaks the issue down into young earth creationism, theistic evolution, and naturalistic evolution in the way that American polls have in some cases.

  • Less than one in three Canadians (29%) believe that God had no part in the creation or development of human beings.
  • Fewer still (26%) believe “that God created human beings pretty much in their present form at one time within the last 10,000 years or so”.
  • A plurality, but still only 34%, say that “human beings have developed over millions of years from less advanced forms of life, but God guided this process”.
  • Belief in creationism is lowest in Quebec (21%), Alberta (22%), and B.C. (22%). In Alberta, the plurality view is that God guided human development (39%), while in Quebec the plurality feels God played no part (40%).
  • Rural residents are 12 points more likely than urban dwellers to believe that God created humans in their present form. Differences by generation are not all that large. The plurality of women (37%) believes that God guided the process, while the plurality of men (35%) believes that God played no part.
  • In polls using the same question (Gallup) put to US residents, findings are different: 45% said God created humans in more or less their present form (compared to 26% in Canada), 40% said that God guided the evolutionary process (compared to 34% in Canada). Only 15% say God played no part (compared to 29% in Canada).
  • According to Decima CEO Bruce Anderson “These results reflect an essential Canadian tendency: we are pretty secular, but pretty hesitant to embrace atheism. Our views on the role of science and spirituality lack consensus but these are not polarizing issues for the most part. It’s more as though for many, these feelings are unresolved, we believe in a higher being, we know what we don’t know, are comfortable not knowing, and choose not to press our views upon one another.”


Quote-mine this!

So, I have recently become aware that Genomicron is cited on an intelligent design wiki entry for “junk DNA“. They quote two paragraphs from my post A word about “junk DNA”. Specifically, a paragraph in which I critique the term “junk DNA” as unnecessarily implying non-function for all non-coding DNA, and a paragraph in which I list many (unsubstantiated) hypotheses about universal functions for non-coding DNA. Here are two paragraphs from the post that they don’t quote:

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions). Case in point: a few years ago, much ado was made of Beaton and Cavalier-Smith’s (1999) titular proclamation, based on a survey of cryptomonad nuclear and nucleomorphic genomes, that “eukaryotic non-coding DNA is functional”. The point was evidently lost that the function proposed by Beaton and Cavalier-Smith (1999) was based entirely on coevolutionary interactions between nucleus size and cell size.

Does non-coding DNA have a function? Some of it does, to be sure. Some of it is involved in chromosome structure and cell division (e.g., telomeres, centromeres). Some of it is undoubtedly regulatory in nature. Some of it is involved in alternative splicing (Kondrashov et al. 2003). A fair portion of it in various genomes shows signs of being evolutionarily conserved, which may imply function (Bejerano et al. 2004; Andolfatto 2005; Kondrashov 2005; Woolfe et al. 2005; Halligan and Keightley 2006). On the other hand, the largest fraction is comprised of transposable elements — some of which become co-opted by the host genome, some of which play major role in generating genomic variation, some of which may be involved in cellular stress response, and yet others of which remain detrimental to host fitness (Kidwell and Lisch 2001; Biémont and Vieira 2006). The upshot is that some non-coding DNA is most certainly functional — but when it is, this usually makes sense only in an evolutionary context, particularly through processes like co-option. More broadly, those who would attribute a universal function for non-coding DNA must bear the following in mind: any proposed function for all non-coding DNA must explain why an onion or a grasshopper needs five times more of it than anyone reading this sentence.

Funny that my post Function, non-function, some function: a brief history of junk DNA, in which I discuss how anti-evolutionists are wrong about the history and the science of non-coding DNA, is not quoted.

Here’s a quote they are welcome to use: Simply saying “junk DNA will turn out to have a function” is not a scientifically actionable prediction unless you specify what that function will be and a way to test the proposed function.



Evolution for Everyone — David Sloan Wilson on CBC.

David Sloan Wilson is Distinguished Professor of Biology and Anthropology at Binghamton University in New York and author of Unto Others, Darwin’s Cathedral, and most recently Evolution for Everyone. I confess that I have not yet read the book, though it is near the top of my pile. (Dr. Wilson and I are on the editorial board of Evolution: Education and Outreach, and he was kind enough to have copies sent to all of us).

On Saturday I happened to be listening to the radio and caught an interview with Dr. Wilson on CBC’s Quirks and Quarks program. You can listen here to a discussion of the book and his ideas about evolution, morality, religion, and other subjects. (Another connection: the host, Bob McDonald, received an honourary Doctor of Letters degree from the University of Guelph at the same convocation at which I received my degree).

Enjoy.


Nonsense from home.

I grew up in and around the small city of Orillia, Ontario. It is a charming place, and was both the hometown of Gordon Lightfoot and the summer home of Stephen Leacock, in the latter case serving as the inspiration for his Sunshine Sketches of a Little Town.

My parents (both since re-married) still live in the area, and I try to get home when I can as a good son should. They also make sure that I am kept up to date with local news of interest, which mostly means stories about the hospital administration’s shenanigans (my mother is a nurse and her husband is an MD, both recently retired and glad of it) and the amazing community project for Zambia that my father and stepmother are hard at work planning.

In addition, my mother enjoys sending me things like the following letter, which appeared in one of the local newspapers. This is, I think, the third rant by a creationist that I have seen in print from this or the smaller paper. A previous one claimed that no one had ever considered the evolution of plants, and thus that creationism must be accurate. I have many botanist colleagues who would be surprised to learn of this omission. In light of the recent poll results that show only 51% of Ontarians accept evolution, I think it is informative. This, by the way, is a lower total than for the USA as a whole, which I find disconcerting. To be fair, the results would probably depend heavily on which part of the province they sampled. Rural areas and small towns differ considerably from the larger cities in various socio-political attitudes. Frankly, I don’t have the time or energy to correct the factual errors and logical fallacies in this latest letter, so I will just post it for your enjoyment (original source).

Evolutionists have their heads in the sand
Orillia Packet & Times
Editorial – Wednesday, May 23, 2007 @ 09:00

Letter to the editor:

Re: M. Brown’s letter “Atheism; a sensible alternative to some”

Atheism: the belief that there is no God. Mr. Albert Einstein, the great theoretical physicist, upon having been asked how much he knew about what there is to be known, said he thought he might know about one hundredth of one per cent without doubt. Most of us know less than he did. All of which leads one to wonder how a person can come to conclude that “there is no God, no creator, no higher intelligence,” when we realize how little we know about anything in general, and origins and beginnings in particular.Atheism does not seem very sensible.

To deny evolution, Mr. Brown writes, is like putting one’s head in the sand, and to dismiss it because we still have apes, is ignorant. Well, where is the evidence for the theory? Where are all the in-between transitional life forms that Mr. Darwin and his followers were sure to be found in the fossil record? After all the digging and searching of the last 150 years, out of hundreds of thousands of fossil discoveries, there is not one clear-cut sample, when there should have been thousands. Dr. Colin Patterson, an evolutionist who was senior paleontologist at the prestigious British Museum of National History and a world-renowned fossil expert, wrote the following about his book entitled “Evolution:” “I fully agree with comments on the lack of direct illustration of evolutionary transitions. If I knew of any, fossil or living, I would certainly have included them. I will lay it on the line; there is not one such fossil for which one could make a watertight argument.”

Surely, this leads open, honest minds to conclude that the theory of evolution and all the resulting evo-babble is unproven, unsubstantiated, without evidence and just plain wrong. As a matter of fact, the earliest fossil record shows that plants and animals appeared suddenly and fully formed, much as we see them today, in complete agreement with the Biblical record. So who, in reality, is putting their head in the sand and ignoring the evidence?

All of which makes one wonder, why evolution is still being taught in our schools, and creation ignored. Why do we so readily allow our children to be misled?

P. Visser

The old saying is not quite accurate: you can go home again, just try not to read the letters to the editor in the local newspaper.


Inter-lineage selection versus "just in case".

I still want to grant the benefit of the doubt to my fellow biologists who recently have made statements about non-coding DNA being potentially useful in the future. Natural selection does not work this way, because it is simply the differential survival and reproduction of entities based on heritable differences. In the most common case, this means individual organisms within populations leaving more or fewer offspring and/or surviving or dying under given conditions in a non-random manner due to heritable trait differences. However, the general principle of natural selection is not restricted to this level, and is a logical consequence in any circumstance in which there is differential survival and reproduction based on inherited variation. There can be selection within the genome among transposons, for example, and some authors also argue that selection can take place among species (as differential speciation and extinction).

The most straightforward way of thinking about natural selection is to imagine that a certain genetic trait is either beneficial or detrimental to an organism, such that it is passed on either more or less commonly to subsequent generations. However, there can be higher-order selection as well, in which some lineages persist longer or branch off to form additional daughter lineages more often than others for non-random reasons. This is not why those traits originated nor why they are maintained from one generation to the next, but it could explain why lineages with those traits are more common or last longer than others.

As an example, consider sex. Sexual reproduction involves the recombination of genes which has two important effects: 1) it allows beneficial mutations to spread more easily in a population, and 2) it prevents the ratchet-like accumulation of deleterious mutations at multiple loci. What this means is that sexual lineages can be expected to evolve more quickly and to last longer than asexual lineages. So, when we look around, we expect to see more sexual lineages than asexual ones, and indeed that is what we see (at least in animals). Sex did not evolve so that lineages would have greater evolutionary potential or would survive for a longer time, but that is nevertheless a significant effect when considering the distribution of biological diversity. However, there is still an issue that sexual reproduction is costly: you only pass on half your genes, you produce “wasteful” males, you have to find a mate, and so on, so we also need to consider immediate benefits that keep the trait around long enough for us to even notice the higher-order effects.

Now back to “junk DNA”. It may be that over the long term, lineages with more non-coding DNA are more flexible and can diverge more often, or that they are more resilient to environmental change and will last longer than those with less DNA. If this is so, then this might explain why we see lineages with lots of non-coding DNA — because those lineages persisted while others disappeared. We would still have to explain the origin of the non-coding DNA and the reason it persists over the shorter term though. There are several possibilities. One, non-coding DNA is beneficial to the organism in some way. Lots of ideas have been proposed for this over the last half century. Two, non-coding DNA could be neutral and is simply not eliminated by selection. Three, non-coding DNA is slightly detrimental, but selection has been too weak (e.g., if populations are small) or mutation too strong (e.g., continual transposable element insertions) for it to be deleted. In any of these situations, it could be possible for non-coding DNA to persist long enough to be co-opted (by chance mutations and subsequent selection) or to have impacts on lineage diversification and/or lifespan.

The problem with this is that species with small genomes are much more common than ones with large genomes and large-genomed species seem to be more sensitive to environmental challenges. So, the most likely scenario is that mutational mechanisms affect DNA amount from the bottom up, while selection comes into play from the top down in terms of effects on cell size and also selection against disruptions of genes. On balance, some lineages end up with large amounts of non-coding DNA, and in some cases this is co-opted into functions like regulation or structure.

It certainly could be that some people are thinking about this from a reasonable perspective based on multiple levels of selection and time scales and are just being sloppy in their descriptions of the net processes. Or maybe they really do think that “junk DNA” is kept because it might become useful. Either way, we need to steer clear of simplified soundbites that obfuscate more than enlighten.